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_maritalStatus(self, marital_status):
"""Extends superclass for convenience
Set the marital status
Keyword arguments:
marital_status -- marital status code
"""
from server.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_relation(self, familyHistory):
"""Extends superclass for convenience
Keyword arguments:
familyHistory -- the relatives
"""
# TODO Combine multiple conditions for same person
from server.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_role(self, role):
"""Extends superclass for convenience
Keyword arguments:
role -- occupation name
"""
if role:
coding = supermod.Coding(display=supermod.string(value=str(role)))
com = supermod.CodeableConcept(coding=[coding])
super(health_Practitioner, self).set_role([com])
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_specialty(self, specialty):
"""Extends superclass for convenience
Keyword arguments
specialty -- person's specialties
"""
for spec in specialty:
code, name = attrgetter('specialty.code', 'specialty.name')(spec)
coding = supermod.Coding(code=supermod.string(value=code),
display=supermod.string(value=name))
com = supermod.CodeableConcept(coding=[coding])
super(health_Practitioner, self).add_specialty(com)
def set_name(self, name):
"""Extends superclass for convenience
Set the observation type
Keyword arguments:
name -- the description of the observation
"""
#TODO Better coding
if name:
n = supermod.CodeableConcept()
n.coding = [supermod.Coding()]
n.coding[0].display = supermod.string(value=name)
super(health_Observation, self).set_name(n)
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_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_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_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_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_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_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_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_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_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_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_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_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
