def runtest(cfg: Config, args: argparse.Namespace,
df: Optional[Datafile]) -> bool:
logger = logging.getLogger()
# Extract parameters from configuration files
try:
adc = ADS1115(address=cfg.get_int('Adc', 'Addr'),
busnum=cfg.get_int('Adc', 'Bus'))
sens = AnalogFlowMeter(adc, cfg.get_int('AnalogFlowSensor', 'Chan'),
cfg.get_expr('AnalogFlowSensor', 'Gain'),
cfg.get_array('AnalogFlowSensor', 'Coeff'))
except BadEntry:
logger.exception("Configuration error")
return False
interval = 1. / args.rate
print("Enter ctrl-c to exit ...", file=sys.stderr)
sens.reset()
try:
for tick in ticker(interval):
vol, secs = sens.amount()
rec = OrderedDict(elapsed=round(secs, 3), vol=round(vol, 3))
writerec(rec)
if df:
df.add_record("flow", rec, ts=tick)
except KeyboardInterrupt:
print("done", file=sys.stderr)
return True
def quick_validate(cfg: Config):
"""
Verify that all required configuration entries are present, raises
a config.BadEntry exception if any are missing.
"""
for k, vals in required.items():
for val in vals:
cfg.get_string(k, val)
def validate(cfg: Config) -> List[str]:
"""
Verify that all required configuration entries are present, returns
a list of all missing entries.
"""
missing = []
for k, vals in required.items():
for val in vals:
try:
cfg.get_string(k, val)
except BadEntry:
missing.append("/".join([k, val]))
return missing
class ValidationTest(unittest.TestCase):
def setUp(self):
path = os.path.join(os.path.dirname(__file__), "example.cfg")
self.cfg = Config(path)
self.badcfg = Config(StringIO(INPUT))
def test_validate(self):
missing = self.cfg.validate()
self.assertEqual(len(missing), 0)
def test_validate_fail(self):
missing = self.badcfg.validate()
self.assertGreater(len(missing), 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)
# 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 runedna(cfg: Config,
deployment: Deployment,
df: Datafile,
prfilt: Callable[[float], float]) -> bool:
logger = logging.getLogger()
logger.info("Starting deployment: %s", deployment.id)
if cfg.has_section("Metadata"):
meta = []
for key in cfg.options("Metadata"):
meta.append(key)
meta.append(cfg.get_string("Metadata", key))
df.add_record("metadata", meta)
# Extract parameters from configuration files
try:
pr = dict()
adc = ADS1115(address=cfg.get_int('Adc', 'Addr'),
busnum=cfg.get_int('Adc', 'Bus'))
pr["Filter"] = PrSensor(adc,
cfg.get_int('Pressure.Filter', 'Chan'),
cfg.get_expr('Pressure.Filter', 'Gain'),
coeff=cfg.get_array('Pressure.Filter', 'Coeff'))
pr["Env"] = PrSensor(adc,
cfg.get_int('Pressure.Env', 'Chan'),
cfg.get_expr('Pressure.Env', 'Gain'),
coeff=cfg.get_array('Pressure.Env', 'Coeff'))
# Discard the first sample
psi_to_dbar(pr["Env"].read())
prmax = cfg.get_float('Pressure.Filter', 'Max')
def checkpr() -> Tuple[float, bool]:
psi = pr["Filter"].read()
return psi, psi < prmax
def checkdepth(limits: Tuple[float, float]) -> Tuple[float, bool]:
dbar = psi_to_dbar(pr["Env"].read())
return prfilt(dbar), limits[0] <= dbar <= limits[1]
pumps = dict()
for key in ("Sample", "Ethanol"):
pumps[key] = Pump(cfg.get_int('Motor.'+key, 'Enable'))
valves = dict()
for key in ("1", "2", "3", "Ethanol"):
vkey = "Valve." + key
valves[key] = Valve(cfg.get_int(vkey, 'Enable'),
cfg.get_int(vkey, 'IN1'),
cfg.get_int(vkey, 'IN2'),
lopen=cfg.get_string(vkey, 'open'),
lclose=cfg.get_string(vkey, 'close'))
fm = AnalogFlowMeter(adc,
cfg.get_int('AnalogFlowSensor', 'Chan'),
cfg.get_expr('AnalogFlowSensor', 'Gain'),
cfg.get_array('AnalogFlowSensor', 'Coeff'))
sample_rate = cfg.get_float('FlowSensor', 'Rate')
ledctl = LedCtl(obj=LED(cfg.get_int("LED", "GPIO")),
fast=cfg.get_float("LED", "fast"),
slow=cfg.get_float("LED", "slow"),
fade=cfg.get_float("LED", "fade"))
limits = dict()
for key in ("Sample", "Ethanol"):
limits[key] = FlowLimits(amount=cfg.get_float('Collect.'+key, 'Amount'),
time=cfg.get_float('Collect.'+key, 'Time'))
deployment.seek_err = cfg.get_float('Deployment', 'SeekErr')
deployment.depth_err = cfg.get_float('Deployment', 'DepthErr')
deployment.pr_rate = cfg.get_float('Deployment', 'PrRate')
deployment.seek_time = cfg.get_int('Deployment', 'SeekTime')
deployment.downcast = cfg.get_bool('Deployment', 'Downcast')
# Each entry in depths is a tuple containing the depth and
# the sample index.
depths = []
for i, key in enumerate(['Sample.1', 'Sample.2', 'Sample.3']):
depths.append((cfg.get_float(key, 'Depth'), i+1))
except BadEntry:
logger.exception("Configuration error")
return False
try:
batteries = [Battery(SMBus(0)), Battery(SMBus(1))]
except Exception:
logger.exception("Battery monitoring disabled")
batteries = []
# Samples are collected in depth order, not index order.
depths.sort(key=lambda e: e[0], reverse=not deployment.downcast)
for target, index in depths:
logger.info("Seeking depth for sample %d; %.2f +/- %.2f",
index, target, deployment.seek_err)
drange = (target-deployment.seek_err, target+deployment.seek_err)
with blinker(ledctl.obj, ledctl.slow):
depth, status = seekdepth(df,
partial(checkdepth, drange),
deployment.pr_rate,
deployment.seek_time)
if not status:
logger.critical("Depth seek time limit expired. Aborting.")
return False
logger.info("Collecting sample %d", index)
drange = (depth-deployment.depth_err, depth+deployment.depth_err)
status = collect(df, index,
(pumps["Sample"], pumps["Ethanol"]),
valves,
fm, sample_rate,
(limits["Sample"], limits["Ethanol"]),
checkpr,
partial(checkdepth, drange), batteries)
return True
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))
class ConfigTestCase(unittest.TestCase):
def setUp(self):
self.cfg = Config(StringIO(INPUT))
self.cfg.load(StringIO(OVERRIDE))
def test_get_int(self):
x = self.cfg.get_int('Valve.1', 'Enable')
self.assertEqual(x, 27)
def test_get_int_hex(self):
x = self.cfg.get_int('Adc', 'Addr')
self.assertEqual(x, 0x48)
def test_get_str(self):
s = self.cfg.get_string('System', 'LogDir')
self.assertEqual(s, "/home/pi/eDNA/logs")
def test_get_float(self):
x = self.cfg.get_float('Foo', 'Bar')
self.assertEqual(x, 2.5)
def test_get_array(self):
x = self.cfg.get_array('Foo', 'Array')
self.assertEqual(x, [5., 6., 7., 8.])
def test_override(self):
x = self.cfg.get_int('Foo', 'Baz')
self.assertEqual(x, 43)
def test_expr(self):
x = self.cfg.get_expr('Adc', 'Gain')
self.assertEqual(x, 2 / 3)
def test_bad_key(self):
self.assertRaises(BadEntry, self.cfg.get_int, 'Valve.5', 'Enable')
def test_get_bool(self):
x = self.cfg.get_bool('Deployment', 'Downcast')
self.assertEqual(x, True)
def test_bool_default(self):
x = self.cfg.get_bool('Foo', 'NotFound')
self.assertEqual(x, False)
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()
def runtest(cfg: Config, args: argparse.Namespace,
df: Optional[Datafile]) -> bool:
logger = logging.getLogger()
# Extract parameters from configuration files
try:
sens = dict()
adc = ADS1115(address=cfg.get_int('Adc', 'Addr'),
busnum=cfg.get_int('Adc', 'Bus'))
sens["Filter"] = PrSensor(adc, cfg.get_int('Pressure.Filter', 'Chan'),
cfg.get_expr('Pressure.Filter', 'Gain'))
prmax = cfg.get_float('Pressure.Filter', 'Max')
def checkpr() -> Tuple[float, bool]:
psi = sens["Filter"].read()
return psi, psi < prmax
pumps = dict()
for key in ("Sample", "Ethanol"):
pumps[key.lower()] = Pump(cfg.get_int('Motor.' + key, 'Enable'))
valves = dict()
for key in ("1", "2", "3", "Ethanol"):
vkey = "Valve." + key
valves[key.lower()] = Valve(cfg.get_int(vkey, 'Enable'),
cfg.get_int(vkey, 'IN1'),
cfg.get_int(vkey, 'IN2'),
lopen=cfg.get_string(vkey, 'open'),
lclose=cfg.get_string(vkey, 'close'))
fm = AnalogFlowMeter(adc, cfg.get_int('AnalogFlowSensor', 'Chan'),
cfg.get_expr('AnalogFlowSensor', 'Gain'),
cfg.get_array('AnalogFlowSensor', 'Coeff'))
except BadEntry:
logger.exception("Configuration error")
return False
if args.pump not in pumps:
logger.critical("Invalid pump name: '%s'", args.pump)
return False
if args.valve not in valves:
logger.critical("Invalid valve: '%s'", args.valve)
return False
interval = 1. / args.rate
print("Enter ctrl-c to exit ...", file=sys.stderr)
try:
fm.reset()
with valves[args.valve]:
with pumps[args.pump]:
for tick in ticker(interval):
amount, secs = fm.amount()
pr, pr_ok = checkpr()
rec = OrderedDict(elapsed=round(secs, 3),
vol=round(amount, 3),
pr=round(pr, 3))
writerec(rec)
if df:
df.add_record("flow", rec, ts=tick)
except KeyboardInterrupt:
print("done", file=sys.stderr)
return True