Merge branch 'main' into add39test

src/semra/pipeline.py

@@ -5,7 +5,7 @@
 import logging
 import time
 from pathlib import Path
-from typing import Any, Literal
+from typing import Any, Literal, Optional
 
 from pydantic import BaseModel, Field, root_validator
 from tqdm.autonotebook import tqdm
@@ -60,7 +60,7 @@ class Input(BaseModel):
     """Represents the input to a mapping assembly."""
 
     source: Literal["pyobo", "bioontologies", "biomappings", "custom", "sssom", "gilda"]
-    prefix: str | None = None
+    prefix: Optional[str] = None
     confidence: float = 1.0
     extras: dict[str, Any] = Field(default_factory=dict)
 
@@ -89,27 +89,27 @@ class Configuration(BaseModel):
         description="A list of pairs of prefixes. Remove all mappings whose source "
         "prefix is the first in a pair and target prefix is second in a pair. Order matters.",
     )
-    remove_prefixes: list[str] | None = None
-    keep_prefixes: list[str] | None = None
+    remove_prefixes: Optional[list[str]] = None
+    keep_prefixes: Optional[list[str]] = None
     remove_imprecise: bool = True
     validate_raw: bool = Field(
         default=False,
         description="Should the raw mappings be validated against Bioregistry "
         "prefixes and local unique identifier regular expressions (when available)?",
     )
 
-    raw_pickle_path: Path | None = None
-    raw_sssom_path: Path | None = None
-    raw_neo4j_path: Path | None = Field(default=None, description="Directory in which Neo4j stuff goes")
-    raw_neo4j_name: str | None = Field(default=None, description="Directory for docker tag for Neo4j")
+    raw_pickle_path: Optional[Path] = None
+    raw_sssom_path: Optional[Path] = None
+    raw_neo4j_path: Optional[Path] = Field(default=None, description="Directory in which Neo4j stuff goes")
+    raw_neo4j_name: Optional[str] = Field(default=None, description="Directory for docker tag for Neo4j")
 
-    processed_pickle_path: Path | None = None
-    processed_sssom_path: Path | None = None
-    processed_neo4j_path: Path | None = Field(default=None, description="Directory in which Neo4j stuff goes")
-    processed_neo4j_name: str | None = Field(default=None, description="Directory for docker tag for Neo4j")
+    processed_pickle_path: Optional[Path] = None
+    processed_sssom_path: Optional[Path] = None
+    processed_neo4j_path: Optional[Path] = Field(default=None, description="Directory in which Neo4j stuff goes")
+    processed_neo4j_name: Optional[str] = Field(default=None, description="Directory for docker tag for Neo4j")
 
-    priority_pickle_path: Path | None = None
-    priority_sssom_path: Path | None = None
+    priority_pickle_path: Optional[Path] = None
+    priority_sssom_path: Optional[Path] = None
     # note that making a priority neo4j doesn't make sense
 
     add_labels: bool = Field(default=False, description="Should PyOBO be used to look up labels for SSSOM output?")

src/semra/sources/chembl.py

@@ -1,4 +1,6 @@
 """Get mappings from ChEMBL."""
+from typing import Optional
+
 import bioregistry
 
 from semra import EXACT_MATCH, UNSPECIFIED_MAPPING, Mapping, MappingSet, Reference, SimpleEvidence
@@ -9,7 +11,7 @@
 ]
 
 
-def get_chembl_compound_mappings(version: str | None = None) -> list[Mapping]:
+def get_chembl_compound_mappings(version: Optional[str] = None) -> list[Mapping]:
     """Get ChEMBL chemical equivalences."""
     import chembl_downloader
 
@@ -36,7 +38,7 @@ def get_chembl_compound_mappings(version: str | None = None) -> list[Mapping]:
     return rows
 
 
-def get_chembl_protein_mappings(version: str | None = None) -> list[Mapping]:
+def get_chembl_protein_mappings(version: Optional[str] = None) -> list[Mapping]:
     """Get ChEMBL to protein mappings."""
     import chembl_downloader
 

src/semra/sources/pubchem.py

@@ -1,6 +1,7 @@
 """Get mappings from PubChem."""
 
 import logging
+from typing import Optional
 
 import bioversions
 import pandas as pd
@@ -16,7 +17,7 @@
 logger = logging.getLogger(__name__)
 
 
-def get_pubchem_mesh_mappings(version: str | None = None) -> list[Mapping]:
+def get_pubchem_mesh_mappings(version: Optional[str] = None) -> list[Mapping]:
     """Get a mapping from PubChem compound identifiers to their equivalent MeSH terms."""
     if version is None:
         version = bioversions.get_version("pubchem")

src/semra/struct.py

@@ -8,7 +8,7 @@
 from collections.abc import Iterable
 from hashlib import md5
 from itertools import islice
-from typing import Annotated, Literal
+from typing import Annotated, Literal, Optional, Union
 
 import pydantic
 from curies import Reference
@@ -65,9 +65,9 @@ def curie(self) -> str:
 
 class MappingSet(pydantic.BaseModel):
     name: str = Field(..., description="Name of the mapping set")
-    version: str | None = Field(default=None, description="The version of the dataset from which the mapping comes")
-    license: str | None = Field(default=None, description="License name or URL for mapping set")
-    confidence: float | None = Field(default=None, description="Mapping set level confidence")
+    version: Optional[str] = Field(default=None, description="The version of the dataset from which the mapping comes")
+    license: Optional[str] = Field(default=None, description="License name or URL for mapping set")
+    confidence: Optional[float] = Field(default=None, description="Mapping set level confidence")
 
     def key(self):
         return self.name, self.version or "", self.license or "", 1.0 if self.confidence is None else self.confidence
@@ -100,7 +100,7 @@ class Config:
         description="A SSSOM-compliant justification",
     )
     mapping_set: MappingSet = Field(..., description="The name of the dataset from which the mapping comes")
-    author: Reference | None = Field(
+    author: Optional[Reference] = Field(
         default=None,
         description="A reference to the author of the mapping (e.g. with ORCID)",
         examples=[
@@ -123,7 +123,7 @@ def mapping_set_names(self) -> set[str]:
         return {self.mapping_set.name}
 
     @property
-    def confidence(self) -> float | None:
+    def confidence(self) -> Optional[float]:
         return self.mapping_set.confidence
 
     @property
@@ -144,7 +144,7 @@ class Config:
     mappings: list[Mapping] = Field(
         ..., description="A list of mappings and their evidences consumed to create this evidence"
     )
-    author: Reference | None = None
+    author: Optional[Reference] = None
     confidence_factor: float = 1.0
 
     def key(self):
@@ -155,7 +155,7 @@ def key(self):
         )
 
     @property
-    def confidence(self) -> float | None:
+    def confidence(self) -> Optional[float]:
         confidences = [mapping.confidence for mapping in self.mappings]
         nn_confidences = [c for c in confidences if c is not None]
         if not nn_confidences:
@@ -178,7 +178,7 @@ def explanation(self) -> str:
 
 
 Evidence = Annotated[
-    ReasonedEvidence | SimpleEvidence,
+    Union[ReasonedEvidence, SimpleEvidence],
     Field(discriminator="evidence_type"),
 ]
 
@@ -202,13 +202,13 @@ def triple(self) -> Triple:
         return self.s, self.p, self.o
 
     @classmethod
-    def from_triple(cls, triple: Triple, evidence: list[Evidence] | None = None) -> Mapping:
+    def from_triple(cls, triple: Triple, evidence: Union[list[Evidence], None] = None) -> Mapping:
         """Instantiate a mapping from a triple."""
         s, p, o = triple
         return cls(s=s, p=p, o=o, evidence=evidence or [])
 
     @property
-    def confidence(self) -> float | None:
+    def confidence(self) -> Optional[float]:
         if not self.evidence:
             return None
         confidences = [e.confidence for e in self.evidence]