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feat: moved identifiers.org namespaces to an asset of the package
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@jonrkarr
jonrkarr committed Jan 12, 2022
1 parent 2db4c27 commit 513b4e3
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Showing 5 changed files with 106 additions and 75 deletions.
3 changes: 3 additions & 0 deletions MANIFEST.in
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Expand Up @@ -8,6 +8,9 @@ include LICENSE
include requirements.txt
include requirements.optional.txt

# identifiers.org namespaces
include biosimulators_utils/utils/identifiers_org.json

# CellML schema
include biosimulators_utils/model_lang/cellml/*.rng

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1 change: 1 addition & 0 deletions biosimulators_utils/utils/identifiers_org.json
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175 changes: 101 additions & 74 deletions biosimulators_utils/utils/identifiers_org.py
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Expand Up @@ -6,15 +6,15 @@
:License: MIT
"""

from ..config import get_app_dirs
from ..warnings import warn, BioSimulatorsWarning
import dataclasses
import datetime
import dateutil.parser
import functools
import json
import os.path
import pkg_resources
import regex as re
import requests_cache
import requests
import typing

__all__ = [
Expand All @@ -24,6 +24,7 @@
'IdentifiersOrgNamespace',
'InvalidIdentifiersOrgUri',
'get_identifiers_org_namespaces',
'download_identifiers_org_namespaces',
'get_identifiers_org_namespace',
'validate_identifiers_org_uri',
]
Expand Down Expand Up @@ -87,87 +88,113 @@ class InvalidIdentifiersOrgUri(Exception):
pass


@functools.lru_cache(maxsize=None)
def get_identifiers_org_namespaces():
IDENTIFIERS_ORG_NAMESPACES = None


def get_identifiers_org_namespaces(reload=False):
""" Get the namespaces registered with `Identifiers.org <https://identifiers.org/>`_.
Args:
reload (:obj:`bool`, optional): whether to reload the namespaces from the Identifiers.org API
Returns:
:obj:`dict`: dictionary that maps the prefix of each Identifiers.org namespace or
a tuple of its provider code and its prefix to its attributes
"""
filename = os.path.join(get_app_dirs().user_cache_dir, 'identifiers-org')
session = requests_cache.CachedSession(filename, expire_after=7 * 24 * 60 * 60)
global IDENTIFIERS_ORG_NAMESPACES

response = session.get(NAMESPACES_ENDPOINT)
response.raise_for_status()
if IDENTIFIERS_ORG_NAMESPACES is None or reload:
filename = pkg_resources.resource_filename('biosimulators_utils', os.path.join('utils', 'identifiers_org.json'))

namespaces = {}
skipped_namespaces = []
for namespace in response.json()['payload']['namespaces']:
resources = []
for resource in namespace['resources']:
resources.append(IdentifiersOrgNamespaceResource(
id=resource['id'],
mir_id=resource['mirId'],
name=resource['name'],
description=resource['description'],
url_pattern=resource['urlPattern'],
official=resource['official'],
provider_code=resource['providerCode'],
sample_id=resource['sampleId'],
home_url=resource['resourceHomeUrl'],
institution=IdentifiersOrgInstitution(
id=resource['institution']['id'],
name=resource['institution']['name'],
home_url=resource['institution']['homeUrl'],
description=resource['institution']['description'],
ror_id=resource['institution']['rorId'],
if os.path.isfile(filename) and not reload:
with open(filename, 'r') as file:
raw_namespaces = json.load(file)
else:
raw_namespaces = download_identifiers_org_namespaces()
with open(filename, 'w') as file:
json.dump(raw_namespaces, file)

namespaces = {}
skipped_namespaces = []
for namespace in raw_namespaces:
resources = []
for resource in namespace['resources']:
resources.append(IdentifiersOrgNamespaceResource(
id=resource['id'],
mir_id=resource['mirId'],
name=resource['name'],
description=resource['description'],
url_pattern=resource['urlPattern'],
official=resource['official'],
provider_code=resource['providerCode'],
sample_id=resource['sampleId'],
home_url=resource['resourceHomeUrl'],
institution=IdentifiersOrgInstitution(
id=resource['institution']['id'],
name=resource['institution']['name'],
home_url=resource['institution']['homeUrl'],
description=resource['institution']['description'],
ror_id=resource['institution']['rorId'],
country=IdentifiersOrgCountry(
code=resource['institution']['location']['countryCode'],
name=resource['institution']['location']['countryName'],
),
),
country=IdentifiersOrgCountry(
code=resource['institution']['location']['countryCode'],
name=resource['institution']['location']['countryName'],
code=resource['location']['countryCode'],
name=resource['location']['countryName'],
),
),
country=IdentifiersOrgCountry(
code=resource['location']['countryCode'],
name=resource['location']['countryName'],
),
deprecated=resource['deprecated'],
deprecated_date=dateutil.parser.parse(resource['deprecationDate']) if resource['deprecationDate'] else None,
))

try:
pattern = re.compile(namespace['pattern'])
except re.error as exception:
msg = "'{}' (prefix '{}'): '{}' is not valid: {}.".format(
namespace['name'], namespace['prefix'], namespace['pattern'], str(exception))
skipped_namespaces.append(msg)
continue

namespace_obj = IdentifiersOrgNamespace(
id=namespace['id'],
mir_id=namespace['mirId'],
prefix=namespace['prefix'],
name=namespace['name'],
description=namespace['description'],
pattern=pattern,
embedded_in_lui=namespace['namespaceEmbeddedInLui'],
sample_id=namespace['sampleId'],
resources=resources,
deprecated=namespace['deprecated'],
deprecated_date=dateutil.parser.parse(namespace['deprecationDate']) if namespace['deprecationDate'] else None,
created=dateutil.parser.parse(namespace['created']),
modified=dateutil.parser.parse(namespace['modified']),
)
namespaces[namespace['prefix'].lower()] = namespace_obj
for resource in namespace['resources']:
namespaces[resource['providerCode'].lower() + '/' + namespace['prefix'].lower()] = namespace_obj

if skipped_namespaces:
msg = '{} namespaces will not be validated because their regular expression patterns are not valid:\n - {}'.format(
len(skipped_namespaces), '\n - '.join(sorted(skipped_namespaces)))
warn(msg, BioSimulatorsWarning)

return namespaces
deprecated=resource['deprecated'],
deprecated_date=dateutil.parser.parse(resource['deprecationDate']) if resource['deprecationDate'] else None,
))

try:
pattern = re.compile(namespace['pattern'])
except re.error as exception:
msg = "'{}' (prefix '{}'): '{}' is not valid: {}.".format(
namespace['name'], namespace['prefix'], namespace['pattern'], str(exception))
skipped_namespaces.append(msg)
continue

namespace_obj = IdentifiersOrgNamespace(
id=namespace['id'],
mir_id=namespace['mirId'],
prefix=namespace['prefix'],
name=namespace['name'],
description=namespace['description'],
pattern=pattern,
embedded_in_lui=namespace['namespaceEmbeddedInLui'],
sample_id=namespace['sampleId'],
resources=resources,
deprecated=namespace['deprecated'],
deprecated_date=dateutil.parser.parse(namespace['deprecationDate']) if namespace['deprecationDate'] else None,
created=dateutil.parser.parse(namespace['created']),
modified=dateutil.parser.parse(namespace['modified']),
)
namespaces[namespace['prefix'].lower()] = namespace_obj
for resource in namespace['resources']:
namespaces[resource['providerCode'].lower() + '/' + namespace['prefix'].lower()] = namespace_obj

if skipped_namespaces:
msg = '{} namespaces will not be validated because their regular expression patterns are not valid:\n - {}'.format(
len(skipped_namespaces), '\n - '.join(sorted(skipped_namespaces)))
warn(msg, BioSimulatorsWarning)

IDENTIFIERS_ORG_NAMESPACES = namespaces

return IDENTIFIERS_ORG_NAMESPACES


def download_identifiers_org_namespaces():
""" Get the namespaces registered with `Identifiers.org <https://identifiers.org/>`_.
Returns:
:obj:`dict`: dictionary that maps the prefix of each Identifiers.org namespace or
a tuple of its provider code and its prefix to its attributes
"""
response = requests.get(NAMESPACES_ENDPOINT)
response.raise_for_status()
return response.json()['payload']['namespaces']


def get_identifiers_org_namespace(prefix):
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1 change: 0 additions & 1 deletion requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,6 @@ pyyaml
rdflib
regex
requests
requests_cache
setuptools
simplejson
termcolor
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1 change: 1 addition & 0 deletions setup.py
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Expand Up @@ -19,6 +19,7 @@
dirname = os.path.dirname(__file__)
package_data = {
name: [
os.path.join('utils', 'identifiers_org.json'),
os.path.join('model_lang', 'cellml', '*.rng'),
os.path.join('viz', 'vega', '**', '*.json'),
],
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