[InterMine Dev] Generic GFF3 source

Thomas TRIPLET thomastriplet at gmail.com
Fri Mar 1 19:42:23 GMT 2013


I did make a build-db too, I even deleted the database. Anyways, it's
working now, although I'm not exactly sure what was wrong.

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


On Fri, Mar 1, 2013 at 2:30 PM, <julie at flymine.org> wrote:

> Try running `ant build-db`, that rebuilds your database. `clean` removes
> the temporary files.
>
>
> http://intermine.readthedocs.org/en/latest/system-requirements/software/ant/#common-ant-targets
>
> Thanks for the fix! I'll update the docs.
>
> > 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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