Merge pull request #144 from datajoint/fix-instant-token

Use a manual sleep due to instant token issue from jwt

CHANGELOG.md

@@ -2,6 +2,13 @@
 
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.6.1] - 2022-11-04
+
+### Added
+
+- Add debug traces for standard routes [#143](https://github.com/datajoint/pharus/pull/143)
+- Set a manual sleep due to `jwt` package not validating tokens issued in less than 1 sec [#143](https://github.com/datajoint/pharus/pull/143)
+
 ## [0.6.0] - 2022-11-03
 
 ### Added
@@ -207,6 +214,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 - Support for DataJoint attribute types: `varchar`, `int`, `float`, `datetime`, `date`, `time`, `decimal`, `uuid`.
 - Check dependency utility to determine child table references.
 
+[0.6.1]: https://github.com/datajoint/pharus/compare/0.6.0...0.6.1
 [0.6.0]: https://github.com/datajoint/pharus/compare/0.5.6...0.6.0
 [0.5.6]: https://github.com/datajoint/pharus/compare/0.5.5...0.5.6
 [0.5.5]: https://github.com/datajoint/pharus/compare/0.5.4...0.5.5

README.rst

@@ -29,13 +29,13 @@ To start the API server, use the command:
 
     .. code-block:: bash
 
-        PHARUS_VERSION=0.6.0 docker-compose -f docker-compose-deploy.yaml up -d
+        PHARUS_VERSION=0.6.1 docker-compose -f docker-compose-deploy.yaml up -d
 
 To stop the API server, use the command:
 
     .. code-block:: bash
 
-        PHARUS_VERSION=0.6.0 docker-compose -f docker-compose-deploy.yaml down
+        PHARUS_VERSION=0.6.1 docker-compose -f docker-compose-deploy.yaml down
 
 References
 ----------

docker-compose-deploy.yaml

@@ -1,5 +1,5 @@
-# PHARUS_VERSION=0.6.0 docker-compose -f docker-compose-deploy.yaml pull
-# PHARUS_VERSION=0.6.0 docker-compose -f docker-compose-deploy.yaml up -d
+# PHARUS_VERSION=0.6.1 docker-compose -f docker-compose-deploy.yaml pull
+# PHARUS_VERSION=0.6.1 docker-compose -f docker-compose-deploy.yaml up -d
 #
 # Intended for production deployment.
 # Note: You must run both commands above for minimal outage

pharus/server.py

@@ -22,6 +22,8 @@
 from datajoint.errors import IntegrityError
 from datajoint.table import foreign_key_error_regexp
 from datajoint.utils import to_camel_case
+import traceback
+import time
 
 app = Flask(__name__)
 # Check if PRIVATE_KEY and PUBIC_KEY is set, if not generate them.
@@ -124,7 +126,7 @@ def api_version() -> str:
             Content-Type: application/json
 
             {
-                "version": "0.6.0"
+                "version": "0.6.1"
             }
 
         :statuscode 200: No error.
@@ -233,6 +235,7 @@ def login() -> dict:
                 auth_info = dict(
                     jwt=result.json()["access_token"], id=result.json()["id_token"]
                 )
+                time.sleep(1)
                 connect_creds = {
                     "databaseAddress": request.args["database_host"],
                     "username": jwt.decode(
@@ -281,7 +284,7 @@ def login() -> dict:
                     raise e
             return dict(**auth_info)
         except Exception as e:
-            return str(e), 500
+            return traceback.format_exc(), 500
 
 
 @app.route(f"{environ.get('PHARUS_PREFIX', '')}/schema", methods=["GET"])
@@ -343,7 +346,7 @@ def schema(connection: dj.Connection) -> dict:
             schemas_name = _DJConnector._list_schemas(connection)
             return dict(schemaNames=schemas_name)
         except Exception as e:
-            return str(e), 500
+            return traceback.format_exc(), 500
 
 
 @app.route(
@@ -420,7 +423,7 @@ def table(
             tables_dict_list = _DJConnector._list_tables(connection, schema_name)
             return dict(tableTypes=tables_dict_list)
         except Exception as e:
-            return str(e), 500
+            return traceback.format_exc(), 500
 
 
 @app.route(
@@ -742,23 +745,23 @@ def record(
                 recordHeader=record_header, records=table_tuples, totalCount=total_count
             )
         except Exception as e:
-            return str(e), 500
+            return traceback.format_exc(), 500
     elif request.method == "POST":
         try:
             _DJConnector._insert_tuple(
                 connection, schema_name, table_name, request.json["records"]
             )
             return "Insert Successful"
         except Exception as e:
-            return str(e), 500
+            return traceback.format_exc(), 500
     elif request.method == "PATCH":
         try:
             _DJConnector._update_tuple(
                 connection, schema_name, table_name, request.json["records"]
             )
             return "Update Successful"
         except Exception as e:
-            return str(e), 500
+            return traceback.format_exc(), 500
     elif request.method == "DELETE":
         try:
             _DJConnector._delete_records(
@@ -789,7 +792,7 @@ def record(
                 409,
             )
         except Exception as e:
-            return str(e), 500
+            return traceback.format_exc(), 500
 
 
 @app.route(
@@ -872,7 +875,7 @@ def definition(
             )
             return table_definition
         except Exception as e:
-            return str(e), 500
+            return traceback.format_exc(), 500
 
 
 @app.route(
@@ -1051,7 +1054,7 @@ def attribute(
                 attributes=attributes_meta["attributes"],
             )
         except Exception as e:
-            return str(e), 500
+            return traceback.format_exc(), 500
 
 
 @app.route(
@@ -1158,14 +1161,14 @@ def dependency(
             )
             return dict(dependencies=dependencies)
         except Exception as e:
-            return str(e), 500
+            return traceback.format_exc(), 500
 
 
 def run():
     """
     Starts API server.
     """
-    app.run(host="0.0.0.0", port=environ.get("PHARUS_PORT", 5000), threaded=True)
+    app.run(host="0.0.0.0", port=environ.get("PHARUS_PORT", 5000), threaded=False)
 
 
 if __name__ == "__main__":

pharus/version.py

@@ -1,2 +1,2 @@
 """Package metadata."""
-__version__ = "0.6.0"
+__version__ = "0.6.1"