def post(self):
numentries = int(self.get_argument("numrecords"))
if numentries < 0:
numentries = 100
logentries = LogEntry.newest_records(numentries)
self.render("error_log.html", logentries=logentries,
user=self.current_user)
def post(self):
self.check_access()
numentries = int(self.get_argument("numrecords"))
if numentries <= 0:
numentries = 100
logentries = LogEntry.newest_records(numentries)
self.render("error_log.html", logentries=logentries)
def post(self):
numentries = int(self.get_argument("numrecords"))
if numentries < 0:
numentries = 100
logentries = LogEntry.newest_records(numentries)
self.render("error_log.html",
logentries=logentries,
user=self.current_user)
def test_artifact_status_put_req_private(self):
obs = artifact_status_put_req(1, '*****@*****.**', 'private')
exp = {
'status': 'success',
'message': 'Artifact visibility changed to private'
}
self.assertEqual(obs, exp)
# testing that the log message is generated
self.assertEqual(
LogEntry.newest_records(1)[0].msg,
'[email protected] changed artifact 1 (study 1) to private')
def test_complete_job(self):
# Complete success
pt = npt.assert_warns(QiitaDBWarning, PrepTemplate.create,
pd.DataFrame({'new_col': {
'1.SKD6.640190': 1
}}), Study(1), '16S')
c_job = ProcessingJob.create(
User('*****@*****.**'),
Parameters.load(Command.get_validator('BIOM'),
values_dict={
'template': pt.id,
'files': dumps({'BIOM': ['file']}),
'artifact_type': 'BIOM'
}), True)
c_job._set_status('running')
fd, fp = mkstemp(suffix='_table.biom')
close(fd)
with open(fp, 'w') as f:
f.write('\n')
self._clean_up_files.append(fp)
exp_artifact_count = get_count('qiita.artifact') + 1
payload = dumps({
'success': True,
'error': '',
'artifacts': {
'OTU table': {
'filepaths': [(fp, 'biom')],
'artifact_type': 'BIOM'
}
}
})
job = self._create_job('complete_job', {
'job_id': c_job.id,
'payload': payload
})
private_task(job.id)
self.assertEqual(job.status, 'success')
self.assertEqual(c_job.status, 'success')
self.assertEqual(get_count('qiita.artifact'), exp_artifact_count)
# Complete job error
payload = dumps({'success': False, 'error': 'Job failure'})
job = self._create_job('complete_job', {
'job_id': 'bcc7ebcd-39c1-43e4-af2d-822e3589f14d',
'payload': payload
})
private_task(job.id)
self.assertEqual(job.status, 'success')
c_job = ProcessingJob('bcc7ebcd-39c1-43e4-af2d-822e3589f14d')
self.assertEqual(c_job.status, 'error')
self.assertEqual(c_job.log, LogEntry.newest_records(numrecords=1)[0])
self.assertEqual(c_job.log.msg, 'Job failure')
# Complete internal error
pt = npt.assert_warns(QiitaDBWarning, PrepTemplate.create,
pd.DataFrame({'new_col': {
'1.SKD6.640190': 1
}}), Study(1), '16S')
c_job = ProcessingJob.create(
User('*****@*****.**'),
Parameters.load(Command.get_validator('BIOM'),
values_dict={
'template': pt.id,
'files': dumps({'BIOM': ['file']}),
'artifact_type': 'BIOM'
}), True)
c_job._set_status('running')
fp = '/surprised/if/this/path/exists.biom'
payload = dumps({
'success': True,
'error': '',
'artifacts': {
'OTU table': {
'filepaths': [(fp, 'biom')],
'artifact_type': 'BIOM'
}
}
})
job = self._create_job('complete_job', {
'job_id': c_job.id,
'payload': payload
})
private_task(job.id)
self.assertEqual(job.status, 'success')
self.assertEqual(c_job.status, 'error')
self.assertIn('No such file or directory', c_job.log.msg)
def get(self):
self.check_access()
logentries = LogEntry.newest_records()
self.render("error_log.html", logentries=logentries)
def test_complete_job(self):
# Complete success
pt = npt.assert_warns(
QiitaDBWarning, PrepTemplate.create,
pd.DataFrame({'new_col': {'1.SKD6.640190': 1}}),
Study(1), '16S')
c_job = ProcessingJob.create(
User('*****@*****.**'),
Parameters.load(
Command.get_validator('BIOM'),
values_dict={'template': pt.id,
'files': dumps({'BIOM': ['file']}),
'artifact_type': 'BIOM'}), True)
c_job._set_status('running')
fd, fp = mkstemp(suffix='_table.biom')
close(fd)
with open(fp, 'w') as f:
f.write('\n')
self._clean_up_files.append(fp)
exp_artifact_count = get_count('qiita.artifact') + 1
payload = dumps(
{'success': True, 'error': '',
'artifacts': {'OTU table': {'filepaths': [(fp, 'biom')],
'artifact_type': 'BIOM'}}})
job = self._create_job('complete_job', {'job_id': c_job.id,
'payload': payload})
private_task(job.id)
self.assertEqual(job.status, 'success')
self.assertEqual(c_job.status, 'success')
self.assertEqual(get_count('qiita.artifact'), exp_artifact_count)
# Complete job error
payload = dumps({'success': False, 'error': 'Job failure'})
job = self._create_job(
'complete_job', {'job_id': 'bcc7ebcd-39c1-43e4-af2d-822e3589f14d',
'payload': payload})
private_task(job.id)
self.assertEqual(job.status, 'success')
c_job = ProcessingJob('bcc7ebcd-39c1-43e4-af2d-822e3589f14d')
self.assertEqual(c_job.status, 'error')
self.assertEqual(c_job.log, LogEntry.newest_records(numrecords=1)[0])
self.assertEqual(c_job.log.msg, 'Job failure')
# Complete internal error
pt = npt.assert_warns(
QiitaDBWarning, PrepTemplate.create,
pd.DataFrame({'new_col': {'1.SKD6.640190': 1}}),
Study(1), '16S')
c_job = ProcessingJob.create(
User('*****@*****.**'),
Parameters.load(
Command.get_validator('BIOM'),
values_dict={'template': pt.id,
'files': dumps({'BIOM': ['file']}),
'artifact_type': 'BIOM'}), True)
c_job._set_status('running')
fp = '/surprised/if/this/path/exists.biom'
payload = dumps(
{'success': True, 'error': '',
'artifacts': {'OTU table': {'filepaths': [(fp, 'biom')],
'artifact_type': 'BIOM'}}})
job = self._create_job('complete_job', {'job_id': c_job.id,
'payload': payload})
private_task(job.id)
self.assertEqual(job.status, 'success')
self.assertEqual(c_job.status, 'error')
self.assertIn('No such file or directory', c_job.log.msg)
def get(self):
logentries = LogEntry.newest_records()
self.render("error_log.html",
logentries=logentries,
user=self.current_user)
def test_artifact_patch_request(self):
a = Artifact(1)
test_user = User('*****@*****.**')
self.assertEqual(a.name, 'Raw data 1')
artifact_patch_request(test_user,
1,
'replace',
'/name/',
req_value='NEW_NAME')
self.assertEqual(a.name, 'NEW_NAME')
# Reset the name
a.name = 'Raw data 1'
# No access
with self.assertRaises(QiitaHTTPError):
artifact_patch_request(User('*****@*****.**'),
1,
'replace',
'/name/',
req_value='NEW_NAME')
# Incorrect path parameter
with self.assertRaises(QiitaHTTPError):
artifact_patch_request(test_user,
1,
'replace',
'/name/wrong/',
req_value='NEW_NAME')
# Missing value
with self.assertRaises(QiitaHTTPError):
artifact_patch_request(test_user, 1, 'replace', '/name/')
# Wrong attribute
with self.assertRaises(QiitaHTTPError):
artifact_patch_request(test_user,
1,
'replace',
'/wrong/',
req_value='NEW_NAME')
# Wrong operation
with self.assertRaises(QiitaHTTPError):
artifact_patch_request(test_user,
1,
'add',
'/name/',
req_value='NEW_NAME')
# Changing visibility
self.assertEqual(a.visibility, 'private')
artifact_patch_request(test_user,
1,
'replace',
'/visibility/',
req_value='sandbox')
self.assertEqual(a.visibility, 'sandbox')
# checking that we have a new entry in the database for this
self.assertEqual(
LogEntry.newest_records(1)[0].msg,
'[email protected] changed artifact 1 (study 1) to sandbox')
# Admin can change to private
artifact_patch_request(User('*****@*****.**'),
1,
'replace',
'/visibility/',
req_value='private')
self.assertEqual(a.visibility, 'private')
# Test user can't change to private
with self.assertRaises(QiitaHTTPError):
artifact_patch_request(test_user,
1,
'replace',
'/visibility/',
req_value='private')
# Unkown req value
with self.assertRaises(QiitaHTTPError):
artifact_patch_request(test_user,
1,
'replace',
'/visibility/',
req_value='wrong')
def get(self):
logentries = LogEntry.newest_records()
self.render("error_log.html", logentries=logentries,
user=self.current_user)
