Merge branch 'release_21.09' into dev

lib/galaxy/app.py

@@ -97,7 +97,31 @@ class HaltableContainer(Container):
             raise exception
 
 
-class MinimalGalaxyApplication(BasicSharedApp, config.ConfiguresGalaxyMixin, HaltableContainer):
+class SentryClientMixin:
+    def configure_sentry_client(self):
+        self.sentry_client = None
+        if self.config.sentry_dsn:
+            event_level = self.config.sentry_event_level.upper()
+            assert event_level in ['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'], f"Invalid sentry event level '{self.config.sentry.event_level}'"
+
+            def postfork_sentry_client():
+                import sentry_sdk
+                from sentry_sdk.integrations.logging import LoggingIntegration
+
+                sentry_logging = LoggingIntegration(
+                    level=logging.INFO,  # Capture info and above as breadcrumbs
+                    event_level=getattr(logging, event_level)  # Send errors as events
+                )
+                self.sentry_client = sentry_sdk.init(
+                    self.config.sentry_dsn,
+                    release=f"{self.config.version_major}.{self.config.version_minor}",
+                    integrations=[sentry_logging]
+                )
+
+            self.application_stack.register_postfork_function(postfork_sentry_client)
+
+
+class MinimalGalaxyApplication(BasicSharedApp, config.ConfiguresGalaxyMixin, HaltableContainer, SentryClientMixin):
     """Encapsulates the state of a minimal Galaxy application"""
 
     def __init__(self, fsmon=False, configure_logging=True, **kwargs) -> None:
@@ -191,27 +215,7 @@ class GalaxyManagerApplication(MinimalManagerApp, MinimalGalaxyApplication):
         self._configure_datatypes_registry(self.installed_repository_manager)
         self._register_singleton(Registry, self.datatypes_registry)
         galaxy.model.set_datatypes_registry(self.datatypes_registry)
-
-        self.sentry_client = None
-        if self.config.sentry_dsn:
-            event_level = self.config.sentry_event_level.upper()
-            assert event_level in ['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'], f"Invalid sentry event level '{self.config.sentry.event_level}'"
-
-            def postfork_sentry_client():
-                import sentry_sdk
-                from sentry_sdk.integrations.logging import LoggingIntegration
-
-                sentry_logging = LoggingIntegration(
-                    level=logging.INFO,  # Capture info and above as breadcrumbs
-                    event_level=getattr(logging, event_level)  # Send errors as events
-                )
-                self.sentry_client = sentry_sdk.init(
-                    self.config.sentry_dsn,
-                    release=f"{self.config.version_major}.{self.config.version_minor}",
-                    integrations=[sentry_logging]
-                )
-
-            self.application_stack.register_postfork_function(postfork_sentry_client)
+        self.configure_sentry_client()
 
 
 class UniverseApplication(StructuredApp, GalaxyManagerApplication):

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

@@ -415,6 +415,10 @@ tool_shed:
   # <project_name> -> Settings -> API Keys.
   #sentry_dsn: null
 
+  # Determines the minimum log level that will be sent as an event to
+  # Sentry. Possible values are DEBUG, INFO, WARNING, ERROR or CRITICAL.
+  #sentry_event_level: ERROR
+
   # 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/tool_shed/webapp/app.py

@@ -11,6 +11,7 @@ import tool_shed.repository_registry
 import tool_shed.repository_types.registry
 import tool_shed.webapp.model
 from galaxy import auth
+from galaxy.app import SentryClientMixin
 from galaxy.config import configure_logging
 from galaxy.managers.citations import CitationsManager
 from galaxy.managers.users import UserManager
@@ -28,7 +29,7 @@ from . import config
 log = logging.getLogger(__name__)
 
 
-class UniverseApplication(BasicSharedApp):
+class UniverseApplication(BasicSharedApp, SentryClientMixin):
     """Encapsulates the state of a Universe application"""
 
     def __init__(self, **kwd) -> None:
@@ -93,6 +94,8 @@ class UniverseApplication(BasicSharedApp):
         self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir
         # Initialize the repository registry.
         self.repository_registry = tool_shed.repository_registry.Registry(self)
+        # Configure Sentry client if configured
+        self.configure_sentry_client()
         #  used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base.
         self.server_starttime = int(time.time())
         log.debug("Tool shed hgweb.config file is: %s", self.hgweb_config_manager.hgweb_config)

lib/tool_shed/webapp/buildapp.py

@@ -248,8 +248,8 @@ def wrap_in_middleware(app, global_conf, application_stack, **local_conf):
     # TODO sentry config is duplicated between tool_shed/galaxy, refactor this.
     sentry_dsn = conf.get('sentry_dsn', None)
     if sentry_dsn:
-        from galaxy.web.framework.middleware.sentry import Sentry
-        app = wrap_if_allowed(app, stack, Sentry, args=(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
     app = wrap_if_allowed(app, stack, XForwardedHostMiddleware)

lib/tool_shed/webapp/config.py

@@ -15,7 +15,7 @@ from galaxy.config import (
 from galaxy.config.schema import AppSchema
 from galaxy.exceptions import ConfigurationError
 from galaxy.util import string_as_bool
-from galaxy.version import VERSION, VERSION_MAJOR
+from galaxy.version import VERSION, VERSION_MAJOR, VERSION_MINOR
 from galaxy.web.formatting import expand_pretty_datetime_format
 
 log = logging.getLogger(__name__)
@@ -67,6 +67,7 @@ class ToolShedAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
         os.umask(self.umask)  # can't get w/o set, so set it back
         self.gid = os.getgid()  # if running under newgrp(1) we'll need to fix the group of data created on the cluster
         self.version_major = VERSION_MAJOR
+        self.version_minor = VERSION_MINOR
         self.version = VERSION
         # Database related configuration
         if not self.database_connection:  # Provide default if not supplied by user

lib/tool_shed/webapp/config_schema.yml

@@ -578,6 +578,14 @@ mapping:
           indicated sentry instance.  This connection string is available in your
           sentry instance under <project_name> -> Settings -> API Keys.
 
+      sentry_event_level:
+        type: str
+        default: ERROR
+        required: false
+        desc: |
+          Determines the minimum log level that will be sent as an event to Sentry.
+          Possible values are DEBUG, INFO, WARNING, ERROR or CRITICAL.
+
       session_duration:
         type: int
         default: 0