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python package for glottolog data curation

Project description

pyglottolog

Programmatic access to Glottolog data.

Build Status codecov PyPI

Install

To install pyglottolog you need a python installation on your system, running python >3.4. Run

pip install pyglottolog

This will also install the command line interface glottolog.

Note: To make use of pyglottolog you also need a local copy of the Glottolog data. This can be

Make sure you remember where this local copy of the data is located - you may have to pass this location as option when using pyglottolog.

A convenient way to clone the data repository, keep it updated and access it from pyglottolog is provided by cldfbench. See the README for details.

Python API

Using pyglottolog, Glottolog data can be accessed programmatically from within python programs. All functionality is mediated through an instance of pyglottolog.Glottolog, e.g.

>>> from pyglottolog import Glottolog
>>> glottolog = Glottolog('.')
>>> print(glottolog)
<Glottolog repos v0.2-259-g27ac0ef at /.../glottolog>

Accessing languoid data

The data in languoid info files in the languoids/tree subdirectory is mainly accessed through two methods:

>>> glottolog.languoid('stan1295')
<Language stan1295>
>>> print(glottolog.languoid('stan1295'))
German [stan1295]

Accessing reference data

>>> print(api.bibfiles['hh.bib']['s:Karang:Tati-Harzani'])
@book{s:Karang:Tati-Harzani,
    author = {'Abd-al-'Ali Kārang},
    title = {Tāti va Harzani},
    publisher = {Tabriz: Tabriz University Press},
    address = {Tabriz},
    pages = {6+160},
    year = {1334 [1953]},
    glottolog_ref_id = {41999},
    hhtype = {grammar_sketch},
    inlg = {Farsi [pes]},
    lgcode = {Harzani [hrz]},
    macro_area = {Eurasia}
}

Performance considerations

Reading the data for Glottolog's almost 25,000 languoids from the same number of files in individual directories isn't particularly quick. So on average computers running

>>> list(glottolog.languoids())

would take around 15 seconds.

Due to this, care should be taken not to read languoid data from disk repeatedly. In particular "N+1"-type problems should be avoided, where one would read all languoid into memory and then look up attributes on each languoid, thereby triggering new reads from disk. This may easily happen, since attributes such as Languoid.family are implemented as properties, which traverse the directory tree and read information from disk at access time.

To make it possible to avoid such problems, many of these properties can be substituted with a call to a similar method of Languoid, which accepts a "node map" (i.e. a dict mapping Languoid.id to Languoid objects) as parameter, e.g. Languoid.ancestors_from_nodemap or Languoid.descendants_from_nodemap. Typical usage would look as follows:

>>> languoids = {l.id: l for l in glottolog.languoids()}
>>> for l in languoids.values():
...    if not l.ancestors_from_nodemap(languoids):
...        print('top-level {0}: {1}'.format(l.level, l.name))

Accessing configuration data

The config subdirectory of Glottolog data contains machine readable metadata like the list of macroareas. This information can be accessed via an instance of Glottolog, too, using the stem of the filename as attribute name:

>>> for ma in glottolog.macroareas.values():
...     print(ma.name)
...     
South America
Eurasia
Africa
Papunesia
North America
Australia

Note that the data read from the INI files is stored as dict, with section names (or explicit id options) as keys and instances of the corresponding class in pyglottolog.config as values.

Command line interface

Command line functionality is implemented via sub-commands of glottolog. The list of available sub-commands can be inspected running

$ glottolog -h
usage: glottolog [-h] [--log-level LOG_LEVEL] [--repos REPOS]
                 [--repos-version REPOS_VERSION]
                 COMMAND ...

optional arguments:
  -h, --help            show this help message and exit
  --log-level LOG_LEVEL
                        log level [ERROR|WARN|INFO|DEBUG] (default: 20)
  --repos REPOS         clone of glottolog/glottolog
  --repos-version REPOS_VERSION
                        version of repository data. Requires a git clone!
                        (default: None)

available commands:
  Run "COMAMND -h" to get help for a specific command.

  COMMAND
    cldf                Dump Glottolog data as CLDF dataset
    create              Create a new languoid directory for a languoid
                        specified by name and level.
    edit                Open a languoid's INI file in a text editor.
    htmlmap             Create an HTML/Javascript map (using leaflet) of
                        Glottolog languoids.
    iso2codes           Map ISO codes to the list of all Glottolog languages
                        and dialects subsumed "under" it.
    langdatastats       List all metadata fields used in languoid INI files
                        and their frequency.
    langsearch          Search Glottolog languoids.
    languoids           Write languoids data to csv files
    refsearch           Search Glottolog references
    searchindex         Index
    show                Display details of a Glottolog object.
    tree                Print the classification tree starting at a specific
                        languoid.

Extracting languoid data

Glottolog data is often integrated with other data or incorporated as reference data in tools, e.g. as LanguageTable in a CLDF dataset.

To make this easier, pyglottolog provides the languoids subcommand, which dumps basic languoid data into a CSVW file with accompanying metadata:

glottolog languoids [--output=OUTDIR] [--version=VERSION]

This will create a CSVW package, i.e.

  • a CSV table glottolog-languoids-VERSION.csv
  • and a JSON description glottolog-languoids-VERSION.csv-metadata.json

where VERSION is the result of running git describe on the data repository, or the version string passed as--version=VERSION in case you are running the command on an export of the repository or a download from ZENODO.

Languoid search

To allow convenient search across all languoid info files, pyglottolog comes with functionality to create and search a Whoosh index. To do so, run

glottolog searchindex

This will take a couple of minutes and build an indeces of about 750 MB size at build/.

Now you can search the index, e.g. using alternative names as query:

$ glottolog langsearch "Abipónok"
1 matches
Abipon [abip1241] language
languoids/tree/guai1249/guai1250/abip1241/md.ini
Abipónok [hu]

1 matches

But you can also exploit the schema defined in pyglottolog.fts.get_langs_index:

$ glottolog langsearch "country:Papua New Guinea"
...

Alamblak [alam1246] language
languoids/tree/sepi1257/sepi1258/east2496/alam1246/md.ini
Papua New Guinea (PG)

900 matches

$ glottolog --repos=. langsearch "iso:mal"
...

Malayalam [mala1464] language
languoids/tree/drav1251/sout3133/sout3138/tami1291/tami1292/tami1293/tami1294/tami1297/tami1298/mala1541/mala1464/md.ini

1 matches

Reference search

The same can be done for reference data: To create a Whoosh index with all reference data, run

glottolog searchindex

Now you can query the index:

$ glottolog refsearch "author:Haspelmath AND title:Atlas"
...
(13 matches)

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