feat: add transcript lookup for genes

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

@@ -11,7 +11,10 @@ import {
   Link,
   InputLabel,
   FormControl,
+<<<<<<< HEAD
   CircularProgress,
+=======
+>>>>>>> 005823a (feat: add transcript lookup for genes)
 } from "@material-ui/core";
 import React, { useEffect, useState } from "react";
 import { GeneAutocomplete } from "../../main/shared/GeneAutocomplete/GeneAutocomplete";
@@ -98,6 +101,10 @@ const GetCoordinates: React.FC = () => {
   const [exonEndOffset, setExonEndOffset] = useState<string>("");
 
   const [geneTranscripts, setGeneTranscripts] = useState([]);
+<<<<<<< HEAD
+=======
+  const [geneTxWarnings, setGeneTxWarnings] = useState<string[]>();
+>>>>>>> 005823a (feat: add transcript lookup for genes)
   const [selectedTranscript, setSelectedTranscript] = useState("");
 
   const [results, setResults] = useState<GenomicData | null>(null);
@@ -125,6 +132,7 @@ const GetCoordinates: React.FC = () => {
     !exonEndText;
 
   useEffect(() => {
+    console.log(inputComplete)
     if (inputComplete) {
       fetchResults();
     }

server/curfu/routers/utilities.py

@@ -82,18 +82,26 @@ async def get_transcripts_for_gene(request: Request, gene: str) -> Dict:
 =======
     normalized = request.app.state.fusor.gene_normalizer.normalize(gene)
     symbol = normalized.gene_descriptor.label
+<<<<<<< HEAD
     print(symbol)
     print(request.app.state.fusor.cool_seq_tool.uta_db)
     transcripts = await request.app.state.fusor.cool_seq_tool.uta_db.get_transcripts(symbol)
     transcripts_dict = transcripts.to_dict()
     tx_for_gene = transcripts_dict["tx_ac"]
     print(transcripts.glimpse())
 >>>>>>> 047cc77 (feat: add transcript lookup for genes)
+=======
+    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"))
+>>>>>>> 005823a (feat: add transcript lookup for genes)
     if transcripts.is_empty():
         return {"warnings": [f"No matching transcripts: {gene}"], "transcripts": []}
     else:
         return {"transcripts": tx_for_gene}
+<<<<<<< HEAD
 
+=======
+>>>>>>> 005823a (feat: add transcript lookup for genes)
 
 @router.get(
     "/api/utilities/get_genomic",
@@ -303,9 +311,13 @@ async def get_sequence(
     """
     _, path = tempfile.mkstemp(suffix=".fasta")
     try:
+<<<<<<< HEAD
         request.app.state.fusor.cool_seq_tool.seqrepo_access.get_fasta_file(
             sequence_id, Path(path)
         )
+=======
+        request.app.state.fusor.cool_seq_tool.seqrepo_access.get_fasta_file(sequence_id, Path(path))
+>>>>>>> 005823a (feat: add transcript lookup for genes)
     except KeyError:
         resp = request.app.state.fusor.cool_seq_tool.seqrepo_access.translate_identifier(  # noqa: E501
             sequence_id, "refseq"

server/curfu/schemas.py

@@ -253,11 +253,15 @@ class GetTranscriptsResponse(Response):
     """Response model for MANE transcript retrieval endpoint."""
 
     transcripts: Optional[List[ManeGeneTranscript]] = None
+<<<<<<< HEAD
 
+=======
+>>>>>>> 005823a (feat: add transcript lookup for genes)
 
 class GetGeneTranscriptsResponse(Response):
     """Response model for MANE transcript retrieval endpoint."""
 
+<<<<<<< HEAD
 <<<<<<< HEAD
 <<<<<<< HEAD
     transcripts: Optional[List[str]] = None
@@ -267,6 +271,9 @@ class GetGeneTranscriptsResponse(Response):
 =======
     transcripts: Optional[Dict]
 >>>>>>> 047cc77 (feat: add transcript lookup for genes)
+=======
+    transcripts: Optional[List[str]] = None
+>>>>>>> 005823a (feat: add transcript lookup for genes)
 
 
 class ServiceInfoResponse(Response):