def test_main(self):
def smear(l):
"given a list of dictionary deltas, return a list of dictionaries"
cur = {}
out = []
for delta in l:
cur.update(delta)
out.append(dict(cur))
return out
json.dump(smear([
{'started': 1234, 'number': 1, 'tests_failed': 1, 'tests_run': 2, 'elapsed': 4, 'path': 'gs://logs/some-job/1', 'job': 'some-job', 'result': 'SUCCESS'},
{'number': 2, 'path': 'gs://logs/some-job/2'},
{'number': 3, 'path': 'gs://logs/some-job/3'},
{'number': 4, 'path': 'gs://logs/some-job/4'},
{'number': 5, 'path': 'gs://logs/other-job/5', 'job': 'other-job', 'elapsed': 8},
{'number': 7, 'path': 'gs://logs/other-job/7', 'result': 'FAILURE'},
]), open('builds.json', 'w'))
json.dump(smear([
{'name': 'example test', 'build': 'gs://logs/some-job/1', 'failure_text': 'some awful stack trace exit 1'},
{'build': 'gs://logs/some-job/2'},
{'build': 'gs://logs/some-job/3'},
{'build': 'gs://logs/some-job/4'},
{'failure_text': 'some other error message'},
{'name': 'unrelated test', 'build': 'gs://logs/other-job/5'},
{'build': 'gs://logs/other-job/7'},
]), open('tests.json', 'w'))
summarize.main(summarize.parse_args(['builds.json', 'tests.json']))
output = json_load_byteified(open('failure_data.json'))
# uncomment when output changes
# import pprint; pprint.pprint(output)
self.assertEqual(output['builds'],
{'cols': {'elapsed': [8, 8, 4, 4, 4, 4],
'executor': [None, None, None, None, None, None],
'pr': [None, None, None, None, None, None],
'result': ['SUCCESS',
'FAILURE',
'SUCCESS',
'SUCCESS',
'SUCCESS',
'SUCCESS'],
'started': [1234, 1234, 1234, 1234, 1234, 1234],
'tests_failed': [1, 1, 1, 1, 1, 1],
'tests_run': [2, 2, 2, 2, 2, 2]},
'job_paths': {'other-job': 'gs://logs/other-job',
'some-job': 'gs://logs/some-job'},
'jobs': {'other-job': {'5': 0, '7': 1},
'some-job': [1, 4, 2]}})
random_hash_1 = output['clustered'][0][1]
random_hash_2 = output['clustered'][1][1]
self.assertEqual(output['clustered'],
[['some awful stack trace exit 1', random_hash_1, 'some awful stack trace exit 1',
[['example test', [['some-job', [1, 2, 3, 4]]]]]],
['some other error message', random_hash_2, 'some other error message',
[['unrelated test', [['other-job', [5, 7]]]],
['example test', [['some-job', [4]]]]]]]
)
def test_main(self):
def smear(l):
"given a list of dictionary deltas, return a list of dictionaries"
cur = {}
out = []
for delta in l:
cur.update(delta)
out.append(dict(cur))
return out
json.dump(
smear([
{
'started': 1234,
'number': 1,
'tests_failed': 1,
'tests_run': 2,
'elapsed': 4,
'path': 'gs://logs/some-job/1',
'job': 'some-job',
'result': 'SUCCESS'
},
{
'number': 2,
'path': 'gs://logs/some-job/2'
},
{
'number': 3,
'path': 'gs://logs/some-job/3'
},
{
'number': 4,
'path': 'gs://logs/some-job/4'
},
{
'number': 5,
'path': 'gs://logs/other-job/5',
'job': 'other-job',
'elapsed': 8
},
{
'number': 7,
'path': 'gs://logs/other-job/7',
'result': 'FAILURE'
},
]), open('builds.json', 'w'))
tests = smear([
{
'name': 'example test',
'build': 'gs://logs/some-job/1',
'failure_text': 'some awful stack trace exit 1'
},
{
'build': 'gs://logs/some-job/2'
},
{
'build': 'gs://logs/some-job/3'
},
{
'build': 'gs://logs/some-job/4'
},
{
'name': 'another test',
'failure_text': 'some other error message'
},
{
'name': 'unrelated test',
'build': 'gs://logs/other-job/5'
},
{}, # intentional dupe
{
'build': 'gs://logs/other-job/7'
},
])
with open('tests.json', 'w') as f:
for t in tests:
f.write(json.dumps(t) + '\n')
json.dump({'node': ['example']}, open('owners.json', 'w'))
summarize.main(
summarize.parse_args([
'builds.json', 'tests.json',
'--output_slices=failure_data_PREFIX.json',
'--owners=owners.json'
]))
output = json_load_byteified(open('failure_data.json'))
# uncomment when output changes
# import pprint; pprint.pprint(output)
self.assertEqual(
output['builds'], {
'cols': {
'elapsed': [8, 8, 4, 4, 4, 4],
'executor': [None, None, None, None, None, None],
'pr': [None, None, None, None, None, None],
'result': [
'SUCCESS', 'FAILURE', 'SUCCESS', 'SUCCESS', 'SUCCESS',
'SUCCESS'
],
'started': [1234, 1234, 1234, 1234, 1234, 1234],
'tests_failed': [1, 1, 1, 1, 1, 1],
'tests_run': [2, 2, 2, 2, 2, 2]
},
'job_paths': {
'other-job': 'gs://logs/other-job',
'some-job': 'gs://logs/some-job'
},
'jobs': {
'other-job': {
'5': 0,
'7': 1
},
'some-job': [1, 4, 2]
}
})
random_hash_1 = output['clustered'][0]['id']
random_hash_2 = output['clustered'][1]['id']
self.assertEqual(output['clustered'], [{
'id':
random_hash_1,
'key':
'some awful stack trace exit 1',
'tests': [{
'jobs': [{
'builds': [4, 3, 2, 1],
'name': 'some-job'
}],
'name': 'example test'
}],
'spans': [29],
'owner':
'node',
'text':
'some awful stack trace exit 1'
}, {
'id':
random_hash_2,
'key':
'some other error message',
'tests': [{
'jobs': [{
'builds': [7, 5],
'name': 'other-job'
}],
'name': 'unrelated test'
}, {
'jobs': [{
'builds': [4],
'name': 'some-job'
}],
'name': 'another test'
}],
'spans': [24],
'owner':
'testing',
'text':
'some other error message'
}])
slice_output = json_load_byteified(
open('failure_data_%s.json' % random_hash_1[:2]))
self.assertEqual(slice_output['clustered'], [output['clustered'][0]])
self.assertEqual(slice_output['builds']['cols']['started'],
[1234, 1234, 1234, 1234])
def main():
args = parse_input_arguments()
acceptable_modules = [
"phaseblock", "summarize", "visualize", "extend", "somatic", "ancestry"
]
if args.module in acceptable_modules:
no_error = True
error_message = []
if args.module == "phaseblock":
if args.bam is None:
no_error = False
error_message.append("The phaseblock module requires a --bam.")
if args.vcf is None:
no_error = False
error_message.append("The phaseblock module requires a --vcf.")
if args.vcf_id is None:
no_error = False
error_message.append(
"The phaseblock module requires a --vcf_id.")
if args.range is None:
no_error = False
error_message.append(
"The phaseblock module requires a --range.")
if no_error:
import phaseblock
x = phaseblock.main(args)
else:
sys.exit("\n".join(error_message))
elif args.module == "extend":
if args.sum is None:
no_error = False
error_message.append("The extend module requires a --sum.")
if args.pb1 is None:
no_error = False
error_message.append("The extend module requires a --pb1.")
if args.pb2 is None:
no_error = False
error_message.append("The extend module requires a --pb2.")
if args.range is None:
no_error = False
error_message.append("The extend module requires a --range.")
if no_error:
import extend
x = extend.main(args)
else:
sys.exit("\n".join(error_message))
elif args.module == "summarize":
if args.pb1 is None:
no_error = False
error_message.append(
"The summarize module requires a --pb1 (phase block file)."
)
if no_error:
import summarize
x = summarize.main(args)
else:
sys.exit("\n".join(error_message))
elif args.module == "somatic":
if args.pb1 is None:
no_error = False
error_message.append(
"The somatic module requires a --pb1 (phase block file).")
if args.range is None:
no_error = False
error_message.append(
"The somatic module requires a --range (genomic range).")
if args.maf is None and args.variant is None:
no_error = False
error_message.append(
"The somatic module requires a --maf (MAF) or --variant (variant IDs)."
)
if args.maf is not None and args.variant is not None:
no_error = False
error_message.append(
"The somatic module can only have a --maf (MAF) or --variant (variant IDs), not both."
)
if args.sum is None:
no_error = False
error_message.append(
"The somatic module requires a --sum (phase block summary file)."
)
if no_error:
import somatic
x = somatic.main(args)
else:
sys.exit("\n".join(error_message))
elif args.module == "ancestry":
if args.pb1 is None:
no_error = False
error_message.append("The ancestry module requires a --pb1.")
if args.vcf is None:
no_error = False
error_message.append("The ancestry module requires a --vcf.")
if args.vcf_id is None:
no_error = False
error_message.append(
"The ancestry module requires a --vcf_id.")
if args.range is None:
no_error = False
error_message.append("The ancestry module requires a --range.")
if args.ibd is None:
no_error = False
error_message.append("The ancestry module requires a --ibd.")
if args.hbd is None:
no_error = False
error_message.append("The ancestry module requires a --hbd.")
if args.dem is None:
no_error = False
error_message.append("The ancestry module requires a --dem.")
if no_error:
import ancestry
x = ancestry.main(args)
else:
sys.exit("\n".join(error_message))
else:
print("Not X")
else:
sys.exit("Module must be one of " + ', '.join(acceptable_modules) +
".")
def search():
term = request.form['input_text']
return summarize.main(term)
def test_main(self):
def smear(l):
"given a list of dictionary deltas, return a list of dictionaries"
cur = {}
out = []
for delta in l:
cur.update(delta)
out.append(dict(cur))
return out
json.dump(smear([
{'started': 1234, 'number': 1, 'tests_failed': 1, 'tests_run': 2,
'elapsed': 4, 'path': 'gs://logs/some-job/1', 'job': 'some-job', 'result': 'SUCCESS'},
{'number': 2, 'path': 'gs://logs/some-job/2'},
{'number': 3, 'path': 'gs://logs/some-job/3'},
{'number': 4, 'path': 'gs://logs/some-job/4'},
{'number': 5, 'path': 'gs://logs/other-job/5', 'job': 'other-job', 'elapsed': 8},
{'number': 7, 'path': 'gs://logs/other-job/7', 'result': 'FAILURE'},
]), open('builds.json', 'w'))
tests = smear([
{'name': 'example test', 'build': 'gs://logs/some-job/1',
'failure_text': 'some awful stack trace exit 1'},
{'build': 'gs://logs/some-job/2'},
{'build': 'gs://logs/some-job/3'},
{'build': 'gs://logs/some-job/4'},
{'name': 'another test', 'failure_text': 'some other error message'},
{'name': 'unrelated test', 'build': 'gs://logs/other-job/5'},
{}, # intentional dupe
{'build': 'gs://logs/other-job/7'},
])
with open('tests.json', 'w') as f:
for t in tests:
f.write(json.dumps(t) + '\n')
json.dump({
'node': ['example']
}, open('owners.json', 'w'))
summarize.main(summarize.parse_args(
['builds.json', 'tests.json',
'--output_slices=failure_data_PREFIX.json',
'--owners=owners.json']))
output = json_load_byteified(open('failure_data.json'))
# uncomment when output changes
# import pprint; pprint.pprint(output)
self.assertEqual(
output['builds'],
{'cols': {'elapsed': [8, 8, 4, 4, 4, 4],
'executor': [None, None, None, None, None, None],
'pr': [None, None, None, None, None, None],
'result': ['SUCCESS',
'FAILURE',
'SUCCESS',
'SUCCESS',
'SUCCESS',
'SUCCESS'],
'started': [1234, 1234, 1234, 1234, 1234, 1234],
'tests_failed': [1, 1, 1, 1, 1, 1],
'tests_run': [2, 2, 2, 2, 2, 2]},
'job_paths': {'other-job': 'gs://logs/other-job',
'some-job': 'gs://logs/some-job'},
'jobs': {'other-job': {'5': 0, '7': 1}, 'some-job': [1, 4, 2]}})
random_hash_1 = output['clustered'][0]['id']
random_hash_2 = output['clustered'][1]['id']
self.assertEqual(
output['clustered'],
[{'id': random_hash_1,
'key': 'some awful stack trace exit 1',
'tests': [{'jobs': [{'builds': [4, 3, 2, 1],
'name': 'some-job'}],
'name': 'example test'}],
'spans': [29],
'owner': 'node',
'text': 'some awful stack trace exit 1'},
{'id': random_hash_2,
'key': 'some other error message',
'tests': [{'jobs': [{'builds': [7, 5],
'name': 'other-job'}],
'name': 'unrelated test'},
{'jobs': [{'builds': [4], 'name': 'some-job'}],
'name': 'another test'}],
'spans': [24],
'owner': 'testing',
'text': 'some other error message'}]
)
slice_output = json_load_byteified(open('failure_data_%s.json' % random_hash_1[:2]))
self.assertEqual(slice_output['clustered'], [output['clustered'][0]])
self.assertEqual(slice_output['builds']['cols']['started'], [1234, 1234, 1234, 1234])