[ensembl-dev] api v60 to v62

Jan Vogel jan.vogel at gmail.com
Fri Jul 8 03:29:38 BST 2011


Hi Stef & Graham, 

did you manage to solve this issue ? I'm running in the same trouble here with e62 and e63 checkouts.

Jan 

On Jun 24, 2011, at 7:23 AM, mailsvl at fastmail.fm wrote:

> Hi everyone,
> 
> We have a script based on ensembl api v60 (where it works without
> errors) and it almost runs flawless with v62 as well except for one
> error:
> 
> Can't call method "display_term" on an undefined value at
> /data/common_modules/ensembl62/ensembl-variation/modules/Bio/EnsEMBL/Variation/VariationFeatureOverlap.pm
> line 530.
> 
> If I remove this call/line everything runs fine:
> 
> $consequence = $transcript_variation->display_consequence if defined
> $transcript_variation->display_consequence;
> 
> ...but then I'm left without the consequences so thats not really an
> option ;) Anyone knows what change from v60 to v62 makes this method now
> run into problems?
> 
> Thanks!
> Stef
> __________________
> http://www.fastmail.fm
> 
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

On Jun 24, 2011, at 8:31 AM, Graham Ritchie wrote:

> Hi Stef,
> 
> This part of the variation API changed quite a lot under the hood for v62, and we did try to maintain the same interface, but you may have found somewhere where the interface has changed. If you could send me a copy of the script, or even just a minimal script that exhibits the same bug, I will be able to try to establish the problem much more quickly.
> 
> Cheers,
> 
> Graham
> 
> 
> On 24 Jun 2011, at 15:23, mailsvl at fastmail.fm wrote:
> 
>> Hi everyone,
>> 
>> We have a script based on ensembl api v60 (where it works without
>> errors) and it almost runs flawless with v62 as well except for one
>> error:
>> 
>> Can't call method "display_term" on an undefined value at
>> /data/common_modules/ensembl62/ensembl-variation/modules/Bio/EnsEMBL/Variation/VariationFeatureOverlap.pm
>> line 530.
>> 
>> If I remove this call/line everything runs fine:
>> 
>> $consequence = $transcript_variation->display_consequence if defined
>> $transcript_variation->display_consequence;
>> 
>> ...but then I'm left without the consequences so thats not really an
>> option ;) Anyone knows what change from v60 to v62 makes this method now
>> run into problems?
>> 
>> Thanks!
>> Stef
>> __________________
>> http://www.fastmail.fm
>> 
>> 
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
> 
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

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