pyspark/dataframe - creating a nested structure - pyspark

i'm using pyspark with dataframe and would like to create a nested structure as below
Before:
Column 1 | Column 2 | Column 3
--------------------------------
A | B | 1
A | B | 2
A | C | 1
After:
Column 1 | Column 4
--------------------------------
A | [B : [1,2]]
A | [C : [1]]
Is this doable?

I don't think you can get that exact output, but you can come close. The problem is your key names for the column 4. In Spark, structs need to have a fixed set of columns known in advance. But let's leave that for later, first, the aggregation:
import pyspark
from pyspark.sql import functions as F
sc = pyspark.SparkContext()
spark = pyspark.sql.SparkSession(sc)
data = [('A', 'B', 1), ('A', 'B', 2), ('A', 'C', 1)]
columns = ['Column1', 'Column2', 'Column3']
data = spark.createDataFrame(data, columns)
data.createOrReplaceTempView("data")
data.show()
# Result
+-------+-------+-------+
|Column1|Column2|Column3|
+-------+-------+-------+
| A| B| 1|
| A| B| 2|
| A| C| 1|
+-------+-------+-------+
nested = spark.sql("SELECT Column1, Column2, STRUCT(COLLECT_LIST(Column3) AS data) AS Column4 FROM data GROUP BY Column1, Column2")
nested.toJSON().collect()
# Result
['{"Column1":"A","Column2":"C","Column4":{"data":[1]}}',
'{"Column1":"A","Column2":"B","Column4":{"data":[1,2]}}']
Which is almost what you want, right? The problem is that if you do not know your key names in advance (that is, the values in Column 2), Spark cannot determine the structure of your data. Also, I am not entirely sure how you can use the value of a column as key for a structure unless you use a UDF (maybe with a PIVOT?):
datatype = 'struct<B:array<bigint>,C:array<bigint>>' # Add any other potential keys here.
#F.udf(datatype)
def replace_struct_name(column2_value, column4_value):
return {column2_value: column4_value['data']}
nested.withColumn('Column5', replace_struct_name(F.col("Column2"), F.col("Column4"))).toJSON().collect()
# Output
['{"Column1":"A","Column2":"C","Column4":{"C":[1]}}',
'{"Column1":"A","Column2":"B","Column4":{"B":[1,2]}}']
This of course has the drawback that the number of keys must be discrete and known in advance, otherwise other key values will be silently ignored.

First, reproducible example of your dataframe.
js = [{"col1": "A", "col2":"B", "col3":1},{"col1": "A", "col2":"B", "col3":2},{"col1": "A", "col2":"C", "col3":1}]
jsrdd = sc.parallelize(js)
sqlContext = SQLContext(sc)
jsdf = sqlContext.read.json(jsrdd)
jsdf.show()
+----+----+----+
|col1|col2|col3|
+----+----+----+
| A| B| 1|
| A| B| 2|
| A| C| 1|
+----+----+----+
Now, lists are not stored as key value pairs. You can either use a dictionary or simple collect_list() after doing a groupby on column2.
jsdf.groupby(['col1', 'col2']).agg(F.collect_list('col3')).show()
+----+----+------------------+
|col1|col2|collect_list(col3)|
+----+----+------------------+
| A| C| [1]|
| A| B| [1, 2]|
+----+----+------------------+

Related

transform distinct row values to different columns with corresponding rows using Pyspark

I'm new to Pyspark and trying to transform data
Given dataframe
Col1
A=id1a A=id2a B=id1b C=id1c B=id2b
D=id1d A=id3a B=id3b C=id2c
A=id4a C=id3c
Required:
A B C
id1a id1b id1c
id2a id2b id2c
id3a id3b id3b
id4a null null
I have tried pivot, but that gives first value.
There might be a better way , however an approach is splitting the column on spaces to create array of the entries and then using higher order functions(spark 2.4+) to split on the '=' for each entry in the splitted array .Then explode and create 2 columns one with the id and one with the value. Then we can assign a row number to each partition and groupby then pivot:
import pyspark.sql.functions as F
df1 = (df.withColumn("Col1",F.split(F.col("Col1"),"\s+")).withColumn("Col1",
F.explode(F.expr("transform(Col1,x->split(x,'='))")))
.select(F.col("Col1")[0].alias("cols"),F.col("Col1")[1].alias("vals")))
from pyspark.sql import Window
w = Window.partitionBy("cols").orderBy("cols")
final = (df1.withColumn("Rnum",F.row_number().over(w)).groupBy("Rnum")
.pivot("cols").agg(F.first("vals")).orderBy("Rnum"))
final.show()
+----+----+----+----+----+
|Rnum| A| B| C| D|
+----+----+----+----+----+
| 1|id1a|id1b|id1c|id1d|
| 2|id2a|id2b|id2c|null|
| 3|id3a|id3b|id3c|null|
| 4|id4a|null|null|null|
+----+----+----+----+----+
this is how df1 looks like after the transformation:
df1.show()
+----+----+
|cols|vals|
+----+----+
| A|id1a|
| A|id2a|
| B|id1b|
| C|id1c|
| B|id2b|
| D|id1d|
| A|id3a|
| B|id3b|
| C|id2c|
| A|id4a|
| C|id3c|
+----+----+
May be I don't know the full picture, but the data format seems to be strange. If nothing can be done at the data source, then some collects, pivots and joins will be needed. Try this.
import pyspark.sql.functions as F
test = sqlContext.createDataFrame([('A=id1a A=id2a B=id1b C=id1c B=id2b',1),('D=id1d A=id3a B=id3b C=id2c',2),('A=id4a C=id3c',3)],schema=['col1','id'])
tst_spl = test.withColumn("item",(F.split('col1'," ")))
tst_xpl = tst_spl.select(F.explode("item"))
tst_map = tst_xpl.withColumn("key",F.split('col','=')[0]).withColumn("value",F.split('col','=')[1]).drop('col')
#%%
tst_pivot = tst_map.groupby(F.lit(1)).pivot('key').agg(F.collect_list(('value'))).drop('1')
#%%
tst_arr = [tst_pivot.select(F.posexplode(coln)).withColumnRenamed('col',coln) for coln in tst_pivot.columns]
tst_fin = reduce(lambda df1,df2:df1.join(df2,on='pos',how='full'),tst_arr).orderBy('pos')
tst_fin.show()
+---+----+----+----+----+
|pos| A| B| C| D|
+---+----+----+----+----+
| 0|id3a|id3b|id1c|id1d|
| 1|id4a|id1b|id2c|null|
| 2|id1a|id2b|id3c|null|
| 3|id2a|null|null|null|
+---+----+----+----+----

How to convert numerical values to a categorical variable using pyspark

pyspark dataframe which have a range of numerical variables.
for eg
my dataframe have a column value from 1 to 100.
1-10 - group1<== the column value for 1 to 10 should contain group1 as value
11-20 - group2
.
.
.
91-100 group10
how can i achieve this using pyspark dataframe
# Creating an arbitrary DataFrame
df = spark.createDataFrame([(1,54),(2,7),(3,72),(4,99)], ['ID','Var'])
df.show()
+---+---+
| ID|Var|
+---+---+
| 1| 54|
| 2| 7|
| 3| 72|
| 4| 99|
+---+---+
Once the DataFrame has been created, we use floor() function to find the integral part of a number. For eg; floor(15.5) will be 15. We need to find the integral part of the Var/10 and add 1 to it, because the indexing starts from 1, as opposed to 0. Finally, we have need to prepend group to the value. Concatenation can be achieved with concat() function, but keep in mind that since the prepended word group is not a column, so we need to put it inside lit() which creates a column of a literal value.
# Requisite packages needed
from pyspark.sql.functions import col, floor, lit, concat
df = df.withColumn('Var',concat(lit('group'),(1+floor(col('Var')/10))))
df.show()
+---+-------+
| ID| Var|
+---+-------+
| 1| group6|
| 2| group1|
| 3| group8|
| 4|group10|
+---+-------+

Pyspark: Delete rows on column condition after groupBy

This is my input dataframe:
id val
1 Y
1 N
2 a
2 b
3 N
Result should be:
id val
1 Y
2 a
2 b
3 N
I want to group by on col id which has both Y and N in the val and then remove the row where the column val contains "N".
Please help me resolve this issue as i am beginner to pyspark
you can first identify the problematic rows with a filter for val=="Y" and then join this dataframe back to the original one. Finally you can filter for Null values and for the rows you want to keep, e.g. val==Y. Pyspark should be able to handle the self-join even if there are a lot of rows.
The example is shown below:
df_new = spark.createDataFrame([
(1, "Y"), (1, "N"), (1,"X"), (1,"Z"),
(2,"a"), (2,"b"), (3,"N")
], ("id", "val"))
df_Y = df_new.filter(col("val")=="Y").withColumnRenamed("val","val_Y").withColumnRenamed("id","id_Y")
df_new = df_new.join(df_Y, df_new["id"]==df_Y["id_Y"],how="left")
df_new.filter((col("val_Y").isNull()) | ((col("val_Y")=="Y") & ~(col("val")=="N"))).select("id","val").show()
The result would be your preferred:
+---+---+
| id|val|
+---+---+
| 1| X|
| 1| Y|
| 1| Z|
| 3| N|
| 2| a|
| 2| b|
+---+---+

Randomly join two dataframes

I have two tables, one called Reasons that has 9 records and another containing IDs with 40k records.
IDs:
+------+------+
|pc_pid|pc_aid|
+------+------+
| 4569| 1101|
| 63961| 1101|
|140677| 4364|
|127113| 7|
| 96097| 480|
| 8309| 3129|
| 45218| 89|
|147036| 3289|
| 88493| 3669|
| 29973| 3129|
|127444| 3129|
| 36095| 89|
|131001| 1634|
|104731| 781|
| 79219| 244|
+-------------+
Reasons:
+-----------------+
| reasons|
+-----------------+
| follow up|
| skin chk|
| annual meet|
|review lab result|
| REF BY DR|
| sick visit|
| body pain|
| test|
| other|
+-----------------+
I want output like this
|pc_pid|pc_aid| reason
+------+------+-------------------
| 4569| 1101| body pain
| 63961| 1101| review lab result
|140677| 4364| body pain
|127113| 7| sick visit
| 96097| 480| test
| 8309| 3129| other
| 45218| 89| follow up
|147036| 3289| annual meet
| 88493| 3669| review lab result
| 29973| 3129| REF BY DR
|127444| 3129| skin chk
| 36095| 89| other
In the reasons I have only 9 records and in the ID dataframe I have 40k records, I want to assign reason randomly to each and every id.
The following solution tries to be more robust to the number of reasons (ie. you can have as many reasons as you can reasonably fit in your cluster). If you just have few reasons (like the OP asks), you can probably broadcast them or embed them in a udf and easily solve this problem.
The general idea is to create an index (sequential) for the reasons and then random values from 0 to N (where N is the number of reasons) on the IDs dataset and then join the two tables using these two new columns. Here is how you can do this:
case class Reasons(s: String)
defined class Reasons
case class Data(id: Long)
defined class Data
Data will hold the IDs (simplified version of the OP) and Reasons will hold some simplified reasons.
val d1 = spark.createDataFrame( Data(1) :: Data(2) :: Data(10) :: Nil)
d1: org.apache.spark.sql.DataFrame = [id: bigint]
d1.show()
+---+
| id|
+---+
| 1|
| 2|
| 10|
+---+
val d2 = spark.createDataFrame( Reasons("a") :: Reasons("b") :: Reasons("c") :: Nil)
+---+
| s|
+---+
| a|
| b|
| c|
+---+
We will later need the number of reasons so we calculate that first.
val numerOfReasons = d2.count()
val d2Indexed = spark.createDataFrame(d2.rdd.map(_.getString(0)).zipWithIndex)
d2Indexed.show()
+---+---+
| _1| _2|
+---+---+
| a| 0|
| b| 1|
| c| 2|
+---+---+
val d1WithRand = d1.select($"id", (rand * numerOfReasons).cast("int").as("rnd"))
The last step is to join on the new columns and the remove them.
val res = d1WithRand.join(d2Indexed, d1WithRand("rnd") === d2Indexed("_2")).drop("_2").drop("rnd")
res.show()
+---+---+
| id| _1|
+---+---+
| 2| a|
| 10| b|
| 1| c|
+---+---+
pyspark random join itself
data_neg = data_pos.sortBy(lambda x: uniform(1, 10000))
data_neg = data_neg.coalesce(1, False).zip(data_pos.coalesce(1, True))
The fastest way to randomly join dataA (huge dataframe) and dataB (smaller dataframe, sorted by any column):
dfB = dataB.withColumn(
"index", F.row_number().over(Window.orderBy("col")) - 1
)
dfA = dataA.withColumn("index", (F.rand() * dfB.count()).cast("bigint"))
df = dfA.join(dfB, on="index", how="left").drop("index")
Since dataB is already sorted, row numbers can be assigned over sorted window with high degree of parallelism. F.rand() is another highly parallel function, so adding index to dataA will be very fast as well.
If dataB is small enough, you may benefit from broadcasting it.
This method is better than using:
zipWithIndex: Can be very expensive to convert dataframe to rdd, zipWithIndex, and then to df.
monotonically_increasing_id: Need to be used with row_number which will collect all the partitions into a single executor.
Reference: https://towardsdatascience.com/adding-sequential-ids-to-a-spark-dataframe-fa0df5566ff6

tidyr::spread() with plain Scala and Spark (rows to columns)

my prototype (written in R with the packages dplyr and tidyr) is hitting a wall in terms of computational complexity - even on my powerfull working station. Therefore, I want to port the code to Spark using Scala.
I looked up all transformations, actions, functions (SparkSQL) and column operations (also SparkSQL) and found all function equivalents except the one for the tidyr::spread() function, available in R.
df %>% tidyr::spread(key = COL_KEY , value = COL_VAL) basically spreads a key-value pair across multiple columns. E.g. the table
COL_KEY | COL_VAL
-----------------
A | 1
B | 1
A | 2
will be transformed to by
A | B
------------
1 | 0
0 | 1
2 | 1
In case there is no "out-of-the-box"-solution available: Could you point me in the right direction? Maybe a user defined function?
I'm free which Spark (and Scala) version to choose (therefore I'd go for the latest, 2.0.0).
Thanks!
Out-of-the-box but requires a shuffle:
df
// A dummy unique key to perform grouping
.withColumn("_id", monotonically_increasing_id)
.groupBy("_id")
.pivot("COL_KEY")
.agg(first("COL_VAL"))
.drop("_id")
// +----+----+
// | A| B|
// +----+----+
// | 1|null|
// |null| 1|
// | 2|null|
// +----+----+
You can optionally follow it with .na.fill(0).
Manually without shuffle:
// Find distinct keys
val keys = df.select($"COL_KEY").as[String].distinct.collect.sorted
// Create column expressions for each key
val exprs = keys.map(key =>
when($"COL_KEY" === key, $"COL_VAL").otherwise(lit(0)).alias(key)
)
df.select(exprs: _*)
// +---+---+
// | A| B|
// +---+---+
// | 1| 0|
// | 0| 1|
// | 2| 0|
// +---+---+