Introduce galaxy_external_url variable

doc/source/admin/galaxy_options.rst

@@ -2279,15 +2279,29 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~~~~~~
+``galaxy_external_url``
+~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    URL (with schema http/https) of the Galaxy instance as accessible
+    from external networks, including ``galaxy_url_prefix`` if
+    necessary. This URL is used to determine links outside of the web
+    application, e.g. when requesting job finish emails.
+:Default: ``None``
+:Type: str
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``galaxy_infrastructure_url``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 :Description:
     URL (with schema http/https) of the Galaxy instance as accessible
-    within your local network. This URL is used as a default by pulsar
-    file staging and Interactive Tool containers for communicating
-    back with Galaxy via the API.
+    within your local network, including ``galaxy_url_prefix`` if
+    necessary. This URL is used as a default by pulsar file staging
+    and Interactive Tool containers for communicating back with Galaxy
+    via the API.
     If you plan to run Interactive Tools make sure the docker
     container can reach this URL.
 :Default: ``http://localhost:8080``

lib/galaxy/config/__init__.py

@@ -706,6 +706,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
     enable_tool_shed_check: bool
     galaxy_data_manager_data_path: str
     galaxy_infrastructure_url: str
+    galaxy_external_url: Optional[str]
     hours_between_check: int
     integrated_tool_panel_config: str
     involucro_path: str

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

@@ -1422,9 +1422,16 @@ galaxy:
   #galaxy_url_prefix: /
 
   # URL (with schema http/https) of the Galaxy instance as accessible
-  # within your local network. This URL is used as a default by pulsar
-  # file staging and Interactive Tool containers for communicating back
-  # with Galaxy via the API.
+  # from external networks, including ``galaxy_url_prefix`` if
+  # necessary. This URL is used to determine links outside of the web
+  # application, e.g. when requesting job finish emails.
+  #galaxy_external_url: null
+
+  # URL (with schema http/https) of the Galaxy instance as accessible
+  # within your local network, including ``galaxy_url_prefix`` if
+  # necessary. This URL is used as a default by pulsar file staging and
+  # Interactive Tool containers for communicating back with Galaxy via
+  # the API.
   # If you plan to run Interactive Tools make sure the docker container
   # can reach this URL.
   #galaxy_infrastructure_url: http://localhost:8080

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

@@ -54,6 +54,9 @@ tool_shed:
   # options.
   #whoosh_index_dir: database/toolshed_whoosh_indexes
 
+  # Cache directory for Pydantic model objects.
+  #model_cache_dir: database/model_cache
+
   # For searching repositories at /api/repositories:
   #repo_name_boost: 0.9
 

lib/galaxy/config/schemas/config_schema.yml

@@ -1642,15 +1642,24 @@ mapping:
           URL prefix for Galaxy application. If Galaxy should be served under a prefix set this to
           the desired prefix value.
 
+      galaxy_external_url:
+        type: str
+        required: false
+        desc: |
+          URL (with schema http/https) of the Galaxy instance as accessible
+          from external networks, including ``galaxy_url_prefix`` if necessary.
+          This URL is used to determine links outside of the web application,
+          e.g. when requesting job finish emails.
+
       galaxy_infrastructure_url:
         type: str
         default: http://localhost:8080
         required: false
         desc: |
           URL (with schema http/https) of the Galaxy instance as accessible
-          within your local network. This URL is used as a default by pulsar
-          file staging and Interactive Tool containers for communicating back with
-          Galaxy via the API.
+          within your local network, including ``galaxy_url_prefix`` if necessary.
+          This URL is used as a default by pulsar file staging and Interactive Tool
+          containers for communicating back with Galaxy via the API.
 
           If you plan to run Interactive Tools make sure the docker container
           can reach this URL.

lib/galaxy/job_execution/actions/post.py

@@ -53,12 +53,11 @@ def execute(cls, app, sa_session, action, job, replacement_dict, final_job_state
         try:
             history_id_encoded = app.security.encode_id(job.history_id)
             link_invocation = None
+            galaxy_url = app.config.galaxy_external_url or app.config.galaxy_infrastructure_url
             if job.workflow_invocation_step:
                 invocation_id_encoded = app.security.encode_id(job.workflow_invocation_step.workflow_invocation_id)
-                link_invocation = (
-                    f"{app.config.galaxy_infrastructure_url}/workflows/invocations/report?id={invocation_id_encoded}"
-                )
-            link = f"{app.config.galaxy_infrastructure_url}/histories/view?id={history_id_encoded}"
+                link_invocation = f"{galaxy_url}/workflows/invocations/report?id={invocation_id_encoded}"
+            link = f"{galaxy_url}/histories/view?id={history_id_encoded}"
             to = job.get_user_email()
             subject = f"Galaxy job completion notification from history '{job.history.name}'"
             outdata = ",\n".join(ds.dataset.display_name() for ds in job.output_datasets)

lib/galaxy/managers/notification.py

@@ -282,7 +282,7 @@ def create_broadcast_notification(self, request: BroadcastNotificationCreateRequ
         This kind of notification is not explicitly associated with any specific user but it is accessible by all users.
         """
         self.ensure_notifications_enabled()
-        notification = self._create_notification_model(request)
+        notification = self._create_notification_model(request, self.config.galaxy_external_url)
         self.sa_session.add(notification)
         with transaction(self.sa_session):
             self.sa_session.commit()

lib/galaxy/webapps/galaxy/services/notifications.py

@@ -57,7 +57,9 @@ def send_notification(
         self.notification_manager.ensure_notifications_enabled()
         self._ensure_user_can_send_notifications(sender_context)
         galaxy_url = (
-            str(sender_context.url_builder("/", qualified=True)).rstrip("/") if sender_context.url_builder else None
+            str(sender_context.url_builder("/", qualified=True)).rstrip("/")
+            if sender_context.url_builder
+            else self.notification_manager.config.galaxy_external_url
         )
         request = NotificationCreateRequest.model_construct(
             notification=payload.notification,

lib/galaxy/webapps/galaxy/services/sharable.py

@@ -117,7 +117,11 @@ def share_with_users(self, trans, id: DecodedDatabaseIdField, payload: ShareWith
         base_status = self._get_sharing_status(trans, item)
         status = self.share_with_status_cls.model_construct(**base_status.model_dump(), extra=extra)
         status.errors.extend(errors)
-        galaxy_url = str(trans.url_builder("/", qualified=True)).rstrip("/") if trans.url_builder else None
+        galaxy_url = (
+            str(trans.url_builder("/", qualified=True)).rstrip("/")
+            if trans.url_builder
+            else trans.app.config.galaxy_external_url
+        )
         self._send_notification_to_users(users_to_notify, item, status, galaxy_url)
         return status