workflow.py 40.3 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 urllib2 
Jerome Mariette's avatar
Jerome Mariette committed
29
import types
Jerome Mariette's avatar
Jerome Mariette committed
30
import logging
Jerome Mariette's avatar
Jerome Mariette committed
31

32
from logging import FileHandler
Jerome Mariette's avatar
Jerome Mariette committed
33
from ConfigParser import ConfigParser, NoOptionError
Jerome Mariette's avatar
Jerome Mariette committed
34
from inspect import getcallargs
Jerome Mariette's avatar
Jerome Mariette committed
35
from urlparse import urlparse
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
39
import jflow.utils as utils
from jflow.workflows_manager import WorkflowsManager, JFlowConfigReader
40
from jflow.parameter import *
Jerome Mariette's avatar
Jerome Mariette committed
41
42
43
44
45
46
47
48
49
50
51
52

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
53

Jerome Mariette's avatar
Jerome Mariette committed
54
55
56
57
58
59
class Workflow(threading.Thread):
    """
    """

    PROPERTIES_FILE_NAME = "workflow.properties"
    MAKEFLOW_LOG_FILE_NAME = "Makeflow.makeflowlog"
60
    DUMP_FILE_NAME = ".workflow.dump"
Jerome Mariette's avatar
Jerome Mariette committed
61
62
63
64
65
    WORKING = ".working"
    STATUS_STARTED = "started"
    STATUS_COMPLETED = "completed"
    STATUS_FAILED = "failed"
    STATUS_ABORTED = "aborted"
Jerome Mariette's avatar
Jerome Mariette committed
66

67
    def __init__(self, args={}, id=None, function= "process", parameters_section=None):
Jerome Mariette's avatar
Jerome Mariette committed
68
69
70
71
72
73
        """ 
        """
        # define as a thread
        threading.Thread.__init__(self)
        self.jflow_config_reader = JFlowConfigReader()
        self.manager = WorkflowsManager()
74
        self.components_to_exec = []
75
        self.components = []
Jerome Mariette's avatar
Jerome Mariette committed
76
77
78
79
80
81
        self.makes = {}
        self.globals = {}
        self.options = Options()
        self.status = self.STATUS_STARTED
        self.start_time = None
        self.end_time = None
82
        self.step = None
Frédéric Escudié's avatar
Frédéric Escudié committed
83
        self.stderr = None
84
        self.dynamic_component_present = False
85
86
        self.function = function
        self.parameters_section = parameters_section
Jerome Mariette's avatar
Jerome Mariette committed
87
        self.comp_pckg = self._import_components()
88
        # intruduce --log-verbose to be able to monitor the new version of makeflow >=4.2.2
Jerome Mariette's avatar
Jerome Mariette committed
89
        self.engine_arguments = ' --log-verbose '
90
        self.component_nameids_is_init = False
Jerome Mariette's avatar
Jerome Mariette committed
91
92
93
        self.component_nameids = {}
        # try to parse engine arguments
        try:
94
95
            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
96
97
98
            if type: self.engine_arguments += ' -T ' + type
            if options : self.engine_arguments += ' -B "' + options + '"'
        except: self.engine_arguments = None
Jerome Mariette's avatar
Jerome Mariette committed
99
        
Jerome Mariette's avatar
Jerome Mariette committed
100
        self.id = id
101
102
103
104
105
106
107
108
109
110
111
        self.name = self.get_name()
        self.description = self.get_description()
        
        # define the parameters 
        self.params_order = []
        self.define_parameters(self.parameters_section)
        # add the metadata parameter
        self.add_parameter("metadata", "Which metadata should be linked to this workflow", is_list=True)
        # if some args are provided, let's fill the parameters
        if args: self._set_parameters(args)

Jerome Mariette's avatar
Jerome Mariette committed
112
113
114
115
        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
116
            if self.stderr is None:
117
                self.set_stderr()
Jerome Mariette's avatar
Jerome Mariette committed
118
            self._serialize()
119
    
120
121
122
123
124
125
126
127
128
129
130
131
132
    def add_input_file(self, name, help, file_format="any", default=None, type=types.StringType, choices=None, 
                       required=False, flag=None, group="default", display_name=None, is_list=False, add_to=None):
        
        if is_list:
            if default == None: default = []
            new_param = InputFileList(name, help, flag=flag, file_format=file_format, default=default, type=type, 
                                      choices=choices, required=required, group=group, display_name=display_name)
        else:
            new_param = InputFile(name, help, flag=flag, file_format=file_format, default=default, type=type, 
                                  choices=choices, 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
133
                self.__getattribute__(add_to).add_sub_parameter(new_param)
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
            except: pass
        # otherwise, add it to the class itself
        else:
            self.params_order.append(name)
            self.__setattr__(name, new_param)

    def add_output_file(self, name, help, file_format="any", default=None, type=types.StringType, choices=None, 
                        required=False, flag=None, group="default", display_name=None, is_list=False, add_to=None):
        if is_list:
            if default == None: default = []
            new_param = OutputFileList(name, help, flag=flag, file_format=file_format, default=default, type=type, 
                                       choices=choices, required=required, group=group, display_name=display_name)
        else:
            new_param = OutputFile(name, help, flag=flag, file_format=file_format, default=default, type=type, 
                                   choices=choices, 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
152
                self.__getattribute__(add_to).add_sub_parameter(new_param)
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
            except: pass
        # otherwise, add it to the class itself
        else:
            self.params_order.append(name)
            self.__setattr__(name, new_param)
    
    def add_multiple_parameter(self, name, help, required=False, flag=None, group="default", display_name=None, is_list=False):
        self.params_order.append(name)
        if is_list:
            new_param = MultiParameterList(name, help, flag=flag, required=required, group=group, display_name=display_name)
        else:
            new_param = MultiParameter(name, help, flag=flag, required=required, group=group, display_name=display_name)
        self.__setattr__(name, new_param)
    
    def add_parameter(self, name, help, default=None, type=types.StringType, choices=None, required=False, 
                      flag=None, group="default", display_name=None, is_list=False, add_to=None):
        if is_list:
            if default == None: default = []
            new_param = ParameterList(name, help, flag=flag, default=default, type=type, choices=choices, 
                                      required=required, group=group, display_name=display_name)
        else:
            new_param = Parameter(name, help, flag=flag, default=default, type=type, choices=choices, 
                                  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
179
                self.__getattribute__(add_to).add_sub_parameter(new_param)
180
181
182
183
184
185
186
187
188
            except: pass
        # otherwise, add it to the class itself
        else:
            self.params_order.append(name)
            self.__setattr__(name, new_param)
    
    def _set_parameters(self, args):
        parameters = self.get_parameters()
        for param in parameters:
Jerome Mariette's avatar
help ok    
Jerome Mariette committed
189
190
191
192
193
194
195
196
197
198
199
200
201
202
            if args[param.name]:
                try: args[param.name] = args[param.name].encode('ascii','ignore')
                except: pass
                if param.__class__ ==  Parameter:
                    new_param = Parameter(param.name, param.help, default=args[param.name], type=param.type, choices=param.choices, 
                                          required=param.required, flag=param.flag, group=param.group, display_name=param.display_name)
                    self.__setattr__(param.name, new_param)
                elif param.__class__ == InputFile:
                    new_param = InputFile(param.name, param.help, file_format=param.file_format, default=args[param.name], type=param.type, 
                                          choices=param.choices, required=param.required, flag=param.flag, 
                                          group=param.group, display_name=param.display_name)
                    self.__setattr__(param.name, new_param)
                elif param.__class__ ==  ParameterList or param.__class__ ==  InputFileList:
                    self.__getattribute__(param.name).extend(args[param.name])
Jerome Mariette's avatar
Jerome Mariette committed
203
204
205
206
207
208
209
210
211
212
                elif param.__class__ == MultiParameter:
                    sub_args = {}
                    for sarg in args[param.name]:
                        sub_args[sarg[0]] = sarg[1]
                    for sub_param in param.sub_parameters:
                        if sub_args.has_key(sub_param.flag):
                            self.__getattribute__(param.name)[sub_param.name] = sub_args[sub_param.flag]
                        else:
                            self.__getattribute__(param.name)[sub_param.name] = self.__getattribute__(param.name).default[sub_param.name]
                            
213
    """
Jerome Mariette's avatar
help ok    
Jerome Mariette committed
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
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
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
    def _get_from_config(self, parameters_section):
        reader = ConfigParser()
        reader.read(self._get_property_path())
        parameters, param_order = [], []
        try:
            params, sub_order, excludes, hash_params = {}, {}, [], {}
            # first grab all parameters name
            for param in reader.items(parameters_section):
                cvalue = reader.get(parameters_section, param[0])
                cparam = param[0].split(".")[0]
                ckey = ".".join(param[0].split(".")[1:])
                if len(ckey.split(".")) > 1:
                    if sub_order.has_key(cparam):
                        if ckey.split(".")[0] not in sub_order[cparam]: sub_order[cparam].append(ckey.split(".")[0])
                    else:
                        sub_order[cparam] =[ckey.split(".")[0]]
                if not params.has_key(cparam):
                    params[cparam] = {ckey: cvalue}
                else:
                    params[cparam][ckey] = cvalue
                if cparam not in param_order: param_order.append(cparam)
            
            for param_name in param_order:
                sub_params, current_params, sub_objs, sub_excludes, hash_sub_params = {}, {}, [], [], {}
                for param in params[param_name]:
                    sub_params_values = param.split(".")
                    if len(sub_params_values) == 2:
                        # TODO: handle exclusive for sub parameter
                        key = None
                        if sub_params_values[1] == "name": 
                            key = "display_name"
                        else:
                            key = sub_params_values[1]
                        if key == "exclude":
                            found = False
                            for exclude_group in sub_excludes:
                                if sub_params_values[0] in exclude_group:
                                    exclude_group.append(params[param_name][param])
                                    found = True
                                elif params[param_name][param] in exclude_group:
                                    exclude_group.append(sub_params_values[0])
                                    found = True
                            if not found: sub_excludes.append([sub_params_values[0], params[param_name][param]])
                        else:
                            if not sub_params.has_key(sub_params_values[0]):
                                sub_params[sub_params_values[0]] = {key: params[param_name][param]}
                                sub_params[sub_params_values[0]]["name"] = sub_params_values[0]
                            else:
                                sub_params[sub_params_values[0]][key] = params[param_name][param]
                    else:
                        if param == "name": current_params["display_name"] = params[param_name][param]
                        elif param == "exclude":
                            found = False
                            for exclude_group in excludes:
                                if param_name in exclude_group:
                                    exclude_group.append(params[param_name][param])
                                    found = True
                                elif params[param_name][param] in exclude_group:
                                    exclude_group.append(param_name)
                                    found = True
                            if not found: excludes.append([param_name, params[param_name][param]])
                        else: current_params[param] = params[param_name][param]
                current_params["name"] = param_name
                if sub_order.has_key(param_name):
                    for sub_param in sub_order[param_name]:
                        sub = Parameter(**sub_params[sub_param])
                        hash_sub_params[sub.name] = sub
                        sub_objs.append(sub)
                    # overwrite the group to exclude some parameters
                    for i, exclude_group in enumerate(sub_excludes):
                        group_name = "exclude-"+str(i)
                        for sparam in set(exclude_group):
                            hash_sub_params[sparam].group = group_name
                current_params["sub_parameters"] = sub_objs
                oparam = Parameter(**current_params)
                parameters.append(oparam)
                hash_params[oparam.name] = oparam
            # overwrite the group to exclude some parameters
            for i, exclude_group in enumerate(excludes):
                group_name = "exclude-"+str(i)
                for param in set(exclude_group):
                    hash_params[param].group = group_name
        except:
            pass
        # finally add the metadata parameter
        metadata = Parameter(name="metadata", flag="--metadata", help="Which metadata should be linked to this workflow", 
                             action="append", display_name="Metadata")
        parameters.append(metadata)
        return [reader.get("global", "name"),
                reader.get("global", "description"),
                parameters]
    
    
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
    def _extend_and_format_args(self, parameters, args):
        extended_args = {}
        for param in parameters:
            try: args[param.name] = args[param.name].encode('ascii','ignore')
            except: pass
            # if this parameter has been modified by the user
            if args.has_key(param.name):
                if param.action == MiltipleAppendAction:
                    extended_args[param.name] = []
                    for arg in args[param.name]:
                        sub_hash = {}
                        for sub_param in param.sub_parameters:
                            # find the value
                            value = None
                            for values in arg:
                                if values[0] == sub_param.flag: 
                                    try: value = values[1].encode('ascii','ignore')
                                    except: value = values[1]
                            if value == None: value = sub_param.default
                            sub_hash[sub_param.name] = value
                        extended_args[param.name].append(sub_hash)
                # if it's an append parameter, the result should be a list
                elif param.action == "append":
                    if args[param.name]:
                        try: value = args[param.name].split(",") 
                        except: value = args[param.name]
                    else: value = []
                    extended_args[param.name] = value
                # if it's a date
                elif param.type == date:
                    if isinstance(args[param.name], str):
                        extended_args[param.name] = date(args[param.name])
                    else:
                        extended_args[param.name] = args[param.name]
                # if it's a boolean
                elif param.type == types.BooleanType:
                    extended_args[param.name] = args[param.name] in [True, 1, 'true', '1', 't', 'y', 'yes']
                elif param.type.__name__ == "MultipleParameters":
                    extended_args[param.name] = {}
                    for sub_param in param.sub_parameters:
                        # find the value
                        value = None
                        for values in args[param.name]:
                            if values[0] == sub_param.flag:
                                try: value = values[1].encode('ascii','ignore')
                                except: value = values[1]
                        if value == None: value = sub_param.default
                        extended_args[param.name][sub_param.name] = value
                else:
                    extended_args[param.name] = args[param.name]
            # otherwise use the default
            else:
                if param.type.__name__ == "MultipleParameters":
                    extended_args[param.name] = {}
                    for sub_param in param.sub_parameters:
                        extended_args[param.name][sub_param.name] = sub_param.default
                else:
                    extended_args[param.name] = param.default
        return extended_args
    """
    
    
369
370
371
372
373
374
375
376
377
378
379
380
381
    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()) + "wf_stderr.old") )
        stderr = os.path.join(self.directory, "wf_stderr.txt")
        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)
        self.stderr = stderr
    
382
    @staticmethod
383
    def config_parser(arg_lines):
384
385
        for arg in arg_lines:
            yield arg
386
    
387
    def get_errors(self):
Frédéric Escudié's avatar
Frédéric Escudié committed
388
389
390
391
392
393
        error = {
                 "title"     : "",
                 "msg"       : list(),
                 "traceback" : list()
        }
        line_idx = 0
394
395
396
        FH_stderr = open( self.stderr )
        lines = FH_stderr.readlines()
        while line_idx < len(lines):
Frédéric Escudié's avatar
Frédéric Escudié committed
397
398
399
400
401
402
            if lines[line_idx].strip().endswith("RunWorflowException"):
                error["title"]     = lines[line_idx].rstrip()
                error["msg"]       = list()
                error["traceback"] = list()
                line_idx += 2 # skip : "Traceback (most recent call last):"
                # Traceback
403
                while lines[line_idx] != lines[line_idx].lstrip():
Frédéric Escudié's avatar
Frédéric Escudié committed
404
405
406
407
                    error["traceback"].append({ 
                                               "location" : lines[line_idx].strip(),
                                               "line"     : lines[line_idx].strip()
                    })
408
                    line_idx += 2
Frédéric Escudié's avatar
Frédéric Escudié committed
409
410
411
412
413
                # Error message
                while line_idx < len(lines) and not lines[line_idx].strip().endswith("RunWorflowException"):
                    error["msg"].append( lines[line_idx].strip() )
                    line_idx += 1
                line_idx -= 1
414
415
            line_idx += 1
        FH_stderr.close()
Frédéric Escudié's avatar
Frédéric Escudié committed
416
417
418
419
420
421
        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
422
    
Philippe Bardou's avatar
Philippe Bardou committed
423
    def get_outputs_per_components(self, web_path):
424
425
        outputs_files = {}
        for current_components in self.components:
Philippe Bardou's avatar
Philippe Bardou committed
426
            #status = self.get_component_status(current_components.get_nameid())
Philippe Bardou's avatar
Philippe Bardou committed
427
            outputs_files[current_components.get_nameid()] = current_components.get_component_outputs(web_path)
Philippe Bardou's avatar
Philippe Bardou committed
428
            #outputs_files["0"] = status["completed"]
429
430
        return outputs_files
    
Jerome Mariette's avatar
Jerome Mariette committed
431
432
433
434
435
436
437
438
439
440
441
442
443
444
    def __setstate__(self, state):
        self.__dict__ = state.copy()
        threading.Thread.__init__(self, name=self.name)
        
    def __getstate__(self):
        """
        Threading uses Lock Object, do not consider these objects when serializing a workflow
        """
        odict = self.__dict__.copy()
        del odict['_Thread__started']
        del odict['_Thread__block']
        del odict['_Thread__stderr']
        return odict
    
445
446
447
448
    def get_parameters_per_groups(self):
        name = self.get_name()
        description = self.get_description()
        parameters = self.get_parameters()
449
450
        pgparameters, parameters_order = {}, []
        for param in parameters:
Jerome Mariette's avatar
Jerome Mariette committed
451
            if param.group not in parameters_order: parameters_order.append(param.group)
452
453
            if pgparameters.has_key(param.group):
                pgparameters[param.group].append(param)
Jerome Mariette's avatar
Jerome Mariette committed
454
            else:
455
456
                pgparameters[param.group] = [param]
        return [pgparameters, parameters_order]
Jerome Mariette's avatar
Jerome Mariette committed
457
    
458
459
460
461
462
463
464
465
    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
    
466
    def get_exec_path(self, software):
467
468
469
470
471
        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)
472
        elif exec_path is None and utils.which(software) == None:
473
474
            sys.stderr.write("Error: '" + software + "' path connot be retrieved either in the PATH and in the application.properties file!\n")
            sys.exit(1)
475
476
477
478
479
        elif exec_path is None and utils.which(software) != None: 
            exec_path = software
        elif exec_path != None and not os.path.isfile(exec_path):
            sys.stderr.write("Error: '" + exec_path + "' set for '" + software + "' does not exists, please provide a valid path!\n")
            sys.exit(1)
480
        return exec_path
481
    
Jerome Mariette's avatar
Jerome Mariette committed
482
483
    def add_component(self, component_name, args=[], kwargs={}, component_prefix="default"):
        # first build and check if this component is OK
484
485
486
487
488
489
490
491
        if self.comp_pckg.has_key(component_name):
            my_pckge = __import__(self.comp_pckg[component_name], globals(), locals(), [component_name], -1)
            # build the object and define required field
            cmpt_object = getattr(my_pckge, component_name)()
            cmpt_object.output_directory = self.get_component_output_directory(component_name, component_prefix)
            cmpt_object.prefix = component_prefix
            if kwargs: cmpt_object.define_parameters(**kwargs)
            else: cmpt_object.define_parameters(*args)
492
493
            
            # there is a dynamic component
494
            if cmpt_object.is_dynamic():
495
496
497
498
                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
499
                    self.components_to_exec.append(cmpt_object)
500
                    self.components.append(cmpt_object)
501
502
503
504
505
506
507
508
509
                    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
510
                    self.components_to_exec = []
511
                    self.components = []
512
513
514
            else:
                if self.component_nameids_is_init:
                    # add the component
515
                    self.components_to_exec.append(cmpt_object)
516
                    self.components.append(cmpt_object)
517
                elif not self.component_nameids_is_init and not self.dynamic_component_present:
Jerome Mariette's avatar
Jerome Mariette committed
518
519
520
                    if self._component_is_duplicated(cmpt_object):
                        raise ValueError("Component " + cmpt_object.__class__.__name__ + " with prefix " + 
                                            cmpt_object.prefix + " already exist in this pipeline!")
521
                    self.components_to_exec.append(cmpt_object)
522
                    self.components.append(cmpt_object)
523
524
525
526
527
528
                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

529
530
            return cmpt_object
        else:
Jerome Mariette's avatar
Jerome Mariette committed
531
            raise ImportError(component_name + " component cannot be loaded, available components are: {0}".format(", ".join(self.comp_pckg.keys())))
Jerome Mariette's avatar
Jerome Mariette committed
532
533
534
535
536
537
538
539
540
    
    def pre_process(self):
        pass
    
    def process(self):
        """ 
        Run the workflow, has to be implemented by subclasses
        """
        raise NotImplementedError
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558

    def get_name(self):
        """ 
        Return the workflow name, has to be implemented by subclasses
        """
        raise NotImplementedErro
    
    def get_description(self):
        """ 
        Return the workflow description, has to be implemented by subclasses
        """
        raise NotImplementedErrorr
    
    def define_parameters(self, parameters_section=None):
        """ 
        Define the workflow parameters, has to be implemented by subclasses
        """
        raise NotImplementedError
Jerome Mariette's avatar
Jerome Mariette committed
559
560
561
562
563
564
565
566
567
568
569
570
571
572
    
    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
573
574
    def wf_execution_wrapper(self):
        getattr(self, self.function)()
Jerome Mariette's avatar
Jerome Mariette committed
575
    
Jerome Mariette's avatar
Jerome Mariette committed
576
577
578
579
    def run(self):
        """
        Only require for Threading
        """
580
581
582
583
584
585
586
        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
587
                self._serialize()
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
            # 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:
                try: 
                    self.wf_execution_wrapper()
                except SystemExit, e: 
                    self.status = self.STATUS_FAILED
                    self.end_time = time.time()
                    self._serialize()
                    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:
                try: 
                    self.wf_execution_wrapper()
                except SystemExit, e: 
                    self.status = self.STATUS_FAILED
                    self.end_time = time.time()
                    self._serialize()
                    raise
                if len(self.components_to_exec) > 0:
                    self._execute_weaver()
620
                self.step = 3
621
622
623
624
625
                self._serialize()
            # if post processing has ne been done yet
            if self.step == 3:
                self.post_process()
                if self.status == self.STATUS_STARTED: self.status = self.STATUS_COMPLETED        
626
627
                self.end_time = time.time()
                self._serialize()
628
629
630
631
        except:
            logging.getLogger("wf." + str(self.id)).exception("RunWorflowException")
            raise
            
Jerome Mariette's avatar
Jerome Mariette committed
632
    
Jerome Mariette's avatar
Jerome Mariette committed
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
    def _download_urlfile(self, input):
        try:
            uri_object = urlparse(input)
            opener = urllib2.urlopen(input)
            block_size = 8000
            jflowconf = JFlowConfigReader()
            tmp_directory = os.path.join(jflowconf.get_tmp_directory(), os.path.basename(tempfile.NamedTemporaryFile().name))
            os.mkdir(tmp_directory) 
            file_path = os.path.join(tmp_directory, os.path.basename(uri_object.path))
            local_file = open(file_path, 'wb')
            if os.path.basename(uri_object.path) is not None and os.path.basename(uri_object.path) != "":
                metadata = opener.info()
                file_size = int(metadata.getheaders("Content-Length")[0])
                while True:
                    buffer = opener.read(block_size)
                    # End of download
                    if not buffer: break
                    # Parts of download
                    local_file.write(buffer)
                local_file.close()
                logging.getLogger("types.urlfile").debug("URL file '{0}' successfully downloaded as: {1}".format(input, file_path))
Jerome Mariette's avatar
Jerome Mariette committed
654
            return [file_path, True]
Jerome Mariette's avatar
Jerome Mariette committed
655
        except:
Jerome Mariette's avatar
Jerome Mariette committed
656
            return [input, False]
Jerome Mariette's avatar
Jerome Mariette committed
657
    
Jerome Mariette's avatar
Jerome Mariette committed
658
659
660
661
    def _prepare_input_files(self, parameters, args):
        kparams = {}
        for param in parameters:
            kparams[param.name] = param
Jerome Mariette's avatar
Jerome Mariette committed
662
663
        new_args = args
        for param in args.keys():
Jerome Mariette's avatar
Jerome Mariette committed
664
665
666
667
668
669
670
671
672
673
674
675
            is_uri, is_local = False, False
            # handle url inputs
            if kparams[param].type.__name__ == "inputfile" or kparams[param].type.__name__ == "urlfile":
                if args[param].__class__.__name__ == "list":
                    for i, val in enumerate(args[param]):
                        new_args[param][i], is_uri = self._download_urlfile(args[param][i])
                else:
                    new_args[param], is_uri = self._download_urlfile(args[param])
            
            # handle upload inputs
            try: is_local = os.path.isfile(args[param])
            except: is_local = False
676
            if not is_uri and not is_local and (kparams[param].type.__name__ == "inputfile" or kparams[param].type.__name__ == "browsefile"):
Jerome Mariette's avatar
Jerome Mariette committed
677
678
679
680
681
682
683
684
                if args[param].__class__.__name__ == "list":
                    for i, val in enumerate(args[param]):
                        if args[param][i]:
                            new_args[param][i] = os.path.join(self.jflow_config_reader.get_tmp_directory(), (args[param][i]))
                else:
                    if args[param]:
                        new_args[param] = os.path.join(self.jflow_config_reader.get_tmp_directory(), (args[param]))

Jerome Mariette's avatar
Jerome Mariette committed
685
686
        return new_args
    
Jerome Mariette's avatar
Jerome Mariette committed
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
    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)
            if self.STATUS_ABORTED in make_states:
                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
    
711
712
713
    def get_resource(self, resource):
        return self.jflow_config_reader.get_resource(resource)
    
Jerome Mariette's avatar
Jerome Mariette committed
714
715
716
717
718
719
720
    def get_component_status(self, component_nameid):
        status = {"time": 0.0,
                  "tasks": 0,
                  "waiting": 0,
                  "running": 0,
                  "failed":0,
                  "aborted": 0,
721
722
                  "completed": 0,
                  "failed_commands": list() }
Jerome Mariette's avatar
Jerome Mariette committed
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
        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
739
                        status["failed_commands"].append( n.command )
Jerome Mariette's avatar
Jerome Mariette committed
740
741
742
743
744
                    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
745
        return status
Jerome Mariette's avatar
Jerome Mariette committed
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
    
    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))

    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:
778
                        for component in self.components_to_exec:
Jerome Mariette's avatar
Jerome Mariette committed
779
                            nest.symbol = component.get_nameid()
780
                            nest.batch = component.batch_options
Jerome Mariette's avatar
Jerome Mariette committed
781
782
783
784
785
786
                            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
787
                        self.end_time = time.time()
Jerome Mariette's avatar
Jerome Mariette committed
788
                        self._serialize()
Jerome Mariette's avatar
Jerome Mariette committed
789
                        raise
790
                self.components_to_exec = []  
Jerome Mariette's avatar
Jerome Mariette committed
791
792
793
794
795
796
797
798
                # 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
799
                    raise
Jerome Mariette's avatar
Jerome Mariette committed
800
801
802

    def _get_current_make(self):
        current_component, make_directory, new_make = [], None, False
803
        for component in self.components_to_exec:
Jerome Mariette's avatar
Jerome Mariette committed
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
            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()

821
822
    def _component_is_duplicated(self, component):
        if component.get_nameid() in self.component_nameids.keys():
Jerome Mariette's avatar
Jerome Mariette committed
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
            return True
        return False

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

    def _import_components(self):
        pckge = {}
        # then import pipeline packages
        pipeline_dir = os.path.dirname(inspect.getfile(self.__class__))
        for importer, modname, ispkg in pkgutil.iter_modules([os.path.join(pipeline_dir, "components")], "workflows." + 
                                                             os.path.basename(pipeline_dir) + ".components."):
Jerome Mariette's avatar
Jerome Mariette committed
839
840
841
842
843
            try:
                m = __import__(modname)
                for class_name, obj in inspect.getmembers(sys.modules[modname], inspect.isclass):
                    if issubclass(obj, jflow.component.Component) and obj.__name__ != jflow.component.Component.__name__:
                        pckge[class_name] = modname
Jerome Mariette's avatar
Jerome Mariette committed
844
            except Exception as e:
Jerome Mariette's avatar
Jerome Mariette committed
845
                logging.getLogger("Workflow._import_components").debug("Component <{0}> cannot be loaded: {1}".format(modname, e))
Jerome Mariette's avatar
Jerome Mariette committed
846
847
848
        # finally import workflows shared packages
        workflows_dir = os.path.dirname(os.path.dirname(inspect.getfile(self.__class__)))
        for importer, modname, ispkg in pkgutil.iter_modules([os.path.join(workflows_dir, "components")], "workflows.components."):
Jerome Mariette's avatar
Jerome Mariette committed
849
850
851
852
853
            try:
                m = __import__(modname)
                for class_name, obj in inspect.getmembers(sys.modules[modname], inspect.isclass):
                    if issubclass(obj, jflow.component.Component) and obj.__name__ != jflow.component.Component.__name__:
                        pckge[class_name] = modname
Jerome Mariette's avatar
Jerome Mariette committed
854
855
            except Exception as e:
                logging.getLogger("Workflow._import_components").debug("Component <{0}> cannot be loaded: {1}".format(modname, e))
Jerome Mariette's avatar
Jerome Mariette committed
856
857
858
859
860
861
862
863
864
865
866
867
        return pckge

    def _import(self, module, symbols):
        """ Import ``symbols`` from ``module`` into global namespace. """
        # Import module
        m = 'weaver.{0}'.format(module)
        m = __import__(m, self.globals, self.globals, symbols, -1)

        # Import symbols from module into global namespace, which we store as
        # an attribute for later use (i.e. during compile)
        for symbol in symbols:
            self.globals[symbol] = getattr(m, symbol)