spark recursively fix circular references in class - scala

My initial data structure contains self-references which are not supported by spark:
initial.toDF
java.lang.UnsupportedOperationException: cannot have circular references in class, but got the circular reference
The initial data structure:
case class FooInitial(bar:String, otherSelf:Option[FooInitial])
val initial = Seq(FooInitial("first", Some(FooInitial("i1", Some(FooInitial("i2", Some(FooInitial("finish", None))))))))
To fix it a semantically similar and desired representation could be:
case class Inner(value:String)
case class Foo(bar:String, otherSelf:Option[Seq[Inner]])
val first = Foo("first", None)
val intermediate1 = Inner("i1")//Foo("i1", None)
val intermediate2 = Inner("i2")//Foo("i2", None)
val finish = Foo("finish", Some(Seq(intermediate1, intermediate2)))
val basic = Seq(first, finish)
basic.foreach(println)
val df = basic.toDF
df.printSchema
df.show
+------+------------+
| bar| otherSelf|
+------+------------+
| first| null|
|finish|[[i1], [i2]]|
+------+------------+
What is a nice functional way to convert from the initial to the other non-self-referencing
representation?

This recursively dereferences the objects:
class MyCollector {
val intermediateElems = new ListBuffer[Foo]
def addElement(initialElement : FooInitial) : MyCollector = {
intermediateElems += Foo(initialElement.bar, None)
intermediateElems ++ addIntermediateElement(initialElement.otherSelf, ListBuffer.empty[Foo])
this
}
#tailrec private def addIntermediateElement(intermediate:Option[FooInitial], l:ListBuffer[Foo]) : ListBuffer[Foo] = {
intermediate match {
case None => l
case Some(s) => {
intermediatePoints += Foo(s.bar + "_inner", None)
addIntermediateElement(s.otherSelf,intermediatePoints)
}
}
}
}
initial.foldLeft(new MyCollector)((myColl,stay)=>myColl.addElement(stay)).intermediatePoints.toArray.foreach(println)
The result is a List of:
Foo(first,None)
Foo(i1_inner,None)
Foo(i2_inner,None)
Foo(finish_inner,None)
which now nicely works for spark.
NOTE: this is not 1:1 for what I asked initially, but good enough for me for now.

Related

Dataset data is updated after inserting into Mysql Database

I have a small scenario where i read text file and calculate average based on date and store the summary into Mysql database.
Following is code
val repo_sum = joined_data.map(SensorReport.generateReport)
repo_sum.show() --- STEP 1
repo_sum.write.mode(SaveMode.Overwrite).jdbc(url, "sensor_report", prop)
repo_sum.show() --- STEP 2
After calculating average in repo_sum dataframe following is the result of STEP 1
+----------+------------------+-----+-----+
| date| flo| hz|count|
+----------+------------------+-----+-----+
|2017-10-05|52.887049194476745|10.27| 5.0|
|2017-10-04| 55.4188048943416|10.27| 5.0|
|2017-10-03| 54.1529270444092|10.27| 10.0|
+----------+------------------+-----+-----+
Then the save command is executed and the dataset values at step 2 is
+----------+-----------------+------------------+-----+
| date| flo| hz|count|
+----------+-----------------+------------------+-----+
|2017-10-05|52.88704919447673|31.578524597238367| 10.0|
|2017-10-04| 55.4188048943416| 32.84440244717079| 10.0|
+----------+-----------------+------------------+-----+
Following is complete code
class StreamRead extends Serializable {
org.apache.spark.sql.catalyst.encoders.OuterScopes.addOuterScope(this);
def main(args: Array[String]) {
val conf = new SparkConf().setAppName("Application").setMaster("local[2]")
val ssc = new StreamingContext(conf, Seconds(2))
val sqlContext = new SQLContext(ssc.sparkContext)
import sqlContext.implicits._
val sensorDStream = ssc.textFileStream("file:///C:/Users/M1026352/Desktop/Spark/StreamData").map(Sensor.parseSensor)
val url = "jdbc:mysql://localhost:3306/streamdata"
val prop = new java.util.Properties
prop.setProperty("user", "root")
prop.setProperty("password", "root")
val tweets = sensorDStream.foreachRDD {
rdd =>
if (rdd.count() != 0) {
val databaseVal = sqlContext.read.jdbc("jdbc:mysql://localhost:3306/streamdata", "sensor_report", prop)
val rdd_group = rdd.groupBy { x => x.date }
val repo_data = rdd_group.map { x =>
val sum_flo = x._2.map { x => x.flo }.reduce(_ + _)
val sum_hz = x._2.map { x => x.hz }.reduce(_ + _)
val sum_flo_count = x._2.size
print(sum_flo_count)
SensorReport(x._1, sum_flo, sum_hz, sum_flo_count)
}
val df = repo_data.toDF()
val joined_data = df.join(databaseVal, Seq("date"), "fullouter")
joined_data.show()
val repo_sum = joined_data.map(SensorReport.generateReport)
repo_sum.show()
repo_sum.write.mode(SaveMode.Overwrite).jdbc(url, "sensor_report", prop)
repo_sum.show()
}
}
ssc.start()
WorkerAndTaskExample.main(args)
ssc.awaitTermination()
}
case class Sensor(resid: String, date: String, time: String, hz: Double, disp: Double, flo: Double, sedPPM: Double, psi: Double, chlPPM: Double)
object Sensor extends Serializable {
def parseSensor(str: String): Sensor = {
val p = str.split(",")
Sensor(p(0), p(1), p(2), p(3).toDouble, p(4).toDouble, p(5).toDouble, p(6).toDouble, p(7).toDouble, p(8).toDouble)
}
}
case class SensorReport(date: String, flo: Double, hz: Double, count: Double)
object SensorReport extends Serializable {
def generateReport(row: Row): SensorReport = {
print(row)
if (row.get(4) == null) {
SensorReport(row.getString(0), row.getDouble(1) / row.getDouble(3), row.getDouble(2) / row.getDouble(3), row.getDouble(3))
} else if (row.get(2) == null) {
SensorReport(row.getString(0), row.getDouble(4), row.getDouble(5), row.getDouble(6))
} else {
val count = row.getDouble(3) + row.getDouble(6)
val flow_avg_update = (row.getDouble(6) * row.getDouble(4) + row.getDouble(1)) / count
val flow_flo_update = (row.getDouble(6) * row.getDouble(5) + row.getDouble(1)) / count
print(count + " : " + flow_avg_update + " : " + flow_flo_update)
SensorReport(row.getString(0), flow_avg_update, flow_flo_update, count)
}
}
}
As far as i understand when save command is executed in spark the whole process runs again, is my understanding is correct please let me know.
In Spark all transformations are lazy, nothing will happen until an action is called. At the same time, this means that if multiple actions are called on the same RDD or dataframe, all computations will be performed multiple times. This includes loading the data and all transformations.
To avoid this, use cache() or persist() (same thing except that cache() can specify different types of storage, the default is RAM memory only). cache() will keep the RDD/dataframe in memory after the first time an action was used on it. Hence, avoiding running the same transformations multiple times.
In this case, since two actions are performed on the dataframe is causing this unexpected behavior, caching the dataframe would solve the problem:
val repo_sum = joined_data.map(SensorReport.generateReport).cache()

How to use the functions.explode to flatten element in dataFrame

I've made this piece of code :
case class RawPanda(id: Long, zip: String, pt: String, happy: Boolean, attributes: Array[Double])
case class PandaPlace(name: String, pandas: Array[RawPanda])
object TestSparkDataFrame extends App{
System.setProperty("hadoop.home.dir", "E:\\Programmation\\Libraries\\hadoop")
val conf = new SparkConf().setAppName("TestSparkDataFrame").set("spark.driver.memory","4g").setMaster("local[*]")
val session = SparkSession.builder().config(conf).getOrCreate()
import session.implicits._
def createAndPrintSchemaRawPanda(session:SparkSession):DataFrame = {
val newPanda = RawPanda(1,"M1B 5K7", "giant", true, Array(0.1, 0.1))
val pandaPlace = PandaPlace("torronto", Array(newPanda))
val df =session.createDataFrame(Seq(pandaPlace))
df
}
val df2 = createAndPrintSchemaRawPanda(session)
df2.show
+--------+--------------------+
| name| pandas|
+--------+--------------------+
|torronto|[[1,M1B 5K7,giant...|
+--------+--------------------+
val pandaInfo = df2.explode(df2("pandas")) {
case Row(pandas: Seq[Row]) =>
pandas.map{
case (Row(
id: Long,
zip: String,
pt: String,
happy: Boolean,
attrs: Seq[Double])) => RawPanda(id, zip, pt , happy, attrs.toArray)
}
}
pandaInfo2.show
+--------+--------------------+---+-------+-----+-----+----------+
| name| pandas| id| zip| pt|happy|attributes|
+--------+--------------------+---+-------+-----+-----+----------+
|torronto|[[1,M1B 5K7,giant...| 1|M1B 5K7|giant| true|[0.1, 0.1]|
+--------+--------------------+---+-------+-----+-----+----------+
The problem that the explode function as I used it is deprecated, so I would like to recaculate the pandaInfo2 dataframe but using the adviced method in the warning.
use flatMap() or select() with functions.explode() instead
But then when I do :
val pandaInfo = df2.select(functions.explode(df("pandas"))
I obtain the same result as I had in df2.
I don't know how to proceed to use flatMap or functions.explode.
How could I use flatMap or functions.explode to obtain the result that I want ?(the one in pandaInfo)
I've seen this post and this other one but none of them helped me.
Calling select with explode function returns a DataFrame where the Array pandas is "broken up" into individual records; Then, if you want to "flatten" the structure of the resulting single "RawPanda" per record, you can select the individual columns using a dot-separated "route":
val pandaInfo2 = df2.select($"name", explode($"pandas") as "pandas")
.select($"name", $"pandas",
$"pandas.id" as "id",
$"pandas.zip" as "zip",
$"pandas.pt" as "pt",
$"pandas.happy" as "happy",
$"pandas.attributes" as "attributes"
)
A less verbose version of the exact same operation would be:
import org.apache.spark.sql.Encoders // going to use this to "encode" case class into schema
val pandaColumns = Encoders.product[RawPanda].schema.fields.map(_.name)
val pandaInfo3 = df2.select($"name", explode($"pandas") as "pandas")
.select(Seq($"name", $"pandas") ++ pandaColumns.map(f => $"pandas.$f" as f): _*)

spark map partitions to fill nan values

I want to fill nan values in spark using the last good known observation - see: Spark / Scala: fill nan with last good observation
My current solution used window functions in order to accomplish the task. But this is not great, as all values are mapped into a single partition.
val imputed: RDD[FooBar] = recordsDF.rdd.mapPartitionsWithIndex { case (i, iter) => fill(i, iter) } should work a lot better. But strangely my fill function is not executed. What is wrong with my code?
+----------+--------------------+
| foo| bar|
+----------+--------------------+
|2016-01-01| first|
|2016-01-02| second|
| null| noValidFormat|
|2016-01-04|lastAssumingSameDate|
+----------+--------------------+
Here is the full example code:
import java.sql.Date
import org.apache.log4j.{ Level, Logger }
import org.apache.spark.SparkConf
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.SparkSession
case class FooBar(foo: Date, bar: String)
object WindowFunctionExample extends App {
Logger.getLogger("org").setLevel(Level.WARN)
val conf: SparkConf = new SparkConf()
.setAppName("foo")
.setMaster("local[*]")
val spark: SparkSession = SparkSession
.builder()
.config(conf)
.enableHiveSupport()
.getOrCreate()
import spark.implicits._
val myDff = Seq(("2016-01-01", "first"), ("2016-01-02", "second"),
("2016-wrongFormat", "noValidFormat"),
("2016-01-04", "lastAssumingSameDate"))
val recordsDF = myDff
.toDF("foo", "bar")
.withColumn("foo", 'foo.cast("Date"))
.as[FooBar]
recordsDF.show
def notMissing(row: FooBar): Boolean = {
row.foo != null
}
val toCarry = recordsDF.rdd.mapPartitionsWithIndex { case (i, iter) => Iterator((i, iter.filter(notMissing(_)).toSeq.lastOption)) }.collectAsMap
println("###################### carry ")
println(toCarry)
println(toCarry.foreach(println))
println("###################### carry ")
val toCarryBd = spark.sparkContext.broadcast(toCarry)
def fill(i: Int, iter: Iterator[FooBar]): Iterator[FooBar] = {
var lastNotNullRow: FooBar = toCarryBd.value(i).get
iter.map(row => {
if (!notMissing(row))1
FooBar(lastNotNullRow.foo, row.bar)
else {
lastNotNullRow = row
row
}
})
}
// The algorithm does not step into the for loop for filling the null values. Strange
val imputed: RDD[FooBar] = recordsDF.rdd.mapPartitionsWithIndex { case (i, iter) => fill(i, iter) }
val imputedDF = imputed.toDS()
println(imputedDF.orderBy($"foo").collect.toList)
imputedDF.show
spark.stop
}
edit
I fixed the code as outlined by the comment. But the toCarryBd contains None values. How can this happen as I did filter explicitly for
def notMissing(row: FooBar): Boolean = {row.foo != null}
iter.filter(notMissing(_)).toSeq.lastOption
non None values.
(2,None)
(5,None)
(4,None)
(7,Some(FooBar(2016-01-04,lastAssumingSameDate)))
(1,Some(FooBar(2016-01-01,first)))
(3,Some(FooBar(2016-01-02,second)))
(6,None)
(0,None)
This leads to NoSuchElementException: None.getwhen trying to access toCarryBd.
Firstly, if your foo field can be null, I would recommend creating the case class as:
case class FooBar(foo: Option[Date], bar: String)
Then, you can rewrite your notMissing function to something like:
def notMissing(row: Option[FooBar]): Boolean = row.isDefined && row.get.foo.isDefined

How to access individual trees in a model created by RandomForestClassifier (spark.ml-version)?

How to access individual trees in a model generated by Spark ML's RandomForestClassifier? I am using the Scala version of RandomForestClassifier.
Actually it has trees attribute:
import org.apache.spark.ml.attribute.NominalAttribute
import org.apache.spark.ml.classification.{
RandomForestClassificationModel, RandomForestClassifier,
DecisionTreeClassificationModel
}
val meta = NominalAttribute
.defaultAttr
.withName("label")
.withValues("0.0", "1.0")
.toMetadata
val data = sqlContext.read.format("libsvm")
.load("data/mllib/sample_libsvm_data.txt")
.withColumn("label", $"label".as("label", meta))
val rf: RandomForestClassifier = new RandomForestClassifier()
.setLabelCol("label")
.setFeaturesCol("features")
val trees: Array[DecisionTreeClassificationModel] = rf.fit(data).trees.collect {
case t: DecisionTreeClassificationModel => t
}
As you can see the only problem is to get types right so we can actually use these:
trees.head.transform(data).show(3)
// +-----+--------------------+-------------+-----------+----------+
// |label| features|rawPrediction|probability|prediction|
// +-----+--------------------+-------------+-----------+----------+
// | 0.0|(692,[127,128,129...| [33.0,0.0]| [1.0,0.0]| 0.0|
// | 1.0|(692,[158,159,160...| [0.0,59.0]| [0.0,1.0]| 1.0|
// | 1.0|(692,[124,125,126...| [0.0,59.0]| [0.0,1.0]| 1.0|
// +-----+--------------------+-------------+-----------+----------+
// only showing top 3 rows
Note:
If you work with pipelines you can extract individual trees as well:
import org.apache.spark.ml.Pipeline
val model = new Pipeline().setStages(Array(rf)).fit(data)
// There is only one stage and know its type
// but lets be thorough
val rfModelOption = model.stages.headOption match {
case Some(m: RandomForestClassificationModel) => Some(m)
case _ => None
}
val trees = rfModelOption.map {
_.trees // ... as before
}.getOrElse(Array())

How to create a custom Transformer from a UDF?

I was trying to create and save a Pipeline with custom stages. I need to add a column to my DataFrame by using a UDF. Therefore, I was wondering if it was possible to convert a UDF or a similar action into a Transformer?
My custom UDF looks like this and I'd like to learn how to do it using an UDF as a custom Transformer.
def getFeatures(n: String) = {
val NUMBER_FEATURES = 4
val name = n.split(" +")(0).toLowerCase
((1 to NUMBER_FEATURES)
.filter(size => size <= name.length)
.map(size => name.substring(name.length - size)))
}
val tokenizeUDF = sqlContext.udf.register("tokenize", (name: String) => getFeatures(name))
It is not a fully featured solution but your can start with something like this:
import org.apache.spark.ml.{UnaryTransformer}
import org.apache.spark.ml.util.Identifiable
import org.apache.spark.sql.types.{ArrayType, DataType, StringType}
class NGramTokenizer(override val uid: String)
extends UnaryTransformer[String, Seq[String], NGramTokenizer] {
def this() = this(Identifiable.randomUID("ngramtokenizer"))
override protected def createTransformFunc: String => Seq[String] = {
getFeatures _
}
override protected def validateInputType(inputType: DataType): Unit = {
require(inputType == StringType)
}
override protected def outputDataType: DataType = {
new ArrayType(StringType, true)
}
}
Quick check:
val df = Seq((1L, "abcdef"), (2L, "foobar")).toDF("k", "v")
val transformer = new NGramTokenizer().setInputCol("v").setOutputCol("vs")
transformer.transform(df).show
// +---+------+------------------+
// | k| v| vs|
// +---+------+------------------+
// | 1|abcdef|[f, ef, def, cdef]|
// | 2|foobar|[r, ar, bar, obar]|
// +---+------+------------------+
You can even try to generalize it to something like this:
import org.apache.spark.sql.catalyst.ScalaReflection.schemaFor
import scala.reflect.runtime.universe._
class UnaryUDFTransformer[T : TypeTag, U : TypeTag](
override val uid: String,
f: T => U
) extends UnaryTransformer[T, U, UnaryUDFTransformer[T, U]] {
override protected def createTransformFunc: T => U = f
override protected def validateInputType(inputType: DataType): Unit =
require(inputType == schemaFor[T].dataType)
override protected def outputDataType: DataType = schemaFor[U].dataType
}
val transformer = new UnaryUDFTransformer("featurize", getFeatures)
.setInputCol("v")
.setOutputCol("vs")
If you want to use UDF not the wrapped function you'll have to extend Transformer directly and override transform method. Unfortunately majority of the useful classes is private so it can be rather tricky.
Alternatively you can register UDF:
spark.udf.register("getFeatures", getFeatures _)
and use SQLTransformer
import org.apache.spark.ml.feature.SQLTransformer
val transformer = new SQLTransformer()
.setStatement("SELECT *, getFeatures(v) AS vs FROM __THIS__")
transformer.transform(df).show
// +---+------+------------------+
// | k| v| vs|
// +---+------+------------------+
// | 1|abcdef|[f, ef, def, cdef]|
// | 2|foobar|[r, ar, bar, obar]|
// +---+------+------------------+
I initially tried to extend the Transformer and UnaryTransformer abstracts but encountered trouble with my application being unable to reach DefaultParamsWriteable.As an example that may be relevant to your problem, I created a simple term normalizer as a UDF following along from this example. My goal is to match terms against patterns and sets to replace them with generic terms. For example:
"\b[A-Z0-9._%+-]+#[A-Z0-9.-]+\.[A-Z]{2,}\b".r -> "emailaddr"
This is the class
import scala.util.matching.Regex
class TermNormalizer(normMap: Map[Any, String]) {
val normalizationMap = normMap
def normalizeTerms(terms: Seq[String]): Seq[String] = {
var termsUpdated = terms
for ((term, idx) <- termsUpdated.view.zipWithIndex) {
for (normalizer <- normalizationMap.keys: Iterable[Any]) {
normalizer match {
case (regex: Regex) =>
if (!regex.findFirstIn(term).isEmpty) termsUpdated =
termsUpdated.updated(idx, normalizationMap(regex))
case (set: Set[String]) =>
if (set.contains(term)) termsUpdated =
termsUpdated.updated(idx, normalizationMap(set))
}
}
}
termsUpdated
}
}
I use it like this:
val testMap: Map[Any, String] = Map("hadoop".r -> "elephant",
"spark".r -> "sparky", "cool".r -> "neat",
Set("123", "456") -> "set1",
Set("789", "10") -> "set2")
val testTermNormalizer = new TermNormalizer(testMap)
val termNormalizerUdf = udf(testTermNormalizer.normalizeTerms(_: Seq[String]))
val trainingTest = sqlContext.createDataFrame(Seq(
(0L, "spark is cool 123", 1.0),
(1L, "adsjkfadfk akjdsfhad 456", 0.0),
(2L, "spark rocks my socks 789 10", 1.0),
(3L, "hadoop is cool 10", 0.0)
)).toDF("id", "text", "label")
val testTokenizer = new Tokenizer()
.setInputCol("text")
.setOutputCol("words")
val tokenizedTrainingTest = testTokenizer.transform(trainingTest)
println(tokenizedTrainingTest
.select($"id", $"text", $"words", termNormalizerUdf($"words"), $"label").show(false))
Now that I read the question a little closer, it sounds like you're asking how to avoid doing it this way lol. Anyways, I'll still post it in case someone in the future is looking for an easy way to apply a transformer-ish like functionality
If you wish to make the transformer writable as well, then you can re-implement the traits such as HasInputCol in the sharedParams library in a public package of your choice and then use them with DefaultParamsWritable trait to make the transformer persistable.
This way you can also avoid having to place part of your code inside the spark core ml packages but you kind of maintain a parallel set of params in your own package. This isnt really a problem given they hardly ever change.
But do track the bug in their JIRA board here that asks for some of the common sharedParams to be made public instead of private to the ml so that people can directly use those from outside classes.