def test_get(self):
"""Test getting content from the bioregistry."""
ncbitaxon_entry = bioregistry.get('ncbitaxon')
self.assertIn('synonyms', ncbitaxon_entry)
self.assertIn('NCBI_Taxon_ID', ncbitaxon_entry['synonyms'])
self.assertIn('miriam', ncbitaxon_entry)
self.assertIn('obofoundry', ncbitaxon_entry)
self.assertIn('ols', ncbitaxon_entry)
self.assertIn('wikidata', ncbitaxon_entry)
def _get_version_type(bioregistry_id) -> Optional[VersionType]:
ols_entry = bioregistry.get(bioregistry_id)
ols_version_type = ols_entry.get('ols_version_type')
ols_version_date_format = ols_entry.get('ols_version_date_format')
if ols_version_date_format:
return VersionType.date
elif ols_version_type:
return getattr(VersionType, ols_version_type)
else:
logger.warning('[%s] missing version type', bioregistry_id)
def resource(prefix: str):
"""Get an entry.
---
parameters:
- name: prefix
in: path
description: The prefix for the entry
required: true
type: string
example: doid
""" # noqa:DAR101,DAR201
prefix = _normalize_prefix_or_404(prefix)
return jsonify(prefix=prefix, **bioregistry.get(prefix)) # type:ignore
def test_name_expansions(self):
"""Test that default names are not capital acronyms."""
for prefix in bioregistry.read_registry():
if bioregistry.is_deprecated(prefix):
continue
entry = bioregistry.get(prefix)
if 'name' in entry:
continue
name = bioregistry.get_name(prefix)
if prefix == name.lower() and name.upper() == name:
with self.subTest(prefix=prefix):
self.fail(msg=f'{prefix} acronym ({name}) is not expanded')
if '.' in prefix and prefix.split('.')[0] == name.lower():
with self.subTest(prefix=prefix):
self.fail(msg=f'{prefix} acronym ({name}) is not expanded')
def test_no_redundant_acronym(self):
"""Test that there is no redundant acronym in the name.
For example, "Amazon Standard Identification Number (ASIN)" is a problematic
name for prefix "asin".
"""
for prefix in bioregistry.read_registry():
if bioregistry.is_deprecated(prefix):
continue
entry = bioregistry.get(prefix)
if 'name' in entry:
continue
name = bioregistry.get_name(prefix)
try:
_, rest = name.rstrip(')').rsplit('(', 1)
except ValueError:
continue
if rest.lower() == prefix.lower():
with self.subTest(prefix=prefix):
self.fail(msg=f'{prefix} has redundany acronym in name "{name}"')