def __set_gnu_identifier(self):
if self.related_person:
puid=safe_attrgetter(self.related_person, self.map['identifier'])
if puid:
ident = supermod.Identifier(
use=supermod.IdentifierUse(value='usual'),
label=supermod.string(value='PUID'),
value=supermod.string(value=puid))
self.add_identifier(value=ident)
def __set_gnu_patient(self):
if self.related_patient:
if RUN_FLASK:
uri = url_for('pat_record', log_id=self.related_patient.id)
else:
uri = dumb_url_generate(['Patient', self.related_patient.id])
display = self.related_patient.rec_name
ref=supermod.ResourceReference()
ref.display = supermod.string(value=display)
ref.reference = supermod.string(value=uri)
self.set_subject(ref)
def __set_gnu_name(self):
family=[]
given=[supermod.string(value=x) for x in safe_attrgetter(
self.related_person, self.map['given'], '').split()]
after_names=[supermod.string(value=x) for x in safe_attrgetter(
self.related_person, self.map['family'], '').split()]
if len(after_names) > 1:
family=after_names[-1:]
given.extend(after_names[:-1])
else:
family=after_names
name=supermod.HumanName(
use=supermod.NameUse(value='usual'),
family=family,
given=given)
self.set_name(name)
def __set_gnu_gender(self):
try:
gender = attrgetter(self.map['gender'])(self.related_person)
coding = supermod.Coding(
system=supermod.uri(value='http://hl7.org/fhir/v3/AdministrativeGender'),
code=supermod.code(value=gender.upper()),
display=supermod.string(value='Male' if gender == 'm' else 'Female')
)
gender=supermod.CodeableConcept(coding=[coding])
self.set_gender(gender)
except:
raise ValueError('No gender')
def __set_gnu_telecom(self):
telecom = []
phone=safe_attrgetter(self.related_person, self.map['phone'])
if phone:
telecom.append(supermod.Contact(
system=supermod.ContactSystem(value='phone'),
value=supermod.string(value=phone),
use=supermod.ContactUse(value='home')))
mobile=safe_attrgetter(self.related_person, self.map['mobile'])
if mobile:
telecom.append(supermod.Contact(
system=supermod.ContactSystem(value='phone'),
value=supermod.string(value=mobile),
use=supermod.ContactUse(value='mobile')))
email=safe_attrgetter(self.related_person, self.map['email'])
if email:
telecom.append(supermod.Contact(
system=supermod.ContactSystem(value='email'),
value=supermod.string(value=email),
use=supermod.ContactUse(value='email')))
for x in telecom:
self.add_telecom(x)
def set_gender(self, gender):
"""Extends superclass for convenience
Keyword arguments:
gender -- practitioner's gender
"""
if gender:
from server.fhir.value_sets import administrativeGender as codes
us = gender.upper()
sd = [x for x in codes.contents if x['code'] == us][0]
coding = supermod.Coding(
system=supermod.uri(value=sd['system']),
code=supermod.code(value=sd['code']),
display=supermod.string(value=sd['display']))
g = supermod.CodeableConcept(coding=[coding])
super(health_Practitioner, self).set_gender(g)
def set_code(self, name, code):
"""Extends superclass for convenience
Keyword arguments:
code -- code value
name -- name of the medication
"""
#TODO Better info, use recognized codes
if name:
c = supermod.Coding()
c.display = supermod.string(value=str(name))
if code:
c.code = supermod.code(value=code)
cc = supermod.CodeableConcept()
cc.coding = [c]
super(health_Medication, self).set_code(cc)
def set_name(self, name):
"""Extends superclass for convenience
Keyword arguments:
name -- the test (Health model)
"""
if name:
conc = supermod.CodeableConcept()
conc.coding = [supermod.Coding()]
conc.coding[0].display = supermod.string(value=name.name)
conc.coding[0].code = supermod.code(value=name.code)
super(health_DiagnosticReport, self).set_name(conc)
else:
# If you don't know what is being tested,
# the data is useless
raise ValueError('No test coding info')
def __set_gnu_address(self):
#FIX Ugly, but clear
if self.related_person:
try:
address=supermod.Address()
address.set_use(supermod.string(value='home'))
line=[]
try:
line.append(str(attrgetter(self.map['addressNumber'](self.related_person))))
except:
pass
try:
line.append(attrgetter(self.map['addressStreet'])(self.related_person))
except:
pass
try:
city = attrgetter(self.map['addressCity'])(self.related_person)
if city:
address.set_city(supermod.string(value=city))
except:
pass
try:
state = attrgetter(self.map['addressState'])(self.related_person)
if state:
address.set_state(supermod.string(value=state))
except:
pass
try:
z = attrgetter(self.map['addressZip'])(self.related_person)
if z:
address.set_zip(supermod.string(value=z))
except:
pass
try:
country = attrgetter(self.map['addressCountry'])(self.related_person)
if country:
address.set_country(supermod.string(value=value))
except:
pass
if line:
address.add_line(supermod.string(value=' '.join(line)))
self.add_address(address)
except:
pass
def set_site(self, site):
"""Extends superclass for convenience
Keyword arguments:
site -- site code where the vaccine was administered
"""
from server.fhir.value_sets import immunizationSite
if site:
m = [
i for i in immunizationSite.contents
if i['code'] == site.upper()
]
if m:
cc = supermod.CodeableConcept()
c = supermod.Coding()
c.display = cc.text = supermod.string(value=m[0]['display'])
c.code = supermod.code(value=m[0]['code'])
cc.coding = [c]
super(health_Immunization, self).set_site(cc)
def set_route(self, route):
"""Extends superclass for convenience
Keyword argument:
route -- how vaccine entered body
"""
from server.fhir.value_sets import immunizationRoute
if route:
ir = [
i for i in immunizationRoute.contents
if i['code'] == route.upper()
]
if ir:
cc = supermod.CodeableConcept()
c = supermod.Coding()
c.display = cc.text = supermod.string(value=ir[0]['display'])
c.code = supermod.code(value=ir[0]['code'])
cc.coding = [c]
super(health_Immunization, self).set_route(cc)
def set_gender(self, gender):
"""Extends superclass for convenience
Set patient gender
Keyword arguments:
gender -- gender code
"""
from server.fhir.value_sets import administrativeGender as gender_codes
if gender:
us = gender.upper() #Standard requires uppercase
try:
sd = [x for x in gender_codes.contents if x['code'] == us][0]
except:
return None
coding = supermod.Coding(
system=supermod.uri(value=sd['system']),
code=supermod.code(value=sd['code']),
display=supermod.string(value=sd['display']))
g = supermod.CodeableConcept(coding=[coding])
super(health_Patient, self).set_gender(g)
def set_valueQuantity(self, value, units=None, code=None, system=None):
"""Extends superclass for convenience
Set actual value of observation
Keyword arguments:
value -- the actual value
units -- units (e.g., g/dL)
code -- the code (e.g., 'XHEHA1')
system -- the code system (e.g., 'http://code.system')
"""
if value:
# This is to handle multi-field
#if self.field == 'temp':
#units = "degrees C"
#code = "258710007"
#system = "http://snomed.info/sct"
#elif self.field == 'press_d':
#units = "mm[Hg]"
#elif self.field == 'press_s':
#units = "mm[Hg]"
#elif self.field == 'pulse':
#units = "beats/min"
#elif self.field == 'rate':
#units= "breaths/min"
q = supermod.Quantity()
q.value = supermod.decimal(value=value)
if units:
q.units = supermod.string(value=str(units))
if code:
q.code = supermod.code(value=str(code))
if system:
q.system = supermod.uri(value=str(system))
super(health_Observation, self).set_valueQuantity(q)
def set_address(self, addresses):
"""Extend superclass
Set the institution's address
Keyword arguments:
addresses - address models (party.address)
"""
ads=[]
for address in addresses:
ad=supermod.Address()
ad.set_use(supermod.string(value='work'))
line=[]
street, zip_, city, state, country = safe_attrgetter(
address,
'street',
'zip',
'city',
'subdivision.name',
'country.name')
# Deal with number in field maybe never
#if number:
#line.append(str(number))
if street:
line.append(street)
if line:
ad.add_line(supermod.string(value=' '.join(line)))
if city:
ad.set_city(supermod.string(value=city))
if state:
ad.set_state(supermod.string(value=state))
if zip_:
ad.set_zip(supermod.string(value=zip_))
if country:
ad.set_country(supermod.string(value=country))
ads.append(ad)
super(health_Organization, self).set_address(ads)
def set_telecom(self, contacts):
"""Extends superclass for convenience
Set telecom information
Keyword arguments:
contacts -- contacts info (Party model)
"""
telecom = []
for contact in contacts:
c=supermod.Contact()
c.value = supermod.string(value=contact.value)
if contact.type == 'phone':
system='phone'
use='work'
else:
use = system = contact.type
c.system=supermod.ContactSystem(value=system)
c.use=supermod.ContactUse(value=use)
telecom.append(c)
if telecom:
super(health_Organization, self).set_telecom(telecom)
def set_address(self, address):
"""Extends superclass for convenience
Set patient's home address
Keyword arguments:
address -- domiciliary unit model
"""
if address:
ad = supermod.Address()
ad.set_use(supermod.string(value='home'))
line = []
number, street, zip_, city, state, country = safe_attrgetter(
address, 'address_street_number', 'address_street',
'address_zip', 'address_city', 'address_subdivision.name',
'address_country.name')
if number:
line.append(str(number))
if street:
line.append(street)
if line:
ad.add_line(supermod.string(value=' '.join(line)))
if city:
ad.set_city(supermod.string(value=city))
if state:
ad.set_state(supermod.string(value=state))
if zip_:
ad.set_zip(supermod.string(value=zip_))
if country:
ad.set_country(supermod.string(value=country))
super(health_Patient, self).set_address([ad])
def add_location(self, location):
if location:
st = supermod.string(value=location)
super(health_OperationOutcome_Issue, self).add_location(st)
def set_details(self, details):
if details:
st = supermod.string(value=details)
super(health_OperationOutcome_Issue, self).set_details(st)