def run():
subject = Subject.objects.get(uuid="26da580a-fc75-4f1a-92b2-be54e2865ceb")
sp = SavedProcedure.objects.get(guid="5bcf6e9d-73a3-48db-9359-e1f110d3019f")
encounter, observations = v2compatlib.sp_to_encounter(sp,subject)
print encounter
for obs in observations:
print obs
def run():
subject = Subject.objects.get(uuid="26da580a-fc75-4f1a-92b2-be54e2865ceb")
sp = SavedProcedure.objects.get(
guid="5bcf6e9d-73a3-48db-9359-e1f110d3019f")
encounter, observations = v2compatlib.sp_to_encounter(sp, subject)
print encounter
for obs in observations:
print obs
def maybe_upload_procedure(saved_procedure):
"""Validates whether an encounter is ready to upload to the emr backend.
Requires all associated BinaryResources be complete.
Parameters:
saved_procedure
The SavedProcedure object which may be uploaded.
"""
result = True
message = ""
logging.debug("Should I upload %s to the MRS?" % saved_procedure.guid)
binaries = saved_procedure.binaryresource_set.all()
ready = True
waiting = []
ready_list = []
# checking all associated binaries
for binary in binaries:
if binary.ready_to_upload():
message = ("Encounter: %s Binary: %s/%s COMPLETE" % (
saved_procedure.guid, binary.guid, len(binaries)))
ready = ready and True
ready_list.append(binary.guid)
else:
logging.debug("BinaryResource: %s completed: %s/%s" %
(binary.pk, binary.upload_progress, binary.total_size))
waiting.append(binary.guid)
message = ("Encounter: %s is WAITING on %s"
% (saved_procedure.guid, waiting))
ready = ready and False
logging.debug("Encounter: %s has %s READY and %s WAITING"
% (saved_procedure.guid,ready_list,waiting))
# We need to bail here if not ready
if not ready:
return result, message
# if uploaded flag already true we don't want to try again
if saved_procedure.uploaded:
message = "Encounter -> %s, Already uploaded." % saved_procedure.guid
logging.info(message)
return result, message
# do the upload
binaries_to_upload = [binary for binary in binaries if not binary.uploaded]
logging.debug('Uploading Encounter -> %s, Binaries to upload = %s'
% (saved_procedure.guid, binaries_to_upload))
files = defaultdict(list)
# Set file for upload
for binary in binaries_to_upload:
files[str(binary.element_id)].append(str(binary.data.path))
# prep text data for upload
client_name = saved_procedure.client.name
savedprocedure_guid = saved_procedure.guid
# decodes and cleans up responses-OpenMRS specific
responses = cjson.decode(saved_procedure.responses,True)
cleaned_responses = []
patient_id = ""
patient_first = ""
patient_last = ""
patient_gender = ""
patient_birthdate = ""
patient_month = ""
patient_day = ""
patient_year = ""
enrolled = 'Yes'
enrolledtemp = responses.get('patientEnrolled', None)
if enrolledtemp:
enrolled = enrolledtemp.get('answer', 'Yes')
del responses['patientEnrolled']
procedure_title = ''
procedure_title_element = responses.get('procedureTitle', None)
if procedure_title_element:
del responses['procedureTitle']
procedure_title = procedure_title_element.get('answer', '')
for eid,attr in responses.items():
if enrolled == "Yes":
if (eid == "patientId"):
patient_id = attr.get('answer')
elif (eid == "patientGender"):
patient_gender = attr.get('answer')
elif (eid == 'patientFirstName'):
patient_first = attr.get('answer')
elif (eid == 'patientLastName'):
patient_last = attr.get('answer')
elif (eid == 'patientBirthdateDay'):
patient_day = attr.get('answer')
elif (eid == 'patientBirthdateMonth'):
patient_month = attr.get('answer')
elif (eid == 'patientBirthdateYear') and (patient_year==""):
patient_year = attr.get('answer')
else:
attr['id'] = eid
cleaned_responses.append(attr)
else:
if (eid == "patientIdNew"):
patient_id = attr.get('answer')
elif (eid == "patientGenderNew"):
patient_gender = attr.get('answer')
elif (eid == 'patientFirstNameNew'):
patient_first = attr.get('answer')
elif (eid == 'patientLastNameNew'):
patient_last = attr.get('answer')
elif (eid == 'patientBirthdateDayNew'):
patient_day = attr.get('answer')
elif (eid == 'patientBirthdateMonthNew'):
patient_month = attr.get('answer')
elif (eid == 'patientBirthdateYearNew'):
patient_year = attr.get('answer')
else:
attr['id'] = eid
cleaned_responses.append(attr)
patient_birthdate = '%s/%s/%s' % (months_dict[patient_month], patient_day,
patient_year)
if patient_id is None:
patient_id = DEFAULT_PATIENT_ID
if patient_gender in ['Male', 'male', 'M', 'm']:
patient_gender = 'M'
elif patient_gender in ['Female', 'female', 'F', 'f']:
patient_gender = 'F'
# Begin upload to the emr
#omrs = openmrslib.OpenMRS16(saved_procedure.upload_username,
# saved_procedure.upload_password,
# settings.OPENMRS_SERVER_URL)
# creates the patient upstream if it does not exist
new_patient = True if enrolled == "No" else False
logging.debug("patient enrolled: %s" % new_patient)
if new_patient:
logging.debug("Creating new patient: patient_id -> %s" % patient_id)
#omrs.create_patient(patient_id,
# patient_first,
# patient_last,
# patient_gender,
# patient_birthdate)
# execute upload
#logging.debug("Uploading to OpenMRS: %s %s %s %s %s "
# % (patient_id, client_name,
# savedprocedure_guid, files, cleaned_responses))
'''
result, msg, _ = omrs.upload_procedure(patient_id,
client_name,
procedure_title,
savedprocedure_guid,
cleaned_responses,
files)
message = 'sp.pk -> %s, %s ' % (saved_procedure.pk, msg)
'''
#edata = {}
#device = Device.objects.get(
#observer = Observer.objects.get(username=client_id)
#procedure = Procedure.objects.get(title=procedure_title)
# mark encounter and binaries as uploaded
logging.debug("API: RESULT = %s" % result )
if result:
saved_procedure.uploaded = True
saved_procedure.save()
for binary in binaries_to_upload:
binary.uploaded = True
binary.save()
logging.debug("Uploaded = True %s" % binaries_to_upload)
flush(saved_procedure)
encounter, obsDict = v2compatlib.sp_to_encounter(saved_procedure,subject)
encounter.save()
observations = v2compatlib.responses_to_observations(encounter, observations, sort=True)
for obs in observations:
obs.save()
if obs.concept.is_complex:
b = BinaryResource.objects.get(sp=saved_procedure, id=obs.node)
smtplib.sender.send_review_notification(obs)
return result, message