Upload 2378 files

.gitattributes

@@ -57,3 +57,11 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+tsammalex-data/tsammalexdata/data/ecoregions.json filter=lfs diff=lfs merge=lfs -text
+tsammalex-data/tsammalexdata/data/Edmond.xml filter=lfs diff=lfs merge=lfs -text
+tsammalex-data/tsammalexdata/data/external/eol.json filter=lfs diff=lfs merge=lfs -text
+tsammalex-data/tsammalexdata/data/external/tdwg/level1.json filter=lfs diff=lfs merge=lfs -text
+tsammalex-data/tsammalexdata/data/external/tdwg/level2.json filter=lfs diff=lfs merge=lfs -text
+tsammalex-data/tsammalexdata/data/external/tdwg/level3.json filter=lfs diff=lfs merge=lfs -text
+tsammalex-data/tsammalexdata/data/external/tdwg/level4.json filter=lfs diff=lfs merge=lfs -text
+tsammalex-data/tsammalexdata/data/external/theplantlist.json filter=lfs diff=lfs merge=lfs -text

tsammalex-data/.gitattributes

@@ -0,0 +1 @@
+*.csv text eol=crlf

tsammalex-data/.gitignore

@@ -0,0 +1,37 @@
+*.py[cod]
+
+# C extensions
+*.so
+
+# Packages
+*.egg
+*.egg-info
+dist
+build
+eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+lib
+lib64
+__pycache__
+
+# Installer logs
+pip-log.txt
+
+# Unit test / coverage reports
+.coverage
+.tox
+nosetests.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+.idea

tsammalex-data/.travis.yml

@@ -0,0 +1,14 @@
+language: python
+python:
+  - "3.4"
+install:
+  - pip install nose
+script:
+  - python setup.py install
+  - nosetests
+notifications:
+  email:
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - [email protected]

tsammalex-data/CONTRIBUTING.md

@@ -0,0 +1,56 @@
+## Contributing
+
+<p>
+    The expansion of the Tsammalex database strongly depends on researchers and communities willing
+    to share their knowledge or collected data. If you are interested in a contribution and have
+    questions, don't hesitate to
+    <a href="http://tsammalex.clld.org/contact">contact</a> one of the editors
+    (Christfried Naumann, Steven Moran or Robert Forkel).
+</p>
+<p>
+    The structure of the database is based on
+    <a href="http://en.wikipedia.org/wiki/Comma-separated_values" title="csv tables"><i class="icon-share"></i> csv tables</a>
+    ("...csv"), i.e., a simple file format that can
+    be opened and edited in editors such as Notepad, or calculation programs such as LibreOffice Calc or
+    Microsoft Excel.
+    <a href="https://github.com/clld/tsammalex-data/tree/master/tsammalexdata/data" title="These csv files"><i class="icon-share"></i> These csv files</a>
+    contain all data on biological species and related linguistic or
+    lexical data, as well as metadata of audio and image files, etc.
+    There is
+    <a href="https://github.com/clld/tsammalex-data/blob/master/tsammalexdata/data/sources.bib" title="a BibTeX"><i class="icon-share"></i> a BibTeX</a>
+    file containing all
+    references cited. Images of species (licensed as Creative Commons or in Public domain) might be
+    uploaded to websites such as Flickr or Wikimedia Commons and linked, or sent to the editors.
+    For more information on the structure of the data and on planned improvements refer to
+    <a href="http://tsammalex.clld.org/static/Tsammalex-Manual.pdf">the manual [PDF]</a>.
+</p>
+<p>
+    Contributions of data must be committed in the form of csv files. In a Windows environment, we recommend
+    using LibreOffice Calc. Open the csv table templates, set the character encoding to UTF-8 (Unicode) and
+    select comma separated table. Have a look into the sketch manual about obligatory vs. optional
+    information, and start entering data. Send these files to the editors.
+</p>
+<p>
+    Alternatively, if you feel comfortable with the
+    <a href="https://help.github.com/articles/using-pull-requests/" title="GitHub collaboration model"><i class="icon-share"></i> GitHub collaboration model</a>
+    you may fork the
+    <a href="https://github.com/clld/tsammalex-data" title="tsammalex-data repository"><i class="icon-share"></i> tsammalex-data repository</a>,
+    add your data and submit a pull request.
+</p>
+<p>
+    Notes:
+</p>
+<ul>
+    <li>Lexical data in "names.csv" must be associated with one species (or another biological taxon, such as a genus).</li>
+    <li>Any species (or other taxon) referred to under "names.csv" must be included previously under "species.csv".</li>
+    <li>
+        The consistency of the data in the tsammalex-data repository is checked by
+        <a href="https://travis-ci.org/clld/tsammalex-data" title="Travis-CI"><i class="icon-share"></i> Travis-CI</a>,
+        so if you choose to add data using pull request, you get the added benefit of having your additions
+        cross-checked while you are working on them.
+    </li>
+    <li>
+        Further information on the rationale behind curating the data in this way are available
+        in <a href="http://clld.org/2015/02/03/open-source-research-data.html" title="this post"><i class="icon-share"></i> this post</a>.
+    </li>
+</ul>

tsammalex-data/MANIFEST.in

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+recursive-include tsammalexdata *.csv *.bib *.json *.xml

tsammalex-data/README.md

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+Tsammalex Data
+==============
+
+[![Build Status](https://travis-ci.org/clld/tsammalex-data.svg?branch=master)](https://travis-ci.org/clld/tsammalex-data)
+
+This repository holds the data served by http://tsammalex.clld.org/
+The data is licensed under a Creative Commons Attribution 4.0 International License.
+
+The data is stored as collection of csv files, suitable for editing with LibreOffice.
+
+
+Adding images
+-------------
+
+Adding an image is done in two steps:
+
+1. Adding a row to ``images.csv``, specifying a publicly available URL to access the image in the ``source_url`` column (this may be a temporary GitHub repository, wikimedia commons or other publicly available webspace).
+2. Providing the image at the specified URL for download.
+
+Notes:
+
+- Use the [md5 hash](http://en.wikipedia.org/wiki/MD5) of the image file as `id` for the row in `images.csv`.
+  Computing this hash can be done using [FCIV on Windows](http://support.microsoft.com/kb/889768), with the 
+  [md5sum command](http://en.wikipedia.org/wiki/Md5sum) on Linux or 
+  with the [md5 command](http://osxdaily.com/2009/10/13/check-md5-hash-on-your-mac/) on mac.
+- When a data release is created, new images will be fetched from the sources and uploaded to [Edmond](http://edmond.mpdl.mpg.de/imeji/collection/d2JGQRxO19XTOEXG) - the MPS' media repository.
+
+
+Referential Integrity
+---------------------
+
+Currently, insuring referential integrity of the data is the responsibility of the editor. In particular editors have
+to make sure
+
+- ``id`` columns hold unique values,
+- ``<name>__id`` columns hold values which exist as ``id`` in the referenced table,
+- ``<name>__ids`` columns hold comma-separated lists of values which exist as ``id`` in the referenced table.
+
+Upon push, referential integrity will be checked by travis-ci.
+
+
+Changing the scientific name of a species
+-----------------------------------------
+
+Since the ``id`` of a species is created from its scientifc name, changing this name involves the following steps:
+
+1. Add a new species with the updated name and ``id`` to ``species.csv``.
+2. Update all references to the ``id`` in ``images.csv`` and ``words.csv``.
+3. **TODO** redirect the old species to the new one by ...
+
+
+Supplemental Data
+-----------------
+
+In addition to the data managed in this repository, we fetch data from other sources to enhance the usability of the site.
+
+- Given a proper scientific name for a species we can fetch a corresponding identifier from [EOL](http://eol.org).
+- Given an EOL identifier, we can information about the biological classification of a species and a common english name.
+- We also use information on terrestrial ecoregions from WWF, which can be referenced using ecoregion identifiers in the format ``AT0101``.
+- WWF ecoregions and countries in which a species occurs can be computed by matching [occurrence information](http://www.gbif.org/occurrence) from [GBIF](http://www.gbif.org) against region borders.
+
+
+Notes
+-----
+
+Notes to self:
+
+- To diff sorted lines, you may run:
+
+    diff -b <(sort words.csv) <(sort words_CN.csv)
+

tsammalex-data/RELEASE.md

@@ -0,0 +1,9 @@
+## Creating a release of Tsammalex Data
+
+1. Make sure the integrity checks for the data pass.
+2. Enrich the taxon data from external sources running the `updatetaxa` command.
+3. Git add, commit and push the updated taxon data.
+4. Upload images to the MPG imeji repository.
+5. Git commit and push the updated image data.
+6. [Create a release](https://help.github.com/articles/creating-releases/) of the repository.
+7. [Import the release](https://github.com/clld/tsammalex/blob/master/RELEASE.md) in http://tsammalex.clld.org

tsammalex-data/setup.py

@@ -0,0 +1,37 @@
+from setuptools import setup, find_packages
+
+
+requires = [
+    'requests',
+    'purl',
+    'pycountry',
+    'flickrapi',
+    'python-dateutil',
+    'BeautifulSoup4',
+    'shapely',
+]
+
+setup(
+    name='tsammalexdata',
+    version='0.0',
+    description='data for the tsammalex site',
+    long_description='',
+    classifiers=[
+        "Programming Language :: Python",
+        "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3.4",
+    ],
+    author='',
+    author_email='',
+    url='',
+    keywords='data linguistics',
+    packages=find_packages(),
+    include_package_data=True,
+    zip_safe=False,
+    install_requires=requires,
+    entry_points={
+        'console_scripts': [
+            'updatetaxa = tsammalexdata.commands:update_taxa']
+    },
+    tests_require=[],
+    test_suite="tsammalexdata")

tsammalex-data/tsammalexdata/README.md

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+The tsammalexdata package
+-------------------------
+
+The ``tsammalexdata`` package provides the following functionality:
+
+- A test suite which can be invoked by travis-ci (or locally) to check integrity of the data.
+- Scripts to enrich the core data with supplemental data from external sources (like EOL of GBIF).
+
+
+Making a release of the data:
+
+1. Make sure the tests pass:
+```
+    $ nosetests
+    ----------------------------------------
+    Ran ...
+
+    OK
+```
+2. Harvest additional data and compute distribution data:
+```bash
+    updatetaxa
+    git add tsammalexdata/data/external/gbif/*.json
+    git commit -a -m"updated taxa info from external sources"
+    git push origin
+```
+3. Upload images.

tsammalex-data/tsammalexdata/__init__.py

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+#
+

tsammalex-data/tsammalexdata/add_source_url.py

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+from __future__ import unicode_literals, print_function
+import json
+
+from purl import URL
+
+from tsammalexdata.util import visit, data_file
+
+
+class Visitor(object):
+    def __init__(self):
+        self.cols = {}
+        with open(data_file('images_md.json'), 'rb') as fp:
+            self.md = json.load(fp)
+        self.count = 0
+
+    def __call__(self, index, row):
+        if index == 0:
+            self.cols = {col: i for i, col in enumerate(row)}
+            return row
+
+        url = URL(row[self.cols['src']])
+        try:
+            for filename in url.path_segments():
+                if filename in self.md:
+                    if self.md[filename].get('source_url'):
+                        row[self.cols['source']] = self.md[filename]['source_url']
+                        self.count += 1
+                        break
+        except IndexError:
+            pass
+        return row
+
+
+if __name__ == '__main__':
+    v = Visitor()
+    visit('images.csv', v)
+    print(v.count)

tsammalex-data/tsammalexdata/add_synonym_col.py

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+from __future__ import unicode_literals, print_function
+
+from tsammalexdata.util import visit
+
+
+class Visitor(object):
+    def __call__(self, index, row):
+        return row[:2] + ['synonyms' if index == 0 else ''] + row[2:]
+
+
+if __name__ == '__main__':
+    visit('taxa.csv', Visitor())

tsammalex-data/tsammalexdata/catalogueoflife.py

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+"""
+Functionality to retrieve information from the Catalogue of Life Web Service
+
+.. seealso:: http://webservice.catalogueoflife.org/col/webservice
+"""
+from __future__ import print_function, unicode_literals, absolute_import, division
+import sys
+import os
+
+from tsammalexdata.util import data_file, jsonload, jsondump, csv_items, DataProvider, unique
+
+
+def text(e, ee):
+    ee = e.find(ee)
+    return (ee.text if ee is not None else '') or ''
+
+
+class CatalogueOfLife(DataProvider):
+    host = 'www.catalogueoflife.org'
+
+    def _get(self, **kw):
+        try:
+            return self.get('col/webservice', type='xml', **kw).find('result')
+        except:
+            return None
+
+    def get_id(self, name):
+        result = self._get(name=name)
+        if result:
+            if text(result, 'name_status') == 'accepted name':
+                return text(result, 'id')
+            if result.find('accepted_name'):
+                return text(result.find('accepted_name'), 'id')
+
+    def get_info(self, id_):
+        result = self._get(id=id_, response='full')
+        if result:
+            # classification: taxon.id name rank url
+            # synonyms: synonym.name
+            res = {k: text(result, k) for k in 'genus species author url'.split()}
+            res['distribution'] = unique(
+                region.split()[0] for region in
+                text(result, 'distribution').split('; ') if region)
+            if result.find('classification'):
+                res['classification'] = {
+                    t.rank.lower(): t.as_dict() for t in
+                    [Taxon(e) for e in result.find('classification').findall('taxon')]}
+            if result.find('synonyms'):
+                res['synonyms'] = filter(
+                    None,
+                    [text(e, 'name') for e in result.find('synonyms').findall('synonym')])
+            return {k: v for k, v in res.items() if v}
+
+    def update(self, taxon, data):
+        if 'distribution' in data:
+            taxon['tdwgregions'] = unique(data['distribution'])
+        classification = data.get('classification', {})
+        for key in 'kingdom phylum class order genus family'.split():
+            if classification.get(key):
+                taxon[key] = classification[key]['name']
+        taxon[self.name + '_url'] = data['url']
+        if 'author' in data:
+            taxon['description'] = data['author']
+
+
+class Taxon(object):
+    def __init__(self, e):
+        for attr in 'id name rank url'.split():
+            setattr(self, attr, text(e, attr))
+
+    def as_dict(self):
+        return dict(id=self.id, name=self.name, url=self.url)
+
+
+if __name__ == '__main__':
+    api = CatalogueOfLife()
+    if sys.argv[1:]:
+        print(api.cli(sys.argv[1]))

tsammalex-data/tsammalexdata/commands.py

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+from __future__ import print_function, unicode_literals, absolute_import, division
+from collections import OrderedDict
+import argparse
+
+from tsammalexdata.util import data_file, jsonload, jsondump, csv_items
+from tsammalexdata.gbif import GBIF
+from tsammalexdata.catalogueoflife import CatalogueOfLife
+from tsammalexdata.eol import EOL
+from tsammalexdata.taxa import item2spec
+from tsammalexdata.distribution import main
+
+
+def update_taxa():
+    parser = argparse.ArgumentParser(
+        description="""\
+Update the supplemental data for taxa from external sources.
+
+We go through the taxa listed in taxa.csv and look for additional information at
+GBIF, EOL and Catalogue Of Life.""")
+    parser.add_argument("--distribution-only", action="store_true")
+    args = parser.parse_args()
+
+    if not args.distribution_only:
+        fname = data_file('taxa.json')
+        taxa = jsonload(fname, default=[], object_pairs_hook=OrderedDict)
+        ids = set(spec['id'] for spec in taxa)
+
+        # add stubs for new entries in taxa.csv:
+        for i, item in enumerate(csv_items('taxa.csv')):
+            if item['id'] not in ids:
+                taxa.insert(i, item2spec(item))
+
+        for cls in [CatalogueOfLife, GBIF, EOL]:
+            with cls() as provider:
+                for i, spec in enumerate(taxa):
+                    if i % 500 == 0:
+                        print(i)
+                    provider.update_taxon(spec)
+
+        jsondump(taxa, fname, indent=4)
+
+    main()

tsammalex-data/tsammalexdata/data/Edmond.xml

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+version https://git-lfs.github.com/spec/v1
+oid sha256:fb7f60b1d6bbffde09e5411b2c19c563b461ab61005a9694076f13031e8a00ad
+size 19873817

tsammalex-data/tsammalexdata/data/audios.csv

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+id,names__id,tags,mime_type,src,creator,date,place,permission,source,source_url,comments

tsammalex-data/tsammalexdata/data/categories.csv

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+id,name,meaning,languages__id,notes
+afr-amfibiee,amfibieë,amphibians,afr,
+afr-bome,bome,trees,afr,
+afr-diere,diere,animals,afr,
+afr-grasse,grasse,grasses,afr,
+afr-insekte,insekte,insects,afr,
+afr-ongewerweldes,ongewerweldes,invertebrates,afr,
+afr-plante,plante,plants,afr,
+afr-reptiele,reptiele,reptiles,afr,
+afr-soogdiere,soogdiere,mammals,afr,
+afr-swamme,swamme,fungi,afr,
+afr-visse,visse,fish,afr,
+afr-voels,voëls,birds,afr,
+deu-amphibien,Amphibien,amphibians,deu,
+deu-baume,Bäume,trees,deu,
+deu-fische,Fische,fish,deu,
+deu-graser,Gräser,grasses,deu,
+deu-insekten,Insekten,insects,deu,
+deu-kletterpflanzen,Kletterpflanzen,climbers,deu,
+deu-pflanzen,Pflanzen,plants,deu,
+deu-pilze,Pilze,fungi,deu,
+deu-reptilien,Reptilien,reptiles,deu,
+deu-saugetiere,Säugetiere,mammals,deu,
+deu-spinnentiere,Spinnentiere,arachnids,deu,
+deu-straucher,Sträucher,shrubs,deu,
+deu-tiere,Tiere,animals,deu,
+deu-vogel,Vögel,birds,deu,
+deu-wirbellose,Wirbellose,invertebrates,deu,
+eng-amphibians,amphibians,,eng,
+eng-animals,animals,,eng,
+eng-arachnids,arachnids,,eng,
+eng-birds,birds,,eng,
+eng-bulbsherbs,bulbs & herbs,,eng,
+eng-creepersclimbers,creepers & climbers,,eng,
+eng-dwarfshrubs,dwarf shrubs,,eng,
+eng-ferns,ferns,,eng,
+eng-fungi,fungi,,eng,
+eng-grassessedges,grasses & sedges,,eng,
+eng-insects,insects,,eng,
+eng-invertebrates,invertebrates,,eng,
+eng-mammals,mammals,,eng,
+eng-molluscs,molluscs,,eng,
+eng-plants,plants,,eng,
+eng-reptiles,reptiles,,eng,
+eng-shrubs,shrubs,,eng,
+eng-succulents,succulents,,eng,
+eng-trees,trees,,eng,
+gwj-ana,ǃánà,vine (life form),gwj,Nakagawa 2013: 1; Tanaka/Sugawara 2010: 121
+gwj-au,ǁʼāū,fish,gwj,Nakagawa 2013: 53; check if really general term
+gwj-dzera,dzérá,bird (life form),gwj,Nakagawa 2013: 167; in Tanaka&Sugawara 2010: 8 = zera
+gwj-gaa,ɡǀa᷇ã,grass (life form),gwj,"Tanaka/Sugawara 2010: 49, 121"
+gwj-guuwahaa,gúũ-wà-háã,"useless/harmless; non-edible, non-medicinal and non-dangerous plants and animals",gwj,"a category opposed to the others, Tanaka/Sugawara 2010: 121"
+gwj-hau,ǁʰàù,animals caught with snare,gwj,"part of the ǀχáa-category (edible vertebrates); Nakagawa 2013: 41; Tanaka/Sugawara 2010: 3, 121"
+gwj-ii,ìī,tree (life form),gwj,Nakagawa 2013: 140; Tanaka/Sugawara 2010: 121; also meaning 'stick'
+gwj-kxooxo,kχʼóo-χo,"larger ungulates that are hunted, “eat-thing”",gwj,"part of the ǀχáa-category (edible vertebrates); Tanaka/Sugawara 2010: 3, 121"
+gwj-kxooxoobi,kχʼôo-χo ǀʔóbi,game with plenty of/fatty meat,gwj,Tanaka/Sugawara 2010: 1
+gwj-paaxo,paa-χò,"dangerous animals, “bite-thing”; synonym: ŋǂīī-ǀùà, ŋǂǐi-ǀoã (carnivores, possible man-killers)",gwj,"Nakagawa 2013: 81; Tanaka/Sugawara 2010: 16, 121; ŋǂīī-ǀùa: “beast-DIM”, mainly felines and canines, maybe a loan from Naro"
+gwj-qxao,ǀqχʼáo,snake (life form),gwj,Tanaka/Sugawara 2010: 120
+gwj-tsoo,tsôo,medicine,gwj,Tanaka/Sugawara 2010: 121
+gwj-tsum,tsṵ̀m̄,plants eaten raw,gwj,Nakagawa 2013: 171
+gwj-uuxo,ǂʔuũ-χò,"edible plants and insects, “eat-thing”",gwj,Tanaka/Sugawara 2010: 121
+gwj-xaa,ǀχáa,"edible vertebrate animals, “meat”",gwj,Tanaka/Sugawara 2010: 121
+gwj-xaaoa,ǀχáa-ǀoa,"small game animals, “small meat”",gwj,Tanaka/Sugawara 2010
+nhr-cgari,cgárí,"tree, thornbush",nhr,Visser 2001: 237
+nhr-chootcgau,chõó tcg'au,"vegetable eaten by whites (eg. lettuce, cabbage, spinach)",nhr,Visser 2001: 234
+nhr-dere,dère,kind of nice food,nhr,Visser 2001: 234
+nhr-ghorokgoose,ghòrò kg'oose,"birds of prey (kite, buzzard, falcon, hawk, eagle, harrier, kestrel)",nhr,Visser 2001: 226
+nhr-hii,hìi,trees,nhr,Visser 2001: 237
+nhr-kgae,kg'ãe,vultures,nhr,Visser 2001: 226
+nhr-khuuga,khúúga,Khoesan medicine (makes you fat),nhr,Visser 2001: 234
+nhr-qgui,qg'ui,thistle,nhr,Visser 2001: 235
+nhr-tcgaberere,tcg'aberere,"vegetable, merogo",nhr,Visser 2001: 236
+nhr-tchaadikgoocoa,tchàa di kg'oo-coa,animals of the field,nhr,Visser 2001: 225
+nhr-tshaatsara,tshàa tsa̠ra,water birds,nhr,Visser 2001: 227
+nhr-tsom,tso̠m,"greens, vegetables",nhr,Visser 2001: 236
+nhr-xaedikgoocoa,x'áé di kg'oo-coa,home animals,nhr,Visser 2001: 225
+nhr-xau,x'aù,fish,nhr,Visser 2001: 225

tsammalex-data/tsammalexdata/data/contributors.csv

@@ -0,0 +1,7 @@
+id,name,sections,editor_ord,editor_sections,affiliation,research_project,homepage,notes
+jn,"Jaulgey, Noémie",,,,"Max Planck Institute for Evolutionary Anthropology, Department of Linguistics, Leipzig, Germany",Tsammalex,,
+nc,"Naumann, Christfried",,1,,"Max Planck Institute for Evolutionary Anthropology, Department of Linguistics, Leipzig, Germany",Tsammalex,http://www.eva.mpg.de/linguistics/staff/christfried-naumann/home.html,
+sl,"Sell, Lena",,,,"Max Planck Institute for Evolutionary Anthropology, Department of Linguistics, Leipzig, Germany",Tsammalex,,
+ms,"Moran, Steven",,2,,"","Dogon Languages",,
+sg,"Segerer, Guillaume",,3,,"LLACAN - Langage, langues et cultures d'Afrique noire","RefLex",,
+fr,"Forkel, Robert",,4,,"Max Planck Institute for Evolutionary Anthropology, Department of Linguistics, Leipzig, Germany",CLLD,,

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tsammalex-data/tsammalexdata/data/external/gbif/acacianebrownii.json

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tsammalex-data/tsammalexdata/data/external/gbif/acacianigrescens.json

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tsammalex-data/tsammalexdata/data/external/gbif/acacianiloticasubspkraussiana.json

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tsammalex-data/tsammalexdata/data/external/gbif/acaciaseyal.json

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