[ensembl-dev] EFG array mapping environment probe2transcript failslooking for transcript_stable_id table

Mon Jul 16 15:21:01 BST 2012

Thanks Nathan, that seemed to work however I immediately hit an issue
when I try to connect to the database to utilise the data.

The problem seems to be with getting the array adaptor - the
Funcgen::DBSQL::DBAdaptor module keeps reverting to default database
settings.  It looks like the problem occurs here:

my ( $dnadb_host, $dnadb_user, $dnadb_port, $dnadb_pass, $dnadb_assm,
$dnadb_name, $dnadb)

    = rearrange( [ 'DNADB_HOST', 'DNADB_USER',

                 'DNADB_PORT', 'DNADB_PASS',

                                  'DNADB_ASSEMBLY', 'DNADB_NAME',

                                  'DNADB'

                ],

                @args );

The @args array is populated but the rearrange method doesn't seem to
work on it.

The error occurs when I run my my scripts but I have also reproduced it
using the array_example.pl script included with the API.

From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf
Of Nathan Johnson
Sent: 11 July 2012 16:55
To: Ensembl developers list
Subject: [ensembl-dev] EFG array mapping environment probe2transcript
failslooking for transcript_stable_id table

Hi Gavin

Please be patient when using the dev list and always keep the
conversation on the list, un-invited off list contact is unacceptable
(see posting guidelines attached).

wrt the error you have found, it seems that this fix has been hanging
around in my local repository for a while and missed check in for some
reason.  I have now checked in the updated methods on the head. You can
try checking out the head code and simply copying the Helper.pm to your
v67 checkout. 

Thanks

Nathan Johnson

Senior Scientific Programmer

Ensembl Regulation

European Bioinformatics Institute

Wellcome Trust Genome Campus

Hinxton

Cambridge CB10 1SD

http://www.ensembl.info/

http://twitter.com/#!/ensembl

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On 11 Jul 2012, at 10:53, Oliver, Gavin wrote:

Hi Nathan,

Sorry to contact you directly but I am not having much luck on the
mailing list.

I am leaving Almac in a couple of weeks (off to the Mayo Clinic) and
have been asked to update our array annotations before I go.  I have not
updated the annotations/APIs etc since v60 and am now trying to update
to v67.

I have got as far as the RunTranscriptXrefs stage but then it is failing
when the Helper.pm module looks for the transcript_stable_id table which
appears to have been removed from the core schema after v64.

Are there any known issues with the current API version?

Best,

Gavin

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