[InterMine Dev] git update, which branch?

sergio contrino sergio at modencode.org
Mon Aug 24 10:35:52 BST 2015


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



More information about the dev mailing list