def create_app(config_filename="config/easyris.cfg",
database_cfg="config/database.cfg",
**kwargs):
app = EasyRis(__name__)
app.config.from_pyfile(config_filename)
kwargs = {k.upper(): v for k, v in kwargs.iteritems()}
app.config.update(**kwargs)
from datetime import timedelta
app.config['PERMANENT_SESSION_LIFETIME'] = timedelta(
hours=int(app.config['PERMANENT_SESSION_LIFETIME']))
# This is to prevent bad url in frontend
app.url_map.strict_slashes = False
# Add basic apis
app.add_url_rule('/', 'entry', entry)
app.add_url_rule('/debug', 'debug', debug)
from easyris.utils.api import cities
from easyris.patient.api import patient
from easyris.user.api import login_
from easyris.examination.api.typology import typology
from easyris.report.api import report
from easyris.examination.api.base import examination
from easyris.log.api import event
# Register blueprint from other modules
app.register_blueprint(patient, url_prefix='/patient')
app.register_blueprint(cities, url_prefix='/cities')
app.register_blueprint(typology, url_prefix='/typology')
app.register_blueprint(examination, url_prefix='/examination')
app.register_blueprint(login_, url_prefix='')
app.register_blueprint(report, url_prefix="/report")
app.register_blueprint(event, url_prefix="/event")
from flask_debugtoolbar import DebugToolbarExtension
app.toolbar = DebugToolbarExtension(app)
app.login_manager = LoginManager()
app.login_manager.init_app(app)
app.before_request(before_request)
def load_user(userid):
# Return an instance of the User model
return app.get_user(userid)
app.login_manager.user_loader(load_user)
# Database connection
from easyris.base.database import parse_db_config, easyris_connect
db_config = parse_db_config(database_cfg)
db_client = easyris_connect(**db_config)
app.config['DB_CLIENT'] = db_client
return app
def run(database_config, n_loaded=50):
db_config = parse_db_config(database_config)
_ = easyris_connect(**db_config)
#client = connect(database, port=port)
Examination.drop_collection()
priority_list = Priority.objects()
typology_list = Typology.objects()
patient_list = Patient.objects()
user1 = User.objects(username='******').first()
user2 = User.objects(username='******').first()
for _ in range(n_loaded):
ip = random.randint(0, len(patient_list) - 1)
it = random.randint(0, len(typology_list) - 1)
ipr = random.randint(0, len(priority_list) - 1)
patient = patient_list[ip]
typology = typology_list[it]
priority = priority_list[ipr]
random_number = random.randint(1, 10)
if random_number > 5:
now = datetime.now()
date_ = datetime(year=now.year, month=now.month, day=now.day)
if random_number == 8:
status_name = 'completed'
status = CompletedExaminationStatus()
else:
status_name = 'new'
status = NewExaminationStatus()
else:
date_ = datetime(year=2016, month=02, day=02)
status_name = 'completed'
status = CompletedExaminationStatus()
examination = Examination(id_patient=patient,
medico_richiedente='Mauro Caffarini',
data_inserimento=date_,
id_priority=priority,
id_typology=typology,
id_technician=user2,
id_creator=user1,
status_name=status_name,
status=status,
codice_esenzione='67577568',
examination_note='ok')
examination.save()
def setUp(self, n_loaded=5, **kwargs):
# TODO: Check overriding in other classes
from easyris.base.database import parse_db_config, \
restore_db,\
easyris_connect
db_filename = "config/database_test.cfg"
db_config = parse_db_config(db_filename)
conn = easyris_connect(**db_config)
self.client = conn
restore_db(db_filename)
def run(database_config="config/database.cfg", **kwargs):
from easyris.base.database import parse_db_config, easyris_connect
db_config = parse_db_config(database_config)
print db_config
conn = easyris_connect(**db_config)
db_name = db_config['database_name']
# Always delete database
if db_name in conn.database_names():
print "Database found. Deleting it!"
conn.drop_database(db_name)
else:
print "Database not found..."
print " ---- Database population ---"
path = os.path.dirname(os.path.realpath(__file__))
# Import city
import_csv(db_name, 'city', os.path.join(path,
"files/codicicomuni2015.csv"))
print "Import patient.csv"
if 'n_loaded' in kwargs.keys():
n_loaded = kwargs['n_loaded']
else:
n_loaded = 100
if 'n_patient' in kwargs.keys():
n_loaded = kwargs['n_patient']
patient_db.run(database_config, n_loaded=n_loaded)
# Import priority_db.csv
import_csv(db_name, 'priority', os.path.join(path,
"files/priority_db.csv"))
# Import nomenclatura_esami.csv
import_csv(db_name, 'typology',
os.path.join(path, "files/nomenclatura_esami.csv"))
print "Populating users, permissions and roles."
user_db.run(database_config)
print "Creating dummy examinations."
if 'n_examination' in kwargs.keys():
n_loaded = kwargs['n_examination']
examination_db.run(database_config, n_loaded=n_loaded * 2)
print "Creating dummy reports."
if 'n_report' in kwargs.keys():
n_loaded = kwargs['n_report']
report_db.run(database_config, n_loaded=n_loaded)
return
def save_event(event_dict):
from easyris.base.database import parse_db_config, easyris_connect
db_config = parse_db_config("config/database.cfg")
db_config['database_name'] = 'easyris_log'
db_client = easyris_connect(**db_config)
print event_dict
event = Event(**event_dict)
event.save()
return "Event saved!"
def run(database_config, n_loaded=100):
db_config = parse_db_config(database_config)
print db_config
conn = easyris_connect(**db_config)
database = db_config['database_name']
db = conn.get_database(database)
print db
if 'city' not in db.collection_names():
# We imported the short version
# We think that we are testing the app!
from easyris.utils.database_setup import import_csv
path = os.path.dirname(os.path.realpath(__file__))
# Import city
print os.path.join(path, "files/codicicomuni_test.csv")
print '------------'
print '------------'
print '------------'
import_csv(database, 'city',
os.path.join(path, "files/codicicomuni_test.csv"))
path = '/'.join(__file__.split('/')[:-1])
print path
filepath = os.path.join(path, 'files/db_test_population.csv')
with open(filepath, 'rb') as csvfile:
patient_csv = csv.reader(csvfile, delimiter=',')
for i, row in enumerate(patient_csv):
if i == 0:
keys_ = [str.lower(r_) for r_ in row]
elif i < n_loaded:
fields_ = dict(zip(keys_, row))
fields_['birthplace'] = str.upper(fields_['birthplace'])
fields_['city'] = str.upper(fields_['city'])
fields_['birthdate'] = datetime.strptime(
fields_['birthdate'], "%Y-%m-%d")
fields_['province'] = None
patient_ = Patient(**fields_)
#print fields_
patient_.save()
def run(database_config, n_loaded=50):
db_config = parse_db_config(database_config)
_ = easyris_connect(**db_config)
Report.drop_collection()
user = User.objects(username='******').first()
examination_list = Examination.objects(status_name='completed',
data_inserimento=datetime.datetime(year=2016,
month=02,
day=02))
# Trovo i pazienti con piu esami
id_patient_list = [e.id_patient.id_patient for e in examination_list]
counter = collections.Counter(id_patient_list)
if len(counter) < n_loaded:
n_loaded = len(counter) / 2
print n_loaded
for i in range(n_loaded):
id_patient = counter.keys()[i]
patient = Patient.objects(id_patient=id_patient).first()
patient_examination = Examination.objects(id_patient=patient.id,
status_name='completed',
data_inserimento=datetime.datetime(year=2016,
month=02,
day=02))
dates_ = np.unique([e.data_inserimento for e in patient_examination])
for d_ in dates_:
data_ = datetime.datetime(d_.year, d_.month, d_.day)
same_date_examination = Examination.objects(id_patient=patient.id,
data_inserimento=data_,
status_name='completed')
report_log = ReportAction(
user=user,
action='create'
)
report = Report(
id_examination = [e for e in same_date_examination],
report_text = "Il paziente bla bla bla",
action_list = [report_log],
id_patient = id_patient,
status=SuspendedReportStatus(),
status_name='suspended'
)
report.save()
for e in same_date_examination:
e.modify(status=ClosedExaminationStatus(),
status_name='closed')
e.save()
def run(database_config):
from easyris.base.database import parse_db_config, easyris_connect
db_config = parse_db_config(database_config)
conn = easyris_connect(**db_config)
actions = ['create', 'read', 'update', 'delete']
actions_examination_status = [
'start', 'go', 'stop', 'pause', 'finish', 'eject'
]
actions_report_status = ['close', 'save', 'print', 'open']
resources = [
'patient', 'examination', 'report', 'examination_status',
'report_status'
]
permission_ = itertools.product(resources, actions)
Permission.drop_collection()
permission_list = []
for it in permission_:
p = Permission(it[1], it[0])
p.save()
permission_list.append(p)
ex_status_permission = itertools.product(['examination'],
actions_examination_status)
for it in ex_status_permission:
p = Permission(it[1], it[0])
p.save()
permission_list.append(p)
report_status_permission = itertools.product(['report'],
actions_report_status)
for it in report_status_permission:
p = Permission(it[1], it[0])
p.save()
permission_list.append(p)
permission_dict = {
'accettazione':
np.array([1, 2, 3, 5, 6, 13, 14, 18, 30]) - 1,
'tecnico':
np.array([2, 6, 7, 8, 14, 15, 16, 18, 21, 22, 23, 24, 25]) - 1,
'medico':
np.array([2, 6, 9, 10, 11, 14, 17, 18, 19, 26, 27, 28, 29, 30]) - 1,
'amministrazione':
np.array([2, 6, 10, 14, 18]) - 1,
'admin':
np.arange(30)
}
Role.drop_collection()
for key_, value_ in permission_dict.iteritems():
role_ = Role(key_, [permission_list[i] for i in value_])
role_.save()
User.drop_collection()
role_medico = Role.objects(role_name='medico').first()
user1 = User(username='******',
password='******',
roles=[role_medico],
first_name='Massimo',
last_name='Caulo',
telephone_number='3289876543',
mobile_number='3212345678',
email='*****@*****.**')
user1.save()
role_acc = Role.objects(role_name='accettazione').first()
user2 = User(username='******',
password='******',
roles=[role_acc],
first_name='Gaetano',
last_name='Di Gaetano',
telephone_number='3289876543',
mobile_number='3212345678',
email='*****@*****.**')
user2.save()
role_tecnico = Role.objects(role_name='tecnico').first()
user3 = User(username='******',
password='******',
roles=[role_tecnico],
first_name='Daniele',
last_name='Petrucci',
telephone_number='3289876543',
mobile_number='3212345678',
email='*****@*****.**')
user3.save()
role_amministrazione = Role.objects(role_name='amministrazione').first()
user4 = User(username='******',
password='******',
roles=[role_amministrazione],
first_name='Carlo',
last_name='Michetti',
telephone_number='3289876543',
mobile_number='3212345678',
email='*****@*****.**')
user4.save()
role_admin = Role.objects(role_name='admin').first()
user5 = User(username='******',
password='******',
roles=[role_admin],
first_name='Piero',
last_name='Chiacchiaretta',
telephone_number='3289876543',
mobile_number='3212345678',
email='*****@*****.**')
user5.save()
user11 = User(username='******',
password='******',
roles=[role_medico],
first_name='Valentina',
last_name='Panara',
telephone_number='3289876543',
mobile_number='3212345678',
email='*****@*****.**')
user11.save()
