cool-seq-tool 0.4.0.dev1__py3-none-any.whl → 0.4.0.dev2__py3-none-any.whl

cool_seq_tool/routers/default.py

@@ -45,7 +45,7 @@ async def genomic_to_transcript_exon_coordinates(
     request_body = request_body.model_dump()
 
     response = GenomicDataResponse(
-        genomic_data=None, warnings=list(), service_meta=service_meta()
+        genomic_data=None, warnings=[], service_meta=service_meta()
     )
 
     try:
@@ -53,9 +53,7 @@ async def genomic_to_transcript_exon_coordinates(
             **request_body
         )
     except Exception as e:
-        logger.error(
-            f"genomic_to_transcript_exon_coordinates unhandled exception {str(e)}"
-        )
+        logger.error("genomic_to_transcript_exon_coordinates unhandled exception %s", e)
         response.warnings.append(UNHANDLED_EXCEPTION_MSG)
 
     return response
@@ -80,7 +78,7 @@ async def transcript_to_genomic_coordinates(
     request_body = request_body.model_dump()
 
     response = GenomicDataResponse(
-        genomic_data=None, warnings=list(), service_meta=service_meta()
+        genomic_data=None, warnings=[], service_meta=service_meta()
     )
 
     try:
@@ -90,7 +88,7 @@ async def transcript_to_genomic_coordinates(
             )
         )
     except Exception as e:
-        logger.error(f"transcript_to_genomic_coordinates unhandled exception {str(e)}")
+        logger.error("transcript_to_genomic_coordinates unhandled exception %s", e)
         response.warnings.append(UNHANDLED_EXCEPTION_MSG)
 
     return response
@@ -119,9 +117,9 @@ async def get_sequence(
     _, path = tempfile.mkstemp(suffix=".fasta")
     try:
         cool_seq_tool.seqrepo_access.get_fasta_file(sequence_id, Path(path))
-    except KeyError:
+    except KeyError as e:
         raise HTTPException(
             status_code=404, detail="No sequence available for requested identifier"
-        )
-    background_tasks.add_task(lambda p: os.unlink(p), path)
+        ) from e
+    background_tasks.add_task(lambda p: os.unlink(p), path)  # noqa: PTH108
     return FileResponse(path)

cool_seq_tool/routers/mane.py

@@ -73,7 +73,7 @@ async def get_mane_data(
     :param ResidueMode residue_mode: Starting residue mode for `start_pos`
         and `end_pos`. Will always return coordinates in inter-residue
     """
-    warnings = list()
+    warnings = []
     mane_data = None
     try:
         mane_data = await cool_seq_tool.mane_transcript.get_mane_transcript(
@@ -90,7 +90,7 @@ async def get_mane_data(
         if not mane_data:
             warnings.append("Unable to retrieve MANE data")
     except Exception as e:
-        logger.exception(f"get_mane_data unhandled exception {e}")
+        logger.exception("get_mane_data unhandled exception %s", e)
         warnings.append(UNHANDLED_EXCEPTION_MSG)
 
     return ManeDataService(

cool_seq_tool/schemas.py

@@ -1,6 +1,6 @@
 """Defines attribute constants, useful object structures, and API response schemas."""
+import datetime
 import re
-from datetime import datetime
 from enum import Enum, IntEnum
 from typing import List, Literal, Optional, Tuple, Union
 
@@ -15,6 +15,8 @@ from pydantic import (
 
 from cool_seq_tool.version import __version__
 
+_now = str(datetime.datetime.now(tz=datetime.timezone.utc))
+
 
 class AnnotationLayer(str, Enum):
     """Create enum for supported annotation layers"""
@@ -79,9 +81,10 @@ class GenomicRequestBody(BaseModelForbidExtra):
     @model_validator(mode="after")
     def check_start_and_end(cls, values):
         """Check that at least one of {``start``, ``end``} is set"""
-        msg = "Must provide either `start` or `end`"
         start, end = values.start, values.end
-        assert start or end, msg
+        if not start or end:
+            msg = "Must provide either `start` or `end`"
+            raise ValueError(msg)
         return values
 
     model_config = ConfigDict(
@@ -112,9 +115,10 @@ class TranscriptRequestBody(BaseModelForbidExtra):
     @model_validator(mode="after")
     def check_exon_start_and_exon_end(cls, values):
         """Check that at least one of {``exon_start``, ``exon_end``} is set"""
-        msg = "Must provide either `exon_start` or `exon_end`"
         exon_start, exon_end = values.exon_start, values.exon_end
-        assert exon_start or exon_end, msg
+        if not exon_start or exon_end:
+            msg = "Must provide either `exon_start` or `exon_end`"
+            raise ValueError(msg)
         return values
 
     model_config = ConfigDict(
@@ -177,20 +181,23 @@ class GenomicData(BaseModelForbidExtra):
         Check that at least one of {``exon_start``, ``exon_end``} is set.
         If not set, set corresponding offset to ``None``
         """
-        msg = "Missing values for `start` or `end`"
         start = values.start
         end = values.end
-        assert start or end, msg
+        if not start and not end:
+            msg = "Missing values for `start` or `end`"
+            raise ValueError(msg)
 
         if start:
-            msg = "Missing value `exon_start`"
-            assert values.exon_start, msg
+            if not values.exon_start:
+                msg = "Missing value `exon_start`"
+                raise ValueError(msg)
         else:
             values.exon_start_offset = None
 
         if end:
-            msg = "Missing value `exon_end`"
-            assert values.exon_end, msg
+            if not values.exon_end:
+                msg = "Missing value `exon_end`"
+                raise ValueError(msg)
         else:
             values.exon_end_offset = None
         return values
@@ -218,7 +225,7 @@ class ServiceMeta(BaseModelForbidExtra):
 
     name: Literal["cool_seq_tool"] = "cool_seq_tool"
     version: StrictStr
-    response_datetime: datetime
+    response_datetime: datetime.datetime
     url: Literal[
         "https://github.com/GenomicMedLab/cool-seq-tool"
     ] = "https://github.com/GenomicMedLab/cool-seq-tool"
@@ -228,8 +235,10 @@ class ServiceMeta(BaseModelForbidExtra):
         """Check version matches semantic versioning regex pattern.
         https://semver.org/#is-there-a-suggested-regular-expression-regex-to-check-a-semver-string
         """
-        version_regex = r"^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(?:-((?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\+([0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?$"  # noqa: E501
-        assert bool(re.match(version_regex, v))
+        version_regex = r"^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(?:-((?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\+([0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?$"
+        if not re.match(version_regex, v):
+            msg = f"Invalid version {v}"
+            raise ValueError(msg)
         return v
 
     model_config = ConfigDict(
@@ -237,7 +246,7 @@ class ServiceMeta(BaseModelForbidExtra):
             "example": {
                 "name": "cool_seq_tool",
                 "version": __version__,
-                "response_datetime": datetime.now(),
+                "response_datetime": _now,
                 "url": "https://github.com/GenomicMedLab/cool-seq-tool",
             }
         }
@@ -267,7 +276,7 @@ class TranscriptExonDataResponse(BaseModelForbidExtra):
                 "service_meta": {
                     "name": "cool_seq_tool",
                     "version": __version__,
-                    "response_datetime": datetime.now(),
+                    "response_datetime": _now,
                     "url": "https://github.com/GenomicMedLab/cool-seq-tool",
                 },
             }
@@ -301,7 +310,7 @@ class GenomicDataResponse(BaseModelForbidExtra):
                 "service_meta": {
                     "name": "cool_seq_tool",
                     "version": __version__,
-                    "response_datetime": datetime.now(),
+                    "response_datetime": _now,
                     "url": "https://github.com/GenomicMedLab/cool-seq-tool",
                 },
             }
@@ -358,7 +367,7 @@ class MappedManeDataService(BaseModelForbidExtra):
                 "service_meta": {
                     "name": "cool_seq_tool",
                     "version": __version__,
-                    "response_datetime": datetime.now(),
+                    "response_datetime": _now,
                     "url": "https://github.com/GenomicMedLab/cool-seq-tool",
                 },
             }
@@ -412,7 +421,7 @@ class ManeDataService(BaseModelForbidExtra):
                 "service_meta": {
                     "name": "cool_seq_tool",
                     "version": __version__,
-                    "response_datetime": datetime.now(),
+                    "response_datetime": _now,
                     "url": "https://github.com/GenomicMedLab/cool-seq-tool",
                 },
             }
@@ -466,7 +475,7 @@ class ToCdnaService(BaseModelForbidExtra):
                 "service_meta": {
                     "name": "cool_seq_tool",
                     "version": __version__,
-                    "response_datetime": datetime.now(),
+                    "response_datetime": _now,
                     "url": "https://github.com/GenomicMedLab/cool-seq-tool",
                 },
             }
@@ -514,7 +523,7 @@ class ToGenomicService(BaseModelForbidExtra):
                 "service_meta": {
                     "name": "cool_seq_tool",
                     "version": __version__,
-                    "response_datetime": datetime.now(),
+                    "response_datetime": _now,
                     "url": "https://github.com/GenomicMedLab/cool-seq-tool",
                 },
             }

cool_seq_tool/sources/mane_transcript_mappings.py

@@ -57,7 +57,7 @@ class ManeTranscriptMappings:
 
         if len(data) == 0:
             logger.warning(
-                f"Unable to get MANE Transcript data for gene: " f"{gene_symbol}"
+                "Unable to get MANE Transcript data for gene: %s", gene_symbol
             )
             return []
 

cool_seq_tool/sources/transcript_mappings.py

@@ -65,7 +65,7 @@ class TranscriptMappings:
 
         :param transcript_file_path: Path to transcript mappings file
         """
-        with open(transcript_file_path) as file:
+        with transcript_file_path.open() as file:
             reader = csv.DictReader(file, delimiter="\t")
             for row in reader:
                 gene = row["Gene name"]
@@ -108,7 +108,7 @@ class TranscriptMappings:
 
         :param Path lrg_refseqgene_path: Path to LRG RefSeqGene file
         """
-        with open(lrg_refseqgene_path) as file:
+        with lrg_refseqgene_path.open() as file:
             reader = csv.DictReader(file, delimiter="\t")
             for row in reader:
                 gene = row["Symbol"]
@@ -146,7 +146,7 @@ class TranscriptMappings:
         :param identifier: Gene identifier to get protein transcripts for
         :return: Protein transcripts for a gene symbol
         """
-        protein_transcripts = list()
+        protein_transcripts = []
         protein_transcripts += self.ensembl_protein_version_for_gene_symbol.get(
             identifier, ""
         )
@@ -160,7 +160,7 @@ class TranscriptMappings:
         :param identifier: Gene identifier to find transcripts for
         :return: cDNA transcripts for a gene symbol
         """
-        genomic_transcripts = list()
+        genomic_transcripts = []
         genomic_transcripts += self.ensembl_transcript_version_for_gene_symbol.get(
             identifier, ""
         )
@@ -179,10 +179,9 @@ class TranscriptMappings:
         :return: Gene symbol
         """
         gene_symbol = self.ensembl_protein_version_to_gene_symbol.get(q)
-        if not gene_symbol:
-            if "." in q:
-                q = q.split(".")[0]
-                gene_symbol = self.ensembl_protein_to_gene_symbol.get(q)
+        if not gene_symbol and "." in q:
+            q = q.split(".")[0]
+            gene_symbol = self.ensembl_protein_to_gene_symbol.get(q)
         return gene_symbol
 
     def get_gene_symbol_from_refeq_protein(self, q: str) -> Optional[str]:
@@ -200,10 +199,9 @@ class TranscriptMappings:
         :return: Gene symbol
         """
         gene_symbol = self.refseq_rna_version_to_gene_symbol.get(q)
-        if not gene_symbol:
-            if "." in q:
-                q = q.split(".")[0]
-                gene_symbol = self.refseq_rna_to_gene_symbol.get(q)
+        if not gene_symbol and "." in q:
+            q = q.split(".")[0]
+            gene_symbol = self.refseq_rna_to_gene_symbol.get(q)
         return gene_symbol
 
     def get_gene_symbol_from_ensembl_transcript(self, q: str) -> Optional[str]:
@@ -213,8 +211,7 @@ class TranscriptMappings:
         :return: Gene symbol
         """
         gene_symbol = self.ensembl_transcript_version_to_gene_symbol.get(q)
-        if not gene_symbol:
-            if "." in q:
-                q = q.split(".")[0]
-                gene_symbol = self.ensembl_transcript_to_gene_symbol.get(q)
+        if not gene_symbol and "." in q:
+            q = q.split(".")[0]
+            gene_symbol = self.ensembl_transcript_to_gene_symbol.get(q)
         return gene_symbol