Merge pull request #14526 from bernt-matthias/topic/fix-test-linters

[22.05] Fix typos in test linter

doc/source/releases/18.09.rst

@@ -220,7 +220,7 @@ Enhancements
   `Pull Request 6480`_
 * Use bootstrap vue classes for workflow import form
   `Pull Request 6489`_
-* Small improvement to the tool xsd docs regarding ``discovered_datasets``
+* Small improvement to the tool xsd docs regarding ``discovered_dataset``
   (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
   `Pull Request 6490`_
 * Implement ``group:`` tags (toward multi-factor analysis with group tagging)

lib/galaxy/tool_util/linters/tests.py

@@ -97,9 +97,9 @@ def lint_tsts(tool_xml, lint_ctx):
             discover_datasets = corresponding_output.find(".//discover_datasets")
             if discover_datasets is not None:
                 if output.tag == "output":
-                    if "count" not in output.attrib and output.find("./discovered_datasets") is None:
+                    if "count" not in output.attrib and output.find("./discovered_dataset") is None:
                         lint_ctx.error(
-                            f"Test {test_idx}: test output '{name}' must have a 'count' attribute and/or 'discovered_datasets' children",
+                            f"Test {test_idx}: test output '{name}' must have a 'count' attribute and/or 'discovered_dataset' children",
                             node=output,
                         )
                         pass

lib/galaxy/tool_util/parser/output_objects.py

@@ -324,7 +324,7 @@ class ToolOutputCollectionStructure:
             )
         if dataset_collector_descriptions and (structured_like or collection_type_from_rules):
             raise ValueError(
-                "Cannot specify dynamic structure (discovered_datasets) and collection type attributes structured_like or collection_type_from_rules."
+                "Cannot specify dynamic structure (discover_datasets) and collection type attributes structured_like or collection_type_from_rules."
             )
         self.dynamic = bool(dataset_collector_descriptions)
 

lib/galaxy/tool_util/xsd/galaxy.xsd

@@ -1853,7 +1853,7 @@ provides a demonstration of using this tag.
 </test>
 ```
 
-Note that this tool uses ``assign_primary_output="true"`` for ``<discover_data_sets>``. Hence, the content of the first discovered dataset (which is the first in the alphabetically sorted list of discovered designations) is checked directly in the ``<output>`` tag of the test.
+Note that this tool uses ``assign_primary_output="true"`` for ``<discover_datasets>``. Hence, the content of the first discovered dataset (which is the first in the alphabetically sorted list of discovered designations) is checked directly in the ``<output>`` tag of the test.
 ]]></xs:documentation>
     </xs:annotation>
     <xs:complexContent>

test/unit/app/tools/test_collect_primary_datasets.py

@@ -55,7 +55,7 @@ class CollectPrimaryDatasetsTestCase(unittest.TestCase, tools_support.UsesTools)
         # Test default metadata stuff
         assert created_hda_1.visible
 
-        # Since discovered_datasets not specified, older name based pattern
+        # Since discover_datasets not specified, older name based pattern
         # didn't result in a dbkey being set.
         assert created_hda_1.dbkey == "?"
 

test/unit/tool_util/test_tool_linters.py

@@ -686,11 +686,18 @@ TESTS_DISCOVER_OUTPUTS = """
     <tests>
         <!-- this should be fine -->
         <test>
-            <output name="data_name" count="2">
-                <discovered_data/>
+            <output name="data_name">
+                <discovered_dataset/>
             </output>
             <output_collection name="collection_name">
-                <element count="2">
+                <element count="2"/>
+            </output_collection>
+        </test>
+        <!-- this should be fine as well -->
+        <test>
+            <output name="data_name" count="2"/>
+            <output_collection name="collection_name">
+                <element>
                     <element/>
                 </element>
             </output_collection>
@@ -1492,21 +1499,21 @@ def test_tests_discover_outputs(lint_ctx):
     tool_source = get_xml_tool_source(TESTS_DISCOVER_OUTPUTS)
     run_lint(lint_ctx, tests.lint_tsts, tool_source)
     assert (
-        "Test 2: test output 'data_name' must have a 'count' attribute and/or 'discovered_datasets' children"
+        "Test 3: test output 'data_name' must have a 'count' attribute and/or 'discovered_dataset' children"
         in lint_ctx.error_messages
     )
     assert (
-        "Test 2: test collection 'collection_name' must have a 'count' attribute or 'element' children"
-        in lint_ctx.error_messages
-    )
-    assert (
-        "Test 2: test collection 'collection_name' must contain nested 'element' tags and/or element childen with a 'count' attribute"
+        "Test 3: test collection 'collection_name' must have a 'count' attribute or 'element' children"
         in lint_ctx.error_messages
     )
     assert (
         "Test 3: test collection 'collection_name' must contain nested 'element' tags and/or element childen with a 'count' attribute"
         in lint_ctx.error_messages
     )
+    assert (
+        "Test 4: test collection 'collection_name' must contain nested 'element' tags and/or element childen with a 'count' attribute"
+        in lint_ctx.error_messages
+    )
     assert not lint_ctx.warn_messages
     assert len(lint_ctx.error_messages) == 4