def test_warning_setsWarningOccurred(self):
args = Namespace(log_file="test.log", verbose=True)
console_stream = StringIO()
logger = utils.Logger(args, console_stream)
logger._file_logger = MockBaseLogger()
self.assertEqual(False, logger.warning_occurred)
logger.warning("oops")
self.assertEqual(True, logger.warning_occurred)
def test_consoleFormat(self):
args = Namespace(log_file="test.log", verbose=None)
console_stream = StringIO()
logger = utils.Logger(args, console_stream)
logger._file_logger = MockBaseLogger()
logger.info("info [{}]", "i")
console_lines = console_stream.getvalue().strip().split("\n")
self.assertEqual(1, len(console_lines))
fields = console_lines[0].split("|")
self.assertEqual(3, len(fields))
self.assertEqual(fields[1], "INFO")
self.assertEqual(fields[2], "info [i]")
def main(command_line_args=None):
'''Connor entry point. See help for more info'''
log = None
if not command_line_args:
command_line_args = sys.argv
try:
start_time = time.time()
args = _parse_command_line_args(command_line_args)
log = utils.Logger(args)
command_validator.preflight(args, log)
log.info('connor begins (v{})', __version__)
log.info('logging to [{}]', args.log_file)
utils.log_environment_info(log, args)
bam_tags = samtools._build_bam_tags()
base_annotated_writer = samtools.build_writer(args.input_bam,
args.annotated_output_bam,
bam_tags,
args)
annotated_writer = LoggingWriter(base_annotated_writer, log)
consensus_writer = samtools.build_writer(args.input_bam,
args.output_bam,
bam_tags,
args)
_dedup_alignments(args, consensus_writer, annotated_writer, log)
annotated_writer.close(log)
consensus_writer.close(log)
warning = ' **See warnings above**' if log.warning_occurred else ''
elapsed_time = int(time.time() - start_time)
log.info("connor complete ({} seconds, {}mb peak memory).{}",
elapsed_time,
utils.peak_memory(),
warning)
except utils.UsageError as usage_error:
message = "connor usage problem: {}".format(str(usage_error))
print(message, file=sys.stderr)
print("See 'connor --help'.", file=sys.stderr)
sys.exit(1)
except Exception: #pylint: disable=broad-except
if log:
show = log.error
else:
show = partial(print, file=sys.stderr)
show("An unexpected error occurred")
show(traceback.format_exc())
exit(1)
def test_notVerbose(self):
args = Namespace(log_file="test.log", verbose=None)
console_stream = StringIO()
file_logger = MockBaseLogger()
logger = utils.Logger(args, console_stream)
logger._file_logger = file_logger
logger.debug("debug [{}]", "d")
logger.info("info [{}]", "i")
logger.warning("warning [{}]", "w")
logger.error("error [{}]", "e")
console_lines = console_stream.getvalue().strip().split("\n")
self.assertEqual(3, len(console_lines))
console_lines[0].endswith("info [i]")
console_lines[1].endswith("warning [w]")
console_lines[2].endswith("error [e]")
self.assertEqual(4, len(file_logger.lines))
file_logger.lines[0].endswith("debug [d]")
file_logger.lines[1].endswith("info [i]")
file_logger.lines[2].endswith("warning [w]")
file_logger.lines[3].endswith("error [e]")