feat!: rename residue mode to coordinate type (#591)

close #590 * `/variation/alignment_mapper/p_to_c`, `/variation/alignment_mapper/c_to_g`, `"/variation/alignment_mapper/p_to_g",`: query string parameter `residue_mode` changed to `coordinate_type`
cancervariants · Jan 6, 2025 · d93df25 · d93df25
1 parent 47db4d5
commit d93df25
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Showing 10 changed files with 56 additions and 56 deletions.
diff --git a/src/variation/main.py b/src/variation/main.py
@@ -678,23 +678,23 @@ async def p_to_c(
     p_ac: str = Query(..., description="Protein RefSeq accession"),
     p_start_pos: int = Query(..., description="Protein start position"),
     p_end_pos: int = Query(..., description="Protein end position"),
-    residue_mode: CoordinateType = Query(
+    coordinate_type: CoordinateType = Query(
         CoordinateType.RESIDUE,
-        description="Residue mode for `p_start_pos` and `p_end_pos`",
+        description="Coordinate type for `p_start_pos` and `p_end_pos`",
     ),
 ) -> ToCdnaService:
     """Translate protein representation to cDNA representation
 
     :param str p_ac: Protein RefSeq accession
     :param int p_start_pos: Protein start position
     :param int p_end_pos: Protein end position
-    :param CoordinateType residue_mode: Residue mode for `p_start_pos` and `p_end_pos`.
+    :param CoordinateType coordinate_type: Coordinate type for `p_start_pos` and `p_end_pos`.
     :return: ToCdnaService containing cDNA representation, warnings, and
         service meta
     """
     try:
         c_data, w = await query_handler.alignment_mapper.p_to_c(
-            p_ac, p_start_pos, p_end_pos, residue_mode
+            p_ac, p_start_pos, p_end_pos, coordinate_type
         )
     except Exception as e:
         _logger.error("Unhandled exception: %s", str(e))
@@ -727,9 +727,9 @@ async def c_to_g(
     cds_start: int | None = Query(
         None, description="CDS start site. If not provided, this will be computed."
     ),
-    residue_mode: CoordinateType = Query(
+    coordinate_type: CoordinateType = Query(
         CoordinateType.RESIDUE,
-        description="Residue mode for `c_start_pos` and `c_end_pos`",
+        description="Coordinate type for `c_start_pos` and `c_end_pos`",
     ),
     target_genome_assembly: Assembly = Query(
         Assembly.GRCH38, description="Genomic assembly to map to"
@@ -742,7 +742,7 @@ async def c_to_g(
     :param int c_end_pos: cDNA end position for codon
     :param Optional[int] cds_start: CDS start site. If not provided, this will be
         computed.
-    :param CoordinateType residue_mode: Residue mode for `c_start_pos` and `c_end_pos`.
+    :param CoordinateType coordinate_type: Coordinate type for `c_start_pos` and `c_end_pos`.
     :param Assembly target_genome_assembly: Genome assembly to get genomic data for
     :return: ToGenomicService containing genomic representation, warnings, and
         service meta
@@ -753,7 +753,7 @@ async def c_to_g(
             c_start_pos,
             c_end_pos,
             cds_start=cds_start,
-            coordinate_type=residue_mode,
+            coordinate_type=coordinate_type,
             target_genome_assembly=target_genome_assembly,
         )
     except Exception as e:
@@ -784,9 +784,9 @@ async def p_to_g(
     p_ac: str = Query(..., description="Protein RefSeq accession"),
     p_start_pos: int = Query(..., description="Protein start position"),
     p_end_pos: int = Query(..., description="Protein end position"),
-    residue_mode: CoordinateType = Query(
+    coordinate_type: CoordinateType = Query(
         CoordinateType.RESIDUE,
-        description="Residue mode for `p_start_pos` and `p_end_pos`",
+        description="Coordinate type for `p_start_pos` and `p_end_pos`",
     ),
     target_genome_assembly: Assembly = Query(
         Assembly.GRCH38, description="Genomic assembly to map to"
@@ -797,7 +797,7 @@ async def p_to_g(
     :param str p_ac: Protein RefSeq accession
     :param int p_start_pos: Protein start position
     :param int p_end_pos: Protein end position
-    :param CoordinateType residue_mode: Residue mode for `p_start_pos` and `p_end_pos`.
+    :param CoordinateType coordinate_type: Coordinate type for `p_start_pos` and `p_end_pos`.
     :param Assembly target_genome_assembly: Genome assembly to get genomic data for
     :return: ToGenomicService containing genomic representation, warnings, and
         service meta
@@ -807,7 +807,7 @@ async def p_to_g(
             p_ac,
             p_start_pos,
             p_end_pos,
-            coordinate_type=residue_mode,
+            coordinate_type=coordinate_type,
             target_genome_assembly=target_genome_assembly,
         )
     except Exception as e:

diff --git a/src/variation/schemas/service_schema.py b/src/variation/schemas/service_schema.py
@@ -28,7 +28,7 @@ class CdnaRepresentation(BaseModel, extra="forbid"):
     c_start_pos: StrictInt
     c_end_pos: StrictInt
     cds_start: StrictInt
-    residue_mode: Literal["inter-residue"] = CoordinateType.INTER_RESIDUE.value
+    coordinate_type: Literal["inter-residue"] = CoordinateType.INTER_RESIDUE.value
 
     model_config = ConfigDict(
         json_schema_extra={
@@ -37,7 +37,7 @@ class CdnaRepresentation(BaseModel, extra="forbid"):
                 "c_start_pos": 1797,
                 "c_end_pos": 1800,
                 "cds_start": 226,
-                "residue_mode": CoordinateType.INTER_RESIDUE.value,
+                "coordinate_type": CoordinateType.INTER_RESIDUE.value,
             }
         }
     )
@@ -58,7 +58,7 @@ class ToCdnaService(BaseModel, extra="forbid"):
                     "c_start_pos": 1797,
                     "c_end_pos": 1800,
                     "cds_start": 226,
-                    "residue_mode": "inter-residue",
+                    "coordinate_type": "inter-residue",
                 },
                 "warnings": [],
                 "service_meta": {
@@ -78,15 +78,15 @@ class GenomicRepresentation(BaseModel, extra="forbid"):
     g_ac: StrictStr
     g_start_pos: StrictInt
     g_end_pos: StrictInt
-    residue_mode: Literal["inter-residue"] = CoordinateType.INTER_RESIDUE.value
+    coordinate_type: Literal["inter-residue"] = CoordinateType.INTER_RESIDUE.value
 
     model_config = ConfigDict(
         json_schema_extra={
             "example": {
                 "g_ac": "NC_000007.13",
                 "g_start_pos": 140453134,
                 "g_end_pos": 140453137,
-                "residue_mode": CoordinateType.INTER_RESIDUE.value,
+                "coordinate_type": CoordinateType.INTER_RESIDUE.value,
             }
         }
     )
@@ -106,7 +106,7 @@ class ToGenomicService(BaseModel, extra="forbid"):
                     "g_ac": "NC_000007.13",
                     "g_start_pos": 140453134,
                     "g_end_pos": 140453137,
-                    "residue_mode": "inter-residue",
+                    "coordinate_type": "inter-residue",
                 },
                 "warnings": [],
                 "service_meta": {

diff --git a/src/variation/translators/genomic_del_dup_base.py b/src/variation/translators/genomic_del_dup_base.py
@@ -116,7 +116,7 @@ async def translate(
         grch38_data = None
         vrs_variation = None
         vrs_seq_loc_ac_status = VrsSeqLocAcStatus.NA
-        residue_mode = CoordinateType.RESIDUE
+        coordinate_type = CoordinateType.RESIDUE
         mane_genes = None
 
         if do_liftover or endpoint_name == Endpoint.NORMALIZE:
@@ -141,7 +141,7 @@ async def translate(
                     pos1 = grch38_data.pos0
                 else:
                     pos1 = grch38_data.pos1
-                residue_mode = CoordinateType.INTER_RESIDUE
+                coordinate_type = CoordinateType.INTER_RESIDUE
                 ac = grch38_data.ac
 
                 if (
@@ -154,7 +154,7 @@ async def translate(
                         pos0,
                         pos0 + (len(ref) - 1),
                         ref,
-                        coordinate_type=residue_mode,
+                        coordinate_type=coordinate_type,
                     )
                     if invalid_ref_msg:
                         warnings.append(invalid_ref_msg)
@@ -198,7 +198,7 @@ async def translate(
             pos0 = grch38_data.pos0 - 1
             pos1 = grch38_data.pos0 if grch38_data.pos1 is None else grch38_data.pos1
             mane_genes = grch38_data.mane_genes
-            residue_mode = CoordinateType.INTER_RESIDUE
+            coordinate_type = CoordinateType.INTER_RESIDUE
             self.is_valid(classification.gene_token, ac, pos0, pos1, errors)
 
             if errors:
@@ -211,7 +211,7 @@ async def translate(
                 pos1,
                 "g",
                 try_longest_compatible=True,
-                coordinate_type=residue_mode,
+                coordinate_type=coordinate_type,
                 gene=classification.gene_token.token
                 if classification.gene_token
                 else None,
@@ -223,7 +223,7 @@ async def translate(
                 vrs_seq_loc_ac_status = mane.status
                 pos0 = mane.pos[0] + mane.coding_start_site
                 pos1 = mane.pos[1] + mane.coding_start_site
-                residue_mode = CoordinateType.INTER_RESIDUE
+                coordinate_type = CoordinateType.INTER_RESIDUE
             else:
                 return None
 
@@ -239,7 +239,7 @@ async def translate(
         if alt_type == AltType.INSERTION:
             alt = classification.inserted_sequence
 
-        start = pos0 if residue_mode == CoordinateType.INTER_RESIDUE else pos0 - 1
+        start = pos0 if coordinate_type == CoordinateType.INTER_RESIDUE else pos0 - 1
         end = pos1 if pos1 else pos0
 
         refget_accession = get_refget_accession(self.seqrepo_access, ac, warnings)

diff --git a/src/variation/translators/genomic_delins.py b/src/variation/translators/genomic_delins.py
@@ -103,7 +103,7 @@ async def translate(
                     warnings,
                     alt=classification.inserted_sequence,
                     cds_start=mane.coding_start_site if gene else None,
-                    residue_mode=CoordinateType.INTER_RESIDUE,
+                    coordinate_type=CoordinateType.INTER_RESIDUE,
                     extensions=extensions,
                 )
         else:
@@ -116,7 +116,7 @@ async def translate(
                 AltType.DELINS,
                 warnings,
                 alt=classification.inserted_sequence,
-                residue_mode=CoordinateType.RESIDUE,
+                coordinate_type=CoordinateType.RESIDUE,
             )
 
         if vrs_allele and vrs_seq_loc_ac:

diff --git a/src/variation/translators/genomic_insertion.py b/src/variation/translators/genomic_insertion.py
@@ -104,7 +104,7 @@ async def translate(
                     warnings,
                     alt=classification.inserted_sequence,
                     cds_start=mane.coding_start_site if gene else None,
-                    residue_mode=CoordinateType.INTER_RESIDUE,
+                    coordinate_type=CoordinateType.INTER_RESIDUE,
                     extensions=extensions,
                 )
         else:
@@ -117,7 +117,7 @@ async def translate(
                 AltType.INSERTION,
                 warnings,
                 alt=classification.inserted_sequence,
-                residue_mode=CoordinateType.RESIDUE,
+                coordinate_type=CoordinateType.RESIDUE,
             )
 
         if vrs_allele and vrs_seq_loc_ac:

diff --git a/src/variation/translators/genomic_reference_agree.py b/src/variation/translators/genomic_reference_agree.py
@@ -101,7 +101,7 @@ async def translate(
                     AltType.REFERENCE_AGREE,
                     warnings,
                     cds_start=mane.coding_start_site if gene else None,
-                    residue_mode=CoordinateType.INTER_RESIDUE,
+                    coordinate_type=CoordinateType.INTER_RESIDUE,
                     extensions=extensions,
                 )
         else:
@@ -113,7 +113,7 @@ async def translate(
                 AnnotationLayer.GENOMIC,
                 AltType.REFERENCE_AGREE,
                 warnings,
-                residue_mode=CoordinateType.RESIDUE,
+                coordinate_type=CoordinateType.RESIDUE,
             )
 
         if vrs_allele and vrs_seq_loc_ac:

diff --git a/src/variation/translators/genomic_substitution.py b/src/variation/translators/genomic_substitution.py
@@ -124,7 +124,7 @@ async def translate(
                     errors,
                     alt=classification.alt,
                     cds_start=mane.coding_start_site if gene else None,
-                    residue_mode=CoordinateType.INTER_RESIDUE,
+                    coordinate_type=CoordinateType.INTER_RESIDUE,
                     extensions=extensions,
                 )
         else:
@@ -137,7 +137,7 @@ async def translate(
                 AltType.SUBSTITUTION,
                 errors,
                 alt=classification.alt,
-                residue_mode=CoordinateType.RESIDUE,
+                coordinate_type=CoordinateType.RESIDUE,
             )
 
         if vrs_allele and vrs_seq_loc_ac:

diff --git a/src/variation/translators/translator.py b/src/variation/translators/translator.py
@@ -90,7 +90,7 @@ def is_valid(
         errors: list[str],
         pos2: int | None = None,
         pos3: int | None = None,
-        residue_mode: CoordinateType = CoordinateType.RESIDUE,
+        coordinate_type: CoordinateType = CoordinateType.RESIDUE,
     ) -> None:
         """Check that positions are valid on a gene. Will mutate `errors` if invalid.
 
@@ -101,7 +101,7 @@ def is_valid(
         :param errors: List of errors. Will get mutated if invalid.
         :param pos2: Position 2 (GRCh38 assembly)
         :param pos3: Position 3 (GRCh38 assembly)
-        :param residue_mode: Residue mode for positions
+        :param coordinate_type: Coordinate type for positions
         """
         gene_start = None
         gene_end = None
@@ -119,7 +119,7 @@ def is_valid(
 
         for pos in [pos0, pos1, pos2, pos3]:
             if pos not in {"?", None}:
-                if residue_mode == CoordinateType.RESIDUE:
+                if coordinate_type == CoordinateType.RESIDUE:
                     pos -= 1
 
                 if not (gene_start <= pos <= gene_end):
@@ -133,7 +133,7 @@ def validate_reference_sequence(
         start_pos: int,
         end_pos: int,
         expected_ref: str,
-        residue_mode: CoordinateType = CoordinateType.RESIDUE,
+        coordinate_type: CoordinateType = CoordinateType.RESIDUE,
     ) -> str | None:
         """Validate that expected reference sequence matches actual reference sequence
         This is also in validator, but there is a ticket to have this method be moved
@@ -143,11 +143,11 @@ def validate_reference_sequence(
         :param start_pos: Start position
         :param end_pos: End position
         :param expected_ref: The expected reference sequence (from input string)
-        :param residue_mode: Residue mode for `start_pos` and `end_pos`
+        :param coordinate_type: Coordinate type for `start_pos` and `end_pos`
         :return: Invalid message if invalid. If valid, `None`
         """
         actual_ref, err_msg = self.seqrepo_access.get_reference_sequence(
-            ac, start=start_pos, end=end_pos, coordinate_type=residue_mode
+            ac, start=start_pos, end=end_pos, coordinate_type=coordinate_type
         )
 
         if not err_msg and (actual_ref != expected_ref):
@@ -227,7 +227,7 @@ async def get_p_or_cdna_translation_result(
                     errors,
                     cds_start=cds_start,
                     alt=alt,
-                    residue_mode=CoordinateType.INTER_RESIDUE,
+                    coordinate_type=CoordinateType.INTER_RESIDUE,
                 )
 
         if not vrs_allele:
@@ -241,7 +241,7 @@ async def get_p_or_cdna_translation_result(
                 errors,
                 cds_start=cds_start,
                 alt=alt,
-                residue_mode=CoordinateType.RESIDUE,
+                coordinate_type=CoordinateType.RESIDUE,
             )
 
         if vrs_allele and vrs_seq_loc_ac: