From bda641b3c5815b58ddca747047ca18cc99c3db0f Mon Sep 17 00:00:00 2001
From: Katie Stahl <kathryn.stahl@nationwidechildrens.org>
Date: Fri, 27 Sep 2024 11:59:38 -0400
Subject: [PATCH] fix: unable to construct tx segment when genomic coordinate
 between exons (#336)

* fix: unable to construct tx segment when genomic coordinate between exons

* build: update cool-seq-tool and fusor versions

* test: add test case for get exon coordinates where genomic coord occurs between exons

* test: remove test case for now

* Update server/tests/integration/test_utilities.py

Co-authored-by: Kori Kuzma <korikuzma@gmail.com>

* styling

---------

Co-authored-by: Kori Kuzma <korikuzma@gmail.com>
---
 .../TxSegmentElementInput.tsx                 | 25 ++++++++-----------
 requirements.txt                              |  4 +--
 server/pyproject.toml                         |  4 +--
 server/src/curfu/routers/constructors.py      |  1 +
 server/src/curfu/routers/utilities.py         |  1 +
 server/tests/integration/test_utilities.py    | 24 ++++++++++++++++--
 6 files changed, 39 insertions(+), 20 deletions(-)

diff --git a/client/src/components/Pages/Structure/Input/TxSegmentElementInput/TxSegmentElementInput.tsx b/client/src/components/Pages/Structure/Input/TxSegmentElementInput/TxSegmentElementInput.tsx
index 0b531e04..613b854c 100644
--- a/client/src/components/Pages/Structure/Input/TxSegmentElementInput/TxSegmentElementInput.tsx
+++ b/client/src/components/Pages/Structure/Input/TxSegmentElementInput/TxSegmentElementInput.tsx
@@ -43,7 +43,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
 
   const [genomicInputType, setGenomicInputType] =
     useState<GenomicInputType | null>(
-      element.inputGene
+      element.inputGene || element.gene
         ? GenomicInputType.GENE
         : element.inputTx
         ? GenomicInputType.TRANSCRIPT
@@ -55,7 +55,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
   // "Text" variables refer to helper or warning text to set under input fields
   // TODO: this needs refactored so badly
   const [txAc, setTxAc] = useState(element.inputTx || "");
-  const [txAcText, setTxAcText] = useState("");
+  const [txAcHelperText, setTxAcHelperText] = useState("");
 
   const [txGene, setTxGene] = useState(element.inputGene || "");
   const [txGeneText, setTxGeneText] = useState("");
@@ -89,9 +89,6 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
   const [endingExonOffsetText, setEndingExonOffsetText] = useState("");
 
   const [geneTranscripts, setGeneTranscripts] = useState([]);
-  const [selectedTranscript, setSelectedTranscript] = useState(
-    element.inputTx || ""
-  );
 
   const [pendingResponse, setPendingResponse] = useState(false);
 
@@ -100,7 +97,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
 
   const genomicInputComplete =
     genomicInputType === GenomicInputType.GENE
-      ? txGene !== "" && selectedTranscript !== ""
+      ? txGene !== "" && txAc !== ""
       : txAc !== "";
 
   // programming horror
@@ -117,7 +114,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
     inputComplete &&
     hasRequiredEnds &&
     txGeneText === "" &&
-    txAcText === "" &&
+    txAcHelperText === "" &&
     txStartingGenomicText === "" &&
     txEndingGenomicText === "" &&
     startingExonText === "" &&
@@ -172,7 +169,6 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
   };
 
   const handleTranscriptSelect = (event: any) => {
-    setSelectedTranscript(event.target.value as string);
     setTxAc(event.target.value as string);
   };
 
@@ -227,7 +223,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
         getTxSegmentElementGC(
           txGene,
           txChrom,
-          selectedTranscript,
+          txAc,
           txStartingGenomic,
           txEndingGenomic
         ).then((txSegmentResponse) => {
@@ -242,6 +238,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
               inputType: txInputType,
               inputStrand: txStrand,
               inputGene: txGene,
+              inputTx: txAc,
               inputChr: txChrom,
               inputGenomicStart: txStartingGenomic,
               inputGenomicEnd: txEndingGenomic,
@@ -266,7 +263,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
             // transcript invalid
             const txWarning = `Unable to get exons for ${txAc}`;
             if (txSegmentResponse.warnings.includes(txWarning)) {
-              setTxAcText("Unrecognized value");
+              setTxAcHelperText("Unrecognized value");
             }
             // exon(s) invalid
             if (startingExon !== undefined) {
@@ -284,7 +281,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
             setPendingResponse(false);
             setErrors(txSegmentResponse.warnings);
           } else {
-            setTxAcText("");
+            setTxAcHelperText("");
             setStartingExonText("");
             setEndingExonText("");
             setErrors([]);
@@ -394,7 +391,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
       <TranscriptField
         fieldValue={txAc}
         valueSetter={setTxAc}
-        errorText={txAcText}
+        errorText={txAcHelperText}
         keyHandler={handleEnterKey}
       />
     </Box>
@@ -436,7 +433,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
                     setChromosome={setTxChrom}
                     setStrand={setTxStrand}
                     setTranscripts={setGeneTranscripts}
-                    setDefaultTranscript={setSelectedTranscript}
+                    setDefaultTranscript={setTxAc}
                   />
                   <FormControl variant="standard">
                     <InputLabel id="transcript-select-label">
@@ -445,7 +442,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
                     <Select
                       labelId="transcript-select-label"
                       id="transcript-select"
-                      value={selectedTranscript}
+                      value={txAc}
                       label="Transcript"
                       onChange={handleTranscriptSelect}
                       placeholder="Transcript"
diff --git a/requirements.txt b/requirements.txt
index 310c4d88..7ac3ee85 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -18,14 +18,14 @@ charset-normalizer==3.3.2
 click==8.1.7
 coloredlogs==15.0.1
 configparser==7.1.0
-cool_seq_tool==0.7.0
+cool_seq_tool==0.7.1
 coverage==7.6.1
 decorator==5.1.1
 distlib==0.3.8
 executing==2.0.1
 fastapi==0.112.1
 filelock==3.15.4
-fusor==0.4.3
+fusor==0.4.4
 ga4gh.vrs==2.0.0a10
 gene-normalizer==0.4.0
 h11==0.14.0
diff --git a/server/pyproject.toml b/server/pyproject.toml
index 60b7021b..b81e1a00 100644
--- a/server/pyproject.toml
+++ b/server/pyproject.toml
@@ -28,8 +28,8 @@ dependencies = [
     "click",
     "boto3",
     "botocore",
-    "fusor ~= 0.4.3",
-    "cool-seq-tool ~= 0.7.0",
+    "fusor ~= 0.4.4",
+    "cool-seq-tool ~= 0.7.1",
     "pydantic == 2.4.2", # validation errors with more recent versions, so don't remove this specific pin
     "gene-normalizer ~= 0.4.0",
 ]
diff --git a/server/src/curfu/routers/constructors.py b/server/src/curfu/routers/constructors.py
index d602dd63..55260dc1 100644
--- a/server/src/curfu/routers/constructors.py
+++ b/server/src/curfu/routers/constructors.py
@@ -115,6 +115,7 @@ async def build_tx_segment_gc(
         seg_start_genomic=start,
         seg_end_genomic=end,
         transcript=transcript,
+        get_nearest_transcript_junction=True,
     )
     return TxSegmentElementResponse(element=tx_segment, warnings=warnings)
 
diff --git a/server/src/curfu/routers/utilities.py b/server/src/curfu/routers/utilities.py
index 0f08d955..ef8fdfa7 100644
--- a/server/src/curfu/routers/utilities.py
+++ b/server/src/curfu/routers/utilities.py
@@ -163,6 +163,7 @@ async def get_exon_coords(
         seg_end_genomic=end,
         transcript=transcript,
         gene=gene,
+        get_nearest_transcript_junction=True,
     )
     warnings = response.errors
     if warnings:
diff --git a/server/tests/integration/test_utilities.py b/server/tests/integration/test_utilities.py
index c027335b..085d024d 100644
--- a/server/tests/integration/test_utilities.py
+++ b/server/tests/integration/test_utilities.py
@@ -213,9 +213,29 @@ def check_coords_response(response: dict, expected_response: dict):
         check_coords_response,
     )
 
+    # check correct response for genomic coordinate that occurs between exons (should get nearest junction)
     await check_response(
-        "/api/utilities/get_exon?chromosome=NC_000001.11&start=154192131&gene=TPM3",
-        {"warnings": ["Must find exactly one row for genomic data, but found: 0"]},
+        "/api/utilities/get_exon?chromosome=NC_000001.11&end=154191900&transcript=NM_152263.3",
+        {
+            "coordinates_data": {
+                "gene": "TPM3",
+                "genomic_ac": "NC_000001.11",
+                "tx_ac": "NM_152263.3",
+                "seg_end": {
+                    "exon_ord": 0,
+                    "offset": 1,
+                    "genomic_location": {
+                        "type": "SequenceLocation",
+                        "sequenceReference": {
+                            "type": "SequenceReference",
+                            "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
+                        },
+                        "start": 154191900,
+                    },
+                },
+                "errors": [],
+            }
+        },
         check_coords_response,
     )