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, ",");
}
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."));
}
}
}
/**
* Garbage collect repository
*
* @throws Exception
*/
public void gc() throws Exception {
HashSet<byte[]> deps = new HashSet<byte[]>();
// deps.add(SERVICE_JAR_FILE);
for (File cmd : commandDir.listFiles()) {
CommandData data = getData(CommandData.class, cmd);
addDependencies(deps, data);
}
for (File service : serviceDir.listFiles()) {
File dataFile = new File(service, "data");
ServiceData data = getData(ServiceData.class, dataFile);
addDependencies(deps, data);
}
int count = 0;
for (File f : repoDir.listFiles()) {
String name = f.getName();
if (!deps.contains(name)) {
if (!name.endsWith(".json")
|| !deps.contains(name.substring(0, name.length() - ".json".length()))) { // Remove
// json
// files
// only
// if
// the
// bin
// is
// going
// as
// well
f.delete();
count++;
} else {
}
}
}
System.out.format("Garbage collection done (%d file(s) removed)%n", count);
}
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;
}
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;
}
static void listPath(File path, FileFilter filter) {
File files[]; // list of files in a directory
indentLevel++; // going down...
// create list of files in this dir
files = path.listFiles(filter);
// Sort with help of Collections API
Arrays.sort(files);
for (int i = 0, n = files.length; i < n; i++) {
for (int indent = 0; indent < indentLevel; indent++) {
System.out.print(" ");
}
if (files[i].isDirectory()) {
System.out.println(files[i].toString());
// recursively descend dir tree
listPath(files[i], filter);
} else {
processFile(files[i]);
}
}
indentLevel--; // and going up
}
// remove temp files, the pipeline.jar operator isn't working.
public void deleteTempFiles() {
System.out.println("\nRemoving these temp files:");
File workingDir = new File(System.getProperty("user.dir"));
File[] toExamine = workingDir.listFiles();
for (File f : toExamine) {
boolean d = false;
String n = f.getName();
if (n.startsWith("pipeinstancelog")) d = true;
else if (n.contains(".DOC.sample")) d = true;
else if (n.contains("allDepths.")) d = true;
else if (n.startsWith("nocalls.")) d = true;
else if (n.startsWith("snpeff.")) d = true;
else if (n.contains("plice")) d = true;
if (d) {
System.out.println("\t" + n);
f.deleteOnExit();
}
}
// delete the temp uncompressed vcf (required by Pipeline.jar)
if (deleteTempVcf) System.out.println("\t" + finalVcf.getName());
}
private void InitUpload() throws ServletException, IOException {
String sConfig = myUtil.ReadFile(myUtil.getConfigFileRealPath(m_request.getServletPath()));
ArrayList aStyle = myUtil.getConfigArray("Style", sConfig);
String sAllowExt, sUploadDir, sBaseUrl, sContentPath;
String sCurrDir, sDir;
int nAllowBrowse;
String sPathShareImage, sPathShareFlash, sPathShareMedia, sPathShareOther;
// param
String sType = myUtil.dealNull(m_request.getParameter("type")).toUpperCase();
String sStyleName = myUtil.dealNull(m_request.getParameter("style"));
String sCusDir = myUtil.dealNull(m_request.getParameter("cusdir"));
String sAction = myUtil.dealNull(m_request.getParameter("action")).toUpperCase();
String s_SKey = myUtil.dealNull(m_request.getParameter("skey"));
// InitUpload
String[] aStyleConfig = new String[1];
boolean bValidStyle = false;
for (int i = 0; i < aStyle.size(); i++) {
aStyleConfig = myUtil.split(aStyle.get(i).toString(), "|||");
if (sStyleName.toLowerCase().equals(aStyleConfig[0].toLowerCase())) {
bValidStyle = true;
break;
}
}
if (!bValidStyle) {
out.print(getOutScript("alert('Invalid Style!')"));
out.close();
return;
}
if (!aStyleConfig[61].equals("1")) {
sCusDir = "";
}
String ss_FileSize = "",
ss_FileBrowse = "",
ss_SpaceSize = "",
ss_SpacePath = "",
ss_PathMode = "",
ss_PathUpload = "",
ss_PathCusDir = "",
ss_PathCode = "",
ss_PathView = "";
if ((aStyleConfig[61].equals("2")) && (!s_SKey.equals(""))) {
ss_FileSize =
(String) myUtil.dealNull(m_session.getAttribute("eWebEditor_" + s_SKey + "_FileSize"));
ss_FileBrowse =
(String) myUtil.dealNull(m_session.getAttribute("eWebEditor_" + s_SKey + "_FileBrowse"));
ss_SpaceSize =
(String) myUtil.dealNull(m_session.getAttribute("eWebEditor_" + s_SKey + "_SpaceSize"));
ss_SpacePath =
(String) myUtil.dealNull(m_session.getAttribute("eWebEditor_" + s_SKey + "_SpacePath"));
ss_PathMode =
(String) myUtil.dealNull(m_session.getAttribute("eWebEditor_" + s_SKey + "_PathMode"));
ss_PathUpload =
(String) myUtil.dealNull(m_session.getAttribute("eWebEditor_" + s_SKey + "_PathUpload"));
ss_PathCusDir =
(String) myUtil.dealNull(m_session.getAttribute("eWebEditor_" + s_SKey + "_PathCusDir"));
ss_PathCode =
(String) myUtil.dealNull(m_session.getAttribute("eWebEditor_" + s_SKey + "_PathCode"));
ss_PathView =
(String) myUtil.dealNull(m_session.getAttribute("eWebEditor_" + s_SKey + "_PathView"));
if (myUtil.IsInt(ss_FileSize)) {
aStyleConfig[11] = ss_FileSize;
aStyleConfig[12] = ss_FileSize;
aStyleConfig[13] = ss_FileSize;
aStyleConfig[14] = ss_FileSize;
aStyleConfig[15] = ss_FileSize;
aStyleConfig[45] = ss_FileSize;
} else {
ss_FileSize = "";
}
if (ss_FileBrowse.equals("0") || ss_FileBrowse.equals("1")) {
aStyleConfig[43] = ss_FileBrowse;
} else {
ss_FileBrowse = "";
}
if (myUtil.IsInt(ss_SpaceSize)) {
aStyleConfig[78] = ss_SpaceSize;
} else {
ss_SpaceSize = "";
}
if (!ss_PathMode.equals("")) {
aStyleConfig[19] = ss_PathMode;
}
if (!ss_PathUpload.equals("")) {
aStyleConfig[3] = ss_PathUpload;
}
if (!ss_PathCode.equals("")) {
aStyleConfig[23] = ss_PathCode;
}
if (!ss_PathView.equals("")) {
aStyleConfig[22] = ss_PathView;
}
sCusDir = ss_PathCusDir;
}
sBaseUrl = aStyleConfig[19];
nAllowBrowse = Integer.valueOf(aStyleConfig[43]).intValue();
if (nAllowBrowse != 1) {
out.print(getOutScript("alert('Do not allow browse!')"));
out.close();
return;
}
if (!sCusDir.equals("")) {
sCusDir = myUtil.replace(sCusDir, "\\", "/");
if ((sCusDir.startsWith("/"))
|| (sCusDir.startsWith("."))
|| (sCusDir.endsWith("."))
|| (sCusDir.indexOf("./") >= 0)
|| (sCusDir.indexOf("/.") >= 0)
|| (sCusDir.indexOf("//") >= 0)
|| (sCusDir.indexOf("..") >= 0)) {
sCusDir = "";
} else {
if (!sCusDir.endsWith("/")) {
sCusDir = sCusDir + "/";
}
}
}
sUploadDir = aStyleConfig[3];
if (!sBaseUrl.equals("3")) {
sUploadDir = myUtil.getRealPathFromRelative(m_request.getServletPath(), sUploadDir);
}
sUploadDir = GetSlashPath(sUploadDir);
sUploadDir =
sUploadDir
+ myUtil.replace(myUtil.replace(sCusDir, "/", sFileSeparator), "\\", sFileSeparator);
if (sType.equals("FILE")) {
sAllowExt = aStyleConfig[6];
} else if (sType.equals("MEDIA")) {
sAllowExt = aStyleConfig[9];
} else if (sType.equals("FLASH")) {
sAllowExt = aStyleConfig[7];
} else {
sAllowExt = aStyleConfig[8];
}
sPathShareImage =
GetSlashPath(
myUtil.getRealPathFromRelative(m_request.getServletPath(), "sharefile/image/"));
sPathShareFlash =
GetSlashPath(
myUtil.getRealPathFromRelative(m_request.getServletPath(), "sharefile/flash/"));
sPathShareMedia =
GetSlashPath(
myUtil.getRealPathFromRelative(m_request.getServletPath(), "sharefile/media/"));
sPathShareOther =
GetSlashPath(
myUtil.getRealPathFromRelative(m_request.getServletPath(), "sharefile/other/"));
String s_Out = "";
if (sAction.equals("FILE")) {
String s_ReturnFlag = myUtil.dealNull(m_request.getParameter("returnflag"));
String s_FolderType = myUtil.dealNull(m_request.getParameter("foldertype"));
String s_Dir = myUtil.dealNull(m_request.getParameter("dir"));
s_Dir = java.net.URLDecoder.decode(s_Dir, "UTF-" + "8");
String s_CurrDir = "";
if (s_FolderType.equals("upload")) {
s_CurrDir = sUploadDir;
} else if (s_FolderType.equals("shareimage")) {
sAllowExt = "";
s_CurrDir = sPathShareImage;
} else if (s_FolderType.equals("shareflash")) {
sAllowExt = "";
s_CurrDir = sPathShareFlash;
} else if (s_FolderType.equals("sharemedia")) {
sAllowExt = "";
s_CurrDir = sPathShareMedia;
} else {
s_FolderType = "shareother";
sAllowExt = "";
s_CurrDir = sPathShareOther;
}
s_Dir = myUtil.replace(s_Dir, "\\", "/");
if ((s_Dir.startsWith("/"))
|| (s_Dir.startsWith("."))
|| (s_Dir.endsWith("."))
|| (s_Dir.indexOf("./") >= 0)
|| (s_Dir.indexOf("/.") >= 0)
|| (s_Dir.indexOf("//") >= 0)
|| (s_Dir.indexOf("..") >= 0)) {
s_Dir = "";
}
String s_Dir2 = myUtil.replace(s_Dir, "/", sFileSeparator);
s_Dir2 = myUtil.replace(s_Dir2, "\\", sFileSeparator);
if (!s_Dir.equals("")) {
if (CheckValidDir(s_CurrDir + s_Dir2)) {
s_CurrDir += s_Dir2;
} else {
s_Dir = "";
}
}
if (CheckValidDir(s_CurrDir)) {
File file = new File(s_CurrDir);
File[] filelist = file.listFiles();
if (filelist != null && filelist.length > 0) {
int n = -1;
for (int i = 0; i < filelist.length; i++) {
if (filelist[i].isFile()) {
String s_FileName = filelist[i].getName();
String s_FileExt = s_FileName.substring(s_FileName.lastIndexOf(".") + 1);
s_FileExt = s_FileExt.toLowerCase();
if (CheckValidExt(sAllowExt, s_FileExt)) {
n++;
s_Out =
s_Out
+ "arr["
+ String.valueOf(n)
+ "]=new Array(\""
+ s_FileName
+ "\", \""
+ String.valueOf(convertFileSize(filelist[i].length()))
+ "\",\""
+ formatDate(new Date(filelist[i].lastModified()))
+ "\");\n";
}
}
}
}
}
s_Out =
"var arr = new Array();\n"
+ s_Out
+ "parent.setFileList('"
+ s_ReturnFlag
+ "', '"
+ s_FolderType
+ "', '"
+ s_Dir
+ "', arr);";
out.print(getOutScript(s_Out));
} else {
s_Out = "var arrUpload = new Array();\n";
s_Out += "var arrShareImage = new Array();\n";
s_Out += "var arrShareFlash = new Array();\n";
s_Out += "var arrShareMedia = new Array();\n";
s_Out += "var arrShareOther = new Array();\n";
s_Out += GetFolderTree(sUploadDir, "Upload", 1, 0).get(0).toString();
sAllowExt = "";
if (sType.equals("FILE")) {
s_Out += GetFolderTree(sPathShareImage, "ShareImage", 1, 0).get(0).toString();
s_Out += GetFolderTree(sPathShareFlash, "ShareFlash", 1, 0).get(0).toString();
s_Out += GetFolderTree(sPathShareMedia, "ShareMedia", 1, 0).get(0).toString();
s_Out += GetFolderTree(sPathShareOther, "ShareOther", 1, 0).get(0).toString();
} else if (sType.equals("MEDIA")) {
s_Out += GetFolderTree(sPathShareMedia, "ShareMedia", 1, 0).get(0).toString();
} else if (sType.equals("FLASH")) {
s_Out += GetFolderTree(sPathShareFlash, "ShareFlash", 1, 0).get(0).toString();
} else {
s_Out += GetFolderTree(sPathShareImage, "ShareImage", 1, 0).get(0).toString();
}
s_Out +=
"parent.setFolderList(arrUpload, arrShareImage, arrShareFlash, arrShareMedia, arrShareOther);";
out.print(getOutScript(s_Out));
}
}