WIP: allow collection inputs to YAML tools.

lib/galaxy/tool_util/parser/yaml.py

@@ -8,6 +8,7 @@ from typing import (
     List,
     Optional,
     Tuple,
+    Union,
 )
 
 import packaging.version
@@ -34,6 +35,7 @@ from galaxy.tool_util_models.tool_source import (
     HelpContent,
     XrefDict,
     YamlTemplateConfigFile,
+    JsonTestCollectionDefDict,
 )
 from galaxy.util import listify
 from .interface import (
@@ -44,6 +46,8 @@ from .interface import (
     PagesSource,
     ToolSource,
     ToolSourceTest,
+    ToolSourceTestInput,
+    ToolSourceTestInputs,
     ToolSourceTests,
 )
 from .output_actions import ToolOutputActionApp
@@ -358,14 +362,24 @@ class YamlToolSource(ToolSource):
         return json.dumps(self.root_dict, ensure_ascii=False, sort_keys=False)
 
 
-def _parse_test(i, test_dict) -> ToolSourceTest:
-    inputs = test_dict["inputs"]
+def __parse_test_inputs(i: int, test_inputs: Union[list, dict]) -> ToolSourceTestInputs:
+    inputs = test_inputs
     if is_dict(inputs):
         new_inputs = []
         for key, value in inputs.items():
             new_inputs.append({"name": key, "value": value, "attributes": {}})
-        test_dict["inputs"] = new_inputs
+        inputs = new_inputs
+    for input in inputs:
+        if is_dict(input["value"]) and "class" in input["value"] and input["value"]["class"] == "Collection":
+            collection_def = JsonTestCollectionDefDict(input["value"])
+            attrib = input.setdefault("attributes", {})
+            attrib["collection"] = collection_def
 
+    return inputs
+
+
+def _parse_test(i: int, test_dict: dict) -> ToolSourceTest:
+    test_dict["inputs"] = __parse_test_inputs(i, deepcopy(test_dict["inputs"]))
     outputs = test_dict["outputs"]
 
     new_outputs = []

lib/galaxy/tool_util/verify/interactor.py

@@ -2001,6 +2001,9 @@ def expanded_inputs_from_json(expanded_inputs_json: ExpandedToolInputsJsonified)
         if isinstance(value, dict) and value.get("model_class"):
             collection_def_dict = cast(XmlTestCollectionDefDict, value)
             loaded_inputs[key] = TestCollectionDef.from_dict(collection_def_dict)
+        elif isinstance(value, dict) and value.get("class") == "Collection":
+            collection_def_dict = cast(JsonTestCollectionDefDict, value)
+            loaded_inputs[key] = TestCollectionDef.from_dict(collection_def_dict)
         else:
             loaded_inputs[key] = value
     return loaded_inputs

test/functional/tools/collection_paired_test_y.yml

@@ -0,0 +1,41 @@
+class: GalaxyTool
+id: collection_paired_test_y
+name: collection_paired_test_y
+version: "0.1.0"
+container: busybox
+shell_command: |
+  cat '$(inputs.f1.forward.path)' '$(inputs.f1.reverse.path)' >> out1.txt
+  echo 'Collection name: $(inputs.f1.name)'
+inputs:
+  - name: f1
+    type: data_collection
+    collection_type: paired
+    label: Input pair
+outputs:
+  - name: out1
+    type: data
+    format: txt
+    from_work_dir: out1.txt
+tests:
+  - inputs:
+      f1:
+        class: Collection
+        collection_type: paired
+        name: collection name
+        elements:
+          - identifier: forward
+            class: File
+            path: simple_line.txt
+          - identifier: reverse
+            class: File
+            path: simple_line_alternative.txt
+    outputs:
+      out1:
+        asserts:
+          - has_line:
+              line: This is a line of text.
+          - has_line:
+              line: This is a different line of text.
+    assert_stdout:
+      - has_line:
+          line: "Collection name: collection name"

test/functional/tools/sample_tool_conf.xml

@@ -186,6 +186,7 @@
   <tool file="output_action_change_format.xml" />
   <tool file="output_action_change_format_paired.xml" />
   <tool file="collection_paired_test.xml" />
+  <tool file="collection_paired_test_y.yml" />
   <tool file="collection_paired_default.xml" />
   <tool file="collection_paired_structured_like.xml" />
   <tool file="collection_paired_conditional_structured_like.xml" />

test/unit/tool_util/test_test_definition_parsing.py

@@ -65,6 +65,18 @@ RECORD_TWO_FILES_EXPECTATIONS = [
     (["inputs", "f1", "fields", 0, "name"], "parent"),
     (["inputs", "f1", "fields", 1, "type"], "File"),
 ]
+COLLECTION_TEST_PAIRED_EXPECTATIONS = [
+    (["inputs", "f1", "model_class"], "TestCollectionDef"),
+    (["inputs", "f1", "collection_type"], "paired"),
+    (["required_files", 0, 0], "simple_line.txt"),
+    (["required_files", 1, 0], "simple_line_alternative.txt"),
+]
+COLLECTION_TEST_PAIRED_Y_EXPECTATIONS = [
+    (["inputs", "f1", "model_class"], "TestCollectionDef"),
+    (["inputs", "f1", "collection_type"], "paired"),
+    (["required_files", 0, 0], "simple_line.txt"),
+    (["required_files", 1, 0], "simple_line_alternative.txt"),
+]
 
 
 class TestTestParsing(TestCase):
@@ -131,6 +143,18 @@ class TestTestParsing(TestCase):
         test_0 = test_dicts[0].to_dict()
         self._verify_each(test_0, RECORD_TWO_FILES_EXPECTATIONS)
 
+    def test_collection_inputs(self):
+        self._init_tool_for_path(functional_test_tool_path("collection_paired_test.xml"))
+        test_dicts = self._parse_tests()
+        test_0 = test_dicts[0].to_dict()
+        self._verify_each(test_0, COLLECTION_TEST_PAIRED_EXPECTATIONS)
+
+    def test_collection_inputs_from_yaml(self):
+        self._init_tool_for_path(functional_test_tool_path("collection_paired_test_y.yml"))
+        test_dicts = self._parse_tests()
+        test_0 = test_dicts[0].to_dict()
+        self._verify_each(test_0, COLLECTION_TEST_PAIRED_Y_EXPECTATIONS)
+
     def test_bigwigtowig_converter(self):
         # defines
         if in_packages():