def __set_rest(self):
r = supermod.Conformance_Rest()
r.mode = supermod.RestfulConformanceMode(value='server')
endpoints = []
for endpoint, mapping in [('Patient', self.patient),
('DiagnosticReport', self.diagnostic_report),
('Practitioner', self.practitioner),
('Procedure', self.procedure),
('Observation', self.observation),
('Condition', self.condition),
('FamilyHistory', self.family_history),
('Medication', self.medication),
('MedicationStatement',
self.medication_statement),
('Immunization', self.immunization),
('Organization', self.organization)]:
e = supermod.Conformance_Resource()
e.type_ = supermod.code(value=endpoint)
e.operation = [
supermod.code(value=operation)
for operation in ['read', 'validate', 'search']
]
for k, v in mapping.resource_search_params.items():
if v is not None: #None are non-implemented
s = supermod.Conformance_SearchParam()
s.name = supermod.string(value=str(k))
s.type_ = supermod.code(value=str(v))
e.add_searchParam(s)
endpoints.append(e)
r.resource = endpoints
self.set_rest([r])
def set_maritalStatus(self, marital_status):
"""Extends superclass for convenience
Set the marital status
Keyword arguments:
marital_status -- marital status code
"""
from fhir.value_sets import maritalStatus as ms
#Health has concubinage and separated, which aren't truly
# matching to the FHIR defined statuses
if marital_status:
us = marital_status.upper() #Codes are uppercase
fhir_status = [x for x in ms.contents\
if x['code'] == us]
if fhir_status:
code = supermod.code(value=fhir_status[0]['code'])
display = supermod.string(value=fhir_status[0]['display'])
else:
code = supermod.code(value='OTH')
display = supermod.string(value='other')
coding = supermod.Coding(system=supermod.uri(
value='http://hl7.org/fhir/v3/MaritalStatus'),
code=code,
display=display)
ms = supermod.CodeableConcept(coding=[coding])
super(health_Patient, self).set_maritalStatus(ms)
def set_interpretation(self, value, lower_limit, upper_limit):
"""Extends superclass for convenience
Set the interpretation
Keyword arguments:
value -- observation value
lower_limit -- the lower normal
upper_limit -- the upper normal
"""
# TODO: Interpretation is complicated
if value and lower_limit and upper_limit:
interp = supermod.CodeableConcept()
interp.coding = [supermod.Coding()]
if value < lower_limit:
v = 'L'
d = 'Low'
elif value > upper_limit:
v = 'H'
d = 'High'
else:
v = 'N'
d = 'Normal'
interp.coding[0].system = supermod.uri(
value='http://hl7.org/fhir/v2/0078')
interp.coding[0].code = supermod.code(value=v)
interp.coding[0].display = supermod.string(value=d)
super(health_Observation, self).set_interpretation(interp)
def set_referenceRange(self, units, lower_limit, upper_limit):
"""Extends superclass for convenience
Set reference range from data model
Keyword arguments:
units -- units name
lower_limit -- lower limit
upper_limit -- upper limit
"""
if units is not None \
and lower_limit is not None \
and upper_limit is not None:
ref = supermod.Observation_ReferenceRange()
#ref.age = supermod.Range() #Not relevant, usually
ref.low = supermod.Quantity()
ref.high = supermod.Quantity()
ref.low.units = ref.high.units = supermod.string(value=units)
ref.low.value = supermod.decimal(value=lower_limit)
ref.high.value = supermod.decimal(value=upper_limit)
ref.meaning = supermod.Coding()
ref.meaning.system = supermod.uri(
value='http://hl7.org/fhir/referencerange-meaning')
ref.meaning.code = supermod.code(value='normal')
ref.meaning.display = supermod.string(value='Normal range')
super(health_Observation, self).set_referenceRange([ref])
def set_relation(self, familyHistory):
"""Extends superclass for convenience
Keyword arguments:
familyHistory -- the relatives
"""
# TODO Combine multiple conditions for same person
from fhir.value_sets import familyMember
for member in familyHistory:
rel = supermod.FamilyHistory_Relation()
rel.relationship = supermod.CodeableConcept()
# Add relationship
t = {'s': 'sibling', 'm': 'maternal', 'f': 'paternal'}
k = ' '.join((t.get(member.xory, ''), member.relative))
info = [d for d in familyMember.contents if d['display'] == k]
c = supermod.Coding()
if info:
c.code = supermod.code(value=info[0]['code'])
c.system = supermod.uri(value=info[0]['system'])
rel.relationship.text = supermod.string(value=k)
c.display = supermod.string(value=k)
rel.relationship.text = supermod.string(value=k)
rel.relationship.coding = [c]
# Add the condition
s = attrgetter(self.map_['condition'])(member)
if s:
con = supermod.FamilyHistory_Condition()
t = supermod.CodeableConcept()
t.coding = [supermod.Coding()]
t.coding[0].display = supermod.string(value=s.name)
t.coding[0].code = supermod.code(value=s.code)
#ICD-10-CM
t.coding[0].system = supermod.uri(
value='urn:oid:2.16.840.1.113883.6.90')
t.text = supermod.string(value=s.name)
con.set_type(t)
rel.add_condition(con)
super(health_FamilyHistory, self).add_relation(rel)
def set_kind(self, kind='product'):
"""Extends superclass for convenience
Keyword arguments:
kind - basically, product or package
"""
if kind in ['product', 'package']:
c = supermod.code(value=kind)
super(health_Medication, self).set_kind(c)
def set_doseQuantity(self, doseQuantity):
"""Extends superclass for convenience
Keyword arguments:
doseQuantity -- amount in mL
"""
if doseQuantity is not None:
v = supermod.decimal(value=str(float(doseQuantity)))
u = supermod.string(value='mL')
s = supermod.uri(value='http://snomed.info/sct')
c = supermod.code(value='258773002')
dq = supermod.Quantity(value=v, units=u, system=s, code=c)
super(health_Immunization, self).set_doseQuantity(dq)
def set_vaccineType(self, vaccineType):
"""Extends superclass for convenience
Keyword arguments:
vaccineType -- the vaccine (Health model)
"""
#TODO Need better coding, much better!
if vaccineType:
cc = supermod.CodeableConcept()
c = supermod.Coding()
c.display = cc.text = supermod.string(value=vaccineType.name.name)
if vaccineType.name.code:
c.code = supermod.code(value=vaccineType.name.code)
cc.coding=[c]
super(health_Immunization, self).set_vaccineType(cc)
def set_site(self, site):
"""Extends superclass for convenience
Keyword arguments:
site -- site code where the vaccine was administered
"""
from 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_code(self, code):
"""Extends superclass for convenience
Keyword arguments:
code -- the pathology info (Health model)
"""
if code:
c = supermod.CodeableConcept()
c.coding = [supermod.Coding()]
c.coding[0].display = supermod.string(value=code.name)
c.coding[0].code = supermod.code(value=code.code)
#ICD-10-CM
c.coding[0].system = supermod.uri(
value='urn:oid:2.16.840.1.113883.6.90')
c.text = supermod.string(value=code.name)
super(health_Condition, self).set_code(c)
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_route(self, route):
"""Extends superclass for convenience
Keyword argument:
route -- how vaccine entered body
"""
from 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
Keyword arguments:
gender -- practitioner's gender
"""
if gender:
from 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_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_communication(self, communication):
"""Extends superclass for convenience
Keyword arguments:
communication -- language
"""
if communication:
from re import sub
code=sub('_','-', communication.code)
name=communication.name
coding = supermod.Coding(
system=supermod.uri(value='urn:ietf:bcp:47'),
code=supermod.code(value=code),
display=supermod.string(value=name)
)
com=supermod.CodeableConcept(coding=[coding],
text=supermod.string(value=name))
super(health_Practitioner, self).add_communication(com)
def set_type(self, type_):
"""Extend superclass
Set the institution's type
Keyword arguments:
type_ - type description
"""
# TODO Use FHIR codes
g = supermod.CodeableConcept()
coding = supermod.Coding(
system=supermod.uri(value='http://hl7.org/fhir/organization-type'),
code=supermod.code(value='prov'),
display=supermod.string(value='Healthcare Provider'))
if type_:
g.text = supermod.string(value=str(type_))
g.coding = [coding]
super(health_Organization, self).set_type(g)
def set_communication(self, communication):
"""Extends superclass for convenience
Set patient language
Keyword arguments:
communication -- the language model
"""
if communication:
from re import sub
code = sub('_', '-', communication.code) #Standard requires dashes
name = communication.name
coding = supermod.Coding(
system=supermod.uri(value='urn:ietf:bcp:47'),
code=supermod.code(value=code),
display=supermod.string(value=name))
com = supermod.CodeableConcept(coding=[coding],
text=supermod.string(value=name))
super(health_Patient, self).set_communication([com])
def set_type(self, type_):
"""Extends superclass for convenience
Keyword arguments:
type_ -- procedure (Health model)
"""
if type_:
concept = supermod.CodeableConcept()
des = type_.description
if des:
concept.text = supermod.string(value=des)
concept.coding = [supermod.Coding()]
name = type_.rec_name
if name:
concept.coding[0].display = supermod.string(value=name)
concept.text = supermod.string(value=name)
concept.coding[0].code = supermod.code(value=type_.name)
#ICD-10-PCS
concept.coding[0].system = supermod.uri(
value='urn:oid:2.16.840.1.113883.6.4')
super(health_Procedure, self).set_type(concept)
def set_gender(self, gender):
"""Extends superclass for convenience
Set patient gender
Keyword arguments:
gender -- gender code
"""
from 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_gnu_dosage(self):
"""Set dosage"""
# TODO Add better dosage info
# FIX On hold since many changes upcoming to the dosage
if self.medication_statement:
d = supermod.MedicationStatement_Dosage()
d.quantity = supermod.Quantity()
f = safe_attrgetter(self.medication_statement,
self.map['dose']['quantity'])
if f:
d.quantity.value = supermod.decimal(value=f)
u = safe_attrgetter(self.medication_statement,
self.map['dose']['units'])
if u:
d.quantity.units = supermod.string(value=u)
d.route = supermod.CodeableConcept()
r = safe_attrgetter(self.medication_statement,
self.map['dose']['route'])
if r:
d.route.coding = [supermod.Coding()]
d.route.coding[0].code = supermod.code(value=r.code)
d.route.coding[0].display = supermod.string(value=r.name)
d.route.text = supermod.string(r.name)
# PRN?
an = safe_attrgetter(self.medication_statement,
self.map['dose']['asNeededBoolean'])
if an:
self.set_asNeededBoolean(supermod.boolean(value=True))
d.timing = supermod.Schedule()
if self.medication_statement.infusion:
d.rate
def set_severity(self, severity):
"""Extends superclass for convenience
Keyword arguments:
severity -- the disease severity
"""
if severity:
# These are the snomed codes
sev = {
'1_mi': ('Mild', '255604002'),
'2_mo': ('Moderate', '6736007'),
'3_sv': ('Severe', '24484000')
}
t = sev.get(severity)
if t:
c = supermod.CodeableConcept()
c.coding = [supermod.Coding()]
c.coding[0].display = supermod.string(value=t[0])
c.coding[0].code = supermod.code(value=t[1])
c.coding[0].system = supermod.uri(
value='http://snomed.info/sct')
c.text = supermod.string(value=t[0])
super(health_Condition, self).set_severity(c)
def __set_format(self):
f = [supermod.code(value='xml')]
#f.append(supermod.code(value='json')) #When JSON is supported
self.set_format(f)
