[InterMine Dev] GeneStructureDisplayer throwing NullPointerException - any ideas?

Sam Hokin shokin at ncgr.org
Thu Apr 28 17:27:45 BST 2016


BOOM! Vivek for the win! That was it - thanks!!!

On 04/27/2016 04:56 PM, Krishnakumar, Vivek wrote:
> Hi Sam,
>
> Just a thought: I've seen NullPointerExceptions in the past with this displayer when the entrez-organism source was not run, i.e.
> the organism information is not populated.
>
> Could this be your issue?
>
> Thanks.
> Vivek
>
> On Wed, Apr 27, 2016, 6:53 PM Sam Hokin <shokin at ncgr.org <mailto:shokin at ncgr.org>> wrote:
>
>     Hi, devs. I've got two mines that are extremely similar, both pulling genomic data from the same chado database. In both cases the
>     objects associated with genes are populated in the same way, namely: transcripts=yes, exons=yes, CDSs=no, introns=no, UTRs=no,
>     fivePrimeUTR=no, threePrimeUTR=no. I mention these because they are what GeneStructureDisplayer replaces in the Gene report.
>
>     However, one of the mines has no error in GeneStructureDisplayer; it shows the list of transcripts and their exons as it should. In
>     the other mine, GeneStructureDisplayer throws a NullPointerException which is, to me, totally uninformative. Since the mines, and
>     webconfig-model.xml, are identical in structure, I can't figure out where to start looking.
>
>     I've attached the full stack trace when I request a Gene report page. I'd really appreciate any ideas on where to look to get the
>     GeneStructureDisplayer to work on this mine!


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