workflow.py 33 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 Parameter, date, MiltipleAppendAction
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="parameters"):
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
83
        self.dynamic_component_present = False
84
85
        self.function = function
        self.parameters_section = parameters_section
Jerome Mariette's avatar
Jerome Mariette committed
86
87
        self.comp_pckg = self._import_components()
        self.engine_arguments = ''
88
        self.component_nameids_is_init = False
Jerome Mariette's avatar
Jerome Mariette committed
89
90
91
        self.component_nameids = {}
        # try to parse engine arguments
        try:
92
93
            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
94
95
96
            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
97
98
        try:
            # Add config information
99
            self.name, self.description, self.parameters = self._get_from_config(self.parameters_section)
Jerome Mariette's avatar
Jerome Mariette committed
100
101
102
        except:
            raise IOError(self.__class__.__name__ + " workflow property file not found or invalid.")
        
Jerome Mariette's avatar
Jerome Mariette committed
103
        self.id = id
Jerome Mariette's avatar
Jerome Mariette committed
104
        self.args = self._extend_and_format_args(self.parameters, args)
Jerome Mariette's avatar
Jerome Mariette committed
105
        self.args = self._prepare_input_files(self.parameters, self.args)
Jerome Mariette's avatar
Jerome Mariette committed
106
        self.metadata = self.args["metadata"]
Jerome Mariette's avatar
Jerome Mariette committed
107
108
109
110
        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)
111
112
            if not hasattr(self, "stderr") or self.stderr is None:
                self.set_stderr()
Jerome Mariette's avatar
Jerome Mariette committed
113
            self._serialize()
114
    
115
116
117
118
119
120
121
122
123
124
125
126
127
    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
    
128
    @staticmethod
129
    def config_parser(arg_lines):
130
131
        for arg in arg_lines:
            yield arg
132
    
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
    def get_errors(self):
        error_msg = list()
        last_stacktrace_location = ""
        FH_stderr = open( self.stderr )
        lines = FH_stderr.readlines()
        line_idx = 0
        while line_idx < len(lines):
            if lines[line_idx].startswith("Traceback"):
                line_idx += 1
                while lines[line_idx] != lines[line_idx].lstrip():
                    last_stacktrace_location = lines[line_idx].lstrip()
                    line_idx += 2
            if not lines[line_idx].strip().endswith("RunWorflowException"):
                error_msg.append( lines[line_idx].strip() )
            line_idx += 1
        FH_stderr.close()
        return { "msg" : error_msg, "location" : last_stacktrace_location }
    
Philippe Bardou's avatar
Philippe Bardou committed
151
    def get_outputs_per_components(self, web_path):
152
153
        outputs_files = {}
        for current_components in self.components:
Philippe Bardou's avatar
Philippe Bardou committed
154
            #status = self.get_component_status(current_components.get_nameid())
Philippe Bardou's avatar
Philippe Bardou committed
155
            outputs_files[current_components.get_nameid()] = current_components.get_component_outputs(web_path)
Philippe Bardou's avatar
Philippe Bardou committed
156
            #outputs_files["0"] = status["completed"]
157
158
        return outputs_files
    
Jerome Mariette's avatar
Jerome Mariette committed
159
160
161
162
163
164
165
166
167
168
169
170
171
172
    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
    
173
174
175
176
    def get_parameters_per_groups(self, parameters_section="parameters"):
        name, description, parameters = self._get_from_config(parameters_section)
        pgparameters, parameters_order = {}, []
        for param in parameters:
Jerome Mariette's avatar
Jerome Mariette committed
177
            if param.group not in parameters_order: parameters_order.append(param.group)
178
179
            if pgparameters.has_key(param.group):
                pgparameters[param.group].append(param)
Jerome Mariette's avatar
Jerome Mariette committed
180
            else:
181
182
                pgparameters[param.group] = [param]
        return [pgparameters, parameters_order]
Jerome Mariette's avatar
Jerome Mariette committed
183
    
184
    def get_exec_path(self, software):
185
186
187
188
189
        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)
190
        elif exec_path is None and utils.which(software) == None:
191
192
            sys.stderr.write("Error: '" + software + "' path connot be retrieved either in the PATH and in the application.properties file!\n")
            sys.exit(1)
193
194
195
196
197
        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)
198
        return exec_path
199
    
Jerome Mariette's avatar
Jerome Mariette committed
200
201
    def add_component(self, component_name, args=[], kwargs={}, component_prefix="default"):
        # first build and check if this component is OK
202
203
204
205
206
207
208
209
        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)
210
211
            
            # there is a dynamic component
212
            if cmpt_object.is_dynamic():
213
214
215
216
                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
217
                    self.components_to_exec.append(cmpt_object)
218
                    self.components.append(cmpt_object)
219
220
221
222
223
224
225
226
227
                    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
228
                    self.components_to_exec = []
229
                    self.components = []
230
231
232
            else:
                if self.component_nameids_is_init:
                    # add the component
233
                    self.components_to_exec.append(cmpt_object)
234
                    self.components.append(cmpt_object)
235
                elif not self.component_nameids_is_init and not self.dynamic_component_present:
Jerome Mariette's avatar
Jerome Mariette committed
236
237
238
                    if self._component_is_duplicated(cmpt_object):
                        raise ValueError("Component " + cmpt_object.__class__.__name__ + " with prefix " + 
                                            cmpt_object.prefix + " already exist in this pipeline!")
239
                    self.components_to_exec.append(cmpt_object)
240
                    self.components.append(cmpt_object)
241
242
243
244
245
246
                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

247
248
            return cmpt_object
        else:
Jerome Mariette's avatar
Jerome Mariette committed
249
            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
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
    
    def pre_process(self):
        pass
    
    def process(self):
        """ 
        Run the workflow, has to be implemented by subclasses
        """
        raise NotImplementedError
    
    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
273
274
    def wf_execution_wrapper(self):
        getattr(self, self.function)()
Jerome Mariette's avatar
Jerome Mariette committed
275
    
Jerome Mariette's avatar
Jerome Mariette committed
276
277
278
279
    def run(self):
        """
        Only require for Threading
        """
280
281
282
283
284
285
286
        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
287
                self._serialize()
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
            # 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()
320
                self.step = 3
321
322
323
324
325
                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        
326
327
                self.end_time = time.time()
                self._serialize()
328
329
330
331
        except:
            logging.getLogger("wf." + str(self.id)).exception("RunWorflowException")
            raise
            
Jerome Mariette's avatar
Jerome Mariette committed
332
    
Jerome Mariette's avatar
Jerome Mariette committed
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
    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
354
            return [file_path, True]
Jerome Mariette's avatar
Jerome Mariette committed
355
        except:
Jerome Mariette's avatar
Jerome Mariette committed
356
            return [input, False]
Jerome Mariette's avatar
Jerome Mariette committed
357
    
Jerome Mariette's avatar
Jerome Mariette committed
358
359
360
361
    def _prepare_input_files(self, parameters, args):
        kparams = {}
        for param in parameters:
            kparams[param.name] = param
Jerome Mariette's avatar
Jerome Mariette committed
362
363
        new_args = args
        for param in args.keys():
Jerome Mariette's avatar
Jerome Mariette committed
364
365
366
367
368
369
370
371
372
373
374
375
            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
376
            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
377
378
379
380
381
382
383
384
                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
385
386
        return new_args
    
Jerome Mariette's avatar
Jerome Mariette committed
387
    def _extend_and_format_args(self, parameters, args):
Jerome Mariette's avatar
Jerome Mariette committed
388
        extended_args = {}
Jerome Mariette's avatar
Jerome Mariette committed
389
        for param in parameters:
Jerome Mariette's avatar
Jerome Mariette committed
390
391
392
393
            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):
394
                if param.action == MiltipleAppendAction:
Jerome Mariette's avatar
Jerome Mariette committed
395
396
397
398
399
400
401
                    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:
402
403
404
                                if values[0] == sub_param.flag: 
                                    try: value = values[1].encode('ascii','ignore')
                                    except: value = values[1]
Jerome Mariette's avatar
Jerome Mariette committed
405
406
407
                            if value == None: value = sub_param.default
                            sub_hash[sub_param.name] = value
                        extended_args[param.name].append(sub_hash)
Jerome Mariette's avatar
Jerome Mariette committed
408
                # if it's an append parameter, the result should be a list
Jerome Mariette's avatar
Jerome Mariette committed
409
                elif param.action == "append":
Jerome Mariette's avatar
Jerome Mariette committed
410
411
412
413
                    if args[param.name]:
                        try: value = args[param.name].split(",") 
                        except: value = args[param.name]
                    else: value = []
Jerome Mariette's avatar
Jerome Mariette committed
414
415
416
417
418
419
420
                    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]
421
422
                # if it's a boolean
                elif param.type == types.BooleanType:
Jerome Mariette's avatar
Jerome Mariette committed
423
                    extended_args[param.name] = args[param.name] in [True, 1, 'true', '1', 't', 'y', 'yes']
Jerome Mariette's avatar
Jerome Mariette committed
424
                elif param.type.__name__ == "MultipleParameters":
Jerome Mariette's avatar
Jerome Mariette committed
425
426
427
428
429
                    extended_args[param.name] = {}
                    for sub_param in param.sub_parameters:
                        # find the value
                        value = None
                        for values in args[param.name]:
430
431
432
                            if values[0] == sub_param.flag:
                                try: value = values[1].encode('ascii','ignore')
                                except: value = values[1]
Jerome Mariette's avatar
Jerome Mariette committed
433
434
                        if value == None: value = sub_param.default
                        extended_args[param.name][sub_param.name] = value
Jerome Mariette's avatar
Jerome Mariette committed
435
436
437
438
                else:
                    extended_args[param.name] = args[param.name]
            # otherwise use the default
            else:
Jerome Mariette's avatar
Jerome Mariette committed
439
                if param.type.__name__ == "MultipleParameters":
Jerome Mariette's avatar
Jerome Mariette committed
440
441
442
443
444
                    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
Jerome Mariette's avatar
Jerome Mariette committed
445
446
        return extended_args
    
447
    def _get_from_config(self, parameters_section):
Jerome Mariette's avatar
Jerome Mariette committed
448
449
        reader = ConfigParser()
        reader.read(self._get_property_path())
450
        parameters, param_order = [], []
Jerome Mariette's avatar
Jerome Mariette committed
451
        try:
Jerome Mariette's avatar
Jerome Mariette committed
452
            params, sub_order, excludes, hash_params = {}, {}, [], {}
Jerome Mariette's avatar
Jerome Mariette committed
453
            # first grab all parameters name
454
455
            for param in reader.items(parameters_section):
                cvalue = reader.get(parameters_section, param[0])
Jerome Mariette's avatar
Jerome Mariette committed
456
                cparam = param[0].split(".")[0]
Jerome Mariette's avatar
Jerome Mariette committed
457
                ckey = ".".join(param[0].split(".")[1:])
458
459
460
461
462
                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]]
Jerome Mariette's avatar
Jerome Mariette committed
463
464
                if not params.has_key(cparam):
                    params[cparam] = {ckey: cvalue}
Jerome Mariette's avatar
Jerome Mariette committed
465
                else:
Jerome Mariette's avatar
Jerome Mariette committed
466
                    params[cparam][ckey] = cvalue
467
                if cparam not in param_order: param_order.append(cparam)
Jerome Mariette's avatar
Jerome Mariette committed
468
            
469
            for param_name in param_order:
Jerome Mariette's avatar
Jerome Mariette committed
470
                sub_params, current_params, sub_objs, sub_excludes, hash_sub_params = {}, {}, [], [], {}
Jerome Mariette's avatar
Jerome Mariette committed
471
472
473
                for param in params[param_name]:
                    sub_params_values = param.split(".")
                    if len(sub_params_values) == 2:
Jerome Mariette's avatar
Jerome Mariette committed
474
                        # TODO: handle exclusive for sub parameter
475
476
477
478
479
                        key = None
                        if sub_params_values[1] == "name": 
                            key = "display_name"
                        else:
                            key = sub_params_values[1]
Jerome Mariette's avatar
Jerome Mariette committed
480
481
482
483
484
485
486
487
488
489
                        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]])
Jerome Mariette's avatar
Jerome Mariette committed
490
                        else:
Jerome Mariette's avatar
Jerome Mariette committed
491
492
493
494
495
                            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]
Jerome Mariette's avatar
Jerome Mariette committed
496
                    else:
497
                        if param == "name": current_params["display_name"] = params[param_name][param]
Jerome Mariette's avatar
Jerome Mariette committed
498
499
500
501
502
503
504
505
506
507
                        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]])
Jerome Mariette's avatar
Jerome Mariette committed
508
509
                        else: current_params[param] = params[param_name][param]
                current_params["name"] = param_name
510
511
512
                if sub_order.has_key(param_name):
                    for sub_param in sub_order[param_name]:
                        sub = Parameter(**sub_params[sub_param])
Jerome Mariette's avatar
Jerome Mariette committed
513
                        hash_sub_params[sub.name] = sub
514
                        sub_objs.append(sub)
Jerome Mariette's avatar
Jerome Mariette committed
515
516
517
518
519
                    # 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
Jerome Mariette's avatar
Jerome Mariette committed
520
521
                current_params["sub_parameters"] = sub_objs
                oparam = Parameter(**current_params)
Jerome Mariette's avatar
Jerome Mariette committed
522
                parameters.append(oparam)
Jerome Mariette's avatar
Jerome Mariette committed
523
524
525
526
527
528
                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
Jerome Mariette's avatar
Jerome Mariette committed
529
530
        except:
            pass
Jerome Mariette's avatar
Jerome Mariette committed
531
        # finally add the metadata parameter
Jerome Mariette's avatar
Jerome Mariette committed
532
533
        metadata = Parameter(name="metadata", flag="--metadata", help="Which metadata should be linked to this workflow", 
                             action="append", display_name="Metadata")
Jerome Mariette's avatar
Jerome Mariette committed
534
        parameters.append(metadata)
Jerome Mariette's avatar
Jerome Mariette committed
535
536
537
538
        return [reader.get("global", "name"),
                reader.get("global", "description"),
                parameters]
    
Jerome Mariette's avatar
Jerome Mariette committed
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
    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
    
563
564
565
    def get_resource(self, resource):
        return self.jflow_config_reader.get_resource(resource)
    
Jerome Mariette's avatar
Jerome Mariette committed
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
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
620
621
622
623
624
625
626
627
    def get_component_status(self, component_nameid):
        status = {"time": 0.0,
                  "tasks": 0,
                  "waiting": 0,
                  "running": 0,
                  "failed":0,
                  "aborted": 0,
                  "completed": 0}
        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
                    elif n.state == Node.ABORTED:
                        status["aborted"] += 1
                    elif n.state == Node.COMPLETED:
                        status["completed"] += 1
        except: pass
        return status        
    
    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:
628
                        for component in self.components_to_exec:
Jerome Mariette's avatar
Jerome Mariette committed
629
                            nest.symbol = component.get_nameid()
630
                            nest.batch = component.batch_options
Jerome Mariette's avatar
Jerome Mariette committed
631
632
633
634
635
636
                            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
637
                        self.end_time = time.time()
Jerome Mariette's avatar
Jerome Mariette committed
638
                        self._serialize()
Jerome Mariette's avatar
Jerome Mariette committed
639
                        raise
640
                self.components_to_exec = []  
Jerome Mariette's avatar
Jerome Mariette committed
641
642
643
644
645
646
647
648
                # 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
649
                    raise
Jerome Mariette's avatar
Jerome Mariette committed
650
651
652

    def _get_current_make(self):
        current_component, make_directory, new_make = [], None, False
653
        for component in self.components_to_exec:
Jerome Mariette's avatar
Jerome Mariette committed
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
            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()

671
672
    def _component_is_duplicated(self, component):
        if component.get_nameid() in self.component_nameids.keys():
Jerome Mariette's avatar
Jerome Mariette committed
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
            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
689
690
691
692
693
            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
694
            except Exception as e:
Jerome Mariette's avatar
Jerome Mariette committed
695
                logging.getLogger("Workflow._import_components").debug("Component <{0}> cannot be loaded: {1}".format(modname, e))
Jerome Mariette's avatar
Jerome Mariette committed
696
697
698
        # 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
699
700
701
702
703
            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
704
705
            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
706
707
708
709
710
711
712
713
714
715
716
717
        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)