diff --git a/linkml_runtime/utils/curienamespace.py b/linkml_runtime/utils/curienamespace.py index 066825d1..04a6c415 100644 --- a/linkml_runtime/utils/curienamespace.py +++ b/linkml_runtime/utils/curienamespace.py @@ -1,40 +1,81 @@ from logging import warning -from typing import Optional, Union, Dict +from typing import Optional, Union, Dict, List from rdflib import Namespace, URIRef +from curies import Converter, Record + +class CurieNamespaceCatalog(object): + catalog: Dict[str, "CurieNamespace"] + def __init__(self) -> None: + self.namespaces = [] + self._converter: Optional[Converter] = None + + @property + def converter(self): + if not self._converter: + self._converter = self._buildConverter() + return self._converter + + def _buildConverter(self): + records = [] + namespaces_to_treat = self.namespaces[:] + while len(namespaces_to_treat) > 0: + ns = namespaces_to_treat.pop(0) + prefix = ns.prefix + uri = str(ns) + all_prefixes = [prefix] + all_uris = [uri] + iteration_needed = True + while iteration_needed: + iteration_needed = False + for possible_synonym in namespaces_to_treat[:]: + if possible_synonym.prefix in all_prefixes: + all_uris.append(str(possible_synonym)) + namespaces_to_treat.remove(possible_synonym) + iteration_needed = True + if str(possible_synonym) in all_uris: + all_prefixes.append(possible_synonym.prefix) + namespaces_to_treat.remove(possible_synonym) + iteration_needed = True + records.append(Record(prefix, uri , [x for x in all_prefixes if not x == prefix], [x for x in all_uris if not x == uri])) + return Converter(records=records) -class CurieNamespace(Namespace): - # We would prefer to use curies.Converter here, but there doesn't appear to be any way to build it incrementally - catalog: Dict[str, "CurieNamespace"] = dict() - @classmethod - def to_curie(cls, uri: Union[str, URIRef]) -> str: - uri = str(uri) - candidate_ns = "" - for prefix, ns in cls.catalog.items(): - if uri.startswith(ns) and len(ns) > len(candidate_ns): - candidate_ns = ns - if candidate_ns: - return candidate_ns.curie(uri[len(candidate_ns):]) - return None + def to_curie(self, uri: Union[str, URIRef]) -> str: + return self.converter.compress(uri) + + def to_uri(self, curie: str) -> Optional[URIRef]: + expanded = self.converter.expand(curie) + return None if expanded is None else URIRef(expanded) + + def add_namespace(self,ns: "CurieNamespace"): + self.namespaces.append(ns) + self._converter = None + @classmethod - def to_uri(cls, curie: str) -> Optional[URIRef]: - prefix, localname = curie.split(':', 1) - ns = CurieNamespace.catalog.get(prefix, None) - return ns[localname] if ns else None + def create(cls, *namespaces: List["CurieNamespace"]): + cat = CurieNamespaceCatalog() + [cat.add_namespace(x) for x in namespaces] + return cat + + def clear(self): + self.catalog = dict() + + def as_dict(self): + return self.catalog.copy() + - def __new__(cls, prefix: str, ns: Union[str, bytes, URIRef]) -> "CurieNamespace": +class CurieNamespace(Namespace): + def __new__(cls, prefix: str, ns: Union[str, URIRef]): rt = Namespace.__new__(cls, str(ns) if not isinstance(ns, bytes) else ns) rt.prefix = prefix - if prefix in CurieNamespace.catalog: - if CurieNamespace.catalog[prefix] != str(rt): - # prefix is bound to a different namespace - warning(f"Prefix: {prefix} already references {CurieNamespace.catalog[prefix]} - not updated to {rt}") - else: - CurieNamespace.catalog[prefix] = rt return rt def curie(self, reference: Optional[str] = '') -> str: return self.prefix + ':' + reference + + def addTo(self, catalog: CurieNamespaceCatalog) -> "CurieNamespace": + catalog.add_namespace(self) + return self diff --git a/poetry.lock b/poetry.lock index c8be3afb..5c61a9d5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,3 +1,5 @@ +# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand. + [[package]] name = "attrs" version = "22.1.0" @@ -5,6 +7,10 @@ description = "Classes Without Boilerplate" category = "main" optional = false python-versions = ">=3.5" +files = [ + {file = "attrs-22.1.0-py2.py3-none-any.whl", hash = "sha256:86efa402f67bf2df34f51a335487cf46b1ec130d02b8d39fd248abfd30da551c"}, + {file = "attrs-22.1.0.tar.gz", hash = "sha256:29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6"}, +] [package.extras] dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy (>=0.900,!=0.940)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "sphinx", "sphinx-notfound-page", "zope.interface"] @@ -19,6 +25,10 @@ description = "Python package for providing Mozilla's CA Bundle." category = "main" optional = false python-versions = ">=3.6" +files = [ + {file = "certifi-2022.9.24-py3-none-any.whl", hash = "sha256:90c1a32f1d68f940488354e36370f6cca89f0f106db09518524c88d6ed83f382"}, + {file = "certifi-2022.9.24.tar.gz", hash = "sha256:0d9c601124e5a6ba9712dbc60d9c53c21e34f5f641fe83002317394311bdce14"}, +] [[package]] name = "charset-normalizer" @@ -27,6 +37,10 @@ description = "The Real First Universal Charset Detector. 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"pytest-mypy (>=0.9.1)"] + +[metadata] +lock-version = "2.0" +python-versions = "^3.7.6" +content-hash = "e29c71ca740857bbca1de0e0b8db14512c5098771d1d9552d70c8929bf62717c" diff --git a/pyproject.toml b/pyproject.toml index 8514ae21..c3b7bde3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -53,7 +53,7 @@ pyyaml = "*" rdflib = ">=6.0.0" requests = "*" prefixmaps = ">=0.1.4" -curies = "^0.4.0" +curies = "^0.4.3" [tool.poetry.dev-dependencies] coverage = "^6.2" diff --git a/tests/test_utils/input/CurieNamespace_test.py b/tests/test_utils/input/CurieNamespace_test.py index ec2c569d..8df2bd65 100644 --- a/tests/test_utils/input/CurieNamespace_test.py +++ b/tests/test_utils/input/CurieNamespace_test.py @@ -23,7 +23,7 @@ from linkml_runtime.utils.formatutils import camelcase, underscore, sfx from linkml_runtime.utils.enumerations import EnumDefinitionImpl from rdflib import Namespace, URIRef, DC -from linkml_runtime.utils.curienamespace import CurieNamespace +from linkml_runtime.utils.curienamespace import CurieNamespace, CurieNamespaceCatalog from linkml_runtime.utils.metamodelcore import Bool, Decimal, ElementIdentifier, NCName, NodeIdentifier, URI, URIorCURIE, XSDDate, XSDDateTime, XSDTime metamodel_version = "1.7.0" @@ -37,7 +37,7 @@ SHEX = CurieNamespace('shex', 'http://www.w3.org/ns/shex#') XSD = CurieNamespace('xsd', 'http://www.w3.org/2001/XMLSchema#') DEFAULT_ = CurieNamespace('', 'http://example.org/') - +namespaceCatalog = CurieNamespaceCatalog.create(LINKML, SHEX, XSD, DEFAULT_) # Types class String(str): diff --git a/tests/test_utils/test_curienamespace.py b/tests/test_utils/test_curienamespace.py index df128c4a..cc5f9ceb 100644 --- a/tests/test_utils/test_curienamespace.py +++ b/tests/test_utils/test_curienamespace.py @@ -90,48 +90,49 @@ def test_curie_as_curie(self): def test_curie_catalog(self): """ Test the CurieNamespace curie to uri and uri to curi conversions""" - from tests.test_utils.input.CurieNamespace_test import Person + from tests.test_utils.input.CurieNamespace_test import Person, namespaceCatalog # Make sure the import doesn't get factored out Person(id="Fred") # Test bidirectional conversion + CurieNamespace("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#").addTo(namespaceCatalog) self.assertEqual('rdf:chaos', - CurieNamespace.to_curie('http://www.w3.org/1999/02/22-rdf-syntax-ns#chaos')) + namespaceCatalog.to_curie('http://www.w3.org/1999/02/22-rdf-syntax-ns#chaos')) self.assertEqual(URIRef('http://www.w3.org/1999/02/22-rdf-syntax-ns#penguins'), - CurieNamespace.to_uri('rdf:penguins')) + namespaceCatalog.to_uri('rdf:penguins')) # Test missing URI and CURIE - self.assertIsNone(CurieNamespace.to_curie('http://nothing.org/never')) - self.assertIsNone(CurieNamespace.to_uri('abcd:efgh')) + self.assertIsNone(namespaceCatalog.to_curie('http://nothing.org/never')) + self.assertIsNone(namespaceCatalog.to_uri('abcd:efgh')) # Test the default namespace - self.assertEqual('http://example.org/ttfn', str(CurieNamespace.to_uri(':ttfn'))) - self.assertEqual(':foul_soap', str(CurieNamespace.to_curie('http://example.org/foul_soap'))) + self.assertEqual('http://example.org/ttfn', str(namespaceCatalog.to_uri(':ttfn'))) + self.assertEqual(':foul_soap', str(namespaceCatalog.to_curie('http://example.org/foul_soap'))) # Make sure we pick the longest path - self.assertEqual(':inst#probe', CurieNamespace.to_curie(URIRef('http://example.org/inst#probe'))) - CurieNamespace('long_ex', 'http://example.org/inst#') - self.assertEqual('long_ex:probe', CurieNamespace.to_curie(URIRef('http://example.org/inst#probe'))) + self.assertEqual(':inst#probe', namespaceCatalog.to_curie(URIRef('http://example.org/inst#probe'))) + CurieNamespace('long_ex', 'http://example.org/inst#').addTo(namespaceCatalog) + self.assertEqual('long_ex:probe', namespaceCatalog.to_curie(URIRef('http://example.org/inst#probe'))) # Test incremental add - CurieNamespace('tester', URIRef('http://fester.bester/tester#')) - self.assertEqual('tester:hip_boots', CurieNamespace.to_curie('http://fester.bester/tester#hip_boots')) + CurieNamespace('tester', URIRef('http://fester.bester/tester#')).addTo(namespaceCatalog) + self.assertEqual('tester:hip_boots', namespaceCatalog.to_curie('http://fester.bester/tester#hip_boots')) # Test multiple prefixes for same suffix - CurieNamespace('ns17', URIRef('http://fester.bester/tester#')) - self.assertEqual('tester:hip_boots', CurieNamespace.to_curie('http://fester.bester/tester#hip_boots')) - self.assertEqual('http://fester.bester/tester#hip_boots', str(CurieNamespace.to_uri('tester:hip_boots'))) - self.assertEqual('http://fester.bester/tester#hip_boots', str(CurieNamespace.to_uri('ns17:hip_boots'))) + CurieNamespace('ns17', URIRef('http://fester.bester/tester#')).addTo(namespaceCatalog) + self.assertEqual('tester:hip_boots', namespaceCatalog.to_curie('http://fester.bester/tester#hip_boots')) + self.assertEqual('http://fester.bester/tester#hip_boots', str(namespaceCatalog.to_uri('tester:hip_boots'))) + self.assertEqual('http://fester.bester/tester#hip_boots', str(namespaceCatalog.to_uri('ns17:hip_boots'))) # Test multiple uris for same prefix # The following should be benign - CurieNamespace('tester', URIRef('http://fester.bester/tester#')) + CurieNamespace('tester', URIRef('http://fester.bester/tester#')).addTo(namespaceCatalog) # Issue warnings for now on this # TODO: test that we log the following # 'Prefix: tester already references http://fester.bester/tester# - # not updated to http://fester.notsogood/tester#' - CurieNamespace('tester', URIRef('http://fester.notsogood/tester#')) + CurieNamespace('tester', URIRef('http://fester.notsogood/tester#')).addTo(namespaceCatalog)