workflow.py 52.8 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
    MAKEFLOW_LOG_FILE_NAME = "Makeflow.makeflowlog"
88
    DUMP_FILE_NAME = ".workflow.dump"
89
    STDERR_FILE_NAME = "wf_stderr.txt"
Jerome Mariette's avatar
Jerome Mariette committed
90
    WORKING = ".working"
91
    OLD_EXTENSION = ".old"
92
    
Jerome Mariette's avatar
Jerome Mariette committed
93
94
95
96
    STATUS_STARTED = "started"
    STATUS_COMPLETED = "completed"
    STATUS_FAILED = "failed"
    STATUS_ABORTED = "aborted"
Jerome Mariette's avatar
Jerome Mariette committed
97
    STATUS_RESETED = "reseted"
98
    
Jerome Mariette's avatar
Jerome Mariette committed
99
100
101
    INPUTFILE_GRAPH_LABEL = "inputfile"
    INPUTFILES_GRAPH_LABEL = "inputfiles"
    INPUTDIRECTORY_GRAPH_LABEL = "inputdirectory"
102
103
    COMPONENT_GRAPH_LABEL = "component"
    
104
    
105
    def __init__(self, args={}, id=None, function= "process"):
Jerome Mariette's avatar
Jerome Mariette committed
106
107
108
109
        # define as a thread
        threading.Thread.__init__(self)
        self.jflow_config_reader = JFlowConfigReader()
        self.manager = WorkflowsManager()
110
        self.components_to_exec = []
111
        self.components = []
Jerome Mariette's avatar
Jerome Mariette committed
112
113
114
115
116
117
        self.makes = {}
        self.globals = {}
        self.options = Options()
        self.status = self.STATUS_STARTED
        self.start_time = None
        self.end_time = None
118
        self.step = None
Frédéric Escudié's avatar
Frédéric Escudié committed
119
        self.stderr = None
Jerome Mariette's avatar
Jerome Mariette committed
120
        self.args = args
121
        self.dynamic_component_present = False
122
123
124
        self.__to_address = None
        self.__subject = None
        self.__message = None
125
        self.function = function
126
        # intruduce --log-verbose to be able to monitor the new version of makeflow >=4.2.2
Jerome Mariette's avatar
Jerome Mariette committed
127
        self.engine_arguments = ' --log-verbose '
128
        self.component_nameids_is_init = False
Jerome Mariette's avatar
Jerome Mariette committed
129
        self.component_nameids = {}
130
        self.reseted_components = []
Jerome Mariette's avatar
Jerome Mariette committed
131
132
        # try to parse engine arguments
        try:
133
134
            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
135
136
137
            if type: self.engine_arguments += ' -T ' + type
            if options : self.engine_arguments += ' -B "' + options + '"'
        except: self.engine_arguments = None
138

Jerome Mariette's avatar
Jerome Mariette committed
139
        self.id = id
140
141
142
143
144
        self.name = self.get_name()
        self.description = self.get_description()
        
        # define the parameters 
        self.params_order = []
145
        self.define_parameters(self.function)
146
        # add the metadata parameter
147
        self.metadata = []
Jerome Mariette's avatar
Jerome Mariette committed
148
        
Jerome Mariette's avatar
Jerome Mariette committed
149
150
151
152
        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
153
            if self.stderr is None:
154
                self.stderr = self._set_stderr()
Jerome Mariette's avatar
Jerome Mariette committed
155
            self._serialize()
Jerome Mariette's avatar
Jerome Mariette committed
156
            
157
158
159
        self.internal_components = self._import_internal_components()
        self.external_components = self._import_external_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
                error["title"]     = lines[line_idx].rstrip()
                error["msg"]       = list()
                error["traceback"] = list()
539
540
541
542
543
                # 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    
544
                while lines[line_idx] != lines[line_idx].lstrip():
Frédéric Escudié's avatar
Frédéric Escudié committed
545
546
547
548
                    error["traceback"].append({ 
                                               "location" : lines[line_idx].strip(),
                                               "line"     : lines[line_idx].strip()
                    })
549
                    line_idx += 2
Frédéric Escudié's avatar
Frédéric Escudié committed
550
                # Error message
551
                while line_idx < len(lines) and not lines[line_idx].strip().startswith("##"):
552
553
554
555
                    try:
                        error["msg"].append( lines[line_idx].strip().split(":", 1)[1][1:] )
                    except:
                        error["msg"].append( lines[line_idx].strip() )
Frédéric Escudié's avatar
Frédéric Escudié committed
556
557
                    line_idx += 1
                line_idx -= 1
558
559
            line_idx += 1
        FH_stderr.close()
Frédéric Escudié's avatar
Frédéric Escudié committed
560
561
562
        last_stack_location = ""
        if len(error["traceback"]) > 0:
            last_stack_location = error["traceback"][-1]["location"].strip()
563
            self.status = self.STATUS_FAILED
Frédéric Escudié's avatar
Frédéric Escudié committed
564
565
566
            return { "msg" : error["msg"], "location" : last_stack_location }
        else:
            return None
567
    
568
    def get_outputs_per_components(self):
569
570
        outputs_files = {}
        for current_components in self.components:
Philippe Bardou's avatar
Philippe Bardou committed
571
            #status = self.get_component_status(current_components.get_nameid())
572
            outputs_files[current_components.get_nameid()] = current_components.get_output_files()
Philippe Bardou's avatar
Philippe Bardou committed
573
            #outputs_files["0"] = status["completed"]
574
575
        return outputs_files
    
Jerome Mariette's avatar
Jerome Mariette committed
576
577
    def __setstate__(self, state):
        self.__dict__ = state.copy()
578
        self.external_components = self._import_external_components()
Jerome Mariette's avatar
Jerome Mariette committed
579
580
581
582
583
584
585
586
587
588
        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']
589
590
        if odict.has_key('external_components') :
            del odict['external_components']
Jerome Mariette's avatar
Jerome Mariette committed
591
592
        return odict
    
593
594
595
596
597
598
599
600
601
602
603
604
605
    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        
606
        smtps, smtpp, froma, fromp, toa, subject, message = self.jflow_config_reader.get_email_options()
607
608
609
610
611
        
        if self.__to_address: toa = self.__to_address
        if self.__subject: subject = self.__subject
        if self.__message: message = self.__message
        
612
        if smtps and smtpp and froma and fromp:
613
614
            if not toa: toa = froma
            if validate_email(froma) and validate_email(toa):
615
616
617
618
619
                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:
620
                        message = Workflow.get_status_under_text_format(self, True, True, True)
Jerome Mariette's avatar
Jerome Mariette committed
621
                    msg = MIMEText(message, 'html')
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
                    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 + "'")
638
    
639
640
641
642
    def get_parameters_per_groups(self):
        name = self.get_name()
        description = self.get_description()
        parameters = self.get_parameters()
643
644
        pgparameters, parameters_order = {}, []
        for param in parameters:
Jerome Mariette's avatar
Jerome Mariette committed
645
            if param.group not in parameters_order: parameters_order.append(param.group)
646
647
            if pgparameters.has_key(param.group):
                pgparameters[param.group].append(param)
Jerome Mariette's avatar
Jerome Mariette committed
648
            else:
649
650
                pgparameters[param.group] = [param]
        return [pgparameters, parameters_order]
Jerome Mariette's avatar
Jerome Mariette committed
651
    
652
653
654
655
656
657
658
659
    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
    
660
    def get_exec_path(self, software):
661
662
663
664
665
        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)
666
        elif exec_path is None and utils.which(software) == None:
667
            raise Exception("'" + software + "' path connot be retrieved either in the PATH and in the application.properties file!")
668
669
670
        elif exec_path is None and utils.which(software) != None: 
            exec_path = software
        elif exec_path != None and not os.path.isfile(exec_path):
671
            raise Exception("'" + exec_path + "' set for '" + software + "' does not exists, please provide a valid path!")
672
        return exec_path
673
    
Jerome Mariette's avatar
Jerome Mariette committed
674
675
    def add_component(self, component_name, args=[], kwargs={}, component_prefix="default"):
        # first build and check if this component is OK
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
        if self.internal_components.has_key(component_name) or self.external_components.has_key(component_name):
            
            if self.internal_components.has_key(component_name) :
                my_pckge = __import__(self.internal_components[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)
            # 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)
693
694
            
            # there is a dynamic component
695
            if cmpt_object.is_dynamic():
696
697
698
699
                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
700
                    self.components_to_exec.append(cmpt_object)
701
                    self.components.append(cmpt_object)
702
703
704
705
706
707
708
709
710
                    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
711
                    self.components_to_exec = []
712
                    self.components = []
713
714
715
            else:
                if self.component_nameids_is_init:
                    # add the component
716
                    self.components_to_exec.append(cmpt_object)
717
                    self.components.append(cmpt_object)
718
                elif not self.component_nameids_is_init and not self.dynamic_component_present:
Jerome Mariette's avatar
Jerome Mariette committed
719
720
721
                    if self._component_is_duplicated(cmpt_object):
                        raise ValueError("Component " + cmpt_object.__class__.__name__ + " with prefix " + 
                                            cmpt_object.prefix + " already exist in this pipeline!")
722
                    self.components_to_exec.append(cmpt_object)
723
                    self.components.append(cmpt_object)
724
725
726
727
728
729
                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

730
731
            return cmpt_object
        else:
732
733
            raise ImportError(component_name + " component cannot be loaded, available components are: {0}".format(
                                           ", ".join(self.internal_components.keys() + self.external_components.keys())))
Jerome Mariette's avatar
Jerome Mariette committed
734
735
736
737
738
739
740
741
    
    def pre_process(self):
        pass
    
    def process(self):
        """ 
        Run the workflow, has to be implemented by subclasses
        """
742
        raise NotImplementedError( "Workflow.process() must be implemented in " + self.__class__.__name__ )
743
744
745

    def get_name(self):
        """ 
746
        Return the workflow name.
747
        """
Jerome Mariette's avatar
Jerome Mariette committed
748
        return self.__class__.__name__.lower()
749
750
751
752
753
    
    def get_description(self):
        """ 
        Return the workflow description, has to be implemented by subclasses
        """
754
        raise NotImplementedError( "Workflow.get_description() must be implemented in " + self.__class__.__name__ )
755
    
756
    def define_parameters(self, function="process"):
757
758
759
        """ 
        Define the workflow parameters, has to be implemented by subclasses
        """
760
        raise NotImplementedError( "Workflow.define_parameters() must be implemented in " + self.__class__.__name__ )
Jerome Mariette's avatar
Jerome Mariette committed
761
762
763
764
765
766
767
768
769
770
771
772
773
774
    
    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
775
776
    def wf_execution_wrapper(self):
        getattr(self, self.function)()
Jerome Mariette's avatar
Jerome Mariette committed
777
    
Jerome Mariette's avatar
Jerome Mariette committed
778
779
780
781
    def run(self):
        """
        Only require for Threading
        """
782
783
784
785
786
787
788
        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
789
790
                # if some args are provided, let's fill the parameters
                self._set_parameters(self.args)
791
                self._serialize()
792
793
794
795
796
797
798
            # 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:
799
800
                try:
                    self.reseted_components = []
801
                    self.components = []
Jerome Mariette's avatar
Jerome Mariette committed
802
                    self.status = self.STATUS_STARTED
803
804
805
806
807
                    self.wf_execution_wrapper()
                except SystemExit, e: 
                    self.status = self.STATUS_FAILED
                    self.end_time = time.time()
                    self._serialize()
808
                    self._send_email()
809
810
811
812
813
814
815
816
817
818
                    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:
819
820
                try:
                    self.reseted_components = []
821
                    self.components = []
Jerome Mariette's avatar
Jerome Mariette committed
822
                    self.status = self.STATUS_STARTED
823
824
825
826
827
                    self.wf_execution_wrapper()
                except SystemExit, e: 
                    self.status = self.STATUS_FAILED
                    self.end_time = time.time()
                    self._serialize()
828
                    self._send_email()
829
830
831
                    raise
                if len(self.components_to_exec) > 0:
                    self._execute_weaver()
832
                self.step = 3
833
834
835
836
                self._serialize()
            # if post processing has ne been done yet
            if self.step == 3:
                self.post_process()
837
                if self.status == self.STATUS_STARTED: self.status = self.STATUS_COMPLETED
838
839
                self.end_time = time.time()
                self._serialize()
840
                self._send_email()
841
842
843
        except Exception as e:
            logging.getLogger("wf." + str(self.id)).exception(str(e))
            utils.display_error_message(str(e))
844

Jerome Mariette's avatar
Jerome Mariette committed
845
846
847
848
849
850
851
852
853
854
855
    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
856
857
858
            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
859
860
861
862
863
864
865
866
867
868
869
870
                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
    
871
872
873
    def get_resource(self, resource):
        return self.jflow_config_reader.get_resource(resource)
    
Jerome Mariette's avatar
Jerome Mariette committed
874
875
876
877
878
879
880
    def get_component_status(self, component_nameid):
        status = {"time": 0.0,
                  "tasks": 0,
                  "waiting": 0,
                  "running": 0,
                  "failed":0,
                  "aborted": 0,
881
882
                  "completed": 0,
                  "failed_commands": list() }
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
        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
906
        return status
Jerome Mariette's avatar
Jerome Mariette committed
907
    
908
909
910
911
912
913
914
915
916
    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:
917
            raise Exception("Impossible to reset component '" + component_name + "'! This one is not part of the workflow!")
918
        self.reseted_components.append(component_name)
Jerome Mariette's avatar
Jerome Mariette committed
919
        self.status = self.STATUS_RESETED
920
921
        self._serialize()
    
922
923
924
925
926
927
928
929
    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
930
931
932
933
934
935
936
937
938
939
940
    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))

941
942
943
944
945
946
947
948
949
950
951
952
953
    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
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
    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:
974
                        for component in self.components_to_exec:
Jerome Mariette's avatar
Jerome Mariette committed
975
                            nest.symbol = component.get_nameid()
976
                            nest.batch = component.batch_options
Jerome Mariette's avatar
Jerome Mariette committed
977
978
979
980
981
982
                            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
983
                        self.end_time = time.time()
Jerome Mariette's avatar
Jerome Mariette committed
984
                        self._serialize()
Jerome Mariette's avatar
Jerome Mariette committed
985
                        raise
986
                self.components_to_exec = []  
Jerome Mariette's avatar
Jerome Mariette committed
987
988
989
990
991
992
993
994
                # 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
995
                    raise
Jerome Mariette's avatar
Jerome Mariette committed
996
997
998

    def _get_current_make(self):
        current_component, make_directory, new_make = [], None, False
999
        for component in self.components_to_exec:
Jerome Mariette's avatar
Jerome Mariette committed
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
            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()

1017
1018
    def _component_is_duplicated(self, component):
        if component.get_nameid() in self.component_nameids.keys():
Jerome Mariette's avatar
Jerome Mariette committed
1019
1020
1021
            return True
        return False