Deployment issue

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Deployment issue

Ewald Grosse-Wilde
Hello,

I am trying to deploy an instance of Apollo 2.4.1 in Ubuntu 18.04, and keep running into an issue. I feel like I am missing something really simple, but for the life of me I can't figure out what I am doing wrong.

I essentially followed the guide here (https://genomearchitect.readthedocs.io/en/latest/Setup.html). To make sure I do not run into problems, I ascertained that only one JDK/JRE is installed (java 8), and set all memory options. When I run apollo as "run local" everything is fine and running (I tested creating the admin, and uploaded a fasta file for a new organism successfully). I tried to deploy, either with mysql or postgresql as a database. For each I adjusted the groovy file as needed, and made sure to create the needed user, and that user names, database names, and passwords in the groovy file match.
match the actual database. I also made sure to copy the groovy file to apollo-config.groovy. I ran "apollo deploy", then copied the WAR file to /var/lib/tomcat8/webapps/apollo.war. I also made sure that the war file is owned by the tomcat8 user. Then I restarted the tomcat8 service. I cannot access the apollo instance, though tomcat8 itself is accessible; looking at the tomcat8 Web Application Manager the apollo app is present and recognized, but not deployed; manual deployment in the manager also fails, with "FAIL - Application at context path [/apollo] could not be started". Looking at the catalina.out I think I might have a database connection issue. 
I have tried multiple times to redo users/databases (dropping/deleting old databases manually beforehand) and even tried using other than the default names (since some page I found claims that hyphenated database names like "apollo-production" can be a problem in Postgresql). So, it is obvious I am missing something. I redid the whole process (after using "apollo clean all") multiple times, and even once started from scratch, deleting all installed dependencies and redoing them. 

All of this means I am likely making a very stupid, basic mistake somewhere. I have attached the catalina.out and the localhost.<>.log from tomcat.

I hope anyone here can help me, thank you in advance!

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catalina.out (27K) Download Attachment
localhost.2019-10-07.log (7K) Download Attachment
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Re: Deployment issue

nathandunn

Thanks for the detailed report.  

One of our amazing users just found and solved this error by setting JAVA_HOME in /etc/default/tomcat8:


I tried to update the doc to reflect the change:


Please feel free to edit the doc to further clarify this if you think it would be helpful.  I can fix any formatting issues.


You should be able to find the appropriate Java version by building with a  `ps -ef` when running ./apollo run-local | grep java ` and then do one when running tomcat?   Sometimes the difference in environments is problematic.

Cheers,

Nathan


On Oct 7, 2019, at 5:59 AM, Ewald Grosse-Wilde <[hidden email]> wrote:

Hello,

I am trying to deploy an instance of Apollo 2.4.1 in Ubuntu 18.04, and keep running into an issue. I feel like I am missing something really simple, but for the life of me I can't figure out what I am doing wrong.

I essentially followed the guide here (https://genomearchitect.readthedocs.io/en/latest/Setup.html). To make sure I do not run into problems, I ascertained that only one JDK/JRE is installed (java 8), and set all memory options. When I run apollo as "run local" everything is fine and running (I tested creating the admin, and uploaded a fasta file for a new organism successfully). I tried to deploy, either with mysql or postgresql as a database. For each I adjusted the groovy file as needed, and made sure to create the needed user, and that user names, database names, and passwords in the groovy file match.
match the actual database. I also made sure to copy the groovy file to apollo-config.groovy. I ran "apollo deploy", then copied the WAR file to /var/lib/tomcat8/webapps/apollo.war. I also made sure that the war file is owned by the tomcat8 user. Then I restarted the tomcat8 service. I cannot access the apollo instance, though tomcat8 itself is accessible; looking at the tomcat8 Web Application Manager the apollo app is present and recognized, but not deployed; manual deployment in the manager also fails, with "FAIL - Application at context path [/apollo] could not be started". Looking at the catalina.out I think I might have a database connection issue. 
I have tried multiple times to redo users/databases (dropping/deleting old databases manually beforehand) and even tried using other than the default names (since some page I found claims that hyphenated database names like "apollo-production" can be a problem in Postgresql). So, it is obvious I am missing something. I redid the whole process (after using "apollo clean all") multiple times, and even once started from scratch, deleting all installed dependencies and redoing them. 

All of this means I am likely making a very stupid, basic mistake somewhere. I have attached the catalina.out and the localhost.<>.log from tomcat.

I hope anyone here can help me, thank you in advance!

<catalina.out><localhost.2019-10-07.log>

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Re: Deployment issue

Ewald Grosse-Wilde

Dear Nathan,


thanks a lot for the very quick help, now everything is working! I had somehow missed that passage in the doc, though it is clear as can be.


Sorry for producing work for you, and again thanks for the help!

Ewald



I will take a look at the doc in a

On 10/7/19 6:16 PM, Nathan Dunn wrote:

Thanks for the detailed report.  

One of our amazing users just found and solved this error by setting JAVA_HOME in /etc/default/tomcat8:


I tried to update the doc to reflect the change:


Please feel free to edit the doc to further clarify this if you think it would be helpful.  I can fix any formatting issues.


You should be able to find the appropriate Java version by building with a  `ps -ef` when running ./apollo run-local | grep java ` and then do one when running tomcat?   Sometimes the difference in environments is problematic.

Cheers,

Nathan


On Oct 7, 2019, at 5:59 AM, Ewald Grosse-Wilde <[hidden email]> wrote:

Hello,

I am trying to deploy an instance of Apollo 2.4.1 in Ubuntu 18.04, and keep running into an issue. I feel like I am missing something really simple, but for the life of me I can't figure out what I am doing wrong.

I essentially followed the guide here (https://genomearchitect.readthedocs.io/en/latest/Setup.html). To make sure I do not run into problems, I ascertained that only one JDK/JRE is installed (java 8), and set all memory options. When I run apollo as "run local" everything is fine and running (I tested creating the admin, and uploaded a fasta file for a new organism successfully). I tried to deploy, either with mysql or postgresql as a database. For each I adjusted the groovy file as needed, and made sure to create the needed user, and that user names, database names, and passwords in the groovy file match.
match the actual database. I also made sure to copy the groovy file to apollo-config.groovy. I ran "apollo deploy", then copied the WAR file to /var/lib/tomcat8/webapps/apollo.war. I also made sure that the war file is owned by the tomcat8 user. Then I restarted the tomcat8 service. I cannot access the apollo instance, though tomcat8 itself is accessible; looking at the tomcat8 Web Application Manager the apollo app is present and recognized, but not deployed; manual deployment in the manager also fails, with "FAIL - Application at context path [/apollo] could not be started". Looking at the catalina.out I think I might have a database connection issue. 
I have tried multiple times to redo users/databases (dropping/deleting old databases manually beforehand) and even tried using other than the default names (since some page I found claims that hyphenated database names like "apollo-production" can be a problem in Postgresql). So, it is obvious I am missing something. I redid the whole process (after using "apollo clean all") multiple times, and even once started from scratch, deleting all installed dependencies and redoing them. 

All of this means I am likely making a very stupid, basic mistake somewhere. I have attached the catalina.out and the localhost.<>.log from tomcat.

I hope anyone here can help me, thank you in advance!

<catalina.out><localhost.2019-10-07.log>

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Re: Deployment issue

nathandunn
Not a problem at all.  There is just a lot of doc in there.

Glad everything worked.  Happy annotating.

Nathan

On Oct 8, 2019, at 12:18 AM, Ewald Grosse-Wilde <[hidden email]> wrote:

Dear Nathan,


thanks a lot for the very quick help, now everything is working! I had somehow missed that passage in the doc, though it is clear as can be.


Sorry for producing work for you, and again thanks for the help!

Ewald



I will take a look at the doc in a

On 10/7/19 6:16 PM, Nathan Dunn wrote:

Thanks for the detailed report.  

One of our amazing users just found and solved this error by setting JAVA_HOME in /etc/default/tomcat8:


I tried to update the doc to reflect the change:


Please feel free to edit the doc to further clarify this if you think it would be helpful.  I can fix any formatting issues.


You should be able to find the appropriate Java version by building with a  `ps -ef` when running ./apollo run-local | grep java ` and then do one when running tomcat?   Sometimes the difference in environments is problematic.

Cheers,

Nathan


On Oct 7, 2019, at 5:59 AM, Ewald Grosse-Wilde <[hidden email]> wrote:

Hello,

I am trying to deploy an instance of Apollo 2.4.1 in Ubuntu 18.04, and keep running into an issue. I feel like I am missing something really simple, but for the life of me I can't figure out what I am doing wrong.

I essentially followed the guide here (https://genomearchitect.readthedocs.io/en/latest/Setup.html). To make sure I do not run into problems, I ascertained that only one JDK/JRE is installed (java 8), and set all memory options. When I run apollo as "run local" everything is fine and running (I tested creating the admin, and uploaded a fasta file for a new organism successfully). I tried to deploy, either with mysql or postgresql as a database. For each I adjusted the groovy file as needed, and made sure to create the needed user, and that user names, database names, and passwords in the groovy file match.
match the actual database. I also made sure to copy the groovy file to apollo-config.groovy. I ran "apollo deploy", then copied the WAR file to /var/lib/tomcat8/webapps/apollo.war. I also made sure that the war file is owned by the tomcat8 user. Then I restarted the tomcat8 service. I cannot access the apollo instance, though tomcat8 itself is accessible; looking at the tomcat8 Web Application Manager the apollo app is present and recognized, but not deployed; manual deployment in the manager also fails, with "FAIL - Application at context path [/apollo] could not be started". Looking at the catalina.out I think I might have a database connection issue. 
I have tried multiple times to redo users/databases (dropping/deleting old databases manually beforehand) and even tried using other than the default names (since some page I found claims that hyphenated database names like "apollo-production" can be a problem in Postgresql). So, it is obvious I am missing something. I redid the whole process (after using "apollo clean all") multiple times, and even once started from scratch, deleting all installed dependencies and redoing them. 

All of this means I am likely making a very stupid, basic mistake somewhere. I have attached the catalina.out and the localhost.<>.log from tomcat.

I hope anyone here can help me, thank you in advance!

<catalina.out><localhost.2019-10-07.log>

--
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].