buildDB problem: Could not load required global properties resource intermine.properties

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buildDB problem: Could not load required global properties resource intermine.properties

Pengcheng Yang
Dear InterMiners,

During building the customized data model, I encountered one problem
listed below. The data model bio-sources was committed at
https://github.com/pengchy/bio-sources.

I have tested removing the data model "locust-anatomy-expression" and
rebuilding, but with the same error for the second data model.

The error message said that "Could not load required global properties
resource intermine.properties". I couldn't find the file
"intermine.properties" under the bio-sources directory.

Thank you and best,

Pengcheng Yang

============ the error messages ==========================

-bash-4.2$ ./gradlew install

BUILD SUCCESSFUL in 22s
112 actionable tasks: 72 executed, 40 up-to-date
-bash-4.2$ ./gradlew builddb --stacktrace

 > Task :bio-source-locust-anatomy-expression:buildDB
Creating schema in objectstore os.bio-test for
/home/pengchy/soft/intermine.4.0/git/bio-sources/locust-anatomy-expression/build/os.bio-test-schema.xml
    [torque] log4j:WARN No appenders could be found for logger
(org.intermine.util.PropertiesUtil).
    [torque] log4j:WARN Please initialize the log4j system properly.
    [torque] log4j:WARN See
http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Creating tables in objectstore os.bio-test with schema
os.bio-test-schema.xml
   [buildDB] log4j:WARN No appenders could be found for logger
(org.intermine.util.PropertiesUtil).
   [buildDB] log4j:WARN Please initialize the log4j system properly.
   [buildDB] log4j:WARN See
http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
   [buildDB] java.lang.RuntimeException: Could not load required global
properties resource intermine.properties
   [buildDB]     at
org.intermine.util.PropertiesUtil.loadGlobalProperties(PropertiesUtil.java:153)
   [buildDB]     at
org.intermine.util.PropertiesUtil.initGlobalProperties(PropertiesUtil.java:58)
   [buildDB]     at
org.intermine.util.PropertiesUtil.getProperties(PropertiesUtil.java:45)
   [buildDB]     at
org.intermine.task.BuildDbTask.setOsName(BuildDbTask.java:63)
   [buildDB]     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
Method)
   [buildDB]     at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
   [buildDB]     at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
   [buildDB]     at java.lang.reflect.Method.invoke(Method.java:498)
   [buildDB]     at
org.apache.tools.ant.IntrospectionHelper$AttributeSetter.setObject(IntrospectionHelper.java:1506)
   [buildDB]     at
org.apache.tools.ant.IntrospectionHelper.setAttribute(IntrospectionHelper.java:411)
   [buildDB]     at
org.apache.tools.ant.RuntimeConfigurable.maybeConfigure(RuntimeConfigurable.java:527)
   [buildDB]     at
org.apache.tools.ant.RuntimeConfigurable.maybeConfigure(RuntimeConfigurable.java:463)
   [buildDB]     at org.apache.tools.ant.Task.maybeConfigure(Task.java:202)
   [buildDB]     at
org.apache.tools.ant.UnknownElement.configure(UnknownElement.java:200)
   [buildDB]     at
org.apache.tools.ant.UnknownElement.maybeConfigure(UnknownElement.java:164)
   [buildDB]     at groovy.util.AntBuilder.performTask(AntBuilder.java:322)
   [buildDB]     at
groovy.util.AntBuilder.nodeCompleted(AntBuilder.java:272)
   [buildDB]     at
groovy.util.BuilderSupport.doInvokeMethod(BuilderSupport.java:154)
   [buildDB]     at
groovy.util.AntBuilder.doInvokeMethod(AntBuilder.java:207)
   [buildDB]     at
groovy.util.BuilderSupport.invokeMethod(BuilderSupport.java:67)
   [buildDB]     at
org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:48)
   [buildDB]     at
org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
   [buildDB]     at
org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
   [buildDB]     at
org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
   [buildDB]     at
org.intermine.plugin.dbmodel.DBModelUtils$_closure5.doCall(DBModelUtils.groovy:88)
   [buildDB]     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
Method)
   [buildDB]     at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
   [buildDB]     at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
   [buildDB]     at java.lang.reflect.Method.invoke(Method.java:498)
   [buildDB]     at
org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
   [buildDB]     at
groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
   [buildDB]     at
org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
   [buildDB]     at
groovy.lang.MetaClassImpl.invokePropertyOrMissing(MetaClassImpl.java:1252)
   [buildDB]     at
groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1215)
   [buildDB]     at
groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
   [buildDB]     at
org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
   [buildDB]     at
org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
   [buildDB]     at
org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
   [buildDB]     at
org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:133)
   [buildDB]     at
org.intermine.plugin.dbmodel.DBModelPlugin$_apply_closure10$_closure40.doCall(DBModelPlugin.groovy:268)
   [buildDB]     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
Method)
   [buildDB]     at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
   [buildDB]     at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
   [buildDB]     at java.lang.reflect.Method.invoke(Method.java:498)
   [buildDB]     at
org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
   [buildDB]     at
groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
   [buildDB]     at
org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
   [buildDB]     at
groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
   [buildDB]     at groovy.lang.Closure.call(Closure.java:414)
   [buildDB]     at groovy.lang.Closure.call(Closure.java:430)
   [buildDB]     at
org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:681)
   [buildDB]     at
org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:656)
   [buildDB]     at
org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:122)
   [buildDB]     at
org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
   [buildDB]     at
org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
   [buildDB]     at
org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
   [buildDB]     at
org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
   [buildDB]     at
org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:111)
   [buildDB]     at
org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92)
   [buildDB]     at
org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70)
   [buildDB]     at
org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:63)
   [buildDB]     at
org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
   [buildDB]     at
org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
   [buildDB]     at
org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:88)
   [buildDB]     at
org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
   [buildDB]     at
org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
   [buildDB]     at
org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
   [buildDB]     at
org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
   [buildDB]     at
org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
   [buildDB]     at
org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
   [buildDB]     at
org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
   [buildDB]     at
org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
   [buildDB]     at
org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
   [buildDB]     at
org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
   [buildDB]     at
org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
   [buildDB]     at
org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
   [buildDB]     at
org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:124)
   [buildDB]     at
org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:80)
   [buildDB]     at
org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:105)
   [buildDB]     at
org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:99)
   [buildDB]     at
org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:625)
   [buildDB]     at
org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:580)
   [buildDB]     at
org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:99)
   [buildDB]     at
org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
   [buildDB]     at
org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
   [buildDB]     at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
   [buildDB]     at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
   [buildDB]     at
org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
   [buildDB]     at java.lang.Thread.run(Thread.java:748)


FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':bio-source-locust-anatomy-expression:buildDB'.
 > java.lang.NullPointerException

* Try:
Run with --info or --debug option to get more log output.

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task
':bio-source-locust-anatomy-expression:buildDB'.
         at
org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:100)
         at
org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70)
         at
org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:63)
         at
org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
         at
org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
         at
org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:88)
         at
org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
         at
org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
         at
org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
         at
org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
         at
org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
         at
org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
         at
org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
         at
org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
         at
org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
         at
org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
         at
org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
         at
org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
         at
org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:124)
         at
org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:80)
         at
org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:105)
         at
org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:99)
         at
org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:625)
         at
org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:580)
         at
org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:99)
         at
org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
         at
org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
         at
org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
Caused by: : java.lang.NullPointerException
         at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:116)
         at
org.intermine.plugin.dbmodel.DBModelUtils$_closure5.doCall(DBModelUtils.groovy:88)
         at
org.intermine.plugin.dbmodel.DBModelPlugin$_apply_closure10$_closure40.doCall(DBModelPlugin.groovy:268)
         at
org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:681)
         at
org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:656)
         at
org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:122)
         at
org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
         at
org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
         at
org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
         at
org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
         at
org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:111)
         at
org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92)
         ... 27 more
Caused by: java.lang.NullPointerException
         at org.intermine.task.BuildDbTask.execute(BuildDbTask.java:284)
         at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
         at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
         ... 38 more


* Get more help at https://help.gradle.org

BUILD FAILED in 7s
10 actionable tasks: 7 executed, 3 up-to-date

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Re: buildDB problem: Could not load required global properties resource intermine.properties

Daniela Butano-2
Dear Pengchy,

I have cloned the bio-source project and installed the bio-sources
locally with success.

cd bio-source

./gradlew install

I have cloned the locustmine projects and added to it the gradle wrapper
+ build.gradle file which were missing on github (but I suppose you have
these and you didn't commit).

I have updated the project.xml file adding the locust-anatomy-expression
source, pointing to the 2.0 version.

Then I have executed:

cd locustmine

./gradlew clean

./gradlew builddb

with success. (Please note that you don't have to execute install in
locustmine!)

In the locustmine database, the table AnatomyExpression, defined in the
locust-anatomy-expression_additions.xml file, has been properly generated

locustmine=# \d anatomyexpression
       Table "public.anatomyexpression"
         Column        |  Type   | Modifiers
----------------------+---------+-----------
  expressionrpkmmin    | real    |
  expressionrankmean   | real    |
  expressionrankmedian | real    |
  expressionrankmax    | real    |
  id                   | integer | not null
  expressionrank1stqu  | real    |
  expressionrpkmmedian | real    |
  expressionrpkm3rdqu  | real    |
  expressionrpkmmax    | real    |
  expressionrpkm1stqu  | real    |
  expressionrankmin    | real    |
  expressionrank3rdqu  | real    |
  expressionrpkmmean   | real    |
  anatomytermid        | integer |
  geneid               | integer |
  class                | text    |
Indexes:
     "anatomyexpression_pkey" UNIQUE CONSTRAINT, btree (id)
     "anatomyexpression__anatomyterm" btree (anatomytermid, id)
     "anatomyexpression__key_gene_anatomyterm" btree (geneid,
anatomytermid, id)

Not sure what's happening to you.
I would suggest to delete your ./m2/repository/org/intermine directory,
then re-install your bio-source and then try again

cd locustmine

./gradlew clean

./gradlew builddb

Please let me know how is going!

Daniela

On 03/02/2020 08:20, Pengcheng Yang wrote:

> Dear InterMiners,
>
> During building the customized data model, I encountered one problem
> listed below. The data model bio-sources was committed at
> https://github.com/pengchy/bio-sources.
>
> I have tested removing the data model "locust-anatomy-expression" and
> rebuilding, but with the same error for the second data model.
>
> The error message said that "Could not load required global properties
> resource intermine.properties". I couldn't find the file
> "intermine.properties" under the bio-sources directory.
>
> Thank you and best,
>
> Pengcheng Yang
>
> ============ the error messages ==========================
>
> -bash-4.2$ ./gradlew install
>
> BUILD SUCCESSFUL in 22s
> 112 actionable tasks: 72 executed, 40 up-to-date
> -bash-4.2$ ./gradlew builddb --stacktrace
>
> > Task :bio-source-locust-anatomy-expression:buildDB
> Creating schema in objectstore os.bio-test for
> /home/pengchy/soft/intermine.4.0/git/bio-sources/locust-anatomy-expression/build/os.bio-test-schema.xml
>    [torque] log4j:WARN No appenders could be found for logger
> (org.intermine.util.PropertiesUtil).
>    [torque] log4j:WARN Please initialize the log4j system properly.
>    [torque] log4j:WARN See
> http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
> Creating tables in objectstore os.bio-test with schema
> os.bio-test-schema.xml
>   [buildDB] log4j:WARN No appenders could be found for logger
> (org.intermine.util.PropertiesUtil).
>   [buildDB] log4j:WARN Please initialize the log4j system properly.
>   [buildDB] log4j:WARN See
> http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
>   [buildDB] java.lang.RuntimeException: Could not load required global
> properties resource intermine.properties
>   [buildDB]     at
> org.intermine.util.PropertiesUtil.loadGlobalProperties(PropertiesUtil.java:153)
>   [buildDB]     at
> org.intermine.util.PropertiesUtil.initGlobalProperties(PropertiesUtil.java:58)
>   [buildDB]     at
> org.intermine.util.PropertiesUtil.getProperties(PropertiesUtil.java:45)
>   [buildDB]     at
> org.intermine.task.BuildDbTask.setOsName(BuildDbTask.java:63)
>   [buildDB]     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
> Method)
>   [buildDB]     at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>   [buildDB]     at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>   [buildDB]     at java.lang.reflect.Method.invoke(Method.java:498)
>   [buildDB]     at
> org.apache.tools.ant.IntrospectionHelper$AttributeSetter.setObject(IntrospectionHelper.java:1506)
>   [buildDB]     at
> org.apache.tools.ant.IntrospectionHelper.setAttribute(IntrospectionHelper.java:411)
>   [buildDB]     at
> org.apache.tools.ant.RuntimeConfigurable.maybeConfigure(RuntimeConfigurable.java:527)
>   [buildDB]     at
> org.apache.tools.ant.RuntimeConfigurable.maybeConfigure(RuntimeConfigurable.java:463)
>   [buildDB]     at
> org.apache.tools.ant.Task.maybeConfigure(Task.java:202)
>   [buildDB]     at
> org.apache.tools.ant.UnknownElement.configure(UnknownElement.java:200)
>   [buildDB]     at
> org.apache.tools.ant.UnknownElement.maybeConfigure(UnknownElement.java:164)
>   [buildDB]     at
> groovy.util.AntBuilder.performTask(AntBuilder.java:322)
>   [buildDB]     at
> groovy.util.AntBuilder.nodeCompleted(AntBuilder.java:272)
>   [buildDB]     at
> groovy.util.BuilderSupport.doInvokeMethod(BuilderSupport.java:154)
>   [buildDB]     at
> groovy.util.AntBuilder.doInvokeMethod(AntBuilder.java:207)
>   [buildDB]     at
> groovy.util.BuilderSupport.invokeMethod(BuilderSupport.java:67)
>   [buildDB]     at
> org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:48)
>   [buildDB]     at
> org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
>   [buildDB]     at
> org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
>   [buildDB]     at
> org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
>   [buildDB]     at
> org.intermine.plugin.dbmodel.DBModelUtils$_closure5.doCall(DBModelUtils.groovy:88)
>   [buildDB]     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
> Method)
>   [buildDB]     at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>   [buildDB]     at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>   [buildDB]     at java.lang.reflect.Method.invoke(Method.java:498)
>   [buildDB]     at
> org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
>   [buildDB]     at
> groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
>   [buildDB]     at
> org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
>   [buildDB]     at
> groovy.lang.MetaClassImpl.invokePropertyOrMissing(MetaClassImpl.java:1252)
>   [buildDB]     at
> groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1215)
>   [buildDB]     at
> groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
>   [buildDB]     at
> org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
>   [buildDB]     at
> org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
>   [buildDB]     at
> org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
>   [buildDB]     at
> org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:133)
>   [buildDB]     at
> org.intermine.plugin.dbmodel.DBModelPlugin$_apply_closure10$_closure40.doCall(DBModelPlugin.groovy:268)
>   [buildDB]     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
> Method)
>   [buildDB]     at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>   [buildDB]     at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>   [buildDB]     at java.lang.reflect.Method.invoke(Method.java:498)
>   [buildDB]     at
> org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
>   [buildDB]     at
> groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
>   [buildDB]     at
> org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
>   [buildDB]     at
> groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
>   [buildDB]     at groovy.lang.Closure.call(Closure.java:414)
>   [buildDB]     at groovy.lang.Closure.call(Closure.java:430)
>   [buildDB]     at
> org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:681)
>   [buildDB]     at
> org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:656)
>   [buildDB]     at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:122)
>   [buildDB]     at
> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
>   [buildDB]     at
> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
>   [buildDB]     at
> org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
>   [buildDB]     at
> org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
>   [buildDB]     at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:111)
>   [buildDB]     at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92)
>   [buildDB]     at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70)
>   [buildDB]     at
> org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:63)
>   [buildDB]     at
> org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
>   [buildDB]     at
> org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
>   [buildDB]     at
> org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:88)
>   [buildDB]     at
> org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
>   [buildDB]     at
> org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
>   [buildDB]     at
> org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
>   [buildDB]     at
> org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
>   [buildDB]     at
> org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
>   [buildDB]     at
> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
>   [buildDB]     at
> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
>   [buildDB]     at
> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
>   [buildDB]     at
> org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
>   [buildDB]     at
> org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
>   [buildDB]     at
> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
>   [buildDB]     at
> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
>   [buildDB]     at
> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:124)
>   [buildDB]     at
> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:80)
>   [buildDB]     at
> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:105)
>   [buildDB]     at
> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:99)
>   [buildDB]     at
> org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:625)
>   [buildDB]     at
> org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:580)
>   [buildDB]     at
> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:99)
>   [buildDB]     at
> org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
>   [buildDB]     at
> org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
>   [buildDB]     at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
>   [buildDB]     at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
>   [buildDB]     at
> org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
>   [buildDB]     at java.lang.Thread.run(Thread.java:748)
>
>
> FAILURE: Build failed with an exception.
>
> * What went wrong:
> Execution failed for task
> ':bio-source-locust-anatomy-expression:buildDB'.
> > java.lang.NullPointerException
>
> * Try:
> Run with --info or --debug option to get more log output.
>
> * Exception is:
> org.gradle.api.tasks.TaskExecutionException: Execution failed for task
> ':bio-source-locust-anatomy-expression:buildDB'.
>         at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:100)
>         at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70)
>         at
> org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:63)
>         at
> org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
>         at
> org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
>         at
> org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:88)
>         at
> org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
>         at
> org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
>         at
> org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
>         at
> org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
>         at
> org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
>         at
> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
>         at
> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
>         at
> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
>         at
> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:124)
>         at
> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:80)
>         at
> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:105)
>         at
> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:99)
>         at
> org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:625)
>         at
> org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:580)
>         at
> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:99)
>         at
> org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
>         at
> org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
>         at
> org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
> Caused by: : java.lang.NullPointerException
>         at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:116)
>         at
> org.intermine.plugin.dbmodel.DBModelUtils$_closure5.doCall(DBModelUtils.groovy:88)
>         at
> org.intermine.plugin.dbmodel.DBModelPlugin$_apply_closure10$_closure40.doCall(DBModelPlugin.groovy:268)
>         at
> org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:681)
>         at
> org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:656)
>         at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:122)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
>         at
> org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
>         at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:111)
>         at
> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92)
>         ... 27 more
> Caused by: java.lang.NullPointerException
>         at org.intermine.task.BuildDbTask.execute(BuildDbTask.java:284)
>         at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
>         at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>         ... 38 more
>
>
> * Get more help at https://help.gradle.org
>
> BUILD FAILED in 7s
> 10 actionable tasks: 7 executed, 3 up-to-date
>
> _______________________________________________
> dev mailing list
> [hidden email]
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Re: buildDB problem: Could not load required global properties resource intermine.properties

Pengcheng Yang
Hi Daniela,

I have found that I run ./gradlew builddb in bio-sources directory,
which should be in my project directory. The problem has been resolved now.

Thank you and best,

Pengcheng

On 2020-2-3 19:20, Daniela Butano wrote:

> Dear Pengchy,
>
> I have cloned the bio-source project and installed the bio-sources
> locally with success.
>
> cd bio-source
>
> ./gradlew install
>
> I have cloned the locustmine projects and added to it the gradle
> wrapper + build.gradle file which were missing on github (but I
> suppose you have these and you didn't commit).
>
> I have updated the project.xml file adding the
> locust-anatomy-expression source, pointing to the 2.0 version.
>
> Then I have executed:
>
> cd locustmine
>
> ./gradlew clean
>
> ./gradlew builddb
>
> with success. (Please note that you don't have to execute install in
> locustmine!)
>
> In the locustmine database, the table AnatomyExpression, defined in
> the locust-anatomy-expression_additions.xml file, has been properly
> generated
>
> locustmine=# \d anatomyexpression
>       Table "public.anatomyexpression"
>         Column        |  Type   | Modifiers
> ----------------------+---------+-----------
>  expressionrpkmmin    | real    |
>  expressionrankmean   | real    |
>  expressionrankmedian | real    |
>  expressionrankmax    | real    |
>  id                   | integer | not null
>  expressionrank1stqu  | real    |
>  expressionrpkmmedian | real    |
>  expressionrpkm3rdqu  | real    |
>  expressionrpkmmax    | real    |
>  expressionrpkm1stqu  | real    |
>  expressionrankmin    | real    |
>  expressionrank3rdqu  | real    |
>  expressionrpkmmean   | real    |
>  anatomytermid        | integer |
>  geneid               | integer |
>  class                | text    |
> Indexes:
>     "anatomyexpression_pkey" UNIQUE CONSTRAINT, btree (id)
>     "anatomyexpression__anatomyterm" btree (anatomytermid, id)
>     "anatomyexpression__key_gene_anatomyterm" btree (geneid,
> anatomytermid, id)
>
> Not sure what's happening to you.
> I would suggest to delete your ./m2/repository/org/intermine
> directory, then re-install your bio-source and then try again
>
> cd locustmine
>
> ./gradlew clean
>
> ./gradlew builddb
>
> Please let me know how is going!
>
> Daniela
>
> On 03/02/2020 08:20, Pengcheng Yang wrote:
>> Dear InterMiners,
>>
>> During building the customized data model, I encountered one problem
>> listed below. The data model bio-sources was committed at
>> https://github.com/pengchy/bio-sources.
>>
>> I have tested removing the data model "locust-anatomy-expression" and
>> rebuilding, but with the same error for the second data model.
>>
>> The error message said that "Could not load required global
>> properties resource intermine.properties". I couldn't find the file
>> "intermine.properties" under the bio-sources directory.
>>
>> Thank you and best,
>>
>> Pengcheng Yang
>>
>> ============ the error messages ==========================
>>
>> -bash-4.2$ ./gradlew install
>>
>> BUILD SUCCESSFUL in 22s
>> 112 actionable tasks: 72 executed, 40 up-to-date
>> -bash-4.2$ ./gradlew builddb --stacktrace
>>
>> > Task :bio-source-locust-anatomy-expression:buildDB
>> Creating schema in objectstore os.bio-test for
>> /home/pengchy/soft/intermine.4.0/git/bio-sources/locust-anatomy-expression/build/os.bio-test-schema.xml
>>    [torque] log4j:WARN No appenders could be found for logger
>> (org.intermine.util.PropertiesUtil).
>>    [torque] log4j:WARN Please initialize the log4j system properly.
>>    [torque] log4j:WARN See
>> http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
>> Creating tables in objectstore os.bio-test with schema
>> os.bio-test-schema.xml
>>   [buildDB] log4j:WARN No appenders could be found for logger
>> (org.intermine.util.PropertiesUtil).
>>   [buildDB] log4j:WARN Please initialize the log4j system properly.
>>   [buildDB] log4j:WARN See
>> http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
>>   [buildDB] java.lang.RuntimeException: Could not load required
>> global properties resource intermine.properties
>>   [buildDB]     at
>> org.intermine.util.PropertiesUtil.loadGlobalProperties(PropertiesUtil.java:153)
>>   [buildDB]     at
>> org.intermine.util.PropertiesUtil.initGlobalProperties(PropertiesUtil.java:58)
>>   [buildDB]     at
>> org.intermine.util.PropertiesUtil.getProperties(PropertiesUtil.java:45)
>>   [buildDB]     at
>> org.intermine.task.BuildDbTask.setOsName(BuildDbTask.java:63)
>>   [buildDB]     at
>> sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>   [buildDB]     at
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>>   [buildDB]     at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>   [buildDB]     at java.lang.reflect.Method.invoke(Method.java:498)
>>   [buildDB]     at
>> org.apache.tools.ant.IntrospectionHelper$AttributeSetter.setObject(IntrospectionHelper.java:1506)
>>   [buildDB]     at
>> org.apache.tools.ant.IntrospectionHelper.setAttribute(IntrospectionHelper.java:411)
>>   [buildDB]     at
>> org.apache.tools.ant.RuntimeConfigurable.maybeConfigure(RuntimeConfigurable.java:527)
>>   [buildDB]     at
>> org.apache.tools.ant.RuntimeConfigurable.maybeConfigure(RuntimeConfigurable.java:463)
>>   [buildDB]     at
>> org.apache.tools.ant.Task.maybeConfigure(Task.java:202)
>>   [buildDB]     at
>> org.apache.tools.ant.UnknownElement.configure(UnknownElement.java:200)
>>   [buildDB]     at
>> org.apache.tools.ant.UnknownElement.maybeConfigure(UnknownElement.java:164)
>>   [buildDB]     at
>> groovy.util.AntBuilder.performTask(AntBuilder.java:322)
>>   [buildDB]     at
>> groovy.util.AntBuilder.nodeCompleted(AntBuilder.java:272)
>>   [buildDB]     at
>> groovy.util.BuilderSupport.doInvokeMethod(BuilderSupport.java:154)
>>   [buildDB]     at
>> groovy.util.AntBuilder.doInvokeMethod(AntBuilder.java:207)
>>   [buildDB]     at
>> groovy.util.BuilderSupport.invokeMethod(BuilderSupport.java:67)
>>   [buildDB]     at
>> org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:48)
>>   [buildDB]     at
>> org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
>>   [buildDB]     at
>> org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
>>   [buildDB]     at
>> org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
>>   [buildDB]     at
>> org.intermine.plugin.dbmodel.DBModelUtils$_closure5.doCall(DBModelUtils.groovy:88)
>>   [buildDB]     at
>> sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>   [buildDB]     at
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>>   [buildDB]     at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>   [buildDB]     at java.lang.reflect.Method.invoke(Method.java:498)
>>   [buildDB]     at
>> org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
>>   [buildDB]     at
>> groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
>>   [buildDB]     at
>> org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
>>   [buildDB]     at
>> groovy.lang.MetaClassImpl.invokePropertyOrMissing(MetaClassImpl.java:1252)
>>   [buildDB]     at
>> groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1215)
>>   [buildDB]     at
>> groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
>>   [buildDB]     at
>> org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
>>   [buildDB]     at
>> org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
>>   [buildDB]     at
>> org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
>>   [buildDB]     at
>> org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:133)
>>   [buildDB]     at
>> org.intermine.plugin.dbmodel.DBModelPlugin$_apply_closure10$_closure40.doCall(DBModelPlugin.groovy:268)
>>   [buildDB]     at
>> sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>   [buildDB]     at
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>>   [buildDB]     at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>   [buildDB]     at java.lang.reflect.Method.invoke(Method.java:498)
>>   [buildDB]     at
>> org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
>>   [buildDB]     at
>> groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
>>   [buildDB]     at
>> org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
>>   [buildDB]     at
>> groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
>>   [buildDB]     at groovy.lang.Closure.call(Closure.java:414)
>>   [buildDB]     at groovy.lang.Closure.call(Closure.java:430)
>>   [buildDB]     at
>> org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:681)
>>   [buildDB]     at
>> org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:656)
>>   [buildDB]     at
>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:122)
>>   [buildDB]     at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
>>   [buildDB]     at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
>>   [buildDB]     at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
>>   [buildDB]     at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
>>   [buildDB]     at
>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:111)
>>   [buildDB]     at
>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92)
>>   [buildDB]     at
>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70)
>>   [buildDB]     at
>> org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:63)
>>   [buildDB]     at
>> org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
>>   [buildDB]     at
>> org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
>>   [buildDB]     at
>> org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:88)
>>   [buildDB]     at
>> org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
>>   [buildDB]     at
>> org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
>>   [buildDB]     at
>> org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
>>   [buildDB]     at
>> org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
>>   [buildDB]     at
>> org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
>>   [buildDB]     at
>> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
>>   [buildDB]     at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
>>   [buildDB]     at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
>>   [buildDB]     at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
>>   [buildDB]     at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
>>   [buildDB]     at
>> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
>>   [buildDB]     at
>> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
>>   [buildDB]     at
>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:124)
>>   [buildDB]     at
>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:80)
>>   [buildDB]     at
>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:105)
>>   [buildDB]     at
>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:99)
>>   [buildDB]     at
>> org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:625)
>>   [buildDB]     at
>> org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:580)
>>   [buildDB]     at
>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:99)
>>   [buildDB]     at
>> org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
>>   [buildDB]     at
>> org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
>>   [buildDB]     at
>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
>>   [buildDB]     at
>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
>>   [buildDB]     at
>> org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
>>   [buildDB]     at java.lang.Thread.run(Thread.java:748)
>>
>>
>> FAILURE: Build failed with an exception.
>>
>> * What went wrong:
>> Execution failed for task
>> ':bio-source-locust-anatomy-expression:buildDB'.
>> > java.lang.NullPointerException
>>
>> * Try:
>> Run with --info or --debug option to get more log output.
>>
>> * Exception is:
>> org.gradle.api.tasks.TaskExecutionException: Execution failed for
>> task ':bio-source-locust-anatomy-expression:buildDB'.
>>         at
>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:100)
>>         at
>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70)
>>         at
>> org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:63)
>>         at
>> org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
>>         at
>> org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
>>         at
>> org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:88)
>>         at
>> org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
>>         at
>> org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
>>         at
>> org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
>>         at
>> org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
>>         at
>> org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
>>         at
>> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
>>         at
>> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
>>         at
>> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
>>         at
>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:124)
>>         at
>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:80)
>>         at
>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:105)
>>         at
>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:99)
>>         at
>> org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:625)
>>         at
>> org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:580)
>>         at
>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:99)
>>         at
>> org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
>>         at
>> org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
>>         at
>> org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
>> Caused by: : java.lang.NullPointerException
>>         at
>> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:116)
>>         at
>> org.intermine.plugin.dbmodel.DBModelUtils$_closure5.doCall(DBModelUtils.groovy:88)
>>         at
>> org.intermine.plugin.dbmodel.DBModelPlugin$_apply_closure10$_closure40.doCall(DBModelPlugin.groovy:268)
>>         at
>> org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:681)
>>         at
>> org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:656)
>>         at
>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:122)
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
>>         at
>> org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
>>         at
>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:111)
>>         at
>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92)
>>         ... 27 more
>> Caused by: java.lang.NullPointerException
>>         at org.intermine.task.BuildDbTask.execute(BuildDbTask.java:284)
>>         at
>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
>>         at
>> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>>         ... 38 more
>>
>>
>> * Get more help at https://help.gradle.org
>>
>> BUILD FAILED in 7s
>> 10 actionable tasks: 7 executed, 3 up-to-date
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
> _______________________________________________
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Re: buildDB problem: Could not load required global properties resource intermine.properties

Daniela Butano-2
Great!

Daniela

On 03/02/2020 12:42, Pengcheng Yang wrote:

> Hi Daniela,
>
> I have found that I run ./gradlew builddb in bio-sources directory,
> which should be in my project directory. The problem has been resolved
> now.
>
> Thank you and best,
>
> Pengcheng
>
> On 2020-2-3 19:20, Daniela Butano wrote:
>> Dear Pengchy,
>>
>> I have cloned the bio-source project and installed the bio-sources
>> locally with success.
>>
>> cd bio-source
>>
>> ./gradlew install
>>
>> I have cloned the locustmine projects and added to it the gradle
>> wrapper + build.gradle file which were missing on github (but I
>> suppose you have these and you didn't commit).
>>
>> I have updated the project.xml file adding the
>> locust-anatomy-expression source, pointing to the 2.0 version.
>>
>> Then I have executed:
>>
>> cd locustmine
>>
>> ./gradlew clean
>>
>> ./gradlew builddb
>>
>> with success. (Please note that you don't have to execute install in
>> locustmine!)
>>
>> In the locustmine database, the table AnatomyExpression, defined in
>> the locust-anatomy-expression_additions.xml file, has been properly
>> generated
>>
>> locustmine=# \d anatomyexpression
>>       Table "public.anatomyexpression"
>>         Column        |  Type   | Modifiers
>> ----------------------+---------+-----------
>>  expressionrpkmmin    | real    |
>>  expressionrankmean   | real    |
>>  expressionrankmedian | real    |
>>  expressionrankmax    | real    |
>>  id                   | integer | not null
>>  expressionrank1stqu  | real    |
>>  expressionrpkmmedian | real    |
>>  expressionrpkm3rdqu  | real    |
>>  expressionrpkmmax    | real    |
>>  expressionrpkm1stqu  | real    |
>>  expressionrankmin    | real    |
>>  expressionrank3rdqu  | real    |
>>  expressionrpkmmean   | real    |
>>  anatomytermid        | integer |
>>  geneid               | integer |
>>  class                | text    |
>> Indexes:
>>     "anatomyexpression_pkey" UNIQUE CONSTRAINT, btree (id)
>>     "anatomyexpression__anatomyterm" btree (anatomytermid, id)
>>     "anatomyexpression__key_gene_anatomyterm" btree (geneid,
>> anatomytermid, id)
>>
>> Not sure what's happening to you.
>> I would suggest to delete your ./m2/repository/org/intermine
>> directory, then re-install your bio-source and then try again
>>
>> cd locustmine
>>
>> ./gradlew clean
>>
>> ./gradlew builddb
>>
>> Please let me know how is going!
>>
>> Daniela
>>
>> On 03/02/2020 08:20, Pengcheng Yang wrote:
>>> Dear InterMiners,
>>>
>>> During building the customized data model, I encountered one problem
>>> listed below. The data model bio-sources was committed at
>>> https://github.com/pengchy/bio-sources.
>>>
>>> I have tested removing the data model "locust-anatomy-expression"
>>> and rebuilding, but with the same error for the second data model.
>>>
>>> The error message said that "Could not load required global
>>> properties resource intermine.properties". I couldn't find the file
>>> "intermine.properties" under the bio-sources directory.
>>>
>>> Thank you and best,
>>>
>>> Pengcheng Yang
>>>
>>> ============ the error messages ==========================
>>>
>>> -bash-4.2$ ./gradlew install
>>>
>>> BUILD SUCCESSFUL in 22s
>>> 112 actionable tasks: 72 executed, 40 up-to-date
>>> -bash-4.2$ ./gradlew builddb --stacktrace
>>>
>>> > Task :bio-source-locust-anatomy-expression:buildDB
>>> Creating schema in objectstore os.bio-test for
>>> /home/pengchy/soft/intermine.4.0/git/bio-sources/locust-anatomy-expression/build/os.bio-test-schema.xml
>>>    [torque] log4j:WARN No appenders could be found for logger
>>> (org.intermine.util.PropertiesUtil).
>>>    [torque] log4j:WARN Please initialize the log4j system properly.
>>>    [torque] log4j:WARN See
>>> http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
>>> Creating tables in objectstore os.bio-test with schema
>>> os.bio-test-schema.xml
>>>   [buildDB] log4j:WARN No appenders could be found for logger
>>> (org.intermine.util.PropertiesUtil).
>>>   [buildDB] log4j:WARN Please initialize the log4j system properly.
>>>   [buildDB] log4j:WARN See
>>> http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
>>>   [buildDB] java.lang.RuntimeException: Could not load required
>>> global properties resource intermine.properties
>>>   [buildDB]     at
>>> org.intermine.util.PropertiesUtil.loadGlobalProperties(PropertiesUtil.java:153)
>>>   [buildDB]     at
>>> org.intermine.util.PropertiesUtil.initGlobalProperties(PropertiesUtil.java:58)
>>>   [buildDB]     at
>>> org.intermine.util.PropertiesUtil.getProperties(PropertiesUtil.java:45)
>>>   [buildDB]     at
>>> org.intermine.task.BuildDbTask.setOsName(BuildDbTask.java:63)
>>>   [buildDB]     at
>>> sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>>   [buildDB]     at
>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>>>   [buildDB]     at
>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>>   [buildDB]     at java.lang.reflect.Method.invoke(Method.java:498)
>>>   [buildDB]     at
>>> org.apache.tools.ant.IntrospectionHelper$AttributeSetter.setObject(IntrospectionHelper.java:1506)
>>>   [buildDB]     at
>>> org.apache.tools.ant.IntrospectionHelper.setAttribute(IntrospectionHelper.java:411)
>>>   [buildDB]     at
>>> org.apache.tools.ant.RuntimeConfigurable.maybeConfigure(RuntimeConfigurable.java:527)
>>>   [buildDB]     at
>>> org.apache.tools.ant.RuntimeConfigurable.maybeConfigure(RuntimeConfigurable.java:463)
>>>   [buildDB]     at
>>> org.apache.tools.ant.Task.maybeConfigure(Task.java:202)
>>>   [buildDB]     at
>>> org.apache.tools.ant.UnknownElement.configure(UnknownElement.java:200)
>>>   [buildDB]     at
>>> org.apache.tools.ant.UnknownElement.maybeConfigure(UnknownElement.java:164)
>>>   [buildDB]     at
>>> groovy.util.AntBuilder.performTask(AntBuilder.java:322)
>>>   [buildDB]     at
>>> groovy.util.AntBuilder.nodeCompleted(AntBuilder.java:272)
>>>   [buildDB]     at
>>> groovy.util.BuilderSupport.doInvokeMethod(BuilderSupport.java:154)
>>>   [buildDB]     at
>>> groovy.util.AntBuilder.doInvokeMethod(AntBuilder.java:207)
>>>   [buildDB]     at
>>> groovy.util.BuilderSupport.invokeMethod(BuilderSupport.java:67)
>>>   [buildDB]     at
>>> org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:48)
>>>   [buildDB]     at
>>> org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
>>>   [buildDB]     at
>>> org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
>>>   [buildDB]     at
>>> org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
>>>   [buildDB]     at
>>> org.intermine.plugin.dbmodel.DBModelUtils$_closure5.doCall(DBModelUtils.groovy:88)
>>>   [buildDB]     at
>>> sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>>   [buildDB]     at
>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>>>   [buildDB]     at
>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>>   [buildDB]     at java.lang.reflect.Method.invoke(Method.java:498)
>>>   [buildDB]     at
>>> org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
>>>
>>>   [buildDB]     at
>>> groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
>>>   [buildDB]     at
>>> org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
>>>   [buildDB]     at
>>> groovy.lang.MetaClassImpl.invokePropertyOrMissing(MetaClassImpl.java:1252)
>>>   [buildDB]     at
>>> groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1215)
>>>   [buildDB]     at
>>> groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
>>>   [buildDB]     at
>>> org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:42)
>>>   [buildDB]     at
>>> org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
>>>   [buildDB]     at
>>> org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
>>>   [buildDB]     at
>>> org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:133)
>>>   [buildDB]     at
>>> org.intermine.plugin.dbmodel.DBModelPlugin$_apply_closure10$_closure40.doCall(DBModelPlugin.groovy:268)
>>>   [buildDB]     at
>>> sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>>   [buildDB]     at
>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>>>   [buildDB]     at
>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>>>   [buildDB]     at java.lang.reflect.Method.invoke(Method.java:498)
>>>   [buildDB]     at
>>> org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
>>>
>>>   [buildDB]     at
>>> groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
>>>   [buildDB]     at
>>> org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294)
>>>   [buildDB]     at
>>> groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022)
>>>   [buildDB]     at groovy.lang.Closure.call(Closure.java:414)
>>>   [buildDB]     at groovy.lang.Closure.call(Closure.java:430)
>>>   [buildDB]     at
>>> org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:681)
>>>   [buildDB]     at
>>> org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:656)
>>>   [buildDB]     at
>>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:122)
>>>   [buildDB]     at
>>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
>>>   [buildDB]     at
>>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
>>>   [buildDB]     at
>>> org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
>>>   [buildDB]     at
>>> org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
>>>   [buildDB]     at
>>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:111)
>>>   [buildDB]     at
>>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92)
>>>   [buildDB]     at
>>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70)
>>>   [buildDB]     at
>>> org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:63)
>>>   [buildDB]     at
>>> org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
>>>   [buildDB]     at
>>> org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
>>>   [buildDB]     at
>>> org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:88)
>>>   [buildDB]     at
>>> org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
>>>   [buildDB]     at
>>> org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
>>>   [buildDB]     at
>>> org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
>>>   [buildDB]     at
>>> org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
>>>   [buildDB]     at
>>> org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
>>>   [buildDB]     at
>>> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
>>>   [buildDB]     at
>>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
>>>   [buildDB]     at
>>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
>>>   [buildDB]     at
>>> org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
>>>   [buildDB]     at
>>> org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
>>>   [buildDB]     at
>>> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
>>>   [buildDB]     at
>>> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
>>>   [buildDB]     at
>>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:124)
>>>   [buildDB]     at
>>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:80)
>>>   [buildDB]     at
>>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:105)
>>>   [buildDB]     at
>>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:99)
>>>   [buildDB]     at
>>> org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:625)
>>>   [buildDB]     at
>>> org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:580)
>>>   [buildDB]     at
>>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:99)
>>>   [buildDB]     at
>>> org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
>>>   [buildDB]     at
>>> org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
>>>   [buildDB]     at
>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
>>>   [buildDB]     at
>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
>>>   [buildDB]     at
>>> org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
>>>   [buildDB]     at java.lang.Thread.run(Thread.java:748)
>>>
>>>
>>> FAILURE: Build failed with an exception.
>>>
>>> * What went wrong:
>>> Execution failed for task
>>> ':bio-source-locust-anatomy-expression:buildDB'.
>>> > java.lang.NullPointerException
>>>
>>> * Try:
>>> Run with --info or --debug option to get more log output.
>>>
>>> * Exception is:
>>> org.gradle.api.tasks.TaskExecutionException: Execution failed for
>>> task ':bio-source-locust-anatomy-expression:buildDB'.
>>>         at
>>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:100)
>>>         at
>>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70)
>>>         at
>>> org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:63)
>>>         at
>>> org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
>>>         at
>>> org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
>>>         at
>>> org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:88)
>>>         at
>>> org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
>>>         at
>>> org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
>>>         at
>>> org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
>>>         at
>>> org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
>>>         at
>>> org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
>>>         at
>>> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
>>>         at
>>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
>>>         at
>>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
>>>         at
>>> org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
>>>         at
>>> org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
>>>         at
>>> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
>>>         at
>>> org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
>>>         at
>>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:124)
>>>         at
>>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:80)
>>>         at
>>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:105)
>>>         at
>>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:99)
>>>         at
>>> org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:625)
>>>         at
>>> org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:580)
>>>         at
>>> org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:99)
>>>         at
>>> org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
>>>         at
>>> org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
>>>         at
>>> org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
>>> Caused by: : java.lang.NullPointerException
>>>         at
>>> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:116)
>>>         at
>>> org.intermine.plugin.dbmodel.DBModelUtils$_closure5.doCall(DBModelUtils.groovy:88)
>>>         at
>>> org.intermine.plugin.dbmodel.DBModelPlugin$_apply_closure10$_closure40.doCall(DBModelPlugin.groovy:268)
>>>         at
>>> org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:681)
>>>         at
>>> org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:656)
>>>         at
>>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:122)
>>>         at
>>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
>>>         at
>>> org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
>>>         at
>>> org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
>>>         at
>>> org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
>>>         at
>>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:111)
>>>         at
>>> org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92)
>>>         ... 27 more
>>> Caused by: java.lang.NullPointerException
>>>         at org.intermine.task.BuildDbTask.execute(BuildDbTask.java:284)
>>>         at
>>> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
>>>         at
>>> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>>>         ... 38 more
>>>
>>>
>>> * Get more help at https://help.gradle.org
>>>
>>> BUILD FAILED in 7s
>>> 10 actionable tasks: 7 executed, 3 up-to-date
>>>
>>> _______________________________________________
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>> _______________________________________________
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> _______________________________________________
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