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Chado/GMOD doesn't parse OBO

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Chado/GMOD doesn't parse OBO

Yasir Suhail
Dear GMOD devs and users,

I am trying to follow the GMOD 2013 tutorial (http://gmod.org/wiki/Chado_Tutorial) and used the latest AMI to start an instance in AWS. It seems that Chado::Builder fails to parse OBO files. Please let me know what I could be doing wrong or other suggestions.
When I try to run make ontologies, this is what I see:

ubuntu@ip-10-170-117-101:~/sources/chado/chado$ make ontologies
./Build ontologies
Available ontologies:
[1] Relationship Ontology
[2] Sequence Ontology
[3] Gene Ontology
[4] Chado Feature Properties
[5] Plant Ontology

Which ontologies would you like to load (Comma delimited)? [0]  3,4,5
fetching files for Gene Ontology
  +http://www.geneontology.org/ontology/gene_ontology.obo
    ./tmp/go/go.obo is up to date
fetching files for Chado Feature Properties
  +load/etc/feature_property.obo
    loading...sh: 1: stag-storenode.pl: not found
System call 'stag-storenode.pl -d 'dbi:Pg:dbname=drupal;host=localhost;port=5432' --user ubuntu  tmp/load/etc/feature_property.oboxml' failed: 32512
failed: 32512 at lib/Bio/Chado/Builder.pm line 367, <STDIN> line 1.
make: *** [ontologies] Error 127
ubuntu@ip-10-170-117-101:~/sources/chado/chado$

Best,
yasir

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Re: Chado/GMOD doesn't parse OBO

Yasir Suhail
So I found that the stag-storenode scripts name was wrong. After changing line 352 of  from
my $stag_string = "stag-storenode.pl -d 'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'";
to
my $stag_string = "stag-storenode -d 'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'";
The previous error goes away but I get:
Maybe DBIx::DBSchema does not work with your database? at /usr/share/perl5/DBIx/DBStag.pm line 427
    DBIx::DBStag::get_pk_col('DBIx::DBStag=HASH(0x20c4b78)', 'cv') called at /usr/share/perl5/DBIx/DBStag.pm line 1265
    DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x20c4b78)', 'Data::Stag::StagImpl=ARRAY(0x2e058e8)') called at /usr/share/perl5/DBIx/DBStag.pm line 1180
    DBIx::DBStag::storenode('DBIx::DBStag=HASH(0x20c4b78)', 'Data::Stag::StagImpl=ARRAY(0x2ccc6f0)') called at /usr/bin/stag-storenode line 88
    eval {...} called at /usr/bin/stag-storenode line 87
    main::store('Data::Stag::BaseHandler=HASH(0x2bafa20)', 'Data::Stag::StagImpl=ARRAY(0x2ccc6f0)') called at /usr/bin/stag-storenode line 137
    main::__ANON__('Data::Stag::BaseHandler=HASH(0x2bafa20)', 'Data::Stag::StagImpl=ARRAY(0x2ccc6f0)') called at /usr/share/perl5/Data/Stag/BaseHandler.pm line 594
    Data::Stag::BaseHandler::end_event('Data::Stag::BaseHandler=HASH(0x2bafa20)', 'cv') called at /usr/share/perl5/Data/Stag/BaseHandler.pm line 742
    Data::Stag::BaseHandler::end_element('Data::Stag::BaseHandler=HASH(0x2bafa20)', 'HASH(0x2ccc378)') called at /usr/share/perl5/XML/Parser/PerlSAX.pm line 239
    XML::Parser::PerlSAX::_handle_end('XML::Parser::PerlSAX=HASH(0x2c9f6c8)', 'XML::Parser::Expat=HASH(0x2bf09a0)', 'cv') called at /usr/share/perl5/XML/Parser/PerlSAX.pm line 79
    XML::Parser::PerlSAX::__ANON__('XML::Parser::Expat=HASH(0x2bf09a0)', 'cv') called at /usr/lib/perl5/XML/Parser/Expat.pm line 470
    XML::Parser::Expat::parse('XML::Parser::Expat=HASH(0x2bf09a0)', 'FileHandle=GLOB(0x2ce7970)') called at /usr/lib/perl5/XML/Parser.pm line 187
    eval {...} called at /usr/lib/perl5/XML/Parser.pm line 186
    XML::Parser::parse('XML::Parser=HASH(0x2bd9cd0)', 'FileHandle=GLOB(0x2ce7970)') called at /usr/share/perl5/XML/Parser/PerlSAX.pm line 146
    XML::Parser::PerlSAX::parse('XML::Parser::PerlSAX=HASH(0x2c9f6c8)', 'Handler', 'Data::Stag::BaseHandler=HASH(0x2bafa20)', 'Source', 'HASH(0x2c9fa88)') called at /usr/share/perl5/Data/Stag/XMLParser.pm line 69
    Data::Stag::XMLParser::parse_fh('Data::Stag::XMLParser=HASH(0x2bd94c0)', 'FileHandle=GLOB(0x2ce7970)') called at /usr/share/perl5/Data/Stag/BaseGenerator.pm line 476
    Data::Stag::BaseGenerator::parse('Data::Stag::XMLParser=HASH(0x2bd94c0)', '-file', 'tmp/load/etc/feature_property.oboxml', '-str', undef, '-fh', undef) called at /usr/share/perl5/Data/Stag/XMLParser.pm line 58
    Data::Stag::XMLParser::parse('Data::Stag::XMLParser=HASH(0x2bd94c0)', '-file', 'tmp/load/etc/feature_property.oboxml', '-str', undef, '-fh', undef) called at /usr/share/perl5/Data/Stag/StagImpl.pm line 275
    Data::Stag::StagImpl::parse('Data::Stag', '-format', undef, '-file', 'tmp/load/etc/feature_property.oboxml', '-handler', 'Data::Stag::BaseHandler=HASH(0x2bafa20)') called at /usr/share/perl5/Data/Stag.pm line 181
    Data::Stag::AUTOLOAD('Data::Stag', '-format', undef, '-file', 'tmp/load/etc/feature_property.oboxml', '-handler', 'Data::Stag::BaseHandler=HASH(0x2bafa20)') called at /usr/bin/stag-storenode line 143
System call 'stag-storenode -d 'dbi:Pg:dbname=drupal;host=localhost;port=5432' --user ubuntu  tmp/load/etc/feature_property.oboxml' failed: 256
failed: 256 at lib/Bio/Chado/Builder.pm line 367, <STDIN> line 1.
make: *** [ontologies] Error 1


On Sun, Nov 1, 2015 at 1:47 AM, Yasir Suhail <[hidden email]> wrote:
Dear GMOD devs and users,

I am trying to follow the GMOD 2013 tutorial (http://gmod.org/wiki/Chado_Tutorial) and used the latest AMI to start an instance in AWS. It seems that Chado::Builder fails to parse OBO files. Please let me know what I could be doing wrong or other suggestions.
When I try to run make ontologies, this is what I see:

ubuntu@ip-10-170-117-101:~/sources/chado/chado$ make ontologies
./Build ontologies
Available ontologies:
[1] Relationship Ontology
[2] Sequence Ontology
[3] Gene Ontology
[4] Chado Feature Properties
[5] Plant Ontology

Which ontologies would you like to load (Comma delimited)? [0]  3,4,5
fetching files for Gene Ontology
  +http://www.geneontology.org/ontology/gene_ontology.obo
    ./tmp/go/go.obo is up to date
fetching files for Chado Feature Properties
  +load/etc/feature_property.obo
    loading...sh: 1: stag-storenode.pl: not found
System call 'stag-storenode.pl -d 'dbi:Pg:dbname=drupal;host=localhost;port=5432' --user ubuntu  tmp/load/etc/feature_property.oboxml' failed: 32512
failed: 32512 at lib/Bio/Chado/Builder.pm line 367, <STDIN> line 1.
make: *** [ontologies] Error 127
ubuntu@ip-10-170-117-101:~/sources/chado/chado$

Best,
yasir


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