New data source derived from BioFileConverter not working

[hendrikweisser]

I've been trying to integrate a new data source into my mine, based on a Java converter class that extends BioFileConverter. The source has been generated in a separate directory using the make_source script (following instructions in the documentation. I can build/install the source (gradlew install), but integration into the mine (gradlew integrate -Psource=...) consistently fails with the error below. (Unfortunately I can't link to the private repository with our sources.)

Interestingly, I can make the integration work by changing the Java class to extend BioDirectoryConverter instead of BioFileConverter (and then picking up the individual file in the directory).

In order to investigate the problem, I've tried to integrate the "kegg-identifiers" example source from here - i.e. I've copied the whole "kegg-identifiers" directory to my sources directory, added an entry to the "settings.gradle" file there and to the "project.xml" of the mine. I even found a suitable input file. The result is the same - installing the source works, but integrating it gives the error below.

[hendrikweisser]

The error:

Execution failed for task ':dbmodel:retrieveSingleSource'.
> /home/hendrik.weisser/.gradle/daemon/4.9/null does not exist.

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

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':dbmodel:retrieveSingleSource'.
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:110)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:77)
        at org.gradle.api.internal.tasks.execution.OutputDirectoryCreatingTaskExecuter.execute(OutputDirectoryCreatingTaskExecuter.java:51)
        at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:59)
        at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
        at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:59)
        at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:101)
        at org.gradle.api.internal.tasks.execution.FinalizeInputFilePropertiesTaskExecuter.execute(FinalizeInputFilePropertiesTaskExecuter.java:44)
        at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:91)
        at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:62)
        at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:59)
        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.api.internal.tasks.execution.EventFiringTaskExecuter$1.run(EventFiringTaskExecuter.java:51)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:300)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:292)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:174)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:90)
        at org.gradle.internal.operations.DelegatingBuildOperationExecutor.run(DelegatingBuildOperationExecutor.java:31)
        at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter.execute(EventFiringTaskExecuter.java:46)
        at org.gradle.execution.taskgraph.LocalTaskInfoExecutor.execute(LocalTaskInfoExecutor.java:42)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$BuildOperationAwareWorkItemExecutor.execute(DefaultTaskExecutionGraph.java:273)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$BuildOperationAwareWorkItemExecutor.execute(DefaultTaskExecutionGraph.java:258)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$ExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:135)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$ExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:130)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$ExecutorWorker.execute(DefaultTaskPlanExecutor.java:200)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$ExecutorWorker.executeWithWork(DefaultTaskPlanExecutor.java:191)
        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$ExecutorWorker.run(DefaultTaskPlanExecutor.java:130)
        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: : /home/hendrik.weisser/.gradle/daemon/4.9/null does not exist.
        at org.intermine.task.FileConverterTask.execute(FileConverterTask.java:128)
        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
        at org.intermine.plugin.integrate.IntegrateUtils$_closure3.doCall(IntegrateUtils.groovy:84)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at org.intermine.plugin.integrate.IntegrateUtils.invokeMethod(IntegrateUtils.groovy)
        at org.intermine.plugin.integrate.IntegrateUtils$_closure2.doCall(IntegrateUtils.groovy:47)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at org.intermine.plugin.integrate.IntegratePlugin$_apply_closure7$_closure20.doCall(IntegratePlugin.groovy:179)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:724)
        at org.gradle.api.internal.AbstractTask$ClosureTaskAction.execute(AbstractTask.java:697)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:131)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:300)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:292)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:174)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:90)
        at org.gradle.internal.operations.DelegatingBuildOperationExecutor.run(DelegatingBuildOperationExecutor.java:31)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:120)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:99)
        ... 31 more
Caused by: /home/hendrik.weisser/.gradle/daemon/4.9/null does not exist.
        at org.apache.tools.ant.types.AbstractFileSet.getDirectoryScanner(AbstractFileSet.java:505)
        at org.intermine.task.FileConverterTask.execute(FileConverterTask.java:102)
        ... 59 more