@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);
}
public ReportContainer(File summaryCsvFile) {
super();
try {
Table csv = Table.readTable(summaryCsvFile.getAbsolutePath());
if (csv.numColumns() == 2) {
initPieChart(csv);
}
} catch (FileNotFoundException e) {
e.printStackTrace();
} catch (UnsupportedEncodingException e) {
e.printStackTrace();
}
}
public static void main(String[] args) {
Table nationalityLIS =
Utils.readTable(
"/home/plibin0/myWorkspace/regadb-io-db/src/net/sf/regadb/io/db/ghb/mapping/LIS-nationality.csv");
Table nationalityDefault =
Utils.readTable(
"/home/plibin0/myWorkspace/regadb-analyses/io-assist-files/countrylist.csv");
int CLISCode = Utils.findColumn(nationalityLIS, "codePost");
int CLISName = Utils.findColumn(nationalityLIS, "internationaleOmschrijving");
int CDefaultCode = Utils.findColumn(nationalityDefault, "ISO 3166-1 2 Letter Code");
int CDefaultName = Utils.findColumn(nationalityDefault, "Common Name");
List<Attribute> regadbAttributesList = Utils.prepareRegaDBAttributes();
Attribute countryOfOrigin = Utils.selectAttribute("Country of origin", regadbAttributesList);
for (int i = 1; i < nationalityLIS.numRows(); i++) {
String LISCode = nationalityLIS.valueAt(CLISCode, i);
String LISName = nationalityLIS.valueAt(CLISName, i);
String match = "";
for (int j = 1; j < nationalityDefault.numRows(); j++) {
String defaultCode = nationalityDefault.valueAt(CDefaultCode, j);
String defaultName = nationalityDefault.valueAt(CDefaultName, j);
if (LISCode.trim().toLowerCase().equals(defaultCode.trim().toLowerCase())) {
match = defaultName;
break;
}
}
System.err.println("\"" + LISCode + "\"" + "," + "\"" + match + "\"");
}
}
public WAbstractItemModel readFromCsv(Table csv) {
WAbstractItemModel model = new WStandardItemModel();
for (int r = 0; r < csv.numRows(); r++) {
if (r != 0) model.insertRow(r - 1);
for (int c = 0; c < csv.numColumns(); c++) {
String value = csv.valueAt(c, r);
if (r == 0) {
model.insertColumn(c);
model.setHeaderData(c, Orientation.Horizontal, value);
} else {
try {
Double d = Double.valueOf(value);
model.setData(r - 1, c, d);
} catch (NumberFormatException e) {
model.setData(r - 1, c, value);
}
}
}
}
return model;
}