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Re: [GUSDEV] LoadTaxon: null value in "taxon_id" violates not-null constraint
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From: <pi...@pc...> - 2006-04-23 14:21:49
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Are you running this without commit on? We did have a problem that the
taxon_ids
were loaded in a separate transaction and so the taxon_ids were not available
for the taxonname insertions when the plugin was run with commit off. I
thought
this was fixed but perhaps the fix was bogus (either didn't work or is a
figment of my imagination) or you don't have the most up to date version.
Can you try running it with commit on?
Deborah
Quoting Fernan Aguero <fe...@ii...>:
> Hi,
>
> I've came across this error while trying to load the ncbi
> taxonomy dumps using LoadTaxon. Any idea if this is due to a
> bad input file or a software bug?
>
> This is a fresh db instance, and this was the first run
> (non-commit mode). Seems like taxon_id is clearly empty for
> ncbi_tax_id=127219
>
> Thanks in advance for any suggestion,
>
> Fernan
>
> LoadTaxon (supported) plugin rev: 4488
> GUS 3.5.1 (SVN snapshot of 11.Apr.2006)
> PostgreSQL 8.1.3 (FreeBSD, i386)
> NCBI taxonomy files from 17.Apr.2006
>
>
> [fernan@omega] ga GUS::Supported::Plugin::LoadTaxon --names names.dmp \
> --nodes nodes.dmp --gencode gencode.dmp --merged merged.dmp --verbose \
> --debug --sqlVerbose
>
>
> Merging taxons: OK
> Updating and inserting SRes.GeneticCode: OK
> Process ncbi_tax_id: OK
> Fails at the first ocurrence of 'Inserting and updating TaxonName'
>
> [ ..... ]
>
> sqlExec:
> INSERT INTO SRes.Taxon ( group_write, other_read, group_read,
> taxon_id, ncbi_tax_id, user_read, genetic_code_id, row_user_id,
> modification_date, other_write, row_project_id,
> row_alg_invocation_id, row_group_id, mitochondrial_genetic_code_id,
> rank, user_write )
> VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ?, ?, ? )
> bindValues (1, 1, 1, 607974, 188885, 1, 20, 1, 0, 1, 6, 1, 19, no rank, 1)
> DbiHandle:sqlExec:insert succeeded 1 row(s)
> Fri Apr 21 21:32:40 2006 Processed ncbi_tax_id : 188885
>
> Fri Apr 21 21:32:40 2006 Inserting and updating TaxonName
>
>
> prepareAndExecute: select t.taxon_id from sres.taxon t where
> t.ncbi_tax_id = 127219
> allNonNullsSet: taxon_name_id not set... = ''
> GUS::Model::SRes::TaxonName->retrieveFromDB($doNotRetrieveAtts=,)
>
> RetrieveFromDB: select * from SRes.TaxonName where
> unique_name_variant is NULL and name_class = ? and name = ? and
> taxon_id is NULL
> bindValues (scientific name, Tellervini)
> Submitting GUS::Model::SRes::TaxonName:
> Table: TaxonName
> unique_name_variant: []
> name_class: [scientific name]
> name: [Tellervini]
> taxon_id: []
>
> HasChangedAttributes='0'
> Setting all foreign keys
> GUS::Model::SRes::TaxonName->Submit: All foreign keys are set...proceeding
> allNonNullsSet: taxon_name_id not set... = ''
> Inserting:
> Table: TaxonName
> unique_name_variant: []
> group_write: [1]
> other_read: [1]
> group_read: [1]
> name: [Tellervini]
> taxon_id: []
> user_read: [1]
> row_user_id: [1]
> modification_date: [now()]
> name_class: [scientific name]
> other_write: [0]
> row_alg_invocation_id: [6]
> row_project_id: [1]
> row_group_id: [1]
> user_write: [1]
>
>
> sqlExec:
> INSERT INTO SRes.TaxonName ( unique_name_variant, group_write,
> other_read, group_read, name, taxon_id, user_read, row_user_id,
> modification_date, name_class, other_write, row_alg_invocation_id,
> row_project_id, taxon_name_id, row_group_id, user_write )
> VALUES ( null, ?, ?, ?, ?, null, ?, ?, now(), ?, ?, ?, ?, ?, ?, ? )
> bindValues (1, 1, 1, Tellervini, 1, 1, scientific name, 0, 6, 1, 2, 1, 1)
> DBD::Pg::st execute failed: ERROR: null value in column "taxon_id"
> violates not-null constraint
> Submitting GUS::Model::Core::AlgorithmInvocation:
> Table: AlgorithmInvocation
> group_read: [1]
> comment_string: []
> user_read: [1]
> algorithm_implementation_id: [5]
> other_write: [0]
> end_time: [now()]
> modification_date: [now()]
> cpu_time: [0]
> row_group_id: [1]
> user_write: [1]
> other_read: [1]
> cpus_used: [1]
> group_write: [1]
> start_time: [now()]
> row_user_id: [1]
> row_alg_invocation_id: [1]
> row_project_id: [1]
> algorithm_invocation_id: [6]
> result: [pending]
>
> HasChangedAttributes='1'
> Setting all foreign keys
> GUS::Model::Core::AlgorithmInvocation->Submit: All foreign keys are
> set...proceeding
> Updating GUS::Model::Core::AlgorithmInvocation=HASH(0x86bcc54)
> Am updateable and have changed atts
> Table: AlgorithmInvocation
> group_read: [1]
> comment_string: []
> user_read: [1]
> algorithm_implementation_id: [5]
> other_write: [0]
> end_time: [now()]
> modification_date: [now()]
> cpu_time: [0]
> row_group_id: [1]
> user_write: [1]
> other_read: [1]
> cpus_used: [1]
> group_write: [1]
> start_time: [now()]
> row_user_id: [1]
> row_alg_invocation_id: [6]
> row_project_id: [1]
> algorithm_invocation_id: [6]
> result: [pending]
>
>
> sqlExec:
> UPDATE Core.AlgorithmInvocation
> SET
> modification_date = ?,
> end_time = ?,
> row_alg_invocation_id = ?
> WHERE algorithm_invocation_id = ?
> bindValues (now(), now(), 6, 6)
> DbiHandle:sqlExec:insert succeeded 1 row(s)
>
> ERROR:
>
> SQL ERROR!! involving
>
> INSERT INTO SRes.TaxonName ( unique_name_variant, group_write,
> other_read, group_read, name, taxon_id, user_read, row_user_id,
> modification_date, name_class, other_write, row_alg_invocation_id,
> row_project_id, taxon_name_id, row_group_id, user_write )
> VALUES ( null, ?, ?, ?, ?, null, ?, ?, now(), ?, ?, ?, ?, ?, ?, ? )
> Values: 1, 1, 1, Tellervini, 1, 1, scientific name, 0, 6, 1, 2, 1, 1
> at
> /scratch/shared/GUS-11.Apr.2006/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
> line 166
> GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x8627670)', '\x{a} SQL ERROR!! involving\x{a} \x{a} INSERT INTO SRes.TaxonName ( u...') called at /scratch/shared/GUS-11.Apr.2006/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line
> 150
>
>
>
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