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 artifact_post_req(user_id,
filepaths,
artifact_type,
name,
prep_template_id,
artifact_id=None):
"""Creates the initial artifact for the prep template
Parameters
----------
user_id : str
User adding the atrifact
filepaths : dict of str
Comma-separated list of files to attach to the artifact,
keyed by file type
artifact_type : str
The type of the artifact
name : str
Name to give the artifact
prep_template_id : int or str castable to int
Prep template to attach the artifact to
artifact_id : int or str castable to int, optional
The id of the imported artifact
Returns
-------
dict of objects
A dictionary containing the new artifact ID
{'status': status,
'message': message,
'artifact': id}
"""
prep_template_id = int(prep_template_id)
prep = PrepTemplate(prep_template_id)
study_id = prep.study_id
# First check if the user has access to the study
access_error = check_access(study_id, user_id)
if access_error:
return access_error
user = User(user_id)
if artifact_id:
# if the artifact id has been provided, import the artifact
qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
cmd = qiita_plugin.get_command('copy_artifact')
params = Parameters.load(cmd,
values_dict={
'artifact': artifact_id,
'prep_template': prep.id
})
job = ProcessingJob.create(user, params, True)
else:
uploads_path = get_mountpoint('uploads')[0][1]
path_builder = partial(join, uploads_path, str(study_id))
cleaned_filepaths = {}
for ftype, file_list in filepaths.items():
# JavaScript sends us this list as a comma-separated list
for fp in file_list.split(','):
# JavaScript will send this value as an empty string if the
# list of files was empty. In such case, the split will
# generate a single element containing the empty string. Check
# for that case here and, if fp is not the empty string,
# proceed to check if the file exists
if fp:
# Check if filepath being passed exists for study
full_fp = path_builder(fp)
exists = check_fp(study_id, full_fp)
if exists['status'] != 'success':
return {
'status': 'error',
'message': 'File does not exist: %s' % fp
}
if ftype not in cleaned_filepaths:
cleaned_filepaths[ftype] = []
cleaned_filepaths[ftype].append(full_fp)
# This should never happen, but it doesn't hurt to actually have
# a explicit check, in case there is something odd with the JS
if not cleaned_filepaths:
return {
'status': 'error',
'message': "Can't create artifact, no files provided."
}
# This try/except will catch the case when the plugins are not
# activated so there is no Validate for the given artifact_type
try:
command = Command.get_validator(artifact_type)
except QiitaDBError as e:
return {'status': 'error', 'message': str(e)}
job = ProcessingJob.create(
user,
Parameters.load(command,
values_dict={
'template': prep_template_id,
'files': dumps(cleaned_filepaths),
'artifact_type': artifact_type,
'name': name,
'analysis': None,
}), True)
# Submit the job
job.submit()
r_client.set(PREP_TEMPLATE_KEY_FORMAT % prep.id,
dumps({
'job_id': job.id,
'is_qiita_job': True
}))
return {'status': 'success', 'message': ''}
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 artifact_post_req(user_id, filepaths, artifact_type, name,
prep_template_id, artifact_id=None):
"""Creates the initial artifact for the prep template
Parameters
----------
user_id : str
User adding the atrifact
filepaths : dict of str
Comma-separated list of files to attach to the artifact,
keyed by file type
artifact_type : str
The type of the artifact
name : str
Name to give the artifact
prep_template_id : int or str castable to int
Prep template to attach the artifact to
artifact_id : int or str castable to int, optional
The id of the imported artifact
Returns
-------
dict of objects
A dictionary containing the new artifact ID
{'status': status,
'message': message,
'artifact': id}
"""
prep_template_id = int(prep_template_id)
prep = PrepTemplate(prep_template_id)
study_id = prep.study_id
# First check if the user has access to the study
access_error = check_access(study_id, user_id)
if access_error:
return access_error
if artifact_id:
# if the artifact id has been provided, import the artifact
job_id = safe_submit(user_id, copy_raw_data, prep, artifact_id)
is_qiita_job = False
else:
uploads_path = get_mountpoint('uploads')[0][1]
path_builder = partial(join, uploads_path, str(study_id))
cleaned_filepaths = {}
for ftype, file_list in viewitems(filepaths):
# JavaScript sends us this list as a comma-separated list
for fp in file_list.split(','):
# JavaScript will send this value as an empty string if the
# list of files was empty. In such case, the split will
# generate a single element containing the empty string. Check
# for that case here and, if fp is not the empty string,
# proceed to check if the file exists
if fp:
# Check if filepath being passed exists for study
full_fp = path_builder(fp)
exists = check_fp(study_id, full_fp)
if exists['status'] != 'success':
return {'status': 'error',
'message': 'File does not exist: %s' % fp}
if ftype not in cleaned_filepaths:
cleaned_filepaths[ftype] = []
cleaned_filepaths[ftype].append(full_fp)
# This should never happen, but it doesn't hurt to actually have
# a explicit check, in case there is something odd with the JS
if not cleaned_filepaths:
return {'status': 'error',
'message': "Can't create artifact, no files provided."}
command = Command.get_validator(artifact_type)
job = ProcessingJob.create(
User(user_id),
Parameters.load(command, values_dict={
'template': prep_template_id,
'files': dumps(cleaned_filepaths),
'artifact_type': artifact_type
}))
job.submit()
job_id = job.id
is_qiita_job = True
r_client.set(PREP_TEMPLATE_KEY_FORMAT % prep.id,
dumps({'job_id': job_id, 'is_qiita_job': is_qiita_job}))
return {'status': 'success', 'message': ''}
