workflow.py 50.5 KB
Newer Older
Jerome Mariette's avatar
Jerome Mariette committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
#
# Copyright (C) 2012 INRA
# 
# 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
20
import re
Jerome Mariette's avatar
Jerome Mariette committed
21
22
23
24
25
26
27
import sys
import uuid
import pkgutil
import tempfile
import pickle
import time
import threading
Jerome Mariette's avatar
Jerome Mariette committed
28
import types
Jerome Mariette's avatar
Jerome Mariette committed
29
import logging
Jerome Mariette's avatar
Jerome Mariette committed
30
import datetime
Jerome Mariette's avatar
Jerome Mariette committed
31
import shutil
Jerome Mariette's avatar
Jerome Mariette committed
32

33
from logging import FileHandler
Jerome Mariette's avatar
Jerome Mariette committed
34
from ConfigParser import ConfigParser, NoOptionError
Jerome Mariette's avatar
Jerome Mariette committed
35
from inspect import getcallargs
Jerome Mariette's avatar
Jerome Mariette committed
36

Jerome Mariette's avatar
Jerome Mariette committed
37
import jflow
Jerome Mariette's avatar
Jerome Mariette committed
38
import jflow.utils as utils
39
from jflow.utils import validate_email
40
from pygraph.classes.digraph import digraph
Jerome Mariette's avatar
Jerome Mariette committed
41
from jflow.workflows_manager import WorkflowsManager, JFlowConfigReader
42
from jflow.utils import get_octet_string_representation, get_nb_octet
43
from jflow.parameter import *
44
from cctools.util import time_format
Jerome Mariette's avatar
Jerome Mariette committed
45
46
47
48
49
50
51
52
53
54
55
56

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

Jerome Mariette's avatar
Jerome Mariette committed
57

58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
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
84

85
86
class Workflow(threading.Thread):
    
Jerome Mariette's avatar
Jerome Mariette committed
87
88
89

    PROPERTIES_FILE_NAME = "workflow.properties"
    MAKEFLOW_LOG_FILE_NAME = "Makeflow.makeflowlog"
90
    DUMP_FILE_NAME = ".workflow.dump"
91
    STDERR_FILE_NAME = "wf_stderr.txt"
Jerome Mariette's avatar
Jerome Mariette committed
92
    WORKING = ".working"
93
    OLD_EXTENSION = ".old"
94
    
Jerome Mariette's avatar
Jerome Mariette committed
95
96
97
98
    STATUS_STARTED = "started"
    STATUS_COMPLETED = "completed"
    STATUS_FAILED = "failed"
    STATUS_ABORTED = "aborted"
Jerome Mariette's avatar
Jerome Mariette committed
99
    STATUS_RESETED = "reseted"
100
    
Jerome Mariette's avatar
Jerome Mariette committed
101
102
103
    INPUTFILE_GRAPH_LABEL = "inputfile"
    INPUTFILES_GRAPH_LABEL = "inputfiles"
    INPUTDIRECTORY_GRAPH_LABEL = "inputdirectory"
104
105
    COMPONENT_GRAPH_LABEL = "component"
    
106
    
107
    def __init__(self, args={}, id=None, function= "process"):
Jerome Mariette's avatar
Jerome Mariette committed
108
109
110
111
        # define as a thread
        threading.Thread.__init__(self)
        self.jflow_config_reader = JFlowConfigReader()
        self.manager = WorkflowsManager()
112
        self.components_to_exec = []
113
        self.components = []
Jerome Mariette's avatar
Jerome Mariette committed
114
115
116
117
118
119
        self.makes = {}
        self.globals = {}
        self.options = Options()
        self.status = self.STATUS_STARTED
        self.start_time = None
        self.end_time = None
120
        self.step = None
Frédéric Escudié's avatar
Frédéric Escudié committed
121
        self.stderr = None
Jerome Mariette's avatar
Jerome Mariette committed
122
        self.args = args
123
        self.dynamic_component_present = False
124
125
126
        self.__to_address = None
        self.__subject = None
        self.__message = None
127
        self.function = function
128
        # intruduce --log-verbose to be able to monitor the new version of makeflow >=4.2.2
Jerome Mariette's avatar
Jerome Mariette committed
129
        self.engine_arguments = ' --log-verbose '
130
        self.component_nameids_is_init = False
Jerome Mariette's avatar
Jerome Mariette committed
131
        self.component_nameids = {}
132
        self.reseted_components = []
Jerome Mariette's avatar
Jerome Mariette committed
133
134
        # try to parse engine arguments
        try:
135
136
            type, options, limit_submission = self.jflow_config_reader.get_batch()
            if limit_submission : self.engine_arguments += ' -J ' + str(limit_submission)
Jerome Mariette's avatar
Jerome Mariette committed
137
138
139
            if type: self.engine_arguments += ' -T ' + type
            if options : self.engine_arguments += ' -B "' + options + '"'
        except: self.engine_arguments = None
140

Jerome Mariette's avatar
Jerome Mariette committed
141
        self.id = id
142
143
144
145
146
        self.name = self.get_name()
        self.description = self.get_description()
        
        # define the parameters 
        self.params_order = []
147
        self.define_parameters(self.function)
148
        # add the metadata parameter
149
        self.metadata = []
Jerome Mariette's avatar
Jerome Mariette committed
150
        
Jerome Mariette's avatar
Jerome Mariette committed
151
152
153
154
        if self.id is not None:
            self.directory = self.manager.get_workflow_directory(self.name, self.id)
            if not os.path.isdir(self.directory):
                os.makedirs(self.directory, 0751)
Frédéric Escudié's avatar
Frédéric Escudié committed
155
            if self.stderr is None:
156
                self.stderr = self._set_stderr()
Jerome Mariette's avatar
Jerome Mariette committed
157
            self._serialize()
Jerome Mariette's avatar
Jerome Mariette committed
158
            
Ibouniyamine Nabihoudine's avatar
Ibouniyamine Nabihoudine committed
159
        self.comp_pckg = self._import_components()
160
    
Jerome Mariette's avatar
Jerome Mariette committed
161
    def add_input_directory(self, name, help, default=None, required=False, flag=None, 
162
163
164
                            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)
Jerome Mariette's avatar
Jerome Mariette committed
165
166
167
168
169
170
171
172
173
174
175
        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)
    
176
    def add_input_file(self, name, help, file_format="any", default=None, type="inputfile", 
177
178
179
180
                       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"
181
        new_param = InputFile(name, help, flag=flag, file_format=file_format, default=default, 
182
                              type=type, required=required, group=group, display_name=display_name, size_limit=size_limit)
Frédéric Escudié's avatar
Frédéric Escudié committed
183
        new_param.linkTrace_nameid = name
184
185
186
187
188
189
        # 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
190
        else:
191
192
193
194
            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", 
195
196
                            required=False, flag=None, group="default", display_name=None, size_limit="0", add_to=None):
        # check if the size provided is correct
197
        if default == None: default = []
198
199
        try: int(get_nb_octet(size_limit))
        except: size_limit="0"
200
201
202
203
204
205
206
        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, 
207
                                  type=type, required=required, group=group, display_name=display_name, size_limit=size_limit)
Frédéric Escudié's avatar
Frédéric Escudié committed
208
        new_param.linkTrace_nameid = name
209
210
211
        # if this input should be added to a particular parameter
        if add_to:
            try:
Jerome Mariette's avatar
help ok    
Jerome Mariette committed
212
                self.__getattribute__(add_to).add_sub_parameter(new_param)
213
214
215
216
217
            except: pass
        # otherwise, add it to the class itself
        else:
            self.params_order.append(name)
            self.__setattr__(name, new_param)
218
219
            
    def add_multiple_parameter(self, name, help, required=False, flag=None, group="default", display_name=None):
220
        self.params_order.append(name)
221
222
223
224
225
226
        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)
227
228
        self.__setattr__(name, new_param)
    
229
230
    def add_parameter(self, name, help, default=None, type=types.StringType, choices=None, 
                      required=False, flag=None, group="default", display_name=None, add_to=None):
231
        new_param = ParameterFactory.factory(name, help, flag=flag, default=default, type=type, choices=choices, 
232
233
234
235
236
237
238
                              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
239
        else:
240
241
242
243
244
245
246
            self.params_order.append(name)
            self.__setattr__(name, new_param)
    
    def add_parameter_list(self, name, help, default=None, type=types.StringType, choices=None, 
                           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, 
247
248
249
250
                                  required=required, group=group, display_name=display_name)
        # if this input should be added to a particular parameter
        if add_to:
            try:
Jerome Mariette's avatar
help ok    
Jerome Mariette committed
251
                self.__getattribute__(add_to).add_sub_parameter(new_param)
252
253
254
255
256
257
            except: pass
        # otherwise, add it to the class itself
        else:
            self.params_order.append(name)
            self.__setattr__(name, new_param)
    
Jerome Mariette's avatar
Jerome Mariette committed
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
    def add_exclusion_rule(self, *args2exclude):
        # first of all, are this parameter exist
        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:
            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
286

Frédéric Escudié's avatar
Frédéric Escudié committed
287
    def _prepare_parameter(self, args, parameter, key="name"):
288
289
        new_param = None
        # Retrieve value
Frédéric Escudié's avatar
Frédéric Escudié committed
290
291
        if args.has_key(parameter.__getattribute__(key)):
            value = args[parameter.__getattribute__(key)]
292
293
294
295
296
        elif parameter != None:
            value = parameter.default
        else:
            value = None
        # Set new parameter
Frédéric Escudié's avatar
Frédéric Escudié committed
297
298
        if parameter.__class__ in [StrParameter, IntParameter, FloatParameter, BoolParameter, DateParameter]:
            if value == "" and parameter.__class__ in [IntParameter, FloatParameter, BoolParameter, DateParameter] : value = None # from GUI
299
300
301
302
            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:
303
            if value == "" : value = [] # from GUI
304
305
306
307
            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:
308
            if value == "" : value = [] # from GUI
309
            iovalues = []
Ibouniyamine Nabihoudine's avatar
Ibouniyamine Nabihoudine committed
310
            prepared_files = parameter.prepare(value)
311
            for file in prepared_files:
312
313
                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,
314
315
                                       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 )
316
            new_param.linkTrace_nameid = parameter.linkTrace_nameid            
317
        elif parameter.__class__ == InputFile:
318
            if value == "" : value = None # from GUI
Ibouniyamine Nabihoudine's avatar
Ibouniyamine Nabihoudine committed
319
            prepared_file = parameter.prepare(value)
320
            new_param = InputFile( parameter.name, parameter.help, file_format=parameter.file_format, default=prepared_file,
321
322
                                   type=parameter.type, choices=parameter.choices, required=parameter.required, flag=parameter.flag, 
                                   group=parameter.group, display_name=parameter.display_name )
323
            new_param.linkTrace_nameid = parameter.linkTrace_nameid
Jerome Mariette's avatar
Jerome Mariette committed
324
325
        elif parameter.__class__ == InputDirectory:
            if value == "" : value = None # from GUI
Ibouniyamine Nabihoudine's avatar
Ibouniyamine Nabihoudine committed
326
            prepared_directory = parameter.prepare(value)
327
            new_param = InputDirectory( parameter.name, parameter.help, default=prepared_directory, choices=parameter.choices, 
Jerome Mariette's avatar
Jerome Mariette committed
328
                                        required=parameter.required, flag=parameter.flag, group=parameter.group, 
329
                                        display_name=parameter.display_name, get_files_fn=parameter.get_files_fn)
Jerome Mariette's avatar
Jerome Mariette committed
330
            new_param.linkTrace_nameid = parameter.linkTrace_nameid
331
332
333
334
        else:
            raise Exception( "Unknown class '" +  parameter.__class__.__name__ + "' for parameter.")
        return new_param

335
336
337
    def _set_parameters(self, args):
        parameters = self.get_parameters()
        for param in parameters:
338
            new_param = None
339
            if param.__class__ == MultiParameter:
340
                new_param = MultiParameter(param.name, param.help, required=param.required, flag=param.flag, group=param.group, display_name=param.display_name)
341
                new_param.sub_parameters = param.sub_parameters
342
343
344
345
346
347
348
                if args[param.name]:
                    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
349
            elif param.__class__ == MultiParameterList:
350
                new_param = MultiParameterList(param.name, param.help, required=param.required, flag=param.flag, group=param.group, display_name=param.display_name)
351
                new_param.sub_parameters = param.sub_parameters
352
353
354
355
356
357
358
359
360
361
                if args.has_key(param.name):
                    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)
362
            else:
363
                new_param = self._prepare_parameter(args, param)
364
            self.__setattr__(param.name, new_param)
Frédéric Escudié's avatar
Frédéric Escudié committed
365

Jerome Mariette's avatar
Jerome Mariette committed
366
    def get_execution_graph(self):
367
        gr = digraph()
368
369
        # build a all_nodes table to store all nodes
        all_nodes = {}
370
371
372
        for ioparameter in self.__dict__.values():
            if issubclass(ioparameter.__class__, InputFile):
                gr.add_node(ioparameter.name)
Jerome Mariette's avatar
Jerome Mariette committed
373
                gr.add_node_attribute(ioparameter.name, self.INPUTFILE_GRAPH_LABEL)
374
                gr.add_node_attribute(ioparameter.name, ioparameter.display_name)
375
                all_nodes[ioparameter.name] = None
376
377
            elif issubclass(ioparameter.__class__, InputFileList):
                gr.add_node(ioparameter.name)
Jerome Mariette's avatar
Jerome Mariette committed
378
379
380
381
382
383
                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)
384
                gr.add_node_attribute(ioparameter.name, ioparameter.display_name)
385
                all_nodes[ioparameter.name] = None
Philippe Bardou's avatar
Philippe Bardou committed
386
            elif issubclass(ioparameter.__class__, MultiParameter):
Jerome Mariette's avatar
Jerome Mariette committed
387
388
389
390
391
392
393
394
395
396
                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)
Philippe Bardou's avatar
Philippe Bardou committed
397
398
399
400
401
402
403
404
405
            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)
406
        for cpt in self.components:
407
408
            gr.add_node(cpt.get_nameid())
            gr.add_node_attribute(cpt.get_nameid(), self.COMPONENT_GRAPH_LABEL)
409
            gr.add_node_attribute(cpt.get_nameid(), cpt.get_nameid())
410
            all_nodes[cpt.get_nameid()] = None
Jerome Mariette's avatar
Jerome Mariette committed
411
412
        for cpt in self.components:
            for ioparameter in cpt.__dict__.values():
Jerome Mariette's avatar
Jerome Mariette committed
413
                if issubclass( ioparameter.__class__, InputFile ) or issubclass( ioparameter.__class__, InputFileList) or issubclass( ioparameter.__class__, InputDirectory):
Frédéric Escudié's avatar
Frédéric Escudié committed
414
415
                    for parent in ioparameter.parent_linkTrace_nameid:
                        try: gr.add_edge((parent, ioparameter.linkTrace_nameid))
Frédéric Escudié's avatar
Frédéric Escudié committed
416
                        except: pass
417
418
419
420
421
422
423
424
425
        # check if all nodes are connected
        for edge in gr.edges():
            if all_nodes.has_key(edge[0]):
                del all_nodes[edge[0]]
            if all_nodes.has_key(edge[1]):
                del all_nodes[edge[1]]
        # then remove all unconnected nodes: to delete inputs not defined by the user
        for orphan_node in all_nodes.keys():
            gr.del_node(orphan_node)
426
        return gr
Frédéric Escudié's avatar
Frédéric Escudié committed
427

Jerome Mariette's avatar
Jerome Mariette committed
428
429
430
431
    def delete(self):
        if self.get_status() in [self.STATUS_COMPLETED, self.STATUS_FAILED, self.STATUS_ABORTED]:
            shutil.rmtree(self.directory)

432
    @staticmethod
433
    def config_parser(arg_lines):
434
435
        for arg in arg_lines:
            yield arg
436
437
438
439
            
    @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))
440
        else: start_time = "-"
441
442
        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)
443
        else: elapsed_time = "-"
Jerome Mariette's avatar
Jerome Mariette committed
444
        elapsed_time = "-" if elapsed_time == "-" else str(datetime.timedelta(seconds=int(str(elapsed_time).split(".")[0])))
445
        if workflow.end_time: end_time = time.asctime(time.localtime(workflow.end_time))
446
447
448
        else: end_time = "-"
        if detailed:
            # Global
449
450
            title = "Workflow #" + utils.get_nb_string(workflow.id) + " (" + workflow.name + ") is " + \
                    workflow.get_status() + ", time elapsed: " + str(elapsed_time) + " (from " + start_time + \
451
452
                    " to " + end_time + ")"
            worflow_errors = ""
453
            error = workflow.get_errors()
454
            if error is not None:
Jerome Mariette's avatar
Jerome Mariette committed
455
456
                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"
457
458
459
            # By components
            components_errors = ""
            status = "Components Status :\n"
460
461
            for i, component in enumerate(workflow.get_components_nameid()):
                status_info = workflow.get_component_status(component)
462
463
464
465
466
467
468
469
470
471
472
                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
                
Jerome Mariette's avatar
Jerome Mariette committed
473
474
475
                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"
476
                else: running = "running:" + str(status_info["running"])
Jerome Mariette's avatar
Jerome Mariette committed
477
478
479
                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"
480
                else: waiting = "waiting:" + str(status_info["waiting"])            
Jerome Mariette's avatar
Jerome Mariette committed
481
482
483
                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"
484
                else: failed = "failed:" + str(status_info["failed"])
Jerome Mariette's avatar
Jerome Mariette committed
485
486
487
                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"
488
                else: aborted = "aborted:" + str(status_info["aborted"])
Jerome Mariette's avatar
Jerome Mariette committed
489
490
491
                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"
492
493
494
495
496
497
498
499
500
                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"  
                    components_errors += "  - " + component + " :\n    " + "\n    ".join(status_info["failed_commands"])
                status += "  - " + component + ", time elapsed " + time_format(status_info["time"]) + \
                    " (total:" + str(status_info["tasks"]) + ", " + waiting + ", " + running + ", " + failed + \
                    ", " + aborted + ", " + completed + ")"
501
                if i<len(workflow.get_components_nameid())-1: status += "\n"
502
503
504
505
506
            # Format str
            pretty_str = title
            pretty_str += ("\n" + worflow_errors) if worflow_errors != "" else ""
            pretty_str += ("\n" + status) if status != "" else ""
            pretty_str += ("\n" + components_errors) if components_errors != "" else ""
Jerome Mariette's avatar
Jerome Mariette committed
507
508
            if html: return pretty_str.replace("\n", "<br />")
            else: return pretty_str
509
        else:
510
511
            pretty_str = utils.get_nb_string(workflow.id) + "\t" + workflow.name + "\t"
            if workflow.get_status() == Workflow.STATUS_STARTED:
Jerome Mariette's avatar
Jerome Mariette committed
512
                pretty_str += "\033[94m"
513
            elif workflow.get_status() == Workflow.STATUS_COMPLETED:
Jerome Mariette's avatar
Jerome Mariette committed
514
                pretty_str += "\033[92m"
515
            elif workflow.get_status() == Workflow.STATUS_FAILED:
Jerome Mariette's avatar
Jerome Mariette committed
516
                pretty_str += "\033[91m"
517
            elif workflow.get_status() == Workflow.STATUS_ABORTED:
Jerome Mariette's avatar
Jerome Mariette committed
518
                pretty_str += "\033[91m"
519
            elif workflow.get_status() == Workflow.STATUS_RESETED:
Jerome Mariette's avatar
Jerome Mariette committed
520
                pretty_str += "\033[3m"
521
            pretty_str += workflow.get_status() + "\033[0m"
Jerome Mariette's avatar
Jerome Mariette committed
522
523
            pretty_str += "\t" + elapsed_time + "\t" + start_time + "\t" + end_time
            return pretty_str
524
    
525
    def get_errors(self):
Frédéric Escudié's avatar
Frédéric Escudié committed
526
527
528
529
530
531
        error = {
                 "title"     : "",
                 "msg"       : list(),
                 "traceback" : list()
        }
        line_idx = 0
532
533
534
        FH_stderr = open( self.stderr )
        lines = FH_stderr.readlines()
        while line_idx < len(lines):
535
            if lines[line_idx].strip().startswith("##"):
Frédéric Escudié's avatar
Frédéric Escudié committed
536
537
538
539
540
                error["title"]     = lines[line_idx].rstrip()
                error["msg"]       = list()
                error["traceback"] = list()
                line_idx += 2 # skip : "Traceback (most recent call last):"
                # Traceback
541
                while lines[line_idx] != lines[line_idx].lstrip():
Frédéric Escudié's avatar
Frédéric Escudié committed
542
543
544
545
                    error["traceback"].append({ 
                                               "location" : lines[line_idx].strip(),
                                               "line"     : lines[line_idx].strip()
                    })
546
                    line_idx += 2
Frédéric Escudié's avatar
Frédéric Escudié committed
547
                # Error message
548
549
                while line_idx < len(lines) and not lines[line_idx].strip().startswith("##"):
                    error["msg"].append( lines[line_idx].strip().split(":", 1)[1][1:] )
Frédéric Escudié's avatar
Frédéric Escudié committed
550
551
                    line_idx += 1
                line_idx -= 1
552
553
            line_idx += 1
        FH_stderr.close()
Frédéric Escudié's avatar
Frédéric Escudié committed
554
555
556
        last_stack_location = ""
        if len(error["traceback"]) > 0:
            last_stack_location = error["traceback"][-1]["location"].strip()
557
            self.status = self.STATUS_FAILED
Frédéric Escudié's avatar
Frédéric Escudié committed
558
559
560
            return { "msg" : error["msg"], "location" : last_stack_location }
        else:
            return None
561
    
562
    def get_outputs_per_components(self):
563
564
        outputs_files = {}
        for current_components in self.components:
Philippe Bardou's avatar
Philippe Bardou committed
565
            #status = self.get_component_status(current_components.get_nameid())
566
            outputs_files[current_components.get_nameid()] = current_components.get_output_files()
Philippe Bardou's avatar
Philippe Bardou committed
567
            #outputs_files["0"] = status["completed"]
568
569
        return outputs_files
    
Jerome Mariette's avatar
Jerome Mariette committed
570
571
572
573
574
575
576
577
578
579
580
581
582
583
    def __setstate__(self, state):
        self.__dict__ = state.copy()
        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()
        del odict['_Thread__started']
        del odict['_Thread__block']
        del odict['_Thread__stderr']
        return odict
    
584
585
586
587
588
589
590
591
592
593
594
595
596
    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        
597
        smtps, smtpp, froma, fromp, toa, subject, message = self.jflow_config_reader.get_email_options()
598
599
600
601
602
        
        if self.__to_address: toa = self.__to_address
        if self.__subject: subject = self.__subject
        if self.__message: message = self.__message
        
603
        if smtps and smtpp and froma and fromp:
604
605
            if not toa: toa = froma
            if validate_email(froma) and validate_email(toa):
606
607
608
609
610
                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:
611
                        message = Workflow.get_status_under_text_format(self, True, True, True)
Jerome Mariette's avatar
Jerome Mariette committed
612
                    msg = MIMEText(message, 'html')
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
                    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()
                    s.starttls()
                    s.login(me, fromp)
                    s.sendmail(me, [you], msg.as_string())
                    s.close()
                except:
                    logging.getLogger("wf." + str(self.id)).debug("Impossible to connect to smtp server '" + smtps + "'")
629
    
630
631
632
633
    def get_parameters_per_groups(self):
        name = self.get_name()
        description = self.get_description()
        parameters = self.get_parameters()
634
635
        pgparameters, parameters_order = {}, []
        for param in parameters:
Jerome Mariette's avatar
Jerome Mariette committed
636
            if param.group not in parameters_order: parameters_order.append(param.group)
637
638
            if pgparameters.has_key(param.group):
                pgparameters[param.group].append(param)
Jerome Mariette's avatar
Jerome Mariette committed
639
            else:
640
641
                pgparameters[param.group] = [param]
        return [pgparameters, parameters_order]
Jerome Mariette's avatar
Jerome Mariette committed
642
    
643
644
645
646
647
648
649
650
    def get_parameters(self):
        params = []
        for param in self.params_order:
            for attribute_value in self.__dict__.values():
                if (issubclass(attribute_value.__class__, AbstractParameter)) and param == attribute_value.name:
                    params.append(attribute_value)
        return params
    
651
    def get_exec_path(self, software):
652
653
654
655
656
        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)
657
        elif exec_path is None and utils.which(software) == None:
658
            raise Exception("'" + software + "' path connot be retrieved either in the PATH and in the application.properties file!")
659
660
661
        elif exec_path is None and utils.which(software) != None: 
            exec_path = software
        elif exec_path != None and not os.path.isfile(exec_path):
662
            raise Exception("'" + exec_path + "' set for '" + software + "' does not exists, please provide a valid path!")
663
        return exec_path
664
    
Jerome Mariette's avatar
Jerome Mariette committed
665
666
    def add_component(self, component_name, args=[], kwargs={}, component_prefix="default"):
        # first build and check if this component is OK
667
668
669
670
671
672
673
674
        if self.comp_pckg.has_key(component_name):
            my_pckge = __import__(self.comp_pckg[component_name], globals(), locals(), [component_name], -1)
            # 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)
675
676
            
            # there is a dynamic component
677
            if cmpt_object.is_dynamic():
678
679
680
681
                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
682
                    self.components_to_exec.append(cmpt_object)
683
                    self.components.append(cmpt_object)
684
685
686
687
688
689
690
691
692
                    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
693
                    self.components_to_exec = []
694
                    self.components = []
695
696
697
            else:
                if self.component_nameids_is_init:
                    # add the component
698
                    self.components_to_exec.append(cmpt_object)
699
                    self.components.append(cmpt_object)
700
                elif not self.component_nameids_is_init and not self.dynamic_component_present:
Jerome Mariette's avatar
Jerome Mariette committed
701
702
703
                    if self._component_is_duplicated(cmpt_object):
                        raise ValueError("Component " + cmpt_object.__class__.__name__ + " with prefix " + 
                                            cmpt_object.prefix + " already exist in this pipeline!")
704
                    self.components_to_exec.append(cmpt_object)
705
                    self.components.append(cmpt_object)
706
707
708
709
710
711
                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

712
713
            return cmpt_object
        else:
Jerome Mariette's avatar
Jerome Mariette committed
714
            raise ImportError(component_name + " component cannot be loaded, available components are: {0}".format(", ".join(self.comp_pckg.keys())))
Jerome Mariette's avatar
Jerome Mariette committed
715
716
717
718
719
720
721
722
    
    def pre_process(self):
        pass
    
    def process(self):
        """ 
        Run the workflow, has to be implemented by subclasses
        """
723
        raise NotImplementedError( "Workflow.process() must be implemented in " + self.__class__.__name__ )
724
725
726

    def get_name(self):
        """ 
727
        Return the workflow name.
728
        """
Jerome Mariette's avatar
Jerome Mariette committed
729
        return self.__class__.__name__.lower()
730
731
732
733
734
    
    def get_description(self):
        """ 
        Return the workflow description, has to be implemented by subclasses
        """
735
        raise NotImplementedError( "Workflow.get_description() must be implemented in " + self.__class__.__name__ )
736
    
737
    def define_parameters(self, function="process"):
738
739
740
        """ 
        Define the workflow parameters, has to be implemented by subclasses
        """
741
        raise NotImplementedError( "Workflow.define_parameters() must be implemented in " + self.__class__.__name__ )
Jerome Mariette's avatar
Jerome Mariette committed
742
743
744
745
746
747
748
749
750
751
752
753
754
755
    
    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):
        return self.component_nameids.keys()
    
Jerome Mariette's avatar
Jerome Mariette committed
756
757
    def wf_execution_wrapper(self):
        getattr(self, self.function)()
Jerome Mariette's avatar
Jerome Mariette committed
758
    
Jerome Mariette's avatar
Jerome Mariette committed
759
760
761
762
    def run(self):
        """
        Only require for Threading
        """
763
764
765
766
767
768
769
        try:
            # if this is the first time the workflow run
            if self.step == None :
                self.start_time = time.time()
                self.step = 0
                self.status = self.STATUS_STARTED
                self.end_time = None
Jerome Mariette's avatar
Jerome Mariette committed
770
771
                # if some args are provided, let's fill the parameters
                self._set_parameters(self.args)
772
                self._serialize()
773
774
775
776
777
778
779
            # if pre_processing has not been done yet
            if self.step == 0:
                self.pre_process()
                self.step = 1
                self._serialize()
            # if collecting components and running workflow has not been done yet
            if self.step == 1:
780
781
                try:
                    self.reseted_components = []
782
                    self.components = []
Jerome Mariette's avatar
Jerome Mariette committed
783
                    self.status = self.STATUS_STARTED
784
785
786
787
788
                    self.wf_execution_wrapper()
                except SystemExit, e: 
                    self.status = self.STATUS_FAILED
                    self.end_time = time.time()
                    self._serialize()
789
                    self._send_email()
790
791
792
793
794
795
796
797
798
799
                    raise
                self.component_nameids_is_init = True
                if self.dynamic_component_present:
                    self.step = 2
                else:
                    self._execute_weaver()
                    self.step = 3
                self._serialize() 
            # if the workflow was a dynamic one
            if self.step == 2:
800
801
                try:
                    self.reseted_components = []
802
                    self.components = []
Jerome Mariette's avatar
Jerome Mariette committed
803
                    self.status = self.STATUS_STARTED
804
805
806
807
808
                    self.wf_execution_wrapper()
                except SystemExit, e: 
                    self.status = self.STATUS_FAILED
                    self.end_time = time.time()
                    self._serialize()
809
                    self._send_email()
810
811
812
                    raise
                if len(self.components_to_exec) > 0:
                    self._execute_weaver()
813
                self.step = 3
814
815
816
817
                self._serialize()
            # if post processing has ne been done yet
            if self.step == 3:
                self.post_process()
818
                if self.status == self.STATUS_STARTED: self.status = self.STATUS_COMPLETED
819
820
                self.end_time = time.time()
                self._serialize()
821
                self._send_email()
822
823
824
        except Exception as e:
            logging.getLogger("wf." + str(self.id)).exception(str(e))
            utils.display_error_message(str(e))
825

Jerome Mariette's avatar
Jerome Mariette committed
826
827
828
829
830
831
832
833
834
835
836
    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()
                make_states.append(log.state)
Jerome Mariette's avatar
Jerome Mariette committed
837
838
839
            if len(self.reseted_components) > 0:
                self.status = self.STATUS_RESETED
            elif self.STATUS_ABORTED in make_states:
Jerome Mariette's avatar
Jerome Mariette committed
840
841
842
843
844
845
846
847
848
849
850
851
                self.status = self.STATUS_ABORTED
            elif self.STATUS_FAILED in make_states:
                self.status = self.STATUS_FAILED
            elif self.status != self.STATUS_COMPLETED:
                self.status = self.STATUS_STARTED
        except: pass
        self._serialize()

    def get_status(self):
        self._update_status_from_log()
        return self.status
    
852
853
854
    def get_resource(self, resource):
        return self.jflow_config_reader.get_resource(resource)
    
Jerome Mariette's avatar
Jerome Mariette committed
855
856
857
858
859
860
861
    def get_component_status(self, component_nameid):
        status = {"time": 0.0,
                  "tasks": 0,
                  "waiting": 0,
                  "running": 0,
                  "failed":0,
                  "aborted": 0,
862
863
                  "completed": 0,
                  "failed_commands": list() }
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
        if component_nameid not in self.reseted_components:
            try:
                log = MakeflowLog(self.component_nameids[component_nameid])
                log.parse()
                symbols = set(n.symbol for n in log.nodes if n.symbol)
                if not symbols: return None
                for n in log.nodes:
                    if not n.symbol: continue
                    if n.symbol == component_nameid:
                        status["tasks"] += 1
                        status["time"]  += n.elapsed_time
                        if n.state == Node.WAITING:
                            status["waiting"] += 1
                        elif n.state == Node.RUNNING:
                            status["running"] += 1
                        elif n.state == Node.FAILED:
                            status["failed"] += 1
                            status["failed_commands"].append( n.command )
                        elif n.state == Node.ABORTED:
                            status["aborted"] += 1
                        elif n.state == Node.COMPLETED:
                            status["completed"] += 1
            except: pass
Frédéric Escudié's avatar
Frédéric Escudié committed
887
        return status
Jerome Mariette's avatar
Jerome Mariette committed
888
    
889
890
891
892
893
894
895
896
897
    def reset_component(self, component_name):
        # first reinit the step to the execution step
        self.step = 1
        found = False
        for cpt in self.components:
            if cpt.get_nameid() == component_name:
                cpt.reset()
                found = True
        if not found:
898
            raise Exception("Impossible to reset component '" + component_name + "'! This one is not part of the workflow!")
899
        self.reseted_components.append(component_name)
Jerome Mariette's avatar
Jerome Mariette committed
900
        self.status = self.STATUS_RESETED
901
902
        self._serialize()
    
903
904
905
906
907
908
909
910
    def minimize(self):
        compts_status = {}
        for i, component in enumerate(self.get_components_nameid()):
            compts_status[component] = self.get_component_status(component)
        return MINIWorkflow(self.id, self.name, self.description, self.get_status(), self.start_time, 
                            self.end_time, self.metadata, self.get_components_nameid(), compts_status, 
                            self.get_errors())
    
Jerome Mariette's avatar
Jerome Mariette committed
911
912
913
914
915
916
917
918
919
920
921
    def makeflow_pretty_print_node(self, dag, node):
        sys.stdout.write('{0:>10} {1} {2}\n'.format('NODE', node.id, node.symbol))
        
        for output_file in sorted(node.output_files):
            sys.stdout.write('{0:>10} {1:>10} {2}\n'.format('', 'OUTPUT', output_file))
    
        for input_file in sorted(node.input_files):
            sys.stdout.write('{0:>10} {1:>10} {2}\n'.format('', 'INPUT', input_file))
            
        sys.stdout.write('{0:>10} {1:>10} {2}\n'.format('', 'COMMAND', node.command))

922
923
924
925
926
927
928
929
930
931
932
933
934
    def _set_stderr(self):
        if hasattr(self, "stderr") and self.stderr is not None:
            os.rename( self.stderr, os.path.join(self.directory, str(time.time()) + self.STDERR_FILE_NAME + self.OLD_EXTENSION) )
        stderr = os.path.join(self.directory, self.STDERR_FILE_NAME)
        logger = logging.getLogger( "wf." + str(self.id) )
        logger.setLevel(logging.DEBUG)
        formatter = logging.Formatter( '## %(asctime)s :: %(message)s' )
        file_handler = FileHandler(stderr, 'a')
        file_handler.setLevel(logging.ERROR)
        file_handler.setFormatter(formatter)
        logger.addHandler(file_handler)
        return stderr

Jerome Mariette's avatar
Jerome Mariette committed
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
    def _execute_weaver(self, engine_wrapper=None):
        # Add nest path and path to script to Python module path to allow
        # for importing modules outside of $PYTHONPATH
        make_directory, new_make = self._get_current_make()
        current_working_directory = os.path.join(os.path.join(self.directory, self.WORKING), make_directory)
        sys.path.insert(0, os.path.abspath(os.path.dirname(current_working_directory)))

        # Load built-ins
        self._import('abstraction', ABSTRACTIONS)
        self._import('dataset', DATASETS)
        self._import('function', FUNCTIONS)
        self._import('nest', NESTS)
        self._import('options', OPTIONS)
        self._import('stack', STACKS)
                
        # Execute nest
        with Nest(current_working_directory, wrapper=engine_wrapper, path=self.jflow_config_reader.get_makeflow_path()) as nest:
            with self.options:
                if new_make:
                    try:
955
                        for component in self.components_to_exec:
Jerome Mariette's avatar
Jerome Mariette committed
956
                            nest.symbol = component.get_nameid()
957
                            nest.batch = component.batch_options
Jerome Mariette's avatar
Jerome Mariette committed
958
959
960
961
962
963
                            self.component_nameids[component.get_nameid()] = os.path.join(current_working_directory, self.MAKEFLOW_LOG_FILE_NAME)
                            component.execute()
                        # create the DAG
                        nest.compile()
                    except Exception as e:
                        self.status = self.STATUS_FAILED
Jerome Mariette's avatar
Jerome Mariette committed
964
                        self.end_time = time.time()
Jerome Mariette's avatar
Jerome Mariette committed
965
                        self._serialize()
Jerome Mariette's avatar
Jerome Mariette committed
966
                        raise
967
                self.components_to_exec = []  
Jerome Mariette's avatar
Jerome Mariette committed
968
969
970
971
972
973
974
975
                # Once a weaver script is compiled, serialize the workflow
                self._serialize()
                try:
                    nest.execute(self.engine_arguments, exit_on_failure=True)
                except:
                    self.status = self.STATUS_FAILED
                    self.end_time = time.time()
                    self._serialize()
Jerome Mariette's avatar
Jerome Mariette committed
976
                    raise
Jerome Mariette's avatar
Jerome Mariette committed
977
978
979

    def _get_current_make(self):
        current_component, make_directory, new_make = [], None, False
980
        for component in self.components_to_exec:
Jerome Mariette's avatar
Jerome Mariette committed
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
            current_component.append(component.get_nameid())
        for make in self.makes:
            if set(current_component) == set(self.makes[make]):
                make_directory = make
        # If the components in the queue have already been compiled
        if make_directory is None:
            make_directory = uuid.uuid4().hex[:10]
            self.makes[make_directory] = current_component
            new_make = True
        return [make_directory, new_make]
    
    def _serialize(self):
        self.dump_path = os.path.join(self.directory, self.DUMP_FILE_NAME)
        workflow_dump = open(self.dump_path, "wb")
        pickle.dump(self, workflow_dump)
        workflow_dump.close()

998
999
    def _component_is_duplicated(self, component):
        if component.get_nameid() in self.component_nameids.keys():
Jerome Mariette's avatar
Jerome Mariette committed
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
            return True
        return False

    def _get_property_path(self):
        """ 
        Return(type:string):  the path to the workflow properties file, None if does not exist
        """
        property_file = os.path.join(os.path.dirname(inspect.getfile(self.__class__)), self.PROPERTIES_FILE_NAME)
        return property_file if os.path.isfile(property_file) else None

    def _import_components(self):
        pckge = {}
        # then import pipeline packages
        pipeline_dir = os.path.dirname(inspect.getfile(self.__class__))
        for importer, modname, ispkg in pkgutil.iter_modules([os.path.join(pipeline_dir, "components")], "workflows." + 
                                                             os.path.basename(pipeline_dir) + ".components."):
Jerome Mariette's avatar
Jerome Mariette committed
1016
1017
1018
1019
1020
            try:
                m = __import__(modname)
                for class_name, obj in inspect.getmembers(sys.modules[modname], inspect.isclass):
                    if issubclass(obj, jflow.component.Component) and obj.__name__ != jflow.component.Component.__name__:
                        pckge[class_name] = modname
Jerome Mariette's avatar
Jerome Mariette committed
1021
            except Exception as e:
1022
                logging.getLogger("wf." + str(self.id)).debug("Component <{0}> cannot be loaded: {1}".format(modname, e))
Jerome Mariette's avatar
Jerome Mariette committed
1023
1024