def test_artifact_post_req_error(self):
# Create a new prep template to attach the 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()])
user_id = '*****@*****.**'
filepaths = {'raw_barcodes': 'uploaded_file.txt',
'raw_forward_seqs': 'update.txt'}
artifact_type = "FASTQ"
name = "TestArtifact"
# The user doesn't have access to the study
obs = artifact_post_req("*****@*****.**", filepaths, artifact_type,
name, pt.id)
exp = {'status': 'error',
'message': 'User does not have access to study'}
self.assertEqual(obs, exp)
# A file does not exist
missing_fps = {'raw_barcodes': 'NOTEXISTS'}
obs = artifact_post_req(user_id, missing_fps, artifact_type,
name, pt.id)
exp = {'status': 'error',
'message': 'File does not exist: NOTEXISTS'}
self.assertEqual(obs, exp)
# Cleaned filepaths is empty
empty_fps = {'raw_barcodes': '', 'raw_forward_seqs': ''}
obs = artifact_post_req(user_id, empty_fps, artifact_type, name, pt.id)
exp = {'status': 'error',
'message': "Can't create artifact, no files provided."}
self.assertEqual(obs, exp)
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_error(self):
# Create a new prep template to attach the 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()])
user_id = '*****@*****.**'
filepaths = {'raw_barcodes': 'uploaded_file.txt',
'raw_forward_seqs': 'update.txt'}
artifact_type = "FASTQ"
name = "TestArtifact"
# The user doesn't have access to the study
obs = artifact_post_req("*****@*****.**", filepaths, artifact_type,
name, pt.id)
exp = {'status': 'error',
'message': 'User does not have access to study'}
self.assertEqual(obs, exp)
# A file does not exist
missing_fps = {'raw_barcodes': 'NOTEXISTS'}
obs = artifact_post_req(user_id, missing_fps, artifact_type,
name, pt.id)
exp = {'status': 'error',
'message': 'File does not exist: NOTEXISTS'}
self.assertEqual(obs, exp)
# Cleaned filepaths is empty
empty_fps = {'raw_barcodes': '', 'raw_forward_seqs': ''}
obs = artifact_post_req(user_id, empty_fps, artifact_type, name, pt.id)
exp = {'status': 'error',
'message': "Can't create artifact, no files provided."}
self.assertEqual(obs, exp)
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()])
new_artifact_id = get_count('qiita.artifact') + 1
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)
obs = r_client.get('prep_template_%d' % pt.id)
self.assertIsNotNone(obs)
redis_info = loads(r_client.get(loads(obs)['job_id']))
while redis_info['status_msg'] == 'Running':
sleep(0.05)
redis_info = loads(r_client.get(loads(obs)['job_id']))
# Instantiate the artifact to make sure it was made and
# to clean the environment
a = Artifact(new_artifact_id)
self._files_to_remove.extend([fp for _, fp, _ in a.filepaths])
# 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()])
new_artifact_id_2 = get_count('qiita.artifact') + 1
obs = artifact_post_req('*****@*****.**', {}, 'FASTQ',
'New Test Artifact 2', pt.id, new_artifact_id)
exp = {'status': 'success', 'message': ''}
self.assertEqual(obs, exp)
obs = r_client.get('prep_template_%d' % pt.id)
self.assertIsNotNone(obs)
redis_info = loads(r_client.get(loads(obs)['job_id']))
while redis_info['status_msg'] == 'Running':
sleep(0.05)
redis_info = loads(r_client.get(loads(obs)['job_id']))
# Instantiate the artifact to make sure it was made and
# to clean the environment
a = Artifact(new_artifact_id_2)
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()])
new_artifact_id = get_count('qiita.artifact') + 1
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)
obs = r_client.get('prep_template_%d' % pt.id)
self.assertIsNotNone(obs)
redis_info = loads(r_client.get(loads(obs)['job_id']))
while redis_info['status_msg'] == 'Running':
sleep(0.05)
redis_info = loads(r_client.get(loads(obs)['job_id']))
# Instantiate the artifact to make sure it was made and
# to clean the environment
a = Artifact(new_artifact_id)
self._files_to_remove.extend([fp for _, fp, _ in a.filepaths])
# 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()])
new_artifact_id_2 = get_count('qiita.artifact') + 1
obs = artifact_post_req(
'*****@*****.**', {}, 'FASTQ', 'New Test Artifact 2', pt.id,
new_artifact_id)
exp = {'status': 'success',
'message': ''}
self.assertEqual(obs, exp)
obs = r_client.get('prep_template_%d' % pt.id)
self.assertIsNotNone(obs)
redis_info = loads(r_client.get(loads(obs)['job_id']))
while redis_info['status_msg'] == 'Running':
sleep(0.05)
redis_info = loads(r_client.get(loads(obs)['job_id']))
# Instantiate the artifact to make sure it was made and
# to clean the environment
a = Artifact(new_artifact_id_2)
self._files_to_remove.extend([fp for _, fp, _ in a.filepaths])