- Update: Type definition for entities() method type definitions. Was…

… previously just Iterable[CURIE], but it is also possible for it to return URIs.

src/oaklib/implementations/funowl/funowl_implementation.py

@@ -1,6 +1,6 @@
 import logging
 from dataclasses import dataclass
-from typing import Any, Iterable, List, Mapping, Optional
+from typing import Any, Iterable, List, Mapping, Optional, Union
 
 import rdflib
 from funowl import (
@@ -27,7 +27,7 @@
 from oaklib.interfaces.basic_ontology_interface import LANGUAGE_TAG
 from oaklib.interfaces.owl_interface import OwlInterface, ReasonerConfiguration
 from oaklib.interfaces.patcher_interface import PatcherInterface
-from oaklib.types import CURIE, PRED_CURIE
+from oaklib.types import CURIE, PRED_CURIE, URI
 
 
 @dataclass
@@ -97,7 +97,7 @@ def label(self, curie: CURIE, lang: Optional[LANGUAGE_TAG] = None) -> str:
             else:
                 raise ValueError(f"Label must be literal, not {label}")
 
-    def entities(self, filter_obsoletes=True, owl_type=None) -> Iterable[CURIE]:
+    def entities(self, filter_obsoletes=True, owl_type=None) -> Iterable[Union[URI, CURIE]]:
         for ax in self._ontology.axioms:
             if isinstance(ax, Declaration):
                 uri = ax.v.full_uri(self.functional_writer.g)

src/oaklib/implementations/kgx/kgx_implementation.py

@@ -4,7 +4,7 @@
 from collections import defaultdict
 from dataclasses import dataclass, field
 from pathlib import Path
-from typing import Any, Dict, Iterable, Iterator, List, Optional, Tuple, Type
+from typing import Any, Dict, Iterable, Iterator, List, Optional, Tuple, Type, Union
 
 import rdflib
 import sqlalchemy.orm
@@ -63,7 +63,7 @@
 from oaklib.interfaces.semsim_interface import SemanticSimilarityInterface
 from oaklib.interfaces.summary_statistics_interface import SummaryStatisticsInterface
 from oaklib.interfaces.validator_interface import ValidatorInterface
-from oaklib.types import CATEGORY_CURIE, CURIE, SUBSET_CURIE
+from oaklib.types import CATEGORY_CURIE, CURIE, SUBSET_CURIE, URI
 from oaklib.utilities.identifier_utils import synonym_type_code_from_curie
 from oaklib.utilities.iterator_utils import chunk
 
@@ -347,7 +347,7 @@ def is_postgres(self):
         # TODO
         return False
 
-    def entities(self, filter_obsoletes=True, owl_type=None) -> Iterable[CURIE]:
+    def entities(self, filter_obsoletes=True, owl_type=None) -> Iterable[Union[URI, CURIE]]:
         q = self.session.query(Node.id)
         logging.debug(f"Entities Query: {q}")
         for row in q:

src/oaklib/implementations/obograph/obograph_implementation.py

@@ -151,7 +151,7 @@ def _all_relationships(self) -> Iterator[RELATIONSHIP]:
                             # directionality is lost in OboGraph representation
                             yield self._tuple_to_curies((n1, EQUIVALENT_CLASS, n2))
 
-    def entities(self, filter_obsoletes=True, owl_type=None) -> Iterable[CURIE]:
+    def entities(self, filter_obsoletes=True, owl_type=None) -> Iterable[Union[URI, CURIE]]:
         od = self.obograph_document
         for g in od.graphs:
             for n in g.nodes:

src/oaklib/implementations/pronto/pronto_implementation.py

@@ -74,7 +74,7 @@
 from oaklib.interfaces.taxon_constraint_interface import TaxonConstraintInterface
 from oaklib.interfaces.validator_interface import ValidatorInterface
 from oaklib.resource import OntologyResource
-from oaklib.types import CURIE, SUBSET_CURIE
+from oaklib.types import CURIE, SUBSET_CURIE, URI
 from oaklib.utilities.axioms.logical_definition_utilities import (
     logical_definition_matches,
 )
@@ -293,7 +293,7 @@ def _create_pred(self, curie: CURIE, exist_ok=True):
         else:
             return self.wrapped_ontology.create_relationship(curie)
 
-    def entities(self, filter_obsoletes=True, owl_type=None) -> Iterable[CURIE]:
+    def entities(self, filter_obsoletes=True, owl_type=None) -> Iterable[Union[URI, CURIE]]:
         for t in self.wrapped_ontology.terms():
             if filter_obsoletes and t.obsolete:
                 continue

src/oaklib/implementations/simpleobo/simple_obo_implementation.py

@@ -120,7 +120,7 @@
 from oaklib.interfaces.taxon_constraint_interface import TaxonConstraintInterface
 from oaklib.interfaces.validator_interface import ValidatorInterface
 from oaklib.resource import OntologyResource
-from oaklib.types import CURIE, PRED_CURIE, SUBSET_CURIE
+from oaklib.types import CURIE, PRED_CURIE, SUBSET_CURIE, URI
 from oaklib.utilities.axioms.logical_definition_utilities import (
     logical_definition_matches,
 )
@@ -255,7 +255,7 @@ def _all_entailed_relationships(self):
         reasoner = RelationGraphReasoner(self)
         yield from reasoner.entailed_edges()
 
-    def entities(self, filter_obsoletes=True, owl_type=None) -> Iterable[CURIE]:
+    def entities(self, filter_obsoletes=True, owl_type=None) -> Iterable[Union[URI, CURIE]]:
         od = self.obo_document
         for s_id, s in od.stanzas.items():
             if filter_obsoletes:

src/oaklib/implementations/sparql/abstract_sparql_implementation.py

@@ -213,7 +213,7 @@ def uri_to_curie(self, uri: URI, strict=True) -> Optional[CURIE]:
             return uri.replace("_", ":")
         return uri
 
-    def entities(self, filter_obsoletes=True, owl_type=None) -> Iterable[CURIE]:
+    def entities(self, filter_obsoletes=True, owl_type=None) -> Iterable[Union[URI, CURIE]]:
         query = SparqlQuery(select=["?s"], distinct=True, where=["?s a ?cls", "FILTER (isIRI(?s))"])
         if owl_type:
             query.where.append(f"?s a {self.curie_to_sparql(owl_type)}")

src/oaklib/implementations/sqldb/sql_implementation.py

@@ -30,7 +30,7 @@
 from linkml_runtime.utils.metamodelcore import URIorCURIE
 from semsql.sqla.semsql import (  # HasMappingStatement,
     AnnotationPropertyNode,
-    Base,
+    Base,URIorCURIE
     ClassNode,
     DeprecatedNode,
     Edge,
@@ -150,7 +150,7 @@
 from oaklib.interfaces.summary_statistics_interface import SummaryStatisticsInterface
 from oaklib.interfaces.taxon_constraint_interface import TaxonConstraintInterface
 from oaklib.interfaces.validator_interface import ValidatorInterface
-from oaklib.types import CATEGORY_CURIE, CURIE, SUBSET_CURIE
+from oaklib.types import CATEGORY_CURIE, CURIE, SUBSET_CURIE, URI
 from oaklib.utilities.axioms.logical_definition_utilities import (
     logical_definition_matches,
 )
@@ -169,6 +169,7 @@
 from oaklib.utilities.iterator_utils import chunk
 from oaklib.utilities.mapping.sssom_utils import inject_mapping_sources
 
+
 SUBJECT_REL_KEY = Tuple[CURIE, Optional[List[PRED_CURIE]], Tuple]
 
 
@@ -407,7 +408,7 @@ def languages(self) -> Iterable[LANGUAGE_TAG]:
             if row.language:
                 yield row.language
 
-    def entities(self, filter_obsoletes=True, owl_type=None) -> Iterable[CURIE]:
+    def entities(self, filter_obsoletes=True, owl_type=None) -> Iterable[Union[URI, CURIE]]:
         # TODO: figure out how to pass through ESCAPE at SQL Alchemy level
         # s = text('SELECT id FROM class_node WHERE id NOT LIKE "\_:%" ESCAPE "\\"')  # noqa W605
         q = self.session.query(Node)

src/oaklib/interfaces/basic_ontology_interface.py

@@ -603,7 +603,7 @@ def ontology_metadata_map(self, ontology: CURIE) -> METADATA_MAP:
             f"ontology_metadata_map() method not implemented for {self.__class__.__name__}"
         )
 
-    def entities(self, filter_obsoletes=True, owl_type=None) -> Iterable[CURIE]:
+    def entities(self, filter_obsoletes=True, owl_type=None) -> Iterable[Union[URI, CURIE]]:
         """
         Yields all known entity CURIEs.