[
https://issues.apache.org/jira/browse/SPARK-24032?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16445514#comment-16445514
]
Cristina Luengo commented on SPARK-24032:
-----------------------------------------
Ok thanks!! Sorry, I didn't really know what to assign it!
The full stack trace is:
Traceback (most recent call last):
File "/home/cluengo/Documents/Projects/vcfLoader/python/rdconnect/main.py",
line 151, in <module>
main(hc,sqlContext)
File "/home/cluengo/Documents/Projects/vcfLoader/python/rdconnect/main.py",
line 141, in main
variantsRN.write.format("org.elasticsearch.spark.sql").options(**es_conf).option("es.nodes",configuration["elasticsearch"]["host"]).option("es.port",configuration["elasticsearch"]["port"]
).save(configuration["elasticsearch"]["index_name"]+"/"+configuration["version"],mode='append')
File "/home/cluengo/spark/python/lib/pyspark.zip/pyspark/sql/readwriter.py",
line 595, in save
File
"/home/cluengo/spark/python/lib/py4j-0.10.4-src.zip/py4j/java_gateway.py", line
1133, in __call__
File "/home/cluengo/spark/python/lib/pyspark.zip/pyspark/sql/utils.py", line
63, in deco
File "/home/cluengo/spark/python/lib/py4j-0.10.4-src.zip/py4j/protocol.py",
line 319, in get_return_value
py4j.protocol.Py4JJavaError: An error occurred while calling o181.save.
: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in
stage 41.0 failed 1 times, most recent failure: Lost task 0.0 in stage 41.0
(TID 200, localhost, executor driver): java.lang.ClassCastException:
scala.collection.mutable.WrappedArray$ofRef cannot be cast to scala.Tuple2
at
org.elasticsearch.spark.sql.DataFrameValueWriter.write(DataFrameValueWriter.scala:53)
at
org.elasticsearch.hadoop.serialization.bulk.AbstractBulkFactory$FieldWriter.doWrite(AbstractBulkFactory.java:152)
at
org.elasticsearch.hadoop.serialization.bulk.AbstractBulkFactory$FieldWriter.write(AbstractBulkFactory.java:118)
at
org.elasticsearch.hadoop.serialization.bulk.TemplatedBulk.writeTemplate(TemplatedBulk.java:80)
at
org.elasticsearch.hadoop.serialization.bulk.TemplatedBulk.write(TemplatedBulk.java:56)
at
org.elasticsearch.hadoop.rest.RestRepository.writeToIndex(RestRepository.java:168)
at org.elasticsearch.spark.rdd.EsRDDWriter.write(EsRDDWriter.scala:67)
at
org.elasticsearch.spark.sql.EsSparkSQL$$anonfun$saveToEs$1.apply(EsSparkSQL.scala:101)
at
org.elasticsearch.spark.sql.EsSparkSQL$$anonfun$saveToEs$1.apply(EsSparkSQL.scala:101)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
at org.apache.spark.scheduler.Task.run(Task.scala:108)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Driver stacktrace:
at
org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1499)
at
org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1487)
at
org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1486)
at
scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
at
org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1486)
at
org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:814)
at
org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:814)
at scala.Option.foreach(Option.scala:257)
at
org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:814)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1714)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1669)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1658)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:630)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2022)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2043)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2075)
at org.elasticsearch.spark.sql.EsSparkSQL$.saveToEs(EsSparkSQL.scala:101)
at
org.elasticsearch.spark.sql.ElasticsearchRelation.insert(DefaultSource.scala:610)
at
org.elasticsearch.spark.sql.DefaultSource.createRelation(DefaultSource.scala:103)
at
org.apache.spark.sql.execution.datasources.DataSource.write(DataSource.scala:472)
at
org.apache.spark.sql.execution.datasources.SaveIntoDataSourceCommand.run(SaveIntoDataSourceCommand.scala:48)
at
org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult$lzycompute(commands.scala:58)
at
org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult(commands.scala:56)
at
org.apache.spark.sql.execution.command.ExecutedCommandExec.doExecute(commands.scala:74)
at
org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:117)
at
org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:117)
at
org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:138)
at
org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at
org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:135)
at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:116)
at
org.apache.spark.sql.execution.QueryExecution.toRdd$lzycompute(QueryExecution.scala:92)
at
org.apache.spark.sql.execution.QueryExecution.toRdd(QueryExecution.scala:92)
at
org.apache.spark.sql.DataFrameWriter.runCommand(DataFrameWriter.scala:610)
at org.apache.spark.sql.DataFrameWriter.save(DataFrameWriter.scala:233)
at org.apache.spark.sql.DataFrameWriter.save(DataFrameWriter.scala:217)
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 py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
at py4j.Gateway.invoke(Gateway.java:280)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:214)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.ClassCastException:
scala.collection.mutable.WrappedArray$ofRef cannot be cast to scala.Tuple2
at
org.elasticsearch.spark.sql.DataFrameValueWriter.write(DataFrameValueWriter.scala:53)
at
org.elasticsearch.hadoop.serialization.bulk.AbstractBulkFactory$FieldWriter.doWrite(AbstractBulkFactory.java:152)
at
org.elasticsearch.hadoop.serialization.bulk.AbstractBulkFactory$FieldWriter.write(AbstractBulkFactory.java:118)
at
org.elasticsearch.hadoop.serialization.bulk.TemplatedBulk.writeTemplate(TemplatedBulk.java:80)
at
org.elasticsearch.hadoop.serialization.bulk.TemplatedBulk.write(TemplatedBulk.java:56)
at
org.elasticsearch.hadoop.rest.RestRepository.writeToIndex(RestRepository.java:168)
at org.elasticsearch.spark.rdd.EsRDDWriter.write(EsRDDWriter.scala:67)
at
org.elasticsearch.spark.sql.EsSparkSQL$$anonfun$saveToEs$1.apply(EsSparkSQL.scala:101)
at
org.elasticsearch.spark.sql.EsSparkSQL$$anonfun$saveToEs$1.apply(EsSparkSQL.scala:101)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
at org.apache.spark.scheduler.Task.run(Task.scala:108)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
... 1 more
Thanks again!
> ElasticSearch update fails on nested field
> ------------------------------------------
>
> Key: SPARK-24032
> URL: https://issues.apache.org/jira/browse/SPARK-24032
> Project: Spark
> Issue Type: Bug
> Components: Spark Core
> Affects Versions: 2.2.0
> Reporter: Cristina Luengo
> Priority: Major
>
> I'm trying to update a nested field on ElasticSearch using a scripted update.
> The code I'm using is:
> update_params = "new_samples: samples"
> update_script = "ctx._source.samples += new_samples"
> es_conf =
> { "es.mapping.id": "id", "es.mapping.exclude": "id", "es.write.operation":
> "upsert", "es.update.script.params": update_params,
> "es.update.script.inline": update_script }
> result.write.format("org.elasticsearch.spark.sql").options(**es_conf).option("es.nodes",configuration["elasticsearch"]["host"]).option("es.port",configuration["elasticsearch"]["port"]
>
> ).save(configuration["elasticsearch"]["index_name"]+"/"+configuration["version"],mode='append')
> And the schema of the field is:
> |– samples: array (nullable = true)|
> | |– element: struct (containsNull = true)|
> | | |– gq: integer (nullable = true)|
> | | |– dp: integer (nullable = true)|
> | | |– gt: string (nullable = true)|
> | | |– adBug: array (nullable = true)|
> | | | |– element: integer (containsNull = true)|
> | | |– ad: double (nullable = true)|
> | | |– sample: string (nullable = true)|
> And I get the following error:
> py4j.protocol.Py4JJavaError: An error occurred while calling o83.save.
> : org.apache.spark.SparkException: Job aborted due to stage failure: Task 0
> in stage 1.0 failed 1 times, most recent failure: Lost task 0.0 in stage 1.0
> (TID 1, localhost, executor driver): java.lang.ClassCastException:
> scala.collection.mutable.WrappedArray$ofRef cannot be cast to scala.Tuple2
> Am I doing something wrong or is this a bug? Thanks.
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