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)))