Examples with DataSet nl.knaw.huygens.timbuctoo.v5.dataset.dto.DataSet used on opensource projects

Example 36 with DataSet

use of nl.knaw.huygens.timbuctoo.v5.dataset.dto.DataSet in project timbuctoo by HuygensING.

the class RsDocumentBuilder method getSourceDescription.

/**
 * Get the source description document. If <code>user</code> == <code>null</code> the source description will
 * only have links to capability lists of published dataSets. Otherwise the source description will have
 * links to capability lists of published dataSets and the dataSets for which the user has read access.
 *
 * @param user User that requests the document, may be <code>null</code>
 * @return the source description document.
 */
public Urlset getSourceDescription(@Nullable User user) {
    RsMd rsMd = new RsMd(Capability.DESCRIPTION.xmlValue);
    Urlset sourceDescription = new Urlset(rsMd);
    for (DataSet dataSet : dataSetRepository.getDataSetsWithReadAccess(user)) {
        DataSetMetaData dataSetMetaData = dataSet.getMetadata();
        String loc = rsUriHelper.uriForRsDocument(dataSetMetaData, Capability.CAPABILITYLIST);
        String descriptionUrl = rsUriHelper.uriForRsDocument(dataSetMetaData, DESCRIPTION_FILENAME);
        UrlItem item = new UrlItem(loc).withMetadata(new RsMd(Capability.CAPABILITYLIST.xmlValue)).addLink(new RsLn(REL_DESCRIBED_BY, descriptionUrl).withType(DESCRIPTION_TYPE));
        sourceDescription.addItem(item);
    }
    return sourceDescription;
}

Example 37 with DataSet

use of nl.knaw.huygens.timbuctoo.v5.dataset.dto.DataSet in project timbuctoo by HuygensING.

the class RsDocumentBuilder method getResourceList.

/**
 * Get the resource list for the dataSet denoted by <code>ownerId</code> and <code>dataSetId</code>.
 * The {@link Optional} is empty if the dataSet is not published and the given <code>user</code> == <code>null</code>
 * or has no read access for the dataSet or the dataSet does not exist.
 *
 * @param user User that requests the list, may be <code>null</code>
 * @param ownerId ownerId
 * @param dataSetId dataSetId
 * @return the resource list for the dataSet denoted by <code>ownerId</code> and <code>dataSetId</code>
 */
public Optional<Urlset> getResourceList(@Nullable User user, String ownerId, String dataSetId) throws IOException {
    Urlset resourceList = null;
    Optional<DataSet> maybeDataSet = dataSetRepository.getDataSet(user, ownerId, dataSetId);
    if (maybeDataSet.isPresent()) {
        DataSetMetaData dataSetMetaData = maybeDataSet.get().getMetadata();
        LogList loglist = maybeDataSet.get().getImportManager().getLogList();
        RsMd rsMd = new RsMd(Capability.RESOURCELIST.xmlValue).withAt(// lastImportDate set on server startup?
        ZonedDateTime.parse(loglist.getLastImportDate()));
        resourceList = new Urlset(rsMd).addLink(new RsLn(REL_UP, rsUriHelper.uriForRsDocument(dataSetMetaData, Capability.CAPABILITYLIST)));
        FileStorage fileStorage = maybeDataSet.get().getFileStorage();
        List<LogEntry> entries = loglist.getEntries();
        entries.sort((e1, e2) -> {
            if (e1.getImportStatus().isPresent() && e2.getImportStatus().isPresent()) {
                return e1.getImportStatus().get().getDate().compareTo(e2.getImportStatus().get().getDate());
            } else if (e1.getImportStatus().isPresent()) {
                return 1;
            } else {
                return -1;
            }
        });
        for (LogEntry logEntry : entries) {
            Optional<String> maybeToken = logEntry.getLogToken();
            if (maybeToken.isPresent()) {
                String loc = rsUriHelper.uriForToken(dataSetMetaData, maybeToken.get());
                Optional<CachedFile> maybeCachedFile = fileStorage.getFile(maybeToken.get());
                if (maybeCachedFile.isPresent()) {
                    UrlItem item = new UrlItem(loc).withMetadata(new RsMd().withType(maybeCachedFile.get().getMimeType().toString()));
                    resourceList.addItem(item);
                }
            }
        }
        rsMd.withCompleted(ZonedDateTime.now(ZoneOffset.UTC));
    }
    return Optional.ofNullable(resourceList);
}

Example 38 with DataSet

use of nl.knaw.huygens.timbuctoo.v5.dataset.dto.DataSet in project timbuctoo by HuygensING.

the class EntityImageFetcher method get.

@Override
public TypedValue get(DataFetchingEnvironment env) {
    if (env.getSource() instanceof SubjectReference) {
        SubjectReference source = env.getSource();
        DataSet dataSet = source.getDataSet();
        Optional<TypedValue> summaryProperty = summaryPropDataRetriever.createSummaryProperty(source, dataSet);
        if (summaryProperty.isPresent()) {
            return summaryProperty.get();
        }
    }
    return null;
}

Example 39 with DataSet

use of nl.knaw.huygens.timbuctoo.v5.dataset.dto.DataSet in project timbuctoo by HuygensING.

the class CollectionMetadataMutation method get.

@Override
public Object get(DataFetchingEnvironment env) {
    DataSet dataSet = MutationHelpers.getDataSet(env, dataSetRepository::getDataSet);
    MutationHelpers.checkAdminPermissions(env, dataSet.getMetadata());
    try {
        String collectionUri = env.getArgument("collectionUri");
        Map data = env.getArgument("metadata");
        final PredicateMutation mutation = new PredicateMutation();
        mutation.entity(collectionUri, getValue(data, "title").map(v -> replace(RDFS_LABEL, value(v))).orElse(null), getValue(data, "archeType").map(v -> replace("http://www.w3.org/2000/01/rdf-schema#subClassOf", subject(v))).orElse(null));
        MutationHelpers.addMutation(dataSet, mutation);
        return new LazyTypeSubjectReference(collectionUri, dataSet);
    } catch (LogStorageFailedException | InterruptedException | ExecutionException e) {
        throw new RuntimeException(e);
    }
}

Example 40 with DataSet

use of nl.knaw.huygens.timbuctoo.v5.dataset.dto.DataSet in project timbuctoo by HuygensING.

the class TimbuctooV4 method run.

@Override
public void run(TimbuctooConfiguration configuration, Environment environment) throws Exception {
    // environment.jersey().property(ServerProperties.TRACING, "ALL");
    // // environment.jersey().property(ServerProperties.TRACING_THRESHOLD, "VERBOSE");
    // Make sure we know what version is running
    Properties properties = new Properties();
    InputStream gitproperties = getClass().getClassLoader().getResourceAsStream("git.properties");
    String currentVersion;
    if (gitproperties != null) {
        properties.load(gitproperties);
        currentVersion = properties.getProperty("git.commit.id");
    } else {
        currentVersion = "NO-GIT-PROPERTIES-FOUND";
        LoggerFactory.getLogger(this.getClass()).error("NO-GIT-PROPERTIES-FOUND");
    }
    LoggerFactory.getLogger(this.getClass()).info("Now launching timbuctoo version: " + currentVersion);
    HttpClientBuilder apacheHttpClientBuilder = new HttpClientBuilder(environment).using(configuration.getHttpClientConfiguration());
    CloseableHttpClient httpClient = apacheHttpClientBuilder.build("httpclient");
    // Support services
    SecurityFactory securityConfig = configuration.getSecurityConfiguration().createNewSecurityFactory(httpClient);
    securityConfig.getHealthChecks().forEachRemaining(check -> {
        register(environment, check.getLeft(), new LambdaHealthCheck(check.getRight()));
    });
    // Database migration
    LinkedHashMap<String, DatabaseMigration> migrations = new LinkedHashMap<>();
    migrations.put("fix-dcarkeywords-displayname-migration", new FixDcarKeywordDisplayNameMigration());
    migrations.put("fix-pids-migration", new MakePidsAbsoluteUrls());
    UriHelper uriHelper = configuration.getUriHelper();
    environment.lifecycle().addServerLifecycleListener(new BaseUriDeriver(configuration));
    TinkerPopConfig tinkerPopConfig = configuration.getDatabaseConfiguration();
    final TinkerPopGraphManager graphManager = new TinkerPopGraphManager(tinkerPopConfig, migrations);
    final PersistenceManager persistenceManager = configuration.getPersistenceManagerFactory().build();
    UrlGenerator uriToRedirectToFromPersistentUrls = (coll, id, rev) -> uriHelper.fromResourceUri(SingleEntity.makeUrl(coll, id, rev));
    final UrlGenerator pathWithoutVersionAndRevision = (coll, id, rev) -> URI.create(SingleEntity.makeUrl(coll, id, null).toString().replaceFirst("^/v2.1/", ""));
    final UrlGenerator uriWithoutRev = (coll, id, rev) -> uriHelper.fromResourceUri(SingleEntity.makeUrl(coll, id, null));
    HandleAdder handleAdder = new HandleAdder(persistenceManager, activeMqBundle);
    // TODO make function when TimbuctooActions does not depend on TransactionEnforcer anymore
    TimbuctooActions.TimbuctooActionsFactory timbuctooActionsFactory = new TimbuctooActions.TimbuctooActionsFactoryImpl(securityConfig.getPermissionFetcher(), Clock.systemDefaultZone(), handleAdder, uriToRedirectToFromPersistentUrls, () -> new TinkerPopOperations(graphManager));
    TransactionEnforcer transactionEnforcer = new TransactionEnforcer(timbuctooActionsFactory);
    graphManager.onGraph(g -> new ScaffoldMigrator(graphManager).execute());
    handleAdder.init(transactionEnforcer);
    final Vres vres = new DatabaseConfiguredVres(transactionEnforcer);
    migrations.put("prepare-for-bia-import-migration", new PrepareForBiaImportMigration(vres, graphManager));
    migrations.put("give-existing-relationtypes-rdf-uris", new RelationTypeRdfUriMigration());
    migrations.put("remove-search-results", new RemoveSearchResultsMigration());
    migrations.put("move-indices-to-isLatest-vertex", new MoveIndicesToIsLatestVertexMigration(vres));
    final ResourceSyncService resourceSyncService = new ResourceSyncService(httpClient, new ResourceSyncContext());
    final JsonMetadata jsonMetadata = new JsonMetadata(vres, graphManager);
    final AutocompleteService.AutocompleteServiceFactory autocompleteServiceFactory = new AutocompleteService.AutocompleteServiceFactory(uriWithoutRev);
    environment.lifecycle().manage(graphManager);
    final CrudServiceFactory crudServiceFactory = new CrudServiceFactory(vres, securityConfig.getUserValidator(), pathWithoutVersionAndRevision);
    final Webhooks webhooks = configuration.getWebhooks().getWebHook(environment);
    DataSetRepository dataSetRepository = configuration.getDataSetConfiguration().createRepository(environment.lifecycle().executorService("dataSet").build(), securityConfig.getPermissionFetcher(), configuration.getDatabases(), configuration.getRdfIdHelper(), (combinedId -> {
        try {
            webhooks.dataSetUpdated(combinedId);
        } catch (IOException e) {
            LOG.error("Webhook call failed", e);
        }
    }), configuration.dataSetsArePublicByDefault());
    environment.lifecycle().manage(new DataSetRepositoryManager(dataSetRepository));
    ErrorResponseHelper errorResponseHelper = new ErrorResponseHelper();
    AuthCheck authCheck = new AuthCheck(securityConfig.getUserValidator(), securityConfig.getPermissionFetcher(), dataSetRepository);
    register(environment, new RdfUpload(authCheck));
    register(environment, new TabularUpload(authCheck, dataSetRepository, errorResponseHelper));
    register(environment, new Rml(dataSetRepository, errorResponseHelper, securityConfig.getUserValidator()));
    SerializerWriterRegistry serializerWriterRegistry = new SerializerWriterRegistry(new CsvWriter(), new JsonLdWriter(), new JsonWriter(), new GraphVizWriter());
    final PaginationArgumentsHelper argHelper = new PaginationArgumentsHelper(configuration.getCollectionFilters());
    final GraphQl graphQlEndpoint = new GraphQl(new RootQuery(dataSetRepository, serializerWriterRegistry, configuration.getArchetypesSchema(), new RdfWiringFactory(dataSetRepository, argHelper, configuration.getDefaultSummaryProps()), new DerivedSchemaTypeGenerator(argHelper), environment.getObjectMapper()), serializerWriterRegistry, securityConfig.getUserValidator(), uriHelper, securityConfig.getPermissionFetcher(), dataSetRepository);
    register(environment, graphQlEndpoint);
    if (securityConfig instanceof TwitterSecurityFactory) {
        final TwitterLogin twitterLogin = new TwitterLogin();
        register(environment, twitterLogin);
    }
    register(environment, new JsonLdEditEndpoint(securityConfig.getUserValidator(), securityConfig.getPermissionFetcher(), dataSetRepository, new HttpClientBuilder(environment).build("json-ld")));
    register(environment, new RootEndpoint(uriHelper, configuration.getUserRedirectUrl()));
    if (securityConfig instanceof OldStyleSecurityFactory) {
        register(environment, new Authenticate(((OldStyleSecurityFactory) securityConfig).getLoggedInUsers()));
    }
    register(environment, new Me(securityConfig.getUserValidator()));
    register(environment, new Search(configuration, uriHelper, graphManager));
    register(environment, new Autocomplete(autocompleteServiceFactory, transactionEnforcer));
    register(environment, new Index(securityConfig.getUserValidator(), crudServiceFactory, transactionEnforcer));
    register(environment, new SingleEntity(securityConfig.getUserValidator(), crudServiceFactory, transactionEnforcer));
    register(environment, new SingleEntityNTriple(transactionEnforcer, uriHelper));
    register(environment, new WomenWritersEntityGet(crudServiceFactory, transactionEnforcer));
    register(environment, new LegacySingleEntityRedirect(uriHelper));
    register(environment, new LegacyIndexRedirect(uriHelper));
    register(environment, new Discover(resourceSyncService));
    if (configuration.isAllowGremlinEndpoint()) {
        register(environment, new Gremlin(graphManager));
    }
    register(environment, new Graph(graphManager, vres));
    register(environment, new RelationTypes(graphManager));
    register(environment, new Metadata());
    register(environment, new nl.knaw.huygens.timbuctoo.server.endpoints.v2.system.vres.Metadata(jsonMetadata));
    register(environment, new MyVres(securityConfig.getUserValidator(), securityConfig.getPermissionFetcher(), transactionEnforcer, uriHelper));
    register(environment, new ListVres(uriHelper, transactionEnforcer));
    register(environment, new VreImage(transactionEnforcer));
    final ExecutorService rfdExecutorService = environment.lifecycle().executorService("rdf-import").build();
    register(environment, new ImportRdf(graphManager, vres, rfdExecutorService, transactionEnforcer));
    register(environment, new Import(new ResourceSyncFileLoader(httpClient), authCheck));
    register(environment, new WellKnown());
    RsDocumentBuilder rsDocumentBuilder = new RsDocumentBuilder(dataSetRepository, configuration.getUriHelper());
    register(environment, new RsEndpoint(rsDocumentBuilder, securityConfig.getUserValidator()));
    // Admin resources
    if (securityConfig instanceof OldStyleSecurityFactory) {
        final OldStyleSecurityFactory oldStyleSecurityFactory = (OldStyleSecurityFactory) securityConfig;
        environment.admin().addTask(new UserCreationTask(new LocalUserCreator(oldStyleSecurityFactory.getLoginCreator(), oldStyleSecurityFactory.getUserCreator(), oldStyleSecurityFactory.getVreAuthorizationCreator())));
    }
    environment.admin().addTask(new DatabaseValidationTask(new DatabaseValidator(graphManager, new LabelsAddedToVertexDatabaseCheck(), new InvariantsCheck(vres), new FullTextIndexCheck()), Clock.systemUTC(), 5000));
    environment.admin().addTask(new DbLogCreatorTask(graphManager));
    environment.admin().addTask(new BdbDumpTask(configuration.getDatabases()));
    if (configuration.getDatabaseBackupper().isPresent()) {
        environment.admin().addTask(new StagingBackup(configuration.getDatabaseBackupper().get().create(configuration.getDatabaseConfiguration().getDatabasePath(), configuration.getDatabases().getDatabaseLocation())));
    }
    // register health checks
    // Dropwizard Health checks are used to check whether requests should be routed to this instance
    // For example, checking if neo4j is in a valid state is not a "HealthCheck" because if the database on one instance
    // is in an invalid state, then this applies to all other instances too. So once the database is in an invalid state
    // timbuctoo will be down.
    // 
    // checking whether this instance is part of the neo4j quorum is a good HealthCheck because running a database query
    // on those instances that are not part of the quorum will block forever, while the other instances will respond
    // just fine.
    register(environment, "Neo4j database connection", graphManager);
    // Log all http requests
    register(environment, new LoggingFilter(1024, currentVersion));
    register(environment, new TransactionFilter(graphManager));
    // Allow all CORS requests
    register(environment, new PromiscuousCorsFilter());
    // Add embedded AMQ (if any) to the metrics
    configuration.getLocalAmqJmxPath(HANDLE_QUEUE).ifPresent(rethrowConsumer(jmxPath -> {
        String dwMetricName = name(this.getClass(), "localAmq");
        ObjectName jmxMetricName = new ObjectName(jmxPath);
        environment.metrics().register(dwMetricName + ".enqueueCount", new JmxAttributeGauge(jmxMetricName, "EnqueueCount"));
        environment.metrics().register(dwMetricName + ".dequeueCount", new JmxAttributeGauge(jmxMetricName, "DequeueCount"));
    }));
    setupObjectMapping(environment);
}