REST API endpoint for manifest creation

Author: sujaypatil96

api/README.md

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+## Setup
+
+To start a local Flask server and test your endpoints:
+
+```bash
+source .venv/bin/activate
+python run_api.py
+```
+
+Access the Swagger UI docs at this location:
+
+```bash
+http://localhost:3001/v1/ui/
+```

api/__init__.py

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+import os
+
+import connexion
+
+from schematic import CONFIG
+
+
+def create_app():
+    connexionapp = connexion.FlaskApp(__name__, specification_dir="openapi/")
+    connexionapp.add_api("api.yaml")
+
+    # get the underlying Flask app instance
+    app = connexionapp.app
+
+    # path to config.yml file saved as a Flask config variable
+    app.config["SCHEMATIC_CONFIG"] = os.path.abspath(
+        os.path.join(__file__, "../../config.yml")
+    )
+
+    # Configure flask app
+    # app.config[] = schematic[]
+    # app.config[] = schematic[]
+    # app.config[] = schematic[]
+
+    # Initialize extension schematic
+    # import MyExtension
+    # myext = MyExtension()
+    # myext.init_app(app)
+
+    return app
+
+# def route_code():
+#     import flask_schematic as sc
+#     sc.method1()
+#

api/openapi/api.yaml

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+openapi: 3.0.0
+info:
+  title: Schematic REST API
+  version: 0.1.0
+  description: >-
+    This service exposes core functionalities from schematic as REST API
+    endpoints
+
+servers:
+  - url: /v1
+
+paths:
+  /manifest/generate:
+    get:
+      summary: >-
+        Endpoints to expose annotation, validation and submission
+        functionalities from schematic
+      description: Endpoint to create dynamically create metadata manifest files
+      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: title
+          schema:
+            type: string
+          description: Title of Manifest
+          example: Patient Metadata Manifest
+          required: false
+        - in: query
+          name: data_type
+          schema:
+            type: string
+            nullable: true
+          description: Data Model Component
+          example: Patient
+          required: true
+        - in: query
+          name: oauth
+          schema:
+            type: boolean
+            default: true
+          description: OAuth or Service Account
+          required: false
+        - in: query
+          name: use_annotations
+          schema:
+            type: boolean
+            default: false
+          description: To Use Annotations
+          required: false
+        - in: query
+          name: dataset_id
+          schema:
+            type: string
+            nullable: true
+          description: Dataset SynID
+          required: true
+      operationId: api.routes.get_manifest_route
+      responses:
+        '201':
+          description: Googlesheet link created.
+          content:
+            application/json:
+              schema:
+                type: string
+      tags:
+        - Manifest Operations

api/routes.py

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+import os
+import shutil
+import tempfile
+import urllib.request
+
+import connexion
+from flask import current_app as app, request, g
+
+from schematic import CONFIG
+
+from schematic.manifest.generator import ManifestGenerator
+
+
+# def before_request(var1, var2):
+#     # Do stuff before your route executes
+#     pass
+# def after_request(var1, var2):
+#     # Do stuff after your route executes
+#     pass
+
+# @before_request
+def get_manifest_route(schema_url, title, oauth, use_annotations):
+    # check if file exists at the path created, i.e., app.config['SCHEMATIC_CONFIG']
+    path_to_config = app.config["SCHEMATIC_CONFIG"]
+
+    if os.path.isfile(path_to_config):
+        CONFIG.load_config(path_to_config)
+    else:
+        raise FileNotFoundError(
+            f"No configuration file was found at this path: {path_to_config}"
+        )
+
+    # retrieve a JSON-LD via URL and store it in a temporary location
+    with urllib.request.urlopen(schema_url) as response:
+        with tempfile.NamedTemporaryFile(delete=False, suffix=".jsonld") as tmp_file:
+            shutil.copyfileobj(response, tmp_file)
+
+    # get path to temporary JSON-LD file
+    jsonld = tmp_file.name
+
+    # request.data[]
+    data_type = connexion.request.args["data_type"]
+
+    # create object of type ManifestGenerator
+    manifest_generator = ManifestGenerator(
+        path_to_json_ld=jsonld,
+        title=title,
+        root=data_type,
+        oauth=oauth,
+        use_annotations=use_annotations,
+    )
+
+    dataset_id = connexion.request.args["dataset_id"]
+
+    # call get_manifest() on manifest_generator
+    result = manifest_generator.get_manifest(sheet_url=True, dataset_id=dataset_id)
+
+    return result