from xml.etree.ElementTree import fromstring
from re import escape, compile
from os.path import join
from galaxy.util import is_in_directory
[docs]class ExpressionValidator(object):
def __init__(self, xml_el):
if type(xml_el) == str:
xml_el = fromstring(xml_el)
self.xml_el = xml_el
[docs] def validate(self, job_directory, string):
regex = "^%s$" % self._expression_to_regex(job_directory, self.xml_el)
match = compile(regex).match(string)
validated = match is not None
if validated:
for group in match.groups():
if not is_in_directory(group, join(job_directory.path, "inputs")) and \
not is_in_directory(group, join(job_directory.path, "outputs")):
validated = False
break
return validated
def _expression_to_regex(self, job_directory, element, default_sep="*spaces*"):
sep = element.get("separate_by", default_sep)
if sep == "*spaces*":
join_on = r" +"
elif sep == "*whitespace*":
join_on = r"\s+"
else:
join_on = escape(sep)
return join_on.join([self._element_to_regex(child, job_directory, join_on) for child in list(element)])
def _element_to_regex(self, element, job_directory, join_on):
tag = element.tag
method_name = "_%s_to_regex" % tag
try:
method = getattr(self, method_name)
except NameError:
raise NameError("Unknown XML validation tag [%s]" % tag)
regex = method(element, job_directory)
if self.__is_true(element.get("single_quote", "false")):
regex = r"'%s'" % regex
if self.__is_true(element.get("double_quote", "false")):
regex = r'"%s"' % regex
min_count = int(element.get("min", "1"))
max_count = int(element.get("max", "1"))
assert max_count > 0
if min_count != 1 or max_count != 1:
single_regex = r"(?:%s)" % regex
first = "%s%s" % (single_regex, "?" if min_count == 0 else "")
rest = r"(?:%s%s){%d,%d}" % (join_on, regex, max(min_count - 1, 0), max_count - 1)
regex = "%s%s" % (first, rest)
return regex
def __is_true(self, str):
return str and str.lower() == "true"
def _literal_to_regex(self, element, job_directory):
return escape(self.__value_or_text(element))
def _regex_to_regex(self, element, job_directory):
return self.__value_or_text(element)
def _parameter_to_regex(self, element, job_directory):
parameter_name = element.get('name')
value_regex = self._expression_to_regex(job_directory, element)
return r"%s(?:=|\s+)%s" % (parameter_name, value_regex)
def _integer_to_regex(self, element, job_directory):
return r"\d+"
def _float_to_regex(self, element, job_directory):
# http://stackoverflow.com/a/9392612
return r"[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?"
def _tool_wrapper_to_regex(self, element, job_directory):
wrapper_name = self.__value_or_text(element, "name")
if not wrapper_name:
raise Exception("Invalid validator - found tool_wrapper element without name.")
path = join(job_directory.path, "tool_files", wrapper_name)
return escape(path)
def _configfile_to_regex(self, element, job_directory):
wrapper_name = self.__value_or_text(element, "name")
path = join(job_directory.path, "configs", wrapper_name)
return escape(path)
def _input_to_regex(self, element, job_directory):
return r"(%s.*)" % escape(join(job_directory.path, "inputs"))
def _output_to_regex(self, element, job_directory):
work_dir_file = element.get("from_work_dir", None)
regex = r"(%s.*)" % escape(join(job_directory.path, "outputs"))
if work_dir_file:
regex = r"%s" % escape(join(job_directory.path, "working", work_dir_file))
return regex
def _group_to_regex(self, element, job_directory):
return self._expression_to_regex(job_directory, element, default_sep="")
def __value_or_text(self, element, attribute="value"):
value = element.get(attribute, None)
if value is None:
value = element.text
return value