[
https://issues.apache.org/jira/browse/SPARK-20847?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16022004#comment-16022004
]
Pablo Alcaraz commented on SPARK-20847:
---------------------------------------
This is fixed by SPARK-14536 in Spark 2.1.1
However the patch does not fix multidimensional columns.
> Error reading NULL int[] element from postgres -- null pointer exception.
> -------------------------------------------------------------------------
>
> Key: SPARK-20847
> URL: https://issues.apache.org/jira/browse/SPARK-20847
> Project: Spark
> Issue Type: Bug
> Components: SQL
> Affects Versions: 2.1.0
> Reporter: Stuart Reynolds
>
> -- maybe fixed already?
> https://github.com/apache/spark/commit/f174cdc7478d0b81f9cfa896284a5ec4c6bb952d
> {code:python}
> def query_int_array():
> import pandas as pd
> from pyspark.sql import SQLContext
> user,password = ... , ....
> hostname = ....
> dbName = ...
> url = "jdbc:postgresql://{hostname}:5432/{dbName}".format(**locals())
> properties = {'user': user, 'password': password}
> sql_create = """DROP TABLE IF EXISTS public._df10;
> CREATE TABLE IF NOT EXISTS public._df10 (
> id integer,
> f_21 integer[]
> );
> INSERT INTO public._df10(id, f_21) VALUES
> (1, ARRAY[1,2]) --OK
> ,(2, ARRAY[3,NULL]) --OK
> ,(3, NULL) --FAIL *****<<<<< PROBLEM
> ;"""
> engine =
> sqlalchemy.create_engine('postgresql+psycopg2://{user}:{password}@{hostname}:5432/{dbName}'.format(**locals()))
> with engine.connect().execution_options(autocommit=True) as con:
> con.execute(sql_create)
> # Export postgres _df10 to spark as table df10
> sc = get_spark_context(master="local")
> sqlContext = SQLContext(sc)
> df10 = sqlContext.read.format("jdbc"). \
> option("url", url). \
> option("driver", "org.postgresql.Driver"). \
> option("useUnicode", "true"). \
> option("continueBatchOnError","true"). \
> option("useSSL", "false"). \
> option("user", user). \
> option("password", password). \
> option("dbtable", "_df10"). \
> load()
> df10.registerTempTable("df10")
> print "DF inferred from postgres:"
> df10.printSchema()
> df10.show()
> print "DF queried from postgres:"
> df10 = sqlContext.sql("select * from df10")
> df10.printSchema()
> df10.show()
> print df10.collect()
> {code}
> Explodes with:
> {noformat}
> DF inferred from postgres:
> root
> |-- id: integer (nullable = true)
> |-- f_21: array (nullable = true)
> | |-- element: integer (containsNull = true)
> 17/05/22 15:46:30 ERROR Executor: Exception in task 0.0 in stage 0.0 (TID 0)
> java.lang.NullPointerException
> at
> org.apache.spark.sql.execution.datasources.jdbc.JdbcUtils$$anonfun$org$apache$spark$sql$execution$datasources$jdbc$JdbcUtils$$makeGetter$13.apply(JdbcUtils.scala:427)
> at
> org.apache.spark.sql.execution.datasources.jdbc.JdbcUtils$$anonfun$org$apache$spark$sql$execution$datasources$jdbc$JdbcUtils$$makeGetter$13.apply(JdbcUtils.scala:425)
> at
> org.apache.spark.sql.execution.datasources.jdbc.JdbcUtils$$anon$1.getNext(JdbcUtils.scala:286)
> at
> org.apache.spark.sql.execution.datasources.jdbc.JdbcUtils$$anon$1.getNext(JdbcUtils.scala:268)
> at org.apache.spark.util.NextIterator.hasNext(NextIterator.scala:73)
> at
> org.apache.spark.util.CompletionIterator.hasNext(CompletionIterator.scala:32)
> at
> org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown
> Source)
> at
> org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
> at
> org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:377)
> at
> org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:231)
> at
> org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:225)
> at
> org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:826)
> at
> org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:826)
> at
> org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
> at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
> at org.apache.spark.scheduler.Task.run(Task.scala:99)
> at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:745)
> 17/05/22 15:46:30 WARN TaskSetManager: Lost task 0.0 in stage 0.0 (TID 0,
> localhost, executor driver): java.lang.NullPointerException
> at
> org.apache.spark.sql.execution.datasources.jdbc.JdbcUtils$$anonfun$org$apache$spark$sql$execution$datasources$jdbc$JdbcUtils$$makeGetter$13.apply(JdbcUtils.scala:427)
> at
> org.apache.spark.sql.execution.datasources.jdbc.JdbcUtils$$anonfun$org$apache$spark$sql$execution$datasources$jdbc$JdbcUtils$$makeGetter$13.apply(JdbcUtils.scala:425)
> at
> org.apache.spark.sql.execution.datasources.jdbc.JdbcUtils$$anon$1.getNext(JdbcUtils.scala:286)
> at
> org.apache.spark.sql.execution.datasources.jdbc.JdbcUtils$$anon$1.getNext(JdbcUtils.scala:268)
> at org.apache.spark.util.NextIterator.hasNext(NextIterator.scala:73)
> at
> org.apache.spark.util.CompletionIterator.hasNext(CompletionIterator.scala:32)
> at
> org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown
> Source)
> at
> org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
> at
> org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:377)
> at
> org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:231)
> at
> org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:225)
> at
> org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:826)
> at
> org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:826)
> at
> org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
> at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
> at org.apache.spark.scheduler.Task.run(Task.scala:99)
> at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:745)
> 17/05/22 15:46:30 ERROR TaskSetManager: Task 0 in stage 0.0 failed 1 times;
> aborting job
> Traceback (most recent call last):
> File
> "/home/builder/.IdeaIC2017.1/config/plugins/python-ce/helpers/pydev/pydevd.py",
> line 1578, in <module>
> globals = debugger.run(setup['file'], None, None, is_module)
> File
> "/home/builder/.IdeaIC2017.1/config/plugins/python-ce/helpers/pydev/pydevd.py",
> line 1015, in run
> pydev_imports.execfile(file, globals, locals) # execute the script
> File "/home/builder/runSparkTest.py", line 476, in <module>
> query_int_array()
> File "/home/builder/runSparkTest.py", line 381, in query_int_array
> df10.show()
> File
> "/usr/local/lib/python2.7/dist-packages/pyspark-2.1.0+hadoop2.7-py2.7.egg/pyspark/sql/dataframe.py",
> line 318, in show
> print(self._jdf.showString(n, 20))
> File "/usr/local/lib/python2.7/dist-packages/py4j/java_gateway.py", line
> 1133, in __call__
> answer, self.gateway_client, self.target_id, self.name)
> File
> "/usr/local/lib/python2.7/dist-packages/pyspark-2.1.0+hadoop2.7-py2.7.egg/pyspark/sql/utils.py",
> line 63, in deco
> return f(*a, **kw)
> File "/usr/local/lib/python2.7/dist-packages/py4j/protocol.py", line 319,
> in get_return_value
> format(target_id, ".", name), value)
> py4j.protocol.Py4JJavaError: An error occurred while calling o37.showString.
> : org.apache.spark.SparkException: Job aborted due to stage failure: Task 0
> in stage 0.0 failed 1 times, most recent failure: Lost task 0.0 in stage 0.0
> (TID 0, localhost, executor driver): java.lang.NullPointerException
> at
> org.apache.spark.sql.execution.datasources.jdbc.JdbcUtils$$anonfun$org$apache$spark$sql$execution$datasources$jdbc$JdbcUtils$$makeGetter$13.apply(JdbcUtils.scala:427)
> at
> org.apache.spark.sql.execution.datasources.jdbc.JdbcUtils$$anonfun$org$apache$spark$sql$execution$datasources$jdbc$JdbcUtils$$makeGetter$13.apply(JdbcUtils.scala:425)
> at
> org.apache.spark.sql.execution.datasources.jdbc.JdbcUtils$$anon$1.getNext(JdbcUtils.scala:286)
> at
> org.apache.spark.sql.execution.datasources.jdbc.JdbcUtils$$anon$1.getNext(JdbcUtils.scala:268)
> at org.apache.spark.util.NextIterator.hasNext(NextIterator.scala:73)
> at
> org.apache.spark.util.CompletionIterator.hasNext(CompletionIterator.scala:32)
> at
> org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown
> Source)
> at
> org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
> at
> org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:377)
> at
> org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:231)
> at
> org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:225)
> at
> org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:826)
> at
> org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:826)
> at
> org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
> at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
> at org.apache.spark.scheduler.Task.run(Task.scala:99)
> at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:745)
> Driver stacktrace:
> at
> org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1435)
> at
> org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1423)
> at
> org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1422)
> at
> scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
> at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
> at
> org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1422)
> at
> org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802)
> at
> org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802)
> at scala.Option.foreach(Option.scala:257)
> at
> org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:802)
> at
> org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1650)
> at
> org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1605)
> at
> org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1594)
> at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
> at
> org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:628)
> at org.apache.spark.SparkContext.runJob(SparkContext.scala:1918)
> at org.apache.spark.SparkContext.runJob(SparkContext.scala:1931)
> at org.apache.spark.SparkContext.runJob(SparkContext.scala:1944)
> at
> org.apache.spark.sql.execution.SparkPlan.executeTake(SparkPlan.scala:333)
> at
> org.apache.spark.sql.execution.CollectLimitExec.executeCollect(limit.scala:38)
> at
> org.apache.spark.sql.Dataset$$anonfun$org$apache$spark$sql$Dataset$$execute$1$1.apply(Dataset.scala:2371)
> at
> org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:57)
> at org.apache.spark.sql.Dataset.withNewExecutionId(Dataset.scala:2765)
> at
> org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$execute$1(Dataset.scala:2370)
> at
> org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$collect(Dataset.scala:2377)
> at
> org.apache.spark.sql.Dataset$$anonfun$head$1.apply(Dataset.scala:2113)
> at
> org.apache.spark.sql.Dataset$$anonfun$head$1.apply(Dataset.scala:2112)
> at org.apache.spark.sql.Dataset.withTypedCallback(Dataset.scala:2795)
> at org.apache.spark.sql.Dataset.head(Dataset.scala:2112)
> at org.apache.spark.sql.Dataset.take(Dataset.scala:2327)
> at org.apache.spark.sql.Dataset.showString(Dataset.scala:248)
> 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:745)
> Caused by: java.lang.NullPointerException
> at
> org.apache.spark.sql.execution.datasources.jdbc.JdbcUtils$$anonfun$org$apache$spark$sql$execution$datasources$jdbc$JdbcUtils$$makeGetter$13.apply(JdbcUtils.scala:427)
> at
> org.apache.spark.sql.execution.datasources.jdbc.JdbcUtils$$anonfun$org$apache$spark$sql$execution$datasources$jdbc$JdbcUtils$$makeGetter$13.apply(JdbcUtils.scala:425)
> at
> org.apache.spark.sql.execution.datasources.jdbc.JdbcUtils$$anon$1.getNext(JdbcUtils.scala:286)
> at
> org.apache.spark.sql.execution.datasources.jdbc.JdbcUtils$$anon$1.getNext(JdbcUtils.scala:268)
> at org.apache.spark.util.NextIterator.hasNext(NextIterator.scala:73)
> at
> org.apache.spark.util.CompletionIterator.hasNext(CompletionIterator.scala:32)
> at
> org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown
> Source)
> at
> org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
> at
> org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:377)
> at
> org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:231)
> at
> org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:225)
> at
> org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:826)
> at
> org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:826)
> at
> org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
> at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
> at org.apache.spark.scheduler.Task.run(Task.scala:99)
> at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> ... 1 more
> {noformat}
--
This message was sent by Atlassian JIRA
(v6.3.15#6346)
---------------------------------------------------------------------
To unsubscribe, e-mail: issues-unsubscr...@spark.apache.org
For additional commands, e-mail: issues-h...@spark.apache.org
