def test_logfile_nested_dirs(self):
with TemporaryDirectory() as temp_dir:
child = os.path.join(temp_dir, "child")
assert not os.path.exists(child)
logfile = os.path.join(child, "nested", "logfile")
with changed_logging(logfile=logfile):
logging.warning("during")
assert os.path.exists(logfile)
def test_debug_file(self):
with NamedTemporaryFile() as logfile:
with changed_logging(logfile=logfile.name, debug=True):
logging.debug("during")
logging.debug("after")
with open(logfile.name) as handle:
content = handle.read()
assert "during" in content
assert "after" not in content
def test_debug(self):
logging.debug("before")
with changed_logging(debug=True):
assert self.logger.getEffectiveLevel() == logging.DEBUG
logging.debug("during")
assert self.logger.getEffectiveLevel() == logging.WARNING
logging.debug("after")
for _, level, msg in self.caplog.record_tuples:
assert level == logging.DEBUG
assert "during" in msg
def test_verbose(self):
logging.info("before")
with changed_logging(verbose=True):
logging.debug("during")
logging.info("during")
assert self.logger.getEffectiveLevel() == logging.INFO
logging.info("after")
assert self.logger.getEffectiveLevel() == logging.WARNING
for _, level, msg in self.caplog.record_tuples:
assert level == logging.INFO
assert "during" in msg
def test_logfile_always_verbose(self):
with NamedTemporaryFile() as logfile:
with changed_logging(logfile=logfile.name):
logging.info("during")
logging.debug("debug")
logging.info("after")
with open(logfile.name) as handle:
content = handle.read()
assert "during" in content
assert "debug" not in content
assert "after" not in content
def test_default(self):
logging.warning("before")
with changed_logging():
logging.warning("during")
logging.info("during")
logging.debug("during")
assert self.logger.getEffectiveLevel() == logging.WARNING
logging.warning("after")
assert self.logger.getEffectiveLevel() == logging.WARNING
assert len(self.caplog.records) == 3
for _, level, _ in self.caplog.record_tuples:
assert level == logging.WARNING
def run_antismash(sequence_file: Optional[str], options: ConfigType) -> int:
""" The complete antismash pipeline. Reads in data, runs detection and
analysis modules over any records found, then outputs the results to
file.
Arguments:
sequence_file: the sequence file to read in records from, can be
None if reusing results
options: command line options
Returns:
0 if requested operations completed succesfully, otherwise 1
Exceptions may also be raised
"""
with logs.changed_logging(logfile=options.logfile, verbose=options.verbose,
debug=options.debug):
result = _run_antismash(sequence_file, options)
return result
