[InterMine Dev] git update, which branch?

Sofia Robb sofia at sofiarobb.com
Wed Aug 19 16:54:23 BST 2015


Yes, i will increase the number of connections allowed to my db, but I will
wait for my tripal load to finish.

Thanks for the info about action vs source. There is so much to learn :)

Performing them separately resulted in all of the postprocesses in the
malariamine tutorial to be successful

<post-process name="create-references"/>
<post-process name="transfer-sequences" dump="true"/>
<post-process name="do-sources"/>
<post-process name="summarise-objectstore"/>
<post-process name="create-autocomplete-index"/>
<post-process name="create-search-index"/>

I will work on my webapp now.

Thank you for your continued support :)
Sofia

On Wed, Aug 19, 2015 at 9:31 AM, sergio contrino <sergio at modencode.org>
wrote:

> hi sofia,
> the bit
>
> Caused by: org.postgresql.util.PSQLException: FATAL: remaining connection
> slots are reserved for non-replication superuser connections
>
> means that you have exhausted the db connection (at the time of running
> the build).
>
> you can check how many connection are open (you can just do something like
> ps awx| grep post | grep -c . )
>
> you can increase the number of connection of a db, but maybe you need to
> wait for the other program to finish?
>
> but your command
>
> ant -v -Dsource=create-references
>
> should be
>
> ant -v -Daction=create-references
>
> thanks
> sergio
>
>
> On 19/08/15 16:18, Sofia Robb wrote:
>
>> I can connect from the command line with the user in my properties file.
>> Did I run my ant command incorrectly?
>>
>> ant -v -Dsource=create-references
>>
>> postprocess:
>> [postprocess] Found 6 post-processes
>> [postprocess]  executing post process: create-references
>> [postprocess] Performing postprocess: create-references
>> [Finalizer] INFO com.zaxxer.hikari.pool.HikariPool - HikariCP pool
>> db.production is being shutdown.
>> [postprocess]  executing post process: transfer-sequences
>> [postprocess] Performing postprocess: transfer-sequences
>> [postprocess]  executing post process: do-sources
>> [postprocess] no postprocess for source: uniprot-malaria, in dir:
>> /var/lib/pgsql/other_data/intermine/bio/sources/uniprot
>> [postprocess] no postprocess for source: malaria-gff, in dir:
>>
>> /var/lib/pgsql/other_data/intermine/bio/sources/example-sources/malaria-gff
>> [postprocess] no postprocess for source: malaria-chromosome-fasta, in
>> dir: /var/lib/pgsql/other_data/intermine/bio/sources/fasta
>> [postprocess] no postprocess for source: interpro, in dir:
>> /var/lib/pgsql/other_data/intermine/bio/sources/interpro
>> [postprocess] no postprocess for source: go, in dir:
>> /var/lib/pgsql/other_data/intermine/bio/sources/go
>> [postprocess] Performing postprocess on source: go-annotation, in dir:
>> /var/lib/pgsql/other_data/intermine/bio/sources/go-annotation
>>
>>
>> Also, this is in my error "Build Failed"
>> Caused by: org.postgresql.util.PSQLException: FATAL: remaining
>> connection slots are reserved for non-replication superuser connections
>> Doesn't sound good. Oh, I am loading data into chado for my tripal
>> install, maybe it has something to do with that? why does it say that no
>> postprocess for my sources can be found?
>>
>> Thanks,
>> Sofia
>>
>> On Wed, Aug 19, 2015 at 9:00 AM, sergio contrino <sergio at modencode.org
>> <mailto:sergio at modencode.org>> wrote:
>>
>>     hi sofia,
>>     it seems that the connection to the database is not happening.
>>     can you try to connect via command line? maybe you need a postgres
>>     restart?
>>     thanks
>>     sergio
>>
>>     On 19/08/15 15:53, Sofia Robb wrote:
>>
>>         Hi Sergio,
>>
>>         I ran the first post-process 'ant -v  -Dsource=create-references'
>>
>>         Here is what I get.
>>
>>         -Sofia
>>
>>         ----------------
>>
>>         -pre-generate-retrieve:
>>                [echo] Retrieving model from os.production...
>>         [postprocess] Failed to retrieve metadata from db.production
>>         (malariamine) - maybe you need to run build-db?
>>                [null] Exiting
>>         /var/lib/pgsql/other_data/intermine/malariamine/dbmodel/build.xml.
>>                [null] Exiting
>>
>> /var/lib/pgsql/other_data/intermine/bio/sources/go-annotation/build.xml.
>>
>>         BUILD FAILED
>>         /var/lib/pgsql/other_data/intermine/imbuild/postprocess.xml:31:
>> The
>>         following error occurred while executing this line:
>>         /var/lib/pgsql/other_data/intermine/imbuild/library.xml:78: The
>>         following error occurred while executing this line:
>>         /var/lib/pgsql/other_data/intermine/imbuild/objectstore.xml:98:
>>         java.sql.SQLException: Timeout of 30000ms encountered waiting for
>>         connection.
>>         at
>>
>> com.zaxxer.hikari.pool.HikariPool.getConnection(HikariPool.java:184)
>>         at
>>
>> com.zaxxer.hikari.HikariDataSource.getConnection(HikariDataSource.java:84)
>>         at org.intermine.sql.Database.getConnection(Database.java:163)
>>         at
>>
>> org.intermine.modelproduction.MetadataManager.retrieve(MetadataManager.java:233)
>>         at
>>
>> org.intermine.task.RetrieveMetadataTask.execute(RetrieveMetadataTask.java:97)
>>         at
>>
>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
>>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>>         at
>>
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>         at java.lang.reflect.Method.invoke(Method.java:606)
>>         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:435)
>>         at org.apache.tools.ant.Target.performTasks(Target.java:456)
>>         at
>>
>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
>>         at
>>
>> org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
>>         at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
>>         at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:440)
>>         at org.intermine.task.Dependencies.execute(Dependencies.java:304)
>>         at
>>
>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
>>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>>         at
>>
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>         at java.lang.reflect.Method.invoke(Method.java:606)
>>         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:435)
>>         at org.apache.tools.ant.Target.performTasks(Target.java:456)
>>         at
>>
>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
>>         at
>>
>> org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
>>         at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
>>         at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:440)
>>         at
>>
>> org.intermine.task.PostProcessTask.doSourcePostProcess(PostProcessTask.java:200)
>>         at
>>
>> org.intermine.task.PostProcessTask.doAllSourcePostProcessing(PostProcessTask.java:155)
>>         at
>>
>> org.intermine.task.PostProcessTask.execute(PostProcessTask.java:110)
>>         at
>>
>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
>>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>>         at
>>
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>         at java.lang.reflect.Method.invoke(Method.java:606)
>>         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:435)
>>         at org.apache.tools.ant.Target.performTasks(Target.java:456)
>>         at
>>
>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
>>         at org.apache.tools.ant.Project.executeTarget(Project.java:1364)
>>         at
>>
>> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
>>         at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
>>         at org.apache.tools.ant.Main.runBuild(Main.java:851)
>>         at org.apache.tools.ant.Main.startAnt(Main.java:235)
>>         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.postgresql.util.PSQLException: FATAL: remaining
>>         connection slots are reserved for non-replication superuser
>>         connections
>>         at
>>
>> org.postgresql.core.v3.ConnectionFactoryImpl.readStartupMessages(ConnectionFactoryImpl.java:574)
>>         at
>>
>> org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:177)
>>         at
>>
>> org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:64)
>>         at
>>
>> org.postgresql.jdbc2.AbstractJdbc2Connection.<init>(AbstractJdbc2Connection.java:138)
>>         at
>>
>> org.postgresql.jdbc3.AbstractJdbc3Connection.<init>(AbstractJdbc3Connection.java:29)
>>         at
>>
>> org.postgresql.jdbc3g.AbstractJdbc3gConnection.<init>(AbstractJdbc3gConnection.java:21)
>>         at
>>
>> org.postgresql.jdbc4.AbstractJdbc4Connection.<init>(AbstractJdbc4Connection.java:31)
>>         at
>>
>> org.postgresql.jdbc4.Jdbc4Connection.<init>(Jdbc4Connection.java:24)
>>         at org.postgresql.Driver.makeConnection(Driver.java:410)
>>         at org.postgresql.Driver.connect(Driver.java:280)
>>         at java.sql.DriverManager.getConnection(DriverManager.java:571)
>>         at java.sql.DriverManager.getConnection(DriverManager.java:215)
>>         at
>>
>> org.postgresql.ds.common.BaseDataSource.getConnection(BaseDataSource.java:99)
>>         at
>>
>> org.postgresql.ds.common.BaseDataSource.getConnection(BaseDataSource.java:82)
>>         at
>>
>> com.zaxxer.hikari.pool.HikariPool.addConnection(HikariPool.java:383)
>>         at
>> com.zaxxer.hikari.pool.HikariPool.access$300(HikariPool.java:54)
>>         at
>>
>> com.zaxxer.hikari.pool.HikariPool$1AddConnection.run(HikariPool.java:295)
>>         at
>>
>> java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
>>         at java.util.concurrent.FutureTask.run(FutureTask.java:262)
>>         at
>>
>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
>>         at
>>
>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
>>         at java.lang.Thread.run(Thread.java:745)
>>
>>         Total time: 1 minute 36 seconds
>>         [Thread-3] INFO com.zaxxer.hikari.pool.HikariPool - HikariCP pool
>>         db.production is being shutdown.
>>         [Thread-13] INFO com.zaxxer.hikari.pool.HikariPool - HikariCP pool
>>         db.production is being shutdown.
>>         [Thread-9] INFO com.zaxxer.hikari.pool.HikariPool - HikariCP pool
>>         db.production is being shutdown.
>>
>>         On Wed, Aug 19, 2015 at 7:41 AM, sergio contrino
>>         <sergio at modencode.org <mailto:sergio at modencode.org>
>>         <mailto:sergio at modencode.org <mailto:sergio at modencode.org>>>
>> wrote:
>>
>>              dear sofia,
>>              could you try to run the post processes one by one and let
>>         us know
>>              which one fails? and can you try to release your webapp even
>> if
>>              you've got a failed post process?
>>              thanks
>>              sergio
>>
>>
>>              On 18/08/15 20:32, Sofia Robb wrote:
>>
>>                  Hi Sergio,
>>
>>                  Ok, the clean checkout worked!  I have gotten through
>>         much of the
>>                  tutorial, but now have another error in post
>>         processing: It said no
>>                  source was set to try ant -Dsource=all. I tried this
>>         and got the
>>                  next error
>>
>>                  Thanks,
>>                  Sofia
>>
>>                  Postprocessing 1st error:
>>
>>                  BUILD FAILED
>>
>>         /var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: no
>>                  source
>>                  set, try "ant -Dsource=all" or "ant
>>         -Dsource=source1,source2"
>>                  at
>> org.intermine.task.Integrate.execute(Integrate.java:86)
>>                  at
>>
>>
>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
>>                  at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
>>         Source)
>>                  at
>>
>>
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>                  at java.lang.reflect.Method.invoke(Method.java:606)
>>                  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:435)
>>                  at
>>         org.apache.tools.ant.Target.performTasks(Target.java:456)
>>                  at
>>
>>
>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
>>                  at
>>         org.apache.tools.ant.Project.executeTarget(Project.java:1364)
>>                  at
>>
>>
>> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
>>                  at
>>         org.apache.tools.ant.Project.executeTargets(Project.java:1248)
>>                  at org.apache.tools.ant.Main.runBuild(Main.java:851)
>>                  at org.apache.tools.ant.Main.startAnt(Main.java:235)
>>                  at
>>         org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>>                  at
>>         org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>>
>>                  Total time: 14 seconds
>>                  [Thread-1] INFO com.zaxxer.hikari.pool.HikariPool -
>>         HikariCP pool
>>                  db.production is being shutdown.
>>
>>
>>                  Postprocessing 2nd error after ant -v -Dsource=all:
>>
>>                  BUILD FAILED
>>
>>         /var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
>>                  following error occurred while executing this line:
>>
>>  /var/lib/pgsql/other_data/intermine/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-malaria", 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-malaria",
>>         type="uniprot",
>>                  skeleton=false>
>>                  at
>>
>>
>> org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:165)
>>                  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:292)
>>                  at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
>>         Source)
>>                  at
>>
>>
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>                  at java.lang.reflect.Method.invoke(Method.java:606)
>>                  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:435)
>>                  at
>>         org.apache.tools.ant.Target.performTasks(Target.java:456)
>>                  at
>>
>>
>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
>>                  at
>>
>>
>> org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
>>                  at
>>         org.apache.tools.ant.Project.executeTargets(Project.java:1248)
>>                  at
>> org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:440)
>>                  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:292)
>>                  at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
>>         Source)
>>                  at
>>
>>
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>                  at java.lang.reflect.Method.invoke(Method.java:606)
>>                  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:435)
>>                  at
>>         org.apache.tools.ant.Target.performTasks(Target.java:456)
>>                  at
>>
>>
>> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
>>                  at
>>         org.apache.tools.ant.Project.executeTarget(Project.java:1364)
>>                  at
>>
>>
>> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
>>                  at
>>         org.apache.tools.ant.Project.executeTargets(Project.java:1248)
>>                  at org.apache.tools.ant.Main.runBuild(Main.java:851)
>>                  at org.apache.tools.ant.Main.startAnt(Main.java:235)
>>                  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-malaria", 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-malaria",
>>         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:147)
>>                  ... 33 more
>>
>>                  Total time: 1 minute 20 seconds
>>                  [Thread-7] INFO com.zaxxer.hikari.pool.HikariPool -
>>         HikariCP pool
>>                  db.common-tgt-items is being shutdown.
>>                  [Thread-18] INFO com.zaxxer.hikari.pool.HikariPool -
>>         HikariCP pool
>>                  db.common-tgt-items is being shutdown.
>>                  [Thread-18] INFO com.zaxxer.hikari.pool.HikariPool -
>>         HikariCP pool
>>                  db.production is being shutdown.
>>
>>
>>                  On Tue, Aug 18, 2015 at 10:33 AM, sergio contrino
>>                  <sergio at modencode.org <mailto:sergio at modencode.org>
>>         <mailto:sergio at modencode.org <mailto:sergio at modencode.org>>
>>                  <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org> <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>>>> wrote:
>>
>>                       hi sofia,
>>                       could you try a fresh checkout?
>>                       where are you running your build from? i would
>>         suggest some
>>                       directory like ~/git/intermine/..
>>                       thanks
>>                       sergio
>>
>>
>>
>>                       On 18/08/15 16:55, Sofia Robb wrote:
>>
>>                           Hi Sergio,
>>
>>                           I tried the clean and the rm the build dir. I
>>         get this
>>                  error:
>>
>>                           Sofia
>>
>>                           BUILD FAILED
>>
>>
>>
>> /var/lib/pgsql/other_data/intermine/malariamine/dbmodel/build.xml:6:
>>                           taskdef class
>> org.intermine.bio.task.SOToModelTask
>>                  cannot be found
>>                              using the classloader
>>
>>
>>
>> AntClassLoader[/var/lib/pgsql/other_data/intermine/malariamine/dbmodel/build/model:/var/lib/pgsql/other_data/intermine/malariamine/dbmodel/build/main:/var/lib/pgsql/other_data/intermine/intermine/model/main/lib/antlr-2.7.6-caching.jar:/var/lib/pgsql/other_data/intermine/intermine/model/main/lib/asm-4.2.jar:/var/lib/pgsql/other_data/intermine/intermine/model/main/lib/asm-util-4.2.jar:/var/lib/pgsql/other_data/intermine/intermine/model/main/lib/cglib-3.1.jar:/var/lib/pgsql/other_data/intermine/intermine/model/main/lib/commons-collections-3.2.jar:/var/lib/pgsql/other_data/intermine/intermine/model/main/lib/commons-io-1.2.jar:/var/lib/pgsql/other_data/intermine/intermine/model/main/lib/commons-lang-2.6.jar:/var/lib/pgsql/other_data/intermine/intermine/model/main/lib/json20110106.jar:/var/lib/pgsql/other_data/intermine/intermine/model/main/lib/log4j.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/HikariCP-1.3.8.jar:/var/lib/pgsql/other_data/intermine/interm
>>
>
>
>>
>>
>>              ine/obje
>>
>>
>>
>>
>>
>> ctstore/main/lib/ant-1.6.5.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/base64.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/commons-beanutils-1.6.1.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/commons-digester-2.1.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/commons-logging-1.0.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/javassist-3.18.2.GA.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/jaxrpc.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/libreadline-java.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/ojdbc14.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/opencsv-2.3.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/postgresql-9.3-1101.jdbc4.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/saaj.jar:/var/lib/p
>>
>
>
>>     gsql
>>
>>
>>              /other
>>
>>
>>
>>
>> _data/intermine/intermine/objectstore/main/lib/slf4j-api-1.7.7.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/slf4j-simple-1.7.7.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/torque-3.2-dev.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/torque-gen-3.2-dev.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/velocity-1.3.jar:/var/lib/pgsql/other_data/intermine/intermine/objectstore/main/lib/xercesImpl-2.9.1.jar:/var/lib/pgsql/other_data/intermine/intermine/integrate/main/lib/mysql-connector-java-5.1.26-bin.jar:/var/lib/pgsql/other_data/intermine/intermine/integrate/main/lib/stax-api-1.0.jar:/var/lib/pgsql/other_data/intermine/intermine/integrate/main/lib/stax-ri-1.0.jar:/var/lib/pgsql/other_data/intermine/intermine/pathquery/main/lib/stax-api-1.0.jar:/var/lib/pgsql/other_data/intermine/intermine/pathquery/main/lib/stax-ri-1.0.jar:/var/lib/pgsql/other_data/intermine/intermine/api/main/li
>>
>
>
>>     b/bo
>>
>>
>>              bo-bro
>>
>>
>>
>>
>> wse-2.5.1.jar:/var/lib/pgsql/other_data/intermine/intermine/api/main/lib/fastutil.jar:/var/lib/pgsql/other_data/intermine/intermine/api/main/lib/kamikaze-2.0.0.jar:/var/lib/pgsql/other_data/intermine/intermine/api/main/lib/lucene-core-3.0.2.jar:/var/lib/pgsql/other_data/intermine/intermine/api/main/lib/lucene-highlighter-3.0.2.jar:/var/lib/pgsql/other_data/intermine/intermine/api/main/lib/lucene-queries-3.0.2.jar:/var/lib/pgsql/other_data/intermine/intermine/api/main/lib/lucene-snowball-3.0.2.jar:/var/lib/pgsql/other_data/intermine/intermine/api/main/lib/xalan.jar:/var/lib/pgsql/other_data/intermine/bio/core/main/lib/bbop.jar:/var/lib/pgsql/other_data/intermine/bio/core/main/lib/biojava-1.7.1.jar:/var/lib/pgsql/other_data/intermine/bio/core/main/lib/jakarta-regexp-1.4.jar:/var/lib/pgsql/other_data/intermine/bio/core/main/lib/jena.jar:/var/lib/pgsql/other_data/intermine/bio/core/main/lib/obo.jar:/var/lib/pgsql/other_data/intermine/malariamine/dbmodel/build/classes]
>>
>>
>>                           On Tue, Aug 18, 2015 at 9:53 AM, Sofia Robb
>>                  <sofia2341 at gmail.com <mailto:sofia2341 at gmail.com>
>>         <mailto:sofia2341 at gmail.com <mailto:sofia2341 at gmail.com>>
>>                           <mailto:sofia2341 at gmail.com
>>         <mailto:sofia2341 at gmail.com> <mailto:sofia2341 at gmail.com
>>         <mailto:sofia2341 at gmail.com>>>
>>                           <mailto:sofia2341 at gmail.com
>>         <mailto:sofia2341 at gmail.com>
>>                  <mailto:sofia2341 at gmail.com
>>         <mailto:sofia2341 at gmail.com>> <mailto:sofia2341 at gmail.com
>>         <mailto:sofia2341 at gmail.com>
>>                  <mailto:sofia2341 at gmail.com
>>         <mailto:sofia2341 at gmail.com>>>>> wrote:
>>
>>                                I tried the clean and rm the build dir. I
>>         get this
>>                  error:
>>
>>
>>                                On Tue, Aug 18, 2015 at 2:47 AM, sergio
>>         contrino
>>                                <sergio at modencode.org
>>         <mailto:sergio at modencode.org>
>>                  <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>> <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>
>>                  <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>>>
>>                           <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>
>>                  <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>> <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>
>>                  <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>>>>> wrote:
>>
>>                                    dear sofia,
>>                                    could you try a
>>                                    ant clean-all build-db
>>                                    or, failing this, to remove manually
>>         the dist
>>                  and build
>>                           directories
>>                                    (something like rm -rf build in
>>                  malariamine/dbmodel)
>>                                    please let us know if this does not
>> help
>>                                    thanks
>>                                    sergio
>>
>>
>>                                    On 17/08/15 20:01, Sofia Robb wrote:
>>
>>                                        Hello Sergio,
>>
>>                                        I updated with  'git pull
>>         upstream master'
>>                  and it
>>                           seemed to
>>                                        be successful.
>>
>>                                        I am running through the
>> malariamine
>>                  tutorial to
>>                           make sure
>>                                        all is in
>>                                        working order, when i try this I
>>         get an error:
>>
>>                                        *]ant clean build-db
>>                                        ...
>>                                             [depend] The class
>>
>>         org.intermine.metadata.MetaDataException
>>                  in file
>>
>>
>>
>>
>> /var/lib/pgsql/other_data/intermine/intermine/objectstore/main/build/classes/org/intermine/metadata/MetaDataException.class
>>                                        is out of date due to
>>
>>         org.intermine.metadata.MetaDataException
>>                  but has
>>                                        not been deleted because its
>>         source file
>>                  could not
>>                           be determined
>>                                             [depend] The class
>>
>>
>>
>>
>> org.intermine.modelproduction.xml.InterMineModelParser$SkeletonClass
>>                                        in
>>                                        file
>>
>>
>>
>>
>> /var/lib/pgsql/other_data/intermine/intermine/objectstore/main/build/classes/org/intermine/modelproduction/xml/InterMineModelParser$SkeletonClass.class
>>                                        is out of date due to
>>
>>
>>           org.intermine.modelproduction.xml.InterMineModelParser but
>>                                        has not been
>>                                        deleted because its source file
>>         could not
>>                  be determined
>>                                             [depend] The class
>>                           org.intermine.model.ShadowClass in file
>>
>>
>>
>>
>> /var/lib/pgsql/other_data/intermine/intermine/objectstore/main/build/classes/org/intermine/model/ShadowClass.class
>>                                        is out of date due to
>>                           org.intermine.model.ShadowClass but
>>                                        has not been
>>                                        deleted because its source file
>>         could not
>>                  be determined
>>                                             [depend] Deleted 1 out of
>>         date files
>>                  in 0 seconds
>>                                              [javac] Compiling 204
>>         source files to
>>
>>
>>
>>
>> /var/lib/pgsql/other_data/intermine/intermine/objectstore/main/build/classes
>>                                        [dependencies] warning: [options]
>>                  bootstrap class
>>                           path not
>>                                        set in
>>                                        conjunction with -source 1.6
>>                                        [dependencies]
>>
>>
>>
>>
>> /var/lib/pgsql/other_data/intermine/intermine/objectstore/main/src/org/intermine/codegen/JavaModelOutput.java:512:
>>                                        error: cannot find symbol
>>                                        [dependencies]
>>               if
>>                           (attr.isPrimitive() ||
>>                                        attr.isNumeric()) {
>>                                        [dependencies]
>>                                                  ^
>>                                        [dependencies]   symbol:   method
>>         isNumeric()
>>                                        [dependencies]   location:
>>         variable attr
>>                  of type
>>                                        AttributeDescriptor
>>                                        [dependencies] Note:
>>
>>
>>
>>
>> /var/lib/pgsql/other_data/intermine/intermine/objectstore/main/src/org/intermine/objectstore/query/QueryField.java
>>                                        uses or overrides a deprecated API.
>>                                        [dependencies] Note: Recompile with
>>                           -Xlint:deprecation for
>>                                        details.
>>                                        [dependencies] Note: Some input
>>         files use
>>                  unchecked or
>>                                        unsafe operations.
>>                                        [dependencies] Note: Recompile with
>>                           -Xlint:unchecked for
>>                                        details.
>>                                        [dependencies] 1 error
>>                                        [dependencies] 1 warning
>>
>>                                        BUILD FAILED
>>
>>
>>
>>         /var/lib/pgsql/other_data/intermine/imbuild/library.xml:78: The
>>                                        following error occurred while
>>         executing
>>                  this line:
>>
>>
>>
>>         /var/lib/pgsql/other_data/intermine/imbuild/library.xml:109: The
>>                                        following error occurred while
>>         executing
>>                  this line:
>>
>>
>>
>>         /var/lib/pgsql/other_data/intermine/imbuild/library.xml:257:
>>                                        Compile
>>                                        failed; see the compiler error
>>         output for
>>                  details.
>>
>>                                        Total time: 14 seconds
>>
>>
>>                                        Thanks,
>>                                        Sofia
>>
>>
>>                                        On Mon, Aug 17, 2015 at 9:43 AM,
>>         sergio
>>                  contrino
>>                                        <sergio at modencode.org
>>         <mailto:sergio at modencode.org>
>>                  <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>> <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>
>>                  <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>>>
>>                           <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>
>>                  <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>> <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>
>>                  <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>>>>
>>                                        <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>
>>                  <mailto:sergio at modencode.org <mailto:
>> sergio at modencode.org>>
>>                           <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>
>>                  <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>>> <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>
>>                  <mailto:sergio at modencode.org <mailto:
>> sergio at modencode.org>>
>>                           <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>
>>                  <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>>>>>>
>>
>>                                        wrote:
>>
>>                                             dear sofia,
>>                                             we are working on beta,
>>         while you can
>>                  update
>>                           to the
>>                                        latest release
>>                                             (1.5.6) using the master
>> branch.
>>                                             thanks!
>>                                             sergio
>>
>>
>>
>>                                             On 17/08/15 16:38, Sofia
>>         Robb wrote:
>>
>>                                                 Hello,
>>
>>                                                 I would like to update my
>>                  intermine. Which
>>                           branch
>>                                        is the best
>>                                                 for me to use?
>>
>>                                                 Thanks,
>>                                                 Sofia
>>
>>                                                    *]git pull upstream
>>
>>                                                 remote: Counting
>>         objects: 5382, done.
>>                                                 remote: Compressing
>>         objects: 100%
>>                  (4/4), done.
>>                                                 remote: Total 5382
>>         (delta 1958),
>>                  reused
>>                           1962 (delta
>>                                        1958),
>>                                                 pack-reused 3420
>>                                                 Receiving objects: 100%
>>                  (5382/5382), 6.57
>>                           MiB |
>>                                        4.48 MiB/s, done.
>>                                                 Resolving deltas: 100%
>>         (3021/3021),
>>                           completed with
>>                                        620 local
>>                                                 objects.
>>                                                   From
>>         github.com:intermine/intermine
>>                                                    * [new branch]
>>         1.5.1-rc   ->
>>                           upstream/1.5.1-rc
>>                                                      898cce9..1137c13
>>         beta       ->
>>                           upstream/beta
>>                                                    * [new branch]
>>                  biogrid-detail-dupes ->
>>
>>           upstream/biogrid-detail-dupes
>>                                                    + 37b68d5...11e56dc
>>         dev        ->
>>                           upstream/dev
>>                                        (forced update)
>>                                                    * [new branch]
>>                  dynamic-objects ->
>>                                        upstream/dynamic-objects
>>                                                    * [new branch]
>>         gradle     ->
>>                           upstream/gradle
>>                                                      787829e..0a759cf
>>                  human-identifiers ->
>>                                                 upstream/human-identifiers
>>                                                      d10b7bd..0e77615
>>         i169       ->
>>                           upstream/i169
>>                                                      60eb6eb..9324602
>>         i797       ->
>>                           upstream/i797
>>                                                    * [new branch]
>>                  keyword-fail-loudly ->
>>
>> upstream/keyword-fail-loudly
>>                                                      c01ea52..7fff99c
>>         like       ->
>>                           upstream/like
>>                                                      b8133ad..9848015
>>         master     ->
>>                           upstream/master
>>                                                    * [new branch]
>>                  new-class-key ->
>>                                        upstream/new-class-key
>>                                                    * [new branch]
>>                  new_jsp_jars ->
>>                                        upstream/new_jsp_jars
>>                                                    * [new branch]
>>                  panther-config-fix ->
>>
>> upstream/panther-config-fix
>>                                                      3e88474..6a29469
>>                  protein-interactions ->
>>
>>           upstream/protein-interactions
>>                                                    * [new branch]
>>                  rm-onto-pubs ->
>>                                        upstream/rm-onto-pubs
>>                                                    * [new tag]
>>                    intermine-1.5.1 ->
>>                                        intermine-1.5.1
>>                                                    * [new tag]
>>                    intermine-1.5.5 ->
>>                                        intermine-1.5.5
>>                                                    * [new tag]
>>                    intermine-1.5.6 ->
>>                                        intermine-1.5.6
>>                                                   From
>>         github.com:intermine/intermine
>>                                                    * [new tag]
>>                    intermine-1.4.2 ->
>>                                        intermine-1.4.2
>>                                                    * [new tag]
>>                    intermine-1.5 ->
>>                           intermine-1.5
>>                                                    * [new tag]
>>                    intermine-1.5.3 ->
>>                                        intermine-1.5.3
>>                                                    * [new tag]
>>                    intermine-1.5.4 ->
>>                                        intermine-1.5.4
>>                                                 You asked to pull from
>>         the remote
>>                           'upstream', but
>>                                        did not specify
>>                                                 a branch. Because this
>>         is not the
>>                  default
>>                                        configured remote
>>                                                 for your current branch,
>>         you must
>>                  specify
>>                           a branch
>>                                        on the
>>                                                 command line.
>>
>>
>>
>>
>> _______________________________________________
>>                                                 dev mailing list
>>         dev at intermine.org <mailto:dev at intermine.org>
>>         <mailto:dev at intermine.org <mailto:dev at intermine.org>>
>>                  <mailto:dev at intermine.org <mailto:dev at intermine.org>
>>         <mailto:dev at intermine.org <mailto:dev at intermine.org>>>
>>                                        <mailto:dev at intermine.org
>>         <mailto:dev at intermine.org>
>>                  <mailto:dev at intermine.org <mailto:dev at intermine.org>>
>>                           <mailto:dev at intermine.org
>>         <mailto:dev at intermine.org> <mailto:dev at intermine.org
>>         <mailto:dev at intermine.org>>>>
>>                  <mailto:dev at intermine.org <mailto:dev at intermine.org>
>>         <mailto:dev at intermine.org <mailto:dev at intermine.org>>
>>                           <mailto:dev at intermine.org
>>         <mailto:dev at intermine.org> <mailto:dev at intermine.org
>>         <mailto:dev at intermine.org>>>
>>                                        <mailto:dev at intermine.org
>>         <mailto:dev at intermine.org>
>>                  <mailto:dev at intermine.org <mailto:dev at intermine.org>>
>>         <mailto:dev at intermine.org <mailto:dev at intermine.org>
>>                  <mailto:dev at intermine.org <mailto:dev at intermine.org>>>>>
>>         http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>>
>>                                             --
>>                                             sergio contrino
>>                  InterMine,
>>                           University
>>                                        of Cambridge
>>         https://sergiocontrino.github.io
>>                                        <https://sergiocontrino.github.io/
>> >
>>         http://www.intermine.org
>>                                        <http://www.intermine.org/>
>>
>>
>>
>>                                    --
>>                                    sergio contrino
>>         InterMine,
>>                  University
>>                           of Cambridge
>>         https://sergiocontrino.github.io
>>                                    <https://sergiocontrino.github.io/>
>>         http://www.intermine.org
>>                                    <http://www.intermine.org/>
>>
>>
>>
>>                           On Tue, Aug 18, 2015 at 2:47 AM, sergio contrino
>>                           <sergio at modencode.org
>>         <mailto:sergio at modencode.org> <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>>
>>                  <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org> <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>>>
>>                           <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>
>>                  <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>> <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>
>>                  <mailto:sergio at modencode.org
>>         <mailto:sergio at modencode.org>>>>> wrote:
>>
>>                                dear sofia,
>>                                could you try a
>>                                ant clean-all build-db
>>                                or, failing this, to remove manually the
>>         dist and
>>                  build
>>                           directories
>>                                (something like rm -rf build in
>>         malariamine/dbmodel)
>>                                please let us know if this does not help
>>                                thanks
>>                                sergio
>>
>>
>>                                On 17/08/15 20:01, Sofia Robb wrote:
>>
>>                                    Hello Sergio,
>>
>>                                    I updated with  'git pull upstream
>>         master' and it
>>                           seemed to be
>>                                    successful.
>>
>>                                    I am running through the malariamine
>>         tutorial
>>                  to make
>>                           sure all is in
>>                                    working order, when i try this I get
>>         an error:
>>
>>                                    *]ant clean build-db
>>                                    ...
>>                                         [depend] The class
>>                           org.intermine.metadata.MetaDataException
>>                                    in file
>>
>>
>>
>>
>> /var/lib/pgsql/other_data/intermine/intermine/objectstore/main/build/classes/org/intermine/metadata/MetaDataException.class
>>                                    is out of date due to
>>                           org.intermine.metadata.MetaDataException
>>                                    but has
>>                                    not been deleted because its source
>>         file could
>>                  not be
>>                           determined
>>                                         [depend] The class
>>
>>
>>
>>
>> org.intermine.modelproduction.xml.InterMineModelParser$SkeletonClass
>>                                    in
>>                                    file
>>
>>
>>
>>
>> /var/lib/pgsql/other_data/intermine/intermine/objectstore/main/build/classes/org/intermine/modelproduction/xml/InterMineModelParser$SkeletonClass.class
>>                                    is out of date due to
>>
>>                    org.intermine.modelproduction.xml.InterMineModelParser
>>                           but has
>>                                    not been
>>                                    deleted because its source file could
>>         not be
>>                  determined
>>                                         [depend] The class
>>                  org.intermine.model.ShadowClass
>>                           in file
>>
>>
>>
>>
>> /var/lib/pgsql/other_data/intermine/intermine/objectstore/main/build/classes/org/intermine/model/ShadowClass.class
>>                                    is out of date due to
>>                  org.intermine.model.ShadowClass
>>                           but has
>>                                    not been
>>                                    deleted because its source file could
>>         not be
>>                  determined
>>                                         [depend] Deleted 1 out of date
>>         files in 0
>>                  seconds
>>                                          [javac] Compiling 204 source
>>         files to
>>
>>
>>
>>
>> /var/lib/pgsql/other_data/intermine/intermine/objectstore/main/build/classes
>>                                    [dependencies] warning: [options]
>>         bootstrap
>>                  class path
>>                           not set in
>>                                    conjunction with -source 1.6
>>                                    [dependencies]
>>
>>
>>
>>
>> /var/lib/pgsql/other_data/intermine/intermine/objectstore/main/src/org/intermine/codegen/JavaModelOutput.java:512:
>>                                    error: cannot find symbol
>>                                    [dependencies]
>>  if
>>                           (attr.isPrimitive() ||
>>                                    attr.isNumeric()) {
>>                                    [dependencies]
>>                                          ^
>
>
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