Add endpoint for first eubopen visualisation

README.md

+# Run development server
 
+```bash
+FLASK_APP=app flask run --host=0.0.0.0
+```

app/__init__.py

@@ -18,6 +18,7 @@ from app.blueprints.visualisation_data.controllers.visualisation_data_controller
 from app.blueprints.utils.controllers.utils_controller import UTILS_BLUEPRINT
 from app.blueprints.entities_join.controllers.entities_join_controller import ENTITIES_JOIN_BLUEPRINT
 from app.blueprints.eubopen.search.controller import EUBOPEN_SEARCH_BLUEPRINT
+from app.blueprints.eubopen.visualisations.controller import EUBOPEN_VISUALISATIONS_BLUEPRINT
 
 
 def create_app():
@@ -89,6 +90,10 @@ def create_app():
         {
             'blueprint': EUBOPEN_SEARCH_BLUEPRINT,
             'url': '/eubopen/search'
+        },
+        {
+            'blueprint': EUBOPEN_VISUALISATIONS_BLUEPRINT,
+            'url': '/eubopen/visualisations'
         }
     ]
 

app/blueprints/eubopen/search/controller.py

@@ -8,7 +8,6 @@ from app.blueprints.eubopen.search import marshmallow_schemas
 from app.blueprints.eubopen.search import services
 
 EUBOPEN_SEARCH_BLUEPRINT = Blueprint('eubopen_search', __name__)
-print('GOING TO REGISTER EUBOPEN BLUEPRINT')
 
 
 @EUBOPEN_SEARCH_BLUEPRINT.route('/autocomplete/<term>', methods=['GET'])

app/blueprints/eubopen/visualisations/controller.py

+"""
+Controller for handling the requests for the eubopen visualisations
+"""
+from flask import Blueprint, jsonify
+
+from app.request_validation.decorators import validate_url_params_with
+from app.blueprints.eubopen.visualisations import services
+
+EUBOPEN_VISUALISATIONS_BLUEPRINT = Blueprint('eubopen_visualisations', __name__)
+
+
+@EUBOPEN_VISUALISATIONS_BLUEPRINT.route('/target_classifications/protein_classification', methods=['GET'])
+def get_protein_target_classification():
+    """
+    :return: the json response with the protein target classification
+    """
+    try:
+        json_data = services.get_protein_target_classification()
+        http_response = jsonify(json_data)
+        return http_response
+    except services.VisualisationServiceError as error:
+        abort(500, msg=f'Internal server error: {str(error)}')

app/blueprints/eubopen/visualisations/services.py

+"""
+Services for the eubopen visualisations
+"""
+
+
+class VisualisationServiceError(Exception):
+    """
+    Base class for errors in this module
+    """
+
+
+def get_protein_target_classification():
+    """
+    :return: the json response with the protein target classification
+    """
+    return {
+        'msg': 'hello'
+    }

app/properties_configuration/config/override.yml

@@ -201,7 +201,7 @@ chembl_target:
     sortable: true
   'target_synonyms':
     based_on: 'target_components'
-    label: 'Target Synonyms'
+    label: 'Synonyms'
   'length':
     label: 'Length'
     label_mini: 'Length'

app/swagger/swagger.yaml

@@ -472,6 +472,20 @@ paths:
           description: "success"
           schema:
             $ref: '#/definitions/COVIDEntitiesRecordsResponse'
+  /eubopen/visualisations/target_classifications/protein_classification:
+    get:
+      tags:
+        - 'Visualisations'
+      summary: 'Get the Protein Target classification tree for EUbOPEN'
+      description: 'Returns the EUbOPEN Protein Target classification tree'
+      operationId: 'get_euobpen_protein_target_classification'
+      produces:
+        - 'application/json'
+      responses:
+        '200':
+          description: "success"
+          schema:
+            $ref: '#/definitions/EUbOPENProteinTargetClassificationResponse'
   /utils/identify_separator:
     post:
       tags:
@@ -669,6 +683,8 @@ definitions:
         type: 'string'
   ProteinTargetClassificationResponse:
     type: "object"
+  EUbOPENProteinTargetClassificationResponse:
+    type: "object"
   OrganismTaxonomyTargetClassificationResponse:
     type: "object"
   GOSlimTargetClassificationResponse:

requirements.txt

@@ -10,6 +10,6 @@ Flask-Caching==1.8.0
 pylibmc==1.6.1
 Flask-Limiter==1.2.1
 pymemcache==3.1.0
-requests==2.23.0
+requests==2.26.0
 Arpeggio==1.9.2
 Werkzeug==1.0.1
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