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Improve resolving of URLs via banana curation
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,94 @@ | ||
| # -*- coding: utf-8 -*- | ||
|
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| """Resolvers for CURIE (e.g., pairs of prefix and identifier).""" | ||
|
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| from typing import Mapping, Optional | ||
|
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| from .resolve import ( | ||
| get_banana, get_format, get_identifiers_org_prefix, get_obofoundry_prefix, get_ols_prefix, get_pattern_re, | ||
| namespace_in_lui, | ||
| ) | ||
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| __all__ = [ | ||
| 'validate', | ||
| 'get_providers', | ||
| 'get_identifiers_org_url', | ||
| 'get_identifiers_org_curie', | ||
| 'get_obofoundry_link', | ||
| 'get_ols_link', | ||
| ] | ||
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| def validate(prefix: str, identifier: str) -> Optional[bool]: | ||
| """Validate the identifier against the prefix's pattern, if it exists.""" | ||
| pattern = get_pattern_re(prefix) | ||
| if pattern is None: | ||
| return None | ||
|
|
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| if namespace_in_lui(prefix) and not identifier.startswith(f'{prefix.upper()}:'): | ||
| # Some cases do not use uppercase | ||
| identifier = f'{prefix.upper()}:{identifier}' | ||
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| return bool(pattern.match(identifier)) | ||
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| def get_providers(prefix: str, identifier: str) -> Mapping[str, str]: | ||
| """Get all providers for the CURIE.""" | ||
| providers = {} | ||
| bioregistry_format = get_format(prefix) | ||
| if bioregistry_format: | ||
| providers['bioregistry'] = bioregistry_format.replace('$1', identifier) | ||
| for provider, get_url in [ | ||
| ('miriam', get_identifiers_org_url), | ||
| ('obofoundry', get_obofoundry_link), | ||
| ('ols', get_ols_link), | ||
| ]: | ||
| link = get_url(prefix, identifier) | ||
| if link: | ||
| providers[provider] = link | ||
| return providers | ||
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|
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| def get_identifiers_org_url(prefix: str, identifier: str) -> Optional[str]: | ||
| """Get the identifiers.org URL for the given CURIE.""" | ||
| curie = get_identifiers_org_curie(prefix, identifier) | ||
| if curie is None: | ||
| return None | ||
| return f'https://identifiers.org/{curie}' | ||
|
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||
|
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| def get_identifiers_org_curie(prefix: str, identifier: str) -> Optional[str]: | ||
| """Get the identifiers.org CURIE for the given CURIE.""" | ||
| miriam_prefix = get_identifiers_org_prefix(prefix) | ||
| if miriam_prefix is None: | ||
| return None | ||
| if not namespace_in_lui(prefix): | ||
| return f'{prefix}:{identifier}' | ||
| banana = get_banana(prefix) | ||
| if banana: | ||
| if identifier.startswith(f'{banana}:'): | ||
| return identifier | ||
| else: | ||
| return f'{banana}:{identifier}' | ||
| else: | ||
| if identifier.startswith(prefix.upper()): | ||
| return identifier | ||
| else: | ||
| return f'{prefix.upper()}:{identifier}' | ||
|
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|
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| def get_obofoundry_link(prefix: str, identifier: str) -> Optional[str]: | ||
| """Get the OBO Foundry URL if possible.""" | ||
| obo_prefix = get_obofoundry_prefix(prefix) | ||
| if obo_prefix is None: | ||
| return None | ||
| return f'http://purl.obolibrary.org/obo/{obo_prefix.upper()}_{identifier}' | ||
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| def get_ols_link(prefix: str, identifier: str) -> Optional[str]: | ||
| """Get the OLS URL if possible.""" | ||
| ols_prefix = get_ols_prefix(prefix) | ||
| obo_link = get_obofoundry_link(prefix, identifier) | ||
| if ols_prefix is None or obo_link is None: | ||
| return None | ||
| return f'https://www.ebi.ac.uk/ols/ontologies/{ols_prefix}/terms?iri={obo_link}' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| # -*- coding: utf-8 -*- | ||
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| """Tests for identifiers.org.""" | ||
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| import unittest | ||
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| import requests | ||
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| from bioregistry import get_identifiers_org_curie, get_identifiers_org_url | ||
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| class TestIdentifiersOrg(unittest.TestCase): | ||
| """Tests for identifiers.org.""" | ||
|
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| def test_url(self): | ||
| """Test formatting URLs.""" | ||
| for prefix, identifier, expected, _reason in [ | ||
| ('efo', '0000400', 'efo:0000400', 'test simple concatenation'), | ||
| ('chebi', 'CHEBI:1234', 'CHEBI:1234', 'test redundant namespace (standard)'), | ||
| ('chebi', '1234', 'CHEBI:1234', 'test exclusion of redundant namespace (standard)'), | ||
| ( | ||
| 'mzspec', | ||
| 'PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2', | ||
| 'mzspec:PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2', | ||
| 'test simple concatenation with false banana', | ||
| ), | ||
| ( | ||
| 'mzspec', | ||
| 'mzspec:PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2', | ||
| 'mzspec:PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2', | ||
| 'test simple concatenation (redundant) with false banana', | ||
| ), | ||
| ]: | ||
| with self.subTest(p=prefix, i=identifier): | ||
| curie = get_identifiers_org_curie(prefix, identifier) | ||
| self.assertEqual(expected, curie, msg='wrong CURIE') | ||
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| url = get_identifiers_org_url(prefix, identifier) | ||
| self.assertEqual(f'https://identifiers.org/{curie}', url, msg='wrong URL') | ||
|
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| # Check that the URL resolves | ||
| res = requests.get(url) | ||
| self.assertEqual(200, res.status_code, msg=res.reason) |
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