I'm trying to create a table from a json datasource.
The problem is that there is a field in the json data that is not always present for every entry and looks like this.
[ { "k1" : "someValue",
"optK" : { "nestedK" : true } },
{ "k1" : "someOtherValue" }
]
When I try to specify the optional field in the schema, all the entries without that field have all null value in the table:
columns: k1 | optK
row1: "someValue" [true]
row2: null null
is it possible to write a schema such that I would have null only in the column where the value is missing?
Like this:
columns: k1 | optK
row1: "someValue" "optV"
row2: "someOtherValue" null
My current code:
import org.apache.spark.sql.expressions.scalalang._
import org.apache.spark.sql.types._
import org.apache.spark.sql.{DataFrame, Dataset, SparkSession}
val session = SparkSession.builder().enableHiveSupport().getOrCreate()
val schema = StructType(Seq(
StructField("k1", StringType, false),
StructField("optK", StructType(Seq(StructField("nestedK", BooleanType, false))), false)
))
val df = session.read.schema(schema).json("data.json")
df.registerTempTable("Mr_Table")
There are several issues in your code/input data:
Input data - JSON keys aren't in quote.
You can use avoid this problem, by one of the following options:
Updating the input data by adding quotes to the json keys
Using .option("allowUnquotedFieldNames",true) in the following way:
val df = session.read.option("allowUnquotedFieldNames",true).schema(schema).json("data.json")
A string field in the input data was defined as boolean in the schema schema should be updated to be:
val schema = StructType(Seq(
StructField("k1", StringType, false),
StructField("optK", StructType(Seq(StructField("nestedK", StringType, false))), false)
))
JSON data format, I've update the sample json input to be in json lines format:
{ k1 : "someValue", optK : { nestedK : "optV" } }
{ k1 : "someOtherValue" }
Running the modify code shows the following:
Spark context available as 'sc' (master = yarn, app id = application_xxx).
Spark session available as 'spark'.
Welcome to
____ __
/ __/__ ___ _____/ /__
_\ \/ _ \/ _ `/ __/ '_/
/___/ .__/\_,_/_/ /_/\_\ version 2.2.0
/_/
Using Scala version 2.11.8 (OpenJDK 64-Bit Server VM, Java 1.8.0_141)
scala> :paste
// Entering paste mode (ctrl-D to finish)
import org.apache.spark.sql.expressions.scalalang._
import org.apache.spark.sql.types._
import org.apache.spark.sql.{DataFrame, Dataset, SparkSession}
val schema = StructType(Seq(
StructField("k1", StringType, false),
StructField("optK", StructType(Seq(StructField("nestedK", StringType, false))), false)
))
val df = spark.read.option("allowUnquotedFieldNames",true).schema(schema).json("s3 location of data.json")
// Exiting paste mode, now interpreting.
import org.apache.spark.sql.expressions.scalalang._
import org.apache.spark.sql.types._
import org.apache.spark.sql.{DataFrame, Dataset, SparkSession}
schema: org.apache.spark.sql.types.StructType = StructType(StructField(k1,StringType,false), StructField(optK,StructType(StructField(nestedK,StringType,false)),false))
df: org.apache.spark.sql.DataFrame = [k1: string, optK: struct<nestedK: string>]
scala> df.show
+--------------+------+
| k1| optK|
+--------------+------+
| someValue|[optV]|
|someOtherValue| null|
+--------------+------+
Related
Scala noob, using Spark 2.3.0.
I'm creating a DataFrame using a udf that creates a JSON String column:
val result: DataFrame = df.withColumn("decrypted_json", instance.decryptJsonUdf(df("encrypted_data")))
it outputs as follows:
+----------------+---------------------------------------+
| encrypted_data | decrypted_json |
+----------------+---------------------------------------+
|eyJleHAiOjE1 ...| {"a":547.65 , "b":"Some Data"} |
+----------------+---------------------------------------+
The UDF is an external code, that I can't change. I would like to split the decrypted_json column into individual columns so the output DataFrame will be like so:
+----------------+----------------------+
| encrypted_data | a | b |
+----------------+--------+-------------+
|eyJleHAiOjE1 ...| 547.65 | "Some Data" |
+----------------+--------+-------------+
Below solution is inspired by one of the solutions given by #Jacek Laskowski:
import org.apache.spark.sql.types._
val JsonSchema = new StructType()
.add($"a".string)
.add($"b".string)
val schema = new StructType()
.add($"encrypted_data".string)
.add($"decrypted_json".array(JsonSchema))
val schemaAsJson = schema.json
import org.apache.spark.sql.types.DataType
val dt = DataType.fromJson(schemaAsJson)
import org.apache.spark.sql.functions._
val rawJsons = Seq("""
{
"encrypted_data" : "eyJleHAiOjE1",
"decrypted_json" : [
{
"a" : "547.65",
"b" : "Some Data"
}
]
}
""").toDF("rawjson")
val people = rawJsons
.select(from_json($"rawjson", schemaAsJson, Map.empty[String, String]) as "json")
.select("json.*") // <-- flatten the struct field
.withColumn("address", explode($"decrypted_json")) // <-- explode the array field
.drop("decrypted_json") // <-- no longer needed
.select("encrypted_data", "address.*") // <-- flatten the struct field
Please go through Link for the original solution with the explanation.
I hope that helps.
Using from_jason you can give parse the JSON into a Struct type then select columns from that dataframe. You will need to know the schema of the json. Here is how -
val sparkSession = //create spark session
import sparkSession.implicits._
val jsonData = """{"a":547.65 , "b":"Some Data"}"""
val schema = {StructType(
List(
StructField("a", DoubleType, nullable = false),
StructField("b", StringType, nullable = false)
))}
val df = sparkSession.createDataset(Seq(("dummy data",jsonData))).toDF("string_column","json_column")
val dfWithParsedJson = df.withColumn("json_data",from_json($"json_column",schema))
dfWithParsedJson.select($"string_column",$"json_column",$"json_data.a", $"json_data.b").show()
Result
+-------------+------------------------------+------+---------+
|string_column|json_column |a |b |
+-------------+------------------------------+------+---------+
|dummy data |{"a":547.65 , "b":"Some Data"}|547.65|Some Data|
+-------------+------------------------------+------+---------+
I am trying to use Spark for processing JSON data with variable structure(nested JSON). Input JSON data could be very large with more than 1000 of keys per row and one batch could be more than 20 GB.
Entire batch has been generated from 30 data sources and 'key2' of each JSON can be used to identify the source and structure for each source is predefined.
What would be the best approach for processing such data?
I have tried using from_json like below but it works only with fixed schema and to use it first I need to group the data based on each source and then apply the schema.
Due to large data volume my preferred choice is to scan the data only once and extract required values from each source, based on predefined schema.
import org.apache.spark.sql.types._
import spark.implicits._
val data = sc.parallelize(
"""{"key1":"val1","key2":"source1","key3":{"key3_k1":"key3_v1"}}"""
:: Nil)
val df = data.toDF
val schema = (new StructType)
.add("key1", StringType)
.add("key2", StringType)
.add("key3", (new StructType)
.add("key3_k1", StringType))
df.select(from_json($"value",schema).as("json_str"))
.select($"json_str.key3.key3_k1").collect
res17: Array[org.apache.spark.sql.Row] = Array([xxx])
This is just a restatement of #Ramesh Maharjan's answer, but with more modern Spark syntax.
I found this method lurking in DataFrameReader which allows you to parse JSON strings from a Dataset[String] into an arbitrary DataFrame and take advantage of the same schema inference Spark gives you with spark.read.json("filepath") when reading directly from a JSON file. The schema of each row can be completely different.
def json(jsonDataset: Dataset[String]): DataFrame
Example usage:
val jsonStringDs = spark.createDataset[String](
Seq(
("""{"firstname": "Sherlock", "lastname": "Holmes", "address": {"streetNumber": 121, "street": "Baker", "city": "London"}}"""),
("""{"name": "Amazon", "employeeCount": 500000, "marketCap": 817117000000, "revenue": 177900000000, "CEO": "Jeff Bezos"}""")))
jsonStringDs.show
jsonStringDs:org.apache.spark.sql.Dataset[String] = [value: string]
+----------------------------------------------------------------------------------------------------------------------+
|value
|
+----------------------------------------------------------------------------------------------------------------------+
|{"firstname": "Sherlock", "lastname": "Holmes", "address": {"streetNumber": 121, "street": "Baker", "city": "London"}}|
|{"name": "Amazon", "employeeCount": 500000, "marketCap": 817117000000, "revenue": 177900000000, "CEO": "Jeff Bezos"} |
+----------------------------------------------------------------------------------------------------------------------+
val df = spark.read.json(jsonStringDs)
df.show(false)
df:org.apache.spark.sql.DataFrame = [CEO: string, address: struct ... 6 more fields]
+----------+------------------+-------------+---------+--------+------------+------+------------+
|CEO |address |employeeCount|firstname|lastname|marketCap |name |revenue |
+----------+------------------+-------------+---------+--------+------------+------+------------+
|null |[London,Baker,121]|null |Sherlock |Holmes |null |null |null |
|Jeff Bezos|null |500000 |null |null |817117000000|Amazon|177900000000|
+----------+------------------+-------------+---------+--------+------------+------+------------+
The method is available from Spark 2.2.0:
http://spark.apache.org/docs/2.2.0/api/scala/index.html#org.apache.spark.sql.DataFrameReader#json(jsonDataset:org.apache.spark.sql.Dataset[String]):org.apache.spark.sql.DataFrame
If you have data as you mentioned in the question as
val data = sc.parallelize(
"""{"key1":"val1","key2":"source1","key3":{"key3_k1":"key3_v1"}}"""
:: Nil)
You don't need to create schema for json data. Spark sql can infer schema from the json string. You just have to use SQLContext.read.json as below
val df = sqlContext.read.json(data)
which will give you schema as below for the rdd data used above
root
|-- key1: string (nullable = true)
|-- key2: string (nullable = true)
|-- key3: struct (nullable = true)
| |-- key3_k1: string (nullable = true)
And you can just select key3_k1 as
df2.select("key3.key3_k1").show(false)
//+-------+
//|key3_k1|
//+-------+
//|key3_v1|
//+-------+
You can manipulate the dataframe as you wish. I hope the answer is helpful
I am not sure if my suggestion can help you although I had a similar case and I solved it as follows:
1) So the idea is to use json rapture (or some other json library) to
load JSON schema dynamically. For instance you could read the 1st
row of the json file to discover the schema(similarly to what I do
here with jsonSchema)
2) Generate schema dynamically. First iterate through the dynamic
fields (notice that I project values of key3 as Map[String, String])
and add a StructField for each one of them to schema
3) Apply the generated schema into your dataframe
import rapture.json._
import jsonBackends.jackson._
val jsonSchema = """{"key1":"val1","key2":"source1","key3":{"key3_k1":"key3_v1", "key3_k2":"key3_v2", "key3_k3":"key3_v3"}}"""
val json = Json.parse(jsonSchema)
import scala.collection.mutable.ArrayBuffer
import org.apache.spark.sql.types.StructField
import org.apache.spark.sql.types.{StringType, StructType}
val schema = ArrayBuffer[StructField]()
//we could do this dynamic as well with json rapture
schema.appendAll(List(StructField("key1", StringType), StructField("key2", StringType)))
val items = ArrayBuffer[StructField]()
json.key3.as[Map[String, String]].foreach{
case(k, v) => {
items.append(StructField(k, StringType))
}
}
val complexColumn = new StructType(items.toArray)
schema.append(StructField("key3", complexColumn))
import org.apache.spark.SparkConf
import org.apache.spark.sql.SparkSession
val sparkConf = new SparkConf().setAppName("dynamic-json-schema").setMaster("local")
val spark = SparkSession.builder().config(sparkConf).getOrCreate()
val jsonDF = spark.read.schema(StructType(schema.toList)).json("""your_path\data.json""")
jsonDF.select("key1", "key2", "key3.key3_k1", "key3.key3_k2", "key3.key3_k3").show()
I used the next data as input:
{"key1":"val1","key2":"source1","key3":{"key3_k1":"key3_v11", "key3_k2":"key3_v21", "key3_k3":"key3_v31"}}
{"key1":"val2","key2":"source2","key3":{"key3_k1":"key3_v12", "key3_k2":"key3_v22", "key3_k3":"key3_v32"}}
{"key1":"val3","key2":"source3","key3":{"key3_k1":"key3_v13", "key3_k2":"key3_v23", "key3_k3":"key3_v33"}}
And the output:
+----+-------+--------+--------+--------+
|key1| key2| key3_k1| key3_k2| key3_k3|
+----+-------+--------+--------+--------+
|val1|source1|key3_v11|key3_v21|key3_v31|
|val2|source2|key3_v12|key3_v22|key3_v32|
|val2|source3|key3_v13|key3_v23|key3_v33|
+----+-------+--------+--------+--------+
An advanced alternative, which I haven't tested yet, would be to generate a case class e.g called JsonRow from the JSON schema in order to have a strongly typed dataset which provides better serialization performance apart the fact that make your code more maintainable. To make this work you need first to create a JsonRow.scala file then you should implement a sbt pre-build script which will modify the content of JsonRow.scala(you might have more than one of course) dynamically based on your source files. To generate class JsonRow dynamically you can use the next code:
def generateClass(members: Map[String, String], name: String) : Any = {
val classMembers = for (m <- members) yield {
s"${m._1}: String"
}
val classDef = s"""case class ${name}(${classMembers.mkString(",")});scala.reflect.classTag[${name}].runtimeClass"""
classDef
}
The method generateClass accepts a map of strings to create the class members and the class name itself. The members of the generated class you can again populate them from you json schema:
import org.codehaus.jackson.node.{ObjectNode, TextNode}
import collection.JavaConversions._
val mapping = collection.mutable.Map[String, String]()
val fields = json.$root.value.asInstanceOf[ObjectNode].getFields
for (f <- fields) {
(f.getKey, f.getValue) match {
case (k: String, v: TextNode) => mapping(k) = v.asText
case (k: String, v: ObjectNode) => v.getFields.foreach(f => mapping(f.getKey) = f.getValue.asText)
case _ => None
}
}
val dynClass = generateClass(mapping.toMap, "JsonRow")
println(dynClass)
This prints out:
case class JsonRow(key3_k2: String,key3_k1: String,key1: String,key2: String,key3_k3: String);scala.reflect.classTag[JsonRow].runtimeClass
Good luck
I have a data set that comes in as XML, and one of the nodes contains JSON. Spark is reading this in as a StringType, so I am trying to use from_json() to convert the JSON to a DataFrame.
I am able to convert a string of JSON, but how do I write the schema to work with an Array?
String without Array - Working nicely
import org.apache.spark.sql.functions._
val schemaExample = new StructType()
.add("FirstName", StringType)
.add("Surname", StringType)
val dfExample = spark.sql("""select "{ \"FirstName\":\"Johnny\", \"Surname\":\"Boy\" }" as theJson""")
val dfICanWorkWith = dfExample.select(from_json($"theJson", schemaExample))
dfICanWorkWith.collect()
// Results \\
res19: Array[org.apache.spark.sql.Row] = Array([[Johnny,Boy]])
String with an Array - Can't figure this one out
import org.apache.spark.sql.functions._
val schemaExample2 = new StructType()
.add("", ArrayType(new StructType()
.add("FirstName", StringType)
.add("Surname", StringType)
)
)
val dfExample2= spark.sql("""select "[{ \"FirstName\":\"Johnny\", \"Surname\":\"Boy\" }, { \"FirstName\":\"Franky\", \"Surname\":\"Man\" }" as theJson""")
val dfICanWorkWith = dfExample2.select(from_json($"theJson", schemaExample2))
dfICanWorkWith.collect()
// Result \\
res22: Array[org.apache.spark.sql.Row] = Array([null])
The problem is that you don't have a fully qualified json. Your json is missing a couple of things:
First you are missing the surrounding {} in which the json is done
Second you are missing the variable value (you set it as "" but did not add it)
Lastly you are missing the closing ]
Try replacing it with:
val dfExample2= spark.sql("""select "{\"\":[{ \"FirstName\":\"Johnny\", \"Surname\":\"Boy\" }, { \"FirstName\":\"Franky\", \"Surname\":\"Man\" }]}" as theJson""")
and you will get:
scala> dfICanWorkWith.collect()
res12: Array[org.apache.spark.sql.Row] = Array([[WrappedArray([Johnny,Boy], [Franky,Man])]])
as of spark 2.4 the schema_of_json function helps:
> SELECT schema_of_json('[{"col":0}]');
array<struct<col:int>>
in your case you can then use the below code to parse that array of son objects:
scala> spark.sql("""select from_json("[{ \"FirstName\":\"Johnny\", \"Surname\":\"Boy\" }, { \"FirstName\":\"Franky\", \"Surname\":\"Man\" }]", 'array<struct<FirstName:string,Surname:string>>' ) as theJson""").show(false)
+------------------------------+
|theJson |
+------------------------------+
|[[Johnny, Boy], [Franky, Man]]|
+------------------------------+
Has anyone parsed a millisecond timestamp using from_json in Spark 2+? How's it done?
So Spark changed the TimestampType to parse epoch numerical values as being in seconds instead of millis in v2.
My input is a hive table that has a json formatted string in a column which I'm trying to parse like this:
val spark = SparkSession
.builder
.appName("Problematic Timestamps")
.enableHiveSupport()
.getOrCreate()
import spark.implicits._
val schema = StructType(
StructField("categoryId", LongType) ::
StructField("cleared", BooleanType) ::
StructField("dataVersion", LongType) ::
StructField("details", DataTypes.createArrayType(StringType)) ::
…
StructField("timestamp", TimestampType) ::
StructField("version", StringType) :: Nil
)
val item_parsed =
spark.sql("select * FROM source.jsonStrInOrc")
.select('itemid, 'locale,
from_json('internalitem, schema)
as 'internalitem,
'version, 'createdat, 'modifiedat)
val item_flattened = item_parsed
.select('itemid, 'locale,
$"internalitem.*",
'version as'outer_version, 'createdat, 'modifiedat)
This can parse a row with a column containing:
{"timestamp": 1494790299549, "cleared": false, "version": "V1", "dataVersion": 2, "categoryId": 2641, "details": [], …}
And that gives me timestamp fields like 49338-01-08 00:39:09.0 from a value 1494790299549 which I'd rather read as: 2017-05-14 19:31:39.549
Now I could set the schema for timestamp to be a long, then divide the value by 1000 and cast to a timestamp, but then I'd have 2017-05-14 19:31:39.000 not 2017-05-14 19:31:39.549. I'm having trouble figuring out how I could either:
Tell from_json to parse a millisecond timestamp (maybe by subclassing the TimestampType in some way to use in the schema)
Use a LongType in the schema and cast that to a Timestamp which preserves the milliseconds.
Addendum on UDFs
I found that trying to do the division in the select and then casting didn't look clean to me, though it's a perfectly valid method. I opted for a UDF that used a java.sql.timestamp which is actually specified in epoch milliseconds.
import java.sql.Timestamp
import org.apache.spark.sql.SparkSession
import org.apache.spark.sql.functions.{explode, from_json, udf}
import org.apache.spark.sql.types.
{BooleanType, DataTypes, IntegerType, LongType,
StringType, StructField, StructType, TimestampType}
val tsmillis = udf { t: Long => new Timestamp (t) }
val spark = SparkSession
.builder
.appName("Problematic Timestamps")
.enableHiveSupport()
.getOrCreate()
import spark.implicits._
val schema = StructType(
StructField("categoryId", LongType) ::
StructField("cleared", BooleanType) ::
StructField("dataVersion", LongType) ::
StructField("details", DataTypes.createArrayType(StringType)) ::
…
StructField("timestamp", LongType) ::
StructField("version", StringType) :: Nil
)
val item_parsed =
spark.sql("select * FROM source.jsonStrInOrc")
.select('itemid, 'locale,
from_json('internalitem, schema)
as 'internalitem,
'version, 'createdat, 'modifiedat)
val item_flattened = item_parsed
.select('itemid, 'locale,
$"internalitem.categoryId", $"internalitem.cleared",
$"internalitem.dataVersion", $"internalitem.details",
tsmillis($"internalitem.timestamp"),
$"internalitem.version",
'version as'outer_version, 'createdat, 'modifiedat)
See how that's in the select.
I think it would be worthwhile to do a performance test to see if using withcolumn division and casting is faster than the udf.
Now I could set the schema for timestamp to be a long, then divide the value by 1000
Actually this exactly what you need, just keep the types right. Let's say you have only Long timestamp field:
val df = spark.range(0, 1).select(lit(1494790299549L).alias("timestamp"))
// df: org.apache.spark.sql.DataFrame = [timestamp: bigint]
If you divide by 1000:
val inSeconds = df.withColumn("timestamp_seconds", $"timestamp" / 1000)
// org.apache.spark.sql.DataFrame = [timestamp: bigint, timestamp_seconds: double]
you'll get timestamp in seconds as double (note that this is SQL, not Scala behavior).
All what is left is cast (Spark < 3.1)
inSeconds.select($"timestamp_seconds".cast("timestamp")).show(false)
// +-----------------------+
// |timestamp_seconds |
// +-----------------------+
// |2017-05-14 21:31:39.549|
// +-----------------------+
or (Spark >= 3.1) timestamp_seconds (or directly timestamp_millis)
import org.apache.spark.sql.functions.{expr, timestamp_seconds}
inSeconds.select(timestamp_seconds($"timestamp_seconds")).show(false)
// +------------------------------------+
// |timestamp_seconds(timestamp_seconds)|
// +------------------------------------+
// |2017-05-14 21:31:39.549 |
// +------------------------------------+
df.select(expr("timestamp_millis(timestamp)")).show(false)
// +---------------------------+
// |timestamp_millis(timestamp)|
// +---------------------------+
// |2017-05-14 21:31:39.549 |
// +---------------------------+
I am trying to load a CSV file into a Spark data frame with spark-csv [1] using an Apache Zeppelin notebook and when loading a numeric field that doesn't have value the parser fails for that line and the line gets skipped.
I would have expected the line to get loaded and the value in the data frame load the line and have the value set to NULL so that aggregations just ignore the value.
%dep
z.reset()
z.addRepo("my-nexus").url("<my_local_nexus_repo_that_is_a_proxy_of_public_repos>")
z.load("com.databricks:spark-csv_2.10:1.1.0")
%spark
import org.apache.spark.sql.SQLContext
import org.apache.spark.sql.types._
import com.databricks.spark.csv._
import org.apache.spark.sql.functions._
val schema = StructType(
StructField("identifier", StringType, true) ::
StructField("name", StringType, true) ::
StructField("height", DoubleType, true) ::
Nil)
val sqlContext = new SQLContext(sc)
val df = sqlContext.read.format("com.databricks.spark.csv")
.schema(schema)
.option("header", "true")
.load("file:///home/spark_user/data.csv")
df.describe("height").show()
Here is the content of the data file: /home/spark_user/data.csv
identifier,name,height
1,sam,184
2,cath,180
3,santa, <-- note that there is not height recorded for Santa !
Here is the output:
+-------+------+
|summary|height|
+-------+------+
| count| 2| <- 2 of 3 lines loaded, ie. sam and cath
| mean| 182.0|
| stddev| 2.0|
| min| 180.0|
| max| 184.0|
+-------+------+
In the logs of zeppelin I can see the following error on parsing santa's line:
ERROR [2015-07-21 16:42:09,940] ({Executor task launch worker-45} CsvRelation.scala[apply]:209) - Exception while parsing line: 3,santa,.
java.lang.NumberFormatException: empty String
at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1842)
at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
at java.lang.Double.parseDouble(Double.java:538)
at scala.collection.immutable.StringLike$class.toDouble(StringLike.scala:232)
at scala.collection.immutable.StringOps.toDouble(StringOps.scala:31)
at com.databricks.spark.csv.util.TypeCast$.castTo(TypeCast.scala:42)
at com.databricks.spark.csv.CsvRelation$$anonfun$com$databricks$spark$csv$CsvRelation$$parseCSV$1.apply(CsvRelation.scala:198)
at com.databricks.spark.csv.CsvRelation$$anonfun$com$databricks$spark$csv$CsvRelation$$parseCSV$1.apply(CsvRelation.scala:180)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
at org.apache.spark.sql.execution.Aggregate$$anonfun$doExecute$1$$anonfun$6.apply(Aggregate.scala:129)
at org.apache.spark.sql.execution.Aggregate$$anonfun$doExecute$1$$anonfun$6.apply(Aggregate.scala:126)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$17.apply(RDD.scala:686)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1$$anonfun$apply$17.apply(RDD.scala:686)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:35)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:277)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:244)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:35)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:277)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:244)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:70)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
at org.apache.spark.scheduler.Task.run(Task.scala:70)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:213)
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)
So you might tell me so far so good ... and you'd be right ;)
Now I want to add an extra column, say age and I always have data in that field.
identifier,name,height,age
1,sam,184,30
2,cath,180,32
3,santa,,70
Now ask politely for some stats about age:
%spark
import org.apache.spark.sql.SQLContext
import org.apache.spark.sql.types._
import com.databricks.spark.csv._
import org.apache.spark.sql.functions._
val schema = StructType(
StructField("identifier", StringType, true) ::
StructField("name", StringType, true) ::
StructField("height", DoubleType, true) ::
StructField("age", DoubleType, true) ::
Nil)
val sqlContext = new SQLContext(sc)
val df = sqlContext.read.format("com.databricks.spark.csv")
.schema(schema)
.option("header", "true")
.load("file:///home/spark_user/data2.csv")
df.describe("age").show()
Results
+-------+----+
|summary| age|
+-------+----+
| count| 2|
| mean|31.0|
| stddev| 1.0|
| min|30.0|
| max|32.0|
+-------+----+
ALL WRONG ! Since santa's height is not known, the whole line is lost and the calculation of age is only based on Sam and Cath while Santa has a perfectly valid age.
My question is what value do I need to plug in Santa's height so that the CSV can be loaded. I have tried to set the schema to be all StringType but then
The next question is more about
I have found in the API that one can handle N/A values using spark. SO I thought maybe I could load my data with all columns set to StringType and then do some cleanup and then only set the schema properly as written below:
%spark
import org.apache.spark.sql.SQLContext
import org.apache.spark.sql.types._
import com.databricks.spark.csv._
import org.apache.spark.sql.functions._
val schema = StructType(
StructField("identifier", StringType, true) ::
StructField("name", StringType, true) ::
StructField("height", StringType, true) ::
StructField("age", StringType, true) ::
Nil)
val sqlContext = new SQLContext(sc)
val df = sqlContext.read.format("com.databricks.spark.csv").schema(schema).option("header", "true").load("file:///home/spark_user/data.csv")
// eg. for each column of my dataframe, replace empty string by null
df.na.replace( "*", Map("" -> null) )
val toDouble = udf[Double, String]( _.toDouble)
df2 = df.withColumn("age", toDouble(df("age")))
df2.describe("age").show()
But df.na.replace() throws an exception and stops:
java.lang.IllegalArgumentException: Unsupported value type java.lang.String ().
at org.apache.spark.sql.DataFrameNaFunctions.org$apache$spark$sql$DataFrameNaFunctions$$convertToDouble(DataFrameNaFunctions.scala:417)
at org.apache.spark.sql.DataFrameNaFunctions$$anonfun$4.apply(DataFrameNaFunctions.scala:337)
at org.apache.spark.sql.DataFrameNaFunctions$$anonfun$4.apply(DataFrameNaFunctions.scala:337)
at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:244)
at scala.collection.immutable.Map$Map1.foreach(Map.scala:109)
at scala.collection.TraversableLike$class.map(TraversableLike.scala:244)
at scala.collection.AbstractTraversable.map(Traversable.scala:105)
at org.apache.spark.sql.DataFrameNaFunctions.replace0(DataFrameNaFunctions.scala:337)
at org.apache.spark.sql.DataFrameNaFunctions.replace(DataFrameNaFunctions.scala:304)
Any help, & tips much appreciated !!
[1] https://github.com/databricks/spark-csv
Spark-csv lacks this option. It has been fixed in master branch. I guess you should use it or wait for the next stable version.