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From: Ricardo B. <rb...@gm...> - 2006-01-10 17:29:26
|
Mike / Steve, We would like to know if you already had created the rules of the version tables. We believe that with these rules we will go to obtain the loads, using th= e ISF. In case that you have some position, you he could inform to me, please. thanks in advance, Ricardo 2006/1/3, bug...@pc... <bug...@pc...>: > > https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=3D257 > > > msa...@pc... changed: > > What |Removed |Added > > -------------------------------------------------------------------------= --- > Status|RESOLVED |REOPENED > Resolution|INVALID | > > > > > ------- Comment #4 from msa...@pc... 2006-01-03 12:05 ------- > version table rules are indeed not being created. this should be > relatively > straight forward to fix. > > > -- > Configure bugmail: > https://www.cbil.upenn.edu/tracker/userprefs.cgi?tab=3Demail > ------- You are receiving this mail because: ------- > You reported the bug, or are watching the reporter. > |
From: Angel P. <an...@ma...> - 2006-01-06 19:33:23
|
Hello, Continuing this discussion, I believe that mike was talking about the GUS/DBAdmin tool that is uses the canonical XML version of the schema. You can find this file in : ${GUS_HOME}/project_home/GusSchema/Definition/config/gus_schema.xml In this file you will notice that the main superclass tables have subclass entries that correspond to the feature views. These superclass entries contain columns that are common to all sub-views, while the subclass entries contain only those columns specific to a feature. In this case CONFIDENCE and SECONDARY_STRUCTURE. Thus the proper way to add this to your schema would be to first create the subclass entry in the gus_schema.xml file: (diff attached that you can apply to the file): <subclass id="DoTS/AAFeature/PsiPred" name="PsiPred" versioned="true" tablespace="USERS" categoryRef="AA Sequence Features" updatable="true"> <columns> <column id="DoTS/PsiPred/CONFIDENCE" name="CONFIDENCE" nullable="true" length="0" precision="0" type="CLOB"/> <column id="DoTS/PsiPred/SECONDARY_STRUCTURE" name="SECONDARY_STRUCTURE" nullable="true" length="0" precision="0" type="CLOB"/> </columns> </subclass> Then you would produce the schema with dbaDumpSchema: dbaDumpSchema -sourceType xml -source gus_schema.xml -targetType oracle -target gus_schema.sql Also a few more handy options for this tool: dbaDumpSchema -sourceType [db|xml] [-source file] -targetType [oracle|postgres|simple|xml|hbm|hbm3] -target file Where "hbm|hbm3" are Hibernate mapping files for versions 2.x and 3.x, respectively. Hibernate is a Java O/R library, which I am quite fond of right now. You'll notice that the table and view definitions for AAFeature now include CLOBs in the SQL. You will still need to create migration scripts, but this goes a long way to getting the changes into the release cycle so that everyone can benefit. In addition to dbaDumpSchema, there is the dbaCompareSchemas script that compares two schema in the XML format to further assist you with migrations. It would have been a much harder task for me to create the Hibernate 3 mapping classes if the DBAdmin project did not exist, so in the hopes of keeping it alive (now that Mike is leaving) I urge everyone to use this as the preferred method of schema change requests. Lastly, this was *never* filed with Bugzilla as a feature request. Please do so, or risk it getting lost in the ether. -angel Jian Lu wrote: > Chris, > > Happy New Year! > > Sorry for late reply since I was on vacation. We have this view which > has been used for our annotation pipeline. Here is the SQL. > > CREATE VIEW DOTS.PSIPRED AS SELECT > AA_FEATURE_ID, > AA_SEQUENCE_ID, > FEATURE_NAME_ID, > PARENT_ID, > NA_FEATURE_ID, > SUBCLASS_VIEW, > SEQUENCE_ONTOLOGY_ID, > DESCRIPTION, > PFAM_ENTRY_ID, > MOTIF_AA_SEQUENCE_ID, > REPEAT_TYPE_ID, > EXTERNAL_DATABASE_RELEASE_ID, > SOURCE_ID, > PREDICTION_ALGORITHM_ID, > IS_PREDICTED, > REVIEW_STATUS_ID, > CLOB1 AS CONFIDENCE, > CLOB2 AS SECONDARY_STRUCTURE, > MODIFICATION_DATE, USER_READ, USER_WRITE, GROUP_READ, GROUP_WRITE, > OTHER_READ, OTHER_WRITE, ROW_USER_ID, ROW_GROUP_ID, ROW_PROJECT_ID, > ROW_ALG_INVOCATION_ID > FROM DOTS.AAFEATUREIMP > WHERE SUBCLASS_VIEW='PsiPred' > WITH CHECK OPTION; > > Thank you. > > Jian > > Chris Stoeckert wrote: > >> Dear Jian, >> >> Awhile back you had requested the addition of two CLOB attributes to >> AAFeatureImp in order to capture ouput from Psipred. I had approved >> that request but learnt from Mike that with the way we are managing >> schema changes to GUS now "the schema representation abstracts the >> imp tables away, so the clobs would be added automatically when used >> by a subclass. Until there's a subclass that's going to have a clob >> column, I can't force them into the imp table." >> >> This simply means that we need to submit a specific view such as for >> Psipred that has clobs as needed. Can you supply that view (or if you >> prefer a more general view) of AAFeatureImp? >> >> Shailesh, where and how are we storing Psipred output you generated >> for PlasmoDB in GUS? >> >> Thanks, >> Chris >> >> Chris Stoeckert, Ph.D. >> >> Research Associate Professor, Dept. of Genetics >> >> 1415 Blockley Hall, Center for Bioinformatics >> >> 423 Guardian Dr., University of Pennsylvania >> >> Philadelphia, PA 19104 >> >> Ph: 215-573-4409 FAX: 215-573-3111 >> >> > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev -- Angel Pizarro Director, Bioinformatics Facility Institute for Translational Medicine and Therapeutics University of Pennsylvania 806 BRB II/III 421 Curie Blvd. Philadelphia, PA 19104-6160 P: 215-573-3736 F: 215-573-9004 |
From: Elisabetta M. <man...@pc...> - 2006-01-06 18:02:10
|
Juan Carlos Perin has installed the RADSA 2.0.0 at CHOP and has kindly provided detailed notes of what he did from start to finish (including GUS installation) to accomplish this goal. His notes can be useful also to those installing RADSA 2.1.0. I've posted them at http://www.cbil.upenn.edu/downloads/RAD/ as well. (JCPerin_InstallingRADSA.doc). Thanks Juan! Elisabetta |
From: Elisabetta M. <man...@pc...> - 2006-01-06 14:54:25
|
(Apologies if you receive this email more than once, it is being mailed to various mailing lists.) Release 2.1.0 of the RADSA is now available at http://www.cbil.upenn.edu/downloads/RAD/. This is compatible with GUS 3.5. The README file included in the tarball contains instructions both for a fresh install and for upgrading from RADSA 2.0.0. As compared to 2.0.0 this new release contains improved code for the user_registration and ontology entry search forms, and other minor modifications. Elisabetta |
From: Michael S. <m...@sa...> - 2006-01-03 17:06:11
|
Hi Ricardo, I looked into the issue and you're correct, rules are not created for =20= the version tables. I've reopened bug 257 and will take a crack at =20 fixing this today. It was a known (but forgotten) issue in the =20 codebase that was non-trivial to fix, but with another change made a =20 while back should now be relatively straight forward. --Mike On Jan 3, 2006, at 5:33 AM, Ricardo Balbi wrote: > Steve, > I think that the problem is the lack of rules for the views of =20 > xxxVer schemas, as this message: > > sqlExec: INSERT INTO DoTSVer.SourceVer select v.*,69,now(),29 from =20 > DoTS.Source v where v.na_feature_id =3D ? > bindValues (15) > DBD::Pg::st execute failed: ERROR: cannot insert into a view > HINT: You need an unconditional ON INSERT DO INSTEAD rule. > > Would you have an file with the creation of these rules? > In my installation there are 76 views for dotsver, 24 views for =20 > protver, 30 views for radver and 4 views for studyver. > > Ricardo. > > 2005/12/30, Steve Fischer <sfi...@pc...>: fabricio- > > perhaps we can set up a time to talk about this on the phone. what > times are you available next week? > > steve > > fab...@de... wrote: > > >Hello all, > > > >We've tried, unsuccessfully, all sugestions to fix ISF problem. > > > >Swicthing the rules from gus schema to those in objects.sql didn't =20= > solve the > >problem about "Cannot insert on a view" when running ISF. > > > >We have a version of ISF working in a previous gus installation =20 > (some months > >ago) > >when this plugin were in beta version yet. So, we got the rules =20 > from that dots > >schema and put them in our deficient gus (ISF problem). But the =20 > same problem > >persists. > > > >Now we have no idea about what we can do to solve this problem. > > > >If you can do something to solve this bug we would be so grateful. > > > >Thanks in advance, > > > >Fabr=EDcio. > > > >---------------------------------------------------------------- > >This message was sent using IMP, the Internet Messaging Program. > > > > > >------------------------------------------------------- > >This SF.net email is sponsored by: Splunk Inc. Do you grep through =20= > log files > >for problems? Stop! Download the new AJAX search engine that makes > >searching your log files as easy as surfing the web. DOWNLOAD =20 > SPLUNK! > >http://ads.osdn.com/?ad_idv37&alloc_id=16865&op=CCk > >_______________________________________________ > >Gusdev-gusdev mailing list > >Gus...@li... > >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through =20 > log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD =20 > SPLUNK! > http://ads.osdn.com/?ad_idv37&alloc_id=16865&opclick > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
From: Jian Lu <jl...@vb...> - 2006-01-03 14:27:20
|
Chris, Happy New Year! Sorry for late reply since I was on vacation. We have this view which has been used for our annotation pipeline. Here is the SQL. CREATE VIEW DOTS.PSIPRED AS SELECT AA_FEATURE_ID, AA_SEQUENCE_ID, FEATURE_NAME_ID, PARENT_ID, NA_FEATURE_ID, SUBCLASS_VIEW, SEQUENCE_ONTOLOGY_ID, DESCRIPTION, PFAM_ENTRY_ID, MOTIF_AA_SEQUENCE_ID, REPEAT_TYPE_ID, EXTERNAL_DATABASE_RELEASE_ID, SOURCE_ID, PREDICTION_ALGORITHM_ID, IS_PREDICTED, REVIEW_STATUS_ID, CLOB1 AS CONFIDENCE, CLOB2 AS SECONDARY_STRUCTURE, MODIFICATION_DATE, USER_READ, USER_WRITE, GROUP_READ, GROUP_WRITE, OTHER_READ, OTHER_WRITE, ROW_USER_ID, ROW_GROUP_ID, ROW_PROJECT_ID, ROW_ALG_INVOCATION_ID FROM DOTS.AAFEATUREIMP WHERE SUBCLASS_VIEW='PsiPred' WITH CHECK OPTION; Thank you. Jian Chris Stoeckert wrote: > Dear Jian, > > Awhile back you had requested the addition of two CLOB attributes to > AAFeatureImp in order to capture ouput from Psipred. I had approved > that request but learnt from Mike that with the way we are managing > schema changes to GUS now "the schema representation abstracts the imp > tables away, so the clobs would be added automatically when used by a > subclass. Until there's a subclass that's going to have a clob > column, I can't force them into the imp table." > > This simply means that we need to submit a specific view such as for > Psipred that has clobs as needed. Can you supply that view (or if you > prefer a more general view) of AAFeatureImp? > > Shailesh, where and how are we storing Psipred output you generated > for PlasmoDB in GUS? > > Thanks, > Chris > > Chris Stoeckert, Ph.D. > > Research Associate Professor, Dept. of Genetics > > 1415 Blockley Hall, Center for Bioinformatics > > 423 Guardian Dr., University of Pennsylvania > > Philadelphia, PA 19104 > > Ph: 215-573-4409 FAX: 215-573-3111 > > |
From: Ricardo B. <rb...@gm...> - 2006-01-03 13:33:51
|
Steve, I think that the problem is the lack of rules for the views of xxxVer schemas, as this message: sqlExec: INSERT INTO DoTSVer.SourceVer select v.*,69,now(),29 from DoTS.Source v where v.na_feature_id =3D ? bindValues (15) DBD::Pg::st execute failed: ERROR: cannot insert into a view HINT: You need an unconditional ON INSERT DO INSTEAD rule. Would you have an file with the creation of these rules? In my installation there are 76 views for dotsver, 24 views for protver, 30 views for radver and 4 views for studyver. Ricardo. 2005/12/30, Steve Fischer <sfi...@pc...>: > > fabricio- > > perhaps we can set up a time to talk about this on the phone. what > times are you available next week? > > steve > > fab...@de... wrote: > > >Hello all, > > > >We've tried, unsuccessfully, all sugestions to fix ISF problem. > > > >Swicthing the rules from gus schema to those in objects.sql didn't solve > the > >problem about "Cannot insert on a view" when running ISF. > > > >We have a version of ISF working in a previous gus installation (some > months > >ago) > >when this plugin were in beta version yet. So, we got the rules from tha= t > dots > >schema and put them in our deficient gus (ISF problem). But the same > problem > >persists. > > > >Now we have no idea about what we can do to solve this problem. > > > >If you can do something to solve this bug we would be so grateful. > > > >Thanks in advance, > > > >Fabr=EDcio. > > > >---------------------------------------------------------------- > >This message was sent using IMP, the Internet Messaging Program. > > > > > >------------------------------------------------------- > >This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files > >for problems? Stop! Download the new AJAX search engine that makes > >searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > >http://ads.osdn.com/?ad_idv37&alloc_id=16865&op=CCk > >_______________________________________________ > >Gusdev-gusdev mailing list > >Gus...@li... > >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_idv37&alloc_id=16865&opclick > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
From: Steve F. <sfi...@pc...> - 2005-12-30 19:39:18
|
fabricio- perhaps we can set up a time to talk about this on the phone. what=20 times are you available next week? steve fab...@de... wrote: >Hello all, > >We've tried, unsuccessfully, all sugestions to fix ISF problem.=20 > >Swicthing the rules from gus schema to those in objects.sql didn't solve= the >problem about "Cannot insert on a view" when running ISF. > >We have a version of ISF working in a previous gus installation (some mo= nths >ago) >when this plugin were in beta version yet. So, we got the rules from tha= t dots >schema and put them in our deficient gus (ISF problem). But the same pro= blem >persists. > >Now we have no idea about what we can do to solve this problem. > >If you can do something to solve this bug we would be so grateful. > >Thanks in advance, > >Fabr=EDcio. > >---------------------------------------------------------------- >This message was sent using IMP, the Internet Messaging Program. > > >------------------------------------------------------- >This SF.net email is sponsored by: Splunk Inc. Do you grep through log f= iles >for problems? Stop! Download the new AJAX search engine that makes >searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! >http://ads.osdn.com/?ad_idv37&alloc_id=16865&op=CCk >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > =20 > |
From: <fab...@de...> - 2005-12-30 11:36:44
|
Hello all, We've tried, unsuccessfully, all sugestions to fix ISF problem.=20 Swicthing the rules from gus schema to those in objects.sql didn't solve = the problem about "Cannot insert on a view" when running ISF. We have a version of ISF working in a previous gus installation (some mon= ths ago) when this plugin were in beta version yet. So, we got the rules from that= dots schema and put them in our deficient gus (ISF problem). But the same prob= lem persists. Now we have no idea about what we can do to solve this problem. If you can do something to solve this bug we would be so grateful. Thanks in advance, Fabr=EDcio. ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. |
From: Steve F. <sfi...@pc...> - 2005-12-24 13:33:14
|
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 >>> > >>> > >>> > >>> > ------------------------------------------------------- >>> > This SF.net email is sponsored by: Splunk Inc. Do you > grep through >>> > log files >>> > for problems? Stop! Download the new AJAX search > engine that makes >>> > searching your log files as easy as surfing > the web. DOWNLOAD >>> > SPLUNK! >>> > > http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dcli= ck > <http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dcl= ick> >>> > _______________________________________________ >>> > Gusdev-gusdev mailing list >>> > Gus...@li... > <mailto:Gus...@li...> >>> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> > >>> >>> >>> >>> ------------------------------------------------------- >>> This SF.net email is sponsored by: Splunk Inc. Do you > grep through >>> log files >>> for problems? Stop! Download the new AJAX search > engine that makes >>> searching your log files as easy as surfing > the web. DOWNLOAD SPLUNK! >>> http://ads.osdn.com/?ad_idv37&alloc_id=16865&opclick > <http://ads.osdn.com/?ad_idv37&alloc_id%16865&opclick> >>> _______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... > <mailto:Gus...@li...> >>> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > <https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev= > >>> >> >> >> >> ------------------------------------------------------- >> This SF.net email is sponsored by: Splunk Inc. Do you > grep through log >> files >> for problems? Stop! Download the new AJAX search engine > that makes >> searching your log files as easy as surfing > the web. DOWNLOAD SPLUNK! >> http://ads.osdn.com/?ad_idv37&alloc_id=16865&op > <http://ads.osdn.com/?ad_idv37&alloc_id%16865&op>=EF=BF=BDk >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... > <mailto:Gus...@li...> >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > <https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev= > > > > > |
From: Chris S. <sto...@pc...> - 2005-12-23 19:25:03
|
Dear Jian, Awhile back you had requested the addition of two CLOB attributes to AAFeatureImp in order to capture ouput from Psipred. I had approved that request but learnt from Mike that with the way we are managing schema changes to GUS now "the schema representation abstracts the imp tables away, so the clobs would be added automatically when used by a subclass. Until there's a subclass that's going to have a clob column, I can't force them into the imp table." This simply means that we need to submit a specific view such as for Psipred that has clobs as needed. Can you supply that view (or if you prefer a more general view) of AAFeatureImp? Shailesh, where and how are we storing Psipred output you generated for PlasmoDB in GUS? Thanks, Chris Chris Stoeckert, Ph.D. Research Associate Professor, Dept. of Genetics 1415 Blockley Hall, Center for Bioinformatics 423 Guardian Dr., University of Pennsylvania Philadelphia, PA 19104 Ph: 215-573-4409 FAX: 215-573-3111 |
From: Ricardo B. <rb...@gm...> - 2005-12-20 17:30:57
|
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From: Ricardo B. <rb...@gm...> - 2005-12-15 10:38:49
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From: Steve F. <sfi...@pc...> - 2005-12-13 21:22:42
|
the install of GUS should have made a primary key _sq, ie, a database=20 "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 =20 > na_sequence_id values in DoTS.NASequence. Off hand, I do not know why =20 > 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 =20 >> tables are empty. Do you know to say me what is happening? The =20 >> error follows below: >> >> [rbalbi1@crithidia bancos]$ ga =20 >> GUS::Supported::Plugin::InsertSequenceFeatures --mapfile $GUS_HOME/=20 >> config/genbank2gus.xml --inputFileOrDir kinetoplastida_nt --=20 >> fileFormat genbank --extDbName "Kinetoplastida_nt" --extDbRlsVer =20 >> "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 =20 >> Kinetoplastida_nt >> Tue Dec 13 14:38:54 2005 ARG extDbRlsVer 2005-12-06 >> Tue Dec 13 14:38:54 2005 ARG 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 /GUS/=20 >> 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 =20 >> kinetoplastida_nt >> Tue Dec 13 14:38:54 2005 ARG makeSourceids >> Tue Dec 13 14:38:54 2005 ARG mapFile /GUS/gus_home/=20 >> 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 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 =20 >> constraint "pk_nasequenceimp" >> >> ERROR: >> >> SQL ERROR!! involving >> >> INSERT INTO DoTS.ExternalNASequence ( sequence, group_read, =20 >> user_read, other_write, modification_date, subclass_view, =20 >> row_group_id, user_write, other_read, group_write, source_id, =20 >> external_database_release_id, c_count, g_count, taxon_id, name, =20 >> row_user_id, description, a_count, t_count, length, row_project_id, =20 >> row_alg_invocation_id, sequence_version, na_sequence_id ) >> VALUES ( ?, ?, ?, ?, now (), ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?,=20 >> ?, ?, ?, ?, ?, ?, ?, ?, ? ) >> Values: =20 >> CAAGGAGGCGGAGAGAATAGAGGGGAGAAAAGAACGGCTTGGGTTTGTCTCTTTATTATACTTTTTATTG= =20 >> TCTTTAGTTCCTTGTGCCTCTTGATATGAATTTTTTCGCTACGCTCGATGCGACCGTCTTGAGACAATTG= =20 >> GCTCTGAATTTCTGACGCAAACGCTCCTCCGTATGACTGTTAGGGGCGGTGTCTTTTTACTTTCACGCCT= =20 >> GCGCACGTTTGTCTTTATTTTGTTCTGCTGTTTGCGTGTATTTCTGTTTGTGTATGCTTGTGCGCTTTTG= =20 >> CTGCATGGGGTGGTGGTGGTTGAAGTCCGTCAAAGTGCCTGTCGCTTTTTTTTTCTCAGGGTTTCTTTTT= =20 >> CTTGCTGGAGGTGCAGTGAAGATTTGTTTTGCTTTGCGAGGGGTGGAAAGCGTGAAACACACGCCTCGGT= =20 >> CCTGGCGGTAGAGGGAGGGGCGAGGGGTGGAGATTTATTTGGGGGAAAAGTGTGCTGCCGATGAGTTTTT= =20 >> TGCCGGATCGGGATCACGGGGAGGAGGAGGTTTGTGACAGTGAACATACGGCACCGCCGCCACAAGAGCA= =20 >> GCGACAGTTGCCTCCCGTGGCTGCGGCGTCTAGCGTGCCGCTGCGGCCGCGCGTTTCCCATGAAGAGCCA= =20 >> CTCACCGCCACGTGTGACGCCCAGGCGGCGGTTTCTCGTGCTGGCGGTGCTGGCGACGGTGGCGGCAACG= =20 >> TCAAGGTTCGCAAGCTGCGGATTTTTGATGACATCACCACCACCACCTCTTCTTCTGAGATGTCTGGAAG= =20 >> GCATGTCAGCACAATTAAGGGGCACTCTGTCCTCAGGCACGCGTTACCGCCGCCTCGGGAGAGCGATATT= =20 >> GCGGAACAAAATATGTCGAGTACTGTTGCGCCAACGCAACCTTCATCCTCGACCCAAGTCGCTCCGGAGG= =20 >> CAGTGGCAGCACCCGTGAGTCTTCATCAAGTGGAAATCTCCGTCAGCAACCGAGCGGGCGACGCGCCTGT= =20 >> TGCACCGGCGGAGGTGAGGTCATCGCGGGGACCAGAAGGGAGGGCTTGGCGAGGCAGCCCGCCGGGAAGT= =20 >> CGCGGCGACGCGCATGGTGAATATACTGTAGTGAGCATGAGTAAGAAGTTTAGTGAAAAAATAGAGGAAT= =20 >> TCTGGGAATTTGGGACGCAGGCGGACACGCACGTTCTTGTGATGTTTGTTTCTTCAGTTTTGTCGTTTGT= =20 >> ATTGACTGTCGTTGCGGCACCTCTCTCCCAGTTGGACAT, 1, 1, 0, =20 >> ExternalNASequence, 1, 1, 1, 1, NW_001081897, 177, 282, 384, 79703, =20 >> NW_001081897, 1, Trypanosoma cruzi strain CL Brener =20 >> tcruzi_1047053482831, whole genome shotgun sequence., 231, 332, =20 >> 1229, 1, 51, 1, 3 at /GUS/gus_home/lib/perl/GUS/ObjRelP/=20 >> DbiDbHandle.pm line 166 >> GUS::ObjRelP::DbiDbHandle::death=20 >> ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9ede9fc)', '\x{a} SQL ERROR!! =20 >> involving\x{a} \x{a} INSERT INTO DoTS.ExternalNASequ...') called =20 >> at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150 >> GUS::ObjRelP::DbiDbHandle::sqlExec=20 >> ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9ede9fc)', =20 >> 'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0xa5bcd8c)', 'ARRAY (0xa5be7ec)'= ,=20 >> '\x{a} INSERT INTO DoTS.ExternalNASequence ( sequence,=20 >> group_r...') called at /GUS/gus_home/lib/perl/GUS/ ObjRelP/DbiRow.pm=20 >> line 666 >> GUS::ObjRelP::DbiRow::quote_and_insert=20 >> ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)', 'HASH=20 >> (0xa5a7fec)') called at /GUS/gus_home/lib/perl/GUS/ObjRelP/ DbiRow.pm=20 >> line 613 >> GUS::ObjRelP::DbiRow::insert=20 >> ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)') called at /= =20 >> GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692 >> GUS::Model::GusRow::submit=20 >> ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)') called at /= =20 >> GUS/gus_home/lib/perl/GUS/Supported/Plugin/ InsertSequenceFeatures.pm=20 >> line 535 >> =20 >> GUS::Supported::Plugin::InsertSequenceFeatures::processSequence=20 >> ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x90f15ac)', =20 >> 'Bio::Seq::RichSeq=3DHASH(0xa4fc60c)', 177) called at /GUS/gus_home/=20 >> lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 326 >> GUS::Supported::Plugin::InsertSequenceFeatures::run=20 >> ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x90f15ac)', =20 >> 'HASH(0xa031ae8)') called at /GUS/gus_home/lib/perl/GUS/PluginMgr/=20 >> GusApplication.pm line 549 >> eval {...} called at /GUS/gus_home/lib/perl/GUS/PluginMgr/=20 >> GusApplication.pm line 541 >> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport=20 >> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', =20 >> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at /GUS/=20 >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459 >> GUS::PluginMgr::GusApplication::doMajorMode_Run=20 >> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', =20 >> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/=20 >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357 >> GUS::PluginMgr::GusApplication::doMajorMode=20 >> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', =20 >> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/=20 >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266 >> GUS::PluginMgr::GusApplication::parseAndRun=20 >> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', 'ARRAY=20 >> (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=20 >> ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9ede9fc)', '\x{a} SQL ERROR!! =20 >> involving\x{a} \x{a} INSERT INTO DoTS.ExternalNASequ...') called =20 >> at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150 >> GUS::ObjRelP::DbiDbHandle::sqlExec=20 >> ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9ede9fc)', =20 >> 'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0xa5bcd8c)', 'ARRAY (0xa5be7ec)'= ,=20 >> '\x{a} INSERT INTO DoTS.ExternalNASequence ( sequence,=20 >> group_r...') called at /GUS/gus_home/lib/perl/GUS/ ObjRelP/DbiRow.pm=20 >> line 666 >> GUS::ObjRelP::DbiRow::quote_and_insert=20 >> ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)', 'HASH=20 >> (0xa5a7fec)') called at /GUS/gus_home/lib/perl/GUS/ObjRelP/ DbiRow.pm=20 >> line 613 >> GUS::ObjRelP::DbiRow::insert=20 >> ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)') called at /= =20 >> GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692 >> GUS::Model::GusRow::submit=20 >> ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)') called at /= =20 >> GUS/gus_home/lib/perl/GUS/Supported/Plugin/ InsertSequenceFeatures.pm=20 >> line 535 >> =20 >> GUS::Supported::Plugin::InsertSequenceFeatures::processSequence=20 >> ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x90f15ac)', =20 >> 'Bio::Seq::RichSeq=3DHASH(0xa4fc60c)', 177) called at /GUS/gus_home/=20 >> lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 326 >> GUS::Supported::Plugin::InsertSequenceFeatures::run=20 >> ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x90f15ac)', =20 >> 'HASH(0xa031ae8)') called at /GUS/gus_home/lib/perl/GUS/PluginMgr/=20 >> GusApplication.pm line 549 >> eval {...} called at /GUS/gus_home/lib/perl/GUS/PluginMgr/=20 >> GusApplication.pm line 541 >> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport=20 >> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', =20 >> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at /GUS/=20 >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459 >> GUS::PluginMgr::GusApplication::doMajorMode_Run=20 >> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', =20 >> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/=20 >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357 >> GUS::PluginMgr::GusApplication::doMajorMode=20 >> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', =20 >> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/=20 >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266 >> GUS::PluginMgr::GusApplication::parseAndRun=20 >> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', 'ARRAY=20 >> (0x90e46d8)') called at /GUS/gus_home/bin/ga line 11 >> >> 2005/12/13, Mark S. Heiges <mh...@ug...>: No need to do it =20 >> 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=EDcio < 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...] Em nome de >> > gus...@li... >> > Enviada em: sexta-feira, 9 de dezembro de 2005 02:09 >> > Para: gus...@li... >> > Assunto: Gusdev-gusdev digest, Vol 1 #741 - 1 msg >> > >> > Send Gusdev-gusdev mailing list submissions to >> > gus...@li... >> > >> > To subscribe or unsubscribe via the World Wide Web, visit >> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> > or, via email, send a message with subject or body 'help' to >> > gus...@li... >> > >> > You can reach the person managing the list at >> > 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 referenc= e. >> > (Michael Saffitz) >> > >> > --__--__-- >> > >> > Message: 1 >> > Cc: gus...@li... >> > From: Michael Saffitz < msa...@pc...> >> > Subject: Re: [GUSDEV] Inserting Sequence Features - Problem with a=20 >> big >> > reference. >> > Date: Thu, 8 Dec 2005 14:39:12 -0500 >> > To: Ricardo Balbi < 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... >> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> > >> > >> > End of Gusdev-gusdev Digest >> > >> > >> > >> > ------------------------------------------------------- >> > This SF.net email is sponsored by: Splunk Inc. Do you grep through >> > log files >> > for problems? Stop! Download the new AJAX search engine that makes >> > searching your log files as easy as surfing the web. DOWNLOAD >> > SPLUNK! >> > http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick >> > _______________________________________________ >> > Gusdev-gusdev mailing list >> > Gus...@li... >> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> > >> >> >> >> ------------------------------------------------------- >> This SF.net email is sponsored by: Splunk Inc. Do you grep through =20 >> log files >> for problems? Stop! Download the new AJAX search engine that makes >> searching your log files as easy as surfing the web. DOWNLOAD SPLUN= K! >> http://ads.osdn.com/?ad_idv37&alloc_id=16865&opclick >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log=20 > files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_idv37&alloc_id=16865&op=CCk > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
From: Mark S. H. <mh...@ug...> - 2005-12-13 19:39:47
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The 'pk_nasequenceimp' unique constraint prevents duplicate =20 na_sequence_id values in DoTS.NASequence. Off hand, I do not know why =20= 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 =20= > tables are empty. Do you know to say me what is happening? The =20 > error follows below: > > [rbalbi1@crithidia bancos]$ ga =20 > GUS::Supported::Plugin::InsertSequenceFeatures --mapfile $GUS_HOME/=20 > config/genbank2gus.xml --inputFileOrDir kinetoplastida_nt --=20 > fileFormat genbank --extDbName "Kinetoplastida_nt" --extDbRlsVer =20 > "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 =20 > Kinetoplastida_nt > Tue Dec 13 14:38:54 2005 ARG extDbRlsVer 2005-12-06 > Tue Dec 13 14:38:54 2005 ARG 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 /GUS/=20 > 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 =20 > kinetoplastida_nt > Tue Dec 13 14:38:54 2005 ARG makeSourceids > Tue Dec 13 14:38:54 2005 ARG mapFile /GUS/gus_home/=20 > 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 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 =20 > constraint "pk_nasequenceimp" > > ERROR: > > SQL ERROR!! involving > > INSERT INTO DoTS.ExternalNASequence ( sequence, group_read, =20 > user_read, other_write, modification_date, subclass_view, =20 > row_group_id, user_write, other_read, group_write, source_id, =20 > external_database_release_id, c_count, g_count, taxon_id, name, =20 > row_user_id, description, a_count, t_count, length, row_project_id, =20= > row_alg_invocation_id, sequence_version, na_sequence_id ) > VALUES ( ?, ?, ?, ?, now=20 > (), ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? ) > Values: =20 > CAAGGAGGCGGAGAGAATAGAGGGGAGAAAAGAACGGCTTGGGTTTGTCTCTTTATTATACTTTTTATTG=20= > TCTTTAGTTCCTTGTGCCTCTTGATATGAATTTTTTCGCTACGCTCGATGCGACCGTCTTGAGACAATTG=20= > GCTCTGAATTTCTGACGCAAACGCTCCTCCGTATGACTGTTAGGGGCGGTGTCTTTTTACTTTCACGCCT=20= > GCGCACGTTTGTCTTTATTTTGTTCTGCTGTTTGCGTGTATTTCTGTTTGTGTATGCTTGTGCGCTTTTG=20= > CTGCATGGGGTGGTGGTGGTTGAAGTCCGTCAAAGTGCCTGTCGCTTTTTTTTTCTCAGGGTTTCTTTTT=20= > CTTGCTGGAGGTGCAGTGAAGATTTGTTTTGCTTTGCGAGGGGTGGAAAGCGTGAAACACACGCCTCGGT=20= > CCTGGCGGTAGAGGGAGGGGCGAGGGGTGGAGATTTATTTGGGGGAAAAGTGTGCTGCCGATGAGTTTTT=20= > TGCCGGATCGGGATCACGGGGAGGAGGAGGTTTGTGACAGTGAACATACGGCACCGCCGCCACAAGAGCA=20= > GCGACAGTTGCCTCCCGTGGCTGCGGCGTCTAGCGTGCCGCTGCGGCCGCGCGTTTCCCATGAAGAGCCA=20= > CTCACCGCCACGTGTGACGCCCAGGCGGCGGTTTCTCGTGCTGGCGGTGCTGGCGACGGTGGCGGCAACG=20= > TCAAGGTTCGCAAGCTGCGGATTTTTGATGACATCACCACCACCACCTCTTCTTCTGAGATGTCTGGAAG=20= > GCATGTCAGCACAATTAAGGGGCACTCTGTCCTCAGGCACGCGTTACCGCCGCCTCGGGAGAGCGATATT=20= > GCGGAACAAAATATGTCGAGTACTGTTGCGCCAACGCAACCTTCATCCTCGACCCAAGTCGCTCCGGAGG=20= > CAGTGGCAGCACCCGTGAGTCTTCATCAAGTGGAAATCTCCGTCAGCAACCGAGCGGGCGACGCGCCTGT=20= > TGCACCGGCGGAGGTGAGGTCATCGCGGGGACCAGAAGGGAGGGCTTGGCGAGGCAGCCCGCCGGGAAGT=20= > CGCGGCGACGCGCATGGTGAATATACTGTAGTGAGCATGAGTAAGAAGTTTAGTGAAAAAATAGAGGAAT=20= > TCTGGGAATTTGGGACGCAGGCGGACACGCACGTTCTTGTGATGTTTGTTTCTTCAGTTTTGTCGTTTGT=20= > ATTGACTGTCGTTGCGGCACCTCTCTCCCAGTTGGACAT, 1, 1, 0, =20 > ExternalNASequence, 1, 1, 1, 1, NW_001081897, 177, 282, 384, 79703, =20= > NW_001081897, 1, Trypanosoma cruzi strain CL Brener =20 > tcruzi_1047053482831, whole genome shotgun sequence., 231, 332, =20 > 1229, 1, 51, 1, 3 at /GUS/gus_home/lib/perl/GUS/ObjRelP/=20 > DbiDbHandle.pm line 166 > GUS::ObjRelP::DbiDbHandle::death=20 > ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9ede9fc)', '\x{a} SQL ERROR!! =20 > involving\x{a} \x{a} INSERT INTO DoTS.ExternalNASequ...') called =20= > at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150 > GUS::ObjRelP::DbiDbHandle::sqlExec=20 > ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9ede9fc)', =20 > 'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0xa5bcd8c)', 'ARRAY=20 > (0xa5be7ec)', '\x{a} INSERT INTO DoTS.ExternalNASequence =20 > ( sequence, group_r...') called at /GUS/gus_home/lib/perl/GUS/=20 > ObjRelP/DbiRow.pm line 666 > GUS::ObjRelP::DbiRow::quote_and_insert=20 > ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)', 'HASH=20 > (0xa5a7fec)') called at /GUS/gus_home/lib/perl/GUS/ObjRelP/=20 > DbiRow.pm line 613 > GUS::ObjRelP::DbiRow::insert=20 > ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)') called at /=20= > GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692 > GUS::Model::GusRow::submit=20 > ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)') called at /=20= > GUS/gus_home/lib/perl/GUS/Supported/Plugin/=20 > InsertSequenceFeatures.pm line 535 > =20 > GUS::Supported::Plugin::InsertSequenceFeatures::processSequence=20 > ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x90f15ac)', =20= > 'Bio::Seq::RichSeq=3DHASH(0xa4fc60c)', 177) called at /GUS/gus_home/=20= > lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 326 > GUS::Supported::Plugin::InsertSequenceFeatures::run=20 > ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x90f15ac)', =20= > 'HASH(0xa031ae8)') called at /GUS/gus_home/lib/perl/GUS/PluginMgr/=20 > GusApplication.pm line 549 > eval {...} called at /GUS/gus_home/lib/perl/GUS/PluginMgr/=20 > GusApplication.pm line 541 > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport=20 > ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', =20 > 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at /GUS/=20= > gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459 > GUS::PluginMgr::GusApplication::doMajorMode_Run=20 > ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', =20 > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/=20 > gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357 > GUS::PluginMgr::GusApplication::doMajorMode=20 > ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', =20 > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/=20 > gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266 > GUS::PluginMgr::GusApplication::parseAndRun=20 > ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', 'ARRAY=20 > (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=20 > ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9ede9fc)', '\x{a} SQL ERROR!! =20 > involving\x{a} \x{a} INSERT INTO DoTS.ExternalNASequ...') called =20= > at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150 > GUS::ObjRelP::DbiDbHandle::sqlExec=20 > ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9ede9fc)', =20 > 'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0xa5bcd8c)', 'ARRAY=20 > (0xa5be7ec)', '\x{a} INSERT INTO DoTS.ExternalNASequence =20 > ( sequence, group_r...') called at /GUS/gus_home/lib/perl/GUS/=20 > ObjRelP/DbiRow.pm line 666 > GUS::ObjRelP::DbiRow::quote_and_insert=20 > ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)', 'HASH=20 > (0xa5a7fec)') called at /GUS/gus_home/lib/perl/GUS/ObjRelP/=20 > DbiRow.pm line 613 > GUS::ObjRelP::DbiRow::insert=20 > ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)') called at /=20= > GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692 > GUS::Model::GusRow::submit=20 > ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)') called at /=20= > GUS/gus_home/lib/perl/GUS/Supported/Plugin/=20 > InsertSequenceFeatures.pm line 535 > =20 > GUS::Supported::Plugin::InsertSequenceFeatures::processSequence=20 > ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x90f15ac)', =20= > 'Bio::Seq::RichSeq=3DHASH(0xa4fc60c)', 177) called at /GUS/gus_home/=20= > lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 326 > GUS::Supported::Plugin::InsertSequenceFeatures::run=20 > ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x90f15ac)', =20= > 'HASH(0xa031ae8)') called at /GUS/gus_home/lib/perl/GUS/PluginMgr/=20 > GusApplication.pm line 549 > eval {...} called at /GUS/gus_home/lib/perl/GUS/PluginMgr/=20 > GusApplication.pm line 541 > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport=20 > ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', =20 > 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at /GUS/=20= > gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459 > GUS::PluginMgr::GusApplication::doMajorMode_Run=20 > ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', =20 > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/=20 > gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357 > GUS::PluginMgr::GusApplication::doMajorMode=20 > ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', =20 > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/=20 > gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266 > GUS::PluginMgr::GusApplication::parseAndRun=20 > ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', 'ARRAY=20 > (0x90e46d8)') called at /GUS/gus_home/bin/ga line 11 > > 2005/12/13, Mark S. Heiges <mh...@ug...>: No need to do it =20 > 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=EDcio < fab...@de...>: Hello Ricardo and =20= > 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...] Em nome de > > gus...@li... > > Enviada em: sexta-feira, 9 de dezembro de 2005 02:09 > > Para: gus...@li... > > Assunto: Gusdev-gusdev digest, Vol 1 #741 - 1 msg > > > > Send Gusdev-gusdev mailing list submissions to > > gus...@li... > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > or, via email, send a message with subject or body 'help' to > > gus...@li... > > > > You can reach the person managing the list at > > 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 =20 > reference. > > (Michael Saffitz) > > > > --__--__-- > > > > Message: 1 > > Cc: gus...@li... > > From: Michael Saffitz < msa...@pc...> > > Subject: Re: [GUSDEV] Inserting Sequence Features - Problem with =20 > a big > > reference. > > Date: Thu, 8 Dec 2005 14:39:12 -0500 > > To: Ricardo Balbi < 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 =20 > 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... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > End of Gusdev-gusdev Digest > > > > > > > > ------------------------------------------------------- > > This SF.net email is sponsored by: Splunk Inc. Do you grep through > > log files > > for problems? Stop! Download the new AJAX search engine that makes > > searching your log files as easy as surfing the web. DOWNLOAD > > SPLUNK! > > http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through =20 > log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD =20 > SPLUNK! > http://ads.osdn.com/?ad_idv37&alloc_id=16865&opclick > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
From: Ricardo B. <rb...@gm...> - 2005-12-13 16:46:55
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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 2005-12-06 Tue Dec 13 14:38:54 2005 ARG 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 /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 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 constrain= t "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: CAAGGAGGCGGAGAGAATAGAGGGGAGAAAAGAACGGCTTGGGTTTGTCTCTTTATTATACTTTTTATTGTCTTT= AGTTCCTTGTGCCTCTTGATATGAATTTTTTCGCTACGCTCGATGCGACCGTCTTGAGACAATTGGCTCTGAATT= TCTGACGCAAACGCTCCTCCGTATGACTGTTAGGGGCGGTGTCTTTTTACTTTCACGCCTGCGCACGTTTGTCTT= TATTTTGTTCTGCTGTTTGCGTGTATTTCTGTTTGTGTATGCTTGTGCGCTTTTGCTGCATGGGGTGGTGGTGGT= TGAAGTCCGTCAAAGTGCCTGTCGCTTTTTTTTTCTCAGGGTTTCTTTTTCTTGCTGGAGGTGCAGTGAAGATTT= GTTTTGCTTTGCGAGGGGTGGAAAGCGTGAAACACACGCCTCGGTCCTGGCGGTAGAGGGAGGGGCGAGGGGTGG= AGATTTATTTGGGGGAAAAGTGTGCTGCCGATGAGTTTTTTGCCGGATCGGGATCACGGGGAGGAGGAGGTTTGT= GACAGTGAACATACGGCACCGCCGCCACAAGAGCAGCGACAGTTGCCTCCCGTGGCTGCGGCGTCTAGCGTGCCG= CTGCGGCCGCGCGTTTCCCATGAAGAGCCACTCACCGCCACGTGTGACGCCCAGGCGGCGGTTTCTCGTGCTGGC= GGTGCTGGCGACGGTGGCGGCAACGTCAAGGTTCGCAAGCTGCGGATTTTTGATGACATCACCACCACCACCTCT= TCTTCTGAGATGTCTGGAAGGCATGTCAGCACAATTAAGGGGCACTCTGTCCTCAGGCACGCGTTACCGCCGCCT= CGGGAGAGCGATATTGCGGAACAAAATATGTCGAGTACTGTTGCGCCAACGCAACCTTCATCCTCGACCCAAGTC= GCTCCGGAGGCAGTGGCAGCACCCGTGAGTCTTCATCAAGTGGAAATCTCCGTCAGCAACCGAGCGGGCGACGCG= CCTGTTGCACCGGCGGAGGTGAGGTCATCGCGGGGACCAGAAGGGAGGGCTTGGCGAGGCAGCCCGCCGGGAAGT= CGCGGCGACGCGCATGGTGAATATACTGTAGTGAGCATGAGTAAGAAGTTTAGTGAAAAAATAGAGGAATTCTGG= GAATTTGGGACGCAGGCGGACACGCACGTTCTTGTGATGTTTGTTTCTTCAGTTTTGTCGTTTGTATTGACTGTC= GTTGCGGCACCTCTCTCCCAGTTGGACAT, 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(0x9ede9f= c)', '\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(0x9ede= 9fc)', '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::ExternalNASequenc= e=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(0= xa4dbff8)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692 GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa= 4dbff8)') called at /GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 535 GUS::Supported::Plugin::InsertSequenceFeatures::processSequence('GUS::Suppo= rted::Plugin::InsertSequenceFeatures=3DHASH(0x90f15ac)', '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(0x90f15ac)', '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 GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::Gu= sApplication=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::GusApplica= tion=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(0x9ede9f= c)', '\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(0x9ede= 9fc)', '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::ExternalNASequenc= e=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(0= xa4dbff8)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692 GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa= 4dbff8)') called at /GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 535 GUS::Supported::Plugin::InsertSequenceFeatures::processSequence('GUS::Suppo= rted::Plugin::InsertSequenceFeatures=3DHASH(0x90f15ac)', '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(0x90f15ac)', '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 GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::Gu= sApplication=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::GusApplica= tion=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...>: > > 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=EDcio <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...] Em nome de > > gus...@li... > > Enviada em: sexta-feira, 9 de dezembro de 2005 02:09 > > Para: gus...@li... > > Assunto: Gusdev-gusdev digest, Vol 1 #741 - 1 msg > > > > Send Gusdev-gusdev mailing list submissions to > > gus...@li... > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > or, via email, send a message with subject or body 'help' to > > gus...@li... > > > > You can reach the person managing the list at > > 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... > > From: Michael Saffitz < 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... > > > > > > > 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... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > End of Gusdev-gusdev Digest > > > > > > > > ------------------------------------------------------- > > This SF.net email is sponsored by: Splunk Inc. Do you grep through > > log files > > for problems? Stop! Download the new AJAX search engine that makes > > searching your log files as easy as surfing the web. DOWNLOAD > > SPLUNK! > > http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_idv37&alloc_id=16865&opclick > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
From: Mark S. H. <mh...@ug...> - 2005-12-13 14:49:59
|
No need to do it manually, those clever GUS developers made a plugin =20 for this. Do ga GUS::Supported::Plugin::InsertSequenceFeaturesUndo --mapFile =20 $GUS_HOME/config/genbank2gus.xml --algInvocationId 26 --commit (Change the mapFile and the algInvocationId =20 (dots.externalnasequence.row_alg_invocation_id) arguments as needed. =20 The values I'm giving are based on the log you posted in your =20 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 =20 > obtain to make the load. However, some registers had been inserted =20= > in the previous executions of the ISF and are taking error of =20 > primary key violated. Is there some way to undo what already was =20 > made to execute the plugin again or I have to delete the rows =20 > manually? > > thanks, > Ricardo > > 2005/12/9, Fabr=EDcio <fab...@de...>: Hello Ricardo and gus-=20= > 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 =20= > views. > > Best regards, > > Fabricio. > > -----Mensagem original----- > De: gus...@li... > [mailto: gus...@li...] Em nome de > gus...@li... > Enviada em: sexta-feira, 9 de dezembro de 2005 02:09 > Para: gus...@li... > Assunto: Gusdev-gusdev digest, Vol 1 #741 - 1 msg > > Send Gusdev-gusdev mailing list submissions to > gus...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > or, via email, send a message with subject or body 'help' to > gus...@li... > > You can reach the person managing the list at > 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... > From: Michael Saffitz < 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... > > > > 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... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > End of Gusdev-gusdev Digest > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through =20 > log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD =20 > SPLUNK! > http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
From: Ricardo B. <rb...@gm...> - 2005-12-13 13:33:16
|
Hi, I obtained to create the rules and I think that now I go to obtain to mak= e 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=EDcio <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...] Em nome de > gus...@li... > Enviada em: sexta-feira, 9 de dezembro de 2005 02:09 > Para: gus...@li... > Assunto: Gusdev-gusdev digest, Vol 1 #741 - 1 msg > > Send Gusdev-gusdev mailing list submissions to > gus...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > or, via email, send a message with subject or body 'help' to > gus...@li... > > You can reach the person managing the list at > 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... > From: Michael Saffitz <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...> > > > 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... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > End of Gusdev-gusdev Digest > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
From: <fab...@de...> - 2005-12-09 10:20:54
|
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...] Em nome de gus...@li... Enviada em: sexta-feira, 9 de dezembro de 2005 02:09 Para: gus...@li... Assunto: Gusdev-gusdev digest, Vol 1 #741 - 1 msg Send Gusdev-gusdev mailing list submissions to gus...@li... To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev or, via email, send a message with subject or body 'help' to gus...@li... You can reach the person managing the list at 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... From: Michael Saffitz <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...> 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... https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev End of Gusdev-gusdev Digest |
From: Michael S. <msa...@pc...> - 2005-12-08 19:39:22
|
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 |
From: Ricardo B. <rb...@gm...> - 2005-12-08 19:34:37
|
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. Do you have a file with all the rules to create in my database ? thanks, Ricardo 2005/12/8, Michael Saffitz <msa...@pc...>: > > > Yes. Is this a 3.5 install? These rules should have been created > automatically. There should be a $GUS_HOME/config/SchemaInstall- > objects.sql file (or similar, if using the trunk) that logged all > created objects/rules in the database-- are the rules in that file? > If so, then the rule was created but incorrectly-- please file a bug > if that's the case, and make sure to submit that file. > > --Mike > > On Dec 8, 2005, at 1:53 PM, Mark S. Heiges wrote: > > > That's error looks specific for Postgres which I don't use. Someone > > else may need to help here. A quick search at google.com for > > "ERROR: cannot insert into a view" or "You need an unconditional > > ON INSERT DO INSTEAD rule" turns up several clues. > > > > -Mark > > > > Mark Heiges > > CryptoDB.org > > C210 Life Sciences Building > > Center for Tropical and Emerging Global Diseases > > University of Georgia, Athens, GA 30602 > > TEL: (706) 542-1447 FAX: (706) 542-3582 > > > > > > On Dec 8, 2005, at 6:04 AM, Ricardo Balbi wrote: > > > >> Thanks Mark, > >> > >> But now I have another error. > >> It follows below: > >> > >> [rbalbi1@crithidia bancos]$ ga > >> GUS::Supported::Plugin::InsertSequenceFeatures --mapfile $GUS_HOME/ > >> config/genbank2gus.xml --inputFileOrDir kinetoplastida_nt -- > >> fileFormat genbank --extDbName "Kinetoplastida_nt" --extDbRlsVer > >> "2005-12-06" --commit > >> Thu Dec 8 09:04:53 2005 ARG algoinvo 1 > >> Thu Dec 8 09:04:53 2005 ARG comment > >> Thu Dec 8 09:04:53 2005 ARG commit 1 > >> Thu Dec 8 09:04:53 2005 ARG debug 0 > >> Thu Dec 8 09:04:53 2005 ARG defaultOrganism > >> Thu Dec 8 09:04:53 2005 ARG extDbName > >> Kinetoplastida_nt > >> Thu Dec 8 09:04:53 2005 ARG extDbRlsVer 2005-12-06 > >> Thu Dec 8 09:04:53 2005 ARG fileFormat genbank > >> Thu Dec 8 09:04:53 2005 ARG gff2GroupTag > >> Thu Dec 8 09:04:53 2005 ARG group > >> Thu Dec 8 09:04:53 2005 ARG gusconfigfile /GUS/ > >> gus_home/config/gus.config > >> Thu Dec 8 09:04:53 2005 ARG handlerExternalDbs > >> Thu Dec 8 09:04:53 2005 ARG help > >> Thu Dec 8 09:04:53 2005 ARG helpHTML > >> Thu Dec 8 09:04:53 2005 ARG inputFileExtension > >> Thu Dec 8 09:04:53 2005 ARG inputFileOrDir > >> kinetoplastida_nt > >> Thu Dec 8 09:04:53 2005 ARG makeSourceids > >> Thu Dec 8 09:04:53 2005 ARG mapFile /GUS/gus_home/ > >> config/genbank2gus.xml > >> Thu Dec 8 09:04:53 2005 ARG naSequenceSubclass > >> Thu Dec 8 09:04:53 2005 ARG project > >> Thu Dec 8 09:04:53 2005 ARG seqIdColumn source_id > >> Thu Dec 8 09:04:53 2005 ARG seqSoTerm > >> Thu Dec 8 09:04:53 2005 ARG seqType > >> Thu Dec 8 09:04:53 2005 ARG soCvsVersion > >> Thu Dec 8 09:04:53 2005 ARG sqlVerbose 0 > >> Thu Dec 8 09:04:53 2005 ARG testNumber > >> Thu Dec 8 09:04:53 2005 ARG user > >> Thu Dec 8 09:04:53 2005 ARG verbose 0 > >> Thu Dec 8 09:04:53 2005 ARG veryVerbose 0 > >> Thu Dec 8 09:04:53 2005 AlgInvocationId 30 > >> Thu Dec 8 09:04:53 2005 COMMIT commit on > >> Thu Dec 8 09:04:55 2005 Processing file > >> 'kinetoplastida_nt'... > >> DBD::Pg::st execute failed: ERROR: cannot insert into a view > >> HINT: You need an unconditional ON INSERT DO INSTEAD rule. > >> > >> ERROR: > >> > >> SQL ERROR!! involving > >> > >> Values: 4 at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm > >> line 166 > >> GUS::ObjRelP::DbiDbHandle::death > >> ('GUS::ObjRelP::DbiDbHandle=3DHASH(0xaa904b0)', '\x{a} SQL ERROR!! > >> involving\x{a} \x{a} Values: 4') called at /GUS/gus_home/lib/perl/ > >> GUS/ObjRelP/DbiDbHandle.pm line 150 > >> GUS::ObjRelP::DbiDbHandle::sqlExec > >> ('GUS::ObjRelP::DbiDbHandle=3DHASH(0xaa904b0)', > >> 'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0xb2b07b0)', 'ARRAY > >> (0xa148314)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm > >> line 1813 > >> GUS::Model::GusRow::version('GUS::Model::DoTS::Source=3DHASH > >> (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm > >> line 1680 > >> GUS::Model::GusRow::submit('GUS::Model::DoTS::Source=3DHASH > >> (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Supported/ > >> Plugin/InsertSequenceFeatures.pm line 731 > >> > >> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees > >> ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x9ca3920)', > >> 'Bio::Seq::RichSeq=3DHASH(0xb0aa2d8)', 4, 177) called at /GUS/ > >> gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm > >> line 330 > >> GUS::Supported::Plugin::InsertSequenceFeatures::run > >> ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x9ca3920)', > >> 'HASH(0xabe05b0)') 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 > >> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport > >> ('GUS::PluginMgr::GusApplication=3DHASH(0x9c82c20)', > >> '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(0x9c82c20)', > >> '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(0x9c82c20)', > >> '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(0x9c82c20)', 'ARRAY > >> (0x9c96700)') 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(0xaa904b0)', '\x{a} SQL ERROR!! > >> involving\x{a} \x{a} Values: 4') called at /GUS/gus_home/lib/perl/ > >> GUS/ObjRelP/DbiDbHandle.pm line 150 > >> GUS::ObjRelP::DbiDbHandle::sqlExec > >> ('GUS::ObjRelP::DbiDbHandle=3DHASH(0xaa904b0)', > >> 'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0xb2b07b0)', 'ARRAY > >> (0xa148314)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm > >> line 1813 > >> GUS::Model::GusRow::version('GUS::Model::DoTS::Source=3DHASH > >> (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm > >> line 1680 > >> GUS::Model::GusRow::submit('GUS::Model::DoTS::Source=3DHASH > >> (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Supported/ > >> Plugin/InsertSequenceFeatures.pm line 731 > >> > >> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees > >> ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x9ca3920)', > >> 'Bio::Seq::RichSeq=3DHASH(0xb0aa2d8)', 4, 177) called at /GUS/ > >> gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm > >> line 330 > >> GUS::Supported::Plugin::InsertSequenceFeatures::run > >> ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x9ca3920)', > >> 'HASH(0xabe05b0)') 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 > >> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport > >> ('GUS::PluginMgr::GusApplication=3DHASH(0x9c82c20)', > >> '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(0x9c82c20)', > >> '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(0x9c82c20)', > >> '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(0x9c82c20)', 'ARRAY > >> (0x9c96700)') called at /GUS/gus_home/bin/ga line 11 > >> > >> Could you help me ? > >> > >> thanks again, > >> Ricardo Balbi > >> > >> > >> > >> > >> > >> 2005/12/7, Mark S. Heiges <mh...@ug...>: One short term > >> solution is to adjust your local schema "alter table > >> SRes.Reference modify (author varchar2(4000))", or something like > >> that, and then restart the loading. > >> > >> You can also file a feature request in the GUS Schema issue tracker > >> to increase that column in a future release - https:// > >> www.cbil.upenn.edu/tracker. > >> > >> On Dec 6, 2005, at 6:48 PM, Ricardo Balbi wrote: > >> > >> > Hi, > >> > > >> > I am trying to load kinetoplastida_nt, using > >> > InsertSequenceFeatures plugin. But I am not obtaining. > >> > Kinetoplastida_nt has a register whose author field exceeds the > >> > maximum size the table sres.reference . > >> > > >> > How I must proceed to load this base? > >> > > >> > It follows below the error: > >> > > >> > [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" --commit > >> > Tue Dec 6 21:32:42 2005 ARG algoinvo 1 > >> > Tue Dec 6 21:32:42 2005 ARG comment > >> > Tue Dec 6 21:32:42 2005 ARG commit 1 > >> > Tue Dec 6 21:32:42 2005 ARG debug 0 > >> > Tue Dec 6 21:32:42 2005 ARG defaultOrganism > >> > Tue Dec 6 21:32:42 2005 ARG extDbName > >> > Kinetoplastida_nt > >> > Tue Dec 6 21:32:42 2005 ARG extDbRlsVer 2005-12-06 > >> > Tue Dec 6 21:32:42 2005 ARG fileFormat genbank > >> > Tue Dec 6 21:32:42 2005 ARG gff2GroupTag > >> > Tue Dec 6 21:32:42 2005 ARG group > >> > Tue Dec 6 21:32:42 2005 ARG gusconfigfile /GUS/ > >> > gus_home/config/gus.config > >> > Tue Dec 6 21:32:42 2005 ARG handlerExternalDbs > >> > Tue Dec 6 21:32:42 2005 ARG help > >> > Tue Dec 6 21:32:42 2005 ARG helpHTML > >> > Tue Dec 6 21:32:42 2005 ARG inputFileExtension > >> > Tue Dec 6 21:32:42 2005 ARG inputFileOrDir > >> > kinetoplastida_nt > >> > Tue Dec 6 21:32:42 2005 ARG makeSourceids > >> > Tue Dec 6 21:32:42 2005 ARG mapFile /GUS/gus_home/ > >> > config/genbank2gus.xml > >> > Tue Dec 6 21:32:42 2005 ARG naSequenceSubclass > >> > Tue Dec 6 21:32:42 2005 ARG project > >> > Tue Dec 6 21:32:42 2005 ARG seqIdColumn source_id > >> > Tue Dec 6 21:32:42 2005 ARG seqSoTerm > >> > Tue Dec 6 21:32:42 2005 ARG seqType > >> > Tue Dec 6 21:32:42 2005 ARG soCvsVersion > >> > Tue Dec 6 21:32:42 2005 ARG sqlVerbose 0 > >> > Tue Dec 6 21:32:42 2005 ARG testNumber > >> > Tue Dec 6 21:32:42 2005 ARG user > >> > Tue Dec 6 21:32:42 2005 ARG verbose 0 > >> > Tue Dec 6 21:32:42 2005 ARG veryVerbose 0 > >> > Tue Dec 6 21:32:42 2005 AlgInvocationId 26 > >> > Tue Dec 6 21:32:42 2005 COMMIT commit on > >> > Tue Dec 6 21:32:44 2005 Processing file > >> 'kinetoplastida_nt'... > >> > DBD::Pg::st execute failed: ERROR: value too long for type > >> > character varying(1000) > >> > > >> > ERROR: > >> > > >> > SQL ERROR!! involving > >> > > >> > INSERT INTO SRes.Reference ( journal_or_book_name, > >> > group_write, other_read, group_read, author, user_read, > >> > row_user_id, reference_id, modification_date, other_write, > >> > row_alg_invocation_id, row_project_id, row_group_id, title, > >> > user_write ) > >> > VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ?, ? ) > >> > Values: Science 309 (5733), 409-415 (2005) PUBMED 16020725, 1, > >> > 1, 1, El-Sayed,N.M., Myler,P.J., Bartholomeu,D.C., Nilsson,D., > >> > Aggarwal,G., Tran,A.N., Ghedin,E., Worthey,E.A., Delcher,A.L., > >> > Blandin,G., Westenberger, S.J., Caler,E., Cerqueira,G.C., > >> > Branche,C., Haas,B., Anupama,A., Arner,E., Aslund,L., Attipoe,P., > >> > Bontempi,E., Bringaud,F., Burton,P., Cadag,E., Campbell,D.A., > >> > Carrington,M., Crabtree,J., Darban,H., da Silveira, J.F., de > >> > Jong,P., Edwards,K., Englund,P.T., Fazelina,G., Feldblyum,T., > >> > Ferella,M., Frasch,A.C., Gull,K., Horn,D., Hou,L., Huang,Y., > >> > Kindlund,E., Klingbeil,M., Kluge,S., Koo,H., Lacerda,D., > >> > Levin, M.J., Lorenzi,H., Louie,T., Machado,C.R., McCulloch,R., > >> > McKenna,A., Mizuno,Y., Mottram,J.C., Nelson,S., Ochaya,S., > >> > Osoegawa,K., Pai,G., Parsons,M., Pentony,M., Pettersson,U., Pop,M., > >> > Ramirez,J.L., Rinta,J., Robertson,L., Salzberg, S.L., Sanchez,D.O., > >> > Seyler,A., Sharma,R., Shetty,J., Simpson,A.J., Sisk,E., Tammi,M.T., > >> > Tarleton,R., Teixeira,S., Van Aken,S., Vogt,C., Ward,P.N., > >> > Wickstead,B., Wortman,J., White,O., Fraser,C.M., Stuart, K.D. and > >> > Andersson,B., 1, 1, 6, 0, 26, 1, 1, The genome sequence of > >> > Trypanosoma cruzi, etiologic agent of Chagas disease, 1 at /GUS/ > >> > gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166 > >> > GUS::ObjRelP::DbiDbHandle::death > >> > ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x91f4d14)', '\x{a} SQL ERROR!! > >> > involving\x{a} \x{a} INSERT INTO SRes.Reference ( j...') called > >> > at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150 > >> > GUS::ObjRelP::DbiDbHandle::sqlExec > >> > ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x91f4d14)', > >> > 'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0x8e826cc)', 'ARRAY > >> > (0x8e82708)', '\x{a} INSERT INTO SRes.Reference > >> > ( journal_or_book_name, grou...') called at /GUS/gus_home/lib/ > >> perl/ > >> > GUS/ObjRelP/DbiRow.pm line 666 > >> > GUS::ObjRelP::DbiRow::quote_and_insert > >> > ('GUS::Model::SRes::Reference=3DHASH(0x987901c)', 'HASH(0x9889d48)') > >> > called at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 613 > >> > GUS::ObjRelP::DbiRow::insert > >> > ('GUS::Model::SRes::Reference=3DHASH(0x987901c)') called at /GUS/ > >> > gus_home/lib/perl/GUS/Model/GusRow.pm line 1692 > >> > > >> > > >> > thanks, > >> > Ricardo > >> > >> > > > > > > > > ------------------------------------------------------- > > This SF.net email is sponsored by: Splunk Inc. Do you grep through > > log files > > for problems? Stop! Download the new AJAX search engine that makes > > searching your log files as easy as surfing the web. DOWNLOAD > > SPLUNK! > > http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
From: Steve F. <sfi...@pc...> - 2005-12-08 19:19:02
|
however, we manage the build of massive projects such as PlasmoDB and AllGenes very successfully with the GUS Pipeline API. a fancy workflow might be nice in concept, but, our simple pipeline api is very effective at managing the build of large datasets. steve Angel Pizarro wrote: > Agreement with Mike here. GUS used to have a set of tables to capture > the state of workflows, such as a build of the dna assemblies. These > tables where agonized over and well thought out, but ultimately went > unused and have subsequently been deleted from the schema. There are > several reasons: > > -Most of the tasks we faced in a workflow where serial and did not > contain any sort of decision points. > -Using flat files to record state and recover from errors works just > fine and is much easier to implement when the above holds true. > > Additionally, there are many workflow-focused open source projects out > there that you can use to define and record the state of complex > asynch workflows that are much more well thought out and are actually > supported by an enthusiastic community. I recommend that if you want > to pursue this further, you take advantage of work being done in the > workflow management systems space, and limit the use of GUS to a data > model that a particular workflow accesses. > > -angel > > Michael Saffitz wrote: > >> >> Hi Ricardo, >> >> GUS doesn't have direct support for workflows or webservices. >> >> There are, however, several groups that are using GUS as the data >> storage system for web services. This usually involves writing a >> small amount of code to extract the data and deliver it. There are >> also some groups that have expressed an interest in using GUS with >> workflows, so this is a good area for collaboration and development. >> >> GUS does have a pipeline API, but I suspect it's not quite what >> you're looking for. >> >> --Mike >> >> >> On Dec 8, 2005, at 1:09 PM, Ricardo Balbi wrote: >> >>> Hi, >>> >>> A doubt: >>> Has support for management of workflows in some schema of gus >>> ? Support for storage of the definition, instances, in and out >>> parameters, etc. >>> Also has support for web services? >>> >>> []'s, >>> Ricardo Balbi >> >> >> >> >> >> ------------------------------------------------------- >> This SF.net email is sponsored by: Splunk Inc. Do you grep through >> log files >> for problems? Stop! Download the new AJAX search engine that makes >> searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! >> http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > |
From: Michael S. <msa...@pc...> - 2005-12-08 19:02:59
|
Yes. Is this a 3.5 install? These rules should have been created automatically. There should be a $GUS_HOME/config/SchemaInstall- objects.sql file (or similar, if using the trunk) that logged all created objects/rules in the database-- are the rules in that file? If so, then the rule was created but incorrectly-- please file a bug if that's the case, and make sure to submit that file. --Mike On Dec 8, 2005, at 1:53 PM, Mark S. Heiges wrote: > That's error looks specific for Postgres which I don't use. Someone > else may need to help here. A quick search at google.com for > "ERROR: cannot insert into a view" or "You need an unconditional > ON INSERT DO INSTEAD rule" turns up several clues. > > -Mark > > Mark Heiges > CryptoDB.org > C210 Life Sciences Building > Center for Tropical and Emerging Global Diseases > University of Georgia, Athens, GA 30602 > TEL: (706) 542-1447 FAX: (706) 542-3582 > > > On Dec 8, 2005, at 6:04 AM, Ricardo Balbi wrote: > >> Thanks Mark, >> >> But now I have another error. >> It follows below: >> >> [rbalbi1@crithidia bancos]$ ga >> GUS::Supported::Plugin::InsertSequenceFeatures --mapfile $GUS_HOME/ >> config/genbank2gus.xml --inputFileOrDir kinetoplastida_nt -- >> fileFormat genbank --extDbName "Kinetoplastida_nt" --extDbRlsVer >> "2005-12-06" --commit >> Thu Dec 8 09:04:53 2005 ARG algoinvo 1 >> Thu Dec 8 09:04:53 2005 ARG comment >> Thu Dec 8 09:04:53 2005 ARG commit 1 >> Thu Dec 8 09:04:53 2005 ARG debug 0 >> Thu Dec 8 09:04:53 2005 ARG defaultOrganism >> Thu Dec 8 09:04:53 2005 ARG extDbName >> Kinetoplastida_nt >> Thu Dec 8 09:04:53 2005 ARG extDbRlsVer 2005-12-06 >> Thu Dec 8 09:04:53 2005 ARG fileFormat genbank >> Thu Dec 8 09:04:53 2005 ARG gff2GroupTag >> Thu Dec 8 09:04:53 2005 ARG group >> Thu Dec 8 09:04:53 2005 ARG gusconfigfile /GUS/ >> gus_home/config/gus.config >> Thu Dec 8 09:04:53 2005 ARG handlerExternalDbs >> Thu Dec 8 09:04:53 2005 ARG help >> Thu Dec 8 09:04:53 2005 ARG helpHTML >> Thu Dec 8 09:04:53 2005 ARG inputFileExtension >> Thu Dec 8 09:04:53 2005 ARG inputFileOrDir >> kinetoplastida_nt >> Thu Dec 8 09:04:53 2005 ARG makeSourceids >> Thu Dec 8 09:04:53 2005 ARG mapFile /GUS/gus_home/ >> config/genbank2gus.xml >> Thu Dec 8 09:04:53 2005 ARG naSequenceSubclass >> Thu Dec 8 09:04:53 2005 ARG project >> Thu Dec 8 09:04:53 2005 ARG seqIdColumn source_id >> Thu Dec 8 09:04:53 2005 ARG seqSoTerm >> Thu Dec 8 09:04:53 2005 ARG seqType >> Thu Dec 8 09:04:53 2005 ARG soCvsVersion >> Thu Dec 8 09:04:53 2005 ARG sqlVerbose 0 >> Thu Dec 8 09:04:53 2005 ARG testNumber >> Thu Dec 8 09:04:53 2005 ARG user >> Thu Dec 8 09:04:53 2005 ARG verbose 0 >> Thu Dec 8 09:04:53 2005 ARG veryVerbose 0 >> Thu Dec 8 09:04:53 2005 AlgInvocationId 30 >> Thu Dec 8 09:04:53 2005 COMMIT commit on >> Thu Dec 8 09:04:55 2005 Processing file >> 'kinetoplastida_nt'... >> DBD::Pg::st execute failed: ERROR: cannot insert into a view >> HINT: You need an unconditional ON INSERT DO INSTEAD rule. >> >> ERROR: >> >> SQL ERROR!! involving >> >> Values: 4 at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm >> line 166 >> GUS::ObjRelP::DbiDbHandle::death >> ('GUS::ObjRelP::DbiDbHandle=HASH(0xaa904b0)', '\x{a} SQL ERROR!! >> involving\x{a} \x{a} Values: 4') called at /GUS/gus_home/lib/perl/ >> GUS/ObjRelP/DbiDbHandle.pm line 150 >> GUS::ObjRelP::DbiDbHandle::sqlExec >> ('GUS::ObjRelP::DbiDbHandle=HASH(0xaa904b0)', >> 'GUS::ObjRelP::DbiDbHandle::st=HASH(0xb2b07b0)', 'ARRAY >> (0xa148314)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm >> line 1813 >> GUS::Model::GusRow::version('GUS::Model::DoTS::Source=HASH >> (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm >> line 1680 >> GUS::Model::GusRow::submit('GUS::Model::DoTS::Source=HASH >> (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Supported/ >> Plugin/InsertSequenceFeatures.pm line 731 >> >> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees >> ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9ca3920)', >> 'Bio::Seq::RichSeq=HASH(0xb0aa2d8)', 4, 177) called at /GUS/ >> gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm >> line 330 >> GUS::Supported::Plugin::InsertSequenceFeatures::run >> ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9ca3920)', >> 'HASH(0xabe05b0)') 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 >> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport >> ('GUS::PluginMgr::GusApplication=HASH(0x9c82c20)', >> '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=HASH(0x9c82c20)', >> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/ >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357 >> GUS::PluginMgr::GusApplication::doMajorMode >> ('GUS::PluginMgr::GusApplication=HASH(0x9c82c20)', >> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/ >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266 >> GUS::PluginMgr::GusApplication::parseAndRun >> ('GUS::PluginMgr::GusApplication=HASH(0x9c82c20)', 'ARRAY >> (0x9c96700)') 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=HASH(0xaa904b0)', '\x{a} SQL ERROR!! >> involving\x{a} \x{a} Values: 4') called at /GUS/gus_home/lib/perl/ >> GUS/ObjRelP/DbiDbHandle.pm line 150 >> GUS::ObjRelP::DbiDbHandle::sqlExec >> ('GUS::ObjRelP::DbiDbHandle=HASH(0xaa904b0)', >> 'GUS::ObjRelP::DbiDbHandle::st=HASH(0xb2b07b0)', 'ARRAY >> (0xa148314)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm >> line 1813 >> GUS::Model::GusRow::version('GUS::Model::DoTS::Source=HASH >> (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm >> line 1680 >> GUS::Model::GusRow::submit('GUS::Model::DoTS::Source=HASH >> (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Supported/ >> Plugin/InsertSequenceFeatures.pm line 731 >> >> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees >> ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9ca3920)', >> 'Bio::Seq::RichSeq=HASH(0xb0aa2d8)', 4, 177) called at /GUS/ >> gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm >> line 330 >> GUS::Supported::Plugin::InsertSequenceFeatures::run >> ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9ca3920)', >> 'HASH(0xabe05b0)') 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 >> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport >> ('GUS::PluginMgr::GusApplication=HASH(0x9c82c20)', >> '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=HASH(0x9c82c20)', >> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/ >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357 >> GUS::PluginMgr::GusApplication::doMajorMode >> ('GUS::PluginMgr::GusApplication=HASH(0x9c82c20)', >> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/ >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266 >> GUS::PluginMgr::GusApplication::parseAndRun >> ('GUS::PluginMgr::GusApplication=HASH(0x9c82c20)', 'ARRAY >> (0x9c96700)') called at /GUS/gus_home/bin/ga line 11 >> >> Could you help me ? >> >> thanks again, >> Ricardo Balbi >> >> >> >> >> >> 2005/12/7, Mark S. Heiges <mh...@ug...>: One short term >> solution is to adjust your local schema "alter table >> SRes.Reference modify (author varchar2(4000))", or something like >> that, and then restart the loading. >> >> You can also file a feature request in the GUS Schema issue tracker >> to increase that column in a future release - https:// >> www.cbil.upenn.edu/tracker. >> >> On Dec 6, 2005, at 6:48 PM, Ricardo Balbi wrote: >> >> > Hi, >> > >> > I am trying to load kinetoplastida_nt, using >> > InsertSequenceFeatures plugin. But I am not obtaining. >> > Kinetoplastida_nt has a register whose author field exceeds the >> > maximum size the table sres.reference . >> > >> > How I must proceed to load this base? >> > >> > It follows below the error: >> > >> > [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" --commit >> > Tue Dec 6 21:32:42 2005 ARG algoinvo 1 >> > Tue Dec 6 21:32:42 2005 ARG comment >> > Tue Dec 6 21:32:42 2005 ARG commit 1 >> > Tue Dec 6 21:32:42 2005 ARG debug 0 >> > Tue Dec 6 21:32:42 2005 ARG defaultOrganism >> > Tue Dec 6 21:32:42 2005 ARG extDbName >> > Kinetoplastida_nt >> > Tue Dec 6 21:32:42 2005 ARG extDbRlsVer 2005-12-06 >> > Tue Dec 6 21:32:42 2005 ARG fileFormat genbank >> > Tue Dec 6 21:32:42 2005 ARG gff2GroupTag >> > Tue Dec 6 21:32:42 2005 ARG group >> > Tue Dec 6 21:32:42 2005 ARG gusconfigfile /GUS/ >> > gus_home/config/gus.config >> > Tue Dec 6 21:32:42 2005 ARG handlerExternalDbs >> > Tue Dec 6 21:32:42 2005 ARG help >> > Tue Dec 6 21:32:42 2005 ARG helpHTML >> > Tue Dec 6 21:32:42 2005 ARG inputFileExtension >> > Tue Dec 6 21:32:42 2005 ARG inputFileOrDir >> > kinetoplastida_nt >> > Tue Dec 6 21:32:42 2005 ARG makeSourceids >> > Tue Dec 6 21:32:42 2005 ARG mapFile /GUS/gus_home/ >> > config/genbank2gus.xml >> > Tue Dec 6 21:32:42 2005 ARG naSequenceSubclass >> > Tue Dec 6 21:32:42 2005 ARG project >> > Tue Dec 6 21:32:42 2005 ARG seqIdColumn source_id >> > Tue Dec 6 21:32:42 2005 ARG seqSoTerm >> > Tue Dec 6 21:32:42 2005 ARG seqType >> > Tue Dec 6 21:32:42 2005 ARG soCvsVersion >> > Tue Dec 6 21:32:42 2005 ARG sqlVerbose 0 >> > Tue Dec 6 21:32:42 2005 ARG testNumber >> > Tue Dec 6 21:32:42 2005 ARG user >> > Tue Dec 6 21:32:42 2005 ARG verbose 0 >> > Tue Dec 6 21:32:42 2005 ARG veryVerbose 0 >> > Tue Dec 6 21:32:42 2005 AlgInvocationId 26 >> > Tue Dec 6 21:32:42 2005 COMMIT commit on >> > Tue Dec 6 21:32:44 2005 Processing file >> 'kinetoplastida_nt'... >> > DBD::Pg::st execute failed: ERROR: value too long for type >> > character varying(1000) >> > >> > ERROR: >> > >> > SQL ERROR!! involving >> > >> > INSERT INTO SRes.Reference ( journal_or_book_name, >> > group_write, other_read, group_read, author, user_read, >> > row_user_id, reference_id, modification_date, other_write, >> > row_alg_invocation_id, row_project_id, row_group_id, title, >> > user_write ) >> > VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ?, ? ) >> > Values: Science 309 (5733), 409-415 (2005) PUBMED 16020725, 1, >> > 1, 1, El-Sayed,N.M., Myler,P.J., Bartholomeu,D.C., Nilsson,D., >> > Aggarwal,G., Tran,A.N., Ghedin,E., Worthey,E.A., Delcher,A.L., >> > Blandin,G., Westenberger, S.J., Caler,E., Cerqueira,G.C., >> > Branche,C., Haas,B., Anupama,A., Arner,E., Aslund,L., Attipoe,P., >> > Bontempi,E., Bringaud,F., Burton,P., Cadag,E., Campbell,D.A., >> > Carrington,M., Crabtree,J., Darban,H., da Silveira, J.F., de >> > Jong,P., Edwards,K., Englund,P.T., Fazelina,G., Feldblyum,T., >> > Ferella,M., Frasch,A.C., Gull,K., Horn,D., Hou,L., Huang,Y., >> > Kindlund,E., Klingbeil,M., Kluge,S., Koo,H., Lacerda,D., >> > Levin, M.J., Lorenzi,H., Louie,T., Machado,C.R., McCulloch,R., >> > McKenna,A., Mizuno,Y., Mottram,J.C., Nelson,S., Ochaya,S., >> > Osoegawa,K., Pai,G., Parsons,M., Pentony,M., Pettersson,U., Pop,M., >> > Ramirez,J.L., Rinta,J., Robertson,L., Salzberg, S.L., Sanchez,D.O., >> > Seyler,A., Sharma,R., Shetty,J., Simpson,A.J., Sisk,E., Tammi,M.T., >> > Tarleton,R., Teixeira,S., Van Aken,S., Vogt,C., Ward,P.N., >> > Wickstead,B., Wortman,J., White,O., Fraser,C.M., Stuart, K.D. and >> > Andersson,B., 1, 1, 6, 0, 26, 1, 1, The genome sequence of >> > Trypanosoma cruzi, etiologic agent of Chagas disease, 1 at /GUS/ >> > gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166 >> > GUS::ObjRelP::DbiDbHandle::death >> > ('GUS::ObjRelP::DbiDbHandle=HASH(0x91f4d14)', '\x{a} SQL ERROR!! >> > involving\x{a} \x{a} INSERT INTO SRes.Reference ( j...') called >> > at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150 >> > GUS::ObjRelP::DbiDbHandle::sqlExec >> > ('GUS::ObjRelP::DbiDbHandle=HASH(0x91f4d14)', >> > 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8e826cc)', 'ARRAY >> > (0x8e82708)', '\x{a} INSERT INTO SRes.Reference >> > ( journal_or_book_name, grou...') called at /GUS/gus_home/lib/ >> perl/ >> > GUS/ObjRelP/DbiRow.pm line 666 >> > GUS::ObjRelP::DbiRow::quote_and_insert >> > ('GUS::Model::SRes::Reference=HASH(0x987901c)', 'HASH(0x9889d48)') >> > called at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 613 >> > GUS::ObjRelP::DbiRow::insert >> > ('GUS::Model::SRes::Reference=HASH(0x987901c)') called at /GUS/ >> > gus_home/lib/perl/GUS/Model/GusRow.pm line 1692 >> > >> > >> > thanks, >> > Ricardo >> >> > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through > log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD > SPLUNK! > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
From: Mark S. H. <mh...@ug...> - 2005-12-08 18:54:14
|
That's error looks specific for Postgres which I don't use. Someone else may need to help here. A quick search at google.com for "ERROR: cannot insert into a view" or "You need an unconditional ON INSERT DO INSTEAD rule" turns up several clues. -Mark Mark Heiges CryptoDB.org C210 Life Sciences Building Center for Tropical and Emerging Global Diseases University of Georgia, Athens, GA 30602 TEL: (706) 542-1447 FAX: (706) 542-3582 On Dec 8, 2005, at 6:04 AM, Ricardo Balbi wrote: > Thanks Mark, > > But now I have another error. > It 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" --commit > Thu Dec 8 09:04:53 2005 ARG algoinvo 1 > Thu Dec 8 09:04:53 2005 ARG comment > Thu Dec 8 09:04:53 2005 ARG commit 1 > Thu Dec 8 09:04:53 2005 ARG debug 0 > Thu Dec 8 09:04:53 2005 ARG defaultOrganism > Thu Dec 8 09:04:53 2005 ARG extDbName > Kinetoplastida_nt > Thu Dec 8 09:04:53 2005 ARG extDbRlsVer 2005-12-06 > Thu Dec 8 09:04:53 2005 ARG fileFormat genbank > Thu Dec 8 09:04:53 2005 ARG gff2GroupTag > Thu Dec 8 09:04:53 2005 ARG group > Thu Dec 8 09:04:53 2005 ARG gusconfigfile /GUS/ > gus_home/config/gus.config > Thu Dec 8 09:04:53 2005 ARG handlerExternalDbs > Thu Dec 8 09:04:53 2005 ARG help > Thu Dec 8 09:04:53 2005 ARG helpHTML > Thu Dec 8 09:04:53 2005 ARG inputFileExtension > Thu Dec 8 09:04:53 2005 ARG inputFileOrDir > kinetoplastida_nt > Thu Dec 8 09:04:53 2005 ARG makeSourceids > Thu Dec 8 09:04:53 2005 ARG mapFile /GUS/gus_home/ > config/genbank2gus.xml > Thu Dec 8 09:04:53 2005 ARG naSequenceSubclass > Thu Dec 8 09:04:53 2005 ARG project > Thu Dec 8 09:04:53 2005 ARG seqIdColumn source_id > Thu Dec 8 09:04:53 2005 ARG seqSoTerm > Thu Dec 8 09:04:53 2005 ARG seqType > Thu Dec 8 09:04:53 2005 ARG soCvsVersion > Thu Dec 8 09:04:53 2005 ARG sqlVerbose 0 > Thu Dec 8 09:04:53 2005 ARG testNumber > Thu Dec 8 09:04:53 2005 ARG user > Thu Dec 8 09:04:53 2005 ARG verbose 0 > Thu Dec 8 09:04:53 2005 ARG veryVerbose 0 > Thu Dec 8 09:04:53 2005 AlgInvocationId 30 > Thu Dec 8 09:04:53 2005 COMMIT commit on > Thu Dec 8 09:04:55 2005 Processing file 'kinetoplastida_nt'... > DBD::Pg::st execute failed: ERROR: cannot insert into a view > HINT: You need an unconditional ON INSERT DO INSTEAD rule. > > ERROR: > > SQL ERROR!! involving > > Values: 4 at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm > line 166 > GUS::ObjRelP::DbiDbHandle::death > ('GUS::ObjRelP::DbiDbHandle=HASH(0xaa904b0)', '\x{a} SQL ERROR!! > involving\x{a} \x{a} Values: 4') called at /GUS/gus_home/lib/perl/ > GUS/ObjRelP/DbiDbHandle.pm line 150 > GUS::ObjRelP::DbiDbHandle::sqlExec > ('GUS::ObjRelP::DbiDbHandle=HASH(0xaa904b0)', > 'GUS::ObjRelP::DbiDbHandle::st=HASH(0xb2b07b0)', 'ARRAY > (0xa148314)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm > line 1813 > GUS::Model::GusRow::version('GUS::Model::DoTS::Source=HASH > (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm > line 1680 > GUS::Model::GusRow::submit('GUS::Model::DoTS::Source=HASH > (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Supported/Plugin/ > InsertSequenceFeatures.pm line 731 > > GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees > ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9ca3920)', > 'Bio::Seq::RichSeq=HASH(0xb0aa2d8)', 4, 177) called at /GUS/ > gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm > line 330 > GUS::Supported::Plugin::InsertSequenceFeatures::run > ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9ca3920)', > 'HASH(0xabe05b0)') 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 > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport > ('GUS::PluginMgr::GusApplication=HASH(0x9c82c20)', > '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=HASH(0x9c82c20)', > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/ > gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357 > GUS::PluginMgr::GusApplication::doMajorMode > ('GUS::PluginMgr::GusApplication=HASH(0x9c82c20)', > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/ > gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266 > GUS::PluginMgr::GusApplication::parseAndRun > ('GUS::PluginMgr::GusApplication=HASH(0x9c82c20)', 'ARRAY > (0x9c96700)') 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=HASH(0xaa904b0)', '\x{a} SQL ERROR!! > involving\x{a} \x{a} Values: 4') called at /GUS/gus_home/lib/perl/ > GUS/ObjRelP/DbiDbHandle.pm line 150 > GUS::ObjRelP::DbiDbHandle::sqlExec > ('GUS::ObjRelP::DbiDbHandle=HASH(0xaa904b0)', > 'GUS::ObjRelP::DbiDbHandle::st=HASH(0xb2b07b0)', 'ARRAY > (0xa148314)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm > line 1813 > GUS::Model::GusRow::version('GUS::Model::DoTS::Source=HASH > (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm > line 1680 > GUS::Model::GusRow::submit('GUS::Model::DoTS::Source=HASH > (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Supported/Plugin/ > InsertSequenceFeatures.pm line 731 > > GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees > ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9ca3920)', > 'Bio::Seq::RichSeq=HASH(0xb0aa2d8)', 4, 177) called at /GUS/ > gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm > line 330 > GUS::Supported::Plugin::InsertSequenceFeatures::run > ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9ca3920)', > 'HASH(0xabe05b0)') 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 > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport > ('GUS::PluginMgr::GusApplication=HASH(0x9c82c20)', > '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=HASH(0x9c82c20)', > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/ > gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357 > GUS::PluginMgr::GusApplication::doMajorMode > ('GUS::PluginMgr::GusApplication=HASH(0x9c82c20)', > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/ > gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266 > GUS::PluginMgr::GusApplication::parseAndRun > ('GUS::PluginMgr::GusApplication=HASH(0x9c82c20)', 'ARRAY > (0x9c96700)') called at /GUS/gus_home/bin/ga line 11 > > Could you help me ? > > thanks again, > Ricardo Balbi > > > > > > 2005/12/7, Mark S. Heiges <mh...@ug...>: One short term > solution is to adjust your local schema "alter table > SRes.Reference modify (author varchar2(4000))", or something like > that, and then restart the loading. > > You can also file a feature request in the GUS Schema issue tracker > to increase that column in a future release - https:// > www.cbil.upenn.edu/tracker. > > On Dec 6, 2005, at 6:48 PM, Ricardo Balbi wrote: > > > Hi, > > > > I am trying to load kinetoplastida_nt, using > > InsertSequenceFeatures plugin. But I am not obtaining. > > Kinetoplastida_nt has a register whose author field exceeds the > > maximum size the table sres.reference . > > > > How I must proceed to load this base? > > > > It follows below the error: > > > > [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" --commit > > Tue Dec 6 21:32:42 2005 ARG algoinvo 1 > > Tue Dec 6 21:32:42 2005 ARG comment > > Tue Dec 6 21:32:42 2005 ARG commit 1 > > Tue Dec 6 21:32:42 2005 ARG debug 0 > > Tue Dec 6 21:32:42 2005 ARG defaultOrganism > > Tue Dec 6 21:32:42 2005 ARG extDbName > > Kinetoplastida_nt > > Tue Dec 6 21:32:42 2005 ARG extDbRlsVer 2005-12-06 > > Tue Dec 6 21:32:42 2005 ARG fileFormat genbank > > Tue Dec 6 21:32:42 2005 ARG gff2GroupTag > > Tue Dec 6 21:32:42 2005 ARG group > > Tue Dec 6 21:32:42 2005 ARG gusconfigfile /GUS/ > > gus_home/config/gus.config > > Tue Dec 6 21:32:42 2005 ARG handlerExternalDbs > > Tue Dec 6 21:32:42 2005 ARG help > > Tue Dec 6 21:32:42 2005 ARG helpHTML > > Tue Dec 6 21:32:42 2005 ARG inputFileExtension > > Tue Dec 6 21:32:42 2005 ARG inputFileOrDir > > kinetoplastida_nt > > Tue Dec 6 21:32:42 2005 ARG makeSourceids > > Tue Dec 6 21:32:42 2005 ARG mapFile /GUS/gus_home/ > > config/genbank2gus.xml > > Tue Dec 6 21:32:42 2005 ARG naSequenceSubclass > > Tue Dec 6 21:32:42 2005 ARG project > > Tue Dec 6 21:32:42 2005 ARG seqIdColumn source_id > > Tue Dec 6 21:32:42 2005 ARG seqSoTerm > > Tue Dec 6 21:32:42 2005 ARG seqType > > Tue Dec 6 21:32:42 2005 ARG soCvsVersion > > Tue Dec 6 21:32:42 2005 ARG sqlVerbose 0 > > Tue Dec 6 21:32:42 2005 ARG testNumber > > Tue Dec 6 21:32:42 2005 ARG user > > Tue Dec 6 21:32:42 2005 ARG verbose 0 > > Tue Dec 6 21:32:42 2005 ARG veryVerbose 0 > > Tue Dec 6 21:32:42 2005 AlgInvocationId 26 > > Tue Dec 6 21:32:42 2005 COMMIT commit on > > Tue Dec 6 21:32:44 2005 Processing file > 'kinetoplastida_nt'... > > DBD::Pg::st execute failed: ERROR: value too long for type > > character varying(1000) > > > > ERROR: > > > > SQL ERROR!! involving > > > > INSERT INTO SRes.Reference ( journal_or_book_name, > > group_write, other_read, group_read, author, user_read, > > row_user_id, reference_id, modification_date, other_write, > > row_alg_invocation_id, row_project_id, row_group_id, title, > > user_write ) > > VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ?, ? ) > > Values: Science 309 (5733), 409-415 (2005) PUBMED 16020725, 1, > > 1, 1, El-Sayed,N.M., Myler,P.J., Bartholomeu,D.C., Nilsson,D., > > Aggarwal,G., Tran,A.N., Ghedin,E., Worthey,E.A., Delcher,A.L., > > Blandin,G., Westenberger, S.J., Caler,E., Cerqueira,G.C., > > Branche,C., Haas,B., Anupama,A., Arner,E., Aslund,L., Attipoe,P., > > Bontempi,E., Bringaud,F., Burton,P., Cadag,E., Campbell,D.A., > > Carrington,M., Crabtree,J., Darban,H., da Silveira, J.F., de > > Jong,P., Edwards,K., Englund,P.T., Fazelina,G., Feldblyum,T., > > Ferella,M., Frasch,A.C., Gull,K., Horn,D., Hou,L., Huang,Y., > > Kindlund,E., Klingbeil,M., Kluge,S., Koo,H., Lacerda,D., > > Levin, M.J., Lorenzi,H., Louie,T., Machado,C.R., McCulloch,R., > > McKenna,A., Mizuno,Y., Mottram,J.C., Nelson,S., Ochaya,S., > > Osoegawa,K., Pai,G., Parsons,M., Pentony,M., Pettersson,U., Pop,M., > > Ramirez,J.L., Rinta,J., Robertson,L., Salzberg, S.L., Sanchez,D.O., > > Seyler,A., Sharma,R., Shetty,J., Simpson,A.J., Sisk,E., Tammi,M.T., > > Tarleton,R., Teixeira,S., Van Aken,S., Vogt,C., Ward,P.N., > > Wickstead,B., Wortman,J., White,O., Fraser,C.M., Stuart, K.D. and > > Andersson,B., 1, 1, 6, 0, 26, 1, 1, The genome sequence of > > Trypanosoma cruzi, etiologic agent of Chagas disease, 1 at /GUS/ > > gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166 > > GUS::ObjRelP::DbiDbHandle::death > > ('GUS::ObjRelP::DbiDbHandle=HASH(0x91f4d14)', '\x{a} SQL ERROR!! > > involving\x{a} \x{a} INSERT INTO SRes.Reference ( j...') called > > at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150 > > GUS::ObjRelP::DbiDbHandle::sqlExec > > ('GUS::ObjRelP::DbiDbHandle=HASH(0x91f4d14)', > > 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8e826cc)', 'ARRAY > > (0x8e82708)', '\x{a} INSERT INTO SRes.Reference > > ( journal_or_book_name, grou...') called at /GUS/gus_home/lib/perl/ > > GUS/ObjRelP/DbiRow.pm line 666 > > GUS::ObjRelP::DbiRow::quote_and_insert > > ('GUS::Model::SRes::Reference=HASH(0x987901c)', 'HASH(0x9889d48)') > > called at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 613 > > GUS::ObjRelP::DbiRow::insert > > ('GUS::Model::SRes::Reference=HASH(0x987901c)') called at /GUS/ > > gus_home/lib/perl/GUS/Model/GusRow.pm line 1692 > > > > > > thanks, > > Ricardo > > |
From: Angel P. <an...@ma...> - 2005-12-08 18:25:49
|
Agreement with Mike here. GUS used to have a set of tables to capture the state of workflows, such as a build of the dna assemblies. These tables where agonized over and well thought out, but ultimately went unused and have subsequently been deleted from the schema. There are several reasons: -Most of the tasks we faced in a workflow where serial and did not contain any sort of decision points. -Using flat files to record state and recover from errors works just fine and is much easier to implement when the above holds true. Additionally, there are many workflow-focused open source projects out there that you can use to define and record the state of complex asynch workflows that are much more well thought out and are actually supported by an enthusiastic community. I recommend that if you want to pursue this further, you take advantage of work being done in the workflow management systems space, and limit the use of GUS to a data model that a particular workflow accesses. -angel Michael Saffitz wrote: > > Hi Ricardo, > > GUS doesn't have direct support for workflows or webservices. > > There are, however, several groups that are using GUS as the data > storage system for web services. This usually involves writing a > small amount of code to extract the data and deliver it. There are > also some groups that have expressed an interest in using GUS with > workflows, so this is a good area for collaboration and development. > > GUS does have a pipeline API, but I suspect it's not quite what > you're looking for. > > --Mike > > > On Dec 8, 2005, at 1:09 PM, Ricardo Balbi wrote: > >> Hi, >> >> A doubt: >> Has support for management of workflows in some schema of gus ? >> Support for storage of the definition, instances, in and out >> parameters, etc. >> Also has support for web services? >> >> []'s, >> Ricardo Balbi > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev -- Angel Pizarro Director, Bioinformatics Facility Institute for Translational Medicine and Therapeutics University of Pennsylvania 806 BRB II/III 421 Curie Blvd. Philadelphia, PA 19104-6160 P: 215-573-3736 F: 215-573-9004 |