def build_fhir_vaccination_protocol(cls, vaccination):
# TODO Better vaccine coding/info
seq = vaccination.dose
authority = vaccination.institution
disease = safe_attrgetter(vaccination, "vaccine.indications") # DEBUG
description = vaccination.observations
if seq:
vp = {"doseSequence": seq, "description": description}
ref = {
"display": safe_attrgetter(authority, "name.rec_name"),
# "reference": "".join(["Institution/", str(authority.id)]),
}
target = {"text": disease}
# Unclear if equivalent concept in Health
status = {"text": "Counts"}
# coding = Coding(code='count',
# display='Counts')
# status.coding = [coding]
# vp["doseStatus"] = status
vp["authority"] = ref
vp["targetDisease"] = [target]
return [vp]
def build_fhir_performer(cls, procedure):
actors = []
surgeon = procedure.name.surgeon
if surgeon:
ref = cls.build_fhir_reference_from_adapter_and_object(
Practitioner, surgeon
)
role = cls.build_codeable_concept(
"304292004", "urn:oid:2.16.840.1.113883.4.642.2.420", "Surgeon"
)
actors.append({"actor": ref, "role": role})
anesthetist = procedure.name.anesthetist
if anesthetist:
ref = cls.build_fhir_reference_from_adapter_and_object(
Practitioner, anesthetist
)
role = cls.build_codeable_concept(
"158970007", "urn:oid:2.16.840.1.113883.4.642.2.420", "Anesthetist"
)
actors.append({"actor": ref, "role": role})
for m in procedure.name.surgery_team:
ref = cls.build_fhir_reference_from_adapter_and_object(Practitioner, m)
if m.role:
code, name = safe_attrgetter(
m, "role.specialty.code", "role.specialty.name"
)
role = cls.build_codeable_concept(code=code, text=name)
actors.append({"actor": ref, "role": role})
else:
actors.append({"actor": ref})
return actors
def build_fhir_performed_period(cls, procedure):
start, end = safe_attrgetter(
procedure, "name.surgery_date", "name.surgery_end_date"
)
if start is not None:
period = {"start": instance(start).to_iso8601_string()}
if end is not None:
period["end"] = instance(end).to_iso8601_string()
return period
def build_fhir_summary(cls, impression):
# Shove Objective in here - evaluation_summary
# Shove HPI in here - present_illness + chief_complaint
# Shove Plan in here - directions
return "CC: {}\n\nHPI: {}\n\nObjective: {}\n\nPlan: {}".format(
*safe_attrgetter(
impression,
"chief_complaint",
"present_illness",
"evaluation_summary",
"directions",
default="",
))
def build_fhir_address(cls, patient):
# Only one currently
du = patient.name.du
if du:
ad = {}
ad["use"] = "home"
ad["type"] = "physical" # TODO Check for this
ad["text"] = patient.name.du_address
line = []
number, street, zip_, city, state, country = safe_attrgetter(
du,
"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["line"] = [" ".join(line)]
if city:
ad["city"] = city
if state:
ad["state"] = state
if zip_:
ad["postalCode"] = zip_
if country:
ad["country"] = country
return [ad]
def build_fhir_expiration_date(cls, vaccination):
date = safe_attrgetter(vaccination, "lot.expiration_date")
if date:
return instance(date).to_iso8601_string()
def build_fhir_lot_number(cls, vaccination):
number = safe_attrgetter(vaccination, "lot.number")
if number:
return str(number)
def build_fhir_dosage(cls, med):
# TODO Can always add more information!
# TODO make into converter / config
code_conv = {
"seconds": "s",
"minutes": "min",
"hours": "h",
"days": "d",
"months": "mo",
"years": "a",
}
dose = {}
# Amount (this should be listed, but could be patient reported)
if med.dose:
dose["doseQuantity"] = {
"value": med.dose,
"unit": med.dose_unit.name
}
# Route
# TODO Standard route values
route = med.route
if route:
cc = {}
c = {}
cc["text"] = c["display"] = route.name
c["code"] = route.code
cc["coding"] = [c]
dose["route"] = cc
# PRN
if med.frequency_prn or (safe_attrgetter(
med, "common_dosage.abbreviation") == "prn"):
dose["asNeededBoolean"] = True
else:
dose["asNeededBoolean"] = False
# TODO
# Site and Method
# timing
# BID | TID | QID | AM | PM | QD | QOD | Q4H | Q6H +.
timing = {}
if med.frequency: # prefer specific information
rep = {}
if med.duration_period != "indefinite":
rep["duration"] = med.duration
rep["durationUnits"] = code_conv.get(med.duration_period)
# Health stores timing as 1 per X s/min/hr
rep["frequency"] = "1"
rep["period"] = med.frequency
rep["periodUnits"] = code_conv.get(med.frequency_unit)
timing["repeat"] = rep
elif med.common_dosage:
c = {
"display": med.common_dosage.abbreviation,
"system": "http://snomed.info/sct",
"code": med.common_dosage.code,
}
timing["code"] = {"text": med.common_dosage.name, "coding": [c]}
else: # No dosage information (either unknown or incomplete)
timing = None
if timing:
dose["timing"] = timing
# Rate - rateRatio
# Only if an infusion -- always mL/hr (I think?)
if med.infusion:
num = {"value": med.infusion_rate, "unit": "mL"}
den = {"value": 1, "unit": "hr"}
dose["rateRatio"] = {"numerator": num, "denominator": den}
return [dose]