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_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)