def conceptsets(self):
"""
:returns: `dict` mapping ConceptSet IDs to `Conceptset` instances.
"""
return to_dict(
Conceptset(api=self, **lowercase(d))
for d in read_dicts(self.data_path('concepticon.tsv')))
def metadata(self):
"""
:returns: `dict` mapping metadata provider IDs to `Metadata` instances.
"""
return to_dict(map(
self._metadata,
[p.stem for p in self.data_path('concept_set_meta').glob('*.tsv')]))
def conceptlists(self):
"""
:returns: `dict` mapping ConceptList IDs to `Conceptlist` instances.
.. note:: Individual concepts can be accessed via `Conceptlist.concepts`.
"""
return to_dict(
Conceptlist(api=self, **lowercase(d))
for d in read_dicts(self.data_path('conceptlists.tsv')))
def bibliography(self) -> typing.Dict[str, Source]:
"""
:returns: `dict` mapping BibTeX IDs to `Reference` instances.
"""
return to_dict(
Source.from_entry(key, entry)
for key, entry in pybtex.database.parse_string(
self.bibfile.read_text(
encoding='utf8'), bib_format='bibtex').entries.items())
def _metadata(self, id_):
values_path = self.data_path('concept_set_meta', id_ + '.tsv')
md_path = self.data_path('concept_set_meta', id_ + '.tsv' + MD_SUFFIX)
assert values_path.exists() and md_path.exists()
md = jsonlib.load(md_path)
return Metadata(id=id_,
meta=md,
values=to_dict(
read_dicts(values_path, schema=md['tableSchema']),
key=operator.itemgetter('CONCEPTICON_ID')))
def bibliography(self):
"""
:returns: `dict` mapping BibTeX IDs to `Reference` instances.
"""
refs = []
with self.bibfile.open(encoding='utf8') as fp:
for key, entry in pybtex.database.parse_string(
fp.read(), bib_format='bibtex').entries.items():
refs.append(Source.from_entry(key, entry))
return to_dict(refs)
def concepts(self):
res = []
if self.path.exists():
for item in self.metadata:
kw, attributes = {}, {}
for k, v in item.items():
if k:
kl = k.lower()
setitem(kw if kl in Concept.public_fields() else attributes, kl, v)
res.append(Concept(list=self, attributes=attributes, **kw))
return to_dict(res)
def bibliography(self):
"""
:returns: `dict` mapping BibTeX IDs to `Reference` instances.
"""
log = logging.getLogger('bibtexparser')
log.setLevel(logging.WARN)
with self.bibfile.open(encoding='utf8') as fp:
refs = []
for rec in bibtexparser.loads(fp.read()).entries:
refs.append(
Reference(id=rec.pop('ID'), type=rec.pop('ENTRYTYPE'), record=rec))
return to_dict(refs)
def test_to_dict(self):
from pyconcepticon.util import to_dict
with self.assertRaises(ValueError):
to_dict([None, None], id)
