Examples with Property nl.knaw.huygens.timbuctoo.v5.graphql.rootquery.dataproviders.Property used on opensource projects

Example 1 with Property

use of nl.knaw.huygens.timbuctoo.v5.graphql.rootquery.dataproviders.Property in project timbuctoo by HuygensING.

the class GraphQl method executeGraphql.

public Response executeGraphql(String query, String acceptHeader, String acceptParam, String queryFromBody, Map variables, String operationName, String authHeader) {
    final SerializerWriter serializerWriter;
    if (acceptParam != null && !acceptParam.isEmpty()) {
        // Accept param overrules header because it's more under the user's control
        acceptHeader = acceptParam;
    }
    if (unSpecifiedAcceptHeader(acceptHeader)) {
        acceptHeader = MediaType.APPLICATION_JSON;
    }
    if (MediaType.APPLICATION_JSON.equals(acceptHeader)) {
        serializerWriter = null;
    } else {
        Optional<SerializerWriter> bestMatch = serializerWriterRegistry.getBestMatch(acceptHeader);
        if (bestMatch.isPresent()) {
            serializerWriter = bestMatch.get();
        } else {
            return Response.status(415).type(MediaType.APPLICATION_JSON_TYPE).entity("{\"errors\": [\"The available mediatypes are: " + String.join(", ", serializerWriterRegistry.getSupportedMimeTypes()) + "\"]}").build();
        }
    }
    if (query != null && queryFromBody != null) {
        return Response.status(400).type(MediaType.APPLICATION_JSON_TYPE).entity("{\"errors\": [\"There's both a query as url paramatere and a query in the body. Please pick one.\"]}").build();
    }
    if (query == null && queryFromBody == null) {
        return Response.status(400).type(MediaType.APPLICATION_JSON_TYPE).entity("{\"errors\": [\"Please provide the graphql query as the query property of a JSON encoded object. " + "E.g. {query: \\\"{\\n  persons {\\n ... \\\"}\"]}").build();
    }
    Optional<User> user;
    try {
        user = userValidator.getUserFromAccessToken(authHeader);
    } catch (UserValidationException e) {
        user = Optional.empty();
    }
    UserPermissionCheck userPermissionCheck = new UserPermissionCheck(user, permissionFetcher, newHashSet(Permission.READ));
    final GraphQLSchema transform = graphqlGetter.get().transform(b -> b.fieldVisibility(new PermissionBasedFieldVisibility(userPermissionCheck, dataSetRepository)));
    final GraphQL.Builder builder = GraphQL.newGraphQL(transform);
    if (serializerWriter != null) {
        builder.queryExecutionStrategy(new SerializerExecutionStrategy());
    }
    GraphQL graphQl = builder.build();
    final ExecutionResult result = graphQl.execute(newExecutionInput().root(new RootData(user)).context(contextData(userPermissionCheck, user)).query(queryFromBody).operationName(operationName).variables(variables == null ? Collections.emptyMap() : variables).build());
    if (serializerWriter == null) {
        return Response.ok().type(MediaType.APPLICATION_JSON_TYPE).entity(result.toSpecification()).build();
    } else {
        if (result.getErrors() != null && !result.getErrors().isEmpty()) {
            return Response.status(415).type(MediaType.APPLICATION_JSON_TYPE).entity(result.toSpecification()).build();
        }
        return Response.ok().type(serializerWriter.getMimeType()).entity((StreamingOutput) os -> {
            serializerWriter.getSerializationFactory().create(os).serialize(new SerializableResult(result.getData()));
        }).build();
    }
}

Example 2 with Property

use of nl.knaw.huygens.timbuctoo.v5.graphql.rootquery.dataproviders.Property in project timbuctoo by HuygensING.

the class BdbRmlDataSourceStore method onChangedSubject.

@Override
public void onChangedSubject(String subject, ChangeFetcher changeFetcher) throws RdfProcessingFailedException {
    try {
        boolean[] wasCollection = new boolean[] { false };
        StreamIterator.iterateAndCloseOrThrow(changeFetcher.getPredicates(subject, TIM_HAS_ROW, Direction.OUT, true, false, true), quad -> {
            wasCollection[0] = true;
            if (quad.getChangeType() == ChangeType.ASSERTED) {
                bdbWrapper.put(subject, quad.getObject());
            }
        });
        if (!wasCollection[0]) {
            try (Stream<CursorQuad> quads = changeFetcher.getPredicates(subject, TIM_HAS_ROW, Direction.IN, true, true, true)) {
                Optional<CursorQuad> isRawRow = quads.findFirst();
                if (isRawRow.isPresent()) {
                    final String collectionUri = isRawRow.get().getObject();
                    Map<String, Property> predicatesToStore = collectionProperties.computeIfAbsent(collectionUri, collection -> getPropertyNames(changeFetcher, collection));
                    switch(isRawRow.get().getChangeType()) {
                        case ASSERTED:
                            // add all unchanged and new predicates
                            StreamIterator.iterateAndCloseOrThrow(changeFetcher.getPredicates(subject, false, true, true), pred -> {
                                final Property property = predicatesToStore.get(pred.getPredicate());
                                if (property != null) {
                                    bdbWrapper.put(subject, property.newName + "\n" + pred.getObject());
                                }
                            });
                            break;
                        case RETRACTED:
                            // remove all unchanged and removed predicates
                            StreamIterator.iterateAndCloseOrThrow(changeFetcher.getPredicates(subject, true, true, false), pred -> {
                                final Property property = predicatesToStore.get(pred.getPredicate());
                                if (property != null) {
                                    bdbWrapper.delete(subject, property.oldName + "\n" + pred.getObject());
                                }
                            });
                            break;
                        case UNCHANGED:
                            // add all added predicates, remove all removed predicates
                            StreamIterator.iterateAndCloseOrThrow(changeFetcher.getPredicates(subject, true, false, true), pred -> {
                                final Property property = predicatesToStore.get(pred.getPredicate());
                                if (property != null) {
                                    if (pred.getChangeType() == ChangeType.RETRACTED) {
                                        bdbWrapper.delete(subject, property.oldName + "\n" + pred.getObject());
                                    } else {
                                        bdbWrapper.put(subject, property.oldName + "\n" + pred.getObject());
                                    }
                                }
                            });
                            break;
                        default:
                            throw new RuntimeException("Should not happen");
                    }
                }
            }
        }
    } catch (DatabaseWriteException e) {
        throw new RdfProcessingFailedException(e);
    }
}

Example 3 with Property

use of nl.knaw.huygens.timbuctoo.v5.graphql.rootquery.dataproviders.Property 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);
}