def install_packages(packages):
if ask_to_install(packages):
logger.info("Dependencies installed. Please launch Faraday Server again")
sys.exit(0)
else:
logger.error("Dependencies not met")
sys.exit(1)
def is_server_running():
pid = daemonize.is_server_running()
if pid is not None:
logger.error("Faraday Server is already running. PID: {}".format(pid))
return True
else:
return False
def setup_environment(check_deps=False):
# Configuration files generation
server.config.copy_default_config_to_local()
if check_deps:
# Check dependencies
installed_deps, missing_deps, conflict_deps = dependencies.check_dependencies(
requirements_file=server.config.REQUIREMENTS_FILE)
logger.info("Checking dependencies...")
if conflict_deps:
logger.info("Some dependencies are old. Update them with \"pip install -r requirements_server.txt -U\"")
if missing_deps:
install_deps = query_yes_no("Do you want to install them?", default="no")
if install_deps:
dependencies.install_packages(missing_deps)
logger.info("Dependencies installed. Please launch Faraday Server again.")
sys.exit(0)
else:
logger.error("Dependencies not met. Please refer to the documentation in order to install them. [%s]",
", ".join(missing_deps))
logger.info("Dependencies met")
# Web configuration file generation
server.config.gen_web_config()
def get_prescriptions(patientid):
"""
Get info of a doctor in the system.
:param doctorid: doctor's uid
:returns: a status, a str ( doctor's info on success, err info on failure)
"""
# print(doctorid)
logger.debug('in get_prescriptions')
resp_list = []
try:
patient = PatientModel.get(PatientModel.email==patientid)
for prescription in PrescriptionModel.select().where(PrescriptionModel.patient==patient):
logger.debug('drug_id: %s, descrip: %s' % (prescription.drug_id, prescription.description))
resp_dict = {}
resp_dict['drug_name'] = prescription.drug_name
resp_dict['after_meal'] = prescription.after_meal
resp_dict['description'] = prescription.description
resp_dict['datetime'] = prescription.datetime
resp_dict['amount'] = prescription.amount
resp_dict['dosage_per_day'] = prescription.dosage_per_day
resp_dict['response_doctor'] = prescription.response_doctor
resp_list.append(resp_dict)
logger.debug('prescriptions:{}'.format(resp_list))
except Exception as ex:
logger.error('Exception: ', ex)
return 0, {'errinfo':'get prescriptions failed'}
else:
return 1, resp_list
def setup_environment(check_deps=False):
# Configuration files generation
server.config.copy_default_config_to_local()
if check_deps:
# Check dependencies
installed_deps, missing_deps = dependencies.check_dependencies(
requirements_file=server.config.REQUIREMENTS_FILE)
logger.info("Checking dependencies...")
if missing_deps:
install_deps = query_yes_no("Do you want to install them?", default="no")
if install_deps:
dependencies.install_packages(missing_deps)
logger.info("Dependencies installed. Please launch Faraday Server again.")
sys.exit(0)
else:
logger.error("Dependencies not met. Please refer to the documentation in order to install them. [%s]",
", ".join(missing_deps))
logger.info("Dependencies met")
# Web configuration file generation
server.config.gen_web_config()
# Reports DB creation
server.couchdb.push_reports()
def get_discharges(patientid):
"""
Get info of a doctor in the system.
:param doctorid: doctor's uid
:returns: a status, a str ( doctor's info on success, err info on failure)
"""
# print(doctorid)
logger.debug('in get_discharges')
resp_list = []
try:
patient = PatientModel.get(PatientModel.email==patientid)
for discharge in DischargeModel.select().where(DischargeModel.patient==patient):
logger.debug('discharge_id: %s, indate: %s' % (discharge.discharge_id, discharge.indate))
resp_dict = {}
resp_dict['indate'] = discharge.indate
resp_dict['outdate'] = discharge.outdate
resp_dict['response_doctor'] = discharge.response_doctor
resp_dict['description'] = discharge.description
resp_dict['datetime'] = discharge.datetime
resp_list.append(resp_dict)
logger.debug('discharges:{}'.format(resp_list))
except Exception as ex:
logger.error('Exception: ', ex)
return 0, {'errinfo':'get discharges failed'}
else:
return 1, resp_list
def is_server_running():
pid = daemonize.is_server_running()
if pid is not None:
logger.error("Faraday Server is already running. PID: {}".format(pid))
return True
else:
return False
def run(self):
for change_doc in self.__stream:
try:
if self.CHANGE_CLS.validate(change_doc):
self.__changes_callback(self.CHANGE_CLS(change_doc))
else:
logger.debug(u'Ignoring change: {}'.format(change_doc))
except Exception, e:
import traceback
logger.debug(traceback.format_exc())
logger.warning(
u"Error while processing change. Ignoring. Offending change: {}"
.format(change_doc))
if change_doc.get('error', None):
if change_doc.get('error') == 'unauthorized':
logger.error(u"Unauthorized access to CouchDB. Make sure faraday-server's"\
" configuration file has CouchDB admin's credentials set")
thread.interrupt_main()
# TODO: A proper fix is needed here
elif change_doc.get('reason') == 'no_db_file':
self.__stream.stop()
break
def check_appointment(doctorid, date):
"""
Get info of appointments for a doctor on a date in the system.
:param appointment_url: appointment's url
:returns: a status, a str ( appointments timeslots info on success,
err info on failure)
"""
# print(doctorid, date)
# info = {}
try:
logger.debug('in check_appointment')
schedule = rediscli.get_data(doctorid+'/'+date)
except Exception as ex:
logger.error('Exception: ', ex)
return 0, 'check_appointment failed'
else:
logger.debug('in check_appointment schedule data:{}'.format(schedule))
if schedule:
logger.debug('in check_appointment schedule data:{}'.format(schedule))
# appointments_json = json.dumps(schedule)
return 1, compatible(schedule)
# no appointment for this doctor on this date
else:
return 1, compatible('{}')
def get_obj(patientid, objid):
"""
Get info of a doctor in the system.
:param doctorid: doctor's uid
:returns: a status, a str ( doctor's info on success, err info on failure)
"""
# print(doctorid)
info = {}
try:
resp_dict = {}
obj = ObjectModel.get(ObjectModel.objid==objid)
storage_url, auth_token = swiftclient.client.get_auth(
conf.auth_url,
conf.account_username,
conf.password,
auth_version=conf.auth_version)
resp_dict['auth_token'] = auth_token
resp_dict['storage_url'] = storage_url + '/' + \
conf.container + '/' + patientid + '/' + objid
except Exception as ex:
logger.error('Exception: ', ex)
return 0, {'errinfo':'get obj failed'}
else:
return 1, resp_dict
def get_objs(patientid):
"""
Get info of a doctor in the system.
:param doctorid: doctor's uid
:returns: a status, a str ( doctor's info on success, err info on failure)
"""
# print(doctorid)
logger.debug('in get_objs')
resp_list = []
try:
patient = PatientModel.get(PatientModel.email==patientid)
for obj in ObjectModel.select().where(ObjectModel.patient==patient):
logger.debug('objid: %s, descrip: %s' % (obj.objid, obj.description))
resp_dict = {}
resp_dict['objid'] = obj.objid
resp_dict['objname'] = obj.objname
resp_dict['description'] = obj.description
resp_dict['datetime'] = obj.datetime
resp_list.append(resp_dict)
logger.debug('objs:{}'.format(resp_list))
except Exception as ex:
logger.error('Exception: ', ex)
return 0, {'errinfo':'get objs failed'}
else:
return 1, resp_list
def get_comments(patientid):
"""
Get info of a doctor in the system.
:param doctorid: doctor's uid
:returns: a status, a str ( doctor's info on success, err info on failure)
"""
# print(doctorid)
logger.debug('in get_comments')
resp_list = []
try:
patient = PatientModel.get(PatientModel.email==patientid)
for comment in CommentModel.select().where(CommentModel.patient==patient):
logger.debug('comment_id: %s, comment: %s' % (comment.comment_id, comment.comment))
resp_dict = {}
resp_dict['comment'] = comment.comment
resp_dict['datetime'] = comment.datetime
resp_dict['response_doctor'] = comment.response_doctor
resp_list.append(resp_dict)
logger.debug('comments:{}'.format(resp_list))
except Exception as ex:
logger.error('Exception: ', ex)
return 0, {'errinfo':'get comments failed'}
else:
return 1, resp_list
def get_doctors():
"""
Get info of doctors in the system.
:returns: a status, a str ( doctor's info on success, err info on failure)
"""
# print(doctorid)
logger.debug('in get_doctors')
resp_list = []
try:
# patient = DoctorModel.get(DoctorModel.email==patientid)
doctors = DoctorModel.select()
print(doctors)
for doc in doctors:
print('doc')
logger.debug('docid: %s' % (doc))
resp_dict = {}
resp_dict['doctorid'] = doc.email
resp_dict['last_name'] = doc.last_name
resp_dict['first_name'] = doc.first_name
resp_list.append(resp_dict)
logger.debug('doctors:{}'.format(resp_list))
except Exception as ex:
logger.error('Exception: ', ex)
return 0, {'errinfo':'get doctors failed'}
else:
return 1, resp_list
def authentication(role, post_data):
"""
Register a patient in the system. The post data is in json format.
:param post_data: dict
:returns: a status, a str( patient's info on success, err info on failure)
"""
# print(post_data)
auth_dict = {}
try:
logger.debug('in authentication')
user = LoginModel.get(LoginModel.username==post_data['username'],
LoginModel.role==role)
except Exception as ex:
logger.error('Exception: ', ex)
return 0, 'auth failed'
else:
logger.debug("user.password:{}, post_data['password']:{}".format(
user.password, post_data['password']))
if user.password==post_data['password']:
try:
# auth_dict['token'] = get_token(post_data['username'], role)
token = get_token(post_data['username'], role)
except Exception as ex:
logger.error('Exception: ', ex)
return 0, 'auth failed, get token failed'
else:
# auth_json = json.dumps(auth_dict)
logger.debug(token)
return 1, token
else:
return 0, 'auth failed, password not match'
def edit_doctor(doctorid, post_data):
"""
Edit a doctor in the system. The post data is a dict.
:param post_data: dict
:returns: a status, a str( doctor's info on success, err info on failure)
"""
# print(post_data)
try:
logger.debug('in edit_doctor')
DoctorModel.update_by_dict(doctorid, post_data)
logger.debug('executed')
# except peewee.IntegrityError:
# logger.warning('in doctor model create except')
# # `username` is a unique column, so this username already exists,
# # making it safe to call .get().
# old_user = AccountModel.get(AccountModel.username == username)
# logger.warning('user exists...')
# resp_dict['info'] = 'user exists, did not create user:%s' % username
# resp.status = falcon.HTTP_409
# try:
# change_user = AccountModel.get(AccountModel.username==username,
# AccountModel.password==password)
# except:
# logger.debug('change user data failed...')
except Exception as ex:
logger.error('Exception: ', ex)
return 0, 'edit_doctor failed, did not edit doctor'
else:
return 1, str(doctorid)
def install_packages(packages):
if ask_to_install(packages):
logger.info(
"Dependencies installed. Please launch Faraday Server again")
sys.exit(0)
else:
logger.error("Dependencies not met")
sys.exit(1)
def __process_new_workspace(self, ws_name):
if ws_name in self.__workspaces:
logger.info(u"Workspace {} already exists. Ignoring change.".format(ws_name))
elif not server.couchdb.server_has_access_to(ws_name):
logger.error(u"Unauthorized access to CouchDB for Workspace {}. Make sure faraday-server's"\
" configuration file has CouchDB admin's credentials set".format(ws_name))
else:
self.__create_and_import_workspace(ws_name)
def log_exception(self, *exc_info):
if isinstance(exc_info[1], tornado.web.HTTPError):
# Delegate HTTPError's to the base class
# We don't want these through normal exception handling
return super(ContextHandler, self).log_exception(*exc_info)
msg = traceback.format_exception(*exc_info)
logger.error('ERROR: %s' % "".join(msg))
def __process_new_workspace(self, ws_name):
if ws_name in self.__workspaces:
logger.info(
u"Workspace {} already exists. Ignoring change.".format(
ws_name))
elif not server.couchdb.server_has_access_to(ws_name):
logger.error(u"Unauthorized access to CouchDB for Workspace {}. Make sure faraday-server's"\
" configuration file has CouchDB admin's credentials set".format(ws_name))
else:
self.__create_and_import_workspace(ws_name)
def get_config(self, option):
query = self.database.session.query(server.models.DatabaseMetadata)
query = query.filter(server.models.DatabaseMetadata.option == option)
try:
result = query.one_or_none()
except MultipleResultsFound:
msg = u'Database {} should not have the option {} defined multiple times'.format(self.__workspace, option)
logger.error(msg)
raise RuntimeError(msg)
return result
def import_workspaces():
couchdb_server_conn, workspaces_list = _open_couchdb_conn()
for workspace_name in workspaces_list:
logger.info(u'Setting up workspace {}'.format(workspace_name))
if not server.couchdb.server_has_access_to(workspace_name):
logger.error(u"Unauthorized access to CouchDB. Make sure faraday-server's"\
" configuration file has CouchDB admin's credentials set")
sys.exit(1)
import_workspace_into_database(workspace_name, couchdb_server_conn=couchdb_server_conn)
def upload_obj(patientid, post_data):
"""
Upload an obj in the system. The post data is a dict.
:param post_data: dict
:returns: a status, a str( obj's info on success, err info on failure)
"""
# print(post_data)
obj = ''
try:
logger.debug('in upload_obj')
logger.debug('auth_url:{}, account_username:{}, password:{}'.format(
conf.auth_url, conf.account_username, conf.password))
resp_dict = {}
storage_url, auth_token = swiftclient.client.get_auth(
conf.auth_url,
conf.account_username,
conf.password,
auth_version=conf.auth_version)
resp_dict['auth_token'] = auth_token
resp_dict['storage_url'] = storage_url + '/' + \
conf.container + '/' + patientid + '/' + \
patientid + '-' + post_data['objname'] + '-' + post_data['datetime']
with database.atomic():
obj = ObjectModel.create_by_dict(patientid, post_data)
logger.debug(obj)
logger.debug('in database.atomic')
# except peewee.IntegrityError:
# logger.warning('in doctor model create except')
# # `username` is a unique column, so this username already exists,
# # making it safe to call .get().
# old_user = AccountModel.get(AccountModel.username == username)
# logger.warning('user exists...')
# resp_dict['info'] = 'user exists, did not create user:%s' % username
# resp.status = falcon.HTTP_409
# try:
# change_user = AccountModel.get(AccountModel.username==username,
# AccountModel.password==password)
# except:
# logger.debug('change user data failed...')
except Exception as ex:
logger.error('Exception: ', ex)
q = ObjectModel.delete().where(ObjectModel.objid==
patientid + '-' + post_data['objname'] + '-' + post_data['datetime'])
q.execute()
return 0, {'errinfo':'create obj failed, did not create obj'}
else:
resp_dict['info'] = 'make PUT request to storage_url with auth_token as "x-storage-token" in headers'
return 1, resp_dict
def _create_and_import_db(db_conn, couchdb_conn):
db_conn.create()
db_conf = server.database.Configuration(db_conn)
db_conf.set_last_seq(couchdb_conn.get_last_seq())
try:
_import_from_couchdb(db_conn, couchdb_conn)
except Exception, e:
import traceback
logger.debug(traceback.format_exc())
logger.error(u'Error while importing workspace {}: {!s}'.format(db_conn.db_name, e))
db_conn.delete()
raise e
def get_config(self, option):
query = self.database.session.query(server.models.DatabaseMetadata)
query = query.filter(server.models.DatabaseMetadata.option == option)
try:
result = query.one_or_none()
except MultipleResultsFound:
msg = u'Database {} should not have the option {} defined multiple times'.format(
self.__workspace, option)
logger.error(msg)
raise RuntimeError(msg)
return result
def __get_config(self, option):
try:
result = self.__db_conn.session\
.query(server.models.DatabaseMetadata)\
.filter(server.models.DatabaseMetadata.option == option)\
.one_or_none()
except MultipleResultsFound:
msg = u'Database {} should not have the option {} defined multiple times'.format(self.__db_conn.db_name, option)
logger.error(msg)
raise RuntimeError(msg)
return result
def make_appointment(post_data):
"""
make_appointment in the system. The post data is in json format.
:param post_data: dict
:returns: a status, a str( appointment's url on success, err info on failure)
with database.atomic():
doctor = DoctorModel.create_by_dict(post_data)
logger.debug(doctor)
logger.debug('in database.atomic')
except peewee.IntegrityError:
logger.warning('in doctor model create except')
1. check if patient and doctor exist in db
2. check if the appointment exist in redis
3. make appointment if 1 and 2 ok
3.2 add the appointment to the doctor's that day's schedule
4. return if appointment exists, with reason if fail
"""
# print(post_data)
try:
logger.debug('in make_appointment')
# check db when patient is ok
rediscli.set_data(
post_data['doctorid']+'/'+post_data['datetimeslot']+'/'+
post_data['patientid'], post_data)
schedule = rediscli.get_data(post_data['doctorid']+'/'+
post_data['datetimeslot'][:8])
if schedule:
schedule = ast.literal_eval(schedule)
schedule[post_data['datetimeslot'][8:]] = '1'
rediscli.set_data(post_data['doctorid']+'/'+post_data['datetimeslot'][:8],
json.dumps(schedule))
else:
schedule = {post_data['datetimeslot'][8:]:'1'}
logger.debug('in make_appointment, schedule:{}'.format(json.dumps(schedule)))
rediscli.set_data(post_data['doctorid']+'/'+post_data['datetimeslot'][:8],
json.dumps(schedule))
except Exception as ex:
logger.error('Exception: ', ex)
# q = DoctorModel.delete().where(DoctorModel.uid==doctor)
# q.execute()
return 0, 'make_appointment failed, did not make_appointment'
else:
return 1, str(post_data['doctorid']+'/'+post_data['datetimeslot']+'/'+
post_data['patientid'])
def check_postgresql():
with app.app_context():
try:
if not db.session.query(Workspace).count():
logger.warn('No workspaces found. Remember to execute CouchDB importer')
except sqlalchemy.exc.ArgumentError:
logger.error(
'\n\b{RED}Please check your PostgreSQL connection string in the file ~/.faraday/config/server.ini on your home directory.{WHITE} \n'.format(RED=Fore.RED, WHITE=Fore.WHITE)
)
sys.exit(1)
except sqlalchemy.exc.OperationalError:
logger.error(
'\n\n{RED}Could not connect to PostgreSQL.\n{WHITE}Please check: \n{YELLOW} * if database is running \n * configuration settings are correct. \n\n{WHITE}For first time installations execute{WHITE}: \n\n {GREEN} python manage.py initdb\n\n'.format(GREEN=Fore.GREEN, YELLOW=Fore.YELLOW, WHITE=Fore.WHITE, RED=Fore.RED))
sys.exit(1)
def __get_config(self, option):
try:
result = self.__db_conn.session\
.query(server.models.DatabaseMetadata)\
.filter(server.models.DatabaseMetadata.option == option)\
.one_or_none()
except MultipleResultsFound:
msg = u'Database {} should not have the option {} defined multiple times'.format(
self.__db_conn.db_name, option)
logger.error(msg)
raise RuntimeError(msg)
return result
def check_postgresql():
with app.app_context():
try:
if not db.session.query(Workspace).count():
logger.warn('No workspaces found. Remeber to execute couchdb importer')
except sqlalchemy.exc.ArgumentError:
logger.error(
'\n\b{RED}Please check you postgresql connection string in server.ini at .faraday on your ohme directory.{WHITE} \n'.format(RED=Fore.RED, WHITE=Fore.WHITE)
)
sys.exit(1)
except sqlalchemy.exc.OperationalError:
logger.error(
'\n\n{RED}Could not connect to postgresql.\n{WHITE}Please check: \n{YELLOW} * if database is running \n * configuration settings are correct. \n\n{WHITE}For first time installations execute{WHITE}: \n\n {GREEN} python manage.py initdb\n\n'.format(GREEN=Fore.GREEN, YELLOW=Fore.YELLOW, WHITE=Fore.WHITE, RED=Fore.RED))
sys.exit(1)
def _open_couchdb_conn():
try:
couchdb_server_conn = server.couchdb.CouchDBServer()
workspaces_list = couchdb_server_conn.list_workspaces()
except RequestError:
logger.error(u"CouchDB is not running at {}. Check faraday-server's"\
" configuration and make sure CouchDB is running".format(
server.couchdb.get_couchdb_url()))
sys.exit(1)
except Unauthorized:
logger.error(u"Unauthorized access to CouchDB. Make sure faraday-server's"\
" configuration file has CouchDB admin's credentials set")
sys.exit(1)
return couchdb_server_conn, workspaces_list
def _open_couchdb_conn():
try:
couchdb_server_conn = server.couchdb.CouchDBServer()
workspaces_list = couchdb_server_conn.list_workspaces()
except RequestError:
logger.error(u"CouchDB is not running at {}. Check faraday-server's"\
" configuration and make sure CouchDB is running".format(
server.couchdb.get_couchdb_url()))
sys.exit(1)
except Unauthorized:
logger.error(u"Unauthorized access to CouchDB. Make sure faraday-server's"\
" configuration file has CouchDB admin's credentials set")
sys.exit(1)
return couchdb_server_conn, workspaces_list
def setup_workspaces():
try:
couchdb = server.couchdb.CouchDBServer()
workspaces_list = couchdb.list_workspaces()
except RequestError:
logger.error(u"CouchDB is not running at {}. Check faraday-server's"\
" configuration and make sure CouchDB is running".format(
server.couchdb.get_couchdb_url()))
sys.exit(1)
except Unauthorized:
logger.error(u"Unauthorized access to CouchDB. Make sure faraday-server's"\
" configuration file has CouchDB admin's credentials set")
sys.exit(1)
for ws in workspaces_list:
setup_workspace(ws)
atexit.register(server.database.close_databases)
def setup_workspaces():
try:
couchdb = server.couchdb.CouchDBServer()
workspaces_list = couchdb.list_workspaces()
except RequestError:
logger.error(u"CouchDB is not running at {}. Check faraday-server's"\
" configuration and make sure CouchDB is running".format(
server.couchdb.get_couchdb_url()))
sys.exit(1)
except Unauthorized:
logger.error(u"Unauthorized access to CouchDB. Make sure faraday-server's"\
" configuration file has CouchDB admin's credentials set")
sys.exit(1)
for ws in workspaces_list:
setup_workspace(ws)
atexit.register(server.database.close_databases)
def run(self):
def signal_handler(*args):
logger.info('Received SIGTERM, shutting down.')
logger.info("Stopping threads, please wait...")
# teardown()
self.raw_report_processor.stop()
site = twisted.web.server.Site(self.__root_resource)
if self.__ssl_enabled:
ssl_context = self.__load_ssl_certs()
self.__listen_func = functools.partial(reactor.listenSSL,
contextFactory=ssl_context)
else:
self.__listen_func = reactor.listenTCP
try:
self.install_signal()
# start threads and processes
self.raw_report_processor = RawReportProcessor()
self.raw_report_processor.start()
# web and static content
self.__listen_func(self.__listen_port,
site,
interface=self.__bind_address)
# websockets
try:
listenWS(self.__build_websockets_resource(),
interface=self.__bind_address)
except:
logger.warn(
'Could not start websockets, address already open. This is ok is you wan to run multiple instances.'
)
logger.info('Faraday Server is ready')
reactor.addSystemEventTrigger('before', 'shutdown', signal_handler)
reactor.run()
except error.CannotListenError as e:
logger.error(str(e))
sys.exit(1)
except Exception as e:
logger.error(
'Something went wrong when trying to setup the Web UI')
logger.exception(e)
sys.exit(1)
def run(self):
for change_doc in self.__stream:
try:
self.__changes_callback(self.CHANGE_CLS(change_doc))
except Exception, e:
import traceback
logger.debug(traceback.format_exc())
logger.warning(u"Error while processing change. Ignoring. Offending change: {}".format(change_doc))
if change_doc.get('error', None):
if change_doc.get('error') == 'unauthorized':
logger.error(u"Unauthorized access to CouchDB. Make sure faraday-server's"\
" configuration file has CouchDB admin's credentials set")
thread.interrupt_main()
# TODO: A proper fix is needed here
elif change_doc.get('reason') == 'no_db_file':
self.__stream.stop()
break
def upload_comment(patientid, doctorid, post_data):
"""
Upload an comment in the system. The post data is a dict.
:param post_data: dict
:returns: a status, a str( comment's info on success, err info on failure)
"""
# print(post_data)
comment = ''
try:
logger.debug('in upload_comment')
resp_dict = {}
with database.atomic():
comment = CommentModel.create_by_dict(patientid, doctorid, post_data)
logger.debug('comment:{}'.format(comment))
logger.debug('in database.atomic')
# except peewee.IntegrityError:
# logger.warning('in doctor model create except')
# # `username` is a unique column, so this username already exists,
# # making it safe to call .get().
# old_user = AccountModel.get(AccountModel.username == username)
# logger.warning('user exists...')
# resp_dict['info'] = 'user exists, did not create user:%s' % username
# resp.status = falcon.HTTP_409
# try:
# change_user = AccountModel.get(AccountModel.username==username,
# AccountModel.password==password)
# except:
# logger.debug('change user data failed...')
except Exception as ex:
logger.error('Exception: ', ex)
q = CommentModel.delete().where(CommentModel.drug_id==
patientid + '-' + doctorid + '-' + post_data['datetime'])
q.execute()
return 0, {'errinfo':'create comment failed, did not create comment'}
else:
# resp_dict['info'] = 'make PUT request to storage_url with auth_token as "x-storage-token" in headers'
resp_dict['comment_id'] = comment.comment_id
return 1, resp_dict
def restart_server(args_port):
devnull = open('/dev/null', 'w')
if args_port:
ports = [args_port]
else:
ports = daemonize.get_ports_running()
if not ports:
logger.error('Faraday Server is not running')
sys.exit(1)
for port in ports:
stop_server(port)
params = ['/usr/bin/env', 'python2.7',\
os.path.join(server.config.FARADAY_BASE, __file__), '--no-setup', '--port', str(port)]
logger.info('Restarting Faraday Server...')
subprocess.Popen(params, stdout=devnull, stderr=devnull)
logger.info('Faraday Server is running as a daemon in port {}'.format(port))
def restart_server(args_port):
devnull = open('/dev/null', 'w')
if args_port:
ports = [args_port]
else:
ports = daemonize.get_ports_running()
if not ports:
logger.error('Faraday Server is not running')
sys.exit(1)
for port in ports:
stop_server(port)
params = ['/usr/bin/env', 'python2.7',\
os.path.join(server.config.FARADAY_BASE, __file__), '--no-setup', '--port', str(port)]
logger.info('Restarting Faraday Server...')
subprocess.Popen(params, stdout=devnull, stderr=devnull)
logger.info('Faraday Server is running as a daemon in port {}'.format(port))
def run(self):
def signal_handler(*args):
logger.info("Stopping threads, please wait...")
# teardown()
self.raw_report_processor.stop()
reactor.stop()
site = twisted.web.server.Site(self.__root_resource)
if self.__ssl_enabled:
ssl_context = self.__load_ssl_certs()
self.__listen_func = functools.partial(
reactor.listenSSL,
contextFactory=ssl_context)
else:
self.__listen_func = reactor.listenTCP
try:
self.install_signal()
# start threads and processes
self.raw_report_processor = RawReportProcessor()
self.raw_report_processor.start()
# web and static content
self.__listen_func(
self.__listen_port, site,
interface=self.__bind_address)
# websockets
try:
listenWS(self.__build_websockets_resource(), interface=self.__bind_address)
except :
logger.warn('Could not start websockets, address already open. This is ok is you wan to run multiple instances.')
logger.info('Faraday Server is ready')
reactor.addSystemEventTrigger('before', 'shutdown', signal_handler)
reactor.run()
except error.CannotListenError as e:
logger.error(str(e))
sys.exit(1)
except Exception as e:
logger.error('Something went wrong when trying to setup the Web UI')
logger.exception(e)
sys.exit(1)
def update_discharge(patientid, doctorid, indate, post_data):
"""
Upload an discharge in the system. The post data is a dict.
:param post_data: dict
:returns: a status, a str( discharge's info on success, err info on failure)
"""
# print(post_data)
discharge = ''
try:
logger.debug('in update_discharge')
resp_dict = {}
DischargeModel.update_by_dict(patientid, doctorid,
indate, post_data)
# except peewee.IntegrityError:
# logger.warning('in doctor model create except')
# # `username` is a unique column, so this username already exists,
# # making it safe to call .get().
# old_user = AccountModel.get(AccountModel.username == username)
# logger.warning('user exists...')
# resp_dict['info'] = 'user exists, did not create user:%s' % username
# resp.status = falcon.HTTP_409
# try:
# change_user = AccountModel.get(AccountModel.username==username,
# AccountModel.password==password)
# except:
# logger.debug('change user data failed...')
except Exception as ex:
logger.error('Exception: ', ex)
return 0, {'errinfo':'update discharge failed, did not create discharge'}
else:
# resp_dict['info'] = 'make PUT request to storage_url with auth_token as "x-storage-token" in headers'
resp_dict['discharge_id'] = patientid + '-' + doctorid + '-' + \
indate
return 1, resp_dict
def create_database(self):
logger.info(u'Creating database for workspace {}'.format(self.__workspace))
self.database.create()
self.database.open_session()
try:
# Add metadata information to database
self.set_last_seq(self.couchdb.get_last_seq())
self.set_migration_status(False)
self.set_schema_version()
self.import_from_couchdb()
# Reaching this far without errors means a successful migration
self.set_migration_status(True)
except Exception, e:
import traceback
logger.debug(traceback.format_exc())
logger.error(u'Error while importing workspace {}: {!s}'.format(self.__workspace, e))
self.delete()
raise e
def delete_obj(patientid, objid):
"""
Get info of a doctor in the system.
:param doctorid: doctor's uid
:returns: a status, a str ( doctor's info on success, err info on failure)
"""
# print(doctorid)
info = {}
try:
resp_dict = {}
conn = swiftclient.client.Connection(conf.auth_url,
conf.account_username,
conf.password,
auth_version=conf.auth_version)
meta, objects = conn.get_container(conf.container,
prefix=patientid + '/' + objid)
logger.debug('meta: %s, \n objects: %s' % (meta, objects))
if objects:
for obj in objects:
conn.delete_object(conf.container, obj['name'])
resp_dict['description_'+obj['name']] = \
'{} have been deleted'.format(obj['name'])
else:
resp_dict['description'] = 'There is no file to be deleted'
logger.debug('resp_dict:%s' % resp_dict)
q = ObjectModel.delete().where(ObjectModel.objid==objid)
q.execute()
resp_dict[objid] = 'deleted from db'
logger.debug('resp_dict:%s' % resp_dict)
except Exception as ex:
logger.error('Exception: ', ex)
return 0, {'errinfo':'delete obj failed, did not delete obj'}
else:
return 1, resp_dict
def get_appointment(appointment_url):
"""
Get info of an appointment in the system.
:param appointment_url: appointment's url
:returns: a status, a str ( appointment's info on success, err info on failure)
"""
# print(appointment_url)
info = {}
try:
logger.debug('in get_appointment')
# check redis
appointment = str(rediscli.get_data(appointment_url))
logger.debug(appointment)
# except UserNotExistException:
# logger.debug('in UserNotExistException')
# return 0, 'get doctor failed, the required Doctor Did Not Exist'
except Exception as ex:
logger.error('Exception: ', ex)
return 0, 'get appointment failed'
else:
# appointment_json = json.dumps({'illness':appointment})
return 1, appointment
def create_database(self):
logger.info(u'Creating database for workspace {}'.format(
self.__workspace))
self.database.create()
self.database.open_session()
try:
# Add metadata information to database
self.set_last_seq(self.couchdb.get_last_seq())
self.set_migration_status(False)
self.set_schema_version()
self.import_from_couchdb()
# Reaching this far without errors means a successful migration
self.set_migration_status(True)
except Exception, e:
import traceback
logger.debug(traceback.format_exc())
logger.error(u'Error while importing workspace {}: {!s}'.format(
self.__workspace, e))
self.delete()
raise e
def main():
os.chdir(FARADAY_BASE)
check_alembic_version()
check_postgresql()
parser = argparse.ArgumentParser()
parser.add_argument('--ssl', action='store_true', help='enable HTTPS')
parser.add_argument('--debug',
action='store_true',
help='run Faraday Server in debug mode')
parser.add_argument('--start',
action='store_true',
help='run Faraday Server in background')
parser.add_argument('--stop',
action='store_true',
help='stop Faraday Server')
parser.add_argument('--restart',
action='store_true',
help='Restart Faraday Server')
parser.add_argument('--nodeps',
action='store_true',
help='Skip dependency check')
parser.add_argument('--no-setup',
action='store_true',
help=argparse.SUPPRESS)
parser.add_argument('--port',
help='Overides server.ini port configuration')
parser.add_argument(
'--websocket_port',
help='Overides server.ini websocket port configuration')
parser.add_argument('--bind_address',
help='Overides server.ini bind_address configuration')
f = open(server.config.VERSION_FILE)
f_version = f.read().strip()
parser.add_argument('-v',
'--version',
action='version',
version='Faraday v{version}'.format(version=f_version))
args = parser.parse_args()
setUpLogger(args.debug)
if args.debug:
server.utils.logger.set_logging_level(server.config.DEBUG)
if args.restart:
restart_server(args.port)
sys.exit()
if args.stop:
if args.port:
sys.exit(0 if stop_server(args.port) else 1)
else:
ports = daemonize.get_ports_running()
if not ports:
logger.info('Faraday Server is not running')
exit_code = 0
for port in ports:
exit_code += 0 if stop_server(port) else 1
sys.exit(exit_code)
else:
if not args.port:
args.port = '5985'
sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
result = sock.connect_ex(
(args.bind_address or server.config.faraday_server.bind_address,
int(args.port or server.config.faraday_server.port)))
if is_server_running(args.port) and result == 0:
sys.exit(1)
if result == 0:
logger.error(
"Faraday Server port in use. Check your processes and run the server again..."
)
sys.exit(1)
# Overwrites config option if SSL is set by argument
if args.ssl:
server.config.ssl.enabled = 'true'
if not args.no_setup:
setup_environment(not args.nodeps)
if args.port:
server.config.faraday_server.port = args.port
if args.bind_address:
server.config.faraday_server.bind_address = args.bind_address
if args.websocket_port:
server.config.faraday_server.websocket_port = args.websocket_port
if args.start:
# Starts a new process on background with --ignore-setup
# and without --start nor --stop
devnull = open('/dev/null', 'w')
params = [
'/usr/bin/env', 'python2.7',
os.path.join(server.config.FARADAY_BASE, __file__), '--no-setup'
]
arg_dict = vars(args)
for arg in arg_dict:
if arg not in ["start", "stop"] and arg_dict[arg]:
params.append('--' + arg)
if arg_dict[arg] != True:
params.append(arg_dict[arg])
logger.info('Faraday Server is running as a daemon')
subprocess.Popen(params, stdout=devnull, stderr=devnull)
elif not args.start:
run_server(args)
def check_admin_access_to(ws_name):
if not server.couchdb.has_permissions_for(
ws_name, credentials=server.couchdb.get_auth_info()):
logger.error(u"Unauthorized access to CouchDB. Make sure faraday-server's"\
" configuration file has CouchDB admin's credentials set")
sys.exit(1)