@Override
public void handleEvent(Event event) {
Vector<File> rawFiles = ((ClinicalData) this.dataType).getRawFiles();
Vector<String> siteIds = this.setOtherIdsUI.getSiteIds();
Vector<String> visitNames = this.setOtherIdsUI.getVisitNames();
// write in a new file
File file =
new File(
this.dataType.getPath().toString()
+ File.separator
+ this.dataType.getStudy().toString()
+ ".columns.tmp");
try {
FileWriter fw = new FileWriter(file);
BufferedWriter out = new BufferedWriter(fw);
out.write(
"Filename\tCategory Code\tColumn Number\tData Label\tData Label Source\tControlled Vocab Code\n");
for (int i = 0; i < rawFiles.size(); i++) {
// site identifier
if (siteIds.elementAt(i).compareTo("") != 0) {
int columnNumber =
FileHandler.getHeaderNumber(rawFiles.elementAt(i), siteIds.elementAt(i));
if (columnNumber != -1) {
out.write(rawFiles.elementAt(i).getName() + "\t\t" + columnNumber + "\tSITE_ID\t\t\n");
}
}
// visit name
if (visitNames.elementAt(i).compareTo("") != 0) {
int columnNumber =
FileHandler.getHeaderNumber(rawFiles.elementAt(i), visitNames.elementAt(i));
if (columnNumber != -1) {
out.write(
rawFiles.elementAt(i).getName() + "\t\t" + columnNumber + "\tVISIT_NAME\t\t\n");
}
}
}
// add lines from existing CMF
try {
BufferedReader br =
new BufferedReader(new FileReader(((ClinicalData) this.dataType).getCMF()));
String line = br.readLine();
while ((line = br.readLine()) != null) {
String[] s = line.split("\t", -1);
if (s[3].compareTo("SITE_ID") != 0 && s[3].compareTo("VISIT_NAME") != 0) {
out.write(line + "\n");
}
}
br.close();
} catch (Exception e) {
this.setOtherIdsUI.displayMessage("Error: " + e.getLocalizedMessage());
e.printStackTrace();
out.close();
}
out.close();
try {
String fileName = ((ClinicalData) this.dataType).getCMF().getName();
((ClinicalData) this.dataType).getCMF().delete();
File fileDest = new File(this.dataType.getPath() + File.separator + fileName);
FileUtils.moveFile(file, fileDest);
((ClinicalData) this.dataType).setCMF(fileDest);
} catch (IOException ioe) {
this.setOtherIdsUI.displayMessage("File error: " + ioe.getLocalizedMessage());
return;
}
} catch (Exception e) {
this.setOtherIdsUI.displayMessage("Error: " + e.getLocalizedMessage());
e.printStackTrace();
}
this.setOtherIdsUI.displayMessage("Column mapping file updated");
WorkPart.updateSteps();
WorkPart.updateFiles();
UsedFilesPart.sendFilesChanged(dataType);
}
@Override
public void handleEvent(Event event) {
this.selectRawFilesUI.openLoadingShell();
new Thread() {
public void run() {
String[] paths = selectRawFilesUI.getPath().split(File.pathSeparator, -1);
for (int i = 0; i < paths.length; i++) {
String path = paths[i];
if (path == null) {
selectRawFilesUI.setIsLoading(false);
return;
}
File rawFile = new File(path);
if (rawFile.exists()) {
if (rawFile.isFile()) {
if (path.contains("%")) {
selectRawFilesUI.setMessage("File name can not contain percent ('%') symbol.");
selectRawFilesUI.setIsLoading(false);
return;
}
String newPath =
dataType.getPath().getAbsolutePath() + File.separator + rawFile.getName();
if (selectRawFilesUI.getFormat().compareTo("Tab delimited raw file") != 0
&& selectRawFilesUI.getFormat().compareTo("SOFT") != 0) {
selectRawFilesUI.setMessage("File format does not exist");
selectRawFilesUI.setIsLoading(false);
return;
}
if (selectRawFilesUI.getFormat().compareTo("SOFT") == 0) {
File newFile = new File(newPath);
if (newFile.exists()) {
selectRawFilesUI.setMessage("File has already been added");
selectRawFilesUI.setIsLoading(false);
return;
} else {
if (createTabFileFromSoft(rawFile, newFile)) {
((ClinicalData) dataType).addRawFile(newFile);
selectRawFilesUI.setMessage("File has been added");
}
}
} else if (selectRawFilesUI.getFormat().compareTo("Tab delimited raw file") == 0) {
if (!checkTabFormat(rawFile)) {
selectRawFilesUI.setIsLoading(false);
return;
}
File copiedRawFile = new File(newPath);
if (!copiedRawFile.exists()) {
try {
FileUtils.copyFile(rawFile, copiedRawFile);
((ClinicalData) dataType).addRawFile(copiedRawFile);
selectRawFilesUI.setMessage("File has been added");
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
selectRawFilesUI.setMessage("File error: " + e.getLocalizedMessage());
selectRawFilesUI.setIsLoading(false);
return;
}
} else {
selectRawFilesUI.setMessage("File has already been added");
selectRawFilesUI.setIsLoading(false);
return;
}
}
} else {
selectRawFilesUI.setMessage("File is a directory");
selectRawFilesUI.setIsLoading(false);
return;
}
} else {
selectRawFilesUI.setMessage("Path does no exist");
selectRawFilesUI.setIsLoading(false);
return;
}
}
selectRawFilesUI.setIsLoading(false);
}
}.start();
this.selectRawFilesUI.waitForThread();
selectRawFilesUI.updateViewer();
WorkPart.updateSteps();
UsedFilesPart.sendFilesChanged(dataType);
}
