GeneStructureDisplayer throwing NullPointerException - any ideas?

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GeneStructureDisplayer throwing NullPointerException - any ideas?

Sam Hokin-3
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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Re: GeneStructureDisplayer throwing NullPointerException - any ideas?

vkrishna
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 <[hidden email]> 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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Re: GeneStructureDisplayer throwing NullPointerException - any ideas?

Sam Hokin-3
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 <[hidden email] <mailto:[hidden email]>> 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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Re: GeneStructureDisplayer throwing NullPointerException - any ideas?

Justin Clark-Casey-2
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 <[hidden email] <mailto:[hidden email]>> 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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> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
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Re: GeneStructureDisplayer throwing NullPointerException - any ideas?

Sam Hokin-3
Well, a NullPointerException is pretty unclear. Yes, if you do the check and throw a RuntimeException("Organism.name is null or
empty") or something like that, it would be very helpful. Generally the IM exceptions are pretty informative; this is one case where
it wasn't at all. But I know it's hard to know in advance what folks are going to mess up. ;)

On 04/28/2016 10:41 AM, Justin Clark-Casey wrote:
> 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?
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Re: GeneStructureDisplayer throwing NullPointerException - any ideas?

Justin Clark-Casey-2
Yeah, that's what I thought :).  Just haven't done a lot of this error
message improvement yet so also wanted to see if anybody else had any
thoughts.  Otherwise, this should be a quick fix - I know how
frustrating it can be to see an error that gives you very little clue as
to what went wrong.

On 2016-04-28 19:06, Sam Hokin wrote:

> Well, a NullPointerException is pretty unclear. Yes, if you do the
> check and throw a RuntimeException("Organism.name is null or empty")
> or something like that, it would be very helpful. Generally the IM
> exceptions are pretty informative; this is one case where it wasn't at
> all. But I know it's hard to know in advance what folks are going to
> mess up. ;)
>
> On 04/28/2016 10:41 AM, Justin Clark-Casey wrote:
>> 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?
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