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Source code for galaxy.tools.parser.xml

import logging
import re
import sys
import traceback
import uuid
from math import isinf

from galaxy.tools.deps import requirements
from galaxy.util import string_as_bool, xml_text, xml_to_string
from galaxy.util.odict import odict
from .interface import (
from .output_actions import ToolOutputActionGroup
from .output_collection_def import dataset_collector_descriptions_from_elem
from .output_objects import (
from .util import (

log = logging.getLogger(__name__)

[docs]class XmlToolSource(ToolSource): """ Responsible for parsing a tool from classic Galaxy representation. """
[docs] 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"
[docs] def parse_version(self): return self.root.get("version", None)
[docs] def parse_id(self): return self.root.get("id")
[docs] 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
[docs] 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
[docs] def parse_tool_type(self): root = self.root if root.get('tool_type', None) is not None: return root.get('tool_type')
[docs] def parse_name(self): return self.root.get("name")
[docs] 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")]
[docs] 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")]
[docs] def parse_description(self): return xml_text(self.root, "description")
[docs] def parse_is_multi_byte(self): return self._get_attribute_as_bool("is_multi_byte", self.default_is_multi_byte)
[docs] def parse_display_interface(self, default): return self._get_attribute_as_bool("display_interface", default)
[docs] def parse_require_login(self, default): return self._get_attribute_as_bool("require_login", default)
[docs] def parse_request_param_translation_elem(self): return self.root.find("request_param_translation")
[docs] def parse_command(self): command_el = self._command_el return ((command_el is not None) and command_el.text) or None
[docs] 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"): definition = { "name": environment_variable_el.get("name"), "template": environment_variable_el.text, } environment_variables.append( definition ) return environment_variables
[docs] 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
[docs] 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"
[docs] def parse_docker_env_pass_through(self): if self.parse_profile() < "18.01": return ["GALAXY_SLOTS"] else: # Pass home, etc... return super(XmlToolSource, self).parse_docker_env_pass_through()
[docs] 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
[docs] 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
[docs] 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
[docs] def parse_parallelism(self): parallelism = self.root.find("parallelism") parallelism_info = None if parallelism is not None and parallelism.get("method"): from galaxy.jobs import ParallelismInfo return ParallelismInfo(parallelism) return parallelism_info
[docs] def parse_hidden(self): hidden = xml_text(self.root, "hidden") if hidden: hidden = string_as_bool(hidden) return hidden
[docs] def parse_redirect_url_params_elem(self): return self.root.find("redirect_url_params")
[docs] def parse_sanitize(self): return self._get_option_value("sanitize", True)
[docs] 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))
[docs] def parse_requirements_and_containers(self): return requirements.parse_requirements_from_xml(self.root)
[docs] def parse_input_pages(self): return XmlPagesSource(self.root)
[docs] 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
[docs] 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
[docs] def parse_outputs(self, tool): out_elem = self.root.find("outputs") outputs = odict() output_collections = odict() if out_elem is None: return outputs, output_collections data_dict = odict() def _parse(data_elem, **kwds): output_def = self._parse_output(data_elem, tool, **kwds) data_dict[output_def.name] = output_def return output_def map(_parse, out_elem.findall("data")) for collection_elem in out_elem.findall("collection"): 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 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="", ): output = ToolOutput(data_elem.get("name")) 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) 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
[docs] def parse_stdio(self): 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) return error_on_exit_code(out_of_memory_exit_code=oom_exit_code) elif detect_errors == "aggressive": return aggressive_error_checks() else: raise ValueError("Unknown detect_errors value encountered [%s]" % detect_errors) elif len(self.root.findall('stdio')) == 0 and not self.legacy_defaults: return error_on_exit_code() else: parser = StdioParser(self.root) return parser.stdio_exit_codes, parser.stdio_regexes
[docs] def parse_strict_shell(self): command_el = self._command_el if command_el is not None: return string_as_bool(command_el.get("strict", "False")) elif self.legacy_defaults: return False else: return True
[docs] def parse_help(self): help_elem = self.root.find('help') return help_elem.text if help_elem is not None else None
[docs] 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")): tests.append(_test_elem_to_dict(test_elem, i)) return rval
[docs] 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 _test_elem_to_dict(test_elem, i): rval = dict( outputs=__parse_output_elems(test_elem), output_collections=__parse_output_collection_elems(test_elem), 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")), 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)), 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): output_collections = [] for output_collection_elem in test_elem.findall("output_collection"): output_collection_def = __parse_output_collection_elem(output_collection_elem) output_collections.append(output_collection_def) return output_collections def __parse_output_collection_elem(output_collection_elem): 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) return TestCollectionOutputDef(name, attrib, element_tests).to_dict() def __parse_element_tests(parent_element): element_tests = {} for element in 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) return element_tests def __parse_test_attributes(output_elem, attrib, parse_elements=False, parse_discovered_datasets=False): 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 = {} # 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', '10000')) 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) 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 if not (assert_list or file or metadata or has_checksum or has_nested_tests): 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, \ 'extra_files type (%s) requires a name attribute' % extra_type 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) root_elem.remove(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) root_elem.remove(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) root_elem.remove(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) child_elem.remove(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 "%s|%s" % (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'] 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 }
[docs]class StdioParser(object):
[docs] 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.error("Exception in parse_stdio! " + str(sys.exc_info()))
[docs] 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("\s", "", code_range) code_ranges = re.split(":", code_range) if (len(code_ranges) == 2): if (code_ranges[0] is None or '' == code_ranges[0]): exit_code.range_start = float("-inf") else: exit_code.range_start = int(code_ranges[0]) if (code_ranges[1] is None or '' == code_ranges[1]): exit_code.range_end = float("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("Invalid tool exit_code range %s - ignored" % code_range) 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("Invalid range start for tool's exit_code %s: exit_code ignored" % code_range) 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 (isinf(exit_code.range_start) and isinf(exit_code.range_end)): log.warning("Tool exit_code range %s will match on " + "all exit codes" % code_range) self.stdio_exit_codes.append(exit_code) except Exception: log.error("Exception in parse_stdio_exit_codes! " + str(sys.exc_info())) trace = sys.exc_info()[2] if trace is not None: trace_msg = repr(traceback.format_tb(trace)) log.error("Traceback: %s" % trace_msg)
[docs] 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: # TODO: Convert the offending XML element to a string log.warning("Ignoring tool's stdio regex element %s - " "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("\s", "", output_srcs) src_list = re.split(",", 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.error("Exception in parse_stdio_exit_codes! " + str(sys.exc_info())) trace = sys.exc_info()[2] if trace is not None: trace_msg = repr(traceback.format_tb(trace)) log.error("Traceback: %s" % trace_msg)
# TODO: This method doesn't have to be part of the Tool class.
[docs] def parse_error_level(self, err_level): """ Parses error level and returns error level enumeration. If unparsable, returns 'fatal' """ from galaxy.jobs.error_level import StdioErrorLevel return_level = StdioErrorLevel.FATAL try: if err_level: if (re.search("log", err_level, re.IGNORECASE)): return_level = StdioErrorLevel.LOG 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.error("Exception in parse_error_level " + str(sys.exc_info())) trace = sys.exc_info()[2] if trace is not None: trace_msg = repr(traceback.format_tb(trace)) log.error("Traceback: %s" % trace_msg) return return_level
[docs]class XmlPagesSource(PagesSource):
[docs] 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(XmlPagesSource, self).__init__(page_sources)
@property def inputs_defined(self): return self.input_elem is not None
[docs]class XmlPageSource(PageSource):
[docs] def __init__(self, parent_elem): self.parent_elem = parent_elem
[docs] 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
[docs] def parse_input_sources(self): return map(XmlInputSource, self.parent_elem)
[docs]class XmlInputSource(InputSource):
[docs] def __init__(self, input_elem): self.input_elem = input_elem self.input_type = self.input_elem.tag
[docs] def parse_input_type(self): return self.input_type
[docs] def elem(self): return self.input_elem
[docs] def get(self, key, value=None): return self.input_elem.get(key, value)
[docs] def get_bool(self, key, default): return string_as_bool(self.get(key, default))
[docs] def parse_label(self): return xml_text(self.input_elem, "label")
[docs] def parse_help(self): return xml_text(self.input_elem, "help")
[docs] def parse_sanitizer_elem(self): return self.input_elem.find("sanitizer")
[docs] def parse_validator_elems(self): return self.input_elem.findall("validator")
[docs] 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
[docs] def parse_static_options(self): static_options = list() elem = self.input_elem for index, option in enumerate(elem.findall("option")): value = option.get("value") selected = string_as_bool(option.get("selected", False)) static_options.append((option.text or value, value, selected)) return static_options
[docs] def parse_optional(self, default=None): """ Return boolean indicating wheter 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)
[docs] 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
[docs] def parse_nested_inputs_source(self): elem = self.input_elem return XmlPageSource(elem)
[docs] 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)
[docs] 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