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Source code for galaxy.jobs.mapper
import importlib
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.getargspec import getfullargspec
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."
ERROR_MESSAGE_RULE_EXCEPTION = "Encountered an unhandled exception while caching job destination dynamic rule."
[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:
"""
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 = getfullargspec(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 JobMappingConfigurationException(message)
else:
expand_function = self.__find_function_by_tool_id(rule_modules)
if not expand_function:
message = ERROR_MESSAGE_NO_RULE_FUNCTION % destination
raise JobMappingConfigurationException(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 JobMappingConfigurationException("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 self.job_wrapper.tool is None:
raise JobMappingException(
"Can't map job to destination, tool '%s' is unavailable" % self.job_wrapper.get_job().tool_id
)
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):
try:
self.cached_job_destination = self.__determine_job_destination(params, raw_job_destination=raw_job_destination)
except (JobMappingConfigurationException, JobMappingException, JobNotReadyException):
raise
except Exception:
# Other exceptions should not bubble up to the job wrapper since they can occur during the fail() method,
# causing jobs to become permanently stuck in a non-terminal state.
log.exception("Caught unhandled exception while attempting to cache job destination:")
raise JobMappingException(ERROR_MESSAGE_RULE_EXCEPTION)
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)