Merge branch 'dev' into 122-test-amqp

fda-metadata-db/setup-schema.sql

@@ -353,7 +353,7 @@ CREATE TABLE IF NOT EXISTS mdb_columns_concepts
     URI     TEXT REFERENCES mdb_concepts (URI),
     created timestamp without time zone NOT NULL DEFAULT NOW(),
     FOREIGN KEY (cDBID, tID, cID) REFERENCES mdb_COLUMNS (cDBID, tID, ID),
-    PRIMARY KEY (cDBID, tID, cID)
+    PRIMARY KEY (cDBID, tID, cID, URI)
 );
 
 CREATE TABLE IF NOT EXISTS mdb_VIEW

fda-units-service/.gitignore

+__pycache__/
\ No newline at end of file

fda-units-service/README.md

@@ -3,3 +3,123 @@
 Suggest and validates units of measurements defined in Ontology of units of Measure (OM) [1] is used. 
 
 [1] https://github.com/HajoRijgersberg/OM
+
+## `POST /api/units/suggest`
+Autosuggests user typed in terms. 
+
+Example http request: 
+POST /api/units/suggest HTTP/1.1
+Content-Type: application/json
+Host: localhost:5010
+Content-Length: 37
+
+```JSON
+{
+  "offset": 0,
+  "ustring": "met"
+}
+```
+
+Response is a JSON object of the following form: 
+
+```JSON
+[
+	{
+		"comment": "The metre is a unit of length defined as the length of the path travelled by light in vacuum during a time interval of 1/299 792 458 of a second.",
+		"name": "metre",
+		"symbol": "m"
+	},
+	{
+		"comment": "Candela per square metre is a unit of luminance defined as candela divided by square metre.",
+		"name": "candela per square metre",
+		"symbol": "cd/m"
+	},
+	{
+		"comment": "Cubic metre is a unit of volume defined as the volume of a cube whose sides measure exactly one metre.",
+		"name": "cubic metre",
+		"symbol": "m3"
+	},
+]
+```
+
+## `POST /api/units/geturi`
+Returns the uri of a certain units contained in the ontology OM. 
+
+Example http request: 
+POST /api/units/geturi HTTP/1.1
+Content-Type: application/json
+Host: localhost:5010
+Content-Length: 22
+
+```JSON
+{
+  "uname": "metre"
+}
+```
+
+Response is a JSON object of the following form: 
+
+```JSON
+{
+	"URI": "http://www.ontology-of-units-of-measure.org/resource/om-2/metre"
+}
+```
+
+## `POST /api/units/validate´
+Validates user typed in units. For example 'diametre' is no unit. 
+
+Example http request:
+POST /api/units/validate HTTP/1.1
+Content-Type: application/json
+Host: localhost:5010
+Content-Length: 24
+
+```JSON
+{
+  "ustring": "metre"
+}
+```
+
+Respose: true / false
+
+## `POST /api/units/saveconcept´
+Is an endpoint for saving concepts in the entity 'mdb_concepts' in the MDB. 
+
+Example http request: 
+POST /api/units/saveconcept HTTP/1.1
+Content-Type: application/json
+Host: localhost:5010
+Content-Length: 97
+
+```JSON
+{
+  "name": "metre",
+  "uri": "http://www.ontology-of-units-of-measure.org/resource/om-2/metre"
+}
+```
+
+The response is a postgres status message, e.g., 
+
+"\"INSERT 0 1\""
+
+## `POST /api/units/savecolumnsconcept'
+Saves values in the entity 'mdb\_columns\_concepts', which realizes the relation between 'mdb\_columns' and 'mdb\_concepts'. Make sure the concept is contained in 'mdb\_concepts'. 
+
+Example http request:
+POST /api/units/savecolumnsconcept HTTP/1.1
+Content-Type: application/json
+Host: localhost:5010
+Content-Length: 122
+
+```JSON
+{
+  "cdbid": "1",
+  "cid": "1",
+  "tid": "1",
+  "uri": "http://www.ontology-of-units-of-measure.org/resource/om-2/metre"
+}
+```
+
+The response is a postgres status message, e.g., 
+
+"\"INSERT 0 1\""

fda-units-service/app.py

@@ -8,6 +8,7 @@ from flasgger.utils import swag_from
 from flasgger import LazyString, LazyJSONEncoder
 from list import list_units, get_uri
 from validate import validator, stringmapper
+from save import insert_mdb_concepts, insert_mdb_columns_concepts
 
 app = Flask(__name__)
 app.config["SWAGGER"] = {"title": "FDA-Units-Service", "uiversion": 3}
@@ -47,32 +48,62 @@ def suggest():
         res = {"success": False, "message": str(e)}
         return jsonify(res), 500
 
-@app.route('/api/units/validate', methods=["POST"], endpoint='validate')
+@app.route('/api/units/validate/<unit>', methods=["GET"], endpoint='validate')
 @swag_from('validate.yml')
-def valitate():
-    input_json = request.get_json()
+def valitate(unit):
     try:
-        unit = str(input_json['ustring'])
-        res = validator(stringmapper(unit))
+        res = validator(unit)
         return str(res), 200
     except Exception as e:
         print(e)
         res = {"success": False, "message": str(e)}
         return jsonify(res)
 
-@app.route('/api/units/geturi', methods=["POST"], endpoint='geturi')
+@app.route('/api/units/uri/<uname>', methods=["GET"], endpoint='uri')
 @swag_from('geturi.yml')
-def geturi():
-    input_json = request.get_json()
+def geturi(uname):
     try:
-        name = str(input_json['uname'])
-        res = get_uri(name)
+        res = get_uri(uname)
         return jsonify(res), 200
     except Exception as e:
         print(e)
         res = {"success": False, "message": str(e)}
         return jsonify(res), 500
 
+@app.route('/api/units/saveconcept', methods=["POST"], endpoint='saveconcept')
+@swag_from('saveconcept.yml')
+def saveconcept():
+    input_json = request.get_json()
+    try:
+        uri = str(input_json['uri'])
+        c_name = str(input_json['name'])
+        if insert_mdb_concepts(uri, c_name) > 0:
+            return jsonify({'uri': uri}), 201
+        else:
+            return jsonify({'status': 'error'}), 400
+    except Exception as e:
+        print(e)
+        res = {"success": False, "message": str(e)}
+        return jsonify(res), 500
+
+@app.route('/api/units/savecolumnsconcept', methods=["POST"], endpoint='savecolumnsconcept')
+@swag_from('savecolumnsconcept.yml')
+def saveconcept():
+    input_json = request.get_json()
+    try:
+        uri = str(input_json['uri'])
+        cid = int(input_json['cid'])
+        tid = int(input_json['tid'])
+        cdbid = int(input_json['cdbid'])
+        if insert_mdb_columns_concepts(cdbid, tid, cid, uri)>0:
+            return jsonify({'uri': uri}), 201
+        else:
+            return jsonify({'status': 'error'}), 400
+    except Exception as e:
+        print(e)
+        res = {"success": False, "message": str(e)}
+        return jsonify(res), 500
+
 rest_server_port = 5010
 eureka_client.init(eureka_server=os.getenv('EUREKA_SERVER', 'http://localhost:9090/eureka/'),
                    app_name="fda-units-service",

fda-units-service/requirements.txt

@@ -4,3 +4,4 @@ py-eureka-client==0.9.1
 docker==5.0.0
 gevent==21.8.0
 rdflib==6.0.2
+psycopg2-binary==2.8.6

fda-units-service/save.py

+from psycopg2 import connect
+import psycopg2.extras
+import json
+
+def insert_mdb_concepts(uri, c_name): 
+    try:
+        # Connecting to metadatabase 
+        conn=connect(
+        dbname="fda",
+        user = "postgres",
+        host = "fda-metadata-db",
+        password = "postgres"
+        )
+
+        cursor = conn.cursor()
+
+        # Insert tblnames into table mdb_TABLES 
+        cursor.execute("INSERT INTO mdb_concepts (URI,name,created) VALUES (%s,%s,current_timestamp) ON CONFLICT (URI) DO NOTHING", (uri,c_name))
+        r = cursor.rowcount
+        conn.commit()
+        conn.close()
+    except Exception as e:
+        print("Error while connecting to metadatabase.",e)
+    return r
+
+def insert_mdb_columns_concepts(cdbid,tid, cid, uri):
+    try:
+        # Connecting to metadatabase
+        conn=connect(
+        dbname="fda",
+        user = "postgres",
+        host = "fda-metadata-db",
+        password = "postgres"
+        )
+
+        cursor = conn.cursor()
+
+        # Insert tblnames into table mdb_TABLES
+        cursor.execute("INSERT INTO mdb_columns_concepts (cDBID,tID, cID,URI,created) VALUES (%s,%s,%s,%s,current_timestamp) ON CONFLICT (cDBID, tID, cID, URI) DO NOTHING", (cdbid,tid,cid,uri))
+        r = cursor.rowcount
+        conn.commit()
+        conn.close()
+    except Exception as e: 
+        print("Error while connecting to metadatabase.",e)
+    return r
\ No newline at end of file

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

@@ -5,16 +5,11 @@ consumes:
 produces:
 - "application/json"
 parameters:
-- in: "body"
-  name: "body"
+- in: "path"
+  type: "string"
+  name: "uname"
   description: "to-do description"
   required: true
-  schema:
-    type: "object"
-    properties:
-      uname:
-        type: "string"
-        example : "metre"
 responses:
   200: 
     description: "OK"

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

+summary: "Save concepts to MDB"
+description: "This is a simple API for saving units and concepts."
+consumes:
+- "application/json"
+produces:
+- "application/json"
+parameters:
+- in: "body"
+  name: "body"
+  description: "to-do description"
+  required: true
+  schema:
+    type: "object"
+    properties:
+      uri:
+        type: "string"
+        example: "http://www.ontology-of-units-of-measure.org/resource/om-2/metre"
+      cid:
+        type: "integer"
+        example: "1"
+      tid: 
+        type: "integer"
+        example: "1"
+      cdbid:
+        type: "integer"
+        example: "1"
+responses:
+  200: 
+    description: "OK"
+  405:
+    description: "Invalid input"

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

+summary: "Save concepts to MDB"
+description: "This is a simple API for saving units and concepts."
+consumes:
+- "application/json"
+produces:
+- "application/json"
+parameters:
+- in: "body"
+  name: "body"
+  description: "to-do description"
+  required: true
+  schema:
+    type: "object"
+    properties:
+      uri:
+        type: "string"
+        example: "http://www.ontology-of-units-of-measure.org/resource/om-2/metre"
+      name:
+        type: "string"
+        example: "metre"
+responses:
+  200: 
+    description: "OK"
+  405:
+    description: "Invalid input"

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

@@ -5,16 +5,11 @@ consumes:
 produces:
 - "application/json"
 parameters:
-- in: "body"
-  name: "body"
+- in: "path"
+  type: "string"
+  name: "unit"
   description: "to-do description"
   required: true
-  schema:
-    type: "object"
-    properties:
-      ustring:
-        type: "string"
-        example : "metre"
 responses:
   200: 
     description: "OK"