Examples with Tuple nl.knaw.huygens.timbuctoo.util.Tuple used on opensource projects

Example 1 with Tuple

use of nl.knaw.huygens.timbuctoo.util.Tuple in project timbuctoo by HuygensING.

the class RootQuery method rebuildSchema.

public synchronized GraphQLSchema rebuildSchema() {
    final TypeDefinitionRegistry staticQuery = schemaParser.parse(this.staticQuery);
    if (archetypes != null && !archetypes.isEmpty()) {
        staticQuery.merge(schemaParser.parse(archetypes + "extend type DataSetMetadata {\n" + "  archetypes: Archetypes! @passThrough\n" + "}\n" + "\n"));
    }
    TypeDefinitionRegistry registry = new TypeDefinitionRegistry();
    registry.merge(staticQuery);
    final RuntimeWiring.Builder wiring = RuntimeWiring.newRuntimeWiring();
    wiring.type("Query", builder -> builder.dataFetcher("promotedDataSets", env -> dataSetRepository.getPromotedDataSets().stream().map(DataSetWithDatabase::new).collect(Collectors.toList())).dataFetcher("allDataSets", env -> dataSetRepository.getDataSets().stream().map(DataSetWithDatabase::new).filter(x -> {
        if (x.isPublished()) {
            return true;
        } else {
            ContextData contextData = env.getContext();
            UserPermissionCheck userPermissionCheck = contextData.getUserPermissionCheck();
            return userPermissionCheck.getPermissions(x.getDataSet().getMetadata()).contains(Permission.READ);
        }
    }).collect(Collectors.toList())).dataFetcher("dataSetMetadata", env -> {
        final String dataSetId = env.getArgument("dataSetId");
        ContextData context = env.getContext();
        final User user = context.getUser().orElse(null);
        Tuple<String, String> splitCombinedId = DataSetMetaData.splitCombinedId(dataSetId);
        return dataSetRepository.getDataSet(user, splitCombinedId.getLeft(), splitCombinedId.getRight()).map(DataSetWithDatabase::new);
    }).dataFetcher("dataSetMetadataList", env -> {
        Stream<DataSetWithDatabase> dataSets = dataSetRepository.getDataSets().stream().map(DataSetWithDatabase::new);
        if (env.getArgument("promotedOnly")) {
            dataSets = dataSets.filter(DataSetWithDatabase::isPromoted);
        }
        if (env.getArgument("publishedOnly")) {
            dataSets = dataSets.filter(DataSetWithDatabase::isPublished);
        }
        return dataSets.filter(x -> {
            ContextData contextData = env.getContext();
            UserPermissionCheck userPermissionCheck = contextData.getUserPermissionCheck();
            return userPermissionCheck.getPermissions(x.getDataSet().getMetadata()).contains(Permission.READ);
        }).collect(Collectors.toList());
    }).dataFetcher("aboutMe", env -> ((RootData) env.getRoot()).getCurrentUser().orElse(null)).dataFetcher("availableExportMimetypes", env -> supportedFormats.getSupportedMimeTypes().stream().map(MimeTypeDescription::create).collect(Collectors.toList())));
    wiring.type("DataSetMetadata", builder -> builder.dataFetcher("currentImportStatus", env -> {
        DataSetMetaData input = env.getSource();
        Optional<User> currentUser = ((RootData) env.getRoot()).getCurrentUser();
        if (!currentUser.isPresent()) {
            throw new RuntimeException("User is not provided");
        }
        return dataSetRepository.getDataSet(currentUser.get(), input.getOwnerId(), input.getDataSetId()).map(dataSet -> dataSet.getImportManager().getImportStatus());
    }).dataFetcher("dataSetImportStatus", env -> {
        Optional<User> currentUser = ((RootData) env.getRoot()).getCurrentUser();
        if (!currentUser.isPresent()) {
            throw new RuntimeException("User is not provided");
        }
        DataSetMetaData input = env.getSource();
        return dataSetRepository.getDataSet(currentUser.get(), input.getOwnerId(), input.getDataSetId()).map(dataSet -> dataSet.getImportManager().getDataSetImportStatus());
    }).dataFetcher("collectionList", env -> getCollections(env.getSource(), ((ContextData) env.getContext()).getUser())).dataFetcher("collection", env -> {
        String collectionId = (String) env.getArguments().get("collectionId");
        if (collectionId != null && collectionId.endsWith("List")) {
            collectionId = collectionId.substring(0, collectionId.length() - "List".length());
        }
        DataSetMetaData input = env.getSource();
        ContextData context = env.getContext();
        final User user = context.getUser().orElse(null);
        final DataSet dataSet = dataSetRepository.getDataSet(user, input.getOwnerId(), input.getDataSetId()).get();
        final TypeNameStore typeNameStore = dataSet.getTypeNameStore();
        String collectionUri = typeNameStore.makeUri(collectionId);
        if (dataSet.getSchemaStore().getStableTypes() == null || dataSet.getSchemaStore().getStableTypes().get(collectionUri) == null) {
            return null;
        } else {
            return getCollection(dataSet, typeNameStore, dataSet.getSchemaStore().getStableTypes().get(collectionUri));
        }
    }).dataFetcher("dataSetId", env -> ((DataSetMetaData) env.getSource()).getCombinedId()).dataFetcher("dataSetName", env -> ((DataSetMetaData) env.getSource()).getDataSetId()).dataFetcher("ownerId", env -> ((DataSetMetaData) env.getSource()).getOwnerId()));
    wiring.type("CurrentImportStatus", builder -> builder.dataFetcher("elapsedTime", env -> {
        final String timeUnit = env.getArgument("unit");
        return ((ImportStatus) env.getSource()).getElapsedTime(timeUnit);
    }));
    wiring.type("DataSetImportStatus", builder -> builder.dataFetcher("lastImportDuration", env -> {
        final String timeUnit = env.getArgument("unit");
        return ((DataSetImportStatus) env.getSource()).getLastImportDuration(timeUnit);
    }));
    wiring.type("EntryImportStatus", builder -> builder.dataFetcher("elapsedTime", env -> {
        final String timeUnit = env.getArgument("unit");
        return ((EntryImportStatus) env.getSource()).getElapsedTime(timeUnit);
    }));
    wiring.type("CollectionMetadata", builder -> builder.dataFetcher("indexConfig", env -> {
        SubjectReference source = env.getSource();
        final QuadStore qs = source.getDataSet().getQuadStore();
        try (Stream<CursorQuad> quads = qs.getQuads(source.getSubjectUri(), TIM_HASINDEXERCONFIG, Direction.OUT, "")) {
            final Map result = quads.findFirst().map(q -> {
                try {
                    return objectMapper.readValue(q.getObject(), Map.class);
                } catch (IOException e) {
                    LOG.error("Value not a Map", e);
                    return new HashMap<>();
                }
            }).orElse(new HashMap());
            if (!result.containsKey("facet") || !(result.get("facet") instanceof List)) {
                result.put("facet", new ArrayList<>());
            }
            if (!result.containsKey("fullText") || !(result.get("fullText") instanceof List)) {
                result.put("fullText", new ArrayList<>());
            }
            return result;
        }
    }).dataFetcher("viewConfig", new ViewConfigFetcher(objectMapper)));
    wiring.type("AboutMe", builder -> builder.dataFetcher("dataSets", env -> (Iterable) () -> dataSetRepository.getDataSetsWithWriteAccess(env.getSource()).stream().map(DataSetWithDatabase::new).iterator()).dataFetcher("dataSetMetadataList", env -> (Iterable) () -> {
        Stream<DataSetWithDatabase> dataSets = dataSetRepository.getDataSets().stream().map(DataSetWithDatabase::new);
        if (env.getArgument("ownOnly")) {
            String userId = ((ContextData) env.getContext()).getUser().map(u -> "u" + u.getPersistentId()).orElse(null);
            dataSets = dataSets.filter(d -> d.getOwnerId().equals(userId));
        }
        Permission permission = Permission.valueOf(env.getArgument("permission"));
        if (permission != Permission.READ) {
            // Read is implied
            UserPermissionCheck check = ((ContextData) env.getContext()).getUserPermissionCheck();
            dataSets = dataSets.filter(d -> check.getPermissions(d).contains(permission));
        }
        return dataSets.iterator();
    }).dataFetcher("id", env -> ((User) env.getSource()).getPersistentId()).dataFetcher("name", env -> ((User) env.getSource()).getDisplayName()).dataFetcher("personalInfo", env -> "http://example.com").dataFetcher("canCreateDataSet", env -> true));
    wiring.type("Mutation", builder -> builder.dataFetcher("setViewConfig", new ViewConfigMutation(dataSetRepository)).dataFetcher("setSummaryProperties", new SummaryPropsMutation(dataSetRepository)).dataFetcher("setIndexConfig", new IndexConfigMutation(dataSetRepository)).dataFetcher("createDataSet", new CreateDataSetMutation(dataSetRepository)).dataFetcher("deleteDataSet", new DeleteDataSetMutation(dataSetRepository)).dataFetcher("publish", new MakePublicMutation(dataSetRepository)).dataFetcher("extendSchema", new ExtendSchemaMutation(dataSetRepository)).dataFetcher("setDataSetMetadata", new DataSetMetadataMutation(dataSetRepository)).dataFetcher("setCollectionMetadata", new CollectionMetadataMutation(dataSetRepository)));
    wiring.wiringFactory(wiringFactory);
    StringBuilder root = new StringBuilder("type DataSets {\n sillyWorkaroundWhenNoDataSetsAreVisible: Boolean\n");
    boolean[] dataSetAvailable = new boolean[] { false };
    dataSetRepository.getDataSets().forEach(dataSet -> {
        final DataSetMetaData dataSetMetaData = dataSet.getMetadata();
        final String name = dataSetMetaData.getCombinedId();
        Map<String, Type> types = dataSet.getSchemaStore().getStableTypes();
        Map<String, List<ExplicitField>> customSchema = dataSet.getCustomSchema();
        final Map<String, Type> customTypes = new HashMap<>();
        for (Map.Entry<String, List<ExplicitField>> entry : customSchema.entrySet()) {
            ExplicitType explicitType = new ExplicitType(entry.getKey(), entry.getValue());
            customTypes.put(entry.getKey(), explicitType.convertToType());
        }
        Map<String, Type> mergedTypes;
        MergeSchemas mergeSchemas = new MergeSchemas();
        mergedTypes = mergeSchemas.mergeSchema(types, customTypes);
        types = mergedTypes;
        if (types != null) {
            dataSetAvailable[0] = true;
            root.append("  ").append(name).append(":").append(name).append(" @dataSet(userId:\"").append(dataSetMetaData.getOwnerId()).append("\", dataSetId:\"").append(dataSetMetaData.getDataSetId()).append("\")\n");
            wiring.type(name, c -> c.dataFetcher("metadata", env -> new DataSetWithDatabase(dataSet)));
            final String schema = typeGenerator.makeGraphQlTypes(name, types, dataSet.getTypeNameStore());
            staticQuery.merge(schemaParser.parse(schema));
        }
    });
    root.append("}\n\nextend type Query {\n  #The actual dataSets\n  dataSets: DataSets @passThrough\n}\n\n");
    if (dataSetAvailable[0]) {
        staticQuery.merge(schemaParser.parse(root.toString()));
    }
    SchemaGenerator schemaGenerator = new SchemaGenerator();
    return schemaGenerator.makeExecutableSchema(staticQuery, wiring.build());
}

Example 2 with Tuple

use of nl.knaw.huygens.timbuctoo.util.Tuple in project timbuctoo by HuygensING.

the class RrTriplesMap method getItems.

Stream<Quad> getItems(ErrorHandler defaultErrorHandler) {
    final int[] numberOfItemsProcessed = new int[1];
    Stream<Quad> quadStream = dataSource.getRows(defaultErrorHandler).peek(e -> {
        numberOfItemsProcessed[0]++;
        if (numberOfItemsProcessed[0] == 1) {
            LoggerFactory.getLogger(RrTriplesMap.class).info("collection '{}' has at least one item", uri);
        }
    }).flatMap(row -> {
        Optional<RdfUri> subjectOpt = subjectMap.generateValue(row);
        if (subjectOpt.isPresent()) {
            RdfUri subject = subjectOpt.get();
            for (Tuple<RrRefObjectMap, String> subscription : subscriptions) {
                subscription.getLeft().onNewSubject(row.getRawValue(subscription.getRight()), subject);
            }
            return predicateObjectMaps.stream().flatMap(predicateObjectMap -> predicateObjectMap.generateValue(subject, row));
        } else {
            defaultErrorHandler.subjectGenerationFailed(uri, row);
            return Stream.empty();
        }
    });
    return quadStream;
}

Example 3 with Tuple

use of nl.knaw.huygens.timbuctoo.util.Tuple in project timbuctoo by HuygensING.

the class TinkerPopOperations method replaceEntity.

@Override
public int replaceEntity(Collection collection, UpdateEntity updateEntity) throws NotFoundException, AlreadyUpdatedException, IOException {
    requireCommit = true;
    GraphTraversal<Vertex, Vertex> entityTraversal = entityFetcher.getEntity(this.traversal, updateEntity.getId(), null, collection.getCollectionName());
    if (!entityTraversal.hasNext()) {
        throw new NotFoundException();
    }
    Vertex entityVertex = entityTraversal.next();
    int curRev = getProp(entityVertex, "rev", Integer.class).orElse(1);
    if (curRev != updateEntity.getRev()) {
        throw new AlreadyUpdatedException();
    }
    int newRev = updateEntity.getRev() + 1;
    entityVertex.property("rev", newRev);
    // update properties
    TinkerPopPropertyConverter tinkerPopPropertyConverter = new TinkerPopPropertyConverter(collection);
    for (TimProperty<?> property : updateEntity.getProperties()) {
        try {
            Tuple<String, Object> nameValue = property.convert(tinkerPopPropertyConverter);
            collection.getWriteableProperties().get(nameValue.getLeft()).setValue(entityVertex, nameValue.getRight());
        } catch (IOException e) {
            throw new IOException(property.getName() + " could not be saved. " + e.getMessage(), e);
        }
    }
    // Set removed values to null.
    Set<String> propertyNames = updateEntity.getProperties().stream().map(prop -> prop.getName()).collect(Collectors.toSet());
    for (String name : Sets.difference(collection.getWriteableProperties().keySet(), propertyNames)) {
        collection.getWriteableProperties().get(name).setJson(entityVertex, null);
    }
    String entityTypesStr = getProp(entityVertex, "types", String.class).orElse("[]");
    boolean wasAddedToCollection = false;
    if (!entityTypesStr.contains("\"" + collection.getEntityTypeName() + "\"")) {
        try {
            ArrayNode entityTypes = arrayToEncodedArray.tinkerpopToJson(entityTypesStr);
            entityTypes.add(collection.getEntityTypeName());
            entityVertex.property("types", entityTypes.toString());
            wasAddedToCollection = true;
        } catch (IOException e) {
            // FIXME potential bug?
            LOG.error(Logmarkers.databaseInvariant, "property 'types' was not parseable: " + entityTypesStr);
        }
    }
    setModified(entityVertex, updateEntity.getModified());
    entityVertex.property("pid").remove();
    Vertex duplicate = duplicateVertex(traversal, entityVertex, indexHandler);
    listener.onPropertyUpdate(collection, Optional.of(entityVertex), duplicate);
    if (wasAddedToCollection) {
        listener.onAddToCollection(collection, Optional.of(entityVertex), duplicate);
    }
    return newRev;
}

Example 4 with Tuple

use of nl.knaw.huygens.timbuctoo.util.Tuple in project timbuctoo by HuygensING.

the class EntityToJsonMapper method mapEntity.

public ObjectNode mapEntity(Collection collection, ReadEntity entity, boolean withRelations, ExtraEntityMappingOptions extraEntityMappingOptions, ExtraRelationMappingOptions relationMappingOptions) {
    final ObjectNode mappedEntity = JsonNodeFactory.instance.objectNode();
    String id = entity.getId().toString();
    mappedEntity.set("@type", jsn(collection.getEntityTypeName()));
    mappedEntity.set("_id", jsn(id));
    mappedEntity.set("^rev", jsn(entity.getRev()));
    mappedEntity.set("^deleted", jsn(entity.getDeleted()));
    mappedEntity.set("^pid", jsn(entity.getPid()));
    if (entity.getRdfUri() != null) {
        mappedEntity.set("^rdfUri", jsn(entity.getRdfUri().toString()));
    }
    mappedEntity.set("^rdfAlternatives", jsnA(entity.getRdfAlternatives().stream().map(JsonBuilder::jsn)));
    JsonNode variationRefs = jsnA(entity.getTypes().stream().map(type -> {
        ObjectNode variationRef = jsnO();
        variationRef.set("id", jsn(id));
        variationRef.set("type", jsn(type));
        return variationRef;
    }));
    mappedEntity.set("@variationRefs", variationRefs);
    Change modified = entity.getModified();
    mappedEntity.set("^modified", mapChange(modified));
    Change created = entity.getCreated();
    mappedEntity.set("^created", mapChange(created));
    // translate TimProperties to Json
    JsonPropertyConverter jsonPropertyConverter = new JsonPropertyConverter(collection);
    entity.getProperties().forEach(prop -> {
        try {
            Tuple<String, JsonNode> convertedProperty = prop.convert(jsonPropertyConverter);
            mappedEntity.set(convertedProperty.getLeft(), convertedProperty.getRight());
        } catch (IOException e) {
            LOG.error(databaseInvariant, propConversionErrorMessage(id, prop));
            LOG.error("Exception message: {}", e.getMessage());
            LOG.debug("Stack trace", e);
        }
    });
    if (!Strings.isNullOrEmpty(entity.getDisplayName())) {
        mappedEntity.set("@displayName", jsn(entity.getDisplayName()));
    }
    extraEntityMappingOptions.execute(entity, mappedEntity);
    if (withRelations) {
        mappedEntity.set("@relationCount", jsn(entity.getRelations().size()));
        mappedEntity.set("@relations", mapRelations(entity.getRelations(), relationMappingOptions));
    }
    return mappedEntity;
}

Example 5 with Tuple

use of nl.knaw.huygens.timbuctoo.util.Tuple in project timbuctoo by HuygensING.

the class RdfUpload method upload.

@Consumes(MediaType.MULTIPART_FORM_DATA)
@POST
public Response upload(@FormDataParam("file") final InputStream rdfInputStream, @FormDataParam("file") final FormDataBodyPart body, @FormDataParam("fileMimeTypeOverride") final MediaType mimeTypeOverride, @FormDataParam("encoding") final String encoding, @FormDataParam("baseUri") final URI baseUri, @FormDataParam("defaultGraph") final URI defaultGraph, @HeaderParam("authorization") final String authHeader, @PathParam("userId") final String userId, @PathParam("dataSet") final String dataSetId, @QueryParam("forceCreation") boolean forceCreation, @QueryParam("async") final boolean async) throws ExecutionException, InterruptedException, LogStorageFailedException, DataStoreCreationException {
    final Either<Response, Response> result = authCheck.getOrCreate(authHeader, userId, dataSetId, forceCreation).flatMap(userAndDs -> authCheck.hasAdminAccess(userAndDs.getLeft(), userAndDs.getRight())).map((Tuple<User, DataSet> userDataSetTuple) -> {
        final MediaType mediaType = mimeTypeOverride == null ? body.getMediaType() : mimeTypeOverride;
        final DataSet dataSet = userDataSetTuple.getRight();
        ImportManager importManager = dataSet.getImportManager();
        if (mediaType == null || !importManager.isRdfTypeSupported(mediaType)) {
            return Response.status(Response.Status.BAD_REQUEST).type(MediaType.APPLICATION_JSON_TYPE).entity("{\"error\": \"We do not support the mediatype '" + mediaType + "'. Make sure to add the correct " + "mediatype to the file parameter. In curl you'd use `-F \"file=@<filename>;type=<mediatype>\"`. In a " + "webbrowser you probably have no way of setting the correct mimetype. So you can use a special " + "parameter " + "to override it: `formData.append(\"fileMimeTypeOverride\", \"<mimetype>\");`\"}").build();
        }
        if (StringUtils.isBlank(encoding)) {
            return Response.status(Response.Status.BAD_REQUEST).entity("Please provide an 'encoding' parameter").build();
        }
        if (StringUtils.isBlank(body.getContentDisposition().getFileName())) {
            return Response.status(400).entity("filename cannot be empty.").build();
        }
        Future<ImportStatus> promise = null;
        try {
            promise = importManager.addLog(baseUri == null ? dataSet.getMetadata().getBaseUri() : baseUri.toString(), defaultGraph == null ? dataSet.getMetadata().getBaseUri() : defaultGraph.toString(), body.getContentDisposition().getFileName(), rdfInputStream, Optional.of(Charset.forName(encoding)), mediaType);
        } catch (LogStorageFailedException e) {
            return Response.serverError().build();
        }
        if (!async) {
            return handleImportManagerResult(promise);
        }
        return Response.accepted().build();
    });
    if (result.isLeft()) {
        return result.getLeft();
    } else {
        return result.get();
    }
}