public void init() throws javax.servlet.ServletException {
super.init();
org.slf4j.Logger logServerStartup = org.slf4j.LoggerFactory.getLogger("serverStartup");
logServerStartup.info(
getClass().getName() + " initialization start - " + UsageLog.setupNonRequestContext());
this.ascLimit = ThreddsConfig.getInt("Opendap.ascLimit", ascLimit);
this.binLimit = ThreddsConfig.getInt("Opendap.binLimit", binLimit);
this.odapVersionString = ThreddsConfig.get("Opendap.serverVersion", odapVersionString);
logServerStartup.info(
getClass().getName()
+ " version= "
+ odapVersionString
+ " ascLimit = "
+ ascLimit
+ " binLimit = "
+ binLimit);
// debugging actions
makeDebugActions();
logServerStartup.info(
getClass().getName()
+ " initialization done - "
+ UsageLog.closingMessageNonRequestContext());
}
/**
* Send given content string as the HTTP response.
*
* @param contents the string to return as the HTTP response.
* @param res the HttpServletResponse
* @throws IOException if an I/O error occurs while writing the response.
*/
public static void returnString(String contents, HttpServletResponse res) throws IOException {
try {
ServletOutputStream out = res.getOutputStream();
IO.copy(new ByteArrayInputStream(contents.getBytes()), out);
log.info(
UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_OK, contents.length()));
} catch (IOException e) {
log.error(" IOException sending string: ", e);
log.info(UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_NOT_FOUND, 0));
res.sendError(HttpServletResponse.SC_NOT_FOUND, "Problem sending string: " + e.getMessage());
}
}
/**
* Write a file to the response stream. Handles Range requests.
*
* @param servlet called from here
* @param req the request
* @param res the response
* @param file to serve
* @param contentType content type, if null, will try to guess
* @throws IOException on write error
*/
public static void returnFile(
HttpServlet servlet,
HttpServletRequest req,
HttpServletResponse res,
File file,
String contentType)
throws IOException {
// No file, nothing to view
if (file == null) {
log.info(
"returnFile(): "
+ UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_NOT_FOUND, 0));
res.sendError(HttpServletResponse.SC_NOT_FOUND);
return;
}
// check that it exists
if (!file.exists()) {
log.info(
"returnFile(): "
+ UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_NOT_FOUND, 0));
res.sendError(HttpServletResponse.SC_NOT_FOUND);
return;
}
// not a directory
if (!file.isFile()) {
log.info(
"returnFile(): "
+ UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_BAD_REQUEST, 0));
res.sendError(HttpServletResponse.SC_BAD_REQUEST);
return;
}
// Set the type of the file
String filename = file.getPath();
if (null == contentType) {
if (filename.endsWith(".html")) contentType = "text/html; charset=iso-8859-1";
else if (filename.endsWith(".xml")) contentType = "text/xml; charset=iso-8859-1";
else if (filename.endsWith(".txt") || (filename.endsWith(".log"))) contentType = CONTENT_TEXT;
else if (filename.indexOf(".log.") > 0) contentType = CONTENT_TEXT;
else if (filename.endsWith(".nc")) contentType = "application/x-netcdf";
else contentType = servlet.getServletContext().getMimeType(filename);
if (contentType == null) contentType = "application/octet-stream";
}
returnFile(req, res, file, contentType);
}
/**
* Write a file to the response stream.
*
* @param servlet called from here
* @param contentPath file root path
* @param path file path reletive to the root
* @param req the request
* @param res the response
* @param contentType content type, or null
* @throws IOException on write error
*/
public static void returnFile(
HttpServlet servlet,
String contentPath,
String path,
HttpServletRequest req,
HttpServletResponse res,
String contentType)
throws IOException {
String filename = ServletUtil.formFilename(contentPath, path);
log.debug("returnFile(): returning file <" + filename + ">.");
// No file, nothing to view
if (filename == null) {
log.info(
"returnFile(): "
+ UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_NOT_FOUND, 0));
res.sendError(HttpServletResponse.SC_NOT_FOUND);
return;
}
// dontallow ..
if (filename.indexOf("..") != -1) {
log.info(
"returnFile(): "
+ UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_FORBIDDEN, 0));
res.sendError(HttpServletResponse.SC_FORBIDDEN);
return;
}
// dont allow access to WEB-INF or META-INF
String upper = filename.toUpperCase();
if (upper.indexOf("WEB-INF") != -1 || upper.indexOf("META-INF") != -1) {
log.info(
"returnFile(): "
+ UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_FORBIDDEN, 0));
res.sendError(HttpServletResponse.SC_FORBIDDEN);
return;
}
returnFile(servlet, req, res, new File(filename), contentType);
}
/**
* Forward this request to the CatalogServices servlet ("/catalog.html").
*
* @param req request
* @param res response
* @throws IOException on IO error
* @throws ServletException other error
*/
public static void forwardToCatalogServices(HttpServletRequest req, HttpServletResponse res)
throws IOException, ServletException {
String reqs = "catalog=" + getReletiveURL(req);
String query = req.getQueryString();
if (query != null) reqs = reqs + "&" + query;
log.info("forwardToCatalogServices(): request string = \"/catalog.html?" + reqs + "\"");
// dispatch to CatalogHtml servlet
RequestForwardUtils.forwardRequestRelativeToCurrentContext("/catalog.html?" + reqs, req, res);
}
private void checkSize(ServerDDS dds, boolean isAscii) throws Exception {
long size = computeSize(dds, isAscii);
// System.err.printf("total (constrained) size=%s\n", size);
log.debug("total (constrained) size={}", size);
double dsize = size / (1000 * 1000);
double maxSize = isAscii ? ascLimit : binLimit; // Mbytes
if (dsize > maxSize) {
log.info("Reject request size = {} Mbytes", dsize);
throw new UnsupportedOperationException(
"Request too big=" + dsize + " Mbytes, max=" + maxSize);
}
}
public static boolean saveFile(
HttpServlet servlet,
String contentPath,
String path,
HttpServletRequest req,
HttpServletResponse res) {
// @todo Need to use logServerAccess() below here.
boolean debugRequest = Debug.isSet("SaveFile");
if (debugRequest) log.debug(" saveFile(): path= " + path);
String filename = contentPath + path; // absolute path
File want = new File(filename);
// backup current version if it exists
int version = getBackupVersion(want.getParent(), want.getName());
String fileSave = filename + "~" + version;
File file = new File(filename);
if (file.exists()) {
try {
IO.copyFile(filename, fileSave);
} catch (IOException e) {
log.error(
"saveFile(): Unable to save copy of file "
+ filename
+ " to "
+ fileSave
+ "\n"
+ e.getMessage());
return false;
}
}
// save new file
try {
OutputStream out = new BufferedOutputStream(new FileOutputStream(filename));
IO.copy(req.getInputStream(), out);
out.close();
if (debugRequest) log.debug("saveFile(): ok= " + filename);
res.setStatus(HttpServletResponse.SC_CREATED);
log.info(UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_CREATED, -1));
return true;
} catch (IOException e) {
log.error(
"saveFile(): Unable to PUT file " + filename + " to " + fileSave + "\n" + e.getMessage());
return false;
}
}
// read or create index
private void readOrCreateIndex(CollectionManager.Force ff, Formatter f) throws IOException {
// force new index or test for new index needed
boolean force =
((ff == CollectionManager.Force.always)
|| (ff == CollectionManager.Force.test && needsUpdate()));
// otherwise, we're good as long as the index file exists
File idx = gc.getIndexFile();
if (force || !idx.exists() || !readIndex(idx.getPath())) {
logger.info("GribCollection {}: createIndex {}", gc.getName(), idx.getPath());
createIndex(idx, ff, f); // write out index
gc.rafLocation = idx.getPath();
gc.setRaf(new RandomAccessFile(idx.getPath(), "r"));
readIndex(gc.getRaf()); // read back in index
}
}
private void sendErrorResponse(HttpServletResponse response, int errorCode, String errorMessage) {
try {
log.info(UsageLog.closingMessageForRequestContext(errorCode, -1));
response.setStatus(errorCode);
response.setHeader("Content-Description", "dods-error");
response.setContentType("text/plain");
PrintWriter pw = new PrintWriter(response.getOutputStream());
pw.println("Error {");
pw.println(" code = " + errorCode + ";");
pw.println(" message = \"" + errorMessage + "\";");
pw.println("};");
pw.flush();
} catch (Exception e) {
System.err.println("sendErrorResponse: " + e);
}
}
/**
* @param request
* @param response
* @return the request state
*/
protected ReqState getRequestState(HttpServletRequest request, HttpServletResponse response) {
ReqState rs = null;
// Assume url was encoded
String baseurl = request.getRequestURL().toString();
baseurl = EscapeStrings.unescapeURL(baseurl);
// Assume query was encoded
String query = request.getQueryString();
query = EscapeStrings.unescapeURLQuery(query);
log.info(String.format("OpendapServlet: nominal url: %s?%s", baseurl, query));
try {
rs = new ReqState(request, response, this, getServerName(), baseurl, query);
} catch (Exception bue) {
rs = null;
}
return rs;
}
/**
* ************************************************************************ Sends an error to the
* client.
*
* @param t The exception that caused the problem.
* @param res The <code>HttpServletResponse</code> for the client.
*/
public static void handleException(Throwable t, HttpServletResponse res) {
try {
String message = t.getMessage();
if (message == null) message = "NULL message " + t.getClass().getName();
if (Debug.isSet("trustedMode")) { // security issue: only show stack if trusted
ByteArrayOutputStream bs = new ByteArrayOutputStream();
PrintStream ps = new PrintStream(bs);
t.printStackTrace(ps);
message = new String(bs.toByteArray());
}
log.info(
UsageLog.closingMessageForRequestContext(
HttpServletResponse.SC_BAD_REQUEST, message.length()));
log.error("handleException", t);
t.printStackTrace(); // debugging - log.error not showing stack trace !!
if (!res.isCommitted()) res.sendError(HttpServletResponse.SC_BAD_REQUEST, message);
} catch (Throwable e) {
log.error("handleException() had problem reporting Exception", e);
t.printStackTrace();
}
}
private boolean testScan(String name, ArrayList group) {
int datatype = name.equals("reflect") ? Level2Record.REFLECTIVITY : Level2Record.VELOCITY_HI;
Level2Record first = (Level2Record) group.get(0);
int n = group.size();
if (debugScans) {
boolean hasBoth = first.hasDopplerData && first.hasReflectData;
System.out.println(
name
+ " "
+ first
+ " has "
+ n
+ " radials resolution= "
+ first.resolution
+ " has both = "
+ hasBoth);
}
boolean ok = true;
double sum = 0.0;
double sum2 = 0.0;
for (int i = 0; i < MAX_RADIAL; i++) radial[i] = 0;
for (int i = 0; i < group.size(); i++) {
Level2Record r = (Level2Record) group.get(i);
/* this appears to be common - seems to be ok, we put missing values in
if (r.getGateCount(datatype) != first.getGateCount(datatype)) {
log.error(raf.getLocation()+" different number of gates ("+r.getGateCount(datatype)+
"!="+first.getGateCount(datatype)+") in record "+name+ " "+r);
ok = false;
} */
if (r.getGateSize(datatype) != first.getGateSize(datatype)) {
log.warn(
raf.getLocation()
+ " different gate size ("
+ r.getGateSize(datatype)
+ ") in record "
+ name
+ " "
+ r);
ok = false;
}
if (r.getGateStart(datatype) != first.getGateStart(datatype)) {
log.warn(
raf.getLocation()
+ " different gate start ("
+ r.getGateStart(datatype)
+ ") in record "
+ name
+ " "
+ r);
ok = false;
}
if (r.resolution != first.resolution) {
log.warn(
raf.getLocation()
+ " different resolution ("
+ r.resolution
+ ") in record "
+ name
+ " "
+ r);
ok = false;
}
if ((r.radial_num < 0) || (r.radial_num >= MAX_RADIAL)) {
log.info(
raf.getLocation()
+ " radial out of range= "
+ r.radial_num
+ " in record "
+ name
+ " "
+ r);
continue;
}
if (radial[r.radial_num] > 0) {
log.warn(
raf.getLocation()
+ " duplicate radial = "
+ r.radial_num
+ " in record "
+ name
+ " "
+ r);
ok = false;
}
radial[r.radial_num] = r.recno + 1;
sum += r.getElevation();
sum2 += r.getElevation() * r.getElevation();
// System.out.println(" elev="+r.getElevation()+" azi="+r.getAzimuth());
}
for (int i = 1; i < radial.length; i++) {
if (0 == radial[i]) {
if (n != (i - 1)) {
log.warn(" missing radial(s)");
ok = false;
}
break;
}
}
double avg = sum / n;
double sd = Math.sqrt((n * sum2 - sum * sum) / (n * (n - 1)));
// System.out.println(" avg elev="+avg+" std.dev="+sd);
return ok;
}
/**
* Handle a request for a raw/static file (i.e., not a catalog or dataset request).
*
* <p>Look in the content (user) directory then the root (distribution) directory for a file that
* matches the given path and, if found, return it as the content of the HttpServletResponse. If
* the file is forbidden (i.e., the path contains a "..", "WEB-INF", or "META-INF" directory),
* send a HttpServletResponse.SC_FORBIDDEN response. If no file matches the request (including an
* "index.html" file if the path ends in "/"), send an HttpServletResponse.SC_NOT_FOUND..
*
* <p>
*
* <ol>
* <li>Make sure the path does not contain ".." directories.
* <li>Make sure the path does not contain "WEB-INF" or "META-INF".
* <li>Check for requested file in the content directory (if the path is a directory, make sure
* the path ends with "/" and check for an "index.html" file).
* <li>Check for requested file in the root directory (if the path is a directory, make sure the
* path ends with "/" and check for an "index.html" file). </ol
*
* @param path the requested path
* @param servlet the servlet handling the request
* @param req the HttpServletRequest
* @param res the HttpServletResponse
* @throws IOException if can't complete request due to IO problems.
*/
public static void handleRequestForRawFile(
String path, HttpServlet servlet, HttpServletRequest req, HttpServletResponse res)
throws IOException {
// Don't allow ".." directories in path.
if (path.indexOf("/../") != -1
|| path.equals("..")
|| path.startsWith("../")
|| path.endsWith("/..")) {
res.sendError(HttpServletResponse.SC_FORBIDDEN, "Path cannot contain \"..\" directory.");
log.info(UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_FORBIDDEN, -1));
return;
}
// Don't allow access to WEB-INF or META-INF directories.
String upper = path.toUpperCase();
if (upper.indexOf("WEB-INF") != -1 || upper.indexOf("META-INF") != -1) {
res.sendError(
HttpServletResponse.SC_FORBIDDEN, "Path cannot contain \"WEB-INF\" or \"META-INF\".");
log.info(UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_FORBIDDEN, -1));
return;
}
// Find a regular file
File regFile = null;
// Look in content directory for regular file.
File cFile = new File(ServletUtil.formFilename(getContentPath(), path));
if (cFile.exists()) {
if (cFile.isDirectory()) {
if (!path.endsWith("/")) {
String newPath = req.getRequestURL().append("/").toString();
ServletUtil.sendPermanentRedirect(newPath, req, res);
}
// If request path is a directory, check for index.html file.
cFile = new File(cFile, "index.html");
if (cFile.exists() && !cFile.isDirectory()) regFile = cFile;
}
// If not a directory, use this file.
else regFile = cFile;
}
if (regFile == null) {
// Look in root directory.
File rFile = new File(ServletUtil.formFilename(getRootPath(), path));
if (rFile.exists()) {
if (rFile.isDirectory()) {
if (!path.endsWith("/")) {
String newPath = req.getRequestURL().append("/").toString();
ServletUtil.sendPermanentRedirect(newPath, req, res);
}
rFile = new File(rFile, "index.html");
if (rFile.exists() && !rFile.isDirectory()) regFile = rFile;
} else regFile = rFile;
}
}
if (regFile == null) {
res.sendError(HttpServletResponse.SC_NOT_FOUND); // 404
log.info(UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_NOT_FOUND, -1));
return;
}
ServletUtil.returnFile(servlet, req, res, regFile, null);
}
/**
* Convenience routine used by handleRequestForContentFile() and handleRequestForRootFile().
*
* @param pathPrefix
* @param path
* @param servlet
* @param req request
* @param res response
* @throws IOException on IO error
*/
private static void handleRequestForContentOrRootFile(
String pathPrefix,
String path,
HttpServlet servlet,
HttpServletRequest req,
HttpServletResponse res)
throws IOException {
if (!pathPrefix.equals("/content/") && !pathPrefix.equals("/root/")) {
log.error(
"handleRequestForContentFile(): The path prefix <"
+ pathPrefix
+ "> must be \"/content/\" or \"/root/\".");
throw new IllegalArgumentException("Path prefix must be \"/content/\" or \"/root/\".");
}
if (!path.startsWith(pathPrefix)) {
log.error(
"handleRequestForContentFile(): path <"
+ path
+ "> must start with \""
+ pathPrefix
+ "\".");
throw new IllegalArgumentException("Path must start with \"" + pathPrefix + "\".");
}
// Don't allow ".." directories in path.
if (path.indexOf("/../") != -1
|| path.equals("..")
|| path.startsWith("../")
|| path.endsWith("/..")) {
res.sendError(HttpServletResponse.SC_FORBIDDEN, "Path cannot contain \"..\" directory.");
log.info(UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_FORBIDDEN, -1));
return;
}
// Find the requested file.
File file =
new File(
ServletUtil.formFilename(getContentPath(), path.substring(pathPrefix.length() - 1)));
if (file.exists()) {
// Do not allow request for a directory.
if (file.isDirectory()) {
if (!path.endsWith("/")) {
String redirectPath = req.getRequestURL().append("/").toString();
ServletUtil.sendPermanentRedirect(redirectPath, req, res);
return;
}
int i = HtmlWriter.getInstance().writeDirectory(res, file, path);
int status = i == 0 ? HttpServletResponse.SC_NOT_FOUND : HttpServletResponse.SC_OK;
log.info(UsageLog.closingMessageForRequestContext(status, i));
return;
}
// Return the requested file.
ServletUtil.returnFile(servlet, req, res, file, null);
} else {
// Requested file not found.
log.info(UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_NOT_FOUND, -1));
res.sendError(HttpServletResponse.SC_NOT_FOUND); // 404
}
}
public void doGet(HttpServletRequest request, HttpServletResponse response) {
log.info("doGet(): " + UsageLog.setupRequestContext(request));
// System.out.printf("opendap doGet: req=%s%n%s%n", ServletUtil.getRequest(request),
// ServletUtil.showRequestDetail(this, request));
String path = null;
ReqState rs = getRequestState(request, response);
try {
path = request.getPathInfo();
log.debug("doGet path={}", path);
if (thredds.servlet.Debug.isSet("showRequestDetail"))
log.debug(ServletUtil.showRequestDetail(this, request));
if (path == null) {
log.info(
"doGet(): "
+ UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_NOT_FOUND, -1));
response.sendError(HttpServletResponse.SC_NOT_FOUND);
return;
}
if (baseURI == null) { // first time, set baseURI
URI reqURI = ServletUtil.getRequestURI(request);
// Build base URI from request (rather than hard-coding "/thredds/dodsC/").
String baseUriString = request.getContextPath() + request.getServletPath() + "/";
baseURI = reqURI.resolve(baseUriString);
log.debug("doGet(): baseURI was set = {}", baseURI);
}
if (path.endsWith("latest.xml")) {
DataRootHandler.getInstance().processReqForLatestDataset(this, request, response);
return;
}
// Redirect all catalog requests at the root level.
if (path.equals("/") || path.equals("/catalog.html") || path.equals("/catalog.xml")) {
ServletUtil.sendPermanentRedirect(ServletUtil.getContextPath() + path, request, response);
return;
}
// Make sure catalog requests match a dataRoot before trying to handle.
if (path.endsWith("/") || path.endsWith("/catalog.html") || path.endsWith("/catalog.xml")) {
if (!DataRootHandler.getInstance().hasDataRootMatch(path)) {
log.info(
"doGet(): "
+ UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_NOT_FOUND, -1));
response.sendError(HttpServletResponse.SC_NOT_FOUND);
return;
}
if (!DataRootHandler.getInstance().processReqForCatalog(request, response))
log.error(
"doGet(): "
+ UsageLog.closingMessageForRequestContext(
ServletUtil.STATUS_FORWARD_FAILURE, -1));
return;
}
if (rs != null) {
String dataSet = rs.getDataSet();
String requestSuffix = rs.getRequestSuffix();
if ((dataSet == null) || dataSet.equals("/") || dataSet.equals("")) {
doGetDIR(rs);
} else if (requestSuffix.equalsIgnoreCase("blob")) {
doGetBLOB(rs);
} else if (requestSuffix.equalsIgnoreCase("close")) {
doClose(rs);
} else if (requestSuffix.equalsIgnoreCase("dds")) {
doGetDDS(rs);
} else if (requestSuffix.equalsIgnoreCase("das")) {
doGetDAS(rs);
} else if (requestSuffix.equalsIgnoreCase("ddx")) {
doGetDDX(rs);
} else if (requestSuffix.equalsIgnoreCase("dods")) {
doGetDAP2Data(rs);
} else if (requestSuffix.equalsIgnoreCase("asc")
|| requestSuffix.equalsIgnoreCase("ascii")) {
doGetASC(rs);
} else if (requestSuffix.equalsIgnoreCase("info")) {
doGetINFO(rs);
} else if (requestSuffix.equalsIgnoreCase("html")
|| requestSuffix.equalsIgnoreCase("htm")) {
doGetHTML(rs);
} else if (requestSuffix.equalsIgnoreCase("ver")
|| requestSuffix.equalsIgnoreCase("version")
|| dataSet.equalsIgnoreCase("/version")
|| dataSet.equalsIgnoreCase("/version/")) {
doGetVER(rs);
} else if (dataSet.equalsIgnoreCase("/help")
|| dataSet.equalsIgnoreCase("/help/")
|| dataSet.equalsIgnoreCase("/" + requestSuffix)
|| requestSuffix.equalsIgnoreCase("help")) {
doGetHELP(rs);
} else {
sendErrorResponse(response, HttpServletResponse.SC_BAD_REQUEST, "Unrecognized request");
return;
}
} else {
sendErrorResponse(response, HttpServletResponse.SC_BAD_REQUEST, "Unrecognized request");
return;
}
log.info(UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_OK, -1));
// plain ol' 404
} catch (FileNotFoundException e) {
sendErrorResponse(response, HttpServletResponse.SC_NOT_FOUND, e.getMessage());
// DAP2Exception bad url
} catch (BadURLException e) {
log.info(UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_BAD_REQUEST, -1));
response.setStatus(HttpServletResponse.SC_BAD_REQUEST);
dap2ExceptionHandler(e, rs);
// all other DAP2Exception
} catch (DAP2Exception de) {
int status =
(de.getErrorCode() == DAP2Exception.NO_SUCH_FILE)
? HttpServletResponse.SC_NOT_FOUND
: HttpServletResponse.SC_BAD_REQUEST;
if ((de.getErrorCode() != DAP2Exception.NO_SUCH_FILE) && (de.getErrorMessage() != null))
log.debug(de.getErrorMessage());
log.info(UsageLog.closingMessageForRequestContext(status, -1));
response.setStatus(status);
dap2ExceptionHandler(de, rs);
// parsing, usually the CE
} catch (ParseException pe) {
log.info(UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_BAD_REQUEST, -1));
response.setStatus(HttpServletResponse.SC_BAD_REQUEST);
parseExceptionHandler(pe, response);
// 403 - request too big
} catch (UnsupportedOperationException e) {
sendErrorResponse(response, HttpServletResponse.SC_FORBIDDEN, e.getMessage());
} catch (java.net.SocketException e) {
log.info("SocketException: " + e.getMessage(), e);
log.info(UsageLog.closingMessageForRequestContext(ServletUtil.STATUS_CLIENT_ABORT, -1));
} catch (IOException e) {
String eName =
e.getClass().getName(); // dont want compile time dependency on ClientAbortException
if (eName.equals("org.apache.catalina.connector.ClientAbortException")) {
log.debug("ClientAbortException: " + e.getMessage());
log.info(UsageLog.closingMessageForRequestContext(ServletUtil.STATUS_CLIENT_ABORT, -1));
return;
}
log.error("path= " + path, e);
sendErrorResponse(response, HttpServletResponse.SC_INTERNAL_SERVER_ERROR, e.getMessage());
// everything else
} catch (Throwable t) {
log.error("path= " + path, t);
t.printStackTrace();
sendErrorResponse(response, HttpServletResponse.SC_INTERNAL_SERVER_ERROR, t.getMessage());
}
}
/**
* Parse CSV file using OpenCSV library and load in given database table. href:
* http://viralpatel.net/blogs/java-load-csv-file-to-database/. Modified by rammar:
* https://github.com/BaderLab/pharmacogenomics/blob/master/src/CSVLoader/CSVLoader.java
*
* @param connection the {@link Connection} SQL.
* @param separator the {@link Character} separator.
* @param csvFile Input CSV InputStream
* @param tableName Database table name to import data
* @param truncateBeforeLoad Truncate the table before inserting new records.
* @throws SQLException if any error is occurred with the SQL Connection.
* @throws java.io.IOException if any error is occurred with the file.
*/
public static void loadCSVToSQLTable(
Connection connection,
char separator,
InputStream csvFile,
String tableName,
boolean truncateBeforeLoad)
throws SQLException, IOException {
String SQL_INSERT = "INSERT INTO ${table}(${keys}) VALUES(${values})";
String TABLE_REGEX = "\\$\\{table\\}";
String KEYS_REGEX = "\\$\\{keys\\}";
String VALUES_REGEX = "\\$\\{values\\}";
CSVReader csvReader;
if (null == connection) {
throw new SQLException("Not a valid connection.");
}
try {
/* Modified by rammar.
*
* I was having issues with the CSVReader using the "\" to escape characters.
* A MySQL CSV file contains quote-enclosed fields and non-quote-enclosed NULL
* values written as "\N". The CSVReader was removing the "\". To detect "\N"
* I must remove the escape character, and the only character you can replace
* it with that you are pretty much guaranteed will not be used to escape
* text is '\0'.
* I read this on:
* http://stackoverflow.com/questions/6008395/opencsv-in-java-ignores-backslash-in-a-field-value
* based on:
* http://sourceforge.net/p/opencsv/support-requests/5/
*/
// PREVIOUS VERSION: csvReader = new CSVReader(new FileReader(csvFile), this.seprator);
csvReader = new CSVReader(new InputStreamReader(csvFile), separator, '"', '\0');
} catch (Exception e) {
throw new IOException("Error occured while executing file. " + e.getMessage());
}
String[] headerRow = csvReader.readNext();
if (null == headerRow) {
throw new FileNotFoundException(
"No columns defined in given CSV file." + "Please check the CSV file format.");
}
String questionmarks = StringUtils.repeat("?,", headerRow.length);
questionmarks = (String) questionmarks.subSequence(0, questionmarks.length() - 1);
/* NOTE from Ron: Header column names must match SQL table fields */
String query = SQL_INSERT.replaceFirst(TABLE_REGEX, tableName);
query = query.replaceFirst(KEYS_REGEX, StringUtils.join(headerRow, ","));
query = query.replaceFirst(VALUES_REGEX, questionmarks);
// System.out.println("Query: " + query); // Modified by rammar to suppress output
String[] nextLine;
Connection con = null;
PreparedStatement ps = null;
try {
con = connection;
con.setAutoCommit(false);
ps = con.prepareStatement(query);
if (truncateBeforeLoad) {
// delete data from table before loading csv
con.createStatement().execute("DELETE FROM " + tableName);
}
final int batchSize = 1000;
int count = 0;
Date date;
while ((nextLine = csvReader.readNext()) != null) {
int index = 1;
for (String string : nextLine) {
date = DateUtilities.convertToDate(string);
if (null != date) {
ps.setDate(index++, new java.sql.Date(date.getTime()));
} else {
/* Section modified by rammar to allow NULL values
* to be input into the DB. */
if (string.length() > 0 && !string.equals("\\N")) {
ps.setString(index++, string);
} else {
ps.setNull(index++, Types.VARCHAR);
// ps.setString(index++, null); // can use this syntax also - not sure which is better
}
}
}
ps.addBatch();
if (++count % batchSize == 0) {
ps.executeBatch();
}
}
ps.executeBatch(); // insert remaining records
logger.info(count + " records loaded into " + tableName + " DB table");
con.commit();
} catch (SQLException | IOException e) {
con.rollback();
throw new IOException(
"Error occured while loading data from file to database." + e.getMessage());
} finally {
if (null != ps) ps.close();
con.close();
csvReader.close();
}
}
/**
* Send a permanent redirect (HTTP status 301 "Moved Permanently") response with the given target
* path.
*
* <p>The given target path may be relative or absolute. If it is relative, it will be resolved
* against the request URL.
*
* @param targetPath the path to which the client is redirected.
* @param req the HttpServletRequest
* @param res the HttpServletResponse
* @throws IOException if can't write the response.
*/
public static void sendPermanentRedirect(
String targetPath, HttpServletRequest req, HttpServletResponse res) throws IOException {
// Absolute URL needed so resolve the target path against the request URL.
URI uri;
try {
uri = new URI(req.getRequestURL().toString());
} catch (URISyntaxException e) {
log.error(
"sendPermanentRedirect(): Bad syntax on request URL <" + req.getRequestURL() + ">.", e);
log.info(
"sendPermanentRedirect(): "
+ UsageLog.closingMessageForRequestContext(
HttpServletResponse.SC_INTERNAL_SERVER_ERROR, 0));
if (!res.isCommitted()) res.sendError(HttpServletResponse.SC_INTERNAL_SERVER_ERROR);
return;
}
String absolutePath = uri.resolve(targetPath).toString();
absolutePath = res.encodeRedirectURL(absolutePath);
res.setStatus(HttpServletResponse.SC_MOVED_PERMANENTLY);
res.addHeader("Location", absolutePath);
String title = "Permanently Moved - 301";
String body =
new StringBuilder()
.append("<p>")
.append("The requested URL <")
.append(req.getRequestURL())
.append("> has been permanently moved (HTTP status code 301).")
.append(" Instead, please use the following URL: <a href=\"")
.append(absolutePath)
.append("\">")
.append(absolutePath)
.append("</a>.")
.append("</p>")
.toString();
String htmlResp =
new StringBuilder()
.append(HtmlWriter.getInstance().getHtmlDoctypeAndOpenTag())
.append("<head><title>")
.append(title)
.append("</title></head><body>")
.append("<h1>")
.append(title)
.append("</h1>")
.append(body)
.append("</body></html>")
.toString();
log.info("sendPermanentRedirect(): redirect to " + absolutePath);
log.info(
"sendPermanentRedirect(): "
+ UsageLog.closingMessageForRequestContext(
HttpServletResponse.SC_MOVED_PERMANENTLY, htmlResp.length()));
// Write the catalog out.
PrintWriter out = res.getWriter();
res.setContentType("text/html");
out.print(htmlResp);
out.flush();
}
/**
* Write a file to the response stream. Handles Range requests.
*
* @param req request
* @param res response
* @param file must exists and not be a directory
* @param contentType must not be null
* @throws IOException or error
*/
public static void returnFile(
HttpServletRequest req, HttpServletResponse res, File file, String contentType)
throws IOException {
res.setContentType(contentType);
// see if its a Range Request
boolean isRangeRequest = false;
long startPos = 0, endPos = Long.MAX_VALUE;
String rangeRequest = req.getHeader("Range");
if (rangeRequest != null) { // bytes=12-34 or bytes=12-
int pos = rangeRequest.indexOf("=");
if (pos > 0) {
int pos2 = rangeRequest.indexOf("-");
if (pos2 > 0) {
String startString = rangeRequest.substring(pos + 1, pos2);
String endString = rangeRequest.substring(pos2 + 1);
startPos = Long.parseLong(startString);
if (endString.length() > 0) endPos = Long.parseLong(endString) + 1;
isRangeRequest = true;
}
}
}
// set content length
long fileSize = file.length();
long contentLength = fileSize;
if (isRangeRequest) {
endPos = Math.min(endPos, fileSize);
contentLength = endPos - startPos;
}
if (contentLength > Integer.MAX_VALUE)
res.addHeader(
"Content-Length", Long.toString(contentLength)); // allow content length > MAX_INT
else res.setContentLength((int) contentLength); // note HEAD only allows this
String filename = file.getPath();
boolean debugRequest = Debug.isSet("returnFile");
if (debugRequest)
log.debug(
"returnFile(): filename = "
+ filename
+ " contentType = "
+ contentType
+ " contentLength = "
+ contentLength);
// indicate we allow Range Requests
res.addHeader("Accept-Ranges", "bytes");
if (req.getMethod().equals("HEAD")) {
log.info(
"returnFile(): "
+ UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_OK, 0));
return;
}
try {
if (isRangeRequest) {
// set before content is sent
res.addHeader("Content-Range", "bytes " + startPos + "-" + (endPos - 1) + "/" + fileSize);
res.setStatus(HttpServletResponse.SC_PARTIAL_CONTENT);
FileCacheRaf.Raf craf = null;
try {
craf = fileCacheRaf.acquire(filename);
IO.copyRafB(
craf.getRaf(), startPos, contentLength, res.getOutputStream(), new byte[60000]);
log.info(
"returnFile(): "
+ UsageLog.closingMessageForRequestContext(
HttpServletResponse.SC_PARTIAL_CONTENT, contentLength));
return;
} finally {
if (craf != null) fileCacheRaf.release(craf);
}
}
// Return the file
ServletOutputStream out = res.getOutputStream();
IO.copyFileB(file, out, 60000);
res.flushBuffer();
out.close();
if (debugRequest) log.debug("returnFile(): returnFile ok = " + filename);
log.info(
"returnFile(): "
+ UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_OK, contentLength));
}
// @todo Split up this exception handling: those from file access vs those from dealing with
// response
// File access: catch and res.sendError()
// response: don't catch (let bubble up out of doGet() etc)
catch (FileNotFoundException e) {
log.error("returnFile(): FileNotFoundException= " + filename);
log.info(
"returnFile(): "
+ UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_NOT_FOUND, 0));
if (!res.isCommitted()) res.sendError(HttpServletResponse.SC_NOT_FOUND);
} catch (java.net.SocketException e) {
log.info("returnFile(): SocketException sending file: " + filename + " " + e.getMessage());
log.info("returnFile(): " + UsageLog.closingMessageForRequestContext(STATUS_CLIENT_ABORT, 0));
} catch (IOException e) {
String eName =
e.getClass().getName(); // dont want compile time dependency on ClientAbortException
if (eName.equals("org.apache.catalina.connector.ClientAbortException")) {
log.info(
"returnFile(): ClientAbortException while sending file: "
+ filename
+ " "
+ e.getMessage());
log.info(
"returnFile(): " + UsageLog.closingMessageForRequestContext(STATUS_CLIENT_ABORT, 0));
return;
}
log.error("returnFile(): IOException (" + e.getClass().getName() + ") sending file ", e);
log.error(
"returnFile(): "
+ UsageLog.closingMessageForRequestContext(HttpServletResponse.SC_NOT_FOUND, 0));
if (!res.isCommitted())
res.sendError(HttpServletResponse.SC_NOT_FOUND, "Problem sending file: " + e.getMessage());
}
}