Beginner Guide

The following is a small guide for users new to pygrametl. It shows the main constructs provided by pygrametl and how to use them to create a simple ETL flow for a simple made-up example. The example is a toy data warehouse for a chain of book stores and is shown below as Data Warehouse example. The warehouse has one fact table and three dimensions organized in a star schema. The fact table stores facts about how many of each book is sold each day. The book dimension stores the name and genre of each book sold, the location dimension stores the city and region of the stores, and the time dimension stores the date of each sale. To keep the example simple, none of the dimensions are snowflaked, nor do they contain any slowly changing attributes. These are however supported by pygrametl through SnowflakedDimension, TypeOneSlowlyChangingDimension, and SlowlyChangingDimension, respectively. In addition, pygrametl provides high-level constructs for creating efficient multiprocess or multithreaded ETL flow, depending on the implementation of Python used (see Parallel). pygrametl also simplifies testing by making it easy to define preconditions and postconditions for each part of an ETL flow without relying on external files for the input and the expected results (see Drawn Table Testing).

Note

When using pygrametl, we strongly recommend using named parameters when instantiating classes as this improves readability and prevents errors in the future if the API changes.

Data Warehouse example

Input Data

Most pygrametl abstractions either produce, consume, or operate on data in rows. A row is a Python dict where the names of the row’s columns are the keys and the values are the data the row contains. For more information about the data sources provided by pygrametl see Data Sources.

Note

The data and Python source code in this guide can be downloaded using the following link.

The most important data for the warehouse are which books have been sold. This information can be extracted from the book stores’ sales records which are stored in the SQLite database sale.sqlite. Of course, storing sales records from multiple book stores is not a common use-case for SQLite. However, SQLite is used in this beginner guide as it makes sharing the input data simple and demonstrates pygrametl’s ability to read and write from any RDBMS that provides a PEP 249 connection. The data is stored in the table sale as shown below:

| book:text             | genre:text | store:text | date:date      | sale:int |
| --------------------- | ---------- | ---------- | -------------- | -------- |
| Nineteen Eighty-Four  | Novel      | Aalborg    | 2005/08/05     | 50       |
| Calvin and Hobbes One | Comic      | Aalborg    | 2005/08/05     | 25       |
| The Silver Spoon      | Cookbook   | Aalborg    | 2005/08/14     | 5        |
| The Silver Spoon      | Cookbook   | Odense     | 2005/09/01     | 7        |
| ....                  |            |            |                |          |

The book titles and genres are extracted from the CMU Book Summary Dataset. As the geographical information stored in the sales records is limited, the location dimension must be pre-filled with data from the CSV file region.csv. This file contains data about cities and regions as shown below (the tabs are added for readability):

city,       region
Aalborg,    North Denmark Region
Odense,     Region of Southern Denmark
....

ETL Flow

The ETL flow is designed to run on CPython and use PostgreSQL as the RDBMS for the data warehouse. The guide assumes PostgreSQL is already installed and running. The ETL flow can easily be run on other Python implementations like Jython. For example, to use Jython the PEP 249 database drivers must simply be replaced with their JDBC equivalents and ConnectionWrapper with JDBCConnectionWrapper. For more information about running pygrametl on Jython see Jython.

We start by creating the database and tables for the data warehouse in PostgreSQL using psql. The SQL script example.sql creates the dw database, the dwuser role with all privileges, and the four tables:

psql -f example.sql

For the ETL flow we start by importing the various functions and classes needed in this beginner guide. The psycopg2 and sqlite3 database drivers must be imported so a connection to PostgreSQL and SQLite can be established. The main pygrametl module is also imported so a ConnectionWrapper can be created. pyggrametl’s datasources module is imported so the sales records (SQLSource) and CSV file (CSVSource) can be read. Finally, classes for interacting with the fact table (FactTable) and the various dimensions (CachedDimension) are imported from tables.

# psycopg2 is a database driver allowing CPython to access PostgreSQL
import psycopg2

# sqlite3 is a database driver allowing CPython to access SQLite
import sqlite3

# pygrametl's __init__ file provides a set of helper functions and more
# importantly the class ConnectionWrapper for wrapping PEP 249 connections
import pygrametl

# pygrametl makes it simple to read external data through datasources
from pygrametl.datasources import SQLSource, CSVSource

# Interacting with the dimensions and the fact table is done through a set
# of classes. A suitable object must be created for each table
from pygrametl.tables import CachedDimension, FactTable

Then a connection to the database containing the sales records and the data warehouses is needed. For CPython, these must be PEP 249 connections. As the data warehouse connection will be shared by multiple pygrametl abstractions, an instance of ConnectionWrapper is created. The first instance created of this class is set as the default connection for pygrametl’s abstractions. This allows pygrametl to be used without having to pass a connection to each abstraction that needs it. A ConnectionWrapper is not needed for the connection to the sales database as it is only used by the CSVSource, so in that case, the PEP 249 connection is used directly. For more information about database connections in pygrametl see Database.

# Creates a PEP 249 connection to the sales database. PARSE_DECLTYPES makes
# sqlite3 return values with the types specified in the database's schema
sale_conn = sqlite3.connect("sale.sqlite",
        detect_types=sqlite3.PARSE_DECLTYPES)

# While SQLite is used in this guide, any RDBMS that provides a PEP 249
# driver can be used with pygrametl. For example, SQLite can be replaced
# with PostgreSQL by simply replacing sale_conn with following two lines
# sale_string = "host='localhost' dbname='sale' user='user' password='pass'"
# sale_conn = psycopg2.connect(sale_string)

# A connection is also created to the data warehouse. The connection is
# then given to a ConnectionWrapper so it becomes implicitly shared between
# all the pygrametl abstractions that needs it without being passed around
dw_string = "host='localhost' dbname='dw' user='dwuser' password='dwpass'"
dw_conn = psycopg2.connect(dw_string)

# Although the ConnectionWrapper is shared automatically between pygrametl
# abstractions, it is saved in a variable so the connection can be closed
dw_conn_wrapper = pygrametl.ConnectionWrapper(connection=dw_conn)

To get data into the ETL flow, two data sources are created. One for the database containing the sales records, and one for the CSV file containing the region information. For more information about the various data sources provided by pygrametl see Data Sources.

# The location dimension stores the name of a location in the column city
# instead of in the column store as done in the input data from the sales
# database. By passing SQLSource a sequence of names matching the number of
# columns in the table it can automatically rename the columns
name_mapping = 'book', 'genre', 'city', 'date', 'sale'

# Extraction of rows from a database using a PEP 249 connection and SQL
query = "SELECT book, genre, store, date, sale FROM sale"
sale_source = SQLSource(connection=sale_conn, query=query,
        names=name_mapping)

# Extraction of rows from a CSV file does not require a PEP 249 connection,
# just an open file handler. pygrametl uses Python's DictReader for CSV
# files and assumes the header of the CSV file contains the name of each
# column. When using CSVSource it is very important to convert the values
# to the correct type before inserting them into a table through pygrametl.
# As region.csv is encoded as UTF-8 and contains the non-ASCII characters æ
# and ø, the encoding open() will use is explicitly set to UTF-8. Of course,
# if a file uses a different encoding than UTF-8 it should be used instead
region_file_handle = open('region.csv', 'r', 16384, "utf-8")
region_source = CSVSource(f=region_file_handle, delimiter=',')

An object must then be created for each dimension and fact table in the data warehouse. pygrametl provides many types of abstractions for dimensions and fact tables, but in this example, we use the simplest ones. For more information about the more advanced dimension and fact table classes, see Dimensions and Fact Tables.

# An instance of CachedDimension is created for each dimension in the data
# warehouse. CachedDimension uses a local cache to significantly reduce the
# number of requests issued to the RDBMS. CachedDimension should generally
# be used instead of Dimension unless the higher memory consumption causes
# problems. For each dimension, the name of the database table, the table's
# primary key, and the table's non-key columns (attributes) are given. In
# addition, for the location dimension, the subset of the attributes that
# should be used to lookup the primary key is given. As mentioned in the
# beginning of this guide, using named parameters is strongly encouraged
book_dimension = CachedDimension(
        name='book',
        key='bookid',
        attributes=['book', 'genre'])

time_dimension = CachedDimension(
        name='time',
        key='timeid',
        attributes=['day', 'month', 'year'])

location_dimension = CachedDimension(
        name='location',
        key='locationid',
        attributes=['city', 'region'],
        lookupatts=['city'])

# A single instance of FactTable is created for the data warehouse's single
# fact table. It is created with the name of the table, a list of columns
# constituting the primary key of the fact table, and a list of measures
fact_table = FactTable(
        name='sale',
        keyrefs=['bookid', 'locationid', 'timeid'],
        measures=['sale'])

As the input dates are datetime objects and the time dimension consists of multiple levels (day, month, and year), the datetime objects must be split into their separate values. For this, a normal Python function is created and passed each of the rows. As pygrametl is a Python package, data transformations can be implemented using standard Python without any syntactic additions or restrictions. This also means that Python’s many packages can be used as part of an ETL flow.

# A normal Python function is used to split the date into its parts
def split_date(row):
    """Splits a date represented by a datetime into its three parts"""

    # First the datetime object is extracted from the row dictionary
    date = row['date']

    # Then each part is reassigned to the row dictionary. It can then be
    # accessed by the caller as the row is a reference to the dict object
    row['year'] = date.year
    row['month'] = date.month
    row['day'] = date.day

Finally, the data can be inserted into the data warehouse. With a few exceptions, the dimension classes in pygrametl provide the same interface, likewise for the fact table classes. When adding members to dimensions or facts to fact tables in pygrametl, the methods lookup(), insert(), ensure() are generally used. lookup() returns the key for the member or the key and measure values for the fact that matches a given row if it exists, insert() adds a member to a dimension or a fact to a fact table, and ensure() performs a lookup() followed by an insert() if lookup() did not find an existing member or fact. Another commonly used method is scdensure(). It is implemented on dimension classes that support slowly changing dimensions and operates like ensure() but takes versioning into account. For the full API of pygrametl’s dimension and fact table classes, see tables

All rows from the CSV file are inserted into the location dimension first. This is necessary for foreign keys to the location dimension to be computed while filling the fact table. The other two dimensions are filled while inserting the facts as the data needed is included in the sales records. To ensure that the data is committed to the database and that the connection is closed correctly, the methods ConnectionWrapper.commit() and ConnectionWrapper.close() are executed at the end.

# The Location dimension is filled with data from the CSV file as the file
# contains all the information required for both columns in the table. If
# the dimension was filled using data from the sales database, it would be
# necessary to update the region attribute with data from the CSV file
# later. To insert the rows the method CachedDimension.insert() is used
[location_dimension.insert(row) for row in region_source]

# The file handle to the CSV file can then be closed
region_file_handle.close()

# All the information needed for the other dimensions are stored in the
# sales database. So with only a single iteration over the sales records
# the ETL flow can split the date and lookup the three dimension keys
# needed for the fact table. While retrieving the dimension keys, pygrametl
# can automatically update the dimensions with new data if ensure() is
# used. This method combines a lookup with an insertion so a new row is
# only inserted into the dimension or fact table if it does not yet exist
for row in sale_source:

    # The date is split into its three parts
    split_date(row)

    # The row is updated with the correct primary keys for each dimension, and
    # any new data are inserted into each of the dimensions at the same time
    row['bookid'] = book_dimension.ensure(row)
    row['timeid'] = time_dimension.ensure(row)

    # CachedDimension.ensure() is not used for the location dimension as it
    # has already been filled. Instead the method CachedDimension.lookup()
    # is used. CachedDimension.lookup() does not insert any data and
    # returns None if a row with the correct lookupatts is not available.
    # This makes error handling very simple to implement. In this case an
    # error is raised if a location is missing from the CSV file as
    # recovery is not possible
    row['locationid'] = location_dimension.lookup(row)
    if not row['locationid']:
        raise ValueError("city was not present in the location dimension")

    # As the number of sales is already aggregated in the sales records, the
    # row can now be inserted into the data warehouse. If aggregation, or
    # other more advanced transformations are required, the full power of
    # Python is available as shown with the call to split_date()
    fact_table.insert(row)

# After all the data have been inserted, the connection is ordered to
# commit and is then closed. This ensures that the data is committed to the
# database and that the resources used by the connection are released
dw_conn_wrapper.commit()
dw_conn_wrapper.close()

# Finally, the connection to the sales database is closed
sale_conn.close()

This small example shows how to quickly create a very simple ETL flow with pygrametl. A combined version with fewer comments can be seen below. However, since this is a very small and simple example, the batching and bulk loading built into some of the more advanced dimension and fact table classes has not been used. For larger ETL flows, these can be used to significantly increase the throughput of an ETL flow. See Dimensions and Fact Tables for more information. The simple parallel capabilities of pygrametl can also be used to further increase the throughput of an ETL flow (see Parallel), and the correctness of an ETL flow should also be checked using a set of automated repeatable tests (see Drawn Table Testing).

import psycopg2
import sqlite3
import pygrametl
from pygrametl.datasources import SQLSource, CSVSource
from pygrametl.tables import CachedDimension, FactTable

# Opening of connections and creation of a ConnectionWrapper
sale_conn = sqlite3.connect("sale.sqlite",
        detect_types=sqlite3.PARSE_DECLTYPES)

dw_string = "host='localhost' dbname='dw' user='dwuser' password='dwpass'"
dw_conn = psycopg2.connect(dw_string)
dw_conn_wrapper = pygrametl.ConnectionWrapper(connection=dw_conn)

# Creation of data sources for the sales database and the CSV file
# containing extra information about cities and regions in Denmark
name_mapping = 'book', 'genre', 'city', 'date', 'sale'
query = "SELECT book, genre, store, date, sale FROM sale"
sale_source = SQLSource(connection=sale_conn, query=query,
        names=name_mapping)

region_file_handle = open('region.csv', 'r', 16384, "utf-8")
region_source = CSVSource(f=region_file_handle, delimiter=',')

# Creation of dimension and fact table abstractions for use in the ETL flow
book_dimension = CachedDimension(
        name='book',
        key='bookid',
        attributes=['book', 'genre'])

time_dimension = CachedDimension(
        name='time',
        key='timeid',
        attributes=['day', 'month', 'year'])

location_dimension = CachedDimension(
        name='location',
        key='locationid',
        attributes=['city', 'region'],
        lookupatts=['city'])

fact_table = FactTable(
        name='sale',
        keyrefs=['bookid', 'locationid', 'timeid'],
        measures=['sale'])

# Python function needed to split the date into its three parts
def split_date(row):
    """Splits a date represented by a datetime into its three parts"""

    # Splitting of the date into parts
    date = row['date']
    row['year'] = date.year
    row['month'] = date.month
    row['day'] = date.day

# The location dimension is loaded from the CSV file
[location_dimension.insert(row) for row in region_source]

# The file handle for the CSV file can then be closed
region_file_handle.close()

# Each row in the sales database is iterated through and inserted
for row in sale_source:

    # Each row is passed to the date split function for splitting
    split_date(row)

    # Lookups are performed to find the key in each dimension for the fact
    # and if the data is not there, it is inserted from the sales row
    row['bookid'] = book_dimension.ensure(row)
    row['timeid'] = time_dimension.ensure(row)

    # The location dimension is pre-filled, so a missing row is an error
    row['locationid'] = location_dimension.lookup(row)
    if not row['locationid']:
        raise ValueError("city was not present in the location dimension")

    # The row can then be inserted into the fact table
    fact_table.insert(row)

# The data warehouse connection is then ordered to commit and close
dw_conn_wrapper.commit()
dw_conn_wrapper.close()

# Finally, the connection to the sales database is closed
sale_conn.close()