[InterMine Dev] setting up chado (tripal) intermine

Krishnakumar, Vivek vKrishna at jcvi.org
Tue Dec 2 18:01:08 GMT 2014


Hi Sofia,

Another issue you will encounter when loading from a Tripal-based Chado database is that the Chado specific tables are not in the postgres default “public” schema of the database. Instead, Tripal puts it in a postgres schema named “chado".

To workaround this, you would need to alter your Chado processor to run the query “ALTER DATABASE <dbname> SET search_path TO chado, public” first, before running any SELECT statements.

Hope this helps!
Vivek

> On Dec 2, 2014, at 12:37 PM, Julie Sullivan <julie at flymine.org> wrote:
> 
> Hi Sofia!
> 
> All your files look fine to me. This line from the tutorial:
> 
> 	(cd ../dbmodel && ant build-db -v); ant -Dsource=chado-db -v
> 
> Assumes that your source is called chado-db. You have named your source 
> in your project XML "drupal".
> 
> So try this instead:
> 
> 	(cd ../dbmodel && ant build-db -v); ant -Dsource=drupal -v
> 
> Julie
> 
> ----
> 
> Hello.
> 
> I am having issues trying to set up my intermine from a chado database
> (actually a chado database within a tripal database).
> 
> I am following the steps in
> http://intermine.readthedocs.org/en/latest/database/data-sources/library/chado/#index-0
> but
> feel as if I must be missing something.
> 
> ERROR:
> 
> BUILD FAILED
> /data/src/intermine/imbuild/integrate.xml:54: can't find source in project
> definition file: chado-db
> 
> my ~/.intermine/simrmine.properties:
> db.flybase.datasource.class=org.postgresql.ds.PGPoolingDataSource
> db.flybase.datasource.dataSourceName=db.flybase
> db.flybase.datasource.serverName=localhost
> db.flybase.datasource.port=5432
> db.flybase.datasource.databaseName=drupal
> db.flybase.datasource.user=xxxx
> db.flybase.datasource.password=xxxx
> db.flybase.datasource.maxCommections=10
> db.flybase.datasource.driver=org.postgresql.Driver
> db.flybase.datasource.platform=PostgreSql
> 
> my project.xml:
> <source name="drupal" type="chado-db" dump="true">
>   <property name="source.db.name" value="flybase"/>
>   <property name="genus" value="Schmidtea"/>
>   <property name="species" value="mediterranea"/>
>   <property name="dataSourceName" value="Flybase"/>
>   <property name="dataSetTitle" value="SmedSxl_v31 data set"/>
>   <property name="converter.class"
> value="org.intermine.bio.dataconversion.ChadoDBConverter"/>
>   <property name="processors"
> value="org.intermine.bio.dataconversion.SequenceProcessor"/>
> </source>
> 
> Thanks,
> Sofia
> 
> _______________________________________________
> dev mailing list
> dev at intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev



More information about the dev mailing list