Merge pull request #156 from x-atlas-consortia/karlburke/flask3updates

Updates for Flask 3 and associated dependencies, including replacing …

src/app.py

@@ -22,7 +22,12 @@
 
 # Use `getLogger()` instead of `getLogger(__name__)` to apply the config to the root logger
 # will be inherited by the sub-module loggers
-logger = logging.getLogger()
+try:
+    logger = logging.getLogger()
+    logger.info(f"Starting. Logger initialized, with logging level {logger.level}")
+except Exception as e:
+    print("Error opening log file during startup")
+    print(str(e))
 
 # Specify the absolute path of the instance folder and use the config file relative to the instance path
 app = Flask(__name__, instance_path=os.path.join(os.path.abspath(os.path.dirname(__file__)), 'instance'),
@@ -31,28 +36,24 @@
 # Use configuration from instance/app.cfg, deployed per-app from examples in the repository.
 try:
     app.config.from_pyfile('app.cfg')
+    logger.info("Application initialized from instance/app.cfg")
 except Exception as e:
+    logger.critical(f"Unable to initialize application from instance/app.cfg due to e='{str(e)}'")
     raise Exception("Failed to get configuration from instance/app.cfg")
 
 worker = None
-
-@app.before_first_request
-def init():
-    global worker
-    try:
-        logger.info("started")
-    except Exception as e:
-        print("Error opening log file during startup")
-        print(str(e))
-
-    try:
-        worker = UUIDWorker(app_config=app.config)
-        logger.info("initialized")
-    except Exception as e:
-        print("Error during startup.")
-        print(str(e))
-        logger.error(e, exc_info=True)
-        print("Check the log file for further information: " + LOG_FILE_NAME)
+try:
+    worker = UUIDWorker(app_config=app.config)
+    logger.info("UUIDWorker instantiated using app.cfg setting.")
+except Exception as e:
+    logger.critical(f"Unable to instantiate a UUIDWorker during startup.")
+    print("Error instantiating a UUIDWorker during startup.")
+    print(str(e))
+    logger.error(e, exc_info=True)
+    print("Check the log file for further information: " + LOG_FILE_NAME)
+
+logger.info('')
+logger.info('')
 
 @app.route('/', methods=['GET'])
 def index():

src/instance/app.cfg.example

@@ -13,7 +13,7 @@ DB_PASSWORD = '123'
 APP_ID_PREFIX = 'HBM'
 #Set to the ID used in the entity-api
 APP_ID = 'hubmap_id'
-APP_BASE_ID = 'base_id'
+APP_BASE_ID = 'hubmap_base_id'
 
 BASE_DIR_TYPES = ['DATA_UPLOAD', 'INGEST_PORTAL_UPLOAD']
 # Entity types which have a uuids_attributes.BASE_ID associated with them

src/requirements.txt

@@ -1,18 +1,18 @@
-Flask==2.1.3
+Flask==3.0.3
 
 # Flask 2.1.3 installs the latest Werkzeug==3.0.0 (released on 9/30/2023) and causing import issues 
 # Use a pinned version 2.3.7 (the latest release before 3.0.0) to mitigate temporaryly
 # Will upgrade Flask to newer version later on across all APIs. 10/3/2023 - Zhou
-Werkzeug==2.3.7
+Werkzeug==3.0.3
 
 # To match the AWS RDS MySQL server 8.0.23, returned by the SELECT VERSION() query.
 mysql-connector-python==8.0.23
 
 # The commons package requires requests>=2.22.0
-requests==2.25.1
+requests==2.32.3
 
 # Use the published package from PyPI as default
 # Use the branch name of commons from github for testing new changes made in commons
 # Default is master branch specified in docker-compose.yml if not set
 # git+https://github.com/hubmapconsortium/commons.git@${COMMONS_BRANCH}#egg=hubmap-commons
-hubmap-commons==2.1.12
+hubmap-commons==2.1.15

src/uuid_worker.py

@@ -321,7 +321,7 @@ def __init__(self, app_config=None):
 
             if 'LARGE_RESPONSE_THRESHOLD' not in app_config \
                 or not isinstance(app_config['LARGE_RESPONSE_THRESHOLD'], int) \
-                or int(app_config['LARGE_RESPONSE_THRESHOLD'] > 9999999):
+                or app_config['LARGE_RESPONSE_THRESHOLD'] > 10*(2**20)-1:
                 self.logger.error(f"There is a problem with the LARGE_RESPONSE_THRESHOLD setting in app.cfg."
                                   f" Defaulting to small value so noticed quickly.")
                 large_response_threshold = 5000000