class TestBCL2FastqRunnerFactory(unittest.TestCase):
dummy_config = DummyConfig()
def test_create_bcl2fastq1x_runner(self):
config = Bcl2FastqConfig(general_config=DUMMY_CONFIG,
bcl2fastq_version="1.8.4",
runfolder_input="test/runfolder",
output="test/output")
factory = BCL2FastqRunnerFactory(self.dummy_config)
runner = factory.create_bcl2fastq_runner(config)
self.assertIsInstance(runner, BCL2Fastq1xRunner)
def test_create_bcl2fastq2x_runner(self):
config = Bcl2FastqConfig(general_config=DUMMY_CONFIG,
bcl2fastq_version="2.15.2",
runfolder_input="test/runfolder",
output="test/output")
factory = BCL2FastqRunnerFactory(self.dummy_config)
runner = factory.create_bcl2fastq_runner(config)
self.assertIsInstance(runner,
BCL2Fastq2xRunner,
msg="runner is: " + str(runner))
def test_create_invalid_version_runner(self):
config = Bcl2FastqConfig(general_config=DUMMY_CONFIG,
bcl2fastq_version="1.7",
runfolder_input="test/runfolder",
output="test/output")
factory = BCL2FastqRunnerFactory(self.dummy_config)
with self.assertRaises(LookupError):
factory.create_bcl2fastq_runner(config)
import unittest
from mock import patch
import tempfile
import os
from bcl2fastq.lib.bcl2fastq_utils import *
from bcl2fastq.lib.illumina import Samplesheet
from test_utils import TestUtils, DummyConfig
DUMMY_CONFIG = DummyConfig()
class TestBcl2FastqConfig(unittest.TestCase):
test_dir = os.path.dirname(os.path.realpath(__file__))
samplesheet_file = test_dir + "/sampledata/new_samplesheet_example.csv"
samplesheet_with_no_tag = test_dir + "/sampledata/no_tag_samplesheet_example.csv"
def test_get_bcl2fastq_version_from_run_parameters(self):
runfolder = TestBcl2FastqConfig.test_dir + "/sampledata/HiSeq-samples/2014-02_13_average_run"
version = Bcl2FastqConfig.get_bcl2fastq_version_from_run_parameters(runfolder, TestUtils.DUMMY_CONFIG)
self.assertEqual(version, "1.8.4")
def test_is_single_read_true(self):
runfolder = TestBcl2FastqConfig.test_dir + "/sampledata/HiSeq-samples/2014-02_13_average_run"
self.assertFalse(Bcl2FastqConfig.is_single_read(runfolder))
def test_is_single_read_false(self):
runfolder = TestBcl2FastqConfig.test_dir + "/sampledata/MiSeq-samples/2014-02_11_50kit_single_read"
self.assertTrue(Bcl2FastqConfig.is_single_read(runfolder))
def get_app(self):
dummy_config = DummyConfig()
return Application(routes(config=dummy_config))
class TestBcl2FastqConfig(unittest.TestCase):
test_dir = os.path.dirname(os.path.realpath(__file__))
samplesheet_file = test_dir + "/sampledata/new_samplesheet_example.csv"
samplesheet_with_no_tag = test_dir + "/sampledata/no_tag_samplesheet_example.csv"
dummy_config = DummyConfig()
def test_get_bcl2fastq_version_from_run_parameters(self):
runfolder = TestBcl2FastqConfig.test_dir + "/sampledata/HiSeq-samples/2014-02_13_average_run"
version = Bcl2FastqConfig.get_bcl2fastq_version_from_run_parameters(
runfolder, self.dummy_config)
self.assertEqual(version, "1.8.4")
def test_is_single_read_true(self):
runfolder = TestBcl2FastqConfig.test_dir + "/sampledata/HiSeq-samples/2014-02_13_average_run"
self.assertFalse(Bcl2FastqConfig.is_single_read(runfolder))
def test_is_single_read_false(self):
runfolder = TestBcl2FastqConfig.test_dir + "/sampledata/MiSeq-samples/2014-02_11_50kit_single_read"
self.assertTrue(Bcl2FastqConfig.is_single_read(runfolder))
def test_get_length_of_indexes(self):
runfolder = TestBcl2FastqConfig.test_dir + "/sampledata/HiSeq-samples/2014-02_13_average_run"
index_and_length = Bcl2FastqConfig.get_length_of_indexes(runfolder)
self.assertEqual(index_and_length, {2: 7})
def test_write_samplesheet(self):
f = tempfile.mktemp()
Bcl2FastqConfig.write_samplesheet(TestUtils.DUMMY_SAMPLESHEET_STRING,
f)
with open(f, "r") as my_file:
content = my_file.read()
self.assertEqual(content, TestUtils.DUMMY_SAMPLESHEET_STRING)
os.remove(f)
def test_samplesheet_gets_written(self):
with patch.object(Bcl2FastqConfig, "write_samplesheet") as ws:
# If we provide a samplesheet to the config this should be written.
# In this case this write call is mocked away to make testing easier,
# but the write it self should be trivial.
config = Bcl2FastqConfig(
general_config=DUMMY_CONFIG,
bcl2fastq_version="1.8.4",
runfolder_input="test/runfolder",
output="test/output",
samplesheet=TestUtils.DUMMY_SAMPLESHEET_STRING)
ws.assert_called_once_with(TestUtils.DUMMY_SAMPLESHEET_STRING,
config.samplesheet_file)
def test_get_bases_mask_per_lane_from_samplesheet(self):
mock_read_index_lengths = {2: 9, 3: 9}
expected_bases_mask = {
1: "y*,i8n*,i8n*,y*",
2: "y*,i6n*,n*,y*",
3: "y*,i6n*,n*,y*",
4: "y*,i7n*,n*,y*",
5: "y*,i7n*,n*,y*",
6: "y*,i7n*,n*,y*",
7: "y*,i7n*,n*,y*",
8: "y*,i7n*,n*,y*",
}
samplesheet = Samplesheet(TestBcl2FastqConfig.samplesheet_file)
actual_bases_mask = Bcl2FastqConfig. \
get_bases_mask_per_lane_from_samplesheet(samplesheet, mock_read_index_lengths, False)
self.assertEqual(expected_bases_mask, actual_bases_mask)
def test_get_bases_mask_per_lane_from_samplesheet_single_read(self):
mock_read_index_lengths = {2: 9, 3: 9}
expected_bases_mask = {
1: "y*,i8n*,i8n*",
2: "y*,i6n*,n*",
3: "y*,i6n*,n*",
4: "y*,i7n*,n*",
5: "y*,i7n*,n*",
6: "y*,i7n*,n*",
7: "y*,i7n*,n*",
8: "y*,i7n*,n*",
}
samplesheet = Samplesheet(TestBcl2FastqConfig.samplesheet_file)
actual_bases_mask = Bcl2FastqConfig. \
get_bases_mask_per_lane_from_samplesheet(samplesheet, mock_read_index_lengths, True)
self.assertEqual(expected_bases_mask, actual_bases_mask)
def test_get_bases_mask_per_lane_from_samplesheet_invalid_length_combo(
self):
# These are to short compared to the length indicated in the samplesheet
mock_read_index_lengths = {2: 4, 3: 4}
samplesheet = Samplesheet(TestBcl2FastqConfig.samplesheet_file)
with self.assertRaises(ArteriaUsageException):
Bcl2FastqConfig. \
get_bases_mask_per_lane_from_samplesheet(samplesheet, mock_read_index_lengths, False)
def test_get_bases_mask_per_lane_from_samplesheet_no_tag(self):
# If we don't have tag for one lane in the samplesheet.
mock_read_index_lengths = {2: 6}
expected_bases_mask = {
1: "y*,n*,y*",
2: "y*,n*,y*",
3: "y*,i6,y*",
4: "y*,i6,y*",
5: "y*,i6,y*",
6: "y*,i6,y*",
7: "y*,n*,y*",
8: "y*,n*,y*",
}
samplesheet = Samplesheet(TestBcl2FastqConfig.samplesheet_with_no_tag)
actual_bases_mask = Bcl2FastqConfig. \
get_bases_mask_per_lane_from_samplesheet(samplesheet, mock_read_index_lengths, False)
self.assertEqual(expected_bases_mask, actual_bases_mask)
class TestBcl2FastqHandlers(AsyncHTTPTestCase):
_start_api_call = 0
def start_api_call_nbr(self):
TestBcl2FastqHandlers._start_api_call += 1
return TestBcl2FastqHandlers._start_api_call
API_BASE = "/api/1.0"
MOCK_BCL2FASTQ_DICT = {
1: "y*,8i,8i,y*",
2: "y*,6i,n*,y*",
3: "y*,6i,n*,y*",
4: "y*,7i,n*,y*",
5: "y*,7i,n*,y*",
6: "y*,7i,n*,y*",
7: "y*,7i,n*,y*",
8: "y*,7i,n*,y*",
}
dummy_config = DummyConfig()
DUMMY_RUNNER_CONF = DummyRunnerConfig(output='/foo/bar/runfolder',
general_config=dummy_config)
def get_app(self):
return Application(routes(config=self.dummy_config))
def test_versions(self):
response = self.fetch(self.API_BASE + "/versions")
self.assertEqual(response.code, 200)
self.assertEqual(sorted(json.loads(response.body)),
sorted(["2.15.2", "1.8.4"]))
def test_start_missing_runfolder_in_body(self):
response = self.fetch(self.API_BASE +
"/start/150415_D00457_0091_AC6281ANXX",
method="POST",
body="")
self.assertEqual(response.code, 500)
def test_start(self):
# Use mock to ensure that this will run without
# creating the runfolder.
with mock.patch.object(os.path, 'isdir', return_value=True), \
mock.patch.object(shutil, 'rmtree', return_value=None), \
mock.patch.object(Bcl2FastqConfig, 'get_bcl2fastq_version_from_run_parameters', return_value="2.15.2"), \
mock.patch.object(BCL2FastqRunnerFactory, "create_bcl2fastq_runner",
return_value=FakeRunner("2.15.2", self.DUMMY_RUNNER_CONF)), \
mock.patch.object(BCL2FastqRunner, 'symlink_output_to_unaligned', return_value=None):
body = {"runfolder_input": "/path/to/runfolder"}
response = self.fetch(self.API_BASE +
"/start/150415_D00457_0091_AC6281ANXX",
method="POST",
body=json_encode(body))
api_call_nbr = self.start_api_call_nbr()
self.assertEqual(response.code, 202)
self.assertEqual(json.loads(response.body)["job_id"], api_call_nbr)
expected_link = "http://localhost:{0}/api/1.0/status/{1}".format(
self.get_http_port(), api_call_nbr)
self.assertEqual(json.loads(response.body)["link"], expected_link)
self.assertEqual(
json.loads(response.body)["bcl2fastq_version"], "2.15.2")
self.assertEqual(json.loads(response.body)["state"], "started")
def test_start_with_empty_body(self):
# Use mock to ensure that this will run without
# creating the runfolder.
with mock.patch.object(os.path, 'isdir', return_value=True), \
mock.patch.object(shutil, 'rmtree', return_value=None), \
mock.patch.object(Bcl2FastqConfig, 'get_bcl2fastq_version_from_run_parameters', return_value="2.15.2"), \
mock.patch.object(BCL2FastqRunnerFactory, "create_bcl2fastq_runner",
return_value=FakeRunner("2.15.2", self.DUMMY_RUNNER_CONF)), \
mock.patch.object(BCL2FastqRunner, 'symlink_output_to_unaligned', return_value=None):
response = self.fetch(self.API_BASE +
"/start/150415_D00457_0091_AC6281ANXX",
method="POST",
body="")
api_call_nbr = self.start_api_call_nbr()
self.assertEqual(response.code, 202)
self.assertEqual(json.loads(response.body)["job_id"], api_call_nbr)
expected_link = "http://localhost:{0}/api/1.0/status/{1}".format(
self.get_http_port(), api_call_nbr)
self.assertEqual(json.loads(response.body)["link"], expected_link)
self.assertEqual(
json.loads(response.body)["bcl2fastq_version"], "2.15.2")
self.assertEqual(json.loads(response.body)["state"], "started")
def test_start_with_disallowed_output_specified(self):
# TODO Please note that this test is not very good, since the
# what we ideally want to test is the output specifed by the request,
# and that that gets rejected, however since the create_bcl2fastq_runner command
# is mocked away here and that is what returns the invalid output the tests is
# a bit misleading. In the future we probably want to refactor this.
# / JD 20170117
runner_conf_with_invalid_output = DummyRunnerConfig(
output='/not/foo/bar/runfolder', general_config=self.dummy_config)
with mock.patch.object(os.path, 'isdir', return_value=True), \
mock.patch.object(shutil, 'rmtree', return_value=None) as rmmock, \
mock.patch.object(Bcl2FastqConfig, 'get_bcl2fastq_version_from_run_parameters', return_value="2.15.2"), \
mock.patch.object(BCL2FastqRunnerFactory, "create_bcl2fastq_runner",
return_value=FakeRunner("2.15.2", runner_conf_with_invalid_output)), \
mock.patch.object(BCL2FastqRunner, 'symlink_output_to_unaligned', return_value=None):
# This output dir is not allowed by the config
body = {'output': '/not/foo/bar'}
response = self.fetch(self.API_BASE +
"/start/150415_D00457_0091_AC6281ANXX",
method="POST",
body=json_encode(body))
self.assertEqual(response.code, 500)
self.assertEqual(
response.reason,
"Invalid output directory /not/foo/bar/runfolder was specified."
" Allowed dirs were: ['/foo/bar']")
rmmock.assert_not_called()
def test_start_with_allowed_output_specified(self):
with mock.patch.object(os.path, 'isdir', return_value=True), \
mock.patch.object(shutil, 'rmtree', return_value=None) as rmmock, \
mock.patch.object(Bcl2FastqConfig, 'get_bcl2fastq_version_from_run_parameters', return_value="2.15.2"), \
mock.patch.object(BCL2FastqRunnerFactory, "create_bcl2fastq_runner",
return_value=FakeRunner("2.15.2", self.DUMMY_RUNNER_CONF)), \
mock.patch.object(BCL2FastqRunner, 'symlink_output_to_unaligned', return_value=None):
body = {'output': '/foo/bar'}
response = self.fetch(self.API_BASE +
"/start/150415_D00457_0091_AC6281ANXX",
method="POST",
body=json_encode(body))
# Just increment it here so it doesn't break the other tests
self.start_api_call_nbr()
self.assertEqual(response.code, 202)
rmmock.assert_called_with('/foo/bar/runfolder')
def test_start_providing_samplesheet(self):
# Use mock to ensure that this will run without
# creating the runfolder.
with mock.patch.object(os.path, 'isdir', return_value=True), \
mock.patch.object(shutil, 'rmtree', return_value=None), \
mock.patch.object(Bcl2FastqConfig, 'get_bcl2fastq_version_from_run_parameters', return_value="2.15.2"), \
mock.patch.object(BCL2FastqRunner, 'symlink_output_to_unaligned', return_value=None), \
mock.patch.object(Bcl2FastqConfig, "write_samplesheet") as ws , \
mock.patch.object(BCL2FastqRunnerFactory, "create_bcl2fastq_runner",
return_value=FakeRunner("2.15.2", self.DUMMY_RUNNER_CONF)):
body = {
"runfolder_input": "/path/to/runfolder",
"samplesheet": TestUtils.DUMMY_SAMPLESHEET_STRING
}
response = self.fetch(self.API_BASE +
"/start/150415_D00457_0091_AC6281ANXX",
method="POST",
body=json_encode(body))
api_call_nbr = self.start_api_call_nbr()
self.assertEqual(response.code, 202)
self.assertEqual(json.loads(response.body)["job_id"], api_call_nbr)
expected_link = "http://localhost:{0}/api/1.0/status/{1}".format(
self.get_http_port(), api_call_nbr)
self.assertEqual(json.loads(response.body)["link"], expected_link)
self.assertEqual(
json.loads(response.body)["bcl2fastq_version"], "2.15.2")
self.assertEqual(json.loads(response.body)["state"], "started")
ws.assert_called_once_with(
TestUtils.DUMMY_SAMPLESHEET_STRING,
"/data/biotank3/runfolders/150415_D00457_0091_AC6281ANXX/SampleSheet.csv"
)
def test_status_with_id(self):
#TODO Add real tests here!
response = self.fetch(self.API_BASE + "/status/1123456546",
method="GET")
self.assertEqual(response.code, 200)
def test_status_without_id(self):
#TODO Add real tests here!
response = self.fetch(self.API_BASE + "/status/", method="GET")
self.assertEqual(response.code, 200)
def test_all_stop_handler(self):
response = self.fetch(self.API_BASE + "/stop/all",
method="POST",
body="")
self.assertEqual(response.code, 200)
def test_stop_handler(self):
response = self.fetch(self.API_BASE + "/stop/3",
method="POST",
body="")
self.assertEqual(response.code, 200)
def test_exception_stop_handler(self):
response = self.fetch(self.API_BASE + "/stop/lll",
method="POST",
body="")
self.assertEqual(response.code, 500)
def test_get_logs(self):
with mock.patch.object(Bcl2FastqLogFileProvider,
"get_log_for_runfolder",
return_value="This is a string"):
response = self.fetch(self.API_BASE + "/logs/coolest_runfolder",
method="GET")
self.assertEqual(response.code, 200)
self.assertEqual(
json.loads(response.body)["log"], "This is a string")
def test_get_logs_trying_to_reach_other_files(self):
response = self.fetch(self.API_BASE + "/logs/../../../etc/shadow",
method="GET")
self.assertEqual(response.code, 404)