public void bad() throws Throwable {
String fn =
".\\src\\testcases\\CWE379_File_Creation_in_Insecure_Dir\\insecureDir"; /* may have to be changed depending on script */
/* POSSIBLE FLAW: potentially insecure directory permissions */
File dir = new File(fn);
if (dir.exists()) {
IO.writeLine("Directory already exists");
if (dir.delete()) {
IO.writeLine("Directory deleted");
} else {
return;
}
}
if (!dir.getParentFile().canWrite()) {
IO.writeLine("Cannot write to parent dir");
}
try {
boolean success = dir.mkdir();
if (success) {
IO.writeLine("Directory created");
File file = new File(dir.getAbsolutePath() + "\\newFile.txt");
file.createNewFile();
}
} catch (Exception e) {
System.out.println(e.getMessage());
}
}
private void good1() throws Throwable {
String fn = ".\\src\\testcases\\CWE379_File_Creation_in_Insecure_Dir\\basic\\insecureDir";
File dir = new File(fn);
if (dir.exists()) {
IO.writeLine("Directory already exists");
if (dir.delete()) {
IO.writeLine("Directory deleted");
} else {
return;
}
}
if (!dir.getParentFile().canWrite()) {
IO.writeLine("Cannot write to parent dir");
}
/* FIX: explicitly set directory permissions */
dir.setExecutable(false, true);
dir.setReadable(true);
dir.setWritable(false, true);
try {
boolean success = dir.mkdir();
if (success) {
IO.writeLine("Directory created");
File file = new File(dir.getAbsolutePath() + "\\newFile.txt");
file.createNewFile();
}
} catch (Exception e) {
System.out.println(e.getMessage());
}
}
public ReaderHandler(LowLevelDbAccess lowLevelDbAccess, String webDir) {
loginInfoDb = new LoginInfo.DB(lowLevelDbAccess);
userDb = new User.DB(lowLevelDbAccess);
feedDb = new Feed.DB(lowLevelDbAccess);
articleDb = new Article.DB(lowLevelDbAccess);
readArticlesCollDb = new ReadArticlesColl.DB(lowLevelDbAccess);
userHelpers = new UserHelpers(loginInfoDb, userDb);
setContextPath("/");
File warPath = new File(webDir);
setWar(warPath.getAbsolutePath());
if (isInJar) {
for (Map.Entry<String, String> entry : PATH_MAPPING.entrySet()) {
addPrebuiltJsp(entry.getKey(), "jsp." + entry.getValue().replaceAll("_", "_005f") + "_jsp");
}
} else {
for (Map.Entry<String, String> entry : PATH_MAPPING.entrySet()) {
addServlet(
new ServletHolder(new RedirectServlet("/" + entry.getValue() + ".jsp")),
entry.getKey());
}
}
setErrorHandler(new ReaderErrorHandler());
}
/**
* return OutputStream of JasperReport object, this page could only be viewed from localhost for
* security concern. parameter can be (id), or (table and type)
*
* @param id - report id, or
* @param table - table name
* @param type - reporttype "s","l","o", case insensitive
* @param client(*) - client domain
* @param version - version number, default to -1
*/
public void process(HttpServletRequest request, HttpServletResponse response) throws Exception {
String clientName = request.getParameter("client");
int objectId = ParamUtils.getIntAttributeOrParameter(request, "id", -1);
if (objectId == -1) {
// try using table and type
objectId =
getReportId(clientName, request.getParameter("table"), request.getParameter("type"));
}
if (objectId == -1) {
logger.error("report not found, request is:" + Tools.toString(request));
throw new NDSException("report not found");
}
int version = ParamUtils.getIntAttributeOrParameter(request, "version", -1);
File reportXMLFile = new File(ReportTools.getReportFile(objectId, clientName));
if (reportXMLFile.exists()) {
// generate jasperreport if file not exists or not newer
String reportName =
reportXMLFile.getName().substring(0, reportXMLFile.getName().lastIndexOf("."));
File reportJasperFile = new File(reportXMLFile.getParent(), reportName + ".jasper");
if (!reportJasperFile.exists()
|| reportJasperFile.lastModified() < reportXMLFile.lastModified()) {
JasperCompileManager.compileReportToFile(
reportXMLFile.getAbsolutePath(), reportJasperFile.getAbsolutePath());
}
InputStream is = new FileInputStream(reportJasperFile);
response.setContentType("application/octetstream;");
response.setContentLength((int) reportJasperFile.length());
// response.setHeader("Content-Disposition","inline;filename=\""+reportJasperFile.getName()+"\"");
ServletOutputStream os = response.getOutputStream();
byte[] b = new byte[8192];
int bInt;
while ((bInt = is.read(b, 0, b.length)) != -1) {
os.write(b, 0, bInt);
}
is.close();
os.flush();
os.close();
} else {
throw new NDSException("Not found report template");
}
}
// Fireup tomcat and register this servlet
public static void main(String[] args) throws LifecycleException, SQLException {
Tomcat tomcat = new Tomcat();
tomcat.setPort(8080);
File base = new File(System.getProperty("java.io.tmpdir"));
Context rootCtx = tomcat.addContext("/", base.getAbsolutePath());
Tomcat.addServlet(rootCtx, "log", new LogService());
rootCtx.addServletMapping("/*", "log");
tomcat.start();
tomcat.getServer().await();
}
private Transformer buildTransformer(String name, File xslDir, TransformerFactory tf)
throws Exception {
Transformer tr =
tf.newTransformer(
new StreamSource(
new FileReader(xslDir.getAbsolutePath() + File.separatorChar + name + ".xsl")));
tr.setOutputProperty(OutputKeys.INDENT, "yes");
tr.setOutputProperty(OutputKeys.METHOD, "html");
tr.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "3");
return tr;
}
/**
* Returns the adapter type for the given file. Will first use the adapter selector function if it
* was specified in init.js, otherwise will use the static type (either set in _init file, as a
* server-wide override in 10gen.properties, or default of DIRECT_10GEN)
*
* @param file to produce type for
* @return adapter type for the specified file
*/
public AdapterType getAdapterType(File file) {
// Q : I think this is the right thing to do
if (inScopeSetup()) {
return AdapterType.DIRECT_10GEN;
}
/*
* cheap hack - prevent any _init.* file from getting run as anythign but DIRECT_10GEN
*/
if (file != null && file.getName().indexOf("_init.") != -1) {
return AdapterType.DIRECT_10GEN;
}
if (_adapterSelector == null) {
return _staticAdapterType;
}
/*
* only let the app select type if file is part of application (i.e.
* don't do it for corejs, core modules, etc...
*/
String fp = file.getAbsolutePath();
String fullRoot = _rootFile.getAbsolutePath(); // there must be a nicer way to do this?
if (!fp.startsWith(fullRoot)) {
return AdapterType.DIRECT_10GEN;
}
Object o = _adapterSelector.call(_initScope, new JSString(fp.substring(fullRoot.length())));
if (o == null) {
return _staticAdapterType;
}
if (!(o instanceof JSString)) {
log("Error : adapter selector not returning string. Ignoring and using static adapter type");
return _staticAdapterType;
}
AdapterType t = getAdapterTypeFromString(o.toString());
return (t == null ? _staticAdapterType : t);
}
@Override
protected void doPost(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
response.setContentType("text/html;charset=UTF-8");
request.setCharacterEncoding("utf-8");
if (jjNumber.isDigit(jjTools.getParameter(request, "maxSize"))) {
maxSize = Long.parseLong(jjTools.getParameter(request, "maxSize"));
}
response.setCharacterEncoding("utf-8");
String name = request.getParameter("name");
name = name == null ? "" : name;
response.setContentType("text/plain");
super.init(getServletConfig());
// response.setContentType("text/plain");
PrintWriter out = response.getWriter();
// out.println();
DiskFileItemFactory fileItemFactory = new DiskFileItemFactory();
// fileItemFactory.setSizeThreshold(1024 * 1024); //1 MB
try {
ServletFileUpload uploadHandler = new ServletFileUpload(fileItemFactory);
List items = uploadHandler.parseRequest(request);
Iterator itr = items.iterator();
while (itr.hasNext()) {
FileItem item = (FileItem) itr.next();
if (item.isFormField()) {
/*
* Field
*/
// out.println("Field Name=" + item.getFieldName() + ", Value=" +
// item.getString());
data.put(item.getFieldName(), item.getString());
} else {
/*
* File
*/
File folderAddress =
new File(request.getServletContext().getRealPath(Save_Folder_Name)); // "/" +
String extension = "";
String nameWithoutExtension = item.getName();
if (item.getName().lastIndexOf(".") > -1) {
extension = item.getName().substring(item.getName().lastIndexOf("."));
nameWithoutExtension =
item.getName()
.substring(
item.getName().lastIndexOf("\\") + 1, item.getName().lastIndexOf("."));
}
folderAddress.mkdirs();
nameWithoutExtension = "P";
File file =
new File(
folderAddress
+ "/"
+ nameWithoutExtension.toLowerCase()
+ jjNumber.getRandom(10)
+ extension.toLowerCase());
String i = "0000000000";
while (file.exists()) {
i = jjNumber.getRandom(10);
file =
new File(
folderAddress
+ "/"
+ nameWithoutExtension.toLowerCase()
+ i
+ extension.toLowerCase());
}
if (!name.equals("")) {
file = new File(folderAddress + "/" + name);
}
// out.println("File Name=" + item.getName()
// + ", Field Name=" + item.getFieldName()
// + ", Content type=" + item.getContentType()
// + ", File Size=" + item.getSize()
// + ", Save Address=" + file);
// out.println(file);
// String urlPath =
// request.getRequestURL().toString().replace("Upload2", "Upload") + "/" +
// file.getName().replace("\\", "/");
// out.println("<html><head><meta http-equiv='Content-Type'
// content='text/html; charset=utf-8'></head><body><input type='text' name='T1' size='58'
// value='" + urlPath + "'></body></html>");
data.put(item.getFieldName(), file.getAbsolutePath());
if (!file.getName().toLowerCase().endsWith(".exe")) {
item.write(file);
}
long size = file.length();
ServerLog.Print("?>>>>>>" + file + " - Size:" + size);
if (size > maxSize) {
file.delete();
out.print("big");
} else {
out.print(
file.getName()
.replace(" ", "%20")
.replace("<pre style=\"word-wrap: break-word; white-space: pre-wrap;\">", ""));
ServerLog.Print("Write pic in: " + file + " size:" + file.length());
String name2 = file.getName().substring(0, file.getName().lastIndexOf("."));
String extension2 =
file.getName()
.substring(file.getName().lastIndexOf(".") + 1, file.getName().length());
File file2 = new File(file.getParent() + "/" + name2 + "_small." + extension2);
if (extension2.toLowerCase().equals("jpg")
|| extension2.toLowerCase().equals("png")
|| extension2.toLowerCase().equals("gif")) {
jjPicture.doChangeSizeOfPic(file, file2, 250);
}
}
}
}
} catch (Exception ex) {
Server.ErrorHandler(ex);
}
out.flush();
out.close();
}
public void doPost(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
// set the response
Shepherd myShepherd = new Shepherd();
Vector rEncounters = new Vector();
// setup data dir
String rootWebappPath = getServletContext().getRealPath("/");
File webappsDir = new File(rootWebappPath).getParentFile();
File shepherdDataDir = new File(webappsDir, CommonConfiguration.getDataDirectoryName());
// if(!shepherdDataDir.exists()){shepherdDataDir.mkdir();}
File encountersDir = new File(shepherdDataDir.getAbsolutePath() + "/encounters");
// if(!encountersDir.exists()){encountersDir.mkdir();}
// set up the files
String gisFilename = "geneGIS_export_" + request.getRemoteUser() + ".csv";
File gisFile = new File(encountersDir.getAbsolutePath() + "/" + gisFilename);
myShepherd.beginDBTransaction();
try {
// set up the output stream
FileOutputStream fos = new FileOutputStream(gisFile);
OutputStreamWriter outp = new OutputStreamWriter(fos);
try {
EncounterQueryResult queryResult =
EncounterQueryProcessor.processQuery(
myShepherd, request, "year descending, month descending, day descending");
rEncounters = queryResult.getResult();
int numMatchingEncounters = rEncounters.size();
// build the CSV file header
StringBuffer locusString = new StringBuffer("");
int numLoci = 2; // most covered species will be loci
try {
numLoci = (new Integer(CommonConfiguration.getProperty("numLoci"))).intValue();
} catch (Exception e) {
System.out.println("numPloids configuration value did not resolve to an integer.");
e.printStackTrace();
}
for (int j = 0; j < numLoci; j++) {
locusString.append(",Locus" + (j + 1) + " A1,Locus" + (j + 1) + " A2");
}
// out.println("<html><body>");
// out.println("Individual ID,Other ID 1,Date,Time,Latitude,Longitude,Area,Sub
// Area,Sex,Haplotype"+locusString.toString());
outp.write(
"Individual ID,Other ID 1,Date,Time,Latitude,Longitude,Area,Sub Area,Sex,Haplotype"
+ locusString.toString()
+ "\n");
for (int i = 0; i < numMatchingEncounters; i++) {
Encounter enc = (Encounter) rEncounters.get(i);
String assembledString = "";
if (enc.getIndividualID() != null) {
assembledString += enc.getIndividualID();
}
if (enc.getAlternateID() != null) {
assembledString += "," + enc.getAlternateID();
} else {
assembledString += ",";
}
String dateString = ",";
if (enc.getYear() > 0) {
dateString += enc.getYear();
if (enc.getMonth() > 0) {
dateString += ("-" + enc.getMonth());
if (enc.getDay() > 0) {
dateString += ("-" + enc.getDay());
}
}
}
assembledString += dateString;
String timeString = ",";
if (enc.getHour() > -1) {
timeString += enc.getHour() + ":" + enc.getMinutes();
}
assembledString += timeString;
if ((enc.getDecimalLatitude() != null) && (enc.getDecimalLongitude() != null)) {
assembledString += "," + enc.getDecimalLatitude();
assembledString += "," + enc.getDecimalLongitude();
} else {
assembledString += ",,";
}
assembledString += "," + enc.getVerbatimLocality();
assembledString += "," + enc.getLocationID();
assembledString += "," + enc.getSex();
// find and print the haplotype
String haplotypeString = ",";
if (enc.getHaplotype() != null) {
haplotypeString += enc.getHaplotype();
}
// find and print the ms markers
String msMarkerString = "";
List<TissueSample> samples = enc.getTissueSamples();
int numSamples = samples.size();
boolean foundMsMarkers = false;
for (int k = 0; k < numSamples; k++) {
if (!foundMsMarkers) {
TissueSample t = samples.get(k);
List<GeneticAnalysis> analyses = t.getGeneticAnalyses();
int aSize = analyses.size();
for (int l = 0; l < aSize; l++) {
GeneticAnalysis ga = analyses.get(l);
if (ga.getAnalysisType().equals("MicrosatelliteMarkers")) {
foundMsMarkers = true;
MicrosatelliteMarkersAnalysis ga2 = (MicrosatelliteMarkersAnalysis) ga;
List<Locus> loci = ga2.getLoci();
int localLoci = loci.size();
for (int m = 0; m < localLoci; m++) {
Locus locus = loci.get(m);
if (locus.getAllele0() != null) {
msMarkerString += "," + locus.getAllele0();
} else {
msMarkerString += ",";
}
if (locus.getAllele1() != null) {
msMarkerString += "," + locus.getAllele1();
} else {
msMarkerString += ",";
}
}
}
}
}
}
// out.println("<p>"+assembledString+haplotypeString+msMarkerString+"</p>");
outp.write(assembledString + haplotypeString + msMarkerString + "\n");
}
outp.close();
outp = null;
// now write out the file
response.setContentType("text/csv");
response.setHeader("Content-Disposition", "attachment;filename=" + gisFilename);
ServletContext ctx = getServletContext();
// InputStream is = ctx.getResourceAsStream("/encounters/"+gisFilename);
InputStream is = new FileInputStream(gisFile);
int read = 0;
byte[] bytes = new byte[BYTES_DOWNLOAD];
OutputStream os = response.getOutputStream();
while ((read = is.read(bytes)) != -1) {
os.write(bytes, 0, read);
}
os.flush();
os.close();
} catch (Exception ioe) {
ioe.printStackTrace();
response.setContentType("text/html");
PrintWriter out = response.getWriter();
out.println(ServletUtilities.getHeader(request));
out.println(
"<html><body><p><strong>Error encountered</strong> with file writing. Check the relevant log.</p>");
out.println(
"<p>Please let the webmaster know you encountered an error at: EncounterSearchExportGeneGISFormat servlet</p></body></html>");
out.println(ServletUtilities.getFooter());
out.close();
outp.close();
outp = null;
}
} catch (Exception e) {
e.printStackTrace();
response.setContentType("text/html");
PrintWriter out = response.getWriter();
out.println(ServletUtilities.getHeader(request));
out.println("<html><body><p><strong>Error encountered</strong></p>");
out.println(
"<p>Please let the webmaster know you encountered an error at: EncounterSearchExportGeneGISFormat servlet</p></body></html>");
out.println(ServletUtilities.getFooter());
out.close();
}
myShepherd.rollbackDBTransaction();
myShepherd.closeDBTransaction();
}
