workflow.py 23.1 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
29
from ConfigParser import ConfigParser, NoOptionError
import types
Jerome Mariette's avatar
Jerome Mariette committed
30
import logging
Jerome Mariette's avatar
Jerome Mariette committed
31
from inspect import getcallargs
Jerome Mariette's avatar
Jerome Mariette committed
32

Jerome Mariette's avatar
Jerome Mariette committed
33
import jflow
Jerome Mariette's avatar
Jerome Mariette committed
34
35
import jflow.utils as utils
from jflow.workflows_manager import WorkflowsManager, JFlowConfigReader
36
from jflow.parameter import Parameter, date, MiltipleAppendAction
Jerome Mariette's avatar
Jerome Mariette committed
37
38
39
40
41
42
43
44
45
46
47
48

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
49

Jerome Mariette's avatar
Jerome Mariette committed
50
51
52
53
54
55
56
57
58
59
60
61
class Workflow(threading.Thread):
    """
    """

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

63
    def __init__(self, args={}, id=None, function= "process", parameters_section="parameters"):
Jerome Mariette's avatar
Jerome Mariette committed
64
65
66
67
68
69
70
71
72
73
74
75
76
        """ 
        """
        # define as a thread
        threading.Thread.__init__(self)
        self.jflow_config_reader = JFlowConfigReader()
        self.manager = WorkflowsManager()
        self.components = []
        self.makes = {}
        self.globals = {}
        self.options = Options()
        self.status = self.STATUS_STARTED
        self.start_time = None
        self.end_time = None
77
78
        self.function = function
        self.parameters_section = parameters_section
Jerome Mariette's avatar
Jerome Mariette committed
79
80
81
82
83
84
85
86
87
        self.comp_pckg = self._import_components()
        self.engine_arguments = ''
        self.component_nameids = {}
        # try to parse engine arguments
        try:
            type, options = self.jflow_config_reader.get_batch()
            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
88
89
90
91
92
93
        try:
            # Add config information
            self.name, self.description, self.parameters = self._get_from_config()
        except:
            raise IOError(self.__class__.__name__ + " workflow property file not found or invalid.")
        
Jerome Mariette's avatar
Jerome Mariette committed
94
        self.id = id
Jerome Mariette's avatar
Jerome Mariette committed
95
        self.args = self._extend_and_format_args(self.parameters, args)
Jerome Mariette's avatar
Jerome Mariette committed
96
        self.metadata = self.args["metadata"]
Jerome Mariette's avatar
Jerome Mariette committed
97
98
99
100
101
        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)
            self._serialize()
102
    
103
    def init_component_nameids(self):
Jerome Mariette's avatar
Jerome Mariette committed
104
105
106
107
        workflow_command_lines = inspect.getsourcelines(getattr(self, self.function))[0]
        for i in range(0, len(workflow_command_lines)):
            line = workflow_command_lines[i]
            if line.find("self.add_component") != -1 and not re.search('^\s*\#', line) :
108
                while re.search('\\\s*$', line) or re.search(',\s*$', line): # While line ends with backslash
Jerome Mariette's avatar
Jerome Mariette committed
109
110
111
112
113
                    # Concatenate next line
                    i += 1
                    next_line = workflow_command_lines[i]
                    if re.search('^\s*\#', next_line) :
                        nex_line = "\\"
114
115
116
117
                    if re.search('\\\s*$', line):
                        line = re.search('(.+)\\\s*$', line).groups()[0] + next_line
                    elif re.search(',\s*$', line):
                        line = re.search('(.+),\s*$', line).groups()[0] + next_line
Jerome Mariette's avatar
Jerome Mariette committed
118
                component_prefix = "default"
119
                component_name = line.strip().split("self.add_component")[1][1:-1].split(",")[0][1:-1]
Jerome Mariette's avatar
Jerome Mariette committed
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
                arguments = re.search("self.add_component\s*\((.+)\)", line).groups()[0]
                named_prefix = re.search("component_prefix\s*=\s*([^,]+)", arguments)
                # Component prefix is in named argument
                if named_prefix:
                    component_prefix = named_prefix.groups()[0].strip().strip('"')
                # Component prefix is missing or in unamed argument
                else :
                    without_named_args = re.sub( ",?\s*\S+\s*=\s*\S+", "" , arguments) # Discard named arguments
                    fields = without_named_args.strip(",").split(",")
                    # Group brackets arguments
                    args_split_clean = []
                    current_idx = 0
                    current_arg = ""
                    while current_idx < len(fields) :
                        current_arg = current_arg + fields[current_idx] + ','
                        open_brackets = current_arg.count("[")
                        close_brackets = current_arg.count("]")
                        if open_brackets == close_brackets:
                            args_split_clean.append( current_arg[:-1] )
                            current_arg = ""
                        current_idx += 1
                    # Find component prefix
                    if len(args_split_clean) >= 4:
                        component_prefix = args_split_clean[3].strip().strip('"')
                if self._component_is_duplicated(component_name+"."+component_prefix):
145
                    raise ValueError("Component " + component_name + " with prefix " + 
Jerome Mariette's avatar
Jerome Mariette committed
146
147
                                     component_prefix + " already exist in this pipeline!")
                self.component_nameids[component_name+"."+component_prefix] = None
148
    
149
    @staticmethod
150
151
152
153
154
155
    def config_parser(arg_lines):
        for arg_line in arg_lines:
            for arg in arg_line.split():
                if not arg.strip():
                    continue
                yield arg
156
    
Jerome Mariette's avatar
Jerome Mariette committed
157
158
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
    
    def add_component(self, component_name, args=[], kwargs={}, component_prefix="default"):
        # first build and check if this component is OK
173
174
175
176
177
178
179
180
        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)
181
182
183
184
185
            # add the component
            self.components.append(cmpt_object)
            # if this one require a dynamic pipeline, execute the first part
            if cmpt_object.is_dynamic:
                self._execute_weaver()
186
187
            return cmpt_object
        else:
Jerome Mariette's avatar
Jerome Mariette committed
188
            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
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
    
    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"):
        # first check if tmp directory exists
        if not os.path.isdir(self.jflow_config_reader.get_tmp_directory()):
            os.makedirs(self.jflow_config_reader.get_tmp_directory(), 0751)
        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()
    
    def run(self):
        """
        Only require for Threading
        """
219
220
        # first init the component list within the workflow
        self.init_component_nameids()
Jerome Mariette's avatar
Jerome Mariette committed
221
222
223
224
225
226
227
228
        self.start_time = time.time()
        self.status = self.STATUS_STARTED
        self.end_time = None  
        # serialize the workflow before pre processing
        self._serialize()
        self.pre_process()
        # serialize the workflow before running
        self._serialize()
Jerome Mariette's avatar
Jerome Mariette committed
229
        try: 
230
            getattr(self, self.function)()
Jerome Mariette's avatar
Jerome Mariette committed
231
        except SystemExit, e: 
Jerome Mariette's avatar
Jerome Mariette committed
232
233
234
            self.status = self.STATUS_FAILED
            self.end_time = time.time()
            self._serialize()
Jerome Mariette's avatar
Jerome Mariette committed
235
            raise
Jerome Mariette's avatar
Jerome Mariette committed
236
237
238
        if len(self.components) > 0:
            self._execute_weaver()
        self._serialize()
Jerome Mariette's avatar
Jerome Mariette committed
239
240
        self.post_process()
        if self.status == self.STATUS_STARTED: self.status = self.STATUS_COMPLETED        
Jerome Mariette's avatar
Jerome Mariette committed
241
242
243
        self.end_time = time.time()
        self._serialize()
    
Jerome Mariette's avatar
Jerome Mariette committed
244
    def _extend_and_format_args(self, parameters, args):
Jerome Mariette's avatar
Jerome Mariette committed
245
        extended_args = {}
Jerome Mariette's avatar
Jerome Mariette committed
246
        for param in parameters:
Jerome Mariette's avatar
Jerome Mariette committed
247
248
249
250
            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):
251
                if param.action == MiltipleAppendAction:
Jerome Mariette's avatar
Jerome Mariette committed
252
253
254
255
256
257
258
259
260
261
262
                    extended_args[param.name] = []
                    for arg in args[param.name]:
                        sub_hash = {}
                        for sub_param in param.sub_parameters:
                            # find the value
                            value = None
                            for values in arg:
                                if values[0] == sub_param.flag: value = values[1]
                            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
263
                # if it's an append parameter, the result should be a list
Jerome Mariette's avatar
Jerome Mariette committed
264
                elif param.action == "append":
Jerome Mariette's avatar
Jerome Mariette committed
265
266
267
268
                    if args[param.name]:
                        try: value = args[param.name].split(",") 
                        except: value = args[param.name]
                    else: value = []
Jerome Mariette's avatar
Jerome Mariette committed
269
270
271
272
273
274
275
                    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]
276
277
                # if it's a boolean
                elif param.type == types.BooleanType:
Jerome Mariette's avatar
Jerome Mariette committed
278
                    extended_args[param.name] = args[param.name] in [True, 1, 'true', '1', 't', 'y', 'yes']
Jerome Mariette's avatar
Jerome Mariette committed
279
280
281
282
283
284
285
286
287
                elif param.type.__name__ == "MiltipleParameters":
                    extended_args[param.name] = {}
                    for sub_param in param.sub_parameters:
                        # find the value
                        value = None
                        for values in args[param.name]:
                            if values[0] == sub_param.flag: value = values[1]
                        if value == None: value = sub_param.default
                        extended_args[param.name][sub_param.name] = value
Jerome Mariette's avatar
Jerome Mariette committed
288
289
290
291
                else:
                    extended_args[param.name] = args[param.name]
            # otherwise use the default
            else:
Jerome Mariette's avatar
Jerome Mariette committed
292
293
294
295
296
297
                if param.type.__name__ == "MiltipleParameters":
                    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
298
299
        return extended_args
    
Jerome Mariette's avatar
Jerome Mariette committed
300
301
302
    def _get_from_config(self):
        reader = ConfigParser()
        reader.read(self._get_property_path())
303
        parameters, param_order = [], []
Jerome Mariette's avatar
Jerome Mariette committed
304
305
        try:
            params = {}
Jerome Mariette's avatar
Jerome Mariette committed
306
            # first grab all parameters name
307
308
            for param in reader.items(self.parameters_section):
                cvalue = reader.get(self.parameters_section, param[0])
Jerome Mariette's avatar
Jerome Mariette committed
309
                cparam = param[0].split(".")[0]
Jerome Mariette's avatar
Jerome Mariette committed
310
                ckey = ".".join(param[0].split(".")[1:])
Jerome Mariette's avatar
Jerome Mariette committed
311
312
                if not params.has_key(cparam):
                    params[cparam] = {ckey: cvalue}
Jerome Mariette's avatar
Jerome Mariette committed
313
                else:
Jerome Mariette's avatar
Jerome Mariette committed
314
                    params[cparam][ckey] = cvalue
315
                if cparam not in param_order: param_order.append(cparam)
Jerome Mariette's avatar
Jerome Mariette committed
316
                    
317
            for param_name in param_order:
Jerome Mariette's avatar
Jerome Mariette committed
318
                sub_params, current_params, sub_objs, sub_order = {}, {}, [], []
Jerome Mariette's avatar
Jerome Mariette committed
319
320
321
322
323
324
325
                for param in params[param_name]:
                    sub_params_values = param.split(".")
                    if len(sub_params_values) == 2:
                        if not sub_params.has_key(sub_params_values[0]):
                            sub_params[sub_params_values[0]] = {sub_params_values[1]: params[param_name][param]}
                        else:
                            sub_params[sub_params_values[0]][sub_params_values[1]] = params[param_name][param]
Jerome Mariette's avatar
Jerome Mariette committed
326
                        sub_order.append(sub_params_values[0])
Jerome Mariette's avatar
Jerome Mariette committed
327
328
                    else:
                        current_params[param] = params[param_name][param]
Jerome Mariette's avatar
Jerome Mariette committed
329
                for sub_param in sorted(sub_params.keys()):
Jerome Mariette's avatar
Jerome Mariette committed
330
331
                    sub = Parameter(**sub_params[sub_param])
                    sub_objs.append(sub)
Jerome Mariette's avatar
Jerome Mariette committed
332
333
                current_params["sub_parameters"] = sub_objs
                oparam = Parameter(**current_params)
Jerome Mariette's avatar
Jerome Mariette committed
334
335
336
                parameters.append(oparam)
        except:
            pass
Jerome Mariette's avatar
Jerome Mariette committed
337
        # finally add the metadata parameter
Jerome Mariette's avatar
Jerome Mariette committed
338
        metadata = Parameter(name="metadata", flag="--metadata", help="Which metadata should be linked to this workflow", action="append")
Jerome Mariette's avatar
Jerome Mariette committed
339
        parameters.append(metadata)
Jerome Mariette's avatar
Jerome Mariette committed
340
341
342
343
        return [reader.get("global", "name"),
                reader.get("global", "description"),
                parameters]
    
Jerome Mariette's avatar
Jerome Mariette committed
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
    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
    
368
369
370
    def get_resource(self, resource):
        return self.jflow_config_reader.get_resource(resource)
    
Jerome Mariette's avatar
Jerome Mariette committed
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
    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:
                        for component in self.components:
                            nest.symbol = component.get_nameid()
435
                            nest.batch = component.batch_options
Jerome Mariette's avatar
Jerome Mariette committed
436
437
438
439
440
441
                            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
442
                        self.end_time = time.time()
Jerome Mariette's avatar
Jerome Mariette committed
443
                        self._serialize()
Jerome Mariette's avatar
Jerome Mariette committed
444
                        raise
Jerome Mariette's avatar
Jerome Mariette committed
445
446
447
448
449
450
451
452
453
                self.components = []
                # 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
454
                    raise
Jerome Mariette's avatar
Jerome Mariette committed
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475

    def _get_current_make(self):
        current_component, make_directory, new_make = [], None, False
        for component in self.components:
            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()

476
477
    def _component_is_duplicated(self, component_nameid):
        if component_nameid in self.component_nameids.keys():
Jerome Mariette's avatar
Jerome Mariette committed
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
            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
494
495
496
497
498
            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
499
            except Exception as e:
Jerome Mariette's avatar
Jerome Mariette committed
500
                logging.getLogger("Workflow._import_components").debug("Component <{0}> cannot be loaded: {1}".format(modname, e))
Jerome Mariette's avatar
Jerome Mariette committed
501
502
503
        # 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
504
505
506
507
508
            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
509
510
            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
511
512
513
514
515
516
517
518
519
520
521
522
        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)