New WebApollo install issue (Grails)

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New WebApollo install issue (Grails)

Shane McCoy
Hey

I am getting this error running ./apollo run-local 8085

..........
    BUILD SUCCESSFUL
    | Compiling 5 source files
    | Compiling 5 source files.....
    ***
    Metrics servlet injected into web.xml
    Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
    ***
    | Running Grails application
    Error occurred during initialization of VM
    Could not reserve enough space for object heap
    Error: Could not create the Java Virtual Machine.
    Error: A fatal exception has occurred. Program will exit.
    | Error Forked Grails VM exited with error

I looked over the same errors on Stack and made adjustments to the memory but I am still getting this error. I am new to Grails but I believe everything is setup correct and i can run a sample app (helloworld).
Here is the changes i made:

    -Xms512m -Xmx1g -XX:PermSize=256m
This is the memory

    free -m
                 total       used       free     shared    buffers     cached
    Mem:          2015       1297        718         56        169        859
    -/+ buffers/cache:        267       1748

Checking if parameters are being read

    $ ps -ef | grep java
    tomcat7  32158     1  1 11:02 ?        00:00:10 /usr/lib/jvm/default-java/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:PermSize=256m -XX:MaxPermSize=256m -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed -classpath /usr/share/tomcat7/bin/bootstrap.jar:/usr/share/tomcat7/bin/tomcat-juli.jar -Dcatalina.base=/var/lib/tomcat7 -Dcatalina.home=/usr/share/tomcat7 -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp org.apache.catalina.startup.Bootstrap start


I have this in my $HOME/.profile

    export JAVA_OPTS="-Xms512m -Xmx1g -XX:MaxPermSize=256m"

in my setenv.sh for Tomcat7

    export CATALINA_OPTS="-Xms512m -Xmx1g \
        -XX:+CMSClassUnloadingEnabled \
        -XX:+CMSPermGenSweepingEnabled \
        -XX:+UseConcMarkSweepGC \
        -XX:MaxPermSize=256m"

Versions: (i went w/ 2.4.5 per Apollo guide)
    $ grails -version
    Grails version: 2.4.5
    $ java -version
    java version "1.7.0_95"
    OpenJDK Runtime Environment (IcedTea 2.6.4) (7u95-2.6.4-0ubuntu0.14.04.1)
    OpenJDK Client VM (build 24.95-b01, mixed mode, sharing)

I am not sure what to change now - it seems the memory would be adequate? I know this isn't Apollo specific but maybe someone here has had the same problem? Please any thoughts would be great. thank you
Shane M.




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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: New WebApollo install issue (Grails)

nathandunn

On Feb 11, 2016, at 11:07 AM, Shane McCoy <[hidden email]> wrote:

Hey

I am getting this error running ./apollo run-local 8085

..........
    BUILD SUCCESSFUL
    | Compiling 5 source files
    | Compiling 5 source files.....
    ***
    Metrics servlet injected into web.xml
    Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
    ***
    | Running Grails application
    Error occurred during initialization of VM
    Could not reserve enough space for object heap
    Error: Could not create the Java Virtual Machine.
    Error: A fatal exception has occurred. Program will exit.
    | Error Forked Grails VM exited with error

I’m guessing that Java is requesting more memory then you have to allocate, and so exiting.  

So, when running it with run-local (for dev purposes), it actually has preset memory, of a max of up to 2 GB, though obviously this is high.  It is in BuildConfig.groovy:

run    : [maxMemory: 2048, minMemory: 64, debug: false , maxPerm: 1024, forkReserve: false],
My guess is that your machine doesn’t have sufficient memory to run this, or there is another process. 

My suggestions would be:
1 - get a machine with at least 4 GB’s of memory, especially if you are going to host to multiple users.  This will enable better caching and performance.    
2 - if (1) is not an immediate option (or to test, or if you are just running locally) your can edit your apollo-config.groovy create a line like this, so it will use less memory:

grails.project.fork = [
// configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
// compile: [maxMemory: 256, minMemory: 64, debug: false, maxPerm: 256, daemon:true],

test : false,
//run : false,
// configure settings for the test-app JVM, uses the daemon by default
//test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
// configure settings for the run-app JVM
run : [maxMemory: 1024, minMemory: 64, debug: false , maxPerm: 512, forkReserve: false],
// configure settings for the run-war JVM
war : [maxMemory: 1024, minMemory: 64, debug: false, maxPerm: 512, forkReserve: false],
// configure settings for the Console UI JVM
console: [maxMemory:
1024, minMemory: 64, debug: false, maxPerm: 512]
]

Setting the java size as done below works for tomcat, but not for the development mode (run-local).  

Nathan 

I looked over the same errors on Stack and made adjustments to the memory but I am still getting this error. I am new to Grails but I believe everything is setup correct and i can run a sample app (helloworld).
Here is the changes i made:

    -Xms512m -Xmx1g -XX:PermSize=256m
This is the memory

    free -m
                 total       used       free     shared    buffers     cached
    Mem:          2015       1297        718         56        169        859
    -/+ buffers/cache:        267       1748

Checking if parameters are being read

    $ ps -ef | grep java
    tomcat7  32158     1  1 11:02 ?        00:00:10 /usr/lib/jvm/default-java/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:PermSize=256m -XX:MaxPermSize=256m -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed -classpath /usr/share/tomcat7/bin/bootstrap.jar:/usr/share/tomcat7/bin/tomcat-juli.jar -Dcatalina.base=/var/lib/tomcat7 -Dcatalina.home=/usr/share/tomcat7 -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp org.apache.catalina.startup.Bootstrap start


I have this in my $HOME/.profile

    export JAVA_OPTS="-Xms512m -Xmx1g -XX:MaxPermSize=256m"

in my setenv.sh for Tomcat7

    export CATALINA_OPTS="-Xms512m -Xmx1g \
        -XX:+CMSClassUnloadingEnabled \
        -XX:+CMSPermGenSweepingEnabled \
        -XX:+UseConcMarkSweepGC \
        -XX:MaxPermSize=256m"

Versions: (i went w/ 2.4.5 per Apollo guide)
    $ grails -version
    Grails version: 2.4.5
    $ java -version
    java version "1.7.0_95"
    OpenJDK Runtime Environment (IcedTea 2.6.4) (7u95-2.6.4-0ubuntu0.14.04.1)
    OpenJDK Client VM (build 24.95-b01, mixed mode, sharing)

I am not sure what to change now - it seems the memory would be adequate? I know this isn't Apollo specific but maybe someone here has had the same problem? Please any thoughts would be great. thank you
Shane M.



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: New WebApollo install issue (Grails)

Shane McCoy
Thanks for the quick reply!
I will see what options I can take -
Shane M.

On Thu, Feb 11, 2016 at 2:18 PM, Nathan Dunn <[hidden email]> wrote:

On Feb 11, 2016, at 11:07 AM, Shane McCoy <[hidden email]> wrote:

Hey

I am getting this error running ./apollo run-local 8085

..........
    BUILD SUCCESSFUL
    | Compiling 5 source files
    | Compiling 5 source files.....
    ***
    Metrics servlet injected into web.xml
    Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
    ***
    | Running Grails application
    Error occurred during initialization of VM
    Could not reserve enough space for object heap
    Error: Could not create the Java Virtual Machine.
    Error: A fatal exception has occurred. Program will exit.
    | Error Forked Grails VM exited with error

I’m guessing that Java is requesting more memory then you have to allocate, and so exiting.  

So, when running it with run-local (for dev purposes), it actually has preset memory, of a max of up to 2 GB, though obviously this is high.  It is in BuildConfig.groovy:

run    : [maxMemory: 2048, minMemory: 64, debug: false , maxPerm: 1024, forkReserve: false],
My guess is that your machine doesn’t have sufficient memory to run this, or there is another process. 

My suggestions would be:
1 - get a machine with at least 4 GB’s of memory, especially if you are going to host to multiple users.  This will enable better caching and performance.    
2 - if (1) is not an immediate option (or to test, or if you are just running locally) your can edit your apollo-config.groovy create a line like this, so it will use less memory:

grails.project.fork = [
// configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
// compile: [maxMemory: 256, minMemory: 64, debug: false, maxPerm: 256, daemon:true],

test : false,
//run : false,
// configure settings for the test-app JVM, uses the daemon by default
//test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
// configure settings for the run-app JVM
run : [maxMemory: 1024, minMemory: 64, debug: false , maxPerm: 512, forkReserve: false],
// configure settings for the run-war JVM
war : [maxMemory: 1024, minMemory: 64, debug: false, maxPerm: 512, forkReserve: false],
// configure settings for the Console UI JVM
console: [maxMemory:
1024, minMemory: 64, debug: false, maxPerm: 512]
]

Setting the java size as done below works for tomcat, but not for the development mode (run-local).  

Nathan 

I looked over the same errors on Stack and made adjustments to the memory but I am still getting this error. I am new to Grails but I believe everything is setup correct and i can run a sample app (helloworld).
Here is the changes i made:

    -Xms512m -Xmx1g -XX:PermSize=256m
This is the memory

    free -m
                 total       used       free     shared    buffers     cached
    Mem:          2015       1297        718         56        169        859
    -/+ buffers/cache:        267       1748

Checking if parameters are being read

    $ ps -ef | grep java
    tomcat7  32158     1  1 11:02 ?        00:00:10 /usr/lib/jvm/default-java/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:PermSize=256m -XX:MaxPermSize=256m -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed -classpath /usr/share/tomcat7/bin/bootstrap.jar:/usr/share/tomcat7/bin/tomcat-juli.jar -Dcatalina.base=/var/lib/tomcat7 -Dcatalina.home=/usr/share/tomcat7 -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp org.apache.catalina.startup.Bootstrap start


I have this in my $HOME/.profile

    export JAVA_OPTS="-Xms512m -Xmx1g -XX:MaxPermSize=256m"

in my setenv.sh for Tomcat7

    export CATALINA_OPTS="-Xms512m -Xmx1g \
        -XX:+CMSClassUnloadingEnabled \
        -XX:+CMSPermGenSweepingEnabled \
        -XX:+UseConcMarkSweepGC \
        -XX:MaxPermSize=256m"

Versions: (i went w/ 2.4.5 per Apollo guide)
    $ grails -version
    Grails version: 2.4.5
    $ java -version
    java version "1.7.0_95"
    OpenJDK Runtime Environment (IcedTea 2.6.4) (7u95-2.6.4-0ubuntu0.14.04.1)
    OpenJDK Client VM (build 24.95-b01, mixed mode, sharing)

I am not sure what to change now - it seems the memory would be adequate? I know this isn't Apollo specific but maybe someone here has had the same problem? Please any thoughts would be great. thank you
Shane M.



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: New WebApollo install issue (Grails)

Shane McCoy
Hey!
So a lot has changed in a year! I'm currently still stuck at 2g but wanted to ask about an issue i have w/ /.apollo deploy
I am getting a blank screen at the URL. I have not added any data for generation yet. I assume i would still get a webapollo ui.
I am using postgresql. I edited apollo-config.groovy
Added (in production only)
datasource.dbCreate = "update" // one of...  ( where does the database name go? I don't understand this line, it seems i'm limited to the options given?)
username: chado database username
password: chado database pw
url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

I haven't changed any other settings and going to http://myipaddress/apollo is a blank page.
I want to use this w/ a already setup postgresql chado database.

I am going off of this guide: http://webapollo.readthedocs.org/en/latest/Setup.html
Thanks!

On Thu, Feb 11, 2016 at 2:29 PM, Shane McCoy <[hidden email]> wrote:
Thanks for the quick reply!
I will see what options I can take -
Shane M.

On Thu, Feb 11, 2016 at 2:18 PM, Nathan Dunn <[hidden email]> wrote:

On Feb 11, 2016, at 11:07 AM, Shane McCoy <[hidden email]> wrote:

Hey

I am getting this error running ./apollo run-local 8085

..........
    BUILD SUCCESSFUL
    | Compiling 5 source files
    | Compiling 5 source files.....
    ***
    Metrics servlet injected into web.xml
    Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
    ***
    | Running Grails application
    Error occurred during initialization of VM
    Could not reserve enough space for object heap
    Error: Could not create the Java Virtual Machine.
    Error: A fatal exception has occurred. Program will exit.
    | Error Forked Grails VM exited with error

I’m guessing that Java is requesting more memory then you have to allocate, and so exiting.  

So, when running it with run-local (for dev purposes), it actually has preset memory, of a max of up to 2 GB, though obviously this is high.  It is in BuildConfig.groovy:

run    : [maxMemory: 2048, minMemory: 64, debug: false , maxPerm: 1024, forkReserve: false],
My guess is that your machine doesn’t have sufficient memory to run this, or there is another process. 

My suggestions would be:
1 - get a machine with at least 4 GB’s of memory, especially if you are going to host to multiple users.  This will enable better caching and performance.    
2 - if (1) is not an immediate option (or to test, or if you are just running locally) your can edit your apollo-config.groovy create a line like this, so it will use less memory:

grails.project.fork = [
// configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
// compile: [maxMemory: 256, minMemory: 64, debug: false, maxPerm: 256, daemon:true],

test : false,
//run : false,
// configure settings for the test-app JVM, uses the daemon by default
//test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
// configure settings for the run-app JVM
run : [maxMemory: 1024, minMemory: 64, debug: false , maxPerm: 512, forkReserve: false],
// configure settings for the run-war JVM
war : [maxMemory: 1024, minMemory: 64, debug: false, maxPerm: 512, forkReserve: false],
// configure settings for the Console UI JVM
console: [maxMemory:
1024, minMemory: 64, debug: false, maxPerm: 512]
]

Setting the java size as done below works for tomcat, but not for the development mode (run-local).  

Nathan 

I looked over the same errors on Stack and made adjustments to the memory but I am still getting this error. I am new to Grails but I believe everything is setup correct and i can run a sample app (helloworld).
Here is the changes i made:

    -Xms512m -Xmx1g -XX:PermSize=256m
This is the memory

    free -m
                 total       used       free     shared    buffers     cached
    Mem:          2015       1297        718         56        169        859
    -/+ buffers/cache:        267       1748

Checking if parameters are being read

    $ ps -ef | grep java
    tomcat7  32158     1  1 11:02 ?        00:00:10 /usr/lib/jvm/default-java/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:PermSize=256m -XX:MaxPermSize=256m -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed -classpath /usr/share/tomcat7/bin/bootstrap.jar:/usr/share/tomcat7/bin/tomcat-juli.jar -Dcatalina.base=/var/lib/tomcat7 -Dcatalina.home=/usr/share/tomcat7 -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp org.apache.catalina.startup.Bootstrap start


I have this in my $HOME/.profile

    export JAVA_OPTS="-Xms512m -Xmx1g -XX:MaxPermSize=256m"

in my setenv.sh for Tomcat7

    export CATALINA_OPTS="-Xms512m -Xmx1g \
        -XX:+CMSClassUnloadingEnabled \
        -XX:+CMSPermGenSweepingEnabled \
        -XX:+UseConcMarkSweepGC \
        -XX:MaxPermSize=256m"

Versions: (i went w/ 2.4.5 per Apollo guide)
    $ grails -version
    Grails version: 2.4.5
    $ java -version
    java version "1.7.0_95"
    OpenJDK Runtime Environment (IcedTea 2.6.4) (7u95-2.6.4-0ubuntu0.14.04.1)
    OpenJDK Client VM (build 24.95-b01, mixed mode, sharing)

I am not sure what to change now - it seems the memory would be adequate? I know this isn't Apollo specific but maybe someone here has had the same problem? Please any thoughts would be great. thank you
Shane M.



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.








This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: New WebApollo install issue (Grails)

Colin
Hi Shaun

>url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

Just wanted to comment on this, actually, it would not be your IP and war here. It is kind of confusing that this "setting" is called a url, because it is actually a JDBC connector string, which actually references your local database, so it would not be using the war file name or even the IP address.

For example, if your database is named "apollodb", then your "url" would be

jdbc:postgresql://localhost/apollodb

It would generally just be localhost unless you have a separate database server. I think it might be worth adding some more comments about that in our setup guide, but I hope that helps!


-Colin

On Sat, Feb 20, 2016 at 2:36 PM, Shane McCoy <[hidden email]> wrote:
Hey!
So a lot has changed in a year! I'm currently still stuck at 2g but wanted to ask about an issue i have w/ /.apollo deploy
I am getting a blank screen at the URL. I have not added any data for generation yet. I assume i would still get a webapollo ui.
I am using postgresql. I edited apollo-config.groovy
Added (in production only)
datasource.dbCreate = "update" // one of...  ( where does the database name go? I don't understand this line, it seems i'm limited to the options given?)
username: chado database username
password: chado database pw
url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

I haven't changed any other settings and going to http://myipaddress/apollo is a blank page.
I want to use this w/ a already setup postgresql chado database.

I am going off of this guide: http://webapollo.readthedocs.org/en/latest/Setup.html
Thanks!

On Thu, Feb 11, 2016 at 2:29 PM, Shane McCoy <[hidden email]> wrote:
Thanks for the quick reply!
I will see what options I can take -
Shane M.

On Thu, Feb 11, 2016 at 2:18 PM, Nathan Dunn <[hidden email]> wrote:

On Feb 11, 2016, at 11:07 AM, Shane McCoy <[hidden email]> wrote:

Hey

I am getting this error running ./apollo run-local 8085

..........
    BUILD SUCCESSFUL
    | Compiling 5 source files
    | Compiling 5 source files.....
    ***
    Metrics servlet injected into web.xml
    Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
    ***
    | Running Grails application
    Error occurred during initialization of VM
    Could not reserve enough space for object heap
    Error: Could not create the Java Virtual Machine.
    Error: A fatal exception has occurred. Program will exit.
    | Error Forked Grails VM exited with error

I’m guessing that Java is requesting more memory then you have to allocate, and so exiting.  

So, when running it with run-local (for dev purposes), it actually has preset memory, of a max of up to 2 GB, though obviously this is high.  It is in BuildConfig.groovy:

run    : [maxMemory: 2048, minMemory: 64, debug: false , maxPerm: 1024, forkReserve: false],
My guess is that your machine doesn’t have sufficient memory to run this, or there is another process. 

My suggestions would be:
1 - get a machine with at least 4 GB’s of memory, especially if you are going to host to multiple users.  This will enable better caching and performance.    
2 - if (1) is not an immediate option (or to test, or if you are just running locally) your can edit your apollo-config.groovy create a line like this, so it will use less memory:

grails.project.fork = [
// configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
// compile: [maxMemory: 256, minMemory: 64, debug: false, maxPerm: 256, daemon:true],

test : false,
//run : false,
// configure settings for the test-app JVM, uses the daemon by default
//test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
// configure settings for the run-app JVM
run : [maxMemory: 1024, minMemory: 64, debug: false , maxPerm: 512, forkReserve: false],
// configure settings for the run-war JVM
war : [maxMemory: 1024, minMemory: 64, debug: false, maxPerm: 512, forkReserve: false],
// configure settings for the Console UI JVM
console: [maxMemory:
1024, minMemory: 64, debug: false, maxPerm: 512]
]

Setting the java size as done below works for tomcat, but not for the development mode (run-local).  

Nathan 

I looked over the same errors on Stack and made adjustments to the memory but I am still getting this error. I am new to Grails but I believe everything is setup correct and i can run a sample app (helloworld).
Here is the changes i made:

    -Xms512m -Xmx1g -XX:PermSize=256m
This is the memory

    free -m
                 total       used       free     shared    buffers     cached
    Mem:          2015       1297        718         56        169        859
    -/+ buffers/cache:        267       1748

Checking if parameters are being read

    $ ps -ef | grep java
    tomcat7  32158     1  1 11:02 ?        00:00:10 /usr/lib/jvm/default-java/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:PermSize=256m -XX:MaxPermSize=256m -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed -classpath /usr/share/tomcat7/bin/bootstrap.jar:/usr/share/tomcat7/bin/tomcat-juli.jar -Dcatalina.base=/var/lib/tomcat7 -Dcatalina.home=/usr/share/tomcat7 -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp org.apache.catalina.startup.Bootstrap start


I have this in my $HOME/.profile

    export JAVA_OPTS="-Xms512m -Xmx1g -XX:MaxPermSize=256m"

in my setenv.sh for Tomcat7

    export CATALINA_OPTS="-Xms512m -Xmx1g \
        -XX:+CMSClassUnloadingEnabled \
        -XX:+CMSPermGenSweepingEnabled \
        -XX:+UseConcMarkSweepGC \
        -XX:MaxPermSize=256m"

Versions: (i went w/ 2.4.5 per Apollo guide)
    $ grails -version
    Grails version: 2.4.5
    $ java -version
    java version "1.7.0_95"
    OpenJDK Runtime Environment (IcedTea 2.6.4) (7u95-2.6.4-0ubuntu0.14.04.1)
    OpenJDK Client VM (build 24.95-b01, mixed mode, sharing)

I am not sure what to change now - it seems the memory would be adequate? I know this isn't Apollo specific but maybe someone here has had the same problem? Please any thoughts would be great. thank you
Shane M.



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Re: New WebApollo install issue (Grails)

nathandunn
In reply to this post by Shane McCoy

Shane the IP will be where the database machine is:

url: jdbc:postgresql://myipaddress/apollo

In this case “apollo” refers to the database name.  

“ myipaddress” is typically localhost or 127.0.0.1 if its not the same machine.  If its on a different machine its, it would be the IP / DNS name of that:

This is one of my dev production ones:

  production {
        dataSource.dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', ''
        dataSource.username = "ndunn"
//    dataSource.password = "<CHANGEME>"
        dataSource.driverClassName = "org.postgresql.Driver"
        dataSource.dialect = org.hibernate.dialect.PostgresPlusDialect
        dataSource.url = "jdbc:postgresql://localhost/apollo-production"
    }


Nathan

On Feb 20, 2016, at 12:36 PM, Shane McCoy <[hidden email]> wrote:

Hey!
So a lot has changed in a year! I'm currently still stuck at 2g but wanted to ask about an issue i have w/ /.apollo deploy
I am getting a blank screen at the URL. I have not added any data for generation yet. I assume i would still get a webapollo ui.
I am using postgresql. I edited apollo-config.groovy
Added (in production only)
datasource.dbCreate = "update" // one of...  ( where does the database name go? I don't understand this line, it seems i'm limited to the options given?)
username: chado database username
password: chado database pw
url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

I haven't changed any other settings and going to http://myipaddress/apollo is a blank page.
I want to use this w/ a already setup postgresql chado database.

I am going off of this guide: http://webapollo.readthedocs.org/en/latest/Setup.html
Thanks!

On Thu, Feb 11, 2016 at 2:29 PM, Shane McCoy <[hidden email]> wrote:
Thanks for the quick reply!
I will see what options I can take -
Shane M.

On Thu, Feb 11, 2016 at 2:18 PM, Nathan Dunn <[hidden email]> wrote:

On Feb 11, 2016, at 11:07 AM, Shane McCoy <[hidden email]> wrote:

Hey

I am getting this error running ./apollo run-local 8085

..........
    BUILD SUCCESSFUL
    | Compiling 5 source files
    | Compiling 5 source files.....
    ***
    Metrics servlet injected into web.xml
    Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
    ***
    | Running Grails application
    Error occurred during initialization of VM
    Could not reserve enough space for object heap
    Error: Could not create the Java Virtual Machine.
    Error: A fatal exception has occurred. Program will exit.
    | Error Forked Grails VM exited with error

I’m guessing that Java is requesting more memory then you have to allocate, and so exiting.  

So, when running it with run-local (for dev purposes), it actually has preset memory, of a max of up to 2 GB, though obviously this is high.  It is in BuildConfig.groovy:

run    : [maxMemory: 2048, minMemory: 64, debug: false , maxPerm: 1024, forkReserve: false],
My guess is that your machine doesn’t have sufficient memory to run this, or there is another process. 

My suggestions would be:
1 - get a machine with at least 4 GB’s of memory, especially if you are going to host to multiple users.  This will enable better caching and performance.    
2 - if (1) is not an immediate option (or to test, or if you are just running locally) your can edit your apollo-config.groovy create a line like this, so it will use less memory:

grails.project.fork = [
// configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
// compile: [maxMemory: 256, minMemory: 64, debug: false, maxPerm: 256, daemon:true],

test : false,
//run : false,
// configure settings for the test-app JVM, uses the daemon by default
//test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
// configure settings for the run-app JVM
run : [maxMemory: 1024, minMemory: 64, debug: false , maxPerm: 512, forkReserve: false],
// configure settings for the run-war JVM
war : [maxMemory: 1024, minMemory: 64, debug: false, maxPerm: 512, forkReserve: false],
// configure settings for the Console UI JVM
console: [maxMemory:
1024, minMemory: 64, debug: false, maxPerm: 512]
]

Setting the java size as done below works for tomcat, but not for the development mode (run-local).  

Nathan 

I looked over the same errors on Stack and made adjustments to the memory but I am still getting this error. I am new to Grails but I believe everything is setup correct and i can run a sample app (helloworld).
Here is the changes i made:

    -Xms512m -Xmx1g -XX:PermSize=256m
This is the memory

    free -m
                 total       used       free     shared    buffers     cached
    Mem:          2015       1297        718         56        169        859
    -/+ buffers/cache:        267       1748

Checking if parameters are being read

    $ ps -ef | grep java
    tomcat7  32158     1  1 11:02 ?        00:00:10 /usr/lib/jvm/default-java/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:PermSize=256m -XX:MaxPermSize=256m -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed -classpath /usr/share/tomcat7/bin/bootstrap.jar:/usr/share/tomcat7/bin/tomcat-juli.jar -Dcatalina.base=/var/lib/tomcat7 -Dcatalina.home=/usr/share/tomcat7 -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp org.apache.catalina.startup.Bootstrap start


I have this in my $HOME/.profile

    export JAVA_OPTS="-Xms512m -Xmx1g -XX:MaxPermSize=256m"

in my setenv.sh for Tomcat7

    export CATALINA_OPTS="-Xms512m -Xmx1g \
        -XX:+CMSClassUnloadingEnabled \
        -XX:+CMSPermGenSweepingEnabled \
        -XX:+UseConcMarkSweepGC \
        -XX:MaxPermSize=256m"

Versions: (i went w/ 2.4.5 per Apollo guide)
    $ grails -version
    Grails version: 2.4.5
    $ java -version
    java version "1.7.0_95"
    OpenJDK Runtime Environment (IcedTea 2.6.4) (7u95-2.6.4-0ubuntu0.14.04.1)
    OpenJDK Client VM (build 24.95-b01, mixed mode, sharing)

I am not sure what to change now - it seems the memory would be adequate? I know this isn't Apollo specific but maybe someone here has had the same problem? Please any thoughts would be great. thank you
Shane M.



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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Re: New WebApollo install issue (Grails)

Shane McCoy
In reply to this post by Colin
Ok, that makes more sense now! thank you very much.
I'll will try with correct settings,
cheers!

On Sat, Feb 20, 2016 at 7:53 PM, Colin <[hidden email]> wrote:
Hi Shaun

>url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

Just wanted to comment on this, actually, it would not be your IP and war here. It is kind of confusing that this "setting" is called a url, because it is actually a JDBC connector string, which actually references your local database, so it would not be using the war file name or even the IP address.

For example, if your database is named "apollodb", then your "url" would be

jdbc:postgresql://localhost/apollodb

It would generally just be localhost unless you have a separate database server. I think it might be worth adding some more comments about that in our setup guide, but I hope that helps!


-Colin

On Sat, Feb 20, 2016 at 2:36 PM, Shane McCoy <[hidden email]> wrote:
Hey!
So a lot has changed in a year! I'm currently still stuck at 2g but wanted to ask about an issue i have w/ /.apollo deploy
I am getting a blank screen at the URL. I have not added any data for generation yet. I assume i would still get a webapollo ui.
I am using postgresql. I edited apollo-config.groovy
Added (in production only)
datasource.dbCreate = "update" // one of...  ( where does the database name go? I don't understand this line, it seems i'm limited to the options given?)
username: chado database username
password: chado database pw
url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

I haven't changed any other settings and going to http://myipaddress/apollo is a blank page.
I want to use this w/ a already setup postgresql chado database.

I am going off of this guide: http://webapollo.readthedocs.org/en/latest/Setup.html
Thanks!

On Thu, Feb 11, 2016 at 2:29 PM, Shane McCoy <[hidden email]> wrote:
Thanks for the quick reply!
I will see what options I can take -
Shane M.

On Thu, Feb 11, 2016 at 2:18 PM, Nathan Dunn <[hidden email]> wrote:

On Feb 11, 2016, at 11:07 AM, Shane McCoy <[hidden email]> wrote:

Hey

I am getting this error running ./apollo run-local 8085

..........
    BUILD SUCCESSFUL
    | Compiling 5 source files
    | Compiling 5 source files.....
    ***
    Metrics servlet injected into web.xml
    Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
    ***
    | Running Grails application
    Error occurred during initialization of VM
    Could not reserve enough space for object heap
    Error: Could not create the Java Virtual Machine.
    Error: A fatal exception has occurred. Program will exit.
    | Error Forked Grails VM exited with error

I’m guessing that Java is requesting more memory then you have to allocate, and so exiting.  

So, when running it with run-local (for dev purposes), it actually has preset memory, of a max of up to 2 GB, though obviously this is high.  It is in BuildConfig.groovy:

run    : [maxMemory: 2048, minMemory: 64, debug: false , maxPerm: 1024, forkReserve: false],
My guess is that your machine doesn’t have sufficient memory to run this, or there is another process. 

My suggestions would be:
1 - get a machine with at least 4 GB’s of memory, especially if you are going to host to multiple users.  This will enable better caching and performance.    
2 - if (1) is not an immediate option (or to test, or if you are just running locally) your can edit your apollo-config.groovy create a line like this, so it will use less memory:

grails.project.fork = [
// configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
// compile: [maxMemory: 256, minMemory: 64, debug: false, maxPerm: 256, daemon:true],

test : false,
//run : false,
// configure settings for the test-app JVM, uses the daemon by default
//test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
// configure settings for the run-app JVM
run : [maxMemory: 1024, minMemory: 64, debug: false , maxPerm: 512, forkReserve: false],
// configure settings for the run-war JVM
war : [maxMemory: 1024, minMemory: 64, debug: false, maxPerm: 512, forkReserve: false],
// configure settings for the Console UI JVM
console: [maxMemory:
1024, minMemory: 64, debug: false, maxPerm: 512]
]

Setting the java size as done below works for tomcat, but not for the development mode (run-local).  

Nathan 

I looked over the same errors on Stack and made adjustments to the memory but I am still getting this error. I am new to Grails but I believe everything is setup correct and i can run a sample app (helloworld).
Here is the changes i made:

    -Xms512m -Xmx1g -XX:PermSize=256m
This is the memory

    free -m
                 total       used       free     shared    buffers     cached
    Mem:          2015       1297        718         56        169        859
    -/+ buffers/cache:        267       1748

Checking if parameters are being read

    $ ps -ef | grep java
    tomcat7  32158     1  1 11:02 ?        00:00:10 /usr/lib/jvm/default-java/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:PermSize=256m -XX:MaxPermSize=256m -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed -classpath /usr/share/tomcat7/bin/bootstrap.jar:/usr/share/tomcat7/bin/tomcat-juli.jar -Dcatalina.base=/var/lib/tomcat7 -Dcatalina.home=/usr/share/tomcat7 -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp org.apache.catalina.startup.Bootstrap start


I have this in my $HOME/.profile

    export JAVA_OPTS="-Xms512m -Xmx1g -XX:MaxPermSize=256m"

in my setenv.sh for Tomcat7

    export CATALINA_OPTS="-Xms512m -Xmx1g \
        -XX:+CMSClassUnloadingEnabled \
        -XX:+CMSPermGenSweepingEnabled \
        -XX:+UseConcMarkSweepGC \
        -XX:MaxPermSize=256m"

Versions: (i went w/ 2.4.5 per Apollo guide)
    $ grails -version
    Grails version: 2.4.5
    $ java -version
    java version "1.7.0_95"
    OpenJDK Runtime Environment (IcedTea 2.6.4) (7u95-2.6.4-0ubuntu0.14.04.1)
    OpenJDK Client VM (build 24.95-b01, mixed mode, sharing)

I am not sure what to change now - it seems the memory would be adequate? I know this isn't Apollo specific but maybe someone here has had the same problem? Please any thoughts would be great. thank you
Shane M.



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







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Re: New WebApollo install issue (Grails)

Shane McCoy
Hey! I made the changes but I am still getting a blank screen.

I checked catalina.out, here is the last output:

/var/log/tomcat7$ tail -f catalina.out
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [PoolCleaner[25416670:1456019437960]] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@1b2e3fc]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 20, 2016 7:51:28 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 20, 2016 7:51:28 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 77106 ms


Is this still a memory issue then?
I have updated tomcat memory to your doc specs already.
Thanks!
shane

On Sat, Feb 20, 2016 at 7:55 PM, Shane McCoy <[hidden email]> wrote:
Ok, that makes more sense now! thank you very much.
I'll will try with correct settings,
cheers!

On Sat, Feb 20, 2016 at 7:53 PM, Colin <[hidden email]> wrote:
Hi Shaun

>url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

Just wanted to comment on this, actually, it would not be your IP and war here. It is kind of confusing that this "setting" is called a url, because it is actually a JDBC connector string, which actually references your local database, so it would not be using the war file name or even the IP address.

For example, if your database is named "apollodb", then your "url" would be

jdbc:postgresql://localhost/apollodb

It would generally just be localhost unless you have a separate database server. I think it might be worth adding some more comments about that in our setup guide, but I hope that helps!


-Colin

On Sat, Feb 20, 2016 at 2:36 PM, Shane McCoy <[hidden email]> wrote:
Hey!
So a lot has changed in a year! I'm currently still stuck at 2g but wanted to ask about an issue i have w/ /.apollo deploy
I am getting a blank screen at the URL. I have not added any data for generation yet. I assume i would still get a webapollo ui.
I am using postgresql. I edited apollo-config.groovy
Added (in production only)
datasource.dbCreate = "update" // one of...  ( where does the database name go? I don't understand this line, it seems i'm limited to the options given?)
username: chado database username
password: chado database pw
url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

I haven't changed any other settings and going to http://myipaddress/apollo is a blank page.
I want to use this w/ a already setup postgresql chado database.

I am going off of this guide: http://webapollo.readthedocs.org/en/latest/Setup.html
Thanks!

On Thu, Feb 11, 2016 at 2:29 PM, Shane McCoy <[hidden email]> wrote:
Thanks for the quick reply!
I will see what options I can take -
Shane M.

On Thu, Feb 11, 2016 at 2:18 PM, Nathan Dunn <[hidden email]> wrote:

On Feb 11, 2016, at 11:07 AM, Shane McCoy <[hidden email]> wrote:

Hey

I am getting this error running ./apollo run-local 8085

..........
    BUILD SUCCESSFUL
    | Compiling 5 source files
    | Compiling 5 source files.....
    ***
    Metrics servlet injected into web.xml
    Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
    ***
    | Running Grails application
    Error occurred during initialization of VM
    Could not reserve enough space for object heap
    Error: Could not create the Java Virtual Machine.
    Error: A fatal exception has occurred. Program will exit.
    | Error Forked Grails VM exited with error

I’m guessing that Java is requesting more memory then you have to allocate, and so exiting.  

So, when running it with run-local (for dev purposes), it actually has preset memory, of a max of up to 2 GB, though obviously this is high.  It is in BuildConfig.groovy:

run    : [maxMemory: 2048, minMemory: 64, debug: false , maxPerm: 1024, forkReserve: false],
My guess is that your machine doesn’t have sufficient memory to run this, or there is another process. 

My suggestions would be:
1 - get a machine with at least 4 GB’s of memory, especially if you are going to host to multiple users.  This will enable better caching and performance.    
2 - if (1) is not an immediate option (or to test, or if you are just running locally) your can edit your apollo-config.groovy create a line like this, so it will use less memory:

grails.project.fork = [
// configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
// compile: [maxMemory: 256, minMemory: 64, debug: false, maxPerm: 256, daemon:true],

test : false,
//run : false,
// configure settings for the test-app JVM, uses the daemon by default
//test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
// configure settings for the run-app JVM
run : [maxMemory: 1024, minMemory: 64, debug: false , maxPerm: 512, forkReserve: false],
// configure settings for the run-war JVM
war : [maxMemory: 1024, minMemory: 64, debug: false, maxPerm: 512, forkReserve: false],
// configure settings for the Console UI JVM
console: [maxMemory:
1024, minMemory: 64, debug: false, maxPerm: 512]
]

Setting the java size as done below works for tomcat, but not for the development mode (run-local).  

Nathan 

I looked over the same errors on Stack and made adjustments to the memory but I am still getting this error. I am new to Grails but I believe everything is setup correct and i can run a sample app (helloworld).
Here is the changes i made:

    -Xms512m -Xmx1g -XX:PermSize=256m
This is the memory

    free -m
                 total       used       free     shared    buffers     cached
    Mem:          2015       1297        718         56        169        859
    -/+ buffers/cache:        267       1748

Checking if parameters are being read

    $ ps -ef | grep java
    tomcat7  32158     1  1 11:02 ?        00:00:10 /usr/lib/jvm/default-java/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:PermSize=256m -XX:MaxPermSize=256m -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed -classpath /usr/share/tomcat7/bin/bootstrap.jar:/usr/share/tomcat7/bin/tomcat-juli.jar -Dcatalina.base=/var/lib/tomcat7 -Dcatalina.home=/usr/share/tomcat7 -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp org.apache.catalina.startup.Bootstrap start


I have this in my $HOME/.profile

    export JAVA_OPTS="-Xms512m -Xmx1g -XX:MaxPermSize=256m"

in my setenv.sh for Tomcat7

    export CATALINA_OPTS="-Xms512m -Xmx1g \
        -XX:+CMSClassUnloadingEnabled \
        -XX:+CMSPermGenSweepingEnabled \
        -XX:+UseConcMarkSweepGC \
        -XX:MaxPermSize=256m"

Versions: (i went w/ 2.4.5 per Apollo guide)
    $ grails -version
    Grails version: 2.4.5
    $ java -version
    java version "1.7.0_95"
    OpenJDK Runtime Environment (IcedTea 2.6.4) (7u95-2.6.4-0ubuntu0.14.04.1)
    OpenJDK Client VM (build 24.95-b01, mixed mode, sharing)

I am not sure what to change now - it seems the memory would be adequate? I know this isn't Apollo specific but maybe someone here has had the same problem? Please any thoughts would be great. thank you
Shane M.



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Re: New WebApollo install issue (Grails)

nathandunn
Try opening in an incognito or another browser of doing a shift reload to flush the cache. 

That being said .. This stack trace looks a bit terse.   Typically shiro (the security plugin) will reload but I don't see that here.  Maybe further up? 

Nathan

On Feb 20, 2016, at 6:04 PM, Shane McCoy <[hidden email]> wrote:

Hey! I made the changes but I am still getting a blank screen.

I checked catalina.out, here is the last output:

/var/log/tomcat7$ tail -f catalina.out
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [PoolCleaner[25416670:1456019437960]] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@1b2e3fc]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 20, 2016 7:51:28 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 20, 2016 7:51:28 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 77106 ms


Is this still a memory issue then?
I have updated tomcat memory to your doc specs already.
Thanks!
shane

On Sat, Feb 20, 2016 at 7:55 PM, Shane McCoy <[hidden email]> wrote:
Ok, that makes more sense now! thank you very much.
I'll will try with correct settings,
cheers!

On Sat, Feb 20, 2016 at 7:53 PM, Colin <[hidden email]> wrote:
Hi Shaun

>url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

Just wanted to comment on this, actually, it would not be your IP and war here. It is kind of confusing that this "setting" is called a url, because it is actually a JDBC connector string, which actually references your local database, so it would not be using the war file name or even the IP address.

For example, if your database is named "apollodb", then your "url" would be

jdbc:postgresql://localhost/apollodb

It would generally just be localhost unless you have a separate database server. I think it might be worth adding some more comments about that in our setup guide, but I hope that helps!


-Colin

On Sat, Feb 20, 2016 at 2:36 PM, Shane McCoy <[hidden email]> wrote:
Hey!
So a lot has changed in a year! I'm currently still stuck at 2g but wanted to ask about an issue i have w/ /.apollo deploy
I am getting a blank screen at the URL. I have not added any data for generation yet. I assume i would still get a webapollo ui.
I am using postgresql. I edited apollo-config.groovy
Added (in production only)
datasource.dbCreate = "update" // one of...  ( where does the database name go? I don't understand this line, it seems i'm limited to the options given?)
username: chado database username
password: chado database pw
url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

I haven't changed any other settings and going to http://myipaddress/apollo is a blank page.
I want to use this w/ a already setup postgresql chado database.

I am going off of this guide: http://webapollo.readthedocs.org/en/latest/Setup.html
Thanks!

On Thu, Feb 11, 2016 at 2:29 PM, Shane McCoy <[hidden email]> wrote:
Thanks for the quick reply!
I will see what options I can take -
Shane M.

On Thu, Feb 11, 2016 at 2:18 PM, Nathan Dunn <[hidden email]> wrote:

On Feb 11, 2016, at 11:07 AM, Shane McCoy <[hidden email]> wrote:

Hey

I am getting this error running ./apollo run-local 8085

..........
    BUILD SUCCESSFUL
    | Compiling 5 source files
    | Compiling 5 source files.....
    ***
    Metrics servlet injected into web.xml
    Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
    ***
    | Running Grails application
    Error occurred during initialization of VM
    Could not reserve enough space for object heap
    Error: Could not create the Java Virtual Machine.
    Error: A fatal exception has occurred. Program will exit.
    | Error Forked Grails VM exited with error

I’m guessing that Java is requesting more memory then you have to allocate, and so exiting.  

So, when running it with run-local (for dev purposes), it actually has preset memory, of a max of up to 2 GB, though obviously this is high.  It is in BuildConfig.groovy:

run    : [maxMemory: 2048, minMemory: 64, debug: false , maxPerm: 1024, forkReserve: false],
My guess is that your machine doesn’t have sufficient memory to run this, or there is another process. 

My suggestions would be:
1 - get a machine with at least 4 GB’s of memory, especially if you are going to host to multiple users.  This will enable better caching and performance.    
2 - if (1) is not an immediate option (or to test, or if you are just running locally) your can edit your apollo-config.groovy create a line like this, so it will use less memory:

grails.project.fork = [
// configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
// compile: [maxMemory: 256, minMemory: 64, debug: false, maxPerm: 256, daemon:true],

test : false,
//run : false,
// configure settings for the test-app JVM, uses the daemon by default
//test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
// configure settings for the run-app JVM
run : [maxMemory: 1024, minMemory: 64, debug: false , maxPerm: 512, forkReserve: false],
// configure settings for the run-war JVM
war : [maxMemory: 1024, minMemory: 64, debug: false, maxPerm: 512, forkReserve: false],
// configure settings for the Console UI JVM
console: [maxMemory:
1024, minMemory: 64, debug: false, maxPerm: 512]
]

Setting the java size as done below works for tomcat, but not for the development mode (run-local).  

Nathan 

I looked over the same errors on Stack and made adjustments to the memory but I am still getting this error. I am new to Grails but I believe everything is setup correct and i can run a sample app (helloworld).
Here is the changes i made:

    -Xms512m -Xmx1g -XX:PermSize=256m
This is the memory

    free -m
                 total       used       free     shared    buffers     cached
    Mem:          2015       1297        718         56        169        859
    -/+ buffers/cache:        267       1748

Checking if parameters are being read

    $ ps -ef | grep java
    tomcat7  32158     1  1 11:02 ?        00:00:10 /usr/lib/jvm/default-java/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:PermSize=256m -XX:MaxPermSize=256m -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed -classpath /usr/share/tomcat7/bin/bootstrap.jar:/usr/share/tomcat7/bin/tomcat-juli.jar -Dcatalina.base=/var/lib/tomcat7 -Dcatalina.home=/usr/share/tomcat7 -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp org.apache.catalina.startup.Bootstrap start


I have this in my $HOME/.profile

    export JAVA_OPTS="-Xms512m -Xmx1g -XX:MaxPermSize=256m"

in my setenv.sh for Tomcat7

    export CATALINA_OPTS="-Xms512m -Xmx1g \
        -XX:+CMSClassUnloadingEnabled \
        -XX:+CMSPermGenSweepingEnabled \
        -XX:+UseConcMarkSweepGC \
        -XX:MaxPermSize=256m"

Versions: (i went w/ 2.4.5 per Apollo guide)
    $ grails -version
    Grails version: 2.4.5
    $ java -version
    java version "1.7.0_95"
    OpenJDK Runtime Environment (IcedTea 2.6.4) (7u95-2.6.4-0ubuntu0.14.04.1)
    OpenJDK Client VM (build 24.95-b01, mixed mode, sharing)

I am not sure what to change now - it seems the memory would be adequate? I know this isn't Apollo specific but maybe someone here has had the same problem? Please any thoughts would be great. thank you
Shane M.



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Re: New WebApollo install issue (Grails)

Shane McCoy
I missed a bit from the log, here is catalina.out from a restart of tomcat7:

 * Stopping Tomcat servlet engine tomcat7                                [ OK ]
 * Starting Tomcat servlet engine tomcat7                                [ OK ]
--------------------------$$:/var/log/tomcat7$ tail -f catalina.out
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor /etc/tomcat7/Catalina/localhost/host-manager.xml
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
^[[AFeb 20, 2016 8:44:43 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 20, 2016 8:44:43 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.

Configuring Shiro ...

Shiro Configured
2016-02-20 20:45:40,539 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column id int8 not null
2016-02-20 20:45:40,543 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,546 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column version int8 not null
2016-02-20 20:45:40,548 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,550 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column program_version varchar(255) not null
2016-02-20 20:45:40,552 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "program_version" contains null values
2016-02-20 20:45:40,554 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_name varchar(255) not null
2016-02-20 20:45:40,555 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_name" contains null values
2016-02-20 20:45:40,558 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_version varchar(255) not null
2016-02-20 20:45:40,559 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_version" contains null values
2016-02-20 20:45:40,562 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column time_executed timestamp not null
2016-02-20 20:45:40,563 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "time_executed" contains null values
2016-02-20 20:45:40,566 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column id int8 not null
2016-02-20 20:45:40,567 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,569 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column version int8 not null
2016-02-20 20:45:40,570 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,573 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column id int8 not null
2016-02-20 20:45:40,574 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,577 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column version int8 not null
2016-02-20 20:45:40,578 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,583 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column is_relationship_type int4 not null
2016-02-20 20:45:40,584 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "is_relationship_type" contains null values
2016-02-20 20:45:40,587 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column id int8 not null
2016-02-20 20:45:40,588 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,590 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column version int8 not null
2016-02-20 20:45:40,591 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,593 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column objectcvterm_id int8 not null
2016-02-20 20:45:40,594 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" contains null values
2016-02-20 20:45:40,598 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column subjectcvterm_id int8 not null
2016-02-20 20:45:40,599 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" contains null values
2016-02-20 20:45:40,602 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column id int8 not null
2016-02-20 20:45:40,602 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,606 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column version int8 not null
2016-02-20 20:45:40,607 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,610 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add column id int8 not null
2016-02-20 20:45:40,612 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,616 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column id int8 not null
2016-02-20 20:45:40,617 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,620 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column version int8 not null
2016-02-20 20:45:40,621 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,632 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column unique_name varchar(255) not null
2016-02-20 20:45:40,633 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "unique_name" contains null values
2016-02-20 20:45:40,636 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column class varchar(255) not null
2016-02-20 20:45:40,637 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "class" contains null values
2016-02-20 20:45:40,641 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column id int8 not null
2016-02-20 20:45:40,642 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,645 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column version int8 not null
2016-02-20 20:45:40,646 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,652 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column child_feature_id int8 not null
2016-02-20 20:45:40,653 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "child_feature_id" contains null values
2016-02-20 20:45:40,656 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column parent_feature_id int8 not null
2016-02-20 20:45:40,657 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "parent_feature_id" contains null values
2016-02-20 20:45:40,660 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column id int8 not null
2016-02-20 20:45:40,661 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,668 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column version int8 not null
2016-02-20 20:45:40,670 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,672 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column publication_id int8 not null
2016-02-20 20:45:40,677 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "publication_id" contains null values
2016-02-20 20:45:40,679 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column id int8 not null
2016-02-20 20:45:40,681 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,684 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column version int8 not null
2016-02-20 20:45:40,685 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,687 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column directory varchar(255)
2016-02-20 20:45:40,688 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,692 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column id int8 not null
2016-02-20 20:45:40,693 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,701 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column version int8 not null
2016-02-20 20:45:40,702 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,704 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column directory varchar(255) not null
2016-02-20 20:45:40,706 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "directory" contains null values
2016-02-20 20:45:40,709 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column id int8 not null
2016-02-20 20:45:40,710 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,715 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column version int8 not null
2016-02-20 20:45:40,716 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,719 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column synonymsgml varchar(255) not null
2016-02-20 20:45:40,720 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "synonymsgml" contains null values
2016-02-20 20:45:40,724 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_feature add constraint FK_8m30ycwh545b4aoxor9sbk1oq foreign key (analysis_id) references analysis
2016-02-20 20:45:40,725 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8m30ycwh545b4aoxor9sbk1oq" for relation "analysis_feature" already exists
2016-02-20 20:45:40,727 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_feature add constraint FK_l94xl424xp988f06gr2b3t5tw foreign key (feature_id) references feature
2016-02-20 20:45:40,728 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_l94xl424xp988f06gr2b3t5tw" for relation "analysis_feature" already exists
2016-02-20 20:45:40,730 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_property add constraint FK_38g8n4bitmdwkrcs217uexrwx foreign key (analysis_id) references analysis
2016-02-20 20:45:40,731 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_38g8n4bitmdwkrcs217uexrwx" for relation "analysis_property" already exists
2016-02-20 20:45:40,733 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_property add constraint FK_9o7xs7saygim8y0sm4ostvpc1 foreign key (type_id) references cvterm
2016-02-20 20:45:40,734 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_9o7xs7saygim8y0sm4ostvpc1" for relation "analysis_property" already exists
2016-02-20 20:45:40,737 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add constraint FK_oksfqluv12ktmut9s6o9jla7a foreign key (cv_id) references cv
2016-02-20 20:45:40,739 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_oksfqluv12ktmut9s6o9jla7a" for relation "cvterm" already exists
2016-02-20 20:45:40,741 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add constraint FK_6d097oy44230tuoo8lb8dkkcp foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,742 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_6d097oy44230tuoo8lb8dkkcp" for relation "cvterm" already exists
2016-02-20 20:45:40,744 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_ke2nrw91sxil8mv7osgv83pw1 foreign key (cv_id) references cv
2016-02-20 20:45:40,745 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ke2nrw91sxil8mv7osgv83pw1" for relation "cvterm_path" already exists
2016-02-20 20:45:40,748 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_tlfh10092i00g6rlv589naqy5 foreign key (objectcvterm_id) references cvterm
2016-02-20 20:45:40,749 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tlfh10092i00g6rlv589naqy5" for relation "cvterm_path" already exists
2016-02-20 20:45:40,751 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_nq02ir0qeydr5tj3071k9gl7b foreign key (subjectcvterm_id) references cvterm
2016-02-20 20:45:40,752 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_nq02ir0qeydr5tj3071k9gl7b" for relation "cvterm_path" already exists
2016-02-20 20:45:40,760 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_jaqi1bk3t2c0m3pybmparp856 foreign key (type_id) references cvterm
2016-02-20 20:45:40,761 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jaqi1bk3t2c0m3pybmparp856" for relation "cvterm_path" already exists
2016-02-20 20:45:40,763 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_r1o1rnfnsf7oipuv1h7h1fln7 foreign key (objectcvterm_id) references cvterm
2016-02-20 20:45:40,766 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,771 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_pwxrfyx6rqu5krq4nj5wa3u4f foreign key (subjectcvterm_id) references cvterm
2016-02-20 20:45:40,775 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,777 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_ob1d0vrfaix8b28j4tvilqnyv foreign key (type_id) references cvterm
2016-02-20 20:45:40,778 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ob1d0vrfaix8b28j4tvilqnyv" for relation "cvterm_relationship" already exists
2016-02-20 20:45:40,781 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add constraint FK_np3tfcu9g867to3qux6raf9y8 foreign key (db_id) references db
2016-02-20 20:45:40,782 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_np3tfcu9g867to3qux6raf9y8" for relation "dbxref" already exists
2016-02-20 20:45:40,786 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref_property add constraint FK_3p1ssctww083s0tt65mmm64uo foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,787 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_3p1ssctww083s0tt65mmm64uo" for relation "dbxref_property" already exists
2016-02-20 20:45:40,792 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref_property add constraint FK_t6ojbvugx8kou45oklsie3rt5 foreign key (type_id) references cvterm
2016-02-20 20:45:40,793 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_t6ojbvugx8kou45oklsie3rt5" for relation "dbxref_property" already exists
2016-02-20 20:45:40,796 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table environmentcvterm add constraint FK_tql9djnqw1d7migfndoj3lrph foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,803 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tql9djnqw1d7migfndoj3lrph" for relation "environmentcvterm" already exists
2016-02-20 20:45:40,805 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table environmentcvterm add constraint FK_rrwb96jjqgtg077yv8pbim3jj foreign key (environment_id) references environment
2016-02-20 20:45:40,807 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_rrwb96jjqgtg077yv8pbim3jj" for relation "environmentcvterm" already exists
2016-02-20 20:45:40,813 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add constraint FK_hc4vrafs0ws7ugdkp0n6u3xdo foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,816 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_hc4vrafs0ws7ugdkp0n6u3xdo" for relation "feature" already exists
2016-02-20 20:45:40,819 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_dbxref add constraint FK_n6n7lheb1qkmlde8u6gvvjxne foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,821 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_n6n7lheb1qkmlde8u6gvvjxne" for relation "feature_dbxref" already exists
2016-02-20 20:45:40,829 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_dbxref add constraint FK_1mrfkxbb3n7fhjxcrkxappdn8 foreign key (feature_featuredbxrefs_id) references feature
2016-02-20 20:45:40,831 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_1mrfkxbb3n7fhjxcrkxappdn8" for relation "feature_dbxref" already exists
2016-02-20 20:45:40,836 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_feature_phenotypes add constraint FK_dy5g29heir5ic3d36okyuihho foreign key (phenotype_id) references phenotype
2016-02-20 20:45:40,839 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_dy5g29heir5ic3d36okyuihho" for relation "feature_feature_phenotypes" already exists
2016-02-20 20:45:40,842 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_feature_phenotypes add constraint FK_aqr7eiyx6puju6elciwubbwmo foreign key (feature_id) references feature
2016-02-20 20:45:40,843 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_aqr7eiyx6puju6elciwubbwmo" for relation "feature_feature_phenotypes" already exists
2016-02-20 20:45:40,847 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_hak8r429shmpho06rbyvwnmt0 foreign key (chromosome_feature_id) references feature
2016-02-20 20:45:40,848 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_hak8r429shmpho06rbyvwnmt0" for relation "feature_genotype" already exists
2016-02-20 20:45:40,856 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_b42u9iq4kuqe5ay544do81n32 foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,857 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_b42u9iq4kuqe5ay544do81n32" for relation "feature_genotype" already exists
2016-02-20 20:45:40,859 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_cm3gqs38fa2lpllgoum8n4kgn foreign key (feature_id) references feature
2016-02-20 20:45:40,861 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cm3gqs38fa2lpllgoum8n4kgn" for relation "feature_genotype" already exists
2016-02-20 20:45:40,863 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_736wxgjs6pip5212ash5i68p foreign key (genotype_id) references genotype
2016-02-20 20:45:40,864 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_736wxgjs6pip5212ash5i68p" for relation "feature_genotype" already exists
2016-02-20 20:45:40,867 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_grails_user add constraint FK_4dgbhgiw0vb9hqy2k5fqg3neh foreign key (feature_owners_id) references feature
2016-02-20 20:45:40,868 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4dgbhgiw0vb9hqy2k5fqg3neh" for relation "feature_grails_user" already exists
2016-02-20 20:45:40,872 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_location add constraint FK_qml7xp9f5uojcw7jwdxcb35le foreign key (feature_id) references feature
2016-02-20 20:45:40,873 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qml7xp9f5uojcw7jwdxcb35le" for relation "feature_location" already exists
2016-02-20 20:45:40,875 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_property add constraint FK_jpvdxc57abfiridcr57x8130 foreign key (feature_id) references feature
2016-02-20 20:45:40,879 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jpvdxc57abfiridcr57x8130" for relation "feature_property" already exists
2016-02-20 20:45:40,881 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_property add constraint FK_36e638geg9tew42b1mp2ehff foreign key (type_id) references cvterm
2016-02-20 20:45:40,882 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_36e638geg9tew42b1mp2ehff" for relation "feature_property" already exists
2016-02-20 20:45:40,885 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_publication add constraint FK_qolh5l4blkx8vfmwcl7f3woan foreign key (feature_feature_publications_id) references feature
2016-02-20 20:45:40,891 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qolh5l4blkx8vfmwcl7f3woan" for relation "feature_publication" already exists
2016-02-20 20:45:40,893 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add constraint FK_8jm56covt0m7m0m191bc5jseh foreign key (child_feature_id) references feature
2016-02-20 20:45:40,894 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "child_feature_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,898 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add constraint FK_72kmd92rdc6gne0nrh026o1j0 foreign key (parent_feature_id) references feature
2016-02-20 20:45:40,899 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "parent_feature_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,907 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship_feature_property add constraint FK_ebgnfbogf1lwdxd8jc17511o7 foreign key (feature_relationship_feature_relationship_properties_id) references feature_relationship
2016-02-20 20:45:40,908 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ebgnfbogf1lwdxd8jc17511o7" for relation "feature_relationship_feature_property" already exists
2016-02-20 20:45:40,911 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship_publication add constraint FK_bdd324e5jb0lpuhs7biy2kacm foreign key (feature_relationship_feature_relationship_publications_id) references feature_relationship
2016-02-20 20:45:40,912 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_bdd324e5jb0lpuhs7biy2kacm" for relation "feature_relationship_publication" already exists
2016-02-20 20:45:40,914 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_nf9qbuay984ixqd2k1425rnyo foreign key (feature_id) references feature
2016-02-20 20:45:40,916 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_nf9qbuay984ixqd2k1425rnyo" for relation "feature_synonym" already exists
2016-02-20 20:45:40,923 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_82wsc3bv9i01t9851xv4xekis foreign key (publication_id) references publication
2016-02-20 20:45:40,926 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "publication_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,929 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_ll4cqdh994s6x8n7vku1q7iwd foreign key (synonym_id) references synonym
2016-02-20 20:45:40,930 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ll4cqdh994s6x8n7vku1q7iwd" for relation "feature_synonym" already exists
2016-02-20 20:45:40,932 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_gsol4u8wrfwbkh1qrx18i3u6 foreign key (feature_synonyms_id) references feature
2016-02-20 20:45:40,933 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gsol4u8wrfwbkh1qrx18i3u6" for relation "feature_synonym" already exists
2016-02-20 20:45:40,935 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm add constraint FK_cuwo3ernssd0t0wjceb7lmm11 foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,936 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cuwo3ernssd0t0wjceb7lmm11" for relation "featurecvterm" already exists
2016-02-20 20:45:40,943 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm add constraint FK_iy7bbt67s7jaemiajsrqalv5o foreign key (feature_id) references feature
2016-02-20 20:45:40,944 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_iy7bbt67s7jaemiajsrqalv5o" for relation "featurecvterm" already exists
2016-02-20 20:45:40,948 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm_dbxref add constraint FK_r9xhefcekikp1od79ectkb22b foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,949 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_r9xhefcekikp1od79ectkb22b" for relation "featurecvterm_dbxref" already exists
2016-02-20 20:45:40,951 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism_organism_property add constraint FK_qyxdgqthtlgixvtdkkhc8g3pu foreign key (organism_organism_properties_id) references organism
2016-02-20 20:45:40,959 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qyxdgqthtlgixvtdkkhc8g3pu" for relation "organism_organism_property" already exists
2016-02-20 20:45:40,961 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organismdbxref add constraint FK_s3vk7onqrk0n4c86xnvqmm3ho foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,962 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_s3vk7onqrk0n4c86xnvqmm3ho" for relation "organismdbxref" already exists
2016-02-20 20:45:40,965 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organismdbxref add constraint FK_l1jfi0wpnyooutd820p5gskr foreign key (organism_id) references organism
2016-02-20 20:45:40,966 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_l1jfi0wpnyooutd820p5gskr" for relation "organismdbxref" already exists
2016-02-20 20:45:40,969 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table permission add constraint FK_4nvoxx3htem6jseb4rmu0aqfp foreign key (organism_id) references organism
2016-02-20 20:45:40,970 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4nvoxx3htem6jseb4rmu0aqfp" for relation "permission" already exists
2016-02-20 20:45:40,972 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_cwgh6naf9gackae2ei11v6p41 foreign key (assay_id) references cvterm
2016-02-20 20:45:40,979 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cwgh6naf9gackae2ei11v6p41" for relation "phenotype" already exists
2016-02-20 20:45:40,981 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_phmfgylejydjqyrvo3imc97go foreign key (attribute_id) references cvterm
2016-02-20 20:45:40,982 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_phmfgylejydjqyrvo3imc97go" for relation "phenotype" already exists
2016-02-20 20:45:40,985 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_jh0fc3orduigl8s7ymentbtrs foreign key (cvalue_id) references cvterm
2016-02-20 20:45:40,986 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jh0fc3orduigl8s7ymentbtrs" for relation "phenotype" already exists
2016-02-20 20:45:40,988 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_gb4wy9qesx6vnekxekm18k9xa foreign key (observable_id) references cvterm
2016-02-20 20:45:40,989 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gb4wy9qesx6vnekxekm18k9xa" for relation "phenotype" already exists
2016-02-20 20:45:40,993 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_cvterm add constraint FK_9e2v7goj5w6nds5jo0x1va1nm foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,999 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_9e2v7goj5w6nds5jo0x1va1nm" for relation "phenotype_cvterm" already exists
2016-02-20 20:45:41,001 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_cvterm add constraint FK_aicsmj1kn20ikm14292g9r2j9 foreign key (phenotype_phenotypecvterms_id) references phenotype
2016-02-20 20:45:41,002 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_aicsmj1kn20ikm14292g9r2j9" for relation "phenotype_cvterm" already exists
2016-02-20 20:45:41,004 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_t52r166gd8710vffy3aompe7d foreign key (environment_id) references environment
2016-02-20 20:45:41,006 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_t52r166gd8710vffy3aompe7d" for relation "phenotype_description" already exists
2016-02-20 20:45:41,011 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_bf1bstadamyw0gsarkb933l5b foreign key (genotype_id) references genotype
2016-02-20 20:45:41,012 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_bf1bstadamyw0gsarkb933l5b" for relation "phenotype_description" already exists
2016-02-20 20:45:41,014 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_8pbyj05khavdl5a648c7pmcil foreign key (type_id) references cvterm
2016-02-20 20:45:41,015 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8pbyj05khavdl5a648c7pmcil" for relation "phenotype_description" already exists
2016-02-20 20:45:41,020 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_q6jvhi3l7ty0m9tpbn09d8pxj foreign key (environment_id) references environment
2016-02-20 20:45:41,021 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_q6jvhi3l7ty0m9tpbn09d8pxj" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,024 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_8rbhsxxdf669tyed8jrr747hv foreign key (genotype_id) references genotype
2016-02-20 20:45:41,027 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8rbhsxxdf669tyed8jrr747hv" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,029 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_gskh1e7b6qa2du48ayu49lr3s foreign key (phenotype_id) references phenotype
2016-02-20 20:45:41,030 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gskh1e7b6qa2du48ayu49lr3s" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,035 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_tk1pgifvuhurefn0y3myfyyt4 foreign key (type_id) references cvterm
2016-02-20 20:45:41,036 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tk1pgifvuhurefn0y3myfyyt4" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,039 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table preference add constraint FK_42b0lk4rcfjcagw84jugd1sgj foreign key (organism_id) references organism
2016-02-20 20:45:41,044 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_42b0lk4rcfjcagw84jugd1sgj" for relation "preference" already exists
2016-02-20 20:45:41,047 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publication add constraint FK_h3g8f3q2krcnwmq2nasbanlay foreign key (type_id) references cvterm
2016-02-20 20:45:41,049 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_h3g8f3q2krcnwmq2nasbanlay" for relation "publication" already exists
2016-02-20 20:45:41,051 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publication_relationship add constraint FK_q6hf14oiq9pomkjrhtndonmeh foreign key (type_id) references cvterm
2016-02-20 20:45:41,052 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_q6hf14oiq9pomkjrhtndonmeh" for relation "publication_relationship" already exists
2016-02-20 20:45:41,055 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publicationdbxref add constraint FK_oh81hma8qx88fhvcmfugx836b foreign key (dbxref_id) references dbxref
2016-02-20 20:45:41,059 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_oh81hma8qx88fhvcmfugx836b" for relation "publicationdbxref" already exists
2016-02-20 20:45:41,061 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table sequence add constraint FK_rux0954nxr4lwvj2qgyjibua7 foreign key (organism_id) references organism
2016-02-20 20:45:41,062 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_rux0954nxr4lwvj2qgyjibua7" for relation "sequence" already exists
2016-02-20 20:45:41,065 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add constraint FK_4ylco1irefvydmsnedglqqdfu foreign key (type_id) references cvterm
2016-02-20 20:45:41,066 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4ylco1irefvydmsnedglqqdfu" for relation "synonym" already exists
2016-02-20 20:45:52,529 [localhost-startStop-1] ERROR liquibase  - Change Set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated) failed.  Error: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
2016-02-20 20:45:52,579 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    ... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
2016-02-20 20:45:52,584 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    ... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
Feb 20, 2016 8:45:52 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 20, 2016 8:45:52 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/apollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [PoolCleaner[25416670:1456022700075]] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@18740d1]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 20, 2016 8:45:52 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 20, 2016 8:45:52 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 80376 ms



On Sat, Feb 20, 2016 at 9:32 PM, Lbl <[hidden email]> wrote:
Try opening in an incognito or another browser of doing a shift reload to flush the cache. 

That being said .. This stack trace looks a bit terse.   Typically shiro (the security plugin) will reload but I don't see that here.  Maybe further up? 

Nathan

On Feb 20, 2016, at 6:04 PM, Shane McCoy <[hidden email]> wrote:

Hey! I made the changes but I am still getting a blank screen.

I checked catalina.out, here is the last output:

/var/log/tomcat7$ tail -f catalina.out
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [PoolCleaner[25416670:1456019437960]] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@1b2e3fc]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 20, 2016 7:51:28 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 20, 2016 7:51:28 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 77106 ms


Is this still a memory issue then?
I have updated tomcat memory to your doc specs already.
Thanks!
shane

On Sat, Feb 20, 2016 at 7:55 PM, Shane McCoy <[hidden email]> wrote:
Ok, that makes more sense now! thank you very much.
I'll will try with correct settings,
cheers!

On Sat, Feb 20, 2016 at 7:53 PM, Colin <[hidden email]> wrote:
Hi Shaun

>url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

Just wanted to comment on this, actually, it would not be your IP and war here. It is kind of confusing that this "setting" is called a url, because it is actually a JDBC connector string, which actually references your local database, so it would not be using the war file name or even the IP address.

For example, if your database is named "apollodb", then your "url" would be

jdbc:postgresql://localhost/apollodb

It would generally just be localhost unless you have a separate database server. I think it might be worth adding some more comments about that in our setup guide, but I hope that helps!


-Colin

On Sat, Feb 20, 2016 at 2:36 PM, Shane McCoy <[hidden email]> wrote:
Hey!
So a lot has changed in a year! I'm currently still stuck at 2g but wanted to ask about an issue i have w/ /.apollo deploy
I am getting a blank screen at the URL. I have not added any data for generation yet. I assume i would still get a webapollo ui.
I am using postgresql. I edited apollo-config.groovy
Added (in production only)
datasource.dbCreate = "update" // one of...  ( where does the database name go? I don't understand this line, it seems i'm limited to the options given?)
username: chado database username
password: chado database pw
url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

I haven't changed any other settings and going to http://myipaddress/apollo is a blank page.
I want to use this w/ a already setup postgresql chado database.

I am going off of this guide: http://webapollo.readthedocs.org/en/latest/Setup.html
Thanks!

On Thu, Feb 11, 2016 at 2:29 PM, Shane McCoy <[hidden email]> wrote:
Thanks for the quick reply!
I will see what options I can take -
Shane M.

On Thu, Feb 11, 2016 at 2:18 PM, Nathan Dunn <[hidden email]> wrote:

On Feb 11, 2016, at 11:07 AM, Shane McCoy <[hidden email]> wrote:

Hey

I am getting this error running ./apollo run-local 8085

..........
    BUILD SUCCESSFUL
    | Compiling 5 source files
    | Compiling 5 source files.....
    ***
    Metrics servlet injected into web.xml
    Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
    ***
    | Running Grails application
    Error occurred during initialization of VM
    Could not reserve enough space for object heap
    Error: Could not create the Java Virtual Machine.
    Error: A fatal exception has occurred. Program will exit.
    | Error Forked Grails VM exited with error

I’m guessing that Java is requesting more memory then you have to allocate, and so exiting.  

So, when running it with run-local (for dev purposes), it actually has preset memory, of a max of up to 2 GB, though obviously this is high.  It is in BuildConfig.groovy:

run    : [maxMemory: 2048, minMemory: 64, debug: false , maxPerm: 1024, forkReserve: false],
My guess is that your machine doesn’t have sufficient memory to run this, or there is another process. 

My suggestions would be:
1 - get a machine with at least 4 GB’s of memory, especially if you are going to host to multiple users.  This will enable better caching and performance.    
2 - if (1) is not an immediate option (or to test, or if you are just running locally) your can edit your apollo-config.groovy create a line like this, so it will use less memory:

grails.project.fork = [
// configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
// compile: [maxMemory: 256, minMemory: 64, debug: false, maxPerm: 256, daemon:true],

test : false,
//run : false,
// configure settings for the test-app JVM, uses the daemon by default
//test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
// configure settings for the run-app JVM
run : [maxMemory: 1024, minMemory: 64, debug: false , maxPerm: 512, forkReserve: false],
// configure settings for the run-war JVM
war : [maxMemory: 1024, minMemory: 64, debug: false, maxPerm: 512, forkReserve: false],
// configure settings for the Console UI JVM
console: [maxMemory:
1024, minMemory: 64, debug: false, maxPerm: 512]
]

Setting the java size as done below works for tomcat, but not for the development mode (run-local).  

Nathan 

I looked over the same errors on Stack and made adjustments to the memory but I am still getting this error. I am new to Grails but I believe everything is setup correct and i can run a sample app (helloworld).
Here is the changes i made:

    -Xms512m -Xmx1g -XX:PermSize=256m
This is the memory

    free -m
                 total       used       free     shared    buffers     cached
    Mem:          2015       1297        718         56        169        859
    -/+ buffers/cache:        267       1748

Checking if parameters are being read

    $ ps -ef | grep java
    tomcat7  32158     1  1 11:02 ?        00:00:10 /usr/lib/jvm/default-java/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:PermSize=256m -XX:MaxPermSize=256m -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed -classpath /usr/share/tomcat7/bin/bootstrap.jar:/usr/share/tomcat7/bin/tomcat-juli.jar -Dcatalina.base=/var/lib/tomcat7 -Dcatalina.home=/usr/share/tomcat7 -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp org.apache.catalina.startup.Bootstrap start


I have this in my $HOME/.profile

    export JAVA_OPTS="-Xms512m -Xmx1g -XX:MaxPermSize=256m"

in my setenv.sh for Tomcat7

    export CATALINA_OPTS="-Xms512m -Xmx1g \
        -XX:+CMSClassUnloadingEnabled \
        -XX:+CMSPermGenSweepingEnabled \
        -XX:+UseConcMarkSweepGC \
        -XX:MaxPermSize=256m"

Versions: (i went w/ 2.4.5 per Apollo guide)
    $ grails -version
    Grails version: 2.4.5
    $ java -version
    java version "1.7.0_95"
    OpenJDK Runtime Environment (IcedTea 2.6.4) (7u95-2.6.4-0ubuntu0.14.04.1)
    OpenJDK Client VM (build 24.95-b01, mixed mode, sharing)

I am not sure what to change now - it seems the memory would be adequate? I know this isn't Apollo specific but maybe someone here has had the same problem? Please any thoughts would be great. thank you
Shane M.



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Re: New WebApollo install issue (Grails)

Shane McCoy
I did try in chrome, chrome canary & firefox, plus clearing cache too.
Thanks!
shane

On Sat, Feb 20, 2016 at 9:51 PM, Shane McCoy <[hidden email]> wrote:
I missed a bit from the log, here is catalina.out from a restart of tomcat7:

 * Stopping Tomcat servlet engine tomcat7                                [ OK ]
 * Starting Tomcat servlet engine tomcat7                                [ OK ]
--------------------------$$:/var/log/tomcat7$ tail -f catalina.out
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor /etc/tomcat7/Catalina/localhost/host-manager.xml
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
^[[AFeb 20, 2016 8:44:43 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 20, 2016 8:44:43 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.

Configuring Shiro ...

Shiro Configured
2016-02-20 20:45:40,539 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column id int8 not null
2016-02-20 20:45:40,543 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,546 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column version int8 not null
2016-02-20 20:45:40,548 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,550 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column program_version varchar(255) not null
2016-02-20 20:45:40,552 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "program_version" contains null values
2016-02-20 20:45:40,554 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_name varchar(255) not null
2016-02-20 20:45:40,555 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_name" contains null values
2016-02-20 20:45:40,558 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_version varchar(255) not null
2016-02-20 20:45:40,559 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_version" contains null values
2016-02-20 20:45:40,562 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column time_executed timestamp not null
2016-02-20 20:45:40,563 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "time_executed" contains null values
2016-02-20 20:45:40,566 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column id int8 not null
2016-02-20 20:45:40,567 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,569 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column version int8 not null
2016-02-20 20:45:40,570 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,573 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column id int8 not null
2016-02-20 20:45:40,574 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,577 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column version int8 not null
2016-02-20 20:45:40,578 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,583 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column is_relationship_type int4 not null
2016-02-20 20:45:40,584 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "is_relationship_type" contains null values
2016-02-20 20:45:40,587 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column id int8 not null
2016-02-20 20:45:40,588 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,590 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column version int8 not null
2016-02-20 20:45:40,591 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,593 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column objectcvterm_id int8 not null
2016-02-20 20:45:40,594 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" contains null values
2016-02-20 20:45:40,598 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column subjectcvterm_id int8 not null
2016-02-20 20:45:40,599 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" contains null values
2016-02-20 20:45:40,602 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column id int8 not null
2016-02-20 20:45:40,602 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,606 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column version int8 not null
2016-02-20 20:45:40,607 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,610 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add column id int8 not null
2016-02-20 20:45:40,612 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,616 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column id int8 not null
2016-02-20 20:45:40,617 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,620 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column version int8 not null
2016-02-20 20:45:40,621 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,632 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column unique_name varchar(255) not null
2016-02-20 20:45:40,633 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "unique_name" contains null values
2016-02-20 20:45:40,636 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column class varchar(255) not null
2016-02-20 20:45:40,637 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "class" contains null values
2016-02-20 20:45:40,641 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column id int8 not null
2016-02-20 20:45:40,642 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,645 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column version int8 not null
2016-02-20 20:45:40,646 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,652 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column child_feature_id int8 not null
2016-02-20 20:45:40,653 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "child_feature_id" contains null values
2016-02-20 20:45:40,656 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column parent_feature_id int8 not null
2016-02-20 20:45:40,657 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "parent_feature_id" contains null values
2016-02-20 20:45:40,660 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column id int8 not null
2016-02-20 20:45:40,661 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,668 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column version int8 not null
2016-02-20 20:45:40,670 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,672 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column publication_id int8 not null
2016-02-20 20:45:40,677 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "publication_id" contains null values
2016-02-20 20:45:40,679 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column id int8 not null
2016-02-20 20:45:40,681 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,684 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column version int8 not null
2016-02-20 20:45:40,685 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,687 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column directory varchar(255)
2016-02-20 20:45:40,688 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,692 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column id int8 not null
2016-02-20 20:45:40,693 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,701 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column version int8 not null
2016-02-20 20:45:40,702 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,704 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column directory varchar(255) not null
2016-02-20 20:45:40,706 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "directory" contains null values
2016-02-20 20:45:40,709 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column id int8 not null
2016-02-20 20:45:40,710 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,715 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column version int8 not null
2016-02-20 20:45:40,716 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,719 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column synonymsgml varchar(255) not null
2016-02-20 20:45:40,720 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "synonymsgml" contains null values
2016-02-20 20:45:40,724 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_feature add constraint FK_8m30ycwh545b4aoxor9sbk1oq foreign key (analysis_id) references analysis
2016-02-20 20:45:40,725 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8m30ycwh545b4aoxor9sbk1oq" for relation "analysis_feature" already exists
2016-02-20 20:45:40,727 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_feature add constraint FK_l94xl424xp988f06gr2b3t5tw foreign key (feature_id) references feature
2016-02-20 20:45:40,728 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_l94xl424xp988f06gr2b3t5tw" for relation "analysis_feature" already exists
2016-02-20 20:45:40,730 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_property add constraint FK_38g8n4bitmdwkrcs217uexrwx foreign key (analysis_id) references analysis
2016-02-20 20:45:40,731 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_38g8n4bitmdwkrcs217uexrwx" for relation "analysis_property" already exists
2016-02-20 20:45:40,733 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_property add constraint FK_9o7xs7saygim8y0sm4ostvpc1 foreign key (type_id) references cvterm
2016-02-20 20:45:40,734 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_9o7xs7saygim8y0sm4ostvpc1" for relation "analysis_property" already exists
2016-02-20 20:45:40,737 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add constraint FK_oksfqluv12ktmut9s6o9jla7a foreign key (cv_id) references cv
2016-02-20 20:45:40,739 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_oksfqluv12ktmut9s6o9jla7a" for relation "cvterm" already exists
2016-02-20 20:45:40,741 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add constraint FK_6d097oy44230tuoo8lb8dkkcp foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,742 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_6d097oy44230tuoo8lb8dkkcp" for relation "cvterm" already exists
2016-02-20 20:45:40,744 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_ke2nrw91sxil8mv7osgv83pw1 foreign key (cv_id) references cv
2016-02-20 20:45:40,745 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ke2nrw91sxil8mv7osgv83pw1" for relation "cvterm_path" already exists
2016-02-20 20:45:40,748 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_tlfh10092i00g6rlv589naqy5 foreign key (objectcvterm_id) references cvterm
2016-02-20 20:45:40,749 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tlfh10092i00g6rlv589naqy5" for relation "cvterm_path" already exists
2016-02-20 20:45:40,751 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_nq02ir0qeydr5tj3071k9gl7b foreign key (subjectcvterm_id) references cvterm
2016-02-20 20:45:40,752 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_nq02ir0qeydr5tj3071k9gl7b" for relation "cvterm_path" already exists
2016-02-20 20:45:40,760 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_jaqi1bk3t2c0m3pybmparp856 foreign key (type_id) references cvterm
2016-02-20 20:45:40,761 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jaqi1bk3t2c0m3pybmparp856" for relation "cvterm_path" already exists
2016-02-20 20:45:40,763 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_r1o1rnfnsf7oipuv1h7h1fln7 foreign key (objectcvterm_id) references cvterm
2016-02-20 20:45:40,766 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,771 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_pwxrfyx6rqu5krq4nj5wa3u4f foreign key (subjectcvterm_id) references cvterm
2016-02-20 20:45:40,775 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,777 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_ob1d0vrfaix8b28j4tvilqnyv foreign key (type_id) references cvterm
2016-02-20 20:45:40,778 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ob1d0vrfaix8b28j4tvilqnyv" for relation "cvterm_relationship" already exists
2016-02-20 20:45:40,781 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add constraint FK_np3tfcu9g867to3qux6raf9y8 foreign key (db_id) references db
2016-02-20 20:45:40,782 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_np3tfcu9g867to3qux6raf9y8" for relation "dbxref" already exists
2016-02-20 20:45:40,786 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref_property add constraint FK_3p1ssctww083s0tt65mmm64uo foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,787 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_3p1ssctww083s0tt65mmm64uo" for relation "dbxref_property" already exists
2016-02-20 20:45:40,792 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref_property add constraint FK_t6ojbvugx8kou45oklsie3rt5 foreign key (type_id) references cvterm
2016-02-20 20:45:40,793 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_t6ojbvugx8kou45oklsie3rt5" for relation "dbxref_property" already exists
2016-02-20 20:45:40,796 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table environmentcvterm add constraint FK_tql9djnqw1d7migfndoj3lrph foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,803 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tql9djnqw1d7migfndoj3lrph" for relation "environmentcvterm" already exists
2016-02-20 20:45:40,805 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table environmentcvterm add constraint FK_rrwb96jjqgtg077yv8pbim3jj foreign key (environment_id) references environment
2016-02-20 20:45:40,807 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_rrwb96jjqgtg077yv8pbim3jj" for relation "environmentcvterm" already exists
2016-02-20 20:45:40,813 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add constraint FK_hc4vrafs0ws7ugdkp0n6u3xdo foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,816 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_hc4vrafs0ws7ugdkp0n6u3xdo" for relation "feature" already exists
2016-02-20 20:45:40,819 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_dbxref add constraint FK_n6n7lheb1qkmlde8u6gvvjxne foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,821 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_n6n7lheb1qkmlde8u6gvvjxne" for relation "feature_dbxref" already exists
2016-02-20 20:45:40,829 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_dbxref add constraint FK_1mrfkxbb3n7fhjxcrkxappdn8 foreign key (feature_featuredbxrefs_id) references feature
2016-02-20 20:45:40,831 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_1mrfkxbb3n7fhjxcrkxappdn8" for relation "feature_dbxref" already exists
2016-02-20 20:45:40,836 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_feature_phenotypes add constraint FK_dy5g29heir5ic3d36okyuihho foreign key (phenotype_id) references phenotype
2016-02-20 20:45:40,839 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_dy5g29heir5ic3d36okyuihho" for relation "feature_feature_phenotypes" already exists
2016-02-20 20:45:40,842 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_feature_phenotypes add constraint FK_aqr7eiyx6puju6elciwubbwmo foreign key (feature_id) references feature
2016-02-20 20:45:40,843 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_aqr7eiyx6puju6elciwubbwmo" for relation "feature_feature_phenotypes" already exists
2016-02-20 20:45:40,847 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_hak8r429shmpho06rbyvwnmt0 foreign key (chromosome_feature_id) references feature
2016-02-20 20:45:40,848 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_hak8r429shmpho06rbyvwnmt0" for relation "feature_genotype" already exists
2016-02-20 20:45:40,856 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_b42u9iq4kuqe5ay544do81n32 foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,857 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_b42u9iq4kuqe5ay544do81n32" for relation "feature_genotype" already exists
2016-02-20 20:45:40,859 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_cm3gqs38fa2lpllgoum8n4kgn foreign key (feature_id) references feature
2016-02-20 20:45:40,861 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cm3gqs38fa2lpllgoum8n4kgn" for relation "feature_genotype" already exists
2016-02-20 20:45:40,863 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_736wxgjs6pip5212ash5i68p foreign key (genotype_id) references genotype
2016-02-20 20:45:40,864 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_736wxgjs6pip5212ash5i68p" for relation "feature_genotype" already exists
2016-02-20 20:45:40,867 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_grails_user add constraint FK_4dgbhgiw0vb9hqy2k5fqg3neh foreign key (feature_owners_id) references feature
2016-02-20 20:45:40,868 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4dgbhgiw0vb9hqy2k5fqg3neh" for relation "feature_grails_user" already exists
2016-02-20 20:45:40,872 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_location add constraint FK_qml7xp9f5uojcw7jwdxcb35le foreign key (feature_id) references feature
2016-02-20 20:45:40,873 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qml7xp9f5uojcw7jwdxcb35le" for relation "feature_location" already exists
2016-02-20 20:45:40,875 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_property add constraint FK_jpvdxc57abfiridcr57x8130 foreign key (feature_id) references feature
2016-02-20 20:45:40,879 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jpvdxc57abfiridcr57x8130" for relation "feature_property" already exists
2016-02-20 20:45:40,881 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_property add constraint FK_36e638geg9tew42b1mp2ehff foreign key (type_id) references cvterm
2016-02-20 20:45:40,882 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_36e638geg9tew42b1mp2ehff" for relation "feature_property" already exists
2016-02-20 20:45:40,885 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_publication add constraint FK_qolh5l4blkx8vfmwcl7f3woan foreign key (feature_feature_publications_id) references feature
2016-02-20 20:45:40,891 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qolh5l4blkx8vfmwcl7f3woan" for relation "feature_publication" already exists
2016-02-20 20:45:40,893 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add constraint FK_8jm56covt0m7m0m191bc5jseh foreign key (child_feature_id) references feature
2016-02-20 20:45:40,894 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "child_feature_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,898 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add constraint FK_72kmd92rdc6gne0nrh026o1j0 foreign key (parent_feature_id) references feature
2016-02-20 20:45:40,899 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "parent_feature_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,907 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship_feature_property add constraint FK_ebgnfbogf1lwdxd8jc17511o7 foreign key (feature_relationship_feature_relationship_properties_id) references feature_relationship
2016-02-20 20:45:40,908 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ebgnfbogf1lwdxd8jc17511o7" for relation "feature_relationship_feature_property" already exists
2016-02-20 20:45:40,911 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship_publication add constraint FK_bdd324e5jb0lpuhs7biy2kacm foreign key (feature_relationship_feature_relationship_publications_id) references feature_relationship
2016-02-20 20:45:40,912 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_bdd324e5jb0lpuhs7biy2kacm" for relation "feature_relationship_publication" already exists
2016-02-20 20:45:40,914 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_nf9qbuay984ixqd2k1425rnyo foreign key (feature_id) references feature
2016-02-20 20:45:40,916 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_nf9qbuay984ixqd2k1425rnyo" for relation "feature_synonym" already exists
2016-02-20 20:45:40,923 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_82wsc3bv9i01t9851xv4xekis foreign key (publication_id) references publication
2016-02-20 20:45:40,926 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "publication_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,929 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_ll4cqdh994s6x8n7vku1q7iwd foreign key (synonym_id) references synonym
2016-02-20 20:45:40,930 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ll4cqdh994s6x8n7vku1q7iwd" for relation "feature_synonym" already exists
2016-02-20 20:45:40,932 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_gsol4u8wrfwbkh1qrx18i3u6 foreign key (feature_synonyms_id) references feature
2016-02-20 20:45:40,933 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gsol4u8wrfwbkh1qrx18i3u6" for relation "feature_synonym" already exists
2016-02-20 20:45:40,935 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm add constraint FK_cuwo3ernssd0t0wjceb7lmm11 foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,936 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cuwo3ernssd0t0wjceb7lmm11" for relation "featurecvterm" already exists
2016-02-20 20:45:40,943 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm add constraint FK_iy7bbt67s7jaemiajsrqalv5o foreign key (feature_id) references feature
2016-02-20 20:45:40,944 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_iy7bbt67s7jaemiajsrqalv5o" for relation "featurecvterm" already exists
2016-02-20 20:45:40,948 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm_dbxref add constraint FK_r9xhefcekikp1od79ectkb22b foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,949 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_r9xhefcekikp1od79ectkb22b" for relation "featurecvterm_dbxref" already exists
2016-02-20 20:45:40,951 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism_organism_property add constraint FK_qyxdgqthtlgixvtdkkhc8g3pu foreign key (organism_organism_properties_id) references organism
2016-02-20 20:45:40,959 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qyxdgqthtlgixvtdkkhc8g3pu" for relation "organism_organism_property" already exists
2016-02-20 20:45:40,961 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organismdbxref add constraint FK_s3vk7onqrk0n4c86xnvqmm3ho foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,962 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_s3vk7onqrk0n4c86xnvqmm3ho" for relation "organismdbxref" already exists
2016-02-20 20:45:40,965 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organismdbxref add constraint FK_l1jfi0wpnyooutd820p5gskr foreign key (organism_id) references organism
2016-02-20 20:45:40,966 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_l1jfi0wpnyooutd820p5gskr" for relation "organismdbxref" already exists
2016-02-20 20:45:40,969 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table permission add constraint FK_4nvoxx3htem6jseb4rmu0aqfp foreign key (organism_id) references organism
2016-02-20 20:45:40,970 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4nvoxx3htem6jseb4rmu0aqfp" for relation "permission" already exists
2016-02-20 20:45:40,972 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_cwgh6naf9gackae2ei11v6p41 foreign key (assay_id) references cvterm
2016-02-20 20:45:40,979 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cwgh6naf9gackae2ei11v6p41" for relation "phenotype" already exists
2016-02-20 20:45:40,981 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_phmfgylejydjqyrvo3imc97go foreign key (attribute_id) references cvterm
2016-02-20 20:45:40,982 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_phmfgylejydjqyrvo3imc97go" for relation "phenotype" already exists
2016-02-20 20:45:40,985 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_jh0fc3orduigl8s7ymentbtrs foreign key (cvalue_id) references cvterm
2016-02-20 20:45:40,986 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jh0fc3orduigl8s7ymentbtrs" for relation "phenotype" already exists
2016-02-20 20:45:40,988 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_gb4wy9qesx6vnekxekm18k9xa foreign key (observable_id) references cvterm
2016-02-20 20:45:40,989 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gb4wy9qesx6vnekxekm18k9xa" for relation "phenotype" already exists
2016-02-20 20:45:40,993 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_cvterm add constraint FK_9e2v7goj5w6nds5jo0x1va1nm foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,999 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_9e2v7goj5w6nds5jo0x1va1nm" for relation "phenotype_cvterm" already exists
2016-02-20 20:45:41,001 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_cvterm add constraint FK_aicsmj1kn20ikm14292g9r2j9 foreign key (phenotype_phenotypecvterms_id) references phenotype
2016-02-20 20:45:41,002 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_aicsmj1kn20ikm14292g9r2j9" for relation "phenotype_cvterm" already exists
2016-02-20 20:45:41,004 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_t52r166gd8710vffy3aompe7d foreign key (environment_id) references environment
2016-02-20 20:45:41,006 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_t52r166gd8710vffy3aompe7d" for relation "phenotype_description" already exists
2016-02-20 20:45:41,011 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_bf1bstadamyw0gsarkb933l5b foreign key (genotype_id) references genotype
2016-02-20 20:45:41,012 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_bf1bstadamyw0gsarkb933l5b" for relation "phenotype_description" already exists
2016-02-20 20:45:41,014 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_8pbyj05khavdl5a648c7pmcil foreign key (type_id) references cvterm
2016-02-20 20:45:41,015 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8pbyj05khavdl5a648c7pmcil" for relation "phenotype_description" already exists
2016-02-20 20:45:41,020 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_q6jvhi3l7ty0m9tpbn09d8pxj foreign key (environment_id) references environment
2016-02-20 20:45:41,021 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_q6jvhi3l7ty0m9tpbn09d8pxj" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,024 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_8rbhsxxdf669tyed8jrr747hv foreign key (genotype_id) references genotype
2016-02-20 20:45:41,027 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8rbhsxxdf669tyed8jrr747hv" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,029 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_gskh1e7b6qa2du48ayu49lr3s foreign key (phenotype_id) references phenotype
2016-02-20 20:45:41,030 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gskh1e7b6qa2du48ayu49lr3s" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,035 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_tk1pgifvuhurefn0y3myfyyt4 foreign key (type_id) references cvterm
2016-02-20 20:45:41,036 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tk1pgifvuhurefn0y3myfyyt4" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,039 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table preference add constraint FK_42b0lk4rcfjcagw84jugd1sgj foreign key (organism_id) references organism
2016-02-20 20:45:41,044 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_42b0lk4rcfjcagw84jugd1sgj" for relation "preference" already exists
2016-02-20 20:45:41,047 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publication add constraint FK_h3g8f3q2krcnwmq2nasbanlay foreign key (type_id) references cvterm
2016-02-20 20:45:41,049 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_h3g8f3q2krcnwmq2nasbanlay" for relation "publication" already exists
2016-02-20 20:45:41,051 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publication_relationship add constraint FK_q6hf14oiq9pomkjrhtndonmeh foreign key (type_id) references cvterm
2016-02-20 20:45:41,052 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_q6hf14oiq9pomkjrhtndonmeh" for relation "publication_relationship" already exists
2016-02-20 20:45:41,055 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publicationdbxref add constraint FK_oh81hma8qx88fhvcmfugx836b foreign key (dbxref_id) references dbxref
2016-02-20 20:45:41,059 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_oh81hma8qx88fhvcmfugx836b" for relation "publicationdbxref" already exists
2016-02-20 20:45:41,061 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table sequence add constraint FK_rux0954nxr4lwvj2qgyjibua7 foreign key (organism_id) references organism
2016-02-20 20:45:41,062 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_rux0954nxr4lwvj2qgyjibua7" for relation "sequence" already exists
2016-02-20 20:45:41,065 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add constraint FK_4ylco1irefvydmsnedglqqdfu foreign key (type_id) references cvterm
2016-02-20 20:45:41,066 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4ylco1irefvydmsnedglqqdfu" for relation "synonym" already exists
2016-02-20 20:45:52,529 [localhost-startStop-1] ERROR liquibase  - Change Set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated) failed.  Error: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
2016-02-20 20:45:52,579 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    ... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
2016-02-20 20:45:52,584 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    ... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
Feb 20, 2016 8:45:52 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 20, 2016 8:45:52 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/apollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [PoolCleaner[25416670:1456022700075]] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@18740d1]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 20, 2016 8:45:52 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 20, 2016 8:45:52 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 80376 ms



On Sat, Feb 20, 2016 at 9:32 PM, Lbl <[hidden email]> wrote:
Try opening in an incognito or another browser of doing a shift reload to flush the cache. 

That being said .. This stack trace looks a bit terse.   Typically shiro (the security plugin) will reload but I don't see that here.  Maybe further up? 

Nathan

On Feb 20, 2016, at 6:04 PM, Shane McCoy <[hidden email]> wrote:

Hey! I made the changes but I am still getting a blank screen.

I checked catalina.out, here is the last output:

/var/log/tomcat7$ tail -f catalina.out
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [PoolCleaner[25416670:1456019437960]] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@1b2e3fc]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 20, 2016 7:51:28 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 20, 2016 7:51:28 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 77106 ms


Is this still a memory issue then?
I have updated tomcat memory to your doc specs already.
Thanks!
shane

On Sat, Feb 20, 2016 at 7:55 PM, Shane McCoy <[hidden email]> wrote:
Ok, that makes more sense now! thank you very much.
I'll will try with correct settings,
cheers!

On Sat, Feb 20, 2016 at 7:53 PM, Colin <[hidden email]> wrote:
Hi Shaun

>url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

Just wanted to comment on this, actually, it would not be your IP and war here. It is kind of confusing that this "setting" is called a url, because it is actually a JDBC connector string, which actually references your local database, so it would not be using the war file name or even the IP address.

For example, if your database is named "apollodb", then your "url" would be

jdbc:postgresql://localhost/apollodb

It would generally just be localhost unless you have a separate database server. I think it might be worth adding some more comments about that in our setup guide, but I hope that helps!


-Colin

On Sat, Feb 20, 2016 at 2:36 PM, Shane McCoy <[hidden email]> wrote:
Hey!
So a lot has changed in a year! I'm currently still stuck at 2g but wanted to ask about an issue i have w/ /.apollo deploy
I am getting a blank screen at the URL. I have not added any data for generation yet. I assume i would still get a webapollo ui.
I am using postgresql. I edited apollo-config.groovy
Added (in production only)
datasource.dbCreate = "update" // one of...  ( where does the database name go? I don't understand this line, it seems i'm limited to the options given?)
username: chado database username
password: chado database pw
url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

I haven't changed any other settings and going to http://myipaddress/apollo is a blank page.
I want to use this w/ a already setup postgresql chado database.

I am going off of this guide: http://webapollo.readthedocs.org/en/latest/Setup.html
Thanks!

On Thu, Feb 11, 2016 at 2:29 PM, Shane McCoy <[hidden email]> wrote:
Thanks for the quick reply!
I will see what options I can take -
Shane M.

On Thu, Feb 11, 2016 at 2:18 PM, Nathan Dunn <[hidden email]> wrote:

On Feb 11, 2016, at 11:07 AM, Shane McCoy <[hidden email]> wrote:

Hey

I am getting this error running ./apollo run-local 8085

..........
    BUILD SUCCESSFUL
    | Compiling 5 source files
    | Compiling 5 source files.....
    ***
    Metrics servlet injected into web.xml
    Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
    ***
    | Running Grails application
    Error occurred during initialization of VM
    Could not reserve enough space for object heap
    Error: Could not create the Java Virtual Machine.
    Error: A fatal exception has occurred. Program will exit.
    | Error Forked Grails VM exited with error

I’m guessing that Java is requesting more memory then you have to allocate, and so exiting.  

So, when running it with run-local (for dev purposes), it actually has preset memory, of a max of up to 2 GB, though obviously this is high.  It is in BuildConfig.groovy:

run    : [maxMemory: 2048, minMemory: 64, debug: false , maxPerm: 1024, forkReserve: false],
My guess is that your machine doesn’t have sufficient memory to run this, or there is another process. 

My suggestions would be:
1 - get a machine with at least 4 GB’s of memory, especially if you are going to host to multiple users.  This will enable better caching and performance.    
2 - if (1) is not an immediate option (or to test, or if you are just running locally) your can edit your apollo-config.groovy create a line like this, so it will use less memory:

grails.project.fork = [
// configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
// compile: [maxMemory: 256, minMemory: 64, debug: false, maxPerm: 256, daemon:true],

test : false,
//run : false,
// configure settings for the test-app JVM, uses the daemon by default
//test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
// configure settings for the run-app JVM
run : [maxMemory: 1024, minMemory: 64, debug: false , maxPerm: 512, forkReserve: false],
// configure settings for the run-war JVM
war : [maxMemory: 1024, minMemory: 64, debug: false, maxPerm: 512, forkReserve: false],
// configure settings for the Console UI JVM
console: [maxMemory:
1024, minMemory: 64, debug: false, maxPerm: 512]
]

Setting the java size as done below works for tomcat, but not for the development mode (run-local).  

Nathan 

I looked over the same errors on Stack and made adjustments to the memory but I am still getting this error. I am new to Grails but I believe everything is setup correct and i can run a sample app (helloworld).
Here is the changes i made:

    -Xms512m -Xmx1g -XX:PermSize=256m
This is the memory

    free -m
                 total       used       free     shared    buffers     cached
    Mem:          2015       1297        718         56        169        859
    -/+ buffers/cache:        267       1748

Checking if parameters are being read

    $ ps -ef | grep java
    tomcat7  32158     1  1 11:02 ?        00:00:10 /usr/lib/jvm/default-java/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:PermSize=256m -XX:MaxPermSize=256m -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed -classpath /usr/share/tomcat7/bin/bootstrap.jar:/usr/share/tomcat7/bin/tomcat-juli.jar -Dcatalina.base=/var/lib/tomcat7 -Dcatalina.home=/usr/share/tomcat7 -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp org.apache.catalina.startup.Bootstrap start


I have this in my $HOME/.profile

    export JAVA_OPTS="-Xms512m -Xmx1g -XX:MaxPermSize=256m"

in my setenv.sh for Tomcat7

    export CATALINA_OPTS="-Xms512m -Xmx1g \
        -XX:+CMSClassUnloadingEnabled \
        -XX:+CMSPermGenSweepingEnabled \
        -XX:+UseConcMarkSweepGC \
        -XX:MaxPermSize=256m"

Versions: (i went w/ 2.4.5 per Apollo guide)
    $ grails -version
    Grails version: 2.4.5
    $ java -version
    java version "1.7.0_95"
    OpenJDK Runtime Environment (IcedTea 2.6.4) (7u95-2.6.4-0ubuntu0.14.04.1)
    OpenJDK Client VM (build 24.95-b01, mixed mode, sharing)

I am not sure what to change now - it seems the memory would be adequate? I know this isn't Apollo specific but maybe someone here has had the same problem? Please any thoughts would be great. thank you
Shane M.



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Re: New WebApollo install issue (Grails)

nathandunn
In reply to this post by Shane McCoy

If you are using postgresql and you don’t have anything in the database you want (or you back it up first) I would drop and re-create the database (with tomcat off).     When it comes back up it will create the database with the create schema for you:

1 - stop tomcat 
1a - backup database? 
2 - dropdb your-apollo-database-name
3 - createdb your-apollo-database-name
4 - start tomcat

Its in a pretty weird state. 

Nathan

On Feb 20, 2016, at 6:51 PM, Shane McCoy <[hidden email]> wrote:

I missed a bit from the log, here is catalina.out from a restart of tomcat7:

 * Stopping Tomcat servlet engine tomcat7                                [ OK ]
 * Starting Tomcat servlet engine tomcat7                                [ OK ]
--------------------------$$:/var/log/tomcat7$ tail -f catalina.out
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor /etc/tomcat7/Catalina/localhost/host-manager.xml
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
^[[AFeb 20, 2016 8:44:43 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 20, 2016 8:44:43 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.

Configuring Shiro ...

Shiro Configured
2016-02-20 20:45:40,539 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column id int8 not null
2016-02-20 20:45:40,543 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,546 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column version int8 not null
2016-02-20 20:45:40,548 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,550 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column program_version varchar(255) not null
2016-02-20 20:45:40,552 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "program_version" contains null values
2016-02-20 20:45:40,554 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_name varchar(255) not null
2016-02-20 20:45:40,555 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_name" contains null values
2016-02-20 20:45:40,558 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_version varchar(255) not null
2016-02-20 20:45:40,559 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_version" contains null values
2016-02-20 20:45:40,562 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column time_executed timestamp not null
2016-02-20 20:45:40,563 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "time_executed" contains null values
2016-02-20 20:45:40,566 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column id int8 not null
2016-02-20 20:45:40,567 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,569 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column version int8 not null
2016-02-20 20:45:40,570 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,573 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column id int8 not null
2016-02-20 20:45:40,574 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,577 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column version int8 not null
2016-02-20 20:45:40,578 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,583 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column is_relationship_type int4 not null
2016-02-20 20:45:40,584 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "is_relationship_type" contains null values
2016-02-20 20:45:40,587 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column id int8 not null
2016-02-20 20:45:40,588 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,590 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column version int8 not null
2016-02-20 20:45:40,591 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,593 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column objectcvterm_id int8 not null
2016-02-20 20:45:40,594 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" contains null values
2016-02-20 20:45:40,598 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column subjectcvterm_id int8 not null
2016-02-20 20:45:40,599 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" contains null values
2016-02-20 20:45:40,602 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column id int8 not null
2016-02-20 20:45:40,602 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,606 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column version int8 not null
2016-02-20 20:45:40,607 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,610 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add column id int8 not null
2016-02-20 20:45:40,612 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,616 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column id int8 not null
2016-02-20 20:45:40,617 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,620 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column version int8 not null
2016-02-20 20:45:40,621 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,632 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column unique_name varchar(255) not null
2016-02-20 20:45:40,633 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "unique_name" contains null values
2016-02-20 20:45:40,636 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column class varchar(255) not null
2016-02-20 20:45:40,637 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "class" contains null values
2016-02-20 20:45:40,641 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column id int8 not null
2016-02-20 20:45:40,642 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,645 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column version int8 not null
2016-02-20 20:45:40,646 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,652 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column child_feature_id int8 not null
2016-02-20 20:45:40,653 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "child_feature_id" contains null values
2016-02-20 20:45:40,656 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column parent_feature_id int8 not null
2016-02-20 20:45:40,657 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "parent_feature_id" contains null values
2016-02-20 20:45:40,660 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column id int8 not null
2016-02-20 20:45:40,661 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,668 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column version int8 not null
2016-02-20 20:45:40,670 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,672 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column publication_id int8 not null
2016-02-20 20:45:40,677 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "publication_id" contains null values
2016-02-20 20:45:40,679 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column id int8 not null
2016-02-20 20:45:40,681 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,684 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column version int8 not null
2016-02-20 20:45:40,685 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,687 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column directory varchar(255)
2016-02-20 20:45:40,688 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,692 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column id int8 not null
2016-02-20 20:45:40,693 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,701 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column version int8 not null
2016-02-20 20:45:40,702 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,704 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column directory varchar(255) not null
2016-02-20 20:45:40,706 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "directory" contains null values
2016-02-20 20:45:40,709 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column id int8 not null
2016-02-20 20:45:40,710 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,715 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column version int8 not null
2016-02-20 20:45:40,716 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,719 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column synonymsgml varchar(255) not null
2016-02-20 20:45:40,720 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "synonymsgml" contains null values
2016-02-20 20:45:40,724 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_feature add constraint FK_8m30ycwh545b4aoxor9sbk1oq foreign key (analysis_id) references analysis
2016-02-20 20:45:40,725 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8m30ycwh545b4aoxor9sbk1oq" for relation "analysis_feature" already exists
2016-02-20 20:45:40,727 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_feature add constraint FK_l94xl424xp988f06gr2b3t5tw foreign key (feature_id) references feature
2016-02-20 20:45:40,728 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_l94xl424xp988f06gr2b3t5tw" for relation "analysis_feature" already exists
2016-02-20 20:45:40,730 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_property add constraint FK_38g8n4bitmdwkrcs217uexrwx foreign key (analysis_id) references analysis
2016-02-20 20:45:40,731 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_38g8n4bitmdwkrcs217uexrwx" for relation "analysis_property" already exists
2016-02-20 20:45:40,733 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_property add constraint FK_9o7xs7saygim8y0sm4ostvpc1 foreign key (type_id) references cvterm
2016-02-20 20:45:40,734 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_9o7xs7saygim8y0sm4ostvpc1" for relation "analysis_property" already exists
2016-02-20 20:45:40,737 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add constraint FK_oksfqluv12ktmut9s6o9jla7a foreign key (cv_id) references cv
2016-02-20 20:45:40,739 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_oksfqluv12ktmut9s6o9jla7a" for relation "cvterm" already exists
2016-02-20 20:45:40,741 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add constraint FK_6d097oy44230tuoo8lb8dkkcp foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,742 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_6d097oy44230tuoo8lb8dkkcp" for relation "cvterm" already exists
2016-02-20 20:45:40,744 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_ke2nrw91sxil8mv7osgv83pw1 foreign key (cv_id) references cv
2016-02-20 20:45:40,745 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ke2nrw91sxil8mv7osgv83pw1" for relation "cvterm_path" already exists
2016-02-20 20:45:40,748 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_tlfh10092i00g6rlv589naqy5 foreign key (objectcvterm_id) references cvterm
2016-02-20 20:45:40,749 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tlfh10092i00g6rlv589naqy5" for relation "cvterm_path" already exists
2016-02-20 20:45:40,751 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_nq02ir0qeydr5tj3071k9gl7b foreign key (subjectcvterm_id) references cvterm
2016-02-20 20:45:40,752 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_nq02ir0qeydr5tj3071k9gl7b" for relation "cvterm_path" already exists
2016-02-20 20:45:40,760 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_jaqi1bk3t2c0m3pybmparp856 foreign key (type_id) references cvterm
2016-02-20 20:45:40,761 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jaqi1bk3t2c0m3pybmparp856" for relation "cvterm_path" already exists
2016-02-20 20:45:40,763 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_r1o1rnfnsf7oipuv1h7h1fln7 foreign key (objectcvterm_id) references cvterm
2016-02-20 20:45:40,766 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,771 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_pwxrfyx6rqu5krq4nj5wa3u4f foreign key (subjectcvterm_id) references cvterm
2016-02-20 20:45:40,775 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,777 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_ob1d0vrfaix8b28j4tvilqnyv foreign key (type_id) references cvterm
2016-02-20 20:45:40,778 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ob1d0vrfaix8b28j4tvilqnyv" for relation "cvterm_relationship" already exists
2016-02-20 20:45:40,781 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add constraint FK_np3tfcu9g867to3qux6raf9y8 foreign key (db_id) references db
2016-02-20 20:45:40,782 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_np3tfcu9g867to3qux6raf9y8" for relation "dbxref" already exists
2016-02-20 20:45:40,786 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref_property add constraint FK_3p1ssctww083s0tt65mmm64uo foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,787 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_3p1ssctww083s0tt65mmm64uo" for relation "dbxref_property" already exists
2016-02-20 20:45:40,792 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref_property add constraint FK_t6ojbvugx8kou45oklsie3rt5 foreign key (type_id) references cvterm
2016-02-20 20:45:40,793 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_t6ojbvugx8kou45oklsie3rt5" for relation "dbxref_property" already exists
2016-02-20 20:45:40,796 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table environmentcvterm add constraint FK_tql9djnqw1d7migfndoj3lrph foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,803 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tql9djnqw1d7migfndoj3lrph" for relation "environmentcvterm" already exists
2016-02-20 20:45:40,805 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table environmentcvterm add constraint FK_rrwb96jjqgtg077yv8pbim3jj foreign key (environment_id) references environment
2016-02-20 20:45:40,807 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_rrwb96jjqgtg077yv8pbim3jj" for relation "environmentcvterm" already exists
2016-02-20 20:45:40,813 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add constraint FK_hc4vrafs0ws7ugdkp0n6u3xdo foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,816 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_hc4vrafs0ws7ugdkp0n6u3xdo" for relation "feature" already exists
2016-02-20 20:45:40,819 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_dbxref add constraint FK_n6n7lheb1qkmlde8u6gvvjxne foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,821 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_n6n7lheb1qkmlde8u6gvvjxne" for relation "feature_dbxref" already exists
2016-02-20 20:45:40,829 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_dbxref add constraint FK_1mrfkxbb3n7fhjxcrkxappdn8 foreign key (feature_featuredbxrefs_id) references feature
2016-02-20 20:45:40,831 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_1mrfkxbb3n7fhjxcrkxappdn8" for relation "feature_dbxref" already exists
2016-02-20 20:45:40,836 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_feature_phenotypes add constraint FK_dy5g29heir5ic3d36okyuihho foreign key (phenotype_id) references phenotype
2016-02-20 20:45:40,839 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_dy5g29heir5ic3d36okyuihho" for relation "feature_feature_phenotypes" already exists
2016-02-20 20:45:40,842 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_feature_phenotypes add constraint FK_aqr7eiyx6puju6elciwubbwmo foreign key (feature_id) references feature
2016-02-20 20:45:40,843 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_aqr7eiyx6puju6elciwubbwmo" for relation "feature_feature_phenotypes" already exists
2016-02-20 20:45:40,847 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_hak8r429shmpho06rbyvwnmt0 foreign key (chromosome_feature_id) references feature
2016-02-20 20:45:40,848 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_hak8r429shmpho06rbyvwnmt0" for relation "feature_genotype" already exists
2016-02-20 20:45:40,856 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_b42u9iq4kuqe5ay544do81n32 foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,857 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_b42u9iq4kuqe5ay544do81n32" for relation "feature_genotype" already exists
2016-02-20 20:45:40,859 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_cm3gqs38fa2lpllgoum8n4kgn foreign key (feature_id) references feature
2016-02-20 20:45:40,861 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cm3gqs38fa2lpllgoum8n4kgn" for relation "feature_genotype" already exists
2016-02-20 20:45:40,863 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_736wxgjs6pip5212ash5i68p foreign key (genotype_id) references genotype
2016-02-20 20:45:40,864 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_736wxgjs6pip5212ash5i68p" for relation "feature_genotype" already exists
2016-02-20 20:45:40,867 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_grails_user add constraint FK_4dgbhgiw0vb9hqy2k5fqg3neh foreign key (feature_owners_id) references feature
2016-02-20 20:45:40,868 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4dgbhgiw0vb9hqy2k5fqg3neh" for relation "feature_grails_user" already exists
2016-02-20 20:45:40,872 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_location add constraint FK_qml7xp9f5uojcw7jwdxcb35le foreign key (feature_id) references feature
2016-02-20 20:45:40,873 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qml7xp9f5uojcw7jwdxcb35le" for relation "feature_location" already exists
2016-02-20 20:45:40,875 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_property add constraint FK_jpvdxc57abfiridcr57x8130 foreign key (feature_id) references feature
2016-02-20 20:45:40,879 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jpvdxc57abfiridcr57x8130" for relation "feature_property" already exists
2016-02-20 20:45:40,881 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_property add constraint FK_36e638geg9tew42b1mp2ehff foreign key (type_id) references cvterm
2016-02-20 20:45:40,882 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_36e638geg9tew42b1mp2ehff" for relation "feature_property" already exists
2016-02-20 20:45:40,885 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_publication add constraint FK_qolh5l4blkx8vfmwcl7f3woan foreign key (feature_feature_publications_id) references feature
2016-02-20 20:45:40,891 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qolh5l4blkx8vfmwcl7f3woan" for relation "feature_publication" already exists
2016-02-20 20:45:40,893 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add constraint FK_8jm56covt0m7m0m191bc5jseh foreign key (child_feature_id) references feature
2016-02-20 20:45:40,894 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "child_feature_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,898 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add constraint FK_72kmd92rdc6gne0nrh026o1j0 foreign key (parent_feature_id) references feature
2016-02-20 20:45:40,899 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "parent_feature_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,907 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship_feature_property add constraint FK_ebgnfbogf1lwdxd8jc17511o7 foreign key (feature_relationship_feature_relationship_properties_id) references feature_relationship
2016-02-20 20:45:40,908 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ebgnfbogf1lwdxd8jc17511o7" for relation "feature_relationship_feature_property" already exists
2016-02-20 20:45:40,911 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship_publication add constraint FK_bdd324e5jb0lpuhs7biy2kacm foreign key (feature_relationship_feature_relationship_publications_id) references feature_relationship
2016-02-20 20:45:40,912 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_bdd324e5jb0lpuhs7biy2kacm" for relation "feature_relationship_publication" already exists
2016-02-20 20:45:40,914 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_nf9qbuay984ixqd2k1425rnyo foreign key (feature_id) references feature
2016-02-20 20:45:40,916 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_nf9qbuay984ixqd2k1425rnyo" for relation "feature_synonym" already exists
2016-02-20 20:45:40,923 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_82wsc3bv9i01t9851xv4xekis foreign key (publication_id) references publication
2016-02-20 20:45:40,926 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "publication_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,929 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_ll4cqdh994s6x8n7vku1q7iwd foreign key (synonym_id) references synonym
2016-02-20 20:45:40,930 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ll4cqdh994s6x8n7vku1q7iwd" for relation "feature_synonym" already exists
2016-02-20 20:45:40,932 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_gsol4u8wrfwbkh1qrx18i3u6 foreign key (feature_synonyms_id) references feature
2016-02-20 20:45:40,933 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gsol4u8wrfwbkh1qrx18i3u6" for relation "feature_synonym" already exists
2016-02-20 20:45:40,935 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm add constraint FK_cuwo3ernssd0t0wjceb7lmm11 foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,936 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cuwo3ernssd0t0wjceb7lmm11" for relation "featurecvterm" already exists
2016-02-20 20:45:40,943 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm add constraint FK_iy7bbt67s7jaemiajsrqalv5o foreign key (feature_id) references feature
2016-02-20 20:45:40,944 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_iy7bbt67s7jaemiajsrqalv5o" for relation "featurecvterm" already exists
2016-02-20 20:45:40,948 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm_dbxref add constraint FK_r9xhefcekikp1od79ectkb22b foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,949 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_r9xhefcekikp1od79ectkb22b" for relation "featurecvterm_dbxref" already exists
2016-02-20 20:45:40,951 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism_organism_property add constraint FK_qyxdgqthtlgixvtdkkhc8g3pu foreign key (organism_organism_properties_id) references organism
2016-02-20 20:45:40,959 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qyxdgqthtlgixvtdkkhc8g3pu" for relation "organism_organism_property" already exists
2016-02-20 20:45:40,961 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organismdbxref add constraint FK_s3vk7onqrk0n4c86xnvqmm3ho foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,962 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_s3vk7onqrk0n4c86xnvqmm3ho" for relation "organismdbxref" already exists
2016-02-20 20:45:40,965 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organismdbxref add constraint FK_l1jfi0wpnyooutd820p5gskr foreign key (organism_id) references organism
2016-02-20 20:45:40,966 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_l1jfi0wpnyooutd820p5gskr" for relation "organismdbxref" already exists
2016-02-20 20:45:40,969 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table permission add constraint FK_4nvoxx3htem6jseb4rmu0aqfp foreign key (organism_id) references organism
2016-02-20 20:45:40,970 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4nvoxx3htem6jseb4rmu0aqfp" for relation "permission" already exists
2016-02-20 20:45:40,972 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_cwgh6naf9gackae2ei11v6p41 foreign key (assay_id) references cvterm
2016-02-20 20:45:40,979 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cwgh6naf9gackae2ei11v6p41" for relation "phenotype" already exists
2016-02-20 20:45:40,981 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_phmfgylejydjqyrvo3imc97go foreign key (attribute_id) references cvterm
2016-02-20 20:45:40,982 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_phmfgylejydjqyrvo3imc97go" for relation "phenotype" already exists
2016-02-20 20:45:40,985 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_jh0fc3orduigl8s7ymentbtrs foreign key (cvalue_id) references cvterm
2016-02-20 20:45:40,986 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jh0fc3orduigl8s7ymentbtrs" for relation "phenotype" already exists
2016-02-20 20:45:40,988 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_gb4wy9qesx6vnekxekm18k9xa foreign key (observable_id) references cvterm
2016-02-20 20:45:40,989 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gb4wy9qesx6vnekxekm18k9xa" for relation "phenotype" already exists
2016-02-20 20:45:40,993 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_cvterm add constraint FK_9e2v7goj5w6nds5jo0x1va1nm foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,999 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_9e2v7goj5w6nds5jo0x1va1nm" for relation "phenotype_cvterm" already exists
2016-02-20 20:45:41,001 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_cvterm add constraint FK_aicsmj1kn20ikm14292g9r2j9 foreign key (phenotype_phenotypecvterms_id) references phenotype
2016-02-20 20:45:41,002 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_aicsmj1kn20ikm14292g9r2j9" for relation "phenotype_cvterm" already exists
2016-02-20 20:45:41,004 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_t52r166gd8710vffy3aompe7d foreign key (environment_id) references environment
2016-02-20 20:45:41,006 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_t52r166gd8710vffy3aompe7d" for relation "phenotype_description" already exists
2016-02-20 20:45:41,011 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_bf1bstadamyw0gsarkb933l5b foreign key (genotype_id) references genotype
2016-02-20 20:45:41,012 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_bf1bstadamyw0gsarkb933l5b" for relation "phenotype_description" already exists
2016-02-20 20:45:41,014 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_8pbyj05khavdl5a648c7pmcil foreign key (type_id) references cvterm
2016-02-20 20:45:41,015 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8pbyj05khavdl5a648c7pmcil" for relation "phenotype_description" already exists
2016-02-20 20:45:41,020 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_q6jvhi3l7ty0m9tpbn09d8pxj foreign key (environment_id) references environment
2016-02-20 20:45:41,021 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_q6jvhi3l7ty0m9tpbn09d8pxj" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,024 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_8rbhsxxdf669tyed8jrr747hv foreign key (genotype_id) references genotype
2016-02-20 20:45:41,027 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8rbhsxxdf669tyed8jrr747hv" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,029 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_gskh1e7b6qa2du48ayu49lr3s foreign key (phenotype_id) references phenotype
2016-02-20 20:45:41,030 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gskh1e7b6qa2du48ayu49lr3s" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,035 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_tk1pgifvuhurefn0y3myfyyt4 foreign key (type_id) references cvterm
2016-02-20 20:45:41,036 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tk1pgifvuhurefn0y3myfyyt4" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,039 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table preference add constraint FK_42b0lk4rcfjcagw84jugd1sgj foreign key (organism_id) references organism
2016-02-20 20:45:41,044 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_42b0lk4rcfjcagw84jugd1sgj" for relation "preference" already exists
2016-02-20 20:45:41,047 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publication add constraint FK_h3g8f3q2krcnwmq2nasbanlay foreign key (type_id) references cvterm
2016-02-20 20:45:41,049 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_h3g8f3q2krcnwmq2nasbanlay" for relation "publication" already exists
2016-02-20 20:45:41,051 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publication_relationship add constraint FK_q6hf14oiq9pomkjrhtndonmeh foreign key (type_id) references cvterm
2016-02-20 20:45:41,052 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_q6hf14oiq9pomkjrhtndonmeh" for relation "publication_relationship" already exists
2016-02-20 20:45:41,055 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publicationdbxref add constraint FK_oh81hma8qx88fhvcmfugx836b foreign key (dbxref_id) references dbxref
2016-02-20 20:45:41,059 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_oh81hma8qx88fhvcmfugx836b" for relation "publicationdbxref" already exists
2016-02-20 20:45:41,061 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table sequence add constraint FK_rux0954nxr4lwvj2qgyjibua7 foreign key (organism_id) references organism
2016-02-20 20:45:41,062 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_rux0954nxr4lwvj2qgyjibua7" for relation "sequence" already exists
2016-02-20 20:45:41,065 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add constraint FK_4ylco1irefvydmsnedglqqdfu foreign key (type_id) references cvterm
2016-02-20 20:45:41,066 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4ylco1irefvydmsnedglqqdfu" for relation "synonym" already exists
2016-02-20 20:45:52,529 [localhost-startStop-1] ERROR liquibase  - Change Set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated) failed.  Error: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
2016-02-20 20:45:52,579 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    ... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
2016-02-20 20:45:52,584 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    ... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
Feb 20, 2016 8:45:52 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 20, 2016 8:45:52 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/apollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [PoolCleaner[25416670:1456022700075]] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@18740d1]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 20, 2016 8:45:52 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 20, 2016 8:45:52 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 80376 ms



On Sat, Feb 20, 2016 at 9:32 PM, Lbl <[hidden email]> wrote:
Try opening in an incognito or another browser of doing a shift reload to flush the cache. 

That being said .. This stack trace looks a bit terse.   Typically shiro (the security plugin) will reload but I don't see that here.  Maybe further up? 

Nathan

On Feb 20, 2016, at 6:04 PM, Shane McCoy <[hidden email]> wrote:

Hey! I made the changes but I am still getting a blank screen.

I checked catalina.out, here is the last output:

/var/log/tomcat7$ tail -f catalina.out
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [PoolCleaner[25416670:1456019437960]] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@1b2e3fc]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 20, 2016 7:51:28 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 20, 2016 7:51:28 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 77106 ms


Is this still a memory issue then?
I have updated tomcat memory to your doc specs already.
Thanks!
shane

On Sat, Feb 20, 2016 at 7:55 PM, Shane McCoy <[hidden email]> wrote:
Ok, that makes more sense now! thank you very much.
I'll will try with correct settings,
cheers!

On Sat, Feb 20, 2016 at 7:53 PM, Colin <[hidden email]> wrote:
Hi Shaun

>url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

Just wanted to comment on this, actually, it would not be your IP and war here. It is kind of confusing that this "setting" is called a url, because it is actually a JDBC connector string, which actually references your local database, so it would not be using the war file name or even the IP address.

For example, if your database is named "apollodb", then your "url" would be

jdbc:postgresql://localhost/apollodb

It would generally just be localhost unless you have a separate database server. I think it might be worth adding some more comments about that in our setup guide, but I hope that helps!


-Colin

On Sat, Feb 20, 2016 at 2:36 PM, Shane McCoy <[hidden email]> wrote:
Hey!
So a lot has changed in a year! I'm currently still stuck at 2g but wanted to ask about an issue i have w/ /.apollo deploy
I am getting a blank screen at the URL. I have not added any data for generation yet. I assume i would still get a webapollo ui.
I am using postgresql. I edited apollo-config.groovy
Added (in production only)
datasource.dbCreate = "update" // one of...  ( where does the database name go? I don't understand this line, it seems i'm limited to the options given?)
username: chado database username
password: chado database pw
url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

I haven't changed any other settings and going to http://myipaddress/apollo is a blank page.
I want to use this w/ a already setup postgresql chado database.

I am going off of this guide: http://webapollo.readthedocs.org/en/latest/Setup.html
Thanks!

On Thu, Feb 11, 2016 at 2:29 PM, Shane McCoy <[hidden email]> wrote:
Thanks for the quick reply!
I will see what options I can take -
Shane M.

On Thu, Feb 11, 2016 at 2:18 PM, Nathan Dunn <[hidden email]> wrote:

On Feb 11, 2016, at 11:07 AM, Shane McCoy <[hidden email]> wrote:

Hey

I am getting this error running ./apollo run-local 8085

..........
    BUILD SUCCESSFUL
    | Compiling 5 source files
    | Compiling 5 source files.....
    ***
    Metrics servlet injected into web.xml
    Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
    ***
    | Running Grails application
    Error occurred during initialization of VM
    Could not reserve enough space for object heap
    Error: Could not create the Java Virtual Machine.
    Error: A fatal exception has occurred. Program will exit.
    | Error Forked Grails VM exited with error

I’m guessing that Java is requesting more memory then you have to allocate, and so exiting.  

So, when running it with run-local (for dev purposes), it actually has preset memory, of a max of up to 2 GB, though obviously this is high.  It is in BuildConfig.groovy:

run    : [maxMemory: 2048, minMemory: 64, debug: false , maxPerm: 1024, forkReserve: false],
My guess is that your machine doesn’t have sufficient memory to run this, or there is another process. 

My suggestions would be:
1 - get a machine with at least 4 GB’s of memory, especially if you are going to host to multiple users.  This will enable better caching and performance.    
2 - if (1) is not an immediate option (or to test, or if you are just running locally) your can edit your apollo-config.groovy create a line like this, so it will use less memory:

grails.project.fork = [
// configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
// compile: [maxMemory: 256, minMemory: 64, debug: false, maxPerm: 256, daemon:true],

test : false,
//run : false,
// configure settings for the test-app JVM, uses the daemon by default
//test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
// configure settings for the run-app JVM
run : [maxMemory: 1024, minMemory: 64, debug: false , maxPerm: 512, forkReserve: false],
// configure settings for the run-war JVM
war : [maxMemory: 1024, minMemory: 64, debug: false, maxPerm: 512, forkReserve: false],
// configure settings for the Console UI JVM
console: [maxMemory:
1024, minMemory: 64, debug: false, maxPerm: 512]
]

Setting the java size as done below works for tomcat, but not for the development mode (run-local).  

Nathan 

I looked over the same errors on Stack and made adjustments to the memory but I am still getting this error. I am new to Grails but I believe everything is setup correct and i can run a sample app (helloworld).
Here is the changes i made:

    -Xms512m -Xmx1g -XX:PermSize=256m
This is the memory

    free -m
                 total       used       free     shared    buffers     cached
    Mem:          2015       1297        718         56        169        859
    -/+ buffers/cache:        267       1748

Checking if parameters are being read

    $ ps -ef | grep java
    tomcat7  32158     1  1 11:02 ?        00:00:10 /usr/lib/jvm/default-java/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:PermSize=256m -XX:MaxPermSize=256m -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed -classpath /usr/share/tomcat7/bin/bootstrap.jar:/usr/share/tomcat7/bin/tomcat-juli.jar -Dcatalina.base=/var/lib/tomcat7 -Dcatalina.home=/usr/share/tomcat7 -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp org.apache.catalina.startup.Bootstrap start


I have this in my $HOME/.profile

    export JAVA_OPTS="-Xms512m -Xmx1g -XX:MaxPermSize=256m"

in my setenv.sh for Tomcat7

    export CATALINA_OPTS="-Xms512m -Xmx1g \
        -XX:+CMSClassUnloadingEnabled \
        -XX:+CMSPermGenSweepingEnabled \
        -XX:+UseConcMarkSweepGC \
        -XX:MaxPermSize=256m"

Versions: (i went w/ 2.4.5 per Apollo guide)
    $ grails -version
    Grails version: 2.4.5
    $ java -version
    java version "1.7.0_95"
    OpenJDK Runtime Environment (IcedTea 2.6.4) (7u95-2.6.4-0ubuntu0.14.04.1)
    OpenJDK Client VM (build 24.95-b01, mixed mode, sharing)

I am not sure what to change now - it seems the memory would be adequate? I know this isn't Apollo specific but maybe someone here has had the same problem? Please any thoughts would be great. thank you
Shane M.



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Re: New WebApollo install issue (Grails)

Shane McCoy
Hi Nathan,
I did as you said and it started up just fine. Thank you!
So this leads me to believe the previous setup I did (1.0.2 i believe) won't be the best guide to a new setup.

I want to be able to use the CHADO schema & use web apollo to edit the genome.
I had set up CHADO on a database and had already uploaded the GFF. Can I get pointers on the proper steps to follow now?
I did back it up prior to deleting and recreating db, but it is pretty small test file and i don't have an issue putting back through the script.
Thanks again!
Shane M. 

On Sun, Feb 21, 2016 at 1:24 AM, Nathan Dunn <[hidden email]> wrote:

If you are using postgresql and you don’t have anything in the database you want (or you back it up first) I would drop and re-create the database (with tomcat off).     When it comes back up it will create the database with the create schema for you:

1 - stop tomcat 
1a - backup database? 
2 - dropdb your-apollo-database-name
3 - createdb your-apollo-database-name
4 - start tomcat

Its in a pretty weird state. 

Nathan

On Feb 20, 2016, at 6:51 PM, Shane McCoy <[hidden email]> wrote:

I missed a bit from the log, here is catalina.out from a restart of tomcat7:

 * Stopping Tomcat servlet engine tomcat7                                [ OK ]
 * Starting Tomcat servlet engine tomcat7                                [ OK ]
--------------------------$$:/var/log/tomcat7$ tail -f catalina.out
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor /etc/tomcat7/Catalina/localhost/host-manager.xml
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
^[[AFeb 20, 2016 8:44:43 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 20, 2016 8:44:43 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.

Configuring Shiro ...

Shiro Configured
2016-02-20 20:45:40,539 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column id int8 not null
2016-02-20 20:45:40,543 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,546 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column version int8 not null
2016-02-20 20:45:40,548 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,550 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column program_version varchar(255) not null
2016-02-20 20:45:40,552 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "program_version" contains null values
2016-02-20 20:45:40,554 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_name varchar(255) not null
2016-02-20 20:45:40,555 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_name" contains null values
2016-02-20 20:45:40,558 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_version varchar(255) not null
2016-02-20 20:45:40,559 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_version" contains null values
2016-02-20 20:45:40,562 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column time_executed timestamp not null
2016-02-20 20:45:40,563 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "time_executed" contains null values
2016-02-20 20:45:40,566 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column id int8 not null
2016-02-20 20:45:40,567 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,569 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column version int8 not null
2016-02-20 20:45:40,570 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,573 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column id int8 not null
2016-02-20 20:45:40,574 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,577 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column version int8 not null
2016-02-20 20:45:40,578 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,583 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column is_relationship_type int4 not null
2016-02-20 20:45:40,584 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "is_relationship_type" contains null values
2016-02-20 20:45:40,587 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column id int8 not null
2016-02-20 20:45:40,588 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,590 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column version int8 not null
2016-02-20 20:45:40,591 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,593 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column objectcvterm_id int8 not null
2016-02-20 20:45:40,594 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" contains null values
2016-02-20 20:45:40,598 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column subjectcvterm_id int8 not null
2016-02-20 20:45:40,599 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" contains null values
2016-02-20 20:45:40,602 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column id int8 not null
2016-02-20 20:45:40,602 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,606 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column version int8 not null
2016-02-20 20:45:40,607 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,610 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add column id int8 not null
2016-02-20 20:45:40,612 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,616 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column id int8 not null
2016-02-20 20:45:40,617 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,620 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column version int8 not null
2016-02-20 20:45:40,621 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,632 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column unique_name varchar(255) not null
2016-02-20 20:45:40,633 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "unique_name" contains null values
2016-02-20 20:45:40,636 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column class varchar(255) not null
2016-02-20 20:45:40,637 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "class" contains null values
2016-02-20 20:45:40,641 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column id int8 not null
2016-02-20 20:45:40,642 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,645 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column version int8 not null
2016-02-20 20:45:40,646 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,652 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column child_feature_id int8 not null
2016-02-20 20:45:40,653 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "child_feature_id" contains null values
2016-02-20 20:45:40,656 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column parent_feature_id int8 not null
2016-02-20 20:45:40,657 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "parent_feature_id" contains null values
2016-02-20 20:45:40,660 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column id int8 not null
2016-02-20 20:45:40,661 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,668 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column version int8 not null
2016-02-20 20:45:40,670 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,672 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column publication_id int8 not null
2016-02-20 20:45:40,677 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "publication_id" contains null values
2016-02-20 20:45:40,679 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column id int8 not null
2016-02-20 20:45:40,681 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,684 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column version int8 not null
2016-02-20 20:45:40,685 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,687 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column directory varchar(255)
2016-02-20 20:45:40,688 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,692 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column id int8 not null
2016-02-20 20:45:40,693 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,701 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column version int8 not null
2016-02-20 20:45:40,702 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,704 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column directory varchar(255) not null
2016-02-20 20:45:40,706 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "directory" contains null values
2016-02-20 20:45:40,709 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column id int8 not null
2016-02-20 20:45:40,710 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,715 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column version int8 not null
2016-02-20 20:45:40,716 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,719 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column synonymsgml varchar(255) not null
2016-02-20 20:45:40,720 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "synonymsgml" contains null values
2016-02-20 20:45:40,724 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_feature add constraint FK_8m30ycwh545b4aoxor9sbk1oq foreign key (analysis_id) references analysis
2016-02-20 20:45:40,725 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8m30ycwh545b4aoxor9sbk1oq" for relation "analysis_feature" already exists
2016-02-20 20:45:40,727 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_feature add constraint FK_l94xl424xp988f06gr2b3t5tw foreign key (feature_id) references feature
2016-02-20 20:45:40,728 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_l94xl424xp988f06gr2b3t5tw" for relation "analysis_feature" already exists
2016-02-20 20:45:40,730 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_property add constraint FK_38g8n4bitmdwkrcs217uexrwx foreign key (analysis_id) references analysis
2016-02-20 20:45:40,731 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_38g8n4bitmdwkrcs217uexrwx" for relation "analysis_property" already exists
2016-02-20 20:45:40,733 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_property add constraint FK_9o7xs7saygim8y0sm4ostvpc1 foreign key (type_id) references cvterm
2016-02-20 20:45:40,734 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_9o7xs7saygim8y0sm4ostvpc1" for relation "analysis_property" already exists
2016-02-20 20:45:40,737 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add constraint FK_oksfqluv12ktmut9s6o9jla7a foreign key (cv_id) references cv
2016-02-20 20:45:40,739 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_oksfqluv12ktmut9s6o9jla7a" for relation "cvterm" already exists
2016-02-20 20:45:40,741 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add constraint FK_6d097oy44230tuoo8lb8dkkcp foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,742 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_6d097oy44230tuoo8lb8dkkcp" for relation "cvterm" already exists
2016-02-20 20:45:40,744 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_ke2nrw91sxil8mv7osgv83pw1 foreign key (cv_id) references cv
2016-02-20 20:45:40,745 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ke2nrw91sxil8mv7osgv83pw1" for relation "cvterm_path" already exists
2016-02-20 20:45:40,748 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_tlfh10092i00g6rlv589naqy5 foreign key (objectcvterm_id) references cvterm
2016-02-20 20:45:40,749 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tlfh10092i00g6rlv589naqy5" for relation "cvterm_path" already exists
2016-02-20 20:45:40,751 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_nq02ir0qeydr5tj3071k9gl7b foreign key (subjectcvterm_id) references cvterm
2016-02-20 20:45:40,752 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_nq02ir0qeydr5tj3071k9gl7b" for relation "cvterm_path" already exists
2016-02-20 20:45:40,760 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_jaqi1bk3t2c0m3pybmparp856 foreign key (type_id) references cvterm
2016-02-20 20:45:40,761 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jaqi1bk3t2c0m3pybmparp856" for relation "cvterm_path" already exists
2016-02-20 20:45:40,763 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_r1o1rnfnsf7oipuv1h7h1fln7 foreign key (objectcvterm_id) references cvterm
2016-02-20 20:45:40,766 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,771 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_pwxrfyx6rqu5krq4nj5wa3u4f foreign key (subjectcvterm_id) references cvterm
2016-02-20 20:45:40,775 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,777 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_ob1d0vrfaix8b28j4tvilqnyv foreign key (type_id) references cvterm
2016-02-20 20:45:40,778 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ob1d0vrfaix8b28j4tvilqnyv" for relation "cvterm_relationship" already exists
2016-02-20 20:45:40,781 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add constraint FK_np3tfcu9g867to3qux6raf9y8 foreign key (db_id) references db
2016-02-20 20:45:40,782 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_np3tfcu9g867to3qux6raf9y8" for relation "dbxref" already exists
2016-02-20 20:45:40,786 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref_property add constraint FK_3p1ssctww083s0tt65mmm64uo foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,787 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_3p1ssctww083s0tt65mmm64uo" for relation "dbxref_property" already exists
2016-02-20 20:45:40,792 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref_property add constraint FK_t6ojbvugx8kou45oklsie3rt5 foreign key (type_id) references cvterm
2016-02-20 20:45:40,793 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_t6ojbvugx8kou45oklsie3rt5" for relation "dbxref_property" already exists
2016-02-20 20:45:40,796 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table environmentcvterm add constraint FK_tql9djnqw1d7migfndoj3lrph foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,803 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tql9djnqw1d7migfndoj3lrph" for relation "environmentcvterm" already exists
2016-02-20 20:45:40,805 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table environmentcvterm add constraint FK_rrwb96jjqgtg077yv8pbim3jj foreign key (environment_id) references environment
2016-02-20 20:45:40,807 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_rrwb96jjqgtg077yv8pbim3jj" for relation "environmentcvterm" already exists
2016-02-20 20:45:40,813 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add constraint FK_hc4vrafs0ws7ugdkp0n6u3xdo foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,816 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_hc4vrafs0ws7ugdkp0n6u3xdo" for relation "feature" already exists
2016-02-20 20:45:40,819 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_dbxref add constraint FK_n6n7lheb1qkmlde8u6gvvjxne foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,821 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_n6n7lheb1qkmlde8u6gvvjxne" for relation "feature_dbxref" already exists
2016-02-20 20:45:40,829 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_dbxref add constraint FK_1mrfkxbb3n7fhjxcrkxappdn8 foreign key (feature_featuredbxrefs_id) references feature
2016-02-20 20:45:40,831 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_1mrfkxbb3n7fhjxcrkxappdn8" for relation "feature_dbxref" already exists
2016-02-20 20:45:40,836 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_feature_phenotypes add constraint FK_dy5g29heir5ic3d36okyuihho foreign key (phenotype_id) references phenotype
2016-02-20 20:45:40,839 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_dy5g29heir5ic3d36okyuihho" for relation "feature_feature_phenotypes" already exists
2016-02-20 20:45:40,842 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_feature_phenotypes add constraint FK_aqr7eiyx6puju6elciwubbwmo foreign key (feature_id) references feature
2016-02-20 20:45:40,843 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_aqr7eiyx6puju6elciwubbwmo" for relation "feature_feature_phenotypes" already exists
2016-02-20 20:45:40,847 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_hak8r429shmpho06rbyvwnmt0 foreign key (chromosome_feature_id) references feature
2016-02-20 20:45:40,848 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_hak8r429shmpho06rbyvwnmt0" for relation "feature_genotype" already exists
2016-02-20 20:45:40,856 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_b42u9iq4kuqe5ay544do81n32 foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,857 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_b42u9iq4kuqe5ay544do81n32" for relation "feature_genotype" already exists
2016-02-20 20:45:40,859 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_cm3gqs38fa2lpllgoum8n4kgn foreign key (feature_id) references feature
2016-02-20 20:45:40,861 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cm3gqs38fa2lpllgoum8n4kgn" for relation "feature_genotype" already exists
2016-02-20 20:45:40,863 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_736wxgjs6pip5212ash5i68p foreign key (genotype_id) references genotype
2016-02-20 20:45:40,864 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_736wxgjs6pip5212ash5i68p" for relation "feature_genotype" already exists
2016-02-20 20:45:40,867 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_grails_user add constraint FK_4dgbhgiw0vb9hqy2k5fqg3neh foreign key (feature_owners_id) references feature
2016-02-20 20:45:40,868 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4dgbhgiw0vb9hqy2k5fqg3neh" for relation "feature_grails_user" already exists
2016-02-20 20:45:40,872 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_location add constraint FK_qml7xp9f5uojcw7jwdxcb35le foreign key (feature_id) references feature
2016-02-20 20:45:40,873 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qml7xp9f5uojcw7jwdxcb35le" for relation "feature_location" already exists
2016-02-20 20:45:40,875 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_property add constraint FK_jpvdxc57abfiridcr57x8130 foreign key (feature_id) references feature
2016-02-20 20:45:40,879 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jpvdxc57abfiridcr57x8130" for relation "feature_property" already exists
2016-02-20 20:45:40,881 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_property add constraint FK_36e638geg9tew42b1mp2ehff foreign key (type_id) references cvterm
2016-02-20 20:45:40,882 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_36e638geg9tew42b1mp2ehff" for relation "feature_property" already exists
2016-02-20 20:45:40,885 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_publication add constraint FK_qolh5l4blkx8vfmwcl7f3woan foreign key (feature_feature_publications_id) references feature
2016-02-20 20:45:40,891 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qolh5l4blkx8vfmwcl7f3woan" for relation "feature_publication" already exists
2016-02-20 20:45:40,893 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add constraint FK_8jm56covt0m7m0m191bc5jseh foreign key (child_feature_id) references feature
2016-02-20 20:45:40,894 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "child_feature_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,898 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add constraint FK_72kmd92rdc6gne0nrh026o1j0 foreign key (parent_feature_id) references feature
2016-02-20 20:45:40,899 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "parent_feature_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,907 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship_feature_property add constraint FK_ebgnfbogf1lwdxd8jc17511o7 foreign key (feature_relationship_feature_relationship_properties_id) references feature_relationship
2016-02-20 20:45:40,908 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ebgnfbogf1lwdxd8jc17511o7" for relation "feature_relationship_feature_property" already exists
2016-02-20 20:45:40,911 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship_publication add constraint FK_bdd324e5jb0lpuhs7biy2kacm foreign key (feature_relationship_feature_relationship_publications_id) references feature_relationship
2016-02-20 20:45:40,912 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_bdd324e5jb0lpuhs7biy2kacm" for relation "feature_relationship_publication" already exists
2016-02-20 20:45:40,914 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_nf9qbuay984ixqd2k1425rnyo foreign key (feature_id) references feature
2016-02-20 20:45:40,916 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_nf9qbuay984ixqd2k1425rnyo" for relation "feature_synonym" already exists
2016-02-20 20:45:40,923 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_82wsc3bv9i01t9851xv4xekis foreign key (publication_id) references publication
2016-02-20 20:45:40,926 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "publication_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,929 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_ll4cqdh994s6x8n7vku1q7iwd foreign key (synonym_id) references synonym
2016-02-20 20:45:40,930 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ll4cqdh994s6x8n7vku1q7iwd" for relation "feature_synonym" already exists
2016-02-20 20:45:40,932 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_gsol4u8wrfwbkh1qrx18i3u6 foreign key (feature_synonyms_id) references feature
2016-02-20 20:45:40,933 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gsol4u8wrfwbkh1qrx18i3u6" for relation "feature_synonym" already exists
2016-02-20 20:45:40,935 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm add constraint FK_cuwo3ernssd0t0wjceb7lmm11 foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,936 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cuwo3ernssd0t0wjceb7lmm11" for relation "featurecvterm" already exists
2016-02-20 20:45:40,943 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm add constraint FK_iy7bbt67s7jaemiajsrqalv5o foreign key (feature_id) references feature
2016-02-20 20:45:40,944 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_iy7bbt67s7jaemiajsrqalv5o" for relation "featurecvterm" already exists
2016-02-20 20:45:40,948 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm_dbxref add constraint FK_r9xhefcekikp1od79ectkb22b foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,949 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_r9xhefcekikp1od79ectkb22b" for relation "featurecvterm_dbxref" already exists
2016-02-20 20:45:40,951 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism_organism_property add constraint FK_qyxdgqthtlgixvtdkkhc8g3pu foreign key (organism_organism_properties_id) references organism
2016-02-20 20:45:40,959 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qyxdgqthtlgixvtdkkhc8g3pu" for relation "organism_organism_property" already exists
2016-02-20 20:45:40,961 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organismdbxref add constraint FK_s3vk7onqrk0n4c86xnvqmm3ho foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,962 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_s3vk7onqrk0n4c86xnvqmm3ho" for relation "organismdbxref" already exists
2016-02-20 20:45:40,965 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organismdbxref add constraint FK_l1jfi0wpnyooutd820p5gskr foreign key (organism_id) references organism
2016-02-20 20:45:40,966 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_l1jfi0wpnyooutd820p5gskr" for relation "organismdbxref" already exists
2016-02-20 20:45:40,969 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table permission add constraint FK_4nvoxx3htem6jseb4rmu0aqfp foreign key (organism_id) references organism
2016-02-20 20:45:40,970 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4nvoxx3htem6jseb4rmu0aqfp" for relation "permission" already exists
2016-02-20 20:45:40,972 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_cwgh6naf9gackae2ei11v6p41 foreign key (assay_id) references cvterm
2016-02-20 20:45:40,979 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cwgh6naf9gackae2ei11v6p41" for relation "phenotype" already exists
2016-02-20 20:45:40,981 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_phmfgylejydjqyrvo3imc97go foreign key (attribute_id) references cvterm
2016-02-20 20:45:40,982 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_phmfgylejydjqyrvo3imc97go" for relation "phenotype" already exists
2016-02-20 20:45:40,985 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_jh0fc3orduigl8s7ymentbtrs foreign key (cvalue_id) references cvterm
2016-02-20 20:45:40,986 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jh0fc3orduigl8s7ymentbtrs" for relation "phenotype" already exists
2016-02-20 20:45:40,988 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_gb4wy9qesx6vnekxekm18k9xa foreign key (observable_id) references cvterm
2016-02-20 20:45:40,989 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gb4wy9qesx6vnekxekm18k9xa" for relation "phenotype" already exists
2016-02-20 20:45:40,993 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_cvterm add constraint FK_9e2v7goj5w6nds5jo0x1va1nm foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,999 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_9e2v7goj5w6nds5jo0x1va1nm" for relation "phenotype_cvterm" already exists
2016-02-20 20:45:41,001 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_cvterm add constraint FK_aicsmj1kn20ikm14292g9r2j9 foreign key (phenotype_phenotypecvterms_id) references phenotype
2016-02-20 20:45:41,002 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_aicsmj1kn20ikm14292g9r2j9" for relation "phenotype_cvterm" already exists
2016-02-20 20:45:41,004 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_t52r166gd8710vffy3aompe7d foreign key (environment_id) references environment
2016-02-20 20:45:41,006 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_t52r166gd8710vffy3aompe7d" for relation "phenotype_description" already exists
2016-02-20 20:45:41,011 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_bf1bstadamyw0gsarkb933l5b foreign key (genotype_id) references genotype
2016-02-20 20:45:41,012 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_bf1bstadamyw0gsarkb933l5b" for relation "phenotype_description" already exists
2016-02-20 20:45:41,014 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_8pbyj05khavdl5a648c7pmcil foreign key (type_id) references cvterm
2016-02-20 20:45:41,015 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8pbyj05khavdl5a648c7pmcil" for relation "phenotype_description" already exists
2016-02-20 20:45:41,020 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_q6jvhi3l7ty0m9tpbn09d8pxj foreign key (environment_id) references environment
2016-02-20 20:45:41,021 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_q6jvhi3l7ty0m9tpbn09d8pxj" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,024 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_8rbhsxxdf669tyed8jrr747hv foreign key (genotype_id) references genotype
2016-02-20 20:45:41,027 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8rbhsxxdf669tyed8jrr747hv" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,029 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_gskh1e7b6qa2du48ayu49lr3s foreign key (phenotype_id) references phenotype
2016-02-20 20:45:41,030 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gskh1e7b6qa2du48ayu49lr3s" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,035 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_tk1pgifvuhurefn0y3myfyyt4 foreign key (type_id) references cvterm
2016-02-20 20:45:41,036 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tk1pgifvuhurefn0y3myfyyt4" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,039 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table preference add constraint FK_42b0lk4rcfjcagw84jugd1sgj foreign key (organism_id) references organism
2016-02-20 20:45:41,044 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_42b0lk4rcfjcagw84jugd1sgj" for relation "preference" already exists
2016-02-20 20:45:41,047 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publication add constraint FK_h3g8f3q2krcnwmq2nasbanlay foreign key (type_id) references cvterm
2016-02-20 20:45:41,049 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_h3g8f3q2krcnwmq2nasbanlay" for relation "publication" already exists
2016-02-20 20:45:41,051 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publication_relationship add constraint FK_q6hf14oiq9pomkjrhtndonmeh foreign key (type_id) references cvterm
2016-02-20 20:45:41,052 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_q6hf14oiq9pomkjrhtndonmeh" for relation "publication_relationship" already exists
2016-02-20 20:45:41,055 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publicationdbxref add constraint FK_oh81hma8qx88fhvcmfugx836b foreign key (dbxref_id) references dbxref
2016-02-20 20:45:41,059 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_oh81hma8qx88fhvcmfugx836b" for relation "publicationdbxref" already exists
2016-02-20 20:45:41,061 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table sequence add constraint FK_rux0954nxr4lwvj2qgyjibua7 foreign key (organism_id) references organism
2016-02-20 20:45:41,062 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_rux0954nxr4lwvj2qgyjibua7" for relation "sequence" already exists
2016-02-20 20:45:41,065 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add constraint FK_4ylco1irefvydmsnedglqqdfu foreign key (type_id) references cvterm
2016-02-20 20:45:41,066 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4ylco1irefvydmsnedglqqdfu" for relation "synonym" already exists
2016-02-20 20:45:52,529 [localhost-startStop-1] ERROR liquibase  - Change Set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated) failed.  Error: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
2016-02-20 20:45:52,579 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    ... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
2016-02-20 20:45:52,584 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    ... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
Feb 20, 2016 8:45:52 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 20, 2016 8:45:52 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/apollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [PoolCleaner[25416670:1456022700075]] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@18740d1]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 20, 2016 8:45:52 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 20, 2016 8:45:52 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 80376 ms



On Sat, Feb 20, 2016 at 9:32 PM, Lbl <[hidden email]> wrote:
Try opening in an incognito or another browser of doing a shift reload to flush the cache. 

That being said .. This stack trace looks a bit terse.   Typically shiro (the security plugin) will reload but I don't see that here.  Maybe further up? 

Nathan

On Feb 20, 2016, at 6:04 PM, Shane McCoy <[hidden email]> wrote:

Hey! I made the changes but I am still getting a blank screen.

I checked catalina.out, here is the last output:

/var/log/tomcat7$ tail -f catalina.out
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [PoolCleaner[25416670:1456019437960]] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@1b2e3fc]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 20, 2016 7:51:28 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 20, 2016 7:51:28 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 77106 ms


Is this still a memory issue then?
I have updated tomcat memory to your doc specs already.
Thanks!
shane

On Sat, Feb 20, 2016 at 7:55 PM, Shane McCoy <[hidden email]> wrote:
Ok, that makes more sense now! thank you very much.
I'll will try with correct settings,
cheers!

On Sat, Feb 20, 2016 at 7:53 PM, Colin <[hidden email]> wrote:
Hi Shaun

>url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

Just wanted to comment on this, actually, it would not be your IP and war here. It is kind of confusing that this "setting" is called a url, because it is actually a JDBC connector string, which actually references your local database, so it would not be using the war file name or even the IP address.

For example, if your database is named "apollodb", then your "url" would be

jdbc:postgresql://localhost/apollodb

It would generally just be localhost unless you have a separate database server. I think it might be worth adding some more comments about that in our setup guide, but I hope that helps!


-Colin

On Sat, Feb 20, 2016 at 2:36 PM, Shane McCoy <[hidden email]> wrote:
Hey!
So a lot has changed in a year! I'm currently still stuck at 2g but wanted to ask about an issue i have w/ /.apollo deploy
I am getting a blank screen at the URL. I have not added any data for generation yet. I assume i would still get a webapollo ui.
I am using postgresql. I edited apollo-config.groovy
Added (in production only)
datasource.dbCreate = "update" // one of...  ( where does the database name go? I don't understand this line, it seems i'm limited to the options given?)
username: chado database username
password: chado database pw
url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

I haven't changed any other settings and going to http://myipaddress/apollo is a blank page.
I want to use this w/ a already setup postgresql chado database.

I am going off of this guide: http://webapollo.readthedocs.org/en/latest/Setup.html
Thanks!

On Thu, Feb 11, 2016 at 2:29 PM, Shane McCoy <[hidden email]> wrote:
Thanks for the quick reply!
I will see what options I can take -
Shane M.

On Thu, Feb 11, 2016 at 2:18 PM, Nathan Dunn <[hidden email]> wrote:

On Feb 11, 2016, at 11:07 AM, Shane McCoy <[hidden email]> wrote:

Hey

I am getting this error running ./apollo run-local 8085

..........
    BUILD SUCCESSFUL
    | Compiling 5 source files
    | Compiling 5 source files.....
    ***
    Metrics servlet injected into web.xml
    Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
    ***
    | Running Grails application
    Error occurred during initialization of VM
    Could not reserve enough space for object heap
    Error: Could not create the Java Virtual Machine.
    Error: A fatal exception has occurred. Program will exit.
    | Error Forked Grails VM exited with error

I’m guessing that Java is requesting more memory then you have to allocate, and so exiting.  

So, when running it with run-local (for dev purposes), it actually has preset memory, of a max of up to 2 GB, though obviously this is high.  It is in BuildConfig.groovy:

run    : [maxMemory: 2048, minMemory: 64, debug: false , maxPerm: 1024, forkReserve: false],
My guess is that your machine doesn’t have sufficient memory to run this, or there is another process. 

My suggestions would be:
1 - get a machine with at least 4 GB’s of memory, especially if you are going to host to multiple users.  This will enable better caching and performance.    
2 - if (1) is not an immediate option (or to test, or if you are just running locally) your can edit your apollo-config.groovy create a line like this, so it will use less memory:

grails.project.fork = [
// configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
// compile: [maxMemory: 256, minMemory: 64, debug: false, maxPerm: 256, daemon:true],

test : false,
//run : false,
// configure settings for the test-app JVM, uses the daemon by default
//test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
// configure settings for the run-app JVM
run : [maxMemory: 1024, minMemory: 64, debug: false , maxPerm: 512, forkReserve: false],
// configure settings for the run-war JVM
war : [maxMemory: 1024, minMemory: 64, debug: false, maxPerm: 512, forkReserve: false],
// configure settings for the Console UI JVM
console: [maxMemory:
1024, minMemory: 64, debug: false, maxPerm: 512]
]

Setting the java size as done below works for tomcat, but not for the development mode (run-local).  

Nathan 

I looked over the same errors on Stack and made adjustments to the memory but I am still getting this error. I am new to Grails but I believe everything is setup correct and i can run a sample app (helloworld).
Here is the changes i made:

    -Xms512m -Xmx1g -XX:PermSize=256m
This is the memory

    free -m
                 total       used       free     shared    buffers     cached
    Mem:          2015       1297        718         56        169        859
    -/+ buffers/cache:        267       1748

Checking if parameters are being read

    $ ps -ef | grep java
    tomcat7  32158     1  1 11:02 ?        00:00:10 /usr/lib/jvm/default-java/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:PermSize=256m -XX:MaxPermSize=256m -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed -classpath /usr/share/tomcat7/bin/bootstrap.jar:/usr/share/tomcat7/bin/tomcat-juli.jar -Dcatalina.base=/var/lib/tomcat7 -Dcatalina.home=/usr/share/tomcat7 -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp org.apache.catalina.startup.Bootstrap start


I have this in my $HOME/.profile

    export JAVA_OPTS="-Xms512m -Xmx1g -XX:MaxPermSize=256m"

in my setenv.sh for Tomcat7

    export CATALINA_OPTS="-Xms512m -Xmx1g \
        -XX:+CMSClassUnloadingEnabled \
        -XX:+CMSPermGenSweepingEnabled \
        -XX:+UseConcMarkSweepGC \
        -XX:MaxPermSize=256m"

Versions: (i went w/ 2.4.5 per Apollo guide)
    $ grails -version
    Grails version: 2.4.5
    $ java -version
    java version "1.7.0_95"
    OpenJDK Runtime Environment (IcedTea 2.6.4) (7u95-2.6.4-0ubuntu0.14.04.1)
    OpenJDK Client VM (build 24.95-b01, mixed mode, sharing)

I am not sure what to change now - it seems the memory would be adequate? I know this isn't Apollo specific but maybe someone here has had the same problem? Please any thoughts would be great. thank you
Shane M.



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Re: New WebApollo install issue (Grails)

nathandunn

So, unfortunately we need to formally add Chado integration back to Apollo.  

We (specifically Deepak) are actively working on it and it should be part of the 2.0.3 release.   We’ll be pinging the community specifically to make sure the export / integration works.  

In the interim the best method that I am aware of is to export a GFF3 from Apollo and import that GFF3 into your Chado schema.  

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Feb 21, 2016, at 9:18 AM, Shane McCoy <[hidden email]> wrote:

Hi Nathan,
I did as you said and it started up just fine. Thank you!
So this leads me to believe the previous setup I did (1.0.2 i believe) won't be the best guide to a new setup.

I want to be able to use the CHADO schema & use web apollo to edit the genome.
I had set up CHADO on a database and had already uploaded the GFF. Can I get pointers on the proper steps to follow now?
I did back it up prior to deleting and recreating db, but it is pretty small test file and i don't have an issue putting back through the script.
Thanks again!
Shane M. 

On Sun, Feb 21, 2016 at 1:24 AM, Nathan Dunn <[hidden email]> wrote:

If you are using postgresql and you don’t have anything in the database you want (or you back it up first) I would drop and re-create the database (with tomcat off).     When it comes back up it will create the database with the create schema for you:

1 - stop tomcat 
1a - backup database? 
2 - dropdb your-apollo-database-name
3 - createdb your-apollo-database-name
4 - start tomcat

Its in a pretty weird state. 

Nathan

On Feb 20, 2016, at 6:51 PM, Shane McCoy <[hidden email]> wrote:

I missed a bit from the log, here is catalina.out from a restart of tomcat7:

 * Stopping Tomcat servlet engine tomcat7                                [ OK ]
 * Starting Tomcat servlet engine tomcat7                                [ OK ]
--------------------------$$:/var/log/tomcat7$ tail -f catalina.out
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor /etc/tomcat7/Catalina/localhost/host-manager.xml
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
^[[AFeb 20, 2016 8:44:43 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 20, 2016 8:44:43 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.

Configuring Shiro ...

Shiro Configured
2016-02-20 20:45:40,539 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column id int8 not null
2016-02-20 20:45:40,543 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,546 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column version int8 not null
2016-02-20 20:45:40,548 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,550 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column program_version varchar(255) not null
2016-02-20 20:45:40,552 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "program_version" contains null values
2016-02-20 20:45:40,554 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_name varchar(255) not null
2016-02-20 20:45:40,555 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_name" contains null values
2016-02-20 20:45:40,558 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_version varchar(255) not null
2016-02-20 20:45:40,559 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_version" contains null values
2016-02-20 20:45:40,562 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column time_executed timestamp not null
2016-02-20 20:45:40,563 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "time_executed" contains null values
2016-02-20 20:45:40,566 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column id int8 not null
2016-02-20 20:45:40,567 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,569 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column version int8 not null
2016-02-20 20:45:40,570 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,573 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column id int8 not null
2016-02-20 20:45:40,574 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,577 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column version int8 not null
2016-02-20 20:45:40,578 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,583 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column is_relationship_type int4 not null
2016-02-20 20:45:40,584 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "is_relationship_type" contains null values
2016-02-20 20:45:40,587 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column id int8 not null
2016-02-20 20:45:40,588 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,590 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column version int8 not null
2016-02-20 20:45:40,591 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,593 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column objectcvterm_id int8 not null
2016-02-20 20:45:40,594 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" contains null values
2016-02-20 20:45:40,598 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column subjectcvterm_id int8 not null
2016-02-20 20:45:40,599 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" contains null values
2016-02-20 20:45:40,602 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column id int8 not null
2016-02-20 20:45:40,602 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,606 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column version int8 not null
2016-02-20 20:45:40,607 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,610 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add column id int8 not null
2016-02-20 20:45:40,612 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,616 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column id int8 not null
2016-02-20 20:45:40,617 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,620 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column version int8 not null
2016-02-20 20:45:40,621 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,632 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column unique_name varchar(255) not null
2016-02-20 20:45:40,633 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "unique_name" contains null values
2016-02-20 20:45:40,636 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column class varchar(255) not null
2016-02-20 20:45:40,637 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "class" contains null values
2016-02-20 20:45:40,641 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column id int8 not null
2016-02-20 20:45:40,642 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,645 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column version int8 not null
2016-02-20 20:45:40,646 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,652 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column child_feature_id int8 not null
2016-02-20 20:45:40,653 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "child_feature_id" contains null values
2016-02-20 20:45:40,656 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column parent_feature_id int8 not null
2016-02-20 20:45:40,657 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "parent_feature_id" contains null values
2016-02-20 20:45:40,660 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column id int8 not null
2016-02-20 20:45:40,661 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,668 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column version int8 not null
2016-02-20 20:45:40,670 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,672 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column publication_id int8 not null
2016-02-20 20:45:40,677 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "publication_id" contains null values
2016-02-20 20:45:40,679 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column id int8 not null
2016-02-20 20:45:40,681 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,684 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column version int8 not null
2016-02-20 20:45:40,685 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,687 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column directory varchar(255)
2016-02-20 20:45:40,688 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,692 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column id int8 not null
2016-02-20 20:45:40,693 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,701 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column version int8 not null
2016-02-20 20:45:40,702 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,704 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column directory varchar(255) not null
2016-02-20 20:45:40,706 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "directory" contains null values
2016-02-20 20:45:40,709 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column id int8 not null
2016-02-20 20:45:40,710 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,715 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column version int8 not null
2016-02-20 20:45:40,716 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,719 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column synonymsgml varchar(255) not null
2016-02-20 20:45:40,720 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "synonymsgml" contains null values
2016-02-20 20:45:40,724 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_feature add constraint FK_8m30ycwh545b4aoxor9sbk1oq foreign key (analysis_id) references analysis
2016-02-20 20:45:40,725 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8m30ycwh545b4aoxor9sbk1oq" for relation "analysis_feature" already exists
2016-02-20 20:45:40,727 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_feature add constraint FK_l94xl424xp988f06gr2b3t5tw foreign key (feature_id) references feature
2016-02-20 20:45:40,728 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_l94xl424xp988f06gr2b3t5tw" for relation "analysis_feature" already exists
2016-02-20 20:45:40,730 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_property add constraint FK_38g8n4bitmdwkrcs217uexrwx foreign key (analysis_id) references analysis
2016-02-20 20:45:40,731 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_38g8n4bitmdwkrcs217uexrwx" for relation "analysis_property" already exists
2016-02-20 20:45:40,733 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_property add constraint FK_9o7xs7saygim8y0sm4ostvpc1 foreign key (type_id) references cvterm
2016-02-20 20:45:40,734 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_9o7xs7saygim8y0sm4ostvpc1" for relation "analysis_property" already exists
2016-02-20 20:45:40,737 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add constraint FK_oksfqluv12ktmut9s6o9jla7a foreign key (cv_id) references cv
2016-02-20 20:45:40,739 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_oksfqluv12ktmut9s6o9jla7a" for relation "cvterm" already exists
2016-02-20 20:45:40,741 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add constraint FK_6d097oy44230tuoo8lb8dkkcp foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,742 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_6d097oy44230tuoo8lb8dkkcp" for relation "cvterm" already exists
2016-02-20 20:45:40,744 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_ke2nrw91sxil8mv7osgv83pw1 foreign key (cv_id) references cv
2016-02-20 20:45:40,745 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ke2nrw91sxil8mv7osgv83pw1" for relation "cvterm_path" already exists
2016-02-20 20:45:40,748 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_tlfh10092i00g6rlv589naqy5 foreign key (objectcvterm_id) references cvterm
2016-02-20 20:45:40,749 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tlfh10092i00g6rlv589naqy5" for relation "cvterm_path" already exists
2016-02-20 20:45:40,751 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_nq02ir0qeydr5tj3071k9gl7b foreign key (subjectcvterm_id) references cvterm
2016-02-20 20:45:40,752 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_nq02ir0qeydr5tj3071k9gl7b" for relation "cvterm_path" already exists
2016-02-20 20:45:40,760 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_jaqi1bk3t2c0m3pybmparp856 foreign key (type_id) references cvterm
2016-02-20 20:45:40,761 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jaqi1bk3t2c0m3pybmparp856" for relation "cvterm_path" already exists
2016-02-20 20:45:40,763 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_r1o1rnfnsf7oipuv1h7h1fln7 foreign key (objectcvterm_id) references cvterm
2016-02-20 20:45:40,766 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,771 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_pwxrfyx6rqu5krq4nj5wa3u4f foreign key (subjectcvterm_id) references cvterm
2016-02-20 20:45:40,775 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,777 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_ob1d0vrfaix8b28j4tvilqnyv foreign key (type_id) references cvterm
2016-02-20 20:45:40,778 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ob1d0vrfaix8b28j4tvilqnyv" for relation "cvterm_relationship" already exists
2016-02-20 20:45:40,781 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add constraint FK_np3tfcu9g867to3qux6raf9y8 foreign key (db_id) references db
2016-02-20 20:45:40,782 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_np3tfcu9g867to3qux6raf9y8" for relation "dbxref" already exists
2016-02-20 20:45:40,786 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref_property add constraint FK_3p1ssctww083s0tt65mmm64uo foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,787 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_3p1ssctww083s0tt65mmm64uo" for relation "dbxref_property" already exists
2016-02-20 20:45:40,792 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref_property add constraint FK_t6ojbvugx8kou45oklsie3rt5 foreign key (type_id) references cvterm
2016-02-20 20:45:40,793 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_t6ojbvugx8kou45oklsie3rt5" for relation "dbxref_property" already exists
2016-02-20 20:45:40,796 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table environmentcvterm add constraint FK_tql9djnqw1d7migfndoj3lrph foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,803 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tql9djnqw1d7migfndoj3lrph" for relation "environmentcvterm" already exists
2016-02-20 20:45:40,805 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table environmentcvterm add constraint FK_rrwb96jjqgtg077yv8pbim3jj foreign key (environment_id) references environment
2016-02-20 20:45:40,807 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_rrwb96jjqgtg077yv8pbim3jj" for relation "environmentcvterm" already exists
2016-02-20 20:45:40,813 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add constraint FK_hc4vrafs0ws7ugdkp0n6u3xdo foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,816 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_hc4vrafs0ws7ugdkp0n6u3xdo" for relation "feature" already exists
2016-02-20 20:45:40,819 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_dbxref add constraint FK_n6n7lheb1qkmlde8u6gvvjxne foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,821 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_n6n7lheb1qkmlde8u6gvvjxne" for relation "feature_dbxref" already exists
2016-02-20 20:45:40,829 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_dbxref add constraint FK_1mrfkxbb3n7fhjxcrkxappdn8 foreign key (feature_featuredbxrefs_id) references feature
2016-02-20 20:45:40,831 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_1mrfkxbb3n7fhjxcrkxappdn8" for relation "feature_dbxref" already exists
2016-02-20 20:45:40,836 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_feature_phenotypes add constraint FK_dy5g29heir5ic3d36okyuihho foreign key (phenotype_id) references phenotype
2016-02-20 20:45:40,839 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_dy5g29heir5ic3d36okyuihho" for relation "feature_feature_phenotypes" already exists
2016-02-20 20:45:40,842 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_feature_phenotypes add constraint FK_aqr7eiyx6puju6elciwubbwmo foreign key (feature_id) references feature
2016-02-20 20:45:40,843 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_aqr7eiyx6puju6elciwubbwmo" for relation "feature_feature_phenotypes" already exists
2016-02-20 20:45:40,847 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_hak8r429shmpho06rbyvwnmt0 foreign key (chromosome_feature_id) references feature
2016-02-20 20:45:40,848 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_hak8r429shmpho06rbyvwnmt0" for relation "feature_genotype" already exists
2016-02-20 20:45:40,856 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_b42u9iq4kuqe5ay544do81n32 foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,857 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_b42u9iq4kuqe5ay544do81n32" for relation "feature_genotype" already exists
2016-02-20 20:45:40,859 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_cm3gqs38fa2lpllgoum8n4kgn foreign key (feature_id) references feature
2016-02-20 20:45:40,861 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cm3gqs38fa2lpllgoum8n4kgn" for relation "feature_genotype" already exists
2016-02-20 20:45:40,863 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_736wxgjs6pip5212ash5i68p foreign key (genotype_id) references genotype
2016-02-20 20:45:40,864 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_736wxgjs6pip5212ash5i68p" for relation "feature_genotype" already exists
2016-02-20 20:45:40,867 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_grails_user add constraint FK_4dgbhgiw0vb9hqy2k5fqg3neh foreign key (feature_owners_id) references feature
2016-02-20 20:45:40,868 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4dgbhgiw0vb9hqy2k5fqg3neh" for relation "feature_grails_user" already exists
2016-02-20 20:45:40,872 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_location add constraint FK_qml7xp9f5uojcw7jwdxcb35le foreign key (feature_id) references feature
2016-02-20 20:45:40,873 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qml7xp9f5uojcw7jwdxcb35le" for relation "feature_location" already exists
2016-02-20 20:45:40,875 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_property add constraint FK_jpvdxc57abfiridcr57x8130 foreign key (feature_id) references feature
2016-02-20 20:45:40,879 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jpvdxc57abfiridcr57x8130" for relation "feature_property" already exists
2016-02-20 20:45:40,881 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_property add constraint FK_36e638geg9tew42b1mp2ehff foreign key (type_id) references cvterm
2016-02-20 20:45:40,882 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_36e638geg9tew42b1mp2ehff" for relation "feature_property" already exists
2016-02-20 20:45:40,885 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_publication add constraint FK_qolh5l4blkx8vfmwcl7f3woan foreign key (feature_feature_publications_id) references feature
2016-02-20 20:45:40,891 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qolh5l4blkx8vfmwcl7f3woan" for relation "feature_publication" already exists
2016-02-20 20:45:40,893 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add constraint FK_8jm56covt0m7m0m191bc5jseh foreign key (child_feature_id) references feature
2016-02-20 20:45:40,894 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "child_feature_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,898 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add constraint FK_72kmd92rdc6gne0nrh026o1j0 foreign key (parent_feature_id) references feature
2016-02-20 20:45:40,899 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "parent_feature_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,907 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship_feature_property add constraint FK_ebgnfbogf1lwdxd8jc17511o7 foreign key (feature_relationship_feature_relationship_properties_id) references feature_relationship
2016-02-20 20:45:40,908 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ebgnfbogf1lwdxd8jc17511o7" for relation "feature_relationship_feature_property" already exists
2016-02-20 20:45:40,911 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship_publication add constraint FK_bdd324e5jb0lpuhs7biy2kacm foreign key (feature_relationship_feature_relationship_publications_id) references feature_relationship
2016-02-20 20:45:40,912 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_bdd324e5jb0lpuhs7biy2kacm" for relation "feature_relationship_publication" already exists
2016-02-20 20:45:40,914 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_nf9qbuay984ixqd2k1425rnyo foreign key (feature_id) references feature
2016-02-20 20:45:40,916 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_nf9qbuay984ixqd2k1425rnyo" for relation "feature_synonym" already exists
2016-02-20 20:45:40,923 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_82wsc3bv9i01t9851xv4xekis foreign key (publication_id) references publication
2016-02-20 20:45:40,926 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "publication_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,929 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_ll4cqdh994s6x8n7vku1q7iwd foreign key (synonym_id) references synonym
2016-02-20 20:45:40,930 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ll4cqdh994s6x8n7vku1q7iwd" for relation "feature_synonym" already exists
2016-02-20 20:45:40,932 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_gsol4u8wrfwbkh1qrx18i3u6 foreign key (feature_synonyms_id) references feature
2016-02-20 20:45:40,933 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gsol4u8wrfwbkh1qrx18i3u6" for relation "feature_synonym" already exists
2016-02-20 20:45:40,935 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm add constraint FK_cuwo3ernssd0t0wjceb7lmm11 foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,936 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cuwo3ernssd0t0wjceb7lmm11" for relation "featurecvterm" already exists
2016-02-20 20:45:40,943 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm add constraint FK_iy7bbt67s7jaemiajsrqalv5o foreign key (feature_id) references feature
2016-02-20 20:45:40,944 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_iy7bbt67s7jaemiajsrqalv5o" for relation "featurecvterm" already exists
2016-02-20 20:45:40,948 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm_dbxref add constraint FK_r9xhefcekikp1od79ectkb22b foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,949 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_r9xhefcekikp1od79ectkb22b" for relation "featurecvterm_dbxref" already exists
2016-02-20 20:45:40,951 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism_organism_property add constraint FK_qyxdgqthtlgixvtdkkhc8g3pu foreign key (organism_organism_properties_id) references organism
2016-02-20 20:45:40,959 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qyxdgqthtlgixvtdkkhc8g3pu" for relation "organism_organism_property" already exists
2016-02-20 20:45:40,961 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organismdbxref add constraint FK_s3vk7onqrk0n4c86xnvqmm3ho foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,962 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_s3vk7onqrk0n4c86xnvqmm3ho" for relation "organismdbxref" already exists
2016-02-20 20:45:40,965 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organismdbxref add constraint FK_l1jfi0wpnyooutd820p5gskr foreign key (organism_id) references organism
2016-02-20 20:45:40,966 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_l1jfi0wpnyooutd820p5gskr" for relation "organismdbxref" already exists
2016-02-20 20:45:40,969 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table permission add constraint FK_4nvoxx3htem6jseb4rmu0aqfp foreign key (organism_id) references organism
2016-02-20 20:45:40,970 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4nvoxx3htem6jseb4rmu0aqfp" for relation "permission" already exists
2016-02-20 20:45:40,972 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_cwgh6naf9gackae2ei11v6p41 foreign key (assay_id) references cvterm
2016-02-20 20:45:40,979 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cwgh6naf9gackae2ei11v6p41" for relation "phenotype" already exists
2016-02-20 20:45:40,981 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_phmfgylejydjqyrvo3imc97go foreign key (attribute_id) references cvterm
2016-02-20 20:45:40,982 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_phmfgylejydjqyrvo3imc97go" for relation "phenotype" already exists
2016-02-20 20:45:40,985 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_jh0fc3orduigl8s7ymentbtrs foreign key (cvalue_id) references cvterm
2016-02-20 20:45:40,986 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jh0fc3orduigl8s7ymentbtrs" for relation "phenotype" already exists
2016-02-20 20:45:40,988 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_gb4wy9qesx6vnekxekm18k9xa foreign key (observable_id) references cvterm
2016-02-20 20:45:40,989 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gb4wy9qesx6vnekxekm18k9xa" for relation "phenotype" already exists
2016-02-20 20:45:40,993 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_cvterm add constraint FK_9e2v7goj5w6nds5jo0x1va1nm foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,999 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_9e2v7goj5w6nds5jo0x1va1nm" for relation "phenotype_cvterm" already exists
2016-02-20 20:45:41,001 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_cvterm add constraint FK_aicsmj1kn20ikm14292g9r2j9 foreign key (phenotype_phenotypecvterms_id) references phenotype
2016-02-20 20:45:41,002 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_aicsmj1kn20ikm14292g9r2j9" for relation "phenotype_cvterm" already exists
2016-02-20 20:45:41,004 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_t52r166gd8710vffy3aompe7d foreign key (environment_id) references environment
2016-02-20 20:45:41,006 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_t52r166gd8710vffy3aompe7d" for relation "phenotype_description" already exists
2016-02-20 20:45:41,011 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_bf1bstadamyw0gsarkb933l5b foreign key (genotype_id) references genotype
2016-02-20 20:45:41,012 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_bf1bstadamyw0gsarkb933l5b" for relation "phenotype_description" already exists
2016-02-20 20:45:41,014 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_8pbyj05khavdl5a648c7pmcil foreign key (type_id) references cvterm
2016-02-20 20:45:41,015 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8pbyj05khavdl5a648c7pmcil" for relation "phenotype_description" already exists
2016-02-20 20:45:41,020 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_q6jvhi3l7ty0m9tpbn09d8pxj foreign key (environment_id) references environment
2016-02-20 20:45:41,021 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_q6jvhi3l7ty0m9tpbn09d8pxj" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,024 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_8rbhsxxdf669tyed8jrr747hv foreign key (genotype_id) references genotype
2016-02-20 20:45:41,027 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8rbhsxxdf669tyed8jrr747hv" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,029 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_gskh1e7b6qa2du48ayu49lr3s foreign key (phenotype_id) references phenotype
2016-02-20 20:45:41,030 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gskh1e7b6qa2du48ayu49lr3s" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,035 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_tk1pgifvuhurefn0y3myfyyt4 foreign key (type_id) references cvterm
2016-02-20 20:45:41,036 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tk1pgifvuhurefn0y3myfyyt4" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,039 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table preference add constraint FK_42b0lk4rcfjcagw84jugd1sgj foreign key (organism_id) references organism
2016-02-20 20:45:41,044 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_42b0lk4rcfjcagw84jugd1sgj" for relation "preference" already exists
2016-02-20 20:45:41,047 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publication add constraint FK_h3g8f3q2krcnwmq2nasbanlay foreign key (type_id) references cvterm
2016-02-20 20:45:41,049 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_h3g8f3q2krcnwmq2nasbanlay" for relation "publication" already exists
2016-02-20 20:45:41,051 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publication_relationship add constraint FK_q6hf14oiq9pomkjrhtndonmeh foreign key (type_id) references cvterm
2016-02-20 20:45:41,052 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_q6hf14oiq9pomkjrhtndonmeh" for relation "publication_relationship" already exists
2016-02-20 20:45:41,055 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publicationdbxref add constraint FK_oh81hma8qx88fhvcmfugx836b foreign key (dbxref_id) references dbxref
2016-02-20 20:45:41,059 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_oh81hma8qx88fhvcmfugx836b" for relation "publicationdbxref" already exists
2016-02-20 20:45:41,061 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table sequence add constraint FK_rux0954nxr4lwvj2qgyjibua7 foreign key (organism_id) references organism
2016-02-20 20:45:41,062 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_rux0954nxr4lwvj2qgyjibua7" for relation "sequence" already exists
2016-02-20 20:45:41,065 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add constraint FK_4ylco1irefvydmsnedglqqdfu foreign key (type_id) references cvterm
2016-02-20 20:45:41,066 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4ylco1irefvydmsnedglqqdfu" for relation "synonym" already exists
2016-02-20 20:45:52,529 [localhost-startStop-1] ERROR liquibase  - Change Set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated) failed.  Error: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
2016-02-20 20:45:52,579 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    ... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
2016-02-20 20:45:52,584 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    ... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
Feb 20, 2016 8:45:52 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 20, 2016 8:45:52 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/apollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [PoolCleaner[25416670:1456022700075]] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@18740d1]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 20, 2016 8:45:52 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 20, 2016 8:45:52 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 80376 ms



On Sat, Feb 20, 2016 at 9:32 PM, Lbl <[hidden email]> wrote:
Try opening in an incognito or another browser of doing a shift reload to flush the cache. 

That being said .. This stack trace looks a bit terse.   Typically shiro (the security plugin) will reload but I don't see that here.  Maybe further up? 

Nathan

On Feb 20, 2016, at 6:04 PM, Shane McCoy <[hidden email]> wrote:

Hey! I made the changes but I am still getting a blank screen.

I checked catalina.out, here is the last output:

/var/log/tomcat7$ tail -f catalina.out
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [PoolCleaner[25416670:1456019437960]] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@1b2e3fc]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 20, 2016 7:51:28 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 20, 2016 7:51:28 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 77106 ms


Is this still a memory issue then?
I have updated tomcat memory to your doc specs already.
Thanks!
shane

On Sat, Feb 20, 2016 at 7:55 PM, Shane McCoy <[hidden email]> wrote:
Ok, that makes more sense now! thank you very much.
I'll will try with correct settings,
cheers!

On Sat, Feb 20, 2016 at 7:53 PM, Colin <[hidden email]> wrote:
Hi Shaun

>url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

Just wanted to comment on this, actually, it would not be your IP and war here. It is kind of confusing that this "setting" is called a url, because it is actually a JDBC connector string, which actually references your local database, so it would not be using the war file name or even the IP address.

For example, if your database is named "apollodb", then your "url" would be

jdbc:postgresql://localhost/apollodb

It would generally just be localhost unless you have a separate database server. I think it might be worth adding some more comments about that in our setup guide, but I hope that helps!


-Colin

On Sat, Feb 20, 2016 at 2:36 PM, Shane McCoy <[hidden email]> wrote:
Hey!
So a lot has changed in a year! I'm currently still stuck at 2g but wanted to ask about an issue i have w/ /.apollo deploy
I am getting a blank screen at the URL. I have not added any data for generation yet. I assume i would still get a webapollo ui.
I am using postgresql. I edited apollo-config.groovy
Added (in production only)
datasource.dbCreate = "update" // one of...  ( where does the database name go? I don't understand this line, it seems i'm limited to the options given?)
username: chado database username
password: chado database pw
url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

I haven't changed any other settings and going to http://myipaddress/apollo is a blank page.
I want to use this w/ a already setup postgresql chado database.

I am going off of this guide: http://webapollo.readthedocs.org/en/latest/Setup.html
Thanks!

On Thu, Feb 11, 2016 at 2:29 PM, Shane McCoy <[hidden email]> wrote:
Thanks for the quick reply!
I will see what options I can take -
Shane M.

On Thu, Feb 11, 2016 at 2:18 PM, Nathan Dunn <[hidden email]> wrote:

On Feb 11, 2016, at 11:07 AM, Shane McCoy <[hidden email]> wrote:

Hey

I am getting this error running ./apollo run-local 8085

..........
    BUILD SUCCESSFUL
    | Compiling 5 source files
    | Compiling 5 source files.....
    ***
    Metrics servlet injected into web.xml
    Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
    ***
    | Running Grails application
    Error occurred during initialization of VM
    Could not reserve enough space for object heap
    Error: Could not create the Java Virtual Machine.
    Error: A fatal exception has occurred. Program will exit.
    | Error Forked Grails VM exited with error

I’m guessing that Java is requesting more memory then you have to allocate, and so exiting.  

So, when running it with run-local (for dev purposes), it actually has preset memory, of a max of up to 2 GB, though obviously this is high.  It is in BuildConfig.groovy:

run    : [maxMemory: 2048, minMemory: 64, debug: false , maxPerm: 1024, forkReserve: false],
My guess is that your machine doesn’t have sufficient memory to run this, or there is another process. 

My suggestions would be:
1 - get a machine with at least 4 GB’s of memory, especially if you are going to host to multiple users.  This will enable better caching and performance.    
2 - if (1) is not an immediate option (or to test, or if you are just running locally) your can edit your apollo-config.groovy create a line like this, so it will use less memory:

grails.project.fork = [
// configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
// compile: [maxMemory: 256, minMemory: 64, debug: false, maxPerm: 256, daemon:true],

test : false,
//run : false,
// configure settings for the test-app JVM, uses the daemon by default
//test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
// configure settings for the run-app JVM
run : [maxMemory: 1024, minMemory: 64, debug: false , maxPerm: 512, forkReserve: false],
// configure settings for the run-war JVM
war : [maxMemory: 1024, minMemory: 64, debug: false, maxPerm: 512, forkReserve: false],
// configure settings for the Console UI JVM
console: [maxMemory:
1024, minMemory: 64, debug: false, maxPerm: 512]
]

Setting the java size as done below works for tomcat, but not for the development mode (run-local).  

Nathan 

I looked over the same errors on Stack and made adjustments to the memory but I am still getting this error. I am new to Grails but I believe everything is setup correct and i can run a sample app (helloworld).
Here is the changes i made:

    -Xms512m -Xmx1g -XX:PermSize=256m
This is the memory

    free -m
                 total       used       free     shared    buffers     cached
    Mem:          2015       1297        718         56        169        859
    -/+ buffers/cache:        267       1748

Checking if parameters are being read

    $ ps -ef | grep java
    tomcat7  32158     1  1 11:02 ?        00:00:10 /usr/lib/jvm/default-java/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:PermSize=256m -XX:MaxPermSize=256m -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed -classpath /usr/share/tomcat7/bin/bootstrap.jar:/usr/share/tomcat7/bin/tomcat-juli.jar -Dcatalina.base=/var/lib/tomcat7 -Dcatalina.home=/usr/share/tomcat7 -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp org.apache.catalina.startup.Bootstrap start


I have this in my $HOME/.profile

    export JAVA_OPTS="-Xms512m -Xmx1g -XX:MaxPermSize=256m"

in my setenv.sh for Tomcat7

    export CATALINA_OPTS="-Xms512m -Xmx1g \
        -XX:+CMSClassUnloadingEnabled \
        -XX:+CMSPermGenSweepingEnabled \
        -XX:+UseConcMarkSweepGC \
        -XX:MaxPermSize=256m"

Versions: (i went w/ 2.4.5 per Apollo guide)
    $ grails -version
    Grails version: 2.4.5
    $ java -version
    java version "1.7.0_95"
    OpenJDK Runtime Environment (IcedTea 2.6.4) (7u95-2.6.4-0ubuntu0.14.04.1)
    OpenJDK Client VM (build 24.95-b01, mixed mode, sharing)

I am not sure what to change now - it seems the memory would be adequate? I know this isn't Apollo specific but maybe someone here has had the same problem? Please any thoughts would be great. thank you
Shane M.



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This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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Re: New WebApollo install issue (Grails)

Shane McCoy
Ok, good to know! I'll keep an eye out for the Chado addition later.
This seems a lot simpler than prior version.
so if i have 2 files: genome.gff & genome.fa

  1. bin/preprare-refseqs.pl --fasta genome.fa --out /opt/apollo/data
  2. bin/flatfile-to-json.pl --gff genome.gff --type gene --tracklabel makergene --autocomplete all --Key Maker Gene --out /opt/apollo/data
  3. and repeat for all the different Types? correct? is there any changes to the options for flatfile-to-json.pl? I have many to add from the same genome
  4. bin/generate-names.pl --verbose --out /opt/apollo/data
  5. ./apollo deploy
  6. add WAR to webapps and start tomcat.
  7. is that about right?
Thanks again!
Shane



On Sun, Feb 21, 2016 at 5:43 PM, Nathan Dunn <[hidden email]> wrote:

So, unfortunately we need to formally add Chado integration back to Apollo.  

We (specifically Deepak) are actively working on it and it should be part of the 2.0.3 release.   We’ll be pinging the community specifically to make sure the export / integration works.  

In the interim the best method that I am aware of is to export a GFF3 from Apollo and import that GFF3 into your Chado schema.  

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Feb 21, 2016, at 9:18 AM, Shane McCoy <[hidden email]> wrote:

Hi Nathan,
I did as you said and it started up just fine. Thank you!
So this leads me to believe the previous setup I did (1.0.2 i believe) won't be the best guide to a new setup.

I want to be able to use the CHADO schema & use web apollo to edit the genome.
I had set up CHADO on a database and had already uploaded the GFF. Can I get pointers on the proper steps to follow now?
I did back it up prior to deleting and recreating db, but it is pretty small test file and i don't have an issue putting back through the script.
Thanks again!
Shane M. 

On Sun, Feb 21, 2016 at 1:24 AM, Nathan Dunn <[hidden email]> wrote:

If you are using postgresql and you don’t have anything in the database you want (or you back it up first) I would drop and re-create the database (with tomcat off).     When it comes back up it will create the database with the create schema for you:

1 - stop tomcat 
1a - backup database? 
2 - dropdb your-apollo-database-name
3 - createdb your-apollo-database-name
4 - start tomcat

Its in a pretty weird state. 

Nathan

On Feb 20, 2016, at 6:51 PM, Shane McCoy <[hidden email]> wrote:

I missed a bit from the log, here is catalina.out from a restart of tomcat7:

 * Stopping Tomcat servlet engine tomcat7                                [ OK ]
 * Starting Tomcat servlet engine tomcat7                                [ OK ]
--------------------------$$:/var/log/tomcat7$ tail -f catalina.out
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor /etc/tomcat7/Catalina/localhost/host-manager.xml
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
^[[AFeb 20, 2016 8:44:43 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 20, 2016 8:44:43 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.

Configuring Shiro ...

Shiro Configured
2016-02-20 20:45:40,539 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column id int8 not null
2016-02-20 20:45:40,543 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,546 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column version int8 not null
2016-02-20 20:45:40,548 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,550 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column program_version varchar(255) not null
2016-02-20 20:45:40,552 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "program_version" contains null values
2016-02-20 20:45:40,554 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_name varchar(255) not null
2016-02-20 20:45:40,555 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_name" contains null values
2016-02-20 20:45:40,558 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_version varchar(255) not null
2016-02-20 20:45:40,559 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_version" contains null values
2016-02-20 20:45:40,562 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column time_executed timestamp not null
2016-02-20 20:45:40,563 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "time_executed" contains null values
2016-02-20 20:45:40,566 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column id int8 not null
2016-02-20 20:45:40,567 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,569 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column version int8 not null
2016-02-20 20:45:40,570 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,573 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column id int8 not null
2016-02-20 20:45:40,574 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,577 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column version int8 not null
2016-02-20 20:45:40,578 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,583 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column is_relationship_type int4 not null
2016-02-20 20:45:40,584 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "is_relationship_type" contains null values
2016-02-20 20:45:40,587 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column id int8 not null
2016-02-20 20:45:40,588 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,590 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column version int8 not null
2016-02-20 20:45:40,591 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,593 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column objectcvterm_id int8 not null
2016-02-20 20:45:40,594 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" contains null values
2016-02-20 20:45:40,598 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column subjectcvterm_id int8 not null
2016-02-20 20:45:40,599 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" contains null values
2016-02-20 20:45:40,602 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column id int8 not null
2016-02-20 20:45:40,602 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,606 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column version int8 not null
2016-02-20 20:45:40,607 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,610 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add column id int8 not null
2016-02-20 20:45:40,612 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,616 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column id int8 not null
2016-02-20 20:45:40,617 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,620 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column version int8 not null
2016-02-20 20:45:40,621 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,632 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column unique_name varchar(255) not null
2016-02-20 20:45:40,633 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "unique_name" contains null values
2016-02-20 20:45:40,636 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column class varchar(255) not null
2016-02-20 20:45:40,637 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "class" contains null values
2016-02-20 20:45:40,641 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column id int8 not null
2016-02-20 20:45:40,642 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,645 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column version int8 not null
2016-02-20 20:45:40,646 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,652 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column child_feature_id int8 not null
2016-02-20 20:45:40,653 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "child_feature_id" contains null values
2016-02-20 20:45:40,656 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column parent_feature_id int8 not null
2016-02-20 20:45:40,657 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "parent_feature_id" contains null values
2016-02-20 20:45:40,660 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column id int8 not null
2016-02-20 20:45:40,661 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,668 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column version int8 not null
2016-02-20 20:45:40,670 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,672 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column publication_id int8 not null
2016-02-20 20:45:40,677 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "publication_id" contains null values
2016-02-20 20:45:40,679 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column id int8 not null
2016-02-20 20:45:40,681 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,684 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column version int8 not null
2016-02-20 20:45:40,685 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,687 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column directory varchar(255)
2016-02-20 20:45:40,688 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,692 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column id int8 not null
2016-02-20 20:45:40,693 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,701 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column version int8 not null
2016-02-20 20:45:40,702 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,704 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column directory varchar(255) not null
2016-02-20 20:45:40,706 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "directory" contains null values
2016-02-20 20:45:40,709 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column id int8 not null
2016-02-20 20:45:40,710 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,715 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column version int8 not null
2016-02-20 20:45:40,716 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,719 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column synonymsgml varchar(255) not null
2016-02-20 20:45:40,720 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "synonymsgml" contains null values
2016-02-20 20:45:40,724 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_feature add constraint FK_8m30ycwh545b4aoxor9sbk1oq foreign key (analysis_id) references analysis
2016-02-20 20:45:40,725 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8m30ycwh545b4aoxor9sbk1oq" for relation "analysis_feature" already exists
2016-02-20 20:45:40,727 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_feature add constraint FK_l94xl424xp988f06gr2b3t5tw foreign key (feature_id) references feature
2016-02-20 20:45:40,728 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_l94xl424xp988f06gr2b3t5tw" for relation "analysis_feature" already exists
2016-02-20 20:45:40,730 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_property add constraint FK_38g8n4bitmdwkrcs217uexrwx foreign key (analysis_id) references analysis
2016-02-20 20:45:40,731 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_38g8n4bitmdwkrcs217uexrwx" for relation "analysis_property" already exists
2016-02-20 20:45:40,733 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_property add constraint FK_9o7xs7saygim8y0sm4ostvpc1 foreign key (type_id) references cvterm
2016-02-20 20:45:40,734 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_9o7xs7saygim8y0sm4ostvpc1" for relation "analysis_property" already exists
2016-02-20 20:45:40,737 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add constraint FK_oksfqluv12ktmut9s6o9jla7a foreign key (cv_id) references cv
2016-02-20 20:45:40,739 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_oksfqluv12ktmut9s6o9jla7a" for relation "cvterm" already exists
2016-02-20 20:45:40,741 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add constraint FK_6d097oy44230tuoo8lb8dkkcp foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,742 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_6d097oy44230tuoo8lb8dkkcp" for relation "cvterm" already exists
2016-02-20 20:45:40,744 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_ke2nrw91sxil8mv7osgv83pw1 foreign key (cv_id) references cv
2016-02-20 20:45:40,745 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ke2nrw91sxil8mv7osgv83pw1" for relation "cvterm_path" already exists
2016-02-20 20:45:40,748 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_tlfh10092i00g6rlv589naqy5 foreign key (objectcvterm_id) references cvterm
2016-02-20 20:45:40,749 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tlfh10092i00g6rlv589naqy5" for relation "cvterm_path" already exists
2016-02-20 20:45:40,751 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_nq02ir0qeydr5tj3071k9gl7b foreign key (subjectcvterm_id) references cvterm
2016-02-20 20:45:40,752 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_nq02ir0qeydr5tj3071k9gl7b" for relation "cvterm_path" already exists
2016-02-20 20:45:40,760 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_jaqi1bk3t2c0m3pybmparp856 foreign key (type_id) references cvterm
2016-02-20 20:45:40,761 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jaqi1bk3t2c0m3pybmparp856" for relation "cvterm_path" already exists
2016-02-20 20:45:40,763 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_r1o1rnfnsf7oipuv1h7h1fln7 foreign key (objectcvterm_id) references cvterm
2016-02-20 20:45:40,766 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,771 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_pwxrfyx6rqu5krq4nj5wa3u4f foreign key (subjectcvterm_id) references cvterm
2016-02-20 20:45:40,775 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,777 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_ob1d0vrfaix8b28j4tvilqnyv foreign key (type_id) references cvterm
2016-02-20 20:45:40,778 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ob1d0vrfaix8b28j4tvilqnyv" for relation "cvterm_relationship" already exists
2016-02-20 20:45:40,781 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add constraint FK_np3tfcu9g867to3qux6raf9y8 foreign key (db_id) references db
2016-02-20 20:45:40,782 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_np3tfcu9g867to3qux6raf9y8" for relation "dbxref" already exists
2016-02-20 20:45:40,786 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref_property add constraint FK_3p1ssctww083s0tt65mmm64uo foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,787 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_3p1ssctww083s0tt65mmm64uo" for relation "dbxref_property" already exists
2016-02-20 20:45:40,792 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref_property add constraint FK_t6ojbvugx8kou45oklsie3rt5 foreign key (type_id) references cvterm
2016-02-20 20:45:40,793 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_t6ojbvugx8kou45oklsie3rt5" for relation "dbxref_property" already exists
2016-02-20 20:45:40,796 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table environmentcvterm add constraint FK_tql9djnqw1d7migfndoj3lrph foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,803 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tql9djnqw1d7migfndoj3lrph" for relation "environmentcvterm" already exists
2016-02-20 20:45:40,805 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table environmentcvterm add constraint FK_rrwb96jjqgtg077yv8pbim3jj foreign key (environment_id) references environment
2016-02-20 20:45:40,807 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_rrwb96jjqgtg077yv8pbim3jj" for relation "environmentcvterm" already exists
2016-02-20 20:45:40,813 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add constraint FK_hc4vrafs0ws7ugdkp0n6u3xdo foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,816 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_hc4vrafs0ws7ugdkp0n6u3xdo" for relation "feature" already exists
2016-02-20 20:45:40,819 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_dbxref add constraint FK_n6n7lheb1qkmlde8u6gvvjxne foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,821 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_n6n7lheb1qkmlde8u6gvvjxne" for relation "feature_dbxref" already exists
2016-02-20 20:45:40,829 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_dbxref add constraint FK_1mrfkxbb3n7fhjxcrkxappdn8 foreign key (feature_featuredbxrefs_id) references feature
2016-02-20 20:45:40,831 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_1mrfkxbb3n7fhjxcrkxappdn8" for relation "feature_dbxref" already exists
2016-02-20 20:45:40,836 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_feature_phenotypes add constraint FK_dy5g29heir5ic3d36okyuihho foreign key (phenotype_id) references phenotype
2016-02-20 20:45:40,839 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_dy5g29heir5ic3d36okyuihho" for relation "feature_feature_phenotypes" already exists
2016-02-20 20:45:40,842 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_feature_phenotypes add constraint FK_aqr7eiyx6puju6elciwubbwmo foreign key (feature_id) references feature
2016-02-20 20:45:40,843 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_aqr7eiyx6puju6elciwubbwmo" for relation "feature_feature_phenotypes" already exists
2016-02-20 20:45:40,847 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_hak8r429shmpho06rbyvwnmt0 foreign key (chromosome_feature_id) references feature
2016-02-20 20:45:40,848 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_hak8r429shmpho06rbyvwnmt0" for relation "feature_genotype" already exists
2016-02-20 20:45:40,856 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_b42u9iq4kuqe5ay544do81n32 foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,857 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_b42u9iq4kuqe5ay544do81n32" for relation "feature_genotype" already exists
2016-02-20 20:45:40,859 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_cm3gqs38fa2lpllgoum8n4kgn foreign key (feature_id) references feature
2016-02-20 20:45:40,861 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cm3gqs38fa2lpllgoum8n4kgn" for relation "feature_genotype" already exists
2016-02-20 20:45:40,863 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_736wxgjs6pip5212ash5i68p foreign key (genotype_id) references genotype
2016-02-20 20:45:40,864 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_736wxgjs6pip5212ash5i68p" for relation "feature_genotype" already exists
2016-02-20 20:45:40,867 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_grails_user add constraint FK_4dgbhgiw0vb9hqy2k5fqg3neh foreign key (feature_owners_id) references feature
2016-02-20 20:45:40,868 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4dgbhgiw0vb9hqy2k5fqg3neh" for relation "feature_grails_user" already exists
2016-02-20 20:45:40,872 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_location add constraint FK_qml7xp9f5uojcw7jwdxcb35le foreign key (feature_id) references feature
2016-02-20 20:45:40,873 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qml7xp9f5uojcw7jwdxcb35le" for relation "feature_location" already exists
2016-02-20 20:45:40,875 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_property add constraint FK_jpvdxc57abfiridcr57x8130 foreign key (feature_id) references feature
2016-02-20 20:45:40,879 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jpvdxc57abfiridcr57x8130" for relation "feature_property" already exists
2016-02-20 20:45:40,881 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_property add constraint FK_36e638geg9tew42b1mp2ehff foreign key (type_id) references cvterm
2016-02-20 20:45:40,882 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_36e638geg9tew42b1mp2ehff" for relation "feature_property" already exists
2016-02-20 20:45:40,885 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_publication add constraint FK_qolh5l4blkx8vfmwcl7f3woan foreign key (feature_feature_publications_id) references feature
2016-02-20 20:45:40,891 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qolh5l4blkx8vfmwcl7f3woan" for relation "feature_publication" already exists
2016-02-20 20:45:40,893 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add constraint FK_8jm56covt0m7m0m191bc5jseh foreign key (child_feature_id) references feature
2016-02-20 20:45:40,894 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "child_feature_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,898 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add constraint FK_72kmd92rdc6gne0nrh026o1j0 foreign key (parent_feature_id) references feature
2016-02-20 20:45:40,899 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "parent_feature_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,907 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship_feature_property add constraint FK_ebgnfbogf1lwdxd8jc17511o7 foreign key (feature_relationship_feature_relationship_properties_id) references feature_relationship
2016-02-20 20:45:40,908 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ebgnfbogf1lwdxd8jc17511o7" for relation "feature_relationship_feature_property" already exists
2016-02-20 20:45:40,911 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship_publication add constraint FK_bdd324e5jb0lpuhs7biy2kacm foreign key (feature_relationship_feature_relationship_publications_id) references feature_relationship
2016-02-20 20:45:40,912 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_bdd324e5jb0lpuhs7biy2kacm" for relation "feature_relationship_publication" already exists
2016-02-20 20:45:40,914 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_nf9qbuay984ixqd2k1425rnyo foreign key (feature_id) references feature
2016-02-20 20:45:40,916 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_nf9qbuay984ixqd2k1425rnyo" for relation "feature_synonym" already exists
2016-02-20 20:45:40,923 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_82wsc3bv9i01t9851xv4xekis foreign key (publication_id) references publication
2016-02-20 20:45:40,926 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "publication_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,929 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_ll4cqdh994s6x8n7vku1q7iwd foreign key (synonym_id) references synonym
2016-02-20 20:45:40,930 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ll4cqdh994s6x8n7vku1q7iwd" for relation "feature_synonym" already exists
2016-02-20 20:45:40,932 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_gsol4u8wrfwbkh1qrx18i3u6 foreign key (feature_synonyms_id) references feature
2016-02-20 20:45:40,933 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gsol4u8wrfwbkh1qrx18i3u6" for relation "feature_synonym" already exists
2016-02-20 20:45:40,935 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm add constraint FK_cuwo3ernssd0t0wjceb7lmm11 foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,936 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cuwo3ernssd0t0wjceb7lmm11" for relation "featurecvterm" already exists
2016-02-20 20:45:40,943 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm add constraint FK_iy7bbt67s7jaemiajsrqalv5o foreign key (feature_id) references feature
2016-02-20 20:45:40,944 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_iy7bbt67s7jaemiajsrqalv5o" for relation "featurecvterm" already exists
2016-02-20 20:45:40,948 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm_dbxref add constraint FK_r9xhefcekikp1od79ectkb22b foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,949 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_r9xhefcekikp1od79ectkb22b" for relation "featurecvterm_dbxref" already exists
2016-02-20 20:45:40,951 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism_organism_property add constraint FK_qyxdgqthtlgixvtdkkhc8g3pu foreign key (organism_organism_properties_id) references organism
2016-02-20 20:45:40,959 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qyxdgqthtlgixvtdkkhc8g3pu" for relation "organism_organism_property" already exists
2016-02-20 20:45:40,961 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organismdbxref add constraint FK_s3vk7onqrk0n4c86xnvqmm3ho foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,962 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_s3vk7onqrk0n4c86xnvqmm3ho" for relation "organismdbxref" already exists
2016-02-20 20:45:40,965 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organismdbxref add constraint FK_l1jfi0wpnyooutd820p5gskr foreign key (organism_id) references organism
2016-02-20 20:45:40,966 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_l1jfi0wpnyooutd820p5gskr" for relation "organismdbxref" already exists
2016-02-20 20:45:40,969 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table permission add constraint FK_4nvoxx3htem6jseb4rmu0aqfp foreign key (organism_id) references organism
2016-02-20 20:45:40,970 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4nvoxx3htem6jseb4rmu0aqfp" for relation "permission" already exists
2016-02-20 20:45:40,972 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_cwgh6naf9gackae2ei11v6p41 foreign key (assay_id) references cvterm
2016-02-20 20:45:40,979 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cwgh6naf9gackae2ei11v6p41" for relation "phenotype" already exists
2016-02-20 20:45:40,981 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_phmfgylejydjqyrvo3imc97go foreign key (attribute_id) references cvterm
2016-02-20 20:45:40,982 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_phmfgylejydjqyrvo3imc97go" for relation "phenotype" already exists
2016-02-20 20:45:40,985 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_jh0fc3orduigl8s7ymentbtrs foreign key (cvalue_id) references cvterm
2016-02-20 20:45:40,986 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jh0fc3orduigl8s7ymentbtrs" for relation "phenotype" already exists
2016-02-20 20:45:40,988 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_gb4wy9qesx6vnekxekm18k9xa foreign key (observable_id) references cvterm
2016-02-20 20:45:40,989 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gb4wy9qesx6vnekxekm18k9xa" for relation "phenotype" already exists
2016-02-20 20:45:40,993 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_cvterm add constraint FK_9e2v7goj5w6nds5jo0x1va1nm foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,999 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_9e2v7goj5w6nds5jo0x1va1nm" for relation "phenotype_cvterm" already exists
2016-02-20 20:45:41,001 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_cvterm add constraint FK_aicsmj1kn20ikm14292g9r2j9 foreign key (phenotype_phenotypecvterms_id) references phenotype
2016-02-20 20:45:41,002 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_aicsmj1kn20ikm14292g9r2j9" for relation "phenotype_cvterm" already exists
2016-02-20 20:45:41,004 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_t52r166gd8710vffy3aompe7d foreign key (environment_id) references environment
2016-02-20 20:45:41,006 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_t52r166gd8710vffy3aompe7d" for relation "phenotype_description" already exists
2016-02-20 20:45:41,011 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_bf1bstadamyw0gsarkb933l5b foreign key (genotype_id) references genotype
2016-02-20 20:45:41,012 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_bf1bstadamyw0gsarkb933l5b" for relation "phenotype_description" already exists
2016-02-20 20:45:41,014 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_8pbyj05khavdl5a648c7pmcil foreign key (type_id) references cvterm
2016-02-20 20:45:41,015 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8pbyj05khavdl5a648c7pmcil" for relation "phenotype_description" already exists
2016-02-20 20:45:41,020 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_q6jvhi3l7ty0m9tpbn09d8pxj foreign key (environment_id) references environment
2016-02-20 20:45:41,021 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_q6jvhi3l7ty0m9tpbn09d8pxj" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,024 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_8rbhsxxdf669tyed8jrr747hv foreign key (genotype_id) references genotype
2016-02-20 20:45:41,027 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8rbhsxxdf669tyed8jrr747hv" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,029 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_gskh1e7b6qa2du48ayu49lr3s foreign key (phenotype_id) references phenotype
2016-02-20 20:45:41,030 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gskh1e7b6qa2du48ayu49lr3s" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,035 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_tk1pgifvuhurefn0y3myfyyt4 foreign key (type_id) references cvterm
2016-02-20 20:45:41,036 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tk1pgifvuhurefn0y3myfyyt4" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,039 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table preference add constraint FK_42b0lk4rcfjcagw84jugd1sgj foreign key (organism_id) references organism
2016-02-20 20:45:41,044 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_42b0lk4rcfjcagw84jugd1sgj" for relation "preference" already exists
2016-02-20 20:45:41,047 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publication add constraint FK_h3g8f3q2krcnwmq2nasbanlay foreign key (type_id) references cvterm
2016-02-20 20:45:41,049 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_h3g8f3q2krcnwmq2nasbanlay" for relation "publication" already exists
2016-02-20 20:45:41,051 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publication_relationship add constraint FK_q6hf14oiq9pomkjrhtndonmeh foreign key (type_id) references cvterm
2016-02-20 20:45:41,052 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_q6hf14oiq9pomkjrhtndonmeh" for relation "publication_relationship" already exists
2016-02-20 20:45:41,055 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publicationdbxref add constraint FK_oh81hma8qx88fhvcmfugx836b foreign key (dbxref_id) references dbxref
2016-02-20 20:45:41,059 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_oh81hma8qx88fhvcmfugx836b" for relation "publicationdbxref" already exists
2016-02-20 20:45:41,061 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table sequence add constraint FK_rux0954nxr4lwvj2qgyjibua7 foreign key (organism_id) references organism
2016-02-20 20:45:41,062 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_rux0954nxr4lwvj2qgyjibua7" for relation "sequence" already exists
2016-02-20 20:45:41,065 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add constraint FK_4ylco1irefvydmsnedglqqdfu foreign key (type_id) references cvterm
2016-02-20 20:45:41,066 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4ylco1irefvydmsnedglqqdfu" for relation "synonym" already exists
2016-02-20 20:45:52,529 [localhost-startStop-1] ERROR liquibase  - Change Set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated) failed.  Error: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
2016-02-20 20:45:52,579 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    ... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
2016-02-20 20:45:52,584 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    ... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
Feb 20, 2016 8:45:52 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 20, 2016 8:45:52 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/apollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [PoolCleaner[25416670:1456022700075]] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@18740d1]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 20, 2016 8:45:52 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 20, 2016 8:45:52 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 80376 ms



On Sat, Feb 20, 2016 at 9:32 PM, Lbl <[hidden email]> wrote:
Try opening in an incognito or another browser of doing a shift reload to flush the cache. 

That being said .. This stack trace looks a bit terse.   Typically shiro (the security plugin) will reload but I don't see that here.  Maybe further up? 

Nathan

On Feb 20, 2016, at 6:04 PM, Shane McCoy <[hidden email]> wrote:

Hey! I made the changes but I am still getting a blank screen.

I checked catalina.out, here is the last output:

/var/log/tomcat7$ tail -f catalina.out
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [PoolCleaner[25416670:1456019437960]] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@1b2e3fc]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 20, 2016 7:51:28 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 20, 2016 7:51:28 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 77106 ms


Is this still a memory issue then?
I have updated tomcat memory to your doc specs already.
Thanks!
shane

On Sat, Feb 20, 2016 at 7:55 PM, Shane McCoy <[hidden email]> wrote:
Ok, that makes more sense now! thank you very much.
I'll will try with correct settings,
cheers!

On Sat, Feb 20, 2016 at 7:53 PM, Colin <[hidden email]> wrote:
Hi Shaun

>url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

Just wanted to comment on this, actually, it would not be your IP and war here. It is kind of confusing that this "setting" is called a url, because it is actually a JDBC connector string, which actually references your local database, so it would not be using the war file name or even the IP address.

For example, if your database is named "apollodb", then your "url" would be

jdbc:postgresql://localhost/apollodb

It would generally just be localhost unless you have a separate database server. I think it might be worth adding some more comments about that in our setup guide, but I hope that helps!


-Colin

On Sat, Feb 20, 2016 at 2:36 PM, Shane McCoy <[hidden email]> wrote:
Hey!
So a lot has changed in a year! I'm currently still stuck at 2g but wanted to ask about an issue i have w/ /.apollo deploy
I am getting a blank screen at the URL. I have not added any data for generation yet. I assume i would still get a webapollo ui.
I am using postgresql. I edited apollo-config.groovy
Added (in production only)
datasource.dbCreate = "update" // one of...  ( where does the database name go? I don't understand this line, it seems i'm limited to the options given?)
username: chado database username
password: chado database pw
url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

I haven't changed any other settings and going to http://myipaddress/apollo is a blank page.
I want to use this w/ a already setup postgresql chado database.

I am going off of this guide: http://webapollo.readthedocs.org/en/latest/Setup.html
Thanks!

On Thu, Feb 11, 2016 at 2:29 PM, Shane McCoy <[hidden email]> wrote:
Thanks for the quick reply!
I will see what options I can take -
Shane M.

On Thu, Feb 11, 2016 at 2:18 PM, Nathan Dunn <[hidden email]> wrote:

On Feb 11, 2016, at 11:07 AM, Shane McCoy <[hidden email]> wrote:

Hey

I am getting this error running ./apollo run-local 8085

..........
    BUILD SUCCESSFUL
    | Compiling 5 source files
    | Compiling 5 source files.....
    ***
    Metrics servlet injected into web.xml
    Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
    ***
    | Running Grails application
    Error occurred during initialization of VM
    Could not reserve enough space for object heap
    Error: Could not create the Java Virtual Machine.
    Error: A fatal exception has occurred. Program will exit.
    | Error Forked Grails VM exited with error

I’m guessing that Java is requesting more memory then you have to allocate, and so exiting.  

So, when running it with run-local (for dev purposes), it actually has preset memory, of a max of up to 2 GB, though obviously this is high.  It is in BuildConfig.groovy:

run    : [maxMemory: 2048, minMemory: 64, debug: false , maxPerm: 1024, forkReserve: false],
My guess is that your machine doesn’t have sufficient memory to run this, or there is another process. 

My suggestions would be:
1 - get a machine with at least 4 GB’s of memory, especially if you are going to host to multiple users.  This will enable better caching and performance.    
2 - if (1) is not an immediate option (or to test, or if you are just running locally) your can edit your apollo-config.groovy create a line like this, so it will use less memory:

grails.project.fork = [
// configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
// compile: [maxMemory: 256, minMemory: 64, debug: false, maxPerm: 256, daemon:true],

test : false,
//run : false,
// configure settings for the test-app JVM, uses the daemon by default
//test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
// configure settings for the run-app JVM
run : [maxMemory: 1024, minMemory: 64, debug: false , maxPerm: 512, forkReserve: false],
// configure settings for the run-war JVM
war : [maxMemory: 1024, minMemory: 64, debug: false, maxPerm: 512, forkReserve: false],
// configure settings for the Console UI JVM
console: [maxMemory:
1024, minMemory: 64, debug: false, maxPerm: 512]
]

Setting the java size as done below works for tomcat, but not for the development mode (run-local).  

Nathan 

I looked over the same errors on Stack and made adjustments to the memory but I am still getting this error. I am new to Grails but I believe everything is setup correct and i can run a sample app (helloworld).
Here is the changes i made:

    -Xms512m -Xmx1g -XX:PermSize=256m
This is the memory

    free -m
                 total       used       free     shared    buffers     cached
    Mem:          2015       1297        718         56        169        859
    -/+ buffers/cache:        267       1748

Checking if parameters are being read

    $ ps -ef | grep java
    tomcat7  32158     1  1 11:02 ?        00:00:10 /usr/lib/jvm/default-java/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:PermSize=256m -XX:MaxPermSize=256m -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed -classpath /usr/share/tomcat7/bin/bootstrap.jar:/usr/share/tomcat7/bin/tomcat-juli.jar -Dcatalina.base=/var/lib/tomcat7 -Dcatalina.home=/usr/share/tomcat7 -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp org.apache.catalina.startup.Bootstrap start


I have this in my $HOME/.profile

    export JAVA_OPTS="-Xms512m -Xmx1g -XX:MaxPermSize=256m"

in my setenv.sh for Tomcat7

    export CATALINA_OPTS="-Xms512m -Xmx1g \
        -XX:+CMSClassUnloadingEnabled \
        -XX:+CMSPermGenSweepingEnabled \
        -XX:+UseConcMarkSweepGC \
        -XX:MaxPermSize=256m"

Versions: (i went w/ 2.4.5 per Apollo guide)
    $ grails -version
    Grails version: 2.4.5
    $ java -version
    java version "1.7.0_95"
    OpenJDK Runtime Environment (IcedTea 2.6.4) (7u95-2.6.4-0ubuntu0.14.04.1)
    OpenJDK Client VM (build 24.95-b01, mixed mode, sharing)

I am not sure what to change now - it seems the memory would be adequate? I know this isn't Apollo specific but maybe someone here has had the same problem? Please any thoughts would be great. thank you
Shane M.



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Re: New WebApollo install issue (Grails)

nathandunn

I think so. 

Keep in mind that anything in the “./bin” directory is actually jbrowse code.  Just make sure you point your organism directory to /opt/apollo/data    

If you have more than one organism they will have to go in different directories. 

Nathan

On Feb 21, 2016, at 5:37 PM, Shane McCoy <[hidden email]> wrote:

Ok, good to know! I'll keep an eye out for the Chado addition later.
This seems a lot simpler than prior version.
so if i have 2 files: genome.gff & genome.fa

  1. bin/preprare-refseqs.pl --fasta genome.fa --out /opt/apollo/data
  2. bin/flatfile-to-json.pl --gff genome.gff --type gene --tracklabel makergene --autocomplete all --Key Maker Gene --out /opt/apollo/data
  3. and repeat for all the different Types? correct? is there any changes to the options for flatfile-to-json.pl? I have many to add from the same genome
  4. bin/generate-names.pl --verbose --out /opt/apollo/data
  5. ./apollo deploy
  6. add WAR to webapps and start tomcat.
  7. is that about right?
Thanks again!
Shane



On Sun, Feb 21, 2016 at 5:43 PM, Nathan Dunn <[hidden email]> wrote:

So, unfortunately we need to formally add Chado integration back to Apollo.  

We (specifically Deepak) are actively working on it and it should be part of the 2.0.3 release.   We’ll be pinging the community specifically to make sure the export / integration works.  

In the interim the best method that I am aware of is to export a GFF3 from Apollo and import that GFF3 into your Chado schema.  

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Feb 21, 2016, at 9:18 AM, Shane McCoy <[hidden email]> wrote:

Hi Nathan,
I did as you said and it started up just fine. Thank you!
So this leads me to believe the previous setup I did (1.0.2 i believe) won't be the best guide to a new setup.

I want to be able to use the CHADO schema & use web apollo to edit the genome.
I had set up CHADO on a database and had already uploaded the GFF. Can I get pointers on the proper steps to follow now?
I did back it up prior to deleting and recreating db, but it is pretty small test file and i don't have an issue putting back through the script.
Thanks again!
Shane M. 

On Sun, Feb 21, 2016 at 1:24 AM, Nathan Dunn <[hidden email]> wrote:

If you are using postgresql and you don’t have anything in the database you want (or you back it up first) I would drop and re-create the database (with tomcat off).     When it comes back up it will create the database with the create schema for you:

1 - stop tomcat 
1a - backup database? 
2 - dropdb your-apollo-database-name
3 - createdb your-apollo-database-name
4 - start tomcat

Its in a pretty weird state. 

Nathan

On Feb 20, 2016, at 6:51 PM, Shane McCoy <[hidden email]> wrote:

I missed a bit from the log, here is catalina.out from a restart of tomcat7:

 * Stopping Tomcat servlet engine tomcat7                                [ OK ]
 * Starting Tomcat servlet engine tomcat7                                [ OK ]
--------------------------$$:/var/log/tomcat7$ tail -f catalina.out
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor /etc/tomcat7/Catalina/localhost/host-manager.xml
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
^[[AFeb 20, 2016 8:44:43 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 20, 2016 8:44:43 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.

Configuring Shiro ...

Shiro Configured
2016-02-20 20:45:40,539 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column id int8 not null
2016-02-20 20:45:40,543 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,546 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column version int8 not null
2016-02-20 20:45:40,548 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,550 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column program_version varchar(255) not null
2016-02-20 20:45:40,552 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "program_version" contains null values
2016-02-20 20:45:40,554 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_name varchar(255) not null
2016-02-20 20:45:40,555 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_name" contains null values
2016-02-20 20:45:40,558 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_version varchar(255) not null
2016-02-20 20:45:40,559 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_version" contains null values
2016-02-20 20:45:40,562 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column time_executed timestamp not null
2016-02-20 20:45:40,563 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "time_executed" contains null values
2016-02-20 20:45:40,566 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column id int8 not null
2016-02-20 20:45:40,567 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,569 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column version int8 not null
2016-02-20 20:45:40,570 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,573 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column id int8 not null
2016-02-20 20:45:40,574 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,577 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column version int8 not null
2016-02-20 20:45:40,578 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,583 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column is_relationship_type int4 not null
2016-02-20 20:45:40,584 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "is_relationship_type" contains null values
2016-02-20 20:45:40,587 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column id int8 not null
2016-02-20 20:45:40,588 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,590 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column version int8 not null
2016-02-20 20:45:40,591 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,593 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column objectcvterm_id int8 not null
2016-02-20 20:45:40,594 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" contains null values
2016-02-20 20:45:40,598 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column subjectcvterm_id int8 not null
2016-02-20 20:45:40,599 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" contains null values
2016-02-20 20:45:40,602 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column id int8 not null
2016-02-20 20:45:40,602 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,606 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column version int8 not null
2016-02-20 20:45:40,607 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,610 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add column id int8 not null
2016-02-20 20:45:40,612 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,616 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column id int8 not null
2016-02-20 20:45:40,617 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,620 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column version int8 not null
2016-02-20 20:45:40,621 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,632 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column unique_name varchar(255) not null
2016-02-20 20:45:40,633 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "unique_name" contains null values
2016-02-20 20:45:40,636 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column class varchar(255) not null
2016-02-20 20:45:40,637 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "class" contains null values
2016-02-20 20:45:40,641 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column id int8 not null
2016-02-20 20:45:40,642 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,645 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column version int8 not null
2016-02-20 20:45:40,646 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,652 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column child_feature_id int8 not null
2016-02-20 20:45:40,653 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "child_feature_id" contains null values
2016-02-20 20:45:40,656 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column parent_feature_id int8 not null
2016-02-20 20:45:40,657 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "parent_feature_id" contains null values
2016-02-20 20:45:40,660 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column id int8 not null
2016-02-20 20:45:40,661 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,668 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column version int8 not null
2016-02-20 20:45:40,670 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,672 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column publication_id int8 not null
2016-02-20 20:45:40,677 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "publication_id" contains null values
2016-02-20 20:45:40,679 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column id int8 not null
2016-02-20 20:45:40,681 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,684 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column version int8 not null
2016-02-20 20:45:40,685 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,687 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column directory varchar(255)
2016-02-20 20:45:40,688 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,692 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column id int8 not null
2016-02-20 20:45:40,693 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,701 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column version int8 not null
2016-02-20 20:45:40,702 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,704 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column directory varchar(255) not null
2016-02-20 20:45:40,706 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "directory" contains null values
2016-02-20 20:45:40,709 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column id int8 not null
2016-02-20 20:45:40,710 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,715 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column version int8 not null
2016-02-20 20:45:40,716 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,719 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column synonymsgml varchar(255) not null
2016-02-20 20:45:40,720 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "synonymsgml" contains null values
2016-02-20 20:45:40,724 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_feature add constraint FK_8m30ycwh545b4aoxor9sbk1oq foreign key (analysis_id) references analysis
2016-02-20 20:45:40,725 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8m30ycwh545b4aoxor9sbk1oq" for relation "analysis_feature" already exists
2016-02-20 20:45:40,727 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_feature add constraint FK_l94xl424xp988f06gr2b3t5tw foreign key (feature_id) references feature
2016-02-20 20:45:40,728 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_l94xl424xp988f06gr2b3t5tw" for relation "analysis_feature" already exists
2016-02-20 20:45:40,730 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_property add constraint FK_38g8n4bitmdwkrcs217uexrwx foreign key (analysis_id) references analysis
2016-02-20 20:45:40,731 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_38g8n4bitmdwkrcs217uexrwx" for relation "analysis_property" already exists
2016-02-20 20:45:40,733 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_property add constraint FK_9o7xs7saygim8y0sm4ostvpc1 foreign key (type_id) references cvterm
2016-02-20 20:45:40,734 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_9o7xs7saygim8y0sm4ostvpc1" for relation "analysis_property" already exists
2016-02-20 20:45:40,737 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add constraint FK_oksfqluv12ktmut9s6o9jla7a foreign key (cv_id) references cv
2016-02-20 20:45:40,739 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_oksfqluv12ktmut9s6o9jla7a" for relation "cvterm" already exists
2016-02-20 20:45:40,741 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add constraint FK_6d097oy44230tuoo8lb8dkkcp foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,742 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_6d097oy44230tuoo8lb8dkkcp" for relation "cvterm" already exists
2016-02-20 20:45:40,744 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_ke2nrw91sxil8mv7osgv83pw1 foreign key (cv_id) references cv
2016-02-20 20:45:40,745 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ke2nrw91sxil8mv7osgv83pw1" for relation "cvterm_path" already exists
2016-02-20 20:45:40,748 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_tlfh10092i00g6rlv589naqy5 foreign key (objectcvterm_id) references cvterm
2016-02-20 20:45:40,749 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tlfh10092i00g6rlv589naqy5" for relation "cvterm_path" already exists
2016-02-20 20:45:40,751 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_nq02ir0qeydr5tj3071k9gl7b foreign key (subjectcvterm_id) references cvterm
2016-02-20 20:45:40,752 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_nq02ir0qeydr5tj3071k9gl7b" for relation "cvterm_path" already exists
2016-02-20 20:45:40,760 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_jaqi1bk3t2c0m3pybmparp856 foreign key (type_id) references cvterm
2016-02-20 20:45:40,761 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jaqi1bk3t2c0m3pybmparp856" for relation "cvterm_path" already exists
2016-02-20 20:45:40,763 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_r1o1rnfnsf7oipuv1h7h1fln7 foreign key (objectcvterm_id) references cvterm
2016-02-20 20:45:40,766 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,771 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_pwxrfyx6rqu5krq4nj5wa3u4f foreign key (subjectcvterm_id) references cvterm
2016-02-20 20:45:40,775 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,777 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_ob1d0vrfaix8b28j4tvilqnyv foreign key (type_id) references cvterm
2016-02-20 20:45:40,778 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ob1d0vrfaix8b28j4tvilqnyv" for relation "cvterm_relationship" already exists
2016-02-20 20:45:40,781 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add constraint FK_np3tfcu9g867to3qux6raf9y8 foreign key (db_id) references db
2016-02-20 20:45:40,782 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_np3tfcu9g867to3qux6raf9y8" for relation "dbxref" already exists
2016-02-20 20:45:40,786 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref_property add constraint FK_3p1ssctww083s0tt65mmm64uo foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,787 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_3p1ssctww083s0tt65mmm64uo" for relation "dbxref_property" already exists
2016-02-20 20:45:40,792 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref_property add constraint FK_t6ojbvugx8kou45oklsie3rt5 foreign key (type_id) references cvterm
2016-02-20 20:45:40,793 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_t6ojbvugx8kou45oklsie3rt5" for relation "dbxref_property" already exists
2016-02-20 20:45:40,796 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table environmentcvterm add constraint FK_tql9djnqw1d7migfndoj3lrph foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,803 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tql9djnqw1d7migfndoj3lrph" for relation "environmentcvterm" already exists
2016-02-20 20:45:40,805 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table environmentcvterm add constraint FK_rrwb96jjqgtg077yv8pbim3jj foreign key (environment_id) references environment
2016-02-20 20:45:40,807 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_rrwb96jjqgtg077yv8pbim3jj" for relation "environmentcvterm" already exists
2016-02-20 20:45:40,813 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add constraint FK_hc4vrafs0ws7ugdkp0n6u3xdo foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,816 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_hc4vrafs0ws7ugdkp0n6u3xdo" for relation "feature" already exists
2016-02-20 20:45:40,819 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_dbxref add constraint FK_n6n7lheb1qkmlde8u6gvvjxne foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,821 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_n6n7lheb1qkmlde8u6gvvjxne" for relation "feature_dbxref" already exists
2016-02-20 20:45:40,829 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_dbxref add constraint FK_1mrfkxbb3n7fhjxcrkxappdn8 foreign key (feature_featuredbxrefs_id) references feature
2016-02-20 20:45:40,831 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_1mrfkxbb3n7fhjxcrkxappdn8" for relation "feature_dbxref" already exists
2016-02-20 20:45:40,836 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_feature_phenotypes add constraint FK_dy5g29heir5ic3d36okyuihho foreign key (phenotype_id) references phenotype
2016-02-20 20:45:40,839 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_dy5g29heir5ic3d36okyuihho" for relation "feature_feature_phenotypes" already exists
2016-02-20 20:45:40,842 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_feature_phenotypes add constraint FK_aqr7eiyx6puju6elciwubbwmo foreign key (feature_id) references feature
2016-02-20 20:45:40,843 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_aqr7eiyx6puju6elciwubbwmo" for relation "feature_feature_phenotypes" already exists
2016-02-20 20:45:40,847 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_hak8r429shmpho06rbyvwnmt0 foreign key (chromosome_feature_id) references feature
2016-02-20 20:45:40,848 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_hak8r429shmpho06rbyvwnmt0" for relation "feature_genotype" already exists
2016-02-20 20:45:40,856 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_b42u9iq4kuqe5ay544do81n32 foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,857 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_b42u9iq4kuqe5ay544do81n32" for relation "feature_genotype" already exists
2016-02-20 20:45:40,859 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_cm3gqs38fa2lpllgoum8n4kgn foreign key (feature_id) references feature
2016-02-20 20:45:40,861 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cm3gqs38fa2lpllgoum8n4kgn" for relation "feature_genotype" already exists
2016-02-20 20:45:40,863 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_736wxgjs6pip5212ash5i68p foreign key (genotype_id) references genotype
2016-02-20 20:45:40,864 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_736wxgjs6pip5212ash5i68p" for relation "feature_genotype" already exists
2016-02-20 20:45:40,867 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_grails_user add constraint FK_4dgbhgiw0vb9hqy2k5fqg3neh foreign key (feature_owners_id) references feature
2016-02-20 20:45:40,868 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4dgbhgiw0vb9hqy2k5fqg3neh" for relation "feature_grails_user" already exists
2016-02-20 20:45:40,872 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_location add constraint FK_qml7xp9f5uojcw7jwdxcb35le foreign key (feature_id) references feature
2016-02-20 20:45:40,873 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qml7xp9f5uojcw7jwdxcb35le" for relation "feature_location" already exists
2016-02-20 20:45:40,875 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_property add constraint FK_jpvdxc57abfiridcr57x8130 foreign key (feature_id) references feature
2016-02-20 20:45:40,879 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jpvdxc57abfiridcr57x8130" for relation "feature_property" already exists
2016-02-20 20:45:40,881 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_property add constraint FK_36e638geg9tew42b1mp2ehff foreign key (type_id) references cvterm
2016-02-20 20:45:40,882 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_36e638geg9tew42b1mp2ehff" for relation "feature_property" already exists
2016-02-20 20:45:40,885 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_publication add constraint FK_qolh5l4blkx8vfmwcl7f3woan foreign key (feature_feature_publications_id) references feature
2016-02-20 20:45:40,891 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qolh5l4blkx8vfmwcl7f3woan" for relation "feature_publication" already exists
2016-02-20 20:45:40,893 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add constraint FK_8jm56covt0m7m0m191bc5jseh foreign key (child_feature_id) references feature
2016-02-20 20:45:40,894 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "child_feature_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,898 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add constraint FK_72kmd92rdc6gne0nrh026o1j0 foreign key (parent_feature_id) references feature
2016-02-20 20:45:40,899 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "parent_feature_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,907 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship_feature_property add constraint FK_ebgnfbogf1lwdxd8jc17511o7 foreign key (feature_relationship_feature_relationship_properties_id) references feature_relationship
2016-02-20 20:45:40,908 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ebgnfbogf1lwdxd8jc17511o7" for relation "feature_relationship_feature_property" already exists
2016-02-20 20:45:40,911 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship_publication add constraint FK_bdd324e5jb0lpuhs7biy2kacm foreign key (feature_relationship_feature_relationship_publications_id) references feature_relationship
2016-02-20 20:45:40,912 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_bdd324e5jb0lpuhs7biy2kacm" for relation "feature_relationship_publication" already exists
2016-02-20 20:45:40,914 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_nf9qbuay984ixqd2k1425rnyo foreign key (feature_id) references feature
2016-02-20 20:45:40,916 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_nf9qbuay984ixqd2k1425rnyo" for relation "feature_synonym" already exists
2016-02-20 20:45:40,923 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_82wsc3bv9i01t9851xv4xekis foreign key (publication_id) references publication
2016-02-20 20:45:40,926 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "publication_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,929 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_ll4cqdh994s6x8n7vku1q7iwd foreign key (synonym_id) references synonym
2016-02-20 20:45:40,930 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ll4cqdh994s6x8n7vku1q7iwd" for relation "feature_synonym" already exists
2016-02-20 20:45:40,932 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_gsol4u8wrfwbkh1qrx18i3u6 foreign key (feature_synonyms_id) references feature
2016-02-20 20:45:40,933 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gsol4u8wrfwbkh1qrx18i3u6" for relation "feature_synonym" already exists
2016-02-20 20:45:40,935 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm add constraint FK_cuwo3ernssd0t0wjceb7lmm11 foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,936 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cuwo3ernssd0t0wjceb7lmm11" for relation "featurecvterm" already exists
2016-02-20 20:45:40,943 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm add constraint FK_iy7bbt67s7jaemiajsrqalv5o foreign key (feature_id) references feature
2016-02-20 20:45:40,944 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_iy7bbt67s7jaemiajsrqalv5o" for relation "featurecvterm" already exists
2016-02-20 20:45:40,948 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm_dbxref add constraint FK_r9xhefcekikp1od79ectkb22b foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,949 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_r9xhefcekikp1od79ectkb22b" for relation "featurecvterm_dbxref" already exists
2016-02-20 20:45:40,951 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism_organism_property add constraint FK_qyxdgqthtlgixvtdkkhc8g3pu foreign key (organism_organism_properties_id) references organism
2016-02-20 20:45:40,959 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qyxdgqthtlgixvtdkkhc8g3pu" for relation "organism_organism_property" already exists
2016-02-20 20:45:40,961 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organismdbxref add constraint FK_s3vk7onqrk0n4c86xnvqmm3ho foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,962 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_s3vk7onqrk0n4c86xnvqmm3ho" for relation "organismdbxref" already exists
2016-02-20 20:45:40,965 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organismdbxref add constraint FK_l1jfi0wpnyooutd820p5gskr foreign key (organism_id) references organism
2016-02-20 20:45:40,966 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_l1jfi0wpnyooutd820p5gskr" for relation "organismdbxref" already exists
2016-02-20 20:45:40,969 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table permission add constraint FK_4nvoxx3htem6jseb4rmu0aqfp foreign key (organism_id) references organism
2016-02-20 20:45:40,970 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4nvoxx3htem6jseb4rmu0aqfp" for relation "permission" already exists
2016-02-20 20:45:40,972 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_cwgh6naf9gackae2ei11v6p41 foreign key (assay_id) references cvterm
2016-02-20 20:45:40,979 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cwgh6naf9gackae2ei11v6p41" for relation "phenotype" already exists
2016-02-20 20:45:40,981 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_phmfgylejydjqyrvo3imc97go foreign key (attribute_id) references cvterm
2016-02-20 20:45:40,982 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_phmfgylejydjqyrvo3imc97go" for relation "phenotype" already exists
2016-02-20 20:45:40,985 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_jh0fc3orduigl8s7ymentbtrs foreign key (cvalue_id) references cvterm
2016-02-20 20:45:40,986 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jh0fc3orduigl8s7ymentbtrs" for relation "phenotype" already exists
2016-02-20 20:45:40,988 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_gb4wy9qesx6vnekxekm18k9xa foreign key (observable_id) references cvterm
2016-02-20 20:45:40,989 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gb4wy9qesx6vnekxekm18k9xa" for relation "phenotype" already exists
2016-02-20 20:45:40,993 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_cvterm add constraint FK_9e2v7goj5w6nds5jo0x1va1nm foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,999 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_9e2v7goj5w6nds5jo0x1va1nm" for relation "phenotype_cvterm" already exists
2016-02-20 20:45:41,001 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_cvterm add constraint FK_aicsmj1kn20ikm14292g9r2j9 foreign key (phenotype_phenotypecvterms_id) references phenotype
2016-02-20 20:45:41,002 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_aicsmj1kn20ikm14292g9r2j9" for relation "phenotype_cvterm" already exists
2016-02-20 20:45:41,004 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_t52r166gd8710vffy3aompe7d foreign key (environment_id) references environment
2016-02-20 20:45:41,006 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_t52r166gd8710vffy3aompe7d" for relation "phenotype_description" already exists
2016-02-20 20:45:41,011 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_bf1bstadamyw0gsarkb933l5b foreign key (genotype_id) references genotype
2016-02-20 20:45:41,012 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_bf1bstadamyw0gsarkb933l5b" for relation "phenotype_description" already exists
2016-02-20 20:45:41,014 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_8pbyj05khavdl5a648c7pmcil foreign key (type_id) references cvterm
2016-02-20 20:45:41,015 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8pbyj05khavdl5a648c7pmcil" for relation "phenotype_description" already exists
2016-02-20 20:45:41,020 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_q6jvhi3l7ty0m9tpbn09d8pxj foreign key (environment_id) references environment
2016-02-20 20:45:41,021 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_q6jvhi3l7ty0m9tpbn09d8pxj" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,024 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_8rbhsxxdf669tyed8jrr747hv foreign key (genotype_id) references genotype
2016-02-20 20:45:41,027 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8rbhsxxdf669tyed8jrr747hv" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,029 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_gskh1e7b6qa2du48ayu49lr3s foreign key (phenotype_id) references phenotype
2016-02-20 20:45:41,030 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gskh1e7b6qa2du48ayu49lr3s" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,035 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_tk1pgifvuhurefn0y3myfyyt4 foreign key (type_id) references cvterm
2016-02-20 20:45:41,036 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tk1pgifvuhurefn0y3myfyyt4" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,039 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table preference add constraint FK_42b0lk4rcfjcagw84jugd1sgj foreign key (organism_id) references organism
2016-02-20 20:45:41,044 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_42b0lk4rcfjcagw84jugd1sgj" for relation "preference" already exists
2016-02-20 20:45:41,047 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publication add constraint FK_h3g8f3q2krcnwmq2nasbanlay foreign key (type_id) references cvterm
2016-02-20 20:45:41,049 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_h3g8f3q2krcnwmq2nasbanlay" for relation "publication" already exists
2016-02-20 20:45:41,051 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publication_relationship add constraint FK_q6hf14oiq9pomkjrhtndonmeh foreign key (type_id) references cvterm
2016-02-20 20:45:41,052 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_q6hf14oiq9pomkjrhtndonmeh" for relation "publication_relationship" already exists
2016-02-20 20:45:41,055 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publicationdbxref add constraint FK_oh81hma8qx88fhvcmfugx836b foreign key (dbxref_id) references dbxref
2016-02-20 20:45:41,059 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_oh81hma8qx88fhvcmfugx836b" for relation "publicationdbxref" already exists
2016-02-20 20:45:41,061 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table sequence add constraint FK_rux0954nxr4lwvj2qgyjibua7 foreign key (organism_id) references organism
2016-02-20 20:45:41,062 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_rux0954nxr4lwvj2qgyjibua7" for relation "sequence" already exists
2016-02-20 20:45:41,065 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add constraint FK_4ylco1irefvydmsnedglqqdfu foreign key (type_id) references cvterm
2016-02-20 20:45:41,066 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4ylco1irefvydmsnedglqqdfu" for relation "synonym" already exists
2016-02-20 20:45:52,529 [localhost-startStop-1] ERROR liquibase  - Change Set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated) failed.  Error: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
2016-02-20 20:45:52,579 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    ... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
2016-02-20 20:45:52,584 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    ... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
Feb 20, 2016 8:45:52 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 20, 2016 8:45:52 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/apollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [PoolCleaner[25416670:1456022700075]] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@18740d1]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 20, 2016 8:45:52 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 20, 2016 8:45:52 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 80376 ms



On Sat, Feb 20, 2016 at 9:32 PM, Lbl <[hidden email]> wrote:
Try opening in an incognito or another browser of doing a shift reload to flush the cache. 

That being said .. This stack trace looks a bit terse.   Typically shiro (the security plugin) will reload but I don't see that here.  Maybe further up? 

Nathan

On Feb 20, 2016, at 6:04 PM, Shane McCoy <[hidden email]> wrote:

Hey! I made the changes but I am still getting a blank screen.

I checked catalina.out, here is the last output:

/var/log/tomcat7$ tail -f catalina.out
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [PoolCleaner[25416670:1456019437960]] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@1b2e3fc]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 20, 2016 7:51:28 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 20, 2016 7:51:28 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 77106 ms


Is this still a memory issue then?
I have updated tomcat memory to your doc specs already.
Thanks!
shane

On Sat, Feb 20, 2016 at 7:55 PM, Shane McCoy <[hidden email]> wrote:
Ok, that makes more sense now! thank you very much.
I'll will try with correct settings,
cheers!

On Sat, Feb 20, 2016 at 7:53 PM, Colin <[hidden email]> wrote:
Hi Shaun

>url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

Just wanted to comment on this, actually, it would not be your IP and war here. It is kind of confusing that this "setting" is called a url, because it is actually a JDBC connector string, which actually references your local database, so it would not be using the war file name or even the IP address.

For example, if your database is named "apollodb", then your "url" would be

jdbc:postgresql://localhost/apollodb

It would generally just be localhost unless you have a separate database server. I think it might be worth adding some more comments about that in our setup guide, but I hope that helps!


-Colin

On Sat, Feb 20, 2016 at 2:36 PM, Shane McCoy <[hidden email]> wrote:
Hey!
So a lot has changed in a year! I'm currently still stuck at 2g but wanted to ask about an issue i have w/ /.apollo deploy
I am getting a blank screen at the URL. I have not added any data for generation yet. I assume i would still get a webapollo ui.
I am using postgresql. I edited apollo-config.groovy
Added (in production only)
datasource.dbCreate = "update" // one of...  ( where does the database name go? I don't understand this line, it seems i'm limited to the options given?)
username: chado database username
password: chado database pw
url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

I haven't changed any other settings and going to http://myipaddress/apollo is a blank page.
I want to use this w/ a already setup postgresql chado database.

I am going off of this guide: http://webapollo.readthedocs.org/en/latest/Setup.html
Thanks!

On Thu, Feb 11, 2016 at 2:29 PM, Shane McCoy <[hidden email]> wrote:
Thanks for the quick reply!
I will see what options I can take -
Shane M.

On Thu, Feb 11, 2016 at 2:18 PM, Nathan Dunn <[hidden email]> wrote:

On Feb 11, 2016, at 11:07 AM, Shane McCoy <[hidden email]> wrote:

Hey

I am getting this error running ./apollo run-local 8085

..........
    BUILD SUCCESSFUL
    | Compiling 5 source files
    | Compiling 5 source files.....
    ***
    Metrics servlet injected into web.xml
    Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
    ***
    | Running Grails application
    Error occurred during initialization of VM
    Could not reserve enough space for object heap
    Error: Could not create the Java Virtual Machine.
    Error: A fatal exception has occurred. Program will exit.
    | Error Forked Grails VM exited with error

I’m guessing that Java is requesting more memory then you have to allocate, and so exiting.  

So, when running it with run-local (for dev purposes), it actually has preset memory, of a max of up to 2 GB, though obviously this is high.  It is in BuildConfig.groovy:

run    : [maxMemory: 2048, minMemory: 64, debug: false , maxPerm: 1024, forkReserve: false],
My guess is that your machine doesn’t have sufficient memory to run this, or there is another process. 

My suggestions would be:
1 - get a machine with at least 4 GB’s of memory, especially if you are going to host to multiple users.  This will enable better caching and performance.    
2 - if (1) is not an immediate option (or to test, or if you are just running locally) your can edit your apollo-config.groovy create a line like this, so it will use less memory:

grails.project.fork = [
// configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
// compile: [maxMemory: 256, minMemory: 64, debug: false, maxPerm: 256, daemon:true],

test : false,
//run : false,
// configure settings for the test-app JVM, uses the daemon by default
//test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
// configure settings for the run-app JVM
run : [maxMemory: 1024, minMemory: 64, debug: false , maxPerm: 512, forkReserve: false],
// configure settings for the run-war JVM
war : [maxMemory: 1024, minMemory: 64, debug: false, maxPerm: 512, forkReserve: false],
// configure settings for the Console UI JVM
console: [maxMemory:
1024, minMemory: 64, debug: false, maxPerm: 512]
]

Setting the java size as done below works for tomcat, but not for the development mode (run-local).  

Nathan 

I looked over the same errors on Stack and made adjustments to the memory but I am still getting this error. I am new to Grails but I believe everything is setup correct and i can run a sample app (helloworld).
Here is the changes i made:

    -Xms512m -Xmx1g -XX:PermSize=256m
This is the memory

    free -m
                 total       used       free     shared    buffers     cached
    Mem:          2015       1297        718         56        169        859
    -/+ buffers/cache:        267       1748

Checking if parameters are being read

    $ ps -ef | grep java
    tomcat7  32158     1  1 11:02 ?        00:00:10 /usr/lib/jvm/default-java/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:PermSize=256m -XX:MaxPermSize=256m -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed -classpath /usr/share/tomcat7/bin/bootstrap.jar:/usr/share/tomcat7/bin/tomcat-juli.jar -Dcatalina.base=/var/lib/tomcat7 -Dcatalina.home=/usr/share/tomcat7 -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp org.apache.catalina.startup.Bootstrap start


I have this in my $HOME/.profile

    export JAVA_OPTS="-Xms512m -Xmx1g -XX:MaxPermSize=256m"

in my setenv.sh for Tomcat7

    export CATALINA_OPTS="-Xms512m -Xmx1g \
        -XX:+CMSClassUnloadingEnabled \
        -XX:+CMSPermGenSweepingEnabled \
        -XX:+UseConcMarkSweepGC \
        -XX:MaxPermSize=256m"

Versions: (i went w/ 2.4.5 per Apollo guide)
    $ grails -version
    Grails version: 2.4.5
    $ java -version
    java version "1.7.0_95"
    OpenJDK Runtime Environment (IcedTea 2.6.4) (7u95-2.6.4-0ubuntu0.14.04.1)
    OpenJDK Client VM (build 24.95-b01, mixed mode, sharing)

I am not sure what to change now - it seems the memory would be adequate? I know this isn't Apollo specific but maybe someone here has had the same problem? Please any thoughts would be great. thank you
Shane M.



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Re: New WebApollo install issue (Grails)

Shane McCoy
ok, I just want to be able to annotate, save & export at this point. So I think the steps I mentioned are all that are needed at the moment.
If I want to remove an organism (start a clean slate) is dropping the db and removing the content of /opt/apollo/data sufficient?
I can continue w/ a new db and organism?
Thanks!

On Sun, Feb 21, 2016 at 10:01 PM, Nathan Dunn <[hidden email]> wrote:

I think so. 

Keep in mind that anything in the “./bin” directory is actually jbrowse code.  Just make sure you point your organism directory to /opt/apollo/data    

If you have more than one organism they will have to go in different directories. 

Nathan

On Feb 21, 2016, at 5:37 PM, Shane McCoy <[hidden email]> wrote:

Ok, good to know! I'll keep an eye out for the Chado addition later.
This seems a lot simpler than prior version.
so if i have 2 files: genome.gff & genome.fa

  1. bin/preprare-refseqs.pl --fasta genome.fa --out /opt/apollo/data
  2. bin/flatfile-to-json.pl --gff genome.gff --type gene --tracklabel makergene --autocomplete all --Key Maker Gene --out /opt/apollo/data
  3. and repeat for all the different Types? correct? is there any changes to the options for flatfile-to-json.pl? I have many to add from the same genome
  4. bin/generate-names.pl --verbose --out /opt/apollo/data
  5. ./apollo deploy
  6. add WAR to webapps and start tomcat.
  7. is that about right?
Thanks again!
Shane



On Sun, Feb 21, 2016 at 5:43 PM, Nathan Dunn <[hidden email]> wrote:

So, unfortunately we need to formally add Chado integration back to Apollo.  

We (specifically Deepak) are actively working on it and it should be part of the 2.0.3 release.   We’ll be pinging the community specifically to make sure the export / integration works.  

In the interim the best method that I am aware of is to export a GFF3 from Apollo and import that GFF3 into your Chado schema.  

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Feb 21, 2016, at 9:18 AM, Shane McCoy <[hidden email]> wrote:

Hi Nathan,
I did as you said and it started up just fine. Thank you!
So this leads me to believe the previous setup I did (1.0.2 i believe) won't be the best guide to a new setup.

I want to be able to use the CHADO schema & use web apollo to edit the genome.
I had set up CHADO on a database and had already uploaded the GFF. Can I get pointers on the proper steps to follow now?
I did back it up prior to deleting and recreating db, but it is pretty small test file and i don't have an issue putting back through the script.
Thanks again!
Shane M. 

On Sun, Feb 21, 2016 at 1:24 AM, Nathan Dunn <[hidden email]> wrote:

If you are using postgresql and you don’t have anything in the database you want (or you back it up first) I would drop and re-create the database (with tomcat off).     When it comes back up it will create the database with the create schema for you:

1 - stop tomcat 
1a - backup database? 
2 - dropdb your-apollo-database-name
3 - createdb your-apollo-database-name
4 - start tomcat

Its in a pretty weird state. 

Nathan

On Feb 20, 2016, at 6:51 PM, Shane McCoy <[hidden email]> wrote:

I missed a bit from the log, here is catalina.out from a restart of tomcat7:

 * Stopping Tomcat servlet engine tomcat7                                [ OK ]
 * Starting Tomcat servlet engine tomcat7                                [ OK ]
--------------------------$$:/var/log/tomcat7$ tail -f catalina.out
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor /etc/tomcat7/Catalina/localhost/host-manager.xml
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
^[[AFeb 20, 2016 8:44:43 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 20, 2016 8:44:43 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.

Configuring Shiro ...

Shiro Configured
2016-02-20 20:45:40,539 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column id int8 not null
2016-02-20 20:45:40,543 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,546 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column version int8 not null
2016-02-20 20:45:40,548 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,550 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column program_version varchar(255) not null
2016-02-20 20:45:40,552 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "program_version" contains null values
2016-02-20 20:45:40,554 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_name varchar(255) not null
2016-02-20 20:45:40,555 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_name" contains null values
2016-02-20 20:45:40,558 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_version varchar(255) not null
2016-02-20 20:45:40,559 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_version" contains null values
2016-02-20 20:45:40,562 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column time_executed timestamp not null
2016-02-20 20:45:40,563 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "time_executed" contains null values
2016-02-20 20:45:40,566 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column id int8 not null
2016-02-20 20:45:40,567 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,569 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column version int8 not null
2016-02-20 20:45:40,570 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,573 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column id int8 not null
2016-02-20 20:45:40,574 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,577 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column version int8 not null
2016-02-20 20:45:40,578 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,583 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column is_relationship_type int4 not null
2016-02-20 20:45:40,584 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "is_relationship_type" contains null values
2016-02-20 20:45:40,587 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column id int8 not null
2016-02-20 20:45:40,588 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,590 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column version int8 not null
2016-02-20 20:45:40,591 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,593 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column objectcvterm_id int8 not null
2016-02-20 20:45:40,594 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" contains null values
2016-02-20 20:45:40,598 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column subjectcvterm_id int8 not null
2016-02-20 20:45:40,599 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" contains null values
2016-02-20 20:45:40,602 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column id int8 not null
2016-02-20 20:45:40,602 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,606 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column version int8 not null
2016-02-20 20:45:40,607 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,610 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add column id int8 not null
2016-02-20 20:45:40,612 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,616 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column id int8 not null
2016-02-20 20:45:40,617 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,620 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column version int8 not null
2016-02-20 20:45:40,621 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,632 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column unique_name varchar(255) not null
2016-02-20 20:45:40,633 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "unique_name" contains null values
2016-02-20 20:45:40,636 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column class varchar(255) not null
2016-02-20 20:45:40,637 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "class" contains null values
2016-02-20 20:45:40,641 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column id int8 not null
2016-02-20 20:45:40,642 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,645 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column version int8 not null
2016-02-20 20:45:40,646 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,652 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column child_feature_id int8 not null
2016-02-20 20:45:40,653 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "child_feature_id" contains null values
2016-02-20 20:45:40,656 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column parent_feature_id int8 not null
2016-02-20 20:45:40,657 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "parent_feature_id" contains null values
2016-02-20 20:45:40,660 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column id int8 not null
2016-02-20 20:45:40,661 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,668 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column version int8 not null
2016-02-20 20:45:40,670 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,672 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column publication_id int8 not null
2016-02-20 20:45:40,677 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "publication_id" contains null values
2016-02-20 20:45:40,679 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column id int8 not null
2016-02-20 20:45:40,681 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,684 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column version int8 not null
2016-02-20 20:45:40,685 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,687 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column directory varchar(255)
2016-02-20 20:45:40,688 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,692 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column id int8 not null
2016-02-20 20:45:40,693 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,701 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column version int8 not null
2016-02-20 20:45:40,702 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,704 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column directory varchar(255) not null
2016-02-20 20:45:40,706 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "directory" contains null values
2016-02-20 20:45:40,709 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column id int8 not null
2016-02-20 20:45:40,710 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,715 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column version int8 not null
2016-02-20 20:45:40,716 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,719 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column synonymsgml varchar(255) not null
2016-02-20 20:45:40,720 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "synonymsgml" contains null values
2016-02-20 20:45:40,724 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_feature add constraint FK_8m30ycwh545b4aoxor9sbk1oq foreign key (analysis_id) references analysis
2016-02-20 20:45:40,725 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8m30ycwh545b4aoxor9sbk1oq" for relation "analysis_feature" already exists
2016-02-20 20:45:40,727 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_feature add constraint FK_l94xl424xp988f06gr2b3t5tw foreign key (feature_id) references feature
2016-02-20 20:45:40,728 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_l94xl424xp988f06gr2b3t5tw" for relation "analysis_feature" already exists
2016-02-20 20:45:40,730 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_property add constraint FK_38g8n4bitmdwkrcs217uexrwx foreign key (analysis_id) references analysis
2016-02-20 20:45:40,731 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_38g8n4bitmdwkrcs217uexrwx" for relation "analysis_property" already exists
2016-02-20 20:45:40,733 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_property add constraint FK_9o7xs7saygim8y0sm4ostvpc1 foreign key (type_id) references cvterm
2016-02-20 20:45:40,734 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_9o7xs7saygim8y0sm4ostvpc1" for relation "analysis_property" already exists
2016-02-20 20:45:40,737 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add constraint FK_oksfqluv12ktmut9s6o9jla7a foreign key (cv_id) references cv
2016-02-20 20:45:40,739 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_oksfqluv12ktmut9s6o9jla7a" for relation "cvterm" already exists
2016-02-20 20:45:40,741 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add constraint FK_6d097oy44230tuoo8lb8dkkcp foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,742 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_6d097oy44230tuoo8lb8dkkcp" for relation "cvterm" already exists
2016-02-20 20:45:40,744 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_ke2nrw91sxil8mv7osgv83pw1 foreign key (cv_id) references cv
2016-02-20 20:45:40,745 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ke2nrw91sxil8mv7osgv83pw1" for relation "cvterm_path" already exists
2016-02-20 20:45:40,748 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_tlfh10092i00g6rlv589naqy5 foreign key (objectcvterm_id) references cvterm
2016-02-20 20:45:40,749 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tlfh10092i00g6rlv589naqy5" for relation "cvterm_path" already exists
2016-02-20 20:45:40,751 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_nq02ir0qeydr5tj3071k9gl7b foreign key (subjectcvterm_id) references cvterm
2016-02-20 20:45:40,752 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_nq02ir0qeydr5tj3071k9gl7b" for relation "cvterm_path" already exists
2016-02-20 20:45:40,760 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_jaqi1bk3t2c0m3pybmparp856 foreign key (type_id) references cvterm
2016-02-20 20:45:40,761 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jaqi1bk3t2c0m3pybmparp856" for relation "cvterm_path" already exists
2016-02-20 20:45:40,763 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_r1o1rnfnsf7oipuv1h7h1fln7 foreign key (objectcvterm_id) references cvterm
2016-02-20 20:45:40,766 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,771 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_pwxrfyx6rqu5krq4nj5wa3u4f foreign key (subjectcvterm_id) references cvterm
2016-02-20 20:45:40,775 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,777 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_ob1d0vrfaix8b28j4tvilqnyv foreign key (type_id) references cvterm
2016-02-20 20:45:40,778 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ob1d0vrfaix8b28j4tvilqnyv" for relation "cvterm_relationship" already exists
2016-02-20 20:45:40,781 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add constraint FK_np3tfcu9g867to3qux6raf9y8 foreign key (db_id) references db
2016-02-20 20:45:40,782 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_np3tfcu9g867to3qux6raf9y8" for relation "dbxref" already exists
2016-02-20 20:45:40,786 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref_property add constraint FK_3p1ssctww083s0tt65mmm64uo foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,787 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_3p1ssctww083s0tt65mmm64uo" for relation "dbxref_property" already exists
2016-02-20 20:45:40,792 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref_property add constraint FK_t6ojbvugx8kou45oklsie3rt5 foreign key (type_id) references cvterm
2016-02-20 20:45:40,793 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_t6ojbvugx8kou45oklsie3rt5" for relation "dbxref_property" already exists
2016-02-20 20:45:40,796 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table environmentcvterm add constraint FK_tql9djnqw1d7migfndoj3lrph foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,803 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tql9djnqw1d7migfndoj3lrph" for relation "environmentcvterm" already exists
2016-02-20 20:45:40,805 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table environmentcvterm add constraint FK_rrwb96jjqgtg077yv8pbim3jj foreign key (environment_id) references environment
2016-02-20 20:45:40,807 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_rrwb96jjqgtg077yv8pbim3jj" for relation "environmentcvterm" already exists
2016-02-20 20:45:40,813 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add constraint FK_hc4vrafs0ws7ugdkp0n6u3xdo foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,816 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_hc4vrafs0ws7ugdkp0n6u3xdo" for relation "feature" already exists
2016-02-20 20:45:40,819 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_dbxref add constraint FK_n6n7lheb1qkmlde8u6gvvjxne foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,821 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_n6n7lheb1qkmlde8u6gvvjxne" for relation "feature_dbxref" already exists
2016-02-20 20:45:40,829 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_dbxref add constraint FK_1mrfkxbb3n7fhjxcrkxappdn8 foreign key (feature_featuredbxrefs_id) references feature
2016-02-20 20:45:40,831 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_1mrfkxbb3n7fhjxcrkxappdn8" for relation "feature_dbxref" already exists
2016-02-20 20:45:40,836 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_feature_phenotypes add constraint FK_dy5g29heir5ic3d36okyuihho foreign key (phenotype_id) references phenotype
2016-02-20 20:45:40,839 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_dy5g29heir5ic3d36okyuihho" for relation "feature_feature_phenotypes" already exists
2016-02-20 20:45:40,842 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_feature_phenotypes add constraint FK_aqr7eiyx6puju6elciwubbwmo foreign key (feature_id) references feature
2016-02-20 20:45:40,843 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_aqr7eiyx6puju6elciwubbwmo" for relation "feature_feature_phenotypes" already exists
2016-02-20 20:45:40,847 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_hak8r429shmpho06rbyvwnmt0 foreign key (chromosome_feature_id) references feature
2016-02-20 20:45:40,848 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_hak8r429shmpho06rbyvwnmt0" for relation "feature_genotype" already exists
2016-02-20 20:45:40,856 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_b42u9iq4kuqe5ay544do81n32 foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,857 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_b42u9iq4kuqe5ay544do81n32" for relation "feature_genotype" already exists
2016-02-20 20:45:40,859 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_cm3gqs38fa2lpllgoum8n4kgn foreign key (feature_id) references feature
2016-02-20 20:45:40,861 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cm3gqs38fa2lpllgoum8n4kgn" for relation "feature_genotype" already exists
2016-02-20 20:45:40,863 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_736wxgjs6pip5212ash5i68p foreign key (genotype_id) references genotype
2016-02-20 20:45:40,864 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_736wxgjs6pip5212ash5i68p" for relation "feature_genotype" already exists
2016-02-20 20:45:40,867 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_grails_user add constraint FK_4dgbhgiw0vb9hqy2k5fqg3neh foreign key (feature_owners_id) references feature
2016-02-20 20:45:40,868 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4dgbhgiw0vb9hqy2k5fqg3neh" for relation "feature_grails_user" already exists
2016-02-20 20:45:40,872 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_location add constraint FK_qml7xp9f5uojcw7jwdxcb35le foreign key (feature_id) references feature
2016-02-20 20:45:40,873 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qml7xp9f5uojcw7jwdxcb35le" for relation "feature_location" already exists
2016-02-20 20:45:40,875 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_property add constraint FK_jpvdxc57abfiridcr57x8130 foreign key (feature_id) references feature
2016-02-20 20:45:40,879 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jpvdxc57abfiridcr57x8130" for relation "feature_property" already exists
2016-02-20 20:45:40,881 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_property add constraint FK_36e638geg9tew42b1mp2ehff foreign key (type_id) references cvterm
2016-02-20 20:45:40,882 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_36e638geg9tew42b1mp2ehff" for relation "feature_property" already exists
2016-02-20 20:45:40,885 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_publication add constraint FK_qolh5l4blkx8vfmwcl7f3woan foreign key (feature_feature_publications_id) references feature
2016-02-20 20:45:40,891 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qolh5l4blkx8vfmwcl7f3woan" for relation "feature_publication" already exists
2016-02-20 20:45:40,893 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add constraint FK_8jm56covt0m7m0m191bc5jseh foreign key (child_feature_id) references feature
2016-02-20 20:45:40,894 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "child_feature_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,898 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add constraint FK_72kmd92rdc6gne0nrh026o1j0 foreign key (parent_feature_id) references feature
2016-02-20 20:45:40,899 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "parent_feature_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,907 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship_feature_property add constraint FK_ebgnfbogf1lwdxd8jc17511o7 foreign key (feature_relationship_feature_relationship_properties_id) references feature_relationship
2016-02-20 20:45:40,908 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ebgnfbogf1lwdxd8jc17511o7" for relation "feature_relationship_feature_property" already exists
2016-02-20 20:45:40,911 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship_publication add constraint FK_bdd324e5jb0lpuhs7biy2kacm foreign key (feature_relationship_feature_relationship_publications_id) references feature_relationship
2016-02-20 20:45:40,912 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_bdd324e5jb0lpuhs7biy2kacm" for relation "feature_relationship_publication" already exists
2016-02-20 20:45:40,914 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_nf9qbuay984ixqd2k1425rnyo foreign key (feature_id) references feature
2016-02-20 20:45:40,916 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_nf9qbuay984ixqd2k1425rnyo" for relation "feature_synonym" already exists
2016-02-20 20:45:40,923 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_82wsc3bv9i01t9851xv4xekis foreign key (publication_id) references publication
2016-02-20 20:45:40,926 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "publication_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,929 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_ll4cqdh994s6x8n7vku1q7iwd foreign key (synonym_id) references synonym
2016-02-20 20:45:40,930 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ll4cqdh994s6x8n7vku1q7iwd" for relation "feature_synonym" already exists
2016-02-20 20:45:40,932 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_gsol4u8wrfwbkh1qrx18i3u6 foreign key (feature_synonyms_id) references feature
2016-02-20 20:45:40,933 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gsol4u8wrfwbkh1qrx18i3u6" for relation "feature_synonym" already exists
2016-02-20 20:45:40,935 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm add constraint FK_cuwo3ernssd0t0wjceb7lmm11 foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,936 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cuwo3ernssd0t0wjceb7lmm11" for relation "featurecvterm" already exists
2016-02-20 20:45:40,943 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm add constraint FK_iy7bbt67s7jaemiajsrqalv5o foreign key (feature_id) references feature
2016-02-20 20:45:40,944 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_iy7bbt67s7jaemiajsrqalv5o" for relation "featurecvterm" already exists
2016-02-20 20:45:40,948 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm_dbxref add constraint FK_r9xhefcekikp1od79ectkb22b foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,949 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_r9xhefcekikp1od79ectkb22b" for relation "featurecvterm_dbxref" already exists
2016-02-20 20:45:40,951 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism_organism_property add constraint FK_qyxdgqthtlgixvtdkkhc8g3pu foreign key (organism_organism_properties_id) references organism
2016-02-20 20:45:40,959 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qyxdgqthtlgixvtdkkhc8g3pu" for relation "organism_organism_property" already exists
2016-02-20 20:45:40,961 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organismdbxref add constraint FK_s3vk7onqrk0n4c86xnvqmm3ho foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,962 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_s3vk7onqrk0n4c86xnvqmm3ho" for relation "organismdbxref" already exists
2016-02-20 20:45:40,965 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organismdbxref add constraint FK_l1jfi0wpnyooutd820p5gskr foreign key (organism_id) references organism
2016-02-20 20:45:40,966 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_l1jfi0wpnyooutd820p5gskr" for relation "organismdbxref" already exists
2016-02-20 20:45:40,969 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table permission add constraint FK_4nvoxx3htem6jseb4rmu0aqfp foreign key (organism_id) references organism
2016-02-20 20:45:40,970 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4nvoxx3htem6jseb4rmu0aqfp" for relation "permission" already exists
2016-02-20 20:45:40,972 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_cwgh6naf9gackae2ei11v6p41 foreign key (assay_id) references cvterm
2016-02-20 20:45:40,979 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cwgh6naf9gackae2ei11v6p41" for relation "phenotype" already exists
2016-02-20 20:45:40,981 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_phmfgylejydjqyrvo3imc97go foreign key (attribute_id) references cvterm
2016-02-20 20:45:40,982 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_phmfgylejydjqyrvo3imc97go" for relation "phenotype" already exists
2016-02-20 20:45:40,985 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_jh0fc3orduigl8s7ymentbtrs foreign key (cvalue_id) references cvterm
2016-02-20 20:45:40,986 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jh0fc3orduigl8s7ymentbtrs" for relation "phenotype" already exists
2016-02-20 20:45:40,988 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_gb4wy9qesx6vnekxekm18k9xa foreign key (observable_id) references cvterm
2016-02-20 20:45:40,989 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gb4wy9qesx6vnekxekm18k9xa" for relation "phenotype" already exists
2016-02-20 20:45:40,993 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_cvterm add constraint FK_9e2v7goj5w6nds5jo0x1va1nm foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,999 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_9e2v7goj5w6nds5jo0x1va1nm" for relation "phenotype_cvterm" already exists
2016-02-20 20:45:41,001 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_cvterm add constraint FK_aicsmj1kn20ikm14292g9r2j9 foreign key (phenotype_phenotypecvterms_id) references phenotype
2016-02-20 20:45:41,002 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_aicsmj1kn20ikm14292g9r2j9" for relation "phenotype_cvterm" already exists
2016-02-20 20:45:41,004 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_t52r166gd8710vffy3aompe7d foreign key (environment_id) references environment
2016-02-20 20:45:41,006 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_t52r166gd8710vffy3aompe7d" for relation "phenotype_description" already exists
2016-02-20 20:45:41,011 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_bf1bstadamyw0gsarkb933l5b foreign key (genotype_id) references genotype
2016-02-20 20:45:41,012 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_bf1bstadamyw0gsarkb933l5b" for relation "phenotype_description" already exists
2016-02-20 20:45:41,014 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_8pbyj05khavdl5a648c7pmcil foreign key (type_id) references cvterm
2016-02-20 20:45:41,015 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8pbyj05khavdl5a648c7pmcil" for relation "phenotype_description" already exists
2016-02-20 20:45:41,020 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_q6jvhi3l7ty0m9tpbn09d8pxj foreign key (environment_id) references environment
2016-02-20 20:45:41,021 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_q6jvhi3l7ty0m9tpbn09d8pxj" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,024 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_8rbhsxxdf669tyed8jrr747hv foreign key (genotype_id) references genotype
2016-02-20 20:45:41,027 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8rbhsxxdf669tyed8jrr747hv" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,029 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_gskh1e7b6qa2du48ayu49lr3s foreign key (phenotype_id) references phenotype
2016-02-20 20:45:41,030 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gskh1e7b6qa2du48ayu49lr3s" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,035 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_tk1pgifvuhurefn0y3myfyyt4 foreign key (type_id) references cvterm
2016-02-20 20:45:41,036 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tk1pgifvuhurefn0y3myfyyt4" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,039 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table preference add constraint FK_42b0lk4rcfjcagw84jugd1sgj foreign key (organism_id) references organism
2016-02-20 20:45:41,044 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_42b0lk4rcfjcagw84jugd1sgj" for relation "preference" already exists
2016-02-20 20:45:41,047 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publication add constraint FK_h3g8f3q2krcnwmq2nasbanlay foreign key (type_id) references cvterm
2016-02-20 20:45:41,049 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_h3g8f3q2krcnwmq2nasbanlay" for relation "publication" already exists
2016-02-20 20:45:41,051 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publication_relationship add constraint FK_q6hf14oiq9pomkjrhtndonmeh foreign key (type_id) references cvterm
2016-02-20 20:45:41,052 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_q6hf14oiq9pomkjrhtndonmeh" for relation "publication_relationship" already exists
2016-02-20 20:45:41,055 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publicationdbxref add constraint FK_oh81hma8qx88fhvcmfugx836b foreign key (dbxref_id) references dbxref
2016-02-20 20:45:41,059 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_oh81hma8qx88fhvcmfugx836b" for relation "publicationdbxref" already exists
2016-02-20 20:45:41,061 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table sequence add constraint FK_rux0954nxr4lwvj2qgyjibua7 foreign key (organism_id) references organism
2016-02-20 20:45:41,062 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_rux0954nxr4lwvj2qgyjibua7" for relation "sequence" already exists
2016-02-20 20:45:41,065 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add constraint FK_4ylco1irefvydmsnedglqqdfu foreign key (type_id) references cvterm
2016-02-20 20:45:41,066 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4ylco1irefvydmsnedglqqdfu" for relation "synonym" already exists
2016-02-20 20:45:52,529 [localhost-startStop-1] ERROR liquibase  - Change Set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated) failed.  Error: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
2016-02-20 20:45:52,579 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    ... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
2016-02-20 20:45:52,584 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    ... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
Feb 20, 2016 8:45:52 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 20, 2016 8:45:52 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/apollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [PoolCleaner[25416670:1456022700075]] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@18740d1]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 20, 2016 8:45:52 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 20, 2016 8:45:52 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 80376 ms



On Sat, Feb 20, 2016 at 9:32 PM, Lbl <[hidden email]> wrote:
Try opening in an incognito or another browser of doing a shift reload to flush the cache. 

That being said .. This stack trace looks a bit terse.   Typically shiro (the security plugin) will reload but I don't see that here.  Maybe further up? 

Nathan

On Feb 20, 2016, at 6:04 PM, Shane McCoy <[hidden email]> wrote:

Hey! I made the changes but I am still getting a blank screen.

I checked catalina.out, here is the last output:

/var/log/tomcat7$ tail -f catalina.out
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [PoolCleaner[25416670:1456019437960]] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@1b2e3fc]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 20, 2016 7:51:28 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 20, 2016 7:51:28 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 77106 ms


Is this still a memory issue then?
I have updated tomcat memory to your doc specs already.
Thanks!
shane

On Sat, Feb 20, 2016 at 7:55 PM, Shane McCoy <[hidden email]> wrote:
Ok, that makes more sense now! thank you very much.
I'll will try with correct settings,
cheers!

On Sat, Feb 20, 2016 at 7:53 PM, Colin <[hidden email]> wrote:
Hi Shaun

>url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

Just wanted to comment on this, actually, it would not be your IP and war here. It is kind of confusing that this "setting" is called a url, because it is actually a JDBC connector string, which actually references your local database, so it would not be using the war file name or even the IP address.

For example, if your database is named "apollodb", then your "url" would be

jdbc:postgresql://localhost/apollodb

It would generally just be localhost unless you have a separate database server. I think it might be worth adding some more comments about that in our setup guide, but I hope that helps!


-Colin

On Sat, Feb 20, 2016 at 2:36 PM, Shane McCoy <[hidden email]> wrote:
Hey!
So a lot has changed in a year! I'm currently still stuck at 2g but wanted to ask about an issue i have w/ /.apollo deploy
I am getting a blank screen at the URL. I have not added any data for generation yet. I assume i would still get a webapollo ui.
I am using postgresql. I edited apollo-config.groovy
Added (in production only)
datasource.dbCreate = "update" // one of...  ( where does the database name go? I don't understand this line, it seems i'm limited to the options given?)
username: chado database username
password: chado database pw
url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

I haven't changed any other settings and going to http://myipaddress/apollo is a blank page.
I want to use this w/ a already setup postgresql chado database.

I am going off of this guide: http://webapollo.readthedocs.org/en/latest/Setup.html
Thanks!

On Thu, Feb 11, 2016 at 2:29 PM, Shane McCoy <[hidden email]> wrote:
Thanks for the quick reply!
I will see what options I can take -
Shane M.

On Thu, Feb 11, 2016 at 2:18 PM, Nathan Dunn <[hidden email]> wrote:

On Feb 11, 2016, at 11:07 AM, Shane McCoy <[hidden email]> wrote:

Hey

I am getting this error running ./apollo run-local 8085

..........
    BUILD SUCCESSFUL
    | Compiling 5 source files
    | Compiling 5 source files.....
    ***
    Metrics servlet injected into web.xml
    Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
    ***
    | Running Grails application
    Error occurred during initialization of VM
    Could not reserve enough space for object heap
    Error: Could not create the Java Virtual Machine.
    Error: A fatal exception has occurred. Program will exit.
    | Error Forked Grails VM exited with error

I’m guessing that Java is requesting more memory then you have to allocate, and so exiting.  

So, when running it with run-local (for dev purposes), it actually has preset memory, of a max of up to 2 GB, though obviously this is high.  It is in BuildConfig.groovy:

run    : [maxMemory: 2048, minMemory: 64, debug: false , maxPerm: 1024, forkReserve: false],
My guess is that your machine doesn’t have sufficient memory to run this, or there is another process. 

My suggestions would be:
1 - get a machine with at least 4 GB’s of memory, especially if you are going to host to multiple users.  This will enable better caching and performance.    
2 - if (1) is not an immediate option (or to test, or if you are just running locally) your can edit your apollo-config.groovy create a line like this, so it will use less memory:

grails.project.fork = [
// configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
// compile: [maxMemory: 256, minMemory: 64, debug: false, maxPerm: 256, daemon:true],

test : false,
//run : false,
// configure settings for the test-app JVM, uses the daemon by default
//test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
// configure settings for the run-app JVM
run : [maxMemory: 1024, minMemory: 64, debug: false , maxPerm: 512, forkReserve: false],
// configure settings for the run-war JVM
war : [maxMemory: 1024, minMemory: 64, debug: false, maxPerm: 512, forkReserve: false],
// configure settings for the Console UI JVM
console: [maxMemory:
1024, minMemory: 64, debug: false, maxPerm: 512]
]

Setting the java size as done below works for tomcat, but not for the development mode (run-local).  

Nathan 

I looked over the same errors on Stack and made adjustments to the memory but I am still getting this error. I am new to Grails but I believe everything is setup correct and i can run a sample app (helloworld).
Here is the changes i made:

    -Xms512m -Xmx1g -XX:PermSize=256m
This is the memory

    free -m
                 total       used       free     shared    buffers     cached
    Mem:          2015       1297        718         56        169        859
    -/+ buffers/cache:        267       1748

Checking if parameters are being read

    $ ps -ef | grep java
    tomcat7  32158     1  1 11:02 ?        00:00:10 /usr/lib/jvm/default-java/bin/java -Djava.util.logging.config.file=/var/lib/tomcat7/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms512m -Xmx1g -XX:PermSize=256m -XX:MaxPermSize=256m -Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m -Djava.endorsed.dirs=/usr/share/tomcat7/endorsed -classpath /usr/share/tomcat7/bin/bootstrap.jar:/usr/share/tomcat7/bin/tomcat-juli.jar -Dcatalina.base=/var/lib/tomcat7 -Dcatalina.home=/usr/share/tomcat7 -Djava.io.tmpdir=/tmp/tomcat7-tomcat7-tmp org.apache.catalina.startup.Bootstrap start


I have this in my $HOME/.profile

    export JAVA_OPTS="-Xms512m -Xmx1g -XX:MaxPermSize=256m"

in my setenv.sh for Tomcat7

    export CATALINA_OPTS="-Xms512m -Xmx1g \
        -XX:+CMSClassUnloadingEnabled \
        -XX:+CMSPermGenSweepingEnabled \
        -XX:+UseConcMarkSweepGC \
        -XX:MaxPermSize=256m"

Versions: (i went w/ 2.4.5 per Apollo guide)
    $ grails -version
    Grails version: 2.4.5
    $ java -version
    java version "1.7.0_95"
    OpenJDK Runtime Environment (IcedTea 2.6.4) (7u95-2.6.4-0ubuntu0.14.04.1)
    OpenJDK Client VM (build 24.95-b01, mixed mode, sharing)

I am not sure what to change now - it seems the memory would be adequate? I know this isn't Apollo specific but maybe someone here has had the same problem? Please any thoughts would be great. thank you
Shane M.



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Re: New WebApollo install issue (Grails)

nathandunn

On Feb 22, 2016, at 5:36 PM, Shane McCoy <[hidden email]> wrote:

ok, I just want to be able to annotate, save & export at this point. So I think the steps I mentioned are all that are needed at the moment.
If I want to remove an organism (start a clean slate) is dropping the db and removing the content of /opt/apollo/data sufficient?
I can continue w/ a new db and organism?
Thanks!

Other user’s might have better insight into their own process for publishing annotations.   

You could definitely do either of the things you mentioned.   If I had the disk space, I would probably opt for the new db if you are changing your reference sequence / scaffolds. 

We also have a “delete_annotations_from_organism.groovy” web services script, as well if you just wanted to remove organisms but save all of the permissions data.  

We also have an outstanding pull request that allow you to (with configuration) do remove all annotations from the interface, but I’m not sure it will make it into 2.0.2. 

Nathan


On Sun, Feb 21, 2016 at 10:01 PM, Nathan Dunn <[hidden email]> wrote:

I think so. 

Keep in mind that anything in the “./bin” directory is actually jbrowse code.  Just make sure you point your organism directory to /opt/apollo/data    

If you have more than one organism they will have to go in different directories. 

Nathan

On Feb 21, 2016, at 5:37 PM, Shane McCoy <[hidden email]> wrote:

Ok, good to know! I'll keep an eye out for the Chado addition later.
This seems a lot simpler than prior version.
so if i have 2 files: genome.gff & genome.fa

  1. bin/preprare-refseqs.pl --fasta genome.fa --out /opt/apollo/data
  2. bin/flatfile-to-json.pl --gff genome.gff --type gene --tracklabel makergene --autocomplete all --Key Maker Gene --out /opt/apollo/data
  3. and repeat for all the different Types? correct? is there any changes to the options for flatfile-to-json.pl? I have many to add from the same genome
  4. bin/generate-names.pl --verbose --out /opt/apollo/data
  5. ./apollo deploy
  6. add WAR to webapps and start tomcat.
  7. is that about right?
Thanks again!
Shane



On Sun, Feb 21, 2016 at 5:43 PM, Nathan Dunn <[hidden email]> wrote:

So, unfortunately we need to formally add Chado integration back to Apollo.  

We (specifically Deepak) are actively working on it and it should be part of the 2.0.3 release.   We’ll be pinging the community specifically to make sure the export / integration works.  

In the interim the best method that I am aware of is to export a GFF3 from Apollo and import that GFF3 into your Chado schema.  

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Feb 21, 2016, at 9:18 AM, Shane McCoy <[hidden email]> wrote:

Hi Nathan,
I did as you said and it started up just fine. Thank you!
So this leads me to believe the previous setup I did (1.0.2 i believe) won't be the best guide to a new setup.

I want to be able to use the CHADO schema & use web apollo to edit the genome.
I had set up CHADO on a database and had already uploaded the GFF. Can I get pointers on the proper steps to follow now?
I did back it up prior to deleting and recreating db, but it is pretty small test file and i don't have an issue putting back through the script.
Thanks again!
Shane M. 

On Sun, Feb 21, 2016 at 1:24 AM, Nathan Dunn <[hidden email]> wrote:

If you are using postgresql and you don’t have anything in the database you want (or you back it up first) I would drop and re-create the database (with tomcat off).     When it comes back up it will create the database with the create schema for you:

1 - stop tomcat 
1a - backup database? 
2 - dropdb your-apollo-database-name
3 - createdb your-apollo-database-name
4 - start tomcat

Its in a pretty weird state. 

Nathan

On Feb 20, 2016, at 6:51 PM, Shane McCoy <[hidden email]> wrote:

I missed a bit from the log, here is catalina.out from a restart of tomcat7:

 * Stopping Tomcat servlet engine tomcat7                                [ OK ]
 * Starting Tomcat servlet engine tomcat7                                [ OK ]
--------------------------$$:/var/log/tomcat7$ tail -f catalina.out
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml_rt is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jstl/xml is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://java.sun.com/jsp/jstl/xml is already defined
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor /etc/tomcat7/Catalina/localhost/host-manager.xml
Feb 20, 2016 8:44:33 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /var/lib/tomcat7/webapps/apollo.war
^[[AFeb 20, 2016 8:44:43 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
Feb 20, 2016 8:44:43 PM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
log4j:WARN No appenders could be found for logger (org.codehaus.groovy.grails.commons.cfg.ConfigurationHelper).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.

Configuring Shiro ...

Shiro Configured
2016-02-20 20:45:40,539 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column id int8 not null
2016-02-20 20:45:40,543 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,546 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column version int8 not null
2016-02-20 20:45:40,548 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,550 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column program_version varchar(255) not null
2016-02-20 20:45:40,552 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "program_version" contains null values
2016-02-20 20:45:40,554 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_name varchar(255) not null
2016-02-20 20:45:40,555 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_name" contains null values
2016-02-20 20:45:40,558 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column source_version varchar(255) not null
2016-02-20 20:45:40,559 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "source_version" contains null values
2016-02-20 20:45:40,562 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis add column time_executed timestamp not null
2016-02-20 20:45:40,563 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "time_executed" contains null values
2016-02-20 20:45:40,566 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column id int8 not null
2016-02-20 20:45:40,567 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,569 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cv add column version int8 not null
2016-02-20 20:45:40,570 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,573 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column id int8 not null
2016-02-20 20:45:40,574 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,577 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column version int8 not null
2016-02-20 20:45:40,578 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,583 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add column is_relationship_type int4 not null
2016-02-20 20:45:40,584 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "is_relationship_type" contains null values
2016-02-20 20:45:40,587 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column id int8 not null
2016-02-20 20:45:40,588 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,590 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column version int8 not null
2016-02-20 20:45:40,591 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,593 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column objectcvterm_id int8 not null
2016-02-20 20:45:40,594 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" contains null values
2016-02-20 20:45:40,598 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add column subjectcvterm_id int8 not null
2016-02-20 20:45:40,599 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" contains null values
2016-02-20 20:45:40,602 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column id int8 not null
2016-02-20 20:45:40,602 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,606 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table db add column version int8 not null
2016-02-20 20:45:40,607 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,610 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add column id int8 not null
2016-02-20 20:45:40,612 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,616 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column id int8 not null
2016-02-20 20:45:40,617 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,620 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column version int8 not null
2016-02-20 20:45:40,621 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,632 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column unique_name varchar(255) not null
2016-02-20 20:45:40,633 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "unique_name" contains null values
2016-02-20 20:45:40,636 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add column class varchar(255) not null
2016-02-20 20:45:40,637 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "class" contains null values
2016-02-20 20:45:40,641 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column id int8 not null
2016-02-20 20:45:40,642 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,645 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column version int8 not null
2016-02-20 20:45:40,646 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,652 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column child_feature_id int8 not null
2016-02-20 20:45:40,653 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "child_feature_id" contains null values
2016-02-20 20:45:40,656 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add column parent_feature_id int8 not null
2016-02-20 20:45:40,657 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "parent_feature_id" contains null values
2016-02-20 20:45:40,660 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column id int8 not null
2016-02-20 20:45:40,661 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,668 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column version int8 not null
2016-02-20 20:45:40,670 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,672 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add column publication_id int8 not null
2016-02-20 20:45:40,677 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "publication_id" contains null values
2016-02-20 20:45:40,679 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column id int8 not null
2016-02-20 20:45:40,681 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,684 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column version int8 not null
2016-02-20 20:45:40,685 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,687 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table genome add column directory varchar(255)
2016-02-20 20:45:40,688 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: relation "genome" does not exist
2016-02-20 20:45:40,692 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column id int8 not null
2016-02-20 20:45:40,693 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,701 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column version int8 not null
2016-02-20 20:45:40,702 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,704 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism add column directory varchar(255) not null
2016-02-20 20:45:40,706 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "directory" contains null values
2016-02-20 20:45:40,709 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column id int8 not null
2016-02-20 20:45:40,710 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "id" contains null values
2016-02-20 20:45:40,715 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column version int8 not null
2016-02-20 20:45:40,716 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "version" contains null values
2016-02-20 20:45:40,719 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add column synonymsgml varchar(255) not null
2016-02-20 20:45:40,720 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "synonymsgml" contains null values
2016-02-20 20:45:40,724 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_feature add constraint FK_8m30ycwh545b4aoxor9sbk1oq foreign key (analysis_id) references analysis
2016-02-20 20:45:40,725 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8m30ycwh545b4aoxor9sbk1oq" for relation "analysis_feature" already exists
2016-02-20 20:45:40,727 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_feature add constraint FK_l94xl424xp988f06gr2b3t5tw foreign key (feature_id) references feature
2016-02-20 20:45:40,728 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_l94xl424xp988f06gr2b3t5tw" for relation "analysis_feature" already exists
2016-02-20 20:45:40,730 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_property add constraint FK_38g8n4bitmdwkrcs217uexrwx foreign key (analysis_id) references analysis
2016-02-20 20:45:40,731 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_38g8n4bitmdwkrcs217uexrwx" for relation "analysis_property" already exists
2016-02-20 20:45:40,733 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table analysis_property add constraint FK_9o7xs7saygim8y0sm4ostvpc1 foreign key (type_id) references cvterm
2016-02-20 20:45:40,734 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_9o7xs7saygim8y0sm4ostvpc1" for relation "analysis_property" already exists
2016-02-20 20:45:40,737 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add constraint FK_oksfqluv12ktmut9s6o9jla7a foreign key (cv_id) references cv
2016-02-20 20:45:40,739 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_oksfqluv12ktmut9s6o9jla7a" for relation "cvterm" already exists
2016-02-20 20:45:40,741 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm add constraint FK_6d097oy44230tuoo8lb8dkkcp foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,742 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_6d097oy44230tuoo8lb8dkkcp" for relation "cvterm" already exists
2016-02-20 20:45:40,744 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_ke2nrw91sxil8mv7osgv83pw1 foreign key (cv_id) references cv
2016-02-20 20:45:40,745 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ke2nrw91sxil8mv7osgv83pw1" for relation "cvterm_path" already exists
2016-02-20 20:45:40,748 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_tlfh10092i00g6rlv589naqy5 foreign key (objectcvterm_id) references cvterm
2016-02-20 20:45:40,749 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tlfh10092i00g6rlv589naqy5" for relation "cvterm_path" already exists
2016-02-20 20:45:40,751 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_nq02ir0qeydr5tj3071k9gl7b foreign key (subjectcvterm_id) references cvterm
2016-02-20 20:45:40,752 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_nq02ir0qeydr5tj3071k9gl7b" for relation "cvterm_path" already exists
2016-02-20 20:45:40,760 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_path add constraint FK_jaqi1bk3t2c0m3pybmparp856 foreign key (type_id) references cvterm
2016-02-20 20:45:40,761 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jaqi1bk3t2c0m3pybmparp856" for relation "cvterm_path" already exists
2016-02-20 20:45:40,763 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_r1o1rnfnsf7oipuv1h7h1fln7 foreign key (objectcvterm_id) references cvterm
2016-02-20 20:45:40,766 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "objectcvterm_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,771 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_pwxrfyx6rqu5krq4nj5wa3u4f foreign key (subjectcvterm_id) references cvterm
2016-02-20 20:45:40,775 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "subjectcvterm_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,777 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table cvterm_relationship add constraint FK_ob1d0vrfaix8b28j4tvilqnyv foreign key (type_id) references cvterm
2016-02-20 20:45:40,778 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ob1d0vrfaix8b28j4tvilqnyv" for relation "cvterm_relationship" already exists
2016-02-20 20:45:40,781 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref add constraint FK_np3tfcu9g867to3qux6raf9y8 foreign key (db_id) references db
2016-02-20 20:45:40,782 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_np3tfcu9g867to3qux6raf9y8" for relation "dbxref" already exists
2016-02-20 20:45:40,786 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref_property add constraint FK_3p1ssctww083s0tt65mmm64uo foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,787 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_3p1ssctww083s0tt65mmm64uo" for relation "dbxref_property" already exists
2016-02-20 20:45:40,792 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table dbxref_property add constraint FK_t6ojbvugx8kou45oklsie3rt5 foreign key (type_id) references cvterm
2016-02-20 20:45:40,793 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_t6ojbvugx8kou45oklsie3rt5" for relation "dbxref_property" already exists
2016-02-20 20:45:40,796 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table environmentcvterm add constraint FK_tql9djnqw1d7migfndoj3lrph foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,803 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tql9djnqw1d7migfndoj3lrph" for relation "environmentcvterm" already exists
2016-02-20 20:45:40,805 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table environmentcvterm add constraint FK_rrwb96jjqgtg077yv8pbim3jj foreign key (environment_id) references environment
2016-02-20 20:45:40,807 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_rrwb96jjqgtg077yv8pbim3jj" for relation "environmentcvterm" already exists
2016-02-20 20:45:40,813 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature add constraint FK_hc4vrafs0ws7ugdkp0n6u3xdo foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,816 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_hc4vrafs0ws7ugdkp0n6u3xdo" for relation "feature" already exists
2016-02-20 20:45:40,819 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_dbxref add constraint FK_n6n7lheb1qkmlde8u6gvvjxne foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,821 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_n6n7lheb1qkmlde8u6gvvjxne" for relation "feature_dbxref" already exists
2016-02-20 20:45:40,829 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_dbxref add constraint FK_1mrfkxbb3n7fhjxcrkxappdn8 foreign key (feature_featuredbxrefs_id) references feature
2016-02-20 20:45:40,831 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_1mrfkxbb3n7fhjxcrkxappdn8" for relation "feature_dbxref" already exists
2016-02-20 20:45:40,836 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_feature_phenotypes add constraint FK_dy5g29heir5ic3d36okyuihho foreign key (phenotype_id) references phenotype
2016-02-20 20:45:40,839 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_dy5g29heir5ic3d36okyuihho" for relation "feature_feature_phenotypes" already exists
2016-02-20 20:45:40,842 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_feature_phenotypes add constraint FK_aqr7eiyx6puju6elciwubbwmo foreign key (feature_id) references feature
2016-02-20 20:45:40,843 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_aqr7eiyx6puju6elciwubbwmo" for relation "feature_feature_phenotypes" already exists
2016-02-20 20:45:40,847 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_hak8r429shmpho06rbyvwnmt0 foreign key (chromosome_feature_id) references feature
2016-02-20 20:45:40,848 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_hak8r429shmpho06rbyvwnmt0" for relation "feature_genotype" already exists
2016-02-20 20:45:40,856 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_b42u9iq4kuqe5ay544do81n32 foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,857 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_b42u9iq4kuqe5ay544do81n32" for relation "feature_genotype" already exists
2016-02-20 20:45:40,859 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_cm3gqs38fa2lpllgoum8n4kgn foreign key (feature_id) references feature
2016-02-20 20:45:40,861 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cm3gqs38fa2lpllgoum8n4kgn" for relation "feature_genotype" already exists
2016-02-20 20:45:40,863 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_genotype add constraint FK_736wxgjs6pip5212ash5i68p foreign key (genotype_id) references genotype
2016-02-20 20:45:40,864 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_736wxgjs6pip5212ash5i68p" for relation "feature_genotype" already exists
2016-02-20 20:45:40,867 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_grails_user add constraint FK_4dgbhgiw0vb9hqy2k5fqg3neh foreign key (feature_owners_id) references feature
2016-02-20 20:45:40,868 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4dgbhgiw0vb9hqy2k5fqg3neh" for relation "feature_grails_user" already exists
2016-02-20 20:45:40,872 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_location add constraint FK_qml7xp9f5uojcw7jwdxcb35le foreign key (feature_id) references feature
2016-02-20 20:45:40,873 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qml7xp9f5uojcw7jwdxcb35le" for relation "feature_location" already exists
2016-02-20 20:45:40,875 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_property add constraint FK_jpvdxc57abfiridcr57x8130 foreign key (feature_id) references feature
2016-02-20 20:45:40,879 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jpvdxc57abfiridcr57x8130" for relation "feature_property" already exists
2016-02-20 20:45:40,881 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_property add constraint FK_36e638geg9tew42b1mp2ehff foreign key (type_id) references cvterm
2016-02-20 20:45:40,882 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_36e638geg9tew42b1mp2ehff" for relation "feature_property" already exists
2016-02-20 20:45:40,885 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_publication add constraint FK_qolh5l4blkx8vfmwcl7f3woan foreign key (feature_feature_publications_id) references feature
2016-02-20 20:45:40,891 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qolh5l4blkx8vfmwcl7f3woan" for relation "feature_publication" already exists
2016-02-20 20:45:40,893 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add constraint FK_8jm56covt0m7m0m191bc5jseh foreign key (child_feature_id) references feature
2016-02-20 20:45:40,894 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "child_feature_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,898 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship add constraint FK_72kmd92rdc6gne0nrh026o1j0 foreign key (parent_feature_id) references feature
2016-02-20 20:45:40,899 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "parent_feature_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,907 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship_feature_property add constraint FK_ebgnfbogf1lwdxd8jc17511o7 foreign key (feature_relationship_feature_relationship_properties_id) references feature_relationship
2016-02-20 20:45:40,908 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ebgnfbogf1lwdxd8jc17511o7" for relation "feature_relationship_feature_property" already exists
2016-02-20 20:45:40,911 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_relationship_publication add constraint FK_bdd324e5jb0lpuhs7biy2kacm foreign key (feature_relationship_feature_relationship_publications_id) references feature_relationship
2016-02-20 20:45:40,912 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_bdd324e5jb0lpuhs7biy2kacm" for relation "feature_relationship_publication" already exists
2016-02-20 20:45:40,914 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_nf9qbuay984ixqd2k1425rnyo foreign key (feature_id) references feature
2016-02-20 20:45:40,916 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_nf9qbuay984ixqd2k1425rnyo" for relation "feature_synonym" already exists
2016-02-20 20:45:40,923 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_82wsc3bv9i01t9851xv4xekis foreign key (publication_id) references publication
2016-02-20 20:45:40,926 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: column "publication_id" referenced in foreign key constraint does not exist
2016-02-20 20:45:40,929 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_ll4cqdh994s6x8n7vku1q7iwd foreign key (synonym_id) references synonym
2016-02-20 20:45:40,930 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_ll4cqdh994s6x8n7vku1q7iwd" for relation "feature_synonym" already exists
2016-02-20 20:45:40,932 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table feature_synonym add constraint FK_gsol4u8wrfwbkh1qrx18i3u6 foreign key (feature_synonyms_id) references feature
2016-02-20 20:45:40,933 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gsol4u8wrfwbkh1qrx18i3u6" for relation "feature_synonym" already exists
2016-02-20 20:45:40,935 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm add constraint FK_cuwo3ernssd0t0wjceb7lmm11 foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,936 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cuwo3ernssd0t0wjceb7lmm11" for relation "featurecvterm" already exists
2016-02-20 20:45:40,943 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm add constraint FK_iy7bbt67s7jaemiajsrqalv5o foreign key (feature_id) references feature
2016-02-20 20:45:40,944 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_iy7bbt67s7jaemiajsrqalv5o" for relation "featurecvterm" already exists
2016-02-20 20:45:40,948 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table featurecvterm_dbxref add constraint FK_r9xhefcekikp1od79ectkb22b foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,949 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_r9xhefcekikp1od79ectkb22b" for relation "featurecvterm_dbxref" already exists
2016-02-20 20:45:40,951 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organism_organism_property add constraint FK_qyxdgqthtlgixvtdkkhc8g3pu foreign key (organism_organism_properties_id) references organism
2016-02-20 20:45:40,959 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_qyxdgqthtlgixvtdkkhc8g3pu" for relation "organism_organism_property" already exists
2016-02-20 20:45:40,961 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organismdbxref add constraint FK_s3vk7onqrk0n4c86xnvqmm3ho foreign key (dbxref_id) references dbxref
2016-02-20 20:45:40,962 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_s3vk7onqrk0n4c86xnvqmm3ho" for relation "organismdbxref" already exists
2016-02-20 20:45:40,965 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table organismdbxref add constraint FK_l1jfi0wpnyooutd820p5gskr foreign key (organism_id) references organism
2016-02-20 20:45:40,966 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_l1jfi0wpnyooutd820p5gskr" for relation "organismdbxref" already exists
2016-02-20 20:45:40,969 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table permission add constraint FK_4nvoxx3htem6jseb4rmu0aqfp foreign key (organism_id) references organism
2016-02-20 20:45:40,970 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4nvoxx3htem6jseb4rmu0aqfp" for relation "permission" already exists
2016-02-20 20:45:40,972 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_cwgh6naf9gackae2ei11v6p41 foreign key (assay_id) references cvterm
2016-02-20 20:45:40,979 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_cwgh6naf9gackae2ei11v6p41" for relation "phenotype" already exists
2016-02-20 20:45:40,981 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_phmfgylejydjqyrvo3imc97go foreign key (attribute_id) references cvterm
2016-02-20 20:45:40,982 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_phmfgylejydjqyrvo3imc97go" for relation "phenotype" already exists
2016-02-20 20:45:40,985 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_jh0fc3orduigl8s7ymentbtrs foreign key (cvalue_id) references cvterm
2016-02-20 20:45:40,986 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_jh0fc3orduigl8s7ymentbtrs" for relation "phenotype" already exists
2016-02-20 20:45:40,988 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype add constraint FK_gb4wy9qesx6vnekxekm18k9xa foreign key (observable_id) references cvterm
2016-02-20 20:45:40,989 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gb4wy9qesx6vnekxekm18k9xa" for relation "phenotype" already exists
2016-02-20 20:45:40,993 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_cvterm add constraint FK_9e2v7goj5w6nds5jo0x1va1nm foreign key (cvterm_id) references cvterm
2016-02-20 20:45:40,999 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_9e2v7goj5w6nds5jo0x1va1nm" for relation "phenotype_cvterm" already exists
2016-02-20 20:45:41,001 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_cvterm add constraint FK_aicsmj1kn20ikm14292g9r2j9 foreign key (phenotype_phenotypecvterms_id) references phenotype
2016-02-20 20:45:41,002 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_aicsmj1kn20ikm14292g9r2j9" for relation "phenotype_cvterm" already exists
2016-02-20 20:45:41,004 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_t52r166gd8710vffy3aompe7d foreign key (environment_id) references environment
2016-02-20 20:45:41,006 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_t52r166gd8710vffy3aompe7d" for relation "phenotype_description" already exists
2016-02-20 20:45:41,011 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_bf1bstadamyw0gsarkb933l5b foreign key (genotype_id) references genotype
2016-02-20 20:45:41,012 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_bf1bstadamyw0gsarkb933l5b" for relation "phenotype_description" already exists
2016-02-20 20:45:41,014 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_description add constraint FK_8pbyj05khavdl5a648c7pmcil foreign key (type_id) references cvterm
2016-02-20 20:45:41,015 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8pbyj05khavdl5a648c7pmcil" for relation "phenotype_description" already exists
2016-02-20 20:45:41,020 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_q6jvhi3l7ty0m9tpbn09d8pxj foreign key (environment_id) references environment
2016-02-20 20:45:41,021 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_q6jvhi3l7ty0m9tpbn09d8pxj" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,024 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_8rbhsxxdf669tyed8jrr747hv foreign key (genotype_id) references genotype
2016-02-20 20:45:41,027 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_8rbhsxxdf669tyed8jrr747hv" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,029 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_gskh1e7b6qa2du48ayu49lr3s foreign key (phenotype_id) references phenotype
2016-02-20 20:45:41,030 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_gskh1e7b6qa2du48ayu49lr3s" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,035 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table phenotype_statement add constraint FK_tk1pgifvuhurefn0y3myfyyt4 foreign key (type_id) references cvterm
2016-02-20 20:45:41,036 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_tk1pgifvuhurefn0y3myfyyt4" for relation "phenotype_statement" already exists
2016-02-20 20:45:41,039 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table preference add constraint FK_42b0lk4rcfjcagw84jugd1sgj foreign key (organism_id) references organism
2016-02-20 20:45:41,044 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_42b0lk4rcfjcagw84jugd1sgj" for relation "preference" already exists
2016-02-20 20:45:41,047 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publication add constraint FK_h3g8f3q2krcnwmq2nasbanlay foreign key (type_id) references cvterm
2016-02-20 20:45:41,049 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_h3g8f3q2krcnwmq2nasbanlay" for relation "publication" already exists
2016-02-20 20:45:41,051 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publication_relationship add constraint FK_q6hf14oiq9pomkjrhtndonmeh foreign key (type_id) references cvterm
2016-02-20 20:45:41,052 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_q6hf14oiq9pomkjrhtndonmeh" for relation "publication_relationship" already exists
2016-02-20 20:45:41,055 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table publicationdbxref add constraint FK_oh81hma8qx88fhvcmfugx836b foreign key (dbxref_id) references dbxref
2016-02-20 20:45:41,059 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_oh81hma8qx88fhvcmfugx836b" for relation "publicationdbxref" already exists
2016-02-20 20:45:41,061 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table sequence add constraint FK_rux0954nxr4lwvj2qgyjibua7 foreign key (organism_id) references organism
2016-02-20 20:45:41,062 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_rux0954nxr4lwvj2qgyjibua7" for relation "sequence" already exists
2016-02-20 20:45:41,065 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - HHH000388: Unsuccessful: alter table synonym add constraint FK_4ylco1irefvydmsnedglqqdfu foreign key (type_id) references cvterm
2016-02-20 20:45:41,066 [localhost-startStop-1] ERROR hbm2ddl.SchemaUpdate  - ERROR: constraint "fk_4ylco1irefvydmsnedglqqdfu" for relation "synonym" already exists
2016-02-20 20:45:52,529 [localhost-startStop-1] ERROR liquibase  - Change Set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated) failed.  Error: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
2016-02-20 20:45:52,579 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing the application: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    ... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
2016-02-20 20:45:52,584 [localhost-startStop-1] ERROR context.GrailsContextLoaderListener  - Error initializing Grails: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
liquibase.exception.MigrationFailedException: Migration failed for change set changelog-2.0.1.groovy::1445460972540-4::nathandunn (generated):
     Reason: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis":
          Caused By: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:347)
    at liquibase.changelog.visitor.UpdateVisitor.visit(UpdateVisitor.java:27)
    at liquibase.changelog.ChangeLogIterator.run(ChangeLogIterator.java:58)
    at liquibase.Liquibase.update(Liquibase.java:114)
    at grails.plugin.databasemigration.MigrationRunner$_runMigrations_closure2.doCall(MigrationRunner.groovy:128)
    at grails.plugin.databasemigration.MigrationRunner.runMigrations(MigrationRunner.groovy:120)
    at grails.plugin.databasemigration.MigrationRunner$_autoRun_closure1.doCall(MigrationRunner.groovy:87)
    at grails.plugin.databasemigration.MigrationUtils.executeInSession(MigrationUtils.groovy:137)
    at grails.plugin.databasemigration.MigrationRunner.autoRun(MigrationRunner.groovy:58)
    at DatabaseMigrationGrailsPlugin$_closure2.doCall(DatabaseMigrationGrailsPlugin.groovy:97)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
Caused by: liquibase.exception.DatabaseException: Error executing SQL ALTER TABLE feature ALTER COLUMN is_analysis TYPE BOOLEAN: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:62)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:104)
    at liquibase.database.AbstractDatabase.execute(AbstractDatabase.java:1091)
    at liquibase.database.AbstractDatabase.executeStatements(AbstractDatabase.java:1075)
    at liquibase.changelog.ChangeSet.execute(ChangeSet.java:317)
    ... 14 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot alter type of a column used by a view or rule
  Detail: rule _RETURN on view so.population_specific_variant depends on column "is_analysis"
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2161)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1890)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:255)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:559)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:403)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:395)
    at liquibase.executor.jvm.JdbcExecutor$1ExecuteStatementCallback.doInStatement(JdbcExecutor.java:92)
    at liquibase.executor.jvm.JdbcExecutor.execute(JdbcExecutor.java:55)
    ... 18 more
Feb 20, 2016 8:45:52 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Feb 20, 2016 8:45:52 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/apollo] startup failed due to previous errors
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesJdbc
SEVERE: The web application [/apollo] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [PoolCleaner[25416670:1456022700075]] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 8:45:52 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@18740d1]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 20, 2016 8:45:52 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 20, 2016 8:45:52 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 80376 ms



On Sat, Feb 20, 2016 at 9:32 PM, Lbl <[hidden email]> wrote:
Try opening in an incognito or another browser of doing a shift reload to flush the cache. 

That being said .. This stack trace looks a bit terse.   Typically shiro (the security plugin) will reload but I don't see that here.  Maybe further up? 

Nathan

On Feb 20, 2016, at 6:04 PM, Shane McCoy <[hidden email]> wrote:

Hey! I made the changes but I am still getting a blank screen.

I checked catalina.out, here is the last output:

/var/log/tomcat7$ tail -f catalina.out
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [PoolCleaner[25416670:1456019437960]] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/apollo] appears to have started a thread named [Timer-0] but has failed to stop it. This is very likely to create a memory leak.
Feb 20, 2016 7:51:28 PM org.apache.catalina.loader.WebappClassLoader checkThreadLocalMapForLeaks
SEVERE: The web application [/apollo] created a ThreadLocal with key of type [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2] (value [org.codehaus.groovy.grails.web.converters.configuration.ConvertersConfigurationHolder$2@1b2e3fc]) and a value of type [java.util.HashMap] (value [{}]) but failed to remove it when the web application was stopped. Threads are going to be renewed over time to try and avoid a probable memory leak.
Feb 20, 2016 7:51:28 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Feb 20, 2016 7:51:28 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 77106 ms


Is this still a memory issue then?
I have updated tomcat memory to your doc specs already.
Thanks!
shane

On Sat, Feb 20, 2016 at 7:55 PM, Shane McCoy <[hidden email]> wrote:
Ok, that makes more sense now! thank you very much.
I'll will try with correct settings,
cheers!

On Sat, Feb 20, 2016 at 7:53 PM, Colin <[hidden email]> wrote:
Hi Shaun

>url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

Just wanted to comment on this, actually, it would not be your IP and war here. It is kind of confusing that this "setting" is called a url, because it is actually a JDBC connector string, which actually references your local database, so it would not be using the war file name or even the IP address.

For example, if your database is named "apollodb", then your "url" would be

jdbc:postgresql://localhost/apollodb

It would generally just be localhost unless you have a separate database server. I think it might be worth adding some more comments about that in our setup guide, but I hope that helps!


-Colin

On Sat, Feb 20, 2016 at 2:36 PM, Shane McCoy <[hidden email]> wrote:
Hey!
So a lot has changed in a year! I'm currently still stuck at 2g but wanted to ask about an issue i have w/ /.apollo deploy
I am getting a blank screen at the URL. I have not added any data for generation yet. I assume i would still get a webapollo ui.
I am using postgresql. I edited apollo-config.groovy
Added (in production only)
datasource.dbCreate = "update" // one of...  ( where does the database name go? I don't understand this line, it seems i'm limited to the options given?)
username: chado database username
password: chado database pw
url: jdbc:postgresql://myipaddress/apollo  (it should be the ipaddress and name of WAR correct?)

I haven't changed any other settings and going to http://myipaddress/apollo is a blank page.
I want to use this w/ a already setup postgresql chado database.

I am going off of this guide: http://webapollo.readthedocs.org/en/latest/Setup.html
Thanks!

On Thu, Feb 11, 2016 at 2:29 PM, Shane McCoy <[hidden email]> wrote:
Thanks for the quick reply!
I will see what options I can take -
Shane M.

On Thu, Feb 11, 2016 at 2:18 PM, Nathan Dunn <[hidden email]> wrote:

On Feb 11, 2016, at 11:07 AM, Shane McCoy <[hidden email]> wrote:

Hey

I am getting this error running ./apollo run-local 8085

..........
    BUILD SUCCESSFUL
    | Compiling 5 source files
    | Compiling 5 source files.....
    ***
    Metrics servlet injected into web.xml
    Metrics Admin servlet-mapping (for /metrics/*) injected into web.xml
    ***
    | Running Grails application
    Error occurred during initialization of VM
    Could not reserve enough space for object heap
    Error: Could not create the Java Virtual Machine.
    Error: A fatal exception has occurred. Program will exit.
    | Error Forked Grails VM exited with error

I’m guessing that Java is requesting more memory then you have to allocate, and so exiting.  

So, when running it with run-local (for dev purposes), it actually has preset memory, of a max of up to 2 GB, though obviously this is high.  It is in BuildConfig.groovy:

run    : [maxMemory: 2048, minMemory: 64, debug: false , maxPerm: 1024, forkReserve: false],
My guess is that your machine doesn’t have sufficient memory to run this, or there is another process. 

My suggestions would be:
1 - get a machine with at least 4 GB’s of memory, especially if you are going to host to multiple users.  This will enable better caching and performance.    
2 - if (1) is not an immediate option (or to test, or if you are just running locally) your can edit your apollo-config.groovy create a line like this, so it will use less memory:

grails.project.fork = [
// configure settings for compilation JVM, note that if you alter the Groovy version forked compilation is required
// compile: [maxMemory: 256, minMemory: 64, debug: false, maxPerm: 256, daemon:true],

test : false,
//run : false,
// configure settings for the test-app JVM, uses the daemon by default
//test: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, daemon:true],
// configure settings for the run-app JVM
run : [maxMemory: 1024, minMemory: 64, debug: false , maxPerm: 512, forkReserve: false],
// configure settings for the run-war JVM
war : [maxMemory: 1024, minMemory: 64, debug: false, maxPerm: 512, forkReserve: false],
// configure settings for the Console UI JVM
console: [maxMemory:
1024, minMemory: 64,