[InterMine Dev] GeneStructureDisplayer throwing NullPointerException - any ideas?

Justin Clark-Casey justincc at intermine.org
Thu Apr 28 17:41:49 BST 2016


In GeneModelCache.getGeneModelOrganismSettings() we could check that organismName != null or "" before proceeding.  Do you think that there is a clearer 
Exception message that we could throw at this stage?

--
Justin Clark-Casey, Synbiomine/InterMine Developer
http://synbiomine.org
http://twitter.com/justincc

On 28/04/16 17:27, Sam Hokin wrote:
> 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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