def initData(): """Load data and mappings from Raw data files and mapping files""" Patient.load() Med.load() Problem.load() Lab.load() Refill.load() VitalSigns.load() Immunization.load() Procedure.load() SocialHistory.load() FamilyHistory.load() Allergy.load()
def initData():
"""Load data and mappings from Raw data files and mapping files"""
Patient.load()
Med.load()
Problem.load()
Lab.load()
Refill.load()
VitalSigns.load()
Immunization.load()
Procedure.load()
SocialHistory.load()
FamilyHistory.load()
ClinicalNote.load()
Allergy.load()
def initData():
"""Load data and mappings from Raw data files and mapping files"""
Patient.load()
VitalSigns.load()
Lab.load()
Procedure.load()
Immunization.load()
FamilyHistory.load()
SocialHistory.load()
Condition.load()
Med.load()
Refill.load()
Document.load()
Allergy.load()
ClinicalNote.load()
Practitioner.load()
Coverage.load()
ExplanationOfBenefit.load()
def writePatientData(self):
pfile = open(os.path.join(self.path, "patient-%s.fhir-bundle.xml" % self.pid), "w")
p = Patient.mpi[self.pid]
now = datetime.datetime.now().isoformat()
base_url = self.base_url
if self.pid == "99912345":
vpatient = generate_patient()
p.dob = vpatient["birthday"]
VitalSigns.loadVitalsPatient(vpatient)
print >> pfile, """<?xml version="1.0" encoding="UTF-8"?>
<Bundle xmlns="http://hl7.org/fhir">
<type value="transaction"/>
"""
if self.pid in Document.documents:
for d in [doc for doc in Document.documents[self.pid] if doc.type == "photograph"]:
data = fetch_document(self.pid, d.file_name)
d.content = data["base64_content"]
d.size = data["size"]
d.hash = data["hash"]
b = d
id = uid("Binary", "%s-photo" % d.id)
d.binary_id = id
template = template_env.get_template("binary.xml")
print >> pfile, template.render(dict(globals(), **locals()))
p.photo_code = d.mime_type
p.photo_binary_id = d.binary_id
p.photo_size = d.size
p.photo_hash = d.hash
p.photo_title = d.title
id = "Patient/%s" % self.pid
pid = id
template = template_env.get_template("patient.xml")
print >> pfile, template.render(dict(globals(), **locals()))
bps = []
othervitals = []
if self.pid in VitalSigns.vitals:
encounters = []
for v in VitalSigns.vitals[self.pid]:
encounter_id = None
e = [i for i in encounters if i["date"] == v.start_date and i["type"] == v.encounter_type]
if len(e) > 0:
encounter_id = e[0]["id"]
else:
encounter_id = uid("Encounter", v.id)
encounters.append({"date": v.start_date, "type": v.encounter_type, "id": encounter_id})
id = encounter_id
template = template_env.get_template("encounter.xml")
print >> pfile, template.render(dict(globals(), **locals()))
for vt in VitalSigns.vitalTypes:
try:
othervitals.append(getVital(v, vt, encounter_id))
except:
pass
try:
systolic = getVital(v, VitalSigns.systolic, encounter_id)
diastolic = getVital(v, VitalSigns.diastolic, encounter_id)
bp = systolic
bp["systolic"] = int(systolic["value"])
bp["diastolic"] = int(diastolic["value"])
bp["site"] = v.bp_site
bp["id"] = v.id
if bp["site"]:
for pc in VitalSigns.bpPositionCodes:
if pc["name"] == bp["site"]:
bp["site_code"] = pc["code"]
bp["site_system"] = pc["system"]
bp["method"] = v.bp_method
if bp["method"]:
for pc in VitalSigns.bpPositionCodes:
if pc["name"] == bp["method"]:
bp["method_code"] = pc["code"]
bp["method_system"] = pc["system"]
bp["position"] = v.bp_position
if bp["position"]:
for pc in VitalSigns.bpPositionCodes:
if pc["name"] == bp["position"]:
bp["position_code"] = pc["code"]
bp["position_system"] = pc["system"]
bps.append(bp)
except:
pass
for bp in bps:
systolicid = uid("Observation", "%s-systolic" % bp["id"])
diastolicid = uid("Observation", "%s-diastolic" % bp["id"])
id = uid("Observation", "%s-bp" % bp["id"])
template = template_env.get_template("blood_pressure.xml")
print >> pfile, template.render(dict(globals(), **locals()))
id = systolicid
o = {
"date": bp["date"],
"code": "8480-6",
"name": "Systolic blood pressure",
"scale": "Qn",
"value": bp["systolic"],
"units": "mm[Hg]",
"unitsCode": "mm[Hg]",
"categoryCode": "vital-signs",
"categoryDisplay": "Vital Signs",
}
template = template_env.get_template("observation.xml")
print >> pfile, template.render(dict(globals(), **locals()))
id = diastolicid
o = {
"date": bp["date"],
"code": "8462-4",
"name": "Diastolic blood pressure",
"scale": "Qn",
"value": bp["diastolic"],
"units": "mm[Hg]",
"unitsCode": "mm[Hg]",
"categoryCode": "vital-signs",
"categoryDisplay": "Vital Signs",
}
template = template_env.get_template("observation.xml")
print >> pfile, template.render(dict(globals(), **locals()))
template = template_env.get_template("observation.xml")
for o in othervitals:
id = uid("Observation", "-".join((o["id"], o["name"].lower().replace(" ", "").replace("_", ""))))
if "units" in o.keys():
o["unitsCode"] = o["units"]
o["categoryCode"] = "vital-signs"
o["categoryDisplay"] = "Vital Signs"
print >> pfile, template.render(dict(globals(), **locals()))
if self.pid in Lab.results:
for o in Lab.results[self.pid]:
id = uid("Observation", "%s-lab" % o.id)
o.categoryCode = "laboratory"
o.categoryDisplay = "Laboratory"
print >> pfile, template.render(dict(globals(), **locals()))
medtemplate = template_env.get_template("medication.xml")
dispensetemplate = template_env.get_template("medication_dispense.xml")
if self.pid in Med.meds:
for m in Med.meds[self.pid]:
medid = id = uid("MedicationOrder", m.id)
print >> pfile, medtemplate.render(dict(globals(), **locals()))
for f in Refill.refill_list(m.pid, m.rxn):
id = uid("MedicationDispense", f.id)
print >> pfile, dispensetemplate.render(dict(globals(), **locals()))
template = template_env.get_template("condition.xml")
if self.pid in Problem.problems:
for c in Problem.problems[self.pid]:
id = uid("Condition", c.id)
print >> pfile, template.render(dict(globals(), **locals()))
template = template_env.get_template("procedure.xml")
if self.pid in Procedure.procedures:
for w in Procedure.procedures[self.pid]:
id = uid("Procedure", w.id)
print >> pfile, template.render(dict(globals(), **locals()))
template = template_env.get_template("immunization.xml")
if self.pid in Immunization.immunizations:
for i in Immunization.immunizations[self.pid]:
id = uid("Immunization", i.id)
i.cvx_system, i.cvx_id = i.cvx.rsplit("cvx", 1)
i.cvx_system += "cvx"
print >> pfile, template.render(dict(globals(), **locals()))
template = template_env.get_template("family_history.xml")
if self.pid in FamilyHistory.familyHistories:
for fh in FamilyHistory.familyHistories[self.pid]:
id = uid("FamilyHistory", fh.id)
print >> pfile, template.render(dict(globals(), **locals()))
template = template_env.get_template("smoking_status.xml")
if self.pid in SocialHistory.socialHistories:
t = SocialHistory.socialHistories[self.pid]
t.smokingStatusText = SMOKINGCODES[t.smokingStatusCode]
id = uid("Observation", "-".join((t.id, "smokingstatus")))
print >> pfile, template.render(dict(globals(), **locals()))
if p.gestage:
template = template_env.get_template("observation.xml")
o = {
"date": p.dob,
"code": "18185-9",
"name": "Gestational age at birth",
"scale": "Qn",
"value": p.gestage,
"units": "weeks",
"unitsCode": "wk",
"categoryCode": "exam",
"categoryDisplay": "Exam",
}
id = uid("Observation", "%s-gestage" % self.pid)
print >> pfile, template.render(dict(globals(), **locals()))
if self.pid in Allergy.allergies:
for al in Allergy.allergies[self.pid]:
if al.statement == "positive":
if al.type == "drugClass":
al.typeDescription = "medication"
al.system = "http://rxnav.nlm.nih.gov/REST/Ndfrt"
elif al.type == "drug":
al.typeDescription = "medication"
al.system = "http://www.nlm.nih.gov/research/umls/rxnorm"
elif al.type == "food":
al.typeDescription = "food"
al.system = "http://fda.gov/UNII/"
elif al.type == "environmental":
al.typeDescription = "environment"
al.system = "http://fda.gov/UNII/"
if al.reaction:
if al.severity.lower() == "mild":
al.severity = "mild"
al.criticality = "CRITL"
elif al.severity.lower() == "severe":
al.severity = "severe"
al.criticality = "CRITH"
elif al.severity.lower() == "life threatening" or al.severity.lower() == "fatal":
al.severity = "severe"
al.criticality = "CRITH"
elif al.severity.lower() == "moderate":
al.severity = "moderate"
al.criticality = "CRITU"
else:
al.severity = None
id = uid("AllergyIntolerance", al.id)
template = template_env.get_template("allergy.xml")
print >> pfile, template.render(dict(globals(), **locals()))
elif al.statement == "negative" and al.type == "general":
if al.code == "160244002":
template = template_env.get_template("no_known_allergies.xml")
id = uid("List", al.id)
al.loinc_code = "52473-6"
al.loinc_display = "Allergy"
al.text = "No known allergies"
print >> pfile, template.render(dict(globals(), **locals()))
elif al.code == "409137002":
template = template_env.get_template("no_known_allergies.xml")
id = uid("List", al.id)
al.loinc_code = "11382-9"
al.loinc_display = "Medication allergy"
al.text = "No known history of drug allergy"
print >> pfile, template.render(dict(globals(), **locals()))
else:
template = template_env.get_template("general_observation.xml")
o = {
"date": al.start,
"system": "http://snomed.info/sct",
"code": al.code,
"name": al.allergen,
"categoryCode": "exam",
"categoryDisplay": "Exam",
}
id = uid("Observation", "%s-allergy" % al.id)
print >> pfile, template.render(dict(globals(), **locals()))
addedPractitioner = False
if self.pid in ClinicalNote.clinicalNotes:
id = "Practitioner/1234"
template = template_env.get_template("practitioner.xml")
print >> pfile, template.render(dict(globals(), **locals()))
addedPractitioner = True
for d in ClinicalNote.clinicalNotes[self.pid]:
if d.mime_type == "text/plain":
data = fetch_document(self.pid, d.file_name)
d.content = data["base64_content"]
b = d
id = uid("Binary", "%s-note" % d.id)
d.binary_id = id
template = template_env.get_template("binary.xml")
print >> pfile, template.render(dict(globals(), **locals()))
id = uid("DocumentReference", "%s-note" % d.id)
d.system = "http://loinc.org"
d.code = "34109-9"
d.display = "Note"
template = template_env.get_template("document.xml")
print >> pfile, template.render(dict(globals(), **locals()))
if self.pid in Document.documents:
if not addedPractitioner:
id = "Practitioner/1234"
template = template_env.get_template("practitioner.xml")
print >> pfile, template.render(dict(globals(), **locals()))
for d in [doc for doc in Document.documents[self.pid] if doc.type != "photograph"]:
data = fetch_document(self.pid, d.file_name)
d.content = data["base64_content"]
d.size = data["size"]
d.hash = data["hash"]
b = d
id = uid("Binary", "%s-document" % d.id)
d.binary_id = id
template = template_env.get_template("binary.xml")
print >> pfile, template.render(dict(globals(), **locals()))
id = uid("DocumentReference", "%s-document" % d.id)
d.system = "http://smarthealthit.org/terms/codes/DocumentType#"
d.code = d.type
d.display = d.type
template = template_env.get_template("document.xml")
print >> pfile, template.render(dict(globals(), **locals()))
if self.pid in ImagingStudy.imagingStudies:
st = {}
for img in ImagingStudy.imagingStudies[self.pid]:
data = fetch_document(self.pid, img.image_file_name)
img.mime_type = "application/dicom"
img.content = data["base64_content"]
img.size = data["size"]
img.hash = data["hash"]
b = img
id = uid("Binary", "%s-dicom" % img.id)
img.binary_id = id
template = template_env.get_template("binary.xml")
print >> pfile, template.render(dict(globals(), **locals()))
if img.study_oid not in st.keys():
st[img.study_oid] = {
"id": img.id,
"title": img.study_title,
"date": img.study_date,
"accession_number": img.study_accession_number,
"modality": img.study_modality,
"oid": img.study_oid,
"series_count": 0,
"images_count": 0,
"series": {},
}
series = st[img.study_oid]["series"]
if img.series_oid not in series.keys():
st[img.study_oid]["series_count"] += 1
series[img.series_oid] = {
"number": st[img.study_oid]["series_count"],
"title": img.series_title,
"oid": img.series_oid,
"images_count": 0,
"images": [],
}
st[img.study_oid]["images_count"] += 1
series[img.series_oid]["images_count"] += 1
series[img.series_oid]["images"].append(
{
"title": img.image_title,
"date": img.image_date,
"file_name": img.image_file_name,
"oid": img.image_oid,
"binary_id": img.binary_id,
"sop": img.image_sop,
"number": series[img.series_oid]["images_count"],
}
)
for i in st:
s = st[i]
id = uid("ImagingStudy", s["id"])
template = template_env.get_template("imagingstudy.xml")
print >> pfile, template.render(dict(globals(), **locals()))
print >> pfile, "\n</Bundle>"
pfile.close()
def writePatientData(self):
pfile = open(os.path.join(self.path, "patient-%s.fhir-bundle.xml"%self.pid), "w")
p = Patient.mpi[self.pid]
now = datetime.datetime.now().isoformat()
if self.pid == '99912345':
vpatient = generate_patient()
p.dob = vpatient["birthday"]
VitalSigns.loadVitalsPatient(vpatient)
print >>pfile, """<?xml version="1.0" encoding="UTF-8"?>
<feed xmlns="http://www.w3.org/2005/Atom">
<title>SMART patient bundle for transactional posting</title>
<id>urn:uuid:%s</id>
<updated>%s</updated>
"""%(uid(), now)
if self.pid in Document.documents:
for d in [doc for doc in Document.documents[self.pid] if doc.type == 'photograph']:
data = fetch_document (self.pid, d.file_name)
d.content = data['base64_content']
d.size = data['size']
d.hash = data['hash']
b = d
id = uid("Binary", "%s-photo" % d.id)
d.binary_id = id
template = template_env.get_template('binary.xml')
print >>pfile, template.render(dict(globals(), **locals()))
p.photo_code = d.mime_type
p.photo_binary_id = d.binary_id
p.photo_size = d.size
p.photo_hash = d.hash
p.photo_title = d.title
id = "Patient/%s"%self.pid
pid = id
template = template_env.get_template('patient.xml')
print >>pfile, template.render(dict(globals(), **locals()))
bps = []
othervitals = []
if self.pid in VitalSigns.vitals:
encounters = []
for v in VitalSigns.vitals[self.pid]:
encounter_id = None
e = [i for i in encounters if i['date'] == v.start_date and i['type'] == v.encounter_type]
if len(e) > 0:
encounter_id = e[0]['id']
else:
encounter_id = uid("Encounter", v.id)
encounters.append ({'date': v.start_date, 'type': v.encounter_type, 'id': encounter_id})
id = encounter_id
template = template_env.get_template('encounter.xml')
print >>pfile, template.render(dict(globals(), **locals()))
for vt in VitalSigns.vitalTypes:
try:
othervitals.append(getVital(v, vt, encounter_id))
except: pass
try:
systolic = getVital(v, VitalSigns.systolic, encounter_id)
diastolic = getVital(v, VitalSigns.diastolic, encounter_id)
bp = systolic
bp['systolic'] = int(systolic['value'])
bp['diastolic'] = int(diastolic['value'])
bp['site'] = v.bp_site
bp['id'] = v.id
if bp['site']:
for pc in VitalSigns.bpPositionCodes:
if pc['name'] == bp['site']:
bp['site_code'] = pc['code']
bp['site_system'] = pc['system']
bp['method'] = v.bp_method
if bp['method']:
for pc in VitalSigns.bpPositionCodes:
if pc['name'] == bp['method']:
bp['method_code'] = pc['code']
bp['method_system'] = pc['system']
bp['position'] = v.bp_position
if bp['position']:
for pc in VitalSigns.bpPositionCodes:
if pc['name'] == bp['position']:
bp['position_code'] = pc['code']
bp['position_system'] = pc['system']
bps.append(bp)
except: pass
for bp in bps:
systolicid = uid("Observation", "%s-systolic" % bp['id'])
diastolicid = uid("Observation", "%s-diastolic" % bp['id'])
id = uid("Observation", "%s-bp" % bp['id'])
template = template_env.get_template('blood_pressure.xml')
print >>pfile, template.render(dict(globals(), **locals()))
id = systolicid
o = {
"date": bp['date'],
"code": "8480-6",
"name": "Systolic blood pressure",
"scale": "Qn",
"value": bp['systolic'],
"units": "mm[Hg]",
"unitsCode": "mm[Hg]"
}
template = template_env.get_template('observation.xml')
print >>pfile, template.render(dict(globals(), **locals()))
id = diastolicid
o = {
"date": bp['date'],
"code": "8462-4",
"name": "Diastolic blood pressure",
"scale": "Qn",
"value": bp['diastolic'],
"units": "mm[Hg]",
"unitsCode": "mm[Hg]"
}
template = template_env.get_template('observation.xml')
print >>pfile, template.render(dict(globals(), **locals()))
template = template_env.get_template('observation.xml')
for o in othervitals:
id = uid("Observation", '-'.join((o["id"], o["name"].lower().replace(' ', '').replace('_', ''))))
if "units" in o.keys():
o["unitsCode"] = o["units"]
print >>pfile, template.render(dict(globals(), **locals()))
if self.pid in Lab.results:
for o in Lab.results[self.pid]:
id = uid("Observation", "%s-lab" % o.id)
print >>pfile, template.render(dict(globals(), **locals()))
medtemplate = template_env.get_template('medication.xml')
dispensetemplate = template_env.get_template('medication_dispense.xml')
if self.pid in Med.meds:
for m in Med.meds[self.pid]:
medid = id = uid("MedicationPrescription", m.id)
print >>pfile, medtemplate.render(dict(globals(), **locals()))
for f in Refill.refill_list(m.pid, m.rxn):
id = uid("MedicationDispense", f.id)
print >>pfile, dispensetemplate.render(dict(globals(), **locals()))
template = template_env.get_template('condition.xml')
if self.pid in Problem.problems:
for c in Problem.problems[self.pid]:
id = uid("Condition", c.id)
print >>pfile, template.render(dict(globals(), **locals()))
template = template_env.get_template('procedure.xml')
if self.pid in Procedure.procedures:
for w in Procedure.procedures[self.pid]:
id = uid("Procedure", w.id)
print >>pfile, template.render(dict(globals(), **locals()))
template = template_env.get_template('immunization.xml')
if self.pid in Immunization.immunizations:
for i in Immunization.immunizations[self.pid]:
id = uid("Immunization", i.id)
i.cvx_system, i.cvx_id = i.cvx.rsplit("cvx",1)
i.cvx_system += "cvx"
print >>pfile, template.render(dict(globals(), **locals()))
template = template_env.get_template('family_history.xml')
if self.pid in FamilyHistory.familyHistories:
for fh in FamilyHistory.familyHistories[self.pid]:
id = uid("FamilyHistory", fh.id)
print >>pfile, template.render(dict(globals(), **locals()))
template = template_env.get_template('smoking_status.xml')
if self.pid in SocialHistory.socialHistories:
t = SocialHistory.socialHistories[self.pid]
t.smokingStatusText = SMOKINGCODES[t.smokingStatusCode]
id = uid("Observation", '-'.join((t.id,"smokingstatus")))
print >>pfile, template.render(dict(globals(), **locals()))
if p.gestage:
template = template_env.get_template('observation.xml')
o = {
"date": p.dob,
"code": "18185-9",
"name": "Gestational age at birth",
"scale": "Qn",
"value": p.gestage,
"units": "weeks",
"unitsCode": "wk"
}
id = uid("Observation", "%s-gestage" % self.pid)
print >>pfile, template.render(dict(globals(), **locals()))
if self.pid in Allergy.allergies:
for al in Allergy.allergies[self.pid]:
if al.statement == 'positive':
id = uid("Substance", '-'.join((al.system.lower(), al.code)))
al.substance_id = id
template = template_env.get_template('substance.xml')
if al.type == 'drugClass':
al.typeDescription = 'drug class'
al.system = "http://rxnav.nlm.nih.gov/REST/Ndfrt"
elif al.type == 'drug':
al.typeDescription = 'drug'
al.system = "http://www.nlm.nih.gov/research/umls/rxnorm"
elif al.type == 'food':
al.typeDescription = 'food',
al.system = "http://fda.gov/UNII/"
elif al.type == 'environmental':
al.typeDescription = 'environmental substance',
al.system = "http://fda.gov/UNII/"
print >>pfile, template.render(dict(globals(), **locals()))
if al.reaction:
if al.severity.lower() == 'mild':
al.severity = 'minor'
al.criticality = 'low'
elif al.severity.lower() == 'severe':
al.severity = 'severe'
al.criticality = 'high'
elif al.severity.lower() == 'life threatening' or al.severity.lower() == 'fatal':
al.severity = 'severe'
al.criticality = 'fatal'
elif al.severity.lower() == 'moderate':
al.severity = 'moderate'
al.criticality = 'medium'
else:
al.severity = None
id = uid("AdverseReaction", al.id)
al.reaction_id = id
template = template_env.get_template('adverse_reaction.xml')
print >>pfile, template.render(dict(globals(), **locals()))
id = uid("AllergyIntolerance", al.id)
template = template_env.get_template('allergy.xml')
print >>pfile, template.render(dict(globals(), **locals()))
elif al.statement == 'negative' and al.type == 'general':
if al.code == '160244002':
template = template_env.get_template('no_known_allergies.xml')
id = uid("List", al.id)
al.loinc_code = '52473-6'
al.loinc_display = 'Allergy'
al.text = 'No known allergies'
print >>pfile, template.render(dict(globals(), **locals()))
elif al.code == '409137002':
template = template_env.get_template('no_known_allergies.xml')
id = uid("List", al.id)
al.loinc_code = '11382-9'
al.loinc_display = 'Medication allergy'
al.text = 'No known history of drug allergy'
print >>pfile, template.render(dict(globals(), **locals()))
else:
template = template_env.get_template('general_observation.xml')
o = {
"date": al.start,
"system": "http://snomed.info/sct",
"code": al.code,
"name": al.allergen
}
id = uid("Observation", "%s-allergy" % al.id)
print >>pfile, template.render(dict(globals(), **locals()))
addedPractitioner = False
if self.pid in ClinicalNote.clinicalNotes:
id = 'Practitioner/1234'
template = template_env.get_template('practitioner.xml')
print >>pfile, template.render(dict(globals(), **locals()))
addedPractitioner = True
for d in ClinicalNote.clinicalNotes[self.pid]:
if d.mime_type == 'text/plain':
data = fetch_document (self.pid, d.file_name)
d.content = data['base64_content']
b = d
id = uid("Binary", "%s-note" % d.id)
d.binary_id = id
template = template_env.get_template('binary.xml')
print >>pfile, template.render(dict(globals(), **locals()))
id = uid("DocumentReference", "%s-note" % d.id)
d.system = "http://loinc.org"
d.code = '34109-9'
d.display = 'Note'
template = template_env.get_template('document.xml')
print >>pfile, template.render(dict(globals(), **locals()))
if self.pid in Document.documents:
if not addedPractitioner:
id = 'Practitioner/1234'
template = template_env.get_template('practitioner.xml')
print >>pfile, template.render(dict(globals(), **locals()))
for d in [doc for doc in Document.documents[self.pid] if doc.type != 'photograph']:
data = fetch_document (self.pid, d.file_name)
d.content = data['base64_content']
d.size = data['size']
d.hash = data['hash']
b = d
id = uid("Binary", "%s-document" % d.id)
d.binary_id = id
template = template_env.get_template('binary.xml')
print >>pfile, template.render(dict(globals(), **locals()))
id = uid("DocumentReference", "%s-document" % d.id)
d.system = 'http://smarthealthit.org/terms/codes/DocumentType#'
d.code = d.type
d.display = d.type
template = template_env.get_template('document.xml')
print >>pfile, template.render(dict(globals(), **locals()))
if self.pid in ImagingStudy.imagingStudies:
st = {}
for img in ImagingStudy.imagingStudies[self.pid]:
data = fetch_document (self.pid, img.image_file_name)
img.mime_type = "application/dicom"
img.content = data['base64_content']
img.size = data['size']
img.hash = data['hash']
b = img
id = uid("Binary", "%s-dicom" % img.id)
img.binary_id = id
template = template_env.get_template('binary.xml')
print >>pfile, template.render(dict(globals(), **locals()))
if img.study_oid not in st.keys():
st[img.study_oid] = {
'id': img.id,
'title': img.study_title,
'date': img.study_date,
'accession_number': img.study_accession_number,
'modality': img.study_modality,
'oid': img.study_oid,
'series_count': 0,
'images_count': 0,
'series': {}
}
series = st[img.study_oid]['series']
if img.series_oid not in series.keys():
st[img.study_oid]['series_count'] += 1
series[img.series_oid] = {
'number': st[img.study_oid]['series_count'],
'title': img.series_title,
'oid': img.series_oid,
'images_count': 0,
'images': []
}
st[img.study_oid]['images_count'] += 1
series[img.series_oid]['images_count'] += 1
series[img.series_oid]['images'].append({
'title': img.image_title,
'date': img.image_date,
'file_name': img.image_file_name,
'oid': img.image_oid,
'binary_id': img.binary_id,
'sop': img.image_sop,
'number': series[img.series_oid]['images_count']
})
for i in st:
s = st[i]
id = uid("ImagingStudy", s['id'])
template = template_env.get_template('imagingstudy.xml')
print >>pfile, template.render(dict(globals(), **locals()))
print >>pfile, "\n</feed>"
pfile.close()
def writePatientData(self, prefix=None):
pfile = open(
os.path.join(self.path, "patient-%s.fhir-bundle.xml" % self.pid),
"w")
p = Patient.mpi[self.pid]
now = datetime.datetime.now().isoformat()
base_url = self.base_url
tag = self.tag
if self.pid == '99912345':
vpatient = generate_patient()
p.dob = vpatient["birthday"]
VitalSigns.loadVitalsPatient(vpatient)
print >> pfile, """<?xml version="1.0" encoding="UTF-8"?>
<Bundle xmlns="http://hl7.org/fhir">
<type value="transaction"/>
"""
if self.pid in Document.documents:
for d in [
doc for doc in Document.documents[self.pid]
if doc.type == 'photograph'
]:
data = fetch_document(self.pid, d.file_name)
d.content = data['base64_content']
d.size = data['size']
d.hash = data['hash']
b = d
id = uid("Binary", "%s-photo" % d.id, prefix)
d.binary_id = id
template = template_env.get_template('binary.xml')
print >> pfile, template.render(dict(globals(), **locals()))
p.photo_code = d.mime_type
p.photo_binary_id = d.binary_id
p.photo_size = d.size
p.photo_hash = d.hash
p.photo_title = d.title
if (prefix == None):
id = "Patient/%s" % self.pid
else:
id = "Patient/%s-%s" % (prefix, self.pid)
pid = id
template = template_env.get_template('patient.xml')
print >> pfile, template.render(dict(globals(), **locals()))
bps = []
othervitals = []
if self.pid in VitalSigns.vitals:
encounters = []
for v in VitalSigns.vitals[self.pid]:
encounter_id = None
e = [
i for i in encounters if i['date'] == v.start_date
and i['type'] == v.encounter_type
]
if len(e) > 0:
encounter_id = e[0]['id']
else:
encounter_id = uid("Encounter", v.id, prefix)
encounters.append({
'date': v.start_date,
'type': v.encounter_type,
'id': encounter_id
})
id = encounter_id
template = template_env.get_template('encounter.xml')
print >> pfile, template.render(dict(
globals(), **locals()))
for vt in VitalSigns.vitalTypes:
try:
othervitals.append(getVital(v, vt, encounter_id))
except:
pass
try:
systolic = getVital(v, VitalSigns.systolic, encounter_id)
diastolic = getVital(v, VitalSigns.diastolic, encounter_id)
bp = systolic
bp['systolic'] = int(systolic['value'])
bp['diastolic'] = int(diastolic['value'])
bp['site'] = v.bp_site
bp['id'] = v.id
if bp['site']:
for pc in VitalSigns.bpPositionCodes:
if pc['name'] == bp['site']:
bp['site_code'] = pc['code']
bp['site_system'] = pc['system']
bp['method'] = v.bp_method
if bp['method']:
for pc in VitalSigns.bpPositionCodes:
if pc['name'] == bp['method']:
bp['method_code'] = pc['code']
bp['method_system'] = pc['system']
bp['position'] = v.bp_position
if bp['position']:
for pc in VitalSigns.bpPositionCodes:
if pc['name'] == bp['position']:
bp['position_code'] = pc['code']
bp['position_system'] = pc['system']
bps.append(bp)
except:
pass
for bp in bps:
systolicid = uid("Observation", "%s-systolic" % bp['id'], prefix)
diastolicid = uid("Observation", "%s-diastolic" % bp['id'], prefix)
id = uid("Observation", "%s-bp" % bp['id'], prefix)
template = template_env.get_template('blood_pressure.xml')
print >> pfile, template.render(dict(globals(), **locals()))
id = systolicid
o = {
"date": bp['date'],
"code": "8480-6",
"name": "Systolic blood pressure",
"scale": "Qn",
"value": bp['systolic'],
"units": "mm[Hg]",
"unitsCode": "mm[Hg]",
"categoryCode": "vital-signs",
"categoryDisplay": "Vital Signs"
}
template = template_env.get_template('observation.xml')
print >> pfile, template.render(dict(globals(), **locals()))
id = diastolicid
o = {
"date": bp['date'],
"code": "8462-4",
"name": "Diastolic blood pressure",
"scale": "Qn",
"value": bp['diastolic'],
"units": "mm[Hg]",
"unitsCode": "mm[Hg]",
"categoryCode": "vital-signs",
"categoryDisplay": "Vital Signs"
}
template = template_env.get_template('observation.xml')
print >> pfile, template.render(dict(globals(), **locals()))
template = template_env.get_template('observation.xml')
for o in othervitals:
id = uid(
"Observation", '-'.join(
(o["id"], o["name"].lower().replace(' ',
'').replace('_', ''))),
prefix)
if "units" in o.keys():
o["unitsCode"] = o["units"]
o["categoryCode"] = "vital-signs"
o["categoryDisplay"] = "Vital Signs"
print >> pfile, template.render(dict(globals(), **locals()))
if self.pid in Lab.results:
for o in Lab.results[self.pid]:
id = uid("Observation", "%s-lab" % o.id, prefix)
o.categoryCode = "laboratory"
o.categoryDisplay = "Laboratory"
print >> pfile, template.render(dict(globals(), **locals()))
medtemplate = template_env.get_template('medication.xml')
dispensetemplate = template_env.get_template('medication_dispense.xml')
if self.pid in Med.meds:
for m in Med.meds[self.pid]:
medid = id = uid("MedicationOrder", m.id, prefix)
print >> pfile, medtemplate.render(dict(globals(), **locals()))
for f in Refill.refill_list(m.pid, m.rxn):
id = uid("MedicationDispense", f.id, prefix)
print >> pfile, dispensetemplate.render(
dict(globals(), **locals()))
template = template_env.get_template('condition.xml')
if self.pid in Problem.problems:
for c in Problem.problems[self.pid]:
id = uid("Condition", c.id, prefix)
print >> pfile, template.render(dict(globals(), **locals()))
template = template_env.get_template('procedure.xml')
if self.pid in Procedure.procedures:
for w in Procedure.procedures[self.pid]:
id = uid("Procedure", w.id, prefix)
print >> pfile, template.render(dict(globals(), **locals()))
template = template_env.get_template('immunization.xml')
if self.pid in Immunization.immunizations:
for i in Immunization.immunizations[self.pid]:
id = uid("Immunization", i.id, prefix)
i.cvx_system, i.cvx_id = i.cvx.rsplit("cvx", 1)
i.cvx_system += "cvx"
print >> pfile, template.render(dict(globals(), **locals()))
template = template_env.get_template('family_history.xml')
if self.pid in FamilyHistory.familyHistories:
for fh in FamilyHistory.familyHistories[self.pid]:
id = uid("FamilyMemberHistory", fh.id, prefix)
print >> pfile, template.render(dict(globals(), **locals()))
template = template_env.get_template('smoking_status.xml')
if self.pid in SocialHistory.socialHistories:
t = SocialHistory.socialHistories[self.pid]
t.smokingStatusText = SMOKINGCODES[t.smokingStatusCode]
id = uid("Observation", '-'.join((t.id, "smokingstatus")), prefix)
print >> pfile, template.render(dict(globals(), **locals()))
if p.gestage:
template = template_env.get_template('observation.xml')
o = {
"date": p.dob,
"code": "18185-9",
"name": "Gestational age at birth",
"scale": "Qn",
"value": p.gestage,
"units": "weeks",
"unitsCode": "wk",
"categoryCode": "exam",
"categoryDisplay": "Exam"
}
id = uid("Observation", "%s-gestage" % self.pid, prefix)
print >> pfile, template.render(dict(globals(), **locals()))
if self.pid in Allergy.allergies:
for al in Allergy.allergies[self.pid]:
if al.statement == 'positive':
if al.type == 'drugClass':
al.typeDescription = 'medication'
al.system = "http://rxnav.nlm.nih.gov/REST/Ndfrt"
elif al.type == 'drug':
al.typeDescription = 'medication'
al.system = "http://www.nlm.nih.gov/research/umls/rxnorm"
elif al.type == 'food':
al.typeDescription = 'food'
al.system = "http://fda.gov/UNII/"
elif al.type == 'environmental':
al.typeDescription = 'environment'
al.system = "http://fda.gov/UNII/"
if al.reaction:
if al.severity.lower() == 'mild':
al.severity = 'mild'
al.criticality = 'CRITL'
elif al.severity.lower() == 'severe':
al.severity = 'severe'
al.criticality = 'CRITH'
elif al.severity.lower(
) == 'life threatening' or al.severity.lower(
) == 'fatal':
al.severity = 'severe'
al.criticality = 'CRITH'
elif al.severity.lower() == 'moderate':
al.severity = 'moderate'
al.criticality = 'CRITU'
else:
al.severity = None
id = uid("AllergyIntolerance", al.id, prefix)
template = template_env.get_template('allergy.xml')
print >> pfile, template.render(dict(
globals(), **locals()))
elif al.statement == 'negative' and al.type == 'general':
if al.code == '160244002':
template = template_env.get_template(
'no_known_allergies.xml')
id = uid("List", al.id, prefix)
al.loinc_code = '52473-6'
al.loinc_display = 'Allergy'
al.text = 'No known allergies'
print >> pfile, template.render(
dict(globals(), **locals()))
elif al.code == '409137002':
template = template_env.get_template(
'no_known_allergies.xml')
id = uid("List", al.id, prefix)
al.loinc_code = '11382-9'
al.loinc_display = 'Medication allergy'
al.text = 'No known history of drug allergy'
print >> pfile, template.render(
dict(globals(), **locals()))
else:
template = template_env.get_template(
'general_observation.xml')
o = {
"date": al.start,
"system": "http://snomed.info/sct",
"code": al.code,
"name": al.allergen,
"categoryCode": "exam",
"categoryDisplay": "Exam"
}
id = uid("Observation", "%s-allergy" % al.id, prefix)
print >> pfile, template.render(
dict(globals(), **locals()))
addedPractitioner = False
if self.pid in ClinicalNote.clinicalNotes:
id = 'Practitioner/SMART-1234'
template = template_env.get_template('practitioner.xml')
print >> pfile, template.render(dict(globals(), **locals()))
addedPractitioner = True
for d in ClinicalNote.clinicalNotes[self.pid]:
if d.mime_type == 'text/plain':
data = fetch_document(self.pid, d.file_name)
d.content = data['base64_content']
b = d
id = uid("Binary", "%s-note" % d.id, prefix)
d.binary_id = id
template = template_env.get_template('binary.xml')
print >> pfile, template.render(dict(
globals(), **locals()))
id = uid("DocumentReference", "%s-note" % d.id, prefix)
d.system = "http://loinc.org"
d.code = '34109-9'
d.display = 'Note'
template = template_env.get_template('document.xml')
print >> pfile, template.render(dict(
globals(), **locals()))
if self.pid in Document.documents:
if not addedPractitioner:
id = 'Practitioner/SMART-1234'
template = template_env.get_template('practitioner.xml')
print >> pfile, template.render(dict(globals(), **locals()))
for d in [
doc for doc in Document.documents[self.pid]
if doc.type != 'photograph'
]:
data = fetch_document(self.pid, d.file_name)
d.content = data['base64_content']
d.size = data['size']
d.hash = data['hash']
b = d
id = uid("Binary", "%s-document" % d.id, prefix)
d.binary_id = id
template = template_env.get_template('binary.xml')
print >> pfile, template.render(dict(globals(), **locals()))
id = uid("DocumentReference", "%s-document" % d.id, prefix)
d.system = 'http://smarthealthit.org/terms/codes/DocumentType#'
d.code = d.type
d.display = d.type
template = template_env.get_template('document.xml')
print >> pfile, template.render(dict(globals(), **locals()))
if self.pid in ImagingStudy.imagingStudies:
st = {}
for img in ImagingStudy.imagingStudies[self.pid]:
data = fetch_document(self.pid, img.image_file_name)
img.mime_type = "application/dicom"
img.content = data['base64_content']
img.size = data['size']
img.hash = data['hash']
b = img
id = uid("Binary", "%s-dicom" % img.id, prefix)
img.binary_id = id
template = template_env.get_template('binary.xml')
print >> pfile, template.render(dict(globals(), **locals()))
if img.study_oid not in st.keys():
st[img.study_oid] = {
'id': img.id,
'title': img.study_title,
'date': img.study_date,
'accession_number': img.study_accession_number,
'modality': img.study_modality,
'oid': img.study_oid,
'series_count': 0,
'images_count': 0,
'series': {}
}
series = st[img.study_oid]['series']
if img.series_oid not in series.keys():
st[img.study_oid]['series_count'] += 1
series[img.series_oid] = {
'number': st[img.study_oid]['series_count'],
'title': img.series_title,
'oid': img.series_oid,
'images_count': 0,
'images': []
}
st[img.study_oid]['images_count'] += 1
series[img.series_oid]['images_count'] += 1
series[img.series_oid]['images'].append({
'title':
img.image_title,
'date':
img.image_date,
'file_name':
img.image_file_name,
'oid':
img.image_oid,
'binary_id':
img.binary_id,
'sop':
img.image_sop,
'number':
series[img.series_oid]['images_count']
})
for i in st:
s = st[i]
id = uid("ImagingStudy", s['id'], prefix)
template = template_env.get_template('imagingstudy.xml')
print >> pfile, template.render(dict(globals(), **locals()))
print >> pfile, "\n</Bundle>"
pfile.close()
