@Override
public void handleEvent(Event event) {
// TODO Auto-generated method stub
File file =
new File(
this.dataType.getPath().toString()
+ File.separator
+ this.dataType.getStudy().toString()
+ ".subject_mapping.tmp");
File stsmf = ((GeneExpressionData) this.dataType).getStsmf();
if (stsmf == null) {
this.setStudyTreeUI.displayMessage("Error: no subject to sample mapping file");
}
String category = "";
TreeNode node = this.setStudyTreeUI.getRoot();
if (!node.hasChildren()) {
this.setStudyTreeUI.displayMessage("You have to set a category code");
return;
}
node = node.getChildren().get(0);
while (node != null) {
if (category.compareTo("") == 0) {
category += node.toString().replace(' ', '_');
} else {
category += "+" + node.toString().replace(' ', '_');
}
if (node.hasChildren()) {
node = node.getChildren().get(0);
} else {
node = null;
}
}
try {
FileWriter fw = new FileWriter(file);
BufferedWriter out = new BufferedWriter(fw);
out.write(
"study_id\tsite_id\tsubject_id\tSAMPLE_ID\tPLATFORM\tTISSUETYPE\tATTR1\tATTR2\tcategory_cd\n");
try {
BufferedReader br = new BufferedReader(new FileReader(stsmf));
String line = br.readLine();
while ((line = br.readLine()) != null) {
String[] fields = line.split("\t", -1);
out.write(
fields[0] + "\t" + fields[1] + "\t" + fields[2] + "\t" + fields[3] + "\t" + fields[4]
+ "\t" + fields[5] + "\t" + fields[6] + "\t" + fields[7] + "\t" + category
+ "\n");
}
br.close();
} catch (Exception e) {
this.setStudyTreeUI.displayMessage("File error: " + e.getLocalizedMessage());
out.close();
e.printStackTrace();
}
out.close();
try {
File fileDest;
if (stsmf != null) {
String fileName = stsmf.getName();
stsmf.delete();
fileDest = new File(this.dataType.getPath() + File.separator + fileName);
} else {
fileDest =
new File(
this.dataType.getPath()
+ File.separator
+ this.dataType.getStudy().toString()
+ ".subject_mapping");
}
FileUtils.moveFile(file, fileDest);
((GeneExpressionData) this.dataType).setSTSMF(fileDest);
} catch (IOException ioe) {
this.setStudyTreeUI.displayMessage("File error: " + ioe.getLocalizedMessage());
return;
}
} catch (Exception e) {
this.setStudyTreeUI.displayMessage("Eerror: " + e.getLocalizedMessage());
e.printStackTrace();
}
this.setStudyTreeUI.displayMessage("Subject to sample mapping file updated");
WorkPart.updateSteps();
WorkPart.updateFiles();
}
@Override
public void handleEvent(Event event) {
// TODO Auto-generated method stub
Vector<String> values = this.setPlatformsUI.getValues();
Vector<String> samples = this.setPlatformsUI.getSamples();
File file =
new File(
this.dataType.getPath().toString()
+ File.separator
+ this.dataType.getStudy().toString()
+ ".subject_mapping.tmp");
File stsmf = ((GeneExpressionData) this.dataType).getStsmf();
if (stsmf == null) {
this.setPlatformsUI.displayMessage("Error: no subject to sample mapping file");
}
try {
FileWriter fw = new FileWriter(file);
BufferedWriter out = new BufferedWriter(fw);
out.write(
"study_id\tsite_id\tsubject_id\tSAMPLE_ID\tPLATFORM\tTISSUETYPE\tATTR1\tATTR2\tcategory_cd\n");
try {
BufferedReader br = new BufferedReader(new FileReader(stsmf));
String line = br.readLine();
while ((line = br.readLine()) != null) {
String[] fields = line.split("\t", -1);
String sample = fields[3];
String platform;
if (samples.contains(sample)) {
platform = values.get(samples.indexOf(sample));
} else {
br.close();
return;
}
out.write(
fields[0] + "\t" + fields[1] + "\t" + fields[2] + "\t" + sample + "\t" + platform
+ "\t" + fields[5] + "\t" + fields[6] + "\t" + fields[7] + "\t" + fields[8]
+ "\n");
}
br.close();
} catch (Exception e) {
this.setPlatformsUI.displayMessage("Error: " + e.getLocalizedMessage());
out.close();
e.printStackTrace();
}
out.close();
try {
File fileDest;
if (stsmf != null) {
String fileName = stsmf.getName();
stsmf.delete();
fileDest = new File(this.dataType.getPath() + File.separator + fileName);
} else {
fileDest =
new File(
this.dataType.getPath()
+ File.separator
+ this.dataType.getStudy().toString()
+ ".subject_mapping");
}
FileUtils.moveFile(file, fileDest);
((GeneExpressionData) this.dataType).setSTSMF(fileDest);
} catch (IOException ioe) {
this.setPlatformsUI.displayMessage("File error: " + ioe.getLocalizedMessage());
return;
}
} catch (Exception e) {
this.setPlatformsUI.displayMessage("Error: " + e.getLocalizedMessage());
e.printStackTrace();
}
this.setPlatformsUI.displayMessage("Subject to sample mapping file updated");
WorkPart.updateSteps();
WorkPart.updateFiles();
}
@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);
}
