refactor: use ResidueMode for residue_mode type

- Inconsistent with using ResidueMode vs str

cool_seq_tool/app.py

@@ -53,5 +53,5 @@ def __init__(
         self.mane_transcript = MANETranscript(
             self.seqrepo_access, self.transcript_mappings,
             self.mane_transcript_mappings, self.uta_db)
-        self.exon_genomic_coords_mapper = ExonGenomicCoordsMapper(self.uta_db,
-                                                                  self.mane_transcript)
+        self.ex_g_coords_mapper = ExonGenomicCoordsMapper(self.uta_db,
+                                                          self.mane_transcript)

cool_seq_tool/handlers/seqrepo_access.py

@@ -20,17 +20,16 @@ class SeqRepoAccess(SeqRepoDataProxy):
 
     def get_reference_sequence(
         self, ac: str, start: Optional[int] = None, end: Optional[int] = None,
-        residue_mode: str = ResidueMode.RESIDUE
+        residue_mode: ResidueMode = ResidueMode.RESIDUE
     ) -> Tuple[str, Optional[str]]:
         """Get reference sequence for an accession given a start and end position.
         If `start` and `end` are not given, it will return the entire reference sequence
 
-        :param str ac: Accession
-        :param Optional[int] start: Start pos change
-        :param Optional[int] end: End pos change. If `None` assumes both
-            `start` and `end` have same values, if `start` exists.
-        :param str residue_mode: Residue mode for start/end positions
-            Must be either `inter-residue` or `residue`
+        :param ac: Accession
+        :param start: Start pos change
+        :param end: End pos change. If `None` assumes both `start` and `end` have same
+            values, if `start` exists.
+        :param residue_mode: Residue mode for `start` and `end`
         :return: Sequence at position (if accession and positions actually
             exist, else return empty string), warning if any
         """

cool_seq_tool/mappers/exon_genomic_coords.py

@@ -354,7 +354,7 @@ def _get_gene_and_alt_ac(
 
     async def _set_mane_genomic_data(
             self, params: Dict, gene: str, alt_ac: str, pos: int, strand: int,
-            is_start: bool, residue_mode: str
+            is_start: bool, residue_mode: ResidueMode
     ) -> Optional[str]:
         """Set genomic data in `params` found from MANE.
 
@@ -365,8 +365,7 @@ async def _set_mane_genomic_data(
         :param strand: Strand
         :param is_start: `True` if `pos` is start position. `False` if `pos` is end
             position.
-        :param residue_mode: Residue mode for start/end positions. Must be either
-            `inter-residue` or `residue`
+        :param residue_mode: Residue mode for `pos`
         :return: Warnings if found
         """
         mane_data = await self.mane_transcript.get_mane_transcript(

cool_seq_tool/mappers/mane_transcript.py

@@ -338,18 +338,18 @@ def _validate_reading_frames(self, ac: str, start_pos: int, end_pos: int,
     def _validate_references(self, ac: str, coding_start_site: int,
                              start_pos: int, end_pos: int,
                              mane_transcript: Dict, expected_ref: str,
-                             anno: AnnotationLayer, residue_mode: str) -> bool:
+                             anno: AnnotationLayer, residue_mode: ResidueMode) -> bool:
         """Return whether or not reference changes are the same.
 
-        :param str ac: Query accession
-        :param int coding_start_site: ac's coding start site
-        :param int start_pos: Original start position change
-        :param int end_pos: Origin end position change
-        :param Dict mane_transcript: Ensembl and RefSeq transcripts with
-            corresponding position change
-        :param str expected_ref: Reference at position given during input
-        :param AnnotationLayer anno: Annotation layer we are starting from
-        :param ResidueMode residue_mode: Residue mode
+        :param ac: Query accession
+        :param coding_start_site: ac's coding start site
+        :param start_pos: Original start position change
+        :param end_pos: Origin end position change
+        :param mane_transcript: Ensembl and RefSeq transcripts with corresponding
+            position change
+        :param expected_ref: Reference at position given during input
+        :param anno: Annotation layer we are starting from
+        :param residue_mode: Residue mode for `start_pos` and `end_pos`
         :return: `True` if reference check passes. `False` otherwise.
         """
         if anno == AnnotationLayer.CDNA:
@@ -432,23 +432,22 @@ def _get_prioritized_transcripts_from_gene(self,
     async def get_longest_compatible_transcript(
             self, gene: str, start_pos: int, end_pos: int,
             start_annotation_layer: AnnotationLayer, ref: Optional[str] = None,
-            residue_mode: str = ResidueMode.RESIDUE,
+            residue_mode: ResidueMode = ResidueMode.RESIDUE,
             mane_transcripts: Optional[Set] = None,
             alt_ac: Optional[str] = None
     ) -> Optional[Dict]:
         """Get longest compatible transcript from a gene.
         Try GRCh38 first, then GRCh37.
         Transcript is compatible if it passes validation checks.
 
-        :param str gene: Gene symbol
-        :param int start_pos: Start position change
-        :param int end_pos: End position change
-        :param  AnnotationLayer start_annotation_layer: Starting annotation layer.
-        :param str ref: Reference at position given during input
-        :param str residue_mode: Residue mode
-        :param Optional[Set] mane_transcripts: Attempted mane transcripts that were not
-            compatible
-        :param Optional[str] alt_ac: Genomic accession
+        :param gene: Gene symbol
+        :param start_pos: Start position change
+        :param end_pos: End position change
+        :param start_annotation_layer: Starting annotation layer.
+        :param ref: Reference at position given during input
+        :param residue_mode: Residue mode for `start_pos` and `end_pos`
+        :param mane_transcripts: Attempted mane transcripts that were not compatible
+        :param alt_ac: Genomic accession
         :return: Data for longest compatible transcript
         """
         inter_residue_pos, _ = get_inter_residue_pos(

cool_seq_tool/routers/__init__.py

@@ -1,7 +1,7 @@
 """Module for routers"""
 from enum import Enum
 
-from cool_seq_tool import CoolSeqTool
+from cool_seq_tool.app import CoolSeqTool
 
 
 cool_seq_tool = CoolSeqTool()

cool_seq_tool/routers/default.py

@@ -14,6 +14,7 @@
     UNHANDLED_EXCEPTION_MSG
 from cool_seq_tool.schemas import GenomicDataResponse, GenomicRequestBody, \
     TranscriptRequestBody
+from cool_seq_tool.utils import service_meta
 
 
 logger = logging.getLogger("cool_seq_tool")
@@ -40,11 +41,11 @@ async def genomic_to_transcript_exon_coordinates(
     request_body = request_body.model_dump()
 
     response = GenomicDataResponse(
-        genomic_data=None, warnings=list(), service_meta=cool_seq_tool.service_meta())
+        genomic_data=None, warnings=list(), service_meta=service_meta())
 
     try:
         response = \
-            await cool_seq_tool.genomic_to_transcript_exon_coordinates(**request_body)
+            await cool_seq_tool.ex_g_coords_mapper.genomic_to_transcript_exon_coordinates(**request_body)  # noqa: E501
     except Exception as e:
         logger.error(f"genomic_to_transcript_exon_coordinates unhandled exception {str(e)}")  # noqa: E501
         response.warnings.append(UNHANDLED_EXCEPTION_MSG)
@@ -71,10 +72,10 @@ async def transcript_to_genomic_coordinates(
     request_body = request_body.model_dump()
 
     response = GenomicDataResponse(
-        genomic_data=None, warnings=list(), service_meta=cool_seq_tool.service_meta())
+        genomic_data=None, warnings=list(), service_meta=service_meta())
 
     try:
-        response = await cool_seq_tool.transcript_to_genomic_coordinates(**request_body)
+        response = await cool_seq_tool.ex_g_coords_mapper.transcript_to_genomic_coordinates(**request_body)  # noqa: E501
     except Exception as e:
         logger.error(f"transcript_to_genomic_coordinates unhandled exception {str(e)}")
         response.warnings.append(UNHANDLED_EXCEPTION_MSG)
@@ -105,7 +106,7 @@ async def get_sequence(
     """
     _, path = tempfile.mkstemp(suffix=".fasta")
     try:
-        cool_seq_tool.get_fasta_file(sequence_id, Path(path))
+        cool_seq_tool.seqrepo_access.get_fasta_file(sequence_id, Path(path))
     except KeyError:
         raise HTTPException(
             status_code=404,

cool_seq_tool/routers/mane.py

@@ -8,6 +8,7 @@
 from cool_seq_tool.routers import cool_seq_tool, SERVICE_NAME, RESP_DESCR, \
     UNHANDLED_EXCEPTION_MSG, Tags
 from cool_seq_tool.schemas import AnnotationLayer, ManeDataService, ResidueMode
+from cool_seq_tool.utils import service_meta
 
 
 logger = logging.getLogger("cool_seq_tool")
@@ -74,5 +75,5 @@ async def get_mane_data(
     return ManeDataService(
         mane_data=mane_data,
         warnings=warnings,
-        service_meta=cool_seq_tool.service_meta()
+        service_meta=service_meta()
     )

cool_seq_tool/routers/mappings.py

@@ -9,6 +9,7 @@
 from cool_seq_tool.routers import cool_seq_tool, SERVICE_NAME, RESP_DESCR, Tags
 from cool_seq_tool.schemas import Assembly, ToGenomicService, ToCdnaService, \
     ResidueMode
+from cool_seq_tool.utils import service_meta
 
 logger = logging.getLogger("cool_seq_tool")
 
@@ -51,7 +52,7 @@ async def p_to_c(
     return ToCdnaService(
         c_data=c_data,
         warnings=[w] if w else [],
-        service_meta=cool_seq_tool.service_meta()
+        service_meta=service_meta()
     )
 
 
@@ -100,7 +101,7 @@ async def c_to_g(
     return ToGenomicService(
         g_data=g_data,
         warnings=[w] if w else [],
-        service_meta=cool_seq_tool.service_meta()
+        service_meta=service_meta()
     )
 
 
@@ -144,5 +145,5 @@ async def p_to_g(
     return ToGenomicService(
         g_data=g_data,
         warnings=[w] if w else [],
-        service_meta=cool_seq_tool.service_meta()
+        service_meta=service_meta()
     )

cool_seq_tool/schemas.py

@@ -419,10 +419,10 @@ class ManeDataService(BaseModelForbidExtra):
 class CdnaRepresentation(BaseModelForbidExtra):
     """Model response for cDNA representation"""
 
-    c_ac: str
-    c_start_pos: str
-    c_end_pos: str
-    cds_start: int
+    c_ac: StrictStr
+    c_start_pos: StrictInt
+    c_end_pos: StrictInt
+    cds_start: StrictInt
     residue_mode: Literal[ResidueMode.INTER_RESIDUE] = ResidueMode.INTER_RESIDUE.value
 
     model_config = ConfigDict(
@@ -432,7 +432,7 @@ class CdnaRepresentation(BaseModelForbidExtra):
                 "c_start_pos": 1797,
                 "c_end_pos": 1800,
                 "cds_start": 226,
-                "residue_mode": "inter-residue",
+                "residue_mode": ResidueMode.INTER_RESIDUE,
             }
         }
     )
@@ -453,7 +453,7 @@ class ToCdnaService(BaseModelForbidExtra):
                     "c_start_pos": 1797,
                     "c_end_pos": 1800,
                     "cds_start": 226,
-                    "residue_mode": "inter-residue",
+                    "residue_mode": ResidueMode.INTER_RESIDUE,
                 },
                 "warnings": [],
                 "service_meta": {
@@ -481,7 +481,7 @@ class GenomicRepresentation(BaseModelForbidExtra):
                 "g_ac": "NC_000007.13",
                 "g_start_pos": 140453134,
                 "g_end_pos": 140453137,
-                "residue_mode": "inter-residue",
+                "residue_mode": ResidueMode.INTER_RESIDUE,
             }
         }
     )
@@ -501,7 +501,7 @@ class ToGenomicService(BaseModelForbidExtra):
                     "g_ac": "NC_000007.13",
                     "g_start_pos": 140453134,
                     "g_end_pos": 140453137,
-                    "residue_mode": "inter-residue",
+                    "residue_mode": ResidueMode.INTER_RESIDUE,
                 },
                 "warnings": [],
                 "service_meta": {

cool_seq_tool/utils.py

@@ -11,15 +11,14 @@
 
 
 def get_inter_residue_pos(
-        start_pos: int, residue_mode: str, end_pos: Optional[int] = None
+        start_pos: int, residue_mode: ResidueMode, end_pos: Optional[int] = None
 ) -> Tuple[Optional[Tuple[int, int]], Optional[str]]:
     """Return inter-residue position
 
-    :param int start_pos: Start position
-    :param str residue_mode: `inter-residue` if start/end are 0 based coords.
-        `residue` if start/end are 1 based coords
-    :param Optional[int] end_pos: End position. If `None` assumes both
-        `start` and `end` have same values.
+    :param start_pos: Start position
+    :param residue_mode: Residue mode for `start_pos` and `end_pos`
+    :param end_pos: End position. If `None` assumes both `start` and `end` have same
+        values.
     :return: Inter-residue coordinates, warning
     """
     residue_mode = residue_mode.lower()

tests/handlers/test_seqrepo_access.py

@@ -1,6 +1,8 @@
 """Module for testing seqrepo access class"""
 import pytest
 
+from cool_seq_tool.schemas import ResidueMode
+
 
 def test_get_reference_sequence(test_seqrepo_access):
     """Test that get_reference_sequence method works correctly"""
@@ -14,7 +16,7 @@ def test_get_reference_sequence(test_seqrepo_access):
     assert resp == ("V", None)
 
     resp = test_seqrepo_access.get_reference_sequence(
-        "NP_004324.2", 599, 600, residue_mode="inter-residue")
+        "NP_004324.2", 599, 600, residue_mode=ResidueMode.INTER_RESIDUE)
     assert resp == ("V", None)
 
     resp = test_seqrepo_access.get_reference_sequence("NP_004324.2", 601, 600)

tests/mappers/test_alignment.py

@@ -23,7 +23,7 @@ def braf_v600e_c():
         "c_start_pos": 1797,
         "c_end_pos": 1800,
         "cds_start": 226,
-        "residue_mode": "inter-residue"
+        "residue_mode": ResidueMode.INTER_RESIDUE
     }
 
 
@@ -35,7 +35,7 @@ def egfr_l858r_c():
         "c_start_pos": 2571,
         "c_end_pos": 2574,
         "cds_start": 261,
-        "residue_mode": "inter-residue"
+        "residue_mode": ResidueMode.INTER_RESIDUE
     }
 
 
@@ -46,7 +46,7 @@ def braf_v600e_grch37():
         "g_ac": "NC_000007.13",
         "g_start_pos": 140453134,
         "g_end_pos": 140453137,
-        "residue_mode": "inter-residue"
+        "residue_mode": ResidueMode.INTER_RESIDUE
     }
 
 
@@ -57,7 +57,7 @@ def braf_v600e_grch38():
         "g_ac": "NC_000007.14",
         "g_start_pos": 140753334,
         "g_end_pos": 140753337,
-        "residue_mode": "inter-residue"
+        "residue_mode": ResidueMode.INTER_RESIDUE
     }
 
 
@@ -68,7 +68,7 @@ def egfr_l858r_grch37():
         "g_ac": "NC_000007.13",
         "g_start_pos": 55259513,
         "g_end_pos": 55259516,
-        "residue_mode": "inter-residue"
+        "residue_mode": ResidueMode.INTER_RESIDUE
     }
 
 
@@ -79,7 +79,7 @@ def egfr_l858r_grch38():
         "g_ac": "NC_000007.14",
         "g_start_pos": 55191820,
         "g_end_pos": 55191823,
-        "residue_mode": "inter-residue"
+        "residue_mode": ResidueMode.INTER_RESIDUE
     }
 
 
@@ -90,7 +90,7 @@ def delins_grch37():
         "g_ac": "NC_000007.13",
         "g_start_pos": 140453131,
         "g_end_pos": 140453137,
-        "residue_mode": "inter-residue"
+        "residue_mode": ResidueMode.INTER_RESIDUE
     }
 
 
@@ -104,7 +104,7 @@ def _expected(assembly):
             "g_ac": g_ac,
             "g_start_pos": 534316,
             "g_end_pos": 534319,
-            "residue_mode": "inter-residue"
+            "residue_mode": ResidueMode.INTER_RESIDUE
         }
 
     return _expected
@@ -159,7 +159,7 @@ async def test_p_to_c(test_alignment_mapper, braf_v600e_c, egfr_l858r_c):
         "c_start_pos": 393,
         "c_end_pos": 396,
         "cds_start": 223,
-        "residue_mode": "inter-residue"
+        "residue_mode": ResidueMode.INTER_RESIDUE
     }