pyspark add multiple columns in grouped applyInPandas (change schema)

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I have a simple function in pandas for handling time-series. My problem is: the number of time-series I want to apply it to is very large. So I want to use pySpark to scale it out.

I face 2 problems:

  • The schema must be passed explicitly can this made somewhat smoother to be passed implicitly?
  • The code fails with: Number of columns of the returned pandas.DataFrame doesn't match specified schema. Expected: 2 Actual: 3 -- how can I ensure that the schema is automatically matched? Notice: I do not want to manually specify it (ideally). In the worst case scenario - could I apply my function to a single time series and have the outputs of the pandas dataframes dtypes converted over to sparks expected schema?

pandas function

import pandas as pd
from pandas import Timestamp

df = pd.DataFrame({'time':['2020-01-01 00:00', '2020-01-01 03:00', '2020-01-01 04:00', '2020-01-06 00:00'], 'category':['1','1','1','1'], 'value':[5, 8, 7, 2]})
df['time'] = pd.to_datetime(df['time'])
display(df)
print(df.shape)

def my_complex_function(pdf):
    # fill missing hours
    pdf = pdf.set_index('time').resample('H').mean().fillna(0)
    
    # some complex computation/business logic which is adding columns/simplified here:
    pdf['foo'] = 'bar'
    pdf['baz'] = 123
    return pdf

print(df.groupby(['category']).apply(my_complex_function).reset_index().shape)

pyspark function

NOTICE: the version of Spark is: v3.0.1

from pyspark.sql import SparkSession
spark = SparkSession.builder.appName("anomlydetection").master("local[4]").config("spark.driver.memory", "2G").getOrCreate()
sdf = spark.createDataFrame(df)
sdf.printSchema()

def my_complex_function_spark(pdf: pd.DataFrame)-> pd.DataFrame:
    # fill missing hours
    pdf = pdf.set_index('time').resample('H').mean().fillna(0)
    
    # some complex computation/business logic which is adding columns/simplified here:
    pdf['foo'] = 'bar'
    pdf['baz'] = 123
    return pdf

# 1) can I somehow implicitly get a reference to the schema?
# 2) this function fails due to schema mismatch
sdf.groupby("category").applyInPandas(my_complex_function_spark, schema=df.schema).show()
pyspark pandas apache-spark group-by python
2 Answers

To define return_schema for ApplyInPandas, a more robust way is to use p.s.t.StructType.fromJson method and df.schema.jsonValue method which can keep all existing column attributes (nullable, metadata etc.) from the original columns. (Note: the mismatched nullable setting can often lead to bugs which are not easy to detect)

Some examples:

  1. append new columns by using StructType.add method, this is the most common use case (example):

    from pyspark.sql.types import StructType

return_schema = StructType.fromJson(df.schema.jsonValue()) \
    .add('foo', 'string', False, "dummu string field") \
    .add('bar', 'integer')

  2. drop existing columns and append new columns:

    return_schema = StructType.fromJson(df.drop("col1", "col2").schema.jsonValue()) \
    .add('foo', 'string')

  3. set up arbitrary order of columns mixed with new columns (for primary data types only, be caution with array, map, struct and the nested data types):

    return_schema = df.selectExpr("col1", "cast('1' as string) as foo", "nested_col", "int(NULL) as bar").schema

    notice for new columns, nullable can be inferred by specifying a NULL or non-NULL zero_value, see below examples:

    cast('1' as string) as foo -> nullable is False
string(NULL) as foo        -> nullable is True

int(123) as bar            -> nullable is False
cast(NULL as int) as bar   -> nullable is True

    so if the metadata attribute for all new columns is not required, this method is fine and provides flexibility. A special case is when the return_schema is unchanged which we can use return_schema = df.schema. the schema of the first example above without the metadata can be:

    return_schema = df.selectExpr("*", "string('') as foo", "int(NULL) as bar").schema

    For complex data types, below is an example of a new StructType column with nullable setting:

    # specify `nullable` attribute of the StructField
my_structs = StructType().add('f1', 'int', False).add('f2', 'string')

# specify `nullable=False` for the StructType
return_schema = df.select("*", F.struct(F.lit(0),F.lit('1')).cast(my_structs).alias('s1')).schema
# specify `nullable=True` for the StructType
return_schema = df.select("*", F.lit(None).cast(my_structs).alias('s2')).schema

My suggestion: No need to manually specify return_schema which can be tedious and error-prone, use as much information as possible from the existing schema and do NOT completely rely on dynamic inferring.

user_95107290

Implicit schema for pandas_udf in PySpark? gives a great hint for the solution.

That approach translates here to the following (see the code below). I need to also support nested structs for my real data - and need perform some more testing on how to get these to work as well.

def my_complex_function_spark(pdf: pd.DataFrame)-> pd.DataFrame:
    # fill missing hours
    
    pdf = pdf.set_index('time').resample('H').mean().fillna(0).reset_index()
    
    # some complex computation/business logic which is adding columns/simplified here:
    pdf['foo'] = 'bar'
    pdf['baz'] = 123
    return pdf

from pyspark.sql.types import *

mapping = {"float64": DoubleType,
           "object":StringType,
           "datetime64[ns]":TimestampType,
           "int64":IntegerType} # Incomplete - extend with your types.

def createUDFSchemaFromPandas(dfp):
  column_types  = [StructField(key, mapping[str(dfp.dtypes[key])]()) for key in dfp.columns]
  schema = StructType(column_types)
  return schema


# certainly use some kind of limit here for real data
df_pd = sdf.toPandas()
df_return = my_complex_function_spark(df_pd)
schema = createUDFSchemaFromPandas(df_return)
sdf.groupby("category").applyInPandas(my_complex_function_spark, schema=schema).show()
user_25879040
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