workflow.py 55.6 KB
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#
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# Copyright (C) 2015 INRA
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# 
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# 
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
# 
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.
#

import inspect
import os
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import re
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import sys
import uuid
import pkgutil
import tempfile
import pickle
import time
import threading
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import types
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import datetime
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import logging
import traceback
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from configparser import ConfigParser, NoOptionError
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from inspect import getcallargs
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from datetime import date as ddate
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import jflow
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import jflow.utils as utils
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from jflow.utils import validate_email
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from pygraph.classes.digraph import digraph
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from jflow.workflows_manager import WorkflowsManager, JFlowConfigReader
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from jflow.utils import get_octet_string_representation, get_nb_octet
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from jflow.parameter import *
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from cctools.util import time_format
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from weaver.script import ABSTRACTIONS
from weaver.script import DATASETS
from weaver.script import FUNCTIONS
from weaver.script import NESTS
from weaver.script import OPTIONS
from weaver.script import STACKS
from weaver.nest import Nest
from weaver.options import Options
from cctools.makeflow import MakeflowLog
from cctools.makeflow.log import Node

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class MINIWorkflow(object):
    
    def __init__(self, id, name, description, status, start_time, end_time, metadata, 
                 component_nameids, compts_status, errors):
        self.id = id
        self.name = name
        self.description = description
        self.status = status
        self.start_time = start_time
        self.end_time = end_time
        self.metadata = metadata
        self.component_nameids = component_nameids
        self.compts_status = compts_status
        self.errors = errors
        
    def get_components_nameid(self):
        return self.component_nameids

    def get_component_status(self, component_nameid):
        return self.compts_status[component_nameid]
    
    def get_errors(self):
        return self.errors
    
    def get_status(self):
        return self.status
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class Workflow(threading.Thread):
    
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    MAKEFLOW_LOG_FILE_NAME = "Makeflow.makeflowlog"
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    DUMP_FILE_NAME = ".workflow.dump"
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    STDERR_FILE_NAME = "wf_stderr.txt"
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    WORKING = ".working"
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    OLD_EXTENSION = ".old"
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    DEFAULT_GROUP = "default"
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    STATUS_STARTED = "started"
    STATUS_COMPLETED = "completed"
    STATUS_FAILED = "failed"
    STATUS_ABORTED = "aborted"
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    STATUS_RESETED = "reseted"
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    INPUTFILE_GRAPH_LABEL = "inputfile"
    INPUTFILES_GRAPH_LABEL = "inputfiles"
    INPUTDIRECTORY_GRAPH_LABEL = "inputdirectory"
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    COMPONENT_GRAPH_LABEL = "component"
    
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    def __init__(self, args={}, id=None, function= "process"):
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        # define as a thread
        threading.Thread.__init__(self)
        self.jflow_config_reader = JFlowConfigReader()
        self.manager = WorkflowsManager()
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        self.components_to_exec = []
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        self.components = []
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        self.makes = {}
        self.globals = {}
        self.options = Options()
        self.status = self.STATUS_STARTED
        self.start_time = None
        self.end_time = None
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        self.__step = None
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        self.stderr = None
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        self.args = args
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        self.dynamic_component_present = False
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        self.__to_address = None
        self.__subject = None
        self.__message = None
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        self.function = function
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        # intruduce --log-verbose to be able to monitor the new version of makeflow >=4.2.2
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        self.engine_arguments = ' --log-verbose '
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        self.component_nameids_is_init = False
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        self.component_nameids = {}
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        self.reseted_components = []
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        # try to parse engine arguments
        try:
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            type, options, limit_submission = self.jflow_config_reader.get_batch()
            if limit_submission : self.engine_arguments += ' -J ' + str(limit_submission)
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            if type: self.engine_arguments += ' -T ' + type
            if options : self.engine_arguments += ' -B "' + options + '"'
        except: self.engine_arguments = None
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        self.id = id
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        self.name = self.get_name()
        self.description = self.get_description()
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        self.__group = self.jflow_config_reader.get_workflow_group(self.__class__.__name__) or self.DEFAULT_GROUP
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        # define the parameters 
        self.params_order = []
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        if self.function != None:
            self.define_parameters(self.function)
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        # add the metadata parameter
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        self.metadata = []
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        if self.id is not None:
            self.directory = self.manager.get_workflow_directory(self.name, self.id)
            if not os.path.isdir(self.directory):
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                os.makedirs(self.directory, 0o751)
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            if self.stderr is None:
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                self.stderr = self._set_stderr()
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            self._serialize()
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        self.internal_components = self._import_internal_components()
        self.external_components = self._import_external_components()
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    def get_workflow_group(self):
        return self.__group
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    def add_input_directory(self, name, help, default=None, required=False, flag=None, 
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                            group="default", display_name=None, get_files_fn=None, add_to=None):
        new_param = InputDirectory(name, help, flag=flag, default=default, required=required, 
                                   group=group, display_name=display_name, get_files_fn=get_files_fn)
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        new_param.linkTrace_nameid = name
        # if this input should be added to a particular parameter
        if add_to:
            try:
                self.__getattribute__(add_to).add_sub_parameter(new_param)
            except: pass
        # otherwise, add it to the class itself
        else:
            self.params_order.append(name)
            self.__setattr__(name, new_param)
    
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    def add_input_file(self, name, help, file_format="any", default=None, type="inputfile", 
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                       required=False, flag=None, group="default", display_name=None, size_limit="0", add_to=None):
        # check if the size provided is correct
        try: int(get_nb_octet(size_limit))
        except: size_limit="0"
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        new_param = InputFile(name, help, flag=flag, file_format=file_format, default=default, 
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                              type=type, required=required, group=group, display_name=display_name, size_limit=size_limit)
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        new_param.linkTrace_nameid = name
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        # if this input should be added to a particular parameter
        if add_to:
            try:
                self.__getattribute__(add_to).add_sub_parameter(new_param)
            except: pass
        # otherwise, add it to the class itself
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        else:
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            self.params_order.append(name)
            self.__setattr__(name, new_param)
            
    def add_input_file_list(self, name, help, file_format="any", default=None, type="inputfile", 
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                            required=False, flag=None, group="default", display_name=None, size_limit="0", add_to=None):
        # check if the size provided is correct
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        if default == None: default = []
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        try: int(get_nb_octet(size_limit))
        except: size_limit="0"
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        if default == None:
            inputs = []
        elif issubclass(default.__class__, list):
            inputs = [IOFile(file, file_format, name, None) for file in default]
        else:
            inputs = [IOFile(default, file_format, name, None)]
        new_param = InputFileList(name, help, flag=flag, file_format=file_format, default=inputs, 
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                                  type=type, required=required, group=group, display_name=display_name, size_limit=size_limit)
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        new_param.linkTrace_nameid = name
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        # if this input should be added to a particular parameter
        if add_to:
            try:
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                self.__getattribute__(add_to).add_sub_parameter(new_param)
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            except: pass
        # otherwise, add it to the class itself
        else:
            self.params_order.append(name)
            self.__setattr__(name, new_param)
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    def add_multiple_parameter(self, name, help, required=False, flag=None, group="default", display_name=None):
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        self.params_order.append(name)
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        new_param = MultiParameter(name, help, flag=flag, required=required, group=group, display_name=display_name)
        self.__setattr__(name, new_param)

    def add_multiple_parameter_list(self, name, help, required=False, flag=None, group="default", display_name=None):
        self.params_order.append(name)
        new_param = MultiParameterList(name, help, flag=flag, required=required, group=group, display_name=display_name)
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        self.__setattr__(name, new_param)
    
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    def add_parameter(self, name, help, default=None, type=str, choices=None, 
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                      required=False, flag=None, group="default", display_name=None, add_to=None):
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        new_param = ParameterFactory.factory(name, help, flag=flag, default=default, type=type, choices=choices, 
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                              required=required, group=group, display_name=display_name)
        # if this input should be added to a particular parameter
        if add_to:
            try:
                self.__getattribute__(add_to).add_sub_parameter(new_param)
            except: pass
        # otherwise, add it to the class itself
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        else:
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            self.params_order.append(name)
            self.__setattr__(name, new_param)
    
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    def add_parameter_list(self, name, help, default=None, type=str, choices=None, 
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                           required=False, flag=None, group="default", display_name=None, add_to=None):
        if default == None: default = []
        new_param = ParameterList(name, help, flag=flag, default=default, type=type, choices=choices, 
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                                  required=required, group=group, display_name=display_name)
        # if this input should be added to a particular parameter
        if add_to:
            try:
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                self.__getattribute__(add_to).add_sub_parameter(new_param)
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            except: pass
        # otherwise, add it to the class itself
        else:
            self.params_order.append(name)
            self.__setattr__(name, new_param)
    
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    def add_exclusion_rule(self, *args2exclude):
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        # first of all, does this parameter exist
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        params2exclude = []
        for arg2exclude in args2exclude:
            try:
                params2exclude.append(self.__getattribute__(arg2exclude))
            except: pass
        # everything is ok, let's go
        if len(params2exclude) == len(args2exclude):
            new_group = "exclude-"+uuid.uuid4().hex[:5]
            for paramsexclude in params2exclude:
                paramsexclude.group = new_group
        # it might be a mutliple param rule
        else:
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            self._log("Exclusion rule cannot be applied within a MultiParameter or a MultiParameterList", raisee=True)
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        # save this for MultiParameter internal exclusion rules, works on command line, not supported on gui
#             for attribute_value in self.__dict__.values():
#                 if issubclass(attribute_value.__class__, MultiParameter) or issubclass(attribute_value.__class__, MultiParameterList):
#                     params2exclude = []
#                     for sub_param in attribute_value.sub_parameters:
#                         if sub_param.name in args2exclude:
#                             params2exclude.append(sub_param)
#                     if len(params2exclude) == len(args2exclude):
#                         new_group = "exclude-"+uuid.uuid4().hex[:5]
#                         flags2exclude = []
#                         for paramsexclude in params2exclude:
#                             paramsexclude.group = new_group
#                             flags2exclude.append(paramsexclude.flag)
#                         attribute_value.type.excludes[new_group] = flags2exclude
#                         break
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    def _prepare_parameter(self, args, parameter, key="name"):
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        new_param = None
        # Retrieve value
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        if parameter.__getattribute__(key) in args:
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            value = args[parameter.__getattribute__(key)]
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        elif parameter.default != None:
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            value = parameter.default
        else:
            value = None
        # Set new parameter
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        if parameter.__class__ in [StrParameter, IntParameter, FloatParameter, BoolParameter, DateParameter]:
            if value == "" and parameter.__class__ in [IntParameter, FloatParameter, BoolParameter, DateParameter] : value = None # from GUI
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            new_param = ParameterFactory.factory( parameter.name, parameter.help, default=value, type=parameter.type, choices=parameter.choices, 
                                                  required=parameter.required, flag=parameter.flag, group=parameter.group, 
                                                  display_name=parameter.display_name )
        elif parameter.__class__ ==  ParameterList:
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            if value == "" : value = [] # from GUI
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            new_param = ParameterList( parameter.name, parameter.help, default=value, type=parameter.type, choices=parameter.choices,
                                       required=parameter.required, flag=parameter.flag, sub_parameters=parameter.sub_parameters,
                                       group=parameter.group, display_name=parameter.display_name )
        elif parameter.__class__ == InputFileList:
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            if value == "" : value = [] # from GUI
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            iovalues = []
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            prepared_files = parameter.prepare(value)
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            for file in prepared_files:
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                iovalues.append(IOFile(file, parameter.file_format, parameter.linkTrace_nameid, None))
            new_param = InputFileList( parameter.name, parameter.help, file_format=parameter.file_format, default=iovalues,
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                                       type=parameter.type, choices=parameter.choices, required=parameter.required, flag=parameter.flag,
                                       group=parameter.group, display_name=parameter.display_name, size_limit=parameter.size_limit )
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            new_param.linkTrace_nameid = parameter.linkTrace_nameid            
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        elif parameter.__class__ == InputFile:
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            if value == "" : value = None # from GUI
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            prepared_file = parameter.prepare(value)
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            new_param = InputFile( parameter.name, parameter.help, file_format=parameter.file_format, default=prepared_file,
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                                   type=parameter.type, choices=parameter.choices, required=parameter.required, flag=parameter.flag, 
                                   group=parameter.group, display_name=parameter.display_name )
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            new_param.linkTrace_nameid = parameter.linkTrace_nameid
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        elif parameter.__class__ == InputDirectory:
            if value == "" : value = None # from GUI
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            prepared_directory = parameter.prepare(value)
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            new_param = InputDirectory( parameter.name, parameter.help, default=prepared_directory, choices=parameter.choices, 
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                                        required=parameter.required, flag=parameter.flag, group=parameter.group, 
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                                        display_name=parameter.display_name, get_files_fn=parameter.get_files_fn)
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            new_param.linkTrace_nameid = parameter.linkTrace_nameid
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        else:
            raise Exception( "Unknown class '" +  parameter.__class__.__name__ + "' for parameter.")
        return new_param

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    def _set_parameters(self, args):
        parameters = self.get_parameters()
        for param in parameters:
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            new_param = None
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            if param.__class__ == MultiParameter:
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                new_param = MultiParameter(param.name, param.help, required=param.required, flag=param.flag, group=param.group, display_name=param.display_name)
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                new_param.sub_parameters = param.sub_parameters
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                if param.name in args:
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                    sub_args = {}
                    for sarg in args[param.name]:
                        sub_args[sarg[0]] = sarg[1]
                    for sub_param in param.sub_parameters:
                        new_sub_parameter = self._prepare_parameter(sub_args, sub_param, "flag")
                        new_param[new_sub_parameter.name] = new_sub_parameter
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            elif param.__class__ == MultiParameterList:
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                new_param = MultiParameterList(param.name, param.help, required=param.required, flag=param.flag, group=param.group, display_name=param.display_name)
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                new_param.sub_parameters = param.sub_parameters
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                if param.name in args:
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                    for idx, sargs in enumerate(args[param.name]):
                        new_multi_param = MultiParameter(param.name + '_' + str(idx), '', required=False, flag=None, group="default", display_name=None)
                        sub_args = {}
                        for sarg in sargs:
                            sub_args[sarg[0]] = sarg[1]
                        for sub_param in param.sub_parameters:
                            new_sub_param = self._prepare_parameter(sub_args, sub_param, "flag")
                            new_multi_param[new_sub_param.name] = new_sub_param
                        new_param.append(new_multi_param)
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            else:
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                new_param = self._prepare_parameter(args, param)
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            self.__setattr__(param.name, new_param)
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    def get_execution_graph(self):
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        gr = digraph()
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        # build a all_nodes table to store all nodes
        all_nodes = {}
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        for ioparameter in list(self.__dict__.values()):
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            if issubclass(ioparameter.__class__, InputFile):
                gr.add_node(ioparameter.name)
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                gr.add_node_attribute(ioparameter.name, self.INPUTFILE_GRAPH_LABEL)
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                gr.add_node_attribute(ioparameter.name, ioparameter.display_name)
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                all_nodes[ioparameter.name] = None
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            elif issubclass(ioparameter.__class__, InputFileList):
                gr.add_node(ioparameter.name)
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                gr.add_node_attribute(ioparameter.name, self.INPUTFILES_GRAPH_LABEL)
                gr.add_node_attribute(ioparameter.name, ioparameter.display_name)
                all_nodes[ioparameter.name] = None
            elif issubclass(ioparameter.__class__, InputDirectory):
                gr.add_node(ioparameter.name)
                gr.add_node_attribute(ioparameter.name, self.INPUTDIRECTORY_GRAPH_LABEL)
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                gr.add_node_attribute(ioparameter.name, ioparameter.display_name)
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                all_nodes[ioparameter.name] = None
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            elif issubclass(ioparameter.__class__, MultiParameter):
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                for subparam in ioparameter.sub_parameters:
                    gr.add_node(subparam.name)
                    all_nodes[subparam.name] = None
                    if issubclass(subparam.__class__, InputFile):
                        gr.add_node_attribute(subparam.name, self.INPUTFILE_GRAPH_LABEL)
                    elif issubclass(subparam.__class__, InputFileList):
                        gr.add_node_attribute(subparam.name, self.INPUTFILES_GRAPH_LABEL)
                    elif issubclass(subparam.__class__, InputDirectory):
                        gr.add_node_attribute(subparam.name, self.INPUTDIRECTORY_GRAPH_LABEL)
                    gr.add_node_attribute(subparam.name, subparam.display_name)
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            elif issubclass(ioparameter.__class__, MultiParameterList):
                for subparam in ioparameter.sub_parameters:
                    gr.add_node(subparam.name)
                    all_nodes[subparam.name] = None                        
                    if issubclass(subparam.__class__, InputDirectory):
                        gr.add_node_attribute(subparam.name, self.INPUTDIRECTORY_GRAPH_LABEL)
                    else:
                        gr.add_node_attribute(subparam.name, self.INPUTFILES_GRAPH_LABEL)
                    gr.add_node_attribute(subparam.name, subparam.display_name)
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        for cpt in self.components:
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            gr.add_node(cpt.get_nameid())
            gr.add_node_attribute(cpt.get_nameid(), self.COMPONENT_GRAPH_LABEL)
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            gr.add_node_attribute(cpt.get_nameid(), cpt.get_nameid())
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            all_nodes[cpt.get_nameid()] = None
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        for cpt in self.components:
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            for ioparameter in list(cpt.__dict__.values()):
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                if issubclass( ioparameter.__class__, InputFile ) or issubclass( ioparameter.__class__, InputFileList) or issubclass( ioparameter.__class__, InputDirectory):
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                    for parent in ioparameter.parent_linkTrace_nameid:
                        try: gr.add_edge((parent, ioparameter.linkTrace_nameid))
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                        except: pass
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                elif issubclass( ioparameter.__class__, InputObject) or issubclass( ioparameter.__class__, InputObjectList):
                    for parent in ioparameter.parent_linkTrace_nameid:
                        try: gr.add_edge((parent, ioparameter.linkTrace_nameid))
                        except: pass
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        # check if all nodes are connected
        for edge in gr.edges():
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            if edge[0] in all_nodes:
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                del all_nodes[edge[0]]
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            if edge[1] in all_nodes:
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                del all_nodes[edge[1]]
        # then remove all unconnected nodes: to delete inputs not defined by the user
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        for orphan_node in list(all_nodes.keys()):
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            gr.del_node(orphan_node)
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        return gr
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    def delete(self):
        if self.get_status() in [self.STATUS_COMPLETED, self.STATUS_FAILED, self.STATUS_ABORTED]:
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            utils.robust_rmtree(self.directory)
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    @staticmethod
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    def config_parser(arg_lines):
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        for arg in arg_lines:
            yield arg
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    @staticmethod
    def get_status_under_text_format(workflow, detailed=False, display_errors=False, html=False):
        if workflow.start_time: start_time = time.asctime(time.localtime(workflow.start_time))
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        else: start_time = "-"
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        if workflow.start_time and workflow.end_time: elapsed_time = str(workflow.end_time-workflow.start_time)
        elif workflow.start_time: elapsed_time = str(time.time()-workflow.start_time)
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        else: elapsed_time = "-"
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        elapsed_time = "-" if elapsed_time == "-" else str(datetime.timedelta(seconds=int(str(elapsed_time).split(".")[0])))
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        if workflow.end_time: end_time = time.asctime(time.localtime(workflow.end_time))
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        else: end_time = "-"
        if detailed:
            # Global
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            title = "Workflow #" + utils.get_nb_string(workflow.id) + " (" + workflow.name + ") is " + \
                    workflow.get_status() + ", time elapsed: " + str(elapsed_time) + " (from " + start_time + \
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                    " to " + end_time + ")"
            worflow_errors = ""
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            error = workflow.get_errors()
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            if error is not None:
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                if html: worflow_errors = "Workflow Error :\n  <span style='color:#ff0000'>" + error["location"] + "\n    " + "\n    ".join(error["msg"]) + "</span>"
                else: worflow_errors = "Workflow Error :\n  \033[91m" + error["location"] + "\n    " + "\n    ".join(error["msg"]) + "\033[0m"
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            # By components
            components_errors = ""
            status = "Components Status :\n"
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            for i, component in enumerate(workflow.get_components_nameid()):
                status_info = workflow.get_component_status(component)
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                try: perc_waiting = (status_info["waiting"]*100.0)/status_info["tasks"]
                except: perc_waiting = 0
                try: perc_running = (status_info["running"]*100.0)/status_info["tasks"]
                except: perc_running = 0
                try: perc_failed = (status_info["failed"]*100.0)/status_info["tasks"]
                except: perc_failed = 0
                try: perc_aborted = (status_info["aborted"]*100.0)/status_info["tasks"]
                except: perc_aborted = 0
                try: perc_completed = (status_info["completed"]*100.0)/status_info["tasks"]
                except: perc_completed = 0
                
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                if status_info["running"] > 0: 
                    if html: running = "<span style='color:#3b3bff'>running:" + str(status_info["running"]) + "</span>"
                    else: running = "\033[94mrunning:" + str(status_info["running"]) + "\033[0m"
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                else: running = "running:" + str(status_info["running"])
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                if status_info["waiting"] > 0: 
                    if html: waiting = "<span style='color:#ffea00'>waiting:" + str(status_info["waiting"]) + "</span>"
                    else: waiting = "\033[93mwaiting:" + str(status_info["waiting"]) + "\033[0m"
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                else: waiting = "waiting:" + str(status_info["waiting"])            
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                if status_info["failed"] > 0: 
                    if html: failed = "<span style='color:#ff0000'>failed:" + str(status_info["failed"]) + "</span>"
                    else: failed = "\033[91mfailed:" + str(status_info["failed"]) + "\033[0m"
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                else: failed = "failed:" + str(status_info["failed"])
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                if status_info["aborted"] > 0: 
                    if html: aborted = "<span style='color:#ff01ba'>aborted:" + str(status_info["aborted"]) + "</span>"
                    else: aborted = "\033[95maborted:" + str(status_info["aborted"]) + "\033[0m"
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                else: aborted = "aborted:" + str(status_info["aborted"])
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                if status_info["completed"] == status_info["tasks"] and status_info["completed"] > 0: 
                    if html: completed = "<span style='color:#14ac00'>completed:" + str(status_info["completed"]) + "</span>"
                    else: completed = "\033[92mcompleted:" + str(status_info["completed"]) + "\033[0m"
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                else: completed = "completed:" + str(status_info["completed"])
                
                if display_errors and len(status_info["failed_commands"]) > 0:
                    if components_errors == "" :
                        components_errors = "Failed Commands :\n"  
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                    components_errors += "  - " + component + " :\n    " + "\n    ".join(status_info["failed_commands"]) + "\n"
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                status += "  - " + component + ", time elapsed " + time_format(status_info["time"]) + \
                    " (total:" + str(status_info["tasks"]) + ", " + waiting + ", " + running + ", " + failed + \
                    ", " + aborted + ", " + completed + ")"
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                if i<len(workflow.get_components_nameid())-1: status += "\n"
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            # Format str
            pretty_str = title
            pretty_str += ("\n" + worflow_errors) if worflow_errors != "" else ""
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            if len(workflow.get_components_nameid()) > 0:
                pretty_str += ("\n" + status) if status != "" else ""
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                pretty_str += ("\n" + components_errors[:-1]) if components_errors != "" else ""
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            if html: return pretty_str.replace("\n", "<br />")
            else: return pretty_str
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        else:
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            pretty_str = utils.get_nb_string(workflow.id) + "\t" + workflow.name + "\t"
            if workflow.get_status() == Workflow.STATUS_STARTED:
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                pretty_str += "\033[94m"
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            elif workflow.get_status() == Workflow.STATUS_COMPLETED:
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                pretty_str += "\033[92m"
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            elif workflow.get_status() == Workflow.STATUS_FAILED:
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                pretty_str += "\033[91m"
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            elif workflow.get_status() == Workflow.STATUS_ABORTED:
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                pretty_str += "\033[91m"
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            elif workflow.get_status() == Workflow.STATUS_RESETED:
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                pretty_str += "\033[3m"
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            pretty_str += workflow.get_status() + "\033[0m"
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            pretty_str += "\t" + elapsed_time + "\t" + start_time + "\t" + end_time
            return pretty_str
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    def get_errors(self):
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        if os.path.isfile(self.stderr):
            error = {
                "title"     : "",
                "msg"       : list(),
                "traceback" : list()
            }
            line_idx = 0
            FH_stderr = open( self.stderr )
            lines = FH_stderr.readlines()
            while line_idx < len(lines):
                if lines[line_idx].strip().startswith("##"):
                    error["title"]     = lines[line_idx].rstrip()
                    error["msg"]       = list()
                    error["traceback"] = list()
                    # skip all lines before the traceback
                    while not lines[line_idx].startswith("Traceback"):
                        line_idx += 1
                    # skip : "Traceback (most recent call last):"
                    line_idx += 1    
                    while lines[line_idx] != lines[line_idx].lstrip():
                        error["traceback"].append({ 
                                                   "location" : lines[line_idx].strip(),
                                                   "line"     : lines[line_idx].strip()
                        })
                        line_idx += 2
                    # Error message
                    while line_idx < len(lines) and not lines[line_idx].strip().startswith("##"):
                        try:
                            error["msg"].append( lines[line_idx].strip().split(":", 1)[1][1:] )
                        except:
                            error["msg"].append( lines[line_idx].strip() )
                        line_idx += 1
                    line_idx -= 1
                line_idx += 1
            FH_stderr.close()
            last_stack_location = ""
            if len(error["traceback"]) > 0:
                last_stack_location = error["traceback"][-1]["location"].strip()
                self.status = self.STATUS_FAILED
                return { "msg" : error["msg"], "location" : last_stack_location }
            else:
                return None
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        else:
            return None
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    def get_outputs_per_components(self):
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        outputs_files = {}
        for current_components in self.components:
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            #status = self.get_component_status(current_components.get_nameid())
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            outputs_files[current_components.get_nameid()] = current_components.get_output_files()
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            #outputs_files["0"] = status["completed"]
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        return outputs_files
    
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    def __setstate__(self, state):
        self.__dict__ = state.copy()
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        self.external_components = self._import_external_components()
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        threading.Thread.__init__(self, name=self.name)
        
    def __getstate__(self):
        """
        Threading uses Lock Object, do not consider these objects when serializing a workflow
        """
        odict = self.__dict__.copy()
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        del odict['_started']
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        if '_tstate_lock' in odict: # python 3.4
            del odict['_tstate_lock']
        else: # python 3.2
            del odict['_block']
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        del odict['_stderr']
        if 'external_components' in odict:
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            del odict['external_components']
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        return odict
    
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    def set_to_address(self, to_address):
        self.__to_address = to_address

    def set_subject(self, subject):
        self.__subject = subject

    def set_message(self, message):
        self.__message = message
    
    def _send_email(self):
        
        import smtplib
        from email.mime.text import MIMEText        
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        smtps, smtpp, froma, fromp, toa, subject, message = self.jflow_config_reader.get_email_options()
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        if self.__to_address: toa = self.__to_address
        if self.__subject: subject = self.__subject
        if self.__message: message = self.__message
        
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        if smtps and smtpp and froma and fromp:
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            if not toa: toa = froma
            if validate_email(froma) and validate_email(toa):
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                try:
                    # Open a plain text file for reading.  For this example, assume that
                    # the text file contains only ASCII characters.
                    # Create a text/plain message
                    if not message:
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                        message = Workflow.get_status_under_text_format(self, True, True, True)
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                    msg = MIMEText(message, 'html')
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                    me = froma
                    you = toa
                    if not subject: subject = "JFlow - Workflow #" + str(self.id) + " is " + self.status
                    msg['Subject'] = subject
                    msg['From'] = me
                    msg['To'] = you
                    # Send the message via our own SMTP server, but don't include the
                    # envelope header.
                    s = smtplib.SMTP(smtps, smtpp)
                    s.ehlo()
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                    # if the SMTP server does not provides TLS or identification
                    try:
                        s.starttls()
                        s.login(me, fromp)
                    except smtplib.SMTPHeloError:
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                        self._log("The server didn't reply properly to the HELO greeting.", level="debug", traceback=traceback.format_exc(chain=False))
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                    except smtplib.SMTPAuthenticationError:
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                        self._log("The server didn't accept the username/password combination.", level="debug", traceback=traceback.format_exc(chain=False))
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                    except smtplib.SMTPException:
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                        self._log("No suitable authentication method was found, or the server does not support the STARTTLS extension.", level="debug", traceback=traceback.format_exc(chain=False))
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                    except RuntimeError:
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                        self._log("SSL/TLS support is not available to your Python interpreter.", level="debug", traceback=traceback.format_exc(chain=False))
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                    except:
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                        self._log("Unhandled error when sending mail.", level="debug", traceback=traceback.format_exc(chain=False))
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                    finally:
                        s.sendmail(me, [you], msg.as_string())
                        s.close()
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                except:
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                    self._log("Impossible to connect to smtp server '" + smtps + "'", level="debug", traceback=traceback.format_exc(chain=False))
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    def get_parameters_per_groups(self):
        name = self.get_name()
        description = self.get_description()
        parameters = self.get_parameters()
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        pgparameters, parameters_order = {}, []
        for param in parameters:
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            if param.group not in parameters_order: parameters_order.append(param.group)
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            if param.group in pgparameters:
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                pgparameters[param.group].append(param)
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            else:
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                pgparameters[param.group] = [param]
        return [pgparameters, parameters_order]
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    def get_parameters(self):
        params = []
        for param in self.params_order:
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            for attribute_value in list(self.__dict__.values()):
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                if (issubclass(attribute_value.__class__, AbstractParameter)) and param == attribute_value.name:
                    params.append(attribute_value)
        return params
    
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    def get_exec_path(self, software):
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        exec_path = self.jflow_config_reader.get_exec(software)
        if exec_path is None and os.path.isfile(os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "../bin", software)):
            exec_path = os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "../bin", software)
        elif exec_path is None and os.path.isfile(os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "bin", software)):
            exec_path = os.path.join(os.path.dirname(inspect.getfile(self.__class__)), "bin", software)
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        elif exec_path is None and utils.which(software) == None:
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            raise Exception("'" + software + "' path connot be retrieved either in the PATH and in the application.properties file!")
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        elif exec_path is None and utils.which(software) != None: 
            exec_path = software
        elif exec_path != None and not os.path.isfile(exec_path):
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            raise Exception("'" + exec_path + "' set for '" + software + "' does not exists, please provide a valid path!")
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        return exec_path
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    def add_component(self, component_name, args=[], kwargs={}, component_prefix="default"):
        # first build and check if this component is OK
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        if component_name in self.internal_components or component_name in self.external_components:
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            if component_name in self.internal_components:
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                my_pckge = __import__(self.internal_components[component_name], globals(), locals(), [component_name])
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                # build the object and define required field
                cmpt_object = getattr(my_pckge, component_name)()
                cmpt_object.output_directory = self.get_component_output_directory(component_name, component_prefix)
                cmpt_object.prefix = component_prefix
                if kwargs: cmpt_object.define_parameters(**kwargs)
                else: cmpt_object.define_parameters(*args)
            # external components
            else :
                cmpt_object = self.external_components[component_name]()
                cmpt_object.output_directory = self.get_component_output_directory(component_name, component_prefix)
                cmpt_object.prefix = component_prefix
                # can't use positional arguments with external components
                cmpt_object.define_parameters(**kwargs)
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            # there is a dynamic component
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            if cmpt_object.is_dynamic():
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                self.dynamic_component_present = True
                # if already init, add the component to the list and check if weaver should be executed
                if self.component_nameids_is_init:
                    # add the component
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                    self.components_to_exec.append(cmpt_object)
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                    self.components.append(cmpt_object)
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                    self._execute_weaver()
                    # update outputs
                    for output in cmpt_object.get_dynamic_outputs():
                        output.update()
                else:
                    if self._component_is_duplicated(cmpt_object):
                        raise ValueError("Component " + cmpt_object.__class__.__name__ + " with prefix " + 
                                            cmpt_object.prefix + " already exist in this pipeline!")
                    self.component_nameids[cmpt_object.get_nameid()] = None
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                    self.components_to_exec = []
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                    self.components = []
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            else:
                if self.component_nameids_is_init:
                    # add the component
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                    self.components_to_exec.append(cmpt_object)
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                    self.components.append(cmpt_object)
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                elif not self.component_nameids_is_init and not self.dynamic_component_present:
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                    if self._component_is_duplicated(cmpt_object):
                        raise ValueError("Component " + cmpt_object.__class__.__name__ + " with prefix " + 
                                            cmpt_object.prefix + " already exist in this pipeline!")
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                    self.components_to_exec.append(cmpt_object)
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                    self.components.append(cmpt_object)
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                else:
                    if self._component_is_duplicated(cmpt_object):
                        raise ValueError("Component " + cmpt_object.__class__.__name__ + " with prefix " + 
                                            cmpt_object.prefix + " already exist in this pipeline!")
                    self.component_nameids[cmpt_object.get_nameid()] = None

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            return cmpt_object
        else:
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            raise ImportError(component_name + " component cannot be loaded, available components are: {0}".format(
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                                           ", ".join(list(self.internal_components.keys()) + list(self.external_components.keys()))))
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    def pre_process(self):
        pass
    
    def process(self):
        """ 
        Run the workflow, has to be implemented by subclasses
        """
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        raise NotImplementedError( "Workflow.process() must be implemented in " + self.__class__.__name__ )
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    def get_name(self):
        """ 
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        Return the workflow name.
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        """
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        return self.__class__.__name__.lower()
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    def get_description(self):
        """ 
        Return the workflow description, has to be implemented by subclasses
        """
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        raise NotImplementedError( "Workflow.get_description() must be implemented in " + self.__class__.__name__ )
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    def define_parameters(self, function="process"):
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        """ 
        Define the workflow parameters, has to be implemented by subclasses
        """
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        raise NotImplementedError( "Workflow.define_parameters() must be implemented in " + self.__class__.__name__ )
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    def post_process(self):
        pass
    
    def get_temporary_file(self, suffix=".txt"):
        tempfile_name = os.path.basename(tempfile.NamedTemporaryFile(suffix=suffix).name)
        return os.path.join(self.jflow_config_reader.get_tmp_directory(), tempfile_name)

    def get_component_output_directory(self, component_name, component_prefix):
        return os.path.join(self.directory, component_name + "_" + component_prefix)
    
    def get_components_nameid(self):
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        return list(self.component_nameids.keys())
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    def wf_execution_wrapper(self):
        getattr(self, self.function)()
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    def run(self):
        """
        Only require for Threading
        """
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        try:
            # if this is the first time the workflow run
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            if self.__step == None :
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                self.start_time = time.time()
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                self.__step = 0
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                self.status = self.STATUS_STARTED
                self.end_time = None
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                # if some args are provided, let's fill the parameters
                self._set_parameters(self.args)
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                self._serialize()
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            # if pre_processing has not been done yet
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            if self.__step == 0:
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                self.pre_process()
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                self.__step = 1
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                self._serialize()
            # if collecting components and running workflow has not been done yet
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            if self.__step == 1:
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                try:
                    self.reseted_components = []
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                    self.components = []
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                    self.status = self.STATUS_STARTED
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                    self.wf_execution_wrapper()
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                except SystemExit: 
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                    self.status = self.STATUS_FAILED
                    self.end_time = time.time()
                    self._serialize()
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                    self._send_email()
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                    raise
                self.component_nameids_is_init = True
                if self.dynamic_component_present:
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                    self.__step = 2
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                else:
                    self._execute_weaver()
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                    self.__step = 3
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                self._serialize() 
            # if the workflow was a dynamic one
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            if self.__step == 2:
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                try:
                    self.reseted_components = []
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                    self.components = []
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                    self.status = self.STATUS_STARTED
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                    self.wf_execution_wrapper()
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                except SystemExit: 
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                    self.status = self.STATUS_FAILED
                    self.end_time = time.time()
                    self._serialize()
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                    self._send_email()
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                    raise
                if len(self.components_to_exec) > 0:
                    self._execute_weaver()
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                self.__step = 3
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                self._serialize()
            # if post processing has ne been done yet
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            if self.__step == 3:
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                self.post_process()
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                if self.status == self.STATUS_STARTED: self.status = self.STATUS_COMPLETED
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                self.end_time = time.time()
                self._serialize()
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                self._send_email()
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        except Exception as e:
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            self._log(str(e), traceback=traceback.format_exc(chain=False))
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            utils.display_error_message(str(e))
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    def _update_status_from_log(self):
        # first update the status from weaver folders
        # TODO update self.end_time
        try:
            working_directory = os.path.join(self.directory, self.WORKING)
            make_states = []
            for wdir in os.listdir(working_directory):
                log_path = os.path.join(working_directory, wdir, self.MAKEFLOW_LOG_FILE_NAME)
                log = MakeflowLog(log_path)
                log.parse()