feat!: update tx segment element with updated cool-seq-tool structure…

… changes
cancervariants · Aug 12, 2024 · fa8c93c · fa8c93c
1 parent 8c1fc23
commit fa8c93c
Show file tree

Hide file tree

Showing 9 changed files with 44 additions and 89 deletions.
diff --git a/client/src/components/Pages/Structure/Input/TxSegmentElementInput/TxSegmentElementInput.tsx b/client/src/components/Pages/Structure/Input/TxSegmentElementInput/TxSegmentElementInput.tsx
@@ -267,8 +267,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
           txAc,
           txChrom,
           txStartingGenomic,
-          txEndingGenomic,
-          txStrand
+          txEndingGenomic
         ).then((txSegmentResponse) => {
           if (
             txSegmentResponse.warnings &&

diff --git a/client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx b/client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx
@@ -193,12 +193,12 @@ const GetCoordinates: React.FC = () => {
         exonEndOffset
       ).then((coordsResponse) => handleResponse(coordsResponse));
     } else if (inputType == "genomic_coords_gene") {
-      getExonCoords(chromosome, start, end, strand, gene).then(
-        (coordsResponse) => handleResponse(coordsResponse)
+      getExonCoords(chromosome, start, end, gene).then((coordsResponse) =>
+        handleResponse(coordsResponse)
       );
     } else if (inputType == "genomic_coords_tx") {
-      getExonCoords(chromosome, start, end, strand, "", txAc).then(
-        (coordsResponse) => handleResponse(coordsResponse)
+      getExonCoords(chromosome, start, end, "", txAc).then((coordsResponse) =>
+        handleResponse(coordsResponse)
       );
     }
   };
@@ -250,10 +250,7 @@ const GetCoordinates: React.FC = () => {
   const genomicCoordinateInfo = (
     <>
       <Box display="flex" justifyContent="space-between" width="100%">
-        <ChromosomeField
-          fieldValue={chromosome}
-          errorText={chromosomeText}
-        />
+        <ChromosomeField fieldValue={chromosome} errorText={chromosomeText} />
         <Box mt="18px">
           <Box className={classes.strand} width="125px">
             <StrandSwitch

diff --git a/client/src/services/ResponseModels.ts b/client/src/services/ResponseModels.ts
@@ -630,22 +630,19 @@ export interface ClientStructuralElement {
  */
 export interface CoordsUtilsResponse {
   warnings?: string[] | null;
-  coordinates_data: GenomicData | null;
+  coordinates_data: GenomicTxData | null;
 }
 /**
- * Model containing genomic and transcript exon data.
+ * Represent aligned genomic/transcript exon data
  */
-export interface GenomicData {
+export interface GenomicTxData {
   gene: string;
-  chr: string;
-  start?: number | null;
-  end?: number | null;
-  exon_start?: number | null;
-  exon_start_offset?: number | null;
-  exon_end?: number | null;
-  exon_end_offset?: number | null;
-  transcript: string;
   strand: Strand;
+  tx_pos_range: [unknown, unknown];
+  alt_pos_range: [unknown, unknown];
+  alt_aln_method: string;
+  tx_exon_id: number;
+  alt_exon_id: number;
 }
 /**
  * Response model for demo fusion object retrieval endpoints.
@@ -672,12 +669,13 @@ export interface ExonCoordsRequest {
  */
 export interface FormattedAssayedFusion {
   fusion_type?: AssayedFusion & string;
-  structure:
+  structure: (
     | TranscriptSegmentElement
     | GeneElement
     | TemplatedSequenceElement
     | LinkerElement
-    | UnknownGeneElement;
+    | UnknownGeneElement
+  )[];
   causative_event?: CausativeEvent | null;
   assay?: Assay | null;
   regulatory_element?: RegulatoryElement | null;
@@ -690,12 +688,13 @@ export interface FormattedAssayedFusion {
  */
 export interface FormattedCategoricalFusion {
   fusion_type?: CategoricalFusion & string;
-  structure:
+  structure: (
     | TranscriptSegmentElement
     | GeneElement
     | TemplatedSequenceElement
     | LinkerElement
-    | MultiplePossibleGenesElement;
+    | MultiplePossibleGenesElement
+  )[];
   regulatory_element?: RegulatoryElement | null;
   critical_functional_domains?: FunctionalDomain[] | null;
   reading_frame_preserved?: boolean | null;
@@ -776,9 +775,9 @@ export interface Response {
 export interface SequenceIDResponse {
   warnings?: string[] | null;
   sequence: string;
-  refseq_id: string | null;
-  ga4gh_id: string | null;
-  aliases: string[] | null;
+  refseq_id?: string | null;
+  ga4gh_id?: string | null;
+  aliases?: string[] | null;
 }
 /**
  * Response model for service_info endpoint.

diff --git a/client/src/services/main.tsx b/client/src/services/main.tsx
@@ -163,13 +163,11 @@ export const getTxSegmentElementGCT = async (
   transcript: string,
   chromosome: string,
   start: string,
-  end: string,
-  strand: string
+  end: string
 ): Promise<TxSegmentElementResponse> => {
   const params: Array<string> = [
     `transcript=${transcript}`,
     `chromosome=${chromosome}`,
-    `strand=${strand === "+" ? "%2B" : "-"}`,
   ];
   if (start !== "") params.push(`start=${start}`);
   if (end !== "") params.push(`end=${end}`);
@@ -251,13 +249,11 @@ export const getExonCoords = async (
   chromosome: string,
   start: string,
   end: string,
-  strand: string,
   gene?: string,
   txAc?: string
 ): Promise<CoordsUtilsResponse> => {
   const argsArray = [
     `chromosome=${chromosome}`,
-    `strand=${strand === "+" ? "%2B" : "-"}`,
     gene && gene !== "" ? `gene=${gene}` : "",
     txAc && txAc !== "" ? `transcript=${txAc}` : "",
     start && start !== "" ? `start=${start}` : "",

diff --git a/server/src/curfu/routers/constructors.py b/server/src/curfu/routers/constructors.py
@@ -15,7 +15,7 @@
     TemplatedSequenceElementResponse,
     TxSegmentElementResponse,
 )
-from curfu.sequence_services import InvalidInputError, get_strand
+from curfu.sequence_services import get_strand
 
 router = APIRouter()
 
@@ -93,7 +93,6 @@ async def build_tx_segment_gct(
     chromosome: str,
     start: int | None = Query(None),
     end: int | None = Query(None),
-    strand: str | None = Query(None),
 ) -> TxSegmentElementResponse:
     """Construct Transcript Segment element by providing transcript and genomic
     coordinates (chromosome, start, end positions).
@@ -107,23 +106,12 @@ async def build_tx_segment_gct(
     :return: Pydantic class with TranscriptSegment element if successful, and
         warnings otherwise.
     """
-    if strand is not None:
-        try:
-            strand_validated = get_strand(strand)
-        except InvalidInputError:
-            warning = f"Received invalid strand value: {strand}"
-            logger.warning(warning)
-            return TxSegmentElementResponse(warnings=[warning], element=None)
-    else:
-        strand_validated = strand
     tx_segment, warnings = await request.app.state.fusor.transcript_segment_element(
         tx_to_genomic_coords=False,
         transcript=parse_identifier(transcript),
         chromosome=parse_identifier(chromosome),
-        start=start,
-        end=end,
-        strand=strand_validated,
-        residue_mode="inter-residue",
+        genomic_start=start,
+        genomic_end=end,
     )
     return TxSegmentElementResponse(element=tx_segment, warnings=warnings)
 
@@ -141,7 +129,6 @@ async def build_tx_segment_gcg(
     chromosome: str,
     start: int | None = Query(None),
     end: int | None = Query(None),
-    strand: str | None = Query(None),
 ) -> TxSegmentElementResponse:
     """Construct Transcript Segment element by providing gene and genomic
     coordinates (chromosome, start, end positions).
@@ -155,23 +142,12 @@ async def build_tx_segment_gcg(
     :return: Pydantic class with TranscriptSegment element if successful, and
         warnings otherwise.
     """
-    if strand is not None:
-        try:
-            strand_validated = get_strand(strand)
-        except InvalidInputError:
-            warning = f"Received invalid strand value: {strand}"
-            logger.warning(warning)
-            return TxSegmentElementResponse(warnings=[warning], element=None)
-    else:
-        strand_validated = strand
     tx_segment, warnings = await request.app.state.fusor.transcript_segment_element(
         tx_to_genomic_coords=False,
         gene=gene,
         chromosome=parse_identifier(chromosome),
-        strand=strand_validated,
-        start=start,
-        end=end,
-        residue_mode="inter-residue",
+        genomic_start=start,
+        genomic_end=end,
     )
     return TxSegmentElementResponse(element=tx_segment, warnings=warnings)
 

diff --git a/server/src/curfu/routers/utilities.py b/server/src/curfu/routers/utilities.py
@@ -16,7 +16,6 @@
     RouteTag,
     SequenceIDResponse,
 )
-from curfu.sequence_services import InvalidInputError, get_strand
 
 router = APIRouter()
 
@@ -107,7 +106,7 @@ async def get_genome_coords(
     if exon_end is not None and exon_end_offset is None:
         exon_end_offset = 0
 
-    response = await request.app.state.fusor.cool_seq_tool.ex_g_coords_mapper.transcript_to_genomic_coordinates(
+    response = await request.app.state.fusor.cool_seq_tool.ex_g_coords_mapper.tx_segment_to_genomic(
         transcript=transcript,
         gene=gene,
         exon_start=exon_start,
@@ -134,7 +133,6 @@ async def get_exon_coords(
     chromosome: str,
     start: int | None = None,
     end: int | None = None,
-    strand: str | None = None,
     gene: str | None = None,
     transcript: str | None = None,
 ) -> CoordsUtilsResponse:
@@ -145,7 +143,6 @@ async def get_exon_coords(
     :param chromosome: chromosome, either as a number/X/Y or as an accession
     :param start: genomic start position
     :param end: genomic end position
-    :param strand: strand of genomic position
     :param gene: gene symbol or ID
     :param transcript: transcript accession ID
     :return: response with exon coordinates if successful, or warnings if failed
@@ -155,23 +152,15 @@ async def get_exon_coords(
         warnings.append("Must provide start and/or end coordinates")
     if transcript is None and gene is None:
         warnings.append("Must provide gene and/or transcript")
-    if strand is not None:
-        try:
-            strand_validated = get_strand(strand)
-        except InvalidInputError:
-            warnings.append(f"Received invalid strand value: {strand}")
-    else:
-        strand_validated = strand
     if warnings:
         for warning in warnings:
             logger.warning(warning)
         return CoordsUtilsResponse(warnings=warnings, coordinates_data=None)
 
-    response = await request.app.state.fusor.cool_seq_tool.ex_g_coords_mapper.genomic_to_transcript_exon_coordinates(
-        alt_ac=chromosome,
-        start=start,
-        end=end,
-        strand=strand_validated,
+    response = await request.app.state.fusor.cool_seq_tool.ex_g_coords_mapper.genomic_to_tx_segment(
+        genomic_ac=chromosome,
+        genomic_start=start,
+        genomic_end=end,
         transcript=transcript,
         gene=gene,
     )

diff --git a/server/src/curfu/schemas.py b/server/src/curfu/schemas.py
@@ -3,13 +3,13 @@
 from enum import Enum
 from typing import Literal
 
-from cool_seq_tool.schemas import GenomicData
+from cool_seq_tool.schemas import GenomicTxData
 from fusor.models import (
     Assay,
     AssayedFusion,
-    AssayedFusionElements,
+    AssayedFusionElement,
     CategoricalFusion,
-    CategoricalFusionElements,
+    CategoricalFusionElement,
     CausativeEvent,
     FunctionalDomain,
     Fusion,
@@ -213,7 +213,7 @@ def validate_number(cls, v) -> int:
 class CoordsUtilsResponse(Response):
     """Response model for genomic coordinates retrieval"""
 
-    coordinates_data: GenomicData | None
+    coordinates_data: GenomicTxData | None
 
 
 class SequenceIDResponse(Response):
@@ -301,7 +301,7 @@ class FormattedAssayedFusion(BaseModel):
     """
 
     fusion_type: FusionType.ASSAYED_FUSION = FusionType.ASSAYED_FUSION
-    structure: AssayedFusionElements
+    structure: list[AssayedFusionElement]
     causative_event: CausativeEvent | None = None
     assay: Assay | None = None
     regulatory_element: RegulatoryElement | None = None
@@ -315,7 +315,7 @@ class FormattedCategoricalFusion(BaseModel):
     """
 
     fusion_type: FusionType.CATEGORICAL_FUSION = FusionType.CATEGORICAL_FUSION
-    structure: CategoricalFusionElements
+    structure: list[CategoricalFusionElement]
     regulatory_element: RegulatoryElement | None = None
     critical_functional_domains: list[FunctionalDomain] | None = None
     reading_frame_preserved: bool | None = None

diff --git a/server/tests/integration/test_constructors.py b/server/tests/integration/test_constructors.py
@@ -159,12 +159,12 @@ async def test_build_segment_gct(
     genomic coordinates and transcript.
     """
     await check_response(
-        "/api/construct/structural_element/tx_segment_gct?transcript=NM_152263.4&chromosome=NC_000001.11&start=154171416&end=154171417&strand=-",
+        "/api/construct/structural_element/tx_segment_gct?transcript=NM_152263.4&chromosome=NC_000001.11&start=154171416&end=154171417",
         {"element": tpm3_tx_t_element},
         check_tx_element_response,
     )
     await check_response(
-        "/api/construct/structural_element/tx_segment_gct?transcript=refseq%3ANM_152263.4&chromosome=NC_000001.11&start=154171416&end=154171417&strand=-",
+        "/api/construct/structural_element/tx_segment_gct?transcript=refseq%3ANM_152263.4&chromosome=NC_000001.11&start=154171416&end=154171417",
         {"element": tpm3_tx_t_element},
         check_tx_element_response,
     )
@@ -178,7 +178,7 @@ async def test_build_segment_gcg(
     genomic coordinates and gene name.
     """
     await check_response(
-        "/api/construct/structural_element/tx_segment_gcg?gene=TPM3&chromosome=NC_000001.11&start=154171416&end=154171417&strand=-",
+        "/api/construct/structural_element/tx_segment_gcg?gene=TPM3&chromosome=NC_000001.11&start=154171416&end=154171417",
         {"element": tpm3_tx_g_element},
         check_tx_element_response,
     )

diff --git a/server/tests/integration/test_utilities.py b/server/tests/integration/test_utilities.py
@@ -136,7 +136,7 @@ def check_coords_response(response: dict, expected_response: dict):
         assert response["coordinates_data"] == expected_response["coordinates_data"]
 
     await check_response(
-        "/api/utilities/get_exon?chromosome=1&transcript=NM_152263.3&start=154192135&strand=-",
+        "/api/utilities/get_exon?chromosome=1&transcript=NM_152263.3&start=154192135",
         {
             "coordinates_data": {
                 "gene": "TPM3",
@@ -145,7 +145,6 @@ def check_coords_response(response: dict, expected_response: dict):
                 "exon_start": 1,
                 "exon_start_offset": 1,
                 "transcript": "NM_152263.3",
-                "strand": -1,
             }
         },
         check_coords_response,