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[Gusdev-gusdev] LoadNRDB plugin questions
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From: MICHAEL L. <lu...@cs...> - 2003-12-09 14:59:30
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Hello Everyone:
I have attempted to load data using the loadnrdb plugin and have recieved
errors. I have a few questions to ask concerning the plugin options.
I entered the following command:
[luchtan@mkiwi luchtan]$ ga GUS::Common::Plugin::LoadNRDB
--temp_login=luchtan
--sourceDB=1:gb,2:emb,3:dbj,4:pir,5:prf,6:sp,7:pdb,8:pat,9:bbs,
10:gnl,11:ref,12:lcl,13:genpept,14:tpe --temp_password=xxxxxxx
--dbi_str="dbi:Oracle:host=xx.xxx.xxx.xx;sid=XXXXX"
--gitax=/home/luchtan
/GUS/loadNRDB/gi_taxid_prot.dmp
--nrdb=/opt/app/oracle/db_storage/data/downloadNRDB/downloadNRDB/nr.Z
--extDbRelId=15 --plugin --delete --verb
ose --maketemp --commit
With the proceeding output:
Reading properties from /var/local/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/luchtan/.gus.properties
Mon Dec 8 17:28:08 2003 ***COMMIT ON***
There are 14 entries in the source database hash
Mon Dec 8 17:28:42 2003 There are 3233042 gi to taxon_id pairs
Mon Dec 8 17:28:47 2003 2000 sets have been processed
and put in the NRDBTemp table
Mon Dec 8 17:28:50 2003 4000 sets have been processed
and put in the NRDBTemp table
Mon Dec 8 17:28:53 2003 5000 sets have been processed
and put in the NRDBTemp table
.
.
.
Mon Dec 8 19:01:59 2003 2956000 sets have been processed
and put in the NRDBTemp table
Mon Dec 8 19:02:00 2003 2957000 sets have been processed
and put in the NRDBTemp table
Mon Dec 8 19:02:03 2003 2958396 total entries have been made
into the NRDBTemp table
Mon Dec 8 19:02:11 2003 2958395 entries in temp table
Submitted set number:1
Submitted set number:2
Submitted set number:3
Submitted set number:4
Submitted set number:5
Submitted set number:6
.
.
.
Submitted set number:3478
Submitted set number:3479
DBD::Oracle::st execute failed: ORA-00942: table or view does not exist
(DBD ERROR: OCIStmtExecute) at /var/local/gus_home/lib/perl/GUS/ObjRel
P/DbiDbHandle.pm line 145, <NRDB> line 19198.
SQL ERROR!! involving
Values: 6805 at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
line 185
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x8645bf4)',
'^J SQL ERROR!! involving^J ^J Values: 6805') called at
/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x8645bf4)',
'GUS::ObjRelP::DbiDbHandle::st=HASH(0x41386b68)', 'ARR
AY(0x849384c)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm
line 1798
GUS::Model::GusRow::version('GUS::Model::DoTS::NRDBEntry=HASH(0x87dcb28)')
called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm
line 1665
GUS::Model::GusRow::submit('GUS::Model::DoTS::NRDBEntry=HASH(0x87dcb28)',
undef, 1) called at /var/local/gus_home/lib/perl/GUS/Model/G
usRow.pm line 1764
GUS::Model::GusRow::submitChildrenInClass('GUS::Model::DoTS::ExternalAASequence=HASH(0x878fa6c)',
'GUS::Model::DoTS::NRDBEntry') calle
d at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1745
GUS::Model::GusRow::submitAllChildren('GUS::Model::DoTS::ExternalAASequence=HASH(0x878fa6c)')
called at /var/local/gus_home/lib/perl/G
US/Model/GusRow.pm line 1684
GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalAASequence=HASH(0x878fa6c)')
called at /var/local/gus_home/lib/perl/GUS/Common/P
lugin/LoadNRDB.pm line 332
GUS::Common::Plugin::LoadNRDB::makeNRDBAndExternalAASequence('GUS::Common::Plugin::LoadNRDB=HASH(0x81069d8)',
'HASH(0x85810c0)', 'HASH
(0x857ea9c)', 15) called at
/var/local/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 127
GUS::Common::Plugin::LoadNRDB::run('GUS::Common::Plugin::LoadNRDB=HASH(0x81069d8)',
'HASH(0x87dd904)') called at /var/local/gus_home/l
ib/perl/GUS/PluginMgr/GusApplication.pm line 430
eval {...} called at
/var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 427
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)',
'GUS::Common::Plugin::LoadNRDB') cal
led at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
283
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)',
'GUS::Common::Plugin::LoadNRDB') called
at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)',
'ARRAY(0x8102dbc)') called at /var/local
/gus_home/bin/ga line 11
write error onstdout: Broken pipe
-----------------------------------------------------------------------------------------------
And that's that.
So something's wrong, but before I get too deep into debugging, I would
like to know what kind of data has been entered already into the database,
and if there is a way to remove it. I would like to run the same with a
--sqlVerbose, but I'm not sure how the plugin will react with the data
already present.
What does the --delete option do? I was under the impression that it
deleted the temp table, or so I was told. The --help reveals this:
--delete!
hint: option to run delete portion
type: boolean
So what is the delete portion?
Supposing that the data has been entered correctly up to a certain point,
I would assume that either
--plugin!
hint: choice of whether to run the remainder of the plug_in
type: boolean
--restart=i
hint: for restarting the interrupted plugin(use with plugin
option), use number from last set number in log
type: int
or
--restart_temp_table!
hint: indicates temp table insertion should be restarted
because table already exits
type: boolean
are the options that I should provide. It is not plainly clear to me.
Is my assumption that I would specify --restart=3479 for this case
correct?
Any help is much appreciated!
Michael Luchtan
http://www.cs.uga.edu/~luchtan
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