TBro can not be installed into chado 1.31 dump

[iimog]

A new dump of an initial chado database version 1.31 has been created (in the update_chado_dump_1.31 branch). However TBro is not able to install into this schema

phing database-initialize -debug

reveals the following error:

     [exec] PHP Fatal error:  Uncaught exception 'PDOException' with message 'SQLSTATE[23502]: Not null violation: 7 ERROR:  null value in column "cv_id" violates not-null constraint
     [exec] DETAIL:  Failing row contains (48298, null, expected_count, null, 106130, 0, 0).' in /tmp/build/tbro/database/cvterms/setup-cvterms.php:169
     [exec] Stack trace:
     [exec] #0 /tmp/build/tbro/database/cvterms/setup-cvterms.php(169): PDOStatement->execute()
     [exec] #1 {main}
     [exec]   thrown in /tmp/build/tbro/database/cvterms/setup-cvterms.php on line 169

This is due to the fact that the CV "Statistical Terms" is missing in the dump. This might be a problem with the chado installation, the used ontologies or TBro. In any case it would be possible for TBro to check for required CVs and create them if they do not already exist.

[fbemm]

Chado introduced quite some changes. Scott Cain presented them at PAG.
Guess we need to check how much they influence TBro.

On 21.04.2016 11:36, Markus Ankenbrand wrote:

A new dump of an initial chado database version 1.31 has been created
(in the update_chado_dump_1.31 branch). However TBro is not able to
install into this schema

|phing database-initialize -debug |

reveals the following error:

|[exec] PHP Fatal error: Uncaught exception 'PDOException' with message
'SQLSTATE[23502]: Not null violation: 7 ERROR: null value in column
"cv_id" violates not-null constraint [exec] DETAIL: Failing row contains
(48298, null, expected_count, null, 106130, 0, 0).' in
/tmp/build/tbro/database/cvterms/setup-cvterms.php:169 [exec] Stack
trace: [exec] #0
/tmp/build/tbro/database/cvterms/setup-cvterms.php(169):
PDOStatement->execute() [exec] #1 {main} [exec] thrown in
/tmp/build/tbro/database/cvterms/setup-cvterms.php on line 169 |

This is due to the fact that the CV "Statistical Terms" is missing in
the dump. This might be a problem with the chado installation, the used
ontologies or TBro. In any case it would be possible for TBro to check
for required CVs and create them if they do not already exist.

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#14

Max Planck Institute for Developmental Biology
Department Weigel - Genome Informatics
Spemannstraße 35, 72076 Tübingen, Germany
Tel +49 7071 6011417, Fax +49 7071 6011412

[greatfireball]

Seems so... @fbemm: Do you know, if there is an overview of changes available?

[greatfireball]

I was on the wrong branch... Looks like https://github.com/GMOD/Chado/blob/1.31/chado/Changes contains some information.

[fbemm]

PDF is attached. Let's see if that works.

On 21.04.2016 11:41, Frank Förster wrote:

Seems so... @fbemm https://github.com/fbemm: Do you know, if there is
an overview of changes available?

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#14 (comment)

Max Planck Institute for Developmental Biology
Department Weigel - Genome Informatics
Spemannstraße 35, 72076 Tübingen, Germany
Tel +49 7071 6011417, Fax +49 7071 6011412

[greatfireball]

Significantly shrunk the amount of data in the "initialize" script to
remove several types of data: all organisms but human, arraydesign data,
statistical terms in cvterm, and the analysis entries.

from the above mentioned https://github.com/GMOD/Chado/blob/1.31/chado/Changes

[greatfireball]

@fbemm PDF/attachment is not shown