Refactor API code (#312)

1. Reuse typed dictionaries to reduce reused kwargs
2. Add simplified function for prefix/identifier arguments
3. Create edges module
4. Switch graph generation to use all edges

src/pyobo/__init__.py

@@ -6,6 +6,8 @@
     get_children,
     get_definition,
     get_descendants,
+    get_edges,
+    get_edges_df,
     get_filtered_properties_df,
     get_filtered_properties_mapping,
     get_filtered_properties_multimapping,
@@ -20,11 +22,15 @@
     get_id_synonyms_mapping,
     get_id_to_alts,
     get_ids,
+    get_literal_properties,
+    get_literal_properties_df,
     get_mappings_df,
     get_metadata,
     get_name,
     get_name_by_curie,
     get_name_id_mapping,
+    get_object_properties,
+    get_object_properties_df,
     get_obsolete,
     get_primary_curie,
     get_primary_identifier,
@@ -80,6 +86,8 @@
     "get_children",
     "get_definition",
     "get_descendants",
+    "get_edges",
+    "get_edges_df",
     "get_filtered_properties_df",
     "get_filtered_properties_mapping",
     "get_filtered_properties_multimapping",
@@ -94,11 +102,15 @@
     "get_id_synonyms_mapping",
     "get_id_to_alts",
     "get_ids",
+    "get_literal_properties",
+    "get_literal_properties_df",
     "get_mappings_df",
     "get_metadata",
     "get_name",
     "get_name_by_curie",
     "get_name_id_mapping",
+    "get_object_properties",
+    "get_object_properties_df",
     "get_obsolete",
     "get_ontology",
     "get_primary_curie",

src/pyobo/api/__init__.py

@@ -6,6 +6,7 @@
     get_primary_curie,
     get_primary_identifier,
 )
+from .edges import get_edges, get_edges_df, get_graph
 from .hierarchy import (
     get_ancestors,
     get_children,
@@ -32,13 +33,16 @@
     get_filtered_properties_df,
     get_filtered_properties_mapping,
     get_filtered_properties_multimapping,
+    get_literal_properties,
+    get_literal_properties_df,
+    get_object_properties,
+    get_object_properties_df,
     get_properties,
     get_properties_df,
     get_property,
 )
 from .relations import (
     get_filtered_relations_df,
-    get_graph,
     get_id_multirelations_mapping,
     get_relation,
     get_relation_mapping,
@@ -61,6 +65,8 @@
     "get_children",
     "get_definition",
     "get_descendants",
+    "get_edges",
+    "get_edges_df",
     "get_equivalent",
     "get_filtered_properties_df",
     "get_filtered_properties_mapping",
@@ -76,11 +82,15 @@
     "get_id_synonyms_mapping",
     "get_id_to_alts",
     "get_ids",
+    "get_literal_properties",
+    "get_literal_properties_df",
     "get_mappings_df",
     "get_metadata",
     "get_name",
     "get_name_by_curie",
     "get_name_id_mapping",
+    "get_object_properties",
+    "get_object_properties_df",
     "get_obsolete",
     "get_ontology",
     "get_primary_curie",

src/pyobo/api/edges.py

@@ -0,0 +1,68 @@
+"""High-level API for edges."""
+
+import networkx as nx
+import pandas as pd
+from tqdm import tqdm
+from typing_extensions import Unpack
+
+from pyobo.api.names import get_ids
+from pyobo.api.utils import get_version_from_kwargs
+from pyobo.constants import (
+    GetOntologyKwargs,
+    check_should_cache,
+    check_should_force,
+    check_should_use_tqdm,
+)
+from pyobo.getters import get_ontology
+from pyobo.struct import Reference
+from pyobo.utils.path import prefix_cache_join
+
+from ..utils.cache import cached_df
+
+__all__ = [
+    "get_edges",
+    "get_edges_df",
+    "get_graph",
+]
+
+
+def get_graph(prefix: str, **kwargs: Unpack[GetOntologyKwargs]) -> nx.DiGraph:
+    """Get the relation graph."""
+    rv = nx.MultiDiGraph()
+    for s in get_ids(prefix, **kwargs):
+        rv.add_node(f"{prefix}:{s}")
+    df = get_edges_df(prefix=prefix, **kwargs)
+    for s, p, o in df.values:
+        rv.add_edge(s, p, key=o)
+    return rv
+
+
+def get_edges_df(prefix, **kwargs: Unpack[GetOntologyKwargs]) -> pd.DataFrame:
+    """Get a dataframe of edges triples."""
+    version = get_version_from_kwargs(prefix, kwargs)
+    path = prefix_cache_join(prefix, name="object_properties.tsv", version=version)
+
+    @cached_df(
+        path=path, dtype=str, force=check_should_force(kwargs), cache=check_should_cache(kwargs)
+    )
+    def _df_getter() -> pd.DataFrame:
+        return get_ontology(prefix, **kwargs).get_edges_df(use_tqdm=check_should_use_tqdm(kwargs))
+
+    return _df_getter()
+
+
+def get_edges(
+    prefix, **kwargs: Unpack[GetOntologyKwargs]
+) -> list[tuple[Reference, Reference, Reference]]:
+    """Get a list of edge triples."""
+    df = get_edges_df(prefix, **kwargs)
+    return [
+        (Reference.from_curie(s), Reference.from_curie(p), Reference.from_curie(o))
+        for s, p, o in tqdm(
+            df.values,
+            desc=f"[{prefix}] parsing edges",
+            unit="edge",
+            unit_scale=True,
+            disable=not check_should_use_tqdm(kwargs),
+        )
+    ]