public void loadProperty() {
try {
File file = new File(confFileName);
log.debug("file=" + file.getAbsolutePath());
confProperties = new Properties();
confProperties.loadFromXML(new FileInputStream(file));
bonitaApiHost = confProperties.getProperty("bonita.api.host");
bonitaApiUsername = confProperties.getProperty("bonita.api.username");
bonitaApiPassword = confProperties.getProperty("bonita.api.password");
bonitaApiHttpUsername = confProperties.getProperty("bonita.api.http.username");
bonitaApiHttpPassword = confProperties.getProperty("bonita.api.http.password");
bonitaApiPath = confProperties.getProperty("bonita.api.path");
rallyApiHost = confProperties.getProperty("rally.api.host");
rallyApiHttpUsername = confProperties.getProperty("rally.api.http.username");
rallyApiHttpPassword = confProperties.getProperty("rally.api.http.password");
rallyProjectIds = confProperties.getProperty("rally.project.ids");
// bonitaProcessId=properties.getProperty("bonita.process.xp_code.id");
workflowServiceUrl = confProperties.getProperty("service.url");
} catch (Exception e) {
log.error("", e);
}
}
/**
* Get dependencies of a source file.
*
* @param path The canonical path of source file.
* @return Path of dependencies.
*/
private ArrayList<String> getDependencies(String path) {
if (!dependenceMap.containsKey(path)) {
ArrayList<String> dependencies = new ArrayList<String>();
Matcher m = PATTERN_REQUIRE.matcher(read(path, charset));
while (m.find()) {
// Decide which root path to use.
// Path wrapped in <> is related to root path.
// Path wrapped in "" is related to parent folder of the source file.
String root = null;
if (m.group(1).equals("<")) {
root = this.root;
} else {
root = new File(path).getParent();
}
// Get path of required file.
String required = m.group(2);
File f = new File(root, required);
if (f.exists()) {
dependencies.add(canonize(f));
} else {
App.exit("Cannot find required file " + required + " in " + path);
}
}
dependenceMap.put(path, dependencies);
}
return dependenceMap.get(path);
}
/**
* The ActionListener implementation
*
* @param event the event.
*/
public void actionPerformed(ActionEvent event) {
String searchText = textField.getText().trim();
if (searchText.equals("") && !saveAs.isSelected() && (fileLength > 10000000)) {
textPane.setText("Blank search text is not allowed for large IdTables.");
} else {
File outputFile = null;
if (saveAs.isSelected()) {
outputFile = chooser.getSelectedFile();
if (outputFile != null) {
String name = outputFile.getName();
int k = name.lastIndexOf(".");
if (k != -1) name = name.substring(0, k);
name += ".txt";
File parent = outputFile.getAbsoluteFile().getParentFile();
outputFile = new File(parent, name);
chooser.setSelectedFile(outputFile);
}
if (chooser.showSaveDialog(this) != JFileChooser.APPROVE_OPTION) System.exit(0);
outputFile = chooser.getSelectedFile();
}
textPane.setText("");
Searcher searcher = new Searcher(searchText, event.getSource().equals(searchPHI), outputFile);
searcher.start();
}
}
public void checkPrintFiles() {
LinkedHashMap<String, File> nameFile = new LinkedHashMap<String, File>();
nameFile.put("Reference directory", referenceDir);
nameFile.put("Pipeline.jar", pJar);
nameFile.put("Pipeline properties", truncPipePropFile);
nameFile.put("Coverage QC bed", bedForCoverageQC);
nameFile.put("Variant calling bed", bedForVarCalling);
nameFile.put("Fasta genome reference", fastaReference);
nameFile.put("Unfiltered bam", unfilteredBam);
nameFile.put("Final bam", finalBam);
nameFile.put("Final vcf", finalVcf);
if (webRootForLinks != null) nameFile.put("Web links dir", webRootForLinks);
nameFile.put("Final output dir", outputDirectory);
boolean missingFile = false;
System.out.println("\nResources (name exists path):");
for (String name : nameFile.keySet()) {
File f = nameFile.get(name);
boolean fExists = true;
if (f == null) {
fExists = false;
missingFile = true;
} else {
fExists = f.exists();
if (fExists == false) missingFile = true;
}
System.out.println(name + "\t" + fExists + "\t" + f);
}
if (missingFile) Misc.printErrAndExit("\nMissing resources! See above.");
}
public boolean accept(File pathname) {
if (pathname.isDirectory()) {
return true;
} else {
return pattern.matcher(pathname.getName()).matches();
}
}
public static BufferedReader getBufferedReader(String fileName, String context) throws Throwable {
includeNames.add(fileName);
if (fileName.startsWith("http://") || fileName.startsWith("https://")) {
String hashedFileName = MD5(fileName);
File remoteCacheFile = new File(cacheDirectoryName + File.separator + hashedFileName);
if (remoteCacheFile.exists()) {
return new BufferedReader(new FileReader(remoteCacheFile));
} else {
URL input = new URL(fileName);
BufferedReader remoteReader = new BufferedReader(new InputStreamReader(input.openStream()));
BufferedWriter cacheWriter =
new BufferedWriter(
new FileWriter(cacheDirectoryName + File.separator + hashedFileName));
String tmpLine = remoteReader.readLine();
while (tmpLine != null) {
cacheWriter.write(tmpLine);
cacheWriter.newLine();
tmpLine = remoteReader.readLine();
}
cacheWriter.close();
return new BufferedReader(
new FileReader(cacheDirectoryName + File.separator + hashedFileName));
}
} else {
if (fileName.startsWith(context)) {
return new BufferedReader(new FileReader(fileName));
} else {
return new BufferedReader(new FileReader(context + fileName));
}
}
}
public String fetchCleanupReviewDirLinkGenXml() {
String s = null;
try {
s = // Organize and Clean Up Section
"<ReviewDirGenerator class='operator.ReviewDirGenerator' destination.dir='"
+ outputDirectory.getCanonicalPath()
+ "' sample='"
+ outputDirectory.getName()
+ "' submitter='"
+ submitter
+ "' analysis.type='"
+ analysisType
+ "'> \n"
+ " <finalVariants /> \n"
+ " <ViewerCSV /> \n"
+ " <InstanceLog class='buffer.InstanceLogFile' /> \n"
+ " <finalBAM /> \n"
+ " <QCOutputFile /> \n"
+ " <bedForVars /> \n"
+ "</ReviewDirGenerator> \n\n";
} catch (IOException e) {
e.printStackTrace();
Misc.printErrAndExit("\nError fetching clean up and review dir links.\n");
}
return s;
}
public void actionPerformed(ActionEvent e) {
if (readOnly) {
return;
}
JFileChooser fc = getFileChooser();
File currentDirectory = fc.getCurrentDirectory();
if (!currentDirectory.exists()) {
JOptionPane.showMessageDialog(
fc,
newFolderParentDoesntExistText,
newFolderParentDoesntExistTitleText,
JOptionPane.WARNING_MESSAGE);
return;
}
File newFolder;
try {
newFolder = fc.getFileSystemView().createNewFolder(currentDirectory);
if (fc.isMultiSelectionEnabled()) {
fc.setSelectedFiles(new File[] {newFolder});
} else {
fc.setSelectedFile(newFolder);
}
} catch (IOException exc) {
JOptionPane.showMessageDialog(
fc,
newFolderErrorText + newFolderErrorSeparator + exc,
newFolderErrorText,
JOptionPane.ERROR_MESSAGE);
return;
}
fc.rescanCurrentDirectory();
}
void put(final URI uri, ArtifactData data) throws Exception {
reporter.trace("put %s %s", uri, data);
File tmp = createTempFile(repoDir, "mtp", ".whatever");
tmp.deleteOnExit();
try {
copy(uri.toURL(), tmp);
byte[] sha = SHA1.digest(tmp).digest();
reporter.trace("SHA %s %s", uri, Hex.toHexString(sha));
ArtifactData existing = get(sha);
if (existing != null) {
reporter.trace("existing");
xcopy(existing, data);
return;
}
File meta = new File(repoDir, Hex.toHexString(sha) + ".json");
File file = new File(repoDir, Hex.toHexString(sha));
rename(tmp, file);
reporter.trace("file %s", file);
data.file = file.getAbsolutePath();
data.sha = sha;
data.busy = false;
CommandData cmddata = parseCommandData(data);
if (cmddata.bsn != null) {
data.name = cmddata.bsn + "-" + cmddata.version;
} else data.name = Strings.display(cmddata.title, cmddata.bsn, cmddata.name, uri);
codec.enc().to(meta).put(data);
reporter.trace("TD = " + data);
} finally {
tmp.delete();
reporter.trace("puted %s %s", uri, data);
}
}
@Override
public void actionPerformed(ActionEvent e) {
if (td.getTabCount() > 0) {
JFileChooser f = new JFileChooser();
f.setFileFilter(new MyFileFilter());
int choose = f.showSaveDialog(getContentPane());
if (choose == JFileChooser.APPROVE_OPTION) {
BufferedWriter brw = null;
try {
File file = f.getSelectedFile();
brw = new BufferedWriter(new FileWriter(file));
int i = td.getSelectedIndex();
TextDocument ta = (TextDocument) td.getComponentAt(i);
ta.write(brw);
ta.fileName = file.getName(); // 將檔案名稱更新為存檔的名稱
td.setTitleAt(td.getSelectedIndex(), ta.fileName);
ta.file = file;
ta.save = true; // 設定已儲存
System.out.println("Save as pass!");
td.setTitleAt(i, ta.fileName); // 更新標題名稱
} catch (Exception exc) {
exc.printStackTrace();
} finally {
try {
brw.close();
} catch (Exception ecx) {
ecx.printStackTrace();
}
}
}
} else {
JOptionPane.showMessageDialog(null, "沒有檔案可以儲存!");
}
}
private byte[] loadClassData(String className) throws IOException {
Playground.println("Loading class " + className + ".class", warning);
File f = new File(System.getProperty("user.dir") + "/" + className + ".class");
byte[] b = new byte[(int) f.length()];
new FileInputStream(f).read(b);
return b;
}
@Override
public void actionPerformed(ActionEvent e) {
JFileChooser f = new JFileChooser();
f.setFileFilter(new MyFileFilter()); // 設定檔案選擇器
int choose = f.showOpenDialog(getContentPane()); // 顯示檔案選取
if (choose == JFileChooser.OPEN_DIALOG) { // 有開啟檔案的話，開始讀檔
BufferedReader br = null;
try {
File file = f.getSelectedFile();
br = new BufferedReader(new FileReader(file));
TextDocument ta = new TextDocument(file.getName(), file);
ta.addKeyListener(new SystemTrackSave());
ta.read(br, null);
td.add(ta);
td.setTitleAt(docCount++, file.getName());
} catch (Exception exc) {
exc.printStackTrace();
} finally {
try {
br.close();
} catch (Exception ecx) {
ecx.printStackTrace();
}
}
}
}
private static void tryResUrls(Picture picture) {
String hi_res = "";
String url = picture.media_url.toString();
for (String ending : Main.endings) {
try {
hi_res = url.replace(url.substring(url.lastIndexOf("_"), url.lastIndexOf(".")), ending);
URL hi_url = new URL(hi_res);
File hi_name = Helper.extractMediaFileNameFromURL(hi_url);
if (hi_name.equals(picture.media_name)) {
picture.hi_url = hi_url;
picture.hi_name = hi_name;
picture.downloaded_hi = true;
break;
} else {
boolean success = Helper.downloadFileFromURLToFileInTemp(hi_url, hi_name);
if (success) {
picture.hi_url = hi_url;
picture.hi_name = hi_name;
picture.downloaded_hi = true;
Helper.moveTempImageToStore(hi_name, new File(Main.blogdir, picture.md5_id));
break;
}
}
} catch (MalformedURLException ex) {
Main.error(String.format("Attempted hi res url %s is a malformed URL.", hi_res));
}
}
}
public static File directoryOf(Class clazz) {
File location = locationOf(clazz);
if (location.isDirectory()) {
return location;
}
return location.getParentFile();
}
private Service getService(File base) throws Exception {
File dataFile = new File(base, "data");
if (!dataFile.isFile()) return null;
ServiceData data = getData(ServiceData.class, dataFile);
return new Service(this, data);
}
public static void main(String[] args) {
File path = new File(".");
String[] list;
if (args.length == 0) list = path.list();
else list = path.list(new DirFilter(args[0]));
Arrays.sort(list, String.CASE_INSENSITIVE_ORDER);
for (String dirItem : list) System.out.println(dirItem);
}
public void valueChanged(ListSelectionEvent evt) {
if (!evt.getValueIsAdjusting()) {
JFileChooser chooser = getFileChooser();
FileSystemView fsv = chooser.getFileSystemView();
JList list = (JList) evt.getSource();
int fsm = chooser.getFileSelectionMode();
boolean useSetDirectory = usesSingleFilePane && (fsm == JFileChooser.FILES_ONLY);
if (chooser.isMultiSelectionEnabled()) {
File[] files = null;
Object[] objects = list.getSelectedValues();
if (objects != null) {
if (objects.length == 1
&& ((File) objects[0]).isDirectory()
&& chooser.isTraversable(((File) objects[0]))
&& (useSetDirectory || !fsv.isFileSystem(((File) objects[0])))) {
setDirectorySelected(true);
setDirectory(((File) objects[0]));
} else {
ArrayList<File> fList = new ArrayList<File>(objects.length);
for (Object object : objects) {
File f = (File) object;
boolean isDir = f.isDirectory();
if ((chooser.isFileSelectionEnabled() && !isDir)
|| (chooser.isDirectorySelectionEnabled() && fsv.isFileSystem(f) && isDir)) {
fList.add(f);
}
}
if (fList.size() > 0) {
files = fList.toArray(new File[fList.size()]);
}
setDirectorySelected(false);
}
}
chooser.setSelectedFiles(files);
} else {
File file = (File) list.getSelectedValue();
if (file != null
&& file.isDirectory()
&& chooser.isTraversable(file)
&& (useSetDirectory || !fsv.isFileSystem(file))) {
setDirectorySelected(true);
setDirectory(file);
if (usesSingleFilePane) {
chooser.setSelectedFile(null);
}
} else {
setDirectorySelected(false);
if (file != null) {
chooser.setSelectedFile(file);
}
}
}
}
}
public boolean accept(File f) {
if (f == null) {
return false;
}
if (f.isDirectory()) {
return true;
}
return pattern.matcher(f.getName()).matches();
}
public boolean accept(File f) {
if (f.isDirectory()) {
return true;
}
String fn = f.getName();
if (fn.toLowerCase().endsWith(".java") || fn.toLowerCase().endsWith(".txt")) {
return true;
}
return false;
}
public void init(Editor _editor) {
this.m_editor = _editor;
File toolRoot = null;
try {
toolRoot =
new File(
SequantoAutomationTool.class
.getProtectionDomain()
.getCodeSource()
.getLocation()
.toURI())
.getParentFile()
.getParentFile();
} catch (java.net.URISyntaxException ex) {
toolRoot =
new File(
SequantoAutomationTool.class
.getProtectionDomain()
.getCodeSource()
.getLocation()
.getPath())
.getParentFile()
.getParentFile();
}
m_generatorPy =
new File(new File(toolRoot, "generator"), "generate_automation_defines.py")
.getAbsolutePath();
m_isWindows = System.getProperty("os.name").toLowerCase().contains("win");
if (m_isWindows) {
for (File root : File.listRoots()) {
File[] files =
root.listFiles(
new FileFilter() {
public boolean accept(File f) {
return f.getName().toLowerCase().startsWith("python");
}
});
if (files != null) {
for (File directory : files) {
m_pythonPath = new File(directory, "python.exe");
break;
}
}
}
if (m_pythonPath == null) {
Base.showMessage(
"ERROR",
String.format(
"Could not python interpreter - Generate Automation tool will not work."));
}
}
}
private void checkForGzippedVcf() {
String vcfName = finalVcf.getName();
if (vcfName.endsWith(".gz")) {
File uncomp = new File(finalVcf.getParentFile(), vcfName.substring(0, vcfName.length() - 3));
if (uncomp.exists() == false) {
deleteTempVcf = true;
if (IO.uncompress(finalVcf, uncomp) == null)
Misc.printErrAndExit("ERROR: failed to uncompress -> " + finalVcf);
}
finalVcf = uncomp;
}
}
public String _isdir(String args[]) {
if (args.length < 2) {
domain.warning("Need at least one file name for ${isdir;...}");
return null;
}
boolean isdir = true;
for (int i = 1; i < args.length; i++) {
File f = new File(args[i]).getAbsoluteFile();
isdir &= f.isDirectory();
}
return isdir ? "true" : "false";
}
public static File getBuildFolder(Sketch data) throws IOException {
File buildFolder;
if (PreferencesData.get("build.path") != null) {
buildFolder = BaseNoGui.absoluteFile(PreferencesData.get("build.path"));
Files.createDirectories(buildFolder.toPath());
} else {
buildFolder =
FileUtils.createTempFolder("build", DigestUtils.md5Hex(data.getMainFilePath()) + ".tmp");
DeleteFilesOnShutdown.add(buildFolder);
}
return buildFolder;
}
@Nonnull
private static File getOutputFileCreatingDirIfNeeded(
@Nonnull String outputDir, @Nonnull String sourceFilePath) {
File outputFile = getOutputFile(outputDir, sourceFilePath);
File parentDir = outputFile.getParentFile();
if (!parentDir.exists()) {
boolean outputDirCreated = parentDir.mkdirs();
assert outputDirCreated : "Failed to create output dir: " + outputDir;
}
return outputFile;
}
public List<CommandData> getCommands(File commandDir) throws Exception {
List<CommandData> result = new ArrayList<CommandData>();
if (!commandDir.exists()) {
return result;
}
for (File f : commandDir.listFiles()) {
CommandData data = getData(CommandData.class, f);
if (data != null) result.add(data);
}
return result;
}
private ArrayList GetFolderTree(String s_Dir, String s_Flag, int n_Indent, int n_TreeIndex) {
String s_List = "";
ArrayList aSubFolders = new ArrayList();
File file = new File(s_Dir);
File[] filelist = file.listFiles();
if (filelist != null && filelist.length > 0) {
for (int i = 0; i < filelist.length; i++) {
if (filelist[i].isDirectory()) {
aSubFolders.add(filelist[i].getName());
}
}
int n_Count = aSubFolders.size();
String s_LastFlag = "";
String s_Folder = "";
for (int i = 1; i <= n_Count; i++) {
if (i < n_Count) {
s_LastFlag = "0";
} else {
s_LastFlag = "1";
}
s_Folder = aSubFolders.get(i - 1).toString();
s_List =
s_List
+ "arr"
+ s_Flag
+ "["
+ String.valueOf(n_TreeIndex)
+ "]=new Array(\""
+ s_Folder
+ "\","
+ String.valueOf(n_Indent)
+ ", "
+ s_LastFlag
+ ");\n";
n_TreeIndex = n_TreeIndex + 1;
ArrayList a_Temp =
GetFolderTree(s_Dir + s_Folder + sFileSeparator, s_Flag, n_Indent + 1, n_TreeIndex);
s_List = s_List + a_Temp.get(0).toString();
n_TreeIndex = Integer.valueOf(a_Temp.get(1).toString()).intValue();
}
}
ArrayList a_Return = new ArrayList();
a_Return.add(s_List);
a_Return.add(String.valueOf(n_TreeIndex));
return a_Return;
}
/**
* Takes a line and looks for an archive group tag. If one is found, the information from the tag
* is returned as an <CODE>ArchiveGroup</CODE>. If a tag is found, the data in the tag is stored
* in the <CODE>HashMap</CODE> provided.
*
* @param currentLine The line in which to look for the archive tag.
* @param template The <CODE>Template</CODE> to which the <CODE>ArchiveGroup</CODE> belongs.
* @return The archive request tag data as an instance of <CODE>ArchiveGroup</CODE>, <CODE>null
* </CODE> if the line passed in does not contain an arFile tag.
*/
private ArchiveGroup parseArchiveGroupTag(String currentLine, Template template) {
ArchiveGroup archiveTag;
Matcher currentMatcher = archiveRequestPattern.matcher(currentLine);
if (currentMatcher.find()) {
String fileName = currentMatcher.group(1);
archiveTag = template.getArchiveGroup(fileName);
if (archiveTag == null) {
File groupFile = new File(fileName);
archiveTag = new ArchiveGroup(groupFile.getParent(), groupFile.getName());
template.addArchiveGroup(archiveTag);
}
} else archiveTag = null;
return archiveTag;
}
public String _fmodified(String args[]) throws Exception {
verifyCommand(args, _fmodifiedHelp, null, 2, Integer.MAX_VALUE);
long time = 0;
Collection<String> names = new ArrayList<String>();
for (int i = 1; i < args.length; i++) {
Processor.split(args[i], names);
}
for (String name : names) {
File f = new File(name);
if (f.exists() && f.lastModified() > time) time = f.lastModified();
}
return "" + time;
}
public List<ServiceData> getServices(File serviceDir) throws Exception {
List<ServiceData> result = new ArrayList<ServiceData>();
if (!serviceDir.exists()) {
return result;
}
for (File sdir : serviceDir.listFiles()) {
File dataFile = new File(sdir, "data");
ServiceData data = getData(ServiceData.class, dataFile);
result.add(data);
}
return result;
}
String ls(String args[], boolean relative) {
if (args.length < 2)
throw new IllegalArgumentException(
"the ${ls} macro must at least have a directory as parameter");
File dir = domain.getFile(args[1]);
if (!dir.isAbsolute())
throw new IllegalArgumentException(
"the ${ls} macro directory parameter is not absolute: " + dir);
if (!dir.exists())
throw new IllegalArgumentException(
"the ${ls} macro directory parameter does not exist: " + dir);
if (!dir.isDirectory())
throw new IllegalArgumentException(
"the ${ls} macro directory parameter points to a file instead of a directory: " + dir);
Collection<File> files = new ArrayList<File>(new SortedList<File>(dir.listFiles()));
for (int i = 2; i < args.length; i++) {
Instructions filters = new Instructions(args[i]);
files = filters.select(files, true);
}
List<String> result = new ArrayList<String>();
for (File file : files) result.add(relative ? file.getName() : file.getAbsolutePath());
return Processor.join(result, ",");
}
