public boolean isAvailable() {
try {
if (((GeneExpressionData) this.dataType).getRawFiles() == null
|| ((GeneExpressionData) this.dataType).getRawFiles().size() == 0) {
return false;
}
File stsmf = ((GeneExpressionData) this.dataType).getStsmf();
if (stsmf == null) {
return false;
}
if (!FileHandler.checkPlatform(stsmf)) {
return false;
}
return true;
} catch (NullPointerException e) {
return false;
}
}
@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);
}
