def test_sra_paired_export_run_set_xml(self):
sra.export(self._inv_obj,
self._tmp_dir,
sra_settings=self._sra_default_config)
with open(os.path.join(self._tmp_dir, 'run_set.xml'), 'rb') as out_fp:
actual_run_set_xml_obj = etree.fromstring(out_fp.read())
self.assertTrue(
utils.assert_xml_equal(self._expected_run_set_xml_obj,
actual_run_set_xml_obj))
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_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_sra_dump_run_set_xml_biis3(self):
with open(os.path.join(self._json_data_dir, 'BII-S-3',
'BII-S-3.json')) as json_fp:
json2sra.convert(json_fp, self._tmp_dir, validate_first=False)
# Now try load the SRA output in test and compare against the expected output in test data directory
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_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_sra_dump_sample_set_xml_biis7(self):
sra_settings = self._sra_default_config
with open(os.path.join(self._json_data_dir, 'BII-S-7',
'BII-S-7.json')) as json_fp:
json2sra.convert(json_fp,
self._tmp_dir,
sra_settings=sra_settings,
validate_first=False)
# Now try load the SRA output in test and compare against the expected output in test data directory
with open(os.path.join(self._tmp_dir, 'sample_set.xml'),
'rb') as ss_fp:
sample_set_xml = ss_fp.read()
actual_sample_set_xml_biis7 = etree.fromstring(sample_set_xml)
self.assertTrue(
utils.assert_xml_equal(self._expected_sample_set_xml_biis7,
actual_sample_set_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)
with open(os.path.join(self._tmp_dir, 'submission.xml'),
'rb') as sub_fp:
submission_xml = sub_fp.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_assert_xml_equal(self):
self.assertTrue(
utils.assert_xml_equal(etree.fromstring(self.x1),
etree.fromstring(self.x2)))
