bug fixes

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

@@ -36,9 +36,6 @@ 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);
 
@@ -113,11 +110,9 @@ export const Summary: React.FC<Props> = ({ setVisibleTab }) => {
         }
       } else {
         setValidationErrors([]);
-        console.log(response.fusion);
         setValidatedFusion(
           response.fusion as CategoricalFusion | AssayedFusion
         );
-        setFormattedFusion(formattedFusion);
       }
     });
   };
@@ -161,6 +156,8 @@ export const Summary: React.FC<Props> = ({ setVisibleTab }) => {
     requestValidatedFusion(formattedFusion);
   }, [fusion]);
 
+  console.log(validatedFusion);
+
   return (
     <>
       {(!validationErrors || validationErrors.length === 0) &&

client/src/services/ResponseModels.ts

@@ -6,9 +6,9 @@
 */
 
 /**
- * Form of evidence supporting identification of the fusion.
+ * Specify possible Fusion types.
  */
-export type Evidence = "observed" | "inferred";
+export type FusionType = "CategoricalFusion" | "AssayedFusion";
 /**
  * Define possible classes of Regulatory Elements. Options are the possible values
  * for /regulatory_class value property in the INSDC controlled vocabulary:
@@ -66,6 +66,20 @@ 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
  */
@@ -81,34 +95,13 @@ export type EventType = "rearrangement" | "read-through" | "trans-splicing";
 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
- * rearrangements detected by whole genome sequencing or by coarser-scale cytogenomic
- * assays. Example: an EWSR1 fusion inferred from a breakapart FISH assay.
+ * Define Fusion class
  */
-export interface AssayedFusion {
-  type?: "AssayedFusion";
+export interface AbstractFusion {
+  type: FusionType;
   regulatoryElement?: RegulatoryElement | null;
-  structure: (
-    | TranscriptSegmentElement
-    | GeneElement
-    | TemplatedSequenceElement
-    | LinkerElement
-    | UnknownGeneElement
-  )[];
+  structure: BaseStructuralElement[];
   readingFramePreserved?: boolean | null;
-  causativeEvent?: CausativeEvent | null;
-  assay?: Assay | null;
 }
 /**
  * Define RegulatoryElement class.
@@ -325,6 +318,43 @@ 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
  */
@@ -664,6 +694,41 @@ export interface ExonCoordsRequest {
   exonEnd?: number | null;
   exonEndOffset?: number | null;
 }
+/**
+ * Assayed fusion with parameters defined as expected in fusor assayed_fusion function
+ * validate attempts to validate a fusion by constructing it by sending kwargs. In the models and frontend, these are camelCase,
+ * but the assayed_fusion and categorical_fusion constructors expect snake_case
+ */
+export interface FormattedAssayedFusion {
+  structure: (
+    | TranscriptSegmentElement
+    | GeneElement
+    | TemplatedSequenceElement
+    | LinkerElement
+    | UnknownGeneElement
+  )[];
+  causative_event?: CausativeEvent | null;
+  assay?: Assay | null;
+  regulatory_element?: RegulatoryElement | null;
+  reading_frame_preserved?: boolean | null;
+}
+/**
+ * Categorical fusion with parameters defined as expected in fusor categorical_fusion function
+ * validate attempts to validate a fusion by constructing it by sending kwargs. In the models and frontend, these are camelCase,
+ * but the assayed_fusion and categorical_fusion constructors expect snake_case
+ */
+export interface FormattedCategoricalFusion {
+  structure: (
+    | TranscriptSegmentElement
+    | GeneElement
+    | TemplatedSequenceElement
+    | LinkerElement
+    | MultiplePossibleGenesElement
+  )[];
+  regulatory_element?: RegulatoryElement | null;
+  critical_functional_domains?: FunctionalDomain[] | null;
+  reading_frame_preserved?: boolean | null;
+}
 /**
  * Response model for gene element construction endoint.
  */
@@ -784,5 +849,5 @@ export interface TxSegmentElementResponse {
  */
 export interface ValidateFusionResponse {
   warnings?: string[] | null;
-  fusion: CategoricalFusion | AssayedFusion | null;
+  fusion: AbstractFusion | null;
 }

client/src/services/main.tsx

@@ -37,6 +37,8 @@ import {
   RegulatoryClass,
   RegulatoryElementResponse,
   ClientRegulatoryElement,
+  FormattedAssayedFusion,
+  FormattedCategoricalFusion,
 } from "./ResponseModels";
 
 export enum ElementType {
@@ -67,6 +69,20 @@ export type ElementUnion =
   | TemplatedSequenceElement
   | TranscriptSegmentElement;
 
+export type AssayedFusionElements =
+  | GeneElement
+  | LinkerElement
+  | UnknownGeneElement
+  | TemplatedSequenceElement
+  | TranscriptSegmentElement;
+
+export type CategoricalFusionElements =
+  | MultiplePossibleGenesElement
+  | GeneElement
+  | LinkerElement
+  | TemplatedSequenceElement
+  | TranscriptSegmentElement;
+
 export type ClientFusion = ClientCategoricalFusion | ClientAssayedFusion;
 
 /**
@@ -387,7 +403,7 @@ export const getGeneNomenclature = async (
  * @returns nomenclature if successful
  */
 export const getFusionNomenclature = async (
-  fusion: AssayedFusion | CategoricalFusion
+  fusion: FormattedAssayedFusion | FormattedCategoricalFusion
 ): Promise<NomenclatureResponse> => {
   const response = await fetch("/api/nomenclature/fusion", {
     method: "POST",

server/src/curfu/routers/nomenclature.py

@@ -186,8 +186,7 @@ def generate_fusion_nomenclature(
     :return: response with fusion nomenclature
     """
     try:
-        valid_fusion = request.app.state.fusor.fusion(**fusion)
+        nomenclature = request.app.state.fusor.generate_nomenclature(fusion)
+        return {"nomenclature": nomenclature}
     except FUSORParametersException as e:
         return {"warnings": [str(e)]}
-    nomenclature = request.app.state.fusor.generate_nomenclature(valid_fusion)
-    return {"nomenclature": nomenclature}

server/src/curfu/schemas.py

@@ -5,10 +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,
@@ -176,7 +180,7 @@ class AssociatedDomainResponse(Response):
 class ValidateFusionResponse(Response):
     """Response model for Fusion validation endpoint."""
 
-    fusion: Fusion | None
+    fusion: AbstractFusion | None
 
 
 class ExonCoordsRequest(BaseModel):
@@ -288,6 +292,31 @@ class ClientAssayedFusion(AssayedFusion):
     ]
 
 
+class FormattedAssayedFusion(BaseModel):
+    """Assayed fusion with parameters defined as expected in fusor assayed_fusion function
+    validate attempts to validate a fusion by constructing it by sending kwargs. In the models and frontend, these are camelCase,
+    but the assayed_fusion and categorical_fusion constructors expect snake_case
+    """
+
+    structure: AssayedFusionElements
+    causative_event: CausativeEvent | None = None
+    assay: Assay | None = None
+    regulatory_element: RegulatoryElement | None = None
+    reading_frame_preserved: bool | None = None
+
+
+class FormattedCategoricalFusion(BaseModel):
+    """Categorical fusion with parameters defined as expected in fusor categorical_fusion function
+    validate attempts to validate a fusion by constructing it by sending kwargs. In the models and frontend, these are camelCase,
+    but the assayed_fusion and categorical_fusion constructors expect snake_case
+    """
+
+    structure: CategoricalFusionElements
+    regulatory_element: RegulatoryElement | None = None
+    critical_functional_domains: list[FunctionalDomain] | None = None
+    reading_frame_preserved: bool | None = None
+
+
 class NomenclatureResponse(Response):
     """Response model for regulatory element nomenclature endpoint."""