workflow.py 67 KB
Newer Older
Jerome Mariette's avatar
Jerome Mariette committed
1
#
Jerome Mariette's avatar
Jerome Mariette committed
2
# Copyright (C) 2015 INRA
Jerome Mariette's avatar
Jerome Mariette committed
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
# 
# 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 datetime
30
31
import logging
import traceback
Jerome Mariette's avatar
Jerome Mariette committed
32

33
from configparser import ConfigParser, NoOptionError
Jerome Mariette's avatar
Jerome Mariette committed
34
from inspect import getcallargs
35
from datetime import date as ddate
Jerome Mariette's avatar
Jerome Mariette committed
36

37
38
from collections import OrderedDict

Jerome Mariette's avatar
Jerome Mariette committed
39
import jflow
Jerome Mariette's avatar
Jerome Mariette committed
40
import jflow.utils as utils
41
from jflow.utils import validate_email
42
from pygraph.classes.digraph import digraph
Ibouniyamine Nabihoudine's avatar
Ibouniyamine Nabihoudine committed
43
44
from jflow.workflows_manager import WorkflowsManager 
from jflow.config_reader import JFlowConfigReader
45
from jflow.utils import get_octet_string_representation, get_nb_octet
46
from jflow.parameter import *
Jerome Mariette's avatar
Jerome Mariette committed
47
from jflow.exceptions import RuleException
48
import jflow.rules as j_rules
49

Jerome Mariette's avatar
Jerome Mariette committed
50
51
from cctools.util import time_format

Jerome Mariette's avatar
Jerome Mariette committed
52
53
54
55
56
57
58
59
60
61
62
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

63
64
from workflows import rules as wf_rules

Jerome Mariette's avatar
Jerome Mariette committed
65

66
67
68
69
70
71
72
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
73
        self._status = status
74
75
76
77
78
79
80
81
82
83
        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

84
85
86
    def get_components_status(self):
        return self.compts_status
    
87
88
89
90
91
92
93
    def get_component_status(self, component_nameid):
        return self.compts_status[component_nameid]
    
    def get_errors(self):
        return self.errors
    
    def get_status(self):
94
        return self._status
95

96
97
class Workflow(threading.Thread):
    
Jerome Mariette's avatar
Jerome Mariette committed
98
    MAKEFLOW_LOG_FILE_NAME = "Makeflow.makeflowlog"
99
    DUMP_FILE_NAME = ".workflow.dump"
100
    STDERR_FILE_NAME = "wf_stderr.txt"
Jerome Mariette's avatar
Jerome Mariette committed
101
    WORKING = ".working"
102
    OLD_EXTENSION = ".old"
103
    DEFAULT_GROUP = "default"
104
    
105
    STATUS_PENDING = "pending"
Jerome Mariette's avatar
Jerome Mariette committed
106
107
108
109
    STATUS_STARTED = "started"
    STATUS_COMPLETED = "completed"
    STATUS_FAILED = "failed"
    STATUS_ABORTED = "aborted"
Jerome Mariette's avatar
Jerome Mariette committed
110
    STATUS_RESETED = "reseted"
111
    
Jerome Mariette's avatar
Jerome Mariette committed
112
113
114
    INPUTFILE_GRAPH_LABEL = "inputfile"
    INPUTFILES_GRAPH_LABEL = "inputfiles"
    INPUTDIRECTORY_GRAPH_LABEL = "inputdirectory"
115
116
    COMPONENT_GRAPH_LABEL = "component"
    
117
    
118
    def __init__(self, args={}, id=None, function= "process"):
Jerome Mariette's avatar
Jerome Mariette committed
119
120
121
122
        # define as a thread
        threading.Thread.__init__(self)
        self.jflow_config_reader = JFlowConfigReader()
        self.manager = WorkflowsManager()
123
        self.components_to_exec = []
124
        self.components = []
Jerome Mariette's avatar
Jerome Mariette committed
125
126
127
        self.makes = {}
        self.globals = {}
        self.options = Options()
128
129
        self._status = self.STATUS_STARTED
        self._postprocess_status = self.STATUS_PENDING
Jerome Mariette's avatar
Jerome Mariette committed
130
131
        self.start_time = None
        self.end_time = None
Jerome Mariette's avatar
Jerome Mariette committed
132
        self.__step = None
Frédéric Escudié's avatar
Frédéric Escudié committed
133
        self.stderr = None
Jerome Mariette's avatar
Jerome Mariette committed
134
        self.args = args
135
        self.dynamic_component_present = False
136
137
138
        self.__to_address = None
        self.__subject = None
        self.__message = None
139
        self.function = function
140
        # intruduce --log-verbose to be able to monitor the new version of makeflow >=4.2.2
Jerome Mariette's avatar
Jerome Mariette committed
141
        self.engine_arguments = ' --log-verbose '
142
        self.component_nameids_is_init = False
Jerome Mariette's avatar
Jerome Mariette committed
143
        self.component_nameids = {}
144
        self.reseted_components = []
Jerome Mariette's avatar
Jerome Mariette committed
145
146
        # try to parse engine arguments
        try:
147
148
            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
149
150
151
            if type: self.engine_arguments += ' -T ' + type
            if options : self.engine_arguments += ' -B "' + options + '"'
        except: self.engine_arguments = None
152

Jerome Mariette's avatar
Jerome Mariette committed
153
        self.id = id
154
155
        self.name = self.get_name()
        self.description = self.get_description()
Ibouniyamine Nabihoudine's avatar
Ibouniyamine Nabihoudine committed
156
        self.__group = self.jflow_config_reader.get_workflow_group(self.__class__.__name__) or Workflow.DEFAULT_GROUP
157
158
159
        
        # define the parameters 
        self.params_order = []
Jerome Mariette's avatar
Jerome Mariette committed
160
161
        if self.function != None:
            self.define_parameters(self.function)
162
        # add the metadata parameter
163
        self.metadata = []
Jerome Mariette's avatar
Jerome Mariette committed
164
        
Jerome Mariette's avatar
Jerome Mariette committed
165
166
167
        if self.id is not None:
            self.directory = self.manager.get_workflow_directory(self.name, self.id)
            if not os.path.isdir(self.directory):
168
                os.makedirs(self.directory, 0o751)
Frédéric Escudié's avatar
Frédéric Escudié committed
169
            if self.stderr is None:
170
                self.stderr = self._set_stderr()
Jerome Mariette's avatar
Jerome Mariette committed
171
            self._serialize()
Jerome Mariette's avatar
Jerome Mariette committed
172
            
173
174
        self.internal_components = self._import_internal_components()
        self.external_components = self._import_external_components()
175

176
177
    def get_workflow_group(self):
        return self.__group
178
            
Jerome Mariette's avatar
Jerome Mariette committed
179
    def add_input_directory(self, name, help, default=None, required=False, flag=None, 
180
                            group="default", display_name=None, get_files_fn=None, add_to=None, rules=None):
181
        new_param = InputDirectory(name, help, flag=flag, default=default, required=required, 
182
                                   group=group, display_name=display_name, get_files_fn=get_files_fn, rules=rules)
Jerome Mariette's avatar
Jerome Mariette committed
183
184
185
186
187
188
189
190
191
192
193
        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)
    
194
    def add_input_file(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,
                       rules=None):
197
198
199
        # check if the size provided is correct
        try: int(get_nb_octet(size_limit))
        except: size_limit="0"
200
        new_param = InputFile(name, help, flag=flag, file_format=file_format, default=default, 
201
202
                              type=type, required=required, group=group, display_name=display_name, size_limit=size_limit,
                              rules=rules)
Frédéric Escudié's avatar
Frédéric Escudié committed
203
        new_param.linkTrace_nameid = name
204
205
206
207
208
209
        # 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
210
        else:
211
212
213
214
            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", 
215
216
                            required=False, flag=None, group="default", display_name=None, size_limit="0", add_to=None,
                            rules=None):
217
        # check if the size provided is correct
218
        if default == None: default = []
219
220
        try: int(get_nb_octet(size_limit))
        except: size_limit="0"
221
222
223
224
225
226
227
        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, 
228
229
                                  type=type, required=required, group=group, display_name=display_name, size_limit=size_limit,
                                  rules=rules)
Frédéric Escudié's avatar
Frédéric Escudié committed
230
        new_param.linkTrace_nameid = name
231
232
233
        # if this input should be added to a particular parameter
        if add_to:
            try:
Jerome Mariette's avatar
help ok    
Jerome Mariette committed
234
                self.__getattribute__(add_to).add_sub_parameter(new_param)
235
236
237
238
239
            except: pass
        # otherwise, add it to the class itself
        else:
            self.params_order.append(name)
            self.__setattr__(name, new_param)
240
            
241
242
    def add_multiple_parameter(self, name, help, required=False, flag=None, group="default", display_name=None,
                               rules=None):
243
        self.params_order.append(name)
244
245
        new_param = MultiParameter(name, help, flag=flag, required=required, group=group, display_name=display_name,
                                   rules=rules)
246
247
        self.__setattr__(name, new_param)

248
    def add_multiple_parameter_list(self, name, help, required=False, flag=None, group="default", display_name=None, rules=None):
249
        self.params_order.append(name)
250
251
        new_param = MultiParameterList(name, help, flag=flag, required=required, group=group, display_name=display_name,
                                       rules=rules)
252
253
        self.__setattr__(name, new_param)
    
254
    def add_parameter(self, name, help, default=None, type=str, choices=None, 
255
                      required=False, flag=None, group="default", display_name=None, add_to=None, rules=None):
256
        new_param = ParameterFactory.factory(name, help, flag=flag, default=default, type=type, choices=choices, 
257
                              required=required, group=group, display_name=display_name, rules=rules)
258
259
260
261
262
263
        # 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
264
        else:
265
266
267
            self.params_order.append(name)
            self.__setattr__(name, new_param)
    
268
    def add_parameter_list(self, name, help, default=None, type=str, choices=None, 
269
                           required=False, flag=None, group="default", display_name=None, add_to=None, rules=None):
270
271
        if default == None: default = []
        new_param = ParameterList(name, help, flag=flag, default=default, type=type, choices=choices, 
272
                                  required=required, group=group, display_name=display_name, rules=rules)
273
274
275
        # if this input should be added to a particular parameter
        if add_to:
            try:
Jerome Mariette's avatar
help ok    
Jerome Mariette committed
276
                self.__getattribute__(add_to).add_sub_parameter(new_param)
277
278
279
280
281
            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
282
#                         break
283

Frédéric Escudié's avatar
Frédéric Escudié committed
284
    def _prepare_parameter(self, args, parameter, key="name"):
285
286
        new_param = None
        # Retrieve value
287
        if parameter.__getattribute__(key) in args:
Frédéric Escudié's avatar
Frédéric Escudié committed
288
            value = args[parameter.__getattribute__(key)]
Jerome Mariette's avatar
Jerome Mariette committed
289
        elif parameter.default != None:
290
291
292
293
            value = parameter.default
        else:
            value = None
        # Set new parameter
Ibouniyamine Nabihoudine's avatar
Ibouniyamine Nabihoudine committed
294
        if parameter.__class__ in [StrParameter, IntParameter, FloatParameter, BoolParameter, DateParameter, PasswordParameter]:
Frédéric Escudié's avatar
Frédéric Escudié committed
295
            if value == "" and parameter.__class__ in [IntParameter, FloatParameter, BoolParameter, DateParameter] : value = None # from GUI
296
297
298
299
            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:
300
            if value == "" : value = [] # from GUI
301
302
303
304
            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:
305
            if value == "" : value = [] # from GUI
306
            iovalues = []
Ibouniyamine Nabihoudine's avatar
Ibouniyamine Nabihoudine committed
307
            prepared_files = parameter.prepare(value)
308
            for file in prepared_files:
309
310
                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,
311
312
                                       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 )
313
            new_param.linkTrace_nameid = parameter.linkTrace_nameid            
314
        elif parameter.__class__ == InputFile:
315
            if value == "" : value = None # from GUI
Ibouniyamine Nabihoudine's avatar
Ibouniyamine Nabihoudine committed
316
            prepared_file = parameter.prepare(value)
317
            new_param = InputFile( parameter.name, parameter.help, file_format=parameter.file_format, default=prepared_file,
318
319
                                   type=parameter.type, choices=parameter.choices, required=parameter.required, flag=parameter.flag, 
                                   group=parameter.group, display_name=parameter.display_name )
320
            new_param.linkTrace_nameid = parameter.linkTrace_nameid
Jerome Mariette's avatar
Jerome Mariette committed
321
322
        elif parameter.__class__ == InputDirectory:
            if value == "" : value = None # from GUI
Ibouniyamine Nabihoudine's avatar
Ibouniyamine Nabihoudine committed
323
            prepared_directory = parameter.prepare(value)
324
            new_param = InputDirectory( parameter.name, parameter.help, default=prepared_directory, choices=parameter.choices, 
Jerome Mariette's avatar
Jerome Mariette committed
325
                                        required=parameter.required, flag=parameter.flag, group=parameter.group, 
326
                                        display_name=parameter.display_name, get_files_fn=parameter.get_files_fn)
Jerome Mariette's avatar
Jerome Mariette committed
327
            new_param.linkTrace_nameid = parameter.linkTrace_nameid
328
329
330
331
        else:
            raise Exception( "Unknown class '" +  parameter.__class__.__name__ + "' for parameter.")
        return new_param

332
    def _set_parameters(self, args):
333
334
        parameters = self.get_parameters()
        for param in parameters:
335
            new_param = None
336
            if param.__class__ == MultiParameter:
337
                new_param = MultiParameter(param.name, param.help, required=param.required, flag=param.flag, group=param.group, display_name=param.display_name)
338
                new_param.sub_parameters = param.sub_parameters
339
                if param.name in args:
340
341
342
343
344
345
                    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
346
            elif param.__class__ == MultiParameterList:
347
                new_param = MultiParameterList(param.name, param.help, required=param.required, flag=param.flag, group=param.group, display_name=param.display_name)
348
                new_param.sub_parameters = param.sub_parameters
349
                if param.name in args:
350
351
352
353
354
355
356
357
358
                    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)
359
            else:
360
                new_param = self._prepare_parameter(args, param)
361
            self.__setattr__(param.name, new_param)
Frédéric Escudié's avatar
Frédéric Escudié committed
362

Jerome Mariette's avatar
Jerome Mariette committed
363
    def get_execution_graph(self):
364
        gr = digraph()
365
366
        # build a all_nodes table to store all nodes
        all_nodes = {}
367
        for ioparameter in list(self.__dict__.values()):
368
369
            if issubclass(ioparameter.__class__, InputFile):
                gr.add_node(ioparameter.name)
Jerome Mariette's avatar
Jerome Mariette committed
370
                gr.add_node_attribute(ioparameter.name, self.INPUTFILE_GRAPH_LABEL)
371
                gr.add_node_attribute(ioparameter.name, ioparameter.display_name)
372
                all_nodes[ioparameter.name] = None
373
374
            elif issubclass(ioparameter.__class__, InputFileList):
                gr.add_node(ioparameter.name)
Jerome Mariette's avatar
Jerome Mariette committed
375
376
377
378
379
380
                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)
381
                gr.add_node_attribute(ioparameter.name, ioparameter.display_name)
382
                all_nodes[ioparameter.name] = None
Philippe Bardou's avatar
Philippe Bardou committed
383
            elif issubclass(ioparameter.__class__, MultiParameter):
Jerome Mariette's avatar
Jerome Mariette committed
384
385
386
387
388
389
390
391
392
393
                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
394
395
396
397
398
399
400
401
402
            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)
403
        for cpt in self.components:
404
405
            gr.add_node(cpt.get_nameid())
            gr.add_node_attribute(cpt.get_nameid(), self.COMPONENT_GRAPH_LABEL)
406
            gr.add_node_attribute(cpt.get_nameid(), cpt.get_nameid())
407
            all_nodes[cpt.get_nameid()] = None
Jerome Mariette's avatar
Jerome Mariette committed
408
        for cpt in self.components:
409
            for ioparameter in list(cpt.__dict__.values()):
Jerome Mariette's avatar
Jerome Mariette committed
410
                if issubclass( ioparameter.__class__, InputFile ) or issubclass( ioparameter.__class__, InputFileList) or issubclass( ioparameter.__class__, InputDirectory):
Frédéric Escudié's avatar
Frédéric Escudié committed
411
412
                    for parent in ioparameter.parent_linkTrace_nameid:
                        try: gr.add_edge((parent, ioparameter.linkTrace_nameid))
Frédéric Escudié's avatar
Frédéric Escudié committed
413
                        except: pass
414
415
416
417
                elif issubclass( ioparameter.__class__, InputObject) or issubclass( ioparameter.__class__, InputObjectList):
                    for parent in ioparameter.parent_linkTrace_nameid:
                        try: gr.add_edge((parent, ioparameter.linkTrace_nameid))
                        except: pass
418
419
        # check if all nodes are connected
        for edge in gr.edges():
420
            if edge[0] in all_nodes:
421
                del all_nodes[edge[0]]
422
            if edge[1] in all_nodes:
423
424
                del all_nodes[edge[1]]
        # then remove all unconnected nodes: to delete inputs not defined by the user
425
        for orphan_node in list(all_nodes.keys()):
426
            gr.del_node(orphan_node)
427
        return gr
Frédéric Escudié's avatar
Frédéric Escudié committed
428

Jerome Mariette's avatar
Jerome Mariette committed
429
430
    def delete(self):
        if self.get_status() in [self.STATUS_COMPLETED, self.STATUS_FAILED, self.STATUS_ABORTED]:
Jerome Mariette's avatar
Jerome Mariette committed
431
            utils.robust_rmtree(self.directory)
Jerome Mariette's avatar
Jerome Mariette committed
432

433
    @staticmethod
434
    def config_parser(arg_lines):
435
436
        for arg in arg_lines:
            yield arg
437
438
439
440
            
    @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))
441
        else: start_time = "-"
442
443
        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)
444
        else: elapsed_time = "-"
Jerome Mariette's avatar
Jerome Mariette committed
445
        elapsed_time = "-" if elapsed_time == "-" else str(datetime.timedelta(seconds=int(str(elapsed_time).split(".")[0])))
446
        if workflow.end_time: end_time = time.asctime(time.localtime(workflow.end_time))
447
448
449
        else: end_time = "-"
        if detailed:
            # Global
450
451
            title = "Workflow #" + utils.get_nb_string(workflow.id) + " (" + workflow.name + ") is " + \
                    workflow.get_status() + ", time elapsed: " + str(elapsed_time) + " (from " + start_time + \
452
453
                    " to " + end_time + ")"
            worflow_errors = ""
454
            error = workflow.get_errors()
455
            if error is not None:
Jerome Mariette's avatar
Jerome Mariette committed
456
457
                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"
458
459
460
            # By components
            components_errors = ""
            status = "Components Status :\n"
461
            components_status = workflow.get_components_status()
462
            for i, component in enumerate(workflow.get_components_nameid()):
463
                status_info = components_status[component]
464
465
466
467
468
469
470
471
472
473
474
                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
475
476
477
                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"
478
                else: running = "running:" + str(status_info["running"])
Jerome Mariette's avatar
Jerome Mariette committed
479
480
481
                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"
482
                else: waiting = "waiting:" + str(status_info["waiting"])            
Jerome Mariette's avatar
Jerome Mariette committed
483
484
485
                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"
486
                else: failed = "failed:" + str(status_info["failed"])
Jerome Mariette's avatar
Jerome Mariette committed
487
488
489
                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"
490
                else: aborted = "aborted:" + str(status_info["aborted"])
Jerome Mariette's avatar
Jerome Mariette committed
491
492
493
                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"
494
495
496
                else: completed = "completed:" + str(status_info["completed"])
                
                if display_errors and len(status_info["failed_commands"]) > 0:
497
498
                    if components_errors == "":
                        components_errors = "Failed Commands :\n"
499
                    components_errors += "  - " + component + " :\n    " + "\n    ".join(status_info["failed_commands"]) + "\n"
500
501
502
                status += "  - " + component + ", time elapsed " + time_format(status_info["time"]) + \
                    " (total:" + str(status_info["tasks"]) + ", " + waiting + ", " + running + ", " + failed + \
                    ", " + aborted + ", " + completed + ")"
503
                if i<len(workflow.get_components_nameid())-1: status += "\n"
504
505
506
            # Format str
            pretty_str = title
            pretty_str += ("\n" + worflow_errors) if worflow_errors != "" else ""
507
508
            if len(workflow.get_components_nameid()) > 0:
                pretty_str += ("\n" + status) if status != "" else ""
509
                pretty_str += ("\n" + components_errors[:-1]) if components_errors != "" else ""
Jerome Mariette's avatar
Jerome Mariette committed
510
511
            if html: return pretty_str.replace("\n", "<br />")
            else: return pretty_str
512
        else:
513
514
            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
515
                pretty_str += "\033[94m"
516
            elif workflow.get_status() == Workflow.STATUS_COMPLETED:
Jerome Mariette's avatar
Jerome Mariette committed
517
                pretty_str += "\033[92m"
518
            elif workflow.get_status() == Workflow.STATUS_FAILED:
Jerome Mariette's avatar
Jerome Mariette committed
519
                pretty_str += "\033[91m"
520
            elif workflow.get_status() == Workflow.STATUS_ABORTED:
Jerome Mariette's avatar
Jerome Mariette committed
521
                pretty_str += "\033[91m"
522
            elif workflow.get_status() == Workflow.STATUS_RESETED:
Jerome Mariette's avatar
Jerome Mariette committed
523
                pretty_str += "\033[3m"
524
            pretty_str += workflow.get_status() + "\033[0m"
Jerome Mariette's avatar
Jerome Mariette committed
525
526
            pretty_str += "\t" + elapsed_time + "\t" + start_time + "\t" + end_time
            return pretty_str
527
    
528
    def get_errors(self):
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
        if os.path.isfile(self.stderr):
            error = {
                "title"     : "",
                "msg"       : list(),
                "traceback" : list()
            }
            line_idx = 0
            FH_stderr = open( self.stderr )
            lines = FH_stderr.readlines()
            while line_idx < len(lines):
                if lines[line_idx].strip().startswith("##"):
                    error["title"]     = lines[line_idx].rstrip()
                    error["msg"]       = list()
                    error["traceback"] = list()
                    # skip all lines before the traceback
                    while not lines[line_idx].startswith("Traceback"):
                        line_idx += 1
                    # skip : "Traceback (most recent call last):"
                    line_idx += 1    
                    while lines[line_idx] != lines[line_idx].lstrip():
                        error["traceback"].append({ 
                                                   "location" : lines[line_idx].strip(),
                                                   "line"     : lines[line_idx].strip()
                        })
                        line_idx += 2
                    # Error message
                    while line_idx < len(lines) and not lines[line_idx].strip().startswith("##"):
                        try:
                            error["msg"].append( lines[line_idx].strip().split(":", 1)[1][1:] )
                        except:
                            error["msg"].append( lines[line_idx].strip() )
                        line_idx += 1
                    line_idx -= 1
                line_idx += 1
            FH_stderr.close()
            last_stack_location = ""
            if len(error["traceback"]) > 0:
                last_stack_location = error["traceback"][-1]["location"].strip()
                return { "msg" : error["msg"], "location" : last_stack_location }
            else:
                return None
Frédéric Escudié's avatar
Frédéric Escudié committed
570
571
        else:
            return None
572

573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
    def print_workflow_outputs(self, logs):
        outputs = self.get_outputs_per_components()
        descriptions = self.get_description_per_components()
        idx = 1
        for output in outputs:
            name = output[:output.index(".")]
            component = str(idx) + ". "
            if output in descriptions and descriptions[output] is not None:
                component += descriptions[output]
            else:
                component += name
            component += ":\n"
            has_outputs = False
            for output_file in outputs[output]:
                if logs or (not output_file.endswith(".stdout") and not output_file.endswith(".stderr")):
                    has_outputs = True
                    component += "  - " + outputs[output][output_file] + "\n"
            if has_outputs:
                print(component)
            idx += 1

594
595
596
597
598
599
    def get_description_per_components(self):
        dag = self.get_execution_graph()
        descriptions = {}
        for current_components in self.components:
            descriptions[current_components.get_nameid()] = current_components.get_description()
        return descriptions
600
                
601
    def get_outputs_per_components(self):
602
        outputs_files = OrderedDict()
603
        for current_components in self.components:
Philippe Bardou's avatar
Philippe Bardou committed
604
            #status = self.get_component_status(current_components.get_nameid())
605
            outputs_files[current_components.get_nameid()] = current_components.get_output_files()
Philippe Bardou's avatar
Philippe Bardou committed
606
            #outputs_files["0"] = status["completed"]
607
608
        return outputs_files
    
Jerome Mariette's avatar
Jerome Mariette committed
609
610
    def __setstate__(self, state):
        self.__dict__ = state.copy()
611
        self.external_components = self._import_external_components()
Jerome Mariette's avatar
Jerome Mariette committed
612
613
614
615
616
617
618
        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()
619
        del odict['_started']
620
621
622
623
        if '_tstate_lock' in odict: # python 3.4
            del odict['_tstate_lock']
        else: # python 3.2
            del odict['_block']
624
625
        del odict['_stderr']
        if 'external_components' in odict:
626
            del odict['external_components']
Jerome Mariette's avatar
Jerome Mariette committed
627
628
        return odict
    
629
630
631
632
633
634
635
636
    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
637
638
639
640

    def _get_cleaned_email_placeholders(self, text):
        """
        @summary: Returns the text after replacement of placeholders by the corresponding workflow values (method or attribute).
Frédéric Escudié's avatar
Frédéric Escudié committed
641
                  Placeholders must be an attribute or a method of the workflow between three sharps: ###attribute### or ###method()###.
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
                  You can add "|date" after the attribute or the method to convert a timestamp in human readable date.
                  Examples: ###id### is replaced by wf.id ; ###get_status()### is replaced by wf.get_status() ; ###start_time|date### is rplaced by wf.start_time in date format.
        @param text: [str] The text containing placeholders.
        @return: [str] The text with placeholders replaced by her real value.
        """
        new_text = text
        placeholders = re.findall("\#\#\#([^\#]+)\#\#\#", text)
        for placeholder in placeholders:
            try:
                placeholder_value = ""
                placeholder_key = placeholder
                is_date = False
                if placeholder.endswith("|date"):
                    placeholder_key = placeholder[:-5]
                    is_date = True
                # Get value
                if placeholder_key.endswith("()"):
                    placeholder_value = str(getattr(self, placeholder_key[:-2])())
                else:
                    placeholder_value = str(getattr(self, placeholder_key))
                # Apply date format
                if is_date:
                    jflow_date_format = self.jflow_config_reader.get_date_format()
                    placeholder_value = time.strftime(jflow_date_format + " %H:%M:%S", time.gmtime(float(placeholder_value)))
                new_text = new_text.replace("###" + placeholder + "###", placeholder_value)
            except:
                pass
        return new_text

671
672
    def _send_email(self):
        import smtplib
673
        from email.mime.text import MIMEText
674
        smtps, smtpp, froma, fromp, toa, subject, message = self.jflow_config_reader.get_email_options()
675
676
677
678
679
        
        if self.__to_address: toa = self.__to_address
        if self.__subject: subject = self.__subject
        if self.__message: message = self.__message
        
680
        if smtps and smtpp and froma and fromp:
681
682
            if not toa: toa = froma
            if validate_email(froma) and validate_email(toa):
683
684
685
686
687
                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:
688
                        message = Workflow.get_status_under_text_format(self, True, True, True)
689
                    message = self._get_cleaned_email_placeholders( message )
Jerome Mariette's avatar
Jerome Mariette committed
690
                    msg = MIMEText(message, 'html')
691
692
                    me = froma
                    you = toa
693
694
695
                    if not subject:
                        subject = "JFlow - Workflow #" + str(self.id) + " is " + self.get_status()
                    subject = self._get_cleaned_email_placeholders( subject )
696
697
698
699
700
701
702
                    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()
Jerome Mariette's avatar
Jerome Mariette committed
703
704
705
706
707
                    # if the SMTP server does not provides TLS or identification
                    try:
                        s.starttls()
                        s.login(me, fromp)
                    except smtplib.SMTPHeloError:
Jerome Mariette's avatar
Jerome Mariette committed
708
                        self._log("The server didn't reply properly to the HELO greeting.", level="warning", traceback=traceback.format_exc(chain=False))
Jerome Mariette's avatar
Jerome Mariette committed
709
                    except smtplib.SMTPAuthenticationError:
Jerome Mariette's avatar
Jerome Mariette committed
710
                        self._log("The server didn't accept the username/password combination.", level="warning", traceback=traceback.format_exc(chain=False))
Jerome Mariette's avatar
Jerome Mariette committed
711
                    except smtplib.SMTPException:
Jerome Mariette's avatar
Jerome Mariette committed
712
                        self._log("No suitable authentication method was found, or the server does not support the STARTTLS extension.", level="warning", traceback=traceback.format_exc(chain=False))
Jerome Mariette's avatar
Jerome Mariette committed
713
                    except RuntimeError:
Jerome Mariette's avatar
Jerome Mariette committed
714
                        self._log("SSL/TLS support is not available to your Python interpreter.", level="warning", traceback=traceback.format_exc(chain=False))
Jerome Mariette's avatar
Jerome Mariette committed
715
                    except:
Jerome Mariette's avatar
Jerome Mariette committed
716
                        self._log("Unhandled error when sending mail.", level="warning", traceback=traceback.format_exc(chain=False))
Jerome Mariette's avatar
Jerome Mariette committed
717
718
719
                    finally:
                        s.sendmail(me, [you], msg.as_string())
                        s.close()
720
                except:
Jerome Mariette's avatar
Jerome Mariette committed
721
                    self._log("Impossible to connect to smtp server '" + smtps + "'", level="warning", traceback=traceback.format_exc(chain=False))
722
    
723
724
725
726
    def get_parameters_per_groups(self):
        name = self.get_name()
        description = self.get_description()
        parameters = self.get_parameters()
727
728
        pgparameters, parameters_order = {}, []
        for param in parameters:
Jerome Mariette's avatar
Jerome Mariette committed
729
            if param.group not in parameters_order: parameters_order.append(param.group)
730
            if param.group in pgparameters:
731
                pgparameters[param.group].append(param)
Jerome Mariette's avatar
Jerome Mariette committed
732
            else:
733
734
                pgparameters[param.group] = [param]
        return [pgparameters, parameters_order]
Jerome Mariette's avatar
Jerome Mariette committed
735
    
736
737
738
    def get_parameters(self):
        params = []
        for param in self.params_order:
739
            for attribute_value in list(self.__dict__.values()):
740
741
742
743
                if (issubclass(attribute_value.__class__, AbstractParameter)) and param == attribute_value.name:
                    params.append(attribute_value)
        return params
    
744
    def get_exec_path(self, software):
745
746
747
748
749
        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)
750
        elif exec_path is None and utils.which(software) == None:
751
            raise Exception("'" + software + "' path connot be retrieved either in the PATH and in the application.properties file!")
752
753
754
        elif exec_path is None and utils.which(software) != None: 
            exec_path = software
        elif exec_path != None and not os.path.isfile(exec_path):
755
            raise Exception("'" + exec_path + "' set for '" + software + "' does not exists, please provide a valid path!")
756
        return exec_path
757
    
Jerome Mariette's avatar
Jerome Mariette committed
758
759
    def add_component(self, component_name, args=[], kwargs={}, component_prefix="default"):
        # first build and check if this component is OK
760
        if component_name in self.internal_components or component_name in self.external_components:
761
            
762
            if component_name in self.internal_components:
Jerome Mariette's avatar
Jerome Mariette committed
763
                my_pckge = __import__(self.internal_components[component_name], globals(), locals(), [component_name])
764
765
766
767
768
769
770
771
772
773
774
775
776
                # 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)
777
778
            
            # there is a dynamic component
779
            if cmpt_object.is_dynamic():
780
781
782
783
                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
784
                    self.components_to_exec.append(cmpt_object)
785
                    self.components.append(cmpt_object)
786
787
788
789
790
791
792
793
794
                    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
795
                    self.components_to_exec = []
796
                    self.components = []
797
798
799
            else:
                if self.component_nameids_is_init:
                    # add the component
800
                    self.components_to_exec.append(cmpt_object)
801
                    self.components.append(cmpt_object)
802
                elif not self.component_nameids_is_init and not self.dynamic_component_present:
Jerome Mariette's avatar
Jerome Mariette committed
803
804
805
                    if self._component_is_duplicated(cmpt_object):
                        raise ValueError("Component " + cmpt_object.__class__.__name__ + " with prefix " + 
                                            cmpt_object.prefix + " already exist in this pipeline!")
806
                    self.components_to_exec.append(cmpt_object)
807
                    self.components.append(cmpt_object)
808
809
810
811
812
813
                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

814
815
            return cmpt_object
        else:
816
            raise ImportError(component_name + " component cannot be loaded, available components are: {0}".format(
817
                                           ", ".join(list(self.internal_components.keys()) + list(self.external_components.keys()))))
Jerome Mariette's avatar
Jerome Mariette committed
818
819
820
821
822
823
824
825
    
    def pre_process(self):
        pass
    
    def process(self):
        """ 
        Run the workflow, has to be implemented by subclasses
        """
826
        raise NotImplementedError( "Workflow.process() must be implemented in " + self.__class__.__name__ )
827
828
829

    def get_name(self):
        """ 
830
        Return the workflow name.
831
        """
Jerome Mariette's avatar
Jerome Mariette committed
832
        return self.__class__.__name__.lower()
833
834
835
836
837
    
    def get_description(self):
        """ 
        Return the workflow description, has to be implemented by subclasses
        """
838
        raise NotImplementedError( "Workflow.get_description() must be implemented in " + self.__class__.__name__ )
839
    
840
    def define_parameters(self, function="process"):
841
842
843
        """ 
        Define the workflow parameters, has to be implemented by subclasses
        """
844
        raise NotImplementedError( "Workflow.define_parameters() must be implemented in " + self.__class__.__name__ )
Jerome Mariette's avatar
Jerome Mariette committed
845
846
847
848
849
850
851
852
853
854
855
856
    
    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):
857
        return list(self.component_nameids.keys())
Jerome Mariette's avatar
Jerome Mariette committed
858
    
Jerome Mariette's avatar
Jerome Mariette committed
859
860
    def wf_execution_wrapper(self):
        getattr(self, self.function)()
Jerome Mariette's avatar
Jerome Mariette committed
861
    
Jerome Mariette's avatar
Jerome Mariette committed
862
863
864
865
    def run(self):
        """
        Only require for Threading
        """
866
867
        try:
            # if this is the first time the workflow run
868
            if self.__step == None:
869
                self.start_time = time.time()
Jerome Mariette's avatar
Jerome Mariette committed
870
                self.__step = 0
871
872
                self._status = self.STATUS_STARTED
                self._postprocess_status = self.STATUS_PENDING
873
                self.end_time = None
Jerome Mariette's avatar
Jerome Mariette committed
874
                # if some args are provided, let's fill the parameters
875