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Re: [Gusdev-gusdev] "RE-GENERATE THE GUS OBJECTS"
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From: Michael L. <lu...@ug...> - 2004-06-11 15:05:25
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Steve-
The problem was not quite fixed. SInce this is all new, the first thing
I have to do is ga +meta , right? Well, first there was a compilation
problem, which was easily fixed. I don't have cvs write, so you might
want to have someone else do it.
GUS::ObjRelP::DbiTable.pm wants to call a method nextValSelect on the
Oracle or Postgres object. There is such a function in PostgreSQL,
called nextValSelect, but commented with the name nextValSQL. Anyway, I
changed the nextValSQL in Oracle.pm to nextValSelect and all worked
fine. Seems like that is the correct thing to do. Unfortunately, our
Sequences have somehow been screwed up. From the sqlplus prompt:
SQL> select core.algorithminvocation_sq.nextval from dual;
NEXTVAL
----------
62
SQL> select core.algorithmimplementation_sq.nextval from dual;
NEXTVAL
----------
62
SQL> select MAX(algorithm_invocation_id) from core.algorithminvocation;
MAX(ALGORITHM_INVOCATION_ID)
----------------------------
30288
And thus the ga +meta has a pk constraint error. Here is the output:
gus_home]# ga +meta
<Core::Algorithm>
<algorithm_id>2</algorithm_id>
<name>GA-Plugin</name>
<description>GUS application framework for plugins</description>
<modification_date>29-OCT-03</modification_date>
<Core::AlgorithmImplementation>
<cvs_revision>1.49</cvs_revision>
<cvs_tag> </cvs_tag>
<executable>GUS::PluginMgr::GusApplication</executable>
<executable_md5>e291775acbf95c5ed6bae9024ad78e79</executable_md5>
<description>update for GUS 3.0</description>
<Core::AlgorithmInvocation>
<start_time>SYSDATE</start_time>
<end_time>SYSDATE</end_time>
<machine_id>0</machine_id>
<cpus_used>1</cpus_used>
<result>meta</result>
</Core::AlgorithmInvocation>
</Core::AlgorithmImplementation>
<user_read>1</user_read>
<user_write>1</user_write>
<group_read>1</group_read>
<group_write>1</group_write>
<other_read>1</other_read>
<other_write>0</other_write>
<row_user_id>3</row_user_id>
<row_group_id>2</row_group_id>
<row_project_id>2</row_project_id>
<row_alg_invocation_id>1</row_alg_invocation_id>
</Core::Algorithm>
DBD::Oracle::st execute failed: ORA-00001: unique constraint
(CORE.PK_ALGORITHMINVOCATION) violated (DB\
D 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, algorithm_i\
mplementation_id, row_project_id, algorithm_invocation_id, 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, 63, 2, 63, 1, 2, meta, 1, 1, 1, 1, 0, 0 at
/var/local/gus_home/lib/perl/GUS/ObjRelP/D\
biDbHandle.pm line 185
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x861c7a0)', '^J SQL ERROR!! i\
nvolving^J ^J INSERT INTO Core.AlgorithmInvocati...') called at
/var/local/gus_home/lib/perl/GUS/Obj\
RelP/DbiDbHandle.pm line 148
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x861c7a0)', 'GUS::ObjRelP::\
DbiDbHandle::st=HASH(0x8740df4)', 'ARRAY(0x8740e84)', '^J INSERT INTO
Core.AlgorithmInvocation ( en\
d_time, row_user_...') called at
/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 681
GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::Core::AlgorithmInvocation=HASH(0x86ac4d0)',\
'HASH(0x8746bf0)') called at
/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 628
GUS::ObjRelP::DbiRow::insert('GUS::Model::Core::AlgorithmInvocation=HASH(0x86ac4d0)') called at\
/var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmInvocation=HASH(0x86ac4d0)', undef, 1) c\
alled at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1764
GUS::Model::GusRow::submitChildrenInClass('GUS::Model::Core::AlgorithmImplementation=HASH(0x869\
6a18)', 'GUS::Model::Core::AlgorithmInvocation') called at
/var/local/gus_home/lib/perl/GUS/Model/GusRo\
w.pm line 1745
GUS::Model::GusRow::submitAllChildren('GUS::Model::Core::AlgorithmImplementation=HASH(0x8696a18\
)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmImplementation=HASH(0x8696a18)', 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(0x861c710)', '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(0x861c710)') called at \
/var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
GUS::Model::GusRow::submit('GUS::Model::Core::Algorithm=HASH(0x861c710)') called at /var/local/\
gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 355
GUS::PluginMgr::GusApplication::doMajorMode_Meta('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c\
)', undef) called at
/var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', u\
ndef) 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
We will write a script to reset all our sequences by selecting the max.
Don't know how this event transpired though...
Michael Luchtan
On Thu, 2004-06-10 at 17:36, Steve Fischer wrote:
> Michael-
>
> i think i have fixed the ga problem.
>
> do this:
> - get the latest from cvs.
> - rm $GUS_HOME/lib/perl/GUS/ObjRelP/*.pm
> - rm $GUS_HOME/lib/perl/GUS/Model/GusRow.pm
> - build GUS install -append
>
> steve
>
> Michael Luchtan wrote:
> > Dave-
> > That seemed to do it. I had to create the core.workflonode view, and
> > core.workflownodeimp, then insert them into tableinfo.
> > So I have successfully done a
> > build GUS install -append
> > without any crashes.
> > Still can't run the ga though. Steve said he was working on it. I
> > don't think that there is anything that happens with the following
> > command that alters the database, so I don't see how it would have reset
> > the SEQ.
> >
> > Thanks,
> > Michael Luchtan
> >
> >
> >
> > On Thu, 2004-06-10 at 15:22, Dave Barkan wrote:
> >
> > > I may have seen something similar to this a few months ago. Make sure
> > > that the table "Core.WorkflowNode" is in your schema and in your
> > > TableInfo (and Core.WorkflowNodeImp for that matter).
> > >
> > > Dave
> > >
> > > On Thu, 10 Jun 2004, Michael Luchtan wrote:
> > >
> > >
> > > > Steve-
> > > > Not all of them, just three:
> > > > [root@mkiwi install]# cd ../GUS/Model/src/java/org/gusdb/model/Core/
> > > > [root@mkiwi Core]# ls WorkflowN*
> > > > WorkflowNoOpNode.java WorkflowNoOpNode_Row.java
> > > > WorkflowNoOpNode_Table.java
> > > >
> > > > Why is this? I guess that is why it is complaining about not finding
> > > > the workflownode object. But these objects should be dynamically
> > > > created, no? Am I missing something in my core.tableinfo or something?
> > > >
> > > > Thanks for the quick reply. I appreciate it.
> > > > Michael Luchtan
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > On Thu, 2004-06-10 at 15:09, Steve Fischer wrote:
> > > >
> > > > > about WorkflowNode: is the file in the following dir?
> > > > >
> > > > > [sfischer@pythia Core]$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
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
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> > > > > > > > > > > > http://2004/guadec.org
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> > > > > > > > > > > -------------------------------------------------------
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> > > > > > > > > > > http://2004/guadec.org
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> > > > > > > > > > -------------------------------------------------------
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> > > > > > > > > > GNOME Users and Developers European Conference, 28-30th June in Norway
> > > > > > > > > > http://2004/guadec.org
> > > > > > > > > > _______________________________________________
> > > > > > > > > > Gusdev-gusdev mailing list
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