Merge pull request #142 from guzman-raphael/memory-leak

Ensure connections are thread-safe

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.
 
+## [0.6.0] - 2022-11-03
+
+### Added
+
+- Allow requests to be thread-safe so that database connections don't cross-pollinate [#142](https://github.com/datajoint/pharus/pull/142)
+- Add `basicquery` and `external` as options to extend with dynamic spec [#142](https://github.com/datajoint/pharus/pull/142)
+
 ## [0.5.6] - 2022-10-29
 
 ### Added
@@ -200,6 +207,7 @@ 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.
 
+[0.6.0]: 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
 [0.5.4]: https://github.com/datajoint/pharus/compare/0.5.3...0.5.4

README.rst

@@ -29,13 +29,13 @@ To start the API server, use the command:
 
     .. code-block:: bash
 
-        PHARUS_VERSION=0.5.6 docker-compose -f docker-compose-deploy.yaml up -d
+        PHARUS_VERSION=0.6.0 docker-compose -f docker-compose-deploy.yaml up -d
 
 To stop the API server, use the command:
 
     .. code-block:: bash
 
-        PHARUS_VERSION=0.5.6 docker-compose -f docker-compose-deploy.yaml down
+        PHARUS_VERSION=0.6.0 docker-compose -f docker-compose-deploy.yaml down
 
 References
 ----------

docker-compose-deploy.yaml

@@ -1,5 +1,5 @@
-# PHARUS_VERSION=0.5.6 docker-compose -f docker-compose-deploy.yaml pull
-# PHARUS_VERSION=0.5.6 docker-compose -f docker-compose-deploy.yaml up -d
+# 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
 #
 # Intended for production deployment.
 # Note: You must run both commands above for minimal outage
@@ -8,8 +8,7 @@
 # With this config and the configuration below in NGINX, you should be able to verify it is
 # running properly with a `curl https://fakeservices.datajoint.io/api/version`.
 version: "2.4"
-x-net:
-  &net
+x-net: &net
   networks:
     - main
 services:
@@ -22,7 +21,7 @@ services:
     #   - PHARUS_SPEC_PATH=tests/init/test_dynamic_api_spec.yaml # for dynamic api spec
   fakeservices.datajoint.io:
     <<: *net
-    image: datajoint/nginx:v0.0.16
+    image: datajoint/nginx:v0.2.3
     environment:
       - ADD_pharus_TYPE=REST
       - ADD_pharus_ENDPOINT=pharus:5000

pharus/component_interface.py

@@ -50,7 +50,7 @@ def __init__(
         name,
         component_config,
         static_config,
-        connect_creds: dict,
+        connection: dj.Connection,
         payload=None,
     ):
         self.name = name
@@ -66,12 +66,7 @@ def __init__(
             self.width = component_config["width"]
         if static_config:
             self.static_variables = types.MappingProxyType(static_config)
-        self.connection = dj.conn(
-            host=connect_creds["databaseAddress"],
-            user=connect_creds["username"],
-            password=connect_creds["password"],
-            reset=True,
-        )
+        self.connection = connection
         self.payload = payload
 
 
@@ -406,6 +401,7 @@ def dj_query_route(self):
 
 
 type_map = {
+    "external": Component,
     "basicquery": FetchComponent,
     "plot:plotly:stored_json": PlotPlotlyStoredjsonComponent,
     "table": TableComponent,

pharus/dynamic_api_gen.py

@@ -11,8 +11,9 @@
 def populate_api():
     header_template = """# Auto-generated rest api
 from .server import app, protected_route
-from .interface import _DJConnector, dj
+from .interface import _DJConnector
 from flask import request
+import datajoint as dj
 from json import loads
 from base64 import b64decode
 from datetime import datetime
@@ -28,14 +29,14 @@ def populate_api():
 
 @app.route('{route}', methods=['{rest_verb}'])
 @protected_route
-def {method_name}(connect_creds: dict) -> dict:
+def {method_name}(connection: dj.Connection) -> dict:
 
     if request.method in ['{rest_verb}']:
         try:
             component_instance = type_map['{component_type}'](name='{component_name}',
                                                               component_config={component},
                                                               static_config={static_config},
-                                                              connect_creds=connect_creds,
+                                                              connection=connection,
                                                               {payload})
             return component_instance.{method_name_type}()
         except Exception as e:
@@ -46,7 +47,7 @@ def {method_name}(connect_creds: dict) -> dict:
 @app.route('{route}', methods=['{rest_verb}'])
 def {method_name}() -> dict:
     if request.method in ['{rest_verb}']:
-        connect_creds = dict(
+        connection = dj.Connection(
             databaseAddress=os.environ["PHARUS_HOST"],
             username=os.environ["PHARUS_USER"],
             password=os.environ["PHARUS_PASSWORD"],
@@ -55,7 +56,7 @@ def {method_name}() -> dict:
             component_instance = type_map['{component_type}'](name='{component_name}',
                                                               component_config={component},
                                                               static_config={static_config},
-                                                              connect_creds=connect_creds,
+                                                              connection=connection,
                                                               {payload})
             return component_instance.{method_name_type}()
         except Exception as e:
@@ -120,8 +121,11 @@ def {method_name}() -> dict:
                     else grid["components"]
                 ).items():
                     if re.match(
-                        r"^(table|metadata|plot|file|slider|dropdown-query|form).*$",
+                        r"""
+                        ^(table|metadata|plot|file|slider|
+                          dropdown-query|form|basicquery|external).*$""",
                         comp["type"],
+                        flags=re.VERBOSE,
                     ):
                         f.write(
                             (active_route_template).format(