[InterMine Dev] dev Digest, Vol 29, Issue 2

wang su wangsu0623 at gmail.com
Mon Oct 3 16:22:56 BST 2011


hi ,
thanks for your help,
but I get another error like

BUILD FAILED
/mnt/Storage/home/wangs/intermine_0_97/imbuild/integrate.xml:54: The following error occurred while executing this line:
/mnt/Storage/home/wangs/intermine_0_97/imbuild/source.xml:201: Exception in XmlDataLoaderTask
	at org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:168)
	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
	at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:616)
	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:390)
	at org.apache.tools.ant.Target.performTasks(Target.java:411)
	at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
	at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
	at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
	at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:441)
	at org.intermine.task.Integrate.performAction(Integrate.java:223)
	at org.intermine.task.Integrate.performAction(Integrate.java:135)
	at org.intermine.task.Integrate.execute(Integrate.java:127)
	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
	at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:616)
	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:390)
	at org.apache.tools.ant.Target.performTasks(Target.java:411)
	at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
	at org.apache.tools.ant.Project.executeTarget(Project.java:1329)
	at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
	at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
	at org.apache.tools.ant.Main.runBuild(Main.java:801)
	at org.apache.tools.ant.Main.startAnt(Main.java:218)
	at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
	at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: org.intermine.objectstore.ObjectStoreException: Failed to instantiate IntegrationWriter class: org.intermine.dataloader.IntegrationWriterDataTrackingImpl
	at org.intermine.dataloader.IntegrationWriterFactory.getIntegrationWriter(IntegrationWriterFactory.java:75)
	at org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:123)
	... 31 more
Caused by: java.lang.reflect.InvocationTargetException
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:616)
	at org.intermine.dataloader.IntegrationWriterFactory.getIntegrationWriter(IntegrationWriterFactory.java:65)
	... 32 more
Caused by: java.lang.IllegalArgumentException: Problem instantiating IntegrationWriterDataTrackingImpl integration.production
	at org.intermine.dataloader.IntegrationWriterDataTrackingImpl.getInstance(IntegrationWriterDataTrackingImpl.java:145)
	at org.intermine.dataloader.IntegrationWriterDataTrackingImpl.getInstance(IntegrationWriterDataTrackingImpl.java:80)
	... 37 more
Caused by: java.lang.reflect.InvocationTargetException
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
	at org.intermine.dataloader.IntegrationWriterDataTrackingImpl.getInstance(IntegrationWriterDataTrackingImpl.java:137)
	... 38 more
Caused by: java.lang.RuntimeException: can't open datasource for {platform=PostgreSQL, datasource.dataSourceName=db.production, datasource.maxConnections=50, datasource.databaseName=pathmine, datasource.class=org.postgresql.ds.PGPoolingDataSource, datasource.password=learningperl, datasource.user=postgres, driver=org.postgresql.Driver, datasource.serverName=localhost} org.postgresql.Driver PostgreSQL
	at org.intermine.sql.Database.getConnection(Database.java:106)
	at org.intermine.dataloader.DataTracker.<init>(DataTracker.java:91)
	... 43 more
Caused by: org.postgresql.util.PSQLException: FATAL: sorry, too many clients already
	at org.postgresql.core.v3.ConnectionFactoryImpl.readStartupMessages(ConnectionFactoryImpl.java:464)
	at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:112)
	at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:66)
	at org.postgresql.jdbc2.AbstractJdbc2Connection.<init>(AbstractJdbc2Connection.java:125)
	at org.postgresql.jdbc3.AbstractJdbc3Connection.<init>(AbstractJdbc3Connection.java:30)
	at org.postgresql.jdbc3g.AbstractJdbc3gConnection.<init>(AbstractJdbc3gConnection.java:22)
	at org.postgresql.jdbc3g.Jdbc3gConnection.<init>(Jdbc3gConnection.java:24)
	at org.postgresql.Driver.makeConnection(Driver.java:393)
	at org.postgresql.Driver.connect(Driver.java:267)
	at java.sql.DriverManager.getConnection(DriverManager.java:620)
	at java.sql.DriverManager.getConnection(DriverManager.java:200)
	at org.postgresql.ds.common.BaseDataSource.getConnection(BaseDataSource.java:91)
	at org.postgresql.ds.common.BaseDataSource.getConnection(BaseDataSource.java:74)
	at org.postgresql.ds.PGConnectionPoolDataSource.getPooledConnection(PGConnectionPoolDataSource.java:60)
	at org.postgresql.ds.jdbc23.AbstractJdbc23PoolingDataSource.getPooledConnection(AbstractJdbc23PoolingDataSource.java:429)
	at org.postgresql.ds.jdbc23.AbstractJdbc23PoolingDataSource.getConnection(AbstractJdbc23PoolingDataSource.java:356)
	at org.intermine.sql.Database.getConnection(Database.java:104)
	... 44 more

Total time: 9 minutes 11 seconds

Thanks

Su
On 2011-10-3, at 下午7:00, dev-request at intermine.org wrote:

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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of dev digest..."
> 
> 
> Today's Topics:
> 
>   1. Re: Changing the default summary views (Julie Sullivan)
>   2. Re: Reports from 'Usage' Tab Emailable? (Julie Sullivan)
>   3. Re: constraints editable by default (Julie Sullivan)
>   4. errors in build a new mine (wang su)
>   5. Re: errors in build a new mine (Julie Sullivan)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 03 Oct 2011 08:43:29 +0100
> From: Julie Sullivan <julie at flymine.org>
> To: dev at intermine.org
> Subject: Re: [InterMine Dev] Changing the default summary views
> Message-ID: <4E8967A1.3050305 at flymine.org>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> That is controlled by the webconfig-model.xml file.
> 
> Here's a list of properties files and what they do:
> 
> 	http://intermine.org/wiki/WebappConfig
> 
> 
> On 30/09/11 20:23, JD Wong wrote:
>> Hi,
>> 
>> Does anybody know how to change what data is displayed when viewing a
>> record?
>> 
>> Thanks!
>> -JD
>> 
>> 
>> 
>> 
>> _______________________________________________
>> dev mailing list
>> dev at intermine.org
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Mon, 03 Oct 2011 08:59:02 +0100
> From: Julie Sullivan <julie at flymine.org>
> To: dev at intermine.org
> Subject: Re: [InterMine Dev] Reports from 'Usage' Tab Emailable?
> Message-ID: <4E896B46.3020705 at flymine.org>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> No, they aren't, but that's a really good idea.  I've made a ticket.
> 
> On 30/09/11 22:47, Kalpana Karra wrote:
>> Wondering if that is a possibility and I am just not seeing it ;)
>> Thanks,
>> -Kalpana
>> 
>> _______________________________________________
>> dev mailing list
>> dev at intermine.org
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>> 
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Mon, 03 Oct 2011 09:16:33 +0100
> From: Julie Sullivan <julie at flymine.org>
> To: dev at intermine.org
> Subject: Re: [InterMine Dev] constraints editable by default
> Message-ID: <4E896F61.7080605 at flymine.org>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Can you go into more detail as to how you are getting a "new" template from an 
> old one?  There are a couple ways to do it.
> 
> If you edit a current template, all "editable" options should remain the same 
> unless changed by you.
> 
> If you make a new template, all "editable" options are by default unlocked.
> 
> How are you making a "new" template?  Renaming?  Because that won't make a new 
> template.  Export/import XML?  I just tested and the editable values were copied 
> over successfully - in FlyMine and on our InterMine 0.98 beta site.
> 
> If you click on "edit query" on the template form to get to the QueryBuilder, 
> then you are editing the query not the template.  All template-related 
> information for that query is lost.  When the template constraints are re-added, 
> they default to be editable.  I would try exporting/importing the XML instead.
> 
> If none of that works for you, upgrade to 0.98 and try again.  It must have been 
> a bug that we've already fixed.  Let me know if that doesn't fix the problem!
> 
> On 30/09/11 22:16, Kalpana Karra wrote:
>> Hi,
>> 
>> Not sure if it was always like this or was changed intentionally in one of the past releases..
>> but..I am finding that if I take an existing template,edit it and start building a new template all
>> the constraints are by default unlocked.
>> 
>>  I have to go through each one and uncheck 'Editable' option. (in YM we do have quite a few  non-editable
> 
> constraints built into most templates)
>> 
>> Could this be changed such that everything remains the same as the template that one starts working off of??
>> 
>> Thanks,
>> -Kalpana
>> 
>> 
>> 
>> 
>> _______________________________________________
>> dev mailing list
>> dev at intermine.org
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>> 
> 
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Mon, 3 Oct 2011 16:15:04 +0800
> From: wang su <wangsu0623 at gmail.com>
> To: dev at intermine.org
> Subject: [InterMine Dev] errors in build a new mine
> Message-ID: <1AF98BD0-136F-47CA-B530-7C049C06DB06 at gmail.com>
> Content-Type: text/plain; charset=us-ascii
> 
> hi ,
> I am loading data into my database 
> # in MINE_NAME/integrate
> ant -v -Dsource=all
> then, there are some errors happened ,before building  this mine, I had  built the malariamine following the start steps. The error is like:
> 
> 
> 
> BUILD FAILED
> /mnt/Storage/home/wangs/intermine_0_97/imbuild/integrate.xml:54: The following error occurred while executing this line:
> /mnt/Storage/home/wangs/intermine_0_97/imbuild/source.xml:330: java.lang.RuntimeException: Exception while dataloading - to allow multiple errors, set the property "dataLoader.allowMultipleErrors" to true
> Problem while loading item identifier 1_1 because
> There is already an equivalent in the database from this source (<Source: name="uniprot-path", type="uniprot", skeleton=false>) from a *previous* run; object from source in this run: "DataSource [description="null", id="4", name="UniProt", url="null"]", object from database: "DataSource [description="null", id="1000001", name="UniProt", url="null"]"; noticed problem while merging field "name" originally read from source: <Source: name="uniprot-path", type="uniprot", skeleton=false>
> 	at org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:164)
> 	at org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:60)
> 	at org.intermine.dataloader.ObjectStoreDataLoaderTask.execute(ObjectStoreDataLoaderTask.java:128)
> 	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> 	at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
> 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> 	at java.lang.reflect.Method.invoke(Method.java:616)
> 	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:390)
> 	at org.apache.tools.ant.Target.performTasks(Target.java:411)
> 	at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
> 	at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
> 	at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
> 	at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:441)
> 	at org.intermine.task.Integrate.performAction(Integrate.java:223)
> 	at org.intermine.task.Integrate.performAction(Integrate.java:136)
> 	at org.intermine.task.Integrate.execute(Integrate.java:127)
> 	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> 	at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
> 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> 	at java.lang.reflect.Method.invoke(Method.java:616)
> 	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:390)
> 	at org.apache.tools.ant.Target.performTasks(Target.java:411)
> 	at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
> 	at org.apache.tools.ant.Project.executeTarget(Project.java:1329)
> 	at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
> 	at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
> 	at org.apache.tools.ant.Main.runBuild(Main.java:801)
> 	at org.apache.tools.ant.Main.startAnt(Main.java:218)
> 	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.lang.IllegalArgumentException: There is already an equivalent in the database from this source (<Source: name="uniprot-path", type="uniprot", skeleton=false>) from a *previous* run; object from source in this run: "DataSource [description="null", id="4", name="UniProt", url="null"]", object from database: "DataSource [description="null", id="1000001", name="UniProt", url="null"]"; noticed problem while merging field "name" originally read from source: <Source: name="uniprot-path", type="uniprot", skeleton=false>
> 	at org.intermine.dataloader.IntegrationWriterDataTrackingImpl.store(IntegrationWriterDataTrackingImpl.java:372)
> 	at org.intermine.dataloader.IntegrationWriterAbstractImpl.store(IntegrationWriterAbstractImpl.java:171)
> 	at org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:146)
> 	... 33 more
> 
> Total time: 1 minute 4 seconds
> 
> 
> 
> Thanks
> Su 
> Tongji University , Shanghai China
> 
> 
> 
> 
> ------------------------------
> 
> Message: 5
> Date: Mon, 03 Oct 2011 09:25:01 +0100
> From: Julie Sullivan <julie at flymine.org>
> To: dev at intermine.org
> Subject: Re: [InterMine Dev] errors in build a new mine
> Message-ID: <4E89715D.8090108 at flymine.org>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Hello Su!
> 
> "Caused by: java.lang.IllegalArgumentException: There is already an equivalent 
> in the database from this source "
> 
> This error message means that you've run the same source twice, UniProt.  Maybe 
> you didn't run the "build-db" task first?
> 
> Try this:
> 
>  1. ant -v build-db
>  2. ant -v -Dsource=all
> 
> Let me know if that doesn't work for you.
> 
> Cheers
> Julie
> 
> On 03/10/11 09:15, wang su wrote:
>> Caused by: java.lang.IllegalArgumentException: There is already an equivalent in the database from this
> 
> source (<Source: name="uniprot-path", type="uniprot", skeleton=false>) from 
> a*previous*  run; object
> 
> from source in this run: "DataSource [description="null", id="4", 
> name="UniProt", url="null"]", object
> 
> from database: "DataSource [description="null", id="1000001", name="UniProt", 
> url="null"]"; noticed problem
> 
> while merging field "name" originally read from source:<Source: 
> name="uniprot-path", type="uniprot", skeleton=false>
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> dev mailing list
> dev at intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
> 
> 
> End of dev Digest, Vol 29, Issue 2
> **********************************




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