build: upgrade FOCA to 0.13.0 (#52)

* build: upgrade FOCA version

Dockerfile

@@ -1,5 +1,5 @@
 ##### BASE IMAGE #####
-FROM elixircloud/foca:20201114
+FROM elixircloud/foca:20240520-py3.12
 
 
 ##### METADATA ##### 

drs_filer/app.py

@@ -2,15 +2,16 @@
 
 import logging
 
-from foca.foca import foca
+from foca import Foca
 
 from drs_filer.ga4gh.drs.endpoints.service_info import RegisterServiceInfo
 
 logger = logging.getLogger(__name__)
 
 
 def main():
-    app = foca("config.yaml")
+    foca = Foca("config.yaml")
+    app = foca.create_app()
 
     # register service info
     with app.app.app_context():

drs_filer/ga4gh/drs/endpoints/register_objects.py

@@ -31,25 +31,26 @@ def register_object(
         A unique identifier for the object.
     """
     # Set parameters
+    foca_config = current_app.config.foca
     db_collection = (
-        current_app.config['FOCA'].db.dbs['drsStore'].
+        foca_config.db.dbs['drsStore'].
         collections['objects'].client
     )
-    url_prefix = current_app.config['FOCA'].endpoints['url_prefix']
-    external_host = current_app.config['FOCA'].endpoints['external_host']
-    external_port = current_app.config['FOCA'].endpoints['external_port']
-    api_path = current_app.config['FOCA'].endpoints['api_path']
+    url_prefix = foca_config.endpoints['url_prefix']
+    external_host = foca_config.endpoints['external_host']
+    external_port = foca_config.endpoints['external_port']
+    api_path = foca_config.endpoints['api_path']
 
     # Set flags and parameters for POST/PUT routes
     replace = True
     was_replaced = False
     if object_id is None:
         replace = False
         id_length = (
-            current_app.config['FOCA'].endpoints['objects']['id_length']
+            foca_config.endpoints['objects']['id_length']
         )
         id_charset: str = (
-            current_app.config['FOCA'].endpoints['objects']['id_charset']
+            foca_config.endpoints['objects']['id_charset']
         )
         # evaluate character set expression or interpret literal string as set
         try:
@@ -120,11 +121,12 @@ def __add_access_ids(data: List) -> List:
     Returns:
         Access methods metadata complete with unique access identifiers.
     """
+    foca_config = current_app.config.foca
     id_charset = eval(
-        current_app.config['FOCA'].endpoints['access_methods']['id_charset']
+        foca_config.endpoints['access_methods']['id_charset']
     )
     id_length = (
-        current_app.config['FOCA'].endpoints['access_methods']['id_length']
+        foca_config.endpoints['access_methods']['id_length']
     )
     access_ids = []
     for method in data:

drs_filer/ga4gh/drs/endpoints/service_info.py

@@ -34,14 +34,14 @@ def __init__(self) -> None:
             db_coll_info: Database collection storing service info objects.
             conf_info: Service info details as per enpoints config.
         """
-        conf = current_app.config['FOCA'].endpoints
+        conf = current_app.config.foca.endpoints
         self.url_prefix = conf['url_prefix']
         self.host_name = conf['external_host']
         self.external_port = conf['external_port']
         self.api_path = conf['api_path']
         self.conf_info = conf['service_info']
         self.db_coll_info = (
-            current_app.config['FOCA'].db.dbs['drsStore']
+            current_app.config.foca.db.dbs['drsStore']
             .collections['service_info'].client
         )
 

drs_filer/ga4gh/drs/server.py

@@ -34,7 +34,7 @@ def GetObject(object_id: str) -> Dict:
         DRS object as dictionary, JSONified if returned in app context.
     """
     db_collection = (
-        current_app.config['FOCA'].db.dbs['drsStore'].
+        current_app.config.foca.db.dbs['drsStore'].
         collections['objects'].client
     )
     obj = db_collection.find_one({"id": object_id})
@@ -112,7 +112,7 @@ def DeleteObject(object_id):
     """
 
     db_collection = (
-        current_app.config['FOCA'].db.dbs['drsStore'].
+        current_app.config.foca.db.dbs['drsStore'].
         collections['objects'].client
     )
     obj = db_collection.find_one({"id": object_id})
@@ -138,7 +138,7 @@ def DeleteAccessMethod(object_id: str, access_id: str) -> str:
     """
 
     db_collection = (
-        current_app.config['FOCA'].db.dbs['drsStore'].
+        current_app.config.foca.db.dbs['drsStore'].
         collections['objects'].client
     )
 

requirements-test.txt

@@ -0,0 +1,4 @@
+flake8
+mongomock
+pytest
+pytest-cov

requirements.txt

@@ -1,3 +1,3 @@
-foca==0.6.0
+foca==0.13.0
 gunicorn==20.0.4
-setuptools==65.5.1
+setuptools==70.0.0

tests/ga4gh/drs/endpoints/test_register_objects.py

@@ -52,12 +52,12 @@ def test_register_object_literal_id_charset():
     app = Flask(__name__)
     endpoint_config = deepcopy(ENDPOINT_CONFIG)
     endpoint_config['objects']['id_charset'] = 'abcdef'
-    app.config['FOCA'] = \
+    app.config.foca = \
         Config(
             db=MongoConfig(**MONGO_CONFIG),
             endpoints=endpoint_config,
         )
-    app.config['FOCA'].db.dbs['drsStore']. \
+    app.config.foca.db.dbs['drsStore']. \
         collections['objects'].client = mongomock.MongoClient().db.collection
 
     request_data = {"name": "mock_name"}
@@ -71,12 +71,12 @@ def test_register_object_invalid_config():
     app = Flask(__name__)
     endpoint_config = deepcopy(ENDPOINT_CONFIG)
     del endpoint_config['url_prefix']
-    app.config['FOCA'] = \
+    app.config.foca = \
         Config(
             db=MongoConfig(**MONGO_CONFIG),
             endpoints=endpoint_config,
         )
-    app.config['FOCA'].db.dbs['drsStore']. \
+    app.config.foca.db.dbs['drsStore']. \
         collections['objects'].client = mongomock.MongoClient().db.collection
 
     request_data = {"name": "mock_name"}
@@ -90,15 +90,15 @@ def test_register_object_exceed_retries():
     identifier.
     """
     app = Flask(__name__)
-    app.config['FOCA'] = \
+    app.config.foca = \
         Config(
             db=MongoConfig(**MONGO_CONFIG),
             endpoints=ENDPOINT_CONFIG,
         )
     mock_resp = MagicMock(side_effect=DuplicateKeyError(''))
-    app.config['FOCA'].db.dbs['drsStore'].collections['objects']. \
+    app.config.foca.db.dbs['drsStore'].collections['objects']. \
         client = MagicMock()
-    app.config['FOCA'].db.dbs['drsStore'].collections['objects']. \
+    app.config.foca.db.dbs['drsStore'].collections['objects']. \
         client.insert_one = mock_resp
 
     request_data = {"name": "mock_name", "access_methods": []}
@@ -110,7 +110,7 @@ def test_register_object_exceed_retries():
 def test_add_access_ids():
     """Test for __add_access_ids()."""
     app = Flask(__name__)
-    app.config['FOCA'] = Config(endpoints=ENDPOINT_CONFIG)
+    app.config.foca = Config(endpoints=ENDPOINT_CONFIG)
     objects = json.loads(open(data_objects_path, "r").read())
     mock_data = objects[0]['access_methods']
     with app.app_context():

tests/ga4gh/drs/endpoints/test_service_info.py

@@ -92,14 +92,14 @@
 def test_get_service_info():
     """Test for getting service info."""
     app = Flask(__name__)
-    app.config['FOCA'] = Config(
+    app.config.foca = Config(
         db=MongoConfig(**MONGO_CONFIG),
         endpoints=ENDPOINT_CONFIG,
     )
     mock_resp = deepcopy(SERVICE_INFO_CONFIG)
-    app.config['FOCA'].db.dbs['drsStore'].collections['service_info'] \
+    app.config.foca.db.dbs['drsStore'].collections['service_info'] \
         .client = mongomock.MongoClient().db.collection
-    app.config['FOCA'].db.dbs['drsStore'].collections['service_info'] \
+    app.config.foca.db.dbs['drsStore'].collections['service_info'] \
         .client.insert_one(mock_resp)
 
     with app.app_context():
@@ -109,11 +109,11 @@ def test_get_service_info():
 def test_get_service_info_na():
     """Test for getting service info if unavailable."""
     app = Flask(__name__)
-    app.config['FOCA'] = Config(
+    app.config.foca = Config(
         db=MongoConfig(**MONGO_CONFIG),
         endpoints=ENDPOINT_CONFIG,
     )
-    app.config['FOCA'].db.dbs['drsStore'].collections['service_info'] \
+    app.config.foca.db.dbs['drsStore'].collections['service_info'] \
         .client = mongomock.MongoClient().db.collection
 
     with app.app_context():
@@ -124,11 +124,11 @@ def test_get_service_info_na():
 def test_set_service_info_from_config():
     """Test for setting service info from config."""
     app = Flask(__name__)
-    app.config['FOCA'] = Config(
+    app.config.foca = Config(
         db=MongoConfig(**MONGO_CONFIG),
         endpoints=ENDPOINT_CONFIG,
     )
-    app.config['FOCA'].db.dbs['drsStore'].collections['service_info'] \
+    app.config.foca.db.dbs['drsStore'].collections['service_info'] \
         .client = mongomock.MongoClient().db.collection
 
     with app.app_context():
@@ -142,11 +142,11 @@ def test_set_service_info_from_config_corrupt():
     app = Flask(__name__)
     mock_resp = deepcopy(ENDPOINT_CONFIG)
     del mock_resp['service_info']['id']
-    app.config['FOCA'] = Config(
+    app.config.foca = Config(
         db=MongoConfig(**MONGO_CONFIG),
         endpoints=mock_resp,
     )
-    app.config['FOCA'].db.dbs['drsStore'].collections['service_info'] \
+    app.config.foca.db.dbs['drsStore'].collections['service_info'] \
         .client = mongomock.MongoClient().db.collection
 
     with app.app_context():
@@ -160,14 +160,14 @@ def test_set_service_info_from_config_skip():
     available.
     """
     app = Flask(__name__)
-    app.config['FOCA'] = Config(
+    app.config.foca = Config(
         db=MongoConfig(**MONGO_CONFIG),
         endpoints=ENDPOINT_CONFIG,
     )
     mock_resp = deepcopy(SERVICE_INFO_CONFIG)
-    app.config['FOCA'].db.dbs['drsStore'].collections['service_info'] \
+    app.config.foca.db.dbs['drsStore'].collections['service_info'] \
         .client = mongomock.MongoClient().db.collection
-    app.config['FOCA'].db.dbs['drsStore'].collections['service_info'] \
+    app.config.foca.db.dbs['drsStore'].collections['service_info'] \
         .client.insert_one(mock_resp)
 
     with app.app_context():
@@ -179,20 +179,20 @@ def test_set_service_info_from_config_skip():
 def test_get_service_info_duplicatekey():
     """Test for duplicated service info config."""
     app = Flask(__name__)
-    app.config['FOCA'] = Config(
+    app.config.foca = Config(
         db=MongoConfig(**MONGO_CONFIG),
         endpoints=ENDPOINT_CONFIG,
     )
 
-    app.config['FOCA'].db.dbs['drsStore'].collections['service_info'] \
+    app.config.foca.db.dbs['drsStore'].collections['service_info'] \
         .client = mongomock.MongoClient().db.collection
     mock = MagicMock(side_effect=[DuplicateKeyError(''), None])
-    app.config['FOCA'].db.dbs['drsStore'] \
+    app.config.foca.db.dbs['drsStore'] \
         .collections['service_info'].client.insert_one = mock
     mock_db_call = MagicMock(name="Find_Obj")
     mock_db_call.return_value.sort.return_value \
         .limit.return_value.next.return_value = deepcopy(SERVICE_INFO_CONFIG)
-    app.config['FOCA'].db.dbs['drsStore'] \
+    app.config.foca.db.dbs['drsStore'] \
         .collections['service_info'].client.find = mock_db_call
     with app.app_context():
         get_service_info = RegisterServiceInfo().get_service_info()
@@ -202,11 +202,11 @@ def test_get_service_info_duplicatekey():
 def test_set_service_info_from_app_context():
     """Test for setting service info from app context."""
     app = Flask(__name__)
-    app.config['FOCA'] = Config(
+    app.config.foca = Config(
         db=MongoConfig(**MONGO_CONFIG),
         endpoints=ENDPOINT_CONFIG,
     )
-    app.config['FOCA'].db.dbs['drsStore'].collections['service_info'] \
+    app.config.foca.db.dbs['drsStore'].collections['service_info'] \
         .client = mongomock.MongoClient().db.collection
 
     with app.app_context():
@@ -220,11 +220,11 @@ def test_set_service_info_from_app_context():
 def test__upsert_service_info_insert():
     """Test for creating service info document in database."""
     app = Flask(__name__)
-    app.config['FOCA'] = Config(
+    app.config.foca = Config(
         db=MongoConfig(**MONGO_CONFIG),
         endpoints=ENDPOINT_CONFIG,
     )
-    app.config['FOCA'].db.dbs['drsStore'].collections['service_info'] \
+    app.config.foca.db.dbs['drsStore'].collections['service_info'] \
         .client = mongomock.MongoClient().db.collection
 
     data = deepcopy(SERVICE_INFO_CONFIG)
@@ -239,14 +239,14 @@ def test__upsert_service_info_insert():
 def test__upsert_service_info_update():
     """Test for replacing service info document in database."""
     app = Flask(__name__)
-    app.config['FOCA'] = Config(
+    app.config.foca = Config(
         db=MongoConfig(**MONGO_CONFIG),
         endpoints=ENDPOINT_CONFIG,
     )
     mock_resp = deepcopy(SERVICE_INFO_CONFIG)
-    app.config['FOCA'].db.dbs['drsStore'].collections['service_info'] \
+    app.config.foca.db.dbs['drsStore'].collections['service_info'] \
         .client = mongomock.MongoClient().db.collection
-    app.config['FOCA'].db.dbs['drsStore'].collections['service_info'] \
+    app.config.foca.db.dbs['drsStore'].collections['service_info'] \
         .client.insert_one(mock_resp)
 
     data = deepcopy(SERVICE_INFO_CONFIG)
@@ -261,7 +261,7 @@ def test__upsert_service_info_update():
 def test__get_headers():
     """Test for response headers getter."""
     app = Flask(__name__)
-    app.config['FOCA'] = Config(
+    app.config.foca = Config(
         db=MongoConfig(**MONGO_CONFIG),
         endpoints=ENDPOINT_CONFIG,
     )