galaxy-test-api 26.0.1.dev0__tar.gz → 26.0.2__tar.gz

galaxy_test_api-26.0.1.dev0/galaxy_test_api.egg-info/PKG-INFO → galaxy_test_api-26.0.2/HISTORY.rst

@@ -1,50 +1,89 @@
-Metadata-Version: 2.4
-Name: galaxy-test-api
-Version: 26.0.1.dev0
-Summary: Galaxy API tests
-Home-page: https://github.com/galaxyproject/galaxy
-Author: Galaxy Project and Community
-Author-email: galaxy-committers@lists.galaxyproject.org
-License: MIT
-Requires-Python: >=3.10
-Description-Content-Type: text/x-rst
-License-File: LICENSE
-Requires-Dist: galaxy-test-base
-Requires-Dist: pytest
-Requires-Dist: python-dateutil
-Requires-Dist: requests
-Requires-Dist: tuspy
-Provides-Extra: driver
-Requires-Dist: galaxy-test-driver; extra == "driver"
-Provides-Extra: test
-Requires-Dist: pytest; extra == "test"
-Dynamic: license-file
+History
+-------
 
+.. to_doc
 
-.. image:: https://badge.fury.io/py/galaxy-test-api.svg
-   :target: https://pypi.org/project/galaxy-test-api/
+-------------------
+26.0.2 (2026-10-25)
+-------------------
 
 
+=========
+Bug fixes
+=========
 
-Overview
---------
+* Fix WES workflow completion and add missing WES docs by `@jmchilton <https://github.com/jmchilton>`_ in `#22857 <https://github.com/galaxyproject/galaxy/pull/22857>`_
+* Fix fasta preview rendering for sequences larger than 100 KB by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23163 <https://github.com/galaxyproject/galaxy/pull/23163>`_
+* Use pydantic-aware serializer for celery control replies by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23525 <https://github.com/galaxyproject/galaxy/pull/23525>`_
+* Fix 500 on the dataset tool-markdown report endpoint by `@jmchilton <https://github.com/jmchilton>`_ in `#23599 <https://github.com/galaxyproject/galaxy/pull/23599>`_
+* Serialize runtime values of unresolved conditionals in populate_state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23649 <https://github.com/galaxyproject/galaxy/pull/23649>`_
+* Fix wait_on callback in test_delete_job_with_message by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23687 <https://github.com/galaxyproject/galaxy/pull/23687>`_
+* Return 400 for request bodies that webob cannot parse by `@rmz-oz <https://github.com/rmz-oz>`_ in `#23839 <https://github.com/galaxyproject/galaxy/pull/23839>`_
+* Fix 500 on reading pages with non-ASCII slugs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23854 <https://github.com/galaxyproject/galaxy/pull/23854>`_
+* Respect allow_uri_if_protocol for single deferred data inputs by `@davelopez <https://github.com/davelopez>`_ in `#24001 <https://github.com/galaxyproject/galaxy/pull/24001>`_
+* Fix CI failures and flaky tests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24028 <https://github.com/galaxyproject/galaxy/pull/24028>`_
+* De-race test_workflow_with_deleted_dataset_step_parameter by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24083 <https://github.com/galaxyproject/galaxy/pull/24083>`_
+* Show workflow integer/float input bounds on the run form by `@jmchilton <https://github.com/jmchilton>`_ in `#24212 <https://github.com/galaxyproject/galaxy/pull/24212>`_
+* Fix dataset permissions set when upload and discovery jobs finish by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24233 <https://github.com/galaxyproject/galaxy/pull/24233>`_
+* Apply default permissions to discovered collection elements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24284 <https://github.com/galaxyproject/galaxy/pull/24284>`_
+* Don't overwrite inputs when skipping database operations on nested collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24286 <https://github.com/galaxyproject/galaxy/pull/24286>`_
+* Better API Handling for Custom Builds by `@jmchilton <https://github.com/jmchilton>`_ in `#24310 <https://github.com/galaxyproject/galaxy/pull/24310>`_
+* Return 400 when a custom build's dataset can't be converted to len by `@jmchilton <https://github.com/jmchilton>`_ in `#24313 <https://github.com/galaxyproject/galaxy/pull/24313>`_
+* Fix numeric column stats in tabular raw_data requests by `@davelopez <https://github.com/davelopez>`_ in `#24359 <https://github.com/galaxyproject/galaxy/pull/24359>`_
+* Import unregistered dataset extensions from model stores as data by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24433 <https://github.com/galaxyproject/galaxy/pull/24433>`_
 
-The Galaxy_ API tests.
+-------------------
+25.1.3 (2026-10-25)
+-------------------
 
-* Code: https://github.com/galaxyproject/galaxy
 
-.. _Galaxy: http://galaxyproject.org/
+=========
+Bug fixes
+=========
 
-History
--------
+* Fix dataset collection tag duplication when copying a history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21984 <https://github.com/galaxyproject/galaxy/pull/21984>`_
+* Restore file doesn't match sniffed datatype message by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21988 <https://github.com/galaxyproject/galaxy/pull/21988>`_
+* Use base64 URL instead of GitHub URL in test_stage_fetch_decompress_true by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22069 <https://github.com/galaxyproject/galaxy/pull/22069>`_
+* Backport FastAPI/Starlette upgrade for BadHost (CVE-2026-48710) by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22778 <https://github.com/galaxyproject/galaxy/pull/22778>`_
+* Use pydantic-aware serializer for celery control replies by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23525 <https://github.com/galaxyproject/galaxy/pull/23525>`_
+* Serialize runtime values of unresolved conditionals in populate_state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23649 <https://github.com/galaxyproject/galaxy/pull/23649>`_
+* Return 400 for request bodies that webob cannot parse by `@rmz-oz <https://github.com/rmz-oz>`_ in `#23839 <https://github.com/galaxyproject/galaxy/pull/23839>`_
+* Fix 500 on reading pages with non-ASCII slugs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23854 <https://github.com/galaxyproject/galaxy/pull/23854>`_
+* Respect allow_uri_if_protocol for single deferred data inputs by `@davelopez <https://github.com/davelopez>`_ in `#24001 <https://github.com/galaxyproject/galaxy/pull/24001>`_
+* Fix CI failures and flaky tests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24028 <https://github.com/galaxyproject/galaxy/pull/24028>`_
+* Fix dataset permissions set when upload and discovery jobs finish by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24233 <https://github.com/galaxyproject/galaxy/pull/24233>`_
+* Apply default permissions to discovered collection elements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24284 <https://github.com/galaxyproject/galaxy/pull/24284>`_
+* Don't overwrite inputs when skipping database operations on nested collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24286 <https://github.com/galaxyproject/galaxy/pull/24286>`_
+* Better API Handling for Custom Builds by `@jmchilton <https://github.com/jmchilton>`_ in `#24310 <https://github.com/galaxyproject/galaxy/pull/24310>`_
+* Fix numeric column stats in tabular raw_data requests by `@davelopez <https://github.com/davelopez>`_ in `#24359 <https://github.com/galaxyproject/galaxy/pull/24359>`_
+* Import unregistered dataset extensions from model stores as data by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24433 <https://github.com/galaxyproject/galaxy/pull/24433>`_
+
+-------------------
+26.0.1 (2026-06-04)
+-------------------
 
-.. to_doc
 
------------
-26.0.1.dev0
------------
+=========
+Bug fixes
+=========
+
+* Hide hidden tools in the tool form by `@bgruening <https://github.com/bgruening>`_ in `#22215 <https://github.com/galaxyproject/galaxy/pull/22215>`_
+* Fix IndexError in SplitPairedAndUnpairedTool for unpaired elements by `@ernestprovo23 <https://github.com/ernestprovo23>`_ in `#22282 <https://github.com/galaxyproject/galaxy/pull/22282>`_
+* Fix \`get_structure\` when it is passed a DCE with nested elements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22453 <https://github.com/galaxyproject/galaxy/pull/22453>`_
+* Treat paused inputs as not-ready in DatabaseOperationTool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22529 <https://github.com/galaxyproject/galaxy/pull/22529>`_
+* Fix crash merging structurally invalid nested collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22546 <https://github.com/galaxyproject/galaxy/pull/22546>`_
+* Raise ToolInputsNotReady for unpopulated structured_like target by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22552 <https://github.com/galaxyproject/galaxy/pull/22552>`_
+* Raises error if decoding fails during relabeling from file by `@guerler <https://github.com/guerler>`_ in `#22595 <https://github.com/galaxyproject/galaxy/pull/22595>`_
+* Fix job access check for collection-only outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22603 <https://github.com/galaxyproject/galaxy/pull/22603>`_
+* Fix data source tool redirect back to Galaxy SPA by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22720 <https://github.com/galaxyproject/galaxy/pull/22720>`_
+* Fix HDA leak in tool form for data managers (#22674) by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22724 <https://github.com/galaxyproject/galaxy/pull/22724>`_
+* Backport FastAPI/Starlette upgrade for BadHost (CVE-2026-48710) by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22778 <https://github.com/galaxyproject/galaxy/pull/22778>`_
 
+============
+Enhancements
+============
 
+* Replace per-term joins in workflow search with EXISTS subqueries by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22548 <https://github.com/galaxyproject/galaxy/pull/22548>`_
 
 -------------------
 26.0.0 (2026-04-08)

{galaxy_test_api-26.0.1.dev0 → galaxy_test_api-26.0.2}/PKG-INFO

@@ -1,11 +1,26 @@
 Metadata-Version: 2.4
 Name: galaxy-test-api
-Version: 26.0.1.dev0
+Version: 26.0.2
 Summary: Galaxy API tests
 Home-page: https://github.com/galaxyproject/galaxy
 Author: Galaxy Project and Community
 Author-email: galaxy-committers@lists.galaxyproject.org
 License: MIT
+Keywords: Galaxy
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Natural Language :: English
+Classifier: Operating System :: POSIX
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Software Development
+Classifier: Topic :: Software Development :: Code Generators
+Classifier: Topic :: Software Development :: Testing
 Requires-Python: >=3.10
 Description-Content-Type: text/x-rst
 License-File: LICENSE
@@ -40,11 +55,87 @@ History
 
 .. to_doc
 
------------
-26.0.1.dev0
------------
+-------------------
+26.0.2 (2026-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix WES workflow completion and add missing WES docs by `@jmchilton <https://github.com/jmchilton>`_ in `#22857 <https://github.com/galaxyproject/galaxy/pull/22857>`_
+* Fix fasta preview rendering for sequences larger than 100 KB by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23163 <https://github.com/galaxyproject/galaxy/pull/23163>`_
+* Use pydantic-aware serializer for celery control replies by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23525 <https://github.com/galaxyproject/galaxy/pull/23525>`_
+* Fix 500 on the dataset tool-markdown report endpoint by `@jmchilton <https://github.com/jmchilton>`_ in `#23599 <https://github.com/galaxyproject/galaxy/pull/23599>`_
+* Serialize runtime values of unresolved conditionals in populate_state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23649 <https://github.com/galaxyproject/galaxy/pull/23649>`_
+* Fix wait_on callback in test_delete_job_with_message by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23687 <https://github.com/galaxyproject/galaxy/pull/23687>`_
+* Return 400 for request bodies that webob cannot parse by `@rmz-oz <https://github.com/rmz-oz>`_ in `#23839 <https://github.com/galaxyproject/galaxy/pull/23839>`_
+* Fix 500 on reading pages with non-ASCII slugs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23854 <https://github.com/galaxyproject/galaxy/pull/23854>`_
+* Respect allow_uri_if_protocol for single deferred data inputs by `@davelopez <https://github.com/davelopez>`_ in `#24001 <https://github.com/galaxyproject/galaxy/pull/24001>`_
+* Fix CI failures and flaky tests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24028 <https://github.com/galaxyproject/galaxy/pull/24028>`_
+* De-race test_workflow_with_deleted_dataset_step_parameter by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24083 <https://github.com/galaxyproject/galaxy/pull/24083>`_
+* Show workflow integer/float input bounds on the run form by `@jmchilton <https://github.com/jmchilton>`_ in `#24212 <https://github.com/galaxyproject/galaxy/pull/24212>`_
+* Fix dataset permissions set when upload and discovery jobs finish by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24233 <https://github.com/galaxyproject/galaxy/pull/24233>`_
+* Apply default permissions to discovered collection elements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24284 <https://github.com/galaxyproject/galaxy/pull/24284>`_
+* Don't overwrite inputs when skipping database operations on nested collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24286 <https://github.com/galaxyproject/galaxy/pull/24286>`_
+* Better API Handling for Custom Builds by `@jmchilton <https://github.com/jmchilton>`_ in `#24310 <https://github.com/galaxyproject/galaxy/pull/24310>`_
+* Return 400 when a custom build's dataset can't be converted to len by `@jmchilton <https://github.com/jmchilton>`_ in `#24313 <https://github.com/galaxyproject/galaxy/pull/24313>`_
+* Fix numeric column stats in tabular raw_data requests by `@davelopez <https://github.com/davelopez>`_ in `#24359 <https://github.com/galaxyproject/galaxy/pull/24359>`_
+* Import unregistered dataset extensions from model stores as data by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24433 <https://github.com/galaxyproject/galaxy/pull/24433>`_
+
+-------------------
+25.1.3 (2026-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
 
+* Fix dataset collection tag duplication when copying a history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21984 <https://github.com/galaxyproject/galaxy/pull/21984>`_
+* Restore file doesn't match sniffed datatype message by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21988 <https://github.com/galaxyproject/galaxy/pull/21988>`_
+* Use base64 URL instead of GitHub URL in test_stage_fetch_decompress_true by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22069 <https://github.com/galaxyproject/galaxy/pull/22069>`_
+* Backport FastAPI/Starlette upgrade for BadHost (CVE-2026-48710) by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22778 <https://github.com/galaxyproject/galaxy/pull/22778>`_
+* Use pydantic-aware serializer for celery control replies by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23525 <https://github.com/galaxyproject/galaxy/pull/23525>`_
+* Serialize runtime values of unresolved conditionals in populate_state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23649 <https://github.com/galaxyproject/galaxy/pull/23649>`_
+* Return 400 for request bodies that webob cannot parse by `@rmz-oz <https://github.com/rmz-oz>`_ in `#23839 <https://github.com/galaxyproject/galaxy/pull/23839>`_
+* Fix 500 on reading pages with non-ASCII slugs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23854 <https://github.com/galaxyproject/galaxy/pull/23854>`_
+* Respect allow_uri_if_protocol for single deferred data inputs by `@davelopez <https://github.com/davelopez>`_ in `#24001 <https://github.com/galaxyproject/galaxy/pull/24001>`_
+* Fix CI failures and flaky tests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24028 <https://github.com/galaxyproject/galaxy/pull/24028>`_
+* Fix dataset permissions set when upload and discovery jobs finish by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24233 <https://github.com/galaxyproject/galaxy/pull/24233>`_
+* Apply default permissions to discovered collection elements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24284 <https://github.com/galaxyproject/galaxy/pull/24284>`_
+* Don't overwrite inputs when skipping database operations on nested collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24286 <https://github.com/galaxyproject/galaxy/pull/24286>`_
+* Better API Handling for Custom Builds by `@jmchilton <https://github.com/jmchilton>`_ in `#24310 <https://github.com/galaxyproject/galaxy/pull/24310>`_
+* Fix numeric column stats in tabular raw_data requests by `@davelopez <https://github.com/davelopez>`_ in `#24359 <https://github.com/galaxyproject/galaxy/pull/24359>`_
+* Import unregistered dataset extensions from model stores as data by `@mvdbeek <https://github.com/mvdbeek>`_ in `#24433 <https://github.com/galaxyproject/galaxy/pull/24433>`_
+
+-------------------
+26.0.1 (2026-06-04)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Hide hidden tools in the tool form by `@bgruening <https://github.com/bgruening>`_ in `#22215 <https://github.com/galaxyproject/galaxy/pull/22215>`_
+* Fix IndexError in SplitPairedAndUnpairedTool for unpaired elements by `@ernestprovo23 <https://github.com/ernestprovo23>`_ in `#22282 <https://github.com/galaxyproject/galaxy/pull/22282>`_
+* Fix \`get_structure\` when it is passed a DCE with nested elements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22453 <https://github.com/galaxyproject/galaxy/pull/22453>`_
+* Treat paused inputs as not-ready in DatabaseOperationTool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22529 <https://github.com/galaxyproject/galaxy/pull/22529>`_
+* Fix crash merging structurally invalid nested collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22546 <https://github.com/galaxyproject/galaxy/pull/22546>`_
+* Raise ToolInputsNotReady for unpopulated structured_like target by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22552 <https://github.com/galaxyproject/galaxy/pull/22552>`_
+* Raises error if decoding fails during relabeling from file by `@guerler <https://github.com/guerler>`_ in `#22595 <https://github.com/galaxyproject/galaxy/pull/22595>`_
+* Fix job access check for collection-only outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22603 <https://github.com/galaxyproject/galaxy/pull/22603>`_
+* Fix data source tool redirect back to Galaxy SPA by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22720 <https://github.com/galaxyproject/galaxy/pull/22720>`_
+* Fix HDA leak in tool form for data managers (#22674) by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22724 <https://github.com/galaxyproject/galaxy/pull/22724>`_
+* Backport FastAPI/Starlette upgrade for BadHost (CVE-2026-48710) by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22778 <https://github.com/galaxyproject/galaxy/pull/22778>`_
+
+============
+Enhancements
+============
 
+* Replace per-term joins in workflow search with EXISTS subqueries by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22548 <https://github.com/galaxyproject/galaxy/pull/22548>`_
 
 -------------------
 26.0.0 (2026-04-08)

{galaxy_test_api-26.0.1.dev0 → galaxy_test_api-26.0.2}/galaxy_test/api/conftest.py

@@ -10,6 +10,7 @@ from typing import (
 
 import pytest
 
+from galaxy.celery import CELERY_APP_DEFAULTS
 from galaxy.tool_util.verify.test_data import TestDataResolver
 from galaxy_test.base.api import (
     AnonymousGalaxyInteractor,
@@ -112,10 +113,7 @@ def celery_worker_parameters():
 
 @pytest.fixture(scope="session")
 def celery_parameters():
-    return {
-        "task_create_missing_queues": True,
-        "task_default_queue": "galaxy.internal",
-    }
+    return CELERY_APP_DEFAULTS
 
 
 @pytest.fixture

{galaxy_test_api-26.0.1.dev0 → galaxy_test_api-26.0.2}/galaxy_test/api/test_authenticate.py

@@ -42,13 +42,14 @@ class TestAuthenticateApi(ApiTestCase):
         tool_runner_response = get(
             urljoin(self.url, "tool_runner?tool_id=test_data_source"),
             cookies={"galaxytoolrunnersession": tool_runner_session_cookie},
+            allow_redirects=False,
         )
-        tool_runner_response.raise_for_status()
+        # On success, the controller redirects back to the SPA so the
+        # frontend can surface a "tool-submitted" toast.
+        assert tool_runner_response.status_code == 302
+        assert "notification=tool-submitted" in tool_runner_response.headers["Location"]
         # Verify that we're not returning the sessioncookie
         assert "galaxysession" not in tool_runner_response.cookies
-        # Verify text message
-        text = tool_runner_response.text
-        assert "A job has been successfully added to the queue." in text
         # Make sure history for original session received job
         current_history_json_response = get(
             urljoin(self.url, "history/current_history_json"), cookies={"galaxysession": galaxy_session_cookie}

{galaxy_test_api-26.0.1.dev0 → galaxy_test_api-26.0.2}/galaxy_test/api/test_dataset_collections.py

@@ -7,6 +7,7 @@ from urllib.parse import quote
 from galaxy.tool_util_models.sample_sheet import SampleSheetColumnDefinitions
 from galaxy.util import galaxy_root_path
 from galaxy_test.base.api_asserts import (
+    assert_error_message_contains,
     assert_has_key,
     assert_object_id_error,
     assert_status_code_is,
@@ -152,6 +153,30 @@ class TestDatasetCollectionsApi(ApiTestCase):
         returned_collections = dataset_collection["elements"]
         assert len(returned_collections) == 1, dataset_collection
 
+    def test_create_list_paired_or_unpaired_rejects_raw_hda_child(self, history_id):
+        element_identifiers = self.dataset_collection_populator.list_identifiers(history_id, contents=[("el1", "hi")])
+        payload = dict(
+            instance_type="history",
+            history_id=history_id,
+            element_identifiers=element_identifiers,
+            collection_type="list:paired_or_unpaired",
+        )
+        create_response = self._post("dataset_collections", payload, json=True)
+        assert_status_code_is(create_response, 400)
+        assert_error_message_contains(create_response, "sub-collection of type 'paired_or_unpaired'")
+
+    def test_create_list_paired_rejects_raw_hda_child(self, history_id):
+        element_identifiers = self.dataset_collection_populator.list_identifiers(history_id, contents=[("el1", "hi")])
+        payload = dict(
+            instance_type="history",
+            history_id=history_id,
+            element_identifiers=element_identifiers,
+            collection_type="list:paired",
+        )
+        create_response = self._post("dataset_collections", payload, json=True)
+        assert_status_code_is(create_response, 400)
+        assert_error_message_contains(create_response, "sub-collection of type 'paired'")
+
     def test_create_record(self, history_id):
         contents = [
             ("condition", "1\t2\t3"),
@@ -750,6 +775,13 @@ class TestDatasetCollectionsApi(ApiTestCase):
                 create_response = self._post("dataset_collections", payload, json=True)
                 self._assert_status_code_is(create_response, 403)
 
+    def test_fetched_list_elements_get_default_permissions(self, history_id):
+        self.dataset_collection_populator.create_list_in_history(
+            history_id, contents=["a\n", "b\n"], direct_upload=True, wait=True
+        )
+        self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+        self.dataset_populator.assert_history_datasets_permissions(history_id, expected_count=2, access_private=False)
+
     def test_dataset_collection_element_security(self):
         with self.dataset_populator.test_history(require_new=False) as history_id:
             dataset_collection = self.dataset_collection_populator.create_list_of_list_in_history(

{galaxy_test_api-26.0.1.dev0 → galaxy_test_api-26.0.2}/galaxy_test/api/test_datasets.py

@@ -3,6 +3,8 @@ import zipfile
 from io import BytesIO
 from urllib.parse import quote
 
+import pytest
+
 from galaxy.model.unittest_utils.store_fixtures import (
     deferred_hda_model_store_dict,
     one_hda_model_store_dict,
@@ -309,6 +311,14 @@ class TestDatasetsApi(ApiTestCase):
             show_response = self._get(f"datasets/{hda['id']}")
             self._assert_status_code_is(show_response, 403)
 
+    @pytest.mark.parametrize("fetch_data", [True, False])
+    def test_show_upload_permissions(self, history_id, fetch_data):
+        role_id = self.dataset_populator.user_private_role_id()
+        hda = self.dataset_populator.new_dataset(history_id, fetch_data=fetch_data, wait=True)
+        show_response = self._get(f"datasets/{hda['id']}")
+        self._assert_status_code_is(show_response, 200)
+        assert show_response.json()["permissions"] == {"manage": [role_id], "access": []}
+
     @requires_admin
     def test_admin_can_update_permissions(self, history_id):
         # Create private dataset
@@ -355,6 +365,22 @@ class TestDatasetsApi(ApiTestCase):
         assert content_type.startswith("text/plain"), content_type
         assert display_response.text == contents
 
+    def test_display_preview_large_fasta_uses_text_plain(self, history_id):
+        # Regression test for https://github.com/galaxyproject/galaxy/issues/22719
+        # A fasta larger than the 100 KB preview limit must still be served as
+        # text/plain so the browser preserves newlines; otherwise the header line
+        # runs into the sequence and the content is rendered as HTML.
+        header = ">seq0 large fasta regression test\n"
+        contents = header + "".join(f"{'ACGT' * 20}\n" for _ in range(2000))
+        hda1 = self.dataset_populator.new_dataset(history_id, content=contents, file_type="fasta", wait=True)
+        display_response = self._get(f"histories/{history_id}/contents/{hda1['id']}/display", {"preview": "True"})
+        self._assert_status_code_is(display_response, 200)
+        content_type = display_response.headers.get("content-type", "")
+        assert content_type.startswith("text/plain"), content_type
+        assert display_response.headers.get("x-content-truncated") == "100000"
+        assert display_response.text.startswith(header)
+        assert len(display_response.text) <= 100000
+
     def test_display_extra_paths(self, history_id: str):
         test_data_resolver = TestDataResolver()
         with open(test_data_resolver.get_filename("1.fasta")) as fh:
@@ -514,6 +540,35 @@ class TestDatasetsApi(ApiTestCase):
         self._assert_status_code_is(response, 400)
         assert_error_message_contains(response, "Conversion")
 
+    def test_raw_data_tabular_numeric_column_stats(self, history_id):
+        # columns: even-count ints, uncastable NA among odd-count castables, all NA, non-finite floats
+        contents = "2\t2\tNA\tnan\n4\tNA\tNA\t3\n6\t4\tNA\tinf\n12\t9\tNA\t6\n"
+        hda = self.dataset_populator.new_dataset(history_id, content=contents, wait=True, file_type="tabular")
+        response = self._get(f"datasets/{hda['id']}", {"data_type": "raw_data", "columns": "[0,1,2,3]"})
+        self._assert_status_code_is(response, 200)
+        even, uncastable, all_na, non_finite = response.json()["meta"]
+
+        assert even["count"] == 4
+        assert even["min"] == 2
+        assert even["max"] == 12
+        assert even["mean"] == 6
+        assert even["median"] == 5
+
+        assert uncastable["count"] == 4
+        assert uncastable["mean"] == 5
+        assert uncastable["median"] == 4
+
+        assert all_na["count"] == 4
+        assert all_na["min"] is None
+        assert "mean" not in all_na
+        assert "median" not in all_na
+
+        assert non_finite["count"] == 4
+        assert non_finite["min"] == 3
+        assert non_finite["max"] == 6
+        assert non_finite["mean"] == 4.5
+        assert non_finite["median"] == 4.5
+
     def test_bam_chunking_through_display_endpoint(self, history_id):
         # This endpoint does not use data providers and instead overrides display_data
         # in the bam datatype. This is the endpoint is very close to the legacy non-API
@@ -968,6 +1023,24 @@ class TestDatasetsApi(ApiTestCase):
         self._assert_status_code_is(response, 200)
         assert quote(name, safe="") in response.headers["Content-Disposition"]
 
+    @skip_without_tool("markdown_report_from_script")
+    def test_report_for_tool_markdown_dataset(self, history_id):
+        run_response = self.dataset_populator.run_tool(
+            "markdown_report_from_script", inputs={"title": "foobar"}, history_id=history_id
+        )
+        self.dataset_populator.wait_for_job(run_response["jobs"][0]["id"], assert_ok=True)
+        report_dataset = next(o for o in run_response["outputs"] if o["output_name"] == "output_report")
+        response = self._get(f"datasets/{report_dataset['id']}/report")
+        self._assert_status_code_is(response, 200)
+        report = response.json()
+        assert report["generate_version"]
+        assert report["generate_time"]
+        content = report["content"]
+        assert "# Dynamically Generated Report" in content
+        # the endpoint returns the embed-expanded markdown, so inline directives are resolved
+        assert "${galaxy generate_galaxy_version()}" not in content
+        assert f"Generated by Galaxy {report['generate_version']}." in content
+
     def test_copy_dataset_from_history_with_copied_from_fields(self, history_id):
         original_hda = self.dataset_populator.new_dataset(history_id, content="original data", wait=True)
         self._assert_copied_from_fields(history_id, original_hda["id"], None, None, None)

{galaxy_test_api-26.0.1.dev0 → galaxy_test_api-26.0.2}/galaxy_test/api/test_framework.py

@@ -1,5 +1,7 @@
 # This file doesn't test any API in particular but is meant to functionally
 # test the API framework itself.
+from requests import post
+
 from galaxy_test.base.decorators import requires_admin
 from ._framework import ApiTestCase
 
@@ -9,6 +11,16 @@ class TestApiFramework(ApiTestCase):
         get_response = self._get("licenses")
         assert get_response.headers["x-frame-options"] == "SAMEORIGIN"
 
+    def test_multipart_empty_boundary(self):
+        # /api/tools POST is still served by the legacy WSGI app.
+        response = post(
+            self._api_url("tools"),
+            data=b"x",
+            headers={"Content-Type": "multipart/form-data; boundary="},
+        )
+        self._assert_status_code_is(response, 400)
+        assert "Invalid boundary" in response.text
+
     # Next several tests test the API's run_as functionality.
     def test_user_cannont_run_as(self):
         run_as_user = self._setup_user("for_run_as@bx.psu.edu")

{galaxy_test_api-26.0.1.dev0 → galaxy_test_api-26.0.2}/galaxy_test/api/test_history_contents.py

@@ -5,6 +5,7 @@ from typing import (
     Union,
 )
 
+from galaxy.model.unittest_utils.store_fixtures import one_hda_model_store_dict
 from galaxy_test.api._framework import ApiTestCase
 from galaxy_test.base.decorators import (
     requires_admin,
@@ -34,6 +35,17 @@ class TestHistoryContentsApi(ApiTestCase):
         self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
         self.library_populator = LibraryPopulator(self.galaxy_interactor)
 
+    def test_contents_from_store_unregistered_extension_imported_as_data(self, history_id):
+        store_dict = one_hda_model_store_dict()
+        store_dict["datasets"][0]["extension"] = "not_a_registered_datatype"
+        as_list = self.dataset_populator.create_contents_from_store(history_id, store_dict=store_dict)
+        assert len(as_list) == 1
+        assert as_list[0]["extension"] == "data"
+        response = self._get(f"histories/{history_id}/contents/archive/contents.zip", {"dry_run": True})
+        self._assert_status_code_is(response, 200)
+        archive_paths = [archive_path for _, archive_path in response.json()]
+        assert archive_paths == ["contents/1.my_cool_name.data"]
+
     def test_index_hda_summary(self, history_id):
         hda1 = self.dataset_populator.new_dataset(history_id)
         contents_response = self._get(f"histories/{history_id}/contents")

{galaxy_test_api-26.0.1.dev0 → galaxy_test_api-26.0.2}/galaxy_test/api/test_jobs.py

@@ -387,6 +387,54 @@ steps:
         assert show_jobs_response.json()["external_id"] is not None
         assert show_jobs_response.json()["command_line"] is not None
 
+    @skip_without_tool("collection_creates_pair")
+    @pytest.mark.require_new_history
+    def test_show_collection_only_job_public(self, history_id):
+        # Regression test for https://github.com/galaxyproject/galaxy/issues/22602.
+        job_id, hdca_id = self._run_collection_only_job(history_id)
+        hdca = self.dataset_populator.get_history_collection_details(history_id, content_id=hdca_id)
+        for element in hdca["elements"]:
+            response = self.dataset_populator.make_dataset_public_raw(history_id, element["object"]["id"])
+            assert_status_code_is_ok(response)
+        with self._different_user(anon=True):
+            show_jobs_response = self._get(f"jobs/{job_id}")
+            self._assert_status_code_is(show_jobs_response, 200)
+            assert show_jobs_response.json()["id"] == job_id
+
+    @skip_without_tool("collection_creates_pair")
+    @pytest.mark.require_new_history
+    def test_show_collection_only_job_private_denied(self, history_id):
+        job_id, hdca_id = self._run_collection_only_job(history_id)
+        hdca = self.dataset_populator.get_history_collection_details(history_id, content_id=hdca_id)
+        for element in hdca["elements"]:
+            self.dataset_populator.make_private(history_id, element["object"]["id"])
+        with self._different_user():
+            show_jobs_response = self._get(f"jobs/{job_id}")
+            self._assert_status_code_is(show_jobs_response, 403)
+
+    @pytest.mark.require_new_history
+    def test_show_job_accessible_via_public_history(self, history_id):
+        self.__history_with_new_dataset(history_id)
+        jobs_response = self._get("jobs", data={"history_id": history_id})
+        job_id = jobs_response.json()[0]["id"]
+        self.dataset_populator.make_public(history_id)
+        with self._different_user():
+            show_jobs_response = self._get(f"jobs/{job_id}")
+            self._assert_status_code_is(show_jobs_response, 200)
+            assert show_jobs_response.json()["id"] == job_id
+
+    def _run_collection_only_job(self, history_id):
+        input_id = self.dataset_populator.new_dataset(history_id, content="a\nb\nc\nd\n", wait=True)["id"]
+        run_response = self.dataset_populator.run_tool(
+            tool_id="collection_creates_pair",
+            inputs={"input1": {"src": "hda", "id": input_id}},
+            history_id=history_id,
+        )
+        job_id = run_response["jobs"][0]["id"]
+        self.dataset_populator.wait_for_job(job_id, assert_ok=True)
+        hdca_id = run_response["output_collections"][0]["id"]
+        return job_id, hdca_id
+
     def _run_detect_errors(self, history_id, inputs):
         payload = self.dataset_populator.run_tool_payload(
             tool_id="detect_errors_aggressive",
@@ -1105,7 +1153,7 @@ steps:
         assert len(empty_search_response.json()) == 0
 
     @pytest.mark.require_new_history
-    @transient_failure(issue=21242)
+    @transient_failure(issue=21242, potentially_fixed=True)
     def test_delete_job_with_message(self, history_id):
         # Setup a job that will take a while to run so we can verify our cancelling
         input_dataset_id = self.__history_with_ok_dataset(history_id)
@@ -1132,9 +1180,9 @@ steps:
             # Check the output dataset is deleted and the info field contains the message
             dataset_details = self._get(f"histories/{history_id}/contents/{output_dataset_id}").json()
             if dataset_details["deleted"] is not True:
-                return False
+                return None
             if dataset_details["misc_info"] != expected_message:
-                return False
+                return None
             return True
 
         assert wait_on(check, "dataset to be deleted with message")

{galaxy_test_api-26.0.1.dev0 → galaxy_test_api-26.0.2}/galaxy_test/api/test_pages.py

@@ -396,7 +396,9 @@ steps:
         response_json = self._create_valid_page_with_slug("pagetoupdate")
         page_id = response_json["id"]
         update_response = self._update_page(page_id, "newannotation", "new.slug", "newtitle", error_code=400)
-        assert update_response["err_msg"] == "String should match pattern '^[a-z0-9-]+$' in ('body', 'slug')"
+        assert update_response["err_msg"].startswith("Page identifier must consist of")
+        update_response = self._update_page(page_id, "newannotation", "new/slug", "newtitle", error_code=400)
+        assert update_response["err_msg"] == "String should match pattern '^[^/:?#]+$' in ('body', 'slug')"
         update_response = self._update_page(page_id, "newannotation", "newslug", "", error_code=400)
         assert update_response["err_msg"] == "String should have at least 1 character in ('body', 'title')"
         update_response = self._update_page(page_id, "newannotation", "newslug", "newtitle")
@@ -407,6 +409,24 @@ steps:
         show_json = show_response.json()
         assert show_json["annotation"] == "newannotation"
 
+    def test_create_and_update_page_with_non_ascii_slug(self):
+        page_id = self._create_valid_page_with_slug("rapport-d-exécution")["id"]
+        update_response = self._update_page(page_id, "newannotation", "rapport-d-exécution", "newtitle")
+        assert update_response["slug"] == "rapport-d-exécution"
+        update_response = self._update_page(page_id, "newannotation", "rapport-d-exécution-2", "newtitle")
+        assert update_response["slug"] == "rapport-d-exécution-2"
+        show_response = self._get(f"pages/{page_id}")
+        self._assert_status_code_is(show_response, 200)
+        assert show_response.json()["title"] == "newtitle"
+
+    def test_show_page_with_non_ascii_slug_set_via_sharing(self):
+        page_id = self._create_valid_page_with_slug("pagetosetnonasciislug")["id"]
+        self._assert_status_code_is_ok(self._set_slug(page_id, "rapport-d-exécution-des-analyses"))
+        show_response = self._get(f"pages/{page_id}")
+        self._assert_status_code_is(show_response, 200)
+        assert show_response.json()["slug"] == "rapport-d-exécution-des-analyses"
+        assert page_id in self._index_ids()
+
     def test_403_on_unowner_show(self):
         response_json = self._create_valid_page_as("others_page_show@bx.psu.edu", "otherspageshow")
         show_response = self._get(f"pages/{response_json['id']}")