def main() -> int:
args = parse_cmdline()
try:
cfg = Config(args.syscfg)
except Exception as e:
print("Error loading system config file; " + str(e), file=sys.stderr)
return 1
logging.basicConfig(format='%(asctime)s %(levelname)s %(message)s',
level=logging.INFO,
datefmt='%Y-%m-%d %H:%M:%S',
stream=sys.stderr)
# eDNA uses the Broadcom SOC pin numbering scheme
GPIO.setmode(GPIO.BCM)
# If we don't suppress warnings, as message will be printed to stderr
# everytime GPIO.setup is called on a pin that isn't in the default
# state (input).
GPIO.setwarnings(False)
status = False
try:
if args.out:
status = runtest(cfg, args, Datafile(args.out))
else:
status = runtest(cfg, args, None)
except Exception as e:
logging.exception("Error running the pump test")
finally:
if args.clean:
GPIO.cleanup()
return 0 if status else 1
def main():
parser = argparse.ArgumentParser(
description="Validate an eDNA deployment configuration")
parser.add_argument("cfg",
metavar="FILE",
nargs="?",
default="",
help="deployment configuration file")
parser.add_argument(
"--sys",
metavar="FILE",
default=os.path.expanduser("~/.config/edna/system.cfg"),
help="location of the system confguration file")
args = parser.parse_args()
try:
cfg = Config(args.sys)
except Exception as e:
print("Error loading system config file; " + str(e), file=sys.stderr)
return 1
if args.cfg:
try:
cfg.load(args.cfg)
except Exception as e:
print("Error loading deployment config file; " + str(e),
file=sys.stderr)
return 1
try:
missing = validate(cfg)
if missing:
print("Missing entries: {}".format(";".join(missing)))
return 1
except Exception as e:
print("Validation failed: {}".format(str(e)), file=sys.stderr)
return 1
return 0
def main() -> int:
args = parse_cmdline()
try:
cfg = Config(args.syscfg)
except Exception as e:
print("Error loading system config file; " + str(e), file=sys.stderr)
return 1
logging.basicConfig(format='%(asctime)s %(levelname)s %(message)s',
level=logging.INFO,
datefmt='%Y-%m-%d %H:%M:%S',
stream=sys.stderr)
status = False
try:
if args.out:
status = runtest(cfg, args, Datafile(args.out))
else:
status = runtest(cfg, args, None)
except Exception:
logging.exception("Error running the sensor test")
return 0 if status else 1
def main() -> int:
args = parse_cmdline()
try:
cfg = Config(args.syscfg)
except Exception as e:
print("Error loading system config file; " + str(e), file=sys.stderr)
return 1
try:
cfg.load(args.cfg)
except Exception as e:
print("Error loading deployment config file; " + str(e), file=sys.stderr)
return 1
# Validate configuration files
missing = cfg.validate()
if missing:
print("Missing configuration entries: {}".format(";".join(missing)))
return 1
# Generate deployment ID and directory name
id = datetime.datetime.now(tz=datetime.timezone.utc).strftime("%Y%m%dT%H%M%S")
dir = os.path.join(args.datadir, "edna_" + id)
deployment = Deployment(id=id, dir=dir)
# Create deployment directory
os.makedirs(deployment.dir, exist_ok=True)
# Initialize logging
init_logging(deployment.dir, deployment.id, debug=args.debug)
# Save configuration to deployment directory
with open(os.path.join(deployment.dir, "deploy.cfg"), "w") as fp:
cfg.write(fp)
# Save deployment ID if specified
if args.id != "":
with open(os.path.join(deployment.dir, "id"), "w") as fp:
print(args.id, file=fp)
signal.signal(signal.SIGINT, abort)
signal.signal(signal.SIGTERM, abort)
logger = logging.getLogger()
# eDNA uses the Broadcom SOC pin numbering scheme
GPIO.setmode(GPIO.BCM)
# If we don't suppress warnings, a message will be printed to stderr
# everytime GPIO.setup is called on a pin that isn't in the default
# state (input).
GPIO.setwarnings(False)
prfilt: Callable[[float], float]
if args.alpha > 0:
prfilt = EMA(args.alpha)
else:
prfilt = lambda x: x
status = False
try:
name = "edna_" + deployment.id + ".ndjson"
with open(os.path.join(deployment.dir, name), "w") as fp:
status = runedna(cfg, deployment, Datafile(fp), prfilt)
except Exception:
logger.exception("Deployment aborted with an exception")
os.makedirs(args.outbox, exist_ok=True)
# Archive the deployment directory to the OUTBOX
arpath = os.path.join(args.outbox, "edna_" + deployment.id + ".tar.gz")
logger.info("Archiving deployment directory to %s", arpath)
with tarfile.open(arpath, "w:gz") as tar:
head, tail = os.path.split(deployment.dir)
os.chdir(head)
tar.add(tail)
if args.clean:
GPIO.cleanup()
return 0 if status else 1
def setUp(self):
path = os.path.join(os.path.dirname(__file__), "example.cfg")
self.cfg = Config(path)
self.badcfg = Config(StringIO(INPUT))
def setUp(self):
self.cfg = Config(StringIO(INPUT))
self.cfg.load(StringIO(OVERRIDE))
def main():
parser = argparse.ArgumentParser(description="Prime an eDNA flow path")
parser.add_argument("cfg",
metavar="FILE",
help="system configuration file")
parser.add_argument("valve",
metavar="N",
type=int,
help="valve# to prime, 1-3")
parser.add_argument("--time",
metavar="SECS",
type=float,
default=30,
help="runtime in seconds")
parser.add_argument("--prmax",
metavar="PSI",
type=float,
default=12,
help="maximum filter pressure in psi")
args = parser.parse_args()
try:
cfg = Config(args.cfg)
except Exception as e:
print("Error loading config file; " + str(e), file=sys.stderr)
sys.exit(1)
if args.valve < 1 or args.valve > 3:
print("Valve number must be between 1 and 3", file=sys.stderr)
sys.exit(1)
logging.basicConfig(format='%(asctime)s %(levelname)s %(message)s',
level=logging.INFO,
datefmt='%Y-%m-%d %H:%M:%S',
stream=sys.stderr)
# eDNA uses the Broadcom SOC pin numbering scheme
GPIO.setmode(GPIO.BCM)
try:
adc = ADS1115(address=0x48, busnum=cfg.get_int('Adc', 'Bus'))
pr_chan = cfg.get_int('Pressure.Filter', 'Chan')
pr_gain = cfg.get_float('Pressure.Filter', 'Gain')
motor = cfg.get_int('Motor.Sample', 'Enable')
GPIO.setup(motor, GPIO.OUT)
# Config file key for valve
vkey = "Valve." + str(args.valve)
sample_valve = Valve(cfg.get_int(vkey, 'Enable'),
cfg.get_int(vkey, 'Power'),
cfg.get_int(vkey, 'Gnd'))
eth_valve = Valve(cfg.get_int('Valve.Ethanol', 'Enable'),
cfg.get_int('Valve.Ethanol', 'Power'),
cfg.get_int('Valve.Ethanol', 'Gnd'))
except BadEntry as e:
print(str(e), file=sys.stderr)
GPIO.cleanup()
sys.exit(2)
try:
prime_cycle(sample_valve, eth_valve, motor,
partial(checkpr, adc, pr_chan, pr_gain, args.prmax),
args.time)
finally:
GPIO.cleanup()