ODM-11747: storing cell metadata

Earthfile

@@ -151,7 +151,6 @@ swagger:
     COPY +build/v1 /usr/share/nginx/html/yaml/
     COPY openapi/swagger/fs /
 
-    RUN rm -f /usr/share/nginx/html/yaml/processorsController.yaml # TODO: Remove this line after 1.61 release
     RUN rm -f /usr/share/nginx/html/yaml/odmApi.yaml
     RUN apk add bash --no-cache && \
         rewrite_entrypoint.sh && \

build.gradle.kts

@@ -82,9 +82,7 @@ tasks {
     }
     val mergeSpecifications by registering(MergeSpecifications::class) {
         dependsOn(downloadSpec)
-        val fileList = sourceFileList.filter { it.asFile.name != processorsControllerFileName } // TODO: use sourceFileList after 1.61 release
-        inputFiles = fileList
-        //inputFiles = sourceFileList
+        inputFiles = sourceFileList
         outputFile = layout.projectDirectory.file(mergedFilePath)
     }
 

openapi/swagger/fs/usr/share/nginx/html/helper/index.html

@@ -1,5 +1,5 @@
 <!--
-  ~ Copyright (c) 2011-2024 Genestack Limited
+  ~ Copyright (c) 2011-2025 Genestack Limited
   ~ All Rights Reserved
   ~ THIS IS UNPUBLISHED PROPRIETARY SOURCE CODE OF GENESTACK LIMITED
   ~ The copyright notice above does not evidence any
@@ -90,6 +90,9 @@ <h4>Query/retrieve data</h4>
           <li>
             <a href="/swagger/?urls.primaryName=preparationUser">preparationUser</a> - API endpoints for retrieving only preparation metadata
           </li>
+          <li>
+            <a href="/swagger/?urls.primaryName=cellUser">cellUser</a> - API endpoints for retrieving cell data or metadata
+          </li>
           <li>
             <a href="/swagger/?urls.primaryName=expressionUser">expressionUser</a> - API endpoints for retrieving any tabular data (not only expression data) except Gene Variant or Flow Cytometry
           </li>
@@ -124,6 +127,9 @@ <h4>Import/curate data</h4>
           <li>
             <a href="/swagger/?urls.primaryName=preparationCurator">preparationCurator</a> - API endpoints to add, delete and update preparations and preparation metadata
           </li>
+          <li>
+              <a href="/swagger/?urls.primaryName=cellCurator">cellCurator</a> - API endpoints for retrieving cell data or metadata
+          </li>
           <li>
             <a href="/swagger/?urls.primaryName=expressionCurator">expressionCurator</a> - API endpoints to add, delete and update any tabular data (not only expression data) except Gene Variant or Flow Cytometry
           </li>

openapi/v1/cellCurator.yaml

@@ -0,0 +1,120 @@
+openapi: 3.1.0
+info:
+  description: |-
+    This swagger page describes the APIs for retrieving cells.
+  title: ODM API
+  version: default-released
+tags:
+  - name: Cells as Curator
+paths:
+  /api/v1/as-curator/cells/{id}:
+    get:
+      operationId: getCellByIdAsCurator
+      parameters:
+        - description: Unique cell identifier. Consists of a cell group accession and a cell barcode, separated by a hyphen, e.g. `GSF123456-AAACCTGAGCGCTCCA-1`.
+          in: path
+          name: id
+          required: true
+          schema:
+            type: string
+      responses:
+        "200":
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/Cell"
+          description: The request was successful. The returned value is the object.
+        "400":
+          content: { }
+          description: Invalid data in the request. See the error message for details.
+        "401":
+          content: { }
+          description: |-
+            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
+             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
+        "404":
+          content: { }
+          description: Object with provided ID could not be found in ODM.
+        "500":
+          content: { }
+          description: "An internal server error occurred. This indicates an unexpected\
+            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+            \ including the error details."
+      security:
+        - Access-token: [ ]
+        - Genestack-API-Token: [ ]
+      summary: Retrieve a cell by ID
+      tags:
+        - Cells as Curator
+  /api/v1/as-curator/cells/by/group/{id}:
+    get:
+      description: |+
+        ## Paging
+        For performance reasons this endpoint returns results in "pages" of limited size together with a `cursor` tag.
+        To retrieve the next page of results please supply this `cursor` tag to resume the query from your previous result and get the next page.
+        If there are no more results you will just retrieve an empty result.
+      operationId: getCellsByGroupAsCurator
+      parameters:
+        - description: Unique identifier (accession) of the cell group.
+          in: path
+          name: id
+          required: true
+          schema:
+            type: string
+        - description: Maximum number of results to return per page (see Paging above).
+            This value must be between 0 and 10000 (inclusive). The default is 2000.
+          in: query
+          name: pageLimit
+          schema:
+            format: int32
+            type: integer
+        - description: The page tag to resume results from (see Paging above). Cell ID is currently used as a cursor.
+          in: query
+          name: cursor
+          schema:
+            type: string
+      responses:
+        "200":
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/CellListResponse"
+          description: The request was successful. The returned value is a list of
+            objects.
+        "400":
+          content: { }
+          description: Cell data cannot be retrieved.
+        "401":
+          content: { }
+          description: |-
+            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
+             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
+        "404":
+          content: { }
+          description: No object exists with the given ID.
+        "500":
+          content: { }
+          description: "An internal server error occurred. This indicates an unexpected\
+            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+            \ including the error details."
+      security:
+        - Access-token: [ ]
+        - Genestack-API-Token: [ ]
+      summary: Retrieve cells from a given group
+      tags:
+        - Cells as Curator
+components:
+  schemas:
+    Cell:
+      $ref: "./schemas/cell/Cell.yaml"
+    CellListResponse:
+      $ref: "./schemas/cell/CellListResponse.yaml"
+  securitySchemes:
+    Access-token:
+      in: header
+      name: Authorization
+      type: apiKey
+    Genestack-API-Token:
+      in: header
+      name: Genestack-API-Token
+      type: apiKey

openapi/v1/cellUser.yaml

@@ -0,0 +1,120 @@
+openapi: 3.1.0
+info:
+  description: |-
+    This swagger page describes the APIs for retrieving cells.
+  title: ODM API
+  version: default-released
+tags:
+  - name: Cells as User
+paths:
+  /api/v1/as-user/cells/{id}:
+    get:
+      operationId: getCellByIdAsUser
+      parameters:
+        - description: Unique cell identifier. Consists of a cell group accession and a cell barcode, separated by a hyphen, e.g. `GSF123456-AAACCTGAGCGCTCCA-1`.
+          in: path
+          name: id
+          required: true
+          schema:
+            type: string
+      responses:
+        "200":
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/Cell"
+          description: The request was successful. The returned value is the object.
+        "400":
+          content: { }
+          description: Invalid data in the request. See the error message for details.
+        "401":
+          content: { }
+          description: |-
+            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
+             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
+        "404":
+          content: { }
+          description: Object with provided ID could not be found in ODM.
+        "500":
+          content: { }
+          description: "An internal server error occurred. This indicates an unexpected\
+            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+            \ including the error details."
+      security:
+        - Access-token: [ ]
+        - Genestack-API-Token: [ ]
+      summary: Retrieve a cell by ID
+      tags:
+        - Cells as User
+  /api/v1/as-user/cells/by/group/{id}:
+    get:
+      description: |+
+        ## Paging
+        For performance reasons this endpoint returns results in "pages" of limited size together with a `cursor` tag.
+        To retrieve the next page of results please supply this `cursor` tag to resume the query from your previous result and get the next page.
+        If there are no more results you will just retrieve an empty result.
+      operationId: getCellsByGroupAsUser
+      parameters:
+        - description: Unique identifier (accession) of the cell group.
+          in: path
+          name: id
+          required: true
+          schema:
+            type: string
+        - description: Maximum number of results to return per page (see Paging above).
+            This value must be between 0 and 10000 (inclusive). The default is 2000.
+          in: query
+          name: pageLimit
+          schema:
+            format: int32
+            type: integer
+        - description: The page tag to resume results from (see Paging above). Cell ID is currently used as a cursor.
+          in: query
+          name: cursor
+          schema:
+            type: string
+      responses:
+        "200":
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/CellListResponse"
+          description: The request was successful. The returned value is a list of
+            objects.
+        "400":
+          content: { }
+          description: Cell data cannot be retrieved.
+        "401":
+          content: { }
+          description: |-
+            User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
+             or  Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
+        "404":
+          content: { }
+          description: No object exists with the given ID.
+        "500":
+          content: { }
+          description: "An internal server error occurred. This indicates an unexpected\
+            \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+            \ including the error details."
+      security:
+        - Access-token: [ ]
+        - Genestack-API-Token: [ ]
+      summary: Retrieve cells from a given group
+      tags:
+        - Cells as User
+components:
+  schemas:
+    Cell:
+      $ref: "./schemas/cell/Cell.yaml"
+    CellListResponse:
+      $ref: "./schemas/cell/CellListResponse.yaml"
+  securitySchemes:
+    Access-token:
+      in: header
+      name: Authorization
+      type: apiKey
+    Genestack-API-Token:
+      in: header
+      name: Genestack-API-Token
+      type: apiKey