workflow.py 46.2 KB
Newer Older
Jerome Mariette's avatar
Jerome Mariette committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
#
# Copyright (C) 2012 INRA
# 
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# 
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
# 
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.
#

import inspect
import os
20
import re
Jerome Mariette's avatar
Jerome Mariette committed
21
22
23
24
25
26
27
import sys
import uuid
import pkgutil
import tempfile
import pickle
import time
import threading
Jerome Mariette's avatar
Jerome Mariette committed
28
import types
Jerome Mariette's avatar
Jerome Mariette committed
29
import logging
Jerome Mariette's avatar
Jerome Mariette committed
30
import datetime
Jerome Mariette's avatar
Jerome Mariette committed
31
import shutil
Jerome Mariette's avatar
Jerome Mariette committed
32

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

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

from weaver.script import ABSTRACTIONS
from weaver.script import DATASETS
from weaver.script import FUNCTIONS
from weaver.script import NESTS
from weaver.script import OPTIONS
from weaver.script import STACKS
from weaver.nest import Nest
from weaver.options import Options
from cctools.makeflow import MakeflowLog
from cctools.makeflow.log import Node

Jerome Mariette's avatar
Jerome Mariette committed
57

58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
class MINIWorkflow(object):
    
    def __init__(self, id, name, description, status, start_time, end_time, metadata, 
                 component_nameids, compts_status, errors):
        self.id = id
        self.name = name
        self.description = description
        self.status = status
        self.start_time = start_time
        self.end_time = end_time
        self.metadata = metadata
        self.component_nameids = component_nameids
        self.compts_status = compts_status
        self.errors = errors
        
    def get_components_nameid(self):
        return self.component_nameids

    def get_component_status(self, component_nameid):
        return self.compts_status[component_nameid]
    
    def get_errors(self):
        return self.errors
    
    def get_status(self):
        return self.status
84

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

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

Jerome Mariette's avatar
Jerome Mariette committed
139
        self.id = id
140
141
142
143
144
        self.name = self.get_name()
        self.description = self.get_description()
        
        # define the parameters 
        self.params_order = []
145
        self.define_parameters(self.function)
146
        # add the metadata parameter
147
        self.add_parameter_list("metadata", "Which metadata should be linked to this workflow")
Jerome Mariette's avatar
Jerome Mariette committed
148
        
Jerome Mariette's avatar
Jerome Mariette committed
149
150
151
152
        if self.id is not None:
            self.directory = self.manager.get_workflow_directory(self.name, self.id)
            if not os.path.isdir(self.directory):
                os.makedirs(self.directory, 0751)
Frédéric Escudié's avatar
Frédéric Escudié committed
153
            if self.stderr is None:
154
                self.set_stderr()
Jerome Mariette's avatar
Jerome Mariette committed
155
            self._serialize()
156
    
157
    def add_input_file(self, name, help, file_format="any", default=None, type="inputfile", 
158
159
160
161
                       required=False, flag=None, group="default", display_name=None, size_limit="0", add_to=None):
        # check if the size provided is correct
        try: int(get_nb_octet(size_limit))
        except: size_limit="0"
162
        new_param = InputFile(name, help, flag=flag, file_format=file_format, default=default, 
163
                              type=type, required=required, group=group, display_name=display_name, size_limit=size_limit)
Frédéric Escudié's avatar
Frédéric Escudié committed
164
        new_param.linkTrace_nameid = name
165
166
167
168
169
170
        # 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
171
        else:
172
173
174
175
            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", 
176
177
                            required=False, flag=None, group="default", display_name=None, size_limit="0", add_to=None):
        # check if the size provided is correct
178
        if default == None: default = []
179
180
        try: int(get_nb_octet(size_limit))
        except: size_limit="0"
181
182
183
184
185
186
187
        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, 
188
                                  type=type, required=required, group=group, display_name=display_name, size_limit=size_limit)
Frédéric Escudié's avatar
Frédéric Escudié committed
189
        new_param.linkTrace_nameid = name
190
191
192
        # if this input should be added to a particular parameter
        if add_to:
            try:
Jerome Mariette's avatar
help ok    
Jerome Mariette committed
193
                self.__getattribute__(add_to).add_sub_parameter(new_param)
194
195
196
197
198
            except: pass
        # otherwise, add it to the class itself
        else:
            self.params_order.append(name)
            self.__setattr__(name, new_param)
199
200
            
    def add_multiple_parameter(self, name, help, required=False, flag=None, group="default", display_name=None):
201
        self.params_order.append(name)
202
203
204
205
206
207
        new_param = MultiParameter(name, help, flag=flag, required=required, group=group, display_name=display_name)
        self.__setattr__(name, new_param)

    def add_multiple_parameter_list(self, name, help, required=False, flag=None, group="default", display_name=None):
        self.params_order.append(name)
        new_param = MultiParameterList(name, help, flag=flag, required=required, group=group, display_name=display_name)
208
209
        self.__setattr__(name, new_param)
    
210
211
    def add_parameter(self, name, help, default=None, type=types.StringType, choices=None, 
                      required=False, flag=None, group="default", display_name=None, add_to=None):
212
        new_param = ParameterFactory.factory(name, help, flag=flag, default=default, type=type, choices=choices, 
213
214
215
216
217
218
219
                              required=required, group=group, display_name=display_name)
        # if this input should be added to a particular parameter
        if add_to:
            try:
                self.__getattribute__(add_to).add_sub_parameter(new_param)
            except: pass
        # otherwise, add it to the class itself
220
        else:
221
222
223
224
225
226
227
            self.params_order.append(name)
            self.__setattr__(name, new_param)
    
    def add_parameter_list(self, name, help, default=None, type=types.StringType, choices=None, 
                           required=False, flag=None, group="default", display_name=None, add_to=None):
        if default == None: default = []
        new_param = ParameterList(name, help, flag=flag, default=default, type=type, choices=choices, 
228
229
230
231
                                  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
232
                self.__getattribute__(add_to).add_sub_parameter(new_param)
233
234
235
236
237
238
            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
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
    def add_exclusion_rule(self, *args2exclude):
        # first of all, are this parameter exist
        params2exclude = []
        for arg2exclude in args2exclude:
            try:
                params2exclude.append(self.__getattribute__(arg2exclude))
            except: pass
        # everything is ok, let's go
        if len(params2exclude) == len(args2exclude):
            new_group = "exclude-"+uuid.uuid4().hex[:5]
            for paramsexclude in params2exclude:
                paramsexclude.group = new_group
        # it might be a mutliple param rule
        else:
            for attribute_value in self.__dict__.values():
                if issubclass(attribute_value.__class__, MultiParameter) or issubclass(attribute_value.__class__, MultiParameterList):
                    params2exclude = []
                    for sub_param in attribute_value.sub_parameters:
                        if sub_param.name in args2exclude:
                            params2exclude.append(sub_param)
                    if len(params2exclude) == len(args2exclude):
                        new_group = "exclude-"+uuid.uuid4().hex[:5]
                        flags2exclude = []
                        for paramsexclude in params2exclude:
                            paramsexclude.group = new_group
                            flags2exclude.append(paramsexclude.flag)
                        attribute_value.type.excludes[new_group] = flags2exclude
                        break
267

Frédéric Escudié's avatar
Frédéric Escudié committed
268
    def _prepare_parameter(self, args, parameter, key="name"):
269
270
        new_param = None
        # Retrieve value
Frédéric Escudié's avatar
Frédéric Escudié committed
271
272
        if args.has_key(parameter.__getattribute__(key)):
            value = args[parameter.__getattribute__(key)]
273
274
275
276
277
278
279
280
281
282
        elif parameter != None:
            value = parameter.default
        else:
            value = None
        # Set new parameter
        if parameter.__class__ ==  StrParameter or parameter.__class__ == IntParameter or parameter.__class__ == FloatParameter or parameter.__class__ == BoolParameter or parameter.__class__ == DateParameter:
            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:
283
            if value == "" : value = [] # from GUI
284
285
286
287
            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:
288
            if value == "" : value = [] # from GUI
289
290
291
292
            iovalues = []
            for file in parameter.prepare_input_files(value):
                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,
293
294
                                       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 )
295
            new_param.linkTrace_nameid = parameter.linkTrace_nameid            
296
        elif parameter.__class__ == InputFile:
297
            if value == "" : value = None # from GUI
298
            new_param = InputFile( parameter.name, parameter.help, file_format=parameter.file_format, default=parameter.prepare_input_file(value),
299
300
                                   type=parameter.type, choices=parameter.choices, required=parameter.required, flag=parameter.flag, 
                                   group=parameter.group, display_name=parameter.display_name )
301
            new_param.linkTrace_nameid = parameter.linkTrace_nameid
302
303
304
305
        else:
            raise Exception( "Unknown class '" +  parameter.__class__.__name__ + "' for parameter.")
        return new_param

306
307
308
    def _set_parameters(self, args):
        parameters = self.get_parameters()
        for param in parameters:
309
            new_param = None
310
            if param.__class__ == MultiParameter:
311
                new_param = MultiParameter(param.name, param.help, required=param.required, flag=param.flag, group=param.group, display_name=param.display_name)
312
                new_param.sub_parameters = param.sub_parameters
313
314
315
316
317
318
319
                if args[param.name]:
                    sub_args = {}
                    for sarg in args[param.name]:
                        sub_args[sarg[0]] = sarg[1]
                    for sub_param in param.sub_parameters:
                        new_sub_parameter = self._prepare_parameter(sub_args, sub_param, "flag")
                        new_param[new_sub_parameter.name] = new_sub_parameter
320
            elif param.__class__ == MultiParameterList:
321
                new_param = MultiParameterList(param.name, param.help, required=param.required, flag=param.flag, group=param.group, display_name=param.display_name)
322
                new_param.sub_parameters = param.sub_parameters
323
324
                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)
325
                    sub_args = {}
326
                    for sarg in sargs:
Jerome Mariette's avatar
Jerome Mariette committed
327
328
                        sub_args[sarg[0]] = sarg[1]
                    for sub_param in param.sub_parameters:
Frédéric Escudié's avatar
Frédéric Escudié committed
329
                        new_sub_param = self._prepare_parameter(sub_args, sub_param, "flag")
330
331
                        new_multi_param[new_sub_param.name] = new_sub_param
                    new_param.append(new_multi_param)
332
            else:
333
                new_param = self._prepare_parameter(args, param)
334
            self.__setattr__(param.name, new_param)
Frédéric Escudié's avatar
Frédéric Escudié committed
335

Jerome Mariette's avatar
Jerome Mariette committed
336
    def get_execution_graph(self):
337
        gr = digraph()
338
339
340
341
342
343
344
        for ioparameter in self.__dict__.values():
            if issubclass(ioparameter.__class__, InputFile):
                gr.add_node(ioparameter.name)
                gr.add_node_attribute(ioparameter.name, self.INPUT_GRAPH_LABEL)
            elif issubclass(ioparameter.__class__, InputFileList):
                gr.add_node(ioparameter.name)
                gr.add_node_attribute(ioparameter.name, self.INPUTS_GRAPH_LABEL)
345
        for cpt in self.components:
346
347
            gr.add_node(cpt.get_nameid())
            gr.add_node_attribute(cpt.get_nameid(), self.COMPONENT_GRAPH_LABEL)
Jerome Mariette's avatar
Jerome Mariette committed
348
349
        for cpt in self.components:
            for ioparameter in cpt.__dict__.values():
Frédéric Escudié's avatar
Frédéric Escudié committed
350
351
352
                if issubclass( ioparameter.__class__, InputFile ) or issubclass( ioparameter.__class__, InputFileList):
                    for parent in ioparameter.parent_linkTrace_nameid:
                        try: gr.add_edge((parent, ioparameter.linkTrace_nameid))
Frédéric Escudié's avatar
Frédéric Escudié committed
353
                        except: pass
354
        return gr
Frédéric Escudié's avatar
Frédéric Escudié committed
355

356
357
358
359
360
361
362
363
364
365
366
367
    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
Frédéric Escudié's avatar
Frédéric Escudié committed
368

Jerome Mariette's avatar
Jerome Mariette committed
369
370
371
372
    def delete(self):
        if self.get_status() in [self.STATUS_COMPLETED, self.STATUS_FAILED, self.STATUS_ABORTED]:
            shutil.rmtree(self.directory)

373
    @staticmethod
374
    def config_parser(arg_lines):
375
376
        for arg in arg_lines:
            yield arg
377
378
379
380
            
    @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))
381
        else: start_time = "-"
382
383
        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)
384
        else: elapsed_time = "-"
Jerome Mariette's avatar
Jerome Mariette committed
385
        elapsed_time = "-" if elapsed_time == "-" else str(datetime.timedelta(seconds=int(str(elapsed_time).split(".")[0])))
386
        if workflow.end_time: end_time = time.asctime(time.localtime(workflow.end_time))
387
388
389
        else: end_time = "-"
        if detailed:
            # Global
390
391
            title = "Workflow #" + utils.get_nb_string(workflow.id) + " (" + workflow.name + ") is " + \
                    workflow.get_status() + ", time elapsed: " + str(elapsed_time) + " (from " + start_time + \
392
393
                    " to " + end_time + ")"
            worflow_errors = ""
394
            error = workflow.get_errors()
395
            if error is not None:
Jerome Mariette's avatar
Jerome Mariette committed
396
397
                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"
398
399
400
            # By components
            components_errors = ""
            status = "Components Status :\n"
401
402
            for i, component in enumerate(workflow.get_components_nameid()):
                status_info = workflow.get_component_status(component)
403
404
405
406
407
408
409
410
411
412
413
                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
414
415
416
                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"
417
                else: running = "running:" + str(status_info["running"])
Jerome Mariette's avatar
Jerome Mariette committed
418
419
420
                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"
421
                else: waiting = "waiting:" + str(status_info["waiting"])            
Jerome Mariette's avatar
Jerome Mariette committed
422
423
424
                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"
425
                else: failed = "failed:" + str(status_info["failed"])
Jerome Mariette's avatar
Jerome Mariette committed
426
427
428
                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"
429
                else: aborted = "aborted:" + str(status_info["aborted"])
Jerome Mariette's avatar
Jerome Mariette committed
430
431
432
                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"
433
434
435
436
437
438
439
440
441
                else: completed = "completed:" + str(status_info["completed"])
                
                if display_errors and len(status_info["failed_commands"]) > 0:
                    if components_errors == "" :
                        components_errors = "Failed Commands :\n"  
                    components_errors += "  - " + component + " :\n    " + "\n    ".join(status_info["failed_commands"])
                status += "  - " + component + ", time elapsed " + time_format(status_info["time"]) + \
                    " (total:" + str(status_info["tasks"]) + ", " + waiting + ", " + running + ", " + failed + \
                    ", " + aborted + ", " + completed + ")"
442
                if i<len(workflow.get_components_nameid())-1: status += "\n"
443
444
445
446
447
            # Format str
            pretty_str = title
            pretty_str += ("\n" + worflow_errors) if worflow_errors != "" else ""
            pretty_str += ("\n" + status) if status != "" else ""
            pretty_str += ("\n" + components_errors) if components_errors != "" else ""
Jerome Mariette's avatar
Jerome Mariette committed
448
449
            if html: return pretty_str.replace("\n", "<br />")
            else: return pretty_str
450
        else:
451
452
            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
453
                pretty_str += "\033[94m"
454
            elif workflow.get_status() == Workflow.STATUS_COMPLETED:
Jerome Mariette's avatar
Jerome Mariette committed
455
                pretty_str += "\033[92m"
456
            elif workflow.get_status() == Workflow.STATUS_FAILED:
Jerome Mariette's avatar
Jerome Mariette committed
457
                pretty_str += "\033[91m"
458
            elif workflow.get_status() == Workflow.STATUS_ABORTED:
Jerome Mariette's avatar
Jerome Mariette committed
459
                pretty_str += "\033[91m"
460
            elif workflow.get_status() == Workflow.STATUS_RESETED:
Jerome Mariette's avatar
Jerome Mariette committed
461
                pretty_str += "\033[3m"
462
            pretty_str += workflow.get_status() + "\033[0m"
Jerome Mariette's avatar
Jerome Mariette committed
463
464
            pretty_str += "\t" + elapsed_time + "\t" + start_time + "\t" + end_time
            return pretty_str
465
    
466
    def get_errors(self):
Frédéric Escudié's avatar
Frédéric Escudié committed
467
468
469
470
471
472
        error = {
                 "title"     : "",
                 "msg"       : list(),
                 "traceback" : list()
        }
        line_idx = 0
473
474
475
        FH_stderr = open( self.stderr )
        lines = FH_stderr.readlines()
        while line_idx < len(lines):
Frédéric Escudié's avatar
Frédéric Escudié committed
476
477
478
479
480
481
            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
482
                while lines[line_idx] != lines[line_idx].lstrip():
Frédéric Escudié's avatar
Frédéric Escudié committed
483
484
485
486
                    error["traceback"].append({ 
                                               "location" : lines[line_idx].strip(),
                                               "line"     : lines[line_idx].strip()
                    })
487
                    line_idx += 2
Frédéric Escudié's avatar
Frédéric Escudié committed
488
489
490
491
492
                # 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
493
494
            line_idx += 1
        FH_stderr.close()
Frédéric Escudié's avatar
Frédéric Escudié committed
495
496
497
498
499
500
        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
501
    
502
    def get_outputs_per_components(self):
503
504
        outputs_files = {}
        for current_components in self.components:
Philippe Bardou's avatar
Philippe Bardou committed
505
            #status = self.get_component_status(current_components.get_nameid())
506
            outputs_files[current_components.get_nameid()] = current_components.get_output_files()
Philippe Bardou's avatar
Philippe Bardou committed
507
            #outputs_files["0"] = status["completed"]
508
509
        return outputs_files
    
Jerome Mariette's avatar
Jerome Mariette committed
510
511
512
513
514
515
516
517
518
519
520
521
522
523
    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
    
524
525
526
527
528
529
530
531
532
533
534
535
536
    def set_to_address(self, to_address):
        self.__to_address = to_address

    def set_subject(self, subject):
        self.__subject = subject

    def set_message(self, message):
        self.__message = message
    
    def _send_email(self):
        
        import smtplib
        from email.mime.text import MIMEText        
537
        smtps, smtpp, froma, fromp, toa, subject, message = self.jflow_config_reader.get_email_options()
538
539
540
541
542
        
        if self.__to_address: toa = self.__to_address
        if self.__subject: subject = self.__subject
        if self.__message: message = self.__message
        
543
        if smtps and smtpp and froma and fromp:
544
545
            if not toa: toa = froma
            if validate_email(froma) and validate_email(toa):
546
547
548
549
550
                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:
551
                        message = Workflow.get_status_under_text_format(self, True, True, True)
Jerome Mariette's avatar
Jerome Mariette committed
552
                    msg = MIMEText(message, 'html')
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
                    me = froma
                    you = toa
                    if not subject: subject = "JFlow - Workflow #" + str(self.id) + " is " + self.status
                    msg['Subject'] = subject
                    msg['From'] = me
                    msg['To'] = you
                    # Send the message via our own SMTP server, but don't include the
                    # envelope header.
                    s = smtplib.SMTP(smtps, smtpp)
                    s.ehlo()
                    s.starttls()
                    s.login(me, fromp)
                    s.sendmail(me, [you], msg.as_string())
                    s.close()
                except:
                    logging.getLogger("wf." + str(self.id)).debug("Impossible to connect to smtp server '" + smtps + "'")
          
570
571
572
573
    def get_parameters_per_groups(self):
        name = self.get_name()
        description = self.get_description()
        parameters = self.get_parameters()
574
575
        pgparameters, parameters_order = {}, []
        for param in parameters:
Jerome Mariette's avatar
Jerome Mariette committed
576
            if param.group not in parameters_order: parameters_order.append(param.group)
577
578
            if pgparameters.has_key(param.group):
                pgparameters[param.group].append(param)
Jerome Mariette's avatar
Jerome Mariette committed
579
            else:
580
581
                pgparameters[param.group] = [param]
        return [pgparameters, parameters_order]
Jerome Mariette's avatar
Jerome Mariette committed
582
    
583
584
585
586
587
588
589
590
    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
    
591
    def get_exec_path(self, software):
592
593
594
595
596
        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)
597
        elif exec_path is None and utils.which(software) == None:
Jerome Mariette's avatar
Jerome Mariette committed
598
            utils.display_error_message("'" + software + "' path connot be retrieved either in the PATH and in the application.properties file!")
599
600
601
        elif exec_path is None and utils.which(software) != None: 
            exec_path = software
        elif exec_path != None and not os.path.isfile(exec_path):
Jerome Mariette's avatar
Jerome Mariette committed
602
            utils.display_error_message("'" + exec_path + "' set for '" + software + "' does not exists, please provide a valid path!")
603
        return exec_path
604
    
Jerome Mariette's avatar
Jerome Mariette committed
605
606
    def add_component(self, component_name, args=[], kwargs={}, component_prefix="default"):
        # first build and check if this component is OK
607
608
609
610
611
612
613
614
        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)
615
616
            
            # there is a dynamic component
617
            if cmpt_object.is_dynamic():
618
619
620
621
                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
622
                    self.components_to_exec.append(cmpt_object)
623
                    self.components.append(cmpt_object)
624
625
626
627
628
629
630
631
632
                    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
633
                    self.components_to_exec = []
634
                    self.components = []
635
636
637
            else:
                if self.component_nameids_is_init:
                    # add the component
638
                    self.components_to_exec.append(cmpt_object)
639
                    self.components.append(cmpt_object)
640
                elif not self.component_nameids_is_init and not self.dynamic_component_present:
Jerome Mariette's avatar
Jerome Mariette committed
641
642
643
                    if self._component_is_duplicated(cmpt_object):
                        raise ValueError("Component " + cmpt_object.__class__.__name__ + " with prefix " + 
                                            cmpt_object.prefix + " already exist in this pipeline!")
644
                    self.components_to_exec.append(cmpt_object)
645
                    self.components.append(cmpt_object)
646
647
648
649
650
651
                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

652
653
            return cmpt_object
        else:
Jerome Mariette's avatar
Jerome Mariette committed
654
            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
655
656
657
658
659
660
661
662
    
    def pre_process(self):
        pass
    
    def process(self):
        """ 
        Run the workflow, has to be implemented by subclasses
        """
663
        raise NotImplementedError( "Workflow.process() must be implemented in " + self.__class__.__name__ )
664
665
666

    def get_name(self):
        """ 
667
        Return the workflow name.
668
        """
Jerome Mariette's avatar
Jerome Mariette committed
669
        return self.__class__.__name__.lower()
670
671
672
673
674
    
    def get_description(self):
        """ 
        Return the workflow description, has to be implemented by subclasses
        """
675
        raise NotImplementedError( "Workflow.get_description() must be implemented in " + self.__class__.__name__ )
676
    
677
    def define_parameters(self, function="process"):
678
679
680
        """ 
        Define the workflow parameters, has to be implemented by subclasses
        """
681
        raise NotImplementedError( "Workflow.define_parameters() must be implemented in " + self.__class__.__name__ )
Jerome Mariette's avatar
Jerome Mariette committed
682
683
684
685
686
687
688
689
690
691
692
693
694
695
    
    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
696
697
    def wf_execution_wrapper(self):
        getattr(self, self.function)()
Jerome Mariette's avatar
Jerome Mariette committed
698
    
Jerome Mariette's avatar
Jerome Mariette committed
699
700
701
702
    def run(self):
        """
        Only require for Threading
        """
703
704
705
706
707
708
709
        try:
            # if this is the first time the workflow run
            if self.step == None :
                self.start_time = time.time()
                self.step = 0
                self.status = self.STATUS_STARTED
                self.end_time = None
Jerome Mariette's avatar
Jerome Mariette committed
710
711
                # if some args are provided, let's fill the parameters
                self._set_parameters(self.args)
712
                self._serialize()
713
714
715
716
717
718
719
            # 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:
720
721
                try:
                    self.reseted_components = []
722
                    self.components = []
Jerome Mariette's avatar
Jerome Mariette committed
723
                    self.status = self.STATUS_STARTED
724
725
726
727
728
                    self.wf_execution_wrapper()
                except SystemExit, e: 
                    self.status = self.STATUS_FAILED
                    self.end_time = time.time()
                    self._serialize()
729
                    self._send_email()
730
731
732
733
734
735
736
737
738
739
                    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:
740
741
                try:
                    self.reseted_components = []
742
                    self.components = []
Jerome Mariette's avatar
Jerome Mariette committed
743
                    self.status = self.STATUS_STARTED
744
745
746
747
748
                    self.wf_execution_wrapper()
                except SystemExit, e: 
                    self.status = self.STATUS_FAILED
                    self.end_time = time.time()
                    self._serialize()
749
                    self._send_email()
750
751
752
                    raise
                if len(self.components_to_exec) > 0:
                    self._execute_weaver()
753
                self.step = 3
754
755
756
757
                self._serialize()
            # if post processing has ne been done yet
            if self.step == 3:
                self.post_process()
758
                if self.status == self.STATUS_STARTED: self.status = self.STATUS_COMPLETED
759
760
                self.end_time = time.time()
                self._serialize()
761
                self._send_email()
762
763
764
        except:
            logging.getLogger("wf." + str(self.id)).exception("RunWorflowException")
            raise
765

Jerome Mariette's avatar
Jerome Mariette committed
766
767
768
769
770
771
772
773
774
775
776
    def _update_status_from_log(self):
        # first update the status from weaver folders
        # TODO update self.end_time
        try:
            working_directory = os.path.join(self.directory, self.WORKING)
            make_states = []
            for wdir in os.listdir(working_directory):
                log_path = os.path.join(working_directory, wdir, self.MAKEFLOW_LOG_FILE_NAME)
                log = MakeflowLog(log_path)
                log.parse()
                make_states.append(log.state)
Jerome Mariette's avatar
Jerome Mariette committed
777
778
779
            if len(self.reseted_components) > 0:
                self.status = self.STATUS_RESETED
            elif self.STATUS_ABORTED in make_states:
Jerome Mariette's avatar
Jerome Mariette committed
780
781
782
783
784
785
786
787
788
789
790
791
                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
    
792
793
794
    def get_resource(self, resource):
        return self.jflow_config_reader.get_resource(resource)
    
Jerome Mariette's avatar
Jerome Mariette committed
795
796
797
798
799
800
801
    def get_component_status(self, component_nameid):
        status = {"time": 0.0,
                  "tasks": 0,
                  "waiting": 0,
                  "running": 0,
                  "failed":0,
                  "aborted": 0,
802
803
                  "completed": 0,
                  "failed_commands": list() }
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
        if component_nameid not in self.reseted_components:
            try:
                log = MakeflowLog(self.component_nameids[component_nameid])
                log.parse()
                symbols = set(n.symbol for n in log.nodes if n.symbol)
                if not symbols: return None
                for n in log.nodes:
                    if not n.symbol: continue
                    if n.symbol == component_nameid:
                        status["tasks"] += 1
                        status["time"]  += n.elapsed_time
                        if n.state == Node.WAITING:
                            status["waiting"] += 1
                        elif n.state == Node.RUNNING:
                            status["running"] += 1
                        elif n.state == Node.FAILED:
                            status["failed"] += 1
                            status["failed_commands"].append( n.command )
                        elif n.state == Node.ABORTED:
                            status["aborted"] += 1
                        elif n.state == Node.COMPLETED:
                            status["completed"] += 1
            except: pass
Frédéric Escudié's avatar
Frédéric Escudié committed
827
        return status
Jerome Mariette's avatar
Jerome Mariette committed
828
    
829
830
831
832
833
834
835
836
837
    def reset_component(self, component_name):
        # first reinit the step to the execution step
        self.step = 1
        found = False
        for cpt in self.components:
            if cpt.get_nameid() == component_name:
                cpt.reset()
                found = True
        if not found:
Jerome Mariette's avatar
Jerome Mariette committed
838
            utils.display_error_message("Impossible to reset component '" + component_name + "'! This one is not part of the workflow")
839
        self.reseted_components.append(component_name)
Jerome Mariette's avatar
Jerome Mariette committed
840
        self.status = self.STATUS_RESETED
841
842
        self._serialize()
    
843
844
845
846
847
848
849
850
    def minimize(self):
        compts_status = {}
        for i, component in enumerate(self.get_components_nameid()):
            compts_status[component] = self.get_component_status(component)
        return MINIWorkflow(self.id, self.name, self.description, self.get_status(), self.start_time, 
                            self.end_time, self.metadata, self.get_components_nameid(), compts_status, 
                            self.get_errors())
    
Jerome Mariette's avatar
Jerome Mariette committed
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
    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:
882
                        for component in self.components_to_exec:
Jerome Mariette's avatar
Jerome Mariette committed
883
                            nest.symbol = component.get_nameid()
884
                            nest.batch = component.batch_options
Jerome Mariette's avatar
Jerome Mariette committed
885
886
887
888
889
890
                            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
891
                        self.end_time = time.time()
Jerome Mariette's avatar
Jerome Mariette committed
892
                        self._serialize()
Jerome Mariette's avatar
Jerome Mariette committed
893
                        raise
894
                self.components_to_exec = []  
Jerome Mariette's avatar
Jerome Mariette committed
895
896
897
898
899
900
901
902
                # 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
903
                    raise
Jerome Mariette's avatar
Jerome Mariette committed
904
905
906

    def _get_current_make(self):
        current_component, make_directory, new_make = [], None, False
907
        for component in self.components_to_exec:
Jerome Mariette's avatar
Jerome Mariette committed
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
            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()

925
926
    def _component_is_duplicated(self, component):
        if component.get_nameid() in self.component_nameids.keys():
Jerome Mariette's avatar
Jerome Mariette committed
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
            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
943
944
945
946
947
            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
948
            except Exception as e:
Jerome Mariette's avatar
Jerome Mariette committed
949
                logging.getLogger("Workflow._import_components").debug("Component <{0}> cannot be loaded: {1}".format(modname, e))
Jerome Mariette's avatar
Jerome Mariette committed
950
951
952
        # 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
953
954
955
956
957
            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
958
959
            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
960
961
962
963
964
965
966
967
968
969
970
        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:
971
            self.globals[symbol] = getattr(m, symbol)