def test_prep_template_jobs_get_req(self):
# Create a new template:
metadata = pd.DataFrame.from_dict(
{
'SKD6.640190': {
'center_name': 'ANL',
'target_subfragment': 'V4',
'center_project_name': 'Test Project',
'ebi_submission_accession': None,
'EMP_status': 'EMP',
'str_column': 'Value for sample 1',
'primer': 'GTGCCAGCMGCCGCGGTAA',
'barcode': 'GTCCGCAAGTTA',
'run_prefix': "s_G1_L001_sequences",
'platform': 'Illumina',
'instrument_model': 'Illumina MiSeq',
'library_construction_protocol': 'AAAA',
'experiment_design_description': 'BBBB'
}
},
orient='index',
dtype=str)
pt = PrepTemplate.create(metadata, Study(1), '16S')
# Check that it returns an empty dictionary when there are no jobs
# attached to the prep template
self.assertEqual(prep_template_jobs_get_req(pt.id, '*****@*****.**'), {})
# Create a job on the template
prep_template_patch_req('*****@*****.**', 'remove',
'/%s/10/columns/target_subfragment/' % pt.id)
# To ensure a deterministic result, wait until the job is completed
self._wait_for_parallel_job('prep_template_%s' % pt.id)
obs = prep_template_jobs_get_req(pt.id, '*****@*****.**')
self.assertEqual(len(obs), 1)
self.assertCountEqual(obs.values(), [{
'error': '',
'status': 'success',
'step': None
}])
obs = prep_template_jobs_get_req(pt.id, '*****@*****.**')
exp = {
'status': 'error',
'message': 'User does not have access to study'
}
self.assertEqual(obs, exp)
def test_prep_template_patch_req_errors(self):
# Operation not supported
obs = prep_template_patch_req('*****@*****.**', 'add',
'/1/investigation_type',
'Cancer Genomics')
exp = {
'status':
'error',
'message':
'Operation "add" not supported. '
'Current supported operations: replace'
}
self.assertEqual(obs, exp)
# Incorrect path parameter
obs = prep_template_patch_req('*****@*****.**', 'replace',
'/investigation_type', 'Cancer Genomics')
exp = {'status': 'error', 'message': 'Incorrect path parameter'}
self.assertEqual(obs, exp)
# Incorrect attribute
obs = prep_template_patch_req('*****@*****.**', 'replace',
'/1/other_attribute', 'Cancer Genomics')
exp = {
'status':
'error',
'message':
'Attribute "other_attribute" not found. '
'Please, check the path parameter'
}
self.assertEqual(obs, exp)
# User doesn't have access
obs = prep_template_patch_req('*****@*****.**', 'replace',
'/1/investigation_type',
'Cancer Genomics')
exp = {
'status': 'error',
'message': 'User does not have access to study'
}
self.assertEqual(obs, exp)
# File does not exists
obs = prep_template_patch_req('*****@*****.**', 'replace', '/1/data',
'unknown_file.txt')
exp = {
'status': 'error',
'message': 'file does not exist',
'file': 'unknown_file.txt'
}
self.assertEqual(obs, exp)
def test_prep_template_patch_req_errors(self):
# Operation not supported
obs = prep_template_patch_req(
'*****@*****.**', 'add', '/1/investigation_type',
'Cancer Genomics')
exp = {'status': 'error',
'message': 'Operation "add" not supported. '
'Current supported operations: replace'}
self.assertEqual(obs, exp)
# Incorrect path parameter
obs = prep_template_patch_req(
'*****@*****.**', 'replace', '/investigation_type',
'Cancer Genomics')
exp = {'status': 'error',
'message': 'Incorrect path parameter'}
self.assertEqual(obs, exp)
# Incorrect attribute
obs = prep_template_patch_req(
'*****@*****.**', 'replace', '/1/other_attribute',
'Cancer Genomics')
exp = {'status': 'error',
'message': 'Attribute "other_attribute" not found. '
'Please, check the path parameter'}
self.assertEqual(obs, exp)
# User doesn't have access
obs = prep_template_patch_req(
'*****@*****.**', 'replace', '/1/investigation_type',
'Cancer Genomics')
exp = {'status': 'error',
'message': 'User does not have access to study'}
self.assertEqual(obs, exp)
# File does not exists
obs = prep_template_patch_req(
'*****@*****.**', 'replace', '/1/data', 'unknown_file.txt')
exp = {'status': 'error',
'message': 'file does not exist',
'file': 'unknown_file.txt'}
self.assertEqual(obs, exp)
def test_prep_template_jobs_get_req(self):
# Create a new template:
metadata = pd.DataFrame.from_dict(
{'SKD6.640190': {'center_name': 'ANL',
'target_subfragment': 'V4',
'center_project_name': 'Test Project',
'ebi_submission_accession': None,
'EMP_status': 'EMP',
'str_column': 'Value for sample 1',
'primer': 'GTGCCAGCMGCCGCGGTAA',
'barcode': 'GTCCGCAAGTTA',
'run_prefix': "s_G1_L001_sequences",
'platform': 'ILLUMINA',
'instrument_model': 'Illumina MiSeq',
'library_construction_protocol': 'AAAA',
'experiment_design_description': 'BBBB'}},
orient='index', dtype=str)
pt = PrepTemplate.create(metadata, Study(1), '16S')
# Check that it returns an empty dictionary when there are no jobs
# attached to the prep template
self.assertEqual(prep_template_jobs_get_req(pt.id, '*****@*****.**'), {})
# Create a job on the template
prep_template_patch_req(
'*****@*****.**', 'remove',
'/%s/10/columns/target_subfragment/' % pt.id)
# To ensure a deterministic result, wait until the job is completed
self._wait_for_parallel_job('prep_template_%s' % pt.id)
obs = prep_template_jobs_get_req(pt.id, '*****@*****.**')
self.assertEqual(len(obs), 1)
self.assertEqual(obs.values(),
[{'error': '', 'status': 'success', 'step': None}])
obs = prep_template_jobs_get_req(pt.id, '*****@*****.**')
exp = {'status': 'error',
'message': 'User does not have access to study'}
self.assertEqual(obs, exp)
def test_prep_template_patch_req(self):
pt = PrepTemplate(1)
# Update investigation type
obs = prep_template_patch_req(
'*****@*****.**', 'replace', '/1/investigation_type',
'Cancer Genomics')
exp = {'status': 'success', 'message': ''}
self.assertEqual(obs, exp)
self.assertEqual(pt.investigation_type, 'Cancer Genomics')
# Update prep template data
obs = prep_template_patch_req(
'*****@*****.**', 'replace', '/1/data', 'update.txt')
self.assertEqual(obs, exp)
obs = r_client.get('prep_template_1')
self.assertIsNotNone(obs)
# 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
redis_info = loads(r_client.get(obs))
while redis_info['status_msg'] == 'Running':
sleep(0.05)
redis_info = loads(r_client.get(obs))
def test_prep_template_patch_req(self):
pt = PrepTemplate(1)
# Update investigation type
obs = prep_template_patch_req('*****@*****.**', 'replace',
'/1/investigation_type',
'Cancer Genomics')
exp = {'status': 'success', 'message': ''}
self.assertEqual(obs, exp)
self.assertEqual(pt.investigation_type, 'Cancer Genomics')
# Update prep template data
obs = prep_template_patch_req('*****@*****.**', 'replace', '/1/data',
'update.txt')
self.assertEqual(obs, exp)
obs = r_client.get('prep_template_1')
self.assertIsNotNone(obs)
# 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
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']))
def test_prep_template_patch_req(self):
metadata = pd.DataFrame.from_dict(
{
'SKD6.640190': {
'center_name': 'ANL',
'target_subfragment': 'V4',
'center_project_name': 'Test Project',
'ebi_submission_accession': None,
'EMP_status': 'EMP',
'str_column': 'Value for sample 1',
'primer': 'GTGCCAGCMGCCGCGGTAA',
'barcode': 'GTCCGCAAGTTA',
'run_prefix': "s_G1_L001_sequences",
'platform': 'ILLUMINA',
'instrument_model': 'Illumina MiSeq',
'library_construction_protocol': 'AAAA',
'experiment_design_description': 'BBBB'
}
},
orient='index',
dtype=str)
pt = PrepTemplate.create(metadata, Study(1), '16S')
# Update investigation type
obs = prep_template_patch_req('*****@*****.**', 'replace',
'/%s/investigation_type' % pt.id,
'Cancer Genomics')
exp = {'status': 'success', 'message': ''}
self.assertEqual(obs, exp)
self.assertEqual(pt.investigation_type, 'Cancer Genomics')
# Update prep template data
obs = prep_template_patch_req('*****@*****.**', 'replace',
'/%s/data' % pt.id, 'update.txt')
self.assertEqual(obs, exp)
obs = r_client.get('prep_template_%s' % pt.id)
self.assertIsNotNone(obs)
self._wait_for_parallel_job('prep_template_%s' % pt.id)
# Delete a prep template column
obs = prep_template_patch_req(
'*****@*****.**', 'remove',
'/%s/10/columns/target_subfragment/' % pt.id)
exp = {'status': 'success', 'message': '', 'row_id': '10'}
self.assertEqual(obs, exp)
self._wait_for_parallel_job('prep_template_%s' % pt.id)
self.assertNotIn('target_subfragment', pt.categories())
# Test all the errors
# Operation not supported
obs = prep_template_patch_req('*****@*****.**', 'add',
'/1/investigation_type',
'Cancer Genomics')
exp = {
'status': 'error',
'message': 'Operation "add" not supported. '
'Current supported operations: replace, remove',
'row_id': '0'
}
self.assertEqual(obs, exp)
# Incorrect path parameter
obs = prep_template_patch_req('*****@*****.**', 'replace',
'/investigation_type', 'Cancer Genomics')
exp = {'status': 'error', 'message': 'Incorrect path parameter'}
self.assertEqual(obs, exp)
# Incorrect attribute
obs = prep_template_patch_req('*****@*****.**', 'replace',
'/1/other_attribute', 'Cancer Genomics')
exp = {
'status':
'error',
'message':
'Attribute "other_attribute" not found. '
'Please, check the path parameter'
}
self.assertEqual(obs, exp)
# User doesn't have access
obs = prep_template_patch_req('*****@*****.**', 'replace',
'/%s/investigation_type' % pt.id,
'Cancer Genomics')
exp = {
'status': 'error',
'message': 'User does not have access to study'
}
self.assertEqual(obs, exp)
# File does not exists
obs = prep_template_patch_req('*****@*****.**', 'replace', '/1/data',
'unknown_file.txt')
exp = {
'status': 'error',
'message': 'file does not exist',
'file': 'unknown_file.txt'
}
self.assertEqual(obs, exp)
def test_prep_template_patch_req(self):
metadata = pd.DataFrame.from_dict(
{'SKD6.640190': {'center_name': 'ANL',
'target_subfragment': 'V4',
'center_project_name': 'Test Project',
'ebi_submission_accession': None,
'EMP_status': 'EMP',
'str_column': 'Value for sample 1',
'primer': 'GTGCCAGCMGCCGCGGTAA',
'barcode': 'GTCCGCAAGTTA',
'run_prefix': "s_G1_L001_sequences",
'platform': 'ILLUMINA',
'instrument_model': 'Illumina MiSeq',
'library_construction_protocol': 'AAAA',
'experiment_design_description': 'BBBB'}},
orient='index', dtype=str)
pt = PrepTemplate.create(metadata, Study(1), '16S')
# Update investigation type
obs = prep_template_patch_req(
'*****@*****.**', 'replace', '/%s/investigation_type' % pt.id,
'Cancer Genomics')
exp = {'status': 'success', 'message': ''}
self.assertEqual(obs, exp)
self.assertEqual(pt.investigation_type, 'Cancer Genomics')
# Update prep template data
obs = prep_template_patch_req(
'*****@*****.**', 'replace', '/%s/data' % pt.id, 'update.txt')
self.assertEqual(obs, exp)
obs = r_client.get('prep_template_%s' % pt.id)
self.assertIsNotNone(obs)
self._wait_for_parallel_job('prep_template_%s' % pt.id)
# Delete a prep template column
obs = prep_template_patch_req(
'*****@*****.**', 'remove',
'/%s/10/columns/target_subfragment/' % pt.id)
exp = {'status': 'success', 'message': '', 'row_id': '10'}
self.assertEqual(obs, exp)
self._wait_for_parallel_job('prep_template_%s' % pt.id)
self.assertNotIn('target_subfragment', pt.categories())
# Change the name of the prep template
obs = prep_template_patch_req(
'*****@*****.**', 'replace', '/%s/name' % pt.id, ' My New Name ')
exp = {'status': 'success', 'message': ''}
self.assertEqual(obs, exp)
self.assertEqual(pt.name, 'My New Name')
# Test all the errors
# Operation not supported
obs = prep_template_patch_req(
'*****@*****.**', 'add', '/1/investigation_type',
'Cancer Genomics')
exp = {'status': 'error',
'message': 'Operation "add" not supported. '
'Current supported operations: replace, remove',
'row_id': '0'}
self.assertEqual(obs, exp)
# Incorrect path parameter
obs = prep_template_patch_req(
'*****@*****.**', 'replace', '/investigation_type',
'Cancer Genomics')
exp = {'status': 'error',
'message': 'Incorrect path parameter'}
self.assertEqual(obs, exp)
# Incorrect attribute
obs = prep_template_patch_req(
'*****@*****.**', 'replace', '/1/other_attribute',
'Cancer Genomics')
exp = {'status': 'error',
'message': 'Attribute "other_attribute" not found. '
'Please, check the path parameter'}
self.assertEqual(obs, exp)
# User doesn't have access
obs = prep_template_patch_req(
'*****@*****.**', 'replace', '/%s/investigation_type' % pt.id,
'Cancer Genomics')
exp = {'status': 'error',
'message': 'User does not have access to study'}
self.assertEqual(obs, exp)
# File does not exists
obs = prep_template_patch_req(
'*****@*****.**', 'replace', '/1/data', 'unknown_file.txt')
exp = {'status': 'error',
'message': 'file does not exist',
'file': 'unknown_file.txt'}
self.assertEqual(obs, exp)
