Investigate reoccuring NPE exception in CVR pipeline

[n1zea144]

Done Condition (What do we need? Why do we need it? Keep this is small as possible!)

Determine cause of reoccurring NPE thrown by CVR pipeline.

Technical Description (How are we going to achieve the above)

java.lang.NullPointerException
    at org.cbioportal.cmo.pipelines.cvr.CVRUtilities.buildCVRMutationRecord(CVRUtilities.java:288)
    at org.cbioportal.cmo.pipelines.cvr.mutation.CVRMutationDataReader.loadMutationRecordsFromJson(CVRMutationDataReader.java:131)
    at org.cbioportal.cmo.pipelines.cvr.mutation.CVRMutationDataReader.open(CVRMutationDataReader.java:101)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
    at org.springframework.aop.support.DelegatingIntroductionInterceptor.doProceed(DelegatingIntroductionInterceptor.java:136)
    at org.springframework.aop.support.DelegatingIntroductionInterceptor.invoke(DelegatingIntroductionInterceptor.java:124)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
    at com.sun.proxy.$Proxy57.open(Unknown Source)
    at org.springframework.batch.item.support.CompositeItemStream.open(CompositeItemStream.java:103)
    at org.springframework.batch.core.step.tasklet.TaskletStep.open(TaskletStep.java:311)
    at org.springframework.batch.core.step.AbstractStep.execute(AbstractStep.java:205)
    at org.springframework.batch.core.job.SimpleStepHandler.handleStep(SimpleStepHandler.java:148)
    at org.springframework.batch.core.job.flow.JobFlowExecutor.executeStep(JobFlowExecutor.java:68)
    at org.springframework.batch.core.job.flow.support.state.StepState.handle(StepState.java:68)
    at org.springframework.batch.core.job.flow.support.SimpleFlow.resume(SimpleFlow.java:169)
    at org.springframework.batch.core.job.flow.support.SimpleFlow.start(SimpleFlow.java:144)
    at org.springframework.batch.core.job.flow.support.state.FlowState.handle(FlowState.java:56)
    at org.springframework.batch.core.job.flow.support.SimpleFlow.resume(SimpleFlow.java:169)
    at org.springframework.batch.core.job.flow.support.SimpleFlow.start(SimpleFlow.java:144)
    at org.springframework.batch.core.job.flow.support.state.FlowState.handle(FlowState.java:56)
    at org.springframework.batch.core.job.flow.support.SimpleFlow.resume(SimpleFlow.java:169)
    at org.springframework.batch.core.job.flow.support.SimpleFlow.start(SimpleFlow.java:144)
    at org.springframework.batch.core.job.flow.FlowJob.doExecute(FlowJob.java:137)
    at org.springframework.batch.core.job.AbstractJob.execute(AbstractJob.java:319)
    at org.springframework.batch.core.launch.support.SimpleJobLauncher$1.run(SimpleJobLauncher.java:147)
    at org.springframework.core.task.SyncTaskExecutor.execute(SyncTaskExecutor.java:50)
    at org.springframework.batch.core.launch.support.SimpleJobLauncher.run(SimpleJobLauncher.java:140)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
    at org.springframework.batch.core.configuration.annotation.SimpleBatchConfiguration$PassthruAdvice.invoke(SimpleBatchConfiguration.java:127)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
    at com.sun.proxy.$Proxy53.run(Unknown Source)
    at org.cbioportal.cmo.pipelines.CVRPipeline.launchCvrPipelineJob(CVRPipeline.java:133)
    at org.cbioportal.cmo.pipelines.CVRPipeline.main(CVRPipeline.java:215)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:49)
    at org.springframework.boot.loader.Launcher.launch(Launcher.java:109)
    at org.springframework.boot.loader.Launcher.launch(Launcher.java:58)
    at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:88)

Potential Issues

Dependencies

Technical Requirements

Outside People/Teams

Changes

[averyniceday]

recurring failures for access cohort - will need to build a custom fetcher that can determine which field is empty

[averyniceday]

P-0069512-T05-XS1 missing normal_ad, normal_dp.

Will add a message in CVR channel about it