Merge pull request #222 from gyorilab/flask3

Update Flask-JWT-Extended, Flask

indra_db_service/api.py

@@ -371,6 +371,7 @@ def get_statements(result_type, method):
 
 
 @app.route("/expand", methods=["POST"])
+@jwt_nontest_optional
 def expand_meta_row():
     start_time = datetime.now()
 

indra_db_service/cli/__init__.py

@@ -10,15 +10,22 @@ def main():
 
 @main.command()
 @click.argument('deployment', nargs=1)
-def push(deployment):
+@click.option('-s', '--settings', 'zappa_settings_file',
+              default='zappa_settings.json',
+              help="Specify the zappa settings file to use. Default is "
+                   "'zappa_settings.json'.")
+def push(deployment, zappa_settings_file):
     """Push a new deployment to the remote lambdas using zappa."""
-    from indra_db_service.cli.zappa_tools import fix_permissions, ZAPPA_CONFIG
+    import json
+    from pathlib import Path
+    from indra_db_service.cli.zappa_tools import fix_permissions
     click.echo(f"Updating {deployment} deployment.")
-    if ZAPPA_CONFIG not in os.listdir('.'):
-        click.echo(f"Please run in directory with {ZAPPA_CONFIG}.")
+    if not Path(zappa_settings_file).exists():
+        click.echo(f"Zappa settings file not found: {zappa_settings_file}")
         return
+    zappa_settings = json.load(open(zappa_settings_file, 'r'))
     os.system(f'zappa update {deployment}')
-    fix_permissions(deployment)
+    fix_permissions(deployment, zappa_settings=zappa_settings)
 
 
 @main.command()

indra_db_service/cli/__main__.py

@@ -0,0 +1,5 @@
+from . import main
+
+
+if __name__ == '__main__':
+    main()

indra_db_service/cli/zappa_tools.py

@@ -1,5 +1,3 @@
-import os
-import json
 import boto3
 
 from indra_db.config import CONFIG
@@ -10,28 +8,15 @@
 aws_role = CONFIG['lambda']['role']
 aws_primary_function = 'indra-db-api-ROOT'
 
-# Load the Zappa config file.
-ZAPPA_CONFIG = 'zappa_settings.json'
 
-
-def load_zappa_settings() -> dict:
-    if not os.path.exists(ZAPPA_CONFIG):
-        raise Exception(f"No valid zappa config file present. "
-                        f"Expecting: {ZAPPA_CONFIG}")
-    with open('zappa_settings.json', 'r') as f:
-        zappa_settings = json.load(f)
-    return zappa_settings
-
-
-def fix_permissions(deployment) -> None:
+def fix_permissions(deployment, zappa_settings) -> None:
     """Add permissions to the lambda function to allow access from API Gateway.
 
     When Zappa runs, it removes permission for the primary endpoint to call
     the lambda functions it creates. This function goes in and fixes those
     permissions, and is intended to be run after a zappa update.
     """
     # Get relevant settings from the zappa config.
-    zappa_settings = load_zappa_settings()
     project_name = zappa_settings[deployment]['project_name']
     region = zappa_settings[deployment]['aws_region']
     if zappa_settings[deployment]['profile_name'].lower() != aws_role.lower():

indra_db_service/config.py

@@ -12,7 +12,7 @@
 
 from os import environ
 from pathlib import Path
-from flask_jwt_extended import jwt_optional
+from flask_jwt_extended import jwt_required
 
 TITLE = "The INDRA Database"
 DEPLOYMENT = environ.get("INDRA_DB_API_DEPLOYMENT")
@@ -39,4 +39,4 @@ def jwt_nontest_optional(func):
     if TESTING["status"]:
         return func
     else:
-        return jwt_optional(func)
+        return jwt_required(optional=True)(func)