Endpoint specification for model/submit

Author: sujaypatil96

api/openapi/api.yaml

@@ -61,7 +61,7 @@ paths:
           required: true
       operationId: api.routes.get_manifest_route
       responses:
-        '201':
+        "201":
           description: Googlesheet link created
           content:
             application/json:
@@ -103,7 +103,7 @@ paths:
           required: true
       operationId: api.routes.validate_manifest_route
       responses:
-        '200':
+        "200":
           description: Manifest Validated
           content:
             application/json:
@@ -120,4 +120,52 @@ paths:
                           type: string
       tags:
         - Model Operations
-        
+  /model/submit:
+    post:
+      summary: Endpoint to facilitate manifest submission
+      description: Endpoint to submit annotated manifest files
+      requestBody:
+        content:
+          multipart/form-data:
+            schema:
+              type: object
+              properties:
+                csv_file:
+                  type: string
+                  format: binary
+      parameters:
+        - in: query
+          name: schema_url
+          schema:
+            type: string
+          description: Data Model URL
+          example: >-
+            https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.model.jsonld
+          required: true
+        - in: query
+          name: data_type
+          schema:
+            type: string
+            nullable: true
+          description: Data Model Component
+          example: Patient
+          required: true
+        - in: query
+          name: dataset_id
+          schema:
+            type: string
+            nullable: true
+          description: Dataset SynID
+          required: true
+      operationId: api.routes.submit_manifest_route
+      responses:
+        "200":
+          description: Manifest submitted
+          content:
+            application/json:
+              schema:
+                type: boolean
+        "500":
+          description: Check schematic log
+      tags:
+        - Model Operations

api/routes.py

@@ -96,3 +96,36 @@ def validate_manifest_route(schema_url, data_type):
     )
 
     return errors
+
+
+def submit_manifest_route(schema_url):
+    # call config_handler()
+    config_handler()
+
+    manifest_file = connexion.request.files["csv_file"]
+
+    # save contents of incoming manifest CSV file to temp file
+    temp_dir = tempfile.gettempdir()
+    # path to temp file where manifest file contents will be saved
+    temp_path = os.path.join(temp_dir, manifest_file.filename)
+    # save content
+    manifest_file.save(temp_path)
+
+    # get path to temporary JSON-LD file
+    jsonld = get_temp_jsonld(schema_url)
+
+    dataset_id = connexion.request.args["dataset_id"]
+
+    data_type = connexion.request.args["data_type"]
+
+    metadata_model = MetadataModel(
+        inputMModelLocation=jsonld, inputMModelLocationType="local"
+    )
+
+    success = metadata_model.submit_metadata_manifest(
+        manifest_path=temp_path,
+        dataset_id=dataset_id,
+        validate_component=data_type,
+    )
+
+    return success

poetry.lock

@@ -55,8 +55,8 @@ rdflib = "^5.0.0"
 setuptools = "^52.0.0"
 synapseclient = "~2.3"  # ~ (not ^) until Data Curator App supports OAuth tokens
 toml = "^0.10.2"
-Flask = "^2.0.1"
-connexion = "^2.7.0"
+Flask = "^1.1.4"
+connexion = {extras = ["swagger-ui"], version = "^2.8.0"}
 
 
 [tool.poetry.dev-dependencies]