Add blueprint for sagger description

app/__init__.py

+"""
+Entry file for the elasticsearch proxy app
+"""
+
+from flask import Flask
+from flask_cors import CORS
+
+from app.config import RUN_CONFIG
+# from app.cache import CACHE
+from app.blueprints.swagger_description.swagger_description_blueprint import SWAGGER_BLUEPRINT
+
+
+def create_app():
+    """
+    Creates the flask app
+    :return: Elasticsearch proxy flask app
+    """
+    base_path = RUN_CONFIG.get('base_path')
+    flask_app = Flask(__name__)
+
+    enable_cors = RUN_CONFIG.get('enable_cors', False)
+
+    if enable_cors:
+        CORS(flask_app)
+
+
+    # with flask_app.app_context():
+    #     CACHE.init_app(flask_app)
+
+        # # pylint: disable=protected-access
+        # if RUN_CONFIG.get('cache_config').get('CACHE_TYPE') == 'memcached':
+        #     CACHE.cache._client.behaviors['tcp_nodelay'] = True
+        #     CACHE.cache._client.behaviors['_noreply'] = True
+        #     CACHE.cache._client.behaviors['no_block'] = True
+        #     CACHE.cache._client.behaviors['remove_failed'] = 10
+        #     CACHE.cache._client.behaviors['retry_timeout'] = 10
+        #     CACHE.cache._client.behaviors['retry_timeout'] = 600
+
+    flask_app.register_blueprint(SWAGGER_BLUEPRINT, url_prefix=f'{base_path}/swagger')
+    return flask_app
+
+
+if __name__ == '__main__':
+    FLASK_APP = create_app()

app/blueprints/swagger_description/swagger_description_blueprint.py

+"""
+Blueprint in charge of sending the swagger configuration in json format.
+"""
+from pathlib import Path
+
+from flask import Blueprint, jsonify
+import yaml
+
+from app.config import RUN_CONFIG
+
+SWAGGER_BLUEPRINT = Blueprint('swagger', __name__)
+
+
+@SWAGGER_BLUEPRINT.route('/swagger.json')
+def get_json():
+    """
+    :return: Responds to the request with the json version of the swagger description
+    """
+
+    yaml_file_path = Path(Path().absolute()).joinpath('app', 'swagger', 'swagger.yaml')
+
+    with open(yaml_file_path, 'r') as stream:
+        swagger_desc = yaml.safe_load(stream)
+        swagger_desc['host'] = RUN_CONFIG.get('server_public_host')
+        swagger_desc['basePath'] = RUN_CONFIG.get('base_path')
+        return jsonify(swagger_desc)

app/config.py

+"""
+    Module that handles the configuration of the app
+"""
+import os
+from pathlib import Path
+import hashlib
+from enum import Enum
+import yaml
+
+CUSTOM_CONFIG_FILE_PATH = os.getenv('CONFIG_FILE_PATH')
+if CUSTOM_CONFIG_FILE_PATH is not None:
+    CONFIG_FILE_PATH = CUSTOM_CONFIG_FILE_PATH
+else:
+    CONFIG_FILE_PATH = str(Path().absolute()) + '/config.yml'
+
+print('------------------------------------------------------------------------------------------------')
+print('CONFIG_FILE_PATH: ', CONFIG_FILE_PATH)
+print('------------------------------------------------------------------------------------------------')
+
+
+class ImproperlyConfiguredError(Exception):
+    """Base class for exceptions in this module."""
+
+
+class RunEnvs(Enum):
+    """
+        Class that defines the possible run environments
+    """
+    DEV = 'DEV'
+    TEST = 'TEST'
+    STAGING = 'STAGING'
+    PROD = 'PROD'
+
+    def __repr__(self):
+        return self.name
+
+    def __str__(self):
+        return self.name
+
+
+def hash_secret(secret):
+    """
+    Returns a a digest of a secret you want to store in memory
+    :param secret: secret you want to hash
+    :return: a sha256 hash of the secret, encoded in hexadecimal
+    """
+
+    hashed = hashlib.sha256(secret.encode('UTF-8')).hexdigest()
+    return hashed
+
+
+def verify_secret(prop_name, value):
+    """
+    Verifies that a value in the current config (hashed) corresponds to the value passed as parameter (unhashed)
+    :param prop_name: name of the property in the configuration
+    :param value: clear text value of the property.
+    :return: True if the value is correct, false otherwise
+    """
+
+    hashed = hashlib.sha256(value.encode('UTF-8')).hexdigest()
+    has_must_be = RUN_CONFIG.get(prop_name)
+
+    return hashed == has_must_be
+
+
+print('Loading run config')
+try:
+    RUN_CONFIG = yaml.load(open(CONFIG_FILE_PATH, 'r'), Loader=yaml.FullLoader)
+    print('Run config loaded')
+except FileNotFoundError:
+    print('Config file not found. Attempting to load config from environment variable DELAYED_JOBS_RAW_CONFIG')
+    RAW_CONFIG = os.getenv('DELAYED_JOBS_RAW_CONFIG')
+    print('raw_config: ', RAW_CONFIG)
+    RUN_CONFIG = yaml.load(RAW_CONFIG, Loader=yaml.FullLoader)
+
+# Load defaults
+ES_CONFIG = RUN_CONFIG.get('elasticsearch', {})
+DEFAULT_ES_CONFIG = {
+    'host': 'https://www.ebi.ac.uk/chembl/glados-es'
+
+}
+RUN_CONFIG['elasticsearch'] = {
+    **DEFAULT_ES_CONFIG,
+    **ES_CONFIG,
+}
+
+CACHE_CONFIG = RUN_CONFIG.get('cache_config', {})
+DEFAULT_CACHE_CONFIG = {
+    'CACHE_TYPE': 'simple'
+}
+RUN_CONFIG['cache_config'] = {
+    **DEFAULT_CACHE_CONFIG,
+    **CACHE_CONFIG,
+}
+
+if RUN_CONFIG.get('base_path') is None:
+    RUN_CONFIG['base_path'] = ''

swagger/swagger.yml → app/swagger/swagger.yaml

@@ -18,12 +18,12 @@ schemes:
 - "https"
 - "http"
 paths:
-  /es_subsets/generate_subset_index_from_ids:
+  /es_subsets/submit_subset_creation_from_ids:
     post:
       tags:
         - 'ES subsets'
       summary: 'Generates a subset index in elasticsearch'
-      description: 'Receives a list of ChEMBL IDs and generates a subset with the items that correspond to
+      description: 'Receives a list of ChEMBL IDs and starts to generate a subset with the items that correspond to
       the ids in the original index'
       operationId: 'generate_subset_index'
       produces:
@@ -50,7 +50,5 @@ definitions:
   SubsetOperationResponse:
     type: 'object'
     properties:
-      subset_created:
-        type: 'object'
-      metadata:
+      task_id:
+        type: 'string'
\ No newline at end of file
-        type: 'object'
\ No newline at end of file

requirements.txt

@@ -5,3 +5,4 @@ pyyaml==5.1.2
 elasticsearch>=7.0.0,<8.0.0 # Recommended by the official documentation
 gunicorn==20.0.4
 marshmallow==3.5.0
+flask-cors==3.0.8
\ No newline at end of file