obographs 0.0.5__tar.gz → 0.0.7__tar.gz

{obographs-0.0.5 → obographs-0.0.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: obographs
-Version: 0.0.5
+Version: 0.0.7
 Summary: A python data model for OBO Graphs
 Keywords: snekpack,cookiecutter
 Author: Charles Tapley Hoyt

{obographs-0.0.5 → obographs-0.0.7}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "uv_build"
 
 [project]
 name = "obographs"
-version = "0.0.5"
+version = "0.0.7"
 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 = "0.0.5"
+current_version = "0.0.7"
 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-0.0.5 → obographs-0.0.7}/src/obographs/__init__.py

@@ -1,5 +1,6 @@
 """A python data model for OBO Graphs."""
 
+from .contrib import guess_primary_graph
 from .model import (
     Definition,
     DomainRangeAxiom,
@@ -69,5 +70,6 @@ __all__ = [
     "StandardizedXref",
     "Synonym",
     "Xref",
+    "guess_primary_graph",
     "read",
 ]

obographs-0.0.7/src/obographs/contrib.py

@@ -0,0 +1,71 @@
+"""Extra functionality that isn't part of the core obographs package."""
+
+from __future__ import annotations
+
+from typing import overload
+
+from .model import Graph, GraphDocument
+from .standardized import StandardizedGraph, StandardizedGraphDocument
+
+__all__ = [
+    "guess_primary_graph",
+]
+
+CANONICAL = {
+    "mamo": "http://identifiers.org/mamo",
+    "swo": "http://www.ebi.ac.uk/swo/swo.json",
+    "ito": "https://identifiers.org/ito:ontology",
+    "apollosv": "http://purl.obolibrary.org/obo/apollo_sv.owl",
+    "cheminf": "http://semanticchemistry.github.io/semanticchemistry/ontology/cheminf.owl",
+    "dideo": "http://purl.obolibrary.org/obo/dideo/release/2022-06-14/dideo.owl",
+    "micro": "http://purl.obolibrary.org/obo/MicrO.owl",
+    "ogsf": "http://purl.obolibrary.org/obo/ogsf-merged.owl",
+    "mfomd": "http://purl.obolibrary.org/obo/MF.owl",
+    "one": "http://purl.obolibrary.org/obo/ONE",
+    "ons": "https://raw.githubusercontent.com/enpadasi/Ontology-for-Nutritional-Studies/master/ons.owl",
+    "ontie": "https://ontology.iedb.org/ontology/ontie.owl",
+}
+
+
+# docstr-coverage:excused `overload`
+@overload
+def guess_primary_graph(
+    graph_document: GraphDocument,
+    prefix: str,
+) -> Graph: ...
+
+
+# docstr-coverage:excused `overload`
+@overload
+def guess_primary_graph(
+    graph_document: StandardizedGraphDocument,
+    prefix: str,
+) -> StandardizedGraph: ...
+
+
+def guess_primary_graph(
+    graph_document: GraphDocument | StandardizedGraphDocument,
+    prefix: str,
+) -> Graph | StandardizedGraph:
+    """Guess the primary graph from a graph document."""
+    if 0 == len(graph_document.graphs):
+        raise ValueError("Could not automatically identify the primary graph from empty list")
+    elif 1 == len(graph_document.graphs):
+        return graph_document.graphs[0]
+
+    id_to_graph = {graph.id: graph for graph in graph_document.graphs if graph.id}
+
+    # Check for standard construction of OBO PURLs
+    for suffix in ["owl", "obo", "json"]:
+        standard_id = f"http://purl.obolibrary.org/obo/{prefix.lower()}.{suffix}"
+        if standard_id in id_to_graph:
+            return id_to_graph[standard_id]
+
+    # Check if we've manually curated a mapping
+    if prefix in CANONICAL and CANONICAL[prefix] in id_to_graph:
+        return id_to_graph[CANONICAL[prefix]]
+
+    raise ValueError(
+        f"Could not automatically identify the primary graph for {prefix=} from "
+        f"{len(id_to_graph):,} graphs:\n\n{sorted(id_to_graph)}"
+    )

{obographs-0.0.5 → obographs-0.0.7}/src/obographs/model.py

@@ -21,7 +21,7 @@ from curies.vocabulary import SynonymScopeOIO
 from pydantic import BaseModel, Field
 
 if TYPE_CHECKING:
-    from .standardized import StandardizedGraph
+    from .standardized import StandardizedGraph, StandardizedGraphDocument
 
 __all__ = [
     "Definition",
@@ -184,11 +184,13 @@ class Graph(BaseModel):
     domainRangeAxioms: list[DomainRangeAxiom] = Field(default_factory=list)  # noqa:N815
     propertyChainAxioms: list[PropertyChainAxiom] = Field(default_factory=list)  # noqa:N815
 
-    def standardize(self, converter: curies.Converter) -> StandardizedGraph:
+    def standardize(
+        self, converter: curies.Converter, *, strict: bool = False
+    ) -> StandardizedGraph:
         """Standardize the graph."""
         from .standardized import StandardizedGraph
 
-        return StandardizedGraph.from_obograph_raw(self, converter)
+        return StandardizedGraph.from_obograph_raw(self, converter, strict=strict)
 
 
 class GraphDocument(BaseModel):
@@ -197,6 +199,12 @@ class GraphDocument(BaseModel):
     graphs: list[Graph]
     meta: Meta | None = None
 
+    def standardize(self, converter: curies.Converter) -> StandardizedGraphDocument:
+        """Standardize the graph."""
+        from .standardized import StandardizedGraphDocument
+
+        return StandardizedGraphDocument.from_obograph_raw(self, converter)
+
 
 def get_id_to_node(graph: Graph) -> dict[str, Node]:
     """Get a dictionary from node ID to nodes."""
@@ -214,17 +222,19 @@ def get_id_to_edges(graph: Graph) -> dict[str, list[tuple[str, str]]]:
 # docstr-coverage:excused `overload`
 @overload
 def read(
-    source: str, *, timeout: TimeoutHint = ..., squeeze: Literal[False] = ...
+    source: str | Path, *, timeout: TimeoutHint = ..., squeeze: Literal[False] = ...
 ) -> GraphDocument: ...
 
 
 # docstr-coverage:excused `overload`
 @overload
-def read(source: str, *, timeout: TimeoutHint = ..., squeeze: Literal[True] = ...) -> Graph: ...
+def read(
+    source: str | Path, *, timeout: TimeoutHint = ..., squeeze: Literal[True] = ...
+) -> Graph: ...
 
 
 def read(
-    source: str, *, timeout: TimeoutHint = None, squeeze: bool = True
+    source: str | Path, *, timeout: TimeoutHint = None, squeeze: bool = True
 ) -> Graph | GraphDocument:
     """Read an OBO Graph document.
 
@@ -239,7 +249,7 @@ def read(
 
     :raises ValueError: If squeeze is set to true and multiple graphs are received
     """
-    if (isinstance(source, str) and source.startswith("https://")) or source.startswith("http://"):
+    if isinstance(source, str) and (source.startswith("https://") or source.startswith("http://")):
         import requests
 
         if source.endswith(".gz"):

{obographs-0.0.5 → obographs-0.0.7}/src/obographs/version.py

@@ -12,7 +12,7 @@ __all__ = [
     "get_version",
 ]
 
-VERSION = "0.0.5"
+VERSION = "0.0.7"
 
 
 def get_git_hash() -> str: