fixing tests and updating data with new models, bug fixes

cancervariants · Jul 31, 2024 · 88503d5 · 88503d5
1 parent 6da6b78
commit 88503d5
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Showing 10 changed files with 131 additions and 196 deletions.
diff --git a/client/src/components/Pages/Structure/Builder/Builder.tsx b/client/src/components/Pages/Structure/Builder/Builder.tsx
@@ -53,7 +53,7 @@ const ELEMENT_TEMPLATE = [
   {
     type: ElementType.geneElement,
     nomenclature: "",
-    element_id: uuid(),
+    elementId: uuid(),
     gene: {
       id: "",
       type: "",
@@ -63,11 +63,11 @@ const ELEMENT_TEMPLATE = [
   {
     type: ElementType.transcriptSegmentElement,
     nomenclature: "",
-    element_id: uuid(),
-    exon_start: null,
-    exon_start_offset: null,
-    exon_end: null,
-    exon_end_offset: null,
+    elementId: uuid(),
+    exonStart: null,
+    exonStartOffset: null,
+    exonEnd: null,
+    exonEndOffset: null,
     gene: {
       id: "",
       type: "",
@@ -77,12 +77,12 @@ const ELEMENT_TEMPLATE = [
   {
     nomenclature: "",
     type: ElementType.linkerSequenceElement,
-    element_id: uuid(),
+    elementId: uuid(),
   },
   {
     nomenclature: "",
     type: ElementType.templatedSequenceElement,
-    element_id: uuid(),
+    elementId: uuid(),
     id: "",
     location: {
       sequence_id: "",
@@ -102,18 +102,18 @@ const ELEMENT_TEMPLATE = [
   },
   {
     type: ElementType.unknownGeneElement,
-    element_id: uuid(),
+    elementId: uuid(),
     nomenclature: "?",
   },
   {
     type: ElementType.multiplePossibleGenesElement,
-    element_id: uuid(),
+    elementId: uuid(),
     nomenclature: "v",
   },
   {
     type: ElementType.regulatoryElement,
     nomenclature: "",
-    element_id: uuid(),
+    elementId: uuid(),
   },
 ];
 
@@ -148,7 +148,7 @@ const Builder: React.FC = () => {
     const sourceClone = Array.from(ELEMENT_TEMPLATE);
     const item = sourceClone[source.index];
     const newItem = Object.assign({}, item);
-    newItem.element_id = uuid();
+    newItem.elementId = uuid();
 
     if (draggableId.includes("RegulatoryElement")) {
       setFusion({ ...fusion, ...{ regulatoryElement: newItem } });
@@ -190,7 +190,7 @@ const Builder: React.FC = () => {
 
   const handleDelete = (uuid: string) => {
     let items: Array<ClientElementUnion> = Array.from(fusion.structure);
-    items = items.filter((item) => item?.element_id !== uuid);
+    items = items.filter((item) => item?.elementId !== uuid);
     setFusion({ ...fusion, ...{ structure: items } });
   };
 
@@ -414,7 +414,7 @@ const Builder: React.FC = () => {
                 style={{ display: "flex" }}
               >
                 <Box className="options-container">
-                  {ELEMENT_TEMPLATE.map(({ element_id, type }, index) => {
+                  {ELEMENT_TEMPLATE.map(({ elementId, type }, index) => {
                     if (
                       (fusion.type === "AssayedFusion" &&
                         type !== ElementType.multiplePossibleGenesElement) ||
@@ -423,8 +423,8 @@ const Builder: React.FC = () => {
                     ) {
                       return (
                         <Draggable
-                          key={element_id}
-                          draggableId={type + element_id}
+                          key={elementId}
+                          draggableId={type + elementId}
                           index={index}
                           isDragDisabled={
                             type === ElementType.regulatoryElement &&
@@ -466,7 +466,7 @@ const Builder: React.FC = () => {
                                 {snapshot.isDragging && (
                                   <Box
                                     style={{ transform: "none !important" }}
-                                    key={element_id}
+                                    key={elementId}
                                     className={`option-item clone ${type}`}
                                   >
                                     {elementNameMap[type].icon}{" "}
@@ -526,8 +526,8 @@ const Builder: React.FC = () => {
                       return (
                         element && (
                           <Draggable
-                            key={element.element_id}
-                            draggableId={element.element_id}
+                            key={element.elementId}
+                            draggableId={element.elementId}
                             index={index}
                           >
                             {(provided) => (

diff --git a/client/src/components/Pages/Structure/Input/GeneElementInput/GeneElementInput.tsx b/client/src/components/Pages/Structure/Input/GeneElementInput/GeneElementInput.tsx
@@ -10,6 +10,7 @@ import {
   getGeneNomenclature,
 } from "../../../../../services/main";
 import StructuralElementInputAccordion from "../StructuralElementInputAccordion";
+import React from "react";
 
 interface GeneElementInputProps extends StructuralElementInputProps {
   element: ClientGeneElement;
@@ -70,7 +71,6 @@ const GeneElementInput: React.FC<GeneElementInputProps> = ({
       setGene={setGene}
       geneText={geneText}
       setGeneText={setGeneText}
-      style={{ width: 125 }}
       tooltipDirection="left"
     />
   );

diff --git a/client/src/components/Pages/Structure/Input/StructuralElementInputAccordion.tsx b/client/src/components/Pages/Structure/Input/StructuralElementInputAccordion.tsx
@@ -72,7 +72,7 @@ const StructuralElementInputAccordion: React.FC<
   inputElements,
   validated,
   icon,
-  pendingResponse
+  pendingResponse,
 }) => {
   const classes = useStyles();
 
@@ -81,20 +81,24 @@ const StructuralElementInputAccordion: React.FC<
       <CardHeader
         avatar={icon}
         action={
-          pendingResponse ?
-          <CircularProgress style={{width: "1.25em", height: "1.25em", padding: "8px"}} /> :
-          <Tooltip title="Delete element">
-            <IconButton
-              style={{ cursor: "pointer" }}
-              onClick={(event) => {
-                event.stopPropagation();
-                handleDelete(element.element_id);
-              }}
-              onFocus={(event) => event.stopPropagation()}
-            >
-              <DeleteIcon />
-            </IconButton>
-          </Tooltip>
+          pendingResponse ? (
+            <CircularProgress
+              style={{ width: "1.25em", height: "1.25em", padding: "8px" }}
+            />
+          ) : (
+            <Tooltip title="Delete element">
+              <IconButton
+                style={{ cursor: "pointer" }}
+                onClick={(event) => {
+                  event.stopPropagation();
+                  handleDelete(element.elementId);
+                }}
+                onFocus={(event) => event.stopPropagation()}
+              >
+                <DeleteIcon />
+              </IconButton>
+            </Tooltip>
+          )
         }
         title={element.nomenclature ? element.nomenclature : null}
         classes={{

diff --git a/...nts/Pages/Structure/Input/TemplatedSequenceElementInput/TemplatedSequenceElementInput.tsx b/...nts/Pages/Structure/Input/TemplatedSequenceElementInput/TemplatedSequenceElementInput.tsx
@@ -21,12 +21,14 @@ const TemplatedSequenceElementInput: React.FC<
   const [chromosome, setChromosome] = useState<string>(
     element.inputChromosome || ""
   );
-  const [strand, setStrand] = useState<string>(element.strand || "+");
+  const [strand, setStrand] = useState<string>(
+    element.strand === 1 ? "+" : "-"
+  );
   const [startPosition, setStartPosition] = useState<string>(
-    element.inputStart || ""
+    element.inputStart !== null ? `${element.inputStart}` : ""
   );
   const [endPosition, setEndPosition] = useState<string>(
-    element.inputEnd || ""
+    element.inputEnd !== null ? `${element.inputEnd}` : ""
   );
   const [inputError, setInputError] = useState<string>("");
 
@@ -74,13 +76,14 @@ const TemplatedSequenceElementInput: React.FC<
           templatedSequenceResponse.element
         ).then((nomenclatureResponse) => {
           if (nomenclatureResponse.nomenclature) {
+            console.log(templatedSequenceResponse.element);
             const templatedSequenceElement: ClientTemplatedSequenceElement = {
               ...templatedSequenceResponse.element,
-              element_id: element.element_id,
+              elementId: element.elementId,
               nomenclature: nomenclatureResponse.nomenclature,
               inputChromosome: chromosome,
-              input_start: startPosition,
-              input_end: endPosition,
+              inputStart: Number(startPosition),
+              inputEnd: Number(endPosition),
             };
             handleSave(index, templatedSequenceElement);
           }

diff --git a/client/src/components/Pages/Structure/Input/TxSegmentElementInput/TxSegmentElementInput.tsx b/client/src/components/Pages/Structure/Input/TxSegmentElementInput/TxSegmentElementInput.tsx
@@ -58,7 +58,9 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
   const [txGene, setTxGene] = useState(element.inputGene || "");
   const [txGeneText, setTxGeneText] = useState("");
 
-  const [txStrand, setTxStrand] = useState<string>(element.inputStrand || "+");
+  const [txStrand, setTxStrand] = useState<string>(
+    element.inputStrand === 1 ? "+" : "-"
+  );
 
   const [txChrom, setTxChrom] = useState(element.inputChr || "");
   const [txChromText, setTxChromText] = useState("");

diff --git a/client/src/services/ResponseModels.ts b/client/src/services/ResponseModels.ts
@@ -534,12 +534,12 @@ export interface ClientTranscriptSegmentElement {
   inputStrand?: Strand | null;
   inputGene?: string | null;
   inputChr?: string | null;
-  inputGenomicStart?: number | null;
-  inputGenomicEnd?: number | null;
-  inputExonStart?: number | null;
-  inputExonStartOffset?: number | null;
-  inputExonEnd?: number | null;
-  inputExonEndOffset?: number | null;
+  inputGenomicStart?: string | null;
+  inputGenomicEnd?: string | null;
+  inputExonStart?: string | null;
+  inputExonStartOffset?: string | null;
+  inputExonEnd?: string | null;
+  inputExonEndOffset?: string | null;
 }
 /**
  * Gene element used client-side.
@@ -560,8 +560,8 @@ export interface ClientTemplatedSequenceElement {
   region: SequenceLocation;
   strand: Strand;
   inputChromosome: string | null;
-  inputStart: number | null;
-  inputEnd: number | null;
+  inputStart: string | null;
+  inputEnd: string | null;
 }
 /**
  * Linker element class used client-side.

diff --git a/server/src/curfu/routers/utilities.py b/server/src/curfu/routers/utilities.py
@@ -107,16 +107,14 @@ async def get_genome_coords(
     if exon_end is not None and exon_end_offset is None:
         exon_end_offset = 0
 
-    response = (
-        await request.app.state.fusor.cool_seq_tool.transcript_to_genomic_coordinates(
-            gene=gene,
-            transcript=transcript,
-            exon_start=exon_start,
-            exon_end=exon_end,
-            exon_start_offset=exon_start_offset,
-            exon_end_offset=exon_end_offset,
-            residue_mode="inter-residue",
-        )
+    response = await request.app.state.fusor.cool_seq_tool.ex_g_coords_mapper.transcript_to_genomic_coordinates(
+        gene=gene,
+        transcript=transcript,
+        exon_start=exon_start,
+        exon_end=exon_end,
+        exon_start_offset=exon_start_offset,
+        exon_end_offset=exon_end_offset,
+        residue_mode="inter-residue",
     )
     warnings = response.warnings
     if warnings:

diff --git a/server/src/curfu/schemas.py b/server/src/curfu/schemas.py
@@ -53,12 +53,12 @@ class ClientTranscriptSegmentElement(TranscriptSegmentElement, ClientStructuralE
     inputStrand: Strand | None = None
     inputGene: str | None = None
     inputChr: str | None = None
-    inputGenomicStart: int | None = None
-    inputGenomicEnd: int | None = None
-    inputExonStart: int | None = None
-    inputExonStartOffset: int | None = None
-    inputExonEnd: int | None = None
-    inputExonEndOffset: int | None = None
+    inputGenomicStart: str | None = None
+    inputGenomicEnd: str | None = None
+    inputExonStart: str | None = None
+    inputExonStartOffset: str | None = None
+    inputExonEnd: str | None = None
+    inputExonEndOffset: str | None = None
 
 
 class ClientLinkerElement(LinkerElement, ClientStructuralElement):
@@ -69,8 +69,8 @@ class ClientTemplatedSequenceElement(TemplatedSequenceElement, ClientStructuralE
     """Templated sequence element used client-side."""
 
     inputChromosome: str | None
-    inputStart: int | None
-    inputEnd: int | None
+    inputStart: str | None
+    inputEnd: str | None
 
 
 class ClientGeneElement(GeneElement, ClientStructuralElement):