chore: clean up some type annotations (#183)

Author: jsstevenson

cool_seq_tool/app.py

@@ -1,6 +1,6 @@
 """Module for initializing data sources."""
 from datetime import datetime
-from typing import Optional, Union, List, Tuple, Dict
+from typing import Optional, TypeVar, Union, List, Tuple, Dict
 from pathlib import Path
 import logging
 
@@ -20,6 +20,10 @@
 
 logger = logging.getLogger("cool_seq_tool")
 
+CoordinatesResponseType = TypeVar(
+    "CoordinatesResponseType", GenomicDataResponse, TranscriptExonDataResponse
+)
+
 
 class CoolSeqTool:
     """Class to initialize data sources."""
@@ -81,8 +85,8 @@ def service_meta() -> ServiceMeta:
 
     @staticmethod
     def _return_warnings(
-            resp: Union[GenomicDataResponse, TranscriptExonDataResponse],
-            warning_msg: str) -> Union[GenomicDataResponse, TranscriptExonDataResponse]:
+            resp: CoordinatesResponseType,
+            warning_msg: str) -> CoordinatesResponseType:
         """Add warnings to response object
 
         :param Union[GenomicDataResponse, TranscriptExonDataResponse] resp:
@@ -97,18 +101,18 @@ def _return_warnings(
 
     async def transcript_to_genomic_coordinates(
             self, gene: Optional[str] = None, transcript: Optional[str] = None,
-            exon_start: Optional[int] = None, exon_start_offset: Optional[int] = 0,  # noqa: E501
-            exon_end: Optional[int] = None, exon_end_offset: Optional[int] = 0,
+            exon_start: Optional[int] = None, exon_start_offset: int = 0,  # noqa: E501
+            exon_end: Optional[int] = None, exon_end_offset: int = 0,
             **kwargs) -> GenomicDataResponse:
         """Get genomic data given transcript data.
         Will use GRCh38 coordinates if possible
 
-        :param Optional[str] gene: Gene symbol
-        :param Optional[str] transcript: Transcript accession
-        :param Optional[int] exon_start: Starting transcript exon number
-        :param Optional[int] exon_end: Ending transcript exon number
-        :param Optional[int] exon_start_offset: Starting exon offset
-        :param Optional[int] exon_end_offset: Ending exon offset
+        :param gene: Gene symbol
+        :param transcript: Transcript accession
+        :param exon_start: Starting transcript exon number
+        :param exon_end: Ending transcript exon number
+        :param exon_start_offset: Starting exon offset
+        :param exon_end_offset: Ending exon offset
         :return: GRCh38 genomic data (inter-residue coordinates)
         """
         resp = GenomicDataResponse(
@@ -138,18 +142,18 @@ async def transcript_to_genomic_coordinates(
 
         tx_exons, warning = await self.uta_db.get_tx_exons(transcript)
         if not tx_exons:
-            return self._return_warnings(resp, warning)
+            return self._return_warnings(resp, warning or "")
 
         tx_exon_coords, warning = self.uta_db.get_tx_exon_coords(
             transcript, tx_exons, exon_start, exon_end)
         if not tx_exon_coords:
-            return self._return_warnings(resp, warning)
+            return self._return_warnings(resp, warning or "")
         tx_exon_start, tx_exon_end = tx_exon_coords
 
         alt_ac_start_end, warning = await self.uta_db.get_alt_ac_start_and_end(
             transcript, tx_exon_start, tx_exon_end, gene=gene)
         if not alt_ac_start_end:
-            return self._return_warnings(resp, warning)
+            return self._return_warnings(resp, warning or "")
         alt_ac_start, alt_ac_end = alt_ac_start_end
 
         gene = alt_ac_start[0] if alt_ac_start else alt_ac_end[0]

cool_seq_tool/data_sources/uta_database.py

@@ -318,8 +318,8 @@ async def get_tx_exons(
 
     @staticmethod
     def _validate_exon(
-            transcript: str, tx_exons: List[str],
-            exon_number: Optional[int] = None) -> Tuple[Optional[List], Optional[str]]:  # noqa: E501
+            transcript: str, tx_exons: List[Tuple[int, int]],
+            exon_number: int) -> Tuple[Optional[Tuple[int, int]], Optional[str]]:
         """Validate that exon number is valid
 
         :param str transcript: Transcript accession
@@ -337,15 +337,15 @@ def _validate_exon(
         return exon, None
 
     def get_tx_exon_coords(
-            self, transcript: str, tx_exons: List[str],
+            self, transcript: str, tx_exons: List[Tuple[int, int]],
             exon_start: Optional[int] = None,
-            exon_end: Optional[int] = None) -> Tuple[Optional[Tuple[List, List]], Optional[str]]:  # noqa: E501
+            exon_end: Optional[int] = None) -> Tuple[Optional[Tuple[Optional[Tuple[int, int]], Optional[Tuple[int, int]]]], Optional[str]]:  # noqa: E501
         """Get transcript exon coordinates
 
-        :param str transcript: Transcript accession
-        :param List tx_exons: List of transcript exons
-        :param Optional[int] exon_start: Start exon number
-        :param Optional[int] exon_end: End exon number
+        :param transcript: Transcript accession
+        :param tx_exons: List of transcript exons
+        :param exon_start: Start exon number
+        :param exon_end: End exon number
         :return: [Transcript start exon coords, Transcript end exon coords],
             and warnings if found
         """
@@ -369,7 +369,8 @@ def get_tx_exon_coords(
     async def get_alt_ac_start_and_end(
             self, tx_ac: str, tx_exon_start: Optional[List[str]] = None,
             tx_exon_end: Optional[List[str]] = None,
-            gene: str = None) -> Tuple[Optional[Tuple[Tuple, Tuple]], Optional[str]]:  # noqa: E501
+            gene: Optional[str] = None
+    ) -> Tuple[Optional[Tuple[Tuple, Tuple]], Optional[str]]:  # noqa: E501
         """Get genomic coordinates for related transcript exon start and end.
 
         :param str tx_ac: Transcript accession

cool_seq_tool/schemas.py

@@ -274,7 +274,7 @@ class TranscriptExonDataResponse(BaseModelForbidExtra):
     """Response model for Transcript Exon Data"""
 
     transcript_exon_data: Optional[TranscriptExonData] = None
-    warnings: Optional[List[StrictStr]] = []
+    warnings: List[StrictStr] = []
     service_meta: ServiceMeta
 
     class Config(BaseModelForbidExtra.Config):
@@ -312,7 +312,7 @@ class GenomicDataResponse(BaseModelForbidExtra):
     """Response model for Genomic Data"""
 
     genomic_data: Optional[GenomicData] = None
-    warnings: Optional[List[StrictStr]] = []
+    warnings: List[StrictStr] = []
     service_meta: ServiceMeta
 
     class Config(BaseModelForbidExtra.Config):