Mercurial > repos > bcclaywell > argo_navis

comparison venv/lib/python2.7/site-packages/planemo/options.py @ 0:d67268158946 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:d67268158946
1 """ Click definitions for various shared options and arguments.
2 """
3
4 import functools
5 import os
6
7 import click
8 from galaxy.tools.deps import docker_util
9 from .config import get_default_callback
10
11
12 def force_option(what="files"):
13 return click.option(
14 "-f",
15 "--force",
16 is_flag=True,
17 help="Overwrite existing %s if present." % what,
18 )
19
20
21 def test_data_option():
22 return click.option(
23 "--test_data",
24 type=click.Path(exists=True, file_okay=False, resolve_path=True),
25 help="test-data directory to for specified tool(s).",
26 )
27
28
29 def tool_data_table_option():
30 return click.option(
31 "--tool_data_table",
32 type=click.Path(exists=True, file_okay=True, resolve_path=True),
33 help="tool_data_table_conf.xml file to for specified tool(s).",
34 )
35
36
37 def galaxy_root_option():
38 return click.option(
39 "--galaxy_root",
40 type=click.Path(exists=True, file_okay=False, resolve_path=True),
41 help="Root of development galaxy directory to execute command with.",
42 )
43
44
45 def galaxy_port_option():
46 return click.option(
47 "--port",
48 type=int,
49 default=None,
50 callback=get_default_callback("9090"),
51 help="Port to serve Galaxy on (default is 9090).",
52 )
53
54
55 def galaxy_host_option():
56 return click.option(
57 "--host",
58 type=str,
59 default=None,
60 callback=get_default_callback("127.0.0.1"),
61 help=("Host to bind Galaxy to. Default is 127.0.0.1 that is "
62 "restricted to localhost connections for security reasons "
63 "set to 0.0.0.0 to bind Galaxy to all ports including "
64 "potentially publicly accessible ones."),
65 )
66
67
68 def dependency_resolvers_option():
69 return click.option(
70 "--dependency_resolvers_config_file",
71 type=click.Path(
72 exists=True,
73 file_okay=True,
74 dir_okay=False,
75 resolve_path=True
76 ),
77 help="Dependency resolver configuration for Galaxy to target.",
78 )
79
80
81 def brew_dependency_resolution():
82 return click.option(
83 "--brew_dependency_resolution",
84 is_flag=True,
85 help="Configure Galaxy to use plain brew dependency resolution.",
86 )
87
88
89 def shed_dependency_resolution():
90 return click.option(
91 "--shed_dependency_resolution",
92 is_flag=True,
93 help=("Configure Galaxy to use brewed Tool Shed dependency"
94 " resolution."),
95 )
96
97
98 def job_config_option():
99 return click.option(
100 "--job_config_file",
101 type=click.Path(
102 exists=True,
103 file_okay=True,
104 dir_okay=False,
105 resolve_path=True
106 ),
107 help="Job configuration file for Galaxy to target.",
108 )
109
110
111 def tool_dependency_dir_option():
112 return click.option(
113 "--tool_dependency_dir",
114 type=click.Path(
115 exists=True,
116 file_okay=False,
117 dir_okay=True,
118 resolve_path=True
119 ),
120 help="Tool dependency dir for Galaxy to target.",
121 )
122
123
124 def install_galaxy_option():
125 return click.option(
126 "--install_galaxy",
127 is_flag=True,
128 help="Download and configure a disposable copy of Galaxy from github."
129 )
130
131
132 def no_cache_galaxy_option():
133 return click.option(
134 "--no_cache_galaxy",
135 is_flag=True,
136 help=("Skip caching of Galaxy source and dependencies obtained with "
137 "--install_galaxy. Not caching this results in faster "
138 "downloads (no git) - so is better on throw away instances such "
139 "with TravisCI. ")
140 )
141
142
143 def brew_option():
144 return click.option(
145 "--brew",
146 type=click.Path(exists=True, file_okay=True, dir_okay=False),
147 help="Homebrew 'brew' executable to use."
148 )
149
150
151 def required_tool_arg():
152 """ Decorate click method as requiring the path to a single tool.
153 """
154 arg_type = click.Path(
155 exists=True,
156 file_okay=True,
157 dir_okay=False,
158 readable=True,
159 resolve_path=True,
160 )
161 return click.argument("path", metavar="TOOL_PATH", type=arg_type)
162
163
164 def _optional_tools_default(ctx, param, value):
165 if param.name == "paths" and len(value) == 0:
166 return [os.path.abspath(os.getcwd())]
167 else:
168 return value
169
170
171 def optional_tools_arg(multiple=False):
172 """ Decorate click method as optionally taking in the path to a tool
173 or directory of tools. If no such argument is given the current working
174 directory will be treated as a directory of tools.
175 """
176 arg_type = click.Path(
177 exists=True,
178 file_okay=True,
179 dir_okay=True,
180 readable=True,
181 resolve_path=True,
182 )
183 name = "paths" if multiple else "path"
184 nargs = -1 if multiple else 1
185 return click.argument(
186 name,
187 metavar="TOOL_PATH",
188 type=arg_type,
189 nargs=nargs,
190 callback=_optional_tools_default,
191 )
192
193
194 class ProjectOrRepositry(click.Path):
195
196 def __init__(self, **kwds):
197 super(ProjectOrRepositry, self).__init__(**kwds)
198
199 def convert(self, value, param, ctx):
200 if value and value.startswith("git:") or value.startswith("git+"):
201 return value
202 else:
203 return super(ProjectOrRepositry, self).convert(value, param, ctx)
204
205
206 def shed_project_arg(multiple=True):
207 arg_type = ProjectOrRepositry(
208 exists=True,
209 file_okay=False,
210 dir_okay=True,
211 writable=True,
212 resolve_path=True,
213 )
214 name = "paths" if multiple else "path"
215 nargs = -1 if multiple else 1
216 return click.argument(
217 name,
218 metavar="PROJECT",
219 default=".",
220 type=arg_type,
221 nargs=nargs,
222 callback=_optional_tools_default,
223 )
224
225
226 def optional_project_arg(exists=True):
227 arg_type = click.Path(
228 exists=exists,
229 file_okay=False,
230 dir_okay=True,
231 writable=True,
232 resolve_path=True,
233 )
234 return click.argument(
235 "path",
236 metavar="PROJECT",
237 default=".",
238 type=arg_type
239 )
240
241
242 def no_cleanup_option():
243 return click.option(
244 "--no_cleanup",
245 is_flag=True,
246 help=("Do not cleanup temp files created for and by Galaxy.")
247 )
248
249
250 def docker_cmd_option():
251 return click.option(
252 "--docker_cmd",
253 default=docker_util.DEFAULT_DOCKER_COMMAND,
254 help="Command used to launch docker (defaults to docker)."
255 )
256
257
258 def docker_sudo_option():
259 return click.option(
260 "--docker_sudo",
261 is_flag=True,
262 help="Flag to use sudo when running docker."
263 )
264
265
266 def docker_sudo_cmd_option():
267 return click.option(
268 "--docker_sudo_cmd",
269 default=None,
270 help="sudo command to use when --docker_sudo is enabled " +
271 "(defaults to sudo).",
272 callback=get_default_callback(docker_util.DEFAULT_SUDO_COMMAND),
273 )
274
275
276 def docker_host_option():
277 return click.option(
278 "--docker_host",
279 default=None,
280 help="Docker host to target when executing docker commands " +
281 "(defaults to localhost).",
282 callback=get_default_callback(docker_util.DEFAULT_HOST),
283 )
284
285
286 def shed_owner_option():
287 return click.option(
288 "--owner",
289 help="Tool Shed repository owner (username)."
290 )
291
292
293 def shed_name_option():
294 return click.option(
295 "--name",
296 help="Tool Shed repository name (defaults to the inferred "
297 "tool directory name)."
298 )
299
300
301 def validate_shed_target_callback(ctx, param, value):
302 target = get_default_callback("toolshed")(ctx, param, value)
303 if target is None:
304 ctx.fail("default_shed_target set to None, must specify a value for "
305 "--shed_target to run this command.")
306 return target
307
308
309 def shed_target_option():
310 return click.option(
311 "-t",
312 "--shed_target",
313 help="Tool Shed to target (this can be 'toolshed', 'testtoolshed', "
314 "'local' (alias for http://localhost:9009/), an arbitrary url "
315 "or mappings defined ~/.planemo.yml.",
316 default=None,
317 callback=validate_shed_target_callback,
318 )
319
320
321 def shed_key_option():
322 return click.option(
323 "--shed_key",
324 help=("API key for Tool Shed access. An API key is required unless "
325 "e-mail and password is specified. This key can be specified "
326 "with either --shed_key or --shed_key_from_env.")
327 )
328
329
330 def shed_key_from_env_option():
331 return click.option(
332 "--shed_key_from_env",
333 help="Environment variable to read API key for Tool Shed access from."
334 )
335
336
337 def shed_email_option():
338 return click.option(
339 "--shed_email",
340 help="E-mail for Tool Shed auth (required unless shed_key is "
341 "specified)."
342 )
343
344
345 def shed_password_option():
346 return click.option(
347 "--shed_password",
348 help="Password for Tool Shed auth (required unless shed_key is "
349 "specified)."
350 )
351
352
353 def shed_skip_upload():
354 return click.option(
355 "--skip_upload",
356 is_flag=True,
357 help=("Skip upload contents as part of operation, only update "
358 "metadata.")
359 )
360
361
362 def shed_skip_metadata():
363 return click.option(
364 "--skip_metadata",
365 is_flag=True,
366 help=("Skip metadata update as part of operation, only upload "
367 "new contents.")
368 )
369
370
371 def shed_message_option():
372 return click.option(
373 "-m",
374 "--message",
375 help="Commit message for tool shed upload."
376 )
377
378
379 def shed_force_create_option():
380 return click.option(
381 "--force_repository_creation",
382 help=("If a repository cannot be found for the specified user/repo "
383 "name pair, then automatically create the repository in the "
384 "toolshed."),
385 is_flag=True,
386 default=False
387 )
388
389
390 def shed_check_diff_option():
391 return click.option(
392 "--check_diff",
393 is_flag=True,
394 help=("Skip uploading if the shed_diff detects there would be no "
395 "'difference' (only attributes populated by the shed would "
396 "be updated.)")
397 )
398
399
400 def shed_upload_options():
401 return _compose(
402 shed_message_option(),
403 shed_force_create_option(),
404 shed_check_diff_option(),
405 )
406
407
408 def shed_realization_options():
409 return _compose(
410 shed_project_arg(multiple=True),
411 recursive_shed_option(),
412 shed_fail_fast_option(),
413 )
414
415
416 def shed_repo_options():
417 return _compose(
418 shed_owner_option(),
419 shed_name_option(),
420 )
421
422
423 def shed_publish_options():
424 """ Common options for commands that require publishing to a
425 a shed.
426 """
427 return _compose(
428 shed_realization_options(),
429 shed_repo_options(),
430 shed_target_options(),
431 )
432
433
434 def shed_read_options():
435 """ Common options that require read access to mapped repositories
436 in a shed.
437 """
438 return _compose(
439 shed_realization_options(),
440 shed_repo_options(),
441 shed_target_options(),
442 )
443
444
445 def shed_target_options():
446 """ Common options for commands that require read-only
447 interactions with a shed.
448 """
449 return _compose(
450 shed_email_option(),
451 shed_key_option(),
452 shed_key_from_env_option(),
453 shed_password_option(),
454 shed_target_option(),
455 )
456
457
458 def galaxy_run_options():
459 return _compose(
460 galaxy_target_options(),
461 galaxy_port_option(),
462 galaxy_host_option(),
463 )
464
465
466 def galaxy_config_options():
467 return _compose(
468 test_data_option(),
469 tool_data_table_option(),
470 dependency_resolvers_option(),
471 tool_dependency_dir_option(),
472 brew_dependency_resolution(),
473 shed_dependency_resolution(),
474 )
475
476
477 def galaxy_target_options():
478 return _compose(
479 galaxy_root_option(),
480 install_galaxy_option(),
481 no_cache_galaxy_option(),
482 no_cleanup_option(),
483 job_config_option(),
484 )
485
486
487 def galaxy_serve_options():
488 return _compose(
489 galaxy_run_options(),
490 galaxy_config_options(),
491 )
492
493
494 def shed_fail_fast_option():
495 return click.option(
496 "--fail_fast",
497 is_flag=True,
498 default=False,
499 help="If multiple repositories are specified and an error occurs "
500 "stop immediately instead of processing remaining repositories."
501 )
502
503
504 def lint_xsd_option():
505 return click.option(
506 "--xsd",
507 is_flag=True,
508 default=False,
509 help=("Include experimental tool XSD validation in linting "
510 "process (requires xmllint on PATH or lxml installed).")
511 )
512
513
514 def report_level_option():
515 return click.option(
516 "--report_level",
517 type=click.Choice(["all", "warn", "error"]),
518 default="all",
519 )
520
521
522 def skip_option():
523 return click.option(
524 "-s",
525 "--skip",
526 default=None,
527 help=("Comma-separated list of lint tests to skip (e.g send ."
528 "--skip 'citations,xml_order' to skip linting of citations "
529 "and best-practice XML ordering.")
530 )
531
532
533 def fail_level_option():
534 return click.option(
535 "--fail_level",
536 type=click.Choice(['warn', 'error']),
537 default="warn"
538 )
539
540
541 def recursive_shed_option():
542 return recursive_option(
543 "Recursively perform command for nested repository directories.",
544 )
545
546
547 def recursive_option(help="Recursively perform command for subdirectories."):
548 return click.option(
549 "-r",
550 "--recursive",
551 is_flag=True,
552 help=help,
553 )
554
555
556 def test_options():
557 return _compose(
558 click.option(
559 "--update_test_data",
560 is_flag=True,
561 help="Update test-data directory with job outputs (normally"
562 " written to directory --job_output_files if specified.)"
563 ),
564 click.option(
565 "--test_output",
566 type=click.Path(file_okay=True, resolve_path=True),
567 callback=get_default_callback("tool_test_output.html"),
568 help=("Output test report (HTML - for humans) defaults to "
569 "tool_test_output.html."),
570 default=None,
571 ),
572 click.option(
573 "--test_output_text",
574 type=click.Path(file_okay=True, resolve_path=True),
575 callback=get_default_callback(None),
576 help=("Output test report (Basic text - for display in CI)"),
577 default=None,
578 ),
579 click.option(
580 "--test_output_markdown",
581 type=click.Path(file_okay=True, resolve_path=True),
582 callback=get_default_callback(None),
583 help=("Output test report (Markdown style - for humans & "
584 "computers)"),
585 default=None,
586 ),
587 click.option(
588 "--test_output_xunit",
589 type=click.Path(file_okay=True, resolve_path=True),
590 callback=get_default_callback(None),
591 help="Output test report (xUnit style - for computers).",
592 default=None,
593 ),
594 click.option(
595 "--test_output_json",
596 type=click.Path(file_okay=True, resolve_path=True),
597 callback=get_default_callback("tool_test_output.json"),
598 help=("Output test report (planemo json) defaults to "
599 "tool_test_output.json."),
600 default=None,
601 ),
602 click.option(
603 "--job_output_files",
604 type=click.Path(file_okay=False, resolve_path=True),
605 help="Write job outputs to specified directory.",
606 default=None,
607 ),
608 click.option(
609 "--summary",
610 type=click.Choice(["none", "minimal", "compact"]),
611 default="minimal",
612 help=("Summary style printed to planemo's standard output (see "
613 "output reports for more complete summary). Set to 'none' "
614 "to disable completely.")
615 )
616 )
617
618
619 def _compose(*functions):
620 def compose2(f, g):
621 return lambda x: f(g(x))
622 return functools.reduce(compose2, functions)
623
624
625 def dependencies_script_options():
626 return _compose(
627 click.option(
628 "--download_cache",
629 type=click.Path(file_okay=False, resolve_path=True),
630 callback=get_default_callback(None),
631 help=("Directory to cache downloaded files, default is $DOWNLOAD_CACHE"),
632 default=None,
633 ),
634 )