From: Steve F. <st...@pc...> - 2004-06-10 19:07:59
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about WorkflowNode: is the file in the following dir? [sfischer@pythia Core]$cd $PROJECT_HOME/GUS/Model/src/java/org/gusdb/model/Core/ [sfischer@pythia Core]$ ls WorkflowN* WorkflowNode.java WorkflowNode_Table.java WorkflowNoOpNode_Row.java WorkflowNode_Row.java WorkflowNoOpNode.java WorkflowNoOpNode_Table.java about ga, i have reproduced the problem here, and will let you know as soon as i have fixed it. it is probably a result of the new postgres compatibility code. steve Michael Luchtan wrote: >So here is the current situation. I have the newest GUS, install, and >CBIL available. When I attempt to build GUS by executing the following >command: >build GUS install -append >Everything seems to go fine until we get the following error message: > [exec] generating java object for DoTS::TranslatedAASequence > [exec] generating java object for RAD3::SpotFamily > [mkdir] Created dir: >/var/local/checkout/GUS/Model/src/java/org/gusdb/model/hand_edited/App > [copy] Copying 2 files to >/var/local/checkout/GUS/Model/src/java/org/gusdb/model/DoTS > [copy] Copying 1 file to >/var/local/checkout/GUS/Model/src/java/org/gusdb/model/SRes > [echo] Starting target: JavaModel > [echo] . > [echo] Installing GUS/Model > [copy] Copying 1291 files to /var/local/gus_home/lib/perl/GUS/Model > [mkdir] Created dir: /var/local/checkout/GUS/Model/classes > [javac] Compiling 1086 source files to >/var/local/checkout/GUS/Model/classes > [javac] >/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/WorkflowEdge_Row.java:119: cannot resolve symbol > [javac] symbol : class WorkflowNode > [javac] location: package Core > [javac] public void >setToWorkflowNode(org.gusdb.model.Core.WorkflowNode >to_workflow_node_id){ > [javac] ^ > [javac] >/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/WorkflowEdge_Row.java:123: cannot resolve symbol > [javac] symbol : class WorkflowNode > [javac] location: package Core > [javac] public org.gusdb.model.Core.WorkflowNode >getToWorkflowNode(boolean retrieveFromDb) > [javac] ^ > [javac] >/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/WorkflowEdge_Row.java:129: cannot resolve symbol > [javac] symbol : class WorkflowNode > [javac] location: package Core > [javac] public void >setFromWorkflowNode(org.gusdb.model.Core.WorkflowNode >from_workflow_node_id){ > [javac] ^ > [javac] >/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/WorkflowEdge_Row.java:133: cannot resolve symbol > [javac] symbol : class WorkflowNode > [javac] location: package Core > [javac] public org.gusdb.model.Core.WorkflowNode >getFromWorkflowNode(boolean retrieveFromDb) > [javac] ^ > [javac] >/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/Workflow_Row.java:175: cannot resolve symbol > [javac] symbol : class WorkflowNode > [javac] location: package Core > [javac] public void >addWorkflowNode(org.gusdb.model.Core.WorkflowNode workflownode){ > [javac] ^ > [javac] >/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/GroupInfo_Row.java:3136: cannot resolve symbol > [javac] symbol : class WorkflowNode > [javac] location: package Core > [javac] public void >addWorkflowNode(org.gusdb.model.Core.WorkflowNode workflownode){ > [javac] ^ > [javac] >/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/ProjectInfo_Row.java:2740: cannot resolve symbol > [javac] symbol : class WorkflowNode > [javac] location: package Core > [javac] public void >addWorkflowNode(org.gusdb.model.Core.WorkflowNode workflownode){ > [javac] ^ > [javac] >/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:2306: cannot resolve symbol > [javac] symbol : class WorkflowNode > [javac] location: package Core > [javac] public void >addWorkflowNode_IAmA_algorithminvocation(org.gusdb.model.Core.WorkflowNode workflownode_iama_algorithminvocation){ > >[javac] ^ > [javac] >/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/AlgorithmInvocation_Row.java:2702: cannot resolve symbol > [javac] symbol : class WorkflowNode > [javac] location: package Core > [javac] public void >addWorkflowNode_IAmA_rowalginvocation(org.gusdb.model.Core.WorkflowNode >workflownode_iama_rowalginvocation){ > >[javac] ^ > [javac] >/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/UserInfo_Row.java:1847: cannot resolve symbol > [javac] symbol : class WorkflowNode > [javac] location: package Core > [javac] public void >addWorkflowNode(org.gusdb.model.Core.WorkflowNode workflownode){ > [javac] ^ > [javac] >/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/WorkflowEdge_Row.java:126: cannot resolve symbol > [javac] symbol : class WorkflowNode > [javac] location: package Core > [javac] return >(org.gusdb.model.Core.WorkflowNode)getParent("to_workflow_node_id", >retrieveFromDb); > [javac] ^ > [javac] >/var/local/checkout/GUS/Model/src/java/org/gusdb/model/Core/WorkflowEdge_Row.java:136: cannot resolve symbol > [javac] symbol : class WorkflowNode > [javac] location: package Core > [javac] return >(org.gusdb.model.Core.WorkflowNode)getParent("from_workflow_node_id", >retrieveFromDb); > [javac] ^ > [javac] 12 errors > >BUILD FAILED >file:/var/local/checkout/install/build.xml:235: Compile failed; see the >compiler error output for details. > >Total time: 14 minutes 11 seconds > > > >Who knows why this isn't working, but I think I know why ga and such is >no longer working. When I attempt to run anything with ga, I get PK >violations. I am under the impressions that ga (or perhaps somewhere >else) has an internal counter to deal with things like primary keys like >algorithm_implementation_id or algorithm_invocation_id when inserting >new entries. >Here is the error I get when trying to update ga for the new SubmitRow >plugin: > >[root@mkiwi install]# ga +update GUS::Common::Plugin::SubmitRow >DBD::Oracle::st execute failed: ORA-00001: unique constraint >(CORE.PK_ALGORITHMIMPLEMENTATION) violated (DBD ERROR: OCIStmtExecute) >at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145. > > SQL ERROR!! involving > > INSERT INTO Core.AlgorithmImplementation ( description, >row_user_id, user_write, group_write, executable_md5, >algorithm_implementation_id, row_project_id, cvs_revision, group_read, >row_group_id, cvs_tag, executable, other_read, modification_date, >user_read, algorithm_id, row_alg_invocation_id, other_write ) > VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, >? ) > Values: make consistent with GUS 3.0, 4, 1, 1, >2e3da77408e21e4e9d7b57ec9b8d412d, 24, 2, 1.8, 1, 2, , >GUS::Common::Plugin::SubmitRow, 1, 1, 3, 1, 0 at >/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185 > >GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x85f2b00)', '^J SQL ERROR!! involving^J ^J INSERT INTO Core.AlgorithmImplemen...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148 > >GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x85f2b00)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8773514)', 'ARRAY(0x877355c)', '^J INSERT INTO Core.AlgorithmImplementation ( description, ro...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 681 > >GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::Core::AlgorithmImplementation=HASH(0x8713d68)', 'HASH(0x81ef630)') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 628 > >GUS::ObjRelP::DbiRow::insert('GUS::Model::Core::AlgorithmImplementation=HASH(0x8713d68)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677 > >GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmImplementation=HASH(0x8713d68)', undef, 1) called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1764 > >GUS::Model::GusRow::submitChildrenInClass('GUS::Model::Core::Algorithm=HASH(0x86f83e8)', 'GUS::Model::Core::AlgorithmImplementation') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1745 > >GUS::Model::GusRow::submitAllChildren('GUS::Model::Core::Algorithm=HASH(0x86f83e8)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684 > >GUS::Model::GusRow::submit('GUS::Model::Core::Algorithm=HASH(0x86f83e8)') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 812 > >GUS::PluginMgr::GusApplication::create_or_update_implementation('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 1, 'GUS::Common::Plugin::SubmitRow') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 466 > >GUS::PluginMgr::GusApplication::doMajorMode_Update('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::SubmitRow') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283 > >GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::SubmitRow') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192 > >GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'ARRAY(0x8102dbc)') called at /var/local/gus_home/bin/ga line 11 >[root@mkiwi install]# > > >How can I get these counters reset? Or is this the wrong direction for >finding a solution to the problem? > >Thanks, >Michael Luchtan > > > > > > > > > >On Wed, 2004-06-09 at 17:00, Steve Fischer wrote: > > >>michael- >> >>it looks like you added a row to TableInfo for the >>SResVer::MassSpecSummary. if so, delete it and build again. >> >>steve >> >>Michael Luchtan wrote: >> >> >> >>>It has been a long time since a build took place here, and I was not >>>really present for the installation of GUS. But in the checkouts >>>directory I checked out GUS from Sanger. I executed the >>>build GUS install -append >>>and got the following errors: >>> [exec] generating java object for SResVer::MassSpecSummary >>> [exec] Error: Package Table Name '' is not in the form of >>>org.gusdb.model.SCHEMA.NAME at /var/lo\ >>>cal/gus_home/lib/perl/GUS/ObjRelP/Generator/RowGenerator.pm line 91 >>> [exec] >>>GUS::ObjRelP::Generator::RowGenerator::_cutPackageTableName('GUS::ObjRelP::Generator::\ >>>JavaRowGenerator=HASH(0x83955d0)', undef) called at >>>/var/local/gus_home/lib/perl/GUS/ObjRelP/Generator\ >>>/JavaRowGenerator.pm line 410 >>> [exec] >>>GUS::ObjRelP::Generator::JavaRowGenerator::_createParentAccessors('GUS::ObjRelP::Gener\ >>>ator::JavaRowGenerator=HASH(0x83955d0)', 'HASH(0x85d48ec)') called at >>>/var/local/gus_home/lib/perl/GUS\ >>>/ObjRelP/Generator/JavaRowGenerator.pm line 127 >>> [exec] >>>GUS::ObjRelP::Generator::JavaRowGenerator::_genAccessors('GUS::ObjRelP::Generator::Jav\ >>>aRowGenerator=HASH(0x83955d0)') called at >>>/var/local/gus_home/lib/perl/GUS/ObjRelP/Generator/JavaRowGe\ >>>nerator.pm line 32 >>> [exec] >>>GUS::ObjRelP::Generator::JavaRowGenerator::generate('GUS::ObjRelP::Generator::JavaRowG\ >>>enerator=HASH(0x83955d0)', undef) called at >>>/var/local/gus_home/lib/perl/GUS/ObjRelP/Generator/Generat\ >>>or.pm line 109 >>> [exec] >>>GUS::ObjRelP::Generator::Generator::generate('GUS::ObjRelP::Generator::Generator=HASH(\ >>>0x81073d4)', undef) called at /var/local/gus_home/bin/generateGusObjects >>>line 67 >>> >>>BUILD FAILED >>>file:/var/local/checkout/GUS/build.xml:114: exec returned: -1 >>> >>> >>>According to the VBI install docs, it is necessary to edit the build.xml >>>and take out the generateGusObjects executable statement first. But >>>after this I get the following errors: >>> [echo] Installing GUS/Model >>> [javac] Compiling 5 source files to >>>/var/local/checkout/GUS/Model/classes >>> [javac] >>>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/SResVer/MassSpecSummary_Table.java:\ >>>17: illegal start of expression >>> [javac] tableAtts.put("", new GUSTableAttribute("", "", >>>"java.lang.notdefyet", -1, , -1, f\ >>>alse, false) ); >>> >>>[javac] ^ >>> [javac] >>>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/SResVer/MassSpecSummary_Table.java:\ >>>17: ')' expected >>> [javac] tableAtts.put("", new GUSTableAttribute("", "", >>>"java.lang.notdefyet", -1, , -1, f\ >>>alse, false) ); >>> >>>[javac] \ >>> ^ >>> [javac] 2 errors >>> >>>BUILD FAILED >>>file:/var/local/checkout/install/build.xml:227: Compile failed; see the >>>compiler error output for deta\ >>>ils. >>> >>> >>>Any help is appreciated.... >>>Michael Luchtan >>> >>> >>> >>> >>> >>>On Wed, 2004-06-09 at 16:10, Steve Fischer wrote: >>> >>> >>> >>> >>>>michael- >>>> >>>>we have seen this. i think if you get the latest from cvs and then >>>>rebuild the objects you will get around this problem. >>>> >>>>then, use submitrow to add rows to tableinfo for the mass spec tables >>>>and rebuild all over again. >>>> >>>>steve >>>> >>>>Michael Luchtan wrote: >>>> >>>> >>>> >>>> >>>> >>>>>Hello-- >>>>>Can you give me a heads up on why I cannot use the submitrow plugin any >>>>>more, now that I have rebuild the perl object layer? Hope I didn't just >>>>>screw myself... >>>>> >>>>>Here is the command/arguement: >>>>> >>>>>luchtan]# ga GUS::Common::Plugin::SubmitRow --tablename Core::UserInfo >>>>>--attrlist >>>>>"login,password,first_name,last_name,e_mail,modification_date" >>>>>--valuelist >>>>>"pablo^^^pablo123^^^pablo^^^mendes^^^pa...@pa...^^^SYSDATE" >>>>>Reading properties from /var/local/gus_home/config/GUS-PluginMgr.prop >>>>>Reading properties from /home/luchtan/.gus.properties >>>>>DBD::Oracle::st execute failed: ORA-00001: unique constraint >>>>>(CORE.PK_ALGORITHMINVOCATION) violated (DBD ERROR: OCIStmtExecute) at >>>>>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145. >>>>> >>>>>SQL ERROR!! involving >>>>> >>>>> INSERT INTO Core.AlgorithmInvocation ( end_time, row_user_id, >>>>>user_write, group_write, cpu_time, algorithm_implementation_id, >>>>>row_project_id, algorithm_invocation_id, comment_string, group_read, >>>>>row_group_id, result, other_read, cpus_used, start_time, >>>>>modification_date, user_read, row_alg_invocation_id, other_write, >>>>>machine_id ) >>>>> VALUES ( SYSDATE, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, ?, ?, ?, >>>>>SYSDATE, SYSDATE, ?, ?, ?, ? ) >>>>>Values: 4, 1, 1, 0, 3, 2, 25, 1, 2, pending, 1, 1, 1, 1, 0, 0 at >>>>>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185 >>>>> >>>>>GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x855e940)', '^J SQL ERROR!! involving^J ^J INSERT INTO Core.AlgorithmInvocati...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148 >>>>> >>>>>GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x855e940)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x873690c)', 'ARRAY(0x87377c4)', '^J INSERT INTO Core.AlgorithmInvocation ( end_time, row_user_...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674 >>>>> >>>>>GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::Core::AlgorithmInvocation=HASH(0x86ae1ac)', 'HASH(0x86a9574)') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 621 >>>>> >>>>>GUS::ObjRelP::DbiRow::insert('GUS::Model::Core::AlgorithmInvocation=HASH(0x86ae1ac)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677 >>>>> >>>>>GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmInvocation=HASH(0x86ae1ac)') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 939 >>>>> >>>>>GUS::PluginMgr::GusApplication::openInvocation('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::SubmitRow=HASH(0x850872c)') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 425 >>>>> >>>>>GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::SubmitRow') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283 >>>>> >>>>>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::SubmitRow') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192 >>>>> >>>>>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'ARRAY(0x8102dbc)') called at /var/local/gus_home/bin/ga line 11 >>>>>Issuing rollback() for database handle being DESTROY'd without explicit >>>>>disconnect(). >>>>> >>>>> >>>>>On Wed, 2004-06-09 at 14:52, Steve Fischer wrote: >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>>I have added instructions for this to the wiki. see if you can find it. >>>>>> >>>>>>steve >>>>>> >>>>>>Michael Luchtan wrote: >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>>Hello- >>>>>>>We are attempting to load some mass spec data into gus. Well, the >>>>>>>version of gus that we have did not contain two of the relevant tables: >>>>>>>DoTS.MassSpecFeature and DoTS.MassSpecSummary >>>>>>>I created the MassSpecFeature view on DoTS.aafeatureimp and the table >>>>>>>dots.massspecsummary. >>>>>>>Now we need to generate the GUS objects for the tables for use in >>>>>>>plug-ins. All of the oerl modules in GUS/Model/* are generated >>>>>>>automagically. It looks like I could just copy some files and change >>>>>>>the names. But they all say something like this: >>>>>>> >>>>>>># THIS CLASS HAS BEEN AUTOMATICALLY GENERATED BY THE >>>>>>>GUS::ObjRelP::Generator >>>>>>># PACKAGE. >>>>>>># >>>>>>># DO NOT EDIT!! >>>>>>> >>>>>>># TO ADD FUNCTIONALITY MANUALLY, COPY THIS FILE TO >>>>>>>InteractionType.pm.man >>>>>>># (or edit that file if it already exists) AND ADD THE FUNCTIONALITY >>>>>>>THERE. >>>>>>># THEN RE-GENERATE THE GUS OBJECTS. >>>>>>> >>>>>>>Any word on how to use the Generator? Any help is appreciated. It >>>>>>>might go well in the Wiki-wiki! >>>>>>> >>>>>>>Michael Luchtan >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>------------------------------------------------------- >>>>>>>This SF.Net email is sponsored by: GNOME Foundation >>>>>>>Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event. >>>>>>>GNOME Users and Developers European Conference, 28-30th June in Norway >>>>>>>http://2004/guadec.org >>>>>>>_______________________________________________ >>>>>>>Gusdev-gusdev mailing list >>>>>>>Gus...@li... >>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>------------------------------------------------------- >>>>>>This SF.Net email is sponsored by: GNOME Foundation >>>>>>Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event. >>>>>>GNOME Users and Developers European Conference, 28-30th June in Norway >>>>>>http://2004/guadec.org >>>>>>_______________________________________________ >>>>>>Gusdev-gusdev mailing list >>>>>>Gus...@li... >>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>------------------------------------------------------- >>>>>This SF.Net email is sponsored by: GNOME Foundation >>>>>Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event. >>>>>GNOME Users and Developers European Conference, 28-30th June in Norway >>>>>http://2004/guadec.org >>>>>_______________________________________________ >>>>>Gusdev-gusdev mailing list >>>>>Gus...@li... >>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> |