Querying multiple backends with Ibis

In our recent Ibis post, we discussed querying & retrieving data using a familiar Pandas-like interface. That discussion focused on the fluent API that Ibis provides to query structure from a SQLite database—in particular, using a single specific backend. In this post, we'll explore Ibis's ability to answer questions about data using two different Ibis backends.

import ibis.omniscidb, dask, intake, sqlalchemy, pandas, pyarrow as arrow, altair, h5py as hdf5

Ibis in the scientific Python ecosystem

Before we delve into the technical details of using Ibis, we'll consider Ibis in the greater historical context of the scientific Python ecosystem. It was started by Wes McKinney, the creator of Pandas, as way to query information on the Hadoop distributed file system and PySpark. More backends were added later as Ibis became a general tool for data queries.

Throughout the rest of this post, we'll highlight the ability of Ibis to generically prescribe query expressions across different data storage systems.

The design of Ibis backends

Currently, Ibis supports more than ten different backends:

>>> import ibis
>>> dir(ibis)
[...HDFS...WebHDFS...bigquery...clickhouse...hdf5...impala...omniscidb...pandas...pyspark...spark...sql...sqlite...]

A backend manages the computation of an Ibis query expression; the query expression itself is independent of the computation. A backend implementation that can be queried with Ibis has one of the three following architectures:

  1. Direct execution backends (e.g., Pandas and HDF5);
  2. Expression-generating backends that create SQLAlchemy expressions (e.g., ibis.sql); or
  3. String-generating backends (e.g., ibis.bigquery and ibis.omniscidb)

We'll unravel some of the different capabilities of each approach below.

A data-driven history of Ibis compatibility

The table below looks at over 2000 issues in the Ibis project. It provides an annual summary of the issues tagged in Ibis for different backends over a span of six years.

    2015
    2016
    2017
    2018
    2019
    2020
Omnisci 31 33 38
Spark 1 22 3
PostgreSQL 2 3 21 10 17 4
BigQuery 15 71 12 2
Pandas 2 49 35 32 4
SQLite 25 2 10 8 1 1
Impala 52 4 15 17 4 2
Kudu 1
Geospatial 7 3
ClickHouse 8 9 1 4
MySQL 2 2 4
SQLAlchemy 17 3 10 2 5

We note an early focus SQLite, SQLAlchemy and Impala. Later, work began on the Pandas backend rounding out the three different types of backgrounds. From this point, improvements were made to these key backends as ClickHouse, Spark and PostgreSQL. For the past two years, Quansight, in partnership with OmniSci, added the ibis.omniscidb string-generating backend. Further, our responsibilities have expanded to support Ibis as community maintainers through Quansight Labs. This collaboration introduced geospatial functionality to Ibis for several backends.

There are currently ongoing efforts to introduce support for SQL Server backends. What other backends would you like to see for Ibis? Maybe our community could benefit from a Dask backend or an Altair backend?

Ibis direct execution backends

Ibis direct execution backends like Pandas and HDF5 operate on conventional in-memory python objects. Pandas is the gold standard for structured data in Python and inspires the API for Ibis.

pd = ibis.pandas.connect({'A': pandas.util.testing.makeDataFrame()})

The object pd is an Ibis backend based on pandas.DataFrame.

expression = pd.table('A').head()

expression is an Ibis query that has expression.compile and expression.execute methods. We'll recognize the execute method when we return pandas.DataFrames from Ibis expression. The compile method does not trigger any computation, rather it constructs an intermediate form that is interpreted by a backend.

>>> assert isinstance(expression.compile(), ibis.expr.types.TableExpr)

In the case of direction execution backends, the expression compiles to an the original Ibis expression. The computation itself is carried out based on a set of recipes defined in Ibis. In general, we would typically do this work directly in Pandas; however this approach is practical in making tests for backend-independent expressions.

Ibis expression-generating backends.

db = ibis.sqlite.connect('lahmansbaseballdb.sqlite')
expression = db.table('halloffame').head()

Expression-generating backends operate on SQL databases that interoperate with SQLAlchemy.

>>> assert isinstance(expression.compile(), sqlalchemy.sql.Select)

In the case of expression-generating backends, the intermediate representation is a sqlalchemy object. SQLAlchemy is the Database Toolkit for Python and Ibis leverages its compatibility with traditional SQL databases.

Ibis string generating backends.

There are two options for downloading Ibis: using pip or using conda.

  • pip: the extra backends from Ibis need to be requested explicitly, e.g.:
pip install --upgrade ibis-framework[omniscidb] ibis-framework[sqlite]
  • conda: all the supported backends (e.g., SQL, Pandas, BigQuery, Omnisci, etc.) are bundled in a single conda package and can be downloaded/installed simultaneously:
conda install -c conda-forge ibis-framework # installs all the backends!

String-generating backends allow Ibis to interface with big data systems that manage their own computation. For example, we may connect to an example Omnisci database.

import ibis.omniscidb
omnisci = ibis.omniscidb.connect(host='metis.omnisci.com',
                                 user='demouser',
                                 password='HyperInteractive',
                                 port=443,
                                 database='omnisci',
                                 protocol='https')

The omnisci object is described as a string-generating backend because the intermediate representation of the query is a flavor of SQL.

expression = omnisci.table('upstream_reservoir').head()

A string-generating expression compiles to ibis.omniscidb flavored SQL, while ibis.bigquery may have a different string representation.

>>> expression.compile()
'SELECT *\nFROM upstream_reservoir\nLIMIT 5'

Acknowledgements

Major credit goes to @xmnlab in his heroic PR to introduce ibis.omniscidb into Ibis. You can watch the drama play out in this Github Issue. We'd like to thank the maintainers of Ibis for their effort in supporting the Ibis community.

Learn more about OmniSci and ibis.omniscidb in this Quansight Labs post: Ibis: Python data analysis productivity framework.