reverting messed up commits

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

@@ -11,10 +11,7 @@ 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";
@@ -101,10 +98,6 @@ 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);
@@ -132,7 +125,6 @@ const GetCoordinates: React.FC = () => {
     !exonEndText;
 
   useEffect(() => {
-    console.log(inputComplete)
     if (inputComplete) {
       fetchResults();
     }

client/src/components/main/shared/TranscriptField/TranscriptField.tsx

@@ -0,0 +1,51 @@
+import { makeStyles, TextField, Typography } from "@material-ui/core";
+import React, { KeyboardEventHandler } from "react";
+import HelpTooltip from "../HelpTooltip/HelpTooltip";
+
+interface Props {
+  fieldValue: string;
+  valueSetter: CallableFunction;
+  errorText: string;
+  keyHandler?: KeyboardEventHandler<HTMLDivElement> | undefined;
+  width?: number | undefined;
+}
+
+const TranscriptField: React.FC<Props> = ({
+  fieldValue,
+  valueSetter,
+  errorText,
+  keyHandler,
+  width,
+}) => {
+  const useStyles = makeStyles(() => ({
+    textField: {
+      width: width ? width : 125,
+    },
+  }));
+  const classes = useStyles();
+
+  return (
+    <HelpTooltip
+      placement="bottom"
+      title={
+        <Typography>
+          RefSeq transcript identifier, e.g.{" "}
+          <Typography variant="overline">NM_002529.3</Typography>.
+        </Typography>
+      }
+    >
+      <TextField
+        margin="dense"
+        value={fieldValue}
+        onChange={(event) => valueSetter(event.target.value)}
+        error={errorText != ""}
+        onKeyDown={keyHandler}
+        label="Transcript"
+        helperText={errorText != "" ? errorText : null}
+        className={classes.textField}
+      />
+    </HelpTooltip>
+  );
+};
+
+export default TranscriptField;

server/curfu/routers/utilities.py

@@ -68,40 +68,17 @@ async def get_transcripts_for_gene(request: Request, gene: str) -> Dict:
     :param str gene: gene term provided by user
     :return: Dict containing transcripts if lookup succeeds, or warnings upon failure
     """
-<<<<<<< HEAD
-<<<<<<< HEAD
     normalized = request.app.state.fusor.gene_normalizer.normalize(gene)
     symbol = normalized.gene_descriptor.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"))
-=======
-    transcripts = await request.app.state.fusor.cool_seq_tool.uta_db.get_transcripts(gene)
->>>>>>> c11b094 (feat!: adding transcript lookup for genes)
-=======
-    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",
@@ -311,13 +288,9 @@ 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

@@ -1,7 +1,6 @@
 """Provide schemas for FastAPI responses."""
 from enum import Enum
 from typing import Dict, List, Literal, Optional, Tuple, Union
-import polars as pl
 
 from cool_seq_tool.schemas import GenomicData
 from fusor.models import (
@@ -253,27 +252,12 @@ 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
-=======
-    transcripts: Optional[pl.DataFrame]
->>>>>>> c11b094 (feat!: adding transcript lookup for genes)
-=======
-    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):