pyobo 0.10.11__py3-none-any.whl → 0.11.0__py3-none-any.whl

pyobo/xrefdb/sources/famplex.py

@@ -1,10 +1,8 @@
-# -*- coding: utf-8 -*-
-
 """Get FamPlex xrefs."""
 
 import logging
+from collections.abc import Mapping
 from functools import lru_cache
-from typing import Mapping, Tuple
 
 import bioregistry
 import pandas as pd
@@ -50,8 +48,8 @@ def get_famplex_xrefs_df(force: bool = False) -> pd.DataFrame:
     return df
 
 
-@lru_cache()
-def get_remapping(force: bool = False) -> Mapping[Tuple[str, str], Tuple[str, str, str]]:
+@lru_cache
+def get_remapping(force: bool = False) -> Mapping[tuple[str, str], tuple[str, str, str]]:
     """Get a mapping from database/identifier pairs to famplex identifiers."""
     df = _get_famplex_df(force=force)
     rv = {}

pyobo/xrefdb/sources/gilda.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Cross references from Gilda.
 
 .. seealso:: https://github.com/indralabs/gilda

pyobo/xrefdb/sources/intact.py

@@ -1,8 +1,6 @@
-# -*- coding: utf-8 -*-
-
 """Get the xrefs from IntAct."""
 
-from typing import Mapping
+from collections.abc import Mapping
 
 import pandas as pd
 
@@ -49,7 +47,8 @@ def get_complexportal_mapping() -> Mapping[str, str]:
     .. code-block:: python
 
         from pyobo import get_filtered_xrefs
-        intact_complexportal_mapping = get_filtered_xrefs('intact', 'complexportal')
+
+        intact_complexportal_mapping = get_filtered_xrefs("intact", "complexportal")
     """
 
     @cached_mapping(
@@ -87,7 +86,8 @@ def get_reactome_mapping() -> Mapping[str, str]:
     .. code-block:: python
 
         from pyobo import get_filtered_xrefs
-        intact_complexportal_mapping = get_filtered_xrefs('intact', 'reactome')
+
+        intact_complexportal_mapping = get_filtered_xrefs("intact", "reactome")
     """
 
     @cached_mapping(

pyobo/xrefdb/sources/ncit.py

@@ -1,8 +1,6 @@
-# -*- coding: utf-8 -*-
-
 """Import NCIT mappings."""
 
-from typing import Iterable
+from collections.abc import Iterable
 
 import pandas as pd
 

pyobo/xrefdb/sources/pubchem.py

@@ -1,12 +1,10 @@
-# -*- coding: utf-8 -*-
-
 """Get xrefs from PubChem Compound to MeSH."""
 
 from typing import Optional
 
-import bioversions
 import pandas as pd
 
+from ...api.utils import safe_get_version
 from ...constants import XREF_COLUMNS
 from ...sources.pubchem import _get_pubchem_extras_url, get_pubchem_id_to_mesh_id
 
@@ -18,7 +16,7 @@ __all__ = [
 def get_pubchem_mesh_df(version: Optional[str] = None) -> pd.DataFrame:
     """Get PubChem Compound-MeSH xrefs."""
     if version is None:
-        version = bioversions.get_version("pubchem")
+        version = safe_get_version("pubchem")
     cid_mesh_url = _get_pubchem_extras_url(version, "CID-MeSH")
     return pd.DataFrame(
         [

pyobo/xrefdb/sources/wikidata.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Get Wikidata xrefs.
 
 Run with ``python -m pyobo.xrefdb.sources.wikidata``.
@@ -7,7 +5,7 @@ Run with ``python -m pyobo.xrefdb.sources.wikidata``.
 
 import json
 import logging
-from typing import Iterable, Tuple
+from collections.abc import Iterable
 
 import bioregistry
 import click
@@ -68,7 +66,7 @@ def get_wikidata_df(prefix: str, wikidata_property: str) -> pd.DataFrame:
 
 def iter_wikidata_mappings(
     wikidata_property: str, *, cache: bool = True
-) -> Iterable[Tuple[str, str]]:
+) -> Iterable[tuple[str, str]]:
     """Iterate over Wikidata xrefs."""
     path = WIKIDATA_MAPPING_DIRECTORY.join(name=f"{wikidata_property}.json")
     if path.exists() and cache:
@@ -81,11 +79,18 @@ def iter_wikidata_mappings(
             json.dump(rows, file, indent=2)
 
     for row in rows:
-        wikidata_id = row["wikidata_id"]["value"][len("http://wikidata.org/entity/") :]
+        wikidata_id = _removeprefix(row["wikidata_id"]["value"], "http://www.wikidata.org/entity/")
+        wikidata_id = _removeprefix(wikidata_id, "http://wikidata.org/entity/")
         entity_id = row["id"]["value"]
         yield wikidata_id, entity_id
 
 
+def _removeprefix(s, prefix):
+    if s.startswith(prefix):
+        return s[len(prefix) :]
+    return s
+
+
 HEADERS = {
     "User-Agent": f"pyobo/{get_version()}",
 }

pyobo/xrefdb/xrefs_pipeline.py

@@ -1,11 +1,10 @@
-# -*- coding: utf-8 -*-
-
 """Pipeline for extracting all xrefs from OBO documents available."""
 
 import gzip
 import itertools as itt
 import logging
-from typing import Iterable, Optional, Tuple, cast
+from collections.abc import Iterable
+from typing import Optional, cast
 
 import bioregistry
 import networkx as nx
@@ -83,7 +82,7 @@ def _iter_metadata(**kwargs):
         yield prefix, version, data["date"], bioregistry.is_deprecated(prefix)
 
 
-def _iter_names(leave: bool = False, **kwargs) -> Iterable[Tuple[str, str, str]]:
+def _iter_names(leave: bool = False, **kwargs) -> Iterable[tuple[str, str, str]]:
     """Iterate over all prefix-identifier-name triples we can get.
 
     :param leave: should the tqdm be left behind?
@@ -100,13 +99,13 @@ def _iter_names(leave: bool = False, **kwargs) -> Iterable[Tuple[str, str, str]]
             yield pubchem.PREFIX, identifier, name
 
 
-def _iter_species(leave: bool = False, **kwargs) -> Iterable[Tuple[str, str, str]]:
+def _iter_species(leave: bool = False, **kwargs) -> Iterable[tuple[str, str, str]]:
     """Iterate over all prefix-identifier-species triples we can get."""
     yield from iter_helper(get_id_species_mapping, leave=leave, **kwargs)
     # TODO ncbigene
 
 
-def _iter_definitions(leave: bool = False, **kwargs) -> Iterable[Tuple[str, str, str]]:
+def _iter_definitions(leave: bool = False, **kwargs) -> Iterable[tuple[str, str, str]]:
     """Iterate over all prefix-identifier-descriptions triples we can get."""
     yield from iter_helper(get_id_definition_mapping, leave=leave, **kwargs)
     yield from _iter_ncbigene(1, 8)
@@ -114,7 +113,7 @@ def _iter_definitions(leave: bool = False, **kwargs) -> Iterable[Tuple[str, str,
 
 def _iter_alts(
     leave: bool = False, strict: bool = True, **kwargs
-) -> Iterable[Tuple[str, str, str]]:
+) -> Iterable[tuple[str, str, str]]:
     for prefix, identifier, alts in iter_helper(
         get_id_to_alts, leave=leave, strict=strict, **kwargs
     ):
@@ -122,7 +121,7 @@ def _iter_alts(
             yield prefix, identifier, alt
 
 
-def _iter_synonyms(leave: bool = False, **kwargs) -> Iterable[Tuple[str, str, str]]:
+def _iter_synonyms(leave: bool = False, **kwargs) -> Iterable[tuple[str, str, str]]:
     """Iterate over all prefix-identifier-synonym triples we can get.
 
     :param leave: should the tqdm be left behind?
@@ -132,26 +131,26 @@ def _iter_synonyms(leave: bool = False, **kwargs) -> Iterable[Tuple[str, str, st
             yield prefix, identifier, synonym
 
 
-def _iter_typedefs(**kwargs) -> Iterable[Tuple[str, str, str, str]]:
+def _iter_typedefs(**kwargs) -> Iterable[tuple[str, str, str, str]]:
     """Iterate over all prefix-identifier-name triples we can get."""
     for prefix, df in iter_helper_helper(get_typedef_df, **kwargs):
         for t in df.values:
             if all(t):
-                yield cast(Tuple[str, str, str, str], (prefix, *t))
+                yield cast(tuple[str, str, str, str], (prefix, *t))
 
 
-def _iter_relations(**kwargs) -> Iterable[Tuple[str, str, str, str, str, str]]:
+def _iter_relations(**kwargs) -> Iterable[tuple[str, str, str, str, str, str]]:
     for prefix, df in iter_helper_helper(get_relations_df, **kwargs):
         for t in df.values:
             if all(t):
-                yield cast(Tuple[str, str, str, str, str, str], (prefix, *t))
+                yield cast(tuple[str, str, str, str, str, str], (prefix, *t))
 
 
-def _iter_properties(**kwargs) -> Iterable[Tuple[str, str, str, str]]:
+def _iter_properties(**kwargs) -> Iterable[tuple[str, str, str, str]]:
     for prefix, df in iter_helper_helper(get_properties_df, **kwargs):
         for t in df.values:
             if all(t):
-                yield cast(Tuple[str, str, str, str], (prefix, *t))
+                yield cast(tuple[str, str, str, str], (prefix, *t))
 
 
 def _iter_xrefs(
@@ -161,7 +160,7 @@ def _iter_xrefs(
     skip_below: Optional[str] = None,
     strict: bool = True,
     **kwargs,
-) -> Iterable[Tuple[str, str, str, str, str]]:
+) -> Iterable[tuple[str, str, str, str, str]]:
     it = iter_helper_helper(
         get_xrefs_df,
         use_tqdm=use_tqdm,
@@ -175,7 +174,7 @@ def _iter_xrefs(
         for row in df.values:
             if any(not element for element in row):
                 continue
-            yield cast(Tuple[str, str, str, str, str], (prefix, *row, prefix))
+            yield cast(tuple[str, str, str, str, str], (prefix, *row, prefix))
     for df in iter_xref_plugins(skip_below=skip_below):
         df.dropna(inplace=True)
         yield from tqdm(df.values, leave=False, total=len(df.index), unit_scale=True)

{pyobo-0.10.11.dist-info → pyobo-0.11.0.dist-info}/LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2020 Charles Tapley Hoyt
+Copyright (c) 2024 Charles Tapley Hoyt
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal