@Before
public void setUp() throws Exception {
lc = new LoggerContext();
converter = new MDCConverter();
converter.start();
MDC.clear();
}
public Object step(int step) {
helper.assertStep(step);
try {
MDC.put("fileset", logFilename);
log.debug("Step " + step);
Job j = activity.getChild();
if (j == null) {
throw helper.cancel(new ERR(), null, "null-job");
} else if (!(j instanceof MetadataImportJob)) {
throw helper.cancel(new ERR(), null, "unexpected-job-type", "job-type", j.ice_id());
}
if (step == 0) {
return importMetadata((MetadataImportJob) j);
} else if (step == 1) {
return pixelData(null); // (ThumbnailGenerationJob) j);
} else if (step == 2) {
return generateThumbnails(null); // (PixelDataJob) j); Nulls image
} else if (step == 3) {
// TODO: indexing and scripting here as well.
store.launchProcessing();
return null;
} else if (step == 4) {
return objects;
} else {
throw helper.cancel(new ERR(), null, "bad-step", "step", "" + step);
}
} catch (MissingLibraryException mle) {
notifyObservers(new ErrorHandler.MISSING_LIBRARY(fileName, mle, usedFiles, format));
throw helper.cancel(new ERR(), mle, "import-missing-library", "filename", fileName);
} catch (UnsupportedCompressionException uce) {
// Handling as UNKNOWN_FORMAT for 4.3.0
notifyObservers(new ErrorHandler.UNKNOWN_FORMAT(fileName, uce, this));
throw helper.cancel(new ERR(), uce, "import-unknown-format", "filename", fileName);
} catch (UnknownFormatException ufe) {
notifyObservers(new ErrorHandler.UNKNOWN_FORMAT(fileName, ufe, this));
throw helper.cancel(new ERR(), ufe, "import-unknown-format", "filename", fileName);
} catch (IOException io) {
notifyObservers(new ErrorHandler.FILE_EXCEPTION(fileName, io, usedFiles, format));
throw helper.cancel(new ERR(), io, "import-file-exception", "filename", fileName);
} catch (FormatException fe) {
notifyObservers(new ErrorHandler.FILE_EXCEPTION(fileName, fe, usedFiles, format));
throw helper.cancel(new ERR(), fe, "import-file-exception", "filename", fileName);
} catch (Cancel c) {
throw c;
} catch (Throwable t) {
notifyObservers(
new ErrorHandler.INTERNAL_EXCEPTION(
fileName, new RuntimeException(t), usedFiles, format));
throw helper.cancel(new ERR(), t, "import-request-failure");
} finally {
try {
long size = logPath.size();
store.updateFileSize(logFile, size);
} catch (Throwable t) {
throw helper.cancel(new ERR(), t, "update-log-file-size");
}
MDC.clear();
}
}
@After
public void tearDown() throws Exception {
lc = null;
converter.stop();
converter = null;
MDC.clear();
}
@Test
public void mdc() throws EvaluationException {
MDC.put("key", "val");
LoggingEvent event = makeEvent("x");
doEvaluateAndCheck("e.mdc['key'] == 'val'", event, true);
MDC.clear();
}
private void calPerf() {
this.bytesRead = (long) (vol.getReadBytes() - this.pbytesRead);
this.pbytesRead = vol.getReadBytes();
MDC.put("bytesRead", Long.toString(bytesRead));
this.bytesWritten = (long) (vol.getActualWriteBytes() - this.pbytesWritten);
this.pbytesWritten = vol.getActualWriteBytes();
MDC.put("bytesWritten", Long.toString(this.bytesWritten));
this.duplicateBytes = (long) (vol.getDuplicateBytes() - this.pduplicateBytes);
this.pduplicateBytes = vol.getDuplicateBytes();
MDC.put("duplicateBytes", Long.toString(this.duplicateBytes));
this.virtualBytesWritten = (long) (vol.getVirtualBytesWritten() - this.pvirtualBytesWritten);
this.pvirtualBytesWritten = vol.getVirtualBytesWritten();
MDC.put("virtualBytesWritten", Long.toString(this.virtualBytesWritten));
this.RIOPS = (long) (vol.getReadOperations() - this.pRIOPS);
this.pRIOPS = vol.getReadOperations();
MDC.put("RIOPS", Long.toString(this.RIOPS));
this.WIOPS = (long) (vol.getWriteOperations() - this.pWIOPS);
this.pWIOPS = vol.getWriteOperations();
this.dseSz = HCServiceProxy.getDSESize();
this.dseCompSz = HCServiceProxy.getDSECompressedSize();
MDC.put("dseSz", Long.toString(this.dseSz));
MDC.put("dseCompSz", Long.toString(this.dseCompSz));
MDC.put("WIOPS", Long.toString(this.WIOPS));
MDC.put("sdfsCpuLoad", Double.toString(perf.getProcessCpuLoad()));
MDC.put("sdfsCpuTime", Double.toString(perf.getProcessCpuTime()));
MDC.put("systemCpuLoad", Double.toString(perf.getSystemCpuLoad()));
MDC.put("systemCpuAverage", Double.toString(perf.getSystemLoadAverage()));
MDC.put("freeMemory", Long.toString(perf.getFreePhysicalMemorySize()));
MDC.put("totalMemory", Long.toString(perf.getTotalPhysicalMemorySize()));
MDC.put("freeSwap", Long.toString(perf.getFreeSwapSpaceSize()));
MDC.put("totalSwap", Long.toString(perf.getTotalSwapSpaceSize()));
log.info(vol.getName());
MDC.clear();
}
@Before
public void setUp() throws Exception {
MDC.clear();
ServerSetup serverSetup = new ServerSetup(port, "localhost", ServerSetup.PROTOCOL_SMTP);
greenMailServer = new GreenMail(serverSetup);
greenMailServer.start();
// give the server a head start
if (EnvUtilForTests.isRunningOnSlowJenkins()) {
Thread.sleep(2000);
} else {
Thread.sleep(50);
}
}
@Before
public void setUp() throws Exception {
OnConsoleStatusListener.addNewInstanceToContext(loggerContext);
MDC.clear();
ServerSetup serverSetup = new ServerSetup(port, "localhost", ServerSetup.PROTOCOL_SMTP);
greenMailServer = new GreenMail(serverSetup);
greenMailServer.start();
// give the server a head start
if (EnvUtilForTests.isRunningOnSlowJenkins()) {
Thread.sleep(2000);
} else {
Thread.sleep(50);
}
}
@Override
public void doFilter(ServletRequest request, ServletResponse response, FilterChain chain)
throws IOException, ServletException {
try {
Principal principal = ((HttpServletRequest) request).getUserPrincipal();
if (principal != null) {
MDC.put(LogConstants.USER, principal.getName());
} else {
MDC.put(LogConstants.USER, "?");
}
chain.doFilter(request, response);
} finally {
MDC.clear();
}
}
@Test
public void LBCLASSIC_104() throws Exception {
buildSMTPAppender(smtpServer.getSmtp().getPort(), SYNCHRONOUS);
smtpAppender.setAsynchronousSending(false);
smtpAppender.setLayout(buildPatternLayout(lc, DEFAULT_PATTERN));
smtpAppender.start();
logger.addAppender(smtpAppender);
MDC.put("key", "val");
logger.debug("hello");
MDC.clear();
logger.error("an error", new Exception("an exception"));
MimeMultipart mp = verify(smtpServer, TEST_SUBJECT);
String body = GreenMailUtil.getBody(mp.getBodyPart(0));
assertTrue("missing HEADER in body", body.startsWith(HEADER.trim()));
assertTrue("missing MDC in body", body.contains("key=val"));
assertTrue("missing FOOTER in body", body.endsWith(FOOTER.trim()));
}
// lost MDC
@Test
public void LBCLASSIC_104() throws Exception {
String subject = "LBCLASSIC_104";
buildSMTPAppender(subject, SYNCHRONOUS);
smtpAppender.setAsynchronousSending(false);
smtpAppender.setLayout(buildPatternLayout(DEFAULT_PATTERN));
smtpAppender.start();
logger.addAppender(smtpAppender);
MDC.put("key", "val");
logger.debug("hello");
MDC.clear();
logger.error("en error", new Exception("test"));
MimeMultipart mp = verifyAndExtractMimeMultipart(subject);
String body = GreenMailUtil.getBody(mp.getBodyPart(0));
assertTrue("missing HEADER in body", body.startsWith(HEADER.trim()));
assertTrue("missing MDC in body", body.contains("key=val"));
assertTrue("missing FOOTER in body", body.endsWith(FOOTER.trim()));
}
/** {@inheritDoc} */
@Override
public void doFilter(ServletRequest request, ServletResponse response, FilterChain chain)
throws IOException, ServletException {
try {
MDC.put(Version.MDC_ATTRIBUTE, Version.getVersion());
MDC.put(CLIENT_ADDRESS_MDC_ATTRIBUTE, request.getRemoteAddr());
MDC.put(SERVER_ADDRESS_MDC_ATTRIBUTE, request.getServerName());
MDC.put(SERVER_PORT_MDC_ATTRIBUTE, Integer.toString(request.getServerPort()));
if (request instanceof HttpServletRequest) {
final HttpSession session = ((HttpServletRequest) request).getSession();
if (session != null) {
MDC.put(JSESSIONID_MDC_ATTRIBUTE, session.getId());
}
}
chain.doFilter(request, response);
} finally {
MDC.clear();
}
}
@Test
public void eventWasPreparedForDeferredProcessing() {
asyncAppender.addAppender(listAppender);
asyncAppender.start();
String k = "k" + diff;
MDC.put(k, "v");
asyncAppender.doAppend(builder.build(diff));
MDC.clear();
asyncAppender.stop();
assertFalse(asyncAppender.isStarted());
// check the event
assertEquals(1, listAppender.list.size());
ILoggingEvent e = listAppender.list.get(0);
// check that MDC values were correctly retained
assertEquals("v", e.getMDCPropertyMap().get(k));
assertFalse(e.hasCallerData());
}
/** Called during {@link #getResponse()}. */
private void cleanup() {
MDC.put("fileset", logFilename);
try {
cleanupReader();
cleanupStore();
log.info(ClassicConstants.FINALIZE_SESSION_MARKER, "Finalizing log file.");
/* hereafter back to normal log destination, not import log file*/
MDC.clear();
try {
/* requires usable session */
setLogFileSize();
} catch (ServerError se) {
log.error("failed to set import log file size", se);
}
cleanupSession();
} finally {
autoClose(); // Doesn't throw
if (resources != null) {
resources.remove(resourcesEntry);
}
}
}
@Test
public void mdc() throws Exception {
HttpServletRequest request = Mockito.mock(HttpServletRequest.class);
Mockito.when(request.getUserPrincipal()).thenReturn(null);
Mockito.when(request.getMethod()).thenReturn("METHOD");
Mockito.when(request.getPathInfo()).thenReturn("/pathinfo");
ServletResponse response = Mockito.mock(ServletResponse.class);
final AtomicBoolean invoked = new AtomicBoolean();
FilterChain chain =
new FilterChain() {
@Override
public void doFilter(ServletRequest servletRequest, ServletResponse servletResponse)
throws IOException, ServletException {
Assert.assertEquals(MDC.get("hostname"), null);
Assert.assertEquals(MDC.get("user"), null);
Assert.assertEquals(MDC.get("method"), "METHOD");
Assert.assertEquals(MDC.get("path"), "/pathinfo");
invoked.set(true);
}
};
MDC.clear();
Filter filter = new MDCFilter();
filter.init(null);
filter.doFilter(request, response, chain);
Assert.assertTrue(invoked.get());
Assert.assertNull(MDC.get("hostname"));
Assert.assertNull(MDC.get("user"));
Assert.assertNull(MDC.get("method"));
Assert.assertNull(MDC.get("path"));
Mockito.when(request.getUserPrincipal())
.thenReturn(
new Principal() {
@Override
public String getName() {
return "name";
}
});
invoked.set(false);
chain =
new FilterChain() {
@Override
public void doFilter(ServletRequest servletRequest, ServletResponse servletResponse)
throws IOException, ServletException {
Assert.assertEquals(MDC.get("hostname"), null);
Assert.assertEquals(MDC.get("user"), "name");
Assert.assertEquals(MDC.get("method"), "METHOD");
Assert.assertEquals(MDC.get("path"), "/pathinfo");
invoked.set(true);
}
};
filter.doFilter(request, response, chain);
Assert.assertTrue(invoked.get());
HostnameFilter.HOSTNAME_TL.set("HOST");
invoked.set(false);
chain =
new FilterChain() {
@Override
public void doFilter(ServletRequest servletRequest, ServletResponse servletResponse)
throws IOException, ServletException {
Assert.assertEquals(MDC.get("hostname"), "HOST");
Assert.assertEquals(MDC.get("user"), "name");
Assert.assertEquals(MDC.get("method"), "METHOD");
Assert.assertEquals(MDC.get("path"), "/pathinfo");
invoked.set(true);
}
};
filter.doFilter(request, response, chain);
Assert.assertTrue(invoked.get());
HostnameFilter.HOSTNAME_TL.remove();
filter.destroy();
}
/**
* Handle a request.
*
* @param request
* @param response
* @throws IOException
* @throws ServletException
*/
public void doPost(HttpServletRequest request, HttpServletResponse response)
throws IOException, ServletException {
MDC.clear();
Date created = new java.util.Date();
long start = created.getTime();
String sendEncoding = request.getHeader("Accept-Encoding");
String recvEncoding = request.getHeader("Content-Encoding");
MDC.put("Accept-Encoding", sendEncoding);
MDC.put("Content-Encoding", recvEncoding);
DispatcherInterface dis = null;
BufferedReader r = null;
BufferedWriter out = null;
try {
Navajo in = null;
if (streamingMode) {
if (sendEncoding != null && sendEncoding.equals(COMPRESS_JZLIB)) {
r =
new BufferedReader(
new java.io.InputStreamReader(new InflaterInputStream(request.getInputStream())));
} else if (sendEncoding != null && sendEncoding.equals(COMPRESS_GZIP)) {
r =
new BufferedReader(
new java.io.InputStreamReader(
new java.util.zip.GZIPInputStream(request.getInputStream()), "UTF-8"));
} else {
r = new BufferedReader(request.getReader());
}
in = NavajoFactory.getInstance().createNavajo(r);
r.close();
r = null;
} else {
logger.info(
"Warning: Using non-streaming mode for "
+ request.getRequestURI()
+ ", file written: "
+ logfileIndex
+ ", total size: "
+ bytesWritten);
InputStream is = request.getInputStream();
ByteArrayOutputStream bos = new ByteArrayOutputStream();
copyResource(bos, is);
is.close();
bos.close();
byte[] bytes = bos.toByteArray();
try {
if (sendEncoding != null && sendEncoding.equals(COMPRESS_JZLIB)) {
r =
new BufferedReader(
new java.io.InputStreamReader(
new InflaterInputStream(new ByteArrayInputStream(bytes))));
} else if (sendEncoding != null && sendEncoding.equals(COMPRESS_GZIP)) {
r =
new BufferedReader(
new java.io.InputStreamReader(
new java.util.zip.GZIPInputStream(new ByteArrayInputStream(bytes)),
"UTF-8"));
} else {
r = new BufferedReader(new java.io.InputStreamReader(new ByteArrayInputStream(bytes)));
}
in = NavajoFactory.getInstance().createNavajo(r);
if (in == null) {
throw new Exception("Invalid Navajo");
}
r.close();
r = null;
} catch (Throwable t) {
// Write request to temp file.
File f = DispatcherFactory.getInstance().getTempDir();
if (f != null) {
bytesWritten += bytes.length;
logfileIndex++;
FileOutputStream fos = new FileOutputStream(new File(f, "request-" + logfileIndex));
copyResource(fos, new ByteArrayInputStream(bytes));
fos.close();
PrintWriter fw =
new PrintWriter(new FileWriter(new File(f, "exception-" + logfileIndex)));
t.printStackTrace(fw);
fw.flush();
fw.close();
}
dumHttp(request, logfileIndex, f);
throw new ServletException(t);
}
}
long stamp = System.currentTimeMillis();
int pT = (int) (stamp - start);
if (in == null) {
throw new ServletException("Invalid request.");
}
Header header = in.getHeader();
if (header == null) {
throw new ServletException("Empty Navajo header.");
}
dis = DispatcherFactory.getInstance();
if (dis == null) {
System.err.println(
"SERIOUS: No dispatcher found. The navajo context did not initialize properly, check the logs to find out why!");
return;
}
// Check for certificate.
Object certObject = request.getAttribute("javax.servlet.request.X509Certificate");
// Call Dispatcher with parsed TML document as argument.
ClientInfo clientInfo =
new ClientInfo(
request.getRemoteAddr(),
"unknown",
recvEncoding,
pT,
(recvEncoding != null
&& (recvEncoding.equals(COMPRESS_GZIP) || recvEncoding.equals(COMPRESS_JZLIB))),
(sendEncoding != null
&& (sendEncoding.equals(COMPRESS_GZIP) || sendEncoding.equals(COMPRESS_JZLIB))),
request.getContentLength(),
created);
Navajo outDoc = handleTransaction(dis, in, certObject, clientInfo);
response.setContentType("text/xml; charset=UTF-8");
response.setHeader("Accept-Ranges", "none");
response.setHeader("Connection", "close");
if (recvEncoding != null && recvEncoding.equals(COMPRESS_JZLIB)) {
response.setHeader("Content-Encoding", COMPRESS_JZLIB);
out =
new BufferedWriter(
new OutputStreamWriter(
new DeflaterOutputStream(response.getOutputStream()), "UTF-8"));
} else if (recvEncoding != null && recvEncoding.equals(COMPRESS_GZIP)) {
response.setHeader("Content-Encoding", COMPRESS_GZIP);
out =
new BufferedWriter(
new OutputStreamWriter(
new java.util.zip.GZIPOutputStream(response.getOutputStream()), "UTF-8"));
} else {
out = new BufferedWriter(response.getWriter());
}
outDoc.write(out);
out.flush();
out.close();
if (in.getHeader() != null
&& outDoc.getHeader() != null
&& !Dispatcher.isSpecialwebservice(in.getHeader().getRPCName())) {
statLogger.info(
"("
+ dis.getApplicationId()
+ "): "
+ new java.util.Date()
+ ": "
+ outDoc.getHeader().getHeaderAttribute("accessId")
+ ":"
+ in.getHeader().getRPCName()
+ "("
+ in.getHeader().getRPCUser()
+ "):"
+ (System.currentTimeMillis() - start)
+ " ms. (st="
+ (outDoc.getHeader().getHeaderAttribute("serverTime")
+ ",rpt="
+ outDoc.getHeader().getHeaderAttribute("requestParseTime")
+ ",at="
+ outDoc.getHeader().getHeaderAttribute("authorisationTime")
+ ",pt="
+ outDoc.getHeader().getHeaderAttribute("processingTime")
+ ",tc="
+ outDoc.getHeader().getHeaderAttribute("threadCount")
+ ",cpu="
+ outDoc.getHeader().getHeaderAttribute("cpuload")
+ ")"
+ " ("
+ sendEncoding
+ "/"
+ recvEncoding
+ ")"));
}
out = null;
} catch (Throwable e) {
logger.error("Error: ", e);
dumHttp(request, -1, null);
if (e instanceof FatalException) {
FatalException fe = (FatalException) e;
if (fe.getMessage().equals("500.13")) {
// Server too busy.
throw new ServletException("500.13", e);
}
}
throw new ServletException(e);
} finally {
dis = null;
if (r != null) {
try {
r.close();
} catch (Exception e) {
// NOT INTERESTED.
}
}
if (out != null) {
try {
out.close();
} catch (Exception e) {
// NOT INTERESTED.
}
}
}
}
public void init(Helper helper) {
this.helper = helper;
helper.setSteps(5);
final ImportConfig config = new ImportConfig();
final String sessionUuid = helper.getEventContext().getCurrentSessionUuid();
if (!(location instanceof ManagedImportLocationI)) {
throw helper.cancel(
new ERR(), null, "bad-location", "location-type", location.getClass().getName());
}
ManagedImportLocationI managedLocation = (ManagedImportLocationI) location;
logPath = managedLocation.getLogFile();
logFilename = logPath.getFullFsPath();
MDC.put("fileset", logFilename);
file = ((ManagedImportLocationI) location).getTarget();
try {
sf = reg.getInternalServiceFactory(sessionUuid, "unused", 3, 1, clientUuid);
store = new OMEROMetadataStoreClient();
store.setCurrentLogFile(logFilename, token);
store.initialize(sf);
registerKeepAlive();
fileName = file.getFullFsPath();
shortName = file.getName();
format = null;
usedFiles = new String[] {fileName};
open(reader, store, file);
format = reader.getFormat();
if (reader.getUsedFiles() != null) {
usedFiles = reader.getUsedFiles();
}
if (usedFiles == null) {
throw new NullPointerException("usedFiles must be non-null");
}
// Process all information which has been passed in as annotations
detectKnownAnnotations();
// Now that we've possibly updated the settings object, copy out
// all the values needed by import.
userSpecifiedTarget = settings.userSpecifiedTarget;
userSpecifiedName =
settings.userSpecifiedName == null ? null : settings.userSpecifiedName.getValue();
userSpecifiedDescription =
settings.userSpecifiedDescription == null
? null
: settings.userSpecifiedDescription.getValue();
userPixels = settings.userSpecifiedPixels;
annotationList = settings.userSpecifiedAnnotationList;
doThumbnails = settings.doThumbnails == null ? true : settings.doThumbnails.getValue();
noStatsInfo = settings.noStatsInfo == null ? false : settings.noStatsInfo.getValue();
IFormatReader baseReader = reader.getImageReader().getReader();
if (log.isInfoEnabled()) {
log.info("File format: " + format);
log.info("Base reader: " + baseReader.getClass().getName());
}
notifyObservers(new ImportEvent.LOADED_IMAGE(shortName, 0, 0, 0));
formatString = baseReader.getClass().getSimpleName();
formatString = formatString.replace("Reader", "");
} catch (Cancel c) {
throw c;
} catch (Throwable t) {
throw helper.cancel(new ERR(), t, "error-on-init");
} finally {
MDC.clear();
}
}
@Before
public void setUp() throws Exception {
smtpServer = new GreenMail();
smtpServer.start();
MDC.clear();
}
/* (non-Javadoc)
* @see org.springframework.ws.server.EndpointInterceptor#afterCompletion(org.springframework.ws.context.MessageContext, java.lang.Object, java.lang.Exception)
*/
@Override
public void afterCompletion(MessageContext messageContext, Object endpoint, Exception ex)
throws Exception {
MDC.clear();
}