def _validate_tree_with_macros(
self, document: Document,
xml_tree: etree.ElementTree) -> List[Diagnostic]:
"""Validates the document after loading all the macros referenced and expands them.
Args:
document (Document): [description]
xml_tree (etree.ElementTree): [description]
Returns:
List[Diagnostic]: [description]
"""
error_range = None
try:
error_range = self._get_macros_range(document, xml_tree)
expanded_tool_tree, _ = xml_macros.load_with_references(
document.path)
expanded_xml = self._remove_macros(expanded_tool_tree)
root = expanded_xml.getroot()
self.xsd_schema.assertValid(root)
return []
except etree.DocumentInvalid as e:
diagnostics = [
Diagnostic(error_range,
f"Validation error on macro: {error.message}",
source=self.server_name)
for error in e.error_log.filter_from_errors()
]
return diagnostics
except etree.XMLSyntaxError as e:
result = Diagnostic(error_range,
f"Syntax error on macro: {e.msg}",
source=self.server_name)
return [result]
def _validate_expanded(self,
tool: GalaxyToolXmlDocument) -> List[Diagnostic]:
"""Validates the document after loading all the macros referenced and expands them.
Args:
document (Document): [description]
xml_tree (etree.ElementTree): [description]
Returns:
List[Diagnostic]: [description]
"""
try:
expanded_tool_tree, _ = xml_macros.load_with_references(tool.path)
expanded_xml = remove_macros(expanded_tool_tree)
root = expanded_xml.getroot()
etree.indent(root, space=DEFAULT_INDENTATION)
content = etree.tostring(root, pretty_print=True, encoding=str)
formatted_xml = etree.fromstring(content)
self.xsd_schema.assertValid(formatted_xml)
return []
except etree.DocumentInvalid as e:
diagnostics = self._build_diagnostics_for_expanded_macros(tool, e)
return diagnostics
except etree.XMLSyntaxError as e:
return self._build_diagnostics_for_macros_file_syntax_error(
tool, e)
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