def test_artifact_post_req(self):
# Create new prep template to attach artifact to
pt = npt.assert_warns(
QiitaDBWarning, PrepTemplate.create,
pd.DataFrame({'new_col': {'1.SKD6.640190': 1}}), Study(1), '16S')
self._files_to_remove.extend([fp for _, fp in pt.get_filepaths()])
filepaths = {'raw_forward_seqs': 'uploaded_file.txt',
'raw_barcodes': 'update.txt'}
obs = artifact_post_req(
'*****@*****.**', filepaths, 'FASTQ', 'New Test Artifact', pt.id)
exp = {'status': 'success',
'message': ''}
self.assertEqual(obs, exp)
wait_for_prep_information_job(pt.id)
# Test importing an artifact
# Create new prep template to attach artifact to
pt = npt.assert_warns(
QiitaDBWarning, PrepTemplate.create,
pd.DataFrame({'new_col': {'1.SKD6.640190': 1}}), Study(1), '16S')
self._files_to_remove.extend([fp for _, fp in pt.get_filepaths()])
obs = artifact_post_req(
'*****@*****.**', {}, 'Demultiplexed', 'New Test Artifact 2',
pt.id, 3)
exp = {'status': 'success',
'message': ''}
self.assertEqual(obs, exp)
wait_for_prep_information_job(pt.id)
# Instantiate the artifact to make sure it was made and
# to clean the environment
a = Artifact(pt.artifact.id)
self._files_to_remove.extend([fp for _, fp, _ in a.filepaths])
def test_artifact_post_req(self):
# Create new prep template to attach artifact to
pt = npt.assert_warns(
QiitaDBWarning, PrepTemplate.create,
pd.DataFrame({'new_col': {'1.SKD6.640190': 1}}), Study(1), '16S')
self._files_to_remove.extend([fp for _, fp in pt.get_filepaths()])
filepaths = {'raw_forward_seqs': 'uploaded_file.txt',
'raw_barcodes': 'update.txt'}
obs = artifact_post_req(
'*****@*****.**', filepaths, 'FASTQ', 'New Test Artifact', pt.id)
exp = {'status': 'success',
'message': ''}
self.assertEqual(obs, exp)
wait_for_prep_information_job(pt.id)
# Test importing an artifact
# Create new prep template to attach artifact to
pt = npt.assert_warns(
QiitaDBWarning, PrepTemplate.create,
pd.DataFrame({'new_col': {'1.SKD6.640190': 1}}), Study(1), '16S')
self._files_to_remove.extend([fp for _, fp in pt.get_filepaths()])
obs = artifact_post_req(
'*****@*****.**', {}, 'Demultiplexed', 'New Test Artifact 2',
pt.id, 3)
exp = {'status': 'success',
'message': ''}
self.assertEqual(obs, exp)
wait_for_prep_information_job(pt.id)
# Instantiate the artifact to make sure it was made and
# to clean the environment
a = Artifact(pt.artifact.id)
self._files_to_remove.extend([fp for _, fp, _ in a.filepaths])
def test_delete_artifact(self):
response = self.post('/artifact/', {'artifact_id': 2})
self.assertEqual(response.code, 200)
# This is needed so the clean up works - this is a distributed system
# so we need to make sure that all processes are done before we reset
# the test database
wait_for_prep_information_job(1)
def test_delete_artifact(self):
response = self.post('/artifact/',
{'artifact_id': 2})
self.assertEqual(response.code, 200)
# This is needed so the clean up works - this is a distributed system
# so we need to make sure that all processes are done before we reset
# the test database
wait_for_prep_information_job(1)
def test_artifact_delete_req(self):
obs = artifact_delete_req(self.artifact.id, '*****@*****.**')
exp = {'status': 'success', 'message': ''}
self.assertEqual(obs, exp)
# This is needed so the clean up works - this is a distributed system
# so we need to make sure that all processes are done before we reset
# the test database
wait_for_prep_information_job(1)
def test_artifact_delete_req(self):
obs = artifact_delete_req(self.artifact.id, '*****@*****.**')
exp = {'status': 'success', 'message': ''}
self.assertEqual(obs, exp)
# This is needed so the clean up works - this is a distributed system
# so we need to make sure that all processes are done before we reset
# the test database
wait_for_prep_information_job(1)
def test_artifact_post_request(self):
# No access
with self.assertRaises(QiitaHTTPError):
artifact_post_req(User('*****@*****.**'), 1)
artifact_post_req(User('*****@*****.**'), 2)
# Wait until the job is completed
wait_for_prep_information_job(1)
# Check that the delete function has been actually called
obs = r_client.get(loads(r_client.get('prep_template_1'))['job_id'])
self.assertIn('Cannot delete artifact 2', obs)
def test_artifact_post_request(self):
# No access
with self.assertRaises(QiitaHTTPError):
artifact_post_req(User('*****@*****.**'), 1)
obs = artifact_post_req(User('*****@*****.**'), 2)
self.assertCountEqual(obs.keys(), ['job'])
# Wait until the job is completed
wait_for_prep_information_job(1)
# Check that the delete function has been actually called
job = ProcessingJob(loads(r_client.get('prep_template_1'))['job_id'])
self.assertEqual(job.status, 'error')
self.assertIn('Cannot delete artifact 2', job.log.msg)
def test_artifact_post_request(self):
# No access
with self.assertRaises(QiitaHTTPError):
artifact_post_req(User('*****@*****.**'), 1)
obs = artifact_post_req(User('*****@*****.**'), 2)
self.assertEqual(obs.keys(), ['job'])
# Wait until the job is completed
wait_for_prep_information_job(1)
# Check that the delete function has been actually called
job = ProcessingJob(loads(r_client.get('prep_template_1'))['job_id'])
self.assertEqual(job.status, 'error')
self.assertIn('Cannot delete artifact 2', job.log.msg)
def test_post_artifact(self):
args = {
'artifact-type': 'FASTQ',
'name': 'New Artifact Handler test',
'prep-template-id': self.prep.id,
'raw_forward_seqs': [self.fwd_fp],
'raw_barcodes': [self.barcodes_fp],
'raw_reverse_seqs': [],
'import-artifact': ''}
response = self.post('/study/new_artifact/', args)
self.assertEqual(response.code, 200)
# make sure new artifact created
wait_for_prep_information_job(self.prep.id)
def test_post_artifact(self):
args = {
'artifact-type': 'FASTQ',
'name': 'New Artifact Handler test',
'prep-template-id': self.prep.id,
'raw_forward_seqs': [self.fwd_fp],
'raw_barcodes': [self.barcodes_fp],
'raw_reverse_seqs': [],
'import-artifact': ''
}
response = self.post('/study/new_artifact/', args)
self.assertEqual(response.code, 200)
# make sure new artifact created
wait_for_prep_information_job(self.prep.id)
def test_post_artifact_ajax_handler(self):
response = self.post('/artifact/2/', {})
self.assertEqual(response.code, 200)
wait_for_prep_information_job(1)
def test_post_artifact_ajax_handler(self):
response = self.post('/artifact/2/', {})
self.assertEqual(response.code, 200)
wait_for_prep_information_job(1)
