Additional fixes

Changed type hints based on more information discovered in mean time.

Author: aucampia

rdflib/graph.py

@@ -38,26 +38,29 @@
 from rdflib.resource import Resource
 from rdflib.serializer import Serializer
 from rdflib.store import Store
-from rdflib.term import (
-    BNode,
-    Genid,
-    IdentifiedNode,
-    Identifier,
-    Literal,
-    Node,
-    RDFLibGenid,
-    URIRef,
-)
+from rdflib.term import BNode, Genid, IdentifiedNode, Literal, Node, RDFLibGenid, URIRef
 
-_SubjectType = IdentifiedNode
-_PredicateType = IdentifiedNode
-_ObjectType = Identifier
+_SubjectType = Node
+_PredicateType = Node
+_ObjectType = Node
 
 _TripleType = Tuple["_SubjectType", "_PredicateType", "_ObjectType"]
 _QuadType = Tuple["_SubjectType", "_PredicateType", "_ObjectType", "Graph"]
+_OptionalQuadType = Tuple[
+    "_SubjectType", "_PredicateType", "_ObjectType", Optional["Graph"]
+]
+_OptionalIdentifiedQuadType = Tuple[
+    "_SubjectType", "_PredicateType", "_ObjectType", Optional["Node"]
+]
 _TriplePatternType = Tuple[
     Optional["_SubjectType"], Optional["_PredicateType"], Optional["_ObjectType"]
 ]
+_QuadPatternType = Tuple[
+    Optional["_SubjectType"],
+    Optional["_PredicateType"],
+    Optional["_ObjectType"],
+    Optional["Graph"],
+]
 _GraphT = TypeVar("_GraphT", bound="Graph")
 
 assert Literal  # avoid warning
@@ -455,7 +458,7 @@ def add(self, triple: "_TripleType"):
         self.__store.add((s, p, o), self, quoted=False)
         return self
 
-    def addN(self, quads: Iterable["_QuadType"]):
+    def addN(self, quads: Iterable["_QuadType"]):  # noqa: N802
         """Add a sequence of triple with context"""
 
         self.__store.addN(
@@ -523,7 +526,9 @@ def triples(
             for _s, _o in p.eval(self, s, o):
                 yield _s, p, _o
         else:
-            for (_s, _p, _o), cg in self.__store.triples((s, p, o), context=self):
+            # type error: Argument 1 to "triples" of "Store" has incompatible type "Tuple[Optional[Node], Optional[Node], Optional[Node]]"; expected "Tuple[Optional[IdentifiedNode], Optional[IdentifiedNode], Optional[Node]]"
+            # NOTE on type error: This is because the store typing is too narrow, willbe fixed in subsequent PR.
+            for (_s, _p, _o), cg in self.__store.triples((s, p, o), context=self):  # type: ignore  [arg-type]
                 yield _s, _p, _o
 
     def __getitem__(self, item):
@@ -1671,11 +1676,21 @@ def __str__(self):
     def _spoc(
         self,
         triple_or_quad: Union[
-            Tuple["_SubjectType", "_PredicateType", "_ObjectType", Optional[Any]],
-            "_TripleType",
+            Tuple[
+                Optional["_SubjectType"],
+                Optional["_PredicateType"],
+                Optional["_ObjectType"],
+                Optional[Any],
+            ],
+            "_TriplePatternType",
         ],
         default: bool = False,
-    ) -> Tuple["_SubjectType", "_PredicateType", "_ObjectType", Optional[Graph]]:
+    ) -> Tuple[
+        Optional["_SubjectType"],
+        Optional["_PredicateType"],
+        Optional["_ObjectType"],
+        Optional[Graph],
+    ]:
         ...
 
     @overload
@@ -1690,8 +1705,13 @@ def _spoc(
         self,
         triple_or_quad: Optional[
             Union[
-                Tuple["_SubjectType", "_PredicateType", "_ObjectType", Optional[Any]],
-                "_TripleType",
+                Tuple[
+                    Optional["_SubjectType"],
+                    Optional["_PredicateType"],
+                    Optional["_ObjectType"],
+                    Optional[Any],
+                ],
+                "_TriplePatternType",
             ]
         ],
         default: bool = False,
@@ -1739,7 +1759,8 @@ def add(
 
         _assertnode(s, p, o)
 
-        self.store.add((s, p, o), context=c, quoted=False)
+        # type error: Argument "context" to "add" of "Store" has incompatible type "Optional[Graph]"; expected "Graph"
+        self.store.add((s, p, o), context=c, quoted=False)  # type: ignore[arg-type]
         return self
 
     @overload
@@ -1758,7 +1779,7 @@ def _graph(self, c: Optional[Union[Graph, Node, str]]) -> Optional[Graph]:
         else:
             return c
 
-    def addN(self, quads: Iterable["_QuadType"]):
+    def addN(self, quads: Iterable["_QuadType"]):  # noqa: N802
         """Add a sequence of triples with context"""
 
         self.store.addN(
@@ -1809,14 +1830,24 @@ def triples(self, triple_or_quad, context=None):
             for (s, p, o), cg in self.store.triples((s, p, o), context=context):
                 yield s, p, o
 
-    def quads(self, triple_or_quad=None):
+    def quads(
+        self,
+        triple_or_quad: Union[
+            "_TriplePatternType",
+            "_QuadPatternType",
+            None,
+        ] = None,
+    ) -> Generator[_OptionalQuadType, None, None]:
         """Iterate over all the quads in the entire conjunctive graph"""
 
         s, p, o, c = self._spoc(triple_or_quad)
 
-        for (s, p, o), cg in self.store.triples((s, p, o), context=c):
+        # type error: Argument 1 to "triples" of "Store" has incompatible type "Tuple[Optional[Node], Optional[Node], Optional[Node]]"; expected "Tuple[Optional[IdentifiedNode], Optional[IdentifiedNode], Optional[Node]]"
+        # NOTE on type error: This is because the store typing is too narrow, willbe fixed in subsequent PR.
+        for (s, p, o), cg in self.store.triples((s, p, o), context=c):  # type: ignore[arg-type]
             for ctx in cg:
-                yield s, p, o, ctx
+                # type error: Incompatible types in "yield" (actual type "Tuple[Optional[Node], Optional[Node], Optional[Node], Any]", expected type "Tuple[Node, Node, Node, Optional[Graph]]")
+                yield s, p, o, ctx  # type: ignore[misc]
 
     def triples_choices(self, triple, context=None):
         """Iterate over all the triples in the entire conjunctive graph"""
@@ -2146,17 +2177,27 @@ def contexts(self, triple=None):
 
     graphs = contexts
 
-    def quads(self, quad):
+    # type error: Return type "Generator[Tuple[Node, Node, Node, Optional[Node]], None, None]" of "quads" incompatible with return type "Generator[Tuple[Node, Node, Node, Optional[Graph]], None, None]" in supertype "ConjunctiveGraph"
+    def quads(  # type: ignore[override]
+        self,
+        quad: Union[
+            "_TriplePatternType",
+            "_QuadPatternType",
+            None,
+        ] = None,
+    ) -> Generator[_OptionalIdentifiedQuadType, None, None]:
         for s, p, o, c in super(Dataset, self).quads(quad):
-            if c.identifier == self.default_context:
+            # type error: Item "None" of "Optional[Graph]" has no attribute "identifier"
+            if c.identifier == self.default_context:  # type: ignore[union-attr]
                 yield s, p, o, None
             else:
-                yield s, p, o, c.identifier
+                # type error: Item "None" of "Optional[Graph]" has no attribute "identifier"  [union-attr]
+                yield s, p, o, c.identifier  # type: ignore[union-attr]
 
     # type error: Return type "Generator[Tuple[Node, URIRef, Node, Optional[IdentifiedNode]], None, None]" of "__iter__" incompatible with return type "Generator[Tuple[IdentifiedNode, IdentifiedNode, Union[IdentifiedNode, Literal]], None, None]" in supertype "Graph"
     def __iter__(  # type: ignore[override]
         self,
-    ) -> Generator[Tuple[Node, URIRef, Node, Optional[IdentifiedNode]], None, None]:
+    ) -> Generator[_OptionalIdentifiedQuadType, None, None]:
         """Iterates over all quads in the store"""
         return self.quads((None, None, None, None))
 
@@ -2182,7 +2223,7 @@ def add(self, triple: "_TripleType"):
         self.store.add((s, p, o), self, quoted=True)
         return self
 
-    def addN(self, quads: Iterable["_QuadType"]) -> "QuotedGraph":
+    def addN(self, quads: Iterable["_QuadType"]) -> "QuotedGraph":  # noqa: N802
         """Add a sequence of triple with context"""
 
         self.store.addN(
@@ -2332,7 +2373,7 @@ def close(self):
     def add(self, triple):
         raise ModificationException()
 
-    def addN(self, quads):
+    def addN(self, quads):  # noqa: N802
         raise ModificationException()
 
     def remove(self, triple):
@@ -2505,7 +2546,7 @@ def add(
             self.batch.append(triple_or_quad)
         return self
 
-    def addN(self, quads: Iterable["_QuadType"]):
+    def addN(self, quads: Iterable["_QuadType"]):  # noqa: N802
         if self.__batch_addn:
             for q in quads:
                 self.add(q)

rdflib/plugins/parsers/ntriples.py

@@ -15,7 +15,7 @@
 from rdflib.exceptions import ParserError as ParseError
 from rdflib.parser import InputSource, Parser
 from rdflib.term import BNode as bNode
-from rdflib.term import Literal, Node
+from rdflib.term import Literal
 from rdflib.term import URIRef as URI
 
 if TYPE_CHECKING:

rdflib/plugins/serializers/rdfxml.py

@@ -207,7 +207,8 @@ def serialize(
 
         subject: IdentifiedNode
         # Write out subjects that can not be inline
-        for subject in store.subjects():
+        # type error: Incompatible types in assignment (expression has type "Node", variable has type "IdentifiedNode")
+        for subject in store.subjects():  # type: ignore[assignment]
             if (None, None, subject) in store:
                 if (subject, None, subject) in store:
                     self.subject(subject, 1)
@@ -218,7 +219,8 @@ def serialize(
         # write out BNodes last (to ensure they can be inlined where possible)
         bnodes = set()
 
-        for subject in store.subjects():
+        # type error: Incompatible types in assignment (expression has type "Node", variable has type "IdentifiedNode")
+        for subject in store.subjects():  # type: ignore[assignment]
             if isinstance(subject, BNode):
                 bnodes.add(subject)
                 continue

rdflib/util.py

@@ -30,6 +30,7 @@
     Any,
     Callable,
     Iterable,
+    Iterator,
     List,
     Optional,
     Set,
@@ -409,13 +410,13 @@ def find_roots(
 
 def get_tree(
     graph: "Graph",
-    root: "IdentifiedNode",
+    root: "Node",
     prop: "URIRef",
-    mapper: Callable[["IdentifiedNode"], "IdentifiedNode"] = lambda x: x,
+    mapper: Callable[["Node"], "Node"] = lambda x: x,
     sortkey: Optional[Callable[[Any], Any]] = None,
-    done: Optional[Set["IdentifiedNode"]] = None,
+    done: Optional[Set["Node"]] = None,
     dir: str = "down",
-) -> Optional[Tuple[IdentifiedNode, List[Any]]]:
+) -> Optional[Tuple[Node, List[Any]]]:
     """
     Return a nested list/tuple structure representing the tree
     built by the transitive property given, starting from the root given
@@ -442,12 +443,11 @@ def get_tree(
     done.add(root)
     tree = []
 
-    branches: Iterable[IdentifiedNode]
+    branches: Iterator[Node]
     if dir == "down":
         branches = graph.subjects(prop, root)
     else:
-        # type error: Incompatible types in assignment (expression has type "Iterable[Node]", variable has type "Iterable[IdentifiedNode]")
-        branches = graph.objects(root, prop)  # type: ignore[assignment]
+        branches = graph.objects(root, prop)
 
     for branch in branches:
         t = get_tree(graph, branch, prop, mapper, sortkey, done, dir)

test/test_graph/test_canonicalization.py

@@ -1,7 +1,6 @@
 import unittest
 from collections import Counter
 from io import StringIO
-from test.testutils import GraphHelper
 from test.utils import GraphHelper
 from typing import TYPE_CHECKING, Set
 
@@ -12,7 +11,6 @@
 from rdflib.compare import to_canonical_graph, to_isomorphic
 from rdflib.namespace import FOAF
 from rdflib.plugins.stores.memory import Memory
-from rdflib.term import Node
 
 if TYPE_CHECKING:
     from rdflib.graph import _TripleType

test/test_graph/test_diff.py

@@ -1,5 +1,4 @@
 import unittest
-from test.testutils import GraphHelper
 from test.utils import GraphHelper
 from typing import TYPE_CHECKING, Set
 from unittest.case import expectedFailure

test/test_namespace/test_namespace.py

@@ -279,7 +279,7 @@ def test_expand_curie_exception_messages(self) -> None:
         assert str(e.value) == "Argument must be a string, not BNode."
 
         with pytest.raises(TypeError) as e:
-            assert g.namespace_manager.expand_curie(Graph()) == None
+            assert g.namespace_manager.expand_curie(Graph()) == None  # type: ignore[arg-type]
         assert str(e.value) == "Argument must be a string, not Graph."
 
     @pytest.mark.parametrize(

test/test_roundtrip.py

@@ -268,10 +268,12 @@ def roundtrip(
         #
         # So we have to scrub the literals' string datatype declarations...
         for c in g2.contexts():
-            for s, p, o in c.triples((None, None, None)):
+            # type error: Incompatible types in assignment (expression has type "Node", variable has type "str")
+            for s, p, o in c.triples((None, None, None)):  # type: ignore[assignment]
                 if type(o) == rdflib.Literal and o.datatype == XSD.string:
                     c.remove((s, p, o))
-                    c.add((s, p, rdflib.Literal(str(o))))
+                    # type error: Argument 1 to "add" of "Graph" has incompatible type "Tuple[str, Node, Literal]"; expected "Tuple[Node, Node, Node]"
+                    c.add((s, p, rdflib.Literal(str(o))))  # type: ignore[arg-type]
 
     if logger.isEnabledFor(logging.DEBUG):
         both, first, second = rdflib.compare.graph_diff(g1, g2)

test/test_typing.py

@@ -22,9 +22,12 @@
 
 from typing import Set, Tuple
 
+import rdflib
+
 # TODO Bug - rdflib.plugins.sparql.prepareQuery() will run fine if this
 # test is run, but mypy can't tell the symbol is exposed.
 import rdflib.plugins.sparql.processor
+from rdflib.term import Node
 
 
 def test_rdflib_query_exercise() -> None:
@@ -56,8 +59,8 @@ def test_rdflib_query_exercise() -> None:
     graph.add((kb_https_uriref, predicate_q, literal_two))
     graph.add((kb_bnode, predicate_p, literal_one))
 
-    expected_nodes_using_predicate_q: Set[rdflib.IdentifiedNode] = {kb_https_uriref}
-    computed_nodes_using_predicate_q: Set[rdflib.IdentifiedNode] = set()
+    expected_nodes_using_predicate_q: Set[Node] = {kb_https_uriref}
+    computed_nodes_using_predicate_q: Set[Node] = set()
     for triple in graph.triples((None, predicate_q, None)):
         computed_nodes_using_predicate_q.add(triple[0])
     assert expected_nodes_using_predicate_q == computed_nodes_using_predicate_q

test/utils/__init__.py

@@ -169,12 +169,15 @@ def quad_set(
         """
         result: GHQuadSet = set()
         for sn, pn, on, gn in graph.quads((None, None, None, None)):
+            gn_id: Identifier
             if isinstance(graph, Dataset):
-                assert isinstance(gn, Identifier)
-                gn_id = gn
+                # type error: Subclass of "Graph" and "Identifier" cannot exist: would have incompatible method signatures
+                assert isinstance(gn, Identifier)  # type: ignore[unreachable]
+                gn_id = gn  # type: ignore[unreachable]
             elif isinstance(graph, ConjunctiveGraph):
                 assert isinstance(gn, Graph)
-                gn_id = gn.identifier
+                # type error: Incompatible types in assignment (expression has type "Node", variable has type "Identifier")
+                gn_id = gn.identifier  # type: ignore[assignment]
             else:
                 raise ValueError(f"invalid graph type {type(graph)}: {graph!r}")
             s, p, o = cls.nodes((sn, pn, on), exclude_blanks)