@SuppressWarnings("unchecked")
@Override
protected void parseFile(String[] argFileString, IMetadataFieldSet argDefaultFields)
throws InvalidDendroFileException {
defaults = (TrimsToTridasDefaults) argDefaultFields;
// TODO run the 'metadata' through the defaults, as
// the user may have specified his own metadata
// Extract 'metadata' ;-)
String userid = argFileString[0].trim();
SafeIntYear startYear = null;
try {
startYear = new SafeIntYear(argFileString[2].trim());
} catch (NumberFormatException e) {
}
// Extract data
ArrayList<TridasValue> ringWidthValues = new ArrayList<TridasValue>();
for (int i = 3; i < argFileString.length; i++) {
TridasValue v = new TridasValue();
if (argFileString[i].startsWith(" ")) {
if (argFileString[i].trim().equals("999")) {
break;
}
v.setValue(argFileString[i].trim());
ringWidthValues.add(v);
log.debug("value = " + String.valueOf(argFileString[i]));
} else {
throw new InvalidDendroFileException(I18n.getText("trims.expectingSpace"), i);
}
}
// Now build up our measurementSeries
TridasMeasurementSeries series = defaults.getMeasurementSeriesWithDefaults();
TridasUnit units = new TridasUnit();
// Set units to 1/100th mm. Is this always the case?
units.setNormalTridas(NormalTridasUnit.HUNDREDTH_MM);
// Build identifier for series
TridasIdentifier seriesId = new ObjectFactory().createTridasIdentifier();
seriesId.setValue(UUID.randomUUID().toString());
seriesId.setDomain(
defaults.getDefaultValue(TridasMandatoryField.IDENTIFIER_DOMAIN).getStringValue());
// Build interpretation group for series
TridasInterpretation interp = new TridasInterpretation();
interp.setFirstYear(startYear.toTridasYear(DatingSuffix.AD));
interp.setLastYear(startYear.add(ringWidthValues.size() - 1).toTridasYear(DatingSuffix.AD));
// Add values to nested value(s) tags
TridasValues valuesGroup = new TridasValues();
valuesGroup.setValues(ringWidthValues);
valuesGroup.setUnit(units);
GenericDefaultValue<TridasVariable> variable =
(GenericDefaultValue<TridasVariable>)
defaults.getDefaultValue(TridasMandatoryField.MEASUREMENTSERIES_VARIABLE);
valuesGroup.setVariable(variable.getValue());
ArrayList<TridasValues> valuesGroupList = new ArrayList<TridasValues>();
valuesGroupList.add(valuesGroup);
// Add all the data to the series
series.setValues(valuesGroupList);
series.setInterpretation(interp);
series.setIdentifier(seriesId);
series.setLastModifiedTimestamp(DateUtils.getTodaysDateTime());
series.setDendrochronologist(userid);
// Add series to our list
mseriesList.add(series);
}
/**
* Parse the specified legacy data file for series
*
* @param file
* @param fileType
*/
private void parseFile(File file, AbstractDendroFormat format) {
ArrayList<Sample> sampleList = new ArrayList<Sample>();
// Create a reader based on the file type supplied
AbstractDendroFileReader reader = TridasIO.getFileReaderFromFormat(format);
if (reader == null) {
Alert.error(containerFrame, "Error", "Unknown file type");
return;
}
// Try and load the file
try {
reader.loadFile(file.getAbsolutePath());
} catch (IOException e) {
Alert.errorLoading(file.getAbsolutePath(), e);
return;
} catch (InvalidDendroFileException e) {
Alert.error(
containerFrame,
"Error",
"The selected file is not a valid "
+ format.getShortName()
+ " file.\nPlease check and try again");
return;
} catch (NullPointerException e) {
Alert.error(containerFrame, "Invalid File", e.getLocalizedMessage());
}
TridasTridas tc = reader.getTridasContainer();
log.debug("Project count: " + tc.getProjects().size());
Boolean hideWarningsFlag = false;
for (TridasProject p : tc.getProjects()) {
for (TridasObject o : p.getObjects()) {
for (TridasElement e : TridasUtils.getElementList(o)) {
log.debug("Element count: " + o.getElements().size());
for (TridasSample s : e.getSamples()) {
for (TridasRadius r : s.getRadiuses()) {
for (TridasMeasurementSeries ms : r.getMeasurementSeries()) {
Sample sample =
EditorFactory.createSampleFromSeries(ms, e, file, format, hideWarningsFlag);
if (sample == null) {
hideWarningsFlag = true;
} else {
sampleList.add(sample);
}
}
}
}
}
}
for (TridasDerivedSeries ds : p.getDerivedSeries()) {
Sample sample =
EditorFactory.createSampleFromSeries(ds, null, file, format, hideWarningsFlag);
if (sample == null) {
hideWarningsFlag = true;
} else {
sampleList.add(sample);
}
}
}
Boolean unitsSet = false;
for (ITridasSeries ser : getSeries(sampleList)) {
for (TridasValues tv : ser.getValues()) {
if (tv.isSetUnit()) {
if (tv.getUnit().isSetNormalTridas()) {
unitsSet = true;
}
}
}
}
if (unitsSet == false && sampleList.size() > 0 && unitsIfNotSpecified == null) {
Object[] possibilities = {"1/1000th mm", "1/100th mm", "1/50th mm", "1/20th mm", "1/10th mm"};
Object s =
JOptionPane.showInputDialog(
containerFrame,
"One or more series has no units defined.\n" + "Please specify units below:",
"Set Units",
JOptionPane.PLAIN_MESSAGE,
null,
possibilities,
"1/1000th mm");
if (s.equals("1/1000th mm")) {
unitsIfNotSpecified = NormalTridasUnit.MICROMETRES;
} else if (s.equals("1/100th mm")) {
unitsIfNotSpecified = NormalTridasUnit.HUNDREDTH_MM;
} else if (s.equals("1/50th mm")) {
unitsIfNotSpecified = NormalTridasUnit.FIFTIETH_MM;
} else if (s.equals("1/20th mm")) {
unitsIfNotSpecified = NormalTridasUnit.TWENTIETH_MM;
} else if (s.equals("1/10th mm")) {
unitsIfNotSpecified = NormalTridasUnit.TENTH_MM;
} else {
Alert.error(containerFrame, "Error", "Invalid measurement units specified");
return;
}
}
for (Sample sample : sampleList) {
ITridasSeries series = sample.getSeries();
try {
for (int i = 0; i < series.getValues().size(); i++) {
TridasValues tv = series.getValues().get(i);
if (tv.isSetUnit()) {
if (!tv.getUnit().isSetNormalTridas()) {
tv.getUnit().setNormalTridas(unitsIfNotSpecified);
}
} else {
TridasUnit unit = new TridasUnit();
unit.setNormalTridas(unitsIfNotSpecified);
tv.setUnit(unit);
tv.setUnitless(null);
}
tv = UnitUtils.convertTridasValues(NormalTridasUnit.MICROMETRES, tv, true);
TridasUnit unit = new TridasUnit();
unit.setNormalTridas(NormalTridasUnit.MICROMETRES);
tv.setUnit(unit);
series.getValues().set(i, tv);
}
} catch (NumberFormatException e) {
Alert.error("Error", "One or more data values are not numbers.");
return;
} catch (ConversionWarningException e) {
Alert.error("Error", "Error converting units");
return;
}
}
for (Sample s : sampleList) {
SeriesIdentity id = new SeriesIdentity(file, format, s);
model.addItem(id);
}
}
