-
Notifications
You must be signed in to change notification settings - Fork 29
/
workflow.py
945 lines (744 loc) · 34.1 KB
/
workflow.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
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
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
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
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
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
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
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
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
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
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
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
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
# -*- coding: utf-8 -*-
#
# Copyright 2017-2022 - Swiss Data Science Center (SDSC)
# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
# Eidgenössische Technische Hochschule Zürich (ETHZ).
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Renku workflow commands."""
import itertools
import re
from collections import defaultdict
from functools import reduce
from pathlib import Path
from typing import TYPE_CHECKING, Any, Dict, List, Optional, Tuple, Union, cast
if TYPE_CHECKING:
from networkx import DiGraph
from renku.command.command_builder import inject
from renku.command.command_builder.command import Command
from renku.command.format.workflow import WORKFLOW_FORMATS
from renku.command.view_model.activity_graph import ActivityGraphViewModel
from renku.command.view_model.composite_plan import CompositePlanViewModel
from renku.command.view_model.plan import plan_view
from renku.core import errors
from renku.core.interface.activity_gateway import IActivityGateway
from renku.core.interface.client_dispatcher import IClientDispatcher
from renku.core.interface.plan_gateway import IPlanGateway
from renku.core.interface.project_gateway import IProjectGateway
from renku.core.plugin.provider import execute
from renku.core.util import communication
from renku.core.util.datetime8601 import local_now
from renku.core.util.os import are_paths_related, get_relative_paths, safe_read_yaml
from renku.core.workflow.activity import create_activity_graph, get_activities_until_paths, sort_activities
from renku.core.workflow.concrete_execution_graph import ExecutionGraph
from renku.core.workflow.plan_factory import delete_indirect_files_list
from renku.core.workflow.value_resolution import CompositePlanValueResolver, ValueResolver
from renku.domain_model.provenance.activity import Activity, ActivityCollection
from renku.domain_model.workflow.composite_plan import CompositePlan
from renku.domain_model.workflow.plan import AbstractPlan, Plan
@inject.autoparams()
def _search_workflows(name: str, plan_gateway: IPlanGateway) -> List[str]:
"""Get all the workflows whose Plan.name start with the given name.
Args:
name(str): The name to search for.
plan_gateway(IPlanGateway): Injected Plan gateway.
Returns:
All Plans whose name starts with ``name``.
"""
return plan_gateway.list_by_name(starts_with=name)
def search_workflows_command():
"""Command to get all the workflows whose Plan.name are greater than or equal to the given name."""
return Command().command(_search_workflows).require_migration().with_database(write=False)
@inject.autoparams()
def _find_workflow(name_or_id: str, plan_gateway: IPlanGateway) -> AbstractPlan:
workflow = plan_gateway.get_by_id(name_or_id) or plan_gateway.get_by_name(name_or_id)
if not workflow:
raise errors.ParameterError(f'The specified workflow "{name_or_id}" cannot be found.')
return workflow
@inject.autoparams()
def _list_workflows(plan_gateway: IPlanGateway, format: str, columns: List[str]):
"""List or manage workflows with subcommands.
Args:
plan_gateway(IPlanGateway): The injected Plan gateway.
format(str): The output format.
columns(List[str]): The columns to show for tabular output.
Returns:
List of workflows formatted by ``format``.
"""
workflows = plan_gateway.get_newest_plans_by_names()
if format not in WORKFLOW_FORMATS:
raise errors.UsageError(f'Provided format "{format}" is not supported ({", ".join(WORKFLOW_FORMATS.keys())})"')
if format == "json-ld":
return WORKFLOW_FORMATS[format](list(workflows.values()), columns=columns)
return WORKFLOW_FORMATS[format](list(map(lambda x: plan_view(x), workflows.values())), columns=columns)
def list_workflows_command():
"""Command to list or manage workflows with subcommands."""
return Command().command(_list_workflows).require_migration().with_database(write=False)
@inject.autoparams()
def _remove_workflow(name: str, force: bool, plan_gateway: IPlanGateway):
"""Remove the remote named <name>.
Args:
name (str): The name of the Plan to remove.
force (bool): Whether to force removal or not.
plan_gateway(IPlanGateway): The injected Plan gateway.
Raises:
errors.ParameterError: If the Plan doesn't exist or was already deleted.
"""
workflows = plan_gateway.get_newest_plans_by_names()
plan = None
if name.startswith("/plans/"):
plan = next(filter(lambda x: x.id == name, workflows.values()), None)
if not plan and name not in workflows:
raise errors.ParameterError(f'The specified workflow is "{name}" is not an active workflow.')
if not force:
prompt_text = f'You are about to remove the following workflow "{name}".' + "\n" + "\nDo you wish to continue?"
communication.confirm(prompt_text, abort=True, warning=True)
plan = plan or workflows[name]
plan.unfreeze()
plan.invalidated_at = local_now()
plan.freeze()
def remove_workflow_command():
"""Command that removes the workflow named <name>."""
return Command().command(_remove_workflow).require_clean().with_database(write=True).with_commit()
def _show_workflow(name_or_id: str):
"""Show the details of a workflow.
Args:
name_or_id(str): Name or id of the Plan to show.
Returns:
Details of the Plan.
"""
workflow = _find_workflow(name_or_id)
return plan_view(workflow)
def show_workflow_command():
"""Command that the details of a workflow."""
return Command().command(_show_workflow).require_migration().with_database(write=False)
@inject.autoparams()
def _compose_workflow(
name: str,
description: str,
mappings: List[str],
defaults: List[str],
links: List[str],
param_descriptions: List[str],
map_inputs: bool,
map_outputs: bool,
map_params: bool,
link_all: bool,
keywords: List[str],
steps: List[str],
sources: List[str],
sinks: List[str],
activity_gateway: IActivityGateway,
plan_gateway: IPlanGateway,
project_gateway: IProjectGateway,
client_dispatcher: IClientDispatcher,
) -> CompositePlan:
"""Compose workflows into a CompositePlan.
Args:
name(str): Name of the new composed Plan.
description(str): Description for the Plan.
mappings(List[str]): Mappings between parameters of this and child Plans.
defaults(List[str]): Default values for parameters.
links(List[str]): Links between parameters of child Plans.
param_descriptions(List[str]): Descriptions of parameters.
map_inputs(bool): Whether or not to automatically expose child inputs.
map_outputs(bool): Whether or not to automatically expose child outputs.
map_params(bool): Whether or not to automatically expose child parameters.
link_all(bool): Whether or not to automatically link child steps' parameters.
keywords(List[str]): Keywords for the Plan.
steps(List[str]): Child steps to include.
sources(List[str]): Starting files when automatically detecting child Plans.
sinks(List[str]): Ending files when automatically detecting child Plans.
activity_gateway(IActivityGateway): Injected activity gateway.
plan_gateway(IPlanGateway): Injected plan gateway.
project_gateway(IProjectGateway): Injected project gateway.
client_dispatcher(IClientDispatcher): Injected client dispatcher.
Returns:
The newly created ``CompositePlan``.
"""
if plan_gateway.get_by_name(name):
raise errors.ParameterError(f"Duplicate workflow name: workflow '{name}' already exists.")
child_workflows = []
plan_activities = []
if steps:
for workflow_name_or_id in steps:
child_workflow = plan_gateway.get_by_id(workflow_name_or_id)
if not child_workflow:
child_workflow = plan_gateway.get_by_name(workflow_name_or_id)
if not child_workflow:
raise errors.ObjectNotFoundError(workflow_name_or_id)
child_workflows.append(child_workflow)
else:
client = client_dispatcher.current_client
sources = sources or []
sources = get_relative_paths(base=client.path, paths=sources)
if not sinks:
usages = activity_gateway.get_all_usage_paths()
generations = activity_gateway.get_all_generation_paths()
sinks = [g for g in generations if all(not are_paths_related(g, u) for u in usages)]
sinks = get_relative_paths(base=client.path, paths=sinks)
activities = list(
get_activities_until_paths(
sinks, sources, activity_gateway=activity_gateway, client_dispatcher=client_dispatcher
)
)
activities = sort_activities(activities)
# we need to get the actual plans from the DB as plan_with_values returns a copy
for i, activity in enumerate(activities, 1):
child_workflow = activity.association.plan
child_workflows.append(child_workflow)
plan_activities.append((i, activity.plan_with_values))
plan = CompositePlan(
description=description,
id=CompositePlan.generate_id(),
keywords=keywords,
name=name,
plans=child_workflows,
project_id=project_gateway.get_project().id,
)
if mappings:
plan.set_mappings_from_strings(mappings)
if defaults:
plan.set_mapping_defaults(defaults)
if plan_activities:
# Since composite is created from activities, we need to add mappings to set defaults to the values of
# the activities, to ensure values from the involved activities are preserved.
# If the user supplies their own mappings, those overrule the automatically added ones.
for i, child_plan in plan_activities:
for param in itertools.chain(child_plan.inputs, child_plan.outputs, child_plan.parameters):
try:
mapping_name = f"{i}-{param.name}"
plan.set_mappings_from_strings([f"{mapping_name}=@step{i}.{param.name}"])
except errors.MappingExistsError:
continue
plan.set_mapping_defaults([f"{mapping_name}={param.actual_value}"])
if links:
plan.set_links_from_strings(links)
graph = ExecutionGraph([plan])
cycles = graph.cycles
if cycles:
cycles = [map(lambda x: x.name, cycle) for cycle in cycles]
raise errors.GraphCycleError(cycles)
if param_descriptions:
plan.set_mapping_descriptions(param_descriptions)
if map_inputs:
plan.map_all_inputs()
if map_outputs:
plan.map_all_outputs()
if map_params:
plan.map_all_parameters()
if link_all:
# NOTE: propagate values to for linking to use
rv = CompositePlanValueResolver(plan)
plan = rv.apply()
graph = ExecutionGraph([plan], virtual_links=True)
cycles = graph.cycles
if cycles:
cycles = [map(lambda x: x.name, cycle) for cycle in cycles]
raise errors.GraphCycleError(cycles)
for virtual_link in graph.virtual_links:
plan.add_link(virtual_link[0], [virtual_link[1]])
plan_gateway.add(plan)
return CompositePlanViewModel.from_composite_plan(plan)
def compose_workflow_command():
"""Command that creates a composite of several workflows."""
return (
Command().command(_compose_workflow).require_migration().require_clean().with_database(write=True).with_commit()
)
@inject.autoparams()
def _edit_workflow(
name: str,
new_name: Optional[str],
description: Optional[str],
set_params: List[str],
map_params: List[str],
rename_params: List[str],
describe_params: List[str],
plan_gateway: IPlanGateway,
):
"""Edits a workflow details.
Args:
name (str): Name of the Plan to edit.
new_name(Optional[str]): New name of the Plan.
description(Optional[str]): New description of the Plan.
set_params(List[str]): New default values for parameters.
map_params(List[str]): New mappings for Plan.
rename_params(List[str]): New names for parameters.
describe_params(List[str]): New descriptions for parameters.
plan_gateway(IPlanGateway): Injected plan gateway.
Returns:
Details of the modified Plan.
"""
derived_from = _find_workflow(name)
workflow = derived_from.derive()
if new_name:
workflow.name = new_name
if description:
workflow.description = description
if isinstance(workflow, Plan):
workflow.set_parameters_from_strings(set_params)
def _mod_params(workflow, changed_params, attr):
for param_string in changed_params:
name, new_value = param_string.split("=", maxsplit=1)
new_value = new_value.strip(' "')
found = False
for collection in [workflow.inputs, workflow.outputs, workflow.parameters]:
for i, param in enumerate(collection):
if param.name == name:
new_param = param.derive(plan_id=workflow.id)
setattr(new_param, attr, new_value)
collection[i] = new_param
found = True
break
if found:
break
else:
raise errors.ParameterNotFoundError(parameter=name, workflow=workflow.name)
_mod_params(workflow, rename_params, "name")
_mod_params(workflow, describe_params, "description")
elif isinstance(workflow, CompositePlan) and len(map_params):
workflow.set_mappings_from_strings(map_params)
plan_gateway.add(workflow)
return plan_view(workflow)
def edit_workflow_command():
"""Command that edits the properties of a given workflow."""
return Command().command(_edit_workflow).require_clean().with_database(write=True).with_commit()
@inject.autoparams()
def _export_workflow(
name_or_id,
client_dispatcher: IClientDispatcher,
format: str,
output: Optional[Union[str, Path]],
values: Optional[str],
):
"""Export a workflow to a given format.
Args:
name_or_id: name or id of the Plan to export
client_dispatcher(IClientDispatcher): Injected client dispatcher.
format(str): Format to export to.
output(Optional[str]): Output path to store result at.
values(Optional[str]): Path to values file to apply before export.
Returns:
The exported workflow as string.
"""
client = client_dispatcher.current_client
workflow = _find_workflow(name_or_id)
output_path: Optional[Path] = None
if output and isinstance(output, str):
output_path = Path(output)
elif output:
output_path = cast(Path, output)
if values:
parsed_values = safe_read_yaml(values)
rv = ValueResolver.get(workflow, parsed_values)
workflow = rv.apply()
if rv.missing_parameters:
communication.warn(
f'Could not resolve the following parameters in "{workflow.name}" workflow: '
f'{",".join(rv.missing_parameters)}'
)
from renku.core.plugin.workflow import workflow_converter
converter = workflow_converter(format)
return converter(workflow=workflow, basedir=client.path, output=output_path, output_format=format)
def export_workflow_command():
"""Command that exports a workflow into a given format."""
return Command().command(_export_workflow).require_clean().with_database(write=False)
@inject.autoparams()
def _lookup_paths_in_paths(client_dispatcher: IClientDispatcher, lookup_paths: List[str], target_paths: List[str]):
"""Return all lookup_paths that are in or under target_paths."""
client = client_dispatcher.current_client
dirs = []
files = set()
for p in lookup_paths:
path = Path(get_relative_paths(client.path, [p])[0])
if path.is_dir():
dirs.append(path)
else:
files.add(path)
target_dirs = []
target_files = set()
for p in target_paths:
path = Path(p)
if path.is_dir():
target_dirs.append(path)
else:
target_files.add(path)
result = set()
for target_file in target_files:
if target_file in files or any(d in target_file.parents for d in dirs):
result.add(str(target_file))
for target_dir in target_dirs:
if target_dir in dirs or any(target_dir in f.parents for f in files):
result.add(str(target_dir))
return result
@inject.autoparams()
def _workflow_inputs(activity_gateway: IActivityGateway, paths: List[str] = None):
"""Get inputs used by workflows.
Args:
activity_gateway(IActivityGateway): The injected activity gateway.
paths(List[str], optional): List of paths to consider as inputs (Default value = None).
Returns:
Set[str]: Set of input file paths.
"""
usage_paths = activity_gateway.get_all_usage_paths()
if not paths:
return usage_paths
return _lookup_paths_in_paths(lookup_paths=paths, target_paths=usage_paths)
def workflow_inputs_command():
"""Command that shows inputs used by workflows."""
return Command().command(_workflow_inputs).require_migration().with_database(write=False)
@inject.autoparams()
def _workflow_outputs(activity_gateway: IActivityGateway, paths: List[str] = None):
"""Get inputs used by workflows.
Args:
activity_gateway(IActivityGateway): The injected activity gateway.
paths(List[str], optional): List of paths to consider as outputs (Default value = None).
Returns:
Set[str]: Set of output file paths.
"""
generation_paths = activity_gateway.get_all_generation_paths()
if not paths:
return generation_paths
return _lookup_paths_in_paths(lookup_paths=paths, target_paths=generation_paths)
def workflow_outputs_command():
"""Command that shows inputs used by workflows."""
return Command().command(_workflow_outputs).require_migration().with_database(write=False)
@inject.params(client_dispatcher=IClientDispatcher, activity_gateway=IActivityGateway, plan_gateway=IPlanGateway)
def execute_workflow(
dag: "DiGraph",
client_dispatcher: IClientDispatcher,
activity_gateway: IActivityGateway,
plan_gateway: IPlanGateway,
provider="cwltool",
config=None,
):
"""Execute a Run with/without subprocesses.
Args:
dag("DiGraph"): The workflow graph to execute.
client_dispatcher(IClientDispatcher): The injected client dispatcher.
activity_gateway(IActivityGateway): The injected activity gateway.
plan_gateway(IPlanGateway): The injected plan gateway.
provider: Provider to run the workflow with (Default value = "cwltool").
config: Config for the workflow provider (Default value = None).
"""
client = client_dispatcher.current_client
inputs = {i.actual_value for p in dag.nodes for i in p.inputs}
# NOTE: Pull inputs from Git LFS or other storage backends
if client.check_external_storage():
client.pull_paths_from_storage(*inputs)
# check whether the none generated inputs of workflows are available
outputs = {o.actual_value for p in dag.nodes for o in p.outputs}
for i in inputs - outputs:
if not Path(i).exists():
raise errors.ParameterError(f"Input '{i}' for the workflow does not exists!")
delete_indirect_files_list(client.path)
if config:
config = safe_read_yaml(config)
started_at_time = local_now()
execute(dag=dag, basedir=client.path, provider=provider, config=config)
ended_at_time = local_now()
activities = []
for plan in dag.nodes:
# NOTE: Update plans are copies of Plan objects. We need to use the original Plan objects to avoid duplicates.
original_plan = plan_gateway.get_by_id(plan.id)
activity = Activity.from_plan(plan=plan, started_at_time=started_at_time, ended_at_time=ended_at_time)
activity.association.plan = original_plan
activity_gateway.add(activity)
activities.append(activity)
if len(activities) > 1:
activity_collection = ActivityCollection(activities=activities)
activity_gateway.add_activity_collection(activity_collection)
def _execute_workflow(
name_or_id: str, set_params: List[str], provider: str, config: Optional[str], values: Optional[str]
):
def _nested_dict():
return defaultdict(_nested_dict)
workflow = _find_workflow(name_or_id)
# apply the provided parameter settings provided by user
override_params = dict()
if values:
override_params.update(safe_read_yaml(values))
if set_params:
from deepmerge import always_merger
for param in set_params:
name, value = param.split("=", maxsplit=1)
keys = name.split(".")
set_param = reduce(lambda x, y: {y: x}, reversed(keys), value) # type: ignore
override_params = always_merger.merge(override_params, set_param)
rv = ValueResolver.get(workflow, override_params)
workflow = rv.apply()
if rv.missing_parameters:
communication.warn(
f'Could not resolve the following parameters in "{workflow.name}" workflow: '
f'{",".join(rv.missing_parameters)}'
)
graph = ExecutionGraph([workflow], virtual_links=True)
execute_workflow(dag=graph.workflow_graph, provider=provider, config=config)
def execute_workflow_command():
"""Command that executes a workflow."""
return (
Command().command(_execute_workflow).require_migration().require_clean().with_database(write=True).with_commit()
)
@inject.autoparams()
def _visualize_graph(
sources: List[str],
targets: List[str],
show_files: bool,
activity_gateway: IActivityGateway,
client_dispatcher: IClientDispatcher,
revision: Optional[str] = None,
):
"""Visualize an activity graph.
Args:
sources(List[str]): Input paths to start the visualized graph at.
targets(List[str]): Output paths to end the visualized graph at.
show_files(bool): Whether or not to show file nodes.
activity_gateway(IActivityGateway): The injected activity gateway.
client_dispatcher(IClientDispatcher): The injected client dispatcher.
revision(Optional[str], optional): Revision or revision range to show
the graph for (Default value = None)
Returns:
Graph visualization view model.
"""
client = client_dispatcher.current_client
sources = sources or []
sources = get_relative_paths(base=client.path, paths=sources)
if not targets:
usages = activity_gateway.get_all_usage_paths()
generations = activity_gateway.get_all_generation_paths()
targets = [g for g in generations if all(not are_paths_related(g, u) for u in usages)]
activities = get_activities_until_paths(
paths=targets,
sources=sources,
revision=revision,
activity_gateway=activity_gateway,
client_dispatcher=client_dispatcher,
)
graph = create_activity_graph(list(activities), with_inputs_outputs=show_files)
return ActivityGraphViewModel(graph)
def visualize_graph_command():
"""Execute the graph visualization command."""
return Command().command(_visualize_graph).require_migration().with_database(write=False)
def _extract_iterate_parameters(values: Dict[str, Any], index_pattern: re.Pattern, tag_separator: str = "@"):
"""Recursively extracts the iteration paramaters from the workflow values given by the user.
Args:
values(Dict[str, Any]): Plan values to iterate over.
index_pattern(re.Pattern): Pattern for parameter indizes.
tag_separator(str, optional): Separator for tagged values (Default value = "@").
Returns:
Tuple of ``(iter_params, params)`` where ``params`` are regular parameters
and ``iter_params`` are parameters with iteration values.
"""
iter_params: Dict[str, Any] = {"indexed": {}, "params": {}, "tagged": {}}
params: Dict[str, Any] = {}
for param_name, param_value in values.items():
if isinstance(param_value, str) and index_pattern.search(param_value):
iter_params["indexed"][param_name] = param_value
params[param_name] = param_value
elif isinstance(param_value, list):
if len(param_value) == 1:
communication.warn(
f"The parameter '{param_name}' has only one element '{param_value}', "
"changing it to be a fixed parameter!"
)
params[param_name] = param_value[0]
continue
if tag_separator in param_name:
name, tag = param_name.split(tag_separator, maxsplit=1)
if tag in iter_params["tagged"]:
iter_params["tagged"][tag][name] = param_value
else:
iter_params["tagged"][tag] = {name: param_value}
params[name] = param_value
else:
iter_params["params"][param_name] = param_value
params[param_name] = param_value
elif isinstance(param_value, dict):
inner_iter_params, inner_params = _extract_iterate_parameters(param_value, index_pattern, tag_separator)
iter_params["params"].update([(f"{param_name}.{ik}", iv) for ik, iv in inner_iter_params["params"].items()])
iter_params["indexed"].update(
[(f"{param_name}.{ik}", iv) for ik, iv in inner_iter_params["indexed"].items()]
)
for tag, param in inner_iter_params["tagged"].items():
if tag in iter_params["tagged"]:
iter_params["tagged"][tag].update([(f"{param_name}.{ik}", iv) for ik, iv in param.items()])
else:
iter_params["tagged"][tag] = dict([(f"{param_name}.{ik}", iv) for ik, iv in param.items()])
params[param_name] = inner_params
else:
params[param_name] = param_value
return iter_params, params
def _validate_iterate_parameters(
workflow: AbstractPlan, workflow_params: Dict[str, Any], iter_params: Dict[str, Any]
) -> Optional[Dict[str, Any]]:
"""Validates the user provided iteration parameters.
Args:
workflow(AbstractPlan): The Plan to validate parameters against.
workflow_params(Dict[str, Any]): The plain parameters to check.
iter_params(Dict[str, Any]): The iterative parameters to check.
Returns:
Dictionary of validated iteration parameters.
"""
import copy
rv = ValueResolver.get(copy.deepcopy(workflow), workflow_params)
rv.apply()
mp_paths = [mp.split(".") for mp in rv.missing_parameters]
for collection in [iter_params["indexed"], iter_params["params"], *iter_params["tagged"].values()]:
remove_keys = []
for p in collection.keys():
parameter_path = p.split(".")
if any(parameter_path[: len(mp)] == mp for mp in mp_paths):
remove_keys.append(p)
for rk in remove_keys:
collection.pop(rk)
# validate tagged
empty_tags = []
for k, tagged_params in iter_params["tagged"].items():
if len(tagged_params) == 0:
empty_tags.append(k)
else:
tagged_params_values = list(tagged_params.values())
tag_size = len(tagged_params_values[0])
for p in tagged_params_values[1:]:
num_params = len(p)
if tag_size != num_params:
communication.error(
f"'{k}' tagged parameters '{tagged_params}' has different number of possible values!"
)
return None
for et in empty_tags:
iter_params["tagged"].pop(et)
if (len(iter_params["indexed"]) == 0) and (len(iter_params["params"]) == 0) and (len(iter_params["tagged"]) == 0):
raise errors.UsageError(
"Please check the provided mappings as none of the "
f"parameters are present in the '{workflow.name}' workflow"
)
if rv.missing_parameters:
communication.confirm(
f'Could not resolve the following parameters in "{workflow.name}" workflow: '
f'{", ".join(rv.missing_parameters)}. Resume the execution?',
abort=True,
)
return iter_params
def _build_iterations(
workflow: AbstractPlan, workflow_params: Dict[str, Any], iter_params: Dict[str, Any], index_pattern: re.Pattern
) -> Tuple[List[AbstractPlan], List[Dict]]:
"""Instantiate the workflows for each iteration.
Args:
workflow(AbstractPlan): The base workflow to use as a template.
workflow_params(Dict[str, Any]): The plain parameters to use.
iter_params(Dict[str, Any]): The iterative parameters to use.
index_pattern(re.Pattern): The pattern for the index placeholder.
Returns:
Tuple of ``(plans, itervalues)`` with ``plans`` being a list of all
plans for each iteration and ``itervalues`` being a list of all values
for each iteration.
"""
import copy
from deepmerge import always_merger
plans = []
execute_plan = []
columns = list(iter_params["params"].keys())
tagged_values = []
for tag in iter_params["tagged"].values():
columns.extend(tag.keys())
tagged_values.append(zip(*tag.values()))
def _flatten(values):
for i in values:
if isinstance(i, (list, tuple)):
for k in i:
yield k
else:
yield i
for i, values in enumerate(itertools.product(*iter_params["params"].values(), *tagged_values)):
plan_params = copy.deepcopy(workflow_params)
iteration_values = {}
for k, v in iter_params["indexed"].items():
value = index_pattern.sub(str(i), v)
set_param = reduce(lambda x, y: {y: x}, reversed(k.split(".")), value) # type: ignore
plan_params = always_merger.merge(plan_params, set_param)
iteration_values[k] = value
for param_key, param_value in zip(columns, _flatten(values)):
set_param = reduce(lambda x, y: {y: x}, reversed(param_key.split(".")), param_value) # type: ignore
plan_params = always_merger.merge(plan_params, set_param)
iteration_values[param_key] = param_value
execute_plan.append(iteration_values)
rv = ValueResolver.get(copy.deepcopy(workflow), plan_params)
plans.append(rv.apply())
return plans, execute_plan
def _iterate_workflow(
name_or_id: str,
mapping_path: str,
mappings: List[str],
dry_run: bool,
provider: str,
config: Optional[str],
):
import ast
from deepmerge import always_merger
from renku.domain_model.tabulate import tabulate
if mapping_path is None and len(mappings) == 0:
raise errors.UsageError("No mapping has been given for the iteration!")
workflow = _find_workflow(name_or_id)
TAG_SEPARATOR = "@"
index_pattern = re.compile(r"{iter_index}")
iter_params: Optional[Dict[str, Any]] = {"indexed": {}, "params": {}, "tagged": {}}
workflow_params = {}
if mapping_path:
mapping = safe_read_yaml(mapping_path)
iter_params, workflow_params = _extract_iterate_parameters(mapping, index_pattern, tag_separator=TAG_SEPARATOR)
for m in mappings:
param_name, param_value = m.split("=", maxsplit=1)
if index_pattern.search(param_value):
iter_params["indexed"][param_name] = param_value # type: ignore
else:
try:
param_value = ast.literal_eval(param_value)
except Exception:
raise errors.ParameterError(
f"The value of '{param_name}' parameter is neither a list nor templated variable!"
)
if isinstance(param_value, list) and len(param_value) == 1:
communication.warn(
f"The parameter '{param_name}' has only one element '{param_value}', "
"changing it to be a fixed parameter!"
)
workflow_params[param_name] = param_value[0]
continue
elif not isinstance(param_value, list):
workflow_params[param_name] = param_value
continue
if TAG_SEPARATOR in param_name:
name, tag = param_name.split(TAG_SEPARATOR, maxsplit=1)
if tag in iter_params["tagged"]:
iter_params["tagged"][tag][name] = param_value
else:
iter_params["tagged"][tag] = {name: param_value}
param_name = name
else:
iter_params["params"][param_name] = param_value
set_param = reduce(lambda x, y: {y: x}, reversed(param_name.split(".")), param_value) # type: ignore
workflow_params = always_merger.merge(workflow_params, set_param)
iter_params = _validate_iterate_parameters(workflow, workflow_params, cast(Dict[str, Any], iter_params))
if iter_params is None:
return
plans, execute_plan = _build_iterations(workflow, workflow_params, iter_params, index_pattern)
communication.echo(f"\n\n{tabulate(execute_plan, execute_plan[0].keys())}")
if not dry_run:
graph = ExecutionGraph(workflows=plans, virtual_links=True)
execute_workflow(dag=graph.workflow_graph, provider=provider, config=config)
def iterate_workflow_command():
"""Command that executes several workflows given a set of variables."""
return (
Command().command(_iterate_workflow).require_migration().require_clean().with_database(write=True).with_commit()
)