diff --git a/doc/source/releases/18.09.rst b/doc/source/releases/18.09.rst index d39ac530a90..2e193ef4ace 100644 --- a/doc/source/releases/18.09.rst +++ b/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 `__). `Pull Request 6490`_ * Implement ``group:`` tags (toward multi-factor analysis with group tagging) diff --git a/lib/galaxy/tool_util/linters/tests.py b/lib/galaxy/tool_util/linters/tests.py index 8985e7e1014..fd99d3f8d3e 100644 --- a/lib/galaxy/tool_util/linters/tests.py +++ b/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 diff --git a/lib/galaxy/tool_util/parser/output_objects.py b/lib/galaxy/tool_util/parser/output_objects.py index 64da29dcf97..48314fb5090 100644 --- a/lib/galaxy/tool_util/parser/output_objects.py +++ b/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) diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd index ec9be7031a5..90cc1ccf6dd 100644 --- a/lib/galaxy/tool_util/xsd/galaxy.xsd +++ b/lib/galaxy/tool_util/xsd/galaxy.xsd @@ -1853,7 +1853,7 @@ provides a demonstration of using this tag. ``` -Note that this tool uses ``assign_primary_output="true"`` for ````. 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 ```` tag of the test. +Note that this tool uses ``assign_primary_output="true"`` for ````. 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 ```` tag of the test. ]]> diff --git a/test/unit/app/tools/test_collect_primary_datasets.py b/test/unit/app/tools/test_collect_primary_datasets.py index 82697984a80..ac2b7ce75b2 100644 --- a/test/unit/app/tools/test_collect_primary_datasets.py +++ b/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 == "?" diff --git a/test/unit/tool_util/test_tool_linters.py b/test/unit/tool_util/test_tool_linters.py index 64f186c0f86..cbc0a2fc88d 100644 --- a/test/unit/tool_util/test_tool_linters.py +++ b/test/unit/tool_util/test_tool_linters.py @@ -686,11 +686,18 @@ TESTS_DISCOVER_OUTPUTS = """ - - + + - + + + + + + + + @@ -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