Hi Everybody,
I’m trying to install Chado following the instructions in the ‘Chado from SVN’ section of the Getting Started page. I have everything working successfully until the make ontologies step. I can successfully use the make ontologies command to install the Relationship Ontology and the Sequence Ontology but am unable to successfully load the Gene Ontology.
It appears that the loading process is trying to insert a row into the cvterm table without values for several fields that are required to be “not null”.
After a long and winding road, the problem seems to be caused by this portion:
property_value: IAO:0000589 "cell and encapsulating structures" xsd:string
of the entry for the GO term GO:0005623 in the go.obo file. [Is IAO the “Information Artifact Ontology?] Is it possible that go.obo needs to provide should some additional information about the IAO, e.g. a ‘name’ and ‘definition’?
What can I do to help make this work?
Thanks,
g.
Here are the details:
When you run make ontologies and select ontologies “1,2,3,4” (for example), this occurs:
fetching files for Relationship Ontology
+http://www.obofoundry.org/ro/ro.obo
updated
loading...done!
fetching files for Sequence Ontology
+http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
updated
loading...done!
fetching files for Gene Ontology
+http://www.geneontology.org/ontology/gene_ontology.obo
updated
loading...System call 'stag-storenode.pl -d 'dbi:Pg:dbname=gmod;host=localhost;port=5432' --user gmod --password 'secret' tmp/go/go.oboxml' failed: 256
FATAL: all hosts have already failed -- aborting
If one digs down a bit into what’s happening, one discovers (beyond how annoying the use of “one” as a third person pronoun is…) that the process is dying within stag-storenode.pl, illustrated here:
gmod@precise32:~/src/gmod-schema-chado$ stag-storenode.pl -d 'dbi:Pg:dbname=gmod;host=localhost;port=5432' --user gmod --password 'secret' tmp/go/go.oboxml
DBD::Pg::st execute failed: ERROR: null value in column "cv_id" violates not-null constraint
DETAIL: Failing row contains (2268, null, null, null, 3088, 0, 0). [for Statement "INSERT INTO cvterm (dbxref_id) VALUES (?)" with ParamValues: 1='3088'] at /usr/local/gmod/lib/perl5/DBIx/DBStag.pm line 3322.
DBD::Pg::st execute failed: ERROR: null value in column "cv_id" violates not-null constraint
DETAIL: Failing row contains (2268, null, null, null, 3088, 0, 0). [for Statement "INSERT INTO cvterm (dbxref_id) VALUES (?)" with ParamValues: 1='3088'] at /usr/local/gmod/lib/perl5/DBIx/DBStag.pm line 3322.
at /usr/local/gmod/lib/perl5/DBIx/DBStag.pm line 3332
DBIx::DBStag::insertrow('DBIx::DBStag=HASH(0x8f839a4)', 'cvterm', 'HASH(0x9493148)', 'cvterm_id') called at /usr/local/gmod/lib/perl5/DBIx/DBStag.pm line 1928
DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x8f839a4)', 'Data::Stag::StagImpl=ARRAY(0x9918b78)') called at /usr/local/gmod/lib/perl5/DBIx/DBStag.pm line 1180
DBIx::DBStag::storenode('DBIx::DBStag=HASH(0x8f839a4)', 'Data::Stag::StagImpl=ARRAY(0x993a4f0)') called at /usr/local/gmod/bin/stag-storenode.pl line 88
eval {...} called at /usr/local/gmod/bin/stag-storenode.pl line 87
main::store('Data::Stag::BaseHandler=HASH(0x961c6a4)', 'Data::Stag::StagImpl=ARRAY(0x993a4f0)') called at /usr/local/gmod/bin/stag-storenode.pl line 137
main::__ANON__('Data::Stag::BaseHandler=HASH(0x961c6a4)', 'Data::Stag::StagImpl=ARRAY(0x993a4f0)') called at /usr/local/gmod/lib/perl5/Data/Stag/BaseHandler.pm line 594
Data::Stag::BaseHandler::end_event('Data::Stag::BaseHandler=HASH(0x961c6a4)', 'cvterm') called at /usr/local/gmod/lib/perl5/Data/Stag/BaseHandler.pm line 742
Data::Stag::BaseHandler::end_element('Data::Stag::BaseHandler=HASH(0x961c6a4)', 'HASH(0x980d2a8)') called at /usr/local/gmod/lib/perl5/XML/Parser/PerlSAX.pm line 239
XML::Parser::PerlSAX::_handle_end('XML::Parser::PerlSAX=HASH(0x974ce40)', 'XML::Parser::Expat=HASH(0x96edf24)', 'cvterm') called at /usr/local/gmod/lib/perl5/XML/Parser/PerlSAX.pm line 79
XML::Parser::PerlSAX::__ANON__('XML::Parser::Expat=HASH(0x96edf24)', 'cvterm') called at /usr/local/gmod/lib/perl5/i686-linux-gnu-thread-multi-64int/XML/Parser/Expat.pm line 470
XML::Parser::Expat::parse('XML::Parser::Expat=HASH(0x96edf24)', 'FileHandle=GLOB(0x9777a34)') called at /usr/local/gmod/lib/perl5/i686-linux-gnu-thread-multi-64int/XML/Parser.pm line 187
eval {...} called at /usr/local/gmod/lib/perl5/i686-linux-gnu-thread-multi-64int/XML/Parser.pm line 186
XML::Parser::parse('XML::Parser=HASH(0x96396b0)', 'FileHandle=GLOB(0x9777a34)') called at /usr/local/gmod/lib/perl5/XML/Parser/PerlSAX.pm line 146
XML::Parser::PerlSAX::parse('XML::Parser::PerlSAX=HASH(0x974ce40)', 'Handler', 'Data::Stag::BaseHandler=HASH(0x961c6a4)', 'Source', 'HASH(0x974d124)') called at /usr/local/gmod/lib/perl5/Data/Stag/XMLParser.pm line 69
Data::Stag::XMLParser::parse_fh('Data::Stag::XMLParser=HASH(0x961c9b0)', 'FileHandle=GLOB(0x9777a34)') called at /usr/local/gmod/lib/perl5/Data/Stag/BaseGenerator.pm line 476
Data::Stag::BaseGenerator::parse('Data::Stag::XMLParser=HASH(0x961c9b0)', '-file', 'tmp/go/go.oboxml', '-str', undef, '-fh', undef) called at /usr/local/gmod/lib/perl5/Data/Stag/XMLParser.pm line 58
Data::Stag::XMLParser::parse('Data::Stag::XMLParser=HASH(0x961c9b0)', '-file', 'tmp/go/go.oboxml', '-str', undef, '-fh', undef) called at /usr/local/gmod/lib/perl5/Data/Stag/StagImpl.pm line 275
Data::Stag::StagImpl::parse('Data::Stag', '-format', undef, '-file', 'tmp/go/go.oboxml', '-handler', 'Data::Stag::BaseHandler=HASH(0x961c6a4)') called at /usr/local/gmod/lib/perl5/Data/Stag.pm line 181
Data::Stag::AUTOLOAD('Data::Stag', '-format', undef, '-file', 'tmp/go/go.oboxml', '-handler', 'Data::Stag::BaseHandler=HASH(0x961c6a4)') called at /usr/local/gmod/bin/stag-storenode.pl line 143
Drilling down into DBIx::DBStag, one hits a call to _storenode with this value for node, leading to a call to insertrow with these arguments:
DB<6> c
DBIx::DBStag::_storenode(/usr/local/gmod/lib/perl5/DBIx/DBStag.pm:1188):
1188: if (!$node) {
$VAR1 = bless( [
'cvterm',
[
bless( [
'@',
[
bless( [
'id',
'IAO:0000589'
], 'Data::Stag::StagImpl' )
]
], 'Data::Stag::StagImpl' ),
bless( [
'dbxref_id',
'dbxref__IAO:0000589'
], 'Data::Stag::StagImpl' )
]
], 'Data::Stag::StagImpl' );
DB<6> c
DBIx::DBStag::_storenode(/usr/local/gmod/lib/perl5/DBIx/DBStag.pm:1930):
1930: $id =
1931: $self->insertrow($element,
1932: \%store_hash,
1933: $pkcol);
$VAR1 = bless( [
'cvterm',
[
bless( [
'dbxref_id',
3088
], 'Data::Stag::StagImpl' )
]
], 'Data::Stag::StagImpl' );
DB<6> c
which leads to this SQL being generated:
DB<5> x $sql
0 'INSERT INTO cvterm (dbxref_id) VALUES (?)'
DB<6>
and run against the cvterm table, which is defined thusly:
Table "public.cvterm"
Column | Type | Modifiers
---------------------+-------------------------+------------------------------------------------------------
cvterm_id | integer | not null default nextval('cvterm_cvterm_id_seq'::regclass)
cv_id | integer | not null
name | character varying(1024) | not null
definition | text |
dbxref_id | integer | not null
is_obsolete | integer | not null default 0
is_relationshiptype | integer | not null default 0
Given that neither cv_id nor name are provided in the insert statement, hilarity is bound to ensue.
The responsible bit of the input file go.oboxml, around line 67, is
<cvterm id="IAO:0000589">
<dbxref_id>dbxref__IAO:0000589</dbxref_id>
</cvterm>
That dbxref_id does seem to be missing a great deal of information when compared to the other dbxref_id’s in the neighborhood.
That bit of XML seems to have been driven by this hunk in go.obo
[Term]
id: GO:0005623
name: cell
namespace: cellular_component
def: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:go_curators]
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
xref_analog: NIF_Subcellular:sao1813327414
xref_analog: Wikipedia:Cell_(biology)
is_a: GO:0005575 ! cellular_component
property_value: IAO:0000589 "cell and encapsulating structures" xsd:string
The go.obo file that I am using begins thusly
format-version: 1.0
version: releases/2014-07-16
date: 16:07:2014 00:43
saved-by: jenkins-slave
phew.
Locked
