public void init(InteractionState interactionState, IForm form, FormTable table) {
Transaction tr = RegaDBMain.getApp().createTransaction();
for (UITestItem ti : testItems) {
Test t = getTest(tr, ti);
if (t != null) {
Label l = new Label(TestComboBox.getLabel(t));
FormField testResultField;
if (ValueTypes.getValueType(t.getTestType().getValueType()) == ValueTypes.NOMINAL_VALUE) {
testResultField = new ComboBox(interactionState, form);
for (TestNominalValue tnv : t.getTestType().getTestNominalValues()) {
((ComboBox) testResultField)
.addItem(new DataComboMessage<TestNominalValue>(tnv, tnv.getValue()));
}
((ComboBox) testResultField).sort();
if (ti.noValueSelected) ((ComboBox) testResultField).addNoSelectionItem();
((ComboBox) testResultField).selectIndex(0);
if (ti.defaultValue != null && interactionState.isEditable())
((ComboBox) testResultField).selectItem(ti.defaultValue);
} else {
testResultField =
FormField.getTextField(
ValueTypes.getValueType(t.getTestType().getValueType()), interactionState, form);
}
table.addLineToTable(l, testResultField);
testFormFields.add(testResultField);
} else {
System.err.println("ViralIsolateForm: test does not exist: '" + ti.description + '\'');
}
}
}
@SuppressWarnings("rawtypes")
@Override
public File run() throws Exception {
File result = File.createTempFile("nadir_", ".csv", getResultDir());
PrintStream out = new PrintStream(new FileOutputStream(result));
TestType tt = pTestType.getTestTypeComboBox().currentValue();
ValueTypes vt = ValueTypes.getValueType(tt.getValueType());
String hql =
"select tr.patient.patientId, tr.test.description, tr.testDate, tr.value from TestResult tr join tr.patient.patientDatasets patient_dataset"
+ " where patient_dataset.id.dataset.datasetIi = :var_dataset"
+ " and tr.testDate <= :var_date"
+ " and tr.test.testIi in (select testIi from Test t where t.testType.testTypeIi = :var_testtype)"
+ " order by tr.patient.patientId, ";
if (vt == ValueTypes.LIMITED_NUMBER)
hql += "cast(substring(tr.value, 2, length(tr.value)) as double)";
else hql += "cast(tr.value as double)";
Transaction t = RegaDBMain.getApp().createTransaction();
Query q = t.createQuery(hql);
q.setParameter("var_dataset", pDataset.getDataset().getDatasetIi());
q.setParameter("var_date", pDate.getDate());
q.setParameter("var_testtype", tt.getTestTypeIi());
out.println("patient_id,test,test_date,value");
List r = q.list();
String prevPatientId = null;
for (Object o : r) {
Object[] oo = (Object[]) o;
String patientId = (String) oo[0];
String test = (String) oo[1];
Date testDate = (Date) oo[2];
String value = (String) oo[3];
if (!patientId.equals(prevPatientId)) {
out.println(
'"'
+ patientId
+ "\",\""
+ test
+ "\",\""
+ DateUtils.format(testDate)
+ "\",\""
+ value
+ '"');
prevPatientId = patientId;
}
}
t.commit();
out.close();
return result;
}
