wip: updating models

client/src/components/Pages/Structure/Input/RegulatoryElementInput/RegulatoryElementInput.tsx

@@ -85,7 +85,7 @@ const RegulatoryElementInput: React.FC<RegulatoryElementInputProps> = ({
           }
           const newRegElement: ClientRegulatoryElement = {
             ...reResponse.regulatoryElement,
-            display_class: regulatoryClassItems[elementClass][1],
+            displayClass: regulatoryClassItems[elementClass][1],
             nomenclature: nomenclatureResponse.nomenclature,
           };
           setRegElement(newRegElement);

client/src/components/Pages/Structure/Input/TemplatedSequenceElementInput/TemplatedSequenceElementInput.tsx

@@ -18,16 +18,15 @@ interface TemplatedSequenceElementInputProps
 const TemplatedSequenceElementInput: React.FC<
   TemplatedSequenceElementInputProps
 > = ({ element, index, handleSave, handleDelete, icon }) => {
-
   const [chromosome, setChromosome] = useState<string>(
-    element.input_chromosome || ""
+    element.inputChromosome || ""
   );
   const [strand, setStrand] = useState<string>(element.strand || "+");
   const [startPosition, setStartPosition] = useState<string>(
-    element.input_start || ""
+    element.inputStart || ""
   );
   const [endPosition, setEndPosition] = useState<string>(
-    element.input_end || ""
+    element.inputEnd || ""
   );
   const [inputError, setInputError] = useState<string>("");
 
@@ -67,7 +66,7 @@ const TemplatedSequenceElementInput: React.FC<
       ) {
         // TODO visible error handling
         setInputError("element validation unsuccessful");
-        setPendingResponse(false)
+        setPendingResponse(false);
         return;
       } else if (templatedSequenceResponse.element) {
         setInputError("");
@@ -79,15 +78,15 @@ const TemplatedSequenceElementInput: React.FC<
               ...templatedSequenceResponse.element,
               element_id: element.element_id,
               nomenclature: nomenclatureResponse.nomenclature,
-              input_chromosome: chromosome,
+              inputChromosome: chromosome,
               input_start: startPosition,
               input_end: endPosition,
             };
             handleSave(index, templatedSequenceElement);
           }
         });
       }
-      setPendingResponse(false)
+      setPendingResponse(false);
     });
   };
 
@@ -167,7 +166,7 @@ const TemplatedSequenceElementInput: React.FC<
     inputElements,
     validated,
     icon,
-    pendingResponse
+    pendingResponse,
   });
 };
 

client/src/components/Pages/Structure/Input/TxSegmentElementInput/TxSegmentElementInput.tsx

@@ -47,12 +47,12 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
   const { fusion } = useContext(FusionContext);
 
   const [txInputType, setTxInputType] = useState<InputType>(
-    (element.input_type as InputType) || InputType.default
+    (element.inputType as InputType) || InputType.default
   );
 
   // "Text" variables refer to helper or warning text to set under input fields
   // TODO: this needs refactored so badly
-  const [txAc, setTxAc] = useState(element.input_tx || "");
+  const [txAc, setTxAc] = useState(element.inputTx || "");
   const [txAcText, setTxAcText] = useState("");
 
   const [txGene, setTxGene] = useState(element.input_gene || "");
@@ -248,7 +248,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
             CheckGenomicCoordWarning(txSegmentResponse.warnings);
           } else {
             const inputParams = {
-              input_type: txInputType,
+              inputType: txInputType,
               input_strand: txStrand,
               input_gene: txGene,
               input_chr: txChrom,
@@ -277,8 +277,8 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
             CheckGenomicCoordWarning(txSegmentResponse.warnings);
           } else {
             const inputParams = {
-              input_type: txInputType,
-              input_tx: txAc,
+              inputType: txInputType,
+              inputTx: txAc,
               input_strand: txStrand,
               input_chr: txChrom,
               input_genomic_start: txStartingGenomic,
@@ -323,8 +323,8 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
             setStartingExonText("");
             setEndingExonText("");
             const inputParams = {
-              input_type: txInputType,
-              input_tx: txAc,
+              inputType: txInputType,
+              inputTx: txAc,
             };
             handleTxElementResponse(txSegmentResponse, inputParams);
           }
@@ -437,10 +437,7 @@ const TxSegmentCompInput: React.FC<TxSegmentElementInputProps> = ({
   const genomicCoordinateInfo = (
     <>
       <Box className="mid-inputs">
-        <ChromosomeField
-          fieldValue={txChrom}
-          errorText={txChromText}
-        />
+        <ChromosomeField fieldValue={txChrom} errorText={txChromText} />
         <Box mt="18px" width="125px">
           <StrandSwitch setStrand={setTxStrand} selectedStrand={txStrand} />
         </Box>

client/src/components/Pages/Summary/Main/Summary.tsx

@@ -3,14 +3,17 @@ import { FusionContext } from "../../../../global/contexts/FusionContext";
 import React, { useContext, useEffect, useState } from "react";
 
 import {
+  AssayedFusionElements,
+  CategoricalFusionElements,
   ClientElementUnion,
   ElementUnion,
   validateFusion,
 } from "../../../../services/main";
 import {
   AssayedFusion,
   CategoricalFusion,
-  FunctionalDomain,
+  FormattedAssayedFusion,
+  FormattedCategoricalFusion,
   GeneElement,
   LinkerElement,
   MultiplePossibleGenesElement,
@@ -33,6 +36,9 @@ export const Summary: React.FC<Props> = ({ setVisibleTab }) => {
   const [validatedFusion, setValidatedFusion] = useState<
     AssayedFusion | CategoricalFusion | null
   >(null);
+  const [formattedFusion, setFormattedFusion] = useState<
+    FormattedAssayedFusion | FormattedCategoricalFusion | null
+  >(null);
   const [validationErrors, setValidationErrors] = useState<string[]>([]);
   const { fusion } = useContext(FusionContext);
 
@@ -54,7 +60,7 @@ export const Summary: React.FC<Props> = ({ setVisibleTab }) => {
       case "LinkerSequenceElement":
         const linkerElement: LinkerElement = {
           type: element.type,
-          linker_sequence: element.linker_sequence,
+          linkerSequence: element.linkerSequence,
         };
         return linkerElement;
       case "TemplatedSequenceElement":
@@ -68,13 +74,13 @@ export const Summary: React.FC<Props> = ({ setVisibleTab }) => {
         const txSegmentElement: TranscriptSegmentElement = {
           type: element.type,
           transcript: element.transcript,
-          exon_start: element.exon_start,
-          exon_start_offset: element.exon_start_offset,
-          exon_end: element.exon_end,
-          exon_end_offset: element.exon_end_offset,
+          exonStart: element.exonStart,
+          exonStartOffset: element.exonStartOffset,
+          exonEnd: element.exonEnd,
+          exonEndOffset: element.exonEndOffset,
           gene: element.gene,
-          element_genomic_start: element.element_genomic_start,
-          element_genomic_end: element.element_genomic_end,
+          elementGenomicStart: element.elementGenomicStart,
+          elementGenomicEnd: element.elementGenomicEnd,
         };
         return txSegmentElement;
       case "MultiplePossibleGenesElement":
@@ -93,7 +99,7 @@ export const Summary: React.FC<Props> = ({ setVisibleTab }) => {
    * @param formattedFusion fusion with client-oriented properties dropped
    */
   const requestValidatedFusion = (
-    formattedFusion: AssayedFusion | CategoricalFusion
+    formattedFusion: FormattedAssayedFusion | FormattedCategoricalFusion
   ) => {
     // make request
     validateFusion(formattedFusion).then((response) => {
@@ -107,52 +113,49 @@ export const Summary: React.FC<Props> = ({ setVisibleTab }) => {
         }
       } else {
         setValidationErrors([]);
+        console.log(response.fusion);
         setValidatedFusion(
           response.fusion as CategoricalFusion | AssayedFusion
         );
+        setFormattedFusion(formattedFusion);
       }
     });
   };
 
   /**
    * On component render, restructure fusion to drop properties used for client state purposes,
+   * fix expected casing for fusor fusion constructors,
    * transmit to validation endpoint, and update local copy.
    */
   useEffect(() => {
-    const structuralElements: ElementUnion[] = fusion.structure?.map(
+    const structure: ElementUnion[] = fusion.structure?.map(
       (element: ClientElementUnion) => fusorifyStructuralElement(element)
     );
     let regulatoryElement: RegulatoryElement | null = null;
     if (fusion.regulatoryElement) {
       regulatoryElement = {
         type: fusion.regulatoryElement.type,
-        associated_gene: fusion.regulatoryElement.associated_gene,
-        regulatory_class: fusion.regulatoryElement.regulatory_class,
+        associatedGene: fusion.regulatoryElement.associatedGene,
+        regulatoryClass: fusion.regulatoryElement.regulatoryClass,
         featureId: fusion.regulatoryElement.featureId,
-        feature_location: fusion.regulatoryElement.feature_location,
+        featureLocation: fusion.regulatoryElement.featureLocation,
       };
     }
-    let formattedFusion: AssayedFusion | CategoricalFusion;
+    let formattedFusion: FormattedAssayedFusion | FormattedCategoricalFusion;
     if (fusion.type === "AssayedFusion") {
       formattedFusion = {
-        ...fusion,
-        structure: structuralElements,
-        regulatoryElement: regulatoryElement,
+        structure: structure as AssayedFusionElements[],
+        causative_event: fusion.causativeEvent,
+        assay: fusion.assay,
+        regulatory_element: regulatoryElement,
+        reading_frame_preserved: fusion.readingFramePreserved,
       };
     } else {
-      const criticalDomains: FunctionalDomain[] =
-        fusion.criticalFunctionalDomains?.map((domain: FunctionalDomain) => ({
-          _id: domain._id,
-          label: domain.label,
-          status: domain.status,
-          associated_gene: domain.associated_gene,
-          sequence_location: domain.sequence_location,
-        }));
       formattedFusion = {
-        ...fusion,
-        structure: structuralElements,
-        regulatoryElement: regulatoryElement,
-        criticalFunctionalDomains: criticalDomains,
+        structure: structure as CategoricalFusionElements[],
+        regulatory_element: regulatoryElement,
+        critical_functional_domains: fusion.criticalFunctionalDomains,
+        reading_frame_preserved: fusion.readingFramePreserved,
       };
     }
     requestValidatedFusion(formattedFusion);

client/src/services/ResponseModels.ts

@@ -5,6 +5,10 @@
 /* Do not modify it by hand - just update the pydantic models and then re-run the script
 */
 
+/**
+ * Form of evidence supporting identification of the fusion.
+ */
+export type Evidence = "observed" | "inferred";
 /**
  * Define possible classes of Regulatory Elements. Options are the possible values
  * for /regulatory_class value property in the INSDC controlled vocabulary:
@@ -71,15 +75,21 @@ export type Strand = 1 | -1;
  * assayed fusion.
  */
 export type EventType = "rearrangement" | "read-through" | "trans-splicing";
-/**
- * Form of evidence supporting identification of the fusion.
- */
-export type Evidence = "observed" | "inferred";
 /**
  * Define possible statuses of functional domains.
  */
 export type DomainStatus = "lost" | "preserved";
 
+/**
+ * Information pertaining to the assay used in identifying the fusion.
+ */
+export interface Assay {
+  type?: "Assay";
+  assayName?: string | null;
+  assayId?: string | null;
+  methodUri?: string | null;
+  fusionDetection?: Evidence | null;
+}
 /**
  * Assayed gene fusions from biological specimens are directly detected using
  * RNA-based gene fusion assays, or alternatively may be inferred from genomic
@@ -413,22 +423,12 @@ export interface CausativeEvent {
   eventType: EventType;
   eventDescription?: string | null;
 }
-/**
- * Information pertaining to the assay used in identifying the fusion.
- */
-export interface Assay {
-  type?: "Assay";
-  assayName?: string | null;
-  assayId?: string | null;
-  methodUri?: string | null;
-  fusionDetection?: Evidence | null;
-}
 /**
  * Response model for domain ID autocomplete suggestion endpoint.
  */
 export interface AssociatedDomainResponse {
   warnings?: string[] | null;
-  geneId: string;
+  gene_id: string;
   suggestions: DomainParams[] | null;
 }
 /**
@@ -717,7 +717,7 @@ export interface NomenclatureResponse {
 export interface NormalizeGeneResponse {
   warnings?: string[] | null;
   term: string;
-  conceptId: string | null;
+  concept_id: string | null;
   symbol: string | null;
   cased: string | null;
 }
@@ -726,7 +726,7 @@ export interface NormalizeGeneResponse {
  */
 export interface RegulatoryElementResponse {
   warnings?: string[] | null;
-  regulatoryElement: RegulatoryElement;
+  regulatory_element: RegulatoryElement;
 }
 /**
  * Abstract Response class for defining API response structures.
@@ -740,8 +740,8 @@ export interface Response {
 export interface SequenceIDResponse {
   warnings?: string[] | null;
   sequence: string;
-  refseqId: string | null;
-  ga4ghId: string | null;
+  refseq_id: string | null;
+  ga4gh_id: string | null;
   aliases: string[] | null;
 }
 /**