def _initialize_api(client_id,
client_secret,
base_url,
username,
password,
timeout_multiplier,
max_wait_time=20):
"""
Creates the ApiCalls object from the api layer.
Sets the instance to use the global _api_instance variable so it behaves as a singleton that can be easily re-init
:param client_id:
:param client_secret:
:param base_url:
:param username:
:param password:
:param timeout_multiplier:
:param max_wait_time:
:return: The ApiCalls instance
"""
global _api_instance
_api_instance = api.ApiCalls(client_id, client_secret, base_url, username,
password, timeout_multiplier, max_wait_time)
if not base_url.endswith('/api/'):
logging.warning(
"base_url does not end in /api/, this configuration might be incorrect"
)
_api_instance = api.ApiCalls(client_id, client_secret, base_url, username,
password, max_wait_time)
return _api_instance
def setUp(self):
print("\nStarting " + self.__module__ + ": " + self._testMethodName)
self.test_api = api.ApiCalls(
client_id=tests_integration.client_id,
client_secret=tests_integration.client_secret,
base_url=tests_integration.base_url,
username=tests_integration.username,
password=tests_integration.password)
def test_valid_assemblies_directory_upload(self):
"""
Test a valid directory of assemblies for upload end to end
:return:
"""
# Set our sample config file to use miseq parser and the correct irida credentials
self.write_to_config_file(
client_id=tests_integration.client_id,
client_secret=tests_integration.client_secret,
username=tests_integration.username,
password=tests_integration.password,
base_url=tests_integration.base_url,
parser="directory")
# instance an api
test_api = api.ApiCalls(client_id=tests_integration.client_id,
client_secret=tests_integration.client_secret,
base_url=tests_integration.base_url,
username=tests_integration.username,
password=tests_integration.password)
# Create a test project, the uploader does not make new projects on its own
# so one must exist to upload samples into
# This may not be the project that the files get uploaded to,
# but one will be made in the case this is the only test being run
project_name = "test_project_assemblies"
project_description = "test_project_description_assemblies"
project = model.Project(name=project_name,
description=project_description)
test_api.send_project(project)
# We always upload to project "1" so that tests will be consistent no matter how many / which tests are run
project_id = "1"
# Do the upload
upload_result = upload_run_single_entry(directory=path.join(
path_to_module, "fake_assemblies_data"),
upload_assemblies=True)
# Make sure the upload was a success
self.assertEqual(upload_result.exit_code, 0)
# Verify the files were uploaded
sample_list = test_api.get_samples(project_id)
test_sample = sample_list[0]
sequence_files = test_api.get_assemblies_files(project_id,
test_sample.sample_name)
self.assertEqual(len(sequence_files), 1)
self.assertEqual(sequence_files[0]['fileName'], 'file_1.fasta')
def _initialize_api(client_id, client_secret, base_url, username, password, max_wait_time=20):
"""
Creates the ApiCalls object from the api layer.
Sets the instance to use the global _api_instance variable so it behaves as a singleton that can be easily re-init
:param client_id:
:param client_secret:
:param base_url:
:param username:
:param password:
:param max_wait_time:
:return: The ApiCalls instance
"""
global _api_instance
_api_instance = api.ApiCalls(client_id, client_secret, base_url, username, password, max_wait_time)
return _api_instance
def test_upload_to_nonexistent_project(self):
"""
Everything is correct except the sample sheet file specifies an invalid project
Samples should not be uploaded
:return:
"""
# try to upload to a non existent project
# Set our sample config file to use miseq parser and the correct irida credentials
self.write_to_config_file(
client_id=tests_integration.client_id,
client_secret=tests_integration.client_secret,
username=tests_integration.username,
password=tests_integration.password,
base_url=tests_integration.base_url,
parser="miseq",
readonly=False)
# instance an api
test_api = api.ApiCalls(client_id=tests_integration.client_id,
client_secret=tests_integration.client_secret,
base_url=tests_integration.base_url,
username=tests_integration.username,
password=tests_integration.password)
# Create a test project, the uploader does not make new projects on its own
# so one must exist to upload samples into
# This may not be the project that the files get uploaded to,
# but one will be made in the case this is the only test being run
project_name = "test_project"
project_description = "test_project_description"
project = model.Project(name=project_name,
description=project_description)
test_api.send_project(project)
# Do the upload
upload_result = upload_run_single_entry(
path.join(path_to_module, "fake_ngs_data_nonexistent_project"))
# Make sure the upload was a failure
self.assertEqual(upload_result.exit_code, 1)
# Verify that the project does not exist
project_id = "1000"
with self.assertRaises(api.exceptions.IridaKeyError):
test_api.get_samples(project_id)
def test_invalid_read_only_miseq_upload(self):
"""
Test failing to upload a readonly miseq directory because readonly is turned off
:return:
"""
# Set our sample config file to use miseq parser and the correct irida credentials
self.write_to_config_file(
client_id=tests_integration.client_id,
client_secret=tests_integration.client_secret,
username=tests_integration.username,
password=tests_integration.password,
base_url=tests_integration.base_url,
parser="miseq",
readonly=False)
# instance an api
test_api = api.ApiCalls(client_id=tests_integration.client_id,
client_secret=tests_integration.client_secret,
base_url=tests_integration.base_url,
username=tests_integration.username,
password=tests_integration.password)
# Create a test project, the uploader does not make new projects on its own
# so one must exist to upload samples into
# This may not be the project that the files get uploaded to,
# but one will be made in the case this is the only test being run
project_name = "test_read_only_project_fail"
project_description = "test_project_description"
project = model.Project(name=project_name,
description=project_description)
test_api.send_project(project)
# try the upload
upload_result = upload_run_single_entry(path.join(
path_to_module, "fake_ngs_data_read_only"),
force_upload=False,
upload_mode=api.MODE_DEFAULT)
# Make sure the upload was a failure
self.assertEqual(upload_result.exit_code, 1)
def generate_api_instance(config_in):
'''
PURPOSE:
Generate api instance for IRIDA platform based on input keys found in csv file
INPUTS:
- KEY_CONFIG --> IRIDA Uploader config file
RETURNS:
- IRIDA_API --> API class instance based on the input keys given in the config
'''
config = configparser.ConfigParser()
config.read(config_in)
settings = config['Settings']
irida_api = api.ApiCalls(settings['client_id'], settings['client_secret'],
settings['base_url'], settings['username'],
settings['password'])
return irida_api
def test_upload_parse_fail(self):
"""
Given an invalid sample sheet, make sure that the upload does not happen
:return:
"""
# try to upload to a non existent project
# Set our sample config file to use miseq parser and the correct irida credentials
self.write_to_config_file(
client_id=tests_integration.client_id,
client_secret=tests_integration.client_secret,
username=tests_integration.username,
password=tests_integration.password,
base_url=tests_integration.base_url,
parser="miseq")
# instance an api
test_api = api.ApiCalls(client_id=tests_integration.client_id,
client_secret=tests_integration.client_secret,
base_url=tests_integration.base_url,
username=tests_integration.username,
password=tests_integration.password)
# Create a test project, the uploader does not make new projects on its own
# so one must exist to upload samples into
# This may not be the project that the files get uploaded to,
# but one will be made in the case this is the only test being run
project_name = "test_project"
project_description = "test_project_description"
project = model.Project(name=project_name,
description=project_description)
test_api.send_project(project)
# Do the upload
upload_result = upload_run_single_entry(
path.join(path_to_module, "fake_ngs_data_parse_fail"))
# Make sure the upload was a failure
self.assertEqual(upload_result.exit_code, 1)
def test_valid_miseq_upload(self):
"""
Test a valid miseq directory for upload from end to end
:return:
"""
# Set our sample config file to use miseq parser and the correct irida credentials
self.write_to_config_file(
client_id=tests_integration.client_id,
client_secret=tests_integration.client_secret,
username=tests_integration.username,
password=tests_integration.password,
base_url=tests_integration.base_url,
parser="miseq")
# instance an api
test_api = api.ApiCalls(client_id=tests_integration.client_id,
client_secret=tests_integration.client_secret,
base_url=tests_integration.base_url,
username=tests_integration.username,
password=tests_integration.password)
# Create a test project, the uploader does not make new projects on its own
# so one must exist to upload samples into
# This may not be the project that the files get uploaded to,
# but one will be made in the case this is the only test being run
project_name = "test_project"
project_description = "test_project_description"
project = model.Project(name=project_name,
description=project_description)
test_api.send_project(project)
# We always upload to project "1" so that tests will be consistent no matter how many / which tests are run
project_id = "1"
# Do the upload
upload_result = upload_run_single_entry(
path.join(path_to_module, "fake_ngs_data"))
# Make sure the upload was a success
self.assertEqual(upload_result.exit_code, 0)
# Verify the files were uploaded
sample_list = test_api.get_samples(project_id)
sample_1_found = False
sample_2_found = False
sample_3_found = False
for sample in sample_list:
if sample.sample_name in ["01-1111", "02-2222", "03-3333"]:
if sample.sample_name == "01-1111":
sample_1_found = True
sequence_files = test_api.get_sequence_files(
project_id, sample.sample_name)
self.assertEqual(len(sequence_files), 2)
res_sequence_file_names = [
sequence_files[0]['fileName'],
sequence_files[1]['fileName']
]
expected_sequence_file_names = [
'01-1111_S1_L001_R1_001.fastq.gz',
'01-1111_S1_L001_R2_001.fastq.gz'
]
self.assertEqual(res_sequence_file_names.sort(),
expected_sequence_file_names.sort())
elif sample.sample_name == "02-2222":
sample_2_found = True
sequence_files = test_api.get_sequence_files(
project_id, sample.sample_name)
self.assertEqual(len(sequence_files), 2)
res_sequence_file_names = [
sequence_files[0]['fileName'],
sequence_files[1]['fileName']
]
expected_sequence_file_names = [
'02-2222_S1_L001_R1_001.fastq.gz',
'02-2222_S1_L001_R2_001.fastq.gz'
]
self.assertEqual(res_sequence_file_names.sort(),
expected_sequence_file_names.sort())
elif sample.sample_name == "03-3333":
sample_3_found = True
sequence_files = test_api.get_sequence_files(
project_id, sample.sample_name)
self.assertEqual(len(sequence_files), 2)
res_sequence_file_names = [
sequence_files[0]['fileName'],
sequence_files[1]['fileName']
]
expected_sequence_file_names = [
'03-3333_S1_L001_R1_001.fastq.gz',
'03-3333_S1_L001_R2_001.fastq.gz'
]
self.assertEqual(res_sequence_file_names.sort(),
expected_sequence_file_names.sort())
self.assertEqual(sample_1_found, True)
self.assertEqual(sample_2_found, True)
self.assertEqual(sample_3_found, True)
def test_valid_directory_upload(self):
"""
Test a valid directory for upload end to end
:return:
"""
# Set our sample config file to use miseq parser and the correct irida credentials
self.write_to_config_file(
client_id=tests_integration.client_id,
client_secret=tests_integration.client_secret,
username=tests_integration.username,
password=tests_integration.password,
base_url=tests_integration.base_url,
parser="directory",
readonly=False)
# instance an api
test_api = api.ApiCalls(client_id=tests_integration.client_id,
client_secret=tests_integration.client_secret,
base_url=tests_integration.base_url,
username=tests_integration.username,
password=tests_integration.password)
# Create a test project, the uploader does not make new projects on its own
# so one must exist to upload samples into
# This may not be the project that the files get uploaded to,
# but one will be made in the case this is the only test being run
project_name = "test_project_2"
project_description = "test_project_description_2"
project = model.Project(name=project_name,
description=project_description)
test_api.send_project(project)
# We always upload to project "1" so that tests will be consistent no matter how many / which tests are run
project_id = "1"
# Do the upload
upload_result = upload_run_single_entry(
path.join(path_to_module, "fake_dir_data"))
# Make sure the upload was a success
self.assertEqual(upload_result.exit_code, 0)
# Verify the files were uploaded
sample_list = test_api.get_samples(project_id)
sample_1_found = False
sample_2_found = False
sample_3_found = False
for sample in sample_list:
if sample.sample_name in [
"my-sample-1", "my-sample-2", "my-sample-3"
]:
if sample.sample_name == "my-sample-1":
sample_1_found = True
sequence_files = test_api.get_sequence_files(
project_id, sample.sample_name)
self.assertEqual(len(sequence_files), 2)
self.assertEqual(sequence_files[0]['fileName'],
'file_1.fastq.gz')
self.assertEqual(sequence_files[1]['fileName'],
'file_2.fastq.gz')
elif sample.sample_name == "my-sample-2":
sample_2_found = True
sequence_files = test_api.get_sequence_files(
project_id, sample.sample_name)
self.assertEqual(len(sequence_files), 2)
self.assertEqual(sequence_files[0]['fileName'],
'samp_F.fastq.gz')
self.assertEqual(sequence_files[1]['fileName'],
'samp_R.fastq.gz')
elif sample.sample_name == "my-sample-3":
sample_3_found = True
sequence_files = test_api.get_sequence_files(
project_id, sample.sample_name)
self.assertEqual(len(sequence_files), 2)
self.assertEqual(sequence_files[0]['fileName'],
'germ_f.fastq.gz')
self.assertEqual(sequence_files[1]['fileName'],
'germ_r.fastq.gz')
self.assertEqual(sample_1_found, True)
self.assertEqual(sample_2_found, True)
self.assertEqual(sample_3_found, True)
