Merge pull request #15553 from mvdbeek/use_sentry_fastapi_integration

[23.0] Use sentry-fastapi integration, expose sampling rate

doc/source/admin/galaxy_options.rst

@@ -2914,6 +2914,19 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``sentry_traces_sample_rate``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Set to a number between 0 and 1. With this option set, every
+    transaction created will have that percentage chance of being sent
+    to Sentry. A value higher than 0 is required to analyze
+    performance.
+:Default: ``0.0``
+:Type: float
+
+
 ~~~~~~~~~~~~~~~
 ``statsd_host``
 ~~~~~~~~~~~~~~~
@@ -5076,14 +5089,15 @@
 :Type: str
 
 
-
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``enable_beacon_integration``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 :Description:
-    Enables user preferences and api endpoint for the beacon integration.
+    Enables user preferences and api endpoint for the beacon
+    integration.
 :Default: ``false``
 :Type: bool
 
 
+

lib/galaxy/app.py

@@ -202,6 +202,7 @@ class SentryClientMixin:
                     self.config.sentry_dsn,
                     release=f"{self.config.version_major}.{self.config.version_minor}",
                     integrations=[sentry_logging],
+                    traces_sample_rate=self.config.sentry_traces_sample_rate,
                 )
 
             self.application_stack.register_postfork_function(postfork_sentry_client)

lib/galaxy/config/sample/galaxy.yml.sample

@@ -1667,6 +1667,11 @@ galaxy:
   # Sentry. Possible values are DEBUG, INFO, WARNING, ERROR or CRITICAL.
   #sentry_event_level: ERROR
 
+  # Set to a number between 0 and 1. With this option set, every
+  # transaction created will have that percentage chance of being sent
+  # to Sentry. A value higher than 0 is required to analyze performance.
+  #sentry_traces_sample_rate: 0.0
+
   # Log to statsd Statsd is an external statistics aggregator
   # (https://github.com/etsy/statsd) Enabling the following options will
   # cause galaxy to log request timing and other statistics to the

lib/galaxy/config/sample/tool_shed.yml.sample

@@ -311,6 +311,11 @@ tool_shed:
   # Sentry. Possible values are DEBUG, INFO, WARNING, ERROR or CRITICAL.
   #sentry_event_level: ERROR
 
+  # Set to a number between 0 and 1. With this option set, every
+  # transaction created will have that percentage chance of being sent
+  # to Sentry. A value higher than 0 is required to analyze performance.
+  #sentry_traces_sample_rate: 0.0
+
   # Galaxy Session Timeout This provides a timeout (in minutes) after
   # which a user will have to log back in. A duration of 0 disables this
   # feature.

lib/galaxy/config/schemas/config_schema.yml

@@ -2108,6 +2108,15 @@ mapping:
           Determines the minimum log level that will be sent as an event to Sentry.
           Possible values are DEBUG, INFO, WARNING, ERROR or CRITICAL.
 
+      sentry_traces_sample_rate:
+        type: float
+        default: 0.0
+        required: false
+        desc: |
+          Set to a number between 0 and 1. With this option set, every transaction created
+          will have that percentage chance of being sent to Sentry. A value higher than 0
+          is required to analyze performance.
+
       statsd_host:
         type: str
         required: false

lib/galaxy/config/schemas/tool_shed_config_schema.yml

@@ -557,6 +557,15 @@ mapping:
           Determines the minimum log level that will be sent as an event to Sentry.
           Possible values are DEBUG, INFO, WARNING, ERROR or CRITICAL.
 
+      sentry_traces_sample_rate:
+        type: float
+        default: 0.0
+        required: false
+        desc: |
+          Set to a number between 0 and 1. With this option set, every transaction created
+          will have that percentage chance of being sent to Sentry. A value higher than 0
+          is required to analyze performance.
+
       session_duration:
         type: int
         default: 0

lib/galaxy/dependencies/conditional-requirements.txt

@@ -2,7 +2,7 @@
 psycopg2-binary==2.9.5
 mysqlclient
 fluent-logger
-sentry-sdk
+sentry-sdk[fastapi]
 pbs_python
 drmaa
 statsd

lib/galaxy/dependencies/pinned-requirements.txt

@@ -61,7 +61,7 @@ ecdsa==0.18.0 ; python_version >= "3.7" and python_version < "3.12"
 edam-ontology==1.25.2 ; python_version >= "3.7" and python_version < "3.12"
 email-validator==1.3.0 ; python_version >= "3.7" and python_version < "3.12"
 fastapi-utils==0.2.1 ; python_version >= "3.7" and python_version < "3.12"
-fastapi==0.89.1 ; python_version >= "3.7" and python_version < "3.12"
+fastapi==0.91.0 ; python_version >= "3.7" and python_version < "3.12"
 flupy==1.2.0 ; python_version >= "3.7" and python_version < "3.12"
 frozenlist==1.3.3 ; python_version >= "3.7" and python_version < "3.12"
 fs==2.4.16 ; python_version >= "3.7" and python_version < "3.12"
@@ -171,7 +171,7 @@ sqlalchemy==1.4.46 ; python_version >= "3.7" and python_version < "3.12"
 sqlitedict==2.1.0 ; python_version >= "3.7" and python_version < "3.12"
 sqlparse==0.4.3 ; python_version >= "3.7" and python_version < "3.12"
 starlette-context==0.3.5 ; python_version >= "3.7" and python_version < "3.12"
-starlette==0.22.0 ; python_version >= "3.7" and python_version < "3.12"
+starlette==0.24.0 ; python_version >= "3.7" and python_version < "3.12"
 supervisor==4.2.5 ; python_version >= "3.7" and python_version < "3.12"
 svgwrite==1.4.3 ; python_version >= "3.7" and python_version < "3.12"
 tempita==0.5.2 ; python_version >= "3.7" and python_version < "3.12"

lib/galaxy/webapps/galaxy/buildapp.py

@@ -66,6 +66,7 @@ def app_pair(global_conf, load_app_kwds=None, wsgi_preflight=True, **kwargs):
         # Call app's shutdown method when the interpeter exits, this cleanly stops
         # the various Galaxy application daemon threads
         app.application_stack.register_postfork_function(atexit.register, app.shutdown)
+
     # Create the universe WSGI application
     webapp = GalaxyWebApplication(app, session_cookie="galaxysession", name="galaxy")
 
@@ -1304,13 +1305,7 @@ def wrap_in_middleware(app, global_conf, application_stack, **local_conf):
         from paste import recursive
 
         app = wrap_if_allowed(app, stack, recursive.RecursiveMiddleware, args=(conf,))
-    # If sentry logging is enabled, log here before propogating up to
-    # the error middleware
-    sentry_dsn = conf.get("sentry_dsn", None)
-    if sentry_dsn:
-        from sentry_sdk.integrations.wsgi import SentryWsgiMiddleware
 
-        app = wrap_if_allowed(app, stack, SentryWsgiMiddleware)
     # Error middleware
     app = wrap_if_allowed(app, stack, ErrorMiddleware, args=(conf,))
     # Transaction logging (apache access.log style)

lib/galaxy/webapps/galaxy/fast_app.py

@@ -107,11 +107,6 @@ def add_galaxy_middleware(app: FastAPI, gx_app):
     GalaxyFileResponse.nginx_x_accel_redirect_base = gx_app.config.nginx_x_accel_redirect_base
     GalaxyFileResponse.apache_xsendfile = gx_app.config.apache_xsendfile
 
-    if gx_app.config.sentry_dsn:
-        from sentry_sdk.integrations.asgi import SentryAsgiMiddleware
-
-        app.add_middleware(SentryAsgiMiddleware)
-
     if gx_app.config.get("allowed_origin_hostnames", None):
         app.add_middleware(
             GalaxyCORSMiddleware,

lib/tool_shed/webapp/buildapp.py

@@ -267,14 +267,7 @@ def wrap_in_middleware(app, global_conf, application_stack, **local_conf):
         from paste.translogger import TransLogger
 
         app = wrap_if_allowed(app, stack, TransLogger)
-    # If sentry logging is enabled, log here before propogating up to
-    # the error middleware
-    # TODO sentry config is duplicated between tool_shed/galaxy, refactor this.
-    sentry_dsn = conf.get("sentry_dsn", None)
-    if sentry_dsn:
-        from sentry_sdk.integrations.wsgi import SentryWsgiMiddleware
 
-        app = wrap_if_allowed(app, stack, SentryWsgiMiddleware)
     # X-Forwarded-Host handling
     from galaxy.web.framework.middleware.xforwardedhost import XForwardedHostMiddleware
 

test/unit/webapps/test_request_scoped_sqlalchemy_sessions.py

@@ -15,6 +15,7 @@ from galaxy.app_unittest_utils.galaxy_mock import MockApp
 from galaxy.webapps.base.api import add_request_id_middleware
 
 app = FastAPI()
+add_request_id_middleware(app)
 GX_APP = None
 
 
@@ -95,7 +96,6 @@ def assert_scoped_session_is_thread_local(gx_app):
 
 @pytest.mark.asyncio
 async def test_request_scoped_sa_session_single_request():
-    add_request_id_middleware(app)
     async with AsyncClient(app=app, base_url="http://test") as client:
         response = await client.get("/")
         assert response.status_code == 200
@@ -106,7 +106,6 @@ async def test_request_scoped_sa_session_single_request():
 
 @pytest.mark.asyncio
 async def test_request_scoped_sa_session_exception():
-    add_request_id_middleware(app)
     async with AsyncClient(app=app, base_url="http://test") as client:
         with pytest.raises(UnexpectedException):
             await client.get("/internal_server_error")
@@ -116,7 +115,6 @@ async def test_request_scoped_sa_session_exception():
 
 @pytest.mark.asyncio
 async def test_request_scoped_sa_session_concurrent_requests_sync():
-    add_request_id_middleware(app)
     async with AsyncClient(app=app, base_url="http://test") as client:
         awaitables = (client.get("/sync_wait") for _ in range(10))
         result = await asyncio.gather(*awaitables)
@@ -131,7 +129,6 @@ async def test_request_scoped_sa_session_concurrent_requests_sync():
 
 @pytest.mark.asyncio
 async def test_request_scoped_sa_session_concurrent_requests_async():
-    add_request_id_middleware(app)
     async with AsyncClient(app=app, base_url="http://test") as client:
         awaitables = (client.get("/async_wait") for _ in range(10))
         result = await asyncio.gather(*awaitables)
@@ -146,7 +143,6 @@ async def test_request_scoped_sa_session_concurrent_requests_async():
 
 @pytest.mark.asyncio
 async def test_request_scoped_sa_session_concurrent_requests_and_background_thread():
-    add_request_id_middleware(app)
     loop = asyncio.get_running_loop()
     target = functools.partial(assert_scoped_session_is_thread_local, GX_APP)
     with concurrent.futures.ThreadPoolExecutor() as pool: