obographs 0.0.4__py3-none-any.whl → 0.0.6__py3-none-any.whl

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",
@@ -197,6 +197,12 @@ 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 +220,19 @@ 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 +247,7 @@ 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/standardized.py

@@ -203,7 +203,7 @@ class StandardizedSynonym(StandardizedBaseModel[Synonym]):
 class StandardizedMeta(StandardizedBaseModel[Meta]):
     """A standardized meta object."""
 
-    definition: StandardizedDefinition | None
+    definition: StandardizedDefinition | None = None
     subsets: list[Reference] | None = None
     xrefs: list[StandardizedXref] | None = None
     synonyms: list[StandardizedSynonym] | None = None
@@ -261,7 +261,9 @@ class StandardizedMeta(StandardizedBaseModel[Meta]):
         return cls(
             definition=StandardizedDefinition.from_obograph_raw(
                 meta.definition, converter, strict=strict
-            ),
+            )
+            if meta.definition is not None
+            else None,
             subsets=[
                 _curie_or_uri_to_ref(subset, converter, strict=strict) for subset in meta.subsets
             ]

obographs/version.py

@@ -12,7 +12,7 @@ __all__ = [
     "get_version",
 ]
 
-VERSION = "0.0.4"
+VERSION = "0.0.6"
 
 
 def get_git_hash() -> str:

{obographs-0.0.4.dist-info → obographs-0.0.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: obographs
-Version: 0.0.4
+Version: 0.0.6
 Summary: A python data model for OBO Graphs
 Keywords: snekpack,cookiecutter
 Author: Charles Tapley Hoyt

obographs-0.0.6.dist-info/RECORD

@@ -0,0 +1,10 @@
+obographs/__init__.py,sha256=55f4bf18441bd7f6c41afa68d094532933b02b21dbdd20679cf8807c1791d494,1601
+obographs/model.py,sha256=b788ef49c630062756c2f5b4d432b8211dd2461efde0b60163ea2e921de85e42,8771
+obographs/py.typed,sha256=01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b,1
+obographs/standardized.py,sha256=43ee42d342f33df38f24151339cdeb6525252af541366149c7719d188901a52f,25863
+obographs/version.py,sha256=2a1a313b49e1a693ffa4dc1a6081dc40aaece02e67d214f42b5502ea75170500,961
+obographs-0.0.6.dist-info/licenses/LICENSE,sha256=4be0ec343e3bf11fd54321a6b576d5616ebb7d18898f741f63c517209e33bcb2,1076
+obographs-0.0.6.dist-info/WHEEL,sha256=65f6765ba93534713730ff2172cd912ef280aa42867625a73f77c2fef0639dae,78
+obographs-0.0.6.dist-info/entry_points.txt,sha256=9a9819cedd2186e28d5d42ddce5e3de1417b0db2b07392ff35f9adc7c86a8619,50
+obographs-0.0.6.dist-info/METADATA,sha256=686e6d277ab0221b4cc2556d637a77c68b3f1814aa204d52f3a681d7a3eaf3fb,12768
+obographs-0.0.6.dist-info/RECORD,,

obographs-0.0.4.dist-info/RECORD

@@ -1,10 +0,0 @@
-obographs/__init__.py,sha256=55f4bf18441bd7f6c41afa68d094532933b02b21dbdd20679cf8807c1791d494,1601
-obographs/model.py,sha256=1f1bda132b83d8e08d7301eddb9be8d58b7e61c5b30e9baab9c24fd22348db53,8457
-obographs/py.typed,sha256=01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b,1
-obographs/standardized.py,sha256=69d26bbd35b49232b8d4bc2ae462f864f4fffcadf3acb7d541783fc8745dbd5e,25791
-obographs/version.py,sha256=c50bb52fc81eb5b19dedfb8583a0c19b6127aff659301cb2d3d51f4d244fefc3,961
-obographs-0.0.4.dist-info/licenses/LICENSE,sha256=4be0ec343e3bf11fd54321a6b576d5616ebb7d18898f741f63c517209e33bcb2,1076
-obographs-0.0.4.dist-info/WHEEL,sha256=65f6765ba93534713730ff2172cd912ef280aa42867625a73f77c2fef0639dae,78
-obographs-0.0.4.dist-info/entry_points.txt,sha256=9a9819cedd2186e28d5d42ddce5e3de1417b0db2b07392ff35f9adc7c86a8619,50
-obographs-0.0.4.dist-info/METADATA,sha256=ac4daf3fa7f23379788e758debc91663ee15663ee1c9fabbf79bc69ca79c5e5b,12768
-obographs-0.0.4.dist-info/RECORD,,