def createTimingResource(self):
from fhirclient.models import timing, fhirdate
timing_resource = timing.Timing()
# once(frequency) per week(period/periodUnit)
repeat = timing.TimingRepeat()
repeat.frequency = int(self.frequency.value)
repeat.periodUnit = self.frequency.unit
repeat.period = float(self.frequency.unit_period)
# Start Date
start_fhirdate = fhirdate.FHIRDate(self.period.start)
end_fhirdate = fhirdate.FHIRDate(self.period.end)
print(start_fhirdate)
print(end_fhirdate)
print(fhirdate.FHIRDate(self.period.start))
from fhirclient.models import period
fhir_period = period.Period()
fhir_period.start = start_fhirdate
fhir_period.end = end_fhirdate
repeat.boundsPeriod = fhir_period
timing_resource.repeat = repeat
return timing_resource
def get_responseperiod_x(start,end):
responseperiod_x = Ext.Extension()
responseperiod_x.url = 'http://fhir.org/guides/argonaut-questionnaire/StructureDefinition/extension-responsePeriod'
responseperiod_x.valuePeriod = P.Period()
responseperiod_x.valuePeriod.start = FD.FHIRDate(start)
responseperiod_x.valuePeriod.end = FD.FHIRDate(end)
return responseperiod_x
def _create_FHIRPeriod(self, start=None, end=None):
"""
Creates a FHIRPeriod object
:param self: needed to call _create_FHIRDate method
:param start: start datetime object
:param end: end datetime object
:returns: FHIRPeriod object
"""
Period = period.Period()
if start is not None:
Period.start = self._create_FHIRDate(start)
else:
Period.start = self._create_FHIRDate(datetime.datetime.now())
if end is not None:
Period.end = self._create_FHIRDate(end)
return Period
def create_fhir_object(self):
"""
method: create_fhir_object()
Create a fhir-client.model.address.Adress object and stores to the self.fhir attribute
:return:
None
"""
# Initialize FHIRclient Address object
# Assign Address object attributes to FHIRclient Address object
fa = fhir_address.Address()
if self.address1:
fa.line = [self.address1]
if self.address2:
fa.line.append(self.address2)
if self.city:
fa.city = self.city
if self.state:
fa.state = self.state
if self.zipcode:
fa.postalCode = self.zipcode
fa.text = self.formatted_address()
if isinstance(self.start_date, date) or isinstance(self.end_date, date):
p = period.Period()
if self.start_date:
fhirdate_start = fhirdate.FHIRDate()
fhirdate_start.date = self.start_date
p.start = fhirdate_start
if self.end_date:
fhirdate_end = fhirdate.FHIRDate()
fhirdate_end.date = self.end_date
p.end = fhirdate_end
fa.period = p
if self.use:
fa.use = self.use.lower()
if self.is_postal and self.is_physical:
fa.type = 'both'
elif self.is_postal:
fa.type = 'postal'
elif self.is_physical:
fa.type = 'physical'
if self.district:
fa.district = self.district
if self.country:
fa.country = self.country
self.fhir = fa
def to_fhir(self) -> period.Period:
fhir_period = period.Period()
fhir_period.start = self.start.to_fhir()
fhir_period.end = self.end.to_fhir()
return fhir_period
if __name__ == "__main__":
ct = ClinicalStudy.from_file("examples/NCT02348489.xml", local_schema=True)
locations = [build_location(x) for x in ct.locations]
foci = build_focus(ct.mesh_terms)
print([x.as_json() for x in foci])
keywords = build_keyword(ct.keywords)
print([x.as_json() for x in keywords])
identifiers = build_identifiers(ct.nct_id, ct.study_id, ct.secondary_id)
print([x.as_json() for x in identifiers])
package = bundle.Bundle()
package.type = "document"
package.identifier = identifier.Identifier(
dict(use='official',
system="https://clinicaltrials.gov/ct2/show/",
value=ct.nct_id))
entries = []
for location in locations:
be = bundle.BundleEntry()
be.resource_type = "Location"
be.resource = location
entries.append(be)
study = researchstudy.ResearchStudy()
study.identifier = identifiers
print("Study Identifier: ", type(study.identifier[0]))
study.period = period.Period(
dict(start=ct.trail.study_first_posted.date.strftime("%Y-%m-%d")))
study.status = build_status(ct.status)
entries.append(study)
package.entry = entries
print(json.dumps(package.as_json(), indent=4, separators=(',', ': ')))
def to_fhir(self):
effective_period = period.Period()
effective_period.start = self.start
effective_period.end = self.end
return effective_period
def make_appts(op, slot=None):
# create Appt based on slot data
logging.info('slot as json = {}',
format(json.dumps(slot.as_json(), sort_keys=True, indent=4)))
appt = Appt.Appointment()
appt.id = '{}{}'.format(slot.id, timestamp())
appt.status = 'proposed'
try: # mapping serviceType
appt.serviceType = [] # codeable pattern
for concept in slot.serviceType:
appt.serviceType.append(map_cc(concept))
except TypeError: # element missing
pass
try: # mapping specialty
appt.specialty = [] # codeable pattern
for concept in slot.specialty: # only the first translation for now
appt.specialty.append(map_cc(concept))
except TypeError: # element missing
pass
# mapping appointmetType
try:
concept = slot.appointmentType
appt.appointmentType = map_cc(concept)
except AttributeError: # element missing
pass
try:
appt.reason = []
for concept in op['reason']:
# create CodeableConcept based on op data - just text for now
appt.reason.append = (CC.CodeableConcept({'text': concept}))
except KeyError: # op missing
pass
appt.start = slot.start
appt.end = slot.end
appt.slot = [FRef.FHIRReference({'reference':
'Slot/{}'.format(slot.id)})] # option a
appt.participant = []
'''
assume a list of participant references from op
'practitioner':[],
'organization':[],
'location-reference':[],
'patient-reference':[],
'patient-resource':[], do this one later...
'''
try:
for url in op['practitioner']:
logging.info('practitioner is = {}'.format(op))
appt.participant.append(map_part(url))
except KeyError:
pass
try:
for url in op['organization']:
appt.participant.append(map_part(url))
except KeyError:
pass
try:
for url in op['location-reference']:
appt.participant.append(map_part(url))
except KeyError:
pass
try:
for url in op['patient-reference']: #TODO add patient stub in for now
appt.participant.append(map_part(url))
except KeyError:
pass
# mapping this comes from the query parameter to requested period there is only one and is required
pd = Period.Period()
fd = FDate.FHIRDate()
try:
fd.origval = op['start'] # start sp
pd.start = fd
except KeyError:
fd.origval = '2017-09-07' # start sp
pd.start = fd
try:
fd.origval = op['end'] # end sp
pd.end = fd
except KeyError:
pass
appt.requestedPeriod = []
appt.requestedPeriod.append(pd)
return (appt)
def createPractitioner(dohmpifield, record):
#extract fields from dohmpi from database
field = []
for i in range(len(dohmpifield)):
f1, = dohmpifield[i] # dohmpi loads from db as a list of onetuples.
field.append(f1) # we make a traditional list to refer to.
fnamei = field.index('provider_first')
lnamei = field.index('provider_last')
genderi = field.index('provider_gender_cd')
deathyi = field.index('deathccyy')
deathmi = field.index('deathmm')
deathdi = field.index('deathdd')
birthi = field.index('provider_dob_dob')
provi = field.index('provider_license_no')
# record is one record from the postgres db
import fhirclient.models.practitioner as p
# set practitioner id as provider licence numberS
p = p.Practitioner({'id': record[provi]})
# resolve name
import fhirclient.models.humanname as hn
name = hn.HumanName()
name.given = [record[fnamei]]
name.family = [record[lnamei]]
p.name = name
# resolve gender
if (record[genderi] == "1"):
p.gender = 'male'
elif (record[genderi] == "2"):
p.gender = 'female'
else:
p.gender = 'unknown'
# build and resolve birthdate
birthdate = record[birthi]
bsep1 = birthdate.index("/")
bsep2 = birthdate.index("/", bsep1 + 1)
birthdate = birthdate[-4:] + "-" + birthdate[0:bsep1] + "-" + birthdate[
bsep1 + 1:bsep2]
p.birthDate = fhirclient.models.fhirdate.FHIRDate(birthdate)
# build and resolve death date
tz = "00:00:00-0600" # Utah is in the Mountain Time Zone, setting time as midnight.
yyyy = record[deathyi]
mm = record[deathmi]
if (len(mm) < 2):
mm = "0%s" % mm
dd = record[deathdi]
if (len(dd) < 2):
dd = "0%s" % dd
deathdate = "%s-%s-%sT%s" % (yyyy, mm, dd, tz)
deathdate = fhirclient.models.fhirdate.FHIRDate(deathdate)
# Create period
import fhirclient.models.period as per
per = per.Period()
per.start = deathdate
import fhirclient.models.fhirreference as ref
location = ref.FHIRReference()
location.reference = 'http://fhir.ehoth.net/deceased'
location.display = 'deceased'
# Create role
import fhirclient.models.practitioner as r
role = r.PractitionerPractitionerRole()
role.healthcareservice = 'deceased'
role.location = [location]
role.period = per
role.managingOrganization = location
#print role.as_json()
p.practitionerRole = [role]
# return practitioner.
return p
def createPatient(dohmpifield, record):
#extract fields from dohmpi from database
field = []
for i in range(len(dohmpifield)):
f1, = dohmpifield[i] # dohmpi loads from db as a list of onetuples.
field.append(f1) # we make a traditional list to refer to.
fnamei = field.index('provider_first')
lnamei = field.index('provider_last')
genderi = field.index('provider_gender_cd')
deathyi = field.index('deathccyy')
deathmi = field.index('deathmm')
deathdi = field.index('deathdd')
birthi = field.index('provider_dob_dob')
provi = field.index('provider_license_no')
# record is one record from the postgres db
import fhirclient.models.patient as p
# set patient id as provider licence numberS
pid = record[provi]
p = p.Patient({})
import fhirclient.models.identifier as idf
identifier = idf.Identifier()
identifier.value = pid
p.identifier = [identifier]
# resolve name
import fhirclient.models.humanname as hn
name = hn.HumanName()
name.given = [record[fnamei]]
name.family = [record[lnamei]]
p.name = [name]
#[name.family, name.given]
# resolve gender
if (record[genderi] == "1"):
p.gender = 'male'
elif (record[genderi] == "2"):
p.gender = 'female'
else:
p.gender = 'unknown'
# build and resolve birthdate
birthdate = record[birthi]
bsep1 = birthdate.index("/")
bsep2 = birthdate.index("/", bsep1 + 1)
year = birthdate[-4:]
month = birthdate[0:bsep1]
if (len(month) < 2):
month = "0%s" % month
date = birthdate[bsep1 + 1:bsep2]
if (len(date) < 2):
date = "0%s" % date
birthdate = year + "-" + month + "-" + date
p.birthDate = fhirclient.models.fhirdate.FHIRDate(birthdate)
# build and resolve death date
tt = "12:00:00" #Setting time to noon
yyyy = record[deathyi]
mm = record[deathmi]
if (len(mm) < 2):
mm = "0%s" % mm
dd = record[deathdi]
if (len(dd) < 2):
dd = "0%s" % dd
deathdate = "%s-%s-%sT%s" % (yyyy, mm, dd, tt)
deathdate = fhirclient.models.fhirdate.FHIRDate(deathdate)
# Create period
import fhirclient.models.period as per
per = per.Period()
per.start = deathdate
p.deceasedBoolean = True
p.deceasedDateTime = deathdate
return p