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Source code for galaxy.tools.toolbox.filters

import logging
import sys

from copy import deepcopy

from galaxy.util import listify

log = logging.getLogger(__name__)


[docs]class FilterFactory(object): """ An instance of this class is responsible for filtering the list of tools presented to a given user in a given context. """
[docs] def __init__(self, toolbox): self.toolbox = toolbox # Prepopulate dict containing filters that are always checked, # other filters that get checked depending on context (e.g. coming from # trackster or no user found are added in build filters). self.default_filters = dict(tool=[_not_hidden, _handle_authorization], section=[], label=[]) # Add dynamic filters to these default filters. config = toolbox.app.config self.__base_modules = listify(getattr(config, "toolbox_filter_base_modules", "galaxy.tools.filters")) self.__init_filters("tool", getattr(config, "tool_filters", ""), self.default_filters) self.__init_filters("section", getattr(config, "tool_section_filters", ""), self.default_filters) self.__init_filters("label", getattr(config, "tool_label_filters", ""), self.default_filters)
[docs] def build_filters(self, trans, **kwds): """ Build list of filters to check tools against given current context. """ filters = deepcopy(self.default_filters) if trans.user: for name, value in trans.user.preferences.items(): if value.strip(): user_filters = listify(value, do_strip=True) category = '' if name == 'toolbox_tool_filters': category = "tool" elif name == 'toolbox_section_filters': category = "section" elif name == 'toolbox_label_filters': category = "label" if category: validate = getattr(trans.app.config, 'user_%s_filters' % category, []) self.__init_filters(category, user_filters, filters, validate=validate) else: if kwds.get("trackster", False): filters["tool"].append(_has_trackster_conf) return filters
def __init_filters(self, key, filters, toolbox_filters, validate=None): for filter in filters: if validate is None or filter in validate or filter in self.default_filters: filter_function = self.build_filter_function(filter) toolbox_filters[key].append(filter_function) else: log.warning("Refusing to load %s filter '%s' which is not defined in config", key, filter) return toolbox_filters
[docs] def build_filter_function(self, filter_name): """Obtain python function (importing a submodule if needed) corresponding to filter_name. """ if ":" in filter_name: # Should be a submodule of filters (e.g. examples:restrict_development_tools) (module_name, function_name) = filter_name.rsplit(":", 1) function = self._import_filter(module_name, function_name) else: # No module found, just load a function from this file or # one that has be explicitly imported. function = getattr(globals(), filter_name.strip()) return function
def _import_filter(self, module_name, function_name): function_name = function_name.strip() for base_module in self.__base_modules: full_module_name = "%s.%s" % (base_module, module_name.strip()) try: __import__(full_module_name) except ImportError: # log.debug("Failed to load module.", exc_info=True) continue module = sys.modules[full_module_name] if hasattr(module, function_name): return getattr(module, function_name) raise Exception("Failed to find filter %s.%s" % (module_name, function_name))
# Stock Filter Functions def _not_hidden(context, tool): return not tool.hidden def _handle_authorization(context, tool): user = context.trans.user if tool.require_login and not user: return False if not tool.allow_user_access(user, attempting_access=False): return False return True def _has_trackster_conf(context, tool): return tool.trackster_conf