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 __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))
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 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)
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