feat: update to latest fusor version

client/src/services/ResponseModels.ts

@@ -10,9 +10,10 @@
  */
 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:
- * https://www.insdc.org/controlled-vocabulary-regulatoryclass
+ * Define possible classes of Regulatory Elements.
+ *
+ * Options are the possible values for ``/regulatory_class`` value property in the
+ * `INSDC controlled vocabulary <https://www.insdc.org/controlled-vocabulary-regulatoryclass>`_.
  */
 export type RegulatoryClass =
   | "attenuator"
@@ -113,8 +114,8 @@ export interface AssayedFusion {
 /**
  * Define RegulatoryElement class.
  *
- * `featureId` would ideally be constrained as a CURIE, but Encode, our preferred
- * feature ID source, doesn't currently have a registered CURIE structure for EH_
+ * ``featureId`` would ideally be constrained as a CURIE, but Encode, our preferred
+ * feature ID source, doesn't currently have a registered CURIE structure for ``EH_``
  * identifiers. Consequently, we permit any kind of free text.
  */
 export interface RegulatoryElement {
@@ -348,6 +349,7 @@ export interface GeneElement {
 }
 /**
  * Define Templated Sequence Element class.
+ *
  * A templated sequence is a contiguous genomic sequence found in the gene
  * product.
  */
@@ -402,7 +404,9 @@ export interface LiteralSequenceExpression {
   [k: string]: unknown;
 }
 /**
- * Define UnknownGene class. This is primarily intended to represent a
+ * Define UnknownGene class.
+ *
+ * This is primarily intended to represent a
  * partner in the result of a fusion partner-agnostic assay, which identifies
  * the absence of an expected gene. For example, a FISH break-apart probe may
  * indicate rearrangement of an MLL gene, but by design, the test cannot
@@ -414,6 +418,8 @@ export interface UnknownGeneElement {
   type?: "UnknownGeneElement";
 }
 /**
+ * Define causative event information for a fusion.
+ *
  * The evaluation of a fusion may be influenced by the underlying mechanism that
  * generated the fusion. Often this will be a DNA rearrangement, but it could also be
  * a read-through or trans-splicing event.
@@ -461,7 +467,9 @@ export interface CategoricalFusion {
   criticalFunctionalDomains?: FunctionalDomain[] | null;
 }
 /**
- * Define MultiplePossibleGenesElement class. This is primarily intended to
+ * Define MultiplePossibleGenesElement class.
+ *
+ * This is primarily intended to
  * represent a partner in a categorical fusion, typifying generalizable
  * characteristics of a class of fusions such as retained or lost regulatory elements
  * and/or functional domains, often curated from biomedical literature for use in
@@ -672,12 +680,13 @@ export interface ExonCoordsRequest {
  */
 export interface FormattedAssayedFusion {
   fusion_type?: AssayedFusion & string;
-  structure:
+  structure: (
     | TranscriptSegmentElement
     | GeneElement
     | TemplatedSequenceElement
     | LinkerElement
-    | UnknownGeneElement;
+    | UnknownGeneElement
+  )[];
   causative_event?: CausativeEvent | null;
   assay?: Assay | null;
   regulatory_element?: RegulatoryElement | null;
@@ -690,12 +699,13 @@ export interface FormattedAssayedFusion {
  */
 export interface FormattedCategoricalFusion {
   fusion_type?: CategoricalFusion & string;
-  structure:
+  structure: (
     | TranscriptSegmentElement
     | GeneElement
     | TemplatedSequenceElement
     | LinkerElement
-    | MultiplePossibleGenesElement;
+    | MultiplePossibleGenesElement
+  )[];
   regulatory_element?: RegulatoryElement | null;
   critical_functional_domains?: FunctionalDomain[] | null;
   reading_frame_preserved?: boolean | null;
@@ -776,9 +786,9 @@ export interface Response {
 export interface SequenceIDResponse {
   warnings?: string[] | null;
   sequence: string;
-  refseq_id: string | null;
-  ga4gh_id: string | null;
-  aliases: string[] | null;
+  refseq_id?: string | null;
+  ga4gh_id?: string | null;
+  aliases?: string[] | null;
 }
 /**
  * Response model for service_info endpoint.

server/pyproject.toml

@@ -28,7 +28,7 @@ dependencies = [
     "click",
     "boto3",
     "botocore",
-    "fusor ~= 0.2.0",
+    "fusor ~= 0.3.0",
     "cool-seq-tool ~= 0.5.1",
     "pydantic == 2.4.2",
     "gene-normalizer ~= 0.4.0",

server/src/curfu/schemas.py

@@ -7,9 +7,9 @@
 from fusor.models import (
     Assay,
     AssayedFusion,
-    AssayedFusionElements,
+    AssayedFusionElement,
     CategoricalFusion,
-    CategoricalFusionElements,
+    CategoricalFusionElement,
     CausativeEvent,
     FunctionalDomain,
     Fusion,
@@ -301,7 +301,7 @@ class FormattedAssayedFusion(BaseModel):
     """
 
     fusion_type: FusionType.ASSAYED_FUSION = FusionType.ASSAYED_FUSION
-    structure: AssayedFusionElements
+    structure: list[AssayedFusionElement]
     causative_event: CausativeEvent | None = None
     assay: Assay | None = None
     regulatory_element: RegulatoryElement | None = None
@@ -315,7 +315,7 @@ class FormattedCategoricalFusion(BaseModel):
     """
 
     fusion_type: FusionType.CATEGORICAL_FUSION = FusionType.CATEGORICAL_FUSION
-    structure: CategoricalFusionElements
+    structure: list[CategoricalFusionElement]
     regulatory_element: RegulatoryElement | None = None
     critical_functional_domains: list[FunctionalDomain] | None = None
     reading_frame_preserved: bool | None = None