Perfectly Random

machine learning and stuff

Handling Avro files in Python

Apache Avro is a data serialization format. We can store data as .avro files on disk. Avro files are typically used with Spark but Spark is completely independent of Avro. Avro is a row-based format that is suitable for evolving data schemas. One benefit of using Avro is that schema and metadata travels with the data. If you have an .avro file, you have the schema of the data as well. The Apache Avro Specification provides easy-to-read yet detailed information.

Sadly, using Avro files with python is unnecessarily error-prone, especially for a beginner. In this post, we will describe the common errors and their solutions.

Official Avro Packages

Python 2 vs Python 3

Python 2 is end-of-life. You should not be writing Python 2 code. However, the official Avro Getting Started (Python) Guide is written for Python 2 and will fail with Python 3. The problem goes deeper than merely outdated official documentation.

There are two official python packages for handling Avro, one for Python 2 and one for Python 3. The packages have different names, which is unusual for the python ecosystem1.

Python Version Package Name Example
Python 2 avro avro.schema.parse
Python 3 avro-python3 avro.schema.Parse

The first problem is that you can actually install avro, which is intended for Python 2, in a Python 3 (virtual) environment. But, when you try to use avro in Python 3, it fails.

# Inside a fresh Python 3 virtual environment
python  --version
# Python 3.7.3

# You can successfully install `avro` in a Python 3 virtualenv even though `avro` is not
# compatible with Python 3.
pip install avro

# Fails when you try to use it!
python -c "import avro.schema"
# Traceback (most recent call last):
#   File "<string>", line 1, in <module>
#   File "/Users/ankur/.virtualenvs/python3-test-env/lib/python3.7/site-packages/avro/schema.py", line 383
#     except Exception, e:
#                     ^
# SyntaxError: invalid syntax

Thankfully, the reverse problem is very unlikely. You should not be able to install avro-python3, which is intended for Python 3, within a Python 2 (virtual) environment, by default.

# Inside a fresh Python 2 virtual environment
python  --version
# Python 2.7.16

# Fails at the installation step itself, thankfully!
pip install avro-python3
# DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
# Collecting avro-python3
#   Downloading https://files.pythonhosted.org/packages/d1/55/4c2e6fecf06cbaa68e0abaf12e1e965969872ed16da3674e6245cab0d5e2/avro-python3-1.9.0.tar.gz
# ERROR: Package 'avro-python3' requires a different Python: 2.7.16 not in '>=3.4'

Even if you install the correct Avro package for your Python environment, the API differs between avro and avro-python3. As an example, for Python 2 (with avro package), you need to use the function avro.schema.parse but for Python 3 (with avro-python3 package), you need to use the function avro.schema.Parse.

While the difference in API does somewhat justify having different package names, this still causes unnecessary confusion. The confusion is exacerbated because the official guide, which still uses Python 2, never mentions that the instructions are only applicable to Python 2.

In the rest of this post, we will only use Python 3 with avro-python3 package because Python 2 is EOL.

Working Example

This is an example usage of avro-python3 in a Python 3 environment.

# Python 3 with `avro-python3` package available
import copy
import json
import avro
from avro.datafile import DataFileWriter, DataFileReader
from avro.io import DatumWriter, DatumReader

# Note that we combined namespace and name to get "full name"
schema = {
    'name': 'avro.example.User',
    'type': 'record',
    'fields': [
        {'name': 'name', 'type': 'string'},
        {'name': 'age', 'type': 'int'}
    ]
}

# Parse the schema so we can use it to write the data
schema_parsed = avro.schema.Parse(json.dumps(schema))

# Write data to an avro file
with open('users.avro', 'wb') as f:
    writer = DataFileWriter(f, DatumWriter(), schema_parsed)
    writer.append({'name': 'Pierre-Simon Laplace', 'age': 77})
    writer.append({'name': 'John von Neumann', 'age': 53})
    writer.close()

# Read data from an avro file
with open('users.avro', 'rb') as f:
    reader = DataFileReader(f, DatumReader())
    metadata = copy.deepcopy(reader.meta)
    schema_from_file = json.loads(metadata['avro.schema'])
    users = [user for user in reader]
    reader.close()

print(f'Schema that we specified:\n {schema}')
print(f'Schema that we parsed:\n {schema_parsed}')
print(f'Schema from users.avro file:\n {schema_from_file}')
print(f'Users:\n {users}')

# Schema that we specified:
#  {'name': 'avro.example.User', 'type': 'record',
#   'fields': [{'name': 'name', 'type': 'string'}, {'name': 'age', 'type': 'int'}]}
# Schema that we parsed:
#  {"type": "record", "name": "User", "namespace": "avro.example",
#   "fields": [{"type": "string", "name": "name"}, {"type": "int", "name": "age"}]}
# Schema from users.avro file:
#  {'type': 'record', 'name': 'User', 'namespace': 'avro.example',
#   'fields': [{'type': 'string', 'name': 'name'}, {'type': 'int', 'name': 'age'}]}
# Users:
#  [{'name': 'Pierre-Simon Laplace', 'age': 77}, {'name': 'John von Neumann', 'age': 53}]

Issue with name, namespace, and full name

An interesting thing to note is what happens with the name and namespace fields. The schema we specified has the full name of the schema that has both name and namespace combined, i.e., 'name': 'avro.example.User'. However, after parsing with avro.schema.Parse(), the name and namespace are separated into individual fields. Further, when we read back the schema from the users.avro file, we also get the name and namespace separated into individual fields.

Avro specification, for some reason, uses the name field for both the full name and the partial name. In other words, the name field can either contain the full name or only the partial name. Ideally, Avro specification should have kept partial_name, namespace, and full_name as separate fields.

This behind-the-scene separation and in-place modification may cause unexpected errors if your code depends on the exact value of name. One common use case is when you’re handling lots of different schemas and you want to identify/index/search by the schema name.

A best practice to guard against possible name errors is to always parse a dict schema into a avro.schema.RecordSchema using avro.schema.Parse(). This will generate the namespace, fullname, and simple_name (partial name), which you can then use with peace of mind.

print(type(schema_parsed))
# <class 'avro.schema.RecordSchema'>
print(schema_parsed.avro_name.fullname)
# avro.example.User
print(schema_parsed.avro_name.simple_name)
# User
print(schema_parsed.avro_name.namespace)
# avro.example

This problem of name and namespace deepens when we use a third-party package called fastavro, as we will see in the next section.

Third-party Avro Packages

fastavro

While avro-python3 is the official Avro package, it appears to be very slow. This is because it is written in pure python. In comparison, fastavro uses C extensions (with regular CPython) making it much faster. Another benefit of using fastavro is that you can install it the same way in both Python 2 and Python 3. fastavro API is also the same2 for both Python 2 and 3.

We will use fastavro 0.22.7 for the following discussion. First, let’s use the fastavro.parse_schema(). Unlike avro.schema.Parse(), fastavro.parse_schema() reads in a schema dict and outputs another schema dict.

import fastavro

# Namespace and name are combined to get "full name"
schema_together = {
    'name': 'avro.example.User',
    'type': 'record',
    'fields': [
        {'name': 'name', 'type': 'string'},
        {'name': 'age', 'type': 'int'}
    ]
}

# Namespace and name are separate
schema_separated = {
    'name': 'User',
    'namespace': 'avro.example',
    'type': 'record',
    'fields': [
        {'name': 'name', 'type': 'string'},
        {'name': 'age', 'type': 'int'}
    ]
}

# fastavro.parse_schema() accepts schema as a dict and returns parsed schema as another dict.
# The parsed schema combines name and namespace into "full name".
schema_together_parsed = fastavro.parse_schema(schema_together)
schema_separated_parsed = fastavro.parse_schema(schema_separated)
print(schema_separated_parsed == schema_together_parsed)
# True
print(schema_separated_parsed)
# {'type': 'record', 'name': 'avro.example.User',
# 'fields': [{'name': 'name', 'type': 'string'},
#            {'name': 'age', 'type': 'int'}],
# '__fastavro_parsed': True}

Parsing a schema dict is not really necessary to write data to disk. Parsing the schema provides two benefits:

  1. It helps us verify that the input schema dict is indeed valid
  2. We get back a canonicalized (as per fastavro) schema dict as a result

But, there is one side effect. Parsed schema combines the name and namespace into full name and then stores the full name in the name field. This is the opposite behavior of avro-python3 and just like with avro-python3, this behind-the-scene, in-place modification can cause unexpected errors. Finally, the schema that gets written to disk is whatever schema dict we pass to the fastavro.writer().

# Continued from above

# User data to store.
users = [{'name': 'Pierre-Simon Laplace', 'age': 77},
         {'name': 'John von Neumann', 'age': 53}]

# Experiment 1: Write data using the schema with `name` and `namespace` combined.
with open('users.avro', 'wb') as f:
    fastavro.writer(f, schema_separated_parsed, users)

with open('users.avro', 'rb') as f:
    reader = fastavro.reader(f)
    users_read_back = [user for user in reader]
    metadata = copy.deepcopy(reader.metadata)
    writer_schema = copy.deepcopy(reader.writer_schema)
    schema_from_file = json.loads(metadata['avro.schema'])

print(writer_schema == schema_from_file)
# True
print(schema_from_file)
# {'type': 'record', 'name': 'avro.example.User',
#  'fields': [{'name': 'name', 'type': 'string'}, {'name': 'age', 'type': 'int'}]}
print(writer_schema)
# {'type': 'record', 'name': 'avro.example.User',
#  'fields': [{'name': 'name', 'type': 'string'}, {'name': 'age', 'type': 'int'}]}

fastavro seems to provide two fields that contain the schema – reader.writer_schema and reader.metadata. Metadata (reader.metadata) includes the schema as reader.metadata['avro.schema']. In the above experiment, both these sources of schema provide the exact same schema that has name and namespace combined into a full name. But, this is not always the case, as we will see in the next experiment.

# Continued from above

# Experiment 2: Write data using the schema that has `name` and `namespace` separate.
# Use the unparsed schema that has name and namespace separate
with open('users.avro', 'wb') as f:
    fastavro.writer(f, schema_separated, users)

with open('users.avro', 'rb') as f:
    reader = fastavro.reader(f)
    users_read_back = [user for user in reader]
    metadata = copy.deepcopy(reader.metadata)
    writer_schema = copy.deepcopy(reader.writer_schema)
    schema_from_file = json.loads(metadata['avro.schema'])

print(writer_schema == schema_from_file)
# False
print(schema_from_file)
# {'name': 'User', 'namespace': 'avro.example', 'type': 'record',
#  'fields': [{'name': 'name', 'type': 'string'}, {'name': 'age', 'type': 'int'}]}
print(writer_schema)
# {'type': 'record', 'name': 'avro.example.User',
#  'fields': [{'name': 'name', 'type': 'string'}, {'name': 'age', 'type': 'int'}]}

The above experiment shows that reader.writer_schema and reader.metadata['avro.schema'] differ in whether or not name and namespace are combined together.

In both experiments, reader.metadata['avro.schema'] is more faithful to the schema dict we used to actually write the data. Therefore, it’s a good practice to use reader.metadata['avro.schema'] instead of reader.writer_schema to get the schema.

avro-python3 vs fastavro

As we saw, avro-python3 and fastavro have opposite behaviors when it comes to handling name, namespace, and full name.

Package Parsing function Behavior
avro-python3 avro.schema.Parse Separates name and namespace
fastavro fastavro.parse_schema Combines name and namespace

The handling of name and namespace may not bother you at all or you may find the above difference in behavior unimportant. But, if your code expects either exactly the partial name or exactly the full name, then you may encounter errors. One common error is when you prefix the namespace to an already fully qualified name in the name field. I highly recommend exercising care when handling name and namespace depending on the package you’re using.

Avro <> DataFrame

As we have seen above, Avro format simply requires a schema and a list of records. We don’t need a dataframe to handle Avro files. However, we can write a pandas dataframe into an Avro file or read an Avro file into a pandas dataframe. To begin with, we can always represent a dataframe as a list of records and vice-versa

  1. List of records – pandas.DataFrame.from_records() –> Dataframe
  2. List of records <– pandas.DataFrame.to_dict(orient='records') – Dataframe

Using the two functions above in conjunction with avro-python3 or fastavro, we can read/write dataframes as Avro. The only additional work wewould need to do is to inter-convert between pandas data types and Avro schema types ourselves.

An alternative solution is to use a third-party package called pandavro, which does some of this inter-conversion for us3.

import copy
import json
import pandas as pd
import pandavro as pdx
from avro.datafile import DataFileReader
from avro.io import DatumReader

# Data to be saved
users = [{'name': 'Pierre-Simon Laplace', 'age': 77},
         {'name': 'John von Neumann', 'age': 53}]
users_df = pd.DataFrame.from_records(users)
print(users_df)

# Save the data without any schema
pdx.to_avro('users.avro', users_df)

# Read the data back
users_df_redux = pdx.from_avro('users.avro')
print(type(users_df_redux))
# <class 'pandas.core.frame.DataFrame'>

# Check the schema for "users.avro"
with open('users.avro', 'rb') as f:
    reader = DataFileReader(f, DatumReader())
    metadata = copy.deepcopy(reader.meta)
    schema_from_file = json.loads(metadata['avro.schema'])
    reader.close()
print(schema_from_file)
# {'type': 'record', 'name': 'Root',
#  'fields': [{'name': 'name', 'type': ['null', 'string']},
#             {'name': 'age', 'type': ['null', 'long']}]}

In the above example, we didn’t specify a schema ourselves and pandavro assigned the name = Root to the schema. We can also provide a schema dict to pandavro.to_avro() function, which will preserve the name and namespace faithfully.

Avro with PySpark

Using Avro with PySpark is fraught with a sequence of issues. Let’s see the common issues step-by-step.

Confusing official guide

The official Spark documentation on Avro contains two seemingly contradictory claims. One the one hand, the official documentation says

Since Spark 2.4 release, Spark SQL provides built-in support for reading and writing Apache Avro data.

Then, in the next line, it says

The spark-avro module is external and not included in spark-submit or spark-shell by default.

Perhaps, there is sufficient technical difference between the two claims to make them consistent with each other. But, use of the word “built-in” is unnecessarily confusing. I recommend that you disregard the first claim that mentions “built-in” support for Avro. Only the second claim is true – you need to provide the spark-avro package to Spark. You can do this by providing the Maven coordinates in the form groupId:artifactId:version as follows4,5:

# Example 1
$SPARK_INSTALLATION/bin/pyspark --packages org.apache.spark:spark-avro_2.12:2.4.4

# Example 2
$SPARK_INSTALLATION/bin/pyspark --packages com.databricks:spark-avro_2.11:4.0.0

You can go to the The Central Repository Search Engine or Maven Repository (recommended) to find the versions. If you provide a Maven coordinate that doesn’t exist on Maven, you will get a dependency error.

You may need to clear the cache in $HOME/.ivy2 to overcome some unknown resolver null issues, as mentioned here and here. You can delete $HOME/.ivy2 folder completely to clear the cache but be aware that you will also delete all other downloaded/installed dependencies if you do so.

spark-avro: Databricks or Apache

The reason why we show two examples in the above snippet is because there are at least two common instances of the spark-avro package. It appears that the original spark-avro package was written by Databricks and then donated to Apache Spark project. Spark 2.4.0 included support for “built-in” for Avro and updated the spark-avro package to have new functionality and better performance while still retaining backward API compatibility with the older Databricks’ version of spark-avro.

Both versions of spark-avro are available to use. If you’re on Spark 2.4.0 or higher, you should use Apache Spark’s spark-avro6. If you’re on Spark 2.4.0 or lower, you need to use the Databricks’ version.

There is still one minor change you need to make to your code to switch between the Databricks’ (older) and Apache Spark’s (newer) versions.

# For Spark 2.4.0 and higher, use Apache Spark's version of spark-avro
df = spark.read.format('avro').load('path/to/avro/data')

# For lower than Spark 2.4.0, use Databricks's version of spark-avro
df = spark.read.format('com.databricks.spark.avro').load('path/to/avro/data')

If you don’t use the correct string in format(), you may see an error like this.

AnalysisException: 'Failed to find data source: avro.
Avro is built-in but external data source module since Spark 2.4.
Please deploy the application as per the deployment section of
"Apache Avro Data Source Guide".;'

Obviously, you also need to provide the corresponding spark-avro to Spark. As we saw, we can simply provide the correct Maven coordinates to the intended spark-avro package. But, there is one more glitch – even if we provide valid Maven coordinates to spark-avro package that installs successfully, we may see an error. Let’s see this in the next section.

Scala version is important

Note the Scala version in the Maven coordinates. In org.apache.spark:spark-avro_2.12:2.4.4, the Scala version is 2.12 and in com.databricks:spark-avro_2.11:4.0.0 the Scala version is 2.11. If you don’t use the correct Scala version, you will find that the spark-avro package installs correctly and the pyspark shell starts successfully but reading Avro data fails.

# Run pyspark shell with Apache Spark's spark-avro package as mentioned in the official docs
$ $SPARK_INSTALLATION/bin/pyspark --packages org.apache.spark:spark-avro_2.12:2.4.4
# Everything successful!

# Inside the resulting pyspark shell
>>> df = spark.read.format("avro").load("users.avro")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  ...
py4j.protocol.Py4JJavaError: An error occurred while calling o35.load.
: java.util.ServiceConfigurationError: org.apache.spark.sql.sources.DataSourceRegister:
Provider org.apache.spark.sql.avro.AvroFileFormat could not be instantiated
    at java.util.ServiceLoader.fail(ServiceLoader.java:232)
    ...
# Failure only when you read the Avro data!

Turns out that the pyspark in the above example was built against Scala 2.11, as shown below. But, we provided a spark-avro package that was built for Scala 2.12.

$ $SPARK_INSTALLATION/bin/pyspark --version
Welcome to
      ____              __
     / __/__  ___ _____/ /__
    _\ \/ _ \/ _ `/ __/  '_/
   /___/ .__/\_,_/_/ /_/\_\   version 2.4.4
      /_/

Using Scala version 2.11.12, Java HotSpot(TM) 64-Bit Server VM, 1.8.0_221
Branch
Compiled by user  on 2019-08-27T21:21:38Z
Revision
Url
Type --help for more information.

This issue is especially egregious because the user is able to install spark-avro for the wrong Scala version without any indication of error, only to fail at the last moment. Once you know about this issue, it can be easily fixed by simply using the correct spark-avro package for your pyspark’s Scala version.

# Run pyspark shell with the correct Scala version for spark-avro
$ $SPARK_INSTALLATION/bin/pyspark --packages org.apache.spark:spark-avro_2.11:2.4.4

# Inside the resulting pyspark shell
>>> df = spark.read.format("avro").load("users.avro")
>>> df.show()
+--------------------+---+
|                name|age|
+--------------------+---+
|Pierre-Simon Laplace| 77|
|    John von Neumann| 53|
+--------------------+---+

Working example, finally!

For this example, we will use Scala 2.11, Spark 2.4.4, and Apache Spark’s spark-avro 2.4.4 within a pyspark shell6.

$ $SPARK_INSTALLATION/bin/pyspark --packages org.apache.spark:spark-avro_2.11:2.4.4

Within the pyspark shell, we can run the following code to write and read Avro.

# Data to store
users = [{'name': 'Pierre-Simon Laplace', 'age': 77},
         {'name': 'John von Neumann', 'age': 53}]

# Create a pyspark dataframe
users_df = spark.createDataFrame(users, 'name STRING, age INT')

# Write to a folder named users
users_df.write.format('avro').mode("overwrite").save('users-folder')

# Read the data back
users_df_redux = spark.read.format('avro').load('./users-folder')

Conclusion

My experience in working with Avro format has been error-prone at every step of the way. The name and namespace ambiguity lies in the Avro specification itself. This is further exacerbated by the contrasting behavior of the two most common Avro packages for python (without spark) – avro-python3 and fastavro. When trying to use the official Avro package for python, the package name and API differences between Python 2 and Python 3 create unnecessary confusion. This makes it difficult to port code over from Python 2. And, even though we should not be writing Python 2 code, the package name and API differences make it difficult to write code that is both Python 2 and Python 3 compatible.

Using Avro with PySpark comes with its own sequence of issues that present themselves unexpectedly. In contrast, using parquet, json, or csv with Spark is so much easier. There is no need to install an external package to use these formats. In that sense, support for parquet, json, or csv is truly built-in.

I wrote this post with the hope that it saves you some time, effort, and frustration. I have tried to list all the issues and solutions that people encounter when using Avro with python. If I missed something or if I made a mistake, please let me know in the comments. Please feel free to share this post with others if they would find it useful.

Footnotes

  1. You can perform pip install pandas for both Python 2 and Python 3. You don’t have to change the name of the package from pandas to pandas-python3 for Python 3. 

  2. Based on my basic usage. 

  3. pandavro makes some decisions while inferring schema such as making all columns nullable. This may not be what you want. For production systems, consider using a pre-determined, version-controlled Avro schema saved as a .avsc file or using a schema store. 

  4. An alternative way to provide a list of packages to Spark is to set the environment variable PYSPARK_SUBMIT_ARGS, as mentioned here. This may be more helpful with Jupyter. 

  5. For Java or Scala, you can list spark-avro as a dependency

  6. For Spark 2.4.0+, using the Databricks’ version of spark-avro creates more problems. One common error is java.lang.ClassNotFoundException: Failed to find data source: org.apache.spark.sql.avro.AvroFileFormat 2