def generate_command(
self, document: Document) -> Optional[GeneratedSnippetResult]:
"""Generates a boilerplate Cheetah code snippet based on the current inputs and outputs
of this tool wrapper."""
tool = GalaxyToolXmlDocument(document)
generator = GalaxyToolCommandSnippetGenerator(tool)
return generator.generate_snippet()
def test_find_tests_section_without_section_returns_none(self) -> None:
document = TestUtils.to_document("<tool></tool>")
tool = GalaxyToolXmlDocument(document)
actual = tool.find_element("notexistent")
assert actual is None
def generate_tests(self,
document: Document) -> Optional[GeneratedSnippetResult]:
"""Generates a code snippet with some tests for the current inputs and outputs
of this tool wrapper."""
tool = GalaxyToolXmlDocument(document)
generator = GalaxyToolTestSnippetGenerator(tool)
return generator.generate_snippet()
def test_get_element_content_range_of_element_returns_expected(self, source: str, element: str, expected: Range) -> None:
document = TestUtils.to_document(source)
tool = GalaxyToolXmlDocument(document)
node = tool.find_element(element)
actual = tool.get_element_content_range(node)
assert actual == expected
def test_get_element_content_range_of_unknown_element_returns_none(self) -> None:
document = TestUtils.to_document("<tool><tests></tests></tool>")
tool = GalaxyToolXmlDocument(document)
node = tool.find_element("unknown")
actual = tool.get_element_content_range(node)
assert actual is None
def test_find_tests_section_returns_expected(self) -> None:
document = TestUtils.to_document("<tool><tests></tests></tool>")
tool = GalaxyToolXmlDocument(document)
actual = tool.find_element("tests")
assert actual
assert actual.name == "tests"
def test_find_snippet_position_returns_expected_result(self, source: str, expected_position: Position) -> None:
document = TestUtils.to_document(source)
tool = GalaxyToolXmlDocument(document)
generator = GalaxyToolCommandSnippetGenerator(tool)
actual_position = generator._find_snippet_insert_position()
assert actual_position == expected_position
def test_generate_snippet_with_tests_section_returns_snippet_only(self) -> None:
document = TestUtils.to_document("<tool><tests></tests></tool>")
tool = GalaxyToolXmlDocument(document)
generator = GalaxyToolTestSnippetGenerator(tool)
result = generator.generate_snippet()
assert "<tests>" not in result.snippet
def test_build_snippet_returns_expected_result(self, tool_file: str, expected_snippet_file: str) -> None:
document = TestUtils.get_test_document_from_file(tool_file)
expected_snippet = TestUtils.get_test_file_contents(expected_snippet_file)
tool = GalaxyToolXmlDocument(document)
generator = GalaxyToolCommandSnippetGenerator(tool)
actual_snippet = generator._build_snippet()
assert actual_snippet == expected_snippet
def test_generate_snippet_with_command_with_cdata_returns_snippet_only(self) -> None:
document = TestUtils.to_document("<tool><command><![CDATA[]]></command></tool>")
tool = GalaxyToolXmlDocument(document)
generator = GalaxyToolCommandSnippetGenerator(tool)
result = generator.generate_snippet()
assert "<command" not in result.snippet
assert "<![CDATA[" not in result.snippet
def test_get_position_after_element_returns_expected_position(
self, source: str, element_name: str, expected_position: Position
) -> None:
document = TestUtils.to_document(source)
tool = GalaxyToolXmlDocument(document)
element = tool.find_element(element_name, maxlevel=4)
assert element is not None
actual_position = tool.get_position_after(element)
assert actual_position == expected_position
def _get_expanded_tool_document(self, tool_document: GalaxyToolXmlDocument) -> GalaxyToolXmlDocument:
"""If the given tool document uses macros, a new tool document with the expanded macros is returned,
otherwise, the same document is returned.
"""
if tool_document.uses_macros:
try:
document = tool_document.document
expanded_tool_tree, _ = xml_macros.load_with_references(document.path)
expanded_tool_tree = cast(etree._ElementTree, expanded_tool_tree)
expanded_source = etree.tostring(expanded_tool_tree, encoding=str)
expanded_document = Document(uri=document.uri, source=expanded_source, version=document.version)
return GalaxyToolXmlDocument(expanded_document)
except BaseException:
return tool_document
return tool_document
def test_analyze_inputs_returns_expected_number_of_leaves(self) -> None:
tool = GalaxyToolXmlDocument(TEST_TOOL_WITH_INPUTS_DOCUMENT)
result = tool.analyze_inputs()
assert len(result.leaves) == 3
def test_uses_macros_returns_expected(self, source: str, expected: bool) -> None:
document = TestUtils.to_document(source)
tool = GalaxyToolXmlDocument(document)
assert tool.uses_macros == expected
def test_is_valid(self, source: str, expected: bool) -> None:
document = TestUtils.to_document(source)
tool = GalaxyToolXmlDocument(document)
assert tool.is_valid == expected
def test_init_sets_properties(self) -> None:
document = TestUtils.to_document("<tool></tool>")
tool = GalaxyToolXmlDocument(document)
assert not tool.xml_document.is_empty