feat: /api/v1/strucvars/csq endpoint with OpenAPI (#607) (#612)

openapi.schema.yaml

@@ -9,6 +9,59 @@ info:
     name: MIT
   version: 0.29.6
 paths:
+  /api/v1/strucvars/csq:
+    get:
+      tags:
+      - strucvars_csq
+      summary: Query for consequence of a variant.
+      operationId: strucvarsCsq
+      parameters:
+      - name: genome_release
+        in: query
+        description: The assembly.
+        required: true
+        schema:
+          $ref: '#/components/schemas/GenomeRelease'
+      - name: chromosome
+        in: query
+        description: Chromosome.
+        required: true
+        schema:
+          type: string
+      - name: start
+        in: query
+        description: 1-based start position.
+        required: true
+        schema:
+          type: integer
+          format: int32
+      - name: stop
+        in: query
+        description: 1-based stop position, ignored for INS.
+        required: false
+        schema:
+          type: integer
+          format: int32
+          nullable: true
+      - name: sv_type
+        in: query
+        description: The variant type to use for annotation.
+        required: true
+        schema:
+          $ref: '#/components/schemas/StrucvarsSvType'
+      responses:
+        '200':
+          description: Strucvars consequence information.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/StrucvarsCsqResponse'
+        '500':
+          description: Internal server error.
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/CustomError'
   /api/v1/versionsInfo:
     get:
       tags:
@@ -62,6 +115,12 @@ components:
           type: string
           description: Version of the Ensembl database, if any.
           nullable: true
+    GenomeRelease:
+      type: string
+      description: Select the genome release to use.
+      enum:
+      - grch37
+      - grch38
     SoftwareVersions:
       type: object
       description: Software version specification.
@@ -75,6 +134,83 @@ components:
         hgvs_rs:
           type: string
           description: Version of the `hgvs` crate.
+    StrucvarsCsqQuery:
+      type: object
+      description: Query parameters of the `/api/v1/strucvars/csq` endpoint.
+      required:
+      - genome_release
+      - chromosome
+      - start
+      - sv_type
+      properties:
+        genome_release:
+          $ref: '#/components/schemas/GenomeRelease'
+        chromosome:
+          type: string
+          description: Chromosome.
+        start:
+          type: integer
+          format: int32
+          description: 1-based start position.
+        stop:
+          type: integer
+          format: int32
+          description: 1-based stop position, ignored for INS.
+          nullable: true
+        sv_type:
+          $ref: '#/components/schemas/StrucvarsSvType'
+    StrucvarsCsqResponse:
+      type: object
+      description: Response of the `/api/v1/strucvars/csq` endpoint.
+      required:
+      - version
+      - query
+      - result
+      properties:
+        version:
+          $ref: '#/components/schemas/VersionsInfoResponse'
+        query:
+          $ref: '#/components/schemas/StrucvarsCsqQuery'
+        result:
+          type: array
+          items:
+            $ref: '#/components/schemas/StrucvarsGeneTranscriptEffects'
+          description: The resulting records for the affected genes.
+    StrucvarsGeneTranscriptEffects:
+      type: object
+      description: Explanation of transcript effect per individual gene.
+      required:
+      - hgnc_id
+      - transcript_effects
+      properties:
+        hgnc_id:
+          type: string
+          description: HGNC identifier
+        transcript_effects:
+          type: array
+          items:
+            $ref: '#/components/schemas/StrucvarsTranscriptEffect'
+          description: Transcript effects for the gene.
+    StrucvarsSvType:
+      type: string
+      description: Structural Variant type.
+      enum:
+      - DEL
+      - DUP
+      - INS
+      - INV
+      - BND
+    StrucvarsTranscriptEffect:
+      type: string
+      description: Enumeration for effect on transcript.
+      enum:
+      - transcript_variant
+      - exon_variant
+      - splice_region_variant
+      - intron_variant
+      - upstream_variant
+      - downstream_variant
+      - intergenic_variant
     VersionsInfoResponse:
       type: object
       description: Response of the `/api/v1/version` endpoint.