WIP: Add connexion

app/app.py

@@ -1,14 +1,22 @@
 import os
 import json
 import flask
+import connexion
+from flask_cors import CORS
 from app import database, geneset, drugset, download, statistics
 
 ROOT_PATH = os.environ.get('ROOT_PATH', '/covid19/')
 # Load any additional configuration parameters via
 #  environment variables--`../.env` can be used
 #  for sensitive information!
 
-app = flask.Flask(__name__, static_url_path=ROOT_PATH + 'static')
+
+connexionApp = connexion.App(__name__)
+connexionApp.add_api(os.path.join(os.path.dirname(__file__), 'swagger.yaml'), base_path=ROOT_PATH)
+app = connexionApp.app
+app.static_url_path = ROOT_PATH + 'static'
+CORS(app)
+
 app.before_first_request(database.init)
 
 
@@ -20,27 +28,23 @@ def route_index():
 def route_genesets_table():
     return geneset.serve_geneset_datatable(int(flask.request.values.get('reviewed')))(**json.loads(flask.request.values.get('body')))
 
-@app.route(ROOT_PATH + 'genesets', methods=['GET', 'POST'])
+@app.route(ROOT_PATH + 'genesets', methods=['GET'])
 def route_genesets():
     if flask.request.method == 'GET':
         reviewed = flask.request.args.get('reviewed', 1)
         return geneset.get_genesets(reviewed)
-    elif flask.request.method == 'POST':
-        return geneset.add_geneset(flask.request.form)
 
 @app.route(ROOT_PATH + 'drugsets_table', methods=['POST'])
 def route_drugsets_table():
     return drugset.serve_drugset_datatable(int(flask.request.values.get('reviewed')))(
         **json.loads(flask.request.values.get('body'))
     )
 
-@app.route(ROOT_PATH + 'drugsets', methods=['GET', 'POST'])
+@app.route(ROOT_PATH + 'drugsets', methods=['GET'])
 def route_drugs():
     if flask.request.method == 'GET':
         reviewed = flask.request.args.get('reviewed', 1)
         return drugset.get_drugsets(reviewed)
-    elif flask.request.method == 'POST':
-        return drugset.add_drugset(flask.request.form)
 
 
 @app.route(ROOT_PATH + 'review', methods=['GET', 'POST'])

app/download.py

@@ -1,14 +1,19 @@
+import flask
 from app.database import Session
 from app.models import Geneset, Drugset
 
 def genesets():
-  sess = Session()
-  for geneset in sess.query(Geneset).filter(Geneset.reviewed == 1):
-    yield geneset.to_gmt() + '\n'
-  sess.close()
+  def geneset_generator():
+    sess = Session()
+    for geneset in sess.query(Geneset).filter(Geneset.reviewed == 1):
+      yield geneset.to_gmt() + '\n'
+    sess.close()
+  return flask.Response(geneset_generator(), mimetype='text/gmt')
 
 def drugsets():
-  sess = Session()
-  for drugset in sess.query(Drugset).filter(Drugset.reviewed == 1):
-    yield drugset.to_gmt() + '\n'
-  sess.close()
+  def drugset_generator():
+    sess = Session()
+    for drugset in sess.query(Drugset).filter(Drugset.reviewed == 1):
+      yield drugset.to_gmt() + '\n'
+    sess.close()
+  return flask.Response(drugset_generator(), mimetype='text/gmt')

app/geneset.py

@@ -27,7 +27,7 @@ def add_geneset(form):
     author_name = form['authorName']
     author_email = form['authorEmail']
     author_aff = form['authorAff']
-    show_contacts = 1 if 'showContacts' in form else 0
+    show_contacts = 1 if form.get('showContacts') else 0
     enrichr_ids = enrichr_submit(gene_set, desc_short)
     enrichr_shortid = enrichr_ids['shortId']
     enrichr_userlistid = enrichr_ids['userListId']

app/swagger.yaml

@@ -0,0 +1,175 @@
+swagger: '2.0'
+info:
+  title: COVID-19 Crowd Generated Gene and Drug Set Library API
+  version: "0.1"
+  description: A collection of drugs and gene sets related to COVID-19 research contributed by the community
+consumes:
+  - application/json
+produces:
+  - application/json
+paths:
+  /genesets:
+    post:
+      operationId: app.geneset.add_geneset
+      consumes:
+      - application/x-www-form-urlencoded
+      parameters:
+      - name: body
+        in: body
+        schema:
+          type: object
+          properties:
+            source:
+              type: string
+              format: url
+              description: The source URL
+            geneSet:
+              type: string
+              description: The actual newline-separated set
+            descrFull:
+              type: string
+              description: A long description of the set
+            descrShort:
+              type: string
+              description: A short description of the set
+            authorName:
+              type: string
+              description: Author Name
+            authorEmail:
+              type: string
+              description: Author Email
+            authorAff:
+              type: string
+              description: Author affiliation
+            showContacts:
+              type: boolean
+              description: true to show, false otherwise (defaults to false)
+            meta:
+              type: object
+              description: Additional key-value metadata properties
+              additionalProperties:
+                type: string
+          required:
+          - source
+          - geneSet
+          - descrFull
+          - descrShort
+          - authorName
+          - authorEmail
+          - authorAff
+          - showContacts
+          - meta
+        required: true
+      responses:
+        200:
+          description: Success
+          schema:
+            type: object
+            properties:
+              success:
+                type: boolean
+                description: true on success, false otherwise
+        500:
+          description: Error occurred
+          schema:
+            type: object
+            properties:
+              success:
+                type: boolean
+                description: true on success, false otherwise
+              error:
+                type: string
+                description: A error string possibly explaining the error
+
+  /genesets.gmt:
+    get:
+      operationId: app.download.genesets
+      description: Download the genesets
+      produces:
+      - text/gmt
+      responses:
+        200:
+          description: A GMT containing all the genesets
+
+  /drugsets:
+    post:
+      operationId: app.drugset.add_drugset
+      consumes:
+      - application/x-www-form-urlencoded
+      parameters:
+      - name: body
+        in: body
+        schema:
+          type: object
+          properties:
+            source:
+              type: string
+              format: url
+              description: The source URL
+            geneSet:
+              type: string
+              description: The actual newline-separated set
+            descrFull:
+              type: string
+              description: A long description of the set
+            descrShort:
+              type: string
+              description: A short description of the set
+            authorName:
+              type: string
+              description: Author Name
+            authorEmail:
+              type: string
+              description: Author Email
+            authorAff:
+              type: string
+              description: Author affiliation
+            showContacts:
+              type: boolean
+              description: true to show, false otherwise (defaults to false)
+            meta:
+              type: object
+              description: Additional key-value metadata properties
+              additionalProperties:
+                type: string
+          required:
+          - source
+          - geneSet
+          - descrFull
+          - descrShort
+          - authorName
+          - authorEmail
+          - authorAff
+          - showContacts
+          - meta
+        required: true
+      responses:
+        200:
+          description: Success
+          schema:
+            type: object
+            properties:
+              success:
+                type: boolean
+                description: true on success, false otherwise
+        500:
+          description: Error occurred
+          schema:
+            type: object
+            properties:
+              success:
+                type: boolean
+                description: true on success, false otherwise
+              error:
+                type: string
+                description: A error string possibly explaining the error
+
+  /drugsets.gmt:
+    get:
+      operationId: app.download.drugsets
+      description: Download the drugsets
+      produces:
+        - text/gmt
+      responses:
+        200:
+          description: A GMT containing all the genesets

app/templates/index.html

@@ -57,7 +57,7 @@ <h1 class="display-5">COVID-19 Crowd Generated Gene and Drug Set Library</h1>
                                    style="width:100%">
                             </table>
                             <div class="row">
-                                <a href="{{ url_for('download_drugsets') }}"><i class="fas fa-download mr-1"
+                                <a href="./drugsets.gmt"><i class="fas fa-download mr-1"
                                                                                 style="font-size: 0.9rem;"></i>Download
                                     all drug sets</a>
                             </div>
@@ -71,7 +71,7 @@ <h1 class="display-5">COVID-19 Crowd Generated Gene and Drug Set Library</h1>
                                    style="width:100%">
                             </table>
                             <div class="row">
-                                <a href="{{ url_for('download_genesets') }}"><i class="fas fa-download mr-1"
+                                <a href="./genesets.gmt"><i class="fas fa-download mr-1"
                                                                                 style="font-size: 0.9rem;"> </i>Download
                                     all gene sets</a>
                             </div>

requirements.txt

@@ -1,10 +1,13 @@
 # Python dependencies
 alembic
+connexion
 cryptography
 Flask
+flask_cors
 pymysql
 python-dotenv
 pytz
 requests
 sqlalchemy
+swagger-ui-bundle
 uwsgi

run.py

@@ -1,7 +1,8 @@
 import os
 import json
-from app.app import app
+from app.app import connexionApp as app
 
+ROOT_PATH = os.environ.get('ROOT_PATH', '/covid19/')
 DEBUG_PORT = json.loads(os.environ.get('DEBUG_PORT', 'null'))
 DEBUG = json.loads(os.environ.get('DEBUG', 'true'))
 # HOST = os.environ.get('HOST', '0.0.0.0')
@@ -16,4 +17,6 @@
     PORT = DEBUG_PORT
 
 # TODO: Add `HOST` when DB `HOST` is fully removed
+print(f'Application at http://0.0.0.0:{PORT}{ROOT_PATH}')
+print(f'Swagger UI at http://0.0.0.0:{PORT}{ROOT_PATH}ui/')
 app.run(host='0.0.0.0', port=PORT, debug=DEBUG)