def test_read_timeout(self):
"""Test against an external website to verify read timeout"""
rave = RWSConnection('https://innovate.mdsol.com')
with mock.patch("requests.sessions.Session.get") as mock_get:
mock_get.side_effect = requests.exceptions.ReadTimeout()
with self.assertRaises(RWSException) as exc:
rave.send_request(rws_requests.ClinicalStudiesRequest(), verify=False,retries=0)
self.assertEqual('Server Read Timeout', str(exc.exception))
def test_no_timeout_unauth(self):
"""No timeout raised, then we get the Authorisation Exception """
rave = RWSConnection('https://innovate.mdsol.com')
with mock.patch("requests.sessions.Session.get") as mock_get:
mock_get.return_value = mock.MagicMock(requests.models.Response, status_code=401,
headers={}, text='Authorization Header not provided')
with self.assertRaises(AuthorizationException) as exc:
rave.send_request(rws_requests.ClinicalStudiesRequest(), timeout=3600, verify=False, retries=0)
self.assertEqual('Authorization Header not provided', str(exc.exception))
def test_read_timeout(self):
"""Test against an external website to verify read timeout"""
rave = RWSConnection('https://innovate.mdsol.com')
with mock.patch("requests.sessions.Session.get") as mock_get:
mock_get.side_effect = requests.exceptions.ReadTimeout()
with self.assertRaises(RWSException) as exc:
rave.send_request(rws_requests.ClinicalStudiesRequest(),
verify=False,
retries=0)
self.assertEqual('Server Read Timeout', str(exc.exception))
def get_rave_subjects():
"""
Gets a list of Patients registered
:return:
"""
client = RWSConnection(domain=RAVE_URL,
username=RAVE_USER,
password=RAVE_PASSWORD)
subjects = client.send_request(
StudySubjectsRequest(STUDY, ENV, subject_key_type='SubjectUUID'))
return subjects
def test_no_timeout_unauth(self):
"""No timeout raised, then we get the Authorisation Exception """
rave = RWSConnection('https://innovate.mdsol.com')
with mock.patch("requests.sessions.Session.get") as mock_get:
mock_get.return_value = mock.MagicMock(
requests.models.Response,
status_code=401,
headers={},
text='Authorization Header not provided')
with self.assertRaises(AuthorizationException) as exc:
rave.send_request(rws_requests.ClinicalStudiesRequest(),
timeout=3600,
verify=False,
retries=0)
self.assertEqual('Authorization Header not provided',
str(exc.exception))
def push_demographics(subject_id, patient_json):
"""
Insert Patient Demography Data
:param subject_uuid: UUID for subject
:param patient_json: returned Patient JSON
:return:
"""
locationoid, subject_uuid = subject_id.split('_')
mapping = []
date_of_birth = patient_json.get('birthDate')
if date_of_birth:
mapping.append(
dict(folder_oid="SCREEN",
form_oid="DM",
field_oid="DM.BRTHDTC",
value=munge_to_rave_date(date_of_birth),
cdash_domain="DM",
cdash_element="BRTHDTC"))
gender = patient_json.get('gender')
if gender:
if gender.lower() in ['male', 'female']:
mapping.append(
dict(folder_oid="SCREEN",
form_oid="DM",
field_oid="DM.SEX",
value=gender.upper(),
cdash_domain="DM",
cdash_element="SEX"))
if mapping:
odm = make_odm(STUDY,
ENV,
locationoid,
subject_uuid,
mapping,
retrieved_datetime=datetime.datetime.now(),
transfer_user='******',
transfer_identifier=audit_id(),
freeze=False)
request = PostDataRequest(str(odm))
client = RWSConnection(domain=RAVE_URL,
username=RAVE_USER,
password=RAVE_PASSWORD)
response = client.send_request(request)
return response
def rws(ctx, url, username, password, raw, verbose, output, virtual_dir):
if ctx.obj is None:
ctx.obj = {}
ctx.obj['URL'] = url
ctx.obj['USERNAME'] = username
ctx.obj['PASSWORD'] = password
ctx.obj['VIRTUAL_DIR'] = virtual_dir
if virtual_dir:
if username and password:
ctx.obj['RWS'] = RWSConnection(url,
username,
password,
virtual_dir=virtual_dir)
else:
# Acceptable for UnAuth Requests
ctx.obj['RWS'] = RWSConnection(url, virtual_dir=virtual_dir)
else:
if username and password:
ctx.obj['RWS'] = RWSConnection(url, username, password)
else:
ctx.obj['RWS'] = RWSConnection(url)
ctx.obj['RAW'] = raw
ctx.obj['OUTPUT'] = output
ctx.obj['VERBOSE'] = verbose
from rwslib.rws_requests.odm_adapter import *
from rwslib.rws_requests.biostats_gateway import *
if __name__ == '__main__':
from _settings import accounts
#Accounts is a dict of dicts like
# accounts = {'innovate' : {'username': '******',
# 'password':'******'},
# 'otherurl' : {'username': '******',
# 'password':'******'},
# }
acc = accounts['innovate']
rave = RWSConnection('innovate', acc['username'], acc['password'])
print rave.send_request(VersionRequest(), retries=3)
print rave.send_request(BuildVersionRequest())
print rave.send_request(DiagnosticsRequest())
print rave.send_request(CacheFlushRequest()).istransactionsuccessful
print "Clinical studies request"
studies = rave.send_request(ClinicalStudiesRequest(),timeout=60)
print len(studies)
print rave.last_result.url
print rave.last_result.text
print rave.request_time
print "Metadata studies request"
__author__ = 'andrew'
from rwslib import RWSConnection
from rwslib.rws_requests import *
from rwslib.rws_requests.odm_adapter import *
from rwslib.rws_requests.biostats_gateway import *
if __name__ == '__main__':
from _settings import accounts
acc = accounts['innovate']
rave = RWSConnection('innovate', acc['username'], acc['password'])
print rave.send_request(VersionRequest())
try:
audits = rave.send_request(AuditRecordsRequest('Mediflex','Dev',startid=4000000,per_page=10000))
print rave.next_link #Get headers, next and last entries?
except:
raise
#print audits
while rave.next_link <> None:
rave.next(AuditRecordsRequest('Mediflex','Dev'))
print rave.next_link
# Variable OID required
MdsolDerivationDef("AGE", form_oid="DM", field_oid="AGE")(
# Variable OID required to be identified as a data step
MdsolDerivationStep(form_oid="DM", field_oid="DOB", data_format="StandardValue", variable_oid="DOB"),
MdsolDerivationStep(function=StepType.Age)
)
)
return odm
if __name__ == '__main__':
from rwslib import RWSConnection
from rwslib.rws_requests import PostMetadataRequest, PostDataRequest
from _settings import accounts
account = accounts['innovate']
r = RWSConnection('innovate', account['username'], account['password'])
if False: # MetaData
projectname = 'TESTSTUDY'
odm_definition = example_metadata(projectname, "Draft1")
request = PostMetadataRequest(projectname, str(odm_definition))
else: #Clinical Data
projectname = 'Mediflex'
odm_definition = example_clinical_data(projectname,"DEV")
request = PostDataRequest(str(odm_definition))
# Uncomment this to see the generated ODM
# print(str(odm_definition))
response = r.send_request(request)
print(str(response))
def push_conmeds(subject_id, conmeds):
"""
Insert a Concomitant Medication Record
:param subject_id: UUID for subject
:param conmeds: list of conmeds
"""
locationoid, subject_uuid = subject_id.split('_')
client = RWSConnection(domain=RAVE_URL,
username=RAVE_USER,
password=RAVE_PASSWORD)
for medrx in conmeds:
# print(medrx)
mapping = []
resource = medrx.get('resource')
# Log context
ctxt = resource.get('id')
print(ctxt)
mapping.append(
dict(folder_oid="SUBJECT",
form_oid="CM",
field_oid="CM.CMINDC",
value=ctxt,
cdash_domain="CM",
log_context_field="CM.CMINDC",
log_context_value=ctxt,
is_new=True))
period = resource.get('effectivePeriod')
if period:
if period.get('start'):
mapping.append(
dict(folder_oid="SUBJECT",
form_oid="CM",
field_oid="CM.CMSTDTC",
value=munge_to_rave_date(
period.get('start').split('T')[0]),
cdash_domain="CM",
log_context_field="CM.CMINDC",
log_context_value=ctxt))
if period.get('end'):
mapping.append(
dict(folder_oid="SUBJECT",
form_oid="CM",
field_oid="CM.CMENDTC",
value=munge_to_rave_date(
period.get('end').split('T')[0]),
cdash_domain="CM",
log_context_field="CM.CMINDC",
log_context_value=ctxt))
# truncate the text, should look into how we get a proper name
if resource.get('dosage'):
dosage = resource.get('dosage')[0]
cmtrt = dosage.get('text')[:198]
mapping.append(
dict(folder_oid="SUBJECT",
form_oid="CM",
field_oid="CM.CMTRT",
value=cmtrt,
cdash_domain="CM",
log_context_field="CM.CMINDC",
log_context_value=ctxt))
if dosage.get('route'):
mapping.append(
dict(folder_oid="SUBJECT",
form_oid="CM",
field_oid="CM.CMROUTE",
value=dosage.get('route').get('text'),
cdash_domain="CM",
log_context_field="CM.CMINDC",
log_context_value=ctxt))
odm = make_odm(STUDY,
ENV,
locationoid,
subject_uuid,
mapping,
retrieved_datetime=datetime.datetime.now(),
transfer_user='******',
transfer_identifier=audit_id(),
freeze=False)
request = PostDataRequest(str(odm))
response = client.send_request(request)
from rwslib.rws_requests.biostats_gateway import *
from rwslib.rwsobjects import RWSException
from rwslib import RWSConnection
import configparser
from rwslib.extras.audit_event.parser import parse
# reading the innovate credentials from the application config files.
config = configparser.ConfigParser()
config.read(r'F:\Codebase\Rave-Data-Ingestor\applicationconfig.ini')
generic_list = []
# making the connection using the rws connection object
rws_connection = RWSConnection(domain=config.get('medidata', 'domain'),
username=config.get('medidata', 'username'),
password=config.get('medidata', 'password'))
study_list = []
# maintaining the generic list for all the studies in the CRO
class clinical_masters:
def get_clinical_studies():
study_data = rws_connection.send_request(ClinicalStudiesRequest())
return study_data
def get_studies_list():
study_data = clinical_masters.get_clinical_studies()
studies_list = []
for study_object in study_data:
studies_list.append(study_object.studyname)
from rwslib.rws_requests.odm_adapter import *
from rwslib.rws_requests.biostats_gateway import *
if __name__ == '__main__':
from _settings import accounts
# Accounts is a dict of dicts like
# accounts = {'innovate' : {'username': '******',
# 'password':'******'},
# 'otherurl' : {'username': '******',
# 'password':'******'},
# }
acc = accounts['innovate']
rave = RWSConnection('innovate', acc['username'], acc['password'])
print(rave.send_request(VersionRequest(), retries=3))
print(rave.send_request(BuildVersionRequest()))
print(rave.send_request(DiagnosticsRequest()))
print(rave.send_request(CacheFlushRequest()).istransactionsuccessful)
print("Clinical studies request")
studies = rave.send_request(ClinicalStudiesRequest(), timeout=60)
print(len(studies))
print(rave.last_result.url)
print(rave.last_result.text)
print(rave.request_time)
print("Metadata studies request")
if __name__ == '__main__':
# An example
logging.basicConfig(level=logging.INFO)
from rwslib._settings import accounts
# Accounts is a dict of dicts like
# accounts = {'innovate' : {'username': '******',
# 'password':'******'},
# 'otherurl' : {'username': '******',
# 'password':'******'},
# }
acc = accounts['innovate']
rv = RWSConnection('innovate', acc['username'], acc['password'])
path, _ = os.path.split(os.path.realpath(__file__))
db_path = os.path.join(path, 'local_cvs.db')
# Make sqllite connection
logging.info('Opening/overwriting sqllite db %s' % db_path)
conn = sqlite3.connect(db_path)
# DBAdaptor takes care of all the database specific parts of the process
db_adaptor = SQLLiteDBAdapter(conn)
lcv = LocalCVBuilder(rv, 'SIMPLESTUDY', 'TEST', db_adaptor)
lcv.execute()
# Once complete you can do further work with the conn object, run SQL statements etc.
dict(folder_oid="SUBJECT",
form_oid="AE",
field_oid="AETERM",
value="AE 3",
log_context_field="AEACNOTH",
log_context_value="XX3"),
dict(folder_oid="SUBJECT",
form_oid="AE",
field_oid="AESTDTC",
value="03 Feb 1981",
log_context_field="AEACNOTH",
log_context_value="XX3"),
dict(folder_oid="SUBJECT",
form_oid="AE",
field_oid="AEACNOTH",
value="XX3",
log_context_field="AEACNOTH",
log_context_value="XX3",
is_new=True),
# Must send a line like this if you want to CREATE a record.
]
odm = make_odm("Mediflex", "Dev", "MDSOL", "222 IJS", mapping_values,
datetime.now(), "EHR Import User", audit_id())
request = PostDataRequest(str(odm))
print(str(odm))
rave = RWSConnection('innovate', 'username', 'password')
print(rave.send_request(request))
def test_classes(self):
test_eventer = TestEventer()
conn = RWSConnection('innovate', "FAKE_USER", "FAKE_PASS")
ODMAdapter(conn, "Mediflex", "Dev", test_eventer)
