[InterMine Dev] git update, which branch?

Sofia Robb sofia2341 at gmail.com
Mon Aug 24 16:04:23 BST 2015


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>
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>> 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
>
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