def resource(prefix: str):
"""Serve the a Bioregistry entry page."""
prefix = _normalize_prefix_or_404(prefix, '.' + resource.__name__)
if not isinstance(prefix, str):
return prefix
example = bioregistry.get_example(prefix)
return render_template(
'resource.html',
prefix=prefix,
name=bioregistry.get_name(prefix),
example=example,
mappings=_get_resource_mapping_rows(prefix),
synonyms=bioregistry.get_synonyms(prefix),
homepage=bioregistry.get_homepage(prefix),
pattern=bioregistry.get_pattern(prefix),
version=bioregistry.get_version(prefix),
has_terms=bioregistry.has_terms(prefix),
obo_download=bioregistry.get_obo_download(prefix),
owl_download=bioregistry.get_owl_download(prefix),
namespace_in_lui=bioregistry.namespace_in_lui(prefix),
deprecated=bioregistry.is_deprecated(prefix),
contact=bioregistry.get_email(prefix),
banana=bioregistry.get_banana(prefix),
description=bioregistry.get_description(prefix),
providers=None if example is None else _get_resource_providers(
prefix, example),
)
def normalize_identifier(prefix: str, identifier: str) -> str:
"""Normalize the identifier."""
# TODO in bioregistry.resolve_identifier there is similar code. just combine with that
banana = bioregistry.get_banana(prefix)
if banana:
if not identifier.startswith(banana):
return f"{banana}:{identifier}"
elif bioregistry.namespace_in_lui(prefix):
banana = f"{prefix.upper()}:"
if not identifier.startswith(banana):
return f"{banana}{identifier}"
return identifier
def resources():
"""Serve the Bioregistry page."""
rows = [
dict(
prefix=prefix,
name=bioregistry.get_name(prefix),
example=bioregistry.get_example(prefix),
homepage=bioregistry.get_homepage(prefix),
pattern=bioregistry.get_pattern(prefix),
namespace_in_lui=bioregistry.namespace_in_lui(prefix),
banana=bioregistry.get_banana(prefix),
description=bioregistry.get_description(prefix),
) for prefix in bioregistry.read_registry()
]
return render_template('resources.html', rows=rows)
def main(url: str, local: bool):
"""Test the API."""
url = url.rstrip('/')
if local:
url = 'http://localhost:5000'
click.echo(f'Testing resolution API on {url}')
failure = False
prefixes = tqdm(bioregistry.read_registry())
for prefix in prefixes:
identifier = bioregistry.get_example(prefix)
if identifier is None:
continue
prefixes.set_postfix({'prefix': prefix})
req_url = f'{url}/{prefix}:{identifier}'
res = requests.get(req_url, allow_redirects=False)
log = partial(_log, req_url=req_url)
if res.status_code == 302: # redirect
continue
elif res.status_code != 404:
text = res.text.splitlines()[3][len('<p>'):-len('</p>')]
log(f'HTTP {res.status_code}: {res.reason} {text}', fg='red')
elif not bioregistry.get_providers(prefix, identifier):
continue
elif '/' in identifier or SLASH_URL_ENCODED in identifier:
log('contains slash 🎩 🎸', fg='red')
elif not bioregistry.validate(prefix, identifier):
pattern = bioregistry.get_pattern(prefix)
if bioregistry.get_banana(prefix):
log(f'banana {pattern} 🍌', fg='red')
else:
log(f'invalid example does not match pattern {pattern}',
fg='red')
else:
log('404 unknown issue', fg='red')
failure = True
return sys.exit(1 if failure else 0)
def test_lui(self):
"""Test the LUI makes sense (spoilers, they don't).
Discussion is ongoing at:
- https://github.com/identifiers-org/identifiers-org.github.io/issues/151
"""
for prefix in bioregistry.read_registry():
if not bioregistry.namespace_in_lui(prefix):
continue
if bioregistry.get_banana(prefix):
continue # rewrite rules are applied to prefixes with bananas
if prefix in {'ark', 'obi'}:
continue # these patterns on identifiers.org are garb
with self.subTest(prefix=prefix):
re_pattern = bioregistry.get_pattern(prefix)
miriam_prefix = bioregistry.get_identifiers_org_prefix(prefix)
self.assertTrue(
re_pattern.startswith(f'^{miriam_prefix.upper()}')
or re_pattern.startswith(miriam_prefix.upper()),
msg=f'{prefix} pattern: {re_pattern}',
)