[InterMine Dev] Generic GFF3 source

julie at flymine.org julie at flymine.org
Fri Mar 1 19:30:22 GMT 2013


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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