Kathiravelu Pradeeban created DRILL-4855:
--------------------------------------------
Summary: Querying MongoDB collection with nested data fails
Key: DRILL-4855
URL: https://issues.apache.org/jira/browse/DRILL-4855
Project: Apache Drill
Issue Type: Bug
Components: Storage - MongoDB
Affects Versions: 1.6.0, 1.7.0
Environment: Centos7 and Ubuntu 16.04
Reporter: Kathiravelu Pradeeban
Priority: Critical
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"});
{ "_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: 1059e3ec-6241-4b4c-a2de-33c4a44c64fe on llovizna:31010]
(state=,code=0)
"tail -f sqlline.log" indicates the below:
2016-08-18 16:10:05,684 [2849e9e2-1bef-6389-2f2c-9f8d1af595fe:foreman] INFO
o.a.drill.exec.work.foreman.Foreman - Query text for query id
2849e9e2-1bef-6389-2f2c-9f8d1af595fe: SELECT camic.provenance.image.case_id
caseid
FROM mongo.users.`contacts` camic
WHERE caseid = 'TCGA-TS2"'
2016-08-18 16:10:06,810 [2849e9e2-1bef-6389-2f2c-9f8d1af595fe:frag:0:0] INFO
o.a.d.e.s.m.MongoScanBatchCreator - Number of record readers initialized : 1
2016-08-18 16:10:06,810 [2849e9e2-1bef-6389-2f2c-9f8d1af595fe:frag:0:0] INFO
o.a.d.e.w.fragment.FragmentExecutor - 2849e9e2-1bef-6389-2f2c-9f8d1af595fe:0:0:
State change requested AWAITING_ALLOCATION --> RUNNING
2016-08-18 16:10:06,811 [2849e9e2-1bef-6389-2f2c-9f8d1af595fe:frag:0:0] INFO
o.a.d.e.w.f.FragmentStatusReporter - 2849e9e2-1bef-6389-2f2c-9f8d1af595fe:0:0:
State to report: RUNNING
2016-08-18 16:10:06,811 [2849e9e2-1bef-6389-2f2c-9f8d1af595fe:frag:0:0] INFO
o.a.d.e.s.mongo.MongoRecordReader - Filters Applied : Document{{}}
2016-08-18 16:10:06,811 [2849e9e2-1bef-6389-2f2c-9f8d1af595fe:frag:0:0] INFO
o.a.d.e.s.mongo.MongoRecordReader - Fields Selected :Document{{_id=0, caseid=1,
provenance=1}}
2016-08-18 16:10:06,812 [2849e9e2-1bef-6389-2f2c-9f8d1af595fe:frag:0:0] WARN
o.a.d.e.e.ExpressionTreeMaterializer - Unable to find value vector of path
`caseid`, returning null instance.
2016-08-18 16:10:06,815 [2849e9e2-1bef-6389-2f2c-9f8d1af595fe:frag:0:0] INFO
o.a.d.e.w.fragment.FragmentExecutor - 2849e9e2-1bef-6389-2f2c-9f8d1af595fe:0:0:
State change requested RUNNING --> FAILED
2016-08-18 16:10:06,816 [2849e9e2-1bef-6389-2f2c-9f8d1af595fe:frag:0:0] INFO
o.a.d.e.w.fragment.FragmentExecutor - 2849e9e2-1bef-6389-2f2c-9f8d1af595fe:0:0:
State change requested FAILED --> FINISHED
2016-08-18 16:10:06,817 [2849e9e2-1bef-6389-2f2c-9f8d1af595fe:frag:0:0] ERROR
o.a.d.e.w.fragment.FragmentExecutor - SYSTEM ERROR: NumberFormatException:
TCGA-TS2"
Fragment 0:0
[Error Id: 1059e3ec-6241-4b4c-a2de-33c4a44c64fe on llovizna:31010]
org.apache.drill.common.exceptions.UserException: SYSTEM ERROR:
NumberFormatException: TCGA-TS2"
Fragment 0:0
[Error Id: 1059e3ec-6241-4b4c-a2de-33c4a44c64fe 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.FiltererGen13.doSetup(FilterTemplate2.java:45)
~[na:na]
at
org.apache.drill.exec.test.generated.FiltererGen13.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$1.run(FragmentExecutor.java:251)
~[drill-java-exec-1.6.0.jar:1.6.0]
at java.security.AccessController.doPrivileged(Native Method)
~[na:1.8.0]
at javax.security.auth.Subject.doAs(Subject.java:422) ~[na:1.8.0]
at
org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1657)
~[hadoop-common-2.7.1.jar:na]
at
org.apache.drill.exec.work.fragment.FragmentExecutor.run(FragmentExecutor.java:251)
[drill-java-exec-1.6.0.jar:1.6.0]
... 4 common frames omitted
2016-08-18 16:10:06,854 [CONTROL-rpc-event-queue] WARN
o.a.drill.exec.work.foreman.Foreman - Dropping request to move to COMPLETED
state as query is already at FAILED state (which is terminal).
2016-08-18 16:10:06,854 [CONTROL-rpc-event-queue] WARN
o.a.d.e.w.b.ControlMessageHandler - Dropping request to cancel fragment.
2849e9e2-1bef-6389-2f2c-9f8d1af595fe:0:0 does not exist.
2016-08-18 16:10:06,855 [USER-rpc-event-queue] INFO
o.a.d.j.i.DrillResultSetImpl$ResultsListener - [#9] Query failed:
org.apache.drill.common.exceptions.UserRemoteException: SYSTEM ERROR:
NumberFormatException: TCGA-TS2"
Fragment 0:0
[Error Id: 1059e3ec-6241-4b4c-a2de-33c4a44c64fe 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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