Re: [GUSDEV] InsertSequenceOntologyOBO error ?

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Thanks Mark !

Yet on ontologies, I just realized there is no "LoadGoOntology" plugin 
in GUS 3.5 
(http://www.gusdb.org/wiki/index.php/Bootstrap%20data#GOOntolgy), anyway 
trying to use "GUS::Supported::Plugin::InsertGeneOntology" I got the 
following errors:

[user@localhost log]$ ga GUS::Supported::Plugin::InsertGeneOntology 
--flatFile function.ontology --filePath /home/user/GO/ 
--functionExtDbName function --createRelease 1.12
Mon May  7 16:17:39 2007        DSN     dbi:Pg:dbname=mydb
Mon May  7 16:17:39 2007        PLUGIN 
GUS::Supported::Plugin::InsertGeneOntology
Mon May  7 16:17:39 2007        ARG     algoinvo        1
Mon May  7 16:17:39 2007        ARG     comment
Mon May  7 16:17:39 2007        ARG     commit  0
Mon May  7 16:17:39 2007        ARG     componentExtDbName
Mon May  7 16:17:39 2007        ARG     createRelease   1
Mon May  7 16:17:39 2007        ARG     debug   0
Mon May  7 16:17:39 2007        ARG     filePath        /home/user/GO/
Mon May  7 16:17:39 2007        ARG     flatFile        function.ontology
Mon May  7 16:17:39 2007        ARG     functionExtDbName       function
Mon May  7 16:17:39 2007        ARG     group
Mon May  7 16:17:39 2007        ARG     gusconfigfile 
$GUS_HOME/config/gus.config
Mon May  7 16:17:39 2007        ARG     help
Mon May  7 16:17:39 2007        ARG     helpHTML
Mon May  7 16:17:39 2007        ARG     loadAgain       0
Mon May  7 16:17:39 2007        ARG     processExtDbName
Mon May  7 16:17:39 2007        ARG     project
Mon May  7 16:17:39 2007        ARG     sqlVerbose      0
Mon May  7 16:17:39 2007        ARG     user
Mon May  7 16:17:39 2007        ARG     verbose 0
Mon May  7 16:17:39 2007        ARG     veryVerbose     0
Mon May  7 16:17:39 2007        AlgInvocationId 36
Mon May  7 16:17:39 2007        COMMIT  commit off
Mon May  7 16:17:39 2007        loading function.ontology in preparation 
for parsing
Mon May  7 16:17:39 2007        parsing all .ontology files in 
preparation for inserting into database
Mon May  7 16:17:40 2007        parsing finished; loading ontology into 
database

ERROR:
USER ERROR: Couldn't find external database function. Use the plugin 
InsertExternalDatabase to insert this information into the database.

STACK TRACE:
  at /usr/lib/perl5/site_perl/5.8.8/Error.pm line 189
         Error::throw('GUS::PluginMgr::PluginUserError=HASH(0x1519d50)') 
called at $GUS_HOME/lib/perl/GUS/PluginMgr/Plugin.pm line 1226

GUS::PluginMgr::Plugin::userError('GUS::Supported::Plugin::InsertGeneOntology=HASH(0xfdd750)', 
'Couldn\'t find external database function. Use the plugin Ins...') 
called at $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertGeneOntology.pm 
line 490

GUS::Supported::Plugin::InsertGeneOntology::getExtDbRelId('GUS::Supported::Plugin::InsertGeneOntology=HASH(0xfdd750)', 
'function', 'CBIL::Bio::GeneOntologyParser::Store=HASH(0x12402c0)') 
called at $GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertGeneOntology.pm 
line 222

GUS::Supported::Plugin::InsertGeneOntology::loadOntology('GUS::Supported::Plugin::InsertGeneOntology=HASH(0xfdd750)', 
'CBIL::Bio::GeneOntologyParser::Parser=HASH(0x1432670)') called at 
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertGeneOntology.pm line 166

GUS::Supported::Plugin::InsertGeneOntology::run('GUS::Supported::Plugin::InsertGeneOntology=HASH(0xfdd750)', 
'HASH(0x14327d0)') called at 
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
         eval {...} called at 
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569

GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)', 
'GUS::Supported::Plugin::InsertGeneOntology', 1) called at 
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485

GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)', 
'GUS::Supported::Plugin::InsertGeneOntology') called at 
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383

GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)', 
'GUS::Supported::Plugin::InsertGeneOntology') called at 
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292

GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)', 
'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11

This is the function.ontology file I was trying to load: 
ftp://ftp.geneontology.org/pub/go/ontology/function.ontology

And when trying to create the external-database I got this error:

[user@localhost log]$ ga GUS::Supported::Plugin::InsertExternalDatabase 
--name function.ontology --verbose
Mon May  7 16:24:19 2007        DSN     dbi:Pg:dbname=mydb
Mon May  7 16:24:19 2007        PLUGIN 
GUS::Supported::Plugin::InsertExternalDatabase
Mon May  7 16:24:19 2007        ARG     algoinvo        1
Mon May  7 16:24:19 2007        ARG     comment
Mon May  7 16:24:19 2007        ARG     commit  0
Mon May  7 16:24:19 2007        ARG     debug   0
Mon May  7 16:24:19 2007        ARG     group
Mon May  7 16:24:19 2007        ARG     gusconfigfile 
$GUS_HOME/config/gus.config
Mon May  7 16:24:19 2007        ARG     help
Mon May  7 16:24:19 2007        ARG     helpHTML
Mon May  7 16:24:19 2007        ARG     name    function.ontology
Mon May  7 16:24:19 2007        ARG     project
Mon May  7 16:24:19 2007        ARG     sqlVerbose      0
Mon May  7 16:24:19 2007        ARG     user
Mon May  7 16:24:19 2007        ARG     verbose 1
Mon May  7 16:24:19 2007        ARG     veryVerbose     0
Mon May  7 16:24:19 2007        AlgInvocationId 37
Mon May  7 16:24:19 2007        COMMIT  commit off
DBD::Pg::st execute failed: ERROR:  duplicate key violates unique 
constraint "pk_externaldatabase"

ERROR:

  SQL ERROR!! involving

     INSERT INTO SRes.ExternalDatabase (  group_write, other_read, 
group_read, name, user_read, row_user_id, external_database_id, 
modification_date, other_write, row_alg_invocation_id, row_project_id, 
row_group_id, user_write )
     VALUES   (  ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ? )
  Values: 1, 1, 1, function.ontology, 1, 1, 7, 0, 37, 1, 1, 1 at 
$GUS_HOME/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166

GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x10e2950)', 
'\x{a} SQL ERROR!! involving\x{a} \x{a}    INSERT INTO 
SRes.ExternalDataba...') called at 
$GUS_HOME/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150

GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x10e2950)', 
'GUS::ObjRelP::DbiDbHandle::st=HASH(0x13c8a80)', 'ARRAY(0x13c8b50)', 
'\x{a}    INSERT INTO SRes.ExternalDatabase (  group_write, other_...') 
called at $GUS_HOME/lib/perl/GUS/ObjRelP/DbiRow.pm line 673

GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::ExternalDatabase=HASH(0x13b2240)', 
'HASH(0x13b1df0)') called at $GUS_HOME/lib/perl/GUS/ObjRelP/DbiRow.pm 
line 620

GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::ExternalDatabase=HASH(0x13b2240)') 
called at $GUS_HOME/lib/perl/GUS/Model/GusRow.pm line 1692

GUS::Model::GusRow::submit('GUS::Model::SRes::ExternalDatabase=HASH(0x13b2240)') 
called at 
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertExternalDatabase.pm line 103

GUS::Supported::Plugin::InsertExternalDatabase::run('GUS::Supported::Plugin::InsertExternalDatabase=HASH(0xf7eeb0)', 
'HASH(0x12eca80)') called at 
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
         eval {...} called at 
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569

GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)', 
'GUS::Supported::Plugin::InsertExternalDatabase', 1) called at 
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485

GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)', 
'GUS::Supported::Plugin::InsertExternalDatabase') called at 
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383

GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)', 
'GUS::Supported::Plugin::InsertExternalDatabase') called at 
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292

GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)', 
'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11

STACK TRACE:
  at $GUS_HOME/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166

GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x10e2950)', 
'\x{a} SQL ERROR!! involving\x{a} \x{a}    INSERT INTO 
SRes.ExternalDataba...') called at 
$GUS_HOME/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150

GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x10e2950)', 
'GUS::ObjRelP::DbiDbHandle::st=HASH(0x13c8a80)', 'ARRAY(0x13c8b50)', 
'\x{a}    INSERT INTO SRes.ExternalDatabase (  group_write, other_...') 
called at $GUS_HOME/lib/perl/GUS/ObjRelP/DbiRow.pm line 673

GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::ExternalDatabase=HASH(0x13b2240)', 
'HASH(0x13b1df0)') called at $GUS_HOME/lib/perl/GUS/ObjRelP/DbiRow.pm 
line 620

GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::ExternalDatabase=HASH(0x13b2240)') 
called at $GUS_HOME/lib/perl/GUS/Model/GusRow.pm line 1692

GUS::Model::GusRow::submit('GUS::Model::SRes::ExternalDatabase=HASH(0x13b2240)') 
called at 
$GUS_HOME/lib/perl/GUS/Supported/Plugin/InsertExternalDatabase.pm line 103

GUS::Supported::Plugin::InsertExternalDatabase::run('GUS::Supported::Plugin::InsertExternalDatabase=HASH(0xf7eeb0)', 
'HASH(0x12eca80)') called at 
/$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 580
         eval {...} called at 
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 569

GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x5052a0)', 
'GUS::Supported::Plugin::InsertExternalDatabase', 1) called at 
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 485

GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x5052a0)', 
'GUS::Supported::Plugin::InsertExternalDatabase') called at 
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 383

GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x5052a0)', 
'GUS::Supported::Plugin::InsertExternalDatabase') called at 
$GUS_HOME/lib/perl/GUS/PluginMgr/GusApplication.pm line 292

GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x5052a0)', 
'ARRAY(0x505dd0)') called at $GUS_HOME/bin/ga line 11

I am using (PostgreSQL) 8.2.2 and Linux FC5 x86_64 on an AMD64 server.

Thanks, Alberto

Mark S. Heiges wrote:
> That plugin requires the file in OBO format. You can download the latest 
> from the SO Project's repository at
> http://song.cvs.sourceforge.net/song/ontology/so.obo
> 
> You can safely ignore the "no 'undoTables()'" message. It just indicates 
> that InsertSequenceOntologyOBO has not implemented some optional record 
> keeping and, as a side effect, is not compatible with the 
> GUS::Community::Plugin::Undo plugin. The "RESULT Inserted n terms into 
> SequenceOntology" message will give an accurate count of what was loaded.
> 
> 
> On May 5, 2007, at 11:04 AM, davila wrote:
> 
>> Hi folks,
>>
>> With GUS 3.5 got from SVN, tryig to use the 
>> GUS::Supported::Plugin::InsertSequenceOntologyOBO plugin I got no rows 
>> inserted, see the log:
>>
>> GUS::Supported::Plugin::InsertSequenceOntologyOBO --inputFile 
>> so.definition --soCvsVersion '1.42' --soVersion
>> '1.419' --user user --group group --commit >so1.log
>>
>> Sat May  5 11:41:22 2007        DSN     dbi:Pg:dbname=mydb
>> Sat May  5 11:41:22 2007        PLUGIN
>> GUS::Supported::Plugin::InsertSequenceOntologyOBO
>> Sat May  5 11:41:22 2007        ARG     algoinvo        1
>> Sat May  5 11:41:22 2007        ARG     comment
>> Sat May  5 11:41:22 2007        ARG     commit  1
>> Sat May  5 11:41:22 2007        ARG     debug   0
>> Sat May  5 11:41:22 2007        ARG     group   dba
>> Sat May  5 11:41:22 2007        ARG     gusconfigfile 
>> $GUS_HOME/gus.config
>> Sat May  5 11:41:22 2007        ARG     help
>> Sat May  5 11:41:22 2007        ARG     helpHTML
>> Sat May  5 11:41:22 2007        ARG     inputFile so.definition
>> Sat May  5 11:41:22 2007        ARG     project
>> Sat May  5 11:41:22 2007        ARG     soCvsVersion    1.42
>> Sat May  5 11:41:22 2007        ARG     soVersion       1.419
>> Sat May  5 11:41:22 2007        ARG     sqlVerbose      0
>> Sat May  5 11:41:22 2007        ARG     user    dba
>> Sat May  5 11:41:22 2007        ARG     verbose 0
>> Sat May  5 11:41:22 2007        ARG     veryVerbose     0
>> Sat May  5 11:41:22 2007        AlgInvocationId 14
>> Sat May  5 11:41:22 2007        COMMIT  commit on
>> Sat May  5 11:41:22 2007        TIME    < 1 sec  (0:00:00)
>> Sat May  5 11:41:22 2007        RESULT  Inserted 0 terms into
>> SequenceOntology
>> Sat May  5 11:41:22 2007        Rows Written    N/A (plugin has no
>> 'undoTables()' method)
>> Sat May  5 11:41:22 2007        AlgInvocationId 14
>> Sat May  5 11:41:22 2007        COMMIT  commit on
>>
>>
>> What exactly means this warining "Rows Written    N/A (plugin has no 
>> 'undoTables()' method)" ?
>>
>> and where one can find and download the most updated "so.definitions" 
>> file ?
>>
>>
>> My sres.gorelationship and sres.sequenceontology are like this:
>>
>>
>> mydb=# \d sres.gorelationship
>>                     Table "sres.gorelationship"
>>          Column          |            Type             | Modifiers
>> -------------------------+-----------------------------+-----------
>>  go_relationship_id      | numeric(10,0)               | not null
>>  parent_term_id          | numeric(10,0)               | not null
>>  child_term_id           | numeric(10,0)               | not null
>>  go_relationship_type_id | numeric(10,0)               | not null
>>  modification_date       | timestamp without time zone | not null
>>  user_read               | numeric(1,0)                | not null
>>  user_write              | numeric(1,0)                | not null
>>  group_read              | numeric(1,0)                | not null
>>  group_write             | numeric(1,0)                | not null
>>  other_read              | numeric(1,0)                | not null
>>  other_write             | numeric(1,0)                | not null
>>  row_user_id             | numeric(12,0)               | not null
>>  row_group_id            | numeric(4,0)                | not null
>>  row_project_id          | numeric(4,0)                | not null
>>  row_alg_invocation_id   | numeric(12,0)               | not null
>> Indexes:
>>     "gorelationship_pk" PRIMARY KEY, btree (go_relationship_id)
>>     "gorelationship_ind01" btree (parent_term_id, child_term_id)
>>     "gorelationship_ind02" btree (child_term_id, parent_term_id)
>>     "gorelationship_ind03" btree (go_relationship_type_id)
>>
>>
>> mydb=# \d sres.sequenceontology
>>                   Table "sres.sequenceontology"
>>         Column         |            Type             | Modifiers
>> -----------------------+-----------------------------+-----------
>>  sequence_ontology_id  | numeric(10,0)               | not null
>>  so_id                 | character varying(12)       | not null
>>  ontology_name         | character varying(30)       | not null
>>  so_version            | character varying(255)      | not null
>>  so_cvs_version        | character varying(10)       | not null
>>  term_name             | character varying(255)      | not null
>>  definition            | character varying(2000)     | not null
>>  modification_date     | timestamp without time zone | not null
>>  user_read             | numeric(1,0)                | not null
>>  user_write            | numeric(1,0)                | not null
>>  group_read            | numeric(1,0)                | not null
>>  group_write           | numeric(1,0)                | not null
>>  other_read            | numeric(1,0)                | not null
>>  other_write           | numeric(1,0)                | not null
>>  row_user_id           | numeric(12,0)               | not null
>>  row_group_id          | numeric(4,0)                | not null
>>  row_project_id        | numeric(4,0)                | not null
>>  row_alg_invocation_id | numeric(12,0)               | not null
>> Indexes:
>>     "pk_sequenceontology" PRIMARY KEY, btree (sequence_ontology_id)
>>
>> Thanks, Alberto
>>