def _get_test_suite_from_document(
self, xml_document: XmlDocument) -> Optional[TestSuiteInfoResult]:
tool = GalaxyToolXmlDocument.from_xml_document(xml_document)
tool_id = tool.get_tool_id()
tests_range = tool.get_tests_range()
if tool_id and tests_range:
tests = tool.get_tests()
test_cases: List[TestInfoResult] = []
id = 1
for test in tests:
range = xml_document.get_full_range(test)
if range:
test_cases.append(
TestInfoResult(
tool_id=tool_id,
test_id=str(id),
uri=xml_document.document.uri,
range=range,
), )
id += 1
return TestSuiteInfoResult(
tool_id=tool_id,
uri=xml_document.document.uri,
range=tests_range,
children=test_cases,
)
return None
def get_macro_names(self, tool_xml: XmlDocument) -> Set[str]:
tool = GalaxyToolXmlDocument.from_xml_document(tool_xml)
macros = self._get_macro_definitions(tool_xml)
imported_macro_files = self._get_imported_macro_files_from_tool(tool)
for file in imported_macro_files.values():
macros.update(file.macros)
return set(macros.keys())
def validate_document(self, xml_document: XmlDocument) -> List[Diagnostic]:
"""Validates the XML document and returns a list of diagnostics
if there are any problems.
Args:
xml_document (XmlDocument): The XML document. Can be a tool wrapper or macro
definition file.
Returns:
List[Diagnostic]: The list of issues found in the document.
"""
syntax_errors = self._check_syntax(xml_document.document)
if syntax_errors:
return syntax_errors
if not xml_document.is_tool_file:
return []
tool = GalaxyToolXmlDocument.from_xml_document(xml_document)
try:
xml_tree = etree.fromstring(tool.source)
return self._validate_tree(xml_tree)
except ExpandMacrosFoundException:
result = self._validate_expanded(tool)
return result
except etree.XMLSyntaxError as e:
return self._build_diagnostics_from_syntax_error(e)
def load_macro_definitions(self,
tool_xml: XmlDocument) -> ToolMacroDefinitions:
tool = GalaxyToolXmlDocument.from_xml_document(tool_xml)
tokens = self._get_token_definitions(tool_xml)
macros = self._get_macro_definitions(tool_xml)
imported_macro_files = self._get_imported_macro_files_from_tool(tool)
for file in imported_macro_files.values():
tokens.update(file.tokens)
macros.update(file.macros)
return ToolMacroDefinitions(
tool_document=tool_xml,
imported_macros=imported_macro_files,
tokens=tokens,
macros=macros,
)
def get_available_refactoring_actions(
self, xml_document: XmlDocument,
params: CodeActionParams) -> List[CodeAction]:
"""Gets a collection of possible refactoring code actions on a selected chunk of the document."""
code_actions = []
text_in_range = xml_document.get_text_in_range(params.range)
target_element_tag = self._get_valid_full_element_tag(text_in_range)
if target_element_tag is not None:
macro = MacroData(name=target_element_tag,
content=text_in_range.strip())
macro_definitions = self.macros.definitions_provider.load_macro_definitions(
xml_document)
tool = GalaxyToolXmlDocument.from_xml_document(xml_document)
code_actions.extend(
self.macros.create_extract_to_macros_file_actions(
tool, macro_definitions, macro, params))
code_actions.extend(
self.macros.create_extract_to_local_macro_actions(
tool, macro, params))
return code_actions