def convert(self, filename): ok = False try: (event, xml) = scorer_to_usebio.convert(filename) self.save(event, xml) ok = True except IOError as err: logging.error("IO error: %s", err) except SyntaxError as err: logging.info( "The selected file '%s' does not look like a valid Scorer results file", filename) logging.error("Error details: %s", err) except scorer_to_usebio.InvalidResultsException as err: logging.error("Conversion error: %s", err) logging.info( "Please raise a support ticket, including the results file you were trying to convert" ) except scorer_to_usebio.InvalidEventType as err: logging.error("Could not convert results: %s", err) logging.info( "Only match point scored events are supported at this time") if ok: self.deleteButton.setEnabled(True) self.statusBar().showMessage( ScorerConverter.status_text['converted_ok']) else: self.deleteButton.setEnabled(False) self.statusBar().showMessage( ScorerConverter.status_text['converted_error'])
def test(self): examples = [] for root, dirs, files in os.walk(EXAMPLES_DIR): for file in files: path = os.path.join(root, file) if os.path.isfile(path) and path.endswith('.xml'): examples.append(path) assert len(examples) > 0 for path in examples: converted = scorer_to_usebio.convert(path, False)[1] expected = ET.parse(os.path.join(CONVERTED_DIR, os.path.basename(path))) converted_text = ET.tostring(converted.getroot()) expected_text = ET.tostring(expected.getroot()) fail_msg = "conversion mismatch for example file {}".format(os.path.normpath(path)) self.assertEqual(converted_text, expected_text, msg=fail_msg)
def test(self): examples = [] for root, dirs, files in os.walk(EXAMPLES_DIR): for file in files: path = os.path.join(root, file) if os.path.isfile(path) and path.endswith('.xml'): examples.append(path) assert len(examples) > 0 for path in examples: converted = scorer_to_usebio.convert(path, False)[1] expected = ET.parse( os.path.join(CONVERTED_DIR, os.path.basename(path))) converted_text = ET.tostring(converted.getroot()) expected_text = ET.tostring(expected.getroot()) fail_msg = "conversion mismatch for example file {}".format( os.path.normpath(path)) self.assertEqual(converted_text, expected_text, msg=fail_msg)
def convert(self, filename): ok = False try: (event, xml) = scorer_to_usebio.convert(filename) self.save(event, xml) ok = True except IOError as err: logging.error("IO error: %s", err) except SyntaxError as err: logging.info("The selected file '%s' does not look like a valid Scorer results file", filename) logging.error("Error details: %s", err) except scorer_to_usebio.InvalidResultsException as err: logging.error("Conversion error: %s", err) logging.info("Please raise a support ticket, including the results file you were trying to convert") except scorer_to_usebio.InvalidEventType as err: logging.error("Could not convert results: %s", err) logging.info("Only match point scored events are supported at this time") if ok: self.deleteButton.setEnabled(True) self.statusBar().showMessage(ScorerConverter.status_text['converted_ok']) else: self.deleteButton.setEnabled(False) self.statusBar().showMessage(ScorerConverter.status_text['converted_error'])