def setup(self):
print "prepering to transfer data from local database to AgBase ..."
self.agbase = AgBase()
self.agbase.set_logging_on(True)
self.user = self.agbase.connect(self.testUser, self.testPwd , self.testServer)
if self.user is None:
print("login failed")
def __init__(self):
# fill out dbname host etc in psycopg2.connect
self.conn = psycopg2.connect("dbname=<database_name> host=<database_host> user=<database_user> password=<database_password>")
self.cur = self.conn.cursor()
self.agbase = AgBase()
self.algorithm = AlgorithmAPI(self.agbase)
self.animal = AnimalAPI(self.agbase)
self.farm = FarmAPI(self.agbase)
self.herd = HerdAPI(self.agbase)
self.measurement = MeasurementAPI(self.agbase)
self.measurement_category = MeasurementCategoryAPI(self.agbase)
self.agbase.set_logging_on(True)
self.user = self.agbase.connect(self.user, self.pwd, self.server)
self.pp = pprint.PrettyPrinter(indent=4)
if self.user is None:
print("login failed")
farms = self.farm.get_farms(self.user)
for farm in farms:
if farm.name == "Demo Farm":
self.frm = farm
cats = self.measurement_category.get_measurement_categories()
for cat in cats:
if cat.name == "Weight":
self.cat = cat
algs = self.algorithm.get_algorithms(self.cat)
for alg in algs:
if alg.name == "bayesy_andy_constrained_prior":
self.alg = alg
def setUp(self):
self.agbase = AgBase()
self.agbase.set_logging_on(True)
self.user = self.agbase.connect(self.testUser, self.testPwd, self.serverIp)
if self.user is None:
self.fail()
self.farm = self.agbase.create_farm("Python Test Farm")
def __init__(self):
parser = argparse.ArgumentParser()
parser.add_argument('--user', required=True, help="AgBase Username")
parser.add_argument('--password', required=True, help="AgBase Password")
#parser.add_argument('--firstDate', required=True, help="First date of the measurements you wish to upload (YYYY/MM/DD)")
#parser.add_argument('--lastDate', required=True, help="Last date of the measurements you wish to upload (YYYY/MM/DD)")
parser.add_argument('--server', required=True, help="AgBase Server")
args = parser.parse_args()
self.agbase = AgBase()
self.algorithm = AlgorithmAPI(self.agbase)
self.animal = AnimalAPI(self.agbase)
self.farm = FarmAPI(self.agbase)
self.herd = HerdAPI(self.agbase)
self.measurement = MeasurementAPI(self.agbase)
self.measurement_category = MeasurementCategoryAPI(self.agbase)
self.agbase.set_logging_on(True)
self.user = self.agbase.connect(args.user, args.password , args.server)
def setUp(self):
print('TestAgBase.setUp')
super(self.__class__, self).setUp()
self.pp = pprint.PrettyPrinter(indent=4)
self.agbase = AgBase()
self.algorithm = AlgorithmAPI(self.agbase)
self.animal = AnimalAPI(self.agbase)
self.farm = FarmAPI(self.agbase)
self.herd = HerdAPI(self.agbase)
self.measurement = MeasurementAPI(self.agbase)
self.measurement_category = MeasurementCategoryAPI(self.agbase)
self.agbase.set_logging_on(True)
self.user = self.agbase.connect(self.testUser, self.testPwd, self.serverIp)
if self.user is None:
self.fail()
print('connected to mooogle with user: {} with id: {}'.format(self.user.email, self.user.id))
def __init__(self):
parser = argparse.ArgumentParser()
parser.add_argument('--user', required=True, help="AgBase Username")
parser.add_argument('--passwd', required=True, help="AgBase Password")
parser.add_argument('--algorithm', required=True, help="The name of the data algorithm you wish "+
"to transfer from local moogle to agbase.(Must be an algorithm name in the moogle database)" +
"and must also be added to the website.")
parser.add_argument('--server', default="<website_address>", help="AgBase Server")
args = parser.parse_args()
self.conn = psycopg2.connect("dbname=<database_name> host=<database_address> user=<database_user> password=<database_password>")
self.cur = self.conn.cursor()
self.agbase = AgBase()
self.algorithm = AlgorithmAPI(self.agbase)
self.animal = AnimalAPI(self.agbase)
self.farm = FarmAPI(self.agbase)
self.herd = HerdAPI(self.agbase)
self.measurement = MeasurementAPI(self.agbase)
self.measurement_category = MeasurementCategoryAPI(self.agbase)
self.agbase.set_logging_on(True)
self.user = self.agbase.connect(args.user, args.passwd , args.server)
self.pp = piprint.PrettyPrinter(indent=4)
if self.user is None:
print("login failed")
farms = self.farm.get_farms(self.user)
for farm in farms:
if farm.name == "Demo Farm":
self.frm = farm
cats = self.measurement_category.get_measurement_categories()
for cat in cats:
if cat.name == "Weight":
self.cat = cat
algs = self.algorithm.get_algorithms(self.cat)
for alg in algs:
if alg.name == args.algorithm: # need to set meathod_id to local moogles method_id in get_day
self.alg = alg
self.moogle_alg_id = self.get_algorithm_id()
def __init__(self):
parser = argparse.ArgumentParser()
parser.add_argument('--user', required=True, help="AgBase Username")
parser.add_argument('--passwd', required=True, help="AgBase Password")
parser.add_argument('--date', required=True, help="Date of the measurements you wish to upload (YYYY:MM:DD)")
parser.add_argument('--server', default="<website_address>", help="AgBase Server")
args = parser.parse_args()
self.conn = psycopg2.connect("dbname=<database_name> host=<database_address> user=<database_user> password=<database_password>")
self.cur = self.conn.cursor()
self.agbase = AgBase()
self.algorithm = AlgorithmAPI(self.agbase)
self.animal = AnimalAPI(self.agbase)
self.farm = FarmAPI(self.agbase)
self.herd = HerdAPI(self.agbase)
self.measurement = MeasurementAPI(self.agbase)
self.measurement_category = MeasurementCategoryAPI(self.agbase)
self.agbase.set_logging_on(True)
self.user = self.agbase.connect(args.user, args.passwd , args.server)
self.pp = pprint.PrettyPrinter(indent=4)
datearr = args.date.split(':',2)
print datearr[0], datearr[1], datearr[2]
self.date = datetime.date(int(datearr[0]), int(datearr[1]), int(datearr[2]))
if self.user is None:
print("login failed")
farms = self.farm.get_farms(self.user)
for farm in farms:
if farm.name == "Demo Farm":
self.frm = farm
cats = self.measurement_category.get_measurement_categories()
for cat in cats:
if cat.name == "Weight":
self.cat = cat
algs = self.algorithm.get_algorithms(self.cat)
for alg in algs:
if alg.name == "bayesy_andy_constrained_prior": # need to change alg id in get_Day function
self.alg = alg
class WeighBridgeEmulator:
user = #
pwd = #
server = #
def __init__(self):
# fill out dbname host etc in psycopg2.connect
self.conn = psycopg2.connect("dbname=<database_name> host=<database_host> user=<database_user> password=<database_password>")
self.cur = self.conn.cursor()
self.agbase = AgBase()
self.algorithm = AlgorithmAPI(self.agbase)
self.animal = AnimalAPI(self.agbase)
self.farm = FarmAPI(self.agbase)
self.herd = HerdAPI(self.agbase)
self.measurement = MeasurementAPI(self.agbase)
self.measurement_category = MeasurementCategoryAPI(self.agbase)
self.agbase.set_logging_on(True)
self.user = self.agbase.connect(self.user, self.pwd, self.server)
self.pp = pprint.PrettyPrinter(indent=4)
if self.user is None:
print("login failed")
farms = self.farm.get_farms(self.user)
for farm in farms:
if farm.name == "Demo Farm":
self.frm = farm
cats = self.measurement_category.get_measurement_categories()
for cat in cats:
if cat.name == "Weight":
self.cat = cat
algs = self.algorithm.get_algorithms(self.cat)
for alg in algs:
if alg.name == "bayesy_andy_constrained_prior":
self.alg = alg
def get_animal_list(self):
query = "select a.id, a.eid from animal as a join animalfarm as af on(a.id = af.animal_id) where a.vid IS NULL;" #limit(500)
self.cur.execute(query)
return self.cur.fetchall()
def get_Day(self, date, animalid):
query = 'select * from weights where weights.animal_id = {animalid} and date <@ tsrange(\'{date}\', \'{date}\'::date + 1, \'[)\') and method_id = 70 and weighbridge_id = 8 order by DATE;'.format(animalid=animalid, date=date)
self.cur.execute(query)
return self.cur.fetchall()
def clean_up(self):
self.cur.close()
self.conn.close()
def create_measurements(self, animal, measurements):
for measurement in measurements:
if(not math.isnan(measurement[5]) or not math.isnan(measurement[6]) or not math.isnan(measurement[7])):
self.measurement.create_measurement(animal, self.alg, self.user, str(measurement[4]), measurement[5], None, measurement[6], None, measurement[7], None)
def upload_animal_measurements_by_day(self):
date = datetime.date(2015, 01, 01) # sets date to first day of the year
animals = self.get_animal_list() # get animal list from the local database
animal_max = len(animals)
self.pp.pprint(animals)
for i in range(0, 100):
print "day: {}/100".format(i)
animal_count = 0
for animalID in animals:
animal_count += 1
print "animal {}/{}".format(animal_count, animal_max)
animal = self.animal.get_animal_by_eid(self.frm, animalID[1])
if(animal == None):
animal = self.animal.create_animal(self.frm, animalID[1]) # creates an animal if it dosnt exist
measurements = self.get_Day(date, animalID[0]) # gets the days measurements for the above animals on the above day
if(len(measurements) > 0): # check to see if there are any measurements on that day
self.create_measurements(animal, measurements)
date += datetime.timedelta(days=1)
class TestHerd(TestCommon):
def setUp(self):
self.agbase = AgBase()
self.agbase.set_logging_on(True)
self.user = self.agbase.connect(self.testUser, self.testPwd, self.serverIp)
if self.user is None:
self.fail()
self.farm = self.agbase.create_farm("Python Test Farm")
def tearDown(self):
print('TestHerd.tearDown')
self.agbase.remove_farm(self.farm)
def test_get_nonexistent_herd(self):
herds = self.agbase.get_herds(self.farm)
if herds is not None and len(herds) != 0:
self.fail()
herd = self.agbase.create_herd(self.farm, "Python Test Herd")
if herd is None:
self.fail()
herd2 = self.agbase.create_herd(self.farm, "Python Test Herd")
if herd2 is None:
self.fail()
print herd2.id
def test_herds(self):
herd = self.agbase.create_herd(self.farm, "Python Test Herd")
if herd is None:
self.fail()
print('created herd: {} with id: {}'.format(herd.name, herd.id))
herds = self.agbase.get_herds()
if herds is None:
self.fail()
for herd in herds:
print('found herd: {} with id: {}'.format(herd.name, herd.id))
herds = self.agbase.get_herds(self.farm)
if herds is None:
self.fail()
for herd in herds:
print('The farm "{}" has a herd named: {}'.format(self.farm.name, herd.name))
deleted = self.agbase.remove_herd(herd)
if not deleted:
self.fail()
class TestAgBase(TestCommon):
def setUp(self):
print('TestAgBase.setUp')
super(self.__class__, self).setUp()
self.pp = pprint.PrettyPrinter(indent=4)
self.agbase = AgBase()
self.algorithm = AlgorithmAPI(self.agbase)
self.animal = AnimalAPI(self.agbase)
self.farm = FarmAPI(self.agbase)
self.herd = HerdAPI(self.agbase)
self.measurement = MeasurementAPI(self.agbase)
self.measurement_category = MeasurementCategoryAPI(self.agbase)
self.agbase.set_logging_on(True)
self.user = self.agbase.connect(self.testUser, self.testPwd, self.serverIp)
if self.user is None:
self.fail()
print('connected to mooogle with user: {} with id: {}'.format(self.user.email, self.user.id))
def test_farms(self):
test_farm = self.farm.create_farm("Python Test Farm")
if test_farm is None:
self.fail()
print('created farm: {} with id: {}'.format(test_farm.name, test_farm.id))
farms = self.farm.get_farms()
if farms is None:
self.fail()
for farm in farms:
print('found farm: {} with id: {}'.format(farm.name, farm.id))
single_query_farm = self.farm.get_farm(test_farm.id)
if single_query_farm.id != test_farm.id:
self.fail()
farms = self.farm.get_farms(self.user)
if farms is None:
self.fail()
for farm in farms:
print('The current user can access farm: {}'.format(farm.name))
deleted = self.farm.remove_farm(test_farm)
if not deleted:
self.fail()
def test_roles(self):
roles = self.agbase.get_roles()
if roles is None:
self.fail()
for role in roles:
print('Found role named {}'.format(role.name))
def test_users(self):
roles = self.agbase.get_roles()
admin_role = None
for role in roles:
if role.name == "Viewer":
admin_role = role
break
test_user = self.agbase.create_user("Test", "Testor", "*****@*****.**", "testpass", admin_role)
if test_user is None:
self.fail()
print('created user: {} with id: {}'.format(test_user.email, test_user.id))
users = self.agbase.get_users()
if users is None:
self.fail()
for user in users:
print('found user: {} {} with email: {}'.format(user.first_name, user.last_name, user.email))
deleted = self.agbase.remove_user(test_user)
if not deleted:
self.fail()
def test_measurement_categories(self):
test_category = self.measurement_category.create_measurement_category('Test Category')
if test_category is None:
self.fail()
print('created measurement category: {} with id: {}'.format(test_category.name, test_category.id))
single_query_category = self.measurement_category.get_measurement_category(test_category.id)
if test_category.id != single_query_category.id:
self.fail()
categories = self.measurement_category.get_measurement_categories()
if categories is None:
self.fail()
for category in categories:
print('found category: {}'.format(category.name))
deleted = self.measurement_category.remove_measurement_category(test_category)
if not deleted:
self.fail()
def test_algorithms(self):
test_category = self.measurement_category.create_measurement_category('Algorithm Test Category')
test_algorithm = self.algorithm.create_algorithm('Test Algorithm', test_category)
print "test_algorithm", test_algorithm.to_json()
if test_algorithm is None:
self.fail()
print('created algorithm {} with id: {}'.format(test_algorithm.name, test_algorithm.id))
single_query_algorithm = self.algorithm.get_algorithm(test_algorithm.id)
print "single_query_algorithm", single_query_algorithm.to_json()
if test_algorithm.id != single_query_algorithm.id:
self.fail()
algorithms = self.algorithm.get_algorithms()
if algorithms is None:
self.fail()
for algorithm in algorithms:
print('found algorithm: {}'.format(algorithm.name))
deleted = self.algorithm.remove_algorithm(test_algorithm)
if not deleted:
self.fail()
self.measurement_category.remove_measurement_category(test_category)
def test_animals(self):
test_farm = self.farm.create_farm('Animal Test Farm')
test_herd = self.herd.create_herd(test_farm, 'Animal Test Herd')
test_eid = "AN-EID-FOR_TESTING"
test_animal = self.animal.create_animal(test_farm, test_eid)
if test_animal is None:
self.fail()
print('created animal {} with id: {}'.format(test_animal.eid, test_animal.id))
result = self.animal.set_animal_herd(test_animal, test_herd)
if result is None:
self.fail()
print "============farm==========",test_farm.to_json()
print "============herd==========",test_herd.to_json()
animals = self.animal.get_animals(test_farm, test_herd)
if animals is None:
self.fail()
for animal in animals:
print('found animal: {}'.format(animal.eid))
updated = self.animal.update_animal_vid(test_animal, "My Pet Cow")
if not updated:
self.fail()
expected_animal = self.animal.get_animal_by_eid(test_farm, test_eid)
if expected_animal.id != test_animal.id:
self.fail()
deleted = self.animal.remove_animal(test_animal)
if not deleted:
self.fail()
self.herd.remove_herd(test_herd)
self.farm.remove_farm(test_farm)
def test_measurements(self):
test_farm = self.farm.create_farm('Animal Test Farm')
test_eid = "AN-EID-FOR_TESTING"
test_animal = self.animal.create_animal(test_farm, test_eid)
test_category = self.measurement_category.create_measurement_category('Algorithm Test Category')
test_algorithm = self.algorithm.create_algorithm('Test Algorithm', test_category)
measurement = self.measurement.create_measurement(test_animal, test_algorithm, self.user, time.strftime("%c"), None, None, 0.3344,None,None,None)
if measurement is None:
self.fail()
print('created measurement with id {}'.format(measurement.id))
animal_measurements = self.measurement.get_measurements_for_animal(test_animal)
if animal_measurements[0].id != measurement.id:
self.fail()
deleted = self.measurement.remove_measurement(measurement)
if not deleted:
self.fail()
eid_measurement = self.measurement.create_measurement_for_eid(test_animal.eid,test_farm, test_algorithm, self.user, time.strftime("%c"), None, None, 0.3344,None,None,None)
if eid_measurement is None:
self.fail()
if eid_measurement.animal_id != test_animal.id:
self.fail()
#self.pp.pprint(repr(eid_measurement))
for keys,values in eid_measurement.__repr__().items():
print(keys)
print(values)
self.measurement.remove_measurement(eid_measurement)
self.animal.remove_animal(test_animal)
self.farm.remove_farm(test_farm)
self.algorithm.remove_algorithm(test_algorithm)
self.measurement_category.remove_measurement_category(test_category)
def test_measurements_bulk_upload(self):
test_farm = self.farm.create_farm('Animal Test Farm')
test_eid = "AN-EID-FOR_TESTING"
test_animal = self.animal.create_animal(test_farm, test_eid)
test_category = self.measurement_category.create_measurement_category('Algorithm Test Category')
test_algorithm = self.algorithm.create_algorithm('Test Algorithm', test_category)
measurement_list = self.measurement.create_bulk_measurement_upload_list(test_animal, test_algorithm, self.user)
measurement_list.add_measurement(time.strftime("%c"), 0.3344)
measurement_list.add_measurement(time.strftime("%c"), 0.4455)
measurement_list.add_measurement(time.strftime("%c"), 0.5566)
success = self.measurement.upload_measurement_list(measurement_list)
if success is not True:
self.fail()
print('created bulk measurements')
animal_measurements = self.measurement.get_measurements_for_animal(test_animal)
if len(animal_measurements) != 3:
self.fail()
self.animal.remove_animal(test_animal)
self.farm.remove_farm(test_farm)
self.algorithm.remove_algorithm(test_algorithm)
self.measurement_category.remove_measurement_category(test_category)
row = worksheet.row(curr_row)
n0 = row[0]
eid0 = row[2]
cell_type_str = ctype_text.get(n0.ctype, "unknown type")
if cell_type_str == "number":
matches.append([int(n0.value), eid0.value])
n0 = row[5]
eid0 = row[7]
cell_type_str = ctype_text.get(n0.ctype, "unknown type")
if cell_type_str == "number":
matches.append([int(n0.value), eid0.value])
# Connect to AgBase
ab = AgBase()
ab.set_logging_on(True)
user = ab.connect(args.user, args.passwd, args.server)
if user is None:
print ("ERROR: Login failed.")
exit(1)
agFarm = FarmAPI(ab)
# Find farm ID
farm = agFarm.get_farm_by_name(user, args.farm)
if farm is None:
print ("ERROR: No such farm: %s" % args.farm)
exit(1)
agAnimal = AnimalAPI(ab)
agMeasurement = MeasurementAPI(ab)
class WeighBridgeEmulator:
def __init__(self):
parser = argparse.ArgumentParser()
parser.add_argument('--user', required=True, help="AgBase Username")
parser.add_argument('--passwd', required=True, help="AgBase Password")
parser.add_argument('--date', required=True, help="Date of the measurements you wish to upload (YYYY:MM:DD)")
parser.add_argument('--server', default="<website_address>", help="AgBase Server")
args = parser.parse_args()
self.conn = psycopg2.connect("dbname=<database_name> host=<database_address> user=<database_user> password=<database_password>")
self.cur = self.conn.cursor()
self.agbase = AgBase()
self.algorithm = AlgorithmAPI(self.agbase)
self.animal = AnimalAPI(self.agbase)
self.farm = FarmAPI(self.agbase)
self.herd = HerdAPI(self.agbase)
self.measurement = MeasurementAPI(self.agbase)
self.measurement_category = MeasurementCategoryAPI(self.agbase)
self.agbase.set_logging_on(True)
self.user = self.agbase.connect(args.user, args.passwd , args.server)
self.pp = pprint.PrettyPrinter(indent=4)
datearr = args.date.split(':',2)
print datearr[0], datearr[1], datearr[2]
self.date = datetime.date(int(datearr[0]), int(datearr[1]), int(datearr[2]))
if self.user is None:
print("login failed")
farms = self.farm.get_farms(self.user)
for farm in farms:
if farm.name == "Demo Farm":
self.frm = farm
cats = self.measurement_category.get_measurement_categories()
for cat in cats:
if cat.name == "Weight":
self.cat = cat
algs = self.algorithm.get_algorithms(self.cat)
for alg in algs:
if alg.name == "bayesy_andy_constrained_prior": # need to change alg id in get_Day function
self.alg = alg
def get_animal_list(self):
query = "select a.id, a.eid from animal as a join animalfarm as af on(a.id = af.animal_id) where a.vid IS NULL;" #limit(500)
self.cur.execute(query)
return self.cur.fetchall()
def get_Day(self, date, animalid):
query = 'select * from weights where weights.animal_id = {animalid} and date <@ tsrange(\'{date}\'::date - 1, \'{date}\', \'[)\') and method_id = 70 and weighbridge_id = 8 order by DATE;'.format(animalid=animalid, date=date)
self.cur.execute(query)
return self.cur.fetchall()
def clean_up(self):
self.cur.close()
self.conn.close()
def upload_animal_measurements_by_day(self):
animals = self.get_animal_list() # get animal list from the local database
animal_max = len(animals)
self.pp.pprint(animals)
listIndex = 0
self.meas_list = []
self.meas_list.append(self.measurement.create_bulk_measurement_upload_list(self.alg,self.user,None,self.frm.id))
animal_count = 0
for animalID in animals:
animal_count += 1
print "animal {}/{}".format(animal_count, animal_max)
measurements = self.get_Day(self.date, animalID[0]) # gets the days measurements for the above animals on the above day
if(len(measurements) > 0): # check to see if there are any measurements on that day
for measurement in measurements:
if(self.meas_list[listIndex].get_measurement_count() >= 500):
self.agbase.log("meas_list Dump >>> " + json.dumps(self.meas_list[listIndex].get_json()))
listIndex += 1
self.meas_list.append(self.measurement.create_bulk_measurement_upload_list(self.alg,self.user,None,self.frm.id))
if(not math.isnan(measurement[5]) or not math.isnan(measurement[6]) or not math.isnan(measurement[7])):
self.meas_list[listIndex].add_measurement(str(measurement[4]), measurement[5], None, measurement[6], None, measurement[7], animalID[1])
for measurementList in self.meas_list:
self.measurement.upload_measurement_list(measurementList)
self.meas_list = []
listIndex = 0
self.meas_list.append(self.measurement.create_bulk_measurement_upload_list(self.alg,self.user,None,self.frm.id))
class LocalToAgBase:
recordLimit = -1
def __init__(self):
parser = argparse.ArgumentParser()
parser.add_argument('--config', default=".agbase", help="AgBase Config File (username password e.t.c)")
parser.add_argument('--user', required=True, help="AgBase Username")
parser.add_argument('--passwd', required=True, help="AgBase Password")
parser.add_argument('--server', default="https://agbase.elec.ac.nz/api/", help="AgBase Server")
parser.add_argument('--print-weights' , action='store_true', help="Prints all the animals and their weights from the database")
parser.add_argument('--upload-animals', action='store_true', help="Uploads all the animals from postgres to agbase")
parser.add_argument('--upload-weights', action='store_true', help="Uploads all the weights from postgres to agbase")
parser.add_argument('--print-animals', action='store_true', help="Print all animals from agbase")
parser.add_argument('--limit', type=int, help="limit the number of animals that get added to agbase")
parser.add_argument('--remove-animals', action='store_true', help="REMOVES ALL ANIMALS AND WEIGHTS")
parser.add_argument('--db-host', default="postgres.elec.ac.nz", help="Local Database Host")
parser.add_argument('--db-user', help="Local Database Username")
parser.add_argument('--db-passwd', help="Local Database Password")
args = parser.parse_args()
self.testUser = args.user
self.testPwd = args.passwd
self.testServer = args.server
conn = psycopg2.connect("dbname=moogle host=%s user=%s password=%s" % (args.db_host, args.db_user, args.db_passwd))
cur = conn.cursor()
self.setup()
if(args.limit):
self.recordLimit = args.limit
if(args.upload_animals):
self.upLoadAnimalsToAgBase(cur)
if(args.upload_weights):
self.uploadWeights(cur)
if(args.print_weights):
self.printWeightsFromAgBase()
if(args.remove_animals):
self.removeAllAnimals()
if(args.print_animals):
self.printAnimalsFromAgBase()
#self.printWeightsFromAgBase()
#self.printHerds(self.agbase.get_farm(31))
cur.close()
conn.close()
def setup(self):
print "prepering to transfer data from local database to AgBase ..."
self.agbase = AgBase()
self.agbase.set_logging_on(True)
self.user = self.agbase.connect(self.testUser, self.testPwd , self.testServer)
if self.user is None:
print("login failed")
def removeAllAnimals(self):
animals = self.agbase.get_animals(self.agbase.get_farm(31),None)
for animal in animals:
self.agbase.remove_animal(animal)
def getWeights(self,cur,method_id,bridge):
cur.execute("select distinct eid, date , w5 ,w50 ,w95 from weights join animal on (weights.animal_id = animal.id) join weighbridge on (weights.weighbridge_id = weighbridge.id) "+
"where (weighbridge.name = '{}')and(weights.method_id = {});".format(bridge,method_id))
return cur.fetchall()
def getWeightsByEid(self,cur,method_id,bridge,eid):
cur.execute("select distinct eid, date , w5 ,w50 ,w95 from weights join animal on (weights.animal_id = animal.id) join weighbridge on (weights.weighbridge_id = weighbridge.id) "+
"where (weighbridge.name = '{}')and(weights.method_id = {})and (animal.eid = '{}');".format(bridge,method_id,eid))
return cur.fetchall()
def printWeights(self,cur,method_id,bridge):
cur.execute("select distinct eid, date , w5 ,w50 ,w95 from weights join animal on (weights.animal_id = animal.id) join weighbridge on (weights.weighbridge_id = weighbridge.id)"+
" where (weighbridge.name = '{}')and(weights.method_id = {});".format(bridge,method_id))
pprint.pprint(cur.fetchall())
def getMethod(self,cur,method_id):
cur.execute("select * from method where method.id = %s;",([method_id]))
return cur.fetchall()
#self.upLoadToAgBase(cur.fetchall())
def getHerds(self,farm):
return self.agbase.get_herds(farm)
def printHerds(self,farm):
herds = self.agbase.get_herds(farm)
for herd in herds:
pprint.pprint("{} : {}".format(herd.name, herd.id))
def getWeighBridges(self,cur,bridge):
cur.execute("select * from weighbridge where (name = '{0}');".format(bridge))
self.upLoadToAgBase(cur.fetchall())
def getAnimals(self,cur,method_id,bridge):
cur.execute('select distinct animal.eid, animal.id from animal join weights on(animal.id = weights.animal_id)join weighbridge on (weights.weighbridge_id = weighbridge.id) '+
'where (weighbridge.name=%s)and(weights.method_id=%s) order by animal.id;', (bridge,method_id));
return cur.fetchall()
def printAnimals(self,cur,method_id,bridge):
cur.execute('select distinct animal.eid, animal.id from animal join weights on(animal.id = weights.animal_id)join weighbridge on (weights.weighbridge_id = weighbridge.id) '+
'where (weighbridge.name=%s)and(weights.method_id=%s) order by animal.id;', (bridge,method_id));
pprint.pprint(cur.fetchall())
def printAnimalsFromAgBase(self):
farm = self.agbase.get_farms(self.user)
animals = self.agbase.get_animals(farm)
if animals is None:
print"no animals in farm 31"
for animal in animals:
print'eid: {}'.format(animal.eid)
print 'animals# {}'.format(len(animals))
def printWeightsFromAgBase(self):
farm = self.agbase.get_farm(31)
animals = self.agbase.get_animals(farm)
if animals is None:
print"no animals in farm 31"
i = 9
for animal in animals:
print'eid: {}'.format(animal.eid)
animal_measurements = self.agbase.get_measurements_for_animal(animal)
for weight in animal_measurements:
print' w5 {}, w50 {}, w95 {}'.format(weight.w05,weight.w50,weight.w95)
print 'animals# {}'.format(len(animals))
def upLoadToAgBase(self,cur): # ul = upload = stuff to put up to server
cur.execute('select method_id from score order by cprs;')
method_id = cur.fetchone()[0]
algName = self.getMethod(cur,method_id)[0][1]
cat = self.agbase.get_measurement_category(27)
alg = self.agbase.create_algorithm(algName, cat)
farm = self.agbase.get_farm(31)
animals = self.getWeights(cur,method_id,"taieri")
pprint.pprint(animals)
for animal in animals: #eid #date w5 w50 w95
self.agbase.create_measurement_for_eid(animal[0], farm, alg, self.user, str(animal[1]),animal[2],animal[3],animal[4])
def uploadWeights(self,cur):
cur.execute('select method_id from score order by cprs;')
method_id = cur.fetchone()[0]
algName = self.getMethod(cur,method_id)[0][1]
cat = self.agbase.create_measurement_category("Weight")
cats = self.agbase.get_measurement_categories()
for ccat in cats:
pprint.pprint("{} {}".format(ccat.name,ccat.id))
alg = self.agbase.create_algorithm(algName, cat)
farm = self.agbase.create_farm("Liquid Calcium")
animals = self.agbase.get_animals(farm)
amax = len(animals)
acount = 0
for animal in animals:
if animal.eid != "":
weights = self.getWeightsByEid(cur,method_id,"taieri",animal.eid)
acount += 1
print("animals {} / {}".format(acount,amax))
wmax = len(weights)
wcount = 0
#make new animal_measurements
measurement_list = self.agbase.create_bulk_measurement_upload_list(animal, alg, self.user)
for weight in weights:
w = list(weight)
wcount += 1
print("measurement {} / {}".format(wcount,wmax))
#self.agbase.create_measurement(animal, alg, self.user, str(w[1]),w[2],w[3],w[4])
if math.isnan(w[2]):
w[2] = None
if math.isnan(w[3]):
w[3] = None
if math.isnan(w[4]):
w[4] = None
print "weight: {}".format(w[2])
measurement_list.add_measurement(time.strftime(str(w[1])), w[2], w[3], w[4])
success = self.agbase.upload_measurement_list(measurement_list)
def upLoadAnimalsToAgBase(self,cur): # ul = upload = stuff to put up to server
cur.execute('select method_id from score order by cprs;')
method_id = cur.fetchone()[0]
farm = self.agbase.create_farm("Liquid Calcium")
herd = self.agbase.create_herd(farm, "Herd 1")
animals = self.getAnimals(cur,method_id,"taieri")
pprint.pprint(animals)
count = 0
minimum = 51
for animal in animals:
print "count: {}/{}".format(count,len(animals))
count += 1
if count >= minimum:
self.agbase.create_animal(farm,animal[0])
print "farm: {}, animal: {}".format(farm, animal)
if count == self.recordLimit:
break
mAnimals = self.agbase.get_animals(farm)
pprint.pprint(mAnimals)
for animal in mAnimals:
self.agbase.set_animal_herd(animal,herd)
class WeighBridgeEmulator:
def __init__(self):
parser = argparse.ArgumentParser()
parser.add_argument('--user', required=True, help="AgBase Username")
parser.add_argument('--passwd', required=True, help="AgBase Password")
parser.add_argument('--algorithm', required=True, help="The name of the data algorithm you wish "+
"to transfer from local moogle to agbase.(Must be an algorithm name in the moogle database)" +
"and must also be added to the website.")
parser.add_argument('--server', default="<website_address>", help="AgBase Server")
args = parser.parse_args()
self.conn = psycopg2.connect("dbname=<database_name> host=<database_address> user=<database_user> password=<database_password>")
self.cur = self.conn.cursor()
self.agbase = AgBase()
self.algorithm = AlgorithmAPI(self.agbase)
self.animal = AnimalAPI(self.agbase)
self.farm = FarmAPI(self.agbase)
self.herd = HerdAPI(self.agbase)
self.measurement = MeasurementAPI(self.agbase)
self.measurement_category = MeasurementCategoryAPI(self.agbase)
self.agbase.set_logging_on(True)
self.user = self.agbase.connect(args.user, args.passwd , args.server)
self.pp = piprint.PrettyPrinter(indent=4)
if self.user is None:
print("login failed")
farms = self.farm.get_farms(self.user)
for farm in farms:
if farm.name == "Demo Farm":
self.frm = farm
cats = self.measurement_category.get_measurement_categories()
for cat in cats:
if cat.name == "Weight":
self.cat = cat
algs = self.algorithm.get_algorithms(self.cat)
for alg in algs:
if alg.name == args.algorithm: # need to set meathod_id to local moogles method_id in get_day
self.alg = alg
self.moogle_alg_id = self.get_algorithm_id()
def get_algorithm_id(self):
query = "select id from method where name = '{}';".format(self.alg.name)
self.cur.execute(query)
return self.cur.fetchone()[0]
def get_animal_list(self):
query = "select a.id, a.eid from animal as a join animalfarm as af on(a.id = af.animal_id) where a.vid IS NULL;" #limit(500)
self.cur.execute(query)
return self.cur.fetchall()
def get_day(self, date, animalid):
query = 'select * from weights where weights.animal_id = {animalid} and date <@ tsrange(\'{date}\', \'{date}\'::date + 1, \'[)\') and method_id = {methodid} and weighbridge_id = 8 order by DATE;'.format(animalid=animalid, date=date, methodid=self.moogle_alg_id)
self.cur.execute(query)
return self.cur.fetchall()
def clean_up(self):
self.cur.close()
self.conn.close()
def upload_animal_measurements_by_day(self):
now = datetime.datetime.now()
date = datetime.date(2015, 01, 01) # sets date to first day of the year
animals = self.get_animal_list() # get animal list from the local database
animal_max = len(animals)
self.pp.pprint(animals)
listIndex = 0
self.meas_list = []
self.meas_list.append(self.measurement.create_bulk_measurement_upload_list(self.alg,self.user,None,self.frm.id))
for i in range(0, 100): #change this if you want it to go for more days
print "day: {}/100".format(i)
animal_count = 0
for animalID in animals:
animal_count += 1
print "animal {}/{}".format(animal_count, animal_max)
measurements = self.get_day(date, animalID[0]) # gets the days measurements for the above animals on the above day
if(len(measurements) > 0): # check to see if there are any measurements on that day
for measurement in measurements:
if(self.meas_list[listIndex].get_measurement_count() >= 500):
self.agbase.log("meas_list Dump >>> " + json.dumps(self.meas_list[listIndex].get_json()))
listIndex += 1
self.meas_list.append(self.measurement.create_bulk_measurement_upload_list(self.alg,self.user,None,self.frm.id))
if(not math.isnan(measurement[5]) or not math.isnan(measurement[6]) or not math.isnan(measurement[7])):
self.meas_list[listIndex].add_measurement(str(measurement[4]), measurement[5], None, measurement[6], None, measurement[7], animalID[1])
date += datetime.timedelta(days=1)
for measurementList in self.meas_list:
self.measurement.upload_measurement_list(measurementList)
self.meas_list = []
listIndex = 0
self.meas_list.append(self.measurement.create_bulk_measurement_upload_list(self.alg,self.user,None,self.frm.id))
class getConditionScores:
def __init__(self):
parser = argparse.ArgumentParser()
parser.add_argument('--user', required=True, help="AgBase Username")
parser.add_argument('--password', required=True, help="AgBase Password")
#parser.add_argument('--firstDate', required=True, help="First date of the measurements you wish to upload (YYYY/MM/DD)")
#parser.add_argument('--lastDate', required=True, help="Last date of the measurements you wish to upload (YYYY/MM/DD)")
parser.add_argument('--server', required=True, help="AgBase Server")
args = parser.parse_args()
self.agbase = AgBase()
self.algorithm = AlgorithmAPI(self.agbase)
self.animal = AnimalAPI(self.agbase)
self.farm = FarmAPI(self.agbase)
self.herd = HerdAPI(self.agbase)
self.measurement = MeasurementAPI(self.agbase)
self.measurement_category = MeasurementCategoryAPI(self.agbase)
self.agbase.set_logging_on(True)
self.user = self.agbase.connect(args.user, args.password , args.server)
#self.first_date = self.getDate(args.firstDate)
#self.last_date = self.getDate(args.lastDate)
def getScores(self):
self.alg = self.algorithm.get_algorithm("DairyNZ BCS")
self.frm = self.farm.get_farm_by_name(self.user,"Demo Farm")
animalList = []
moreAnimals = True
offset = 0
limit = 500
while moreAnimals is True: # amimals # more comlicated because there are more then the 1024 limit
tempAnimalList = self.animal.get_animals(self.frm, None, limit, offset)
if(len(tempAnimalList) != (limit+offset)):
moreAnimals = False
offset += limit
for animal in tempAnimalList:
animalList.append(animal)
measurementList = {} # holds all of the measurements indexed by eid
length = len(animalList)
count = 0
for animal in animalList: # goes through the animal list and sends a query to the datebase
print "Animal {}/{}".format(count, length)
count += 1
measurementList[animal.eid] = self.measurement.get_measurements_for_animal(animal,self.alg)
count = 0
for animal in animalList:
print "Animal {}/{}".format(count, length)
count += 1
for measurement in measurementList[animal.eid]:
print "eid: {}, condition score: {}, timestamp: {}".format(animal.eid,measurement.w50,measurement.time_stamp)
def getDate(self, raw_date):
date_parts = raw_date.split('/',2)
if(len(date_parts) == 3):
date = datetime.date(int(date_parts[0]),int(date_parts[1]),int(date_parts[2]))
print 'date: ', date
return int((date-datetime.date(1970,1,1)).total_seconds() * 1000)
return None