)
from galaxy.tool_util.output_checker import DETECTED_JOB_STATE
from galaxy.util import (
DATABASE_MAX_STRING_SIZE,
ExecutionTimer,
in_directory,
ParamsWithSpecs,
shrink_stream_by_size,
unicodify,
)
from galaxy.util.bunch import Bunch
from galaxy.util.logging import get_logger
from galaxy.util.monitors import Monitors
from .state_handler_factory import build_state_handlers
log = get_logger(__name__)
STOP_SIGNAL = object()
JOB_RUNNER_PARAMETER_UNKNOWN_MESSAGE = "Invalid job runner parameter for this plugin: %s"
JOB_RUNNER_PARAMETER_MAP_PROBLEM_MESSAGE = "Job runner parameter '%s' value '%s' could not be converted to the correct type"
JOB_RUNNER_PARAMETER_VALIDATION_FAILED_MESSAGE = "Job runner parameter %s failed validation"
GALAXY_LIB_ADJUST_TEMPLATE = """GALAXY_LIB="%s"; if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"; else PYTHONPATH="$GALAXY_LIB"; fi; export PYTHONPATH; fi;"""
GALAXY_VENV_TEMPLATE = """GALAXY_VIRTUAL_ENV="%s"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi;"""
class RunnerParams(ParamsWithSpecs):
def _param_unknown_error(self, name):
"""
Actions to be run at job completion (or output hda creation, as in the case of
immediate_actions listed below. Currently only used in workflows.
"""
import datetime
import socket
from markupsafe import escape
from galaxy.util import send_mail
from galaxy.util.logging import get_logger
log = get_logger(__name__)
class DefaultJobAction(object):
"""
Base job action.
"""
name = "DefaultJobAction"
verbose_name = "Default Job"
@classmethod
def execute(cls, app, sa_session, action, job, replacement_dict=None):
pass
@classmethod
def get_short_str(cls, pja):
if pja.action_arguments:
return "%s -> %s" % (pja.action_type, escape(pja.action_arguments))
else: