[InterMine Dev] git update, which branch?

Sofia Robb sofia2341 at gmail.com
Thu Aug 20 17:47:04 BST 2015


Sergio and Vivek,

I followed the documentation and changed the encoding. The create db errors
while running project_build are gone but I still have my objectStore
errors. Any ideas?

Thanks,
Sofia

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.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:606)
at
org.intermine.objectstore.ObjectStoreFactory.getObjectStore(ObjectStoreFactory.java:61)
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: ObjectStore
'os.common-translated-std' not found in properties
at
org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl.getInstance(ObjectStoreFastCollectionsForTranslatorImpl.java:97)
... 37 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:606)
at
org.intermine.objectstore.ObjectStoreFactory.getObjectStore(ObjectStoreFactory.java:61)
at
org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl.getInstance(ObjectStoreFastCollectionsForTranslatorImpl.java:90)
... 37 more
Caused by: java.lang.IllegalArgumentException: Unable to get
sub-ObjectStore for Translating ObjectStore (check properties file)
at
org.intermine.objectstore.translating.ObjectStoreTranslatingImpl.getInstance(ObjectStoreTranslatingImpl.java:87)
... 43 more

Total time: 1 minute 28 seconds
Thu Aug 20 11:43:42 CDT 2015

On Wed, Aug 19, 2015 at 12:12 PM, Krishnakumar, Vivek <vKrishna at jcvi.org>
wrote:

> Hi Sofia,
>
> When running createdb, by default, it uses the postgres
> `template1`database as a reference to instantiate an empty DB.
>
> While setting up postgres, did you happen to follow the documentation here
> (
> http://intermine.readthedocs.org/en/latest/system-requirements/software/postgres/postgres/#character-set-encoding),
> which shows how to alter the `template1` database with the required
> SQL_ASCII encoding, and Locale settings?
>
> Thank you.
> Vivek
>
> On Aug 19, 2015, at 1:52 PM, Sofia Robb <sofia at sofiarobb.com> wrote:
>
> Thanks for the help Vivek. While rerunning like you suggested (I am still
> getting the objectStore error, also as you saw) I noticed some other errors
> that I did not see before.
>
> There seems to be an issue with the encoding.
>
>
> making db copy: createdb -E SQL_ASCII -U intermine -h localhost -T
> malariamine malariamine:malaria-chromosome-fasta
>
> createdb: database creation failed: ERROR:  encoding "SQL_ASCII" does not
> match locale "en_US.UTF-8"
> DETAIL:  The chosen LC_CTYPE setting requires encoding "UTF8".
> Wed Aug 19 12:33:00 CDT 2015
>
> making db copy: createdb -E SQL_ASCII -U intermine -h localhost -T
> malariamine malariamine:go-annotation
>
> createdb: database creation failed: ERROR:  encoding "SQL_ASCII" does not
> match locale "en_US.UTF-8"
> DETAIL:  The chosen LC_CTYPE setting requires encoding "UTF8".
> Wed Aug 19 12:40:18 CDT 2015
>
>
> On Wed, Aug 19, 2015 at 11:31 AM, Krishnakumar, Vivek <vKrishna at jcvi.org>
> wrote:
>
>> Hi Sofia,
>>
>> Actually, I take back what I said. After looking at your error stack
>> trace a but closer, the failure of your MalariaMine build is not due to the
>> Entrez eutils web services, but rather due to some issues with the
>> InterMine ObjectStore.
>>
>> Sorry for the confusion.
>>
>> Thank you.
>> Vivek
>>
>> On Aug 19, 2015, at 1:25 PM, Vivek Krishnakumar <vkrishna at jcvi.org>
>> wrote:
>>
>> Hi Sofia,
>>
>> Just wanted to chime in on this thread since our most recent development
>> build of ThaleMine (InterMine for Arabidopsis,
>> https://apps.araport.org/thalemine/) failed at the same step as yours,
>> i.e. entrez-organism.
>>
>> This failure has nothing to do with InterMine itself, but because the
>> remote Entrez eutils services might have been unavailable while your build
>> was running.
>>
>> The web service call is structured something like this:
>> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=taxonomy&retmode=xml&id=10090,10116,7227,9606,4932,6239,3702,7955,
>> where the ids in this list correspond to the organisms you are loading into
>> your mine.
>>
>> However, as of writing this email, I can see that the eutils web services
>> are back up online.
>>
>> As such, I would urge you to please try rebuilding MalariaMine again.
>>
>> Thank you.
>>
>> Regards,
>> Vivek
>>
>> On Aug 19, 2015, at 12:47 PM, Sofia Robb <sofia at sofiarobb.com> wrote:
>>
>> I ran this command '../bio/scripts/project_build -b -v localhost
>> ~/malariamine-dump' and I get the following error:
>>
>>
>>
>> action update-publications took 284 seconds
>>
>> Wed Aug 19 11:13:45 CDT 2015
>>
>> starting command: ant -v -Dsource=entrez-organism
>>
>>
>> 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.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:606)
>> at
>> org.intermine.objectstore.ObjectStoreFactory.getObjectStore(ObjectStoreFactory.java:61)
>> 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: ObjectStore
>> 'os.common-translated-std' not found in properties
>> at
>> org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl.getInstance(ObjectStoreFastCollectionsForTranslatorImpl.java:97)
>> ... 37 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:606)
>> at
>> org.intermine.objectstore.ObjectStoreFactory.getObjectStore(ObjectStoreFactory.java:61)
>> at
>> org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl.getInstance(ObjectStoreFastCollectionsForTranslatorImpl.java:90)
>> ... 37 more
>> Caused by: java.lang.IllegalArgumentException: Unable to get
>> sub-ObjectStore for Translating ObjectStore (check properties file)
>> at
>> org.intermine.objectstore.translating.ObjectStoreTranslatingImpl.getInstance(ObjectStoreTranslatingImpl.java:87)
>> ... 43 more
>>
>> Total time: 1 minute 19 seconds
>> Wed Aug 19 11:15:05 CDT 2015
>>
>> finished
>>
>>
>> ERROR: 256
>> failed with exit code 0: ant -v -Dsource=entrez-organism
>>
>> check log: pbuild.log
>>
>> On Wed, Aug 19, 2015 at 9:54 AM, Sofia Robb <sofia at sofiarobb.com> wrote:
>>
>>> 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]
>>>>>                                          ^
>>>>
>>>>
>>>
>> _______________________________________________
>> dev mailing list
>> dev at intermine.org
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>>
>>
>>
>
>
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