[InterMine Dev] malariamine failed to build

Victor Ruotti ruotti at wisc.edu
Fri Mar 18 23:05:17 GMT 2011


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: dev-bounces at intermine.org on behalf of Victor Ruotti
>>> Sent: Fri 3/18/2011 4:43 PM
>>> To: dev at intermine.org
>>> 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
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> dev mailing list
>>> dev at intermine.org
>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>> 
>>> 
>> 
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