Examples with Entity nl.knaw.huygens.timbuctoo.v5.serializable.dto.Entity used on opensource projects

Example 1 with Entity

use of nl.knaw.huygens.timbuctoo.v5.serializable.dto.Entity 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 Entity

use of nl.knaw.huygens.timbuctoo.v5.serializable.dto.Entity in project timbuctoo by HuygensING.

the class TabularUpload method upload.

@Consumes(MediaType.MULTIPART_FORM_DATA)
@Produces(MediaType.APPLICATION_JSON)
@POST
public Response upload(@FormDataParam("file") final InputStream rdfInputStream, @FormDataParam("file") final FormDataBodyPart body, @FormDataParam("file") final FormDataContentDisposition fileInfo, @FormDataParam("fileMimeTypeOverride") final MediaType mimeTypeOverride, FormDataMultiPart formData, @HeaderParam("authorization") final String authHeader, @PathParam("userId") final String ownerId, @PathParam("dataSetId") final String dataSetId, @QueryParam("forceCreation") boolean forceCreation) throws DataStoreCreationException, FileStorageFailedException, ExecutionException, InterruptedException, LogStorageFailedException {
    final Either<Response, Response> result = authCheck.getOrCreate(authHeader, ownerId, dataSetId, forceCreation).flatMap(userAndDs -> authCheck.hasAdminAccess(userAndDs.getLeft(), userAndDs.getRight())).map(userAndDs -> {
        final MediaType mediaType = mimeTypeOverride == null ? body.getMediaType() : mimeTypeOverride;
        Optional<Loader> loader = LoaderFactory.createFor(mediaType.toString(), formData.getFields().entrySet().stream().filter(entry -> entry.getValue().size() > 0).filter(entry -> entry.getValue().get(0) != null).filter(entry -> MediaTypes.typeEqual(MediaType.TEXT_PLAIN_TYPE, entry.getValue().get(0).getMediaType())).collect(Collectors.toMap(Map.Entry::getKey, entry -> entry.getValue().get(0).getValue())));
        if (!loader.isPresent()) {
            return errorResponseHelper.error(400, "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>\");`");
        }
        final DataSet dataSet = userAndDs.getRight();
        ImportManager importManager = dataSet.getImportManager();
        if (StringUtils.isBlank(fileInfo.getName())) {
            return Response.status(400).entity("filename cannot be empty.").build();
        }
        try {
            String fileToken = importManager.addFile(rdfInputStream, fileInfo.getFileName(), mediaType);
            Future<ImportStatus> promise = importManager.generateLog(dataSet.getMetadata().getBaseUri(), dataSet.getMetadata().getBaseUri(), new TabularRdfCreator(loader.get(), fileToken, fileInfo.getFileName()));
            return handleImportManagerResult(promise);
        } catch (FileStorageFailedException | LogStorageFailedException e) {
            LOG.error("Tabular upload failed", e);
            return Response.serverError().build();
        }
    });
    if (result.isLeft()) {
        return result.getLeft();
    } else {
        return result.get();
    }
}

Example 3 with Entity

use of nl.knaw.huygens.timbuctoo.v5.serializable.dto.Entity in project timbuctoo by HuygensING.

the class JsonCrudService method getCollection.

public List<ObjectNode> getCollection(String collectionName, int rows, int start, boolean withRelations) throws InvalidCollectionException {
    final Collection collection = mappings.getCollection(collectionName).orElseThrow(() -> new InvalidCollectionException(collectionName));
    DataStream<ReadEntity> entities = timDbAccess.getCollection(collection, start, rows, withRelations, (traversalSource, vre) -> {
    }, (entity1, entityVertex, target, relationRef) -> {
    });
    List<ObjectNode> result = entities.map(entity -> entityToJsonMapper.mapEntity(collection, entity, withRelations, (readEntity, resultJson) -> {
    }, (relationRef, resultJson) -> {
    }));
    return result;
}

Example 4 with Entity

use of nl.knaw.huygens.timbuctoo.v5.serializable.dto.Entity in project timbuctoo by HuygensING.

the class Index method createNew.

@POST
public Response createNew(@PathParam("collection") String collectionName, @HeaderParam("Authorization") String authHeader, ObjectNode body) throws URISyntaxException {
    Optional<User> user;
    try {
        user = userValidator.getUserFromAccessToken(authHeader);
    } catch (UserValidationException e) {
        user = Optional.empty();
    }
    Optional<User> newUser = user;
    if (!user.isPresent()) {
        return Response.status(Response.Status.UNAUTHORIZED).build();
    } else {
        return transactionEnforcer.executeAndReturn(timbuctooActions -> {
            JsonCrudService crudService = crudServiceFactory.newJsonCrudService(timbuctooActions);
            try {
                UUID id = crudService.create(collectionName, body, newUser.get());
                return commitAndReturn(Response.created(SingleEntity.makeUrl(collectionName, id)).build());
            } catch (InvalidCollectionException e) {
                return rollbackAndReturn(Response.status(Response.Status.NOT_FOUND).entity(jsnO("message", jsn(e.getMessage()))).build());
            } catch (IOException e) {
                return rollbackAndReturn(Response.status(Response.Status.BAD_REQUEST).entity(jsnO("message", jsn(e.getMessage()))).build());
            } catch (PermissionFetchingException e) {
                return rollbackAndReturn(Response.status(Response.Status.FORBIDDEN).entity(jsnO("message", jsn(e.getMessage()))).build());
            }
        });
    }
}

Example 5 with Entity

use of nl.knaw.huygens.timbuctoo.v5.serializable.dto.Entity in project timbuctoo by HuygensING.

the class SingleEntity method put.

@PUT
public Response put(@PathParam("collection") String collectionName, @HeaderParam("Authorization") String authHeader, @PathParam("id") UUIDParam id, ObjectNode body) {
    Optional<User> user;
    try {
        user = userValidator.getUserFromAccessToken(authHeader);
    } catch (UserValidationException e) {
        user = Optional.empty();
    }
    Optional<User> newUser = user;
    if (!newUser.isPresent()) {
        return Response.status(Response.Status.UNAUTHORIZED).build();
    } else {
        UpdateMessage updateMessage = transactionEnforcer.executeAndReturn(timbuctooActions -> {
            JsonCrudService crudService = crudServiceFactory.newJsonCrudService(timbuctooActions);
            try {
                crudService.replace(collectionName, id.get(), body, newUser.get());
                return commitAndReturn(UpdateMessage.success());
            } catch (InvalidCollectionException e) {
                return rollbackAndReturn(UpdateMessage.failure(e.getMessage(), Response.Status.NOT_FOUND));
            } catch (NotFoundException e) {
                return rollbackAndReturn(UpdateMessage.failure("not found", Response.Status.NOT_FOUND));
            } catch (IOException e) {
                return rollbackAndReturn(UpdateMessage.failure(e.getMessage(), Response.Status.BAD_REQUEST));
            } catch (AlreadyUpdatedException e) {
                return rollbackAndReturn(UpdateMessage.failure("Entry was already updated", Response.Status.EXPECTATION_FAILED));
            } catch (PermissionFetchingException e) {
                return rollbackAndReturn(UpdateMessage.failure(e.getMessage(), Response.Status.FORBIDDEN));
            }
        });
        // committed in the database
        if (updateMessage.isSuccess()) {
            return transactionEnforcer.executeAndReturn(timbuctooActions -> {
                JsonCrudService crudService = crudServiceFactory.newJsonCrudService(timbuctooActions);
                try {
                    JsonNode jsonNode = crudService.get(collectionName, id.get());
                    return commitAndReturn(Response.ok(jsonNode).build());
                } catch (InvalidCollectionException e) {
                    return rollbackAndReturn(Response.status(Response.Status.NOT_FOUND).entity(jsnO("message", jsn("Collection '" + collectionName + "' was available a moment ago, but not anymore: " + e.getMessage()))).build());
                } catch (NotFoundException e) {
                    return rollbackAndReturn(Response.status(Response.Status.NOT_FOUND).entity(jsnO("message", jsn("not found"))).build());
                }
            });
        } else {
            return Response.status(updateMessage.getResponseStatus()).entity(jsnO("message", jsn(updateMessage.getException().get()))).build();
        }
    }
}