galaxy-test-api 25.1.dev0__tar.gz → 25.1.2__tar.gz

{galaxy_test_api-25.1.dev0 → galaxy_test_api-25.1.2}/HISTORY.rst

@@ -3,11 +3,127 @@ History
 
 .. to_doc
 
----------
-25.1.dev0
----------
+-------------------
+25.1.2 (2026-03-09)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Allow workflow download with missing file source references by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21814 <https://github.com/galaxyproject/galaxy/pull/21814>`_
+* Fix pick_value output inheriting hidden state from input datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21995 <https://github.com/galaxyproject/galaxy/pull/21995>`_
+
+-------------------
+25.1.1 (2026-02-03)
+-------------------
+
+
+=========
+Bug fixes
+=========
 
+* Sample sheet column fix by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21446 <https://github.com/galaxyproject/galaxy/pull/21446>`_
+* Record input parameter invocation inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21452 <https://github.com/galaxyproject/galaxy/pull/21452>`_
+* Maintain column definitions on map over by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21468 <https://github.com/galaxyproject/galaxy/pull/21468>`_
+* Fix subworkflow runs for disconnected required inputs with defaults by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21488 <https://github.com/galaxyproject/galaxy/pull/21488>`_
+* Fix type annotation for invocation report ``errors`` field by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21508 <https://github.com/galaxyproject/galaxy/pull/21508>`_
+* Fix job cache collection copy by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21558 <https://github.com/galaxyproject/galaxy/pull/21558>`_
+* Fix option propagation for workflow inputs connected to multiple subworkflows by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21712 <https://github.com/galaxyproject/galaxy/pull/21712>`_
+* Fix collection job state not preserved during history export/import by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21716 <https://github.com/galaxyproject/galaxy/pull/21716>`_
 
+============
+Enhancements
+============
+
+* Add database operation tool to convert sample sheets to list collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21625 <https://github.com/galaxyproject/galaxy/pull/21625>`_
+
+-------------------
+25.1.0 (2025-12-12)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix a transiently failing API test. by `@jmchilton <https://github.com/jmchilton>`_ in `#20278 <https://github.com/galaxyproject/galaxy/pull/20278>`_
+* Fix `multiple="true"` data collection map over for shell_command tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20859 <https://github.com/galaxyproject/galaxy/pull/20859>`_
+* Fix default conditional test parameters... by `@jmchilton <https://github.com/jmchilton>`_ in `#20942 <https://github.com/galaxyproject/galaxy/pull/20942>`_
+* Test and fix CORS on exceptions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21105 <https://github.com/galaxyproject/galaxy/pull/21105>`_
+* Fix type annotation in test_run_workflow_use_cached_job_implicit_conv… by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21138 <https://github.com/galaxyproject/galaxy/pull/21138>`_
+* Fix proxy endpoint encoding by `@davelopez <https://github.com/davelopez>`_ in `#21169 <https://github.com/galaxyproject/galaxy/pull/21169>`_
+* Fix optional subworkflow input scheduling bug by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21435 <https://github.com/galaxyproject/galaxy/pull/21435>`_
+* Maintain columns on sample sheet map over by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21436 <https://github.com/galaxyproject/galaxy/pull/21436>`_
+
+============
+Enhancements
+============
+
+* Don't serialize view of item in delete/purge request by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18732 <https://github.com/galaxyproject/galaxy/pull/18732>`_
+* Add tags to output datasets from tool form by `@PlushZ <https://github.com/PlushZ>`_ in `#19225 <https://github.com/galaxyproject/galaxy/pull/19225>`_
+* Implement Sample Sheets  by `@jmchilton <https://github.com/jmchilton>`_ in `#19305 <https://github.com/galaxyproject/galaxy/pull/19305>`_
+* Consider collections in on_strings for parameters accepting multiple datasets by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19817 <https://github.com/galaxyproject/galaxy/pull/19817>`_
+* Empower Users to More Pragmatically Import Datasets & Collections From Tables by `@jmchilton <https://github.com/jmchilton>`_ in `#20288 <https://github.com/galaxyproject/galaxy/pull/20288>`_
+* Prepare ``ToolBox.dynamic_tool_to_tool()`` for CWL formats by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20364 <https://github.com/galaxyproject/galaxy/pull/20364>`_
+* Test case for using URL-based workflow inputs with implicit conversions. by `@jmchilton <https://github.com/jmchilton>`_ in `#20509 <https://github.com/galaxyproject/galaxy/pull/20509>`_
+* Implement Data Landing Requests by `@jmchilton <https://github.com/jmchilton>`_ in `#20592 <https://github.com/galaxyproject/galaxy/pull/20592>`_
+* Clean up code from pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20642 <https://github.com/galaxyproject/galaxy/pull/20642>`_
+* Add more info to inheritance chain by `@arash77 <https://github.com/arash77>`_ in `#20701 <https://github.com/galaxyproject/galaxy/pull/20701>`_
+* Attempt to reuse previously materialized datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20718 <https://github.com/galaxyproject/galaxy/pull/20718>`_
+* Add configfiles support and various enhancements for user defined tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20761 <https://github.com/galaxyproject/galaxy/pull/20761>`_
+* Modernize tools in the filters/ dir by `@natefoo <https://github.com/natefoo>`_ in `#20840 <https://github.com/galaxyproject/galaxy/pull/20840>`_
+* Replace tour_generator webhook with internal API and frontend by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#20868 <https://github.com/galaxyproject/galaxy/pull/20868>`_
+* Allow addressing user defined tools in job config by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20932 <https://github.com/galaxyproject/galaxy/pull/20932>`_
+* Limit admin requirement of selected tool data api endpoints by `@guerler <https://github.com/guerler>`_ in `#20949 <https://github.com/galaxyproject/galaxy/pull/20949>`_
+* Allow sending and tracking landing request origin by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20957 <https://github.com/galaxyproject/galaxy/pull/20957>`_
+* Track landing request with invocation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20960 <https://github.com/galaxyproject/galaxy/pull/20960>`_
+* Use workflow-style payload in data landing request by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21107 <https://github.com/galaxyproject/galaxy/pull/21107>`_
+* Tighter API for tool run tagging. by `@jmchilton <https://github.com/jmchilton>`_ in `#21210 <https://github.com/galaxyproject/galaxy/pull/21210>`_
+
+=============
+Other changes
+=============
+
+* Merge `release_25.0` into `dev` by `@davelopez <https://github.com/davelopez>`_ in `#20484 <https://github.com/galaxyproject/galaxy/pull/20484>`_
+* Sample Sheet Bug Fixes around Preserving Collection Metadata by `@jmchilton <https://github.com/jmchilton>`_ in `#20749 <https://github.com/galaxyproject/galaxy/pull/20749>`_
+* Validate sample sheet column definitions in workflow definitions on backend. by `@jmchilton <https://github.com/jmchilton>`_ in `#20880 <https://github.com/galaxyproject/galaxy/pull/20880>`_
+* Fix ``TOOL_WITH_SHELL_COMMAND``  import source by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21070 <https://github.com/galaxyproject/galaxy/pull/21070>`_
+
+-------------------
+25.0.4 (2025-11-18)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix PUT /api/workflows for user defined tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20987 <https://github.com/galaxyproject/galaxy/pull/20987>`_
+* Run landing request state through validator by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21087 <https://github.com/galaxyproject/galaxy/pull/21087>`_
+* Fix workflow run form input restrictions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21095 <https://github.com/galaxyproject/galaxy/pull/21095>`_
+* Create new datasets when creating skipped database operation tool outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21142 <https://github.com/galaxyproject/galaxy/pull/21142>`_
+* Fix proxy url validation for non-printable characters by `@davelopez <https://github.com/davelopez>`_ in `#21280 <https://github.com/galaxyproject/galaxy/pull/21280>`_
+
+============
+Enhancements
+============
+
+* Use job cache also for implicit conversions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21021 <https://github.com/galaxyproject/galaxy/pull/21021>`_
+* Harden proxy redirect validation by `@davelopez <https://github.com/davelopez>`_ in `#21185 <https://github.com/galaxyproject/galaxy/pull/21185>`_
+
+=============
+Other changes
+=============
+
+* Backport `Fix proxy endpoint encoding` by `@davelopez <https://github.com/davelopez>`_ in `#21184 <https://github.com/galaxyproject/galaxy/pull/21184>`_
+
+-------------------
+25.0.3 (2025-09-23)
+-------------------
+
+No recorded changes since last release
 
 -------------------
 25.0.2 (2025-08-13)

{galaxy_test_api-25.1.dev0/galaxy_test_api.egg-info → galaxy_test_api-25.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: galaxy-test-api
-Version: 25.1.dev0
+Version: 25.1.2
 Summary: Galaxy API tests
 Home-page: https://github.com/galaxyproject/galaxy
 Author: Galaxy Project and Community
@@ -54,11 +54,127 @@ History
 
 .. to_doc
 
----------
-25.1.dev0
----------
+-------------------
+25.1.2 (2026-03-09)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Allow workflow download with missing file source references by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21814 <https://github.com/galaxyproject/galaxy/pull/21814>`_
+* Fix pick_value output inheriting hidden state from input datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21995 <https://github.com/galaxyproject/galaxy/pull/21995>`_
+
+-------------------
+25.1.1 (2026-02-03)
+-------------------
+
+
+=========
+Bug fixes
+=========
 
+* Sample sheet column fix by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21446 <https://github.com/galaxyproject/galaxy/pull/21446>`_
+* Record input parameter invocation inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21452 <https://github.com/galaxyproject/galaxy/pull/21452>`_
+* Maintain column definitions on map over by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21468 <https://github.com/galaxyproject/galaxy/pull/21468>`_
+* Fix subworkflow runs for disconnected required inputs with defaults by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21488 <https://github.com/galaxyproject/galaxy/pull/21488>`_
+* Fix type annotation for invocation report ``errors`` field by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21508 <https://github.com/galaxyproject/galaxy/pull/21508>`_
+* Fix job cache collection copy by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21558 <https://github.com/galaxyproject/galaxy/pull/21558>`_
+* Fix option propagation for workflow inputs connected to multiple subworkflows by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21712 <https://github.com/galaxyproject/galaxy/pull/21712>`_
+* Fix collection job state not preserved during history export/import by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21716 <https://github.com/galaxyproject/galaxy/pull/21716>`_
 
+============
+Enhancements
+============
+
+* Add database operation tool to convert sample sheets to list collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21625 <https://github.com/galaxyproject/galaxy/pull/21625>`_
+
+-------------------
+25.1.0 (2025-12-12)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix a transiently failing API test. by `@jmchilton <https://github.com/jmchilton>`_ in `#20278 <https://github.com/galaxyproject/galaxy/pull/20278>`_
+* Fix `multiple="true"` data collection map over for shell_command tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20859 <https://github.com/galaxyproject/galaxy/pull/20859>`_
+* Fix default conditional test parameters... by `@jmchilton <https://github.com/jmchilton>`_ in `#20942 <https://github.com/galaxyproject/galaxy/pull/20942>`_
+* Test and fix CORS on exceptions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21105 <https://github.com/galaxyproject/galaxy/pull/21105>`_
+* Fix type annotation in test_run_workflow_use_cached_job_implicit_conv… by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21138 <https://github.com/galaxyproject/galaxy/pull/21138>`_
+* Fix proxy endpoint encoding by `@davelopez <https://github.com/davelopez>`_ in `#21169 <https://github.com/galaxyproject/galaxy/pull/21169>`_
+* Fix optional subworkflow input scheduling bug by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21435 <https://github.com/galaxyproject/galaxy/pull/21435>`_
+* Maintain columns on sample sheet map over by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21436 <https://github.com/galaxyproject/galaxy/pull/21436>`_
+
+============
+Enhancements
+============
+
+* Don't serialize view of item in delete/purge request by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18732 <https://github.com/galaxyproject/galaxy/pull/18732>`_
+* Add tags to output datasets from tool form by `@PlushZ <https://github.com/PlushZ>`_ in `#19225 <https://github.com/galaxyproject/galaxy/pull/19225>`_
+* Implement Sample Sheets  by `@jmchilton <https://github.com/jmchilton>`_ in `#19305 <https://github.com/galaxyproject/galaxy/pull/19305>`_
+* Consider collections in on_strings for parameters accepting multiple datasets by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19817 <https://github.com/galaxyproject/galaxy/pull/19817>`_
+* Empower Users to More Pragmatically Import Datasets & Collections From Tables by `@jmchilton <https://github.com/jmchilton>`_ in `#20288 <https://github.com/galaxyproject/galaxy/pull/20288>`_
+* Prepare ``ToolBox.dynamic_tool_to_tool()`` for CWL formats by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20364 <https://github.com/galaxyproject/galaxy/pull/20364>`_
+* Test case for using URL-based workflow inputs with implicit conversions. by `@jmchilton <https://github.com/jmchilton>`_ in `#20509 <https://github.com/galaxyproject/galaxy/pull/20509>`_
+* Implement Data Landing Requests by `@jmchilton <https://github.com/jmchilton>`_ in `#20592 <https://github.com/galaxyproject/galaxy/pull/20592>`_
+* Clean up code from pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20642 <https://github.com/galaxyproject/galaxy/pull/20642>`_
+* Add more info to inheritance chain by `@arash77 <https://github.com/arash77>`_ in `#20701 <https://github.com/galaxyproject/galaxy/pull/20701>`_
+* Attempt to reuse previously materialized datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20718 <https://github.com/galaxyproject/galaxy/pull/20718>`_
+* Add configfiles support and various enhancements for user defined tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20761 <https://github.com/galaxyproject/galaxy/pull/20761>`_
+* Modernize tools in the filters/ dir by `@natefoo <https://github.com/natefoo>`_ in `#20840 <https://github.com/galaxyproject/galaxy/pull/20840>`_
+* Replace tour_generator webhook with internal API and frontend by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#20868 <https://github.com/galaxyproject/galaxy/pull/20868>`_
+* Allow addressing user defined tools in job config by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20932 <https://github.com/galaxyproject/galaxy/pull/20932>`_
+* Limit admin requirement of selected tool data api endpoints by `@guerler <https://github.com/guerler>`_ in `#20949 <https://github.com/galaxyproject/galaxy/pull/20949>`_
+* Allow sending and tracking landing request origin by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20957 <https://github.com/galaxyproject/galaxy/pull/20957>`_
+* Track landing request with invocation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20960 <https://github.com/galaxyproject/galaxy/pull/20960>`_
+* Use workflow-style payload in data landing request by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21107 <https://github.com/galaxyproject/galaxy/pull/21107>`_
+* Tighter API for tool run tagging. by `@jmchilton <https://github.com/jmchilton>`_ in `#21210 <https://github.com/galaxyproject/galaxy/pull/21210>`_
+
+=============
+Other changes
+=============
+
+* Merge `release_25.0` into `dev` by `@davelopez <https://github.com/davelopez>`_ in `#20484 <https://github.com/galaxyproject/galaxy/pull/20484>`_
+* Sample Sheet Bug Fixes around Preserving Collection Metadata by `@jmchilton <https://github.com/jmchilton>`_ in `#20749 <https://github.com/galaxyproject/galaxy/pull/20749>`_
+* Validate sample sheet column definitions in workflow definitions on backend. by `@jmchilton <https://github.com/jmchilton>`_ in `#20880 <https://github.com/galaxyproject/galaxy/pull/20880>`_
+* Fix ``TOOL_WITH_SHELL_COMMAND``  import source by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21070 <https://github.com/galaxyproject/galaxy/pull/21070>`_
+
+-------------------
+25.0.4 (2025-11-18)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix PUT /api/workflows for user defined tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20987 <https://github.com/galaxyproject/galaxy/pull/20987>`_
+* Run landing request state through validator by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21087 <https://github.com/galaxyproject/galaxy/pull/21087>`_
+* Fix workflow run form input restrictions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21095 <https://github.com/galaxyproject/galaxy/pull/21095>`_
+* Create new datasets when creating skipped database operation tool outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21142 <https://github.com/galaxyproject/galaxy/pull/21142>`_
+* Fix proxy url validation for non-printable characters by `@davelopez <https://github.com/davelopez>`_ in `#21280 <https://github.com/galaxyproject/galaxy/pull/21280>`_
+
+============
+Enhancements
+============
+
+* Use job cache also for implicit conversions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21021 <https://github.com/galaxyproject/galaxy/pull/21021>`_
+* Harden proxy redirect validation by `@davelopez <https://github.com/davelopez>`_ in `#21185 <https://github.com/galaxyproject/galaxy/pull/21185>`_
+
+=============
+Other changes
+=============
+
+* Backport `Fix proxy endpoint encoding` by `@davelopez <https://github.com/davelopez>`_ in `#21184 <https://github.com/galaxyproject/galaxy/pull/21184>`_
+
+-------------------
+25.0.3 (2025-09-23)
+-------------------
+
+No recorded changes since last release
 
 -------------------
 25.0.2 (2025-08-13)

{galaxy_test_api-25.1.dev0 → galaxy_test_api-25.1.2}/galaxy_test/api/test_dataset_collections.py

@@ -16,6 +16,7 @@ from galaxy_test.base.decorators import requires_new_user
 from galaxy_test.base.populators import (
     DatasetCollectionPopulator,
     DatasetPopulator,
+    skip_without_tool,
 )
 from ._framework import ApiTestCase
 
@@ -427,6 +428,154 @@ class TestDatasetCollectionsApi(ApiTestCase):
         assert row_1[0] == 45
         # TODO: test case where column definition does not match supplied data
 
+    @skip_without_tool("cat1")
+    def test_sample_sheet_map_over_preserves_columns(self, history_id):
+        """Test that mapping cat1 over a sample sheet preserves columns metadata."""
+        # Create a sample sheet collection with columns metadata
+        contents = [
+            ("sample1", "content1"),
+            ("sample2", "content2"),
+            ("sample3", "content3"),
+        ]
+        sample_sheet_identifiers = self.dataset_collection_populator.list_identifiers(history_id, contents)
+        payload = dict(
+            name="test sample sheet",
+            instance_type="history",
+            history_id=history_id,
+            element_identifiers=sample_sheet_identifiers,
+            collection_type="sample_sheet",
+            column_definitions=[
+                {"type": "int", "name": "replicate", "optional": False},
+                {"type": "string", "name": "condition", "optional": False},
+            ],
+            rows={
+                "sample1": [1, "control"],
+                "sample2": [2, "treatment"],
+                "sample3": [3, "control"],
+            },
+        )
+        create_response = self._post("dataset_collections", payload, json=True)
+        sample_sheet = self._check_create_response(create_response)
+        hdca_id = sample_sheet["id"]
+
+        # Verify the input sample sheet has columns metadata
+        input_elements = sample_sheet["elements"]
+        assert len(input_elements) == 3
+        assert input_elements[0]["columns"] == [1, "control"]
+        assert input_elements[1]["columns"] == [2, "treatment"]
+        assert input_elements[2]["columns"] == [3, "control"]
+
+        # Run cat1 on the sample sheet collection in batch mode (mapping over it)
+        inputs = {
+            "input1": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
+        }
+        run = self.dataset_populator.run_tool("cat1", inputs=inputs, history_id=history_id)
+        self.dataset_populator.wait_for_history_jobs(history_id)
+
+        # Get the implicit output collection
+        implicit_collections = run["implicit_collections"]
+        assert len(implicit_collections) == 1, f"Expected 1 implicit collection, got {len(implicit_collections)}"
+        output_collection = implicit_collections[0]
+
+        # Fetch the full collection details including elements
+        collection_details = self.dataset_populator.get_history_collection_details(
+            history_id, content_id=output_collection["id"]
+        )
+        assert collection_details["column_definitions"] == sample_sheet["column_definitions"]
+
+        # Verify that the output collection preserved the columns metadata
+        output_elements = collection_details["elements"]
+        assert len(output_elements) == 3, f"Expected 3 output elements, got {len(output_elements)}"
+
+        # Check that columns metadata was preserved for each element
+        self._assert_has_keys(output_elements[0], "columns")
+        assert output_elements[0]["columns"] == [
+            1,
+            "control",
+        ], f"Expected [1, 'control'], got {output_elements[0]['columns']}"
+        assert output_elements[0]["element_identifier"] == "sample1"
+
+        self._assert_has_keys(output_elements[1], "columns")
+        assert output_elements[1]["columns"] == [
+            2,
+            "treatment",
+        ], f"Expected [2, 'treatment'], got {output_elements[1]['columns']}"
+        assert output_elements[1]["element_identifier"] == "sample2"
+
+        self._assert_has_keys(output_elements[2], "columns")
+        assert output_elements[2]["columns"] == [
+            3,
+            "control",
+        ], f"Expected [3, 'control'], got {output_elements[2]['columns']}"
+        assert output_elements[2]["element_identifier"] == "sample3"
+
+    def test_copy_sample_sheet_collection(self, history_id):
+        """Test that copying a sample sheet collection preserves columns metadata."""
+        # Create a sample sheet collection with columns metadata
+        contents = [
+            ("sample1", "content1"),
+            ("sample2", "content2"),
+        ]
+        sample_sheet_identifiers = self.dataset_collection_populator.list_identifiers(history_id, contents)
+        payload = dict(
+            name="original sample sheet",
+            instance_type="history",
+            history_id=history_id,
+            element_identifiers=sample_sheet_identifiers,
+            collection_type="sample_sheet",
+            column_definitions=[
+                {"type": "int", "name": "replicate", "optional": False},
+                {"type": "string", "name": "condition", "optional": False},
+            ],
+            rows={
+                "sample1": [1, "control"],
+                "sample2": [2, "treatment"],
+            },
+        )
+        create_response = self._post("dataset_collections", payload, json=True)
+        original_collection = self._check_create_response(create_response)
+        original_hdca_id = original_collection["id"]
+
+        # Verify the original sample sheet has columns metadata
+        original_elements = original_collection["elements"]
+        assert len(original_elements) == 2
+        assert original_elements[0]["columns"] == [1, "control"]
+        assert original_elements[1]["columns"] == [2, "treatment"]
+
+        # Copy the collection using the new copy_collection method
+        copy_response = self.dataset_collection_populator.copy_collection(
+            history_id, original_hdca_id, copy_elements=True, wait=False
+        )
+        copied_collection = copy_response.json()
+
+        # Fetch the full details of the copied collection
+        copied_collection_details = self.dataset_populator.get_history_collection_details(
+            history_id, content_id=copied_collection["id"]
+        )
+
+        # Verify the copied collection has the same columns metadata
+        copied_elements = copied_collection_details["elements"]
+        assert len(copied_elements) == 2, f"Expected 2 elements, got {len(copied_elements)}"
+
+        # Check that columns metadata was preserved for each element
+        self._assert_has_keys(copied_elements[0], "columns")
+        assert copied_elements[0]["columns"] == [
+            1,
+            "control",
+        ], f"Expected [1, 'control'], got {copied_elements[0]['columns']}"
+        assert copied_elements[0]["element_identifier"] == "sample1"
+
+        self._assert_has_keys(copied_elements[1], "columns")
+        assert copied_elements[1]["columns"] == [
+            2,
+            "treatment",
+        ], f"Expected [2, 'treatment'], got {copied_elements[1]['columns']}"
+        assert copied_elements[1]["element_identifier"] == "sample2"
+
+        # Verify column definitions are preserved
+        assert copied_collection_details["column_definitions"] == original_collection["column_definitions"]
+        assert copied_collection_details["collection_type"] == "sample_sheet"
+
     def test_workbook_download(self):
         xlsx_file = self.dataset_collection_populator.download_workbook(
             "sample_sheet",

{galaxy_test_api-25.1.dev0 → galaxy_test_api-25.1.2}/galaxy_test/api/test_datasets.py

@@ -672,7 +672,7 @@ class TestDatasetsApi(ApiTestCase):
             history_id, output_hda_id, stop_job=True, use_query_params=use_query_params
         )
         self._assert_status_code_is_ok(delete_response)
-        deleted_hda = delete_response.json()
+        deleted_hda = self.dataset_populator.get_history_dataset_details(history_id, content_id=output_hda_id)
         assert deleted_hda["deleted"], deleted_hda
 
         # The job should be cancelled

{galaxy_test_api-25.1.dev0 → galaxy_test_api-25.1.2}/galaxy_test/api/test_histories.py

@@ -729,6 +729,18 @@ class ImportExportTests(BaseHistories):
             history_id=imported_history_id, hid=1, assert_ok=False, hda_checker=check_failed, job_checker=check_failed
         )
 
+        # Also check collection state is preserved - regression test for issue #20450
+        imported_collection = self.dataset_populator.get_history_collection_details(
+            history_id=imported_history_id,
+            history_content_type="dataset_collection",
+            assert_ok=False,
+        )
+        assert "job_state_summary" in imported_collection, imported_collection
+        assert imported_collection["job_state_summary"].get("error", 0) == 1, (
+            f"Expected error count of 1 after import, got {imported_collection['job_state_summary']}. "
+            "Collection job state was not preserved during history export/import (issue #20450)."
+        )
+
     def test_import_metadata_regeneration(self):
         if self.task_based:
             raise SkipTest("skipping test_import_metadata_regeneration for task based...")

{galaxy_test_api-25.1.dev0 → galaxy_test_api-25.1.2}/galaxy_test/api/test_history_contents.py

@@ -692,7 +692,7 @@ class TestHistoryContentsApi(ApiTestCase):
         assert not dataset_collection["deleted"]
 
         delete_response = self._delete(collection_url)
-        self._assert_status_code_is(delete_response, 200)
+        self._assert_status_code_is_ok(delete_response)
 
         show_response = self._get(collection_url)
         dataset_collection = show_response.json()

{galaxy_test_api-25.1.dev0 → galaxy_test_api-25.1.2}/galaxy_test/api/test_jobs.py

@@ -736,7 +736,7 @@ steps:
         output = run_response["outputs"][0]
         # Delete second jobs input while second job is waiting for first job
         delete_response = self._delete(f"histories/{history_id}/contents/{hda1['id']}")
-        self._assert_status_code_is(delete_response, 200)
+        self._assert_status_code_is_ok(delete_response)
         self.dataset_populator.wait_for_history_jobs(history_id, assert_ok=False)
         dataset_details = self._get(f"histories/{history_id}/contents/{output['id']}").json()
         assert dataset_details["state"] == "paused"
@@ -773,11 +773,11 @@ steps:
         self._search(search_payload, expected_search_count=1)
         # Now we delete the original input HDA that was used -- we should still be able to find the job
         delete_respone = self._delete(f"histories/{history_id}/contents/{dataset_id}")
-        self._assert_status_code_is(delete_respone, 200)
+        self._assert_status_code_is_ok(delete_respone)
         self._search(search_payload, expected_search_count=1)
         # Now we also delete the copy -- we shouldn't find a job
         delete_respone = self._delete(f"histories/{new_history_id}/contents/{new_dataset_id}")
-        self._assert_status_code_is(delete_respone, 200)
+        self._assert_status_code_is_ok(delete_respone)
         self._search(search_payload, expected_search_count=0)
 
     @pytest.mark.require_new_history
@@ -803,7 +803,7 @@ steps:
         tool_response = self._job_search(tool_id="cat1", history_id=history_id, inputs=inputs)
         output_id = tool_response.json()["outputs"][0]["id"]
         delete_respone = self._delete(f"histories/{history_id}/contents/{output_id}")
-        self._assert_status_code_is(delete_respone, 200)
+        self._assert_status_code_is_ok(delete_respone)
         search_payload = self._search_payload(history_id=history_id, tool_id="cat1", inputs=inputs)
         self._search(search_payload, expected_search_count=0)
 
@@ -847,7 +847,7 @@ steps:
         # and use the correct input job definition, the job should not be found
         output_id = tool_response.json()["outputs"][0]["id"]
         delete_respone = self._delete(f"histories/{history_id}/contents/{output_id}")
-        self._assert_status_code_is(delete_respone, 200)
+        self._assert_status_code_is_ok(delete_respone)
         search_payload = self._search_payload(history_id=history_id, tool_id="multi_data_param", inputs=inputs)
         self._search(search_payload, expected_search_count=0)
 
@@ -863,14 +863,14 @@ steps:
         output_id = tool_response.json()["outputs"][0]["id"]
         # We delete a single tool output, no job should be returned
         delete_respone = self._delete(f"histories/{history_id}/contents/{output_id}")
-        self._assert_status_code_is(delete_respone, 200)
+        self._assert_status_code_is_ok(delete_respone)
         search_payload = self._search_payload(history_id=history_id, tool_id="collection_creates_list", inputs=inputs)
         self._search(search_payload, expected_search_count=0)
         tool_response = self._job_search(tool_id="collection_creates_list", history_id=history_id, inputs=inputs)
         output_collection_id = tool_response.json()["output_collections"][0]["id"]
         # We delete a collection output, no job should be returned
         delete_respone = self._delete(f"histories/{history_id}/contents/dataset_collections/{output_collection_id}")
-        self._assert_status_code_is(delete_respone, 200)
+        self._assert_status_code_is_ok(delete_respone)
         search_payload = self._search_payload(history_id=history_id, tool_id="collection_creates_list", inputs=inputs)
         self._search(search_payload, expected_search_count=0)
 
@@ -902,11 +902,11 @@ steps:
         self._search(search_payload, expected_search_count=1)
         # Now we delete the original input HDCA that was used -- we should still be able to find the job
         delete_respone = self._delete(f"histories/{history_id}/contents/dataset_collections/{list_id_a}")
-        self._assert_status_code_is(delete_respone, 200)
+        self._assert_status_code_is_ok(delete_respone)
         self._search(search_payload, expected_search_count=1)
         # Now we also delete the copy -- we shouldn't find a job
         delete_respone = self._delete(f"histories/{history_id}/contents/dataset_collections/{new_list_a}")
-        self._assert_status_code_is(delete_respone, 200)
+        self._assert_status_code_is_ok(delete_respone)
         self._search(search_payload, expected_search_count=0)
 
     @pytest.mark.require_new_history