Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.jobs.mapper

import importlib
import inspect
import logging

import galaxy.jobs.rules
from galaxy.jobs import stock_rules
from galaxy.jobs.dynamic_tool_destination import map_tool_to_destination
from galaxy.util.submodules import import_submodules
from .rule_helper import RuleHelper

log = logging.getLogger(__name__)

DYNAMIC_RUNNER_NAME = "dynamic"
DYNAMIC_DESTINATION_ID = "dynamic_legacy_from_url"

ERROR_MESSAGE_NO_RULE_FUNCTION = "Galaxy misconfigured - cannot find dynamic rule function name for destination %s."
ERROR_MESSAGE_RULE_FUNCTION_NOT_FOUND = "Galaxy misconfigured - no rule function named %s found in dynamic rule modules."


[docs]class JobMappingException(Exception):
[docs] def __init__(self, failure_message): self.failure_message = failure_message
[docs]class JobNotReadyException(Exception):
[docs] def __init__(self, job_state=None, message=None): self.job_state = job_state self.message = message
STOCK_RULES = dict( choose_one=stock_rules.choose_one, burst=stock_rules.burst, docker_dispatch=stock_rules.docker_dispatch, dtd=map_tool_to_destination, )
[docs]class JobRunnerMapper(object): """ This class is responsible to managing the mapping of jobs (in the form of job_wrappers) to job runner url strings. """
[docs] def __init__(self, job_wrapper, url_to_destination, job_config): self.job_wrapper = job_wrapper self.url_to_destination = url_to_destination self.job_config = job_config self.rules_module = galaxy.jobs.rules if job_config.dynamic_params is not None: module_name = job_config.dynamic_params['rules_module'] self.rules_module = importlib.import_module(module_name)
def __invoke_expand_function(self, expand_function, destination): function_arg_names = inspect.getargspec(expand_function).args app = self.job_wrapper.app possible_args = { "job_id": self.job_wrapper.job_id, "tool": self.job_wrapper.tool, "tool_id": self.job_wrapper.tool.id, "job_wrapper": self.job_wrapper, "rule_helper": RuleHelper(app), "app": app, "referrer": destination } actual_args = {} # Send through any job_conf.xml defined args to function for destination_param in destination.params.keys(): if destination_param in function_arg_names: actual_args[destination_param] = destination.params[destination_param] # Populate needed args for possible_arg_name in possible_args: if possible_arg_name in function_arg_names: actual_args[possible_arg_name] = possible_args[possible_arg_name] # Don't hit the DB to load the job object if not needed require_db = False for param in ["job", "user", "user_email", "resource_params", "workflow_invocation_uuid"]: if param in function_arg_names: require_db = True break if require_db: job = self.job_wrapper.get_job() user = job.user user_email = user and str(user.email) if "job" in function_arg_names: actual_args["job"] = job if "user" in function_arg_names: actual_args["user"] = user if "user_email" in function_arg_names: actual_args["user_email"] = user_email if "resource_params" in function_arg_names: actual_args["resource_params"] = self.job_wrapper.get_resource_parameters(job) if "workflow_invocation_uuid" in function_arg_names: param_values = job.raw_param_dict() workflow_invocation_uuid = param_values.get("__workflow_invocation_uuid__", None) actual_args["workflow_invocation_uuid"] = workflow_invocation_uuid if "workflow_resource_params" in function_arg_names: param_values = job.raw_param_dict() workflow_resource_params = param_values.get("__workflow_resource_params__", None) actual_args["workflow_resource_params"] = workflow_resource_params return expand_function(**actual_args) def __job_params(self, job): app = self.job_wrapper.app param_values = job.get_param_values(app, ignore_errors=True) return param_values def __convert_url_to_destination(self, url): """ Job runner URLs are deprecated, but dynamic mapper functions may still be returning them. Runners are expected to be able to convert these to destinations. This method calls JobHandlerQueue.DefaultJobDispatcher.url_to_destination, which in turn calls the url_to_destination method for the appropriate runner. """ dest = self.url_to_destination(url) dest['id'] = DYNAMIC_DESTINATION_ID return dest def __find_function_by_tool_id(self, rule_modules): # default look for function with name matching an id of tool, unless one specified for tool_id in self.job_wrapper.tool.all_ids: matching_func = self.__last_matching_function_in_modules(rule_modules, tool_id) if matching_func: return matching_func return None def __get_expand_function(self, destination): """ Returns the function that matches the rule. If a rules_module override is specified, search within that rules_module, or default to the plugin's top level rules_module. """ rules_module_name = destination.params.get('rules_module') rule_modules = self.__get_rule_modules_or_defaults(rules_module_name) expand_function = None expand_function_name = destination.params.get('function') if expand_function_name: expand_function = self.__last_matching_function_in_modules( rule_modules, expand_function_name) if not expand_function: message = ERROR_MESSAGE_RULE_FUNCTION_NOT_FOUND % expand_function_name raise Exception(message) else: expand_function = self.__find_function_by_tool_id(rule_modules) if not expand_function: message = ERROR_MESSAGE_NO_RULE_FUNCTION % destination raise Exception(message) return expand_function def __get_rule_modules_or_defaults(self, rules_module_name): """ Returns the rules under the given rules_module_name or default to returning the rules of the top-level rules module for the plugin """ if rules_module_name: rules_module = importlib.import_module(rules_module_name) else: rules_module = self.rules_module return import_submodules(rules_module, ordered=True) def __last_matching_function_in_modules(self, rule_modules, function_name): # self.rule_modules is sorted in reverse order, so find first # with function for rule_module in rule_modules: if hasattr(rule_module, function_name): return getattr(rule_module, function_name) return None def __handle_dynamic_job_destination(self, destination): expand_type = destination.params.get('type', "python") expand_function = None if expand_type == "python": expand_function = self.__get_expand_function(destination) elif expand_type in STOCK_RULES: expand_function = STOCK_RULES[expand_type] else: raise Exception("Unhandled dynamic job runner type specified - %s" % expand_type) return self.__handle_rule(expand_function, destination) def __handle_rule(self, rule_function, destination): job_destination = self.__invoke_expand_function(rule_function, destination) if not isinstance(job_destination, galaxy.jobs.JobDestination): job_destination_rep = str(job_destination) # Should be either id or url if '://' in job_destination_rep: job_destination = self.__convert_url_to_destination(job_destination_rep) else: job_destination = self.job_config.get_destination(job_destination_rep) return job_destination def __determine_job_destination(self, params, raw_job_destination=None): if raw_job_destination is None: raw_job_destination = self.job_wrapper.tool.get_job_destination(params) if raw_job_destination.runner == DYNAMIC_RUNNER_NAME: job_destination = self.__handle_dynamic_job_destination(raw_job_destination) log.debug("(%s) Mapped job to destination id: %s", self.job_wrapper.job_id, job_destination.id) # Recursively handle chained dynamic destinations if job_destination.runner == DYNAMIC_RUNNER_NAME: return self.__determine_job_destination(params, raw_job_destination=job_destination) else: job_destination = raw_job_destination log.debug("(%s) Mapped job to destination id: %s", self.job_wrapper.job_id, job_destination.id) return job_destination def __cache_job_destination(self, params, raw_job_destination=None): self.cached_job_destination = self.__determine_job_destination( params, raw_job_destination=raw_job_destination) return self.cached_job_destination
[docs] def get_job_destination(self, params): """ cached_job_destination is a public property that is sometimes externally set to short-circuit the mapper, such as during resubmits. get_job_destination will respect that and not run the mapper if so. """ if not hasattr(self, 'cached_job_destination'): return self.__cache_job_destination(params) return self.cached_job_destination
[docs] def cache_job_destination(self, raw_job_destination): """ Force update of cached_job_destination to mapper determined job destination, overwriting any externally set cached_job_destination """ return self.__cache_job_destination( None, raw_job_destination=raw_job_destination)