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Python Transformation

Python transformations complement R and SQL transformations where computations or other operations are too difficult. Common data operations like joining, sorting, or grouping are still easier and faster to do in SQL Transformations.

Environment

The Python script is running in an isolated Docker environment. The Python version is updated regularly, few weeks after the official release. The update is always announced on the status page.

When we update the Python version, we offer — for a limited time — the option to switch to the previous version. You can switch the version in the transformation detail by clicking on the Change Backend label:

Screenshot - Transformations Versions

This feature is intended to help you postpone the update to a more convenient time for you in case there are any problems with the new version. You should update the transformation code to the new version soon, as the old version is considered unsupported.

If the Python label is not displayed, there is no previous version offered. It is still possible to change the version via the API though.

Memory and Processing Constraints

The Docker container running the Python transformation has 8GB of allocated memory and the maximum running time is 6 hours. The container is also limited to the equivalent of 2 Intel Broadwell 2.3 GHz processors.

File locations

The Python script itself will be compiled to /data/script.py. To access your input and output tables, use relative (in/tables/file.csv, out/tables/file.csv) or absolute (/data/in/tables/file.csv, /data/out/tables/file.csv) paths. To access downloaded files, use the in/user/tag or /data/in/user/tag path. If you want to dig really deep, have a look at the full Common Interface specification. Temporary files can be written to a /tmp/ folder. Do not use the /data/ folder for those files you do not wish to exchange with Keboola.

Python Script Requirements

Python is sensitive to indentation. Make sure not to mix tabs and spaces. All files are assumed to be in UTF; # coding=utf-8 at the beginning of the script is not needed. If you define a main function, do not wrap it within the if __name__ == '__main__': block as it will not be run. Simply calling it from within the script is enough:

def main():
    print("Hello Keboola")

main()

Packages

You can list extra packages in the UI. These packages are installed using pip. Generally, any package available on PyPI can be installed. However, some packages have external dependencies, which might not be available. Feel free to contact us if you run into problems. When the package is installed, you still need to import from it.

Screenshot - Package Configuration

The latest versions of packages are always installed at the time of the release (you can check that in the repository). In case your code relies on a specific package version, you can override the installed version by calling, e.g.:

import subprocess
import sys
subprocess.call([sys.executable, '-m', 'pip', 'install', '--disable-pip-version-check', '--no-cache-dir', '--force-reinstall', 'pandas==0.20.0'])

Some packages are already installed in the environment (see their full list), and they do not need to be listed in the transformation.

CSV Format

Tables from Storage are imported to the Python script from CSV files. CSV files can be read by standard Python functions from the csv packages. It is recommended to explicitly specify the formatting options. You can read CSV files either to vectors (numbered columns), or to dictionaries (named columns). Your input tables are stored as CSV files in in/tables/, and your output tables in out/tables/.

If you can process the file line-by-line, then the most effective way is to read each line, process it and write it immediately. The following two examples show two ways of reading and manipulating a CSV file.

Development Tutorial

To develop and debug Python transformations, you can replicate the execution environment on your local machine. To do so, you need to have Python installed, preferably the same version as us.

To simulate the input and output mapping, all you need to do is create the right directories with the right files. The following image shows the directory structure:

Screenshot - Data folder structure

The script itself is expected to be in the data directory; its name is arbitrary. It is possible to use relative directories, so that you can move the script to a Keboola transformation with no changes. To develop a Python transformation which takes a sample CSV file locally, take the following steps:

  • Put the Python code into a file, for example script.py, in the working directory.
  • Put all the input mapping tables inside the in/tables subdirectory of the working directory.
  • If using binary files, place them inside the in/user subdirectory of the working directory, and make sure that their name is without any extension.
  • Store the result CSV files inside the out/tables subdirectory.

Use this sample script:

import csv

csvlt = '\n'
csvdel = ','
csvquo = '"'
with open('in/tables/source.csv', mode='rt', encoding='utf-8') as in_file, open('out/tables/result.csv', mode='wt', encoding='utf-8') as out_file:
    writer = csv.DictWriter(out_file, fieldnames=['col1', 'col2'], lineterminator=csvlt, delimiter=csvdel, quotechar=csvquo)
    writer.writeheader()

    lazy_lines = (line.replace('\0', '') for line in in_file)
    reader = csv.DictReader(lazy_lines, lineterminator=csvlt, delimiter=csvdel, quotechar=csvquo)
    for row in reader:
        # do something and write row
        writer.writerow({'col1': row['first'] + 'ping', 'col2': int(row['second']) * 42})

A finished example of the above is attached below in data.zip. Download it and test the script in your local Python installation. The result.csv output file will be created. This script can be used in your transformations without any modifications. All you need to do is

  • create a table in Storage by uploading the sample CSV file),
  • create an input mapping from that table, setting its destination to source.csv (as expected by the Python script),
  • create an output mapping from result.csv (produced by the Python script) to a new table in your Storage,
  • copy & paste the above script into the transformation code, and finally,
  • save and run the transformation.

Screenshot - Sample Input Output Mapping

Going Further

The above steps are usually sufficient for daily development and debugging of moderately complex Python transformations, although they do not reproduce the transformation execution environment exactly. To create a development environment with the exact same configuration as the transformation environment, use our Docker image.

Example 1 – Using Dictionaries

The following piece of code reads a table with two columns, named first and second, from the source.csv input mapping file into the row dictionary using csvReader. It then adds ping to the first column and multiplies the second column by 42. After that, it saves the row to the result.csv output mapping file.

import csv

csvlt = '\n'
csvdel = ','
csvquo = '"'
with open('in/tables/source.csv', mode='rt', encoding='utf-8') as in_file, open('out/tables/result.csv', mode='wt', encoding='utf-8') as out_file:
    writer = csv.DictWriter(out_file, fieldnames=['col1', 'col2'], lineterminator=csvlt, delimiter=csvdel, quotechar=csvquo)
    writer.writeheader()

    lazy_lines = (line.replace('\0', '') for line in in_file)
    reader = csv.DictReader(lazy_lines, lineterminator=csvlt, delimiter=csvdel, quotechar=csvquo)
    for row in reader:
        # do something and write row
        writer.writerow({'col1': row['first'] + 'ping', 'col2': int(row['second']) * 42})

The above example shows how to process the file line-by-line; this is the most memory-efficient way which allows you to process data files of any size. The expression lazy_lines = (line.replace('\0', '') for line in in_file) is a Generator which makes sure that Null characters are properly handled. It is also important to use encoding='utf-8' when reading and writing files.

Example 2 – Using Lists

The following piece of code reads a table with some of its columns from the source.csv input mapping file into the row list of strings. It then adds ping to the first column and multiplies the second column by 42. After that, it saves the row to the result.csv output mapping file.

import csv

csvlt = '\n'
csvdel = ','
csvquo = '"'
with open('/data/in/tables/source.csv', mode='rt', encoding='utf-8') as in_file, open('/data/out/tables/result.csv', mode='wt', encoding='utf-8') as out_file:
    writer = csv.writer(out_file, lineterminator=csvlt, delimiter=csvdel, quotechar=csvquo)
    lazy_lines = (line.replace('\0', '') for line in in_file)
    reader = csv.reader(lazy_lines, lineterminator=csvlt, delimiter=csvdel, quotechar=csvquo)
    for row in reader:
        # do something and write row
        writer.writerow([row[0] + 'ping', int(row[1]) * 42])

Example 3 – Using CSV dialect

You can simplify the above code using our pre-installed Keboola dialect.

import csv

with open('/data/in/tables/source.csv', mode='rt', encoding='utf-8') as in_file, open('/data/out/tables/result.csv', mode='wt', encoding='utf-8') as out_file:
    lazy_lines = (line.replace('\0', '') for line in in_file)
    reader = csv.DictReader(lazy_lines, dialect='kbc')
    writer = csv.DictWriter(out_file, dialect='kbc', fieldnames=reader.fieldnames)
    writer.writeheader()
    for row in reader:
        # do something and write row
        writer.writerow({"first": row['first'] + 'ping', "second": int(row['second']) * 42})

The kbc dialect is automatically available in the transformation environment. If you want it in your local environment, it is defined as csv.register_dialect('kbc', lineterminator='\n', delimiter = ',', quotechar = '"').