Java Code Examples for org.slf4j.MDC#MDCCloseable

@Override
@Transactional
public void deleteChain(WeblichtChain aChain) throws IOException
{
    entityManager.remove(
            entityManager.contains(aChain) ? aChain : entityManager.merge(aChain));
    
    File gaz = getChainFile(aChain);
    if (gaz.exists()) {
        gaz.delete();
    }
    
    try (MDC.MDCCloseable closable = MDC.putCloseable(Logging.KEY_PROJECT_ID,
            String.valueOf(aChain.getRecommender().getProject().getId()))) {
        log.info("Removed chain [{}] from recommender [{}]({}) in project [{}]({})",
                aChain.getName(), aChain.getRecommender().getName(),
                aChain.getRecommender().getId(),
                aChain.getRecommender().getProject().getName(),
                aChain.getRecommender().getProject().getId());
    }
}
 

@Override
@Transactional
public void createLayer(AnnotationLayer aLayer)
{
    if (isNull(aLayer.getId())) {
        entityManager.persist(aLayer);
    }
    else {
        entityManager.merge(aLayer);
    }
    
    try (MDC.MDCCloseable closable = MDC.putCloseable(Logging.KEY_PROJECT_ID,
            String.valueOf(aLayer.getProject().getId()))) {
        Project project = aLayer.getProject();
        log.info("Created layer [{}]({}) in project [{}]({})", aLayer.getName(),
                aLayer.getId(), project.getName(), project.getId());
    }
}
 

@Override
@Transactional
public void createTagSet(TagSet aTagSet)
{
    if (isNull(aTagSet.getId())) {
        entityManager.persist(aTagSet);
    }
    else {
        entityManager.merge(aTagSet);
    }
    
    try (MDC.MDCCloseable closable = MDC.putCloseable(Logging.KEY_PROJECT_ID,
            String.valueOf(aTagSet.getProject().getId()))) {
        Project project = aTagSet.getProject();
        log.info("Created tagset [{}]({}) in project [{}]({})", aTagSet.getName(),
                aTagSet.getId(), project.getName(), project.getId());
    }
}
 

@Override
public void upgradeCas(CAS aCas, SourceDocument aSourceDocument, String aUser)
    throws UIMAException, IOException
{
    upgradeCas(aCas, aSourceDocument.getProject());
    
    try (MDC.MDCCloseable closable = MDC.putCloseable(
            Logging.KEY_PROJECT_ID,
            String.valueOf(aSourceDocument.getProject().getId()))) {
        Project project = aSourceDocument.getProject();
        log.info(
                "Upgraded CAS of user [{}] for "
                        + "document [{}]({}) in project [{}]({})",
                aUser, aSourceDocument.getName(), aSourceDocument.getId(), project.getName(),
                project.getId());
    }
}
 

/**
 * Provides exporting constraints as a file.
 */
@Override
public File exportConstraintAsFile(ConstraintSet aSet)
{
    String constraintRulesPath = repositoryProperties.getPath().getAbsolutePath() + "/"
            + PROJECT_FOLDER + "/" + aSet.getProject().getId() + "/"
            + ConstraintsService.CONSTRAINTS + "/";
    String filename = aSet.getId() + ".txt";
    File constraintsFile = new File(constraintRulesPath, filename);
    if (constraintsFile.exists()) {
        try (MDC.MDCCloseable closable = MDC.putCloseable(Logging.KEY_PROJECT_ID,
                String.valueOf(aSet.getProject().getId()))) {
            log.info("Exported constraints set [{}] from project [{}]({})",
                    aSet.getName(), aSet.getProject().getName(), aSet.getProject().getId());
        }
        return constraintsFile;
    }
    else {
        try (MDC.MDCCloseable closable = MDC.putCloseable(Logging.KEY_PROJECT_ID,
                String.valueOf(aSet.getProject().getId()))) {
            log.info("Unable to read constraints set file [{}] in project [{}]({})",
                    filename, aSet.getProject().getName(), aSet.getProject().getId());
        }
        return null;
    }
}
 

@Override
public void writeConstraintSet(ConstraintSet aSet, InputStream aContent)
    throws IOException
{
    String constraintRulesPath = repositoryProperties.getPath().getAbsolutePath() + "/"
            + PROJECT_FOLDER + "/" + aSet.getProject().getId() + "/"
            + ConstraintsService.CONSTRAINTS + "/";
    String filename = aSet.getId() + ".txt";
    FileUtils.forceMkdir(new File(constraintRulesPath));
    FileUtils.copyInputStreamToFile(aContent, new File(constraintRulesPath, filename));

    
    try (MDC.MDCCloseable closable = MDC.putCloseable(Logging.KEY_PROJECT_ID,
            String.valueOf(aSet.getProject().getId()))) {
        log.info("Saved constraints set [{}] in project [{}]({})",
                aSet.getName(), aSet.getProject().getName(), aSet.getProject().getId());
    }
}
 

@Override
public String readConstrainSet(ConstraintSet aSet)
    throws IOException
{
    String constraintRulesPath = repositoryProperties.getPath().getAbsolutePath() + "/"
            + PROJECT_FOLDER + "/" + aSet.getProject().getId() + "/"
            + ConstraintsService.CONSTRAINTS + "/";
    String filename = aSet.getId() + ".txt";
    
    String data;
    try (BOMInputStream is = new BOMInputStream(
            new FileInputStream(new File(constraintRulesPath, filename)))) {
        data = IOUtils.toString(is, "UTF-8");
    }

    try (MDC.MDCCloseable closable = MDC.putCloseable(Logging.KEY_PROJECT_ID,
            String.valueOf(aSet.getProject().getId()))) {
        log.info("Read constraints set [{}] in project [{}]({})",
                aSet.getName(), aSet.getProject().getName(), aSet.getProject().getId());
    }
    
    return data;
}
 

@Override
public void removeCurationDocumentContent(SourceDocument aSourceDocument, String aUsername)
    throws IOException
{
    if (new File(casStorageService.getAnnotationFolder(aSourceDocument),
            WebAnnoConst.CURATION_USER + ".ser").exists()) {
        FileUtils.forceDelete(new File(casStorageService.getAnnotationFolder(aSourceDocument),
                WebAnnoConst.CURATION_USER + ".ser"));

        try (MDC.MDCCloseable closable = MDC.putCloseable(Logging.KEY_PROJECT_ID,
                String.valueOf(aSourceDocument.getProject().getId()))) {
            Project project = aSourceDocument.getProject();
            log.info("Removed curation of source document [{}]({}) from project [{}]({})",
                    aSourceDocument.getName(), aSourceDocument.getId(), project.getName(),
                    project.getId());
        }
    }
}
 

@Override
@Transactional
public void createAnnotationDocument(AnnotationDocument aAnnotationDocument)
{
    Validate.notNull(aAnnotationDocument, "Annotation document must be specified");
    
    if (isNull(aAnnotationDocument.getId())) {
        entityManager.persist(aAnnotationDocument);
        
        try (MDC.MDCCloseable closable = MDC.putCloseable(Logging.KEY_PROJECT_ID,
                String.valueOf(aAnnotationDocument.getProject().getId()))) {
            log.info(
                    "Created annotation document [{}] for user [{}] for source document "
                    + "[{}]({}) in project [{}]({})",
                    aAnnotationDocument.getId(), aAnnotationDocument.getUser(), 
                    aAnnotationDocument.getDocument().getName(),
                    aAnnotationDocument.getDocument().getId(),
                    aAnnotationDocument.getProject().getName(),
                    aAnnotationDocument.getProject().getId());
        }
    }
    else {
        entityManager.merge(aAnnotationDocument);
    }
}
 

@Override
@Transactional
public void deleteGazeteers(Gazeteer aGazeteer) throws IOException
{
    entityManager.remove(
            entityManager.contains(aGazeteer) ? aGazeteer : entityManager.merge(aGazeteer));
    
    File gaz = getGazeteerFile(aGazeteer);
    if (gaz.exists()) {
        gaz.delete();
    }
    
    try (MDC.MDCCloseable closable = MDC.putCloseable(Logging.KEY_PROJECT_ID,
            String.valueOf(aGazeteer.getRecommender().getProject().getId()))) {
        log.info("Removed gazeteer [{}] from recommender [{}]({}) in project [{}]({})",
                aGazeteer.getName(), aGazeteer.getRecommender().getName(),
                aGazeteer.getRecommender().getId(),
                aGazeteer.getRecommender().getProject().getName(),
                aGazeteer.getRecommender().getProject().getId());
    }
}
 

@Override
@Transactional
public void removeProject(Project aProject)
    throws IOException
{
    long start = System.currentTimeMillis();
    
    // remove metadata from DB
    Project project = aProject;
    if (!entityManager.contains(project)) {
        project = entityManager.merge(project);
    }
    
    applicationEventPublisher.publishEvent(new BeforeProjectRemovedEvent(this, aProject));

    for (ProjectPermission permissions : getProjectPermissions(aProject)) {
        entityManager.remove(permissions);
    }
            
    entityManager.remove(project);
    
    // remove the project directory from the file system
    String path = repositoryProperties.getPath().getAbsolutePath() + "/" + PROJECT_FOLDER + "/"
            + aProject.getId();
    try {
        FastIOUtils.delete(new File(path));
    }
    catch (FileNotFoundException e) {
        try (MDC.MDCCloseable closable = MDC.putCloseable(Logging.KEY_PROJECT_ID,
                String.valueOf(aProject.getId()))) {
            log.info("Project directory to be deleted was not found: [{}]. Ignoring.", path);
        }
    }

    try (MDC.MDCCloseable closable = MDC.putCloseable(Logging.KEY_PROJECT_ID,
            String.valueOf(aProject.getId()))) {
        log.info("Removed project [{}]({}) ({})", aProject.getName(), aProject.getId(),
                formatDurationWords(System.currentTimeMillis() - start, true, true));
    }
}
 

@Override
@Transactional
public void removeSourceDocument(SourceDocument aDocument)
    throws IOException
{
    Validate.notNull(aDocument, "Source document must be specified");
    
    // BeforeDocumentRemovedEvent is triggered first, since methods that rely 
    // on it might need to have access to the associated annotation documents 
    applicationEventPublisher.publishEvent(new BeforeDocumentRemovedEvent(this, aDocument));
    
    for (AnnotationDocument annotationDocument : listAllAnnotationDocuments(aDocument)) {
        removeAnnotationDocument(annotationDocument);
    }
    
    entityManager.remove(
            entityManager.contains(aDocument) ? aDocument : entityManager.merge(aDocument));

    String path = repositoryProperties.getPath().getAbsolutePath() + "/" + PROJECT_FOLDER + "/"
            + aDocument.getProject().getId() + "/" + DOCUMENT_FOLDER + "/" + aDocument.getId();
    
    // remove from file both source and related annotation file
    if (new File(path).exists()) {
        FileUtils.forceDelete(new File(path));
    }
    
    try (MDC.MDCCloseable closable = MDC.putCloseable(Logging.KEY_PROJECT_ID,
            String.valueOf(aDocument.getProject().getId()))) {
        Project project = aDocument.getProject();
        log.info("Removed source document [{}]({}) from project [{}]({})", aDocument.getName(),
                aDocument.getId(), project.getName(), project.getId());
    }
}
 

@Override
@Transactional
public void removeProjectPermission(ProjectPermission aPermission)
{
    entityManager.remove(aPermission);
    
    try (MDC.MDCCloseable closable = MDC.putCloseable(Logging.KEY_PROJECT_ID,
            String.valueOf(aPermission.getProject().getId()))) {
        log.info("Removed permission [{}] for user [{}] on project [{}]({})",
                aPermission.getLevel(), aPermission.getUser(),
                aPermission.getProject().getName(), aPermission.getProject().getId());
    }
}
 

@Override
public void upgradeCas(CAS aCas, SourceDocument aSourceDocument, String aUser,
        CasUpgradeMode aMode)
    throws UIMAException, IOException
{
    switch (aMode) {
    case NO_CAS_UPGRADE:
        return;
    case AUTO_CAS_UPGRADE: {
        boolean upgraded = upgradeCasIfRequired(aCas, aSourceDocument);
        if (!upgraded) {
            try (MDC.MDCCloseable closable = MDC.putCloseable(Logging.KEY_PROJECT_ID,
                    String.valueOf(aSourceDocument.getProject().getId()))) {
                log.debug(
                        "CAS of user [{}] for document [{}]({}) in project [{}]({}) is already "
                                + "compatible with project type system - skipping upgrade",
                        aUser, aSourceDocument.getName(), aSourceDocument.getId(),
                        aSourceDocument.getProject().getName(),
                        aSourceDocument.getProject().getId());
            }
        }
        return;
    }
    case FORCE_CAS_UPGRADE:
        upgradeCas(aCas, aSourceDocument, aUser);
        return;
    }
}
 

@Override
@Transactional
public void removeConstraintSet(ConstraintSet aSet)
{
    entityManager.remove(entityManager.merge(aSet));
    
    try (MDC.MDCCloseable closable = MDC.putCloseable(Logging.KEY_PROJECT_ID,
            String.valueOf(aSet.getProject().getId()))) {
        log.info("Removed constraints set [{}] in project [{}]({})",
                aSet.getName(), aSet.getProject().getName(), aSet.getProject().getId());
    }
}
 

public static MDC.MDCCloseable safePutCloseable(String key, String value) {
  try {
    return MDC.putCloseable(key, value);
  } catch (Exception e) {
    log.error("Failed to put MDC", e);
    // Returning null here is ok as try-with-resources ignores null resources.
    return null;
  }
}
 

@Override
protected void doGet(HttpServletRequest req, HttpServletResponse resp) throws IOException {
    String[] pathParts;
    if(req.getPathInfo() != null){
        pathParts = req.getPathInfo().split("/");
    }else{
        pathParts = req.getServletPath().split("/");
    }


    if (pathParts.length < 2) {
        resp.sendError(404);
        return;
    }

    try (MDC.MDCCloseable ignored = MDC.putCloseable("provider", req.getServletPath())) {
        String action = pathParts[1];
        if (action.equals("authenticate")) {
            authenticate(req, resp);
        } else if (action.equals("callback")) {
            oauth2callback(req, resp);
        } else if (action.equals("token")) {
            getToken(req, resp);
        } else if (action.equals("session")) {
            setupSession(req, resp);
        }else if (action.equals("logout")) {
            logoutSession(req, resp);
        } else {
            logger.warn("Unknown request {}", req.getServletPath() + req.getPathInfo() + "?" + req.getQueryString());
            resp.sendError(404);
        }
    }
}
 

@Override
@Transactional
public void createOrUpdateGazeteer(Gazeteer aGazeteer)
{
    if (aGazeteer.getId() == null) {
        entityManager.persist(aGazeteer);
        
        try (MDC.MDCCloseable closable = MDC.putCloseable(Logging.KEY_PROJECT_ID,
                String.valueOf(aGazeteer.getRecommender().getProject().getId()))) {
            log.info("Created gazeteer [{}] for recommender [{}]({}) in project [{}]({})",
                    aGazeteer.getName(), aGazeteer.getRecommender().getName(),
                    aGazeteer.getRecommender().getId(),
                    aGazeteer.getRecommender().getProject().getName(),
                    aGazeteer.getRecommender().getProject().getId());
        }
    }
    else {
        entityManager.merge(aGazeteer);
        
        try (MDC.MDCCloseable closable = MDC.putCloseable(Logging.KEY_PROJECT_ID,
                String.valueOf(aGazeteer.getRecommender().getProject().getId()))) {
            log.info("Updated gazeteer [{}] for recommender [{}]({}) in project [{}]({})",
                    aGazeteer.getName(), aGazeteer.getRecommender().getName(),
                    aGazeteer.getRecommender().getId(),
                    aGazeteer.getRecommender().getProject().getName(),
                    aGazeteer.getRecommender().getProject().getId());
        }
    }
}
 

@EventListener
@Transactional
public void beforeProjectRemove(BeforeProjectRemovedEvent aEvent)
    throws IOException
{
    Project project = aEvent.getProject();
    
    Validate.notNull(project, "Project must be specified");

    // Since the project is being deleted anyway, we don't bother sending around
    // BeforeDocumentRemovedEvent anymore. If we did, we would likely trigger a
    // a lot of CPU usage and DB bashing (e.g. for re-calculating the project state
    // (ProjectServiceImpl.recalculateProjectState).
    // List<SourceDocument> sourceDocuments = listSourceDocuments(project);
    // for (SourceDocument doc : sourceDocuments) {
    // applicationEventPublisher.publishEvent(new BeforeDocumentRemovedEvent(this, doc));
    // }

    // There should be a cascade-on-delete for annotation documents when the respective
    // source document is deleted, but that is not there at the moment...
    String deleteAnnotationDocumentsQuery = String.join("\n",
            "DELETE FROM AnnotationDocument",
            "WHERE project = :project");
    entityManager.createQuery(deleteAnnotationDocumentsQuery)
            .setParameter("project", project)
            .executeUpdate();

    // Delete all the source documents for the given project
    String deleteSourceDocumentsQuery = String.join("\n",
            "DELETE FROM SourceDocument",
            "WHERE project = :project");
    entityManager.createQuery(deleteSourceDocumentsQuery)
            .setParameter("project", project)
            .executeUpdate();
    
    // Delete all the source documents files for the given project
    File docFolder = new File(repositoryProperties.getPath().getAbsolutePath() + "/"
            + PROJECT_FOLDER + "/" + project.getId() + "/" + DOCUMENT_FOLDER + "/");
    if (docFolder.exists()) {
        FastIOUtils.delete(docFolder);
    }
    
    try (MDC.MDCCloseable closable = MDC.putCloseable(Logging.KEY_PROJECT_ID,
            String.valueOf(project.getId()))) {
        log.info("Removed all documents from project [{}]({}) being deleted", project.getName(),
                project.getId());
    }
}
 

@Override
@Transactional
public File exportAnnotationDocument(SourceDocument aDocument, String aUser,
        FormatSupport aFormat, String aFileName, Mode aMode, boolean aStripExtension,
        Map<Pair<Project, String>, Object> aBulkOperationContext)
    throws UIMAException, IOException, ClassNotFoundException
{
    Map<Pair<Project, String>, Object> bulkOperationContext = aBulkOperationContext;
    if (bulkOperationContext == null) {
        bulkOperationContext = new HashMap<>();
    }
    
    String username;
    // for Correction, it will export the corrected document (of the logged in user)
    // (CORRECTION_USER.ser is the automated result displayed for the user to correct it, not
    // the final result) for automation, it will export either the corrected document
    // (Annotated) or the automated document
    if (aMode.equals(ANNOTATION) || aMode.equals(AUTOMATION) || aMode.equals(CORRECTION)) {
        username = aUser;
    }
    // The merge result will be exported
    else {
        username = CURATION_USER;
    }

    // Read file
    File exportFile;
    try (CasStorageSession session = CasStorageSession.openNested()) {
        CAS cas = casStorageService.readCas(aDocument, username);
        exportFile = exportCasToFile(cas, aDocument, aFileName, aFormat, aStripExtension,
                aBulkOperationContext);
    }

    Project project = aDocument.getProject();
    try (MDC.MDCCloseable closable = MDC.putCloseable(KEY_PROJECT_ID,
            String.valueOf(project.getId()))) {
        log.info("Exported annotations [{}]({}) for user [{}] from project [{}]({}) "
                + "using format [{}]", aDocument.getName(), aDocument.getId(), aUser, 
                project.getName(), project.getId(), aFormat.getId());
    }

    return exportFile;
}