[InterMine Dev] git update, which branch?

Sofia Robb sofia at sofiarobb.com
Mon Aug 24 17:55:43 BST 2015


Ok, It was something silly. I was on the wrong branch. I was using beta not
the master. So i changed it and everything works just fine. I did
everything up to '../bio/scripts/project_build -b -v localhost
~/malariamine-dump'

Thanks,
Sofia

On Mon, Aug 24, 2015 at 9:28 AM, sergio contrino <sergio at modencode.org>
wrote:

> ok sofia, let us know how it ends.
> regarding your createdb statement, i think it is fine (we tend to use
> directly the user (-U) rather than the owner (-O)) and you should now be
> able to omit the -E SQL_ASCII clause (after updating template1 db).
> thanks
> sergio
>
>
> On 24/08/15 16:04, Sofia Robb wrote:
>
>> Hi Sergio,
>>
>> Thats weird. I did all of this, but I will do it again.  I also did the
>> steps on this page
>>
>> http://intermine.readthedocs.org/en/latest/system-requirements/software/postgres/postgres/#character-set-encoding
>> .
>>
>>
>> I have a question.The tutorial says when you are creating a db just use
>> createdb. This does not allow me to add a user, I changed to my postgres
>> user, then used this command to create malariamine 'createdb -O
>> intermine -E SQL_ASCII -W  malariamine'
>>
>>
>> I will do as you suggest and get the master again and drop my dbs and
>> try again.
>>
>> Thanks,
>> Sofia
>>
>>
>>
>>
>>
>> On Mon, Aug 24, 2015 at 3:35 AM, sergio contrino <sergio at modencode.org
>> <mailto:sergio at modencode.org>> wrote:
>>
>>     hi sofia,
>>     i run the complete build without problems from a master checkout.
>>     did you drop and recreated the 2 dbs (malariamine and
>>     items-malariamine)?
>>     if you did, i would suggest that again you start anew from a new
>>     checkout, this time just using the final 'build a complete
>>     malariamine' step.
>>     please note that you will need to correct the
>>     dbmodel/resources/genomic_priorities.properties
>>     as outlined in the tutorial.
>>     if this does not work, please send us your properties file
>>     (malariamine.properties in your ~/.intermine directory)
>>     thanks
>>     sergio
>>
>>
>>     On 21/08/15 14:54, Sofia Robb wrote:
>>
>>         Hi Sergio,
>>
>>         Yes, that is the step I am on.
>>
>>         Sofia
>>
>>         On Fri, Aug 21, 2015 at 4:33 AM, sergio contrino
>>         <sergio at modencode.org <mailto:sergio at modencode.org>
>>         <mailto:sergio at modencode.org <mailto:sergio at modencode.org>>>
>> wrote:
>>
>>              hi sofia,
>>              are you running the 'Build complete MalariaMine' step from
>>         the tutorial?
>>              thanks
>>              sergio
>>
>>
>>              On 20/08/15 17:48, Sofia Robb wrote:
>>
>>                  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
>>
>>
>>              --
>>              sergio contrino                  InterMine, University of
>>         Cambridge
>>         https://sergiocontrino.github.io http://www.intermine.org
>>
>>
>>
>>     --
>>     sergio contrino                  InterMine, University of Cambridge
>>     https://sergiocontrino.github.io http://www.intermine.org
>>
>>
>>
> --
> sergio contrino                  InterMine, University of Cambridge
> https://sergiocontrino.github.io           http://www.intermine.org
>
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