@Override
@SuppressWarnings("unchecked")
protected void process(File csvFile) throws Exception {
Transaction t = createTransaction();
Query q = createQuery(t);
List<Object[]> list = (List<Object[]>) q.list();
if (list.size() < 1) throw new EmptyResultException();
ArrayList<String> row;
Table out = new Table();
for (Object[] o : list) {
TestResult tr = (TestResult) o[0];
PatientAttributeValue pc = (PatientAttributeValue) o[1];
PatientAttributeValue bdt = (PatientAttributeValue) o[2];
Date bd = DateUtils.parseDate(bdt.getValue());
Date tDate = tr.getTestDate();
int testCode = TestCode.T4.getCode();
if (bd != null
&& tDate != null
&& DateUtils.getDateOffset(bd, Calendar.YEAR, 15).after(tDate)) {
// < 15 years old at time of test
testCode = TestCode.T4PERCENT.getCode();
if (!tr.getTest()
.getTestType()
.getDescription()
.equals(StandardObjects.getCd4PercentageTestType().getDescription())) continue;
} else {
if (tr.getTest()
.getTestType()
.getDescription()
.equals(StandardObjects.getCd4PercentageTestType().getDescription())) continue;
}
String value = tr.getValue();
row = new ArrayList<String>();
row.add(getCentreName());
row.add(OriginCode.ARC.getCode() + "");
row.add(pc.getValue());
row.add(getFormattedDate(tDate));
row.add(TypeOfInformationCode.LAB_RESULT.getCode() + "");
row.add(testCode + "");
row.add(getFormattedDecimal(value, 0, 0));
row.add("");
out.addRow(row);
}
t.commit();
out.exportAsCsv(new FileOutputStream(csvFile), ';', false);
}
@Override
public void setAttributeValue(Attribute attribute, Instance instance, Patient patient) {
RegaService rs = ruleService.getRegaService();
PatientAttributeValue pav =
rs.getPatientAttributeValue(
patient, ClinicalAttributeFactory.CLINICAL_REGA_ATTRIBUTE_RECENT_BLOOD_HB);
if (pav == null) return; // The is no recent blood hb for this patient
String strVal = pav.getValue();
Double dVal;
if (strVal.equals("N/A")) {
return; // There is no value
} else if (strVal.contains("/")) {
dVal = Double.parseDouble(strVal.replace('/', '.'));
} else {
dVal = Double.parseDouble(strVal);
}
logger.info("Recent Blood HB for " + patient.getPatientId() + " is " + dVal);
instance.setValue(attribute, dVal);
}