[InterMine Dev] Generic GFF3 source

Thomas TRIPLET thomastriplet at gmail.com
Fri Mar 1 19:18:55 GMT 2013


For some reason, the folder resources wasn't created along with other
folders when creating the new gff source. I created the folder manually,
but I am getting another error message now:

/home/intermine/imbuild/integrate.xml:54: The following error occurred
while executing this line:
/home/intermine/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 0_1 because
There is already an equivalent in the database from this source (<Source:
name="aniger-gff", type="csfg-aniger-gff", skeleton=false>) from a
*previous* run; object from source in this run: "Organism
[commonName="null", genus="null", id="1", name="null", shortName="null",
species="null", taxonId="5061"]", object from database: "Organism
[commonName="null", genus="null", id="9000000", name="null",
shortName="null", species="null", taxonId="5061"]"; noticed problem while
merging field "shortName" originally read from source: <Source:
name="aniger-gff", type="csfg-aniger-gff", skeleton=false>
 at
org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:164)
at
org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:60)
 at
org.intermine.dataloader.ObjectStoreDataLoaderTask.execute(ObjectStoreDataLoaderTask.java:128)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
 [...]


This is weird, as I made a "clean" before, so there's no previous run.


By the way, the following (form the doc) does not work:
<property name="src.data.dir" location="/DATA/*.gff3"/>

You have to write:
<property name="src.data.dir" location="/DATA/"/>
<property name="src.data.dir.includes" location="*.gff3"/>

--
Thomas Triplet, Jr. Eng., Ph.D.
http://www.thomastriplet.net


On Fri, Mar 1, 2013 at 12:22 PM, <julie at flymine.org> wrote:

> So this path does exist:
>
> /home/intermine/bio/sources/csfg-aniger-gff/main/resources
>
> > Hi,
> > I've created a custom GFF source for a previous version of my project,
> but
> > I'd like to use the generic GFF3 source for InterMine v1.2, but I'm
> > getting
> > the following error message:
> >
> > integrate:
> > [integrate] action:
> >
> > BUILD FAILED
> > /home/intermine/imbuild/integrate.xml:54: Error in project.xml: Can't
> find
> > directories for sources: 'gff3',  looked in:
> >
> >
> /home/intermine/bio/sources/example-sources/malaria-gff/main/src/org/intermine/bio
> > [...]
> >
> > It seems that there's no GFF3 source. And the documentation is a bit
> > inconsistent on that matter: it says at first that you need to create a
> > specific data source, then it says it's optional.
> >
> > Same on the page to create the GFF data source: it says that just
> creating
> > the data source will work as is, but I get the following error message
> > (ran
> > build after creating the source and updating project.xml):
> >
> > BUILD FAILED
> > /home/intermine/imbuild/integrate.xml:54: The following error occurred
> > while executing this line:
> > /home/intermine/imbuild/library.xml:78: The following error occurred
> while
> > executing this line:
> > /home/intermine/imbuild/library.xml:141:
> > /home/intermine/bio/sources/csfg-aniger-gff/main/resources does not
> exist.
> >  at
> >
> org.apache.tools.ant.types.AbstractFileSet.getDirectoryScanner(AbstractFileSet.java:483)
> > at org.apache.tools.ant.taskdefs.Zip.grabResources(Zip.java:1547)
> >  at org.apache.tools.ant.taskdefs.Zip.getResourcesToAdd(Zip.java:1286)
> > at org.apache.tools.ant.taskdefs.Zip.getResourcesToAdd(Zip.java:1220)
> >
> > So is there a generic GFF source, or should I implement a custom one?
> >
> > Thanks!
> > Thomas
> >
> > --
> > Thomas Triplet, Jr. Eng., Ph.D.
> > http://www.thomastriplet.net
> > _______________________________________________
> > dev mailing list
> > dev at intermine.org
> > http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
> >
>
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