CODEWITHSUNDEEP
scalaapache-sparkapache-spark-sqlnanapache-spark-dataset
Georg Heiler
Georg Heiler

Reputation: 17676

Spark / Scala: fill nan with last good observation

I am using the spark 2.0.1 and want to fill nan values with the last good known value in the column.

The only reference for spark I could find Spark / Scala: forward fill with last observation or Fill in null with previously known good value with pyspark which seem to use RDD.

I would rather like to stay in the data frame / dataset world and possible handle multiple nan values. Is this possible?

My assumption is that the data (initially loaded from e.g. a CSV file is ordered by time and this order is preserved in the distributed setting e.g. filling by close / last good known value is correct. Maybe filling with the previous value is enough as for most records there are no 2 or more nan records in a row. Does this actually hold? The point is that a 

myDf.sort("foo").show

Would destroy any order e.g. all null values will come first.

A small example:

import java.sql.{ Date, Timestamp }
case class FooBar(foo:Date, bar:String)
val myDf = Seq(("2016-01-01","first"),("2016-01-02","second"),("2016-wrongFormat","noValidFormat"), ("2016-01-04","lastAssumingSameDate"))
         .toDF("foo","bar")
         .withColumn("foo", 'foo.cast("Date"))
         .as[FooBar]

Results in 

+----------+--------------------+
|       foo|                 bar|
+----------+--------------------+
|2016-01-01|               first|
|2016-01-02|              second|
|      null|       noValidFormat|
|2016-01-04|lastAssumingSameDate|
+----------+--------------------+

I would like to fix the value with the last good known value. How can I achieve this?

+----------+--------------------+
|       foo|                 bar|
+----------+--------------------+
|2016-01-01|               first|
|2016-01-02|              second|
|2016-01-02|       noValidFormat|
|2016-01-04|lastAssumingSameDate|
+----------+--------------------+

edit

in my case, it would be good enough to fill the value from the row above, as there are only very limited faulty values.

edit2

I try to add an index column

val myDf = Seq(("2016-01-01", "first"), ("2016-01-02", "second"), ("2016-wrongFormat", "noValidFormat"), ("2016-01-04", "lastAssumingSameDate"))
    .toDF("foo", "bar")
    .withColumn("foo", 'foo.cast("Date"))
    .as[FooBar]
    .withColumn("rowId", monotonically_increasing_id())

And then fill with the last value.

myDf.withColumn("fooLag", lag('foo, 1) over Window.orderBy('rowId)).show

But that reads the following warning: No Partition Defined for Window operation! Moving all data to a single partition, this can cause serious performance degradation. How could I introduce meaningful partitions?

+----------+--------------------+-----+----------+
|       foo|                 bar|rowId|    fooLag|
+----------+--------------------+-----+----------+
|2016-01-01|               first|    0|      null|
|2016-01-02|              second|    1|2016-01-01|
|      null|       noValidFormat|    2|2016-01-02|
|2016-01-04|lastAssumingSameDate|    3|      null|
+----------+--------------------+-----+----------+

Upvotes: 4

Views: 3399

Answers (2)

Sanskar Suman
Sanskar Suman

Reputation: 63

//filling null fields with last non known null I tried and this actually worked !!

val dftxt1 = spark.read.option("header","true").option("sep","\t").csv("/sdata/ph/com/r/ph_com_r_ita_javelin/inbound/abc.txt").toDF("line_name", "merge_key", "line_id")
dftxt2.select("line_name","merge_key","line_id").write.mode("overwrite").insertInto("dbname.tablename")

val df = spark.sql("select * from dbname.tablename")

val Df1 = df.withColumn("rowId", monotonically_increasing_id())

import org.apache.spark.sql.expressions.Window

val partitionWindow = Window.orderBy("rowId")

val Df2 = Df1.withColumn("line_id", last("line_id", true) over (partitionWindow))

Df2.show

Upvotes: 2

Georg Heiler
Georg Heiler

Reputation: 17676

This is an intermediate answer. However, it is not great as no partitions / only a single partition is used. I am still looking for a better way to solve the problem

df
    .withColumn("rowId", monotonically_increasing_id())
    .withColumn("replacement", lag('columnWithNull, 1) over Window.orderBy('rowId))
    .withColumn("columnWithNullReplaced",
      when($"columnWithNull" isNull, "replacement").otherwise($"columnWithNull")

    )

edit

I am working on building a better solution using mapPartitionsWithIndex https://gist.github.com/geoHeil/6a23d18ccec085d486165089f9f430f2 is not complete yet.

edit2

adding 

if (i == 0) {
          lastNotNullRow = toCarryBd.value.get(i + 1).get
        } else {
          lastNotNullRow = toCarryBd.value.get(i - 1).get
        }

will lead to the desired result.

Upvotes: 1

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