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  1. Apache Drill
  2. DRILL-4855

Querying MongoDB collection with nested data fails

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    Details

    • Type: Bug
    • Status: Resolved
    • Priority: Critical
    • Resolution: Invalid
    • Affects Version/s: 1.6.0, 1.7.0
    • Fix Version/s: None
    • Component/s: Storage - MongoDB
    • Labels:
      None
    • Environment:

      Centos7 and Ubuntu 16.04

      Description

      To reproduce:

      1. Create a json file called small.json with the below line:

      {"_id":

      {"$oid":"56a784b76952647b7b51c562"}

      ,"provenance":{"image":

      {"case_id":"TCGA-TS2","subject_id":"TCGA"}

      }}

      2. Create a Mongo DB with the small.json as below:

      mongoimport --db users --collection contacts --type small.json

      3. Create a Mongo Query involving the nested data to confirm everything is fine.

      use users;
      db.contacts.find(

      { "provenance.image.case_id": "TCGA-TS2"}

      );

      This returns:

      { "_id" : ObjectId("56a784b76952647b7b51c562"), "provenance" : { "image" :

      { "case_id" : "TCGA-TS2", "subject_id" : "TCGA" }

      } }

      4. Create a Drill query for the same:

      SELECT camic.provenance.image.case_id caseid
      FROM mongo.users.`contacts` camic
      WHERE caseid = 'TCGA-TS2';

      The above query fails with the below error message.

      Error: SYSTEM ERROR: NumberFormatException: TCGA-TS2

      Fragment 0:0

      [Error Id: 142d9f37-fe13-4757-8009-e713d55bc1d8 on llovizna:31010] (state=,code=0)

      "tail -f sqlline.log" indicates the below:

      2016-08-18 16:33:32,097 [2849e462-ade5-621f-5e4b-59e93c07ff11:foreman] INFO o.a.drill.exec.work.foreman.Foreman - Query text for query id 2849e462-ade5-621f-5e4b-59e93c07ff11: SELECT camic.provenance.image.case_id caseid
      FROM mongo.users.`contacts` camic
      WHERE caseid = 'TCGA-TS2'
      2016-08-18 16:33:33,369 [2849e462-ade5-621f-5e4b-59e93c07ff11:frag:0:0] INFO o.a.d.e.s.m.MongoScanBatchCreator - Number of record readers initialized : 1
      2016-08-18 16:33:33,371 [2849e462-ade5-621f-5e4b-59e93c07ff11:frag:0:0] INFO o.a.d.e.w.fragment.FragmentExecutor - 2849e462-ade5-621f-5e4b-59e93c07ff11:0:0: State change requested AWAITING_ALLOCATION --> RUNNING
      2016-08-18 16:33:33,371 [2849e462-ade5-621f-5e4b-59e93c07ff11:frag:0:0] INFO o.a.d.e.w.f.FragmentStatusReporter - 2849e462-ade5-621f-5e4b-59e93c07ff11:0:0: State to report: RUNNING
      2016-08-18 16:33:33,371 [2849e462-ade5-621f-5e4b-59e93c07ff11:frag:0:0] INFO o.a.d.e.s.mongo.MongoRecordReader - Filters Applied : Document{{}}
      2016-08-18 16:33:33,371 [2849e462-ade5-621f-5e4b-59e93c07ff11:frag:0:0] INFO o.a.d.e.s.mongo.MongoRecordReader - Fields Selected :Document{{_id=0, caseid=1, provenance=1}}
      2016-08-18 16:33:33,372 [2849e462-ade5-621f-5e4b-59e93c07ff11:frag:0:0] WARN o.a.d.e.e.ExpressionTreeMaterializer - Unable to find value vector of path `caseid`, returning null instance.
      2016-08-18 16:33:33,375 [2849e462-ade5-621f-5e4b-59e93c07ff11:frag:0:0] INFO o.a.d.e.w.fragment.FragmentExecutor - 2849e462-ade5-621f-5e4b-59e93c07ff11:0:0: State change requested RUNNING --> FAILED
      2016-08-18 16:33:33,375 [2849e462-ade5-621f-5e4b-59e93c07ff11:frag:0:0] INFO o.a.d.e.w.fragment.FragmentExecutor - 2849e462-ade5-621f-5e4b-59e93c07ff11:0:0: State change requested FAILED --> FINISHED
      2016-08-18 16:33:33,376 [2849e462-ade5-621f-5e4b-59e93c07ff11:frag:0:0] ERROR o.a.d.e.w.fragment.FragmentExecutor - SYSTEM ERROR: NumberFormatException: TCGA-TS2

      Fragment 0:0

      [Error Id: efb49b38-0515-4b20-9d24-052944f04a73 on llovizna:31010]
      org.apache.drill.common.exceptions.UserException: SYSTEM ERROR: NumberFormatException: TCGA-TS2

      Fragment 0:0

      [Error Id: efb49b38-0515-4b20-9d24-052944f04a73 on llovizna:31010]
      at org.apache.drill.common.exceptions.UserException$Builder.build(UserException.java:543) ~[drill-common-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.work.fragment.FragmentExecutor.sendFinalState(FragmentExecutor.java:318) [drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.work.fragment.FragmentExecutor.cleanup(FragmentExecutor.java:185) [drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.work.fragment.FragmentExecutor.run(FragmentExecutor.java:287) [drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.common.SelfCleaningRunnable.run(SelfCleaningRunnable.java:38) [drill-common-1.6.0.jar:1.6.0]
      at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0]
      at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0]
      at java.lang.Thread.run(Thread.java:744) [na:1.8.0]
      Caused by: java.lang.NumberFormatException: TCGA-TS2
      at org.apache.drill.exec.expr.fn.impl.StringFunctionHelpers.nfeI(StringFunctionHelpers.java:95) ~[drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.expr.fn.impl.StringFunctionHelpers.varTypesToInt(StringFunctionHelpers.java:120) ~[drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.test.generated.FiltererGen20.doSetup(FilterTemplate2.java:45) ~[na:na]
      at org.apache.drill.exec.test.generated.FiltererGen20.setup(FilterTemplate2.java:54) ~[na:na]
      at org.apache.drill.exec.physical.impl.filter.FilterRecordBatch.generateSV2Filterer(FilterRecordBatch.java:197) ~[drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.physical.impl.filter.FilterRecordBatch.setupNewSchema(FilterRecordBatch.java:109) ~[drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.record.AbstractSingleRecordBatch.innerNext(AbstractSingleRecordBatch.java:78) ~[drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.record.AbstractRecordBatch.next(AbstractRecordBatch.java:162) ~[drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.record.AbstractRecordBatch.next(AbstractRecordBatch.java:119) ~[drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.record.AbstractRecordBatch.next(AbstractRecordBatch.java:109) ~[drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.record.AbstractSingleRecordBatch.innerNext(AbstractSingleRecordBatch.java:51) ~[drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.physical.impl.svremover.RemovingRecordBatch.innerNext(RemovingRecordBatch.java:94) ~[drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.record.AbstractRecordBatch.next(AbstractRecordBatch.java:162) ~[drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.record.AbstractRecordBatch.next(AbstractRecordBatch.java:119) ~[drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.record.AbstractRecordBatch.next(AbstractRecordBatch.java:109) ~[drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.record.AbstractSingleRecordBatch.innerNext(AbstractSingleRecordBatch.java:51) ~[drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.physical.impl.project.ProjectRecordBatch.innerNext(ProjectRecordBatch.java:129) ~[drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.record.AbstractRecordBatch.next(AbstractRecordBatch.java:162) ~[drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.physical.impl.BaseRootExec.next(BaseRootExec.java:104) ~[drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.physical.impl.ScreenCreator$ScreenRoot.innerNext(ScreenCreator.java:81) ~[drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.physical.impl.BaseRootExec.next(BaseRootExec.java:94) ~[drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.work.fragment.FragmentExecutor$1.run(FragmentExecutor.java:257) ~[drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.work.fragment.FragmentExecutor$1.run(FragmentExecutor.java:251) ~[drill-java-exec-1.6.0.jar:1.6.0]
      at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0]
      at javax.security.auth.Subject.doAs(Subject.java:422) ~[na:1.8.0]
      at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1657) ~[hadoop-common-2.7.1.jar:na]
      at org.apache.drill.exec.work.fragment.FragmentExecutor.run(FragmentExecutor.java:251) [drill-java-exec-1.6.0.jar:1.6.0]
      ... 4 common frames omitted
      2016-08-18 16:33:33,426 [CONTROL-rpc-event-queue] WARN o.a.drill.exec.work.foreman.Foreman - Dropping request to move to COMPLETED state as query is already at FAILED state (which is terminal).
      2016-08-18 16:33:33,426 [CONTROL-rpc-event-queue] WARN o.a.d.e.w.b.ControlMessageHandler - Dropping request to cancel fragment. 2849e462-ade5-621f-5e4b-59e93c07ff11:0:0 does not exist.
      2016-08-18 16:33:33,427 [USER-rpc-event-queue] INFO o.a.d.j.i.DrillResultSetImpl$ResultsListener - 14 Query failed:
      org.apache.drill.common.exceptions.UserRemoteException: SYSTEM ERROR: NumberFormatException: TCGA-TS2

      Fragment 0:0

      [Error Id: efb49b38-0515-4b20-9d24-052944f04a73 on llovizna:31010]
      at org.apache.drill.exec.rpc.user.QueryResultHandler.resultArrived(QueryResultHandler.java:119) [drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.rpc.user.UserClient.handleReponse(UserClient.java:113) [drill-java-exec-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.rpc.BasicClientWithConnection.handle(BasicClientWithConnection.java:46) [drill-rpc-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.rpc.BasicClientWithConnection.handle(BasicClientWithConnection.java:31) [drill-rpc-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.rpc.RpcBus.handle(RpcBus.java:67) [drill-rpc-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.rpc.RpcBus$RequestEvent.run(RpcBus.java:374) [drill-rpc-1.6.0.jar:1.6.0]
      at org.apache.drill.common.SerializedExecutor$RunnableProcessor.run(SerializedExecutor.java:89) [drill-rpc-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.rpc.RpcBus$SameExecutor.execute(RpcBus.java:252) [drill-rpc-1.6.0.jar:1.6.0]
      at org.apache.drill.common.SerializedExecutor.execute(SerializedExecutor.java:123) [drill-rpc-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.rpc.RpcBus$InboundHandler.decode(RpcBus.java:285) [drill-rpc-1.6.0.jar:1.6.0]
      at org.apache.drill.exec.rpc.RpcBus$InboundHandler.decode(RpcBus.java:257) [drill-rpc-1.6.0.jar:1.6.0]
      at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:89) [netty-codec-4.0.27.Final.jar:4.0.27.Final]
      at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:339) [netty-transport-4.0.27.Final.jar:4.0.27.Final]
      at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:324) [netty-transport-4.0.27.Final.jar:4.0.27.Final]
      at io.netty.handler.timeout.IdleStateHandler.channelRead(IdleStateHandler.java:254) [netty-handler-4.0.27.Final.jar:4.0.27.Final]
      at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:339) [netty-transport-4.0.27.Final.jar:4.0.27.Final]
      at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:324) [netty-transport-4.0.27.Final.jar:4.0.27.Final]
      at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:103) [netty-codec-4.0.27.Final.jar:4.0.27.Final]
      at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:339) [netty-transport-4.0.27.Final.jar:4.0.27.Final]
      at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:324) [netty-transport-4.0.27.Final.jar:4.0.27.Final]
      at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:242) [netty-codec-4.0.27.Final.jar:4.0.27.Final]
      at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:339) [netty-transport-4.0.27.Final.jar:4.0.27.Final]
      at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:324) [netty-transport-4.0.27.Final.jar:4.0.27.Final]
      at io.netty.channel.ChannelInboundHandlerAdapter.channelRead(ChannelInboundHandlerAdapter.java:86) [netty-transport-4.0.27.Final.jar:4.0.27.Final]
      at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:339) [netty-transport-4.0.27.Final.jar:4.0.27.Final]
      at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:324) [netty-transport-4.0.27.Final.jar:4.0.27.Final]
      at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:847) [netty-transport-4.0.27.Final.jar:4.0.27.Final]
      at io.netty.channel.epoll.AbstractEpollStreamChannel$EpollStreamUnsafe.epollInReady(AbstractEpollStreamChannel.java:618) [netty-transport-native-epoll-4.0.27.Final-linux-x86_64.jar:na]
      at io.netty.channel.epoll.EpollEventLoop.processReady(EpollEventLoop.java:329) [netty-transport-native-epoll-4.0.27.Final-linux-x86_64.jar:na]
      at io.netty.channel.epoll.EpollEventLoop.run(EpollEventLoop.java:250) [netty-transport-native-epoll-4.0.27.Final-linux-x86_64.jar:na]
      at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:111) [netty-common-4.0.27.Final.jar:4.0.27.Final]
      at java.lang.Thread.run(Thread.java:744) [na:1.8.0]

      5. Please note the below returns the correct output:

      SELECT camic.provenance.image.case_id caseid
      FROM mongo.users.`contacts` camic;

      -----------

      caseid

      -----------

      TCGA-TS2

      -----------
      1 row selected (1,135 seconds)

      So the issue is with the WHERE clause:
      WHERE caseid = 'TCGA-TS2"';

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            • Assignee:
              Unassigned
              Reporter:
              pradeeban Kathiravelu Pradeeban
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              Dates

              • Created:
                Updated:
                Resolved: