[GUSDEV] LoadTaxon: null value in "taxon_id" violates not-null constraint

[Fernan A. <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