|
99
|
1 #!/usr/bin/env python
|
|
|
2
|
|
|
3 import argparse
|
|
|
4 import datetime as dt
|
|
|
5 import json
|
|
|
6 import logging
|
|
|
7 import os
|
|
|
8 import sys
|
|
|
9 import tempfile
|
|
|
10 from collections import namedtuple
|
|
|
11 from concurrent.futures import thread, ThreadPoolExecutor
|
|
|
12
|
|
|
13 import yaml
|
|
|
14
|
|
|
15 from galaxy.tool_util.verify.interactor import (
|
|
|
16 DictClientTestConfig,
|
|
|
17 GalaxyInteractorApi,
|
|
|
18 verify_tool,
|
|
|
19 )
|
|
|
20
|
|
|
21 DESCRIPTION = """Script to quickly run a tool test against a running Galaxy instance."""
|
|
|
22 DEFAULT_SUITE_NAME = "Galaxy Tool Tests"
|
|
|
23 ALL_TESTS = -1
|
|
|
24 ALL_TOOLS = "*"
|
|
|
25 ALL_VERSION = "*"
|
|
|
26 LATEST_VERSION = None
|
|
|
27
|
|
|
28
|
|
|
29 TestReference = namedtuple("TestReference", ["tool_id", "tool_version", "test_index"])
|
|
|
30 TestException = namedtuple("TestException", ["tool_id", "exception", "was_recorded"])
|
|
|
31
|
|
|
32
|
|
|
33 class Results:
|
|
|
34
|
|
|
35 def __init__(self, default_suitename, test_json, append=False):
|
|
|
36 self.test_json = test_json or "-"
|
|
|
37 test_results = []
|
|
|
38 test_exceptions = []
|
|
|
39 suitename = default_suitename
|
|
|
40 if append:
|
|
|
41 assert test_json != "-"
|
|
|
42 with open(test_json) as f:
|
|
|
43 previous_results = json.load(f)
|
|
|
44 test_results = previous_results["tests"]
|
|
|
45 if "suitename" in previous_results:
|
|
|
46 suitename = previous_results["suitename"]
|
|
|
47 self.test_results = test_results
|
|
|
48 self.test_exceptions = test_exceptions
|
|
|
49 self.suitename = suitename
|
|
|
50
|
|
|
51 def register_result(self, result):
|
|
|
52 self.test_results.append(result)
|
|
|
53
|
|
|
54 def register_exception(self, test_exception):
|
|
|
55 self.test_exceptions.append(test_exception)
|
|
|
56
|
|
|
57 def already_successful(self, test_reference):
|
|
|
58 test_id = _test_id_for_reference(test_reference)
|
|
|
59 for test_result in self.test_results:
|
|
|
60 if test_result.get('id') != test_id:
|
|
|
61 continue
|
|
|
62
|
|
|
63 has_data = test_result.get('has_data', False)
|
|
|
64 if has_data:
|
|
|
65 test_data = test_result.get("data", {})
|
|
|
66 if 'status' in test_data and test_data['status'] == 'success':
|
|
|
67 return True
|
|
|
68
|
|
|
69 return False
|
|
|
70
|
|
|
71 def write(self):
|
|
|
72 tests = sorted(self.test_results, key=lambda el: el['id'])
|
|
|
73 n_passed, n_failures, n_skips = 0, 0, 0
|
|
|
74 n_errors = len([e for e in self.test_exceptions if not e.was_recorded])
|
|
|
75 for test in tests:
|
|
|
76 has_data = test.get('has_data', False)
|
|
|
77 if has_data:
|
|
|
78 test_data = test.get("data", {})
|
|
|
79 if 'status' not in test_data:
|
|
|
80 raise Exception(f"Test result data {test_data} doesn't contain a status key.")
|
|
|
81 status = test_data['status']
|
|
|
82 if status == "success":
|
|
|
83 n_passed += 1
|
|
|
84 elif status == "error":
|
|
|
85 n_errors += 1
|
|
|
86 elif status == "skip":
|
|
|
87 n_skips += 1
|
|
|
88 elif status == "failure":
|
|
|
89 n_failures += 1
|
|
|
90 report_obj = {
|
|
|
91 'version': '0.1',
|
|
|
92 'suitename': self.suitename,
|
|
|
93 'results': {
|
|
|
94 'total': n_passed + n_failures + n_skips + n_errors,
|
|
|
95 'errors': n_errors,
|
|
|
96 'failures': n_failures,
|
|
|
97 'skips': n_skips,
|
|
|
98 },
|
|
|
99 'tests': tests,
|
|
|
100 }
|
|
|
101 if self.test_json == "-":
|
|
|
102 print(json.dumps(report_obj))
|
|
|
103 else:
|
|
|
104 with open(self.test_json, "w") as f:
|
|
|
105 json.dump(report_obj, f)
|
|
|
106
|
|
|
107 def info_message(self):
|
|
|
108 messages = []
|
|
|
109 passed_tests = self._tests_with_status('success')
|
|
|
110 messages.append("Passed tool tests ({}): {}".format(
|
|
|
111 len(passed_tests),
|
|
|
112 [t["id"] for t in passed_tests]
|
|
|
113 ))
|
|
|
114 failed_tests = self._tests_with_status('failure')
|
|
|
115 messages.append("Failed tool tests ({}): {}".format(
|
|
|
116 len(failed_tests),
|
|
|
117 [t["id"] for t in failed_tests]
|
|
|
118 ))
|
|
|
119 skiped_tests = self._tests_with_status('skip')
|
|
|
120 messages.append("Skipped tool tests ({}): {}".format(
|
|
|
121 len(skiped_tests),
|
|
|
122 [t["id"] for t in skiped_tests]
|
|
|
123 ))
|
|
|
124 errored_tests = self._tests_with_status('error')
|
|
|
125 messages.append("Errored tool tests ({}): {}".format(
|
|
|
126 len(errored_tests),
|
|
|
127 [t["id"] for t in errored_tests]
|
|
|
128 ))
|
|
|
129 return "\n".join(messages)
|
|
|
130
|
|
|
131 @property
|
|
|
132 def success_count(self):
|
|
|
133 self._tests_with_status('success')
|
|
|
134
|
|
|
135 @property
|
|
|
136 def skip_count(self):
|
|
|
137 self._tests_with_status('skip')
|
|
|
138
|
|
|
139 @property
|
|
|
140 def error_count(self):
|
|
|
141 return self._tests_with_status('error') + len(self.test_exceptions)
|
|
|
142
|
|
|
143 @property
|
|
|
144 def failure_count(self):
|
|
|
145 return self._tests_with_status('failure')
|
|
|
146
|
|
|
147 def _tests_with_status(self, status):
|
|
|
148 return [t for t in self.test_results if t.get("data", {}).get("status") == status]
|
|
|
149
|
|
|
150
|
|
|
151 def test_tools(
|
|
|
152 galaxy_interactor,
|
|
|
153 test_references,
|
|
|
154 results,
|
|
|
155 log=None,
|
|
|
156 parallel_tests=1,
|
|
|
157 history_per_test_case=False,
|
|
|
158 no_history_cleanup=False,
|
|
|
159 retries=0,
|
|
|
160 verify_kwds=None,
|
|
|
161 ):
|
|
|
162 """Run through tool tests and write report.
|
|
|
163
|
|
|
164 Refactor this into Galaxy in 21.01.
|
|
|
165 """
|
|
|
166 verify_kwds = (verify_kwds or {}).copy()
|
|
|
167 tool_test_start = dt.datetime.now()
|
|
|
168 history_created = False
|
|
|
169 if history_per_test_case:
|
|
|
170 test_history = None
|
|
|
171 else:
|
|
|
172 history_created = True
|
|
|
173 test_history = galaxy_interactor.new_history(history_name=f"History for {results.suitename}")
|
|
|
174 verify_kwds.update({
|
|
|
175 "no_history_cleanup": no_history_cleanup,
|
|
|
176 "test_history": test_history,
|
|
|
177 })
|
|
|
178 with ThreadPoolExecutor(max_workers=parallel_tests) as executor:
|
|
|
179 try:
|
|
|
180 for test_reference in test_references:
|
|
|
181 _test_tool(
|
|
|
182 executor=executor,
|
|
|
183 test_reference=test_reference,
|
|
|
184 results=results,
|
|
|
185 galaxy_interactor=galaxy_interactor,
|
|
|
186 log=log,
|
|
|
187 retries=retries,
|
|
|
188 verify_kwds=verify_kwds,
|
|
|
189 )
|
|
|
190 finally:
|
|
|
191 # Always write report, even if test was cancelled.
|
|
|
192 try:
|
|
|
193 executor.shutdown(wait=True)
|
|
|
194 except KeyboardInterrupt:
|
|
|
195 executor._threads.clear()
|
|
|
196 thread._threads_queues.clear()
|
|
|
197 results.write()
|
|
|
198 if log:
|
|
|
199 log.info("Report written to '%s'", os.path.abspath(results.test_json))
|
|
|
200 log.info(results.info_message())
|
|
|
201 log.info("Total tool test time: {}".format(dt.datetime.now() - tool_test_start))
|
|
|
202 if history_created and not no_history_cleanup:
|
|
|
203 galaxy_interactor.delete_history(test_history)
|
|
|
204
|
|
|
205
|
|
|
206 def _test_id_for_reference(test_reference):
|
|
|
207 tool_id = test_reference.tool_id
|
|
|
208 tool_version = test_reference.tool_version
|
|
|
209 test_index = test_reference.test_index
|
|
|
210
|
|
|
211 if tool_version and tool_id.endswith("/" + tool_version):
|
|
|
212 tool_id = tool_id[:-len("/" + tool_version)]
|
|
|
213
|
|
|
214 label_base = tool_id
|
|
|
215 if tool_version:
|
|
|
216 label_base += "/" + str(tool_version)
|
|
|
217
|
|
|
218 test_id = label_base + "-" + str(test_index)
|
|
|
219 return test_id
|
|
|
220
|
|
|
221
|
|
|
222 def _test_tool(
|
|
|
223 executor,
|
|
|
224 test_reference,
|
|
|
225 results,
|
|
|
226 galaxy_interactor,
|
|
|
227 log,
|
|
|
228 retries,
|
|
|
229 verify_kwds,
|
|
|
230 ):
|
|
|
231 tool_id = test_reference.tool_id
|
|
|
232 tool_version = test_reference.tool_version
|
|
|
233 test_index = test_reference.test_index
|
|
|
234 # If given a tool_id with a version suffix, strip it off so we can treat tool_version
|
|
|
235 # correctly at least in client_test_config.
|
|
|
236 if tool_version and tool_id.endswith("/" + tool_version):
|
|
|
237 tool_id = tool_id[:-len("/" + tool_version)]
|
|
|
238
|
|
|
239 test_id = _test_id_for_reference(test_reference)
|
|
|
240
|
|
|
241 def run_test():
|
|
|
242 run_retries = retries
|
|
|
243 job_data = None
|
|
|
244 job_exception = None
|
|
|
245
|
|
|
246 def register(job_data_):
|
|
|
247 nonlocal job_data
|
|
|
248 job_data = job_data_
|
|
|
249
|
|
|
250 try:
|
|
|
251 while run_retries >= 0:
|
|
|
252 job_exception = None
|
|
|
253 try:
|
|
|
254 if log:
|
|
|
255 log.info("Executing test '%s'", test_id)
|
|
|
256 verify_tool(
|
|
|
257 tool_id, galaxy_interactor, test_index=test_index, tool_version=tool_version,
|
|
|
258 register_job_data=register, **verify_kwds
|
|
|
259 )
|
|
|
260 if log:
|
|
|
261 log.info("Test '%s' passed", test_id)
|
|
|
262 break
|
|
|
263 except Exception as e:
|
|
|
264 if log:
|
|
|
265 log.warning("Test '%s' failed", test_id, exc_info=True)
|
|
|
266
|
|
|
267 job_exception = e
|
|
|
268 run_retries -= 1
|
|
|
269 finally:
|
|
|
270 if job_data is not None:
|
|
|
271 results.register_result({
|
|
|
272 "id": test_id,
|
|
|
273 "has_data": True,
|
|
|
274 "data": job_data,
|
|
|
275 })
|
|
|
276 if job_exception is not None:
|
|
|
277 was_recorded = job_data is not None
|
|
|
278 test_exception = TestException(tool_id, job_exception, was_recorded)
|
|
|
279 results.register_exception(test_exception)
|
|
|
280
|
|
|
281 executor.submit(run_test)
|
|
|
282
|
|
|
283
|
|
|
284 def build_case_references(
|
|
|
285 galaxy_interactor,
|
|
|
286 tool_id=ALL_TOOLS,
|
|
|
287 tool_version=LATEST_VERSION,
|
|
|
288 test_index=ALL_TESTS,
|
|
|
289 page_size=0,
|
|
|
290 page_number=0,
|
|
|
291 check_against=None,
|
|
|
292 log=None,
|
|
|
293 ):
|
|
|
294 test_references = []
|
|
|
295 if tool_id == ALL_TOOLS:
|
|
|
296 tests_summary = galaxy_interactor.get_tests_summary()
|
|
|
297 for tool_id, tool_versions_dict in tests_summary.items():
|
|
|
298 for tool_version, summary in tool_versions_dict.items():
|
|
|
299 for test_index in range(summary["count"]):
|
|
|
300 test_reference = TestReference(tool_id, tool_version, test_index)
|
|
|
301 test_references.append(test_reference)
|
|
|
302 else:
|
|
|
303 assert tool_id
|
|
|
304 tool_test_dicts = galaxy_interactor.get_tool_tests(tool_id, tool_version=tool_version) or {}
|
|
|
305 for i, tool_test_dict in enumerate(tool_test_dicts):
|
|
|
306 this_tool_version = tool_test_dict.get("tool_version", tool_version)
|
|
|
307 this_test_index = i
|
|
|
308 if test_index == ALL_TESTS or i == test_index:
|
|
|
309 test_reference = TestReference(tool_id, this_tool_version, this_test_index)
|
|
|
310 test_references.append(test_reference)
|
|
|
311
|
|
|
312 if check_against:
|
|
|
313 filtered_test_references = []
|
|
|
314 for test_reference in test_references:
|
|
|
315 if check_against.already_successful(test_reference):
|
|
|
316 if log is not None:
|
|
|
317 log.debug(f"Found successful test for {test_reference}, skipping")
|
|
|
318 continue
|
|
|
319 filtered_test_references.append(test_reference)
|
|
|
320 log.info(f"Skipping {len(test_references)-len(filtered_test_references)} out of {len(test_references)} tests.")
|
|
|
321 test_references = filtered_test_references
|
|
|
322
|
|
|
323 if page_size > 0:
|
|
|
324 slice_start = page_size * page_number
|
|
|
325 slice_end = page_size * (page_number + 1)
|
|
|
326 test_references = test_references[slice_start:slice_end]
|
|
|
327
|
|
|
328 return test_references
|
|
|
329
|
|
|
330
|
|
|
331 def main(argv=None):
|
|
|
332 if argv is None:
|
|
|
333 argv = sys.argv[1:]
|
|
|
334
|
|
|
335 args = _arg_parser().parse_args(argv)
|
|
|
336 log = setup_global_logger(__name__, verbose=args.verbose)
|
|
|
337 client_test_config_path = args.client_test_config
|
|
|
338 if client_test_config_path is not None:
|
|
|
339 log.debug(f"Reading client config path {client_test_config_path}")
|
|
|
340 with open(client_test_config_path) as f:
|
|
|
341 client_test_config = yaml.full_load(f)
|
|
|
342 else:
|
|
|
343 client_test_config = {}
|
|
|
344
|
|
|
345 def get_option(key):
|
|
|
346 arg_val = getattr(args, key, None)
|
|
|
347 if arg_val is None and key in client_test_config:
|
|
|
348 val = client_test_config.get(key)
|
|
|
349 else:
|
|
|
350 val = arg_val
|
|
|
351 return val
|
|
|
352
|
|
|
353 output_json_path = get_option("output_json")
|
|
|
354 galaxy_interactor_kwds = {
|
|
|
355 "galaxy_url": get_option("galaxy_url"),
|
|
|
356 "master_api_key": get_option("admin_key"),
|
|
|
357 "api_key": get_option("key"),
|
|
|
358 "keep_outputs_dir": args.output,
|
|
|
359 "download_attempts": get_option("download_attempts"),
|
|
|
360 "download_sleep": get_option("download_sleep"),
|
|
|
361 }
|
|
|
362 tool_id = args.tool_id
|
|
|
363 tool_version = args.tool_version
|
|
|
364 tools_client_test_config = DictClientTestConfig(client_test_config.get("tools"))
|
|
|
365 verbose = args.verbose
|
|
|
366
|
|
|
367 galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds)
|
|
|
368 results = Results(args.suite_name, output_json_path, append=args.append)
|
|
|
369 check_against = None if not args.skip_successful else results
|
|
|
370 test_references = build_case_references(
|
|
|
371 galaxy_interactor,
|
|
|
372 tool_id=tool_id,
|
|
|
373 tool_version=tool_version,
|
|
|
374 test_index=args.test_index,
|
|
|
375 page_size=args.page_size,
|
|
|
376 page_number=args.page_number,
|
|
|
377 check_against=check_against,
|
|
|
378 log=log,
|
|
|
379 )
|
|
|
380 log.debug(f"Built {len(test_references)} test references to executed.")
|
|
|
381 verify_kwds = dict(
|
|
|
382 client_test_config=tools_client_test_config,
|
|
|
383 force_path_paste=args.force_path_paste,
|
|
|
384 skip_with_reference_data=not args.with_reference_data,
|
|
|
385 quiet=not verbose,
|
|
|
386 )
|
|
|
387 test_tools(
|
|
|
388 galaxy_interactor,
|
|
|
389 test_references,
|
|
|
390 results,
|
|
|
391 log=log,
|
|
|
392 parallel_tests=args.parallel_tests,
|
|
|
393 history_per_test_case=args.history_per_test_case,
|
|
|
394 no_history_cleanup=args.no_history_cleanup,
|
|
|
395 verify_kwds=verify_kwds,
|
|
|
396 )
|
|
|
397 exceptions = results.test_exceptions
|
|
|
398 if exceptions:
|
|
|
399 exception = exceptions[0]
|
|
|
400 if hasattr(exception, "exception"):
|
|
|
401 exception = exception.exception
|
|
|
402 raise exception
|
|
|
403
|
|
|
404
|
|
|
405 def setup_global_logger(name, log_file=None, verbose=False):
|
|
|
406 formatter = logging.Formatter('%(asctime)s %(levelname)-5s - %(message)s')
|
|
|
407 console = logging.StreamHandler()
|
|
|
408 console.setFormatter(formatter)
|
|
|
409
|
|
|
410 logger = logging.getLogger(name)
|
|
|
411 logger.setLevel(logging.DEBUG if verbose else logging.INFO)
|
|
|
412 logger.addHandler(console)
|
|
|
413
|
|
|
414 if not log_file:
|
|
|
415 # delete = false is chosen here because it is always nice to have a log file
|
|
|
416 # ready if you need to debug. Not having the "if only I had set a log file"
|
|
|
417 # moment after the fact.
|
|
|
418 temp = tempfile.NamedTemporaryFile(prefix="ephemeris_", delete=False)
|
|
|
419 log_file = temp.name
|
|
|
420 file_handler = logging.FileHandler(log_file)
|
|
|
421 logger.addHandler(file_handler)
|
|
|
422 logger.info(f"Storing log file in: {log_file}")
|
|
|
423 return logger
|
|
|
424
|
|
|
425
|
|
|
426 def _arg_parser():
|
|
|
427 parser = argparse.ArgumentParser(description=DESCRIPTION)
|
|
|
428 parser.add_argument('-u', '--galaxy-url', default="http://localhost:8080", help='Galaxy URL')
|
|
|
429 parser.add_argument('-k', '--key', default=None, help='Galaxy User API Key')
|
|
|
430 parser.add_argument('-a', '--admin-key', default=None, help='Galaxy Admin API Key')
|
|
|
431 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.')
|
|
|
432 parser.add_argument('-t', '--tool-id', default=ALL_TOOLS, help='Tool ID')
|
|
|
433 parser.add_argument('--tool-version', default=None, help='Tool Version (if tool id supplied). Defaults to just latest version, use * to test all versions')
|
|
|
434 parser.add_argument('-i', '--test-index', default=ALL_TESTS, type=int, help='Tool Test Index (starting at 0) - by default all tests will run.')
|
|
|
435 parser.add_argument('-o', '--output', default=None, help='directory to dump outputs to')
|
|
|
436 parser.add_argument('--append', default=False, action="store_true", help="Extend a test record json (created with --output-json) with additional tests.")
|
|
|
437 parser.add_argument('--skip-successful', default=False, action="store_true", help="When used with --append, skip previously run successful tests.")
|
|
|
438 parser.add_argument('-j', '--output-json', default=None, help='output metadata json')
|
|
|
439 parser.add_argument('--verbose', default=False, action="store_true", help="Verbose logging.")
|
|
|
440 parser.add_argument('-c', '--client-test-config', default=None, help="Test config YAML to help with client testing")
|
|
|
441 parser.add_argument('--suite-name', default=DEFAULT_SUITE_NAME, help="Suite name for tool test output")
|
|
|
442 parser.add_argument('--with-reference-data', dest="with_reference_data", default=False, action="store_true")
|
|
|
443 parser.add_argument('--skip-with-reference-data', dest="with_reference_data", action="store_false", help="Skip tests the Galaxy server believes use data tables or loc files.")
|
|
|
444 parser.add_argument('--history-per-suite', dest="history_per_test_case", default=False, action="store_false", help="Create new history per test suite (all tests in same history).")
|
|
|
445 parser.add_argument('--history-per-test-case', dest="history_per_test_case", action="store_true", help="Create new history per test case.")
|
|
|
446 parser.add_argument('--no-history-cleanup', default=False, action="store_true", help="Perserve histories created for testing.")
|
|
|
447 parser.add_argument('--parallel-tests', default=1, type=int, help="Parallel tests.")
|
|
|
448 parser.add_argument('--retries', default=0, type=int, help="Retry failed tests.")
|
|
|
449 parser.add_argument('--page-size', default=0, type=int, help="If positive, use pagination and just run one 'page' to tool tests.")
|
|
|
450 parser.add_argument('--page-number', default=0, type=int, help="If page size is used, run this 'page' of tests - starts with 0.")
|
|
|
451 parser.add_argument('--download-attempts', default=1, type=int, help="Galaxy may return a transient 500 status code for download if test results are written but not yet accessible.")
|
|
|
452 parser.add_argument('--download-sleep', default=1, type=int, help="If download attempts is greater than 1, the amount to sleep between download attempts.")
|
|
|
453 return parser
|
|
|
454
|
|
|
455
|
|
|
456 if __name__ == "__main__":
|
|
|
457 main()
|
