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comparison env/lib/python3.9/site-packages/cwltool/argparser.py @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000 (2021-03-22)
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1 """Command line argument parsing for cwltool."""
2
3 import argparse
4 import os
5 from typing import (
6 Any,
7 AnyStr,
8 Dict,
9 List,
10 MutableMapping,
11 MutableSequence,
12 Optional,
13 Sequence,
14 Union,
15 cast,
16 )
17
18 from schema_salad.ref_resolver import file_uri
19
20 from .loghandler import _logger
21 from .process import Process, shortname
22 from .resolver import ga4gh_tool_registries
23 from .software_requirements import SOFTWARE_REQUIREMENTS_ENABLED
24 from .utils import DEFAULT_TMP_PREFIX, onWindows
25
26
27 def arg_parser() -> argparse.ArgumentParser:
28 parser = argparse.ArgumentParser(
29 description="Reference executor for Common Workflow Language standards. "
30 "Not for production use."
31 )
32 parser.add_argument("--basedir", type=str)
33 parser.add_argument(
34 "--outdir",
35 type=str,
36 default=os.path.abspath("."),
37 help="Output directory. The default is the current directory.",
38 )
39
40 parser.add_argument(
41 "--parallel",
42 action="store_true",
43 default=False,
44 help="[experimental] Run jobs in parallel. ",
45 )
46 envgroup = parser.add_mutually_exclusive_group()
47 envgroup.add_argument(
48 "--preserve-environment",
49 type=str,
50 action="append",
51 help="Preserve specific environment variable when running "
52 "CommandLineTools without a software container. May be provided "
53 "multiple times. The default is to preserve only the PATH.",
54 metavar="ENVVAR",
55 default=["PATH"],
56 dest="preserve_environment",
57 )
58 envgroup.add_argument(
59 "--preserve-entire-environment",
60 action="store_true",
61 help="Preserve all environment variables when running CommandLineTools "
62 "without a software container.",
63 default=False,
64 dest="preserve_entire_environment",
65 )
66
67 containergroup = parser.add_mutually_exclusive_group()
68 containergroup.add_argument(
69 "--rm-container",
70 action="store_true",
71 default=True,
72 help="Delete Docker container used by jobs after they exit (default)",
73 dest="rm_container",
74 )
75
76 containergroup.add_argument(
77 "--leave-container",
78 action="store_false",
79 default=True,
80 help="Do not delete Docker container used by jobs after they exit",
81 dest="rm_container",
82 )
83
84 cidgroup = parser.add_argument_group(
85 "Options for recording the Docker container identifier into a file."
86 )
87 cidgroup.add_argument(
88 # Disabled as containerid is now saved by default
89 "--record-container-id",
90 action="store_true",
91 default=False,
92 help=argparse.SUPPRESS,
93 dest="record_container_id",
94 )
95
96 cidgroup.add_argument(
97 "--cidfile-dir",
98 type=str,
99 help="Store the Docker container ID into a file in the specified directory.",
100 default=None,
101 dest="cidfile_dir",
102 )
103
104 cidgroup.add_argument(
105 "--cidfile-prefix",
106 type=str,
107 help="Specify a prefix to the container ID filename. "
108 "Final file name will be followed by a timestamp. "
109 "The default is no prefix.",
110 default=None,
111 dest="cidfile_prefix",
112 )
113
114 parser.add_argument(
115 "--tmpdir-prefix",
116 type=str,
117 help="Path prefix for temporary directories. If --tmpdir-prefix is not "
118 "provided, then the prefix for temporary directories is influenced by "
119 "the value of the TMPDIR, TEMP, or TMP environment variables. Taking "
120 "those into consideration, the current default is {}.".format(
121 DEFAULT_TMP_PREFIX
122 ),
123 default=DEFAULT_TMP_PREFIX,
124 )
125
126 intgroup = parser.add_mutually_exclusive_group()
127 intgroup.add_argument(
128 "--tmp-outdir-prefix",
129 type=str,
130 help="Path prefix for intermediate output directories. Defaults to the "
131 "value of --tmpdir-prefix.",
132 default="",
133 )
134
135 intgroup.add_argument(
136 "--cachedir",
137 type=str,
138 default="",
139 help="Directory to cache intermediate workflow outputs to avoid "
140 "recomputing steps. Can be very helpful in the development and "
141 "troubleshooting of CWL documents.",
142 )
143
144 tmpgroup = parser.add_mutually_exclusive_group()
145 tmpgroup.add_argument(
146 "--rm-tmpdir",
147 action="store_true",
148 default=True,
149 help="Delete intermediate temporary directories (default)",
150 dest="rm_tmpdir",
151 )
152
153 tmpgroup.add_argument(
154 "--leave-tmpdir",
155 action="store_false",
156 default=True,
157 help="Do not delete intermediate temporary directories",
158 dest="rm_tmpdir",
159 )
160
161 outgroup = parser.add_mutually_exclusive_group()
162 outgroup.add_argument(
163 "--move-outputs",
164 action="store_const",
165 const="move",
166 default="move",
167 help="Move output files to the workflow output directory and delete "
168 "intermediate output directories (default).",
169 dest="move_outputs",
170 )
171
172 outgroup.add_argument(
173 "--leave-outputs",
174 action="store_const",
175 const="leave",
176 default="move",
177 help="Leave output files in intermediate output directories.",
178 dest="move_outputs",
179 )
180
181 outgroup.add_argument(
182 "--copy-outputs",
183 action="store_const",
184 const="copy",
185 default="move",
186 help="Copy output files to the workflow output directory and don't "
187 "delete intermediate output directories.",
188 dest="move_outputs",
189 )
190
191 pullgroup = parser.add_mutually_exclusive_group()
192 pullgroup.add_argument(
193 "--enable-pull",
194 default=True,
195 action="store_true",
196 help="Try to pull Docker images",
197 dest="pull_image",
198 )
199
200 pullgroup.add_argument(
201 "--disable-pull",
202 default=True,
203 action="store_false",
204 help="Do not try to pull Docker images",
205 dest="pull_image",
206 )
207
208 parser.add_argument(
209 "--rdf-serializer",
210 help="Output RDF serialization format used by --print-rdf (one of "
211 "turtle (default), n3, nt, xml)",
212 default="turtle",
213 )
214
215 parser.add_argument(
216 "--eval-timeout",
217 help="Time to wait for a Javascript expression to evaluate before giving "
218 "an error, default 20s.",
219 type=float,
220 default=20,
221 )
222
223 provgroup = parser.add_argument_group(
224 "Options for recording provenance information of the execution"
225 )
226 provgroup.add_argument(
227 "--provenance",
228 help="Save provenance to specified folder as a "
229 "Research Object that captures and aggregates "
230 "workflow execution and data products.",
231 type=str,
232 )
233
234 provgroup.add_argument(
235 "--enable-user-provenance",
236 default=False,
237 action="store_true",
238 help="Record user account info as part of provenance.",
239 dest="user_provenance",
240 )
241 provgroup.add_argument(
242 "--disable-user-provenance",
243 default=False,
244 action="store_false",
245 help="Do not record user account info in provenance.",
246 dest="user_provenance",
247 )
248 provgroup.add_argument(
249 "--enable-host-provenance",
250 default=False,
251 action="store_true",
252 help="Record host info as part of provenance.",
253 dest="host_provenance",
254 )
255 provgroup.add_argument(
256 "--disable-host-provenance",
257 default=False,
258 action="store_false",
259 help="Do not record host info in provenance.",
260 dest="host_provenance",
261 )
262 provgroup.add_argument(
263 "--orcid",
264 help="Record user ORCID identifier as part of "
265 "provenance, e.g. https://orcid.org/0000-0002-1825-0097 "
266 "or 0000-0002-1825-0097. Alternatively the environment variable "
267 "ORCID may be set.",
268 dest="orcid",
269 default=os.environ.get("ORCID", ""),
270 type=str,
271 )
272 provgroup.add_argument(
273 "--full-name",
274 help="Record full name of user as part of provenance, "
275 "e.g. Josiah Carberry. You may need to use shell quotes to preserve "
276 "spaces. Alternatively the environment variable CWL_FULL_NAME may "
277 "be set.",
278 dest="cwl_full_name",
279 default=os.environ.get("CWL_FULL_NAME", ""),
280 type=str,
281 )
282
283 printgroup = parser.add_mutually_exclusive_group()
284 printgroup.add_argument(
285 "--print-rdf",
286 action="store_true",
287 help="Print corresponding RDF graph for workflow and exit",
288 )
289 printgroup.add_argument(
290 "--print-dot",
291 action="store_true",
292 help="Print workflow visualization in graphviz format and exit",
293 )
294 printgroup.add_argument(
295 "--print-pre",
296 action="store_true",
297 help="Print CWL document after preprocessing.",
298 )
299 printgroup.add_argument(
300 "--print-deps", action="store_true", help="Print CWL document dependencies."
301 )
302 printgroup.add_argument(
303 "--print-input-deps",
304 action="store_true",
305 help="Print input object document dependencies.",
306 )
307 printgroup.add_argument(
308 "--pack",
309 action="store_true",
310 help="Combine components into single document and print.",
311 )
312 printgroup.add_argument(
313 "--version", action="store_true", help="Print version and exit"
314 )
315 printgroup.add_argument(
316 "--validate", action="store_true", help="Validate CWL document only."
317 )
318 printgroup.add_argument(
319 "--print-supported-versions",
320 action="store_true",
321 help="Print supported CWL specs.",
322 )
323 printgroup.add_argument(
324 "--print-subgraph",
325 action="store_true",
326 help="Print workflow subgraph that will execute. Can combined with "
327 "--target or --single-step",
328 )
329 printgroup.add_argument(
330 "--print-targets", action="store_true", help="Print targets (output parameters)"
331 )
332 printgroup.add_argument(
333 "--make-template", action="store_true", help="Generate a template input object"
334 )
335
336 strictgroup = parser.add_mutually_exclusive_group()
337 strictgroup.add_argument(
338 "--strict",
339 action="store_true",
340 help="Strict validation (unrecognized or out of place fields are error)",
341 default=True,
342 dest="strict",
343 )
344 strictgroup.add_argument(
345 "--non-strict",
346 action="store_false",
347 help="Lenient validation (ignore unrecognized fields)",
348 default=True,
349 dest="strict",
350 )
351
352 parser.add_argument(
353 "--skip-schemas",
354 action="store_true",
355 help="Skip loading of schemas",
356 default=False,
357 dest="skip_schemas",
358 )
359
360 doccachegroup = parser.add_mutually_exclusive_group()
361 doccachegroup.add_argument(
362 "--no-doc-cache",
363 action="store_false",
364 help="Disable disk cache for documents loaded over HTTP",
365 default=True,
366 dest="doc_cache",
367 )
368 doccachegroup.add_argument(
369 "--doc-cache",
370 action="store_true",
371 help="Enable disk cache for documents loaded over HTTP",
372 default=True,
373 dest="doc_cache",
374 )
375
376 volumegroup = parser.add_mutually_exclusive_group()
377 volumegroup.add_argument("--verbose", action="store_true", help="Default logging")
378 volumegroup.add_argument(
379 "--quiet", action="store_true", help="Only print warnings and errors."
380 )
381 volumegroup.add_argument(
382 "--debug", action="store_true", help="Print even more logging"
383 )
384
385 parser.add_argument(
386 "--strict-memory-limit",
387 action="store_true",
388 help="When running with "
389 "software containers and the Docker engine, pass either the "
390 "calculated memory allocation from ResourceRequirements or the "
391 "default of 1 gigabyte to Docker's --memory option.",
392 )
393
394 parser.add_argument(
395 "--timestamps",
396 action="store_true",
397 help="Add timestamps to the errors, warnings, and notifications.",
398 )
399 parser.add_argument(
400 "--js-console", action="store_true", help="Enable javascript console output"
401 )
402 parser.add_argument(
403 "--disable-js-validation",
404 action="store_true",
405 help="Disable javascript validation.",
406 )
407 parser.add_argument(
408 "--js-hint-options-file",
409 type=str,
410 help="File of options to pass to jshint. "
411 'This includes the added option "includewarnings". ',
412 )
413 dockergroup = parser.add_mutually_exclusive_group()
414 dockergroup.add_argument(
415 "--user-space-docker-cmd",
416 metavar="CMD",
417 help="(Linux/OS X only) Specify the path to udocker. Implies --udocker",
418 )
419 dockergroup.add_argument(
420 "--udocker",
421 help="(Linux/OS X only) Use the udocker runtime for running containers "
422 "(equivalent to --user-space-docker-cmd=udocker).",
423 action="store_const",
424 const="udocker",
425 dest="user_space_docker_cmd",
426 )
427
428 dockergroup.add_argument(
429 "--singularity",
430 action="store_true",
431 default=False,
432 help="[experimental] Use "
433 "Singularity runtime for running containers. "
434 "Requires Singularity v2.6.1+ and Linux with kernel "
435 "version v3.18+ or with overlayfs support "
436 "backported.",
437 )
438 dockergroup.add_argument(
439 "--no-container",
440 action="store_false",
441 default=True,
442 help="Do not execute jobs in a "
443 "Docker container, even when `DockerRequirement` "
444 "is specified under `hints`.",
445 dest="use_container",
446 )
447
448 dependency_resolvers_configuration_help = argparse.SUPPRESS
449 dependencies_directory_help = argparse.SUPPRESS
450 use_biocontainers_help = argparse.SUPPRESS
451 conda_dependencies = argparse.SUPPRESS
452
453 if SOFTWARE_REQUIREMENTS_ENABLED:
454 dependency_resolvers_configuration_help = "Dependency resolver "
455 "configuration file describing how to adapt 'SoftwareRequirement' "
456 "packages to current system."
457 dependencies_directory_help = (
458 "Defaut root directory used by dependency resolvers configuration."
459 )
460 use_biocontainers_help = "Use biocontainers for tools without an "
461 "explicitly annotated Docker container."
462 conda_dependencies = (
463 "Short cut to use Conda to resolve 'SoftwareRequirement' packages."
464 )
465
466 parser.add_argument(
467 "--beta-dependency-resolvers-configuration",
468 default=None,
469 help=dependency_resolvers_configuration_help,
470 )
471 parser.add_argument(
472 "--beta-dependencies-directory", default=None, help=dependencies_directory_help
473 )
474 parser.add_argument(
475 "--beta-use-biocontainers",
476 default=None,
477 help=use_biocontainers_help,
478 action="store_true",
479 )
480 parser.add_argument(
481 "--beta-conda-dependencies",
482 default=None,
483 help=conda_dependencies,
484 action="store_true",
485 )
486
487 parser.add_argument(
488 "--tool-help", action="store_true", help="Print command line help for tool"
489 )
490
491 parser.add_argument(
492 "--relative-deps",
493 choices=["primary", "cwd"],
494 default="primary",
495 help="When using --print-deps, print paths "
496 "relative to primary file or current working directory.",
497 )
498
499 parser.add_argument(
500 "--enable-dev",
501 action="store_true",
502 help="Enable loading and running unofficial development versions of "
503 "the CWL standards.",
504 default=False,
505 )
506
507 parser.add_argument(
508 "--enable-ext",
509 action="store_true",
510 help="Enable loading and running 'cwltool:' extensions to the CWL standards.",
511 default=False,
512 )
513
514 colorgroup = parser.add_mutually_exclusive_group()
515 colorgroup.add_argument(
516 "--enable-color",
517 action="store_true",
518 help="Enable logging color (default enabled)",
519 default=not onWindows(),
520 )
521 colorgroup.add_argument(
522 "--disable-color",
523 action="store_false",
524 dest="enable_color",
525 help="Disable colored logging (default false)",
526 default=onWindows(),
527 )
528
529 parser.add_argument(
530 "--default-container",
531 help="Specify a default software container to use for any "
532 "CommandLineTool without a DockerRequirement.",
533 )
534 parser.add_argument(
535 "--no-match-user",
536 action="store_true",
537 help="Disable passing the current uid to `docker run --user`",
538 )
539 parser.add_argument(
540 "--custom-net",
541 type=str,
542 help="Passed to `docker run` as the '--net' parameter when "
543 "NetworkAccess is true, which is its default setting.",
544 )
545 parser.add_argument(
546 "--disable-validate",
547 dest="do_validate",
548 action="store_false",
549 default=True,
550 help=argparse.SUPPRESS,
551 )
552
553 reggroup = parser.add_mutually_exclusive_group()
554 reggroup.add_argument(
555 "--enable-ga4gh-tool-registry",
556 action="store_true",
557 help="Enable tool resolution using GA4GH tool registry API",
558 dest="enable_ga4gh_tool_registry",
559 default=True,
560 )
561 reggroup.add_argument(
562 "--disable-ga4gh-tool-registry",
563 action="store_false",
564 help="Disable tool resolution using GA4GH tool registry API",
565 dest="enable_ga4gh_tool_registry",
566 default=True,
567 )
568
569 parser.add_argument(
570 "--add-ga4gh-tool-registry",
571 action="append",
572 help="Add a GA4GH tool registry endpoint to use for resolution, default %s"
573 % ga4gh_tool_registries,
574 dest="ga4gh_tool_registries",
575 default=[],
576 )
577
578 parser.add_argument(
579 "--on-error",
580 help="Desired workflow behavior when a step fails. One of 'stop' (do "
581 "not submit any more steps) or 'continue' (may submit other steps that "
582 "are not downstream from the error). Default is 'stop'.",
583 default="stop",
584 choices=("stop", "continue"),
585 )
586
587 checkgroup = parser.add_mutually_exclusive_group()
588 checkgroup.add_argument(
589 "--compute-checksum",
590 action="store_true",
591 default=True,
592 help="Compute checksum of contents while collecting outputs",
593 dest="compute_checksum",
594 )
595 checkgroup.add_argument(
596 "--no-compute-checksum",
597 action="store_false",
598 help="Do not compute checksum of contents while collecting outputs",
599 dest="compute_checksum",
600 )
601
602 parser.add_argument(
603 "--relax-path-checks",
604 action="store_true",
605 default=False,
606 help="Relax requirements on path names to permit "
607 "spaces and hash characters.",
608 dest="relax_path_checks",
609 )
610
611 parser.add_argument(
612 "--force-docker-pull",
613 action="store_true",
614 default=False,
615 help="Pull latest software container image even if it is locally present",
616 dest="force_docker_pull",
617 )
618 parser.add_argument(
619 "--no-read-only",
620 action="store_true",
621 default=False,
622 help="Do not set root directory in the container as read-only",
623 dest="no_read_only",
624 )
625
626 parser.add_argument(
627 "--overrides",
628 type=str,
629 default=None,
630 help="Read process requirement overrides from file.",
631 )
632
633 subgroup = parser.add_mutually_exclusive_group()
634 subgroup.add_argument(
635 "--target",
636 "-t",
637 action="append",
638 help="Only execute steps that contribute to listed targets (can be "
639 "provided more than once).",
640 )
641 subgroup.add_argument(
642 "--single-step",
643 type=str,
644 default=None,
645 help="Only executes a single step in a workflow. The input object must "
646 "match that step's inputs. Can be combined with --print-subgraph.",
647 )
648
649 parser.add_argument(
650 "--mpi-config-file",
651 type=str,
652 default=None,
653 help="Platform specific configuration for MPI (parallel launcher, its "
654 "flag etc). See README section 'Running MPI-based tools' for details "
655 "of the format.",
656 )
657
658 parser.add_argument(
659 "workflow",
660 type=str,
661 nargs="?",
662 default=None,
663 metavar="cwl_document",
664 help="path or URL to a CWL Workflow, "
665 "CommandLineTool, or ExpressionTool. If the `inputs_object` has a "
666 "`cwl:tool` field indicating the path or URL to the cwl_document, "
667 " then the `cwl_document` argument is optional.",
668 )
669 parser.add_argument(
670 "job_order",
671 nargs=argparse.REMAINDER,
672 metavar="inputs_object",
673 help="path or URL to a YAML or JSON "
674 "formatted description of the required input values for the given "
675 "`cwl_document`.",
676 )
677
678 return parser
679
680
681 def get_default_args() -> Dict[str, Any]:
682 """Get default values of cwltool's command line options."""
683 ap = arg_parser()
684 args = ap.parse_args([])
685 return vars(args)
686
687
688 class FSAction(argparse.Action):
689 objclass = None # type: str
690
691 def __init__(
692 self, option_strings: List[str], dest: str, nargs: Any = None, **kwargs: Any
693 ) -> None:
694 """Fail if nargs is used."""
695 if nargs is not None:
696 raise ValueError("nargs not allowed")
697 super().__init__(option_strings, dest, **kwargs)
698
699 def __call__(
700 self,
701 parser: argparse.ArgumentParser,
702 namespace: argparse.Namespace,
703 values: Union[AnyStr, Sequence[Any], None],
704 option_string: Optional[str] = None,
705 ) -> None:
706 setattr(
707 namespace,
708 self.dest,
709 {
710 "class": self.objclass,
711 "location": file_uri(str(os.path.abspath(cast(AnyStr, values)))),
712 },
713 )
714
715
716 class FSAppendAction(argparse.Action):
717 objclass = None # type: str
718
719 def __init__(
720 self, option_strings: List[str], dest: str, nargs: Any = None, **kwargs: Any
721 ) -> None:
722 """Initialize."""
723 if nargs is not None:
724 raise ValueError("nargs not allowed")
725 super().__init__(option_strings, dest, **kwargs)
726
727 def __call__(
728 self,
729 parser: argparse.ArgumentParser,
730 namespace: argparse.Namespace,
731 values: Union[AnyStr, Sequence[Any], None],
732 option_string: Optional[str] = None,
733 ) -> None:
734 g = getattr(namespace, self.dest)
735 if not g:
736 g = []
737 setattr(namespace, self.dest, g)
738 g.append(
739 {
740 "class": self.objclass,
741 "location": file_uri(str(os.path.abspath(cast(AnyStr, values)))),
742 }
743 )
744
745
746 class FileAction(FSAction):
747 objclass = "File"
748
749
750 class DirectoryAction(FSAction):
751 objclass = "Directory"
752
753
754 class FileAppendAction(FSAppendAction):
755 objclass = "File"
756
757
758 class DirectoryAppendAction(FSAppendAction):
759 objclass = "Directory"
760
761
762 def add_argument(
763 toolparser: argparse.ArgumentParser,
764 name: str,
765 inptype: Any,
766 records: List[str],
767 description: str = "",
768 default: Any = None,
769 input_required: bool = True,
770 ) -> None:
771 if len(name) == 1:
772 flag = "-"
773 else:
774 flag = "--"
775
776 # if input_required is false, don't make the command line
777 # parameter required.
778 required = default is None and input_required
779 if isinstance(inptype, MutableSequence):
780 if inptype[0] == "null":
781 required = False
782 if len(inptype) == 2:
783 inptype = inptype[1]
784 else:
785 _logger.debug("Can't make command line argument from %s", inptype)
786 return None
787
788 ahelp = description.replace("%", "%%")
789 action = None # type: Optional[Union[argparse.Action, str]]
790 atype = None # type: Any
791
792 if inptype == "File":
793 action = cast(argparse.Action, FileAction)
794 elif inptype == "Directory":
795 action = cast(argparse.Action, DirectoryAction)
796 elif isinstance(inptype, MutableMapping) and inptype["type"] == "array":
797 if inptype["items"] == "File":
798 action = cast(argparse.Action, FileAppendAction)
799 elif inptype["items"] == "Directory":
800 action = cast(argparse.Action, DirectoryAppendAction)
801 else:
802 action = "append"
803 elif isinstance(inptype, MutableMapping) and inptype["type"] == "enum":
804 atype = str
805 elif isinstance(inptype, MutableMapping) and inptype["type"] == "record":
806 records.append(name)
807 for field in inptype["fields"]:
808 fieldname = name + "." + shortname(field["name"])
809 fieldtype = field["type"]
810 fielddescription = field.get("doc", "")
811 add_argument(toolparser, fieldname, fieldtype, records, fielddescription)
812 return
813 elif inptype == "string":
814 atype = str
815 elif inptype == "int":
816 atype = int
817 elif inptype == "double":
818 atype = float
819 elif inptype == "float":
820 atype = float
821 elif inptype == "boolean":
822 action = "store_true"
823 else:
824 _logger.debug("Can't make command line argument from %s", inptype)
825 return None
826
827 if inptype != "boolean":
828 typekw = {"type": atype}
829 else:
830 typekw = {}
831
832 toolparser.add_argument(
833 flag + name,
834 required=required,
835 help=ahelp,
836 action=action, # type: ignore
837 default=default,
838 **typekw
839 )
840
841
842 def generate_parser(
843 toolparser: argparse.ArgumentParser,
844 tool: Process,
845 namemap: Dict[str, str],
846 records: List[str],
847 input_required: bool = True,
848 ) -> argparse.ArgumentParser:
849 toolparser.description = tool.tool.get("doc", None)
850 toolparser.add_argument("job_order", nargs="?", help="Job input json file")
851 namemap["job_order"] = "job_order"
852
853 for inp in tool.tool["inputs"]:
854 name = shortname(inp["id"])
855 namemap[name.replace("-", "_")] = name
856 inptype = inp["type"]
857 description = inp.get("doc", "")
858 default = inp.get("default", None)
859 add_argument(
860 toolparser, name, inptype, records, description, default, input_required
861 )
862
863 return toolparser