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

Example 11 with DataSetMetaData

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

the class DataSetRepository method publishDataSet.

public void publishDataSet(User user, String ownerId, String dataSetName) throws DataSetPublishException {
    Optional<DataSet> dataSet = getDataSet(user, ownerId, dataSetName);
    try {
        if (dataSet.isPresent() && permissionFetcher.getPermissions(user, dataSet.get().getMetadata()).contains(Permission.ADMIN)) {
            DataSetMetaData dataSetMetaData = dataSet.get().getMetadata();
            dataSetMetaData.publish();
            try {
                dataStorage.getDataSetStorage(ownerId, dataSetName).saveMetaData(dataSetMetaData);
            } catch (DataStorageSaveException e) {
                throw new DataSetPublishException(e);
            }
        }
    } catch (PermissionFetchingException e) {
        throw new DataSetPublishException(e);
    }
}

Example 12 with DataSetMetaData

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

the class DataSetRepository method createDataSet.

public DataSet createDataSet(User user, String dataSetId) throws DataStoreCreationException, IllegalDataSetNameException {
    // The ownerId might not be valid (i.e. a safe string). We make it safe here:
    // dataSetId is under the control of the user so we simply throw if it's not valid
    String ownerPrefix = "u" + user.getPersistentId();
    final String baseUri = rdfIdHelper.dataSetBaseUri(ownerPrefix, dataSetId);
    String uriPrefix;
    if (!baseUri.endsWith("/") && !baseUri.endsWith("#") && !baseUri.endsWith("?")) {
        // #boo&foo=bar
        if (baseUri.contains("#") || baseUri.contains("?")) {
            if (baseUri.endsWith("&")) {
                uriPrefix = baseUri;
            } else {
                uriPrefix = baseUri + "&";
            }
        } else {
            uriPrefix = baseUri + "/";
        }
    } else {
        uriPrefix = baseUri;
    }
    final DataSetMetaData dataSet = new BasicDataSetMetaData(ownerPrefix, dataSetId, baseUri, uriPrefix, false, publicByDefault);
    try {
        dataStorage.getDataSetStorage(ownerPrefix, dataSetId).saveMetaData(dataSet);
    } catch (DataStorageSaveException e) {
        throw new DataStoreCreationException(e);
    }
    synchronized (dataSetMap) {
        Map<String, DataSet> userDataSets = dataSetMap.computeIfAbsent(ownerPrefix, key -> new HashMap<>());
        if (!userDataSets.containsKey(dataSetId)) {
            try {
                permissionFetcher.initializeOwnerAuthorization(user, dataSet.getOwnerId(), dataSet.getDataSetId());
                userDataSets.put(dataSetId, dataSet(dataSet, executorService, rdfBaseUri, dataStoreFactory, () -> onUpdated.accept(dataSet.getCombinedId()), dataStorage.getDataSetStorage(ownerPrefix, dataSetId)));
            } catch (PermissionFetchingException | AuthorizationCreationException | IOException e) {
                throw new DataStoreCreationException(e);
            }
        }
        return userDataSets.get(dataSetId);
    }
}

Example 13 with DataSetMetaData

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

the class DataSet method dataSet.

public static DataSet dataSet(DataSetMetaData metadata, ExecutorService executorService, String rdfPrefix, BdbEnvironmentCreator dataStoreFactory, Runnable onUpdated, DataSetStorage dataSetStorage) throws IOException, DataStoreCreationException {
    String userId = metadata.getOwnerId();
    String dataSetId = metadata.getDataSetId();
    File descriptionFile = dataSetStorage.getResourceSyncDescriptionFile();
    FileStorage fileStorage = dataSetStorage.getFileStorage();
    ImportManager importManager = new ImportManager(dataSetStorage.getLogList(), fileStorage, fileStorage, dataSetStorage.getLogStorage(), executorService, dataSetStorage.getRdfIo(), onUpdated);
    try {
        importManager.subscribeToRdf(new RdfDescriptionSaver(descriptionFile, metadata.getBaseUri(), importManager.getImportStatus()));
    } catch (ParserConfigurationException | SAXException e) {
        LOG.error("Could not construct import manager of data set", e);
    }
    final TupleBinding<String> stringBinding = TupleBinding.getPrimitiveBinding(String.class);
    try {
        StringStringIsCleanHandler stringStringIsCleanHandler = new StringStringIsCleanHandler();
        BdbTripleStore quadStore = new BdbTripleStore(dataStoreFactory.getDatabase(userId, dataSetId, "rdfData", true, stringBinding, stringBinding, stringStringIsCleanHandler));
        final BdbTypeNameStore typeNameStore = new BdbTypeNameStore(new BdbBackedData(dataStoreFactory.getDatabase(userId, dataSetId, "typenames", false, stringBinding, stringBinding, stringStringIsCleanHandler)), rdfPrefix);
        final BdbSchemaStore schema = new BdbSchemaStore(new BdbBackedData(dataStoreFactory.getDatabase(userId, dataSetId, "schema", false, stringBinding, stringBinding, stringStringIsCleanHandler)), importManager.getImportStatus());
        final BdbTruePatchStore truePatchStore = new BdbTruePatchStore(dataStoreFactory.getDatabase(userId, dataSetId, "truePatch", true, stringBinding, stringBinding, stringStringIsCleanHandler));
        final TupleBinding<Integer> integerBinding = TupleBinding.getPrimitiveBinding(Integer.class);
        final UpdatedPerPatchStore updatedPerPatchStore = new UpdatedPerPatchStore(dataStoreFactory.getDatabase(userId, dataSetId, "updatedPerPatch", true, integerBinding, stringBinding, new IsCleanHandler<Integer, String>() {

            @Override
            public Integer getKey() {
                return Integer.MAX_VALUE;
            }

            @Override
            public String getValue() {
                return "isClean";
            }
        }));
        final BdbRmlDataSourceStore rmlDataSourceStore = new BdbRmlDataSourceStore(dataStoreFactory.getDatabase(userId, dataSetId, "rmlSource", true, stringBinding, stringBinding, stringStringIsCleanHandler), importManager.getImportStatus());
        VersionStore versionStore = new VersionStore(dataStoreFactory.getDatabase(userId, dataSetId, "versions", false, stringBinding, integerBinding, new IsCleanHandler<String, Integer>() {

            @Override
            public String getKey() {
                return "isClean";
            }

            @Override
            public Integer getValue() {
                return Integer.MAX_VALUE;
            }
        }));
        final StoreUpdater storeUpdater = new StoreUpdater(dataStoreFactory, quadStore, typeNameStore, truePatchStore, updatedPerPatchStore, Lists.newArrayList(schema, rmlDataSourceStore), versionStore, importManager.getImportStatus());
        importManager.subscribeToRdf(storeUpdater);
        ImmutableDataSet dataSet = ImmutableDataSet.builder().ownerId(userId).dataSetName(dataSetId).bdbEnvironmentCreator(dataStoreFactory).metadata(metadata).quadStore(quadStore).typeNameStore(typeNameStore).schemaStore(schema).dataSource(new RdfDataSourceFactory(rmlDataSourceStore)).schemaStore(schema).importManager(importManager).dataSetStorage(dataSetStorage).build();
        importManager.init(dataSet);
        if (!quadStore.isClean() || !typeNameStore.isClean() || !schema.isClean() || !truePatchStore.isClean() || !updatedPerPatchStore.isClean() || !rmlDataSourceStore.isClean() || !versionStore.isClean()) {
            LOG.error("Data set '{}__{}' data is corrupted, starting to reimport.", userId, dataSetId);
            quadStore.empty();
            typeNameStore.empty();
            schema.empty();
            truePatchStore.empty();
            updatedPerPatchStore.empty();
            rmlDataSourceStore.empty();
            versionStore.empty();
            importManager.reprocessLogs();
        } else {
            // process unprocessed logs
            importManager.processLogs();
        }
        return dataSet;
    } catch (BdbDbCreationException e) {
        throw new DataStoreCreationException(e.getCause());
    }
}

Example 14 with DataSetMetaData

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

the class RawUploadRdfSaverTest method setUp.

@Before
public void setUp() throws Exception {
    rdfSerializer = mock(RdfSerializer.class);
    dataSetMetadata = new BasicDataSetMetaData("userid", "dataset", "http://timbuctoo.huygens.knaw.nl/v5/datasets/userid/dataset", "http://example.org/prefix/", false, false);
    instance = instanceWithRdfSerializer(rdfSerializer, dataSetMetadata);
}

Example 15 with DataSetMetaData

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

the class MutationHelpers method checkAdminPermissions.

public static void checkAdminPermissions(DataFetchingEnvironment env, DataSetMetaData dataSetMetaData) throws RuntimeException {
    ContextData contextData = env.getContext();
    UserPermissionCheck userPermissionCheck = contextData.getUserPermissionCheck();
    if (!userPermissionCheck.getPermissions(dataSetMetaData).contains(Permission.ADMIN)) {
        throw new RuntimeException("You are not admin of this dataset");
    }
}