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Repository for tracking uncategorizable issues related to backend pipelines work
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CMO pipelines: REDCap fetcher #636

Closed ao508 closed 3 years ago

ao508 commented 3 years ago

Theory is that we just need to make some adjustments to the execution context. Maybe more memory or if it's having trouble parsing values out of the execution context then change the class types to something compatible.

Stacktrace 

2021-08-04 19:02:01 [main] INFO  org.springframework.batch.core.job.SimpleStepHandler - Executing step: [exportRawTimelineDataStep]
2021-08-04 19:02:01 [main] INFO  org.mskcc.cmo.ks.redcap.pipeline.RawTimelineDataStepListener - Starting a timeline data step
2021-08-04 19:02:01 [main] INFO  org.mskcc.cmo.ks.redcap.pipeline.TimelineReader - Getting timeline header for project: mskimpact_pediatrics_supp_timeline
2021-08-04 19:02:01 [main] INFO  org.mskcc.cmo.ks.redcap.source.internal.RedcapSessionManager - Getting attributes for project...
2021-08-04 19:02:02 [main] INFO  org.mskcc.cmo.ks.redcap.source.internal.RedcapSessionManager - Getting data for project...
2021-08-04 19:02:02 [main] INFO  org.mskcc.cmo.ks.redcap.source.internal.RedcapSessionManager - Getting attributes for project...
2021-08-04 19:02:02 [main] INFO  org.springframework.batch.core.step.AbstractStep - Step: [exportRawTimelineDataStep] executed in 521ms
2021-08-04 19:02:02 [main] ERROR org.springframework.batch.core.job.AbstractJob - Encountered fatal error executing job
org.springframework.batch.core.JobExecutionException: Flow execution ended unexpectedly
    at org.springframework.batch.core.job.flow.FlowJob.doExecute(FlowJob.java:143)
    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.$Proxy41.run(Unknown Source)
    at org.mskcc.cmo.ks.redcap.RedcapPipeline.launchJob(RedcapPipeline.java:213)
    at org.mskcc.cmo.ks.redcap.RedcapPipeline.main(RedcapPipeline.java:390)
Caused by: org.springframework.batch.core.job.flow.FlowExecutionException: Ended flow=redcapRawExportJob at state=redcapRawExportJob.exportRawTimelineDataStep with exception
    at org.springframework.batch.core.job.flow.support.SimpleFlow.resume(SimpleFlow.java:178)
    at org.springframework.batch.core.job.flow.support.SimpleFlow.start(SimpleFlow.java:144)
    at org.springframework.batch.core.job.flow.FlowJob.doExecute(FlowJob.java:137)
    ... 17 more
Caused by: java.lang.IllegalArgumentException: Unable to deserialize the execution context
    at org.springframework.batch.core.repository.dao.JdbcExecutionContextDao$ExecutionContextRowMapper.mapRow(JdbcExecutionContextDao.java:328)
    at org.springframework.batch.core.repository.dao.JdbcExecutionContextDao$ExecutionContextRowMapper.mapRow(JdbcExecutionContextDao.java:312)
    at org.springframework.jdbc.core.RowMapperResultSetExtractor.extractData(RowMapperResultSetExtractor.java:94)
    at org.springframework.jdbc.core.RowMapperResultSetExtractor.extractData(RowMapperResultSetExtractor.java:61)
    at org.springframework.jdbc.core.JdbcTemplate$1.doInPreparedStatement(JdbcTemplate.java:679)
    at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:617)
    at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:669)
    at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:700)
    at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:712)
    at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:768)
    at org.springframework.batch.core.repository.dao.JdbcExecutionContextDao.getExecutionContext(JdbcExecutionContextDao.java:129)
    at org.springframework.batch.core.repository.support.SimpleJobRepository.getLastStepExecution(SimpleJobRepository.java:224)
    at sun.reflect.GeneratedMethodAccessor73.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
    at com.sun.proxy.$Proxy37.getLastStepExecution(Unknown Source)
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$PassthruAdvice.invoke(SimpleBatchConfiguration.java:127)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
    at com.sun.proxy.$Proxy37.getLastStepExecution(Unknown Source)
    at org.springframework.batch.core.job.SimpleStepHandler.handleStep(SimpleStepHandler.java:115)
    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)
    ... 19 more
Caused by: com.fasterxml.jackson.databind.JsonMappingException: The class with java.util.Arrays$ArrayList and name of java.util.Arrays$ArrayList is not trusted. If you believe this class is safe to deserialize, please provide an explicit mapping using Jackson annotations or a custom ObjectMapper. If the serialization is only done by a trusted source, you can also enable default typing. (through reference chain: java.util.HashMap["standardTimelineDataFields"])
    at com.fasterxml.jackson.databind.JsonMappingException.wrapWithPath(JsonMappingException.java:397)
    at com.fasterxml.jackson.databind.JsonMappingException.wrapWithPath(JsonMappingException.java:356)
    at com.fasterxml.jackson.databind.deser.std.ContainerDeserializerBase.wrapAndThrow(ContainerDeserializerBase.java:181)
    at com.fasterxml.jackson.databind.deser.std.MapDeserializer._readAndBindStringKeyMap(MapDeserializer.java:552)
    at com.fasterxml.jackson.databind.deser.std.MapDeserializer.deserialize(MapDeserializer.java:377)
    at com.fasterxml.jackson.databind.deser.std.MapDeserializer.deserialize(MapDeserializer.java:29)
    at com.fasterxml.jackson.databind.jsontype.impl.AsPropertyTypeDeserializer._deserializeTypedForId(AsPropertyTypeDeserializer.java:132)
    at com.fasterxml.jackson.databind.jsontype.impl.AsPropertyTypeDeserializer.deserializeTypedFromObject(AsPropertyTypeDeserializer.java:99)
    at com.fasterxml.jackson.databind.deser.std.MapDeserializer.deserializeWithType(MapDeserializer.java:413)
    at com.fasterxml.jackson.databind.deser.impl.TypeWrappedDeserializer.deserialize(TypeWrappedDeserializer.java:68)
    at com.fasterxml.jackson.databind.ObjectMapper._readMapAndClose(ObjectMapper.java:4524)
    at com.fasterxml.jackson.databind.ObjectMapper.readValue(ObjectMapper.java:3511)
    at org.springframework.batch.core.repository.dao.Jackson2ExecutionContextStringSerializer.deserialize(Jackson2ExecutionContextStringSerializer.java:123)
    at org.springframework.batch.core.repository.dao.Jackson2ExecutionContextStringSerializer.deserialize(Jackson2ExecutionContextStringSerializer.java:102)
    at org.springframework.batch.core.repository.dao.JdbcExecutionContextDao$ExecutionContextRowMapper.mapRow(JdbcExecutionContextDao.java:325)
    ... 55 more
Caused by: java.lang.IllegalArgumentException: The class with java.util.Arrays$ArrayList and name of java.util.Arrays$ArrayList is not trusted. If you believe this class is safe to deserialize, please provide an explicit mapping using Jackson annotations or a custom ObjectMapper. If the serialization is only done by a trusted source, you can also enable default typing.
    at org.springframework.batch.core.repository.dao.Jackson2ExecutionContextStringSerializer$TrustedTypeIdResolver.typeFromId(Jackson2ExecutionContextStringSerializer.java:329)
    at com.fasterxml.jackson.databind.jsontype.impl.TypeDeserializerBase._findDeserializer(TypeDeserializerBase.java:154)
    at com.fasterxml.jackson.databind.jsontype.impl.AsArrayTypeDeserializer._deserialize(AsArrayTypeDeserializer.java:97)
    at com.fasterxml.jackson.databind.jsontype.impl.AsArrayTypeDeserializer.deserializeTypedFromArray(AsArrayTypeDeserializer.java:53)
    at com.fasterxml.jackson.databind.jsontype.impl.AsPropertyTypeDeserializer.deserializeTypedFromAny(AsPropertyTypeDeserializer.java:193)
    at com.fasterxml.jackson.databind.deser.std.UntypedObjectDeserializer$Vanilla.deserializeWithType(UntypedObjectDeserializer.java:710)
    at com.fasterxml.jackson.databind.deser.std.MapDeserializer._readAndBindStringKeyMap(MapDeserializer.java:542)
    ... 66 more
2021-08-04 19:02:02 [main] INFO  org.springframework.batch.core.launch.support.SimpleJobLauncher - Job: [FlowJob: [name=redcapRawExportJob]] completed with the following parameters: [{stableId=mskimpact, directory=/data/portal-cron/cbio-portal-data/redcap-snapshot/mskimpact, rawData=true}] and the following status: [FAILED] in 1m55s62ms
2021-08-04 19:02:02 [main] ERROR org.mskcc.cmo.ks.redcap.RedcapPipeline - RedcapPipeline job failed with exit status: exitCode=FAILED;exitDescription=org.springframework.batch.core.JobExecutionException: Flow execution ended unexpectedly
    at org.springframework.batch.core.job.flow.FlowJob.doExecute(FlowJob.java:143)
    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.$Proxy41.run(Unknown Source)
    at org.mskcc.cmo.ks.redcap.RedcapPipeline.launchJob(RedcapPipeline.java:213)
    at org.mskcc.cmo.ks.redcap.RedcapPipeline.main(RedcapPipeline.java:390)
Caused by: org.springframework.batch.core.job.flow.FlowExecutionException: Ended flow=redcapRawExportJob at state=redcapRawExportJob.exportRawTimelineDataStep with exception
    at org.springframework.batch.core.job.flow.support.SimpleFlow.resume(SimpleFlow.java:178)
    at org.springframework.batch.core.job.flow.support.SimpleFlow.start(SimpleFlow.java:144)
    at org.springframework.batch.core.job.flow.FlowJob.doExecute(FlowJob.java:137)
    ... 17 more
Caused by: java.lang.IllegalArgumentException: Unable to deserialize the execution context
    at org.springframework.batch.core.repository.dao.JdbcExecutionContextDao$ExecutionContextRowMapper.mapRow(JdbcExecutionContextDao.java:328)
    at org.springframework.batch.core.repository.dao.JdbcExecutionContextDao$ExecutionContextRowMapper.mapRow(JdbcExecutionContextDao.java:312)
    at org.springframework.jdbc.core.RowMapperResultSetExtractor.extractData(RowMapperResultSetExtractor.java:94)
    at org.springframework.jdbc.core.RowMapperResultSetExtractor.extractData(RowMapperResultSetExtractor.java:61)
    at org.springframework.jdbc.core.JdbcTemplate$1.doInPreparedStatement(JdbcTemplate.java:679)
    at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:617)
    at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:669)
    at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:700)
    at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:712)
    at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:768)
    at org.springframework.batch.core.repository.dao.JdbcExecutionContextDao.getExecutionContext(JdbcExecutionContextDao.java:129)
    at org.springframework.batch.core.repository.support.SimpleJobRepository.getLastStepExecution(SimpleJobRepository.java:224)
    at sun.reflect.GeneratedMethodAccessor73.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
    at com.sun.proxy.$Proxy37.getLastStepExecution(Unknown Source)
    at sun.reflect.GeneratedMethodAccessor73.invoke(Unknown Source)
    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$PassthruAdvice.invoke(SimpleBatchConfiguration.java:127)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
    at com.sun.proxy.$Proxy37.getLastStepExecution(Unknown Source)
    at org.springframework.batch.core.job.SimpleStepHandler.handleStep(SimpleStepHandler.java:115)
    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)
    ... 19 more
Caused by: com.fasterxml.jackson.databind.JsonMappingException: The class with java.util.Arrays$ArrayList and name of java.util.Arrays$ArrayList is not trusted. If you believe this class is safe to deserialize, please provide an explicit mapping using Jackson annotations or a custom ObjectMapper. If the serialization is only done by a trusted source, you can also enable default typing. (through reference chain: java.util.HashMap["standardTimelineDataFields"])
    at com.fasterxml.jackson.databind.JsonMappingException.wrapWithPath(JsonMappingException.java:397)
    at com.fasterxml.jackson.databind.JsonMappingException.wrapWithPath(JsonMappingException.java:356)
    at com.fasterxml.jackson.databind.deser.std.ContainerDeserializerBase.wrapAndThrow(ContainerDeserializerBase.java:181)
    at com.fasterxml.jackson.databind.deser.std.MapDeserializer._readAndBindStringKeyMap(MapDeserializer.java:552)
    at com.fasterxml.jackson.databind.deser.std.MapDeserializer.deserialize(MapDeserializer.java:377)
    at com.fasterxml.jackson.databind.deser.std.MapDeserializer.deserialize(MapDeserializer.java:29)
    at com.fasterxml.jackson.databind.jsontype.impl.AsPropertyTypeDeserializer._deserializeTypedForId(AsPropertyTypeDeserializer.java:132)
    at com.fasterxml.jackson.databind.jsontype.impl.AsPropertyTypeDeserializer.deserializeTypedFromObject(AsPropertyTypeDeserializer.java:99)
    at com.fasterxml.jackson.databind.deser.std.MapDeserializer.deserializeWithType(MapDeserializer.java:413)
    at com.fasterxml.jackson.databind.deser.impl.TypeWrappedDeserializer.deserialize(TypeWrappedDeserializer.java:68)
    at com.fasterxml.jackson.databind.ObjectMapper._readMapAndClose(ObjectMapper.java:4524)
    at com.fasterxml.jackson.databind.ObjectMapper.readValue(ObjectMapper.java:3511)
    at org.springframework.batch.core.repository.dao.Jackson2ExecutionContextStringSerializer.deserialize(Jackson2ExecutionContextStringSerializer.java:123)
    at org.springframework.batch.core.repository.dao.Jackson2ExecutionContextStringSerializer.deserialize(Jackson2ExecutionContextStringSerializer.java:102)
    at org.springframework.batch.core.repository.dao.JdbcExecutionContextDao$ExecutionContextRowMapper.mapRow(JdbcExecutionContextDao.java:325)
    ... 55 more
Caused by: java.lang.IllegalArgumentException: The class with java.util.Arrays$ArrayList and name of java.util.Arrays$ArrayList is not trusted. If you believe this class is safe to deserialize, please provide an explicit mapping using Jackson annotations or a custom ObjectMapper. If the serialization is only done by a trusted source, you can also enable default typing.
    at org.springframework.batch.core.repository.dao.Jackson2ExecutionContextStringSerializer$TrustedTypeIdResolver.typeFromId(Jackson2ExecutionContextStringSerializer.java:329)
    at com.fasterxml.jackson.databind.jsontype.impl.TypeDeserializerBase._findDeserializer(TypeDeserializerBase.java:154)
    at com.fasterxml.jackson.databind.jsontype.impl.AsArrayTypeDeserializer._deserialize(AsArrayTypeDeserializer.java:97)
    at com.fasterxml.jackson.databind.jsontype.impl.AsArrayTypeDeserializer.deserializeTypedFromArray(AsArrayTypeDeserializer.java:53)
    at com.fasterxml.jackson.databind.jsontype.impl.AsPropertyTypeDeserializer.deserializeTypedFromAny(AsPropertyTypeDeserializer.java:193)
    at com.fasterxml.jackson.databind.deser.std.UntypedObjectDeserializer$Vanilla.deserializeWithType(UntypedObjectDeserializer.java:710)
    at com.fasterxml.jackson.databind.deser.std.MapDeserializer._readAndBindStringKeyMap(MapDeserializer.java:542)
    ... 66 more
ao508 commented 3 years ago

Also need to investigate whether the DDP fetcher is failing for a similar reason as REDCap ^