From 0a22cb1049e2e9492091b319c7bca3aef31db21b Mon Sep 17 00:00:00 2001
From: Katie Stahl <kathryn.stahl@nationwidechildrens.org>
Date: Wed, 25 Sep 2024 14:51:05 -0400
Subject: [PATCH 1/6] fix: unable to construct tx segment when genomic
 coordinate between exons

---
 .../TxSegmentElementInput.tsx                 | 26 ++++++++-----------
 server/src/curfu/routers/constructors.py      |  1 +
 server/src/curfu/routers/utilities.py         |  1 +
 3 files changed, 13 insertions(+), 15 deletions(-)

diff --git a/client/src/components/Pages/Structure/Input/TxSegmentElementInput/TxSegmentElementInput.tsx b/client/src/components/Pages/Structure/Input/TxSegmentElementInput/TxSegmentElementInput.tsx
index e83895e1..220b4ba1 100644
--- a/client/src/components/Pages/Structure/Input/TxSegmentElementInput/TxSegmentElementInput.tsx
+++ b/client/src/components/Pages/Structure/Input/TxSegmentElementInput/TxSegmentElementInput.tsx
@@ -33,7 +33,6 @@ interface TxSegmentElementInputProps extends StructuralElementInputProps {
 
 const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
   element,
-  index,
   handleSave,
   handleDelete,
   icon,
@@ -44,7 +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
@@ -54,7 +53,7 @@ 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("");
@@ -88,9 +87,6 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
   const [endingExonOffsetText, setEndingExonOffsetText] = useState("");
 
   const [geneTranscripts, setGeneTranscripts] = useState([]);
-  const [selectedTranscript, setSelectedTranscript] = useState(
-    element.inputTx || ""
-  );
 
   const [pendingResponse, setPendingResponse] = useState(false);
 
@@ -99,7 +95,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
 
   const genomicInputComplete =
     genomicInputType === GenomicInputType.GENE
-      ? txGene !== "" && selectedTranscript !== ""
+      ? txGene !== "" && txAc !== ""
       : txAc !== "";
 
   // programming horror
@@ -116,7 +112,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
     inputComplete &&
     hasRequiredEnds &&
     txGeneText === "" &&
-    txAcText === "" &&
+    txAcHelperText === "" &&
     txStartingGenomicText === "" &&
     txEndingGenomicText === "" &&
     startingExonText === "" &&
@@ -171,7 +167,6 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
   };
 
   const handleTranscriptSelect = (event: any) => {
-    setSelectedTranscript(event.target.value as string);
     setTxAc(event.target.value as string);
   };
 
@@ -226,7 +221,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
         getTxSegmentElementGC(
           txGene,
           txChrom,
-          selectedTranscript,
+          txAc,
           txStartingGenomic,
           txEndingGenomic
         ).then((txSegmentResponse) => {
@@ -240,6 +235,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
               inputType: txInputType,
               inputStrand: txStrand,
               inputGene: txGene,
+              inputTx: txAc,
               inputChr: txChrom,
               inputGenomicStart: txStartingGenomic,
               inputGenomicEnd: txEndingGenomic,
@@ -263,7 +259,7 @@ 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) {
@@ -279,7 +275,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
               }
             }
           } else {
-            setTxAcText("");
+            setTxAcHelperText("");
             setStartingExonText("");
             setEndingExonText("");
             const inputParams = {
@@ -388,7 +384,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
       <TranscriptField
         fieldValue={txAc}
         valueSetter={setTxAc}
-        errorText={txAcText}
+        errorText={txAcHelperText}
         keyHandler={handleEnterKey}
       />
     </Box>
@@ -430,7 +426,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
                     setChromosome={setTxChrom}
                     setStrand={setTxStrand}
                     setTranscripts={setGeneTranscripts}
-                    setDefaultTranscript={setSelectedTranscript}
+                    setDefaultTranscript={setTxAc}
                   />
                   <FormControl variant="standard">
                     <InputLabel id="transcript-select-label">
@@ -439,7 +435,7 @@ 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/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:

From a96b423eba0ae3b405a797b87cd12259c891e4ba Mon Sep 17 00:00:00 2001
From: Katie Stahl <kathryn.stahl@nationwidechildrens.org>
Date: Thu, 26 Sep 2024 10:59:53 -0400
Subject: [PATCH 2/6] build: update cool-seq-tool and fusor versions

---
 requirements.txt      | 32 ++++++++++++++++++++++++++++----
 server/pyproject.toml |  4 ++--
 2 files changed, 30 insertions(+), 6 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 0c7c0fdf..7ac3ee85 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -8,46 +8,69 @@ asyncpg==0.29.0
 attrs==24.2.0
 biocommons.seqrepo==0.6.9
 bioutils==0.5.8.post1
-boto3==1.35.4
-botocore==1.35.4
+black==24.8.0
+boto3==1.35.3
+botocore==1.35.3
 canonicaljson==2.0.0
 certifi==2024.7.4
+cfgv==3.4.0
 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
-fusor==0.4.2
+filelock==3.15.4
+fusor==0.4.4
 ga4gh.vrs==2.0.0a10
 gene-normalizer==0.4.0
 h11==0.14.0
 hgvs==1.5.4
+httpcore==1.0.5
+httpx==0.27.0
 humanfriendly==10.0
+identify==2.6.0
 idna==3.7
 importlib_metadata==8.4.0
+iniconfig==2.0.0
 ipython==8.26.0
 jedi==0.19.1
 Jinja2==3.1.4
 jmespath==1.0.1
 MarkupSafe==2.1.5
 matplotlib-inline==0.1.7
+mypy-extensions==1.0.0
+nodeenv==1.9.1
+packaging==24.1
 Parsley==1.3
 parso==0.8.4
+pathspec==0.12.1
 pexpect==4.9.0
+platformdirs==4.2.2
+pluggy==1.5.0
 polars==1.5.0
+pre-commit==3.8.0
 prompt_toolkit==3.0.47
 psycopg2==2.9.9
+psycopg2-binary==2.9.9
 ptyprocess==0.7.0
 pure_eval==0.2.3
 pydantic==2.4.2
+pydantic-to-typescript2==1.0.4
 pydantic_core==2.10.1
 Pygments==2.18.0
 pysam==0.22.1
+pytest==8.3.2
+pytest-asyncio==0.24.0
+pytest-cov==5.0.0
 python-dateutil==2.9.0.post0
+PyYAML==6.0.2
 requests==2.32.3
+ruff==0.5.0
 s3transfer==0.10.2
 six==1.16.0
 sniffio==1.3.1
@@ -60,6 +83,7 @@ traitlets==5.14.3
 typing_extensions==4.12.2
 urllib3==1.26.19
 uvicorn==0.30.6
+virtualenv==20.26.3
 wags_tails==0.1.4
 wcwidth==0.2.13
 yoyo-migrations==8.2.0
diff --git a/server/pyproject.toml b/server/pyproject.toml
index 80bda160..b81e1a00 100644
--- a/server/pyproject.toml
+++ b/server/pyproject.toml
@@ -28,8 +28,8 @@ dependencies = [
     "click",
     "boto3",
     "botocore",
-    "fusor ~= 0.4.2",
-    "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",
 ]

From 3d6eed327acf6f0f0561065e90ee7e2d0a41dc89 Mon Sep 17 00:00:00 2001
From: Katie Stahl <kathryn.stahl@nationwidechildrens.org>
Date: Thu, 26 Sep 2024 12:45:37 -0400
Subject: [PATCH 3/6] test: add test case for get exon coordinates where
 genomic coord occurs between exons

---
 server/tests/integration/test_utilities.py | 26 ++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/server/tests/integration/test_utilities.py b/server/tests/integration/test_utilities.py
index c027335b..8ff4b3a8 100644
--- a/server/tests/integration/test_utilities.py
+++ b/server/tests/integration/test_utilities.py
@@ -219,6 +219,32 @@ 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&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,
+    )
+
 
 @pytest.mark.asyncio()
 async def test_get_sequence_id(check_response):

From 08d98e8bceb10e55d7d78f0d95bc7bd89fb198d8 Mon Sep 17 00:00:00 2001
From: Katie Stahl <kathryn.stahl@nationwidechildrens.org>
Date: Thu, 26 Sep 2024 13:21:34 -0400
Subject: [PATCH 4/6] test: remove test case for now

---
 server/tests/integration/test_utilities.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/server/tests/integration/test_utilities.py b/server/tests/integration/test_utilities.py
index 8ff4b3a8..f2c162fb 100644
--- a/server/tests/integration/test_utilities.py
+++ b/server/tests/integration/test_utilities.py
@@ -213,11 +213,12 @@ def check_coords_response(response: dict, expected_response: dict):
         check_coords_response,
     )
 
-    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"]},
-        check_coords_response,
-    )
+    # TODO: add back / adjust this test when https://github.com/GenomicMedLab/cool-seq-tool/issues/372 is addressed
+    # 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"]},
+    #     check_coords_response,
+    # )
 
     # check correct response for genomic coordinate that occurs between exons (should get nearest junction)
     await check_response(

From 6a895676109bd8fbe2df02606afe43a6b049099a Mon Sep 17 00:00:00 2001
From: Katie Stahl <kathryn.stahl@nationwidechildrens.org>
Date: Fri, 27 Sep 2024 11:15:49 -0400
Subject: [PATCH 5/6] Update server/tests/integration/test_utilities.py

Co-authored-by: Kori Kuzma <korikuzma@gmail.com>
---
 server/tests/integration/test_utilities.py | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/server/tests/integration/test_utilities.py b/server/tests/integration/test_utilities.py
index f2c162fb..7c8211cd 100644
--- a/server/tests/integration/test_utilities.py
+++ b/server/tests/integration/test_utilities.py
@@ -213,12 +213,6 @@ def check_coords_response(response: dict, expected_response: dict):
         check_coords_response,
     )
 
-    # TODO: add back / adjust this test when https://github.com/GenomicMedLab/cool-seq-tool/issues/372 is addressed
-    # 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"]},
-    #     check_coords_response,
-    # )
 
     # check correct response for genomic coordinate that occurs between exons (should get nearest junction)
     await check_response(

From 3845c401607f0bde6e25d8780282e9253bc7163e Mon Sep 17 00:00:00 2001
From: Katie Stahl <kathryn.stahl@nationwidechildrens.org>
Date: Fri, 27 Sep 2024 11:21:45 -0400
Subject: [PATCH 6/6] styling

---
 server/tests/integration/test_utilities.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/server/tests/integration/test_utilities.py b/server/tests/integration/test_utilities.py
index 7c8211cd..085d024d 100644
--- a/server/tests/integration/test_utilities.py
+++ b/server/tests/integration/test_utilities.py
@@ -213,7 +213,6 @@ 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&end=154191900&transcript=NM_152263.3",