Re: [Gusdev-gusdev] GBParser Failures...:(

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Hello Steve--

Here is the first occurence of the dbdbihandle error:
Inserting:
Table: NAEntry
	created_date: [2003-5-03 00:00:00]   <--------
	row_user_id: [6]
	user_write: [1]
	group_write: [1]
	created_rel_ver: [135]
	na_sequence_id: [1911]
	row_project_id: [2]
	group_read: [1]
	row_group_id: [3]
	other_read: [1]
	source_id: [AY140947]
	modification_date: [SYSDATE]
	user_read: [1]
	row_alg_invocation_id: [139]
	other_write: [0]
	version: [1]
	division: [INV]
DBD::Oracle::st execute failed: ORA-01861: literal does not match format
string (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 144, <GEN0> line
74.

On the sql prompt we checked the dots.NAentry table, which is this:
SQL> describe dots.naentry;
 Name                                      Null?    Type
 ----------------------------------------- --------
----------------------------
 NA_ENTRY_ID                               NOT NULL NUMBER(10)
 NA_SEQUENCE_ID                            NOT NULL NUMBER(10)
 SOURCE_ID                                 NOT NULL VARCHAR2(15)
 STATUS                                             VARCHAR2(12)
 DIVISION                                           VARCHAR2(15)
 VERSION                                            NUMBER(12)
 NID                                                VARCHAR2(15)
 CREATED_DATE                                       DATE
 CREATED_REL_VER                                    NUMBER(5)
 UPDATE_DATE                                        DATE
 UPDATE_REL_VER                                     NUMBER(5)
 MODIFICATION_DATE                         NOT NULL DATE
 USER_READ                                 NOT NULL NUMBER(1)
 USER_WRITE                                NOT NULL NUMBER(1)
 GROUP_READ                                NOT NULL NUMBER(1)
 GROUP_WRITE                               NOT NULL NUMBER(1)
 OTHER_READ                                NOT NULL NUMBER(1)
 OTHER_WRITE                               NOT NULL NUMBER(1)
 ROW_USER_ID                               NOT NULL NUMBER(12)
 ROW_GROUP_ID                              NOT NULL NUMBER(3)
 ROW_PROJECT_ID                            NOT NULL NUMBER(3)
 ROW_ALG_INVOCATION_ID                     NOT NULL NUMBER(12)

We are guessing that the type mismatch is with the created_date attribute,
which for some reason the parser is attempting to enter in the wrong
format.  Thanks,

Michael Luchtan
http://www.cs.uga.edu/~luchtan

On Tue, 13 May 2003, Steve Fischer wrote:

> michael-
>
> look in the log that captures stdout for sql errors on or near line 144
> of DbDbiHandle.pm
>
> that was the main clue last time.
>
> steve
>
> MICHAEL LUCHTAN wrote:
>
> >Hello-
> >We have advanced a little further in our effort to get the gbparser plugin
> >running on a new GUS installation.  Thank you for the help so far, and we
> >have resolved the dependency regarding the Dots.sequencetype table, but
> >unfortunately we have new dependency errors.  Here a snapshot from the
> >generated error log:
> >
> >
> >
> > ------------------ 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: 2003-5-03 00:00:00, 6, 1, 1, 135, 1809, 2, 1, 3, 1, 205,
> >AY140947, 1, 138, 0, 1, INV at
> >/home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184
> >
> >GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x8afbd68)',
> >'^J SQL ERROR!! involving^J ^J    INSERT INTO DoTS.NAEntry (  create...')
> >called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147
> >
> >GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x8afbd68)',
> >'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8f3e0ec)', 'ARRAY(0x8f3c990)', '^J
> >INSERT INTO DoTS.NAEntry (  created_date, row_user_id, user...') called at
> >/home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674
> >
> >GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::NAEntry=HASH(0x8d72bf0)',
> >'HASH(0x8f3c810)') called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
> >line 621
> >
> >GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::NAEntry=HASH(0x8d72bf0)')
> >called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
> >
> >GUS::Model::GusRow::submit('GUS::Model::DoTS::NAEntry=HASH(0x8d72bf0)',
> >undef, 1) called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1765
> >
> >GUS::Model::GusRow::submitChildrenInClass('GUS::Model::DoTS::ExternalNASequence=HASH(0x8d6b500)',
> >'GUS::Model::DoTS::NAEntry') called at
> >/home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1746
> >
> >GUS::Model::GusRow::submitAllChildren('GUS::Model::DoTS::ExternalNASequence=HASH(0x8d6b500)')
> >called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
> >
> >GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalNASequence=HASH(0x8d6b500)')
> >called at /home/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 284
> >
> >GUS::Common::Plugin::GBParser::processEntry('GUS::Common::Plugin::GBParser=HASH(0x84be838)',
> >'CBIL::Bio::GenBank::ArrayStream=HASH(0x8ccac48)') called at
> >/home/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 185
> >	eval {...} called at
> >/home/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 184
> >
> >GUS::Common::Plugin::GBParser::run('GUS::Common::Plugin::GBParser=HASH(0x84be838)',
> >'HASH(0x8c60dc8)') called at
> >/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 389
> >	eval {...} called at
> >/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 385
> >
> >GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >'GUS::Common::Plugin::GBParser') called at
> >/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 284
> >
> >GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >'GUS::Common::Plugin::GBParser') called at
> >/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 193
> >
> >GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11
> >
> >
> >Thank you...
> >
> >Michael Luchtan
> >http://www.cs.uga.edu/~luchtan
> >
> >
> >
> >
> >-------------------------------------------------------
> >Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara
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> >
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>
>
>
>
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