public void fillData(Set<TestResult> testResults) {
Transaction tra = RegaDBMain.getApp().createTransaction();
for (int i = 0; i < testItems.size(); i++) {
TestItem ti = testItems.get(i);
Test test = getTest(tra, ti);
if (test == null) continue;
TestResult theTr = null;
for (TestResult tr : testResults) {
if (tr.getTest().getDescription().equals(test.getDescription())) {
theTr = tr;
break;
}
}
FormField f = testFormFields.get(i);
if (theTr != null) {
if (f instanceof ComboBox) {
((ComboBox) f).selectItem(theTr.getTestNominalValue().getValue());
} else {
if (theTr.getValue() != null) f.setText(theTr.getValue());
else f.setText(new String(theTr.getData()));
}
}
}
}
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 + '\'');
}
}
}
public void saveData(Set<TestResult> testResults) {
Transaction tra = RegaDBMain.getApp().createTransaction();
for (int i = 0; i < testItems.size(); i++) {
TestResult tr = null;
for (TestResult vi_tr : testResults) {
if (vi_tr.getTest().getDescription().equals(testItems.get(i).description)) {
tr = vi_tr;
break;
}
}
FormField f = testFormFields.get(i);
if (f instanceof ComboBox) {
DataComboMessage<TestNominalValue> dcm =
(DataComboMessage<TestNominalValue>) ((ComboBox) f).currentItem();
if (dcm != null && dcm.getValue() != null) {
TestItem ti = testItems.get(i);
if (tr == null) tr = createTestResult(getTest(tra, ti));
tr.setTestNominalValue(
((DataComboMessage<TestNominalValue>) ((ComboBox) f).currentItem()).getDataValue());
} else if (tr != null) {
removeTestResult(tr);
}
} else {
if (f.text() != null && !f.text().trim().equals("")) {
TestItem ti = testItems.get(i);
if (tr == null) tr = createTestResult(getTest(tra, ti));
tr.setValue(f.text());
} else if (tr != null) {
removeTestResult(tr);
}
}
}
}
@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;
}
public TestListWidget(InteractionState is, List<UITestItem> testItems, Set<TestResult> results) {
this.testItems = new ArrayList<UITestItem>(testItems);
Transaction tr = RegaDBMain.getApp().createTransaction();
Iterator<UITestItem> i = this.testItems.iterator();
while (i.hasNext()) {
UITestItem ti = i.next();
Test t = getTest(tr, ti);
if (!showTest(is, t, results)) i.remove();
}
}
public void loadTable(
Collection<String> drugClasses,
boolean showMutations,
boolean showAllAlgorithms,
Set<TestResult> testResults,
TestType gssTestType) {
clear();
if (gssTestType == null) {
return;
}
Transaction t = RegaDBMain.getApp().createTransaction();
List<DrugClass> sortedDrugClasses_ = t.getDrugClassesSortedOnResistanceRanking();
// drug names - column position
HashMap<String, Integer> algoColumn = new HashMap<String, Integer>();
int col = 0;
getElementAt(0, col).addWidget(new WText(""));
col = getColumnCount();
getElementAt(0, col).addWidget(new WText(""));
int maxWidth = 0;
for (Test test : getAlgorithms(t, gssTestType, showAllAlgorithms)) {
col = getColumnCount();
getElementAt(0, col).addWidget(new TableHeader(test.getDescription()));
getElementAt(0, col).setStyleClass("column-title");
algoColumn.put(test.getDescription(), col);
maxWidth += test.getDescription().length();
}
// drug names - row position
HashMap<String, Integer> drugColumn = new HashMap<String, Integer>();
List<DrugGeneric> genericDrugs;
int row;
boolean firstGenericDrugInThisClass;
for (DrugClass dc : sortedDrugClasses_) {
if (!drugClasses.contains(dc.getClassId())) continue;
genericDrugs = t.getDrugGenericSortedOnResistanceRanking(dc);
firstGenericDrugInThisClass = true;
for (DrugGeneric dg : genericDrugs) {
row = getRowCount();
if (firstGenericDrugInThisClass) {
getElementAt(row, 0).addWidget(new TableHeader(dc.getClassId() + ":"));
firstGenericDrugInThisClass = false;
getElementAt(row, 0).setStyleClass("form-label-area");
}
getElementAt(row, 1).addWidget(new TableHeader(dg.getGenericId()));
drugColumn.put(dg.getGenericId(), row);
getElementAt(row, 1).setStyleClass("form-label-area");
}
}
ViralIsolateFormConfig config =
RegaDBSettings.getInstance().getInstituteConfig().getViralIsolateFormConfig();
// clear table
for (int i = 1; i < getRowCount(); i++) {
for (int j = 2; j < getColumnCount(); j++) {
ViralIsolateFormUtils.putResistanceTableResult(
null, getElementAt(i, j), config, false, showMutations);
}
}
Integer colN;
Integer rowN;
for (TestResult tr : testResults) {
if (tr.getTest().getAnalysis() != null
&& Equals.isSameTestType(gssTestType, tr.getTest().getTestType())) {
if (!drugClasses.contains(tr.getDrugGeneric().getDrugClass().getClassId())) continue;
colN = algoColumn.get(tr.getTest().getDescription());
rowN = drugColumn.get(ViralIsolateFormUtils.getFixedGenericId(tr));
if (colN != null && rowN != null) {
ViralIsolateFormUtils.putResistanceTableResult(
tr, getElementAt(rowN, colN), config, false, showMutations);
}
}
}
}