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comparison planemo/lib/python3.7/site-packages/galaxy/tool_util/verify/script.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
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0:d30785e31577 1:56ad4e20f292
1 #!/usr/bin/env python
2 from __future__ import print_function
3
4 import argparse
5 import json
6 import sys
7
8 from .interactor import (
9 GalaxyInteractorApi,
10 verify_tool,
11 )
12
13 DESCRIPTION = """Script to quickly run a tool test against a running Galaxy instance."""
14 ALL_TESTS = "*all_tests*"
15
16
17 def main(argv=None):
18 if argv is None:
19 argv = sys.argv[1:]
20
21 args = _arg_parser().parse_args(argv)
22 galaxy_interactor_kwds = {
23 "galaxy_url": args.galaxy_url,
24 "master_api_key": args.admin_key,
25 "api_key": args.key,
26 "keep_outputs_dir": args.output,
27 }
28 tool_id = args.tool_id
29 tool_version = args.tool_version
30
31 galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds)
32 raw_test_index = args.test_index
33 if raw_test_index == ALL_TESTS:
34 tool_test_dicts = galaxy_interactor.get_tool_tests(tool_id, tool_version=tool_version)
35 test_indices = list(range(len(tool_test_dicts)))
36 else:
37 test_indices = [int(raw_test_index)]
38
39 test_results = []
40
41 if args.append:
42 with open(args.output_json, "r") as f:
43 previous_results = json.load(f)
44 test_results = previous_results["tests"]
45
46 exceptions = []
47 verbose = args.verbose
48 for test_index in test_indices:
49 if tool_version:
50 tool_id_and_version = "%s/%s" % (tool_id, tool_version)
51 else:
52 tool_id_and_version = tool_id
53
54 test_identifier = "tool %s test # %d" % (tool_id_and_version, test_index)
55
56 def register(job_data):
57 test_results.append({
58 'id': tool_id + "-" + str(test_index),
59 'has_data': True,
60 'data': job_data,
61 })
62
63 try:
64 verify_tool(
65 tool_id, galaxy_interactor, test_index=test_index, tool_version=tool_version,
66 register_job_data=register, quiet=not verbose, force_path_paste=args.force_path_paste
67 )
68
69 if verbose:
70 print("%s passed" % test_identifier)
71
72 except Exception as e:
73 if verbose:
74 print("%s failed, %s" % (test_identifier, e))
75 exceptions.append(e)
76
77 report_obj = {
78 'version': '0.1',
79 'tests': test_results,
80 }
81 output_json = args.output_json
82 if output_json:
83 if args.output_json == "-":
84 assert not args.append
85 print(json.dumps(report_obj))
86 else:
87 with open(args.output_json, "w") as f:
88 json.dump(report_obj, f)
89
90 if exceptions:
91 raise exceptions[0]
92
93
94 def _arg_parser():
95 parser = argparse.ArgumentParser(description=DESCRIPTION)
96 parser.add_argument('-u', '--galaxy-url', default="http://localhost:8080", help='Galaxy URL')
97 parser.add_argument('-k', '--key', default=None, help='Galaxy User API Key')
98 parser.add_argument('-a', '--admin-key', default=None, help='Galaxy Admin API Key')
99 parser.add_argument('--force_path_paste', default=False, action="store_true", help='This requires Galaxy-side config option "allow_path_paste" enabled. Allows for fetching test data locally. Only for admins.')
100 parser.add_argument('-t', '--tool-id', default=None, help='Tool ID')
101 parser.add_argument('--tool-version', default=None, help='Tool Version')
102 parser.add_argument('-i', '--test-index', default=ALL_TESTS, help='Tool Test Index (starting at 0) - by default all tests will run.')
103 parser.add_argument('-o', '--output', default=None, help='directory to dump outputs to')
104 parser.add_argument('--append', default=False, action="store_true", help="Extend a test record json (created with --output-json) with additional tests.")
105 parser.add_argument('-j', '--output-json', default=None, help='output metadata json')
106 parser.add_argument('--verbose', default=False, action="store_true", help="Verbose logging.")
107 return parser
108
109
110 if __name__ == "__main__":
111 main()