def test_unique_two_delete_not_found(self):
# Delete the zip code from an existing address that doesn't have a zip code.
p = Pump("data/org_def.json")
p.update_data = {1: {u'uri': u'http://vivo.ufl.edu/individual/n765319', u'zip': u'None'}}
[add, sub] = p.update()
self.assertTrue(len(add) == 0 and len(sub) == 0)
def test_unique_one_delete(self):
from rdflib import URIRef, Literal, XSD
p = Pump()
p.update_data = {1: {u'uri': u'http://vivo.ufl.edu/individual/n111669', u'abbreviation': u'None'}}
[add, sub] = p.update()
self.assertTrue(
len(add) == 0 and len(sub) == 1 and (URIRef("http://vivo.ufl.edu/individual/n111669"),
URIRef("http://vivoweb.org/ontology/core#abbreviation"),
Literal("JWRU", datatype=XSD.string)) in sub)
def test_without_lang(self):
from rdflib import URIRef, Literal
p = Pump("data/org_def.json", verbose=True)
p.update_data = {1: {u'uri': u'http://vivo.ufl.edu/individual/n928712', u'name': u'Ad ver tising'}}
[add, sub] = p.update()
self.assertTrue(
len(add) == 1 and len(sub) == 1 and (URIRef("http://vivo.ufl.edu/individual/n928712"),
URIRef("http://www.w3.org/2000/01/rdf-schema#label"),
Literal("Ad ver tising")) in add)
def test_unique_one_add(self):
from rdflib import URIRef, Literal
p = Pump()
p.update_data = {1: {u'uri': u'http://vivo.ufl.edu/individual/n1001011525', u'abbreviation': u'PH9'}}
[add, sub] = p.update()
self.assertTrue(
len(add) == 1 and len(sub) == 0 and (URIRef("http://vivo.ufl.edu/individual/n1001011525"),
URIRef("http://vivoweb.org/ontology/core#abbreviation"),
Literal("PH9")) in add)
def test_with_lang(self):
from rdflib import URIRef, Literal
p = Pump("data/building_def.json", verbose=True)
p.update_data = {1: {u'uri': u'http://vivo.ufl.edu/individual/n1001011525', u'name': u'Building 42'}}
[add, sub] = p.update()
self.assertTrue(
len(add) == 1 and len(sub) == 1 and (URIRef("http://vivo.ufl.edu/individual/n1001011525"),
URIRef("http://www.w3.org/2000/01/rdf-schema#label"),
Literal("Building 42", lang="en-US")) in add)
def test_without_datatype(self):
from rdflib import URIRef, Literal
p = Pump("data/building_def.json", verbose=True)
p.update_data = {1: {u'uri': u'http://vivo.ufl.edu/individual/n1001011525', u'url': u'http://a'}}
[add, sub] = p.update()
self.assertTrue(
len(add) == 4 and len(sub) == 0 and (None,
URIRef("http://vivoweb.org/ontology/core#linkURI"),
Literal("http://a")) in add)
def test_multiple_one_change_nothing(self):
# Do nothing if the multiple values specified match those in VIVO
p = Pump("data/person_def.json", verbose=True)
p.update_data = {1: {u'uri': u'http://vivo.ufl.edu/individual/n1723097935',
u'types': u'person;thing;agent;fac;uf;ufc'}}
[add, sub] = p.update()
self.assertTrue(len(add) == 0 and len(sub) == 0)
def test_with_datatype(self):
from rdflib import URIRef, Literal, XSD
p = Pump("data/building_def.json", verbose=True)
p.update_data = {1: {u'uri': u'http://vivo.ufl.edu/individual/n1001011525', u'abbreviation': u'PH9'}}
[add, sub] = p.update()
self.assertTrue(
len(add) == 1 and len(sub) == 0 and (URIRef("http://vivo.ufl.edu/individual/n1001011525"),
URIRef("http://vivoweb.org/ontology/core#abbreviation"),
Literal("PH9", datatype=XSD.string)) in add)
def test_multiple_one_delete(self):
# Empty the set of values
p = Pump("data/person_def.json", verbose=True)
p.update_data = {1: {u'uri': u'http://vivo.ufl.edu/individual/n25674',
u'research_areas': u'None'}}
[add, sub] = p.update()
self.assertTrue(len(add) == 0 and len(sub) == 4)
def test_inject_empty_original_graph(self):
from rdflib import Graph, URIRef
p = Pump(verbose=True)
p.original_graph = Graph()
p.update_data = {1: {u'uri': u'http://vivo.ufl.edu/individual/n8984374104', u'abbreviation': u'None'}}
[add, sub] = p.update()
self.assertTrue(
len(add) == 1 and len(sub) == 0 and (None,
URIRef("http://www.w3.org/1999/02/22-rdf-syntax-ns#type"),
URIRef("http://vivoweb.org/ontology/core#Building")) in add)
def test_unique_three_add_partial_path(self):
from rdflib import URIRef, Literal
p = Pump("data/grant_def.json", verbose=True)
# WARNING. This test passes by constructing a new datetime interval. Not clear if this is the desired result.
p.update_data = {1: {u'uri': u'http://vivo.ufl.edu/individual/n42774', u'start_date': u'2006-03-01'}}
[add, sub] = p.update()
self.assertTrue(
len(add) == 5 and len(sub) == 0 and (None,
URIRef("http://vivoweb.org/ontology/core#dateTime"),
Literal("2006-03-01")) in add)
def test_unique_three_add_fullpath(self):
from rdflib import URIRef, Literal
p = Pump("data/grant_def.json")
# Add a start date to a grant. There is no date time interval, so a full path will need to be created
p.update_data = {1: {u'uri': u'http://vivo.ufl.edu/individual/n51914', u'start_date': u'2015-03-01'}}
[add, sub] = p.update()
self.assertTrue(
len(add) == 5 and len(sub) == 0 and (None,
URIRef("http://vivoweb.org/ontology/core#dateTime"),
Literal("2015-03-01")) in add)
def test_unique_two_delete(self):
from rdflib import URIRef, Literal, XSD
# Delete the zip code on an existing address
p = Pump("data/org_def.json")
p.update_data = {1: {u'uri': u'http://vivo.ufl.edu/individual/n87597', u'zip': u'None'}}
[add, sub] = p.update()
self.assertTrue(
len(add) == 0 and len(sub) == 1 and (URIRef("http://vivo.ufl.edu/individual/n994294"),
URIRef("http://vivoweb.org/ontology/core#addressPostalCode"),
Literal("32611", datatype=XSD.string)) in sub)
def test_unique_two_add_to_existing(self):
from rdflib import URIRef, Literal
# Add a zip code to the provost's office at UF. An address already exists, the zip needs to be
# added to the existing address
p = Pump("data/org_def.json")
p.update_data = {1: {u'uri': u'http://vivo.ufl.edu/individual/n765319', u'zip': u'32653'}}
[add, sub] = p.update()
self.assertTrue(
len(add) == 1 and len(sub) == 0 and (URIRef("http://vivo.ufl.edu/individual/n119803"),
URIRef("http://vivoweb.org/ontology/core#addressPostalCode"),
Literal("32653")) in add)
def test_unique_two_add_fullpath(self):
from rdflib import URIRef, Literal
p = Pump("data/org_def.json")
# Add a zip code to Lee County Extension Office. There is no address, so a full path will need
# to be created
p.update_data = {1: {u'uri': u'http://vivo.ufl.edu/individual/n7023301', u'zip': u'32653'}}
[add, sub] = p.update()
self.assertTrue(
len(add) == 4 and len(sub) == 0 and (None,
URIRef("http://vivoweb.org/ontology/core#addressPostalCode"),
Literal("32653")) in add)
def test_unique_three_delete(self):
from rdflib import URIRef, Literal, XSD
# WARNING: Delete start date value from existing datetime interval. This may not be the desirable data
# management action
p = Pump("data/grant_def.json", verbose=True)
p.update_data = {1: {u'uri': u'http://vivo.ufl.edu/individual/n650082272', u'start_date': u'None'}}
[add, sub] = p.update()
self.assertTrue(
len(add) == 0 and len(sub) == 1 and (None,
URIRef("http://vivoweb.org/ontology/core#dateTime"),
Literal("2006-07-01T00:00:00", datatype=XSD.dateTime)) in sub)
def main():
"""
The main function. Does the work of Simple VIVO
:return: None
"""
import sys
from datetime import datetime
from vivopump import get_args
from pump import Pump
return_code = 0
print datetime.now(), "Start"
args = get_args()
# Create a Pump and use it to perform the requested actions based on arguments
p = Pump(args.defn, args.src, args.verbose, args.nofilters, args.inter, args.intra, args.rdfprefix,
query_parms={'queryuri': args.queryuri,
'username': args.username,
'password': args.password,
'prefix': args.prefix,
'uriprefix': args.uriprefix})
if args.action == 'get':
n_rows = p.get()
print datetime.now(), n_rows, "rows in", args.src
elif args.action == 'update':
try:
[add_graph, sub_graph] = p.update()
except IOError:
print "File not found"
return_code = 1
else:
add_file = open(args.rdfprefix + '_add.rdf', 'w')
print >>add_file, add_graph.serialize(format='nt')
add_file.close()
sub_file = open(args.rdfprefix + '_sub.rdf', 'w')
print >>sub_file, sub_graph.serialize(format='nt')
sub_file.close()
print datetime.now(), len(add_graph), 'triples to add', len(sub_graph), 'triples to sub'
elif args.action == 'summarize':
print p.summarize()
elif args.action == 'serialize':
print p.serialize()
elif args.action == 'test':
print p.test()
else:
print datetime.now(), "Unknown action. Try sv -h for help"
print datetime.now(), "Finish"
sys.exit(return_code)
def test_multiple_one_change(self):
from rdflib import URIRef
# Change the set of values adding one and removing another
p = Pump("data/person_def.json", verbose=True)
p.update_data = {1: {u'uri': u'http://vivo.ufl.edu/individual/n1723097935',
u'types': u'person;thing;agent;fac;uf;pd'}}
[add, sub] = p.update()
self.assertTrue(len(add) == 1 and len(sub) == 1 and
(URIRef("http://vivo.ufl.edu/individual/n1723097935"),
URIRef("http://www.w3.org/1999/02/22-rdf-syntax-ns#type"),
URIRef("http://vivoweb.org/ontology/core#Postdoc")) in add and
(URIRef("http://vivo.ufl.edu/individual/n1723097935"),
URIRef("http://www.w3.org/1999/02/22-rdf-syntax-ns#type"),
URIRef("http://vivo.ufl.edu/ontology/vivo-ufl/UFCurrentEntity")) in sub)
def test_multiple_one_add(self):
from rdflib import URIRef
# Add multiple values for an attribute to an entity that has no values for the attribute
p = Pump("data/person_def.json", verbose=True)
p.update_data = {1: {u'uri': u'http://vivo.ufl.edu/individual/n1723097935',
u'research_areas': u'http://vivo.ufl.edu/individual/n2551317090;http://vivo.ufl.edu/individual/n157098'}}
[add, sub] = p.update()
self.assertTrue(
len(add) == 2 and len(sub) == 0 and (URIRef("http://vivo.ufl.edu/individual/n1723097935"),
URIRef("http://vivoweb.org/ontology/core#hasResearchArea"),
URIRef("http://vivo.ufl.edu/individual/n2551317090")) in add and
(URIRef("http://vivo.ufl.edu/individual/n1723097935"),
URIRef("http://vivoweb.org/ontology/core#hasResearchArea"),
URIRef("http://vivo.ufl.edu/individual/n157098")) in add)
def test_unique_three_change_xsd(self):
from rdflib import URIRef, Literal, XSD
p = Pump("data/grant_def.json", verbose=True)
# WARNING. This test passes by changing the start date value on an existing datetime interval. Not sure
# if this is the desired behavior.
p.update_data = {1: {u'uri': u'http://vivo.ufl.edu/individual/n650082272', u'start_date': u'2006-03-02'}}
[add, sub] = p.update()
self.assertTrue(
len(add) == 1 and len(sub) == 1 and (None,
URIRef("http://vivoweb.org/ontology/core#dateTime"),
Literal("2006-03-02")) in add and
(None,
URIRef("http://vivoweb.org/ontology/core#dateTime"),
Literal("2006-07-01T00:00:00", datatype=XSD.dateTime)) in sub)
def test_pump_update(self):
p = Pump("data/building_def.json")
[add, sub] = p.update("data/buildings.txt")
self.assertEqual(74, len(add))
self.assertEqual(76, len(sub))
for name, val in program_defaults.items():
vars(args)[name] = val
if args.verbose:
print datetime.now(), "Arguments\n", vars(args)
# Create a Pump and use it to perform the requested actions based on arguments
p = Pump(args.defn, args.src, args.verbose, args.nofilters, query_parms={'query_uri': args.queryuri,
'username': args.pwd, 'password': args.pwd},
uri_prefix=args.uriprefix)
if args.action == 'get':
n_rows = p.get(args.src, args.inter, args.intra)
print datetime.now(), n_rows, "rows in", args.src
elif args.action == 'update':
[add_graph, sub_graph] = p.update(args.src, args.inter, args.intra)
add_file = open(args.rdfprefix + '_add.rdf', 'w')
print >>add_file, add_graph.serialize(format='nt')
add_file.close()
sub_file = open(args.rdfprefix + '_sub.rdf', 'w')
print >>sub_file, sub_graph.serialize(format='nt')
sub_file.close()
print datetime.now(), len(add_graph), 'triples to add', len(sub_graph), 'triples to sub'
elif args.action == 'summarize':
print p.summarize()
elif args.action == 'serialize':
print p.serialize()
else:
print datetime.now(), "Unknown action. Try sv -h for help"
print datetime.now(), "Finish"
class Manager:
AUTO_START_GPIO_PIN = 16
ONCE_BY_HOUR_TICK = 360 # 1h
def __init__(self, refPath, dataPath, dbFilename):
GPIO.cleanup()
GPIO.setmode(GPIO.BCM)
GPIO.setup(self.AUTO_START_GPIO_PIN, GPIO.IN, pull_up_down=GPIO.PUD_UP)
self.__i2c = I2C(2)
self.__analog = Analog(sel.__i2c.getLock(), 0x49)
self.default = Default()
self.database = Database(dataPath, dbFilename)
self.waterlevel = Waterlevel(debug, self.database)
self.light = Light(self.database)
self.curtain = Curtain(self.database)
self.pressure = Pressure(self.database, self.default, self.__analog)
self.temperature = Temperature("28-0417716a37ff", self.database)
self.redox = Redox(debug, self.database, self.default, self.__analog)
self.ph = PH(debug, self.database, self.default, self.__analog,
self.temperature)
self.robot = Robot(debug, self.database)
self.pump = Pump(debug, self.database, self.default, self.robot,
self.redox, self.ph, self.temperature)
self.panel = Panel(debug, self.database, self.default, self.pump,
self.redox, self.ph, self.__i2c)
self.statistic = Statistic(debug, self.pump, self.robot, self.redox,
self.ph, self.temperature, self.pressure,
self.waterlevel)
self.refPath = refPath
self.__autoSaveTick = 0
self.__today = date.today().day - 1
debug.TRACE(debug.DEBUG, "Initialisation done (Verbosity level: %s)\n",
debug)
def __del__(self):
GPIO.cleanup()
def __onceByHour(self):
if self.__autoSaveTick == self.ONCE_BY_HOUR_TICK:
self.database.backup()
self.__autoSaveTick = 0
# All seems to be OK, we can remove the previous version
backup = os.path.join(self.refPath, "PoolSurvey_bak")
if os.path.exists(backup):
os.system("rm -frd %s" % backup)
self.__autoSaveTick += 1
def __onceByDay(self):
if self.__today != date.today().day:
self.__today = date.today().day
self.pressure.onceByDay()
self.pump.onceByDay()
self.statistic.onceByDay()
def isAutoStart(self):
return GPIO.input(self.AUTO_START_GPIO_PIN) == GPIO.LOW
def start(self):
debug.TRACE(debug.DEBUG, "Manager is started\n")
self.__running = True
while self.__running:
debug.TAG(debug.DETAIL, "%ds Tick" % REFRESH_TICK)
self.temperature.update()
self.__onceByDay()
self.pump.update()
if self.pump.guardPeriodElapsed():
self.robot.update()
self.ph.update()
self.redox.update()
self.waterlevel.update()
self.pressure.update()
self.panel.update()
self.statistic.update()
self.__onceByHour()
time.sleep(REFRESH_TICK)
debug.TRACE(debug.DEBUG, "Manager is stopped\n")
self.pump.switchOff()
self.statistic.save()
def stop(self):
self.__running = False
def test_not_found(self):
p = Pump("data/person_def.json", verbose=True)
p.update_data = {1: {u'uri': u'http://vivo.ufl.edu/individual/n12345678',
u'remove': u'True'}}
[add, sub] = p.update()
self.assertTrue(len(add) == 0 and len(sub) == 0)
def test_small_case(self):
p = Pump("data/person_def.json", verbose=True)
p.update_data = {1: {u'uri': u'http://vivo.ufl.edu/individual/n2084211328',
u'remove': u'True'}}
[add, sub] = p.update()
self.assertTrue(len(add) == 0 and len(sub) == 1)
def test_no_update_file(self):
p = Pump()
with self.assertRaises(IOError):
p.update('data/no_update_file.txt')
def test_normal_inject(self):
p = Pump()
p.update_data = {1: {u'uri': u'http://vivo.ufl.edu/individual/n8984374104', u'abbreviation': u'None'}}
p.update()
self.assertTrue("8984374104" in str(p.update_data)) # Using the injected data, not default
def test_missing_uri_column_inject(self):
p = Pump()
p.update_data = {1: {u'overview': u'None'}}
with self.assertRaises(KeyError):
p.update()
def test_default_usage(self):
p = Pump()
p.update()
self.assertTrue("data/pump_def.json" in p.summarize()) # Using the default definition
