def createsuperuser():
"""
Create a super user of the system, requiring Email and password.
"""
email = prompt('User E-Mail')
email_confirm = prompt('Confirm E-Mail')
if not email == email_confirm:
sys.exit('\nCould not create user: E-Mail did not match')
if not EMAIL_REGEX.match(email):
sys.exit('\nCould not create user: Invalid E-Mail addresss')
password = prompt_pass('User password')
password_confirm = prompt_pass('Confirmed password')
if not password == password_confirm:
sys.exit('\nCould not create user: Passwords did not match')
datastore = SQLAlchemyUserDatastore(db, User, Role)
datastore.create_user(
email=email,
password=encrypt_password(password),
active=True,
super_user=True)
db.session.commit()
def do_setup(app):
"""Create a new settings database from scratch"""
if config.SERVER_MODE is False:
print("NOTE: Configuring authentication for DESKTOP mode.")
email = config.DESKTOP_USER
p1 = ''.join([
random.choice(string.ascii_letters + string.digits)
for n in range(32)
])
else:
print("NOTE: Configuring authentication for SERVER mode.\n")
# Prompt the user for their default username and password.
print("""
Enter the email address and password to use for the initial pgAdmin user \
account:\n""")
email = ''
while email == '':
email = input("Email address: ")
def pprompt():
return getpass.getpass(), getpass.getpass('Retype password:'******'Passwords do not match. Try again')
p1, p2 = pprompt()
# Setup Flask-Security
user_datastore = SQLAlchemyUserDatastore(db, User, Role)
security = Security(app, user_datastore)
with app.app_context():
password = encrypt_password(p1)
db.create_all()
user_datastore.create_role(name='Administrators',
description='pgAdmin Administrators Role')
user_datastore.create_user(email=email, password=password)
db.session.flush()
user_datastore.add_role_to_user(email, 'Administrators')
# Get the user's ID and create the default server group
user = User.query.filter_by(email=email).first()
server_group = ServerGroup(user_id=user.id, name="Servers")
db.session.merge(server_group)
# Set the schema version
version = Version(name='ConfigDB',
value=config.SETTINGS_SCHEMA_VERSION)
db.session.merge(version)
db.session.commit()
# Done!
print("")
print("The configuration database has been created at {0}".format(
config.SQLITE_PATH))
def do_setup(app):
"""Create a new settings database from scratch"""
if config.SERVER_MODE is False:
print("NOTE: Configuring authentication for DESKTOP mode.")
email = config.DESKTOP_USER
p1 = "".join([random.choice(string.ascii_letters + string.digits) for n in xrange(32)])
else:
print("NOTE: Configuring authentication for SERVER mode.\n")
# Prompt the user for their default username and password.
print("Enter the email address and password to use for the initial pgAdmin user account:\n")
email = ""
while email == "":
email = raw_input("Email address: ")
pprompt = lambda: (getpass.getpass(), getpass.getpass("Retype password: "******"Passwords do not match. Try again")
p1, p2 = pprompt()
# Setup Flask-Security
user_datastore = SQLAlchemyUserDatastore(db, User, Role)
security = Security(app, user_datastore)
with app.app_context():
password = encrypt_password(p1)
db.create_all()
user_datastore.create_role(name="Administrators", description="pgAdmin Administrators Role")
user_datastore.create_user(email=email, password=password)
db.session.flush()
user_datastore.add_role_to_user(email, "Administrators")
# Get the user's ID and create the default server group
user = User.query.filter_by(email=email).first()
server_group = ServerGroup(user_id=user.id, name="Servers")
db.session.merge(server_group)
# Set the schema version
version = Version(name="ConfigDB", value=config.SETTINGS_SCHEMA_VERSION)
db.session.merge(version)
db.session.commit()
# Done!
print("")
print("The configuration database has been created at %s" % config.SQLITE_PATH)
class UserRepository(object):
def __init__(self):
self.ud = SQLAlchemyUserDatastore(db, User, Role)
def get(self, email):
return self.ud.get_user(email)
def create(self, username, email, pwd):
user = self.ud.create_user(
email=email,
username=username,
password=pwd
)
db.session.commit()
return user
def login(self, email, pwd):
user = self.get(email)
if user:
if user.password == pwd:
return login_user(user)
return False
def register(self, username, email, pwd):
user = self.get(email)
if not user:
user_obj = self.create(username, email, pwd)
return login_user(user_obj)
else:
return False
# create tabdata queries
replace_tabdata_query(
db, name="Tabdata_hexbin",
description="Hexbin of geographical data",
parameters='{ "locationColumn" : 0, "valueColumn" : 0, "textColumn" : 0 }',
template="tabdata_hexbin_query.html")
replace_tabdata_query(
db, name="Tabdata_markercluster",
description="Markercluster map of geographical data",
parameters='{ "locationColumn" : 0, "valueColumn" : 0, "textColumn" : 0 }',
template="tabdata_markercluster_query.html")
# create users
user_datastore = SQLAlchemyUserDatastore(db, User, Role)
if user_datastore.find_user(nickname="admin") is None:
admin = user_datastore.create_user(
nickname="admin", email="*****@*****.**", password="******")
db.session.add(admin)
db.session.commit()
create_gps_cache()
if not os.path.exists(SQLALCHEMY_MIGRATE_REPO):
api.create(SQLALCHEMY_MIGRATE_REPO, 'database repository')
api.version_control(SQLALCHEMY_DATABASE_URI, SQLALCHEMY_MIGRATE_REPO)
else:
api.version_control(SQLALCHEMY_DATABASE_URI,
SQLALCHEMY_MIGRATE_REPO,
api.version(SQLALCHEMY_MIGRATE_REPO))
class UserTest(MarionTest):
def setUp(self):
self.user_datastore = SQLAlchemyUserDatastore(tutorial.db, User, Role)
tutorial.db.create_all()
#u = User( nickname='test1', email='*****@*****.**' )
self.user = self.user_datastore.create_user(nickname='test1',
email='*****@*****.**',
password='******')
tutorial.db.session.add(self.user)
tutorial.db.session.commit()
# must commit before ID exists
self.first_id = self.user.id
def get_user(self):
return User.query.get(1)
def _login(self, email="*****@*****.**", password="******"):
data = {'email': email, 'password': password, 'remember': 'y'}
#print( "login: "******""
with open(filename, 'r') as f:
result = f.read()
return result
def test_upload_form(self):
self._login()
rv = self.client.post(
'/upload_file/',
buffered=True,
content_type='multipart/form-data',
data={'file_1': (BytesIO(b'Hello, World!'), 'test.txt')},
follow_redirects=True)
# check to see if the file is there
filename = os.path.join(self._user_basedir, 'test.txt')
self.assertTrue(os.path.isfile(filename))
self.assertEqual(self.fileContents(filename), "Hello, World!")
def test_upload_api(self):
self._login()
rv = self.client.post(
'/api/1.0/upload',
buffered=True,
content_type='multipart/form-data',
data={'files': (BytesIO(b'Hello, World!'), 'test.txt')},
follow_redirects=True)
# check to see if the file is there
filename = os.path.join(self._user_basedir, 'test.txt')
self.assertTrue(os.path.isfile(filename))
self.assertEqual(self.fileContents(filename), "Hello, World!")
self._logout()
def clear_test_data_directory(self):
if os.path.exists(self._user_basedir):
shutil.rmtree(self._user_basedir)
dataset_description = "Description"
dataset_query = "Query"
def add_basic_dataset(self):
rv = self.client.post("/add_dataset/",
buffered=True,
data={
'descriptionField': self.dataset_description,
'queryField': self.dataset_query
},
follow_redirects=True)
def test_add_dataset_form(self):
self._login()
u = self.get_user()
self.add_basic_dataset()
self.assertEqual(len(list(u.datasets)), 1)
self.assertEqual(u.datasets[0].description, self.dataset_description)
self.assertEqual(u.datasets[0].query_text, self.dataset_query)
def add_tabfiles(self, dataset_id, filename):
with open(os.path.join('test_data', filename), 'rb') as f1:
rv = self.client.post("/edit_dataset/" + str(dataset_id),
buffered=True,
data={'file_1': (f1, filename)},
follow_redirects=True)
f1.close()
print(rv)
def test_dataset_h5_up_to_date(self):
self._login()
u = self.get_user()
self.add_basic_dataset()
d = u.datasets[0]
self.add_tabfiles(d.id, 'metamaterials_1.tab')
self.assertEqual(len(list(d.csv_files)), 1)
self.assertEqual(d.h5_file_is_up_to_date(), False)
self.client.post('/regenerate_h5/' + str(d.id))
self.assertEqual(d.h5_file_is_up_to_date(), True)
self.add_tabfiles(d.id, 'metamaterials_2.tab')
self.assertEqual(len(list(d.csv_files)), 2)
self.assertEqual(d.h5_file_is_up_to_date(), False)
self.client.post('/regenerate_h5/' + str(d.id))
self.assertEqual(d.h5_file_is_up_to_date(), True)
class GPSTest(MarionTest):
"""
Tests both the GPS lookup and some biblio functions that rely on it
"""
def setUp(self):
self.user_datastore = SQLAlchemyUserDatastore(tutorial.db, User, Role)
tutorial.db.create_all()
# u = User( nickname='test1', email='*****@*****.**' )
self.remap_from = "University of Oxford"
self.remap_to = "Oxford, United Kingdom"
self.cache_loc = "Oxford, United Kingdom"
self.cache_lat = 51.7519
self.cache_lon = -1.2578
self.user = self.user_datastore.create_user(nickname='test1',
email='*****@*****.**',
password='******')
tutorial.db.session.add(self.user)
tutorial.db.session.commit()
oxford_remap = Gps_remap(from_location=self.remap_from,
to_location=self.remap_to)
tutorial.db.session.add(oxford_remap)
oxford_lookup = Gps_cache(location=self.cache_loc,
latitude=self.cache_lat,
longitude=self.cache_lon)
tutorial.db.session.add(oxford_lookup)
tutorial.db.session.commit()
def _logout(self):
logout_user()
def tearDown(self):
self._logout()
tutorial.db.session.remove()
tutorial.db.drop_all()
def test_retrieval(self):
remap = Gps_remap.query.get(self.remap_from)
self.assertEqual(remap.from_location, self.remap_from)
cache = Gps_cache.query.get(self.cache_loc)
self.assertAlmostEqual(cache.latitude, self.cache_lat)
self.assertAlmostEqual(cache.longitude, self.cache_lon)
def test_has_keys(self):
self.assertAlmostEqual(remap_has_key(self.remap_from), True)
self.assertAlmostEqual(cache_has_key(self.cache_loc), True)
def test_simplified_guess(self):
self.assertEqual(
next_guess("Inst Angew Phys, D-76131 Karlsruhe, Germany"),
"Inst Angew Phys, D-76131 Karlsruhe, Germany")
self.assertEqual(
next_guess(
"Soochow Univ, Sch Phys Sci & Technol, Suzhou 215006, Jiangsu, Peoples R China"
),
"Sch Phys Sci & Technol, Suzhou 215006, Jiangsu, Peoples R China")
def test_get_location(self):
self.assertEqual(get_location("blorfing"), None)
self.assertAlmostEqual(
get_location(self.cache_loc)['lat'], self.cache_lat)
self.assertAlmostEqual(get_location("london")['lon'], -0.1277583)
def test_get_locations_and_unknowns(self):
locs, unks = get_locations_and_unknowns(
["University of Oxford", "blorfing"], False)
self.assertAlmostEqual(locs["University of Oxford"]['lon'],
self.cache_lon)
self.assertEqual(unks[0], "blorfing")
def test_paper_lat_lon_query(self):
"""
"""
with wos_reader.open_wos_h5("test_data/irwin.h5") as w5:
locresults = wos_reader_query.paperLatLonQuery(
w5, get_locations_and_unknowns_nocache)
tmp = self.maxDiff
self.maxDiff = None
irwin_network = {
'not_located': [
'Kyushu Univ, Dept Phys, Fukuoka 812, Japan',
'Natl Res Inst Astron & Geophys, Dept Astron, Cairo 11421, Egypt; Natl Res Inst Astron & Geophys, Kottamia Ctr Sci Excellence Astron & Space Sci KC, Cairo 11421, Egypt',
'Natl Res Inst Astron & Geophys, Dept Astron, Cairo 11421, Egypt'
],
'paper_locations': {
'10.1051/mmnp/20138208': {
'edges': {
0: {
'to': 1,
'text': '10.1051/mmnp/20138208',
'from': 0,
'val': 0
},
1: {
'to': 2,
'text': '10.1051/mmnp/20138208',
'from': 0,
'val': 0
},
2: {
'to': 3,
'text': '10.1051/mmnp/20138208',
'from': 0,
'val': 0
},
3: {
'to': 4,
'text': '10.1051/mmnp/20138208',
'from': 0,
'val': 0
},
4: {
'to': 2,
'text': '10.1051/mmnp/20138208',
'from': 1,
'val': 0
},
5: {
'to': 3,
'text': '10.1051/mmnp/20138208',
'from': 1,
'val': 0
},
6: {
'to': 4,
'text': '10.1051/mmnp/20138208',
'from': 1,
'val': 0
},
7: {
'to': 3,
'text': '10.1051/mmnp/20138208',
'from': 2,
'val': 0
},
8: {
'to': 4,
'text': '10.1051/mmnp/20138208',
'from': 2,
'val': 0
},
9: {
'to': 4,
'text': '10.1051/mmnp/20138208',
'from': 3,
'val': 0
}
},
'nodes': {
0: {
'text':
'10.1051/mmnp/20138208: Univ Southern Denmark, MEMPHYS Ctr Biomembrane Phys, Dept Phys Chem & Pharm, DK-5230 Odense M, Denmark',
'val': 0,
'lon': 10.4033399,
'lat': 55.37906169999999
},
1: {
'text':
'10.1051/mmnp/20138208: Univ Potsdam, Inst Phys & Astron, D-14476 Potsdam, Germany; Tech Univ Tampere, Dept Phys, FI-33101 Tampere, Finland',
'val': 0,
'lon': 23.7610254,
'lat': 61.4981508
},
2: {
'text':
'10.1051/mmnp/20138208: Univ Oxford, Rudolf Peierls Ctr Theoret Phys, Oxford OX1 3NP, England',
'val': 0,
'lon': -1.259116,
'lat': 51.7595933
},
3: {
'text':
'10.1051/mmnp/20138208: Inst Theoret Phys NSC KIPT, UA-61108 Kharkov, Ukraine; Max Planck Inst Phys Komplexer Syst, D-01187 Dresden, Germany',
'val': 0,
'lon': 13.7090684,
'lat': 51.0266014
},
4: {
'text':
'10.1051/mmnp/20138208: Humboldt Univ, Inst Phys, D-12489 Berlin, Germany',
'val': 0,
'lon': 13.5470509,
'lat': 52.4370179
}
}
}
},
'failed_papers': ['', '10.1016/j.newast.2014.02.011']
}
self.assertEqual(locresults['paper_locations'].keys(),
irwin_network['paper_locations'].keys())
self.assertEqual(set(locresults['failed_papers']),
set(irwin_network['failed_papers']))
self.assertEqual(set(locresults['not_located']),
set(irwin_network['not_located']))
self.maxDiff = tmp
def test_paper_hexbin_query(self):
with wos_reader.open_wos_h5("test_data/irwin.h5") as w5:
locresults = wos_reader_query.paperHexbinQuery(
w5, get_locations_and_unknowns_nocache)
expected_results = {
'not_located': [
'Kyushu Univ, Dept Phys, Fukuoka 812, Japan',
'Natl Res Inst Astron & Geophys, Dept Astron, Cairo 11421, Egypt',
'Natl Res Inst Astron & Geophys, Dept Astron, Cairo 11421, Egypt; Natl Res Inst Astron & Geophys, Kottamia Ctr Sci Excellence Astron & Space Sci KC, Cairo 11421, Egypt'
],
'paper_locations': {
'10.1051/mmnp/20138208': {
'nodes': {
'3': {
'val': 0,
'text':
'10.1051/mmnp/20138208: Humboldt Univ, Inst Phys, D-12489 Berlin, Germany',
'lat': 52.4370179,
'lon': 13.5470509
},
'2': {
'val': 0,
'text':
'10.1051/mmnp/20138208: Univ Potsdam, Inst Phys & Astron, D-14476 Potsdam, Germany; Tech Univ Tampere, Dept Phys, FI-33101 Tampere, Finland',
'lat': 61.4981508,
'lon': 23.7610254
},
'1': {
'val': 0,
'text':
'10.1051/mmnp/20138208: Univ Oxford, Rudolf Peierls Ctr Theoret Phys, Oxford OX1 3NP, England',
'lat': 51.7595933,
'lon': -1.259116
},
'0': {
'val': 0,
'text':
'10.1051/mmnp/20138208: Univ Southern Denmark, MEMPHYS Ctr Biomembrane Phys, Dept Phys Chem & Pharm, DK-5230 Odense M, Denmark',
'lat': 55.37906169999999,
'lon': 10.4033399
},
'4': {
'val': 0,
'text':
'10.1051/mmnp/20138208: Inst Theoret Phys NSC KIPT, UA-61108 Kharkov, Ukraine; Max Planck Inst Phys Komplexer Syst, D-01187 Dresden, Germany',
'lat': 51.0266014,
'lon': 13.7090684
}
},
'edges': {
'3': {
'val': 0,
'to': 4,
'from': 0,
'text': '10.1051/mmnp/20138208'
},
'2': {
'val': 0,
'to': 3,
'from': 0,
'text': '10.1051/mmnp/20138208'
},
'1': {
'val': 0,
'to': 2,
'from': 0,
'text': '10.1051/mmnp/20138208'
},
'0': {
'val': 0,
'to': 1,
'from': 0,
'text': '10.1051/mmnp/20138208'
},
'7': {
'val': 0,
'to': 3,
'from': 2,
'text': '10.1051/mmnp/20138208'
},
'6': {
'val': 0,
'to': 4,
'from': 1,
'text': '10.1051/mmnp/20138208'
},
'5': {
'val': 0,
'to': 3,
'from': 1,
'text': '10.1051/mmnp/20138208'
},
'4': {
'val': 0,
'to': 2,
'from': 1,
'text': '10.1051/mmnp/20138208'
},
'9': {
'val': 0,
'to': 4,
'from': 3,
'text': '10.1051/mmnp/20138208'
},
'8': {
'val': 0,
'to': 4,
'from': 2,
'text': '10.1051/mmnp/20138208'
}
}
}
},
'failed_papers': ['', '10.1016/j.newast.2014.02.011'],
'hexbin': {
'nodes': [{
'text':
'10.1051/mmnp/20138208: Univ Southern Denmark, MEMPHYS Ctr Biomembrane Phys, Dept Phys Chem & Pharm, DK-5230 Odense M, Denmark',
'lng': 10.4033399,
'lat': 55.37906169999999,
'pubcount': 1
}, {
'text':
'10.1051/mmnp/20138208: Univ Oxford, Rudolf Peierls Ctr Theoret Phys, Oxford OX1 3NP, England',
'lng': -1.259116,
'lat': 51.7595933,
'pubcount': 1
}, {
'text':
'10.1051/mmnp/20138208: Univ Potsdam, Inst Phys & Astron, D-14476 Potsdam, Germany; Tech Univ Tampere, Dept Phys, FI-33101 Tampere, Finland',
'lng': 23.7610254,
'lat': 61.4981508,
'pubcount': 1
}, {
'text':
'10.1051/mmnp/20138208: Humboldt Univ, Inst Phys, D-12489 Berlin, Germany',
'lng': 13.5470509,
'lat': 52.4370179,
'pubcount': 1
}, {
'text':
'10.1051/mmnp/20138208: Inst Theoret Phys NSC KIPT, UA-61108 Kharkov, Ukraine; Max Planck Inst Phys Komplexer Syst, D-01187 Dresden, Germany',
'lng': 13.7090684,
'lat': 51.0266014,
'pubcount': 1
}],
'edges': [{
'fromlng': 10.4033399,
'fromlat': 55.37906169999999,
'tolng': -1.259116,
'weight': 1,
'tolat': 51.7595933
}, {
'fromlng': 10.4033399,
'fromlat': 55.37906169999999,
'tolng': 23.7610254,
'weight': 1,
'tolat': 61.4981508
}, {
'fromlng': 10.4033399,
'fromlat': 55.37906169999999,
'tolng': 13.5470509,
'weight': 1,
'tolat': 52.4370179
}, {
'fromlng': 10.4033399,
'fromlat': 55.37906169999999,
'tolng': 13.7090684,
'weight': 1,
'tolat': 51.0266014
}, {
'fromlng': -1.259116,
'fromlat': 51.7595933,
'tolng': 23.7610254,
'weight': 1,
'tolat': 61.4981508
}, {
'fromlng': -1.259116,
'fromlat': 51.7595933,
'tolng': 13.5470509,
'weight': 1,
'tolat': 52.4370179
}, {
'fromlng': -1.259116,
'fromlat': 51.7595933,
'tolng': 13.7090684,
'weight': 1,
'tolat': 51.0266014
}, {
'fromlng': 23.7610254,
'fromlat': 61.4981508,
'tolng': 13.5470509,
'weight': 1,
'tolat': 52.4370179
}, {
'fromlng': 23.7610254,
'fromlat': 61.4981508,
'tolng': 13.7090684,
'weight': 1,
'tolat': 51.0266014
}, {
'fromlng': 13.5470509,
'fromlat': 52.4370179,
'tolng': 13.7090684,
'weight': 1,
'tolat': 51.0266014
}]
}
}
self.assertEqual(len(locresults['hexbin']['nodes']),
len(expected_results['hexbin']['nodes']))
self.assertEqual(len(locresults['hexbin']['edges']),
len(expected_results['hexbin']['edges']))
def do_setup(app):
"""Create a new settings database from scratch"""
if config.SERVER_MODE is False:
print("NOTE: Configuring authentication for DESKTOP mode.")
email = config.DESKTOP_USER
p1 = ''.join([
random.choice(string.ascii_letters + string.digits)
for n in range(32)
])
else:
print("NOTE: Configuring authentication for SERVER mode.\n")
# Prompt the user for their default username and password.
print("""
Enter the email address and password to use for the initial pgAdmin user \
account:\n""")
email_filter = re.compile(
"^[a-zA-Z0-9.!#$%&'*+\/=?^_`{|}~-]+@[a-zA-Z0-9]"
"(?:[a-zA-Z0-9-]{0,61}[a-zA-Z0-9])?(?:\.[a-zA-Z0-9]"
"(?:[a-zA-Z0-9-]{0,61}[a-zA-Z0-9])?)*$")
email = ''
input("Email address: ")
while email == '' or not email_filter.match(email):
print('Invalid email address. Please try again.')
email = input("Email address: ")
def pprompt():
return getpass.getpass(), getpass.getpass('Retype password:'******'Passwords do not match. Please try again.')
p1, p2 = pprompt()
# Setup Flask-Security
user_datastore = SQLAlchemyUserDatastore(db, User, Role)
Security(app, user_datastore)
with app.app_context():
password = encrypt_password(p1)
db.create_all()
user_datastore.create_role(
name='Administrator',
description='pgAdmin Administrator Role'
)
user_datastore.create_role(
name='User',
description='pgAdmin User Role'
)
user_datastore.create_user(email=email, password=password)
db.session.flush()
user_datastore.add_role_to_user(email, 'Administrator')
# Get the user's ID and create the default server group
user = User.query.filter_by(email=email).first()
server_group = ServerGroup(user_id=user.id, name="Servers")
db.session.merge(server_group)
# Set the schema version
version = Version(
name='ConfigDB', value=config.SETTINGS_SCHEMA_VERSION
)
db.session.merge(version)
db.session.commit()
# Done!
print("")
print(
"The configuration database has been created at {0}".format(
config.SQLITE_PATH
)
)
app.config['SQLALCHEMY_DATABASE_URI'] = 'sqlite:///videlish.db'
Base.metadata.bind = engine
DBSession = sessionmaker(bind=engine)
session = DBSession()
# Setup Flask-Security
user_datastore = SQLAlchemyUserDatastore(db, User, Role)
security = Security(app, user_datastore)
newRecipe1 = Recipe(name = 'Spanish Omlet', host = 'YouTube', credit = 'Tasty', hostId = 'ah4YoiIbRpc', photo = "https://img.youtube.com/vi/ah4YoiIbRpc/mqdefault.jpg"
)
newRecipe2 = Recipe(name = 'Almond Butter Oatmeal Muffins', host = 'YouTube', credit = 'Quaker', hostId = 'OqfNwI0Qxww', photo = "https://img.youtube.com/vi/OqfNwI0Qxww/mqdefault.jpg" )
user1 = Account(name = 'Emma Green', username = '******')
user_datastore.create_user(email='*****@*****.**', password='******')
recipeLike1 = RecipeLike(account = user1, recipe=newRecipe1)
session.add(newRecipe1)
session.add(newRecipe2)
session.add(user1)
session.commit()
session.add(recipeLike1)
session.commit()
def create_user():
user_datastore = SQLAlchemyUserDatastore(db, User, Role)
user_datastore.create_user(email='admin', password='******')
db.session.commit()
from flask.ext.security import Security, SQLAlchemyUserDatastore
from flask_wtf.csrf import CsrfProtect
from config import FIRST_USER_PASS, FIRST_USER_NAME
# Initialize the app and database, import the config
app = Flask(__name__)
app.config.from_object('config')
db = SQLAlchemy(app)
CsrfProtect(app)
app.killswitch = 0
# setup db, create the db, setup security, and add first user
from app import models
userstore = SQLAlchemyUserDatastore(db, models.User, None)
sec = Security(app, userstore)
db.create_all()
try:
userstore.create_user(email=FIRST_USER_NAME, password=FIRST_USER_PASS)
db.session.commit()
except: db.session.rollback()
#this loads all views
from app.views import main, admin
#admin setup
_admin = Admin(app, 'NYX Admin', template_mode='bootstrap3',
index_view=admin.ProtectedIndexView())
_admin.add_link(MenuLink(name='Back to Site', url='/'))
_admin.add_view(admin.UserModelView(models.User, db.session))
_admin.add_view(admin.BotModelView(models.Bot, db.session))
def create_app(config_name):
from models import (
User,
Role,
)
from places.models import (
Category,
Feature,
Place,
)
app = Flask(__name__)
app.config.from_object(config[config_name])
config[config_name].init_app(app)
user_datastore = SQLAlchemyUserDatastore(db, User, Role)
security.init_app(app,user_datastore)
principal.init_app(app)
# jwt.init_app(app)
api.init_app(app)
admin.init_app(app)
assets.init_app(app)
assets.register('css_all', css_all)
assets.register('js_vendor', js_vendor)
with app.app_context():
db.init_app(app)
db.create_all()
if not Role.query.first():
admin_role = Role(name='admin',description='Administrator')
db.session.add(admin_role)
db.session.commit()
else:
admin_role = Role.query.filter(Role.name=='admin').first()
if not User.query.first():
user_datastore.create_user(
email='*****@*****.**',
password=encrypt_password('Haukola'),
roles=[admin_role]
)
db.session.commit()
# attach routes and custom error pages here
admin.add_view(UserModelView(User, db.session, category='Auth'))
admin.add_view(AdminModelView(Role, db.session, category='Auth'))
admin.add_view(PlaceAdmin(Place, db.session))
admin.add_view(CategoryAdmin(Category, db.session))
admin.add_view(FeatureAdmin(Feature, db.session))
admin.add_view(LogoutView(name='Logout', endpoint='logout'))
admin.add_view(LoginView(name='Login', endpoint='login'))
sitemap_view = Sitemap.as_view('sitemap')
app.add_url_rule('/sitemap', view_func=sitemap_view)
tapvendors_csv_view = TAPVendorsCSV.as_view('tapvendors_csv')
app.add_url_rule('/csv/tapvendors', view_func=tapvendors_csv_view)
railstations_csv_view = RailStationsCSV.as_view('railstations_csv')
app.add_url_rule('/csv/railstations', view_func=railstations_csv_view)
placemap_view = Placemap.as_view('placemap')
app.add_url_rule('/placemap/',
view_func=placemap_view,
methods=['GET'],
)
placemaptapvendors_view = Placemap.as_view('placemaptapvendors')
app.add_url_rule('/placemap/tapvendors',
view_func=placemaptapvendors_view,
methods=['GET'],
)
placemaprailstations_view = Railmap.as_view('placemaprailstations')
app.add_url_rule('/placemap/railstations',
view_func=placemaprailstations_view,
methods=['GET'],
)
return app
duration = 86400
elif user['duration'] == 'week':
duration = 604800
else:
<<<<<<< HEAD
duration = 13148730
=======
duration = 2592000
# if user['duration'] == 'week':
# duration = 604800
# elif user['duration'] == 'month':
# duration = 2592000
# else:
# duration = 13148730
>>>>>>> master
admin_user_object = user_datastore.create_user(email=user['email'], name=user['name'], password=user['pass'], dhbox_duration=duration)
db.session.commit()
login_user(admin_user_object)
the_new_dhbox = DockerBackend.setup_new_dhbox(admin_user, admin_pass, admin_email)
return str('Successfully created a new DH Box.')
@app.route('/kill_dhbox', methods=['POST'])
@login_required
def kill_dhbox():
the_next = request.form.get('next')
user = request.form.get('user')
print(user)
if current_user.has_role("admin"):
pass
elif user != current_user.name:
# -*- coding: utf-8 -*-
from flask.ext.security import SQLAlchemyUserDatastore
from app import create_app
from app.core import db
from app.data.users import User, Role
app = create_app("dev")
user_datastore = SQLAlchemyUserDatastore(db, User, Role)
# security = Security(app, user_datastore)
# Create a user to test with
# db.drop_all()
# db.create_all()
role = user_datastore.create_role(name="root", description="Site administrator")
user_datastore.create_user(email='*****@*****.**', password='******', roles=[role])
user_datastore.create_user(email='*****@*****.**', password='******')
db.session.commit()
class Test(object):
id = 1
en_title = "title"
ru_title = u"тайтл"
class GPSTest(MarionTest):
"""
Tests both the GPS lookup and some biblio functions that rely on it
"""
def setUp(self):
self.user_datastore = SQLAlchemyUserDatastore(tutorial.db, User, Role)
tutorial.db.create_all()
# u = User( nickname='test1', email='*****@*****.**' )
self.remap_from = "University of Oxford"
self.remap_to = "Oxford, United Kingdom"
self.cache_loc = "Oxford, United Kingdom"
self.cache_lat = 51.7519
self.cache_lon = -1.2578
self.user = self.user_datastore.create_user(nickname='test1',
email='*****@*****.**',
password='******')
tutorial.db.session.add(self.user)
tutorial.db.session.commit()
oxford_remap = Gps_remap(from_location=self.remap_from,
to_location=self.remap_to)
tutorial.db.session.add(oxford_remap)
oxford_lookup = Gps_cache(location=self.cache_loc,
latitude=self.cache_lat,
longitude=self.cache_lon)
tutorial.db.session.add(oxford_lookup)
tutorial.db.session.commit()
def _logout(self):
logout_user()
def tearDown(self):
self._logout()
tutorial.db.session.remove()
tutorial.db.drop_all()
def test_retrieval(self):
remap = Gps_remap.query.get(self.remap_from)
self.assertEqual(remap.from_location, self.remap_from)
cache = Gps_cache.query.get(self.cache_loc)
self.assertAlmostEqual(cache.latitude, self.cache_lat)
self.assertAlmostEqual(cache.longitude, self.cache_lon)
def test_has_keys(self):
self.assertAlmostEqual(remap_has_key(self.remap_from), True)
self.assertAlmostEqual(cache_has_key(self.cache_loc), True)
def test_simplified_guess(self):
self.assertEqual(next_guess("Inst Angew Phys, D-76131 Karlsruhe, Germany"),
"Inst Angew Phys, D-76131 Karlsruhe, Germany")
self.assertEqual(next_guess("Soochow Univ, Sch Phys Sci & Technol, Suzhou 215006, Jiangsu, Peoples R China"),
"Sch Phys Sci & Technol, Suzhou 215006, Jiangsu, Peoples R China")
def test_get_location(self):
self.assertEqual(get_location("blorfing"), None)
self.assertAlmostEqual(get_location(self.cache_loc)['lat'],
self.cache_lat)
self.assertAlmostEqual(get_location("london")['lon'], -0.1277583)
def test_get_locations_and_unknowns(self):
locs, unks = get_locations_and_unknowns(
["University of Oxford", "blorfing"],
False)
self.assertAlmostEqual(locs["University of Oxford"]['lon'],
self.cache_lon)
self.assertEqual(unks[0], "blorfing")
def test_paper_lat_lon_query(self):
"""
"""
with wos_reader.open_wos_h5("test_data/irwin.h5") as w5:
locresults = wos_reader_query.paperLatLonQuery(
w5, get_locations_and_unknowns_nocache)
tmp = self.maxDiff
self.maxDiff = None
irwin_network = {'not_located': ['Kyushu Univ, Dept Phys, Fukuoka 812, Japan', 'Natl Res Inst Astron & Geophys, Dept Astron, Cairo 11421, Egypt; Natl Res Inst Astron & Geophys, Kottamia Ctr Sci Excellence Astron & Space Sci KC, Cairo 11421, Egypt', 'Natl Res Inst Astron & Geophys, Dept Astron, Cairo 11421, Egypt'], 'paper_locations': {'10.1051/mmnp/20138208': {'edges': {0: {'to': 1, 'text': '10.1051/mmnp/20138208', 'from': 0, 'val': 0}, 1: {'to': 2, 'text': '10.1051/mmnp/20138208', 'from': 0, 'val': 0}, 2: {'to': 3, 'text': '10.1051/mmnp/20138208', 'from': 0, 'val': 0}, 3: {'to': 4, 'text': '10.1051/mmnp/20138208', 'from': 0, 'val': 0}, 4: {'to': 2, 'text': '10.1051/mmnp/20138208', 'from': 1, 'val': 0}, 5: {'to': 3, 'text': '10.1051/mmnp/20138208', 'from': 1, 'val': 0}, 6: {'to': 4, 'text': '10.1051/mmnp/20138208', 'from': 1, 'val': 0}, 7: {'to': 3, 'text': '10.1051/mmnp/20138208', 'from': 2, 'val': 0}, 8: {'to': 4, 'text': '10.1051/mmnp/20138208', 'from': 2, 'val': 0}, 9: {'to': 4, 'text': '10.1051/mmnp/20138208', 'from': 3, 'val': 0}}, 'nodes': {0: {'text': '10.1051/mmnp/20138208: Univ Southern Denmark, MEMPHYS Ctr Biomembrane Phys, Dept Phys Chem & Pharm, DK-5230 Odense M, Denmark', 'val': 0, 'lon': 10.4033399, 'lat': 55.37906169999999}, 1: {'text': '10.1051/mmnp/20138208: Univ Potsdam, Inst Phys & Astron, D-14476 Potsdam, Germany; Tech Univ Tampere, Dept Phys, FI-33101 Tampere, Finland', 'val': 0, 'lon': 23.7610254, 'lat': 61.4981508}, 2: {'text': '10.1051/mmnp/20138208: Univ Oxford, Rudolf Peierls Ctr Theoret Phys, Oxford OX1 3NP, England', 'val': 0, 'lon': -1.259116, 'lat': 51.7595933}, 3: {'text': '10.1051/mmnp/20138208: Inst Theoret Phys NSC KIPT, UA-61108 Kharkov, Ukraine; Max Planck Inst Phys Komplexer Syst, D-01187 Dresden, Germany', 'val': 0, 'lon': 13.7090684, 'lat': 51.0266014}, 4: {'text': '10.1051/mmnp/20138208: Humboldt Univ, Inst Phys, D-12489 Berlin, Germany', 'val': 0, 'lon': 13.5470509, 'lat': 52.4370179}}}}, 'failed_papers': ['', '10.1016/j.newast.2014.02.011']}
self.assertEqual(locresults['paper_locations'].keys(),
irwin_network['paper_locations'].keys())
self.assertEqual(set(locresults['failed_papers']),
set(irwin_network['failed_papers']))
self.assertEqual(set(locresults['not_located']),
set(irwin_network['not_located']))
self.maxDiff = tmp
def test_paper_hexbin_query(self):
with wos_reader.open_wos_h5("test_data/irwin.h5") as w5:
locresults = wos_reader_query.paperHexbinQuery(
w5,
get_locations_and_unknowns_nocache)
expected_results = {'not_located': ['Kyushu Univ, Dept Phys, Fukuoka 812, Japan', 'Natl Res Inst Astron & Geophys, Dept Astron, Cairo 11421, Egypt', 'Natl Res Inst Astron & Geophys, Dept Astron, Cairo 11421, Egypt; Natl Res Inst Astron & Geophys, Kottamia Ctr Sci Excellence Astron & Space Sci KC, Cairo 11421, Egypt'], 'paper_locations': {'10.1051/mmnp/20138208': {'nodes': {'3': {'val': 0, 'text': '10.1051/mmnp/20138208: Humboldt Univ, Inst Phys, D-12489 Berlin, Germany', 'lat': 52.4370179, 'lon': 13.5470509}, '2': {'val': 0, 'text': '10.1051/mmnp/20138208: Univ Potsdam, Inst Phys & Astron, D-14476 Potsdam, Germany; Tech Univ Tampere, Dept Phys, FI-33101 Tampere, Finland', 'lat': 61.4981508, 'lon': 23.7610254}, '1': {'val': 0, 'text': '10.1051/mmnp/20138208: Univ Oxford, Rudolf Peierls Ctr Theoret Phys, Oxford OX1 3NP, England', 'lat': 51.7595933, 'lon': -1.259116}, '0': {'val': 0, 'text': '10.1051/mmnp/20138208: Univ Southern Denmark, MEMPHYS Ctr Biomembrane Phys, Dept Phys Chem & Pharm, DK-5230 Odense M, Denmark', 'lat': 55.37906169999999, 'lon': 10.4033399}, '4': {'val': 0, 'text': '10.1051/mmnp/20138208: Inst Theoret Phys NSC KIPT, UA-61108 Kharkov, Ukraine; Max Planck Inst Phys Komplexer Syst, D-01187 Dresden, Germany', 'lat': 51.0266014, 'lon': 13.7090684}}, 'edges': {'3': {'val': 0, 'to': 4, 'from': 0, 'text': '10.1051/mmnp/20138208'}, '2': {'val': 0, 'to': 3, 'from': 0, 'text': '10.1051/mmnp/20138208'}, '1': {'val': 0, 'to': 2, 'from': 0, 'text': '10.1051/mmnp/20138208'}, '0': {'val': 0, 'to': 1, 'from': 0, 'text': '10.1051/mmnp/20138208'}, '7': {'val': 0, 'to': 3, 'from': 2, 'text': '10.1051/mmnp/20138208'}, '6': {'val': 0, 'to': 4, 'from': 1, 'text': '10.1051/mmnp/20138208'}, '5': {'val': 0, 'to': 3, 'from': 1, 'text': '10.1051/mmnp/20138208'}, '4': {'val': 0, 'to': 2, 'from': 1, 'text': '10.1051/mmnp/20138208'}, '9': {'val': 0, 'to': 4, 'from': 3, 'text': '10.1051/mmnp/20138208'}, '8': {'val': 0, 'to': 4, 'from': 2, 'text': '10.1051/mmnp/20138208'}}}}, 'failed_papers': ['', '10.1016/j.newast.2014.02.011'], 'hexbin': {'nodes': [{'text': '10.1051/mmnp/20138208: Univ Southern Denmark, MEMPHYS Ctr Biomembrane Phys, Dept Phys Chem & Pharm, DK-5230 Odense M, Denmark', 'lng': 10.4033399, 'lat': 55.37906169999999, 'pubcount': 1}, {'text': '10.1051/mmnp/20138208: Univ Oxford, Rudolf Peierls Ctr Theoret Phys, Oxford OX1 3NP, England', 'lng': -1.259116, 'lat': 51.7595933, 'pubcount': 1}, {'text': '10.1051/mmnp/20138208: Univ Potsdam, Inst Phys & Astron, D-14476 Potsdam, Germany; Tech Univ Tampere, Dept Phys, FI-33101 Tampere, Finland', 'lng': 23.7610254, 'lat': 61.4981508, 'pubcount': 1}, {'text': '10.1051/mmnp/20138208: Humboldt Univ, Inst Phys, D-12489 Berlin, Germany', 'lng': 13.5470509, 'lat': 52.4370179, 'pubcount': 1}, {'text': '10.1051/mmnp/20138208: Inst Theoret Phys NSC KIPT, UA-61108 Kharkov, Ukraine; Max Planck Inst Phys Komplexer Syst, D-01187 Dresden, Germany', 'lng': 13.7090684, 'lat': 51.0266014, 'pubcount': 1}], 'edges': [{'fromlng': 10.4033399, 'fromlat': 55.37906169999999, 'tolng': -1.259116, 'weight': 1, 'tolat': 51.7595933}, {'fromlng': 10.4033399, 'fromlat': 55.37906169999999, 'tolng': 23.7610254, 'weight': 1, 'tolat': 61.4981508}, {'fromlng': 10.4033399, 'fromlat': 55.37906169999999, 'tolng': 13.5470509, 'weight': 1, 'tolat': 52.4370179}, {'fromlng': 10.4033399, 'fromlat': 55.37906169999999, 'tolng': 13.7090684, 'weight': 1, 'tolat': 51.0266014}, {'fromlng': -1.259116, 'fromlat': 51.7595933, 'tolng': 23.7610254, 'weight': 1, 'tolat': 61.4981508}, {'fromlng': -1.259116, 'fromlat': 51.7595933, 'tolng': 13.5470509, 'weight': 1, 'tolat': 52.4370179}, {'fromlng': -1.259116, 'fromlat': 51.7595933, 'tolng': 13.7090684, 'weight': 1, 'tolat': 51.0266014}, {'fromlng': 23.7610254, 'fromlat': 61.4981508, 'tolng': 13.5470509, 'weight': 1, 'tolat': 52.4370179}, {'fromlng': 23.7610254, 'fromlat': 61.4981508, 'tolng': 13.7090684, 'weight': 1, 'tolat': 51.0266014}, {'fromlng': 13.5470509, 'fromlat': 52.4370179, 'tolng': 13.7090684, 'weight': 1, 'tolat': 51.0266014}]}}
self.assertEqual(len(locresults['hexbin']['nodes']),
len(expected_results['hexbin']['nodes']))
self.assertEqual(len(locresults['hexbin']['edges']),
len(expected_results['hexbin']['edges']))
def init_db():
fake_app = create_app()
with fake_app.test_request_context():
db.create_all()
datastore = SQLAlchemyUserDatastore(db, User, Role)
print("\n** ADDING ROLES **")
for role in ['admin', 'manager']:
try:
print("adding role '%s'" % role)
datastore.create_role(name=role, description=role)
datastore.commit()
print(" ...OK")
except IntegrityError as r:
print(" '%s' role already exists" % role)
db.session.rollback()
print("\n** ADDING USERS **")
users = [
fake_app.config['ADMIN_USER'], fake_app.config['MANAGER_USER'],
fake_app.config['CLERK_USER']
]
for user in users:
if user:
name = user['name']
email = user['email']
role = user['role']
password = user['password']
try:
print("adding user '%s'" % name)
password = encrypt_password(password)
datastore.create_user(email=email,
password=password,
name=name,
active=True)
datastore.commit()
print(" ...OK")
except IntegrityError as e:
print(" user '%s' already exists" % name)
db.session.rollback()
if role:
try:
print("adding '%s' role to user '%s'" % (role, name))
this_user = db.session.query(User)\
.filter(User.name == name).first()
this_role = db.session.query(Role).filter(
Role.name == role).first()
datastore.add_role_to_user(this_user, this_role)
datastore.commit()
print(" ...OK")
except IntegrityError as e:
print(" unable to add role '%s' to user '%s'" %
(role, name))
from alembic.config import Config
from alembic import command
path = os.path.join(os.path.dirname(__file__), 'alembic.ini')
alembic_cfg = Config(path)
command.stamp(alembic_cfg, 'head')
