gusdev-gusdev Mailing List for Genomic Unified Schema Development (Page 2)

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I don't know what the officially supported mechanism is for this (there may not be one ) but this is what I have used to manually insert that row.

INSERT INTO Core.DatabaseVersion
  (DATABASE_VERSION_ID, VERSION, MODIFICATION_DATE, USER_READ, USER_WRITE, 
   GROUP_READ, GROUP_WRITE, OTHER_READ, OTHER_WRITE, ROW_USER_ID, 
   ROW_GROUP_ID, ROW_PROJECT_ID, ROW_ALG_INVOCATION_ID) 
VALUES (1, 3.6, current_timestamp,1,1,1,1,1,0,1,1,1,1);

On Mar 23, 2012, at 2:41 PM, John Iodice wrote:

> Hi Nicolas,
> 
> I think this is related to the table core.DatabaseVersion, and that this table should have a single row in it with "3.6" in the VERSION column. But I don't know how that gets there. 
> 
> Is this what you have? If that table is empty, my suggestion (unless somebody else has a better one) is to insert a record with that value in that column.
> 
> -- John
> 
> On Fri, Mar 23, 2012 at 5:03 AM, Nicolas Joannin <nic...@gm...> wrote:
> Hi again,
> 
> Thanks again for the help!
> I just have one last question:
> In the Install Guide for GUS, it is written that one should register the GUS application framework with the following command:
> $ ga +meta --commit
> 
> I'm not quite sure what this does, and when I do run it, I get the following message:
> 
> Nicolas-work-iMac:bin Nicolas$ ga +meta --commit
> 
> ERROR: Database version does not match required version for Plugin.
> Database Version:     Plugin Version: 3.6
> 
> Is this registration something I should worry about? If so, any suggestions as to what this problem might be?
> 
> Best regards,
> Nicolas
> 
> 
> 
> 
> On Fri, Mar 23, 2012 at 13:05, Mark Heiges <mh...@ug...> wrote:
> whew!
> 
> On Mar 23, 2012, at 12:01 AM, Nicolas Joannin wrote:
> 
> > Indeed, again, my mistake!
> > Thank you all for your help: BUILD SUCCESSFUL ;)
> >
> > Best regards,
> > Nicolas
> >
> >
> > On Fri, Mar 23, 2012 at 12:40, Mark Heiges <mh...@ug...> wrote:
> > Check the dbiDsn setting in your gus.config. What you sent earlier (dbiDsn=dbi:Pg:dbname=<my_db_name>)  looks correct to me; make sure that hasn't changed. The error is symptomatic of missing the 'dbname=' prefix
> >
> >
> >
> >
> >
> > On Mar 22, 2012, at 11:20 PM, Nicolas Joannin wrote:
> >
> > > Hi Mark,
> > >
> > > Thanks: indeed, I made the mistake of adjusting the PATH with $GUS_HOME/bin etc. before actually exporting GUS_HOME.
> > >
> > > I've rerun the build GUS install -append and it now has a new error:
> > > perlGeneratedModel:
> > >      [echo] generating Perl Objects
> > >      [exec] GUS::ObjRelP::DbiDbHandle connect('varDB_2012','postgres',...) failed: missing "=" after "varDB_2012" in connection info string at /Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 173
> > >      [exec] Can't bless non-reference value at /Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 21.
> > >
> > > BUILD FAILED
> > > /Users/Nicolas/GUS/project_home/install/build.xml:38: The following error occurred while executing this line:
> > > /Users/Nicolas/GUS/project_home/GUS/build.xml:258: exec returned: 255
> > >
> > > Thanks again for your help!
> > > Best regards,
> > > Nicolas
> > >
> > >
> > > Full output:
> > >
> > > Nicolas-work-iMac:bin Nicolas$ ./build GUS install -append
> > > Buildfile: /Users/Nicolas/GUS/project_home/install/build.xml
> > >
> > > install:
> > >      [echo]  proj=GUS
> > >      [echo]  comp=
> > >
> > > defaultComponentInstall:
> > >      [echo] .
> > >      [echo] Installing CBIL/Bio
> > >
> > > recordBuildState:
> > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > >
> > > defaultComponentInstall:
> > >      [echo] .
> > >      [echo] Installing CBIL/CSP
> > >
> > > defaultJavaCompile:
> > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > >
> > > recordBuildState:
> > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > >
> > > defaultComponentInstall:
> > >      [echo] .
> > >      [echo] Installing CBIL/Util
> > >
> > > recordBuildState:
> > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > >
> > > defaultComponentInstall:
> > >      [echo] .
> > >      [echo] Installing CBIL/Cider
> > >
> > > recordBuildState:
> > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > >
> > > defaultComponentInstall:
> > >      [echo] .
> > >      [echo] Installing CBIL/HQ
> > >
> > > recordBuildState:
> > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > >
> > > defaultComponentInstall:
> > >      [echo] .
> > >      [echo] Installing CBIL/TranscriptExpression
> > >
> > > recordBuildState:
> > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > >
> > > defaultComponentInstall:
> > >      [echo] .
> > >      [echo] Installing CBIL/ObjectMapper
> > >
> > > recordBuildState:
> > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > >
> > > defaultComponentInstall:
> > >      [echo] .
> > >      [echo] Installing GUS/Supported
> > >
> > > defaultJavaCompile:
> > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > >
> > > recordBuildState:
> > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > >
> > > defaultComponentInstall:
> > >      [echo] .
> > >      [echo] Installing GUS/Community
> > >
> > > recordBuildState:
> > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > >
> > > defaultComponentInstall:
> > >      [echo] .
> > >      [echo] Installing GUS/DBAdmin
> > >
> > > defaultJavaCompile:
> > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > >
> > > recordBuildState:
> > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > >
> > > defaultComponentInstall:
> > >      [echo] .
> > >      [echo] Installing GUS/GOPredict
> > >
> > > defaultJavaCompile:
> > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > >
> > > recordBuildState:
> > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > >
> > > defaultComponentInstall:
> > >      [echo] .
> > >      [echo] Installing GusSchema/Definition
> > >
> > > recordBuildState:
> > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > >
> > > defaultComponentInstall:
> > >      [echo] .
> > >      [echo] Installing GUS/DBAdmin
> > >
> > > defaultJavaCompile:
> > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > >
> > > recordBuildState:
> > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > >
> > > defaultComponentInstall:
> > >      [echo] .
> > >      [echo] Installing GUS/ObjRelP
> > >
> > > recordBuildState:
> > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > >
> > > perlGeneratedModel:
> > >      [echo] generating Perl Objects
> > >      [exec] GUS::ObjRelP::DbiDbHandle connect('varDB_2012','postgres',...) failed: missing "=" after "varDB_2012" in connection info string at /Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 173
> > >      [exec] Can't bless non-reference value at /Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 21.
> > >
> > > BUILD FAILED
> > > /Users/Nicolas/GUS/project_home/install/build.xml:38: The following error occurred while executing this line:
> > > /Users/Nicolas/GUS/project_home/GUS/build.xml:258: exec returned: 255
> > >
> > > Total time: 20 seconds
> > >
> > > On Fri, Mar 23, 2012 at 12:00, Mark Heiges <mh...@ug...> wrote:
> > > The includeantruntime warning is an ant 1.8 "feature". I'm pretty sure you can ignore that warning in this case, I don't see any abnormal repercussions from it, but we've not used that version of ant ourselves. You can google that warning for more information if you're curious.
> > >
> > > The generateGusObjects error makes me suspect that your PATH doesn't include $GUS_HOME/bin . You'll want something like
> > >        export PATH=$GUS_HOME/bin:$PROJECT_HOME/install/bin:$PATH
> > >
> > > At this point the schema is installed in your database (log in with a client and confirm). So the next time run  "build GUS install -append" (without the -installDBSchema) and it should resume with the "generating Perl Objects".
> > >
> > >
> > > On Mar 22, 2012, at 9:59 PM, Nicolas Joannin wrote:
> > >
> > > > Hi Mark,
> > > >
> > > > I got the code from the subversion repository, but that was a couple weeks ago, I think.
> > > > I've just tried with the latest svn update.
> > > >
> > > > I started all from scratch: I deleted the GUS folder I was working in and replaced it with the new.
> > > > I run the install a first time and encountered the same ojdbc5.jar problem.
> > > >
> > > > So I added that file to the proper directory and rerun the install.
> > > >
> > > > This time I get different errors (see full output below):
> > > >
> > > > defaultJavaCompile:
> > > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > > >
> > > > [InstallSchema] ERROR [main] (InstallSchemaTask.java:122) - Null version, skipping.  Note:  You will need to manually add a version number to the DB
> > > >
> > > > BUILD FAILED
> > > > /Users/Nicolas/GUS/project_home/install/build.xml:38: The following error occurred while executing this line:
> > > > /Users/Nicolas/GUS/project_home/GUS/build.xml:258: Execute failed: java.io.IOException: Cannot run program "generateGusObjects" (in directory "/Users/Nicolas/GUS/project_home/install"): error=2, No such file or directory
> > > >
> > > > The first one (with the "warning: 'includeantruntime'") occurs several times.
> > > >
> > > > Thanks for the quick responses!
> > > > Best regards,
> > > > Nicolas
> > > >
> > > >
> > > > Here's the full output:
> > > >
> > > > Nicolas-work-iMac:bin Nicolas$ ./build GUS install -append -installDBSchema
> > > > Buildfile: /Users/Nicolas/GUS/project_home/install/build.xml
> > > >
> > > > install:
> > > >      [echo]  proj=GUS
> > > >      [echo]  comp=
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing CBIL/Bio
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing CBIL/CSP
> > > >
> > > > defaultJavaCompile:
> > > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing CBIL/Util
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing CBIL/Cider
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing CBIL/HQ
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing CBIL/TranscriptExpression
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing CBIL/ObjectMapper
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing GUS/Supported
> > > >
> > > > defaultJavaCompile:
> > > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing GUS/Community
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing GUS/DBAdmin
> > > >
> > > > defaultJavaCompile:
> > > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing GUS/GOPredict
> > > >
> > > > defaultJavaCompile:
> > > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing GusSchema/Definition
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing GUS/DBAdmin
> > > >
> > > > defaultJavaCompile:
> > > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > InstallSchema:
> > > > [InstallSchema]  INFO [main] (InstallSchemaTask.java:79) - Reading database from /Users/Nicolas/GUS/project_home/GusSchema/Definition/config/gus_schema.xml
> > > > [InstallSchema]  INFO [main] (SchemaReader.java:48) - Reading Database
> > > > [InstallSchema]  INFO [main] (Database.java:161) - Resolving Database References
> > > > [InstallSchema]  INFO [main] (DatabaseValidator.java:57) - Validating Database: 'null'
> > > > [InstallSchema]  INFO [main] (InstallSchemaTask.java:87) -  Overriding individual tablespace specifications with value "GUS" from property file
> > > > [InstallSchema]  INFO [main] (DatabaseValidator.java:57) - Validating Database: 'null'
> > > > [InstallSchema]  INFO [main] (SchemaWriter.java:33) - Writing Database
> > > > [InstallSchema]  INFO [main] (DatabaseValidator.java:57) - Validating Database: 'null'
> > > > [InstallSchema]  INFO [main] (SchemaWriter.java:33) - Writing Database
> > > > [InstallSchema] ERROR [main] (InstallSchemaTask.java:122) - Null version, skipping.  Note:  You will need to manually add a version number to the DB
> > > > [InstallSchema] ERROR [main] (InstallSchemaTask.java:122) - Null version, skipping.  Note:  You will need to manually add a version number to the DB
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing GUS/ObjRelP
> > > >
> > > > componentPartCopySub:
> > > >      [copy] Copying 3 files to /Users/Nicolas/GUS/gus_home/bin
> > > >
> > > > componentPartCopySub:
> > > >     [mkdir] Created dir: /Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP
> > > >      [copy] Copying 18 files to /Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP
> > > >
> > > > componentPartCopySub:
> > > >     [mkdir] Created dir: /Users/Nicolas/GUS/gus_home/doc/GUS/ObjRelP
> > > >      [copy] Copying 3 files to /Users/Nicolas/GUS/gus_home/doc/GUS/ObjRelP
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > perlGeneratedModel:
> > > >     [mkdir] Created dir: /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/Core
> > > >     [mkdir] Created dir: /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/DoTS
> > > >     [mkdir] Created dir: /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/RAD
> > > >     [mkdir] Created dir: /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/SRes
> > > >     [mkdir] Created dir: /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/TESS
> > > >     [mkdir] Created dir: /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/PROT
> > > >     [mkdir] Created dir: /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/Study
> > > >      [echo] generating Perl Objects
> > > >
> > > > BUILD FAILED
> > > > /Users/Nicolas/GUS/project_home/install/build.xml:38: The following error occurred while executing this line:
> > > > /Users/Nicolas/GUS/project_home/GUS/build.xml:258: Execute failed: java.io.IOException: Cannot run program "generateGusObjects" (in directory "/Users/Nicolas/GUS/project_home/install"): error=2, No such file or directory
> > > >       at java.lang.ProcessBuilder.start(ProcessBuilder.java:460)
> > > >       at java.lang.Runtime.exec(Runtime.java:593)
> > > >       at org.apache.tools.ant.taskdefs.Execute$Java13CommandLauncher.exec(Execute.java:862)
> > > >       at org.apache.tools.ant.taskdefs.Execute.launch(Execute.java:481)
> > > >       at org.apache.tools.ant.taskdefs.Execute.execute(Execute.java:495)
> > > >       at org.apache.tools.ant.taskdefs.ExecTask.runExecute(ExecTask.java:631)
> > > >       at org.apache.tools.ant.taskdefs.ExecTask.runExec(ExecTask.java:672)
> > > >       at org.apache.tools.ant.taskdefs.ExecTask.execute(ExecTask.java:498)
> > > >       at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> > > >       at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
> > > >       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> > > >       at java.lang.reflect.Method.invoke(Method.java:597)
> > > >       at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> > > >       at org.apache.tools.ant.Task.perform(Task.java:348)
> > > >       at org.apache.tools.ant.Target.execute(Target.java:392)
> > > >       at org.apache.tools.ant.Target.performTasks(Target.java:413)
> > > >       at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
> > > >       at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
> > > >       at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
> > > >       at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
> > > >       at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> > > >       at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> > > >       at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> > > >       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> > > >       at java.lang.reflect.Method.invoke(Method.java:597)
> > > >       at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> > > >       at org.apache.tools.ant.Task.perform(Task.java:348)
> > > >       at org.apache.tools.ant.Target.execute(Target.java:392)
> > > >       at org.apache.tools.ant.Target.performTasks(Target.java:413)
> > > >       at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
> > > >       at org.apache.tools.ant.Project.executeTarget(Project.java:1368)
> > > >       at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
> > > >       at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
> > > >       at org.apache.tools.ant.Main.runBuild(Main.java:811)
> > > >       at org.apache.tools.ant.Main.startAnt(Main.java:217)
> > > >       at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
> > > >       at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
> > > > Caused by: java.io.IOException: error=2, No such file or directory
> > > >       at java.lang.UNIXProcess.forkAndExec(Native Method)
> > > >       at java.lang.UNIXProcess.<init>(UNIXProcess.java:53)
> > > >       at java.lang.ProcessImpl.start(ProcessImpl.java:91)
> > > >       at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
> > > >       ... 36 more
> > > >
> > > > Total time: 30 seconds
> > > >
> > > >
> > > >
> > > > On Fri, Mar 23, 2012 at 10:37, Mark Heiges <mh...@ug...> wrote:
> > > > Hi Nicolas, Are you using code from the gus subversion repository? If so, do an svn update. This bug was fixed this morning. If not from subversion, where did you get your code?
> > > >
> > > > -Mark
> > > >
> > > > On Mar 22, 2012, at 9:24 PM, Nicolas Joannin wrote:
> > > >
> > > > > Good morning Mark, Rodrigo and John,
> > > > >
> > > > > Indeed, the ojdbc5.jar file helped to get further ahead :)
> > > > > Unfortunately, there are still some errors (see below).
> > > > >
> > > > > Best regards,
> > > > > Nicolas
> > > > >
> > > > >
> > > > >
> > > > > Nicolas-work-iMac:bin Nicolas$ ./build GUS install -append -installDBSchema
> > > > > Buildfile: /Users/Nicolas/GUS/project_home/install/build.xml
> > > > >
> > > > > install:
> > > > >      [echo]  proj=GUS
> > > > >      [echo]  comp=
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing CBIL/Bio
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing CBIL/CSP
> > > > >
> > > > > defaultJavaCompile:
> > > > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing CBIL/Util
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing CBIL/Cider
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing CBIL/HQ
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing CBIL/TranscriptExpression
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing CBIL/ObjectMapper
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing GUS/Supported
> > > > >
> > > > > defaultJavaCompile:
> > > > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing GUS/Community
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing GUS/DBAdmin
> > > > >
> > > > > defaultJavaCompile:
> > > > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing GUS/GOPredict
> > > > >
> > > > > defaultJavaCompile:
> > > > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing GusSchema/Definition
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing GUS/DBAdmin
> > > > >
> > > > > defaultJavaCompile:
> > > > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file: /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > InstallSchema:
> > > > > [InstallSchema]  INFO [main] (InstallSchemaTask.java:79) - Reading database from /Users/Nicolas/GUS/project_home/GusSchema/Definition/config/gus_schema.xml
> > > > > [InstallSchema]  INFO [main] (SchemaReader.java:48) - Reading Database
> > > > > [InstallSchema]  INFO [main] (Database.java:161) - Resolving Database References
> > > > > [InstallSchema]  INFO [main] (DatabaseValidator.java:57) - Validating Database: 'null'
> > > > > [InstallSchema]  INFO [main] (InstallSchemaTask.java:87) -  Overriding individual tablespace specifications with value "GUS" from property file
> > > > > [InstallSchema]  INFO [main] (DatabaseValidator.java:57) - Validating Database: 'null'
> > > > > [InstallSchema]  INFO [main] (SchemaWriter.java:33) - Writing Database
> > > > > [InstallSchema]  INFO [main] (DatabaseValidator.java:57) - Validating Database: 'null'
> > > > > [InstallSchema]  INFO [main] (SchemaWriter.java:33) - Writing Database
> > > > >
> > > > > BUILD FAILED
> > > > > /Users/Nicolas/GUS/project_home/install/build.xml:38: The following error occurred while executing this line:
> > > > > /Users/Nicolas/GUS/project_home/GUS/build.xml:16: The following error occurred while executing this line:
> > > > > /Users/Nicolas/GUS/project_home/GusSchema/build.xml:63: java.io.IOException: Error executing SQL: '
> > > > >
> > > > > CREATE TABLE Core.AlgorithmInvocation (
> > > > >        ALGORITHM_INVOCATION_ID NUMERIC(12,0)  NOT NULL,
> > > > >        ALGORITHM_IMPLEMENTATION_ID NUMERIC(5,0)  NOT NULL,
> > > > >        START_TIME TIMESTAMP NOT NULL,
> > > > >        END_TIME TIMESTAMP NOT NULL,
> > > > >        CPUS_USED NUMERIC(5,0) ,
> > > > >        CPU_TIME FLOAT(126) ,
> > > > >        RESULT VARCHAR(350)  NOT NULL,
> > > > >        COMMENT_STRING VARCHAR(255) ,
> > > > >        MODIFICATION_DATE TIMESTAMP NOT NULL,
> > > > >        USER_READ NUMERIC(1,0)  NOT NULL,
> > > > >        USER_WRITE NUMERIC(1,0)  NOT NULL,
> > > > >        GROUP_READ NUMERIC(1,0)  NOT NULL,
> > > > >        GROUP_WRITE NUMERIC(1,0)  NOT NULL,
> > > > >        OTHER_READ NUMERIC(1,0)  NOT NULL,
> > > > >        OTHER_WRITE NUMERIC(1,0)  NOT NULL,
> > > > >        ROW_USER_ID NUMERIC(12,0)  NOT NULL,
> > > > >        ROW_GROUP_ID NUMERIC(4,0)  NOT NULL,
> > > > >        ROW_PROJECT_ID NUMERIC(4,0)  NOT NULL,
> > > > >        ROW_ALG_INVOCATION_ID NUMERIC(12,0)  NOT NULL)' Error: ERROR: precision for type float must be less than 54 bits
> > > > >       at org.gusdb.dbadmin.util.JDBCStreamWriter.flush(JDBCStreamWriter.java:57)
> > > > >       at org.gusdb.dbadmin.writer.RelationalDatabaseWriter.writeTable(RelationalDatabaseWriter.java:67)
> > > > >       at org.gusdb.dbadmin.writer.RelationalDatabaseWriter.writeTables(RelationalDatabaseWriter.java:43)
> > > > >       at org.gusdb.dbadmin.writer.PostgresWriter.writeDatabase(PostgresWriter.java:68)
> > > > >       at org.gusdb.dbadmin.writer.SchemaWriter.write(SchemaWriter.java:34)
> > > > >       at org.gusdb.dbadmin.util.InstallSchemaTask.execute(InstallSchemaTask.java:99)
> > > > >       at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> > > > >       at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
> > > > >       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> > > > >       at java.lang.reflect.Method.invoke(Method.java:597)
> > > > >       at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> > > > >       at org.apache.tools.ant.Task.perform(Task.java:348)
> > > > >       at org.apache.tools.ant.Target.execute(Target.java:392)
> > > > >       at org.apache.tools.ant.Target.performTasks(Target.java:413)
> > > > >       at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
> > > > >       at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
> > > > >       at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
> > > > >       at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
> > > > >       at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> > > > >       at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
> > > > >       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> > > > >       at java.lang.reflect.Method.invoke(Method.java:597)
> > > > >       at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> > > > >       at org.apache.tools.ant.Task.perform(Task.java:348)
> > > > >       at org.apache.tools.ant.Target.execute(Target.java:392)
> > > > >       at org.apache.tools.ant.Target.performTasks(Target.java:413)
> > > > >       at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
> > > > >       at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
> > > > >       at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
> > > > >       at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
> > > > >       at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> > > > >       at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> > > > >       at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> > > > >       at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> > > > >       at java.lang.reflect.Method.invoke(Method.java:597)
> > > > >       at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> > > > >       at org.apache.tools.ant.Task.perform(Task.java:348)
> > > > >       at org.apache.tools.ant.Target.execute(Target.java:392)
> > > > >       at org.apache.tools.ant.Target.performTasks(Target.java:413)
> > > > >       at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
> > > > >       at org.apache.tools.ant.Project.executeTarget(Project.java:1368)
> > > > >       at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
> > > > >       at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
> > > > >       at org.apache.tools.ant.Main.runBuild(Main.java:811)
> > > > >       at org.apache.tools.ant.Main.startAnt(Main.java:217)
> > > > >       at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
> > > > >       at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
> > > > >
> > > > > Total time: 20 seconds
> > > > >
> > > > >
> > > > > On Thu, Mar 22, 2012 at 23:23, Mark Heiges <mh...@ug...> wrote:
> > > > > I have confirmed that the ojdbc jar is required for the code to compile.
> > > > >
> > > > > -Mark
> > > > >
> > > > > On Mar 22, 2012, at 10:09 AM, John Iodice wrote:
> > > > >
> > > > > > Hi Nicolas,
> > > > > >
> > > > > > That dbVendor setting looks right; I think that your configuration is correct for a Postgres install (and that I was mistaken to think that the install is looking for oracle.jdbc.OracleDriver because it's configured to use Oracle).
> > > > > >
> > > > > > Looking in my own $GUS_HOME/lib/java/db_driver directory, I see that I have both Oracle and Postgres drivers, though I only use Oracle. Maybe both are required to compile the Java? These are the files I have there:
> > > > > >
> > > > > > $ ls $GUS_HOME/lib/java/db_driver/
> > > > > > ojdbc5.jar  postgresql-8.3-603.jdbc3.jar
> > > > > >
> > > > > > I see that ojdbc5.jar does contain oracle/jdbc/OracleDriver.class. I suggest you try downloading that jarfile. You can get it from here: http://www.oracle.com/technetwork/database/enterprise-edition/jdbc-111060-084321.html
> > > > > >
> > > > > > -- John
> > > > > >
> > > >
> > > >
> > > >
> > >
> > >
> > >
> >
> >
> >
> 
> 
> 
> 
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