def test_isatab2sra_dump_run_set_xml_biis7(self):
isatab2sra.convert(self._biis7_dir,
self._tmp_dir,
validate_first=False)
with open(os.path.join(self._tmp_dir, 'run_set.xml'), 'rb') as rs_fp:
run_set_xml = rs_fp.read()
actual_run_set_xml_biis7 = etree.fromstring(run_set_xml)
self.assertTrue(
utils.assert_xml_equal(self._expected_run_set_xml_biis7,
actual_run_set_xml_biis7))
def test_isatab2sra_dump_sample_set_xml_biis3(self):
isatab2sra.convert(self._biis3_dir,
self._tmp_dir,
validate_first=False)
sample_set_xml = open(os.path.join(self._tmp_dir, 'sample_set.xml'),
'rb').read()
actual_sample_set_xml_biis3 = etree.fromstring(sample_set_xml)
self.assertTrue(
utils.assert_xml_equal(self._expected_sample_set_xml_biis3,
actual_sample_set_xml_biis3))
def test_isatab2sra_dump_experiment_set_xml_biis7(self):
isatab2sra.convert(self._biis7_dir,
self._tmp_dir,
validate_first=False)
experiment_set_xml = open(
os.path.join(self._tmp_dir, 'experiment_set.xml'), 'rb').read()
actual_experiment_set_xml_biis7 = etree.fromstring(experiment_set_xml)
self.assertTrue(
utils.assert_xml_equal(self._expected_experiment_set_xml_biis7,
actual_experiment_set_xml_biis7))
def test_isatab2sra_dump_submission_xml_biis3(self):
isatab2sra.convert(self._biis3_dir,
self._tmp_dir,
validate_first=False)
with open(os.path.join(self._tmp_dir, 'submission.xml'),
'rb') as sub_fp:
submission_xml = sub_fp.read()
actual_submission_xml_biis3 = etree.fromstring(submission_xml)
self.assertTrue(
utils.assert_xml_equal(self._expected_submission_xml_biis3,
actual_submission_xml_biis3))
def test_isatab2sra_dump_project_set_xml_biis3(self):
isatab2sra.convert(self._biis3_dir,
self._tmp_dir,
validate_first=False)
with open(os.path.join(self._tmp_dir, 'project_set.xml'),
'rb') as ps_fp:
project_set_xml = ps_fp.read()
actual_project_set_xml_biis3 = etree.fromstring(project_set_xml)
self.assertTrue(
utils.assert_xml_equal(self._expected_project_set_xml_biis3,
actual_project_set_xml_biis3))
def test_isatab2sra_dump_submission_xml_biis7(self):
sra_settings = {
"sra_broker": "",
"sra_center": "OXFORD",
"sra_project": "OXFORD",
"sra_lab": "Oxford e-Research Centre",
"sra_broker_inform_on_status": "*****@*****.**",
"sra_broker_inform_on_error": "*****@*****.**",
"sra_broker_contact_name": "PRS"
}
isatab2sra.convert(self._biis3_dir, self._tmp_dir, sra_settings=sra_settings, validate_first=False)
submission_xml = open(os.path.join(self._tmp_dir, 'submission.xml'), 'rb').read()
actual_submission_xml_biis7 = etree.fromstring(submission_xml)
self.assertTrue(utils.assert_xml_equal(self._expected_submission_xml_biis7, actual_submission_xml_biis7))
def test_isatab2sra_dump_submission_xml_biis7(self):
sra_settings = {
"sra_broker": "",
"sra_center": "OXFORD",
"sra_project": "OXFORD",
"sra_lab": "Oxford e-Research Centre",
"sra_broker_inform_on_status": "*****@*****.**",
"sra_broker_inform_on_error": "*****@*****.**",
"sra_broker_contact_name": "PRS"
}
isatab2sra.convert(self._biis3_dir, self._tmp_dir, sra_settings=sra_settings, validate_first=False)
submission_xml = open(os.path.join(self._tmp_dir, 'submission.xml'), 'rb').read()
actual_submission_xml_biis7 = etree.fromstring(submission_xml)
self.assertTrue(utils.assert_xml_equal(self._expected_submission_xml_biis7, actual_submission_xml_biis7))
def test_isatab2sra_zip_return(self):
b = isatab2sra.convert(self._biis3_dir,
self._tmp_dir,
validate_first=False)
self.assertIsInstance(b, BytesIO)
with ZipFile(b) as zip_file:
self.assertEqual(len(zip_file.namelist()), 5)
def test_isatab2sra_dump_project_set_xml_biis7(self):
isatab2sra.convert(self._biis7_dir, self._tmp_dir, validate_first=False)
project_set_xml = open(os.path.join(self._tmp_dir, 'project_set.xml'), 'rb').read()
actual_project_set_xml_biis7 = etree.fromstring(project_set_xml)
self.assertTrue(utils.assert_xml_equal(self._expected_project_set_xml_biis7, actual_project_set_xml_biis7))
def test_isatab2sra_dump_run_set_xml_biis3(self):
isatab2sra.convert(self._biis3_dir, self._tmp_dir, validate_first=False)
run_set_xml = open(os.path.join(self._tmp_dir, 'run_set.xml'), 'rb').read()
actual_run_set_xml_biis3 = etree.fromstring(run_set_xml)
self.assertTrue(utils.assert_xml_equal(self._expected_run_set_xml_biis3, actual_run_set_xml_biis3))
def test_isatab2sra_zip_return(self):
b = isatab2sra.convert(self._biis3_dir, self._tmp_dir, validate_first=False)
self.assertIsInstance(b, BytesIO)
with ZipFile(b) as zip_file:
self.assertEquals(len(zip_file.namelist()), 5)
def test_isatab2sra_zip_return(self):
b = isatab2sra.convert(self._biis3_dir, self._tmp_dir, validate_first=False) # TODO: To use new parser, need dervives_from completed
self.assertIsInstance(b, BytesIO)
with ZipFile(b) as zip_file:
self.assertEquals(len(zip_file.namelist()), 5)