text: import json
  import logging
  import math
  import re
  import uuid
  from typing import Optional
  
  import packaging.version
  
  from galaxy.tool_util.deps import requirements
  from galaxy.tool_util.parser.util import (
      DEFAULT_DELTA,
      DEFAULT_DELTA_FRAC
  )
  from galaxy.util import (
      string_as_bool,
      xml_text,
      xml_to_string
  )
  from .interface import (
      InputSource,
      PageSource,
      PagesSource,
      RequiredFiles,
      TestCollectionDef,
      TestCollectionOutputDef,
      ToolSource,
  )
  from .output_actions import ToolOutputActionGroup
  from .output_collection_def import dataset_collector_descriptions_from_elem
  from .output_objects import (
      ToolExpressionOutput,
      ToolOutput,
      ToolOutputCollection,
      ToolOutputCollectionStructure
  )
  from .stdio import (
      aggressive_error_checks,
      error_on_exit_code,
      StdioErrorLevel,
      ToolStdioExitCode,
      ToolStdioRegex,
  )
  
  
  log = logging.getLogger(__name__)
  
  
  class XmlToolSource(ToolSource):
      """ Responsible for parsing a tool from classic Galaxy representation.
      """
  
      language = 'xml'
  
      def __init__(self, xml_tree, source_path=None, macro_paths=None):
          self.xml_tree = xml_tree
          self.root = xml_tree.getroot()
          self._source_path = source_path
          self._macro_paths = macro_paths or []
          self.legacy_defaults = self.parse_profile() == "16.01"
  
      def to_string(self):
          return xml_to_string(self.root)
  
      def parse_version(self):
          return self.root.get("version", None)
  
      def parse_id(self):
          return self.root.get("id")
  
      def parse_tool_module(self):
          root = self.root
          if root.find("type") is not None:
              type_elem = root.find("type")
              module = type_elem.get('module', 'galaxy.tools')
              cls = type_elem.get('class')
              return module, cls
  
          return None
  
      def parse_action_module(self):
          root = self.root
          action_elem = root.find("action")
          if action_elem is not None:
              module = action_elem.get('module')
              cls = action_elem.get('class')
              return module, cls
          else:
              return None
  
      def parse_tool_type(self):
          root = self.root
          if root.get('tool_type', None) is not None:
              return root.get('tool_type')
  
      def parse_name(self):
          return self.root.get("name")
  
      def parse_edam_operations(self):
          edam_ops = self.root.find("edam_operations")
          if edam_ops is None:
              return []
          return [edam_op.text for edam_op in edam_ops.findall("edam_operation")]
  
      def parse_edam_topics(self):
          edam_topics = self.root.find("edam_topics")
          if edam_topics is None:
              return []
          return [edam_topic.text for edam_topic in edam_topics.findall("edam_topic")]
  
      def parse_xrefs(self):
          xrefs = self.root.find("xrefs")
          if xrefs is None:
              return []
          return [dict(value=xref.text.strip(), reftype=xref.attrib['type']) for xref in xrefs.findall("xref") if xref.get("type")]
  
      def parse_description(self):
          return xml_text(self.root, "description")
  
      def parse_display_interface(self, default):
          return self._get_attribute_as_bool("display_interface", default)
  
      def parse_require_login(self, default):
          return self._get_attribute_as_bool("require_login", default)
  
      def parse_request_param_translation_elem(self):
          return self.root.find("request_param_translation")
  
      def parse_command(self):
          command_el = self._command_el
          return ((command_el is not None) and command_el.text) or None
  
      def parse_expression(self):
          """ Return string containing command to run.
          """
          expression_el = self.root.find("expression")
          if expression_el is not None:
              expression_type = expression_el.get("type")
              if expression_type != "ecma5.1":
                  raise Exception(f"Unknown expression type [{expression_type}] encountered")
              return expression_el.text
          return None
  
      def parse_environment_variables(self):
          environment_variables_el = self.root.find("environment_variables")
          if environment_variables_el is None:
              return []
  
          environment_variables = []
          for environment_variable_el in environment_variables_el.findall("environment_variable"):
              template = environment_variable_el.text
              inject = environment_variable_el.get("inject")
              if inject:
                  assert not template, "Cannot specify inject and environment variable template."
                  assert inject in ["api_key"]
              if template:
                  assert not inject, "Cannot specify inject and environment variable template."
              definition = {
                  "name": environment_variable_el.get("name"),
                  "template": template,
                  "inject": inject,
                  "strip": string_as_bool(environment_variable_el.get("strip", False)),
              }
              environment_variables.append(
                  definition
              )
          return environment_variables
  
      def parse_home_target(self):
          target = "job_home" if self.parse_profile() >= "18.01" else "shared_home"
          command_el = self._command_el
          command_legacy = (command_el is not None) and command_el.get("use_shared_home", None)
          if command_legacy is not None:
              target = "shared_home" if string_as_bool(command_legacy) else "job_home"
          return target
  
      def parse_tmp_target(self):
          # Default to not touching TMPDIR et. al. but if job_tmp is set
          # in job_conf then do. This is a very conservative approach that shouldn't
          # break or modify any configurations by default.
          return "job_tmp_if_explicit"
  
      def parse_interpreter(self):
          interpreter = None
          command_el = self._command_el
          if command_el is not None:
              interpreter = command_el.get("interpreter", None)
          if interpreter and not self.legacy_defaults:
              log.warning("Deprecated interpreter attribute on command element is now ignored.")
              interpreter = None
          return interpreter
  
      def parse_version_command(self):
          version_cmd = self.root.find("version_command")
          if version_cmd is not None:
              return version_cmd.text
          else:
              return None
  
      def parse_version_command_interpreter(self):
          if self.parse_version_command() is not None:
              version_cmd = self.root.find("version_command")
              version_cmd_interpreter = version_cmd.get("interpreter", None)
              if version_cmd_interpreter:
                  return version_cmd_interpreter
          return None
  
      def parse_parallelism(self):
          parallelism = self.root.find("parallelism")
          parallelism_info = None
          if parallelism is not None and parallelism.get("method"):
              return ParallelismInfo(parallelism)
          return parallelism_info
  
      def parse_interactivetool(self):
          interactivetool_el = self.root.find("entry_points")
          rtt = []
          if interactivetool_el is None:
              return rtt
          for ep_el in interactivetool_el.findall("entry_point"):
              port = ep_el.find("port")
              assert port is not None, ValueError('A port is required for InteractiveTools')
              port = port.text.strip()
              url = ep_el.find("url")
              if url is not None:
                  url = url.text.strip()
              name = ep_el.get('name', None)
              if name:
                  name = name.strip()
              requires_domain = string_as_bool(ep_el.attrib.get("requires_domain", False))
              rtt.append(dict(port=port, url=url, name=name, requires_domain=requires_domain))
          return rtt
  
      def parse_hidden(self):
          hidden = xml_text(self.root, "hidden")
          if hidden:
              hidden = string_as_bool(hidden)
          return hidden
  
      def parse_redirect_url_params_elem(self):
          return self.root.find("redirect_url_params")
  
      def parse_sanitize(self):
          return self._get_option_value("sanitize", True)
  
      def parse_refresh(self):
          return self._get_option_value("refresh", False)
  
      def _get_option_value(self, key, default):
          root = self.root
          for option_elem in root.findall("options"):
              if key in option_elem.attrib:
                  return string_as_bool(option_elem.get(key))
          return default
  
      @property
      def _command_el(self):
          return self.root.find("command")
  
      def _get_attribute_as_bool(self, attribute, default, elem=None):
          if elem is None:
              elem = self.root
          return string_as_bool(elem.get(attribute, default))
  
      def parse_required_files(self) -> Optional[RequiredFiles]:
          required_files = self.root.find("required_files")
          if required_files is None:
              return None
  
          def parse_include_exclude_list(tag_name):
              as_list = []
              for ref in required_files.findall(tag_name):
                  path = ref.get("path")
                  assert path is not None, f'"path" must be specified in {tag_name}'
                  path_type = ref.get("type", "literal")
                  as_list.append({"path": path, "path_type": path_type})
              return as_list
  
          as_dict = {}
          as_dict["extend_default_excludes"] = self._get_attribute_as_bool("extend_default_excludes", True, elem=required_files)
          as_dict["includes"] = parse_include_exclude_list("include")
          as_dict["excludes"] = parse_include_exclude_list("exclude")
          return RequiredFiles.from_dict(as_dict)
  
      def parse_requirements_and_containers(self):
          return requirements.parse_requirements_from_xml(self.root)
  
      def parse_input_pages(self):
          return XmlPagesSource(self.root)
  
      def parse_provided_metadata_style(self):
          style = None
          out_elem = self.root.find("outputs")
          if out_elem is not None and "provided_metadata_style" in out_elem.attrib:
              style = out_elem.attrib["provided_metadata_style"]
  
          if style is None:
              style = "legacy" if self.parse_profile() < "17.09" else "default"
  
          assert style in ["legacy", "default"]
          return style
  
      def parse_provided_metadata_file(self):
          provided_metadata_file = "galaxy.json"
          out_elem = self.root.find("outputs")
          if out_elem is not None and "provided_metadata_file" in out_elem.attrib:
              provided_metadata_file = out_elem.attrib["provided_metadata_file"]
  
          return provided_metadata_file
  
      def parse_outputs(self, tool):
          out_elem = self.root.find("outputs")
          outputs = {}
          output_collections = {}
          if out_elem is None:
              return outputs, output_collections
  
          data_dict = {}
  
          def _parse(data_elem, **kwds):
              output_def = self._parse_output(data_elem, tool, **kwds)
              data_dict[output_def.name] = output_def
              return output_def
  
          for _ in out_elem.findall("data"):
              _parse(_)
  
          def _parse_expression(output_elem, **kwds):
              output_def = self._parse_expression_output(output_elem, tool, **kwds)
              output_def.filters = output_elem.findall('filter')
              data_dict[output_def.name] = output_def
              return output_def
  
          def _parse_collection(collection_elem):
              name = collection_elem.get("name")
              label = xml_text(collection_elem, "label")
              default_format = collection_elem.get("format", "data")
              collection_type = collection_elem.get("type", None)
              collection_type_source = collection_elem.get("type_source", None)
              collection_type_from_rules = collection_elem.get("type_from_rules", None)
              structured_like = collection_elem.get("structured_like", None)
              inherit_format = False
              inherit_metadata = False
              if structured_like:
                  inherit_format = string_as_bool(collection_elem.get("inherit_format", None))
                  inherit_metadata = string_as_bool(collection_elem.get("inherit_metadata", None))
              default_format_source = collection_elem.get("format_source", None)
              default_metadata_source = collection_elem.get("metadata_source", "")
              filters = collection_elem.findall('filter')
  
              dataset_collector_descriptions = None
              if collection_elem.find("discover_datasets") is not None:
                  dataset_collector_descriptions = dataset_collector_descriptions_from_elem(collection_elem, legacy=False)
              structure = ToolOutputCollectionStructure(
                  collection_type=collection_type,
                  collection_type_source=collection_type_source,
                  collection_type_from_rules=collection_type_from_rules,
                  structured_like=structured_like,
                  dataset_collector_descriptions=dataset_collector_descriptions,
              )
              output_collection = ToolOutputCollection(
                  name,
                  structure,
                  label=label,
                  filters=filters,
                  default_format=default_format,
                  inherit_format=inherit_format,
                  inherit_metadata=inherit_metadata,
                  default_format_source=default_format_source,
                  default_metadata_source=default_metadata_source,
              )
              outputs[output_collection.name] = output_collection
  
              for data_elem in collection_elem.findall("data"):
                  _parse(
                      data_elem,
                      default_format=default_format,
                      default_format_source=default_format_source,
                      default_metadata_source=default_metadata_source,
                  )
  
              for data_elem in collection_elem.findall("data"):
                  output_name = data_elem.get("name")
                  data = data_dict[output_name]
                  assert data
                  del data_dict[output_name]
                  output_collection.outputs[output_name] = data
              output_collections[name] = output_collection
  
          for out_child in out_elem:
              if out_child.tag == "data":
                  _parse(out_child)
              elif out_child.tag == "collection":
                  _parse_collection(out_child)
              elif out_child.tag == "output":
                  output_type = out_child.get("type")
                  if output_type == "data":
                      _parse(out_child)
                  elif output_type == "collection":
                      out_child.attrib["type"] = out_child.get("collection_type")
                      out_child.attrib["type_source"] = out_child.get("collection_type_source")
                      _parse_collection(out_child)
                  else:
                      _parse_expression(out_child)
              else:
                  log.warning(f"Unknown output tag encountered [{out_child.tag}]")
  
          for output_def in data_dict.values():
              outputs[output_def.name] = output_def
          return outputs, output_collections
  
      def _parse_output(
          self,
          data_elem,
          tool,
          default_format="data",
          default_format_source=None,
          default_metadata_source="",
          expression_type=None,
      ):
          from_expression = data_elem.get("from")
          output = ToolOutput(data_elem.get("name"), from_expression=from_expression)
          output_format = data_elem.get("format", default_format)
          auto_format = string_as_bool(data_elem.get("auto_format", "false"))
          if auto_format and output_format != "data":
              raise ValueError("Setting format and auto_format is not supported at this time.")
          elif auto_format:
              output_format = "_sniff_"
          output.format = output_format
          output.change_format = data_elem.findall("change_format")
          output.format_source = data_elem.get("format_source", default_format_source)
          output.default_identifier_source = data_elem.get("default_identifier_source", 'None')
          output.metadata_source = data_elem.get("metadata_source", default_metadata_source)
          output.parent = data_elem.get("parent", None)
          output.label = xml_text(data_elem, "label")
          output.count = int(data_elem.get("count", 1))
          output.filters = data_elem.findall('filter')
          output.tool = tool
          output.from_work_dir = data_elem.get("from_work_dir", None)
          if output.from_work_dir and getattr(tool, 'profile', 0) < 21.09:
              # We started quoting from_work_dir outputs in 21.09.
              # Prior to quoting, trailing spaces had no effect.
              # This ensures that old tools continue to work.
              output.from_work_dir = output.from_work_dir.strip()
          output.hidden = string_as_bool(data_elem.get("hidden", ""))
          output.actions = ToolOutputActionGroup(output, data_elem.find('actions'))
          output.dataset_collector_descriptions = dataset_collector_descriptions_from_elem(data_elem, legacy=self.legacy_defaults)
          return output
  
      def _parse_expression_output(self, output_elem, tool, **kwds):
          output_type = output_elem.get("type")
          from_expression = output_elem.get("from")
          output = ToolExpressionOutput(
              output_elem.get("name"),
              output_type,
              from_expression,
          )
          output.path = output_elem.get("value")
          output.label = xml_text(output_elem, "label")
  
          output.hidden = string_as_bool(output_elem.get("hidden", ""))
          output.actions = ToolOutputActionGroup(output, output_elem.find('actions'))
          output.dataset_collector_descriptions = []
          return output
  
      def parse_stdio(self):
          """
          parse error handling from command and stdio tag
  
          returns list of exit codes, list of regexes
  
          - exit_codes contain all non-zero exit codes (:-1 and 1:) if
            detect_errors is default (if not legacy), exit_code, or aggressive
          - the oom_exit_code if given and detect_errors is exit_code
          - exit codes and regexes from the stdio tag
            these are prepended to the list, i.e. are evaluated prior to regexes
            and exit codes derived from the properties of the command tag.
            thus more specific regexes of the same or more severe error level
            are triggered first.
  
          """
  
          command_el = self._command_el
          detect_errors = None
          if command_el is not None:
              detect_errors = command_el.get("detect_errors")
  
          if detect_errors and detect_errors != "default":
              if detect_errors == "exit_code":
                  oom_exit_code = None
                  if command_el is not None:
                      oom_exit_code = command_el.get("oom_exit_code", None)
                  if oom_exit_code is not None:
                      int(oom_exit_code)
                  exit_codes, regexes = error_on_exit_code(out_of_memory_exit_code=oom_exit_code)
              elif detect_errors == "aggressive":
                  exit_codes, regexes = aggressive_error_checks()
              else:
                  raise ValueError(f"Unknown detect_errors value encountered [{detect_errors}]")
          elif len(self.root.findall('stdio')) == 0 and not self.legacy_defaults:
              exit_codes, regexes = error_on_exit_code()
          else:
              exit_codes = []
              regexes = []
  
          if len(self.root.findall('stdio')) > 0:
              parser = StdioParser(self.root)
              exit_codes = parser.stdio_exit_codes + exit_codes
              regexes = parser.stdio_regexes + regexes
  
          return exit_codes, regexes
  
      def parse_strict_shell(self):
          command_el = self._command_el
          if packaging.version.parse(self.parse_profile()) < packaging.version.parse('20.09'):
              default = "False"
          else:
              default = "True"
          if command_el is not None:
              return string_as_bool(command_el.get("strict", default))
          else:
              return string_as_bool(default)
  
      def parse_help(self):
          help_elem = self.root.find('help')
          return help_elem.text if help_elem is not None else None
  
      @property
      def macro_paths(self):
          return self._macro_paths
  
      @property
      def source_path(self):
          return self._source_path
  
      def parse_tests_to_dict(self):
          tests_elem = self.root.find("tests")
          tests = []
          rval = dict(
              tests=tests
          )
  
          if tests_elem is not None:
              for i, test_elem in enumerate(tests_elem.findall("test")):
                  profile = self.parse_profile()
                  tests.append(_test_elem_to_dict(test_elem, i, profile))
  
          return rval
  
      def parse_profile(self):
          # Pre-16.04 or default XML defaults
          # - Use standard error for error detection.
          # - Don't run shells with -e
          # - Auto-check for implicit multiple outputs.
          # - Auto-check for $param_file.
          # - Enable buggy interpreter attribute.
          return self.root.get("profile", "16.01")
  
      def parse_license(self):
          return self.root.get("license")
  
      def parse_python_template_version(self):
          python_template_version = self.root.get("python_template_version", None)
          if python_template_version is not None:
              python_template_version = packaging.version.parse(python_template_version)
          return python_template_version
  
      def parse_creator(self):
          creators_el = self.root.find("creator")
          if creators_el is None:
              return None
  
          creators = []
          for creator_el in creators_el:
              creator_as_dict = {}
              if creator_el.tag == "person":
                  clazz = "Person"
              elif creator_el.tag == "organization":
                  clazz = "Organization"
              else:
                  continue
              creator_as_dict["class"] = clazz
              creator_as_dict.update(creator_el.attrib)
              creators.append(creator_as_dict)
          return creators
  
  
  def _test_elem_to_dict(test_elem, i, profile=None):
      rval = dict(
          outputs=__parse_output_elems(test_elem),
          output_collections=__parse_output_collection_elems(test_elem, profile=profile),
          inputs=__parse_input_elems(test_elem, i),
          expect_num_outputs=test_elem.get("expect_num_outputs"),
          command=__parse_assert_list_from_elem(test_elem.find("assert_command")),
          command_version=__parse_assert_list_from_elem(test_elem.find("assert_command_version")),
          stdout=__parse_assert_list_from_elem(test_elem.find("assert_stdout")),
          stderr=__parse_assert_list_from_elem(test_elem.find("assert_stderr")),
          expect_exit_code=test_elem.get("expect_exit_code"),
          expect_failure=string_as_bool(test_elem.get("expect_failure", False)),
          expect_test_failure=string_as_bool(test_elem.get("expect_test_failure", False)),
          maxseconds=test_elem.get("maxseconds", None),
      )
      _copy_to_dict_if_present(test_elem, rval, ["num_outputs"])
      return rval
  
  
  def __parse_input_elems(test_elem, i):
      __expand_input_elems(test_elem)
      return __parse_inputs_elems(test_elem, i)
  
  
  def __parse_output_elems(test_elem):
      outputs = []
      for output_elem in test_elem.findall("output"):
          name, file, attributes = __parse_output_elem(output_elem)
          outputs.append({"name": name, "value": file, "attributes": attributes})
      return outputs
  
  
  def __parse_output_elem(output_elem):
      attrib = dict(output_elem.attrib)
      name = attrib.pop('name', None)
      if name is None:
          raise Exception("Test output does not have a 'name'")
  
      file, attributes = __parse_test_attributes(output_elem, attrib, parse_discovered_datasets=True)
      return name, file, attributes
  
  
  def __parse_command_elem(test_elem):
      assert_elem = test_elem.find("command")
      return __parse_assert_list_from_elem(assert_elem)
  
  
  def __parse_output_collection_elems(test_elem, profile=None):
      output_collections = []
      for output_collection_elem in test_elem.findall("output_collection"):
          output_collection_def = __parse_output_collection_elem(output_collection_elem, profile=profile)
          output_collections.append(output_collection_def)
      return output_collections
  
  
  def __parse_output_collection_elem(output_collection_elem, profile=None):
      attrib = dict(output_collection_elem.attrib)
      name = attrib.pop('name', None)
      if name is None:
          raise Exception("Test output collection does not have a 'name'")
      element_tests = __parse_element_tests(output_collection_elem, profile=profile)
      return TestCollectionOutputDef(name, attrib, element_tests).to_dict()
  
  
  def __parse_element_tests(parent_element, profile=None):
      element_tests = {}
      for idx, element in enumerate(parent_element.findall("element")):
          element_attrib = dict(element.attrib)
          identifier = element_attrib.pop('name', None)
          if identifier is None:
              raise Exception("Test primary dataset does not have a 'identifier'")
          element_tests[identifier] = __parse_test_attributes(element, element_attrib, parse_elements=True, profile=profile)
          if profile and profile >= "20.09":
              element_tests[identifier][1]["expected_sort_order"] = idx
  
      return element_tests
  
  
  def __parse_test_attributes(output_elem, attrib, parse_elements=False, parse_discovered_datasets=False, profile=None):
      assert_list = __parse_assert_list(output_elem)
  
      # Allow either file or value to specify a target file to compare result with
      # file was traditionally used by outputs and value by extra files.
      file = attrib.pop('file', attrib.pop('value', None))
  
      # File no longer required if an list of assertions was present.
      attributes = {}
  
      if 'value_json' in attrib:
          attributes['object'] = json.loads(attrib.pop('value_json'))
  
      # Method of comparison
      attributes['compare'] = attrib.pop('compare', 'diff').lower()
      # Number of lines to allow to vary in logs (for dates, etc)
      attributes['lines_diff'] = int(attrib.pop('lines_diff', '0'))
      # Allow a file size to vary if sim_size compare
      attributes['delta'] = int(attrib.pop('delta', DEFAULT_DELTA))
      attributes['delta_frac'] = float(attrib['delta_frac']) if 'delta_frac' in attrib else DEFAULT_DELTA_FRAC
      attributes['sort'] = string_as_bool(attrib.pop('sort', False))
      attributes['decompress'] = string_as_bool(attrib.pop('decompress', False))
      extra_files = []
      if 'ftype' in attrib:
          attributes['ftype'] = attrib['ftype']
      for extra in output_elem.findall('extra_files'):
          extra_files.append(__parse_extra_files_elem(extra))
      metadata = {}
      for metadata_elem in output_elem.findall('metadata'):
          metadata[metadata_elem.get('name')] = metadata_elem.get('value')
      md5sum = attrib.get("md5", None)
      checksum = attrib.get("checksum", None)
      element_tests = {}
      if parse_elements:
          element_tests = __parse_element_tests(output_elem, profile=profile)
  
      primary_datasets = {}
      if parse_discovered_datasets:
          for primary_elem in (output_elem.findall("discovered_dataset") or []):
              primary_attrib = dict(primary_elem.attrib)
              designation = primary_attrib.pop('designation', None)
              if designation is None:
                  raise Exception("Test primary dataset does not have a 'designation'")
              primary_datasets[designation] = __parse_test_attributes(primary_elem, primary_attrib)
  
      has_checksum = md5sum or checksum
      has_nested_tests = extra_files or element_tests or primary_datasets
      has_object = 'object' in attributes
      if not (assert_list or file or metadata or has_checksum or has_nested_tests or has_object):
          raise Exception("Test output defines nothing to check (e.g. must have a 'file' check against, assertions to check, metadata or checksum tests, etc...)")
      attributes['assert_list'] = assert_list
      attributes['extra_files'] = extra_files
      attributes['metadata'] = metadata
      attributes['md5'] = md5sum
      attributes['checksum'] = checksum
      attributes['elements'] = element_tests
      attributes['primary_datasets'] = primary_datasets
      return file, attributes
  
  
  def __parse_assert_list(output_elem):
      assert_elem = output_elem.find("assert_contents")
      return __parse_assert_list_from_elem(assert_elem)
  
  
  def __parse_assert_list_from_elem(assert_elem):
      assert_list = None
  
      def convert_elem(elem):
          """ Converts and XML element to a dictionary format, used by assertion checking code. """
          tag = elem.tag
          attributes = dict(elem.attrib)
          converted_children = []
          for child_elem in elem:
              converted_children.append(convert_elem(child_elem))
          return {"tag": tag, "attributes": attributes, "children": converted_children}
      if assert_elem is not None:
          assert_list = []
          for assert_child in list(assert_elem):
              assert_list.append(convert_elem(assert_child))
  
      return assert_list
  
  
  def __parse_extra_files_elem(extra):
      # File or directory, when directory, compare basename
      # by basename
      attrib = dict(extra.attrib)
      extra_type = attrib.pop('type', 'file')
      extra_name = attrib.pop('name', None)
      assert extra_type == 'directory' or extra_name is not None, \
          f'extra_files type ({extra_type}) requires a name attribute'
      extra_value, extra_attributes = __parse_test_attributes(extra, attrib)
      return {
          "value": extra_value,
          "name": extra_name,
          "type": extra_type,
          "attributes": extra_attributes
      }
  
  
  def __expand_input_elems(root_elem, prefix=""):
      __append_prefix_to_params(root_elem, prefix)
  
      repeat_elems = root_elem.findall('repeat')
      indices = {}
      for repeat_elem in repeat_elems:
          name = repeat_elem.get("name")
          if name not in indices:
              indices[name] = 0
              index = 0
          else:
              index = indices[name] + 1
              indices[name] = index
  
          new_prefix = __prefix_join(prefix, name, index=index)
          __expand_input_elems(repeat_elem, new_prefix)
          __pull_up_params(root_elem, repeat_elem)
  
      cond_elems = root_elem.findall('conditional')
      for cond_elem in cond_elems:
          new_prefix = __prefix_join(prefix, cond_elem.get("name"))
          __expand_input_elems(cond_elem, new_prefix)
          __pull_up_params(root_elem, cond_elem)
  
      section_elems = root_elem.findall('section')
      for section_elem in section_elems:
          new_prefix = __prefix_join(prefix, section_elem.get("name"))
          __expand_input_elems(section_elem, new_prefix)
          __pull_up_params(root_elem, section_elem)
  
  
  def __append_prefix_to_params(elem, prefix):
      for param_elem in elem.findall('param'):
          param_elem.set("name", __prefix_join(prefix, param_elem.get("name")))
  
  
  def __pull_up_params(parent_elem, child_elem):
      for param_elem in child_elem.findall('param'):
          parent_elem.append(param_elem)
  
  
  def __prefix_join(prefix, name, index=None):
      name = name if index is None else "%s_%d" % (name, index)
      return name if not prefix else f"{prefix}|{name}"
  
  
  def _copy_to_dict_if_present(elem, rval, attributes):
      for attribute in attributes:
          if attribute in elem.attrib:
              rval[attribute] = elem.get(attribute)
      return rval
  
  
  def __parse_inputs_elems(test_elem, i):
      raw_inputs = []
      for param_elem in test_elem.findall("param"):
          raw_inputs.append(__parse_param_elem(param_elem, i))
  
      return raw_inputs
  
  
  def __parse_param_elem(param_elem, i=0):
      attrib = dict(param_elem.attrib)
      if 'values' in attrib:
          value = attrib['values'].split(',')
      elif 'value' in attrib:
          value = attrib['value']
      elif 'value_json' in attrib:
          value = json.loads(attrib['value_json'])
      else:
          value = None
  
      children_elem = param_elem
      if children_elem is not None:
          # At this time, we can assume having children only
          # occurs on DataToolParameter test items but this could
          # change and would cause the below parsing to change
          # based upon differences in children items
          attrib['metadata'] = {}
          attrib['composite_data'] = []
          attrib['edit_attributes'] = []
          # Composite datasets need to be renamed uniquely
          composite_data_name = None
          for child in children_elem:
              if child.tag == 'composite_data':
                  file_name = child.get("value")
                  attrib['composite_data'].append(file_name)
                  if composite_data_name is None:
                      # Generate a unique name; each test uses a
                      # fresh history.
                      composite_data_name = '_COMPOSITE_RENAMED_t%d_%s' \
                          % (i, uuid.uuid1().hex)
              elif child.tag == 'metadata':
                  attrib['metadata'][child.get("name")] = child.get("value")
              elif child.tag == 'edit_attributes':
                  attrib['edit_attributes'].append(child)
              elif child.tag == 'collection':
                  attrib['collection'] = TestCollectionDef.from_xml(child, __parse_param_elem)
          if composite_data_name:
              # Composite datasets need implicit renaming;
              # inserted at front of list so explicit declarations
              # take precedence
              attrib['edit_attributes'].insert(0, {'type': 'name', 'value': composite_data_name})
      name = attrib.pop('name')
      return {
          "name": name,
          "value": value,
          "attributes": attrib
      }
  
  
  class StdioParser:
  
      def __init__(self, root):
          try:
              self.stdio_exit_codes = list()
              self.stdio_regexes = list()
  
              # We should have a single <stdio> element, but handle the case for
              # multiples.
              # For every stdio element, add all of the exit_code and regex
              # subelements that we find:
              for stdio_elem in (root.findall('stdio')):
                  self.parse_stdio_exit_codes(stdio_elem)
                  self.parse_stdio_regexes(stdio_elem)
          except Exception:
              log.exception("Exception in parse_stdio!")
  
      def parse_stdio_exit_codes(self, stdio_elem):
          """
          Parse the tool's <stdio> element's <exit_code> subelements.
          This will add all of those elements, if any, to self.stdio_exit_codes.
          """
          try:
              # Look for all <exit_code> elements. Each exit_code element must
              # have a range/value.
              # Exit-code ranges have precedence over a single exit code.
              # So if there are value and range attributes, we use the range
              # attribute. If there is neither a range nor a value, then print
              # a warning and skip to the next.
              for exit_code_elem in (stdio_elem.findall("exit_code")):
                  exit_code = ToolStdioExitCode()
                  # Each exit code has an optional description that can be
                  # part of the "desc" or "description" attributes:
                  exit_code.desc = exit_code_elem.get("desc")
                  if exit_code.desc is None:
                      exit_code.desc = exit_code_elem.get("description")
                  # Parse the error level:
                  exit_code.error_level = (
                      self.parse_error_level(exit_code_elem.get("level")))
                  code_range = exit_code_elem.get("range")
                  if code_range is None:
                      code_range = exit_code_elem.get("value")
                  if code_range is None:
                      log.warning("Tool stdio exit codes must have a range or value")
                      continue
                  # Parse the range. We look for:
                  #   :Y
                  #  X:
                  #  X:Y   - Split on the colon. We do not allow a colon
                  #          without a beginning or end, though we could.
                  # Also note that whitespace is eliminated.
                  # TODO: Turn this into a single match - it should be
                  # more efficient.
                  code_range = re.sub(r"\s", "", code_range)
                  code_ranges = re.split(r":", code_range)
                  if (len(code_ranges) == 2):
                      if (code_ranges[0] is None or '' == code_ranges[0]):
                          exit_code.range_start = -math.inf
                      else:
                          exit_code.range_start = int(code_ranges[0])
                      if (code_ranges[1] is None or '' == code_ranges[1]):
                          exit_code.range_end = math.inf
                      else:
                          exit_code.range_end = int(code_ranges[1])
                  # If we got more than one colon, then ignore the exit code.
                  elif (len(code_ranges) > 2):
                      log.warning(f"Invalid tool exit_code range {code_range} - ignored")
                      continue
                  # Else we have a singular value. If it's not an integer, then
                  # we'll just write a log message and skip this exit_code.
                  else:
                      try:
                          exit_code.range_start = int(code_range)
                      except Exception:
                          log.error(code_range)
                          log.warning(f"Invalid range start for tool's exit_code {code_range}: exit_code ignored")
                          continue
                      exit_code.range_end = exit_code.range_start
                  # TODO: Check if we got ">", ">=", "<", or "<=":
                  # Check that the range, regardless of how we got it,
                  # isn't bogus. If we have two infinite values, then
                  # the start must be -inf and the end must be +inf.
                  # So at least warn about this situation:
                  if math.isinf(exit_code.range_start) and math.isinf(exit_code.range_end):
                      log.warning(f"Tool exit_code range {code_range} will match on all exit codes")
                  self.stdio_exit_codes.append(exit_code)
          except Exception:
              log.exception("Exception in parse_stdio_exit_codes!")
  
      def parse_stdio_regexes(self, stdio_elem):
          """
          Look in the tool's <stdio> elem for all <regex> subelements
          that define how to look for warnings and fatal errors in
          stdout and stderr. This will add all such regex elements
          to the Tols's stdio_regexes list.
          """
          try:
              # Look for every <regex> subelement. The regular expression
              # will have "match" and "source" (or "src") attributes.
              for regex_elem in (stdio_elem.findall("regex")):
                  # TODO: Fill in ToolStdioRegex
                  regex = ToolStdioRegex()
                  # Each regex has an optional description that can be
                  # part of the "desc" or "description" attributes:
                  regex.desc = regex_elem.get("desc")
                  if regex.desc is None:
                      regex.desc = regex_elem.get("description")
                  # Parse the error level
                  regex.error_level = (
                      self.parse_error_level(regex_elem.get("level")))
                  regex.match = regex_elem.get("match")
                  if regex.match is None:
                      log.warning(f"Ignoring tool's stdio regex element with attributes {regex_elem.attrib} - "
                                  "the 'match' attribute must exist")
                      continue
                  # Parse the output sources. We look for the "src", "source",
                  # and "sources" attributes, in that order. If there is no
                  # such source, then the source defaults to stderr & stdout.
                  # Look for a comma and then look for "err", "error", "out",
                  # and "output":
                  output_srcs = regex_elem.get("src")
                  if output_srcs is None:
                      output_srcs = regex_elem.get("source")
                  if output_srcs is None:
                      output_srcs = regex_elem.get("sources")
                  if output_srcs is None:
                      output_srcs = "output,error"
                  output_srcs = re.sub(r"\s", "", output_srcs)
                  src_list = re.split(r",", output_srcs)
                  # Just put together anything to do with "out", including
                  # "stdout", "output", etc. Repeat for "stderr", "error",
                  # and anything to do with "err". If neither stdout nor
                  # stderr were specified, then raise a warning and scan both.
                  for src in src_list:
                      if re.search("both", src, re.IGNORECASE):
                          regex.stdout_match = True
                          regex.stderr_match = True
                      if re.search("out", src, re.IGNORECASE):
                          regex.stdout_match = True
                      if re.search("err", src, re.IGNORECASE):
                          regex.stderr_match = True
                      if (not regex.stdout_match and not regex.stderr_match):
                          log.warning("Tool id %s: unable to determine if tool "
                                      "stream source scanning is output, error, "
                                      "or both. Defaulting to use both." % self.id)
                          regex.stdout_match = True
                          regex.stderr_match = True
                  self.stdio_regexes.append(regex)
          except Exception:
              log.exception("Exception in parse_stdio_exit_codes!")
  
      # TODO: This method doesn't have to be part of the Tool class.
      def parse_error_level(self, err_level):
          """
          Parses error level and returns error level enumeration. If
          unparsable, returns 'fatal'
          """
          return_level = StdioErrorLevel.FATAL
          try:
              if err_level:
                  if (re.search("log", err_level, re.IGNORECASE)):
                      return_level = StdioErrorLevel.LOG
                  elif (re.search("qc", err_level, re.IGNORECASE)):
                      return_level = StdioErrorLevel.QC
                  elif (re.search("warning", err_level, re.IGNORECASE)):
                      return_level = StdioErrorLevel.WARNING
                  elif (re.search("fatal_oom", err_level, re.IGNORECASE)):
                      return_level = StdioErrorLevel.FATAL_OOM
                  elif (re.search("fatal", err_level, re.IGNORECASE)):
                      return_level = StdioErrorLevel.FATAL
                  else:
                      log.debug("Tool %s: error level %s did not match log/warning/fatal" %
                                (self.id, err_level))
          except Exception:
              log.exception("Exception in parse_error_level")
          return return_level
  
  
  class XmlPagesSource(PagesSource):
  
      def __init__(self, root):
          self.input_elem = root.find("inputs")
          page_sources = []
          if self.input_elem is not None:
              pages_elem = self.input_elem.findall("page")
              for page in (pages_elem or [self.input_elem]):
                  page_sources.append(XmlPageSource(page))
          super().__init__(page_sources)
  
      @property
      def inputs_defined(self):
          return self.input_elem is not None
  
  
  class XmlPageSource(PageSource):
  
      def __init__(self, parent_elem):
          self.parent_elem = parent_elem
  
      def parse_display(self):
          display_elem = self.parent_elem.find("display")
          if display_elem is not None:
              display = xml_to_string(display_elem)
          else:
              display = None
          return display
  
      def parse_input_sources(self):
          return list(map(XmlInputSource, self.parent_elem))
  
  
  class XmlInputSource(InputSource):
  
      def __init__(self, input_elem):
          self.input_elem = input_elem
          self.input_type = self.input_elem.tag
  
      def parse_input_type(self):
          return self.input_type
  
      def elem(self):
          return self.input_elem
  
      def get(self, key, value=None):
          return self.input_elem.get(key, value)
  
      def get_bool(self, key, default):
          return string_as_bool(self.get(key, default))
  
      def parse_label(self):
          return xml_text(self.input_elem, "label")
  
      def parse_help(self):
          return xml_text(self.input_elem, "help")
  
      def parse_sanitizer_elem(self):
          return self.input_elem.find("sanitizer")
  
      def parse_validator_elems(self):
          return self.input_elem.findall("validator")
  
      def parse_dynamic_options_elem(self):
          """ Return a galaxy.tools.parameters.dynamic_options.DynamicOptions
          if appropriate.
          """
          options_elem = self.input_elem.find('options')
          return options_elem
  
      def parse_static_options(self):
          """
          >>> from galaxy.util import parse_xml_string_to_etree
          >>> xml = '<param><option value="a">A</option><option value="b">B</option></param>'
          >>> xis = XmlInputSource(parse_xml_string_to_etree(xml).getroot())
          >>> xis.parse_static_options()
          [('A', 'a', False), ('B', 'b', False)]
          >>> xml = '<param><option value="a"/><option value="b"/><option value="a" selected="true"/></param>'
          >>> xis = XmlInputSource(parse_xml_string_to_etree(xml).getroot())
          >>> xis.parse_static_options()
          [('a', 'a', True), ('b', 'b', False)]
          """
          static_options = list()
          elem = self.input_elem
          for option in elem.findall("option"):
              value = option.get("value")
              text = option.text or value
              selected = string_as_bool(option.get("selected", False))
              present = False
              for i, o in enumerate(static_options):
                  if o[1] == value:
                      present = True
                      static_options[i] = (text, value, selected)
                      break
              if not present:
                  static_options.append((text, value, selected))
          return static_options
  
      def parse_optional(self, default=None):
          """ Return boolean indicating whether parameter is optional. """
          elem = self.input_elem
          if self.get('type') == "data_column":
              # Allow specifing force_select for backward compat., but probably
              # should use optional going forward for consistency with other
              # parameters.
              if "force_select" in elem.attrib:
                  force_select = string_as_bool(elem.get("force_select"))
              else:
                  force_select = not string_as_bool(elem.get("optional", False))
              return not force_select
  
          if default is None:
              default = self.default_optional
          return self.get_bool("optional", default)
  
      def parse_conversion_tuples(self):
          elem = self.input_elem
          conversions = []
          for conv_elem in elem.findall("conversion"):
              name = conv_elem.get("name")  # name for commandline substitution
              conv_extensions = conv_elem.get("type")  # target datatype extension
              conversions.append((name, conv_extensions))
          return conversions
  
      def parse_nested_inputs_source(self):
          elem = self.input_elem
          return XmlPageSource(elem)
  
      def parse_test_input_source(self):
          elem = self.input_elem
          input_elem = elem.find("param")
          assert input_elem is not None, "<conditional> must have a child <param>"
          return XmlInputSource(input_elem)
  
      def parse_when_input_sources(self):
          elem = self.input_elem
  
          sources = []
          for case_elem in elem.findall("when"):
              value = case_elem.get("value")
              case_page_source = XmlPageSource(case_elem)
              sources.append((value, case_page_source))
          return sources
  
  
  class ParallelismInfo:
      """
      Stores the information (if any) for running multiple instances of the tool in parallel
      on the same set of inputs.
      """
  
      def __init__(self, tag):
          self.method = tag.get('method')
          if isinstance(tag, dict):
              items = tag.items()
          else:
              items = tag.attrib.items()
          self.attributes = dict([item for item in items if item[0] != 'method'])
          if len(self.attributes) == 0:
              # legacy basic mode - provide compatible defaults
              self.attributes['split_size'] = 20
              self.attributes['split_mode'] = 'number_of_parts'
  