malariamine failed to build

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malariamine failed to build

Victor
Hi,
I followed the instructions on getting all the prerequisites as well as setting up intermine the 0_96 release.
I was trying to build the malaria mine and got the following error.
I was able to create both malariamine and itemsmalariamine. Also able to log in with the username and password.

Something related with not being able to open the datasource. I might be missing something I'm sure.
Any ideas would be greatly appreciated.
Thanks,
Victor


BUILD FAILED
/Users/victor/intermine/intermine_0_96/imbuild/integrate.xml:54: The following error occurred while executing this line:
/Users/victor/intermine/intermine_0_96/imbuild/source.xml:330: java.lang.RuntimeException: Exception while dataloading - to allow multiple errors, set the property "dataLoader.allowMultipleErrors" to true
Problem while loading item identifier 1_2 because
can't open datasource for {platform=PostgreSQL, datasource.dataSourceName=db.common-tgt-items, datasource.maxConnections=10, datasource.databaseName=items-malariamine, datasource.class=org.postgresql.ds.PGPoolingDataSource, datasource.password=mypassword, datasource.user=postgres, datasource.serverName=localhost, driver=org.postgresql.Driver} org.postgresql.Driver PostgreSQL




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Re: malariamine failed to build

Vallejos, Andrew
RE: [InterMine Dev] malariamine failed to build

I believe this error is caused by mis-configuration in your ~/.intermine/malariamine.properties file.  Check to make sure your postgres username, password, and host are all et properly.

-Andrew 

-----Original Message-----
From: [hidden email] on behalf of Victor Ruotti
Sent: Fri 3/18/2011 4:43 PM
To: [hidden email]
Subject: [InterMine Dev] malariamine failed to build

Hi,
I followed the instructions on getting all the prerequisites as well as setting up intermine the 0_96 release.
I was trying to build the malaria mine and got the following error.
I was able to create both malariamine and itemsmalariamine. Also able to log in with the username and password.

Something related with not being able to open the datasource. I might be missing something I'm sure.
Any ideas would be greatly appreciated.
Thanks,
Victor


BUILD FAILED
/Users/victor/intermine/intermine_0_96/imbuild/integrate.xml:54: The following error occurred while executing this line:
/Users/victor/intermine/intermine_0_96/imbuild/source.xml:330: java.lang.RuntimeException: Exception while dataloading - to allow multiple errors, set the property "dataLoader.allowMultipleErrors" to true
Problem while loading item identifier 1_2 because
can't open datasource for {platform=PostgreSQL, datasource.dataSourceName=db.common-tgt-items, datasource.maxConnections=10, datasource.databaseName=items-malariamine, datasource.class=org.postgresql.ds.PGPoolingDataSource, datasource.password=mypassword, datasource.user=postgres, datasource.serverName=localhost, driver=org.postgresql.Driver} org.postgresql.Driver PostgreSQL




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Re: malariamine failed to build

Victor
Hi Andrew,
Good seeing you in the forum.
I'm able to log in with the same user name and password via the terminal to both the malariamine and the items-malariamine.
hostname is localhost for now.
wireless-181:bin victor$ psql -d malariamine
Password: 
psql (8.4.7)
Type "help" for help.

malariamine=# \q
wireless-181:bin victor$ psql -d items-malariamine
Password: 
psql (8.4.7)
Type "help" for help.

items-malariamine=# 

Victor

On Mar 18, 2011, at 4:45 PM, Vallejos, Andrew wrote:

I believe this error is caused by mis-configuration in your ~/.intermine/malariamine.properties file.  Check to make sure your postgres username, password, and host are all et properly.

-Andrew 

-----Original Message-----
From: [hidden email] on behalf of Victor Ruotti
Sent: Fri 3/18/2011 4:43 PM
To: [hidden email]
Subject: [InterMine Dev] malariamine failed to build

Hi,
I followed the instructions on getting all the prerequisites as well as setting up intermine the 0_96 release.
I was trying to build the malaria mine and got the following error.
I was able to create both malariamine and itemsmalariamine. Also able to log in with the username and password.

Something related with not being able to open the datasource. I might be missing something I'm sure.
Any ideas would be greatly appreciated.
Thanks,
Victor


BUILD FAILED
/Users/victor/intermine/intermine_0_96/imbuild/integrate.xml:54: The following error occurred while executing this line:
/Users/victor/intermine/intermine_0_96/imbuild/source.xml:330: java.lang.RuntimeException: Exception while dataloading - to allow multiple errors, set the property "dataLoader.allowMultipleErrors" to true
Problem while loading item identifier 1_2 because
can't open datasource for {platform=PostgreSQL, datasource.dataSourceName=db.common-tgt-items, datasource.maxConnections=10, datasource.databaseName=items-malariamine, datasource.class=org.postgresql.ds.PGPoolingDataSource, datasource.password=mypassword, datasource.user=postgres, datasource.serverName=localhost, driver=org.postgresql.Driver} org.postgresql.Driver PostgreSQL




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Re: malariamine failed to build

Victor
I think I got it
My connection limit was set to the to -1. Changed that to 50 and that works.
Victor
[integrate] Creating index: CREATE INDEX DataSet__key_title ON DataSet (name)
[integrate] Creating index: CREATE INDEX DataSource__key_name ON DataSource (name)
[integrate] Creating index: CREATE INDEX Gene__key_secondaryidentifier ON Gene (secondaryIdentifier)
[integrate] Creating index: CREATE INDEX Gene__key_primaryidentifier ON Gene (primaryIdentifier)
[integrate] Creating index: CREATE INDEX Ontology__key_title ON Ontology (name)
[integrate] Creating index: CREATE INDEX OntologyTerm__key_name_ontology ON OntologyTerm (name, ontologyid)
[integrate] Creating index: CREATE INDEX Organism__key_taxonid ON Organism (taxonId)
[integrate] Creating index: CREATE INDEX ProteinDomain__key_identifier ON ProteinDomain (primaryIdentifier)
[integrate] Creating index: CREATE INDEX Publication__key_pubmed ON Publication (pubMedId)
[integrate] Creating index: CREATE INDEX Synonym__key_synonym ON Synonym (subjectid, intermine_value)

do-action:

-post-action:

action:

default:

BUILD SUCCESSFUL
Total time: 1 minute 51 seconds


On Mar 18, 2011, at 5:08 PM, Victor Ruotti wrote:

Hi Andrew,
Good seeing you in the forum.
I'm able to log in with the same user name and password via the terminal to both the malariamine and the items-malariamine.
hostname is localhost for now.
wireless-181:bin victor$ psql -d malariamine
Password: 
psql (8.4.7)
Type "help" for help.

malariamine=# \q
wireless-181:bin victor$ psql -d items-malariamine
Password: 
psql (8.4.7)
Type "help" for help.

items-malariamine=# 

Victor

On Mar 18, 2011, at 4:45 PM, Vallejos, Andrew wrote:

I believe this error is caused by mis-configuration in your ~/.intermine/malariamine.properties file.  Check to make sure your postgres username, password, and host are all et properly.

-Andrew 

-----Original Message-----
From: [hidden email] on behalf of Victor Ruotti
Sent: Fri 3/18/2011 4:43 PM
To: [hidden email]
Subject: [InterMine Dev] malariamine failed to build

Hi,
I followed the instructions on getting all the prerequisites as well as setting up intermine the 0_96 release.
I was trying to build the malaria mine and got the following error.
I was able to create both malariamine and itemsmalariamine. Also able to log in with the username and password.

Something related with not being able to open the datasource. I might be missing something I'm sure.
Any ideas would be greatly appreciated.
Thanks,
Victor


BUILD FAILED
/Users/victor/intermine/intermine_0_96/imbuild/integrate.xml:54: The following error occurred while executing this line:
/Users/victor/intermine/intermine_0_96/imbuild/source.xml:330: java.lang.RuntimeException: Exception while dataloading - to allow multiple errors, set the property "dataLoader.allowMultipleErrors" to true
Problem while loading item identifier 1_2 because
can't open datasource for {platform=PostgreSQL, datasource.dataSourceName=db.common-tgt-items, datasource.maxConnections=10, datasource.databaseName=items-malariamine, datasource.class=org.postgresql.ds.PGPoolingDataSource, datasource.password=mypassword, datasource.user=postgres, datasource.serverName=localhost, driver=org.postgresql.Driver} org.postgresql.Driver PostgreSQL




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[hidden email]
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Re: malariamine failed to build

Victor
Getting closer.
I got one more error when trying to load the malaria GFF file.
Thanks in advance for any clues you may have.
Victor

 [copy] Copying /Users/victor/.intermine/malariamine.properties to /Users/victor/intermine/intermine_0_96/bio/sources/example-sources/malaria-gff/build/main/intermine.properties
     [copy] Copying 1 file to /Users/victor/intermine/intermine_0_96/bio/sources/example-sources/malaria-gff/build/main
     [copy] Copying /Users/victor/intermine/intermine_0_96/malariamine/default.intermine.integrate.properties to /Users/victor/intermine/intermine_0_96/bio/sources/example-sources/malaria-gff/build/main/default.intermine.properties
 [property] Loading /Users/victor/intermine/intermine_0_96/bio/sources/example-sources/malaria-gff/build/main/intermine.properties

-pre-init-deps:

library.-init-deps:
     [null] Exiting /Users/victor/intermine/intermine_0_96/bio/sources/example-sources/malaria-gff/build.xml.

BUILD FAILED
/Users/victor/intermine/intermine_0_96/imbuild/integrate.xml:54: The following error occurred while executing this line:
/Users/victor/intermine/intermine_0_96/imbuild/library.xml:78: Expected project bio/sources/malaria-gff/main to be located at /Users/victor/intermine/intermine_0_96/imbuild/../bio/sources/malaria-gff/main but location doesn't exist
at org.intermine.task.Dependencies.getProjectBaseDir(Dependencies.java:531)
at org.intermine.task.Dependencies.followProjectDependencies(Dependencies.java:446)
at org.intermine.task.Dependencies.iterateOverDependencies(Dependencies.java:487)

On Mar 18, 2011, at 5:28 PM, Victor Ruotti wrote:

I think I got it
My connection limit was set to the to -1. Changed that to 50 and that works.
Victor
[integrate] Creating index: CREATE INDEX DataSet__key_title ON DataSet (name)
[integrate] Creating index: CREATE INDEX DataSource__key_name ON DataSource (name)
[integrate] Creating index: CREATE INDEX Gene__key_secondaryidentifier ON Gene (secondaryIdentifier)
[integrate] Creating index: CREATE INDEX Gene__key_primaryidentifier ON Gene (primaryIdentifier)
[integrate] Creating index: CREATE INDEX Ontology__key_title ON Ontology (name)
[integrate] Creating index: CREATE INDEX OntologyTerm__key_name_ontology ON OntologyTerm (name, ontologyid)
[integrate] Creating index: CREATE INDEX Organism__key_taxonid ON Organism (taxonId)
[integrate] Creating index: CREATE INDEX ProteinDomain__key_identifier ON ProteinDomain (primaryIdentifier)
[integrate] Creating index: CREATE INDEX Publication__key_pubmed ON Publication (pubMedId)
[integrate] Creating index: CREATE INDEX Synonym__key_synonym ON Synonym (subjectid, intermine_value)

do-action:

-post-action:

action:

default:

BUILD SUCCESSFUL
Total time: 1 minute 51 seconds


On Mar 18, 2011, at 5:08 PM, Victor Ruotti wrote:

Hi Andrew,
Good seeing you in the forum.
I'm able to log in with the same user name and password via the terminal to both the malariamine and the items-malariamine.
hostname is localhost for now.
wireless-181:bin victor$ psql -d malariamine
Password: 
psql (8.4.7)
Type "help" for help.

malariamine=# \q
wireless-181:bin victor$ psql -d items-malariamine
Password: 
psql (8.4.7)
Type "help" for help.

items-malariamine=# 

Victor

On Mar 18, 2011, at 4:45 PM, Vallejos, Andrew wrote:

I believe this error is caused by mis-configuration in your ~/.intermine/malariamine.properties file.  Check to make sure your postgres username, password, and host are all et properly.

-Andrew 

-----Original Message-----
From: [hidden email] on behalf of Victor Ruotti
Sent: Fri 3/18/2011 4:43 PM
To: [hidden email]
Subject: [InterMine Dev] malariamine failed to build

Hi,
I followed the instructions on getting all the prerequisites as well as setting up intermine the 0_96 release.
I was trying to build the malaria mine and got the following error.
I was able to create both malariamine and itemsmalariamine. Also able to log in with the username and password.

Something related with not being able to open the datasource. I might be missing something I'm sure.
Any ideas would be greatly appreciated.
Thanks,
Victor


BUILD FAILED
/Users/victor/intermine/intermine_0_96/imbuild/integrate.xml:54: The following error occurred while executing this line:
/Users/victor/intermine/intermine_0_96/imbuild/source.xml:330: java.lang.RuntimeException: Exception while dataloading - to allow multiple errors, set the property "dataLoader.allowMultipleErrors" to true
Problem while loading item identifier 1_2 because
can't open datasource for {platform=PostgreSQL, datasource.dataSourceName=db.common-tgt-items, datasource.maxConnections=10, datasource.databaseName=items-malariamine, datasource.class=org.postgresql.ds.PGPoolingDataSource, datasource.password=mypassword, datasource.user=postgres, datasource.serverName=localhost, driver=org.postgresql.Driver} org.postgresql.Driver PostgreSQL




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[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev


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dev mailing list
[hidden email]
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[hidden email]
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Re: malariamine failed to build

Alex Kalderimis
In reply to this post by Victor
It may just be a typo, but the database name you have in the description does not match that in the stack-trace (they differ by a hyphen)

-----
sent from my phone - please excuse any brevity

----- Reply message -----
From: "Victor Ruotti" <[hidden email]>
To: <[hidden email]>
Subject: [InterMine Dev] malariamine failed to build
Date: Fri, Mar 18, 2011 21:43


Hi,
I followed the instructions on getting all the prerequisites as well as setting up intermine the 0_96 release.
I was trying to build the malaria mine and got the following error.
I was able to create both malariamine and itemsmalariamine. Also able to log in with the username and password.

Something related with not being able to open the datasource. I might be missing something I'm sure.
Any ideas would be greatly appreciated.
Thanks,
Victor


BUILD FAILED
/Users/victor/intermine/intermine_0_96/imbuild/integrate.xml:54: The following error occurred while executing this line:
/Users/victor/intermine/intermine_0_96/imbuild/source.xml:330: java.lang.RuntimeException: Exception while dataloading - to allow multiple errors, set the property "dataLoader.allowMultipleErrors" to true
Problem while loading item identifier 1_2 because
can't open datasource for {platform=PostgreSQL, datasource.dataSourceName=db.common-tgt-items, datasource.maxConnections=10, datasource.databaseName=items-malariamine, datasource.class=org.postgresql.ds.PGPoolingDataSource, datasource.password=mypassword, datasource.user=postgres, datasource.serverName=localhost, driver=org.postgresql.Driver} org.postgresql.Driver PostgreSQL




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dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev