Merge pull request #47 from MassBank/dev-frontend

Use similarity search in backend & request via peak list and reference spectra within frontend

Author: michaelwenk

api/openapi.yml

@@ -26,7 +26,7 @@ paths:
           $ref: "./schemas/FilterSchemas.yaml#/components/schemas/MSType"
         required: false
       - in: query
-        name: ion-mode
+        name: ion_mode
         description: Filter by ion mode. If none is given, both is assumed.
         schema:
           $ref: "./schemas/FilterSchemas.yaml#/components/schemas/IonMode"
@@ -109,7 +109,7 @@ paths:
       summary: Get a list of records
       operationId: getRecords
       responses:
-        '200':
+        "200":
           description: "A list of records"
           content:
             application/json:
@@ -128,7 +128,7 @@ paths:
       summary: Get a MassBank record
       operationId: getRecord
       responses:
-        '200':
+        "200":
           description: "A MassBank record"
           content:
             application/json:
@@ -146,18 +146,18 @@ paths:
       summary: The SVG image for an accession
       operationId: getSVG
       responses:
-        '200':
+        "200":
           description: "A compound SVG"
           content:
-           image/svg+xml:
+            image/svg+xml:
               schema:
                 type: string
-  /records/count:    
+  /records/count:
     get:
       summary: The number of all records
       operationId: getCount
       responses:
-        '200':
+        "200":
           description: "The record count"
           content:
             application/json:
@@ -168,7 +168,7 @@ paths:
       summary: get filter options
       operationId: getFilterOptions
       responses:
-        '200':
+        "200":
           description: "All Filter options"
           content:
             application/json:
@@ -192,7 +192,7 @@ paths:
             $ref: "./schemas/FilterSchemas.yaml#/components/schemas/MSType"
           required: false
         - in: query
-          name: ion-mode
+          name: ion_mode
           description: Filter by ion mode. If none is given, both is assumed.
           schema:
             $ref: "./schemas/FilterSchemas.yaml#/components/schemas/IonMode"
@@ -204,7 +204,7 @@ paths:
             $ref: "./schemas/FilterSchemas.yaml#/components/schemas/Contributor"
           required: false
       responses:
-        '200':
+        "200":
           description: "All browse options"
           content:
             application/json:
@@ -215,9 +215,94 @@ paths:
       summary: get massbank metadata
       operationId: getMetadata
       responses:
-        '200':
+        "200":
           description: "Metadata for database and datasets"
           content:
             application/json:
               schema:
                 $ref: "./schemas/FilterOptions.yaml#/components/schemas/Metadata"
+
+  /similarity:
+    parameters:
+      - in: query
+        name: peak_list
+        description: Filter by peak list.
+        schema:
+          $ref: "./schemas/FilterSchemas.yaml#/components/schemas/PeakList"
+        required: true
+      - in: query
+        name: reference_spectra_list
+        description: Filter by reference spectra list.
+        schema:
+          type: array
+          items:
+            type: string
+          example:
+            - MSBNK-IPB_Halle-PB001341
+            - MSBNK-IPB_Halle-PB006202
+            - MSBNK-IPB_Halle-PB006203
+            - MSBNK-IPB_Halle-PB001342
+            - MSBNK-IPB_Halle-PB001343
+        required: false
+      - in: query
+        name: instrument_type
+        description: Filter by a list of instrument type, which will be associated by OR.
+        schema:
+          $ref: "./schemas/FilterSchemas.yaml#/components/schemas/InstrumentType"
+        required: false
+      - in: query
+        description: Filter by a List of MS types, which are associated by OR. If none is given, all is assumed.
+        name: ms_type
+        schema:
+          $ref: "./schemas/FilterSchemas.yaml#/components/schemas/MSType"
+        required: false
+      - in: query
+        name: ion_mode
+        description: Filter by ion mode. If none is given, both is assumed.
+        schema:
+          $ref: "./schemas/FilterSchemas.yaml#/components/schemas/IonMode"
+        required: false
+      - in: query
+        name: exact_mass
+        description: Filter by exact mass.
+        schema:
+          $ref: "./schemas/FilterSchemas.yaml#/components/schemas/ExactMass"
+      - in: query
+        name: mass_tolerance
+        description: "Tolerance for mass filters. Default: 0.3"
+        schema:
+          $ref: "./schemas/FilterSchemas.yaml#/components/schemas/MassTolerance"
+      - in: query
+        name: formula
+        description: Filter by formula.
+        schema:
+          $ref: "./schemas/FilterSchemas.yaml#/components/schemas/Formula"
+        required: false
+      - in: query
+        name: limit
+        description: "Maximum number of results. Default: 20"
+        schema:
+          $ref: "./schemas/FilterSchemas.yaml#/components/schemas/Limit"
+        required: false
+      - in: query
+        name: intensity_cutoff
+        description: "The Instensity cutoff for Peaklist search. Default: 5"
+        schema:
+          $ref: "./schemas/FilterSchemas.yaml#/components/schemas/IntensityCutoff"
+        required: false
+      - in: query
+        name: contributor
+        description: a contributor (institution)
+        schema:
+          $ref: "./schemas/FilterSchemas.yaml#/components/schemas/Contributor"
+        required: false
+    get:
+      summary: Get a list of records with similarity scores
+      operationId: getSimilarity
+      responses:
+        "200":
+          description: "A list of similar records"
+          content:
+            application/json:
+              schema:
+                $ref: "./schemas/SimilaritySearchResult.yaml"

api/schemas/FilterSchemas.yaml

@@ -10,7 +10,7 @@ components:
       type: array
       items:
         type: string
-        enum: [ MS,MS2,MS3,MS4 ]
+        enum: [MS, MS2, MS3, MS4]
     IonMode:
       type: string
       description: "enum: [ POSITIVE, NEGATIVE ]"
@@ -44,8 +44,8 @@ components:
       type: array
       items:
         type: string
-        description: "A tuple of m/z and intensity, e.g. (193.4,57)"
-        pattern: "\\([0-9]+(\\.[0-9]*)?,[0-9]+\\)"
+        description: "A tuple of m/z and intensity, e.g. (193.4;57)"
+        pattern: "\\([0-9]+(\\.[0-9]*)?;[0-9]+\\)"
     IntensityCutoff:
       type: integer
       default: 5

api/schemas/SimilaritySearchResult.yaml

@@ -0,0 +1,15 @@
+type: object
+properties:
+  data:
+    type: array
+    description: A ranked list of records with similarity scores.
+    items:
+      description: A record with similarity score.
+      type: object
+      properties:
+        accession:
+          description: MassBank accession id.
+          type: string
+        score:
+          description: Similarity score to the query spectrum.
+          type: number

cmd/mb3server/.openapi-generator/FILES

@@ -37,5 +37,7 @@ src/model_ms_focused_ion_inner.go
 src/model_search_result.go
 src/model_search_result_data_inner.go
 src/model_search_result_data_inner_spectra_inner.go
+src/model_similarity_search_result.go
+src/model_similarity_search_result_data_inner.go
 src/model_string_count_inner.go
 src/routers.go

cmd/mb3server/.openapi-generator/VERSION

@@ -1 +1 @@
-6.6.0
+7.7.0