Merge branch 'release_23.1' into dev

lib/galaxy/datatypes/converters/tar_to_directory.xml

@@ -1,7 +1,7 @@
 <tool id="CONVERTER_tar_to_directory" name="Convert tar to directory" version="1.0.1" profile="17.05">
     <!-- Don't use tar directly so we can verify safety of results - tar -xzf '$input1'; -->
     <requirements>
-        <requirement type="package" version="19.9">galaxy-util</requirement>
+        <requirement type="package" version="23.1">galaxy-util</requirement>
     </requirements>
     <command>
         mkdir '$output1.files_path';

lib/galaxy/model/metadata.py

@@ -670,7 +670,6 @@ def from_external_value(self, value, parent, path_rewriter=None):
                 # directory. Correct.
                 file_name = path_rewriter(file_name)
             mf.update_from_file(file_name)
-            os.unlink(file_name)
             value = mf.id
         return value
 

lib/galaxy/model/store/__init__.py

@@ -457,6 +457,16 @@ def handle_dataset_object_edit(dataset_instance, dataset_attrs):
                 self._attach_dataset_sources(dataset_attrs["dataset"], dataset_instance)
                 if "id" in dataset_attrs["dataset"] and self.import_options.allow_edit:
                     dataset_instance.dataset.id = dataset_attrs["dataset"]["id"]
+                    for dataset_association in dataset_instance.dataset.history_associations:
+                        if (
+                            dataset_association is not dataset_instance
+                            and dataset_association.extension == dataset_instance.extension
+                        ):
+                            dataset_association.metadata = dataset_instance.metadata
+                            dataset_association.blurb = dataset_instance.blurb
+                            dataset_association.peek = dataset_instance.peek
+                            dataset_association.info = dataset_instance.info
+                            dataset_association.tool_version = dataset_instance.tool_version
                 if job:
                     dataset_instance.dataset.job_id = job.id
 

test/integration/test_dataset_copy_metadata_files.py

@@ -0,0 +1,75 @@
+from galaxy_test.api.test_workflows import RunsWorkflowFixtures
+from galaxy_test.base.populators import (
+    DatasetPopulator,
+    WorkflowPopulator,
+)
+from galaxy_test.driver.integration_util import IntegrationTestCase
+
+
+class TestDirectoryStrategyMetadataFileIntegrationTestCase(IntegrationTestCase, RunsWorkflowFixtures):
+    dataset_populator: DatasetPopulator
+    workflow_populator: WorkflowPopulator
+    framework_tool_and_types = True
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["metadata_strategy"] = "directory"
+
+    def setUp(self):
+        super().setUp()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+        self.workflow_populator = WorkflowPopulator(self.galaxy_interactor)
+
+    def test_metadata_copied_to_copied_outputs(self, history_id):
+        summary = self.workflow_populator.run_workflow(
+            """
+class: GalaxyWorkflow
+label: Tests metadata copied to copied outputs
+inputs:
+  bam_file:
+    type: collection
+    collection_type: list
+outputs:
+  copied_bam:
+    outputSource: extract/output
+steps:
+  build_list:
+    tool_id: __BUILD_LIST__
+    in:
+      datasets_0|input: bam_file
+  sleep:
+    tool_id: cat_data_and_sleep
+    tool_state:
+      sleep_time: 2
+    in:
+      input1:
+        source: build_list/output
+  extract:
+    tool_id: __EXTRACT_DATASET__
+    tool_state:
+      which:
+        which_dataset: first
+    in:
+      input:
+        source: sleep/out_file1
+test_data:
+  bam_file:
+    value: 1.bam
+    file_type: bam
+    type: File
+""",
+            history_id=history_id,
+            wait=True,
+            assert_ok=True,
+        )
+        invocation = self.workflow_populator.get_invocation(summary.invocation_id, step_details=True)
+        copied_bam = invocation["outputs"]["copied_bam"]
+        dataset = self.dataset_populator.get_history_dataset_details(history_id, content_id=copied_bam["id"])
+        assert dataset["peek"] == "Binary bam alignments file"
+        assert len(dataset["meta_files"]) == 1
+
+
+class TestExtendedMetadataStrategyMetadataFileIntegrationTestCase(TestDirectoryStrategyMetadataFileIntegrationTestCase):
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["metadata_strategy"] = "directory"