treedb

Glottolog treedb

|PyPI version| |License| |Supported Python| |Wheel|

|Build|

This tool loads the content of the languoids/tree_ directory from the Glottolog_ master repo_ into a normalized SQLite_ database.

Each file under in that directory contains the definition of one Glottolog languoid_. Loading their content into a relational database allows to perform some advanced consistency checks (example_) and in general to execute queries that inspect the languoid tree relations in a compact and performant way (e.g. without repeatedly traversing the directory tree).

See pyglottolog_ for the more general official Python API to work with the repo without a mandatory initial loading step (also provides programmatic access to the references_ and a convenient command-line interface).

The database can be exported into a ZIP file containing one CSV file for each database table, or written into a single denormalized CSV file with one row per languoid (via a provided SQL query_).

As sqlite_ is the most widely used_ database, the database file itself (e.g. treedb.sqlite3) can be queried directly from most programming environments. It can also be examined using graphical interfaces such as DBeaver_, or via the sqlite3 cli_.

Python users can also use the provided SQLAlchemy_ models_ to build queries or additional abstractions programmatically using SQLAlchemy core_ or the ORM_ (as more maintainable alternative to hand-written SQL queries).

Links

• GitHub: https://github.com/glottolog/treedb
• PyPI: https://pypi.org/project/treedb/
• Example: https://nbviewer.jupyter.org/github/glottolog/treedb/blob/master/Stats.ipynb
• Changelog: https://github.com/glottolog/treedb/blob/master/CHANGES.rst
• Issue Tracker: https://github.com/glottolog/treedb/issues
• Download: https://pypi.org/project/treedb/#files

Quickstart

Install treedb (and dependencies):

.. code:: bash

$ pip install treedb

Clone the Glottolog master repo_ :

.. code:: bash

$ git clone https://github.com/glottolog/glottolog.git

Note: treedb expects to find it under ./glottolog/ by default (i.e. under the current directory), use treedb.set_root() to point it to a different path.

Load ./glottolog/languoids/tree/**/md.ini into an in-memory sqlite3 database. Write the denormalized example query into treedb.query.csv:

.. code:: bash

$ python -c "import treedb; treedb.load(); treedb.write_csv()"

Usage from Python

Start a Python shell:

.. code:: bash

$ python

Import the package:

.. code:: python

>>> import treedb

Use treedb.iterlanguoids() to iterate over languoids as (, dict) pairs:

.. code:: python

>>> next(treedb.iterlanguoids())
(('abin1243',), {'id': 'abin1243', 'parent_id': None, 'level': 'language', ...

Note: This is a low-level interface, which does not require loading.

Load the database into treedb.sqlite3 (and set the default engine):

.. code:: python

>>> treedb.load('treedb.sqlite3')
...
<treedb._proxies.SqliteEngineProxy filename='treedb.sqlite3' ...>

Run consistency checks:

.. code:: python

>>> treedb.check()
...
True

Export into a ZIP file containing one CSV file per database table:

.. code:: python

>>> treedb.csv_zipfile()
...Path('treedb.zip')

Execute the example query and write it into a CSV file with one row per languoid:

.. code:: python

>>> treedb.write_csv()
...Path('treedb.query.csv')

Rebuild the database (e.g. after an update):

.. code:: python

>>> treedb.load(rebuild=True)
...
<treedb._proxies.SqliteEngineProxy filename='treedb.sqlite3' ...>

Execute a simple query with sqlalchemy core and write it to a CSV file:

.. code:: python

>>> import sqlalchemy as sa
>>> treedb.write_csv(sa.select(treedb.Languoid), filename='languoids.csv')
...Path('languoids.csv')

Get one row from the languoid table via sqlalchemy core (in Glottocode order):

.. code:: python

>>> next(treedb.iterrows(sa.select(treedb.Languoid)))
('3adt1234', '3Ad-Tekles', 'dialect', 'nort3292', None, None, None, None)

Get one Languoid model instance via sqlalchemy orm (in Glottocode order):

.. code:: python

>>> session = treedb.Session()
>>> session.query(treedb.Languoid).first()
<Languoid id='3adt1234' level='dialect' name='3Ad-Tekles'>
>>> session.close()

See also

• pyglottolog_ |--| official Python API to access https://github.com/glottolog/glottolog

License

This tool is distributed under the MIT license_.

.. _Glottolog: https://glottolog.org/ .. _master repo: https://github.com/glottolog/glottolog .. _languoids/tree: https://github.com/glottolog/glottolog/tree/master/languoids/tree .. _SQLite: https://sqlite.org .. _languoid: https://glottolog.org/meta/glossary#Languoid .. _example: https://github.com/glottolog/treedb/blob/36c7cdcdd017e7aa4386ef085ee84fb3036c01ca/treedb/checks.py#L154-L169 .. _pyglottolog: https://github.com/glottolog/pyglottolog .. _references: https://github.com/glottolog/glottolog/tree/master/references .. _SQL query: https://github.com/glottolog/treedb/blob/master/treedb/queries.py .. _most widely used: https://www.sqlite.org/mostdeployed.html .. _DBeaver: https://dbeaver.io/ .. _sqlite3 cli: https://sqlite.org/cli.html .. _SQLAlchemy: https://www.sqlalchemy.org .. _models: https://github.com/glottolog/treedb/blob/master/treedb/models.py .. _SQLAlchemy Core: https://docs.sqlalchemy.org/en/latest/core/ .. _ORM: https://docs.sqlalchemy.org/en/latest/orm/ .. _venv: https://docs.python.org/3/library/venv.html

.. _MIT license: https://opensource.org/licenses/MIT

.. |--| unicode:: U+2013

.. |PyPI version| image:: https://img.shields.io/pypi/v/treedb.svg :target: https://pypi.org/project/treedb/ :alt: Latest PyPI Version .. |License| image:: https://img.shields.io/pypi/l/treedb.svg :target: https://github.com/glottolog/treedb/blob/master/LICENSE.txt :alt: License .. |Supported Python| image:: https://img.shields.io/pypi/pyversions/treedb.svg :target: https://pypi.org/project/treedb/ :alt: Supported Python Versions .. |Wheel| image:: https://img.shields.io/pypi/wheel/treedb.svg :target: https://pypi.org/project/treedb/#files :alt: Wheel format

.. |Build| image:: https://github.com/glottolog/treedb/actions/workflows/build.yaml/badge.svg?branch=master :target: https://github.com/glottolog/treedb/actions/workflows/build.yaml?query=branch%3Amaster :alt: Build .. |Codecov| image:: https://codecov.io/gh/glottolog/treedb/branch/master/graph/badge.svg :target: https://codecov.io/gh/glottolog/treedb :alt: Codecov