-
Notifications
You must be signed in to change notification settings - Fork 85
/
options.py
843 lines (680 loc) · 21.9 KB
/
options.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
""" Click definitions for various shared options and arguments.
"""
from __future__ import absolute_import
import functools
import os
import click
from galaxy.tools.deps import docker_util
from .config import get_default_callback
def force_option(what="files"):
return click.option(
"-f",
"--force",
is_flag=True,
help="Overwrite existing %s if present." % what,
)
def skip_venv_option():
return click.option(
"--skip_venv",
is_flag=True,
help=("Do not create or source a virtualenv environment for Galaxy, "
"this should be used or instance to preserve an externally "
"configured virtual environment or conda environment.")
)
def test_data_option():
return click.option(
"--test_data",
type=click.Path(exists=True, file_okay=False, resolve_path=True),
help="test-data directory to for specified tool(s).",
)
def tool_data_table_option():
return click.option(
"--tool_data_table",
type=click.Path(exists=True, file_okay=True, resolve_path=True),
help="tool_data_table_conf.xml file to for specified tool(s).",
)
def galaxy_root_option():
return click.option(
"--galaxy_root",
type=click.Path(exists=True, file_okay=False, resolve_path=True),
help="Root of development galaxy directory to execute command with.",
)
def galaxy_sqlite_database_option():
return click.option(
"--galaxy_sqlite_database",
callback=get_default_callback(None, resolve_path=True),
type=click.Path(exists=True, file_okay=False, resolve_path=True),
help="Preseeded Galaxy sqlite database to target.",
)
def galaxy_cwl_root_option():
return click.option(
"--cwl_galaxy_root",
type=click.Path(exists=True, file_okay=False, resolve_path=True),
help=("Root of development galaxy directory to execute command with"
" (must be branch of Galaxy with CWL support, this option"
" is experimental and will be replaced with --galaxy_root when"
" and if CWL support is merged into Galaxy."),
)
def galaxy_port_option():
return click.option(
"--port",
type=int,
default=None,
callback=get_default_callback("9090"),
help="Port to serve Galaxy on (default is 9090).",
)
def galaxy_host_option():
return click.option(
"--host",
type=str,
default=None,
callback=get_default_callback("127.0.0.1"),
help=("Host to bind Galaxy to. Default is 127.0.0.1 that is "
"restricted to localhost connections for security reasons "
"set to 0.0.0.0 to bind Galaxy to all ports including "
"potentially publicly accessible ones."),
)
def dependency_resolvers_option():
return click.option(
"--dependency_resolvers_config_file",
type=click.Path(
exists=True,
file_okay=True,
dir_okay=False,
resolve_path=True
),
help="Dependency resolver configuration for Galaxy to target.",
)
def enable_cwl_option():
return click.option(
"--cwl",
is_flag=True,
help=("Configure Galaxy for use with CWL tool."
" (this option is experimental and will be replaced when"
" and if CWL support is merged into Galaxy)."),
)
def cwl_conformance_test():
return click.option(
"--conformance-test",
is_flag=True,
help=("Generate CWL conformance test object describing job. "
"Required by CWL conformance test suite and implemented "
"by cwltool reference implementation."),
)
def brew_dependency_resolution():
return click.option(
"--brew_dependency_resolution",
is_flag=True,
help="Configure Galaxy to use plain brew dependency resolution.",
)
def conda_dependency_resolution():
return click.option(
"--conda_dependency_resolution",
is_flag=True,
help="Configure Galaxy to use only conda for dependency resolution.",
)
def shed_dependency_resolution():
return click.option(
"--shed_dependency_resolution",
is_flag=True,
help=("Configure Galaxy to use brewed Tool Shed dependency"
" resolution."),
)
def job_config_option():
return click.option(
"--job_config_file",
type=click.Path(
exists=True,
file_okay=True,
dir_okay=False,
resolve_path=True
),
help="Job configuration file for Galaxy to target.",
)
def tool_dependency_dir_option():
return click.option(
"--tool_dependency_dir",
type=click.Path(
exists=True,
file_okay=False,
dir_okay=True,
resolve_path=True
),
help="Tool dependency dir for Galaxy to target.",
)
def install_galaxy_option():
return click.option(
"--install_galaxy",
is_flag=True,
help="Download and configure a disposable copy of Galaxy from github."
)
def no_cache_galaxy_option():
return click.option(
"--no_cache_galaxy",
is_flag=True,
help=("Skip caching of Galaxy source and dependencies obtained with "
"--install_galaxy. Not caching this results in faster "
"downloads (no git) - so is better on throw away instances such "
"with TravisCI. ")
)
def galaxy_branch_option():
return click.option(
"--galaxy_branch",
callback=get_default_callback(None),
help=("Branch of Galaxy to target (defaults to master) if a Galaxy "
"root isn't specified.")
)
def galaxy_source_option():
return click.option(
"--galaxy_source",
callback=get_default_callback(None),
help=("Git source of Galaxy to target (defaults to the official "
"galaxyproject github source if a Galaxy root isn't "
"specified.")
)
def skip_install_option():
return click.option(
"--skip_install",
is_flag=True,
help="Skip installation - only source requirements already available."
)
def brew_option():
return click.option(
"--brew",
type=click.Path(exists=True, file_okay=True, dir_okay=False),
help="Homebrew 'brew' executable to use."
)
def conda_prefix_option():
return click.option(
"--conda_prefix",
type=click.Path(file_okay=False, dir_okay=True),
help="Conda prefix to use for conda dependency commands."
)
def conda_exec_option():
return click.option(
"--conda_exec",
type=click.Path(exists=True, file_okay=True, dir_okay=False),
help="Location of conda executable."
)
def conda_debug_option():
return click.option(
"--conda_debug",
is_flag=True,
help="Enable more verbose conda logging."
)
def conda_ensure_channels_option():
return click.option(
"--conda_ensure_channels",
type=str,
help=("Ensure conda is configured with specified comma separated "
"list of channels."),
default="r,bioconda"
)
def conda_copy_dependencies_option():
return click.option(
"--conda_copy_dependencies",
is_flag=True,
help=("Conda dependency resolution for Galaxy will copy dependencies "
"instead of attempting to link them.")
)
def conda_auto_install_option():
return click.option(
"--conda_auto_install",
is_flag=True,
help=("Conda dependency resolution for Galaxy will auto install "
"will attempt to install requested but missing packages.")
)
def conda_auto_init_option():
return click.option(
"--conda_auto_init",
is_flag=True,
help=("Conda dependency resolution for Galaxy will auto install "
"conda itself using miniconda if not availabe on conda_prefix.")
)
def required_tool_arg():
""" Decorate click method as requiring the path to a single tool.
"""
arg_type = click.Path(
exists=True,
file_okay=True,
dir_okay=False,
readable=True,
resolve_path=True,
)
return click.argument("path", metavar="TOOL_PATH", type=arg_type)
def required_job_arg():
""" Decorate click method as requiring the path to a single tool.
"""
arg_type = click.Path(
exists=True,
file_okay=True,
dir_okay=False,
readable=True,
resolve_path=True,
)
return click.argument("job_path", metavar="JOB_PATH", type=arg_type)
def _optional_tools_default(ctx, param, value):
if param.name == "paths" and len(value) == 0:
return [os.path.abspath(os.getcwd())]
else:
return value
def optional_tools_arg(multiple=False):
""" Decorate click method as optionally taking in the path to a tool
or directory of tools. If no such argument is given the current working
directory will be treated as a directory of tools.
"""
arg_type = click.Path(
exists=True,
file_okay=True,
dir_okay=True,
readable=True,
resolve_path=True,
)
name = "paths" if multiple else "path"
nargs = -1 if multiple else 1
return click.argument(
name,
metavar="TOOL_PATH",
type=arg_type,
nargs=nargs,
callback=_optional_tools_default,
)
class ProjectOrRepositry(click.Path):
def __init__(self, **kwds):
super(ProjectOrRepositry, self).__init__(**kwds)
def convert(self, value, param, ctx):
if value and value.startswith("git:") or value.startswith("git+"):
return value
else:
return super(ProjectOrRepositry, self).convert(value, param, ctx)
def shed_project_arg(multiple=True):
arg_type = ProjectOrRepositry(
exists=True,
file_okay=False,
dir_okay=True,
writable=True,
resolve_path=True,
)
name = "paths" if multiple else "path"
nargs = -1 if multiple else 1
return click.argument(
name,
metavar="PROJECT",
type=arg_type,
nargs=nargs,
callback=_optional_tools_default,
)
def optional_project_arg(exists=True):
arg_type = click.Path(
exists=exists,
file_okay=False,
dir_okay=True,
writable=True,
resolve_path=True,
)
return click.argument(
"path",
metavar="PROJECT",
default=".",
type=arg_type
)
def no_cleanup_option():
return click.option(
"--no_cleanup",
is_flag=True,
help=("Do not cleanup temp files created for and by Galaxy.")
)
def docker_cmd_option():
return click.option(
"--docker_cmd",
default=docker_util.DEFAULT_DOCKER_COMMAND,
help="Command used to launch docker (defaults to docker)."
)
def docker_sudo_option():
return click.option(
"--docker_sudo",
is_flag=True,
help="Flag to use sudo when running docker."
)
def docker_sudo_cmd_option():
return click.option(
"--docker_sudo_cmd",
default=None,
help="sudo command to use when --docker_sudo is enabled " +
"(defaults to sudo).",
callback=get_default_callback(docker_util.DEFAULT_SUDO_COMMAND),
)
def docker_host_option():
return click.option(
"--docker_host",
default=None,
help="Docker host to target when executing docker commands " +
"(defaults to localhost).",
callback=get_default_callback(docker_util.DEFAULT_HOST),
)
def shed_owner_option():
return click.option(
"--owner",
help="Tool Shed repository owner (username)."
)
def shed_name_option():
return click.option(
"--name",
help="Tool Shed repository name (defaults to the inferred "
"tool directory name)."
)
def validate_shed_target_callback(ctx, param, value):
target = get_default_callback("toolshed")(ctx, param, value)
if target is None:
ctx.fail("default_shed_target set to None, must specify a value for "
"--shed_target to run this command.")
return target
def shed_target_option():
return click.option(
"-t",
"--shed_target",
help="Tool Shed to target (this can be 'toolshed', 'testtoolshed', "
"'local' (alias for http://localhost:9009/), an arbitrary url "
"or mappings defined ~/.planemo.yml.",
default=None,
callback=validate_shed_target_callback,
)
def shed_key_option():
return click.option(
"--shed_key",
help=("API key for Tool Shed access. An API key is required unless "
"e-mail and password is specified. This key can be specified "
"with either --shed_key or --shed_key_from_env.")
)
def shed_key_from_env_option():
return click.option(
"--shed_key_from_env",
help="Environment variable to read API key for Tool Shed access from."
)
def shed_email_option():
return click.option(
"--shed_email",
help="E-mail for Tool Shed auth (required unless shed_key is "
"specified)."
)
def shed_password_option():
return click.option(
"--shed_password",
help="Password for Tool Shed auth (required unless shed_key is "
"specified)."
)
def shed_skip_upload():
return click.option(
"--skip_upload",
is_flag=True,
help=("Skip upload contents as part of operation, only update "
"metadata.")
)
def shed_skip_metadata():
return click.option(
"--skip_metadata",
is_flag=True,
help=("Skip metadata update as part of operation, only upload "
"new contents.")
)
def shed_message_option():
return click.option(
"-m",
"--message",
help="Commit message for tool shed upload."
)
def shed_force_create_option():
return click.option(
"--force_repository_creation",
help=("If a repository cannot be found for the specified user/repo "
"name pair, then automatically create the repository in the "
"toolshed."),
is_flag=True,
default=False
)
def shed_check_diff_option():
return click.option(
"--check_diff",
is_flag=True,
help=("Skip uploading if the shed_diff detects there would be no "
"'difference' (only attributes populated by the shed would "
"be updated.)")
)
def shed_upload_options():
return _compose(
shed_message_option(),
shed_force_create_option(),
shed_check_diff_option(),
)
def shed_realization_options():
return _compose(
shed_project_arg(multiple=True),
recursive_shed_option(),
shed_fail_fast_option(),
)
def shed_repo_options():
return _compose(
shed_owner_option(),
shed_name_option(),
)
def shed_publish_options():
""" Common options for commands that require publishing to a
a shed.
"""
return _compose(
shed_realization_options(),
shed_repo_options(),
shed_target_options(),
)
def shed_read_options():
""" Common options that require read access to mapped repositories
in a shed.
"""
return _compose(
shed_realization_options(),
shed_repo_options(),
shed_target_options(),
)
def shed_target_options():
""" Common options for commands that require read-only
interactions with a shed.
"""
return _compose(
shed_email_option(),
shed_key_option(),
shed_key_from_env_option(),
shed_password_option(),
shed_target_option(),
)
def conda_target_options():
return _compose(
conda_prefix_option(),
conda_exec_option(),
conda_debug_option(),
conda_ensure_channels_option(),
)
def galaxy_run_options():
return _compose(
galaxy_target_options(),
galaxy_port_option(),
galaxy_host_option(),
)
def galaxy_config_options():
return _compose(
test_data_option(),
tool_data_table_option(),
dependency_resolvers_option(),
tool_dependency_dir_option(),
brew_dependency_resolution(),
shed_dependency_resolution(),
conda_target_options(),
conda_dependency_resolution(),
conda_copy_dependencies_option(),
conda_auto_install_option(),
conda_auto_init_option(),
)
def galaxy_target_options():
return _compose(
galaxy_root_option(),
galaxy_sqlite_database_option(),
install_galaxy_option(),
galaxy_branch_option(),
galaxy_source_option(),
skip_venv_option(),
no_cache_galaxy_option(),
no_cleanup_option(),
job_config_option(),
)
def galaxy_serve_options():
return _compose(
galaxy_run_options(),
galaxy_config_options(),
)
def shed_fail_fast_option():
return click.option(
"--fail_fast",
is_flag=True,
default=False,
help="If multiple repositories are specified and an error occurs "
"stop immediately instead of processing remaining repositories."
)
def lint_xsd_option():
return click.option(
"--xsd",
is_flag=True,
default=False,
help=("Include experimental tool XSD validation in linting "
"process (requires xmllint on PATH or lxml installed).")
)
def report_level_option():
return click.option(
"--report_level",
type=click.Choice(["all", "warn", "error"]),
default="all",
)
def report_xunit():
return click.option(
"--report_xunit",
type=click.Path(file_okay=True, resolve_path=True),
help="Output an XUnit report, useful for CI testing",
default=None,
)
def skip_option():
return click.option(
"-s",
"--skip",
default=None,
help=("Comma-separated list of lint tests to skip (e.g send ."
"--skip 'citations,xml_order' to skip linting of citations "
"and best-practice XML ordering.")
)
def fail_level_option():
return click.option(
"--fail_level",
type=click.Choice(['warn', 'error']),
default="warn"
)
def recursive_shed_option():
return recursive_option(
"Recursively perform command for nested repository directories.",
)
def recursive_option(help="Recursively perform command for subdirectories."):
return click.option(
"-r",
"--recursive",
is_flag=True,
help=help,
)
def tool_test_json():
target_path = click.Path(
file_okay=True,
dir_okay=False,
resolve_path=True,
)
return click.argument(
'path',
metavar="FILE_PATH",
type=target_path,
default="tool_test_output.json",
)
def test_report_options():
return _compose(
click.option(
"--test_output",
type=click.Path(file_okay=True, resolve_path=True),
callback=get_default_callback("tool_test_output.html",
resolve_path=True),
help=("Output test report (HTML - for humans) defaults to "
"tool_test_output.html."),
default=None,
),
click.option(
"--test_output_text",
type=click.Path(file_okay=True, resolve_path=True),
callback=get_default_callback(None, resolve_path=True),
help=("Output test report (Basic text - for display in CI)"),
default=None,
),
click.option(
"--test_output_markdown",
type=click.Path(file_okay=True, resolve_path=True),
callback=get_default_callback(None, resolve_path=True),
help=("Output test report (Markdown style - for humans & "
"computers)"),
default=None,
),
)
def test_options():
return _compose(
click.option(
"--update_test_data",
is_flag=True,
help="Update test-data directory with job outputs (normally"
" written to directory --job_output_files if specified.)"
),
test_report_options(),
click.option(
"--test_output_xunit",
type=click.Path(file_okay=True, resolve_path=True),
callback=get_default_callback(None, resolve_path=True),
help="Output test report (xUnit style - for computers).",
default=None,
),
click.option(
"--test_output_json",
type=click.Path(file_okay=True, resolve_path=True),
callback=get_default_callback("tool_test_output.json",
resolve_path=True),
help=("Output test report (planemo json) defaults to "
"tool_test_output.json."),
default=None,
),
click.option(
"--job_output_files",
type=click.Path(file_okay=False, resolve_path=True),
help="Write job outputs to specified directory.",
default=None,
),
click.option(
"--summary",
type=click.Choice(["none", "minimal", "compact"]),
default="minimal",
help=("Summary style printed to planemo's standard output (see "
"output reports for more complete summary). Set to 'none' "
"to disable completely.")
)
)
def _compose(*functions):
def compose2(f, g):
return lambda x: f(g(x))
return functools.reduce(compose2, functions)
def dependencies_script_options():
return _compose(
click.option(
"--download_cache",
type=click.Path(file_okay=False, resolve_path=True),
callback=get_default_callback(None),
help=("Directory to cache downloaded files, default is $DOWNLOAD_CACHE"),
default=None,
),
)