merge recent changes + fixes

client/src/components/Pages/Structure/Input/TxSegmentElementInput/TxSegmentElementInput.tsx

@@ -6,8 +6,8 @@ import {
 } from "../../../../../services/ResponseModels";
 import React, { useEffect, useState, KeyboardEvent, useContext } from "react";
 import {
-  getTxSegmentElementECT,
-  getTxSegmentElementGCG,
+  getTxSegmentElementEC,
+  getTxSegmentElementGC,
   getTxSegmentNomenclature,
 } from "../../../../../services/main";
 import { GeneAutocomplete } from "../../../../main/shared/GeneAutocomplete/GeneAutocomplete";
@@ -26,8 +26,8 @@ interface TxSegmentElementInputProps extends StructuralElementInputProps {
 
 export enum InputType {
   default = "default",
-  gcg = "genomic_coords",
-  ect = "exon_coords_tx",
+  gc = "genomic_coords",
+  ec = "exon_coords",
 }
 
 const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
@@ -56,7 +56,6 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
   );
 
   const [txChrom, setTxChrom] = useState(element.inputChr || "");
-  const [txChromText, setTxChromText] = useState("");
 
   const [txStartingGenomic, setTxStartingGenomic] = useState(
     element.inputGenomicStart || ""
@@ -100,12 +99,12 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
 
   // programming horror
   const inputComplete =
-    (txInputType === InputType.gcg &&
+    (txInputType === InputType.gc &&
       txGene !== "" &&
       txChrom !== "" &&
       selectedTranscript !== "" &&
       (txStartingGenomic !== "" || txEndingGenomic !== "")) ||
-    (txInputType === InputType.ect &&
+    (txInputType === InputType.ec &&
       txAc !== "" &&
       (startingExon !== "" || endingExon !== ""));
 
@@ -212,16 +211,18 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
     setEndingExonOffsetText("");
   };
 
+  console.log(pendingResponse);
+
   /**
    * Request construction of tx segment element from server and handle response
    */
   const buildTranscriptSegmentElement = () => {
     setPendingResponse(true);
     // fire constructor request
     switch (txInputType) {
-      case InputType.gcg:
+      case InputType.gc:
         clearGenomicCoordWarnings();
-        getTxSegmentElementGCG(
+        getTxSegmentElementGC(
           txGene,
           txChrom,
           selectedTranscript,
@@ -247,8 +248,8 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
           }
         });
         break;
-      case InputType.ect:
-        getTxSegmentElementECT(
+      case InputType.ec:
+        getTxSegmentElementEC(
           txAc,
           startingExon as string,
           endingExon as string,
@@ -407,7 +408,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
 
   const renderTxOptions = () => {
     switch (txInputType) {
-      case InputType.gcg:
+      case InputType.gc:
         return (
           <Box>
             <Box className="mid-inputs" minWidth="325px">
@@ -444,7 +445,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
             {genomicCoordinateInfo}
           </Box>
         );
-      case InputType.ect:
+      case InputType.ec:
         return (
           <Box>
             {txInputField}
@@ -583,7 +584,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
    */
   const selectInputType = (selection: InputType) => {
     if (txInputType !== "default") {
-      if (selection === "exon_coords_tx") {
+      if (selection === "exon_coords") {
         clearGenomicCoordWarnings();
       } else {
         clearExonWarnings();
@@ -624,7 +625,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
                 Select input data
               </MenuItem>
               <MenuItem value="genomic_coords">Genomic coordinates</MenuItem>
-              <MenuItem value="exon_coords_tx">
+              <MenuItem value="exon_coords">
                 Exon coordinates, transcript
               </MenuItem>
             </Select>

client/src/components/Utilities/GetCoordinates/GetCoordinates.tsx

@@ -109,7 +109,7 @@ const GetCoordinates: React.FC = () => {
       gene !== "" &&
       chromosome !== "" &&
       (start !== "" || end !== "")) ||
-    (inputType === "exon_coords_tx" &&
+    (inputType === "exon_coords" &&
       txAc !== "" &&
       (exonStart !== "" || exonEnd !== ""));
 
@@ -191,7 +191,7 @@ const GetCoordinates: React.FC = () => {
 
   const fetchResults = () => {
     setIsLoading(true);
-    if (inputType == "exon_coords_tx") {
+    if (inputType == "exon_coords") {
       getGenomicCoords(
         gene,
         txAc,
@@ -347,7 +347,7 @@ const GetCoordinates: React.FC = () => {
             </Box>
           </>
         );
-      case "exon_coords_tx":
+      case "exon_coords":
         return (
           <>
             <Box>
@@ -410,7 +410,7 @@ const GetCoordinates: React.FC = () => {
               Select input data
             </MenuItem>
             <MenuItem value="genomic_coords">Genomic coordinates</MenuItem>
-            <MenuItem value="exon_coords_tx">Exon coordinates</MenuItem>
+            <MenuItem value="exon_coords">Exon coordinates</MenuItem>
           </Select>
         </Box>
       </Box>

client/src/services/ResponseModels.ts

@@ -530,7 +530,7 @@ export interface ClientTranscriptSegmentElement {
   gene: Gene;
   elementGenomicStart?: SequenceLocation | null;
   elementGenomicEnd?: SequenceLocation | null;
-  inputType: "genomic_coords_gene" | "genomic_coords_tx" | "exon_coords_tx";
+  inputType: "genomic_coords_gene" | "genomic_coords_tx" | "exon_coords";
   inputTx?: string | null;
   inputStrand?: Strand | null;
   inputGene?: string | null;

client/src/services/main.tsx

@@ -130,7 +130,7 @@ export const getTemplatedSequenceElement = async (
   return responseJson;
 };
 
-export const getTxSegmentElementECT = async (
+export const getTxSegmentElementEC = async (
   transcript: string,
   exonStart: string,
   exonEnd: string,
@@ -153,13 +153,13 @@ export const getTxSegmentElementECT = async (
     params.push(`exon_end_offset=${exonEndOffset}`);
   }
   const url =
-    "api/construct/structural_element/tx_segment_ect?" + params.join("&");
+    "api/construct/structural_element/tx_segment_ec?" + params.join("&");
   const response = await fetch(url);
   const responseJson = await response.json();
   return responseJson;
 };
 
-export const getTxSegmentElementGCG = async (
+export const getTxSegmentElementGC = async (
   gene: string,
   chromosome: string,
   transcript: string,
@@ -176,7 +176,7 @@ export const getTxSegmentElementGCG = async (
   if (start !== "") params.push(`start=${start}`);
   if (end !== "") params.push(`end=${end}`);
   const url =
-    "api/construct/structural_element/tx_segment_gcg?" + params.join("&");
+    "api/construct/structural_element/tx_segment_gc?" + params.join("&");
   const response = await fetch(url);
   const responseJson = await response.json();
   return responseJson;

server/src/curfu/routers/constructors.py

@@ -43,13 +43,13 @@ def build_gene_element(request: Request, term: str = Query("")) -> GeneElementRe
 
 
 @router.get(
-    "/api/construct/structural_element/tx_segment_ect",
+    "/api/construct/structural_element/tx_segment_ec",
     operation_id="buildTranscriptSegmentElementECT",
     response_model=TxSegmentElementResponse,
     response_model_exclude_none=True,
     tags=[RouteTag.CONSTRUCTORS],
 )
-async def build_tx_segment_ect(
+async def build_tx_segment_ec(
     request: Request,
     transcript: str,
     exon_start: int | None = Query(None),
@@ -81,21 +81,21 @@ async def build_tx_segment_ect(
 
 
 @router.get(
-    "/api/construct/structural_element/tx_segment_gcg",
-    operation_id="buildTranscriptSegmentElementGCG",
+    "/api/construct/structural_element/tx_segment_gc",
+    operation_id="buildTranscriptSegmentElementGC",
     response_model=TxSegmentElementResponse,
     response_model_exclude_none=True,
     tags=[RouteTag.CONSTRUCTORS],
 )
-async def build_tx_segment_gcg(
+async def build_tx_segment_gc(
     request: Request,
     gene: str,
     chromosome: str,
     transcript: str,
     start: int | None = Query(None),
     end: int | None = Query(None),
 ) -> TxSegmentElementResponse:
-    """Construct Transcript Segment element by providing gene and genomic
+    """Construct Transcript Segment element by providing gene and/or transcript and genomic
     coordinates (chromosome, start, end positions).
     \f
     :param request: the HTTP request context, supplied by FastAPI. Use to access

server/src/curfu/routers/demo.py

@@ -100,7 +100,7 @@ def clientify_structural_element(
     if element.type == StructuralElementType.TRANSCRIPT_SEGMENT_ELEMENT:
         nm = tx_segment_nomenclature(element)
         element_args["nomenclature"] = nm
-        element_args["inputType"] = "exon_coords_tx"
+        element_args["inputType"] = "exon_coords"
         element_args["inputTx"] = element.transcript.split(":")[1]
         element_args["inputExonStart"] = str(element.exonStart)
         element_args["inputExonStartOffset"] = str(element.exonStartOffset)

server/src/curfu/routers/lookup.py

@@ -3,7 +3,12 @@
 from fastapi import APIRouter, Query, Request
 
 from curfu import LookupServiceError
-from curfu.schemas import NormalizeGeneResponse, ResponseDict, RouteTag
+from curfu.schemas import (
+    GetGeneTranscriptsResponse,
+    NormalizeGeneResponse,
+    ResponseDict,
+    RouteTag,
+)
 
 router = APIRouter()
 
@@ -37,3 +42,28 @@ def normalize_gene(request: Request, term: str = Query("")) -> NormalizeGeneResp
         response["symbol"] = None
         response["cased"] = None
     return NormalizeGeneResponse(**response)
+
+
+@router.get(
+    "/api/utilities/get_transcripts_for_gene",
+    operation_id="getTranscriptsFromGene",
+    response_model=GetGeneTranscriptsResponse,
+    response_model_exclude_none=True,
+)
+async def get_transcripts_for_gene(request: Request, gene: str) -> dict:
+    """Get all transcripts for gene term.
+    \f
+    :param Request request: the HTTP request context, supplied by FastAPI. Use to access
+        FUSOR and UTA-associated tools.
+    :param str gene: gene term provided by user
+    :return: Dict containing transcripts if lookup succeeds, or warnings upon failure
+    """
+    normalized = request.app.state.fusor.gene_normalizer.normalize(gene)
+    symbol = normalized.gene.label
+    transcripts = await request.app.state.fusor.cool_seq_tool.uta_db.get_transcripts(
+        gene=symbol
+    )
+    tx_for_gene = list(transcripts.rows_by_key("tx_ac"))
+    if transcripts.is_empty():
+        return {"warnings": [f"No matching transcripts: {gene}"], "transcripts": []}
+    return {"transcripts": tx_for_gene}

server/src/curfu/routers/utilities.py

@@ -12,7 +12,6 @@
 from curfu import logger
 from curfu.schemas import (
     CoordsUtilsResponse,
-    GetGeneTranscriptsResponse,
     GetTranscriptsResponse,
     RouteTag,
     SequenceIDResponse,
@@ -50,31 +49,6 @@ def get_mane_transcripts(request: Request, term: str) -> dict:
     return {"transcripts": transcripts}
 
 
-@router.get(
-    "/api/utilities/get_transcripts_for_gene",
-    operation_id="getTranscriptsFromGene",
-    response_model=GetGeneTranscriptsResponse,
-    response_model_exclude_none=True,
-)
-async def get_transcripts_for_gene(request: Request, gene: str) -> dict:
-    """Get all transcripts for gene term.
-    \f
-    :param Request request: the HTTP request context, supplied by FastAPI. Use to access
-        FUSOR and UTA-associated tools.
-    :param str gene: gene term provided by user
-    :return: Dict containing transcripts if lookup succeeds, or warnings upon failure
-    """
-    normalized = request.app.state.fusor.gene_normalizer.normalize(gene)
-    symbol = normalized.gene.label
-    transcripts = await request.app.state.fusor.cool_seq_tool.uta_db.get_transcripts(
-        gene=symbol
-    )
-    tx_for_gene = list(transcripts.rows_by_key("tx_ac"))
-    if transcripts.is_empty():
-        return {"warnings": [f"No matching transcripts: {gene}"], "transcripts": []}
-    return {"transcripts": tx_for_gene}
-
-
 @router.get(
     "/api/utilities/get_genomic",
     operation_id="getGenomicCoords",

server/src/curfu/schemas.py

@@ -54,7 +54,7 @@ class ClientTranscriptSegmentElement(TranscriptSegmentElement, ClientStructuralE
     inputType: (
         Literal["genomic_coords_gene"]
         | Literal["genomic_coords_tx"]
-        | Literal["exon_coords_tx"]
+        | Literal["exon_coords"]
     )
     inputTx: str | None = None
     inputStrand: Strand | None = None

server/tests/integration/test_constructors.py

@@ -124,28 +124,28 @@ def check_temp_seq_response(response: dict, expected_response: dict):
 
 
 @pytest.mark.asyncio()
-async def test_build_tx_segment_ect(
+async def test_build_tx_segment_ec(
     check_response, check_tx_element_response, ntrk1_tx_element_start
 ):
     """Test correct functioning of transcript segment element construction using exon
     coordinates and transcript.
     """
     await check_response(
-        "/api/construct/structural_element/tx_segment_ect?transcript=NM_002529.3&exon_start=2&exon_start_offset=1",
+        "/api/construct/structural_element/tx_segment_ec?transcript=NM_002529.3&exon_start=2&exon_start_offset=1",
         {"element": ntrk1_tx_element_start},
         check_tx_element_response,
     )
 
     # test require exonStart or exonEnd
     await check_response(
-        "/api/construct/structural_element/tx_segment_ect?transcript=NM_002529.3",
+        "/api/construct/structural_element/tx_segment_ec?transcript=NM_002529.3",
         {"warnings": ["Must provide either `exon_start` or `exon_end`"]},
         check_tx_element_response,
     )
 
     # test handle invalid transcript
     await check_response(
-        "/api/construct/structural_element/tx_segment_ect?transcript=NM_0012529.3&exon_start=3",
+        "/api/construct/structural_element/tx_segment_ec?transcript=NM_0012529.3&exon_start=3",
         {"warnings": ["Unable to get exons for NM_0012529.3"]},
         check_tx_element_response,
     )
@@ -171,14 +171,14 @@ async def test_build_segment_gct(
 
 
 @pytest.mark.asyncio()
-async def test_build_segment_gcg(
+async def test_build_segment_gc(
     check_response, check_tx_element_response, tpm3_tx_g_element
 ):
     """Test correct functioning of transcript segment element construction using
     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",
+        "/api/construct/structural_element/tx_segment_gc?gene=TPM3&chromosome=NC_000001.11&start=154171416&end=154171417",
         {"element": tpm3_tx_g_element},
         check_tx_element_response,
     )