Merge pull request #21936 from mvdbeek/backport_paired_or_unpaired_mapping_fix

[26.0] Backport paired or unpaired mapping fix

lib/galaxy/tool_util/client/staging.py

@@ -112,7 +112,7 @@ class StagingInterface(metaclass=abc.ABCMeta):
                     decompress=upload_target.properties.get("decompress") or DEFAULT_DECOMPRESS,
                     hashes=upload_target.properties.get("hashes"),
                 )
-                name = _file_path_to_name(file_path)
+                name = upload_target.properties.get("name") or _file_path_to_name(file_path)
                 if file_path is not None:
                     src = _attach_file(fetch_payload, file_path)
                     fetch_payload["targets"][0]["elements"][0].update(src)
@@ -134,7 +134,9 @@ class StagingInterface(metaclass=abc.ABCMeta):
                     fetch_payload["targets"][0]["elements"][0]["tags"] = tags
                 fetch_payload["targets"][0]["elements"][0]["name"] = name
             elif isinstance(upload_target, FileLiteralTarget):
-                fetch_payload = _fetch_payload(history_id)
+                file_type = upload_target.properties.get("filetype", None) or DEFAULT_FILE_TYPE
+                dbkey = upload_target.properties.get("dbkey", None) or DEFAULT_DBKEY
+                fetch_payload = _fetch_payload(history_id, file_type=file_type, dbkey=dbkey)
                 # For file literals - take them as is - never convert line endings.
                 fetch_payload["targets"][0]["elements"][0].update(
                     {
@@ -146,6 +148,9 @@ class StagingInterface(metaclass=abc.ABCMeta):
                 tags = upload_target.properties.get("tags")
                 if tags:
                     fetch_payload["targets"][0]["elements"][0]["tags"] = tags
+                name = upload_target.properties.get("name")
+                if name:
+                    fetch_payload["targets"][0]["elements"][0]["name"] = name
             elif isinstance(upload_target, DirectoryUploadTarget):
                 fetch_payload = _fetch_payload(history_id, file_type=upload_target.file_type)
                 element = fetch_payload["targets"][0]["elements"][0]
@@ -191,7 +196,7 @@ class StagingInterface(metaclass=abc.ABCMeta):
                 file_type = upload_target.properties.get("filetype", None) or DEFAULT_FILE_TYPE
                 dbkey = upload_target.properties.get("dbkey", None) or DEFAULT_DBKEY
                 upload_payload = _upload_payload(history_id, file_type=file_type, to_posix_lines=dbkey)
-                name = _file_path_to_name(file_path)
+                name = upload_target.properties.get("name") or _file_path_to_name(file_path)
                 upload_payload["inputs"]["files_0|auto_decompress"] = False
                 upload_payload["inputs"]["auto_decompress"] = False
                 if file_path is not None:
@@ -216,7 +221,8 @@ class StagingInterface(metaclass=abc.ABCMeta):
                 return self._tools_post(upload_payload)
             elif isinstance(upload_target, FileLiteralTarget):
                 # For file literals - take them as is - never convert line endings.
-                payload = _upload_payload(history_id, file_type="auto", auto_decompress=False, to_posix_lines=False)
+                file_type = upload_target.properties.get("filetype", None) or DEFAULT_FILE_TYPE
+                payload = _upload_payload(history_id, file_type=file_type, auto_decompress=False, to_posix_lines=False)
                 payload["inputs"]["files_0|url_paste"] = upload_target.contents
                 return self._tools_post(payload)
             elif isinstance(upload_target, DirectoryUploadTarget):
@@ -246,10 +252,13 @@ class StagingInterface(metaclass=abc.ABCMeta):
                 raise ValueError(f"Unsupported type for upload_target: {type(upload_target)}")
 
         def create_collection_func(
-            element_identifiers: List[Dict[str, Any]], collection_type: str, rows: Optional[Dict[str, Any]] = None
+            element_identifiers: List[Dict[str, Any]],
+            collection_type: str,
+            rows: Optional[Dict[str, Any]] = None,
+            name: Optional[str] = None,
         ) -> Dict[str, Any]:
             payload = {
-                "name": "dataset collection",
+                "name": name or "dataset collection",
                 "instance_type": "history",
                 "history_id": history_id,
                 "element_identifiers": element_identifiers,

lib/galaxy/tool_util/cwl/util.py

@@ -138,7 +138,11 @@ def path_or_uri_to_uri(path_or_uri: str) -> str:
 class CollectionCreateFunc(Protocol):
 
     def __call__(
-        self, element_identifiers: List[Dict[str, Any]], collection_type: str, rows: Optional[Dict[str, Any]] = None
+        self,
+        element_identifiers: List[Dict[str, Any]],
+        collection_type: str,
+        rows: Optional[Dict[str, Any]] = None,
+        name: Optional[str] = None,
     ) -> Dict[str, Any]:
         """Create a collection from these identifiers."""
 
@@ -253,6 +257,8 @@ def galactic_job_json(
             kwd["hashes"] = value["hashes"]
         if value.get("metadata"):
             kwd["metadata"] = value["metadata"]
+        if "name" in value:
+            kwd["name"] = value["name"]
         if composite_data_raw:
             composite_data = []
             for entry in composite_data_raw:
@@ -268,7 +274,7 @@ def galactic_job_json(
         if file_path is None:
             contents = value.get("contents")
             if contents is not None:
-                return upload_file_literal(contents, **kwd)
+                return upload_file_literal(contents, filetype=filetype, **kwd)
 
             return value
 
@@ -360,6 +366,8 @@ def galactic_job_json(
         kwds = {}
         if collection_type.startswith("sample_sheet"):
             kwds["rows"] = value["rows"]
+        if "name" in value:
+            kwds["name"] = value["name"]
         collection = collection_create_func(elements, collection_type, **kwds)
         dataset_collections.append(collection)
         hdca_id = collection["id"]

lib/galaxy/tool_util_models/__init__.py

@@ -218,7 +218,7 @@ def _check_collection_type(v: str) -> str:
         raise ValueError("Invalid empty collection_type specified.")
     collection_levels = v.split(":")
     for collection_level in collection_levels:
-        if collection_level not in ["list", "paired"]:
+        if collection_level not in ["list", "paired", "paired_or_unpaired", "record", "sample_sheet"]:
             raise ValueError(f"Invalid collection_type specified [{v}]")
     return v
 

lib/galaxy/workflow/modules.py

@@ -40,6 +40,7 @@ from galaxy.model import (
 )
 from galaxy.model.base import ensure_object_added_to_session
 from galaxy.model.dataset_collections import matching
+from galaxy.model.dataset_collections.adapters import PromoteCollectionElementToCollectionAdapter
 from galaxy.model.dataset_collections.query import HistoryQuery
 from galaxy.model.dataset_collections.type_description import COLLECTION_TYPE_DESCRIPTION_FACTORY
 from galaxy.model.dataset_collections.types.sample_sheet_util import validate_column_definitions
@@ -638,6 +639,20 @@ class WorkflowModule:
 
                 subcollection_type_description = history_query.can_map_over(data) or None
                 if subcollection_type_description:
+                    # Translate paired_or_unpaired to concrete mapping type for
+                    # flat collections. Mirrors logic in basic.py:2675-2679 that
+                    # the API tool execution path uses.
+                    _sub_ct = subcollection_type_description.collection_type
+                    _hdca_ct = data.collection.collection_type
+                    if _sub_ct == "paired_or_unpaired" and not _hdca_ct.endswith("paired_or_unpaired"):
+                        if _hdca_ct.endswith("paired"):
+                            subcollection_type_description = dataset_collection_type_descriptions.for_collection_type(
+                                "paired"
+                            )
+                        else:
+                            subcollection_type_description = dataset_collection_type_descriptions.for_collection_type(
+                                "single_datasets"
+                            )
                     subcollection_type_list = subcollection_type_description.collection_type.split(":")
                     for collection_type in reversed(subcollection_type_list):
                         if type_list:
@@ -2414,9 +2429,25 @@ class ToolModule(WorkflowModule):
             def callback(input, prefixed_name: str, **kwargs):
                 input_dict = all_inputs_by_name[prefixed_name]
 
-                replacement: Union[model.Dataset, NoReplacement] = NO_REPLACEMENT
+                replacement: Union[model.Dataset, NoReplacement, PromoteCollectionElementToCollectionAdapter] = (
+                    NO_REPLACEMENT
+                )
                 if iteration_elements and prefixed_name in iteration_elements:  # noqa: B023
                     replacement = iteration_elements[prefixed_name]  # noqa: B023
+                    # When mapping flat collections over paired_or_unpaired via
+                    # single_datasets, wrap each element in an adapter so the
+                    # tool sees a paired_or_unpaired collection.
+                    if (
+                        collection_info  # noqa: B023
+                        and isinstance(replacement, model.DatasetCollectionElement)
+                        and not replacement.child_collection
+                    ):
+                        mapping_type = collection_info.subcollection_mapping_type(prefixed_name)  # noqa: B023
+                        if (
+                            hasattr(mapping_type, "collection_type")
+                            and mapping_type.collection_type == "single_datasets"
+                        ):
+                            replacement = PromoteCollectionElementToCollectionAdapter(replacement)
                 else:
                     replacement = progress.replacement_for_input(trans, step, input_dict)
 

lib/galaxy_test/api/test_tool_execute.py

@@ -525,6 +525,18 @@ def test_map_over_paired_or_unpaired_with_list(target_history: TargetHistory, re
     output_collection.assert_has_dataset_element("foo").with_contents_stripped("text for foo element")
 
 
+@requires_tool_id("collection_paired_or_unpaired")
+def test_map_over_paired_or_unpaired_with_sample_sheet(target_history: TargetHistory, required_tool: RequiredTool):
+    contents = [("foo", "text for foo element")]
+    hdca = target_history.with_sample_sheet(contents)
+    execute = required_tool.execute().with_inputs(
+        {"f1": {"batch": True, "values": [{"map_over_type": "single_datasets", **hdca.src_dict}]}}
+    )
+    execute.assert_has_n_jobs(1).assert_creates_n_implicit_collections(1)
+    output_collection = execute.assert_creates_implicit_collection(0)
+    output_collection.assert_has_dataset_element("foo").with_contents_stripped("text for foo element")
+
+
 @requires_tool_id("collection_paired_or_unpaired")
 def test_map_over_paired_or_unpaired_with_list_of_lists(target_history: TargetHistory, required_tool: RequiredTool):
     hdca = target_history.with_example_list_of_lists()

lib/galaxy_test/base/populators.py

@@ -2650,6 +2650,7 @@ class BaseWorkflowPopulator(BasePopulator):
         raw_yaml: bool = False,
         use_cached_job: bool = False,
         copy_inputs_to_history: bool = False,
+        job_dir: Optional[str] = None,
     ):
         """High-level wrapper around workflow API, etc. to invoke format 2 workflows."""
         workflow_populator = self
@@ -2683,9 +2684,33 @@ class BaseWorkflowPopulator(BasePopulator):
         replacement_parameters = test_data_dict.pop("replacement_parameters", {})
         if history_id is None:
             history_id = self.dataset_populator.new_history()
-        inputs, label_map, has_uploads = load_data_dict(
-            history_id, test_data_dict, self.dataset_populator, self.dataset_collection_populator
-        )
+        if _uses_class_syntax(test_data_dict):
+            # Copy because galactic_job_json() mutates the dict in-place
+            job_copy = dict(test_data_dict)
+            # Extract raw parameters before staging — galactic_job_json
+            # doesn't understand type: raw and would misinterpret them
+            raw_params = {}
+            for k, v in list(job_copy.items()):
+                if isinstance(v, dict) and v.get("type") == "raw":
+                    raw_params[k] = v["value"]
+                    del job_copy[k]
+            staged_job, datasets = stage_inputs(
+                self.dataset_populator.galaxy_interactor,
+                history_id,
+                job_copy,
+                use_path_paste=False,
+                job_dir=job_dir,
+            )
+            if datasets:
+                self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+            staged_job.update(raw_params)
+            label_map = staged_job
+            inputs = staged_job
+            has_uploads = bool(datasets)
+        else:
+            inputs, label_map, has_uploads = load_data_dict(
+                history_id, test_data_dict, self.dataset_populator, self.dataset_collection_populator
+            )
         workflow_request: dict[str, Any] = dict(
             history=f"hist_id={history_id}",
             workflow_id=workflow_id,
@@ -3952,6 +3977,16 @@ class DatasetCollectionPopulator(BaseDatasetCollectionPopulator):
         return create_response
 
 
+def _uses_class_syntax(test_data_dict: dict) -> bool:
+    """Detect Planemo-style class: Collection/File syntax in test data."""
+    for value in test_data_dict.values():
+        if isinstance(value, dict) and "class" in value:
+            return True
+        if isinstance(value, list):  # CWL list shorthand
+            return True
+    return False
+
+
 LoadDataDictResponseT = tuple[dict[str, Any], dict[str, Any], bool]
 
 
@@ -4075,6 +4110,17 @@ def stage_inputs(
     job_dir: Optional[str] = None,
 ) -> tuple[dict[str, Any], list[dict[str, Any]]]:
     """Alternative to load_data_dict that uses production-style workflow inputs."""
+    test_data_resolver = TestDataResolver()
+
+    def resolve_data(filename):
+        result = galaxy_interactor._find_in_test_data_directories(filename)
+        if result and os.path.exists(result):
+            return result
+        try:
+            return test_data_resolver.get_filename(filename)
+        except Exception:
+            return None
+
     kwds = {}
     if job_dir is not None:
         kwds["job_dir"] = job_dir
@@ -4084,7 +4130,7 @@ def stage_inputs(
         job=job,
         use_path_paste=use_path_paste,
         to_posix_lines=to_posix_lines,
-        resolve_data=galaxy_interactor._find_in_test_data_directories,
+        resolve_data=resolve_data,
         **kwds,
     )
 
@@ -4746,6 +4792,15 @@ class TargetHistory:
             )
         )
 
+    def with_sample_sheet(self, contents: Optional[ListContentsDescription] = None) -> "HasSrcDict":
+        if contents is None:
+            contents = [("foo", "text for foo element")]
+        create_response = self._dataset_collection_populator.create_sample_sheet(
+            self._history_id, contents=contents, column_definitions=[], rows={c[0]: [] for c in contents}
+        )
+        api_asserts.assert_status_code_is_ok(create_response)
+        return HasSrcDict("hdca", create_response.json())
+
     def with_example_list_of_pairs(self) -> "HasSrcDict":
         return HasSrcDict("hdca", self._dataset_collection_populator.example_list_of_pairs(self._history_id))
 

lib/galaxy_test/workflow/directory_index.gxwf-tests.yml

@@ -2,9 +2,9 @@
     Test that passing directory indexes works
   job:
     reference:
-      type: File
-      value: 1.fasta
-      file_type: fasta
+      class: File
+      path: 1.fasta
+      filetype: fasta
   outputs:
     output:
       class: File

lib/galaxy_test/workflow/empty_collection_sort.gxwf-tests.yml

@@ -1,12 +1,16 @@
-- doc: | 
+- doc: |
     Test to verify collection operations like the sort tool work fine with empty collections.
   job:
     input:
+      class: Collection
       collection_type: list
       elements:
       - identifier: i1
-        content: "0"
-    filter_file: i1
+        class: File
+        contents: "0"
+    filter_file:
+      class: File
+      contents: "i1"
   outputs:
     output:
       class: Collection

lib/galaxy_test/workflow/filter_null.gxwf-tests.yml

@@ -2,10 +2,12 @@
     Test to verify filter null tool keeps non-null datasets.
   job:
     input_collection:
+      class: Collection
       collection_type: list
       elements:
         - identifier: first
-          content: "abc"
+          class: File
+          contents: "abc"
     when:
       value: true
       type: raw
@@ -18,10 +20,12 @@
     Test to verify filter null tool discards null datasets.
   job:
     input_collection:
+      class: Collection
       collection_type: list
       elements:
         - identifier: first
-          content: "abc"
+          class: File
+          contents: "abc"
     when:
       value: false
       type: raw

lib/galaxy_test/workflow/flat_over_paired_or_unpaired.gxwf-tests.yml

@@ -0,0 +1,40 @@
+- doc: |
+    A flat list mapped over a paired_or_unpaired tool input via
+    single_datasets produces a list output.
+  job:
+    input1:
+      class: Collection
+      collection_type: list
+      elements:
+        - identifier: el1
+          class: File
+          contents: "element 1"
+        - identifier: el2
+          class: File
+          contents: "element 2"
+  outputs:
+    wf_output:
+      class: Collection
+      collection_type: list
+
+- doc: |
+    A flat sample_sheet mapped over a paired_or_unpaired tool input via
+    single_datasets produces a sample_sheet output.
+  job:
+    input1:
+      class: Collection
+      collection_type: sample_sheet
+      rows:
+        el1: []
+        el2: []
+      elements:
+        - identifier: el1
+          class: File
+          contents: "element 1"
+        - identifier: el2
+          class: File
+          contents: "element 2"
+  outputs:
+    wf_output:
+      class: Collection
+      collection_type: sample_sheet

lib/galaxy_test/workflow/flat_over_paired_or_unpaired.gxwf.yml

@@ -0,0 +1,13 @@
+class: GalaxyWorkflow
+inputs:
+  input1:
+    type: collection
+    collection_type: paired_or_unpaired
+outputs:
+  wf_output:
+    outputSource: tool_step/out1
+steps:
+  tool_step:
+    tool_id: collection_paired_or_unpaired
+    in:
+      f1: input1

lib/galaxy_test/workflow/flatten_collection_over_execution.gxwf-tests.yml

@@ -1,11 +1,13 @@
-- doc: | 
+- doc: |
     Test to verify collection flatten collection operation mid workflow.
   job:
     input_fastqs:
+      class: Collection
       collection_type: list
       elements:
         - identifier: samp1
-          content: "0 mycoolline\n1 mysecondline\n"
+          class: File
+          contents: "0 mycoolline\n1 mysecondline\n"
   outputs:
     out:
       class: Collection

lib/galaxy_test/workflow/integer_into_data_column.gxwf-tests.yml

@@ -2,9 +2,9 @@
     Test to verify text parameter can be connected to data column param
   job:
     input:
-      type: File
-      value: 2.tabular
-      file_type: tabular
+      class: File
+      path: 2.tabular
+      filetype: tabular
     column:
       value: "2"
       type: raw

lib/galaxy_test/workflow/map_over_expression.gxwf-tests.yml

@@ -2,12 +2,15 @@
     Test to verify text parameter can be connected to data column param
   job:
     text_input1:
+      class: Collection
       collection_type: list
       elements:
         - identifier: A
-          content: A
+          class: File
+          contents: A
         - identifier: B
-          content: B
+          class: File
+          contents: B
   outputs:
     out1:
       class: Collection

lib/galaxy_test/workflow/multi_select_mapping.gxwf-tests.yml

@@ -5,15 +5,17 @@
     string.
   job:
     input:
-      type: collection
+      class: Collection
       collection_type: list
       elements:
         - identifier: the_example_2
-          content: '"ex2"'
-          ext: 'expression.json'
+          class: File
+          contents: '"ex2"'
+          filetype: 'expression.json'
         - identifier: the_example_5
-          content: '"ex5"'
-          ext: 'expression.json'
+          class: File
+          contents: '"ex5"'
+          filetype: 'expression.json'
   outputs:
     output:
       class: Collection

lib/galaxy_test/workflow/multiple_integer_into_data_column.gxwf-tests.yml

@@ -2,9 +2,9 @@
     Test to verify text parameter can be connected to data column param
   job:
     input:
-      type: File
-      value: 2.tabular
-      file_type: tabular
+      class: File
+      path: 2.tabular
+      filetype: tabular
     column:
       value: [1, 2]
       type: raw

lib/galaxy_test/workflow/optional_conditional_inputs_to_build_list.gxwf-tests.yml

@@ -2,9 +2,9 @@
     Test optional unspecified input into conditional step works
   job:
     required_dataset:
-      type: File
-      value: 2.tabular
-      file_type: tabular
+      class: File
+      path: 2.tabular
+      filetype: tabular
   outputs:
     out:
       class: Collection

lib/galaxy_test/workflow/output_parameter.gxwf-tests.yml

@@ -2,7 +2,7 @@
     Test to verify exact output parameter verification works propery.
   job:
     text_int:
-      type: File
-      content: "43"
+      class: File
+      contents: "43"
   outputs:
     out_int: 43

lib/galaxy_test/workflow/rename_based_on_input_collection.gxwf-tests.yml

@@ -1,21 +1,22 @@
-- doc: | 
+- doc: |
     Test output dataset renaming when the target basename is based on an input collection.
   job:
     fasta_input:
-      value: 1.fasta
-      type: File
+      class: File
+      path: 1.fasta
       name: fasta1
-      file_type: fasta
+      filetype: fasta
     fastq_inputs:
+      class: Collection
       collection_type: list
       name: the_dataset_pair
       elements:
         - identifier: forward
-          value: 1.fastq
-          type: File
+          class: File
+          path: 1.fastq
         - identifier: reverse
-          value: 1.fastq
-          type: File
+          class: File
+          path: 1.fastq
   outputs:
     output:
       class: File

lib/galaxy_test/workflow/subcollection_rank_sorting.gxwf-tests.yml

@@ -1,11 +1,25 @@
-- doc: | 
+- doc: |
     Test to verify a tool that takes in a list or nested list is sent the most
     specific list possible during workflow execution (the nested list). This should
     not trigger subcollection mapping.
   job:
     input:
-      type: collection
+      class: Collection
       collection_type: list:list
+      elements:
+        - identifier: test_level_1
+          class: Collection
+          type: list
+          elements:
+            - identifier: data1
+              class: File
+              contents: "TestData123"
+            - identifier: data2
+              class: File
+              contents: "TestData123"
+            - identifier: data3
+              class: File
+              contents: "TestData123"
   outputs:
     out:
       asserts:
@@ -15,8 +29,26 @@
     Once again with mapping, should reduce the result into a flat list.
   job:
     input:
-      type: collection
+      class: Collection
       collection_type: list:list:list
+      elements:
+        - identifier: test_level_2
+          class: Collection
+          type: list:list
+          elements:
+            - identifier: test_level_1
+              class: Collection
+              type: list
+              elements:
+                - identifier: data1
+                  class: File
+                  contents: "TestData123"
+                - identifier: data2
+                  class: File
+                  contents: "TestData123"
+                - identifier: data3
+                  class: File
+                  contents: "TestData123"
   outputs:
     out:
       class: Collection
@@ -34,8 +66,30 @@
     two levels should be mapped over.
   job:
     input:
-      type: collection
+      class: Collection
       collection_type: list:list:list:list
+      elements:
+        - identifier: test_level_3
+          class: Collection
+          type: list:list:list
+          elements:
+            - identifier: test_level_2
+              class: Collection
+              type: list:list
+              elements:
+                - identifier: test_level_1
+                  class: Collection
+                  type: list
+                  elements:
+                    - identifier: data1
+                      class: File
+                      contents: "TestData123"
+                    - identifier: data2
+                      class: File
+                      contents: "TestData123"
+                    - identifier: data3
+                      class: File
+                      contents: "TestData123"
   outputs:
     out:
       class: Collection

lib/galaxy_test/workflow/subcollection_rank_sorting_paired.gxwf-tests.yml

@@ -1,11 +1,22 @@
-- doc: | 
+- doc: |
     Test to verify a tool that takes in a paired or list of paired is sent the most
     specific list possible during workflow execution (the list of paired datasets). This should
     not trigger subcollection mapping.
   job:
     input:
-      type: collection
+      class: Collection
       collection_type: list:paired
+      elements:
+        - identifier: test_level_1
+          class: Collection
+          type: paired
+          elements:
+            - identifier: forward
+              class: File
+              contents: "TestData123"
+            - identifier: reverse
+              class: File
+              contents: "TestData123"
   outputs:
     out:
       asserts:
@@ -16,8 +27,23 @@
     Once again with mapping, should reduce the result into a flat list.
   job:
     input:
-      type: collection
+      class: Collection
       collection_type: list:list:paired
+      elements:
+        - identifier: test_level_2
+          class: Collection
+          type: list:paired
+          elements:
+            - identifier: test_level_1
+              class: Collection
+              type: paired
+              elements:
+                - identifier: forward
+                  class: File
+                  contents: "TestData123"
+                - identifier: reverse
+                  class: File
+                  contents: "TestData123"
   outputs:
     out:
       class: Collection
@@ -34,8 +60,27 @@
     Once again with double mapping, should reduce the result into a nested list (list:list).
   job:
     input:
-      type: collection
+      class: Collection
       collection_type: list:list:list:paired
+      elements:
+        - identifier: test_level_3
+          class: Collection
+          type: list:list:paired
+          elements:
+            - identifier: test_level_2
+              class: Collection
+              type: list:paired
+              elements:
+                - identifier: test_level_1
+                  class: Collection
+                  type: paired
+                  elements:
+                    - identifier: forward
+                      class: File
+                      contents: "TestData123"
+                    - identifier: reverse
+                      class: File
+                      contents: "TestData123"
   outputs:
     out:
       class: Collection

lib/galaxy_test/workflow/test_framework_workflows.py

@@ -70,6 +70,7 @@ class TestWorkflow(ApiTestCase):
                     yaml_content,
                     test_data=test_job["job"],
                     history_id=history_id,
+                    job_dir=str(workflow_path.parent),
                 )
                 if TEST_WORKFLOW_AFTER_RERUN:
                     run_summary = self.workflow_populator.rerun(run_summary)

lib/galaxy_test/workflow/triply_nested_list_mapping.gxwf-tests.yml

@@ -1,10 +1,28 @@
-- doc: | 
+- doc: |
     Test that a basic list:list:list parameter is consumed directly by the tool
     and not mapped over.
   job:
     input:
-      type: collection
+      class: Collection
       collection_type: list:list:list
+      elements:
+        - identifier: test_level_2
+          class: Collection
+          type: list:list
+          elements:
+            - identifier: test_level_1
+              class: Collection
+              type: list
+              elements:
+                - identifier: data1
+                  class: File
+                  contents: "TestData123"
+                - identifier: data2
+                  class: File
+                  contents: "TestData123"
+                - identifier: data3
+                  class: File
+                  contents: "TestData123"
   outputs:
     out:
       asserts:
@@ -13,12 +31,34 @@
       - that: has_text
         text: "collection_type<list:list>"
 
-- doc: | 
+- doc: |
     Test that mapping over a list:list:list input parameter.
   job:
     input:
-      type: collection
+      class: Collection
       collection_type: list:list:list:list
+      elements:
+        - identifier: test_level_3
+          class: Collection
+          type: list:list:list
+          elements:
+            - identifier: test_level_2
+              class: Collection
+              type: list:list
+              elements:
+                - identifier: test_level_1
+                  class: Collection
+                  type: list
+                  elements:
+                    - identifier: data1
+                      class: File
+                      contents: "TestData123"
+                    - identifier: data2
+                      class: File
+                      contents: "TestData123"
+                    - identifier: data3
+                      class: File
+                      contents: "TestData123"
   outputs:
     out:
       class: Collection

lib/galaxy_test/workflow/zip_collection.gxwf-tests.yml

@@ -1,8 +1,12 @@
-- doc: | 
+- doc: |
     Test simple use of __ZIP_COLLECTION__ in a workflow.
   job:
-    test_input_1: "samp1\t10.0\nsamp2\t20.0\n"
-    test_input_2: "samp1\t20.0\nsamp2\t40.0\n"
+    test_input_1:
+      class: File
+      contents: "samp1\t10.0\nsamp2\t20.0\n"
+    test_input_2:
+      class: File
+      contents: "samp1\t20.0\nsamp2\t40.0\n"
   outputs:
     out:
       asserts:

test/unit/tool_util/test_cwl_util.py

@@ -1,6 +1,11 @@
 import tempfile
 
-from galaxy.tool_util.cwl.util import output_properties
+from galaxy.tool_util.cwl.util import (
+    FileLiteralTarget,
+    galactic_job_json,
+    output_properties,
+    UploadTarget,
+)
 
 
 def test_output_properties_in_memory():
@@ -23,3 +28,126 @@ def test_output_properties_path():
     assert props["nameext"] == ".txt"
     assert props["size"] == 11
     assert props["checksum"] == "sha1$2aae6c35c94fcfb415dbe95f408b9ce91ee846ed"
+
+
+def _mock_upload_func(upload_target: UploadTarget):
+    """Mock upload that captures the target for inspection."""
+    dataset_id = f"dataset_{id(upload_target)}"
+    return {"outputs": [{"id": dataset_id}]}
+
+
+def _mock_collection_create_func(element_identifiers, collection_type, rows=None, name=None):
+    return {"id": f"collection_{collection_type}"}
+
+
+def test_galactic_job_json_file_literal_filetype():
+    """FileLiteralTarget receives filetype when specified via class: File + contents."""
+    captured_targets = []
+
+    def upload_func(upload_target):
+        captured_targets.append(upload_target)
+        return _mock_upload_func(upload_target)
+
+    job = {
+        "input1": {
+            "class": "File",
+            "contents": "some text",
+            "filetype": "txt",
+        }
+    }
+    result_job, datasets = galactic_job_json(
+        job, ".", upload_func, _mock_collection_create_func, tool_or_workflow="workflow"
+    )
+    assert len(captured_targets) == 1
+    target = captured_targets[0]
+    assert isinstance(target, FileLiteralTarget)
+    assert target.contents == "some text"
+    assert target.properties.get("filetype") == "txt"
+
+
+def test_galactic_job_json_file_literal_no_filetype():
+    """FileLiteralTarget receives filetype=None when not specified."""
+    captured_targets = []
+
+    def upload_func(upload_target):
+        captured_targets.append(upload_target)
+        return _mock_upload_func(upload_target)
+
+    job = {
+        "input1": {
+            "class": "File",
+            "contents": "some text",
+        }
+    }
+    result_job, datasets = galactic_job_json(
+        job, ".", upload_func, _mock_collection_create_func, tool_or_workflow="workflow"
+    )
+    assert len(captured_targets) == 1
+    target = captured_targets[0]
+    assert isinstance(target, FileLiteralTarget)
+    assert target.properties.get("filetype") is None
+
+
+def test_galactic_job_json_file_literal_tags_and_dbkey():
+    """FileLiteralTarget receives tags and dbkey."""
+    captured_targets = []
+
+    def upload_func(upload_target):
+        captured_targets.append(upload_target)
+        return _mock_upload_func(upload_target)
+
+    job = {
+        "input1": {
+            "class": "File",
+            "contents": "some text",
+            "filetype": "fastq",
+            "tags": ["group:sample1"],
+            "dbkey": "hg38",
+        }
+    }
+    result_job, datasets = galactic_job_json(
+        job, ".", upload_func, _mock_collection_create_func, tool_or_workflow="workflow"
+    )
+    assert len(captured_targets) == 1
+    target = captured_targets[0]
+    assert isinstance(target, FileLiteralTarget)
+    assert target.properties["filetype"] == "fastq"
+    assert target.properties["tags"] == ["group:sample1"]
+    assert target.properties["dbkey"] == "hg38"
+
+
+def test_galactic_job_json_collection_element_filetype():
+    """Collection elements with class: File + contents get filetype forwarded."""
+    captured_targets = []
+
+    def upload_func(upload_target):
+        captured_targets.append(upload_target)
+        return _mock_upload_func(upload_target)
+
+    job = {
+        "reads": {
+            "class": "Collection",
+            "collection_type": "paired",
+            "elements": [
+                {
+                    "identifier": "forward",
+                    "class": "File",
+                    "contents": "forward reads",
+                    "filetype": "fastqsanger",
+                },
+                {
+                    "identifier": "reverse",
+                    "class": "File",
+                    "contents": "reverse reads",
+                    "filetype": "fastqsanger",
+                },
+            ],
+        }
+    }
+    result_job, datasets = galactic_job_json(
+        job, ".", upload_func, _mock_collection_create_func, tool_or_workflow="workflow"
+    )
+    assert len(captured_targets) == 2
+    for target in captured_targets:
+        assert isinstance(target, FileLiteralTarget)
+        assert target.properties.get("filetype") == "fastqsanger"