add transcript

cancervariants · Jul 10, 2024 · 3bdd399 · 3bdd399
1 parent b5a2b7b
commit 3bdd399
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Showing 2 changed files with 5 additions and 70 deletions.
diff --git a/client/src/services/main.tsx b/client/src/services/main.tsx
@@ -145,36 +145,17 @@ export const getTxSegmentElementECT = async (
   return responseJson;
 };
 
-export const getTxSegmentElementGCT = async (
-  transcript: string,
-  chromosome: string,
-  start: string,
-  end: string,
-  strand: 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=${end}`);
-  const url =
-    "api/construct/structural_element/tx_segment_gct?" + params.join("&");
-  const response = await fetch(url);
-  const responseJson = await response.json();
-  return responseJson;
-};
-
 export const getTxSegmentElementGCG = async (
   gene: string,
+  transcript: string,
   chromosome: string,
   start: string,
   end: string,
   strand: string
 ): Promise<TxSegmentElementResponse> => {
   const params: Array<string> = [
     `gene=${gene}`,
+    `transcript=${transcript}`,
     `chromosome=${chromosome}`,
     `strand=${strand === "+" ? "%2B" : "-"}`,
   ];

diff --git a/server/curfu/routers/constructors.py b/server/curfu/routers/constructors.py
@@ -82,55 +82,6 @@ async def build_tx_segment_ect(
     )
     return TxSegmentElementResponse(element=tx_segment, warnings=warnings)
 
-
-@router.get(
-    "/api/construct/structural_element/tx_segment_gct",
-    operation_id="buildTranscriptSegmentElementGCT",
-    response_model=TxSegmentElementResponse,
-    response_model_exclude_none=True,
-    tags=[RouteTag.CONSTRUCTORS],
-)
-async def build_tx_segment_gct(
-    request: Request,
-    transcript: str,
-    chromosome: str,
-    start: Optional[int] = Query(None),
-    end: Optional[int] = Query(None),
-    strand: Optional[str] = Query(None),
-) -> TxSegmentElementResponse:
-    """Construct Transcript Segment element by providing transcript and genomic
-    coordinates (chromosome, start, end positions).
-    \f
-    :param request: the HTTP request context, supplied by FastAPI. Use to access
-        FUSOR and UTA-associated tools.
-    :param transcript: transcript accession identifier
-    :param chromosome: chromosome (TODO how to identify?)
-    :param start: starting position (TODO assume residue-based?)
-    :param end: ending position
-    :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",
-    )
-    return TxSegmentElementResponse(element=tx_segment, warnings=warnings)
-
-
 @router.get(
     "/api/construct/structural_element/tx_segment_gcg",
     operation_id="buildTranscriptSegmentElementGCG",
@@ -141,6 +92,7 @@ async def build_tx_segment_gct(
 async def build_tx_segment_gcg(
     request: Request,
     gene: str,
+    transcript: str,
     chromosome: str,
     start: Optional[int] = Query(None),
     end: Optional[int] = Query(None),
@@ -152,6 +104,7 @@ async def build_tx_segment_gcg(
     :param request: the HTTP request context, supplied by FastAPI. Use to access
         FUSOR and UTA-associated tools.
     :param gene: gene (TODO how to identify?)
+    :param transcript: transcript accession identifier
     :param chromosome: chromosome (TODO how to identify?)
     :param start: starting position (TODO assume residue-based?)
     :param end: ending position
@@ -170,6 +123,7 @@ async def build_tx_segment_gcg(
     tx_segment, warnings = await request.app.state.fusor.transcript_segment_element(
         tx_to_genomic_coords=False,
         gene=gene,
+        transcript=parse_identifier(transcript),
         chromosome=parse_identifier(chromosome),
         strand=strand_validated,
         start=start,