From ba9cc04f3c819030ea67e3bb9a928bf8c444f745 Mon Sep 17 00:00:00 2001
From: Kori Kuzma <korikuzma@gmail.com>
Date: Fri, 19 Jul 2024 09:16:36 -0400
Subject: [PATCH] refactor: resolve Pylance warnings (#366)
* replace constr with Annotated and StringConstraints
---
src/gene/schemas.py | 20 ++++++++++++--------
1 file changed, 12 insertions(+), 8 deletions(-)
diff --git a/src/gene/schemas.py b/src/gene/schemas.py
index e70dca2..56febb9 100644
--- a/src/gene/schemas.py
+++ b/src/gene/schemas.py
@@ -1,7 +1,7 @@
"""Contains data models for representing VICC normalized gene records."""
from enum import Enum, IntEnum
-from typing import Literal
+from typing import Annotated, Literal
from ga4gh.core import domain_models
from ga4gh.vrs import models
@@ -11,12 +11,12 @@
StrictBool,
StrictInt,
StrictStr,
- constr,
+ StringConstraints,
)
from gene import __version__
-CURIE = constr(pattern=r"^\w[^:]*:.+$")
+CURIE_REGEX = r"^\w[^:]*:.+$"
class SymbolStatus(str, Enum):
@@ -69,7 +69,9 @@ class GeneSequenceLocation(BaseModel):
type: Literal["SequenceLocation"] = "SequenceLocation"
start: StrictInt
end: StrictInt
- sequence_id: constr(pattern=r"^ga4gh:SQ.[0-9A-Za-z_\-]{32}$")
+ sequence_id: Annotated[
+ str, StringConstraints(pattern=r"^ga4gh:SQ.[0-9A-Za-z_\-]{32}$")
+ ]
class BaseGene(BaseModel):
@@ -77,7 +79,7 @@ class BaseGene(BaseModel):
/search and /normalize_unmerged.
"""
- concept_id: CURIE
+ concept_id: Annotated[str, StringConstraints(pattern=CURIE_REGEX)]
symbol: StrictStr
symbol_status: SymbolStatus | None = None
label: StrictStr | None = None
@@ -86,8 +88,8 @@ class BaseGene(BaseModel):
locations: list[models.SequenceLocation] | list[GeneSequenceLocation] = []
aliases: list[StrictStr] = []
previous_symbols: list[StrictStr] = []
- xrefs: list[CURIE] = []
- associated_with: list[CURIE] = []
+ xrefs: list[Annotated[str, StringConstraints(pattern=CURIE_REGEX)]] = []
+ associated_with: list[Annotated[str, StringConstraints(pattern=CURIE_REGEX)]] = []
gene_type: StrictStr | None = None
@@ -460,7 +462,9 @@ class UnmergedNormalizationService(BaseNormalizationService):
attributes.
"""
- normalized_concept_id: CURIE | None = None
+ normalized_concept_id: (
+ Annotated[str, StringConstraints(pattern=CURIE_REGEX)] | None
+ ) = None
source_matches: dict[SourceName, MatchesNormalized]
model_config = ConfigDict(