pass around formatted fusion to reduce repeated code

client/src/components/Pages/Summary/JSON/SummaryJSON.tsx

@@ -1,118 +1,23 @@
 import copy from "clipboard-copy";
 import React, { useEffect, useState } from "react";
+import { validateFusion } from "../../../../services/main";
 import {
-  ClientElementUnion,
-  ElementUnion,
-  validateFusion,
-} from "../../../../services/main";
-import {
-  AssayedFusion,
-  CategoricalFusion,
-  FunctionalDomain,
-  GeneElement,
-  LinkerElement,
-  MultiplePossibleGenesElement,
-  TemplatedSequenceElement,
-  TranscriptSegmentElement,
-  UnknownGeneElement,
+  FormattedAssayedFusion,
+  FormattedCategoricalFusion,
 } from "../../../../services/ResponseModels";
-import { FusionType } from "../Main/Summary";
 import "./SummaryJSON.scss";
 
 interface Props {
-  fusion: FusionType;
+  formattedFusion: FormattedAssayedFusion | FormattedCategoricalFusion;
 }
 
-export const SummaryJSON: React.FC<Props> = ({ fusion }) => {
+export const SummaryJSON: React.FC<Props> = ({ formattedFusion }) => {
   const [isDown, setIsDown] = useState<boolean>(false);
   const [isCopied, setIsCopied] = useState<boolean>(false);
   const [printedFusion, setPrintedFusion] = useState<string>("");
   const [validationErrors, setValidationErrors] = useState<string[]>([]);
 
-  /**
-   * On component render, restructure fusion to drop properties used for client state purposes,
-   * transmit to validation endpoint, and update local copy.
-   */
   useEffect(() => {
-    const structuralElements: ElementUnion[] = fusion.structure?.map(
-      (element: ClientElementUnion) => {
-        switch (element.type) {
-          case "GeneElement":
-            const geneElement: GeneElement = {
-              type: element.type,
-              gene: element.gene,
-            };
-            return geneElement;
-          case "LinkerSequenceElement":
-            const linkerElement: LinkerElement = {
-              type: element.type,
-              linker_sequence: element.linker_sequence,
-            };
-            return linkerElement;
-          case "TemplatedSequenceElement":
-            const templatedSequenceElement: TemplatedSequenceElement = {
-              type: element.type,
-              region: element.region,
-              strand: element.strand,
-            };
-            return templatedSequenceElement;
-          case "TranscriptSegmentElement":
-            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,
-              gene: element.gene,
-              element_genomic_start: element.element_genomic_start,
-              element_genomic_end: element.element_genomic_end,
-            };
-            return txSegmentElement;
-          case "MultiplePossibleGenesElement":
-          case "UnknownGeneElement":
-            const newElement:
-              | MultiplePossibleGenesElement
-              | UnknownGeneElement = {
-              type: element.type,
-            };
-            return newElement;
-          default:
-            throw new Error("Unrecognized element type");
-        }
-      }
-    );
-    const regulatoryElements = fusion.regulatoryElements?.map((re) => ({
-      type: re.type,
-      associated_gene: re.associated_gene,
-      regulatory_class: re.regulatory_class,
-      featureId: re.featureId,
-      genomic_location: re.genomic_location,
-    }));
-    let formattedFusion: AssayedFusion | CategoricalFusion;
-    if (fusion.type === "AssayedFusion") {
-      formattedFusion = {
-        ...fusion,
-        structure: structuralElements,
-        regulatoryElements: regulatoryElements,
-      };
-    } else {
-      const criticalDomains: FunctionalDomain[] =
-        fusion.criticalFunctionalDomains?.map((domain) => ({
-          _id: domain._id,
-          label: domain.label,
-          status: domain.status,
-          associated_gene: domain.associated_gene,
-          sequence_location: domain.sequence_location,
-        }));
-      formattedFusion = {
-        ...fusion,
-        structure: structuralElements,
-        regulatoryElements: regulatoryElements,
-        criticalFunctionalDomains: criticalDomains,
-      };
-    }
-
     // make request
     validateFusion(formattedFusion).then((response) => {
       if (response.warnings && response.warnings?.length > 0) {
@@ -126,7 +31,7 @@ export const SummaryJSON: React.FC<Props> = ({ fusion }) => {
         setPrintedFusion(JSON.stringify(response.fusion, null, 2));
       }
     });
-  }, [fusion]); // should be blank?
+  }, [formattedFusion]);
 
   const handleCopy = () => {
     copy(printedFusion);

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

@@ -60,7 +60,7 @@ export const Success: React.FC<Props> = ({ fusion }) => {
         </TabPanel>
         <TabPanel value={currentTab} index={1}>
           <div className="summary-sub-tab">
-            {fusion && <SummaryJSON fusion={fusion} />}
+            {fusion && <SummaryJSON formattedFusion={fusion} />}
           </div>
         </TabPanel>
       </div>

client/src/services/ResponseModels.ts

@@ -6,9 +6,9 @@
 */
 
 /**
- * Specify possible Fusion types.
+ * Form of evidence supporting identification of the fusion.
  */
-export type FusionType = "CategoricalFusion" | "AssayedFusion";
+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:
@@ -66,20 +66,6 @@ export type Range = [number | null, number | null];
  * A character string of Residues that represents a biological sequence using the conventional sequence order (5'-to-3' for nucleic acid sequences, and amino-to-carboxyl for amino acid sequences). IUPAC ambiguity codes are permitted in Sequence Strings.
  */
 export type SequenceString = string;
-/**
- * Define possible structural element type values.
- */
-export type StructuralElementType =
-  | "TranscriptSegmentElement"
-  | "TemplatedSequenceElement"
-  | "LinkerSequenceElement"
-  | "GeneElement"
-  | "UnknownGeneElement"
-  | "MultiplePossibleGenesElement";
-/**
- * Form of evidence supporting identification of the fusion.
- */
-export type Evidence = "observed" | "inferred";
 /**
  * Create enum for positive and negative strand
  */
@@ -95,13 +81,34 @@ export type EventType = "rearrangement" | "read-through" | "trans-splicing";
 export type DomainStatus = "lost" | "preserved";
 
 /**
- * Define Fusion class
+ * 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
+ * rearrangements detected by whole genome sequencing or by coarser-scale cytogenomic
+ * assays. Example: an EWSR1 fusion inferred from a breakapart FISH assay.
  */
-export interface AbstractFusion {
-  type: FusionType;
+export interface AssayedFusion {
+  type?: "AssayedFusion";
   regulatoryElement?: RegulatoryElement | null;
-  structure: BaseStructuralElement[];
+  structure: (
+    | TranscriptSegmentElement
+    | GeneElement
+    | TemplatedSequenceElement
+    | LinkerElement
+    | UnknownGeneElement
+  )[];
   readingFramePreserved?: boolean | null;
+  causativeEvent?: CausativeEvent | null;
+  assay?: Assay | null;
 }
 /**
  * Define RegulatoryElement class.
@@ -318,43 +325,6 @@ export interface SequenceReference {
   circular?: boolean | null;
   [k: string]: unknown;
 }
-/**
- * Define base structural element class.
- */
-export interface BaseStructuralElement {
-  type: StructuralElementType;
-  [k: string]: unknown;
-}
-/**
- * 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
- * rearrangements detected by whole genome sequencing or by coarser-scale cytogenomic
- * assays. Example: an EWSR1 fusion inferred from a breakapart FISH assay.
- */
-export interface AssayedFusion {
-  type?: "AssayedFusion";
-  regulatoryElement?: RegulatoryElement | null;
-  structure: (
-    | TranscriptSegmentElement
-    | GeneElement
-    | TemplatedSequenceElement
-    | LinkerElement
-    | UnknownGeneElement
-  )[];
-  readingFramePreserved?: boolean | null;
-  causativeEvent?: CausativeEvent | null;
-  assay?: Assay | null;
-}
 /**
  * Define TranscriptSegment class
  */
@@ -849,5 +819,5 @@ export interface TxSegmentElementResponse {
  */
 export interface ValidateFusionResponse {
   warnings?: string[] | null;
-  fusion: AbstractFusion | null;
+  fusion: CategoricalFusion | AssayedFusion | null;
 }

server/src/curfu/schemas.py

@@ -5,14 +5,14 @@
 
 from cool_seq_tool.schemas import GenomicData
 from fusor.models import (
-    AbstractFusion,
     Assay,
     AssayedFusion,
     AssayedFusionElements,
     CategoricalFusion,
     CategoricalFusionElements,
     CausativeEvent,
     FunctionalDomain,
+    Fusion,
     GeneElement,
     LinkerElement,
     MultiplePossibleGenesElement,
@@ -180,7 +180,7 @@ class AssociatedDomainResponse(Response):
 class ValidateFusionResponse(Response):
     """Response model for Fusion validation endpoint."""
 
-    fusion: AbstractFusion | None
+    fusion: Fusion | None
 
 
 class ExonCoordsRequest(BaseModel):