def generate(cls, patient_file_name=RI_PATIENTS_FILE):
"""Generates a patient file from raw data; replaces old patients file"""
# Open the patient data file for writing generated data
f = open(PATIENTS_FILE, 'w')
top = True # Starting at the top of the file (need to write header here...)
# Open the raw data file and read in the first (header) record
pats = csv.reader(file(patient_file_name, 'U'), dialect='excel-tab')
header = pats.next()
# Read in patient data:
for pat in pats:
# create patient from header and row values
p = dict((zip(header, pat)))
# Add synthetic data
patient_name = rndName(p['GENDER'])
p['fname'] = patient_name[0]
p['initial'] = patient_name[1]
p['lname'] = patient_name[2]
# Add random day of year to year of birth to get dob value
# Make it for the prior year so vists, tests come after birth
p['dob'] = rndDate(int(p['YOB']) - 1).isoformat()
# Map raw GENDER to SMART encoding values
# (For the moment, SMART only handles 'male' and 'female'...)
gender = 'male' if p['GENDER'] == 'M' else 'female'
p['gender'] = gender
p['email'] = toEmail(patient_name)
# Finally, add a random address:
adr = rndAddress()
p = dict(p.items() + adr.items())
p['home'] = '' if randint(0, 1) else rndTelephone()
p['cell'] = '' if randint(0, 1) else rndTelephone()
p['gestage'] = '' if randint(0, 1) else rndGestAge()
# Write out the new patient data file:
# Start with the header (writing only once at the top of the file):
if top:
head = p.keys()
print >> f, "\t".join(head)
top = False
# Then write out the row:
print >> f, "\t".join([p[field] for field in head])
f.close()
def generate(cls,patient_file_name=RI_PATIENTS_FILE):
"""Generates a patient file from raw data; replaces old patients file"""
# Open the patient data file for writing generated data
f = open(PATIENTS_FILE,'w')
top = True # Starting at the top of the file (need to write header here...)
# Open the raw data file and read in the first (header) record
pats = csv.reader(file(patient_file_name,'U'),dialect='excel-tab')
header = pats.next()
# Read in patient data:
for pat in pats:
p=dict((zip(header,pat))) # create patient from header and row values
# Add synthetic data
patient_name = rndName(p['GENDER'])
p['fname']=patient_name[0]
p['initial']=patient_name[1]
p['lname']=patient_name[2]
# Add random day of year to year of birth to get dob value
# Make it for the prior year so vists, tests come after birth
p['dob']=rndDate(int(p['YOB'])-1).isoformat()
# Map raw GENDER to SMART encoding values
# (For the moment, SMART only handles 'male' and 'female'...)
gender = 'male' if p['GENDER']=='M' else 'female'
p['gender'] = gender
p['email'] = toEmail(patient_name)
# Finally, add a random address:
adr = rndAddress()
p = dict(p.items() + adr.items())
p['home'] = '' if randint(0,1) else rndTelephone()
p['cell'] = '' if randint(0,1) else rndTelephone()
p['gestage'] = '' if randint(0,1) else rndGestAge()
# Write out the new patient data file:
# Start with the header (writing only once at the top of the file):
if top:
head = p.keys()
print >>f, "\t".join(head)
top = False
# Then write out the row:
print >>f, "\t".join([ p[field] for field in head])
f.close()
def toJSON(self, prefix=""):
if prefix:
prefix += "-"
patient = Patient.mpi[self.pid]
return {
"request": {
"method": "PUT",
"url": "Observation/" + prefix + "smokingstatus-" + self.id
},
"resource": {
"id":
prefix + "smokingstatus-" + self.id,
"resourceType":
"Observation",
"status":
"final",
"identifier": [{
"use": "official",
"system":
"http://www.bmc.nl/zorgportal/identifiers/observations",
"value": prefix + self.id
}],
"text": {
"status":
"generated",
"div":
'<div xmlns="http://www.w3.org/1999/xhtml">' +
'Tobacco smoking status: %s</div>' % self.smokingStatusText
},
"performer": [{
"reference":
"Practitioner/" + prefix + "Practitioner-" + patient.gp
}],
"effectiveDateTime":
rndDate(2016).isoformat(),
"code": {
"coding": [{
"system": "http://loinc.org",
"code": "72166-2",
"display": "Tobacco smoking status"
}],
"text":
"Tobacco smoking status"
},
"subject": {
"reference": "Patient/" + prefix + self.pid
},
"category": [{
"coding": [{
"system": "http://hl7.org/fhir/observation-category",
"code": "social-history",
"display": "Social History"
}],
"text":
"Social History"
}],
"valueCodeableConcept": {
"coding": [{
"system": "http://snomed.info/sct",
"code": self.smokingStatusCode,
"display": self.smokingStatusText
}],
"text":
self.smokingStatusText
}
}
}