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

Example 1 with DataSetRepository

use of nl.knaw.huygens.timbuctoo.v5.dataset.DataSetRepository 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 DataSetRepository

use of nl.knaw.huygens.timbuctoo.v5.dataset.DataSetRepository 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 3 with DataSetRepository

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

the class ViewConfigMutation method get.

@Override
public Object get(DataFetchingEnvironment env) {
    String collectionUri = env.getArgument("collectionUri");
    Object viewConfig = env.getArgument("viewConfig");
    DataSet dataSet = MutationHelpers.getDataSet(env, dataSetRepository::getDataSet);
    MutationHelpers.checkAdminPermissions(env, dataSet.getMetadata());
    try {
        MutationHelpers.addMutation(dataSet, new PredicateMutation().entity(collectionUri, replace(HAS_VIEW_CONFIG, value(OBJECT_MAPPER.writeValueAsString(viewConfig)))));
        return viewConfig;
    } catch (LogStorageFailedException | InterruptedException | ExecutionException | JsonProcessingException e) {
        throw new RuntimeException(e);
    }
}

Example 4 with DataSetRepository

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

the class PermissionBasedFieldVisibilityTest method getFieldDefinitionsShowsNonDataSetFields.

@Test
public void getFieldDefinitionsShowsNonDataSetFields() throws Exception {
    final DataSetRepository dataSetRepository = mock(DataSetRepository.class);
    DataSet dataSet = createDataSetWithUserPermissions("user__dataSetUserHasAccessTo", Sets.newHashSet(Permission.READ));
    DataSet dataSet2 = createDataSetWithUserPermissions("user__dataSetUserDoesNotHasAccessTo", Sets.newHashSet());
    Collection<DataSet> dataSetCollection = Sets.newHashSet(dataSet, dataSet2);
    given(dataSetRepository.getDataSets()).willReturn(dataSetCollection);
    final PermissionBasedFieldVisibility permissionBasedFieldVisibility = new PermissionBasedFieldVisibility(userPermissionCheck, dataSetRepository);
    final GraphQLFieldsContainer graphQlFieldsContainer = createGraphQlFieldsContainer("user__dataSetUserHasAccessTo", "user__dataSetUserDoesNotHasAccessTo", "nonDataSetField");
    List<GraphQLFieldDefinition> retrievedGraphQlFieldDefinitions = permissionBasedFieldVisibility.getFieldDefinitions(graphQlFieldsContainer);
    assertThat(retrievedGraphQlFieldDefinitions, contains(hasProperty("name", is("user__dataSetUserHasAccessTo")), hasProperty("name", is("nonDataSetField"))));
}

Example 5 with DataSetRepository

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

the class PermissionBasedFieldVisibilityTest method getFieldDefinitionReturnsFieldDefinitionIfNotDataSetField.

@Test
public void getFieldDefinitionReturnsFieldDefinitionIfNotDataSetField() throws Exception {
    final DataSetRepository dataSetRepository = mock(DataSetRepository.class);
    DataSet dataSet = createDataSetWithUserPermissions("user__dataSetUserHasAccessTo", Sets.newHashSet(Permission.READ));
    DataSet dataSet2 = createDataSetWithUserPermissions("user__dataSetUserDoesNotHasAccessTo", Sets.newHashSet());
    Collection<DataSet> dataSetCollection = Sets.newHashSet(dataSet, dataSet2);
    given(dataSetRepository.getDataSets()).willReturn(dataSetCollection);
    final PermissionBasedFieldVisibility permissionBasedFieldVisibility = new PermissionBasedFieldVisibility(userPermissionCheck, dataSetRepository);
    final GraphQLFieldsContainer graphQlFieldsContainer = createGraphQlFieldsContainer("user__dataSetUserHasAccessTo", "user__dataSetUserDoesNotHasAccessTo", "nonDataSetField");
    GraphQLFieldDefinition retrievedGraphQlFieldDefinition = permissionBasedFieldVisibility.getFieldDefinition(graphQlFieldsContainer, // new String to make sure the
    new String("nonDataSetField"));
    // contents are compared not the instance.
    assertThat(retrievedGraphQlFieldDefinition, hasProperty("name", is("nonDataSetField")));
}