obographs 0.0.7__tar.gz → 0.0.9__tar.gz

{obographs-0.0.7 → obographs-0.0.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: obographs
-Version: 0.0.7
+Version: 0.0.9
 Summary: A python data model for OBO Graphs
 Keywords: snekpack,cookiecutter
 Author: Charles Tapley Hoyt

{obographs-0.0.7 → obographs-0.0.9}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "uv_build"
 
 [project]
 name = "obographs"
-version = "0.0.7"
+version = "0.0.9"
 description = "A python data model for OBO Graphs"
 readme = "README.md"
 authors = [
@@ -232,7 +232,7 @@ known-first-party = [
 docstring-code-format = true
 
 [tool.bumpversion]
-current_version = "0.0.7"
+current_version = "0.0.9"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?(?:\\+(?P<build>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?"
 serialize = [
     "{major}.{minor}.{patch}-{release}+{build}",

{obographs-0.0.7 → obographs-0.0.9}/src/obographs/model.py

@@ -184,6 +184,23 @@ class Graph(BaseModel):
     domainRangeAxioms: list[DomainRangeAxiom] = Field(default_factory=list)  # noqa:N815
     propertyChainAxioms: list[PropertyChainAxiom] = Field(default_factory=list)  # noqa:N815
 
+    def _get_property(self, predicate: str) -> str | None:
+        if self.meta is not None:
+            for prop in self.meta.basicPropertyValues or []:
+                if prop.pred == predicate and prop.val:
+                    return prop.val
+        return None
+
+    @property
+    def name(self) -> str | None:
+        """Get the title."""
+        return self._get_property("http://purl.org/dc/terms/title")
+
+    @property
+    def version(self) -> str | None:
+        """Get the version."""
+        return self._get_property("http://www.w3.org/2002/07/owl#versionInfo")
+
     def standardize(
         self, converter: curies.Converter, *, strict: bool = False
     ) -> StandardizedGraph:
@@ -222,19 +239,31 @@ def get_id_to_edges(graph: Graph) -> dict[str, list[tuple[str, str]]]:
 # docstr-coverage:excused `overload`
 @overload
 def read(
-    source: str | Path, *, timeout: TimeoutHint = ..., squeeze: Literal[False] = ...
+    source: str | Path,
+    *,
+    timeout: TimeoutHint = ...,
+    squeeze: Literal[False] = ...,
+    encoding: str = ...,
 ) -> GraphDocument: ...
 
 
 # docstr-coverage:excused `overload`
 @overload
 def read(
-    source: str | Path, *, timeout: TimeoutHint = ..., squeeze: Literal[True] = ...
+    source: str | Path,
+    *,
+    timeout: TimeoutHint = ...,
+    squeeze: Literal[True] = ...,
+    encoding: str = ...,
 ) -> Graph: ...
 
 
 def read(
-    source: str | Path, *, timeout: TimeoutHint = None, squeeze: bool = True
+    source: str | Path,
+    *,
+    timeout: TimeoutHint = None,
+    squeeze: bool = True,
+    encoding: str = "utf-8",
 ) -> Graph | GraphDocument:
     """Read an OBO Graph document.
 
@@ -244,6 +273,7 @@ def read(
         only has a single graph and return a :class:`Graph` object. If `true` and
         multiple graphs are received, will raise an error. Set this to `false` to return
         a GraphDocument containing all graphs.
+    :param encoding: The encoding to use for reading the graph
 
     :returns: A graph or graph document
 
@@ -264,10 +294,10 @@ def read(
         if not path.is_file():
             raise FileNotFoundError
         if path.suffix.endswith(".gz"):
-            with gzip.open(path, mode="rt") as file:
+            with gzip.open(path, mode="rt", encoding=encoding) as file:
                 graph_document = GraphDocument.model_validate(json.load(file))
         else:
-            with path.open() as file:
+            with path.open(mode="rt", encoding=encoding) as file:
                 graph_document = GraphDocument.model_validate(json.load(file))
     else:
         raise TypeError(f"Unhandled source: {source}")

{obographs-0.0.7 → obographs-0.0.9}/src/obographs/standardized.py

@@ -4,11 +4,12 @@ from __future__ import annotations
 
 import logging
 from abc import ABC, abstractmethod
+from collections.abc import Iterable
 from typing import Generic, TypeVar, cast
 
 import curies.preprocessing
 from curies import Converter, Reference, Triple, vocabulary
-from curies.vocabulary import SynonymScopeOIO
+from curies.vocabulary import SynonymScopeOIO, has_title, owl_version_info
 from pydantic import BaseModel, Field
 from typing_extensions import Self
 
@@ -209,7 +210,7 @@ class StandardizedMeta(StandardizedBaseModel[Meta]):
     synonyms: list[StandardizedSynonym] | None = None
     comments: list[str] | None = None
     deprecated: bool = False
-    version: str | None = None
+    version_iri: str | None = None
     properties: list[StandardizedProperty] | None = None
 
     @classmethod
@@ -272,7 +273,7 @@ class StandardizedMeta(StandardizedBaseModel[Meta]):
             xrefs=xrefs or None,
             synonyms=synonyms or None,
             comments=meta.comments,
-            version=meta.version,
+            version_iri=meta.version,
             deprecated=meta.deprecated,
             properties=props or None,
         )
@@ -287,7 +288,7 @@ class StandardizedMeta(StandardizedBaseModel[Meta]):
             xrefs=[xref.to_raw(converter) for xref in self.xrefs] if self.xrefs else None,
             synonyms=[s.to_raw(converter) for s in self.synonyms] if self.synonyms else None,
             comments=self.comments,
-            version=self.version,  # TODO might need some kind of expansion?
+            version=self.version_iri,
             deprecated=self.deprecated,
             basicPropertyValues=[p.to_raw(converter) for p in self.properties]
             if self.properties
@@ -411,8 +412,11 @@ class StandardizedDomainRangeAxiom(StandardizedBaseModel[DomainRangeAxiom]):
         cls, obj: DomainRangeAxiom, converter: Converter, *, strict: bool = False
     ) -> Self | None:
         """Parse a raw object."""
+        predicate = _curie_or_uri_to_ref(obj.predicateId, converter, strict=strict)
+        if predicate is None:
+            return None
         return cls(
-            predicate=_curie_or_uri_to_ref(obj.predicateId, converter, strict=strict),
+            predicate=predicate,
             domains=_parse_list(obj.domainClassIds, converter, strict=strict) or [],
             ranges=_parse_list(obj.rangeClassIds, converter, strict=strict) or [],
             all_values_from_edges=[
@@ -528,11 +532,11 @@ class StandardizedLogicalDefinition(StandardizedBaseModel[LogicalDefinition]):
         """Parse a raw object."""
         return cls(
             node=_curie_or_uri_to_ref(obj.definedClassId, converter, strict=strict),
-            geni=_parse_list(obj.genusIds, converter, strict=strict),
-            restrictions=[
+            geni=_parse_list(obj.genusIds, converter, strict=strict) or [],
+            restrictions=_schwoop(
                 StandardizedExistentialRestriction.from_obograph_raw(r, converter, strict=strict)
                 for r in obj.restrictions or []
-            ],
+            ),
             meta=StandardizedMeta.from_obograph_raw(obj.meta, converter, strict=strict),
         )
 
@@ -577,22 +581,22 @@ class StandardizedGraph(StandardizedBaseModel[Graph]):
                 for edge in graph.edges
                 if (s_edge := StandardizedEdge.from_obograph_raw(edge, converter, strict=strict))
             ],
-            equivalent_node_sets=[
+            equivalent_node_sets=_schwoop(
                 StandardizedEquivalentNodeSet.from_obograph_raw(e, converter, strict=strict)
                 for e in graph.equivalentNodesSets or []
-            ],
-            logical_definition_axioms=[
+            ),
+            logical_definition_axioms=_schwoop(
                 StandardizedLogicalDefinition.from_obograph_raw(e, converter, strict=strict)
                 for e in graph.logicalDefinitionAxioms or []
-            ],
-            property_chain_axioms=[
+            ),
+            property_chain_axioms=_schwoop(
                 StandardizedPropertyChainAxiom.from_obograph_raw(e, converter, strict=strict)
                 for e in graph.propertyChainAxioms or []
-            ],
-            domain_range_axioms=[
+            ),
+            domain_range_axioms=_schwoop(
                 StandardizedDomainRangeAxiom.from_obograph_raw(e, converter, strict=strict)
                 for e in graph.domainRangeAxioms or []
-            ],
+            ),
         )
 
     def to_raw(self, converter: Converter) -> Graph:
@@ -623,12 +627,24 @@ class StandardizedGraph(StandardizedBaseModel[Graph]):
     @property
     def name(self) -> str | None:
         """Look up the name of the graph."""
-        r = self._get_property(Reference(prefix="dcterms", identifier="title"))
+        r = self._get_property(has_title)
+        if isinstance(r, Reference):
+            raise TypeError
+        return r
+
+    @property
+    def version(self) -> str | None:
+        """Get the version."""
+        r = self._get_property(owl_version_info)
         if isinstance(r, Reference):
             raise TypeError
         return r
 
 
+def _schwoop(x: Iterable[X | None]) -> list[X]:
+    return [y for y in x if y is not None]
+
+
 class StandardizedGraphDocument(StandardizedBaseModel[GraphDocument]):
     """A standardized graph document."""
 

{obographs-0.0.7 → obographs-0.0.9}/src/obographs/version.py

@@ -12,7 +12,7 @@ __all__ = [
     "get_version",
 ]
 
-VERSION = "0.0.7"
+VERSION = "0.0.9"
 
 
 def get_git_hash() -> str: