8

I am trying to apply string indexer on multiple columns. Here is my code

val stringIndexers = Categorical_Model.map { colName =>new StringIndexer().setInputCol(colName).setOutputCol(colName + "_indexed")}

var dfStringIndexed = stringIndexers(0).fit(df3).transform(df3) // 'fit's a model then 'transform's data
for(x<-1 to stringIndexers.length-1)
{dfStringIndexed = stringIndexers(x).fit(dfStringIndexed).transform(dfStringIndexed)
}
dfStringIndexed = dfStringIndexed.drop(Categorical_Model: _*)

The Schema shows up with all columns having nullable as false

The stringIndexers array shows up like this

stringIndexers: Array[org.apache.spark.ml.feature.StringIndexer] = Array(strIdx_c53c3bdf464c, strIdx_61e685c520f7, strIdx_d6e59b2fc69d, ......)


dfStringIndexed.show(10)

This throws the following error

org.apache.spark.SparkException: Failed to execute user defined function($anonfun$9: (string) =&gt; double)

Why is it that print schema is showing up but no data is available .

Update: If I loop the string Indexers manually like so instead of the loop. This code works. Which is wierd.

var dfStringIndexed = stringIndexers(0).fit(df3).transform(df3) // 'fit's a model then 'transform's data
dfStringIndexed = stringIndexers(1).fit(dfStringIndexed).transform(dfStringIndexed)
dfStringIndexed = stringIndexers(2).fit(dfStringIndexed).transform(dfStringIndexed)
dfStringIndexed = stringIndexers(3).fit(dfStringIndexed).transform(dfStringIndexed)
dfStringIndexed = stringIndexers(4).fit(dfStringIndexed).transform(dfStringIndexed)

Adding Stacktrace on request

Driver stacktrace:
  at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1602)
  at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1590)
  at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1589)
  at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
  at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
  at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1589)
  at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:831)
  at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:831)
  at scala.Option.foreach(Option.scala:257)
  at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:831)
  at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1823)
  at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1772)
  at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1761)
  at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
  at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:642)
  at org.apache.spark.SparkContext.runJob(SparkContext.scala:2034)
  at org.apache.spark.SparkContext.runJob(SparkContext.scala:2055)
  at org.apache.spark.SparkContext.runJob(SparkContext.scala:2074)
  at org.apache.spark.sql.execution.SparkPlan.executeTake(SparkPlan.scala:363)
  at org.apache.spark.sql.execution.CollectLimitExec.executeCollect(limit.scala:38)
  at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$collectFromPlan(Dataset.scala:3273)
  at org.apache.spark.sql.Dataset$$anonfun$head$1.apply(Dataset.scala:2484)
  at org.apache.spark.sql.Dataset$$anonfun$head$1.apply(Dataset.scala:2484)
  at org.apache.spark.sql.Dataset$$anonfun$52.apply(Dataset.scala:3254)
  at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:77)
  at org.apache.spark.sql.Dataset.withAction(Dataset.scala:3253)
  at org.apache.spark.sql.Dataset.head(Dataset.scala:2484)
  at org.apache.spark.sql.Dataset.take(Dataset.scala:2698)
  at org.apache.spark.sql.Dataset.showString(Dataset.scala:254)
  at org.apache.spark.sql.Dataset.show(Dataset.scala:723)
  at org.apache.spark.sql.Dataset.show(Dataset.scala:682)
  ... 63 elided
Caused by: org.apache.spark.SparkException: Failed to execute user defined function($anonfun$9: (string) => double)
  at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIteratorForCodegenStage1.processNext(Unknown Source)
  at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
  at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$10$$anon$1.hasNext(WholeStageCodegenExec.scala:614)
  at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:253)
  at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:247)
  at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:830)
  at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:830)
  at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
  at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
  at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
  at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
  at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
  at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
  at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
  at org.apache.spark.scheduler.Task.run(Task.scala:109)
  at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:345)
  ... 3 more
Caused by: org.apache.spark.SparkException: StringIndexer encountered NULL value. To handle or skip NULLS, try setting StringIndexer.handleInvalid.
  at org.apache.spark.ml.feature.StringIndexerModel$$anonfun$9.apply(StringIndexer.scala:251)
  at org.apache.spark.ml.feature.StringIndexerModel$$anonfun$9.apply(StringIndexer.scala:246)
  ... 19 more
Improve this question
5
  • Can you add the stacktrace to your question? Commented Jul 22, 2019 at 9:44
  • Added the stack trace to the question Commented Jul 22, 2019 at 10:11
  • The error is that in some column that you are tring the StringIndexer has null values. Check stackoverflow.com/questions/44671597/… Commented Jul 22, 2019 at 10:35
  • 1
    It have checked that already . On print Schema i get Nullable = false and no nulls .Also when i am manuallly looping it is working Commented Jul 22, 2019 at 10:39
  • Have you try another approach like using fold and building a new dataframe each iteration..? Commented Jul 22, 2019 at 10:45

1 Answer 1

Reset to default
7

I have also been getting a similar issue, even on a tiny subset of 50 rows, none of which have nulls in the column I am string indexing. But it didn't work even when I ran it manually.

I can avoid the error by including .setHandleInvalid("keep"), and I've checked the outputs and it's not doing anything strange like setting everything to be 0 or the same value or anything. I'm still unhappy about that being the resolution as it seems quite unsafe. Would be very interested to know if you found a more reasonable answer and resolution!

dfStringIndexed = stringIndexers(1).setHandleInvalid("keep").fit(dfStringIndexed).transform(dfStringIndexed)

I think it might also be fixed by changing the nullability of your column, even if it doesn't contain nulls in it, which I did as per here

Can I change the nullability of a column in my Spark dataframe?

Improve this answer
Sign up to request clarification or add additional context in comments.

Comments

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Start asking to get answers

Find the answer to your question by asking.

Ask question

Explore related questions

See similar questions with these tags.