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Source code for galaxy.tools.parameters.sanitize

Tool Parameter specific sanitizing.
import logging
import string

import galaxy.util

log = logging.getLogger(__name__)

[docs]class ToolParameterSanitizer: """ Handles tool parameter specific sanitizing. >>> from galaxy.util import XML >>> sanitizer = ToolParameterSanitizer.from_element(XML( ... ''' ... <sanitizer invalid_char=""> ... <valid initial="string.ascii_letters"/> ... </sanitizer> ... ''')) >>> sanitizer.sanitize_param(''.join(sorted(c for c in string.printable))) == ''.join(sorted(c for c in string.ascii_letters)) True >>> slash = chr(92) >>> sanitizer = ToolParameterSanitizer.from_element(XML( ... ''' ... <sanitizer> ... <valid initial="none"> ... <add preset="string.printable"/> ... <remove value="&quot;"/> ... <remove value="%s"/> ... </valid> ... <mapping initial="none"> ... <add source="&quot;" target="%s&quot;"/> ... <add source="%s" target="%s%s"/> ... </mapping> ... </sanitizer> ... ''' % (slash, slash, slash, slash, slash))) >>> text = '%s"$rm&#!' % slash >>> [c for c in sanitizer.sanitize_param(text)] == [slash, slash, slash, '"', '$', 'r', 'm', '&', '#', '!'] True """ VALID_PRESET = {"default": (f"{string.ascii_letters + string.digits} -=_.()/+*^,:?!"), "none": ""} MAPPING_PRESET = {"default": galaxy.util.mapped_chars, "none": {}} DEFAULT_INVALID_CHAR = "X" # class methods
[docs] @classmethod def from_element(cls, elem): """Loads the proper filter by the type attribute of elem""" # TODO: Add ability to generically specify a method to use for sanitizing input via specification in tool XML rval = ToolParameterSanitizer() rval._invalid_char = elem.get("invalid_char", cls.DEFAULT_INVALID_CHAR) rval.sanitize = galaxy.util.string_as_bool(elem.get("sanitize", "True")) for valid_elem in elem.findall("valid"): rval._valid_chars = rval.get_valid_by_name(valid_elem.get("initial", "default")) for action_elem in valid_elem: preset = rval.get_valid_by_name(action_elem.get("preset", "none")) valid_value = [val for val in action_elem.get("value", [])] if action_elem.tag.lower() == "add": for val in preset + valid_value: if val not in rval._valid_chars: rval._valid_chars.append(val) elif action_elem.tag.lower() == "remove": for val in preset + valid_value: while val in rval._valid_chars: rval._valid_chars.remove(val) else: log.debug(f"Invalid action tag in valid: {action_elem.tag}") for mapping_elem in elem.findall("mapping"): rval._mapped_chars = rval.get_mapping_by_name(mapping_elem.get("initial", "default")) for action_elem in mapping_elem: map_source = action_elem.get("source", None) map_target = action_elem.get("target", None) preset = rval.get_mapping_by_name(action_elem.get("preset", "none")) if action_elem.tag.lower() == "add": rval._mapped_chars.update(preset) if None not in [map_source, map_target]: rval._mapped_chars[map_source] = map_target elif action_elem.tag.lower() == "remove": for map_key in preset.keys(): if map_key in rval._mapped_chars: del rval._mapped_chars[map_key] if map_source is not None and map_key in rval._mapped_chars: del rval._mapped_chars[map_key] else: log.debug(f"Invalid action tag in mapping: {action_elem.tag}") return rval
[docs] @classmethod def get_valid_by_name(cls, name): rval = [] for split_name in name.split(","): # Remove ';' (if present) and everything after it split_name = split_name.split(";", 1)[0] split_name = split_name.strip() value = [] if split_name.startswith("string."): string_constant = split_name[7:] if string_constant in ("letters", "lowercase", "uppercase"): split_name = f"string.ascii_{string_constant}" try: value = eval(split_name) except NameError as e: log.debug(f"Invalid string preset specified: {e}") elif split_name in cls.VALID_PRESET: value = cls.VALID_PRESET[split_name] else: log.debug(f"Invalid preset name specified: {split_name}") rval.extend([val for val in value if val not in rval]) return rval
[docs] @classmethod def get_mapping_by_name(cls, name): rval = {} for split_name in name.split(","): split_name = split_name.strip() if split_name in cls.MAPPING_PRESET: rval.update(cls.MAPPING_PRESET[split_name]) else: log.debug(f"Invalid preset name specified: {split_name}") return rval
# end class methods
[docs] def __init__(self): self._valid_chars = [] # List of valid characters self._mapped_chars = {} # Replace a char with a any number of characters self._invalid_char = self.DEFAULT_INVALID_CHAR # Replace invalid characters with this character self.sanitize = True # Simply pass back the passed in value
[docs] def restore_text(self, text): """Restores sanitized text""" if self.sanitize: for key, value in self._mapped_chars.items(): text = text.replace(value, key) return text
[docs] def sanitize_text(self, text): """Restricts the characters that are allowed in a text""" if not self.sanitize: return text rval = [] for c in text: if c in self._valid_chars: rval.append(c) elif c in self._mapped_chars: rval.append(self._mapped_chars[c]) else: rval.append(self._invalid_char) return "".join(rval)
[docs] def sanitize_param(self, value): """Clean incoming parameters (strings or lists)""" if not self.sanitize: return value if isinstance(value, str): return self.sanitize_text(value) elif isinstance(value, list): return list(map(self.sanitize_text, value)) else: raise Exception(f"Unknown parameter type ({type(value)}:{value})")