implement tasks API and adapt notification tests

Author: bernt-matthias

bioblend/_tests/GalaxyTestBase.py

@@ -18,12 +18,14 @@
 @test_util.skip_unless_galaxy()
 class GalaxyTestBase(unittest.TestCase):
     gi: GalaxyInstance
+    config: Dict[str, Any]
 
     @classmethod
     def setUpClass(cls):
         galaxy_key = os.environ["BIOBLEND_GALAXY_API_KEY"]
         galaxy_url = os.environ["BIOBLEND_GALAXY_URL"]
         cls.gi = GalaxyInstance(url=galaxy_url, key=galaxy_key)
+        cls.config = cls.gi.config.get_config()
 
     def _test_dataset(self, history_id: str, contents: str = "1\t2\t3", **kwargs: Any) -> str:
         tool_output = self.gi.tools.paste_content(contents, history_id, **kwargs)

bioblend/_tests/TestGalaxyNotifications.py

@@ -9,6 +9,8 @@
     Optional,
 )
 
+from galaxy.tool_util.verify.wait import wait_on
+
 from bioblend.galaxy import GalaxyInstance
 from . import (
     GalaxyTestBase,
@@ -32,6 +34,8 @@ def test_notification_status(self):
         if not self.gi.users.get_current_user()["is_admin"]:
             self.skipTest("This tests requires the current user to be an admin, which is not the case.")
 
+        task_based = self.gi.config.get_config()["enable_celery_tasks"]
+
         # user creation for the test
         user1 = self._create_local_test_user(password="password")
         user2 = self._create_local_test_user(password="password")
@@ -56,14 +60,14 @@ def test_notification_status(self):
             [user1["id"]],
             message="test_notification_status 1",
         )
-        assert created_response_1["total_notifications_sent"] == 1
+        self._assert_notifications_sent(task_based, created_response_1, 1)
 
         # Both user1 and user2 will receive this notification
         created_response_2 = self._send_test_notification_to(
             [user1["id"], user2["id"]],
             message="test_notification_status 2",
         )
-        assert created_response_2["total_notifications_sent"] == 2
+        self._assert_notifications_sent(task_based, created_response_2, 2)
 
         # All users will receive this broadcasted notification
         self._send_test_broadcast_notification(message="test_notification_status 3")
@@ -146,11 +150,16 @@ def test_get_user_notifications(self):
         if not self.gi.users.get_current_user()["is_admin"]:
             self.skipTest("This tests requires the current user to be an admin, which is not the case.")
 
+        task_based = self.gi.config.get_config()["enable_celery_tasks"]
+
         # send the notifications
         user_id = [self.gi.users.get_current_user()["id"]]
-        self._send_test_notification_to(user_id, message="test_notification_status 1")
-        self._send_test_notification_to(user_id, message="test_notification_status 2")
-        self._send_test_notification_to(user_id, message="test_notification_status 3")
+        send_response = self._send_test_notification_to(user_id, message="test_notification_status 1")
+        self._assert_notifications_sent(task_based, send_response, 1)
+        send_response = self._send_test_notification_to(user_id, message="test_notification_status 2")
+        self._assert_notifications_sent(task_based, send_response, 1)
+        send_response = self._send_test_notification_to(user_id, message="test_notification_status 3")
+        self._assert_notifications_sent(task_based, send_response, 1)
 
         # this should fetch all the notifications
         created_response_1 = self.gi.notifications.get_user_notifications()
@@ -239,6 +248,7 @@ def test_show_notification(self):
             self.skipTest("This Galaxy instance is not configured to use notifications.")
         if not self.gi.users.get_current_user()["is_admin"]:
             self.skipTest("This tests requires the current user to be an admin, which is not the case.")
+        task_based = self.gi.config.get_config()["enable_celery_tasks"]
 
         # user creation for the test
         user = self._create_local_test_user(password="password")
@@ -247,10 +257,11 @@ def test_show_notification(self):
         user_gi = GalaxyInstance(url=self.gi.base_url, email=user["email"], password="password")
 
         # send the test notification
-        notification_response = self._send_test_notification_to([user["id"]], message="test_notification_status")[
-            "notification"
-        ]
-        notification_id = notification_response["id"]
+        send_response = self._send_test_notification_to([user["id"]], message="test_notification_status")
+        self._assert_notifications_sent(task_based, send_response, 1)
+
+        notifications = user_gi.notifications.get_user_notifications()
+        notification_id = notifications[0]["id"]
 
         # Fetch the notification
         notification = user_gi.notifications.show_notification(notification_id)
@@ -269,6 +280,7 @@ def test_update_notifications(self):
             self.skipTest("This Galaxy instance is not configured to use notifications.")
         if not self.gi.users.get_current_user()["is_admin"]:
             self.skipTest("This tests requires the current user to be an admin, which is not the case.")
+        task_based = self.gi.config.get_config()["enable_celery_tasks"]
 
         # user creation for the test
         user = self._create_local_test_user(password="password")
@@ -277,12 +289,14 @@ def test_update_notifications(self):
         user_gi = GalaxyInstance(url=self.gi.base_url, email=user["email"], password="password")
 
         # send the test notifications and save their ids
-        notification_1_id = self._send_test_notification_to([user["id"]], message="test_notification_status 1")[
-            "notification"
-        ]["id"]
-        notification_2_id = self._send_test_notification_to([user["id"]], message="test_notification_status 2")[
-            "notification"
-        ]["id"]
+        send_response = self._send_test_notification_to([user["id"]], message="test_notification_status 1")
+        self._assert_notifications_sent(task_based, send_response, 1)
+        send_response = self._send_test_notification_to([user["id"]], message="test_notification_status 2")
+        self._assert_notifications_sent(task_based, send_response, 1)
+
+        notifications = user_gi.notifications.get_user_notifications()
+        notification_1_id = notifications[0]["id"]
+        notification_2_id = notifications[1]["id"]
 
         # fetch the notifications
         notification_1 = user_gi.notifications.show_notification(notification_1_id)
@@ -349,6 +363,7 @@ def test_delete_notifications(self):
             self.skipTest("This Galaxy instance is not configured to use notifications.")
         if not self.gi.users.get_current_user()["is_admin"]:
             self.skipTest("This tests requires the current user to be an admin, which is not the case.")
+        task_based = self.gi.config.get_config()["enable_celery_tasks"]
 
         # user creation for the test
         user = self._create_local_test_user(password="password")
@@ -357,15 +372,17 @@ def test_delete_notifications(self):
         user_gi = GalaxyInstance(url=self.gi.base_url, email=user["email"], password="password")
 
         # send the test notifications and save their ids
-        notification_1 = self._send_test_notification_to([user["id"]], message="test_notification_status 1")
-        print(notification_1)
-        notification_1_id = notification_1["notification"]["id"]
-        notification_2_id = self._send_test_notification_to([user["id"]], message="test_notification_status 2")[
-            "notification"
-        ]["id"]
-        notification_3_id = self._send_test_notification_to([user["id"]], message="test_notification_status 3")[
-            "notification"
-        ]["id"]
+        send_response = self._send_test_notification_to([user["id"]], message="test_notification_status 1")
+        self._assert_notifications_sent(task_based, send_response, 1)
+        send_response = self._send_test_notification_to([user["id"]], message="test_notification_status 2")
+        self._assert_notifications_sent(task_based, send_response, 1)
+        send_response = self._send_test_notification_to([user["id"]], message="test_notification_status 3")
+        self._assert_notifications_sent(task_based, send_response, 1)
+
+        notifications = user_gi.notifications.get_user_notifications()
+        notification_1_id = notifications[0]["id"]
+        notification_2_id = notifications[1]["id"]
+        notification_3_id = notifications[2]["id"]
 
         # delete a single notifications
         response_1 = user_gi.notifications.delete_user_notification(notification_id=notification_1_id)
@@ -545,4 +562,16 @@ def _send_test_notification_to(
             user_ids=user_ids,
             expiration_time=(datetime.utcnow() + timedelta(days=1)),
         )
+        print(f"_send_test_notification_to {notification=}")
         return notification
+
+    def _assert_notifications_sent(self, task_based, response, expected_count: int = 0):
+        def task_success():
+            return None if self.gi.tasks.get_task_status(task_id) != "SUCCESS" else True
+
+        if task_based:
+            task_id = response["id"]
+            assert task_id is not None
+            wait_on(task_success, "Task successful", 60)
+        else:
+            assert response["total_notifications_sent"] == expected_count

bioblend/galaxy/__init__.py

@@ -22,6 +22,7 @@
     notifications,
     quotas,
     roles,
+    tasks,
     tool_data,
     tool_dependencies,
     tools,
@@ -111,6 +112,7 @@ def __init__(
         self.folders = folders.FoldersClient(self)
         self.tool_dependencies = tool_dependencies.ToolDependenciesClient(self)
         self.notifications = notifications.NotificationClient(self)
+        self.tasks = tasks.TasksClient(self)
 
     def __repr__(self) -> str:
         """

bioblend/galaxy/tasks/__init__.py

@@ -0,0 +1,36 @@
+"""
+Contains possible interaction dealing with Galaxy tasks.
+"""
+
+from typing import TYPE_CHECKING
+
+from bioblend.galaxy.client import Client
+
+if TYPE_CHECKING:
+    from uuid import UUID
+
+    from bioblend.galaxy import GalaxyInstance
+
+
+class TasksClient(Client):
+    """
+    This endpoint only works on Galaxy 22.05 or later.
+    """
+
+    module = "tasks"
+
+    def __init__(self, galaxy_instance: "GalaxyInstance") -> None:
+        super().__init__(galaxy_instance)
+
+    def get_task_status(self, task_id: "UUID") -> str:
+        """
+        Determine state of task ID
+
+        :type task_id: UUID
+        :param task_id: the task ID
+
+        :rtype: str
+        :return: String indicating task state
+        """
+        url = self._make_url() + f"/{task_id}/state"
+        return self._get(url=url)

setup.cfg

@@ -82,6 +82,7 @@ console_scripts =
 [options.extras_require]
 testing =
     pytest
+    galaxy-tool-util
 
 [options.package_data]
 bioblend =

tox.ini

@@ -6,6 +6,7 @@ commands =
     pytest {posargs}
 deps =
     pytest
+    galaxy-tool-util
 passenv =
     BIOBLEND_GALAXY_API_KEY
     BIOBLEND_GALAXY_MASTER_API_KEY