Re: [Gusdev-gusdev] (no subject)

[Deborah F. P. <pi...@pc...>]

The parser requires a value for --gbRel which should be a number, the 
release number issued by genbank and generally found in their 
README.genbank file at ftp://ftp.ncbi.nih.gov/genbank/. The parser dies 
otherwise. Could you have given it this source_id like designation, 
AAEE0100000000, as the release number?

                                                     Debbie

On Mon, 27 Sep 2004, Deborah F. Pinney wrote:

> I think the error is actually created_rel_ver which should be a number not a 
> string. This seems to be the source_id. The date is OK. I'm not sure why the 
> parser is using the source_id as the created_rel_ver value.
>
>                                             -Debbie
>
> On Mon, 27 Sep 2004, Ed Robinson wrote:
>
>> Everything is parsing now, but I am still getting a SQL error so nothing 
>> is going in.  Here is the SQL:
>> 
>>  INSERT INTO DoTS.NAEntry (  created_date, row_user_id, user_write, 
>> group_write, created_rel_ver, na_sequence_id, row_project_id, group_read, 
>> row_group_id, other_read, na_entry_id, source_id, modification_date, 
>> user_read, row_alg_invocation_id, other_write, version, division )
>>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? 
>> )
>> Values: 2004-4-05 00:00:00, 1, 1, 1, AAEE0100000000, 43, 1, 1, 1, 1, 43, 
>> AAEE01000001, 1, 104, 0, 1, INV
>> 
>> As far as I can tell, it's all good except for the format of the date. 
>> Here is the full error from the error log.  All 18 chromosomes return the 
>> same error:
>> 
>> Again, thanks for everyone's help on this.
>> 
>> 
>> -Ed
>> 
>> ----
>> 
>> ------------------ entry number 1 -----------------
>> 
>> SQL ERROR!! involving
>> 
>>    INSERT INTO DoTS.NAEntry (  created_date, row_user_id, user_write, 
>> group_write, created_rel_ver, na_sequence_id, row_project_id, group_read, 
>> row_group_id, other_read, na_entry_id, source_id, modification_date, 
>> user_read, row_alg_invocation_id, other_write, version, division )
>>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? 
>> )
>> Values: 2004-4-05 00:00:00, 1, 1, 1, AAEE0100000000, 43, 1, 1, 1, 1, 43, 
>> AAEE01000001, 1, 104, 0, 1, INV at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185
>>        GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x8ab7b78)', 
>> '^J SQL ERROR!! involving^J ^J    INSERT INTO DoTS.NAEntry (  create...') 
>> called at /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm 
>> line 148
>>        GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x8ab7b78)', 
>> 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x9ce0958)', 'ARRAY(0x9ce0808)', '^J 
>> INSERT INTO DoTS.NAEntry (  created_date, row_user_id, user...') called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 681
>>        GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::NAEntry=HASH(0x949ea18)', 
>> 'HASH(0x9cc906c)') called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 628
>>        GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::NAEntry=HASH(0x949ea18)') 
>> called at /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 
>> 1677
>>        GUS::Model::GusRow::submit('GUS::Model::DoTS::NAEntry=HASH(0x949ea18)', 
>> undef, 1) called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 1764
>>        GUS::Model::GusRow::submitChildrenInClass('GUS::Model::DoTS::ExternalNASequence=HASH(0x94a084c)', 
>> 'GUS::Model::DoTS::NAEntry') called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 1745
>>        GUS::Model::GusRow::submitAllChildren('GUS::Model::DoTS::ExternalNASequence=HASH(0x94a084c)') 
>> called at /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 
>> 1684
>>        GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalNASequence=HASH(0x94a084c)') 
>> called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 
>> 284
>>        GUS::Common::Plugin::GBParser::processEntry('GUS::Common::Plugin::GBParser=HASH(0x8106d54)', 
>> 'CBIL::Bio::GenBank::ArrayStream=HASH(0x90e130c)') called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 
>> 185
>>        eval {...} called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 
>> 184
>>        GUS::Common::Plugin::GBParser::run('GUS::Common::Plugin::GBParser=HASH(0x8106d54)', 
>> 'HASH(0x8d0a8f8)') called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 
>> 453
>>        eval {...} called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 
>> 450
>>        GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 
>> 'GUS::Common::Plugin::GBParser', 1) called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 
>> 383
>>        GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 
>> 'GUS::Common::Plugin::GBParser') called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 
>> 289
>>        GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 
>> 'GUS::Common::Plugin::GBParser') called at 
>> /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 
>> 198
>> 
>>        GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 
>> 'ARRAY(0x8102dec)') called at /var/local/GUSTest/gus_home/bin/ga line 11
>> 
>> 
>> Ed Robinson
>> 255 Deerfield Rd
>> Bogart, GA 30622
>> (706)425-9181
>> http://www.electedrobinson.com
>> 
>> --Learn more about the face of your neighbor, and less about your own.
>>         -Sargent Shriver
>> 
>> 
>> 
>> 
>> 
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>
>
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