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From: Steve F. <st...@pc...> - 2004-06-18 01:24:53
|
terry-
i don't know what is causing that problem.
there is an undocumented flag to turn off java compiling (you can find
stuff like by snooping in:
$PROJECT_HOME/install/bin/build.pl
the flag is:
build GUS install -skipJavaCompiling -append
try that until somebody figures out what is going on with the rmic
steve
Terry Clark wrote:
>Dear Gus Developers,
>
>I am starting a GUS project in a new laboratory using
>today's CVS checkout of GUS and an FTP today of CBIL tools.
>The build is breaking with the Java rmic, with the ominous suggestion
> [rmic] error: An error has occurred in the compiler;
> please file a bug report (http://java.sun.com/cgi-bin/bugreport.cgi).
> [rmic] 1 error
>The rmic messages do not look quite right, but this is outside of
>what I am familiar with; and the rmic nest in build.xml
>used to be commented out so I do not have successful examples
>to compare to.
>
>Any ideas how to get by this? Maybe I am missing a component?
>The Java distribution I am using is from the file "j2eesdk-1_4_01-linux.bin"
>for Linux. The CLASSPATH in the build shell is
> CLASSPATH=/usr/java1.4/jdk/lib/dt.jar:/usr/java1.4/jdk/lib/tools.jar:/usr/java1.4/jdk/jre/lib/rt.jar
> JAVA_HOME=/usr/java1.4/jdk
>
>Thanks,
>
>Terry
>
>p.s. Here is stderr and stdout from the build.
>
>
>ant -f /farm/gus/projects/install/build.xml install -Dproj=GUS -DtargetDir=/farm/gus/gushome -Dcomp= -DprojectsDir=/farm/gus/projects -Dappend=true -logger org.apache.tools.ant.NoBannerLogger | grep ']'
>
> [rmic] java.lang.IncompatibleClassChangeError: field sun.tools.java.Type.idJavaLangObject was not found.
> [rmic] at _Jv_ResolvePoolEntry(java.lang.Class, int) (/lib/ssa/libgcj.so.4.0.0)
> [rmic] at sun.tools.java.Type.<clinit>() (Unknown Source)
> [rmic] at java.lang.Class.initializeClass() (/lib/ssa/libgcj.so.4.0.0)
> [rmic] at _Jv_ResolvePoolEntry(java.lang.Class, int) (/lib/ssa/libgcj.so.4.0.0)
> [rmic] at sun.tools.javac.BatchEnvironment.classExists(sun.tools.java.Identifier) (Unknown Source)
> [rmic] at sun.tools.java.Environment.resolvePackageQualifiedName(sun.tools.java.Identifier) (Unknown Source)
> [rmic] at sun.rmi.rmic.Main.doCompile() (Unknown Source)
> [rmic] at sun.rmi.rmic.Main.compile(java.lang.String[]) (Unknown Source)
> [rmic] at _Jv_CallAnyMethodA(java.lang.Object, java.lang.Class, _Jv_Method, boolean, java.lang.Class[], jvalue, jvalue) (/lib/ssa/libgcj.so.4.0.0)
> [rmic] at _Jv_CallAnyMethodA(java.lang.Object, java.lang.Class, _Jv_Method, boolean, java.lang.Class[], java.lang.Object[]) (/lib/ssa/libgcj.so.4.0.0)
> [rmic] at java.lang.reflect.Method.invoke(java.lang.Object, java.lang.Object[]) (/lib/ssa/libgcj.so.4.0.0)
> [rmic] at org.apache.tools.ant.taskdefs.rmic.SunRmic.execute() (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
> [rmic] at org.apache.tools.ant.taskdefs.Rmic.execute() (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
> [rmic] at org.apache.tools.ant.Task.perform() (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
> [rmic] at org.apache.tools.ant.Target.execute() (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
> [rmic] at org.apache.tools.ant.Target.performTasks() (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
> [rmic] at org.apache.tools.ant.Project.executeTarget(java.lang.String) (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
> [rmic] at org.apache.tools.ant.taskdefs.Ant.execute() (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
> [rmic] at org.apache.tools.ant.Task.perform() (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
> [rmic] at org.apache.tools.ant.Target.execute() (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
> [rmic] at org.apache.tools.ant.Target.performTasks() (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
> [rmic] at org.apache.tools.ant.Project.executeTarget(java.lang.String) (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
> [rmic] at org.apache.tools.ant.Project.executeTargets(java.util.Vector) (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
> [rmic] at org.apache.tools.ant.Main.runBuild(java.lang.ClassLoader) (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
> [rmic] at org.apache.tools.ant.Main.start(java.lang.String[], java.util.Properties, java.lang.ClassLoader) (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
> [rmic] at org.apache.tools.ant.Main.main(java.lang.String[]) (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
>
>BUILD FAILED
>file:/farm/gus/projects/GUS/build.xml:305: Rmic failed; see the compiler error output for details.
>
>Total time: 6 seconds
> [echo] .
> [echo] Installing CBIL/Bio
> [echo] .
> [echo] Installing CBIL/CSP
> [javac] Since compiler setting isn't classic or modern,ignoring fork setting.
> [jar] Building jar: /farm/gus/gushome/lib/java/CBIL-CSP.jar
> [echo] .
> [echo] Installing CBIL/Util
> [echo] .
> [echo] Installing CBIL/HQ
> [echo] .
> [echo] Installing CBIL/ObjectMapper
> [concat] Warning: Could not find any of the files specified in concat task.
> [echo] .
> [echo] Installing GUS/Common
> [echo] .
> [echo] Installing GUS/DBAdmin
> [echo] .
> [echo] Installing GUS/GOPredict
> [javac] Since compiler setting isn't classic or modern,ignoring fork setting.
> [jar] Building jar: /farm/gus/gushome/lib/java/GUS-GOPredict.jar
> [echo] .
> [echo] Installing GUS/ObjRelP
> [rmic] RMI Compiling 1 class to /farm/gus/projects/GUS/ObjRelJ/src/java
> [rmic] error: An error has occurred in the compiler; please file a bug report (http://java.sun.com/cgi-bin/bugreport.cgi).
> [rmic] 1 error
>
>
>
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|
|
From: Terry C. <tc...@it...> - 2004-06-18 00:32:36
|
Dear Gus Developers,
I am starting a GUS project in a new laboratory using
today's CVS checkout of GUS and an FTP today of CBIL tools.
The build is breaking with the Java rmic, with the ominous suggestion
[rmic] error: An error has occurred in the compiler;
please file a bug report (http://java.sun.com/cgi-bin/bugreport.cgi).
[rmic] 1 error
The rmic messages do not look quite right, but this is outside of
what I am familiar with; and the rmic nest in build.xml
used to be commented out so I do not have successful examples
to compare to.
Any ideas how to get by this? Maybe I am missing a component?
The Java distribution I am using is from the file "j2eesdk-1_4_01-linux.bin"
for Linux. The CLASSPATH in the build shell is
CLASSPATH=/usr/java1.4/jdk/lib/dt.jar:/usr/java1.4/jdk/lib/tools.jar:/usr/java1.4/jdk/jre/lib/rt.jar
JAVA_HOME=/usr/java1.4/jdk
Thanks,
Terry
p.s. Here is stderr and stdout from the build.
ant -f /farm/gus/projects/install/build.xml install -Dproj=GUS -DtargetDir=/farm/gus/gushome -Dcomp= -DprojectsDir=/farm/gus/projects -Dappend=true -logger org.apache.tools.ant.NoBannerLogger | grep ']'
[rmic] java.lang.IncompatibleClassChangeError: field sun.tools.java.Type.idJavaLangObject was not found.
[rmic] at _Jv_ResolvePoolEntry(java.lang.Class, int) (/lib/ssa/libgcj.so.4.0.0)
[rmic] at sun.tools.java.Type.<clinit>() (Unknown Source)
[rmic] at java.lang.Class.initializeClass() (/lib/ssa/libgcj.so.4.0.0)
[rmic] at _Jv_ResolvePoolEntry(java.lang.Class, int) (/lib/ssa/libgcj.so.4.0.0)
[rmic] at sun.tools.javac.BatchEnvironment.classExists(sun.tools.java.Identifier) (Unknown Source)
[rmic] at sun.tools.java.Environment.resolvePackageQualifiedName(sun.tools.java.Identifier) (Unknown Source)
[rmic] at sun.rmi.rmic.Main.doCompile() (Unknown Source)
[rmic] at sun.rmi.rmic.Main.compile(java.lang.String[]) (Unknown Source)
[rmic] at _Jv_CallAnyMethodA(java.lang.Object, java.lang.Class, _Jv_Method, boolean, java.lang.Class[], jvalue, jvalue) (/lib/ssa/libgcj.so.4.0.0)
[rmic] at _Jv_CallAnyMethodA(java.lang.Object, java.lang.Class, _Jv_Method, boolean, java.lang.Class[], java.lang.Object[]) (/lib/ssa/libgcj.so.4.0.0)
[rmic] at java.lang.reflect.Method.invoke(java.lang.Object, java.lang.Object[]) (/lib/ssa/libgcj.so.4.0.0)
[rmic] at org.apache.tools.ant.taskdefs.rmic.SunRmic.execute() (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
[rmic] at org.apache.tools.ant.taskdefs.Rmic.execute() (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
[rmic] at org.apache.tools.ant.Task.perform() (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
[rmic] at org.apache.tools.ant.Target.execute() (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
[rmic] at org.apache.tools.ant.Target.performTasks() (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
[rmic] at org.apache.tools.ant.Project.executeTarget(java.lang.String) (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
[rmic] at org.apache.tools.ant.taskdefs.Ant.execute() (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
[rmic] at org.apache.tools.ant.Task.perform() (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
[rmic] at org.apache.tools.ant.Target.execute() (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
[rmic] at org.apache.tools.ant.Target.performTasks() (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
[rmic] at org.apache.tools.ant.Project.executeTarget(java.lang.String) (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
[rmic] at org.apache.tools.ant.Project.executeTargets(java.util.Vector) (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
[rmic] at org.apache.tools.ant.Main.runBuild(java.lang.ClassLoader) (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
[rmic] at org.apache.tools.ant.Main.start(java.lang.String[], java.util.Properties, java.lang.ClassLoader) (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
[rmic] at org.apache.tools.ant.Main.main(java.lang.String[]) (/usr/lib/lib-org-apache-tools-ant-1.5.2.so)
BUILD FAILED
file:/farm/gus/projects/GUS/build.xml:305: Rmic failed; see the compiler error output for details.
Total time: 6 seconds
[echo] .
[echo] Installing CBIL/Bio
[echo] .
[echo] Installing CBIL/CSP
[javac] Since compiler setting isn't classic or modern,ignoring fork setting.
[jar] Building jar: /farm/gus/gushome/lib/java/CBIL-CSP.jar
[echo] .
[echo] Installing CBIL/Util
[echo] .
[echo] Installing CBIL/HQ
[echo] .
[echo] Installing CBIL/ObjectMapper
[concat] Warning: Could not find any of the files specified in concat task.
[echo] .
[echo] Installing GUS/Common
[echo] .
[echo] Installing GUS/DBAdmin
[echo] .
[echo] Installing GUS/GOPredict
[javac] Since compiler setting isn't classic or modern,ignoring fork setting.
[jar] Building jar: /farm/gus/gushome/lib/java/GUS-GOPredict.jar
[echo] .
[echo] Installing GUS/ObjRelP
[rmic] RMI Compiling 1 class to /farm/gus/projects/GUS/ObjRelJ/src/java
[rmic] error: An error has occurred in the compiler; please file a bug report (http://java.sun.com/cgi-bin/bugreport.cgi).
[rmic] 1 error
|
|
From: Steve F. <st...@pc...> - 2004-06-17 16:06:17
|
michael- would you consider putting this on the gus wiki? steve Michael Luchtan wrote: >Here you go: >We wanted to enter new data into GUS. Mass Spec data. This required >the use of a plug-in that was provided by Martin Fraunholz. The plugin >needed two perl modules that we did not have. DoTS::MassSpecSummary and >DoTS::MassSpecFeature. These are plug-ins of the type that are >automatically generated by a gus install with regards to the tables that >are in the GUS schema > >We did not have these modules in our $GUS_HOME/lib/perl/GUS/Model/DoTS/ >directory, because we did not have these tables in our schema. >Obviously >this required us to update our gus installation. > >So this is what we did: >1. Create the tables > * Very important to add the primary key constraints >2. Add the tables description to Core.TableInfo > * Very important to describe correctly the table for perl objects >automatic generation >3. Download GUS from CVS >4. Build > * If the build resets all sequences to 1, we have a clue on how to >fix them. > >Describing the steps in detail: > >1. Create the tables: >If the table that you want to create has been incorporated into later >versions of GUS, then chances are you can find the sql to create the >table somewhere in the latest version of GUS from CVS. > >Look in >$PROJECT_HOME/GUS/Model/schema/oracle/ >There are 6 types of files containing the sql commands for each schema. >For example, for DoTS schema: > dots-constraints.sql > dots-indexes.sql > dots-pkey-constraints.sql > dots-sequences.sql > dots-tables.sql > dots-views.sql > >- Create table commands > >create table dots.massspecsummary( > mass_spec_summary_id number(12) not null, > aa_sequence_id number(12) not null, > prediction_algorithm_id number(12) not null, > external_database_release_id number(12) null, > developmental_stage varchar2(20) not null, > is_expressed number(1) not null, > number_of_spans number(12) not null, > sequence_count number(12) not null, > spectrum_count number(12) not null, > aa_seq_percent_covered float(22) not null, > aa_seq_length number(12) not null, > aa_seq_molecular_weight number(12) not null, > aa_seq_pi float(22) not null, > modification_date date not null, > user_read number(1) not null, > user_write number(1) not null, > group_read number(1) not null, > group_write number(1) not null, > other_read number(1) not null, > other_write number(1) not null, > row_user_id number(12) not null, > row_group_id number(3) not null, > row_project_id number(4) not null, > row_alg_invocation_id number(12) not null) > storage( maxextents unlimited ); > >- Add the primary key constraints. >If the table has a primary key, you must make sure to enter the >constraint. > > alter table dots.massspecsummary add constraint >PK_MASSSPECSUMARY > primary key (MASS_SPEC_SUMMARY_ID); > >- Add the foreign key constraints, create the views, indexes, and >sequences. Again the sql for this can usually be found somewhere in >$PROJECT_HOME/GUS/Model/schema/oracle/ > >2. Add the tables description to Core.TableInfo > >The description of the new tables then need to be entered into >Core.TableInfo, since this is the place that the GUS installation will >look for tables to automatically create modules for. It is imperative >that you set the attributes correctly, otherwise the build will not >work. > >table_id -> Unique identifier to the tables (automatic generated by >SubmitRow plug-in). >name -> Name of the table without the schema prefix 'Schema::'. eg: for >DoTS::MassSpecSummary, the table name is MassSpecSummary. >table_type -> controlled vocabulary, many to many, standard, version, >view. >primary_key_column -> Which is the column from this new table you're >describing that identifies uniquely the data inside? (This column must >be set as primary key on the database schema) >database_id -> Here you supply information about the schemas Core, DoTS, >SRes, RAD3, TESS. You must provide the database_id for the correct entry >in the Core.DatabaseInfo table. >is_versioned -> If the table is to be in a Ver schema. >is_view -> This must be set to 1 if you're describing a view. Otherwise, >set it to 0. >view_on_table_id -> Insert the table_id of the table where your new view >gets its data, null otherwise. >superclass_table_id -> Insert the table_id of the table of which your >new table is a child, null if it is not a child table. >is_updatable -> this seems to always be set to 1. > >Example: > >ga GUS::Common::Plugin::SubmitRow > --tablename Core::TableInfo > --attrlist >"name,table_type,primary_key_column,database_id,is_versioned,is_view,is_updatable" > --valuelist >"MassSpecSummary^^^standard^^^mass_spec_summary_id^^^5^^^0^^^0^^^1" > >3. Download GUS from CVS > Go ahead and get the latest version. You might want to make a >back up copy of what > you presently have. > > >4. Build >If you have customized some modules, you might want to make back-ups of >them in a temporary directory. >The last step is to rebuild the GUS installation by executing the >command: > > build GUS install -append > >Our first attempt to rebuild reset all our sequences to 1. We developed >a perl script to autofix all sequences based on the primary_keys current >value. But this is not supposed to happen with the latest version of >GUS from CVS. >If it happens, it is an easy fix. Just ask for the script... > > > >On Wed, 2004-06-16 at 13:20, Sucheta Tripathy wrote: > > >>Hi Michael, >> >>I am sure I will find my answer if I browse through the source forge page, >>but just to get a qucik answer I am writing to you.In case you have some >>time please address this. >> >>I know you added some tables and re-generated the objects, I just wanted >>to make sure what is the sequence of events. >> >>I understand it to be >> >>1. Change the table definition >>2. Rebuild the schema by giving install -append option. >> >>In our case I have the old CVS, not updated. I am afraid if I will be >>stuck at the re building stage. And also what happens to the plugins that >>are modified by us locally.And also what happens to the data already >>present in the tables? >> >> >> >>Many thanks >> >>Sucheta >> >> >> >>>No worry about this. >>>The class was not defined because I had not done the following: >>>alter table dots.massspecsummary add constraint PK_MASSSPECSUMMARY >>>primary key\ >>> (mass_spec_summary_id); >>> >>> >>>On Wed, 2004-06-16 at 11:01, Michael Luchtan wrote: >>> >>> >>>>Hello- >>>>Is this class some kind of standard notation for the gus development >>>>team? I would assume that it means that the class has not been defined >>>>yet. I get the following error message sometimes when trying to run >>>> >>>>build GUS install -append >>>> >>>> [javac] Compiling 1095 source files to >>>>/var/local/checkout/GUS/Model/classes >>>> [javac] >>>>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/MassSpecSummary_Row.java:312: >>>>\ >>>>cannot resolve symbol >>>> [javac] symbol : class notdefyet >>>> [javac] location: class org.gusdb.model.DoTS.MassSpecSummary_Row >>>> [javac] notdefyet pk = get(); >>>> [javac] ^ >>>> [javac] >>>>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/MassSpecSummary_Row.java:312: >>>>\ >>>>cannot resolve symbol >>>> [javac] symbol : method get () >>>> [javac] location: class org.gusdb.model.DoTS.MassSpecSummary_Row >>>> [javac] notdefyet pk = get(); >>>> [javac] ^ >>>> [javac] >>>>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/MassSpecSummary_Row.java:312: >>>>\ >>>>cannot resolve symbol >>>> [javac] symbol : method get () >>>> [javac] location: class org.gusdb.model.DoTS.MassSpecSummary_Row >>>> [javac] notdefyet pk = get(); >>>> [javac] ^ >>>> [javac] >>>>/var/local/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/MassSpecSummary_Row.java:320: >>>>\ >>>>cannot resolve symbol >>>> [javac] symbol : class notdefyet >>>> [javac] location: class org.gusdb.model.DoTS.MassSpecSummary_Row >>>> [javac] set(new notdefyet(pk)); >>>> [javac] ^ >>>> [javac] 3 errors >>>> >>>>BUILD FAILED >>>>file:/var/local/checkout/install/build.xml:235: Compile failed; see the >>>>compiler error output for deta\ >>>>ils. >>>> >>>>Am I doing something wrong that would cause this class to not be >>>>defined, or is this just part of the latest version from CVS? >>>> >>>> >>> >>>------------------------------------------------------- >>>This SF.Net email is sponsored by The 2004 JavaOne(SM) Conference >>>Learn from the experts at JavaOne(SM), Sun's Worldwide Java Developer >>>Conference, June 28 - July 1 at the Moscone Center in San Francisco, CA >>>REGISTER AND SAVE! http://java.sun.com/javaone/sf Priority Code NWMGYKND >>>_______________________________________________ >>>Gusdev-gusdev mailing list >>>Gus...@li... >>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >>> >>> > > > >------------------------------------------------------- >This SF.Net email is sponsored by The 2004 JavaOne(SM) Conference >Learn from the experts at JavaOne(SM), Sun's Worldwide Java Developer >Conference, June 28 - July 1 at the Moscone Center in San Francisco, CA >REGISTER AND SAVE! http://java.sun.com/javaone/sf Priority Code NWMGYKND >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
|
From: Michael L. <lu...@ug...> - 2004-06-17 14:19:35
|
Here you go:
We wanted to enter new data into GUS. Mass Spec data. This required
the use of a plug-in that was provided by Martin Fraunholz. The plugin
needed two perl modules that we did not have. DoTS::MassSpecSummary and
DoTS::MassSpecFeature. These are plug-ins of the type that are
automatically generated by a gus install with regards to the tables that
are in the GUS schema
We did not have these modules in our $GUS_HOME/lib/perl/GUS/Model/DoTS/
directory, because we did not have these tables in our schema.
Obviously
this required us to update our gus installation.
So this is what we did:
1. Create the tables
* Very important to add the primary key constraints
2. Add the tables description to Core.TableInfo
* Very important to describe correctly the table for perl objects
automatic generation
3. Download GUS from CVS
4. Build
* If the build resets all sequences to 1, we have a clue on how to
fix them.
Describing the steps in detail:
1. Create the tables:
If the table that you want to create has been incorporated into later
versions of GUS, then chances are you can find the sql to create the
table somewhere in the latest version of GUS from CVS.
Look in
$PROJECT_HOME/GUS/Model/schema/oracle/
There are 6 types of files containing the sql commands for each schema.
For example, for DoTS schema:
dots-constraints.sql
dots-indexes.sql
dots-pkey-constraints.sql
dots-sequences.sql
dots-tables.sql
dots-views.sql
- Create table commands
create table dots.massspecsummary(
mass_spec_summary_id number(12) not null,
aa_sequence_id number(12) not null,
prediction_algorithm_id number(12) not null,
external_database_release_id number(12) null,
developmental_stage varchar2(20) not null,
is_expressed number(1) not null,
number_of_spans number(12) not null,
sequence_count number(12) not null,
spectrum_count number(12) not null,
aa_seq_percent_covered float(22) not null,
aa_seq_length number(12) not null,
aa_seq_molecular_weight number(12) not null,
aa_seq_pi float(22) not null,
modification_date date not null,
user_read number(1) not null,
user_write number(1) not null,
group_read number(1) not null,
group_write number(1) not null,
other_read number(1) not null,
other_write number(1) not null,
row_user_id number(12) not null,
row_group_id number(3) not null,
row_project_id number(4) not null,
row_alg_invocation_id number(12) not null)
storage( maxextents unlimited );
- Add the primary key constraints.
If the table has a primary key, you must make sure to enter the
constraint.
alter table dots.massspecsummary add constraint
PK_MASSSPECSUMARY
primary key (MASS_SPEC_SUMMARY_ID);
- Add the foreign key constraints, create the views, indexes, and
sequences. Again the sql for this can usually be found somewhere in
$PROJECT_HOME/GUS/Model/schema/oracle/
2. Add the tables description to Core.TableInfo
The description of the new tables then need to be entered into
Core.TableInfo, since this is the place that the GUS installation will
look for tables to automatically create modules for. It is imperative
that you set the attributes correctly, otherwise the build will not
work.
table_id -> Unique identifier to the tables (automatic generated by
SubmitRow plug-in).
name -> Name of the table without the schema prefix 'Schema::'. eg: for
DoTS::MassSpecSummary, the table name is MassSpecSummary.
table_type -> controlled vocabulary, many to many, standard, version,
view.
primary_key_column -> Which is the column from this new table you're
describing that identifies uniquely the data inside? (This column must
be set as primary key on the database schema)
database_id -> Here you supply information about the schemas Core, DoTS,
SRes, RAD3, TESS. You must provide the database_id for the correct entry
in the Core.DatabaseInfo table.
is_versioned -> If the table is to be in a Ver schema.
is_view -> This must be set to 1 if you're describing a view. Otherwise,
set it to 0.
view_on_table_id -> Insert the table_id of the table where your new view
gets its data, null otherwise.
superclass_table_id -> Insert the table_id of the table of which your
new table is a child, null if it is not a child table.
is_updatable -> this seems to always be set to 1.
Example:
ga GUS::Common::Plugin::SubmitRow
--tablename Core::TableInfo
--attrlist
"name,table_type,primary_key_column,database_id,is_versioned,is_view,is_updatable"
--valuelist
"MassSpecSummary^^^standard^^^mass_spec_summary_id^^^5^^^0^^^0^^^1"
3. Download GUS from CVS
Go ahead and get the latest version. You might want to make a
back up copy of what
you presently have.
4. Build
If you have customized some modules, you might want to make back-ups of
them in a temporary directory.
The last step is to rebuild the GUS installation by executing the
command:
build GUS install -append
Our first attempt to rebuild reset all our sequences to 1. We developed
a perl script to autofix all sequences based on the primary_keys current
value. But this is not supposed to happen with the latest version of
GUS from CVS.
If it happens, it is an easy fix. Just ask for the script...
On Wed, 2004-06-16 at 13:20, Sucheta Tripathy wrote:
> Hi Michael,
>
> I am sure I will find my answer if I browse through the source forge page,
> but just to get a qucik answer I am writing to you.In case you have some
> time please address this.
>
> I know you added some tables and re-generated the objects, I just wanted
> to make sure what is the sequence of events.
>
> I understand it to be
>
> 1. Change the table definition
> 2. Rebuild the schema by giving install -append option.
>
> In our case I have the old CVS, not updated. I am afraid if I will be
> stuck at the re building stage. And also what happens to the plugins that
> are modified by us locally.And also what happens to the data already
> present in the tables?
>
>
>
> Many thanks
>
> Sucheta
>
> > No worry about this.
> > The class was not defined because I had not done the following:
> > alter table dots.massspecsummary add constraint PK_MASSSPECSUMMARY
> > primary key\
> > (mass_spec_summary_id);
> >
> >
> > On Wed, 2004-06-16 at 11:01, Michael Luchtan wrote:
> >> Hello-
> >> Is this class some kind of standard notation for the gus development
> >> team? I would assume that it means that the class has not been defined
> >> yet. I get the following error message sometimes when trying to run
> >>
> >> build GUS install -append
> >>
> >> [javac] Compiling 1095 source files to
> >> /var/local/checkout/GUS/Model/classes
> >> [javac]
> >> /var/local/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/MassSpecSummary_Row.java:312:
> >> \
> >> cannot resolve symbol
> >> [javac] symbol : class notdefyet
> >> [javac] location: class org.gusdb.model.DoTS.MassSpecSummary_Row
> >> [javac] notdefyet pk = get();
> >> [javac] ^
> >> [javac]
> >> /var/local/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/MassSpecSummary_Row.java:312:
> >> \
> >> cannot resolve symbol
> >> [javac] symbol : method get ()
> >> [javac] location: class org.gusdb.model.DoTS.MassSpecSummary_Row
> >> [javac] notdefyet pk = get();
> >> [javac] ^
> >> [javac]
> >> /var/local/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/MassSpecSummary_Row.java:312:
> >> \
> >> cannot resolve symbol
> >> [javac] symbol : method get ()
> >> [javac] location: class org.gusdb.model.DoTS.MassSpecSummary_Row
> >> [javac] notdefyet pk = get();
> >> [javac] ^
> >> [javac]
> >> /var/local/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/MassSpecSummary_Row.java:320:
> >> \
> >> cannot resolve symbol
> >> [javac] symbol : class notdefyet
> >> [javac] location: class org.gusdb.model.DoTS.MassSpecSummary_Row
> >> [javac] set(new notdefyet(pk));
> >> [javac] ^
> >> [javac] 3 errors
> >>
> >> BUILD FAILED
> >> file:/var/local/checkout/install/build.xml:235: Compile failed; see the
> >> compiler error output for deta\
> >> ils.
> >>
> >> Am I doing something wrong that would cause this class to not be
> >> defined, or is this just part of the latest version from CVS?
> >
> >
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by The 2004 JavaOne(SM) Conference
> > Learn from the experts at JavaOne(SM), Sun's Worldwide Java Developer
> > Conference, June 28 - July 1 at the Moscone Center in San Francisco, CA
> > REGISTER AND SAVE! http://java.sun.com/javaone/sf Priority Code NWMGYKND
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
>
|
|
From: Michael L. <lu...@ug...> - 2004-06-16 15:39:45
|
No worry about this. The class was not defined because I had not done the following: alter table dots.massspecsummary add constraint PK_MASSSPECSUMMARY primary key\ (mass_spec_summary_id); On Wed, 2004-06-16 at 11:01, Michael Luchtan wrote: > Hello- > Is this class some kind of standard notation for the gus development > team? I would assume that it means that the class has not been defined > yet. I get the following error message sometimes when trying to run > > build GUS install -append > > [javac] Compiling 1095 source files to > /var/local/checkout/GUS/Model/classes > [javac] > /var/local/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/MassSpecSummary_Row.java:312: \ > cannot resolve symbol > [javac] symbol : class notdefyet > [javac] location: class org.gusdb.model.DoTS.MassSpecSummary_Row > [javac] notdefyet pk = get(); > [javac] ^ > [javac] > /var/local/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/MassSpecSummary_Row.java:312: \ > cannot resolve symbol > [javac] symbol : method get () > [javac] location: class org.gusdb.model.DoTS.MassSpecSummary_Row > [javac] notdefyet pk = get(); > [javac] ^ > [javac] > /var/local/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/MassSpecSummary_Row.java:312: \ > cannot resolve symbol > [javac] symbol : method get () > [javac] location: class org.gusdb.model.DoTS.MassSpecSummary_Row > [javac] notdefyet pk = get(); > [javac] ^ > [javac] > /var/local/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/MassSpecSummary_Row.java:320: \ > cannot resolve symbol > [javac] symbol : class notdefyet > [javac] location: class org.gusdb.model.DoTS.MassSpecSummary_Row > [javac] set(new notdefyet(pk)); > [javac] ^ > [javac] 3 errors > > BUILD FAILED > file:/var/local/checkout/install/build.xml:235: Compile failed; see the > compiler error output for deta\ > ils. > > Am I doing something wrong that would cause this class to not be > defined, or is this just part of the latest version from CVS? |
|
From: Michael L. <lu...@ug...> - 2004-06-16 15:11:55
|
Hello-
Is this class some kind of standard notation for the gus development
team? I would assume that it means that the class has not been defined
yet. I get the following error message sometimes when trying to run
build GUS install -append
[javac] Compiling 1095 source files to
/var/local/checkout/GUS/Model/classes
[javac]
/var/local/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/MassSpecSummary_Row.java:312: \
cannot resolve symbol
[javac] symbol : class notdefyet
[javac] location: class org.gusdb.model.DoTS.MassSpecSummary_Row
[javac] notdefyet pk = get();
[javac] ^
[javac]
/var/local/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/MassSpecSummary_Row.java:312: \
cannot resolve symbol
[javac] symbol : method get ()
[javac] location: class org.gusdb.model.DoTS.MassSpecSummary_Row
[javac] notdefyet pk = get();
[javac] ^
[javac]
/var/local/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/MassSpecSummary_Row.java:312: \
cannot resolve symbol
[javac] symbol : method get ()
[javac] location: class org.gusdb.model.DoTS.MassSpecSummary_Row
[javac] notdefyet pk = get();
[javac] ^
[javac]
/var/local/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/MassSpecSummary_Row.java:320: \
cannot resolve symbol
[javac] symbol : class notdefyet
[javac] location: class org.gusdb.model.DoTS.MassSpecSummary_Row
[javac] set(new notdefyet(pk));
[javac] ^
[javac] 3 errors
BUILD FAILED
file:/var/local/checkout/install/build.xml:235: Compile failed; see the
compiler error output for deta\
ils.
Am I doing something wrong that would cause this class to not be
defined, or is this just part of the latest version from CVS?
--
Michael Luchtan
http://www.cs.uga.edu/~luchtan
|
|
From: Michael L. <lu...@ug...> - 2004-06-15 14:20:56
|
Hello- If you would like to help us write some documentation on updating a working GUS installation, please read the following and offer advice and or answer the questions at the end. We wanted to enter new data into GUS. Mass Spec data. This required the use of a plug-in that was provided by Martin Fraunholz. The plugin needed two perl modules that we did not have. DoTS::MassSpecSummary and DoTS::MassSpecFeature. These are plug-ins of the type that are automatically generated by a gus install with regards to the tables that in the GUS schema (how this is done we will explain later). We did not have these modules in our $GUS_HOME/lib/perl/GUS/Model/DoTS/ directory. This is because we did not have these tables in our schema. So the problems are: How to create the tables (easily done) and how to get the modules to be generated. And what order to do it in. First thing to do is to create the tables. You can get the sql commands to do this from the latest version of CVS. in checkoutdir/GUS/Model/schema/oracle/dots-tables.sql The description of the new tables then need to be entered into Core.TableInfo, since (supposedly) this is the place that the GUS installation will look for tables to create modules for. Then, rebuild the GUS installation by executing the command: build GUS install -append This did not create the modules as we expected. Additionally, all sequences contained in GUS were reset to 1. We have written a script to set the sequences back to where they should be. Did we miss some step in between that would have created the modules? Is there a command that would have regenerated the GUS objects without reseting the sequences back to 1? Thanks in advance, -- Michael Luchtan http://www.cs.uga.edu/~luchtan |
|
From: Jonathan S. <js...@pc...> - 2004-06-12 14:29:15
|
Gregory: This logic is in GUS::Model::GusRow::addChild. An object may not have more than one parent from any given table/class. The child object is removed from its previous parent whenever a new parent claims (adds) it. Thus, I believe, an object that had two keys to the same parent table could not belong to both parent objects at the same time. Though I prefer my original suggestion since it is faster, this suggests another work around. Sorry for the all caps, but, I DO NOT RECOMMEND THIS! Rather than getting the children via getChildren, you could SQL query for the ids then instantiate the children directly. Cheers, Jonathan ------------------------------------------------------------------------ --- Jonathan Schug Center for Bioinformatics js...@pc... Computational Biology and Informatics Lab (215) 573-3113 voice University of Pennsylvania, (215) 573-3111 fax 1401a Blockley Hall, Philadelphia, PA 19014-6021 |
|
From: Jonathan S. <js...@pc...> - 2004-06-12 13:55:54
|
Gregory:
I'm looking into this problem. It may be due to the violation you
suggest.
Perhaps a better work-around/solution is to maintain a cache of
objects, e.g., { na_sequence_id => GUS::Model::DoTS::NASequence }.
Then as you scan through your list of Similarities you can easily see
if you have already processed that na_sequence_id already and readily
get your hands on the object if you really want to reprocess it. Of
course this is solution may require more memory, but it sounds as
though you already have multiple objects in memory at one time.
Note to GUS developers: I seem to remember that we have discussed this
idea before, but let me float it again. Should we consider changing
retrieveFromDB or adding another, similar, routine that actually
returns a pointer to the (cached) object? If the object can not be
retrieved from the DB then it returns undef. If the object is already
loaded, it returns that object. If the object is novel, then it
returns the caller's notion of the object. Here are a couple of ways
to use such a method.
my $_obj = GUS::Model::Schema::Table->new({ table_id => 123 });
$_obj = _$obj->uniquelyRetrieveFromDb();
if (!_obj) {
die "Could not find object 123 in db.";
}
OR
my $_obj = GUS::Model::Schema::Table
->new({ table_id => 123 })
->uniquelyRetrieveFromDb();
if (!$_obj) {
die "Could not find object 123 in db.";
}
Thoughts?
Jonathan Schug
------------------------------------------------------------------------
---
Jonathan Schug Center for Bioinformatics
js...@pc... Computational Biology and Informatics Lab
(215) 573-3113 voice University of Pennsylvania,
(215) 573-3111 fax 1401a Blockley Hall, Philadelphia, PA
19014-6021
|
|
From: Gregory C. K. <gck...@cs...> - 2004-06-11 17:40:57
|
Hi,
I ran into a problem with the GUS object layer yesterday. I'm not sure if
this behavior is a bug or intended, so I'd appreciate some input.
I pull two objects ($seq1, $seq2) representing the same row out of the
database (for example, if I'm iterating through a list of Similarities and
if two share a subject sequence, getSequenceObject('subject') will do
this). I use $seq1->getChildren() to find a RepeatType (or features,
etc.) that points to it, and then I do the same with the other
($seq2->getChildren()). It looks like the second getChildren() leads to
an addChild() that goes back and removes the RepeatType from
$seq1->{'children'}.
So, $seq1->{'children'} looked like this after $seq1->getChildren():
{
'GUS::Model::DoTS::RepeatType' => {
'GUS::Model::DoTS::RepeatType=HASH(0x8b6a110)' => 1
}
};
It looks like this after $seq2->getChildren():
{
'GUS::Model::DoTS::RepeatType' => {}
};
and $seq1->{'retrievedChildren'} still shows:
{
'GUS::Model::DoTS::RepeatType' => 1
};
As a side effect of a second lookup, I seem to have knocked the RepeatType
out of a different sequence's list of children, even though the two
sequence objects represent the same row. That seems wrong to me, though
it might be my punishment for violating an implicit "one row, one object"
rule. I seem to be able to get around this with a call to
retrieveChildrenFromDB() before a getChildren(), but that's messy and
slow. Is this the intended behavior, and if so, what's a better way to
deal with it?
Gregory Kettler gck...@cs...
Preuss Lab, MGCB, University of Chicago
|
|
From: Sucheta T. <su...@vb...> - 2004-06-11 15:41:19
|
Yes, I did. This is the place where GI number of each Genbank file is recorded. In other words, If you have a chromosome the specific GI number for that chromosome goes here, not the GI numbers of the individual genes, that are present in the chromosome/scaffold. Sucheta At 11:32 AM 6/11/2004 -0400, Steve Fischer wrote: >have you looked in dots.externalnasequence.secondary_identifier? > >steve > >Sucheta Tripathy wrote: > >> >>Hello all, >> >>As it appears the GI numbers of each gene from a genbank entry(which has >>whole chromosome data in it), does not seem to get anywhere into GUS tables. >> >>Just a thought - WIll it not be nice to store it in some place like >>dots.nagene.na_gene_id by modifying the column? >> >>Any suggestions. >> >>Sucheta >> >> >>------------------------------------------------------- >>This SF.Net email is sponsored by the new InstallShield X. >> >>> From Windows to Linux, servers to mobile, InstallShield X is the >> >>one installation-authoring solution that does it all. Learn more and >>evaluate today! http://www.installshield.com/Dev2Dev/0504 >>_______________________________________________ >>Gusdev-gusdev mailing list >>Gus...@li... >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
|
From: Steve F. <sfi...@pc...> - 2004-06-11 15:32:34
|
have you looked in dots.externalnasequence.secondary_identifier? steve Sucheta Tripathy wrote: > > Hello all, > > As it appears the GI numbers of each gene from a genbank entry(which > has whole chromosome data in it), does not seem to get anywhere into > GUS tables. > > Just a thought - WIll it not be nice to store it in some place like > dots.nagene.na_gene_id by modifying the column? > > Any suggestions. > > Sucheta > > > ------------------------------------------------------- > This SF.Net email is sponsored by the new InstallShield X. > >> From Windows to Linux, servers to mobile, InstallShield X is the > > one installation-authoring solution that does it all. Learn more and > evaluate today! http://www.installshield.com/Dev2Dev/0504 > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: Steve F. <sfi...@pc...> - 2004-06-11 15:20:23
|
michael- oops, i had forgotten to check in my change to Oracle.pm. done.
about the sequences, sorry about that. yeah, it looks like you have to
fix the sequence. I don't know how to do that.
steve
Michael Luchtan wrote:
>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
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>-------------------------------------------------------
>>>>>>>>>>>>>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
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>-------------------------------------------------------
>>>>>>This SF.Net email is sponsored by the new InstallShield X.
>>>>>>From Windows to Linux, servers to mobile, InstallShield X is the
>>>>>>one installation-authoring solution that does it all. Learn more and
>>>>>>evaluate today! http://www.installshield.com/Dev2Dev/0504
>>>>>>_______________________________________________
>>>>>>Gusdev-gusdev mailing list
>>>>>>Gus...@li...
>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>
>>>>>>
>>>>>>
>>>>>-------------------------------------------------------
>>>>>This SF.Net email is sponsored by the new InstallShield X.
>>>>>>From Windows to Linux, servers to mobile, InstallShield X is the
>>>>>one installation-authoring solution that does it all. Learn more and
>>>>>evaluate today! http://www.installshield.com/Dev2Dev/0504
>>>>>_______________________________________________
>>>>>Gusdev-gusdev mailing list
>>>>>Gus...@li...
>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>
>>>>>
>>>>>
>>>>>
>>>>-------------------------------------------------------
>>>>This SF.Net email is sponsored by the new InstallShield X.
>>>>From Windows to Linux, servers to mobile, InstallShield X is the
>>>>one installation-authoring solution that does it all. Learn more and
>>>>evaluate today! http://www.installshield.com/Dev2Dev/0504
>>>>_______________________________________________
>>>>Gusdev-gusdev mailing list
>>>>Gus...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>>
>>>>
>>>-------------------------------------------------------
>>>This SF.Net email is sponsored by the new InstallShield X.
>>>>From Windows to Linux, servers to mobile, InstallShield X is the
>>>one installation-authoring solution that does it all. Learn more and
>>>evaluate today! http://www.installshield.com/Dev2Dev/0504
>>>_______________________________________________
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>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>>
|
|
From: Michael L. <lu...@ug...> - 2004-06-11 15:05:25
|
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
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > > -------------------------------------------------------
> > > > > > > > > > > > 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
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> > > > > > > > > > > _______________________________________________
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|
|
From: Sucheta T. <su...@vb...> - 2004-06-11 15:05:24
|
Hello all, As it appears the GI numbers of each gene from a genbank entry(which has whole chromosome data in it), does not seem to get anywhere into GUS tables. Just a thought - WIll it not be nice to store it in some place like dots.nagene.na_gene_id by modifying the column? Any suggestions. Sucheta |
|
From: Steve F. <st...@pc...> - 2004-06-10 21:34:41
|
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
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>-------------------------------------------------------
>>>>>>>>>>>This SF.Net email is sponsored by: GNOME Foundation
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>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>-------------------------------------------------------
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|
From: Michael L. <lu...@ug...> - 2004-06-10 19:50:10
|
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
> > > >>>>>>>
> > > >>>>>>>
> > > >>>>>>>
> > > >>>>>>>
> > > >>>>>>>
> > > >>>>>>>
> > > >>>>>>>
> > > >>>>>>>
> > > >>>>>>>-------------------------------------------------------
> > > >>>>>>>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
> > > >>>>>>>_______________________________________________
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> > > >>>>>>>Gus...@li...
> > > >>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > > >>>>>>>
> > > >>>>>>>
> > > >>>>>>>
> > > >>>>>>>
> > > >>>>>>>
> > > >>>>>>>
> > > >>>>>>>
> > > >>>>>>>
> > > >>>>>>-------------------------------------------------------
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> > > >>>>>>_______________________________________________
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> > > >>>>>>Gus...@li...
> > > >>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > > >>>>>>
> > > >>>>>>
> > > >>>>>>
> > > >>>>>>
> > > >>>>>>
> > > >>>>>>
> > > >>>>>-------------------------------------------------------
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> > > >>>>>_______________________________________________
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> > > >>>>>
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> > > >>>>>
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> > > >>>>>
> > > >>>>>
> > >
> > >
> > >
> > > -------------------------------------------------------
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|
|
From: Dave B. <db...@pc...> - 2004-06-10 19:22:38
|
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
> > >>>>>>>
> > >>>>>>>
> > >>>>>>>
> > >>>>>>>
> > >>>>>>>
> > >>>>>>>
> > >>>>>>>
> > >>>>>>>
> > >>>>>>>-------------------------------------------------------
> > >>>>>>>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
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> > >>>>>>_______________________________________________
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> > >>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>-------------------------------------------------------
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> > >>>>>Hackers Unite! GUADEC: The world's #1 Open Source Desktop Event.
> > >>>>>GNOME Users and Developers European Conference, 28-30th June in Norway
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> > >>>>>_______________________________________________
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> > >>>>>
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> > >>>>>
> > >>>>>
> > >>>>>
> >
> >
> >
> > -------------------------------------------------------
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|
|
From: Michael S. <msa...@pc...> - 2004-06-10 19:19:58
|
Michael, All primary keys are generated using sequences from within the database. It's assumed in the design of GUS that a table, i.e. DOTS.NAFEATUREIMP will have a corresponding sequence, DOTS.NAFEATUREIMP_SQ. Careful note! In Oracle, sequences are completely orthogonal to tables-- there's nothing preventing one from using the nafeatureimp_sq sequence to generate an id for any other table. The object model uses the above assumption to automatically generate the proper id for a row. If data has been loaded outside of the object model, then it's possible that your sequences are out of sync with their corresponding table (although based on what Steve's said, I'm not implying that this is the case here). Anyway, most of this is just FYI... I'll try to add a Wiki page on this shortly. --Mike On Jun 10, 2004, at 2:04 PM, Michael Luchtan wrote: > 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. |
|
From: Michael L. <lu...@ug...> - 2004-06-10 19:17:17
|
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
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>-------------------------------------------------------
> >>>>>>>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
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
>
>
>
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|
|
From: Steve F. <st...@pc...> - 2004-06-10 19:07:59
|
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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
|
|
From: Michael L. <lu...@ug...> - 2004-06-10 18:13:41
|
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
> >>>
> >>>
> >>>
> >>>
>
|
|
From: Steve F. <st...@pc...> - 2004-06-10 14:37:40
|
paul- i have put version 1.5.0 on the download site http://www.cbil.upenn.edu/downloads/CBIL/releases/ dave- i have added instructions to the cbil wiki. steve Dave Barkan wrote: >Hey Paul, > >I recommitted the relevant files; Steve is in the process of creating the >new CBIL release. When he is done, everything should work fine. > >Let me know how the LoadGoOntology plugin runs; it is newly refactored. >It works fine for me but I think you are the first to use it since, so >good luck ;-) (There shouldn't be any problems). > >Dave > >On Wed, 9 Jun 2004, Paul Mooney wrote: > > > >>Hi, >> >>I get an error when running the LoadGoOntology plugin. >>It is up-to-date WRT cvs. >>I have the CBIL_v1-4-0.tar.gz file, the Store.pm being identical to the >>one in my $GUS_HOME directory path. >>Do I need a newer CBIL utilities ? >> >>Wed Jun 9 14:00:09 2004 loading all .ontology files in >>/nfs/team81/pjm/temp/GUS_installation/GO/ in preparation for parsing >>Wed Jun 9 14:00:10 2004 parsing all .ontology files in >>preparation for inserting into database >>Wed Jun 9 14:00:39 2004 parsing finished; loading ontology into >>database >>Can't locate object method "getDescription" via package >>"CBIL::Bio::GeneOntologyParser::Store" (perhaps you forgot to load >>"CBIL::Bio::GeneOntologyParser::Store"?) at >>/nfs/team81/pjm/GUS/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm >>line 452. >> >>Paul. >> >> >> >>------------------------------------------------------- >>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 > > |
|
From: Dave B. <db...@pc...> - 2004-06-10 14:10:09
|
Hey Paul, I recommitted the relevant files; Steve is in the process of creating the new CBIL release. When he is done, everything should work fine. Let me know how the LoadGoOntology plugin runs; it is newly refactored. It works fine for me but I think you are the first to use it since, so good luck ;-) (There shouldn't be any problems). Dave On Wed, 9 Jun 2004, Paul Mooney wrote: > Hi, > > I get an error when running the LoadGoOntology plugin. > It is up-to-date WRT cvs. > I have the CBIL_v1-4-0.tar.gz file, the Store.pm being identical to the > one in my $GUS_HOME directory path. > Do I need a newer CBIL utilities ? > > Wed Jun 9 14:00:09 2004 loading all .ontology files in > /nfs/team81/pjm/temp/GUS_installation/GO/ in preparation for parsing > Wed Jun 9 14:00:10 2004 parsing all .ontology files in > preparation for inserting into database > Wed Jun 9 14:00:39 2004 parsing finished; loading ontology into > database > Can't locate object method "getDescription" via package > "CBIL::Bio::GeneOntologyParser::Store" (perhaps you forgot to load > "CBIL::Bio::GeneOntologyParser::Store"?) at > /nfs/team81/pjm/GUS/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm > line 452. > > Paul. > > > > ------------------------------------------------------- > 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 > |
|
From: Michael S. <msa...@pc...> - 2004-06-09 21:05:19
|
Plus it should be:
SResVer::MassSpecSummaryVER
(note the Ver on the end of the table)
I think MassSpecSummary should be in DoTS, not SRES.
--Mike
On Jun 9, 2004, at 5:00 PM, 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
>>>>
>>>>
>
>
>
> -------------------------------------------------------
> 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
|
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