add descriptions, update flasgger endpoints

fda-units-service/app.py

@@ -87,7 +87,7 @@ def validate(unit):
     except Exception as e:
         logging.error(e)
         res = {"success": False, "message": str(e)}
-        return jsonify(res)
+        return jsonify(res), 500
 
 
 @app.route('/api/units/uri/<uname>', methods=["GET"], endpoint='uri')
@@ -141,7 +141,7 @@ def save_column_concept():
         res = {"success": False, "message": str(e)}
         return jsonify(res), 500
 
-@app.route('/api/units/getconcept/<cname>', methods=["GET"], endpoint='get_concept')
+@app.route('/api/ontologies/getconcept/<cname>', methods=["GET"], endpoint='get_concept')
 @swag_from('getconcept.yml')
 def get_concept(cname):
     logging.debug('endpoint get concept, cname=%s, body=%s', cname, request)
@@ -156,33 +156,33 @@ def get_concept(cname):
 
 ONTOLOGIES_DIRECTORY = 'ontologies'
 
-@app.route('/api/ontologies', methods=["POST"], endpoint='upload_onto')
-@swag_from('ontologie.yml')
+@app.route('/api/ontology', methods=["POST"], endpoint='upload_onto')
+@swag_from('ontologies.yml')
 def post_ontologies():
     if 'file' not in request.files:
         return "no file", 500
     file = request.files['file']
     if file.filename == '':
-        return "no file selected", 500
+        return "no file selected", 400
     if file and allowed_file(file.filename):
         filename = secure_filename(file.filename)
         if ontology_exists(Path(filename).stem):
-            return "ontology name already exists", 500
+            return "ontology name already exists", 409
         setup_ontology_dir()
         file.save(os.path.join(ONTOLOGIES_DIRECTORY, filename))
         logging.debug('created ontology: %s', filename)
-        return "created", 200
+        return "created", 201
 
 @app.route('/api/ontologies', methods=["GET"], endpoint='get_ontos')
-@swag_from('ontologies.yml')
+@swag_from('ontology.yml')
 def get_ontologies():
     print(list_ontologies())
     return jsonify(list_ontologies())
 
-@app.route('/api/ontologies/<name>', methods=["GET"], endpoint='get_onto')
-@swag_from('ontologie.yml')
-def get_ontologies(name):
-    ontology = get_ontology(name)
+@app.route('/api/ontologies/<o_name>', methods=["GET"], endpoint='get_onto')
+@swag_from('ontologybyname.yml')
+def get_ontologies(o_name):
+    ontology = get_ontology(o_name)
     if ontology is None:
         return "ontology does not exist", 404
     return ontology

fda-units-service/onto_feat.py

@@ -3,6 +3,7 @@ import glob
 import sys
 import os
 from pathlib import Path
+import rdflib
 
 ALLOWED_EXTENSIONS = {'ttl', 'nt'}
 

fda-units-service/us-yml/getconcept.yml

@@ -8,7 +8,7 @@ parameters:
 - in: "path"
   type: "string"
   name: "cname"
-  description: "Enter a table name or attribute name.´"
+  description: "Enter a concept name."
   required: true
 responses:
   200: 

fda-units-service/us-yml/ontologies.yml

-summary: "Get list of ontologies"
-description: "This is a simple API for getting the list of all ontologies contained in DB-Repo."
+summary: "Post / Upload ontology"
+description: "This is a simple API for posting ontologies (.nt, .ttl files) to DB-Repo."
 consumes:
 - "application/json"
 produces:
 - "application/json"
+parameters:
+- name: file
+  required: false
+  in: formData
+  type: file
 responses:
   200:
     description: "OK"
+  201:
+    description: "Created"
+  400:
+    description: "Bad request"
   405:
     description: "Invalid input"
+  409:
+    description: "Conflict"
\ No newline at end of file

fda-units-service/us-yml/ontologie.yml → fda-units-service/us-yml/ontology.yml

 summary: "Get ontology"
-description: "This is a simple API for getting ontologies (.nt, .ttl files) used in DB-Repo."
+description: "This is a simple API for listing all ontologies (.nt, .ttl files) used in DB-Repo."
 consumes:
 - "application/json"
 produces:
 - "application/json"
-parameters:
-- name: file
-  required: false
-  in: formData
-  type: file
 responses:
   200:
     description: "OK"
-  201:
-    description: "Created"
   405:
     description: "Invalid input"
\ No newline at end of file

fda-units-service/us-yml/ontologybyname.yml

+summary: "Get ontology"
+description: "This is a simple API for getting a certain ontologies (.nt, .ttl files) stored in DB-Repo."
+consumes:
+- "application/json"
+produces:
+- "application/json"
+parameters:
+  - name: o_name
+    in: path
+    required: true
+    type: string
+    default: "VOCAB_QUDT-UNITS-ALL-v2.1"
+responses:
+  200:
+    description: "OK"
+  404:
+    description: "Not found"
+  405:
+    description: "Invalid input"

fda-units-service/us-yml/suggest.yml

@@ -7,7 +7,7 @@ produces:
 parameters:
 - in: "body"
   name: "body"
-  description: "to-do description"
+  description: "Json containing ustring, i.e., string of a unit, and an offset."
   required: true
   schema:
     type: "object"

fda-units-service/us-yml/validate.yml

@@ -8,7 +8,7 @@ parameters:
 - in: "path"
   type: "string"
   name: "unit"
-  description: "to-do description"
+  description: "Validates unit against om-2."
   required: true
 responses:
   200: