/** Método de ejecución del hilo. */
public void run() {
running = true;
while (!stopped) { // El hilo sigue corriendo.
if (done) { // We are waiting for a task now.
synchronized (this) {
try {
if (logger.isDebugEnabled())
logger.debug("Wait until we get a task to execute. Id: " + this.toString());
this.wait(); // Wait until we get a task to execute.
} catch (InterruptedException e) {
stopped = true;
logger.error("Run InterruptedException =" + this.getAdress(), e);
}
}
} else { // There is a task....let us execute it.
try {
if (logger.isDebugEnabled()) logger.debug("Se ejecuta Id: " + this.toString());
execute();
} catch (Exception e) {
logger.error("#### Run exception =" + this.getAdress(), e);
} finally {
reset();
}
}
}
}
public void update(DbConnection db) throws ISicresRPAdminDAOException {
DynamicTable tableInfo = new DynamicTable();
DynamicRows rowsInfo = new DynamicRows();
DynamicRow rowInfo = new DynamicRow();
SicresUserPermisosTabla table = new SicresUserPermisosTabla();
try {
if (logger.isDebugEnabled()) {
logger.debug("Actualizando scr_usrperms.");
}
tableInfo.setTableObject(table);
tableInfo.setClassName(table.getClass().getName());
tableInfo.setTablesMethod("getTableName");
tableInfo.setColumnsMethod("getUpdateColumnNames");
rowInfo.addRow(this);
rowInfo.setClassName(this.getClass().getName());
rowInfo.setValuesMethod("update");
rowsInfo.add(rowInfo);
DynamicFns.update(db, table.getById(getIdUsr()), tableInfo, rowsInfo);
if (logger.isDebugEnabled()) {
logger.debug("Actualizado scr_usrperms.");
}
} catch (Exception e) {
logger.error("Error actualizando scr_usrperms", e);
throw new ISicresRPAdminDAOException(ISicresRPAdminDAOException.SCR_USRPERMS_UPDATE);
}
}
public void add(DbConnection db) throws ISicresRPAdminDAOException {
DynamicTable tableInfo = new DynamicTable();
DynamicRows rowsInfo = new DynamicRows();
DynamicRow rowInfo = new DynamicRow();
SicresUserPermisosTabla table = new SicresUserPermisosTabla();
try {
if (logger.isDebugEnabled()) {
logger.debug("Añadiendo scr_usrperms...");
}
tableInfo.setTableObject(table);
tableInfo.setClassName(table.getClass().getName());
tableInfo.setTablesMethod("getTableName");
tableInfo.setColumnsMethod("getAllColumnNames");
rowInfo.addRow(this);
rowInfo.setClassName(this.getClass().getName());
rowInfo.setValuesMethod("insert");
rowsInfo.add(rowInfo);
DynamicFns.insert(db, tableInfo, rowsInfo);
if (logger.isDebugEnabled()) {
logger.debug("scr_usrperms añadida.");
}
} catch (Exception e) {
logger.error("Error añadiendo scr_usrperms.", e);
throw new ISicresRPAdminDAOException(ISicresRPAdminDAOException.SCR_USRPERMS_INSERT, e);
}
}
/**
* Execute an OS command and return the result of stdout.
*
* @param command Command to run
* @return Returns output of the command in a string
* @throws ReplicatorException Thrown if command execution fails
*/
public String exec(String command) throws ReplicatorException {
String[] osArray = {"sh", "-c", command};
ProcessExecutor pe = new ProcessExecutor();
pe.setCommands(osArray);
if (logger.isDebugEnabled()) {
logger.debug("Executing OS command: " + command);
}
pe.run();
if (logger.isDebugEnabled()) {
logger.debug("OS command stdout: " + pe.getStdout());
logger.debug("OS command stderr: " + pe.getStderr());
logger.debug("OS command exit value: " + pe.getExitValue());
}
if (!pe.isSuccessful()) {
logger.error(
"OS command failed: command="
+ command
+ " rc="
+ pe.getExitValue()
+ " stdout="
+ pe.getStdout()
+ " stderr="
+ pe.getStderr());
throw new ReplicatorException("OS command failed: command=" + command);
}
return pe.getStdout();
}
/**
* Creates a new {@link UML2VoidReturnParameter} instance.
*
* @param dslOperation the {@link org.eclipse.uml2.uml.Operation} that is adopted by this class.
* @param factory The {@link UML2AdapterFactory} used to create nested elements.
* @generated NOT
*/
public UML2VoidReturnParameter(
org.eclipse.uml2.uml.Operation dslOperation, UML2AdapterFactory factory) {
/* Eventually log the entry into this method. */
if (LOGGER.isDebugEnabled()) {
String msg;
msg = "UML2VoidReturnParameter("; // $NON-NLS-1$ //$NON-NLS-2$
msg += "dslOperation = " + dslOperation; // $NON-NLS-1$ //$NON-NLS-2$
msg += ", factory = " + factory; // $NON-NLS-1$ //$NON-NLS-2$
msg += ") - enter"; // $NON-NLS-1$ //$NON-NLS-2$
LOGGER.debug(msg);
}
// no else.
/* Initialize adapted operation. */
this.dslOperation = dslOperation;
this.factory = factory;
/* Eventually log the exit from this method. */
if (LOGGER.isDebugEnabled()) {
LOGGER.debug("UML2Parameter() - exit"); // $NON-NLS-1$
}
// no else.
}
public ModelAndView searchProjects(
HttpServletRequest request, HttpServletResponse response, ProjectVo command)
throws Exception {
if (logger.isDebugEnabled()) {
logger.debug("searchProjects(HttpServletRequest, HttpServletResponse, ProjectVo) - start");
}
modelAndView = new ModelAndView("volunteer/viewProjectList"); // jsp page
List<CodeLookupVo> projectCodeList =
CodeLookupUtil.getCodeListByCategory(VMSConstants.PROJECT_STATUS);
modelAndView.addObject("projectCodeList", projectCodeList);
List<ProjectVo> projectList = projectManagementService.getProjectsbyProjectVo(command);
logger.debug("The project size is" + projectList.size());
modelAndView.addObject("projectList", projectList);
modelAndView.addObject("command", command);
PagedListHolder projectPagedListHolder = new PagedListHolder(projectList);
if (!projectList.isEmpty()) {
int page = ServletRequestUtils.getIntParameter(request, "p", 0);
projectPagedListHolder.setPage(page);
projectPagedListHolder.setPageSize(VMSConstants.MAX_PAGE_SIZE);
}
modelAndView.addObject("pagedListHolder", projectPagedListHolder);
if (logger.isDebugEnabled()) {
logger.debug("searchProjects(HttpServletRequest, HttpServletResponse, ProjectVo) - end");
}
return modelAndView;
}
/**
* Gets the events fired from SynthesisQueue thread and it forwards them. to
* ImplementationPlatform it also sets the appropriate flags
*
* @param event the event.
*/
public void outputStatusChanged(final SynthesizedOutputEvent event) {
if (event.isType(OutputStartedEvent.EVENT_TYPE)) {
final OutputStartedEvent outputStartedEvent = (OutputStartedEvent) event;
final SpeakableText startedSpeakable = outputStartedEvent.getSpeakable();
if (LOGGER.isDebugEnabled()) {
LOGGER.debug("output started " + startedSpeakable);
}
isBusy = true;
fireOutputStarted(startedSpeakable);
} else if (event.isType(OutputEndedEvent.EVENT_TYPE)) {
final OutputEndedEvent outputEndedEvent = (OutputEndedEvent) event;
final SpeakableText endedSpeakable = outputEndedEvent.getSpeakable();
if (LOGGER.isDebugEnabled()) {
LOGGER.debug("audio playing ended");
}
isBusy = false;
fireOutputEnded(endedSpeakable);
} else if (event.isType(QueueEmptyEvent.EVENT_TYPE)) {
if (LOGGER.isDebugEnabled()) {
LOGGER.debug("output queue is empty");
}
speakableQueueEmpty = true;
fireQueueEmpty();
synchronized (emptyLock) {
emptyLock.notifyAll();
}
}
}
/**
* @param sort, the column number to sort
* @return the new xml string of the array sorted
* @throws NumberFormatException
* <p>The sort of this array is cyclic : it begins by UNSORTED, then if the user click again
* the array will be <br>
* sorted ASCENDING, then DESCENDING, and finally UNSORTED.
*/
private String sortColomn(String sort) throws NumberFormatException {
if (tableModel != null && sorter != null) {
int sortingColumn = new Integer(sort).intValue();
int sortingStatus = -2;
if (logger.isDebugEnabled()) {
logger.debug("GetTableServlet: Sort column :" + sortingColumn);
}
if (sorter.getSortingStatus(sortingColumn) == TableSorter.ASCENDING) {
for (int i = 0; i < sorter.getColumnCount(); i++) {
sorter.setSortingStatus(i, TableSorter.NOT_SORTED);
}
sorter.setSortingStatus(sortingColumn, TableSorter.DESCENDING);
sortingStatus = TableSorter.DESCENDING;
} else if (sorter.getSortingStatus(sortingColumn) == TableSorter.DESCENDING) {
for (int i = 0; i < sorter.getColumnCount(); i++) {
sorter.setSortingStatus(i, TableSorter.NOT_SORTED);
}
sorter.setSortingStatus(sortingColumn, TableSorter.NOT_SORTED);
sortingStatus = TableSorter.NOT_SORTED;
} else if (sorter.getSortingStatus(sortingColumn) == TableSorter.NOT_SORTED) {
for (int i = 0; i < sorter.getColumnCount(); i++) {
sorter.setSortingStatus(i, TableSorter.NOT_SORTED);
}
sorter.setSortingStatus(sortingColumn, TableSorter.ASCENDING);
sortingStatus = TableSorter.ASCENDING;
}
if (logger.isDebugEnabled()) {
logger.debug("GetTableServlet: sorting status " + sortingStatus);
}
return toJSon(sortingColumn, sortingStatus);
}
return null;
}
@Override
public boolean equals(final Object obj) {
try {
if ((obj != null) && (obj instanceof FlurKey)) {
final FlurKey other = (FlurKey) obj;
if (((gemarkungsId != null)
&& (other.getGemarkungsId() != null)
&& gemarkungsId.equals(other.getGemarkungsId()))
|| ((gemarkungsId == null) && (other.getGemarkungsId() == null))) {
if (LOG.isDebugEnabled()) {
LOG.debug("Gemarkung stimmt überein");
}
if (((flurId != null) && (other.getFlurId() != null) && flurId.equals(other.getFlurId()))
|| ((flurId == null) && (other.getFlurId() == null))) {
if (LOG.isDebugEnabled()) {
LOG.debug("Alle Felder stimmen überein --> equals");
}
return true;
}
}
}
return false;
} catch (Exception ex) {
LOG.error("Fehler in equals Flurkey", ex);
}
return false;
}
protected synchronized void doCancel() {
if (isTerminated()) {
if (LOG.isDebugEnabled()) {
LOG.debug(
"Receiving Cancel, but is already terminated. callID:"
+ (getSipSession() != null ? getSipSession().getCallId() : ""));
}
} else if (isNoAnswered()) {
if (LOG.isDebugEnabled()) {
LOG.debug(
"Receiving Cancel, not answered. terminating, callID"
+ (getSipSession() != null ? getSipSession().getCallId() : ""));
}
if (_joinDelegate != null) {
_joinDelegate.done(JoinCompleteEvent.Cause.CANCELED, new CanceledException());
}
this.setSIPCallState(SIPCall.State.DISCONNECTED);
terminate(CallCompleteEvent.Cause.CANCEL, null, null);
} else {
if (LOG.isDebugEnabled()) {
LOG.debug(
"Receiving Cancel, but is already answered. terminating, callID"
+ (getSipSession() != null ? getSipSession().getCallId() : ""));
}
this.setSIPCallState(SIPCall.State.DISCONNECTED);
terminate(CallCompleteEvent.Cause.CANCEL, null, null);
}
}
/* (non-Javadoc)
* @see org.eclipse.jface.viewers.ViewerDropAdapter#performDrop(java.lang.Object)
*/
@Override
public boolean performDrop(Object data) {
if (LOG.isDebugEnabled()) {
LOG.debug("performDrop...");
}
boolean success = false;
try {
for (DropPerformer adapter : performerSet) {
if (adapter.isActive()) {
if (adapter.performDrop(data, getCurrentTarget(), getViewer())) {
success = true;
if (LOG.isDebugEnabled()) {
LOG.debug("performDrop, success: " + adapter);
}
}
} else if (LOG.isDebugEnabled()) {
LOG.debug("performDrop, adapter is not active: " + adapter);
}
}
} catch (RuntimeException e) {
LOG.error("Error while performing drop.", e);
throw e;
}
return success;
}
@Override
public Status investigate(final long hostId) {
final HostVO host = _hostDao.findById(hostId);
if (host == null) {
return null;
}
final Enumeration<Investigator> en = _investigators.enumeration();
Status hostState = null;
Investigator investigator = null;
while (en.hasMoreElements()) {
investigator = en.nextElement();
hostState = investigator.isAgentAlive(host);
if (hostState != null) {
if (s_logger.isDebugEnabled()) {
s_logger.debug(
investigator.getName()
+ " was able to determine host "
+ hostId
+ " is in "
+ hostState.toString());
}
return hostState;
}
if (s_logger.isDebugEnabled()) {
s_logger.debug(
investigator.getName() + " unable to determine the state of the host. Moving on.");
}
}
return null;
}
protected Status testIpAddress(Long hostId, String testHostIp) {
try {
Answer pingTestAnswer = _agentMgr.send(hostId, new PingTestCommand(testHostIp));
if (pingTestAnswer == null) {
if (s_logger.isDebugEnabled()) {
s_logger.debug("host (" + testHostIp + ") returns null answer");
}
return null;
}
if (pingTestAnswer.getResult()) {
if (s_logger.isDebugEnabled()) {
s_logger.debug(
"host (" + testHostIp + ") has been successfully pinged, returning that host is up");
}
// computing host is available, but could not reach agent, return false
return Status.Up;
} else {
if (s_logger.isDebugEnabled()) {
s_logger.debug(
"host (" + testHostIp + ") cannot be pinged, returning null ('I don't know')");
}
return null;
}
} catch (AgentUnavailableException e) {
return null;
} catch (OperationTimedoutException e) {
return null;
}
}
@Override
public boolean waitMsecs(int msecs) {
if (msecs < 0) {
throw new RuntimeException("waitMsecs: msecs cannot be negative!");
}
long maxMsecs = time.getMilliseconds() + msecs;
int curMsecTimeout = 0;
lock.lock();
try {
while (!eventOccurred) {
curMsecTimeout = Math.min(msecs, msecPeriod);
if (LOG.isDebugEnabled()) {
LOG.debug("waitMsecs: Wait for " + curMsecTimeout);
}
try {
boolean signaled = cond.await(curMsecTimeout, TimeUnit.MILLISECONDS);
if (LOG.isDebugEnabled()) {
LOG.debug("waitMsecs: Got timed signaled of " + signaled);
}
} catch (InterruptedException e) {
throw new IllegalStateException(
"waitMsecs: Caught interrupted " + "exception on cond.await() " + curMsecTimeout, e);
}
if (time.getMilliseconds() > maxMsecs) {
return false;
}
msecs = Math.max(0, msecs - curMsecTimeout);
progressable.progress(); // go around again
}
} finally {
lock.unlock();
}
return true;
}
/**
* Function to try and obtain a handler using the name of the current SOAP service and operation.
*
* @param opName the name of the operation
* @return OperationHandler to handle the operation
* @throws AxisFault
*/
private OperationHandler getHandler(String serviceName, String operationName) {
if (serviceName == null) {
if (log.isDebugEnabled()) {
log.debug("Service Name was null!");
}
return null;
}
if (operationName == null) {
if (log.isDebugEnabled()) {
log.debug("Operation Name was null!");
}
return null;
}
Map<String, OperationHandler> handlers = serviceHandlers.get(serviceName);
if (handlers == null) {
if (log.isDebugEnabled()) {
log.debug("No Service Handlers found for: " + serviceName);
}
return null;
}
OperationHandler handler = handlers.get(operationName);
if (handler == null) {
if (log.isDebugEnabled()) {
log.debug("Handler not found for: " + serviceName + "/" + operationName);
}
}
return handler;
}
protected DomainRouterVO waitRouter(final DomainRouterVO router) {
DomainRouterVO vm = _routerDao.findById(router.getId());
if (s_logger.isDebugEnabled()) {
s_logger.debug("Router " + router.getInstanceName() + " is not fully up yet, we will wait");
}
while (vm.getState() == State.Starting) {
try {
Thread.sleep(1000);
} catch (final InterruptedException e) {
}
// reload to get the latest state info
vm = _routerDao.findById(router.getId());
}
if (vm.getState() == State.Running) {
if (s_logger.isDebugEnabled()) {
s_logger.debug("Router " + router.getInstanceName() + " is now fully up");
}
return router;
}
s_logger.warn(
"Router " + router.getInstanceName() + " failed to start. current state: " + vm.getState());
return null;
}
private static PirsfDatRecord parseSubFamilyLine(String line) {
PirsfDatRecord instance = null;
String[] chunks = line.split(" ");
for (int i = 0; i < chunks.length; i++) {
if (i == 0) {
if (chunks[i].length() > 1) {
final String modelAccession = chunks[i].substring(1);
instance = new PirsfDatRecord(modelAccession);
if (LOGGER.isDebugEnabled()) {
LOGGER.debug("Found a new model accession with sub families: " + modelAccession);
}
}
} else if (i > 1) {
final String subfamily = chunks[i];
if (LOGGER.isDebugEnabled()) {
LOGGER.debug(
"Found a new subfamily named "
+ subfamily
+ " for model accession: "
+ instance.getModelAccession());
}
instance.addSubFamily(subfamily);
}
}
return instance;
}
public static synchronized Properties getConfig() {
if (config == null) {
config = new Properties();
InputStream is = null;
try {
is = DAOConfig.class.getClassLoader().getResourceAsStream("dao_config.properties");
config.load(is);
} catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug(e.getMessage());
}
throw new RuntimeException("failed to read dao configuration file");
} finally {
if (is != null) {
try {
is.close();
} catch (IOException e) {
if (log.isDebugEnabled()) {
log.debug(e.getMessage());
}
}
}
}
}
return config;
}
public ModelAndView postFeedback(
HttpServletRequest request, HttpServletResponse response, ProjectFeedbackVo feedbackVo)
throws Exception {
if (logger.isDebugEnabled()) {
logger.debug(
"postExperienceAndFb(HttpServletRequest, HttpServletResponse, ProjectInfoVo) - start");
}
ProjectVo projectVo = (ProjectVo) modelAndView.getModel().get("projectVo");
modelAndView = new ModelAndView("volunteer/viewProject");
if (!StringUtil.isNullOrEmpty(feedbackVo.getTitle())) {
feedbackVo.setPrjId(projectVo.getPrjId());
projectFeedbackService.createProjectFeedback(feedbackVo);
modelAndView.addObject(
"riMsg",
Messages.getString("message.common.submitreview.msg", new String[] {"Project Feedback"}));
}
List<ProjectMemberVo> memberList =
memberManagementService.getMemberListbyProject(projectVo.getPrjId());
List<ProjectExperienceVo> experienceList =
projectExperienceService.getProjectExperienceListbyProjectId(projectVo.getPrjId());
List<ProjectFeedbackVo> feedbackList =
projectFeedbackService.getProjectFeedbackListbyProjectId(projectVo.getPrjId());
PagedListHolder feedbackPagedListHolder = new PagedListHolder(feedbackList);
if (!feedbackList.isEmpty()) {
int page = ServletRequestUtils.getIntParameter(request, "p1", 0);
feedbackPagedListHolder.setPage(page);
feedbackPagedListHolder.setPageSize(100);
}
PagedListHolder exPagedListHolder = new PagedListHolder(experienceList);
if (!experienceList.isEmpty()) {
int page = ServletRequestUtils.getIntParameter(request, "p2", 0);
exPagedListHolder.setPage(page);
exPagedListHolder.setPageSize(100);
}
modelAndView.addObject("fbPagedListHolder", feedbackPagedListHolder);
modelAndView.addObject("exPagedListHolder", exPagedListHolder);
modelAndView.addObject("memberList", memberList);
modelAndView.addObject("experienceList", experienceList);
modelAndView.addObject("feedbackList", feedbackList);
modelAndView.addObject("projectVo", projectVo);
modelAndView.addObject("feedbackVo", new ProjectFeedbackVo());
modelAndView.addObject("experienceVo", new ProjectExperienceVo());
if (logger.isDebugEnabled()) {
logger.debug(
"postExperienceAndFb(HttpServletRequest, HttpServletResponse, ProjectInfoVo) - end");
}
return modelAndView;
}
public Integer getRegisterDeptOfic(String guid, String entidad) throws SecurityException {
Transaction tran = null;
Integer deptId = null;
try {
Session session = HibernateUtil.currentSession(entidad);
// tran = session.beginTransaction();
// Obtener el grupo ldap de la tabla de grupos
List list = ISicresQueries.getUserLdapPgrp(session, guid);
if (list != null && !list.isEmpty()) {
Iuserldapgrphdr udeptGrpHdr = (Iuserldapgrphdr) list.get(0);
if (log.isDebugEnabled()) {
log.debug(" Iuserldapgrphdr [" + udeptGrpHdr + "] con el log [" + log + "]");
}
// Obtener el departamento invesdoc asociado al grupo ldap
list = ISicresQueries.getUserDeptHdr(session, udeptGrpHdr.getId());
if (list != null && !list.isEmpty()) {
Iuserdepthdr udeptHdr = (Iuserdepthdr) list.get(0);
if (log.isDebugEnabled()) {
log.debug(" Iuserdepthdr [" + udeptHdr + "] con el log [" + log + "]");
}
deptId = udeptHdr.getId();
}
}
// HibernateUtil.commitTransaction(tran);
} catch (Exception e) {
// HibernateUtil.rollbackTransaction(tran);
log.error("Impossible to verify user with guid[" + guid + "]", e);
throw new SecurityException(SecurityException.ERROR_USER_NOTFOUND);
} /*
* finally { HibernateUtil.closeSession(); }
*/
return deptId;
}
private void validateConfig() throws ConfigXMLParsingException {
if (logger.isDebugEnabled()) {
logger.debug("validateConfig() - start"); // $NON-NLS-1$
}
assertConfigForTag(localEntityId == null, "LOCAL_ENTITY_ID");
assertConfigForTag(postAttrSAML == null, "SAML_POST_ATTRIBUTE_NAME");
if (SAMLTokenEncrypted) validateSAMLDecryptorKey("SAML_TOKEN_ENCRYPTION");
validateDecryptKey("SAML_ENCRYPTED_ASSERTION_DECRYPTOR");
// validateSignerKeyKey("SAML_SIGNATURE_VERIFIER");
assertConfigForTag(metadataProvider == null, "SAML_METADATA_PROVIDER");
assertConfigForTag(idpURL == null, "IDP_URL");
assertConfigForTag(verifySignature == null, "ASSERTION_SIGNATURE_VERIFICATION");
if (contextDataExtractor != null) {
assertConfigForAttribute(contextDataStore == null, "ATTRIBUTE_NAME", "STOREAS");
assertConfigForAttribute(
contextDataStore != ContextDataStoreType.none && contextDataStoreParam == null,
"ATTRIBUTE_NAME",
"STOREIN");
}
createDefaultInvalidSessionHandler(invalidSessionHandler == null);
createDefaultErrorHandler(errorHandler == null);
if (logger.isDebugEnabled()) {
logger.debug("validateConfig() - end"); // $NON-NLS-1$
}
}
/**
* return the first playable for this session
*
* @return the first Playable
*/
protected Playable getFirstPlayable() {
if (logger.isDebugEnabled()) {
logger.debug("calling getFirstPlayable()");
}
Playable playable = null;
PlayList playlist = this.getPlayList();
if (playlist != null) {
if (playlist.size() > 0) {
Object o = playlist.get(0);
if (o instanceof Playable) {
playable = (Playable) o;
}
} else {
if (logger.isDebugEnabled()) {
logger.debug(
"the size of the playlist is " + playlist.size() + " --> could not provide first");
}
}
}
if (logger.isDebugEnabled()) {
logger.debug("end of calling getFirstPlayable() returns " + playable);
}
return playable;
}
public Application get(final URI uri) throws InvalidApplicationException, RedirectException {
Application app = getCached(uri);
if (LOG.isDebugEnabled()) {
LOG.debug(
toString() + " found app=" + app + " for url=" + uri + ",_cache.size=" + _cache.size());
}
if (app == null) {
app = findApplication(uri);
putCached(uri, app);
if (LOG.isDebugEnabled()) {
LOG.debug(
toString()
+ " cached app="
+ app
+ " for url="
+ uri
+ ",_cache.size="
+ _cache.size());
}
} else {
Utils.setLogContext(app, null);
LOG.info(app + " has been found.");
}
return app;
}
@Override
public void setup(SourceResolver resolver, Map objectModel, String src, Parameters par) {
if (log.isDebugEnabled()) log.debug("begin setup");
try {
super.setup(resolver, objectModel, src, par);
ContextManager cm = (ContextManager) this.manager.lookup(ContextManager.ROLE);
try {
if (cm.hasSessionContext()) {
cm.deleteContext("authentication");
}
} catch (Exception exe) {
}
userid = par.getParameter("username", null);
password = par.getParameter("password", null);
try {
String jaasRealmTmp = par.getParameter("jaasRealm", null);
if (jaasRealmTmp != null && !jaasRealmTmp.equalsIgnoreCase("")) {
jaasRealm = jaasRealmTmp;
}
} catch (Exception se) {
}
try {
String toUpper = par.getParameter("toUpperCase", null);
if (toUpper != null && !toUpper.equalsIgnoreCase("true")) {
userid = userid.toUpperCase();
}
} catch (Exception se) {
}
if (log.isDebugEnabled()) log.debug("trying to login as " + userid + " on the webpage");
} catch (Exception ex) {
new ProcessingException(ex.getMessage());
}
if (log.isDebugEnabled()) log.debug("end setup");
}
public List<TemplateNode> getChildren(NodeRef node, String types) {
List<TemplateNode> results = new ArrayList<TemplateNode>();
PagedResults pagedDocs = queryChildren(node, types);
CMISResultSet resultSet = (CMISResultSet) pagedDocs.getResult();
for (NodeRef nodeRef : resultSet.getNodeRefs()) {
TemplateNode tnode =
new TemplateNode(nodeRef, serviceRegistry, imageResolver.getImageResolver());
if (tnode.getIsDocument()) {
if (logger.isDebugEnabled()) {
logger.debug("add result :" + tnode.getNodeRef());
}
results.add(tnode);
}
}
PagedResults pagedFolders = queryChildren(node, FOLDER);
CMISResultSet resultSetFolders = (CMISResultSet) pagedFolders.getResult();
for (NodeRef nodeRef : resultSetFolders.getNodeRefs()) {
// folder
if (logger.isDebugEnabled()) {
logger.debug("search in folder ..." + nodeRef);
}
List<TemplateNode> tmp = getChildren(nodeRef, types);
results.addAll(tmp);
}
return results;
}
public Object getDAO(String key, Connection conn) throws FactoryException {
if (logger.isDebugEnabled()) {
logger.debug("getDAO(String, Connection) - start");
}
IDAO dao = null;
try {
if (null != key) {
Class cls = (Class) this.daoInstances.get(key);
if (null != cls) {
dao = (IDAO) ClassHelper.newInstance(cls.getName());
if (null != conn && !conn.isClosed()) dao.setConnection(conn);
}
}
} catch (Exception e) {
logger.error("getDAO(String, Connection)", e);
FactoryException fe = new FactoryException(e);
throw fe;
}
if (null == dao) {
FactoryException fe = new FactoryException("申请的ｄａｏ没有注册到系统中�?");
throw fe;
}
if (logger.isDebugEnabled()) {
logger.debug("getDAO(String, Connection) - end");
}
return dao;
}
public void load(int identificador, DbConnection db) throws ISicresRPAdminDAOException {
DynamicTable tableInfo = new DynamicTable();
DynamicRows rowsInfo = new DynamicRows();
DynamicRow rowInfo = new DynamicRow();
SicresUserPermisosTabla table = new SicresUserPermisosTabla();
if (logger.isDebugEnabled()) {
logger.debug("Obteniendo datos de scr_usrperms...");
}
try {
tableInfo.setTableObject(table);
tableInfo.setClassName(table.getClass().getName());
tableInfo.setTablesMethod("getTableName");
tableInfo.setColumnsMethod("getAllColumnNames");
rowInfo.addRow(this);
rowInfo.setClassName(this.getClass().getName());
rowInfo.setValuesMethod("loadAllValues");
rowsInfo.add(rowInfo);
if (!DynamicFns.select(db, table.getById(identificador), tableInfo, rowsInfo)) {
throw new ISicresRPAdminDAOException(ISicresRPAdminDAOException.SCR_USRPERMS_NOT_FOUND);
}
if (logger.isDebugEnabled()) {
logger.debug("Datos de scr_usrperms obtenidos.");
}
} catch (Exception e) {
if (e instanceof ISicresRPAdminDAOException)
logger.warn("No se ha encontrado fila en scr_usrperms");
else logger.error("Error obteniendo datos de scr_usrperms");
throw new ISicresRPAdminDAOException(ISicresRPAdminDAOException.EXC_GENERIC_EXCEPCION, e);
}
}
public void setInitializationData(IConfigurationElement config, String propertyName, Object data)
throws CoreException {
beanRef = (String) data;
if (logger.isDebugEnabled()) {
logger.debug(
"Initializing bean '" + beanRef + "' for extension " + config.getAttribute("id"));
}
try {
bean = getContainerInstance().getBean(beanRef);
if (logger.isDebugEnabled()) {
logger.debug("Got bean of class '" + bean.getClass().getName() + "'");
}
} catch (Exception e) {
logger.error(
"Unable to get bean instance for bean id '"
+ beanRef
+ "' of class '"
+ (bean != null ? bean.getClass().getName() : "n/a")
+ "'",
e);
ForceExceptionUtils.throwNewCoreException(e);
}
}
/**
* This method is called to execute the action that the StepInstance must perform.
*
* @param stepInstance containing the parameters for executing.
* @param temporaryFileDirectory
* @throws Exception could be anything thrown by the execute method.
*/
@Override
public void execute(StepInstance stepInstance, String temporaryFileDirectory) {
// Retrieve raw results for protein range.
Map<String, RawProtein<PfamHmmer3RawMatch>> rawMatches =
rawMatchDAO.getRawMatchesForProteinIdsInRange(
stepInstance.getBottomProtein(),
stepInstance.getTopProtein(),
getSignatureLibraryRelease());
if (LOGGER.isDebugEnabled()) {
LOGGER.debug("PfamA: Retrieved " + rawMatches.size() + " proteins to post-process.");
int matchCount = 0;
for (final RawProtein rawProtein : rawMatches.values()) {
matchCount += rawProtein.getMatches().size();
}
LOGGER.debug("PfamA: A total of " + matchCount + " raw matches.");
}
// Post process
try {
Map<String, RawProtein<PfamHmmer3RawMatch>> filteredMatches =
getPostProcessor().process(rawMatches);
if (LOGGER.isDebugEnabled()) {
LOGGER.debug(
"PfamA: " + filteredMatches.size() + " proteins passed through post processing.");
int matchCount = 0;
for (final RawProtein rawProtein : filteredMatches.values()) {
matchCount += rawProtein.getMatches().size();
}
LOGGER.debug("PfamA: A total of " + matchCount + " matches PASSED.");
}
filteredMatchDAO.persist(filteredMatches.values());
} catch (IOException e) {
throw new IllegalStateException(
"IOException thrown when attempting to post process filtered matches.", e);
}
}
/**
* Resolve a constraint against an RDF/XML document.
*
* <p>Resolution is by filtration of a URL stream, and thus very slow.
*/
public Resolution resolve(Constraint constraint) throws QueryException {
if (logger.isDebugEnabled()) {
logger.debug("Resolve " + constraint);
}
// check the model
ConstraintElement modelElement = constraint.getModel();
if (modelElement instanceof Variable) {
if (logger.isDebugEnabled()) logger.debug("Ignoring solutions for " + constraint);
return new EmptyResolution(constraint, false);
} else if (!(modelElement instanceof LocalNode)) {
throw new QueryException("Failed to localize Lucene Graph before resolution " + constraint);
}
/* temporary hack because $_from is not resolved before transformation occurs, and hence
* no LuceneConstraint's are created when doing ... from <lucene-model> where ... .
*/
if (!(constraint instanceof LuceneConstraint)) {
constraint = new LuceneConstraint(constraint);
}
// generate the tuples
try {
FullTextStringIndex stringIndex =
getFullTextStringIndex(((LocalNode) modelElement).getValue());
return new FullTextStringIndexTuples(
stringIndex, (LuceneConstraint) constraint, resolverSession);
} catch (IOException ioe) {
throw new QueryException("Failed to open string index", ioe);
} catch (FullTextStringIndexException ef) {
throw new QueryException("Query failed against string index\n" + new StackTrace(ef));
} catch (TuplesException te) {
throw new QueryException("Failed to query string index", te);
}
}