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Re: [GUSDEV] RES: Re: Inserting Sequence Features - Problem with a big reference.
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From: Steve F. <sfi...@pc...> - 2005-12-24 13:33:14
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Ricardo-
Mike is moving from Philadelphia to Seattle, and has taken a new job. =20
We are hoping to fill his position soon.
The version tables are used by the GUS object layer to save rows that=20
have been updated. We use it so that we can track the history of=20
changes to the database.
steve
Ricardo Balbi wrote:
> ops !!!
>
> I forgot the file ... sorry.
> I am sending it now
>
> 2005/12/20, Ricardo Balbi <rb...@gm... <mailto:rb...@gm...>>:
>
> Mark / Michael / Steve,
> I think that I discovered the problem.
> When I spoke that the rules did not exist were because I was not
> obtaining to see them.
> Later that I created the rules again, started to happen the
> error of duplicated key.=20
> Analyzing better the database I perceived that they had rules
> repeated for each view, the cause of the error of duplicated key.
> I droped the repeated rules and the error of absence of rules
> came back to happen.
> I perceived that the rules that were lacking were the rules of
> the xxxVer schemas.
> I created these rules that were lacking based in another
> installation that I made, because the file
> /GUS/gus_home/config/SchemaInstall-objects.sql does not create
> these rules.
> However, I think that the creation of the rules is missed. I am
> sending the file for analysis.=20
>
> Do you have any file with the correct creation of these rules?=20
>
> A doubt:=20
> Why the xxxVer schemas exist?=20
> Why to keep this type of versioning?
>
> excuses for my english :-)
>
> thanks,
> Ricardo Balbi
>
>
>
> 2005/12/15, Ricardo Balbi <rb...@gm...
> <mailto:rb...@gm...>>:
>
> No Steve, there is no rows in DoTS.NASequenceImp. The table is
> empty.
> I tried three times without success, therefore the sequence is
> with number three. I do not know because this is happening
> since the sequence always is developed and the only field of
> the primary key is na_sequence_id.=20
>
> Do you have some idea?
>
> thanks,
> Ricardo
>
> I know about the sequence and I have been reseted it before
> run the ISF plugin.
>
> 2005/12/13, Steve Fischer < sfi...@pc...
> <mailto:sfi...@pc...>>:
>
> the install of GUS should have made a primary key _sq, ie,
> a database
> "sequence" that generates the next primary key for that
> table.
>
> it looks like the na_sequence_id that is being written is 3.
>
> is there any row in DoTS.NASequenceImp with a
> na_sequence_id of 3?
>
> steve
>
> Mark S. Heiges wrote:
>
>> The 'pk_nasequenceimp' unique constraint prevents duplicate
>> na_sequence_id values in DoTS.NASequence. Off hand, I do
> not know why
>> values are being duplicated.
>> Anyone else want to pitch in?
>>
>>
>> On Dec 13, 2005, at 11:46 AM, Ricardo Balbi wrote:
>>
>>> Hi Mark,
>>>
>>> I executed the ISFU plugin, but now I am taking another
> error. All
>>> tables are empty. Do you know to say me what is
> happening? The
>>> error follows below:
>>>
>>> [rbalbi1@crithidia bancos]$ ga
>>> GUS::Supported::Plugin::InsertSequenceFeatures --mapfile
> $GUS_HOME/
>>> config/genbank2gus.xml --inputFileOrDir kinetoplastida_nt --
>>> fileFormat genbank --extDbName "Kinetoplastida_nt"
> --extDbRlsVer
>>> "2005-12-06" -- sqlVerbose --commit
>>> Tue Dec 13 14:38:54 2005 ARG algoinvo 1
>>> Tue Dec 13 14:38:54 2005 ARG comment
>>> Tue Dec 13 14:38:54 2005 ARG commit 0
>>> Tue Dec 13 14:38:54 2005 ARG debug 0
>>> Tue Dec 13 14:38:54 2005 ARG defaultOrganism
>>> Tue Dec 13 14:38:54 2005 ARG extDbName
>>> Kinetoplastida_nt
>>> Tue Dec 13 14:38:54 2005 ARG extDbRlsVer =20
> 2005-12-06
>>> Tue Dec 13 14:38:54 2005 ARG =20
> fileFormat genbank
>>> Tue Dec 13 14:38:54 2005 ARG gff2GroupTag
>>> Tue Dec 13 14:38:54 2005 ARG group
>>> Tue Dec 13 14:38:54 2005 ARG gusconfigfile =20
> /GUS/
>>> gus_home/config/gus.config
>>> Tue Dec 13 14:38:54 2005 ARG handlerExternalDbs
>>> Tue Dec 13 14:38:54 2005 ARG help
>>> Tue Dec 13 14:38:54 2005 ARG helpHTML
>>> Tue Dec 13 14:38:54 2005 ARG inputFileExtension
>>> Tue Dec 13 14:38:54 2005 ARG inputFileOrDir
>>> kinetoplastida_nt
>>> Tue Dec 13 14:38:54 2005 ARG makeSourceids
>>> Tue Dec 13 14:38:54 2005 ARG mapFile
> /GUS/gus_home/
>>> config/genbank2gus.xml
>>> Tue Dec 13 14:38:54 2005 ARG naSequenceSubclass
>>> Tue Dec 13 14:38:54 2005 ARG project
>>> Tue Dec 13 14:38:54 2005 ARG seqIdColumn =20
> source_id
>>> Tue Dec 13 14:38:54 2005 ARG seqSoTerm
>>> Tue Dec 13 14:38:54 2005 ARG seqType
>>> Tue Dec 13 14:38:54 2005 ARG soCvsVersion
>>> Tue Dec 13 14:38:54 2005 ARG sqlVerbose 0
>>> Tue Dec 13 14:38:54 2005 ARG testNumber
>>> Tue Dec 13 14:38:54 2005 ARG user
>>> Tue Dec 13 14:38:54 2005 ARG verbose 0
>>> Tue Dec 13 14:38:54 2005 ARG veryVerbose 0
>>> Tue Dec 13 14:38:54 2005 AlgInvocationId 51
>>> Tue Dec 13 14:38:54 2005 COMMIT commit off
>>> Tue Dec 13 14:38:56 2005 Processing file
> 'kinetoplastida_nt'...
>>> DBD::Pg::st execute failed: ERROR: duplicate key
> violates unique
>>> constraint "pk_nasequenceimp"
>>>
>>> ERROR:
>>>
>>> SQL ERROR!! involving
>>>
>>> INSERT INTO DoTS.ExternalNASequence ( sequence,
> group_read,
>>> user_read, other_write, modification_date, subclass_view,
>>> row_group_id, user_write, other_read, group_write,
> source_id,
>>> external_database_release_id, c_count, g_count,
> taxon_id, name,
>>> row_user_id, description, a_count, t_count, length,
> row_project_id,
>>> row_alg_invocation_id, sequence_version, na_sequence_id )
>>> VALUES ( ?, ?, ?, ?, now (), ?, ?, ?, ?, ?, ?, ?,
> ?, ?, ?, ?,
>>> ?, ?, ?, ?, ?, ?, ?, ?, ? )
>>> Values:
>>>
> CAAGGAGGCGGAGAGAATAGAGGGGAGAAAAGAACGGCTTGGGTTTGTCTCTTTATTAT=
ACTTTTTATTG
>
>>>
> TCTTTAGTTCCTTGTGCCTCTTGATATGAATTTTTTCGCTACGCTCGATGCGACCGTCT=
TGAGACAATTG
>>>
> GCTCTGAATTTCTGACGCAAACGCTCCTCCGTATGACTGTTAGGGGCGGTGTCTTTTTA=
CTTTCACGCCT
>>>
> GCGCACGTTTGTCTTTATTTTGTTCTGCTGTTTGCGTGTATTTCTGTTTGTGTATGCTT=
GTGCGCTTTTG
>
>>>
> CTGCATGGGGTGGTGGTGGTTGAAGTCCGTCAAAGTGCCTGTCGCTTTTTTTTTCTCAG=
GGTTTCTTTTT
>>>
> CTTGCTGGAGGTGCAGTGAAGATTTGTTTTGCTTTGCGAGGGGTGGAAAGCGTGAAACA=
CACGCCTCGGT
>>>
> CCTGGCGGTAGAGGGAGGGGCGAGGGGTGGAGATTTATTTGGGGGAAAAGTGTGCTGCC=
GATGAGTTTTT
>
>>>
> TGCCGGATCGGGATCACGGGGAGGAGGAGGTTTGTGACAGTGAACATACGGCACCGCCG=
CCACAAGAGCA
>>>
> GCGACAGTTGCCTCCCGTGGCTGCGGCGTCTAGCGTGCCGCTGCGGCCGCGCGTTTCCC=
ATGAAGAGCCA
>>>
> CTCACCGCCACGTGTGACGCCCAGGCGGCGGTTTCTCGTGCTGGCGGTGCTGGCGACGG=
TGGCGGCAACG
>
>>>
> TCAAGGTTCGCAAGCTGCGGATTTTTGATGACATCACCACCACCACCTCTTCTTCTGAG=
ATGTCTGGAAG
>>>
> GCATGTCAGCACAATTAAGGGGCACTCTGTCCTCAGGCACGCGTTACCGCCGCCTCGGG=
AGAGCGATATT
>>>
> GCGGAACAAAATATGTCGAGTACTGTTGCGCCAACGCAACCTTCATCCTCGACCCAAGT=
CGCTCCGGAGG
>
>>>
> CAGTGGCAGCACCCGTGAGTCTTCATCAAGTGGAAATCTCCGTCAGCAACCGAGCGGGC=
GACGCGCCTGT
>>>
> TGCACCGGCGGAGGTGAGGTCATCGCGGGGACCAGAAGGGAGGGCTTGGCGAGGCAGCC=
CGCCGGGAAGT
>>>
> CGCGGCGACGCGCATGGTGAATATACTGTAGTGAGCATGAGTAAGAAGTTTAGTGAAAA=
AATAGAGGAAT
>
>>>
> TCTGGGAATTTGGGACGCAGGCGGACACGCACGTTCTTGTGATGTTTGTTTCTTCAGTT=
TTGTCGTTTGT
>>> ATTGACTGTCGTTGCGGCACCTCTCTCCCAGTTGGACAT, 1, 1, 0,
>>> ExternalNASequence, 1, 1, 1, 1, NW_001081897, 177, 282,
> 384, 79703,
>>> NW_001081897, 1, Trypanosoma cruzi strain CL Brener
>>> tcruzi_1047053482831, whole genome shotgun sequence.,
> 231, 332,
>>> 1229, 1, 51, 1, 3 at /GUS/gus_home/lib/perl/GUS/ObjRelP/
>>> DbiDbHandle.pm line 166
>>> GUS::ObjRelP::DbiDbHandle::death
>>> ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9ede9fc)', '\x{a} SQL
> ERROR!!
>>> involving\x{a} \x{a} INSERT INTO
> DoTS.ExternalNASequ...' ) called
>>> at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
> line 150
>>> GUS::ObjRelP::DbiDbHandle::sqlExec
>>> ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9ede9fc)',
>>> 'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0xa5bcd8c)', 'ARRAY
> (0xa5be7ec)',
>>> '\x{a} INSERT INTO DoTS.ExternalNASequence ( sequence,
>>> group_r...') called at /GUS/gus_home/lib/perl/GUS/
> ObjRelP/DbiRow.pm
>>> line 666
>>> GUS::ObjRelP::DbiRow::quote_and_insert
>>> ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)',
> 'HASH
>>> (0xa5a7fec)') called at
> /GUS/gus_home/lib/perl/GUS/ObjRelP/ DbiRow.pm
>>> line 613
>>> GUS::ObjRelP::DbiRow::insert
>>> ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)')
> called at /
>>> GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
>>> GUS::Model::GusRow::submit
>>> ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)')
> called at /
>>> GUS/gus_home/lib/perl/GUS/Supported/Plugin/
> InsertSequenceFeatures.pm
>>> line 535
>>>
>>>
> GUS::Supported::Plugin::InsertSequenceFeatures::processSequ=
ence
>>>
> ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x9=
0f15ac)',
>
>>> 'Bio::Seq::RichSeq=3DHASH(0xa4fc60c)', 177) called at
> /GUS/gus_home/
>>> lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 326
>>> GUS::Supported::Plugin::InsertSequenceFeatures::run
>>>
> ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x9=
0f15ac)',
>>> 'HASH(0xa031ae8)') called at
> /GUS/gus_home/lib/perl/GUS/PluginMgr/
>>> GusApplication.pm line 549
>>> eval {...} called at
> /GUS/gus_home/lib/perl/GUS/PluginMgr/
>>> GusApplication.pm line 541
>>> =20
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport
>>> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1)
> called at /GUS/
>>> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459
>>> GUS::PluginMgr::GusApplication::doMajorMode_Run
>>> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures') called
> at /GUS/
>>> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357
>>> GUS::PluginMgr::GusApplication::doMajorMode
>>> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures') called
> at /GUS/
>>> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266
>>> GUS::PluginMgr::GusApplication::parseAndRun
>>> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', 'ARRAY
>>> (0x90e46d8)') called at /GUS/gus_home/bin/ga line 11
>>>
>>> STACK TRACE:
>>> at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
> line 166
>>> GUS::ObjRelP::DbiDbHandle::death
>>> ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9ede9fc)', '\x{a} SQL
> ERROR!!
>>> involving\x{a} \x{a} INSERT INTO
> DoTS.ExternalNASequ...') called
>>> at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
> line 150
>>> GUS::ObjRelP::DbiDbHandle::sqlExec
>>> ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9ede9fc)',
>>> 'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0xa5bcd8c)', 'ARRAY
> (0xa5be7ec)',
>>> '\x{a} INSERT INTO DoTS.ExternalNASequence ( sequence,
>>> group_r...') called at /GUS/gus_home/lib/perl/GUS/
> ObjRelP/DbiRow.pm
>>> line 666
>>> GUS::ObjRelP::DbiRow::quote_and_insert
>>> ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)',
> 'HASH
>>> (0xa5a7fec)') called at
> /GUS/gus_home/lib/perl/GUS/ObjRelP/ DbiRow.pm
>>> line 613
>>> GUS::ObjRelP::DbiRow::insert
>>> ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)')
> called at /
>>> GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
>>> GUS::Model::GusRow::submit
>>> ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)')
> called at /
>>> GUS/gus_home/lib/perl/GUS/Supported/Plugin/
> InsertSequenceFeatures.pm
>>> line 535
>>>
>>>
> GUS::Supported::Plugin::InsertSequenceFeatures::processSequ=
ence
>>>
> ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x9=
0f15ac)',
>>> 'Bio::Seq::RichSeq=3DHASH(0xa4fc60c)', 177) called at
> /GUS/gus_home/
>>> lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 326
>>> GUS::Supported::Plugin::InsertSequenceFeatures::run
>>>
> ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x9=
0f15ac)',
>
>>> 'HASH(0xa031ae8)') called at
> /GUS/gus_home/lib/perl/GUS/PluginMgr/
>>> GusApplication.pm line 549
>>> eval {...} called at
> /GUS/gus_home/lib/perl/GUS/PluginMgr/
>>> GusApplication.pm line 541
>>> =20
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport
>>> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1)
> called at /GUS/
>>> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459
>>> GUS::PluginMgr::GusApplication::doMajorMode_Run
>>> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures') called
> at /GUS/
>>> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357
>>> GUS::PluginMgr::GusApplication::doMajorMode
>>> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)',
>>> 'GUS::Supported::Plugin::InsertSequenceFeatures') called
> at /GUS/
>>> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266
>>> GUS::PluginMgr::GusApplication::parseAndRun
>>> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', 'ARRAY
>>> (0x90e46d8)') called at /GUS/gus_home/bin/ga line 11
>>>
>>> 2005/12/13, Mark S. Heiges <mh...@ug...
> <mailto:mh...@ug...>>: No need to do it
>>> manually, those clever GUS developers made a plugin
>>> for this. Do
>>>
>>> ga GUS::Supported::Plugin::InsertSequenceFeaturesUndo
> --mapFile
>>> $GUS_HOME/config/genbank2gus.xml --algInvocationId 26
> --commit
>>>
>>> (Change the mapFile and the algInvocationId
>>> (dots.externalnasequence.row_alg_invocation_id)
> arguments as needed.
>>> The values I'm giving are based on the log you posted in
> your
>>> 2005-12-06 email).
>>>
>>> On Dec 13, 2005, at 8:33 AM, Ricardo Balbi wrote:
>>>
>>> > Hi,
>>> > I obtained to create the rules and I think that now
> I go to
>>> > obtain to make the load. However, some registers had
> been inserted
>>> > in the previous executions of the ISF and are taking
> error of
>>> > primary key violated. Is there some way to undo what
> already was
>>> > made to execute the plugin again or I have to delete
> the rows
>>> > manually?
>>> >
>>> > thanks,
>>> > Ricardo
>>> >
>>> > 2005/12/9, Fabr=EF=BF=BDcio < fab...@de...
> <mailto:fab...@de...> >: Hello Ricardo and gus-
>>> > devers.
>>> >
>>> > I'm dealing with this same problem in my current Gus +
> Postgres
>>> > installation.
>>> >
>>> > My platform is:
>>> >
>>> > Postgres 8.1 in linux.
>>> >
>>> > I will follow mike's tip and see object.sql file to
> modify rules in
>>> > views.
>>> >
>>> > Best regards,
>>> >
>>> > Fabricio.
>>> >
>>> > -----Mensagem original-----
>>> > De: gus...@li...
> <mailto:gus...@li...>
>>> > [mailto: gus...@li...
> <mailto:gus...@li...>] Em nome=
de
>>> > gus...@li...
> <mailto:gus...@li...>
>>> > Enviada em: sexta-feira, 9 de dezembro de 2005 02:09
>>> > Para: gus...@li...
> <mailto:gus...@li...>
>>> > Assunto: Gusdev-gusdev digest, Vol 1 #741 - 1 msg
>>> >
>>> > Send Gusdev-gusdev mailing list submissions to
>>> > gus...@li...
> <mailto:gus...@li...>
>>> >
>>> > To subscribe or unsubscribe via the World Wide Web, visit
>>> > =20
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>> > or, via email, send a message with subject or body
> 'help' to
>>> > gus...@li...
> <mailto:gus...@li...>
>>> >
>>> > You can reach the person managing the list at
>>> > gus...@li...
> <mailto:gus...@li...>
>>> >
>>> > When replying, please edit your Subject line so it is
> more specific
>>> > than "Re: Contents of Gusdev-gusdev digest..."
>>> >
>>> >
>>> > Today's Topics:
>>> >
>>> > 1. Re: Inserting Sequence Features - Problem with a
> big reference.
>>> > (Michael Saffitz)
>>> >
>>> > --__--__--
>>> >
>>> > Message: 1
>>> > Cc: gus...@li...
> <mailto:gus...@li...>
>>> > From: Michael Saffitz < msa...@pc...
> <mailto:msa...@pc...>>
>>> > Subject: Re: [GUSDEV] Inserting Sequence Features -
> Problem with a
>>> big
>>> > reference.
>>> > Date: Thu, 8 Dec 2005 14:39:12 -0500
>>> > To: Ricardo Balbi < rb...@gm...
> <mailto:rb...@gm...> >
>>> >
>>> >
>>> > On Dec 8, 2005, at 2:34 PM, Ricardo Balbi wrote:
>>> >
>>> > > Yes Michael, this is a 3.5 install.
>>> > > The file exists and the rules too, but they had not
> been created. I
>>> > > created one manually.
>>> > > I will file a bug and submit the sql file.
>>> > >
>>> >
>>> > Hmmm... Ok. Do you still have the log from the
> install? I believe
>>> > this has worked for others, so it may be particular to
> your setup.
>>> > Please include in the bug report your version of
> Postgres, platform,
>>> > etc.
>>> >
>>> > > Do you have a file with all the rules to create in
> my database ?
>>> >
>>> > Yes, that object.sql file should have everything that
> belongs in the
>>> > database.
>>> >
>>> > --Mike
>>> >
>>> >
>>> >
>>> > --__--__--
>>> >
>>> > _______________________________________________
>>> > Gusdev-gusdev mailing list
>>> > Gus...@li...
> <mailto:Gus...@li...>
>>> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>> >
>>> >
>>> > End of Gusdev-gusdev Digest
>>> >
>>> >
>>> >
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>>
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