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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 (
InputSource,
PageSource,
PagesSource,
TestCollectionDef,
TestCollectionOutputDef,
ToolSource,
ToolStdioExitCode,
ToolStdioRegex,
)
from .output_actions import ToolOutputActionGroup
from .output_collection_def import dataset_collector_descriptions_from_elem
from .output_objects import (
ToolOutput,
ToolOutputCollection,
ToolOutputCollectionStructure
)
from .util import (
aggressive_error_checks,
error_on_exit_code,
)
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_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_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_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
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_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 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]class XmlInputSource(InputSource):
[docs] def __init__(self, input_elem):
self.input_elem = input_elem
self.input_type = self.input_elem.tag
[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_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