Allow uploading individual HDAs via fetch API.

lib/galaxy/tools/parameters/output_collect.py

@@ -247,6 +247,42 @@ def collect_dynamic_outputs(
                 filenames,
             )
             collection_builder.populate()
+        elif destination_type == "hdas":
+            history = job.history
+
+            datasets = []
+
+            def collect_elements_for_history(elements):
+                for element in elements:
+                    if "elements" in element:
+                        collect_elements_for_history(element["elements"])
+                    else:
+                        discovered_file = discovered_file_for_unnamed_output(element, job_working_directory)
+                        fields_match = discovered_file.match
+                        designation = fields_match.designation
+                        ext = fields_match.ext
+                        dbkey = fields_match.dbkey
+                        info = element.get("info", None)
+                        link_data = discovered_file.match.link_data
+
+                        # Create new primary dataset
+                        name = fields_match.name or designation
+
+                        dataset = job_context.create_dataset(
+                            ext=ext,
+                            designation=designation,
+                            visible=True,
+                            dbkey=dbkey,
+                            name=name,
+                            filename=discovered_file.path,
+                            info=info,
+                            link_data=link_data
+                        )
+                        dataset.raw_set_dataset_state('ok')
+                        datasets.append(dataset)
+
+            collect_elements_for_history(elements)
+            job.history.add_datasets(job_context.sa_session, datasets)
 
     for name, has_collection in output_collections.items():
         if name not in tool.output_collections:

lib/galaxy/webapps/galaxy/api/_fetch_util.py

@@ -15,7 +15,7 @@ from galaxy.util import (
 
 log = logging.getLogger(__name__)
 
-VALID_DESTINATION_TYPES = ["library", "library_folder", "hdca"]
+VALID_DESTINATION_TYPES = ["library", "library_folder", "hdca", "hdas"]
 ELEMENTS_FROM_TYPE = ["archive", "bagit", "bagit_archive", "directory"]
 # These elements_from cannot be sym linked to because they only exist during upload.
 ELEMENTS_FROM_TRANSIENT_TYPES = ["archive", "bagit_archive"]

test/integration/test_upload_configuration_options.py

@@ -737,10 +737,10 @@ class FetchByPathTestCase(BaseUploadContentConfigurationTestCase):
 
     def test_fetch_recursive_archive(self):
         history_id, library, destination = self.library_populator.setup_fetch_to_folder("recursive_archive")
-        bed_test_data_path = self.test_data_resolver.get_filename("testdir1.zip")
+        archive_test_data_path = self.test_data_resolver.get_filename("testdir1.zip")
         targets = [{
             "destination": destination,
-            "items_from": "archive", "src": "path", "path": bed_test_data_path,
+            "items_from": "archive", "src": "path", "path": archive_test_data_path,
         }]
         payload = {
             "history_id": history_id,  # TODO: Shouldn't be needed :(
@@ -756,6 +756,23 @@ class FetchByPathTestCase(BaseUploadContentConfigurationTestCase):
         dataset = self.library_populator.get_library_contents_with_path(library["id"], "/dir1/file3")
         assert dataset["file_size"] == 11, dataset
 
+    def test_fetch_recursive_archive_history(self):
+        destination = {"type": "hdas"}
+        archive = self.test_data_resolver.get_filename("testdir1.zip")
+        targets = [{
+            "destination": destination,
+            "items_from": "archive", "src": "path", "path": archive,
+        }]
+        payload = {
+            "history_id": self.history_id,  # TODO: Shouldn't be needed :(
+            "targets": json.dumps(targets),
+        }
+        self.dataset_populator.fetch(payload)
+        contents_response = self.dataset_populator._get_contents_request(self.history_id)
+        assert contents_response.status_code == 200
+        contents = contents_response.json()
+        assert len(contents) == 3
+
     def test_fetch_recursive_archive_to_library(self):
         bed_test_data_path = self.test_data_resolver.get_filename("testdir1.zip")
         targets = [{