Py4JJavaError: An error occurred while calling o840.showString - pyspark

Question

I am trying to parse a log file with millions of records. It contains host name, timestamp, status code etc. After successfully parsing host and status code and url, when I am trying to parse timestamp, I am getting an error. following is my code:
lines=sc.textFile(filepath)
df_log= lines.map(lambda x: Row(header=x)).toDF()
timestamp_pattern= r'\[\d{2}\/\w{3}\/\d{4}\:\d{2}\:\d{2}\:\d{2}\s\S+\d{4}]'
df2=df_log.select(regexp_extract(col('header'),timestamp_pattern,1).alias("timestamp"))
everything is working fine till here. after this when I am trying to df2.show(10). I am getting following error:
Py4JJavaErrorTraceback (most recent call last) <ipython-input-112-5a86d13b2926> in <module>()
----> 1 df2.show(1)
/opt/cloudera/parcels/SPARK2/lib/spark2/python/pyspark/sql/dataframe.pyc in show(self, n, truncate)
316 """
317 if isinstance(truncate, bool) and truncate:
--> 318 print(self._jdf.showString(n, 20))
319 else:
320 print(self._jdf.showString(n, int(truncate)))
/opt/cloudera/parcels/SPARK2/lib/spark2/python/lib/py4j-0.10.4-src.zip/py4j/java_gateway.py in __call__(self, *args) 1131 answer = self.gateway_client.send_command(command) 1132 return_value
= get_return_value(
-> 1133 answer, self.gateway_client, self.target_id, self.name) 1134 1135 for temp_arg in temp_args:
/opt/cloudera/parcels/SPARK2/lib/spark2/python/pyspark/sql/utils.pyc in deco(*a, **kw)
61 def deco(*a, **kw):
62 try:
---> 63 return f(*a, **kw)
64 except py4j.protocol.Py4JJavaError as e:
65 s = e.java_exception.toString()
/opt/cloudera/parcels/SPARK2/lib/spark2/python/lib/py4j-0.10.4-src.zip/py4j/protocol.py in get_return_value(answer, gateway_client, target_id, name)
317 raise Py4JJavaError(
318 "An error occurred while calling {0}{1}{2}.\n".
--> 319 format(target_id, ".", name), value)
320 else:
321 raise Py4JError(
Py4JJavaError: An error occurred while calling o965.showString. : org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 2.0 failed 4 times, most recent failure: Lost task 0.3 in stage 2.0 (TID 5, ip-20-0-31-210.ec2.internal, executor 2): java.lang.IndexOutOfBoundsException: No group 1 at java.util.regex.Matcher.group(Matcher.java:538) 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:325) 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$$failJobAndIndependentStages(DAGScheduler.scala:1430) at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1418) at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1417) at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59) at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48) at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1417) at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:797) at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:797) at scala.Option.foreach(Option.scala:257) at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:797) at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1645) at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1600) at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1589) at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48) at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:623) at org.apache.spark.SparkContext.runJob(SparkContext.scala:1930) at org.apache.spark.SparkContext.runJob(SparkContext.scala:1943) at org.apache.spark.SparkContext.runJob(SparkContext.scala:1956) 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$1.apply(Dataset.scala:2378) at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:57) at org.apache.spark.sql.Dataset.withNewExecutionId(Dataset.scala:2772) at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$execute$1(Dataset.scala:2377) at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$collect(Dataset.scala:2384) at org.apache.spark.sql.Dataset$$anonfun$head$1.apply(Dataset.scala:2120) at org.apache.spark.sql.Dataset$$anonfun$head$1.apply(Dataset.scala:2119) at org.apache.spark.sql.Dataset.withTypedCallback(Dataset.scala:2802) at org.apache.spark.sql.Dataset.head(Dataset.scala:2119) at org.apache.spark.sql.Dataset.take(Dataset.scala:2334) at org.apache.spark.sql.Dataset.showString(Dataset.scala:248) at sun.reflect.GeneratedMethodAccessor71.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357) at py4j.Gateway.invoke(Gateway.java:280) at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132) at py4j.commands.CallCommand.execute(CallCommand.java:79) at py4j.GatewayConnection.run(GatewayConnection.java:214) at java.lang.Thread.run(Thread.java:748) Caused by: java.lang.IndexOutOfBoundsException: No group 1 at java.util.regex.Matcher.group(Matcher.java:538) at org.apache.spark.sql.catalyst.expressions.GeneratedClass$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:325) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) ... 1 more
Please help me with this.
following is the excerpt of the records in the log file for referance:
109.169.248.247 - - [12/Dec/2015:18:25:11 +0100] GET /administrator/ HTTP/1.1 200 4263 - Mozilla/5.0 (Windows NT 6.0; rv:34.0) Gecko/20100101 Firefox/34.0 -
109.169.248.247 - - [12/Dec/2015:18:25:11 +0100] GET /administrator/ HTTP/1.1 200 4263 - Mozilla/5.0 (Windows NT 6.0; rv:34.0) Gecko/20100101 Firefox/34.0 -
109.169.248.247 - - [12/Dec/2015:18:25:11 +0100] GET /administrator/ HTTP/1.1 200 4263 - Mozilla/5.0 (Windows NT 6.0; rv:34.0) Gecko/20100101 Firefox/34.0 -
109.169.248.247 - - [12/Dec/2015:18:25:11 +0100] POST /administrator/index.php HTTP/1.1 200 4494 http://almhuette-raith.at/administrator/ Mozilla/5.0 (Windows NT 6.0; rv:34.0) Gecko/20100101 Firefox/34.0 -
46.72.177.4 - - [12/Dec/2015:18:31:08 +0100] GET /administrator/ HTTP/1.1 200 4263 - Mozilla/5.0 (Windows NT 6.0; rv:34.0) Gecko/20100101 Firefox/34.0 -
46.72.177.4 - - [12/Dec/2015:18:31:08 +0100] POST /administrator/index.php HTTP/1.1 200 4494 http://almhuette-raith.at/administrator/ Mozilla/5.0 (Windows NT 6.0; rv:34.0) Gecko/20100101 Firefox/34.0 -
83.167.113.100 - - [12/Dec/2015:18:31:25 +0100] GET /administrator/ HTTP/1.1 200 4263 - Mozilla/5.0 (Windows NT 6.0; rv:34.0) Gecko/20100101 Firefox/34.0 -
83.167.113.100 - - [12/Dec/2015:18:31:25 +0100] POST /administrator/index.php HTTP/1.1 200 4494 http://almhuette-raith.at/administrator/ Mozilla/5.0 (Windows NT 6.0; rv:34.0) Gecko/20100101 Firefox/34.0 -
95.29.198.15 - - [12/Dec/2015:18:32:10 +0100] GET /administrator/ HTTP/1.1 200 4263 - Mozilla/5.0 (Windows NT 6.0; rv:34.0) Gecko/20100101 Firefox/34.0 -
95.29.198.15 - - [12/Dec/2015:18:32:11 +0100] POST /administrator/index.php HTTP/1.1 200 4494 http://almhuette-raith.at/administrator/ Mozilla/5.0 (Windows NT 6.0; rv:34.0) Gecko/20100101 Firefox/34.0 -
109.184.11.34 - - [12/Dec/2015:18:32:56 +0100] GET /administrator/ HTTP/1.1 200 4263 - Mozilla/5.0 (Windows NT 6.0; rv:34.0) Gecko/20100101 Firefox/34.0 -
109.184.11.34 - - [12/Dec/2015:18:32:56 +0100] POST /administrator/index.php HTTP/1.1 200 4494 http://almhuette-raith.at/administrator/ Mozilla/5.0 (Windows NT 6.0; rv:34.0) Gecko/20100101 Firefox/34.0 -
`

Answer 1

change last line to -
timestamp_pattern= r'\[\d{2}\/\w{3}\/\d{4}\:\d{2}\:\d{2}\:\d{2}\s\S+\d{4}]'
df2=df_log.select(regexp_extract(col('header'),timestamp_pattern,0).alias("timestamp"))
note: I changed the groupId from 1 to 0 since there is no group set in your timestamp_pattern