Examples with LogStorageFailedException nl.knaw.huygens.timbuctoo.v5.filestorage.exceptions.LogStorageFailedException used on opensource projects

Example 6 with LogStorageFailedException

use of nl.knaw.huygens.timbuctoo.v5.filestorage.exceptions.LogStorageFailedException 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 7 with LogStorageFailedException

use of nl.knaw.huygens.timbuctoo.v5.filestorage.exceptions.LogStorageFailedException in project timbuctoo by HuygensING.

the class RawUploadRdfSaverTest method usageTest.

@Test
public void usageTest() throws LogStorageFailedException {
    RdfToStringFaker rdfSerializer = new RdfToStringFaker();
    RawUploadRdfSaver instance = instanceWithRdfSerializer(rdfSerializer, dataSetMetadata);
    final String collection1 = instance.addCollection("collection1");
    ImportPropertyDescriptions importPropertyDescriptions = new ImportPropertyDescriptions();
    importPropertyDescriptions.getOrCreate(1).setPropertyName("propName1");
    importPropertyDescriptions.getOrCreate(2).setPropertyName("propName2");
    instance.addPropertyDescriptions(collection1, importPropertyDescriptions);
    instance.addEntity(collection1, ImmutableMap.of("propName1", "value1", "propName2", "val2"));
    instance.addEntity(collection1, ImmutableMap.of("propName1", "entVal1", "propName2", "entVal2"));
    final String collection2 = instance.addCollection("collection2");
    ImportPropertyDescriptions importPropertyDescriptions1 = new ImportPropertyDescriptions();
    importPropertyDescriptions1.getOrCreate(1).setPropertyName("prop3");
    importPropertyDescriptions1.getOrCreate(2).setPropertyName("prop4");
    instance.addPropertyDescriptions(collection2, importPropertyDescriptions1);
    instance.addEntity(collection2, ImmutableMap.of("prop3", "value1", "prop4", "val2"));
    instance.addEntity(collection2, ImmutableMap.of("prop3", "entVal1", "prop4", "entVal2"));
    String generatedRdf = rdfSerializer.toString();
    // Use assertEquals because the failing Hamcrest output is hard to compare
    String graphName = dataSetMetadata.getBaseUri();
    String fileUri = dataSetMetadata.getUriPrefix() + "rawData/fileName/";
    String prop = fileUri + "props/";
    String rowData = fileUri + "entities/";
    assertEquals(fileUri + " " + RDF_TYPE + " " + TIM_TABULAR_FILE + " " + graphName + "\n" + graphName + " " + PROV_DERIVED_FROM + " " + fileUri + " " + graphName + "\n" + fileUri + " " + TIM_MIMETYPE + " " + "application/octet-stream" + "^^" + STRING + " " + graphName + "\n" + fileUri + " " + RDFS_LABEL + " " + FILE_NAME + "^^" + STRING + " " + graphName + "\n" + fileUri + " " + PROV_ATTIME + " " + DATE + "^^" + XSD_DATETIMESTAMP + " " + graphName + "\n" + collection1 + " " + RDF_TYPE + " " + collection1 + "type " + graphName + "\n" + collection1 + " " + RDF_TYPE + " " + TIM_TABULAR_COLLECTION + " " + graphName + "\n" + collection1 + " " + RDFS_LABEL + " collection1" + "^^" + STRING + " " + graphName + "\n" + fileUri + " " + TIM_HASCOLLECTION + " " + collection1 + " " + graphName + "\n" + fileUri + " " + TIMBUCTOO_NEXT + " " + collection1 + " " + graphName + "\n" + prop + "tim_id " + RDF_TYPE + " " + TIM_PROP_DESC + " " + graphName + "\n" + collection1 + " " + TIM_HAS_PROPERTY + " " + prop + "tim_id " + graphName + "\n" + prop + "tim_id " + TIM_PROP_ID + " -1" + "^^" + INTEGER + " " + graphName + "\n" + prop + "tim_id " + RDFS_LABEL + " tim_id" + "^^" + STRING + " " + graphName + "\n" + prop + "propName1 " + RDF_TYPE + " " + TIM_PROP_DESC + " " + graphName + "\n" + collection1 + " " + TIM_HAS_PROPERTY + " " + prop + "propName1 " + graphName + "\n" + prop + "propName1 " + TIM_PROP_ID + " 1" + "^^" + INTEGER + " " + graphName + "\n" + prop + "propName1 " + RDFS_LABEL + " propName1" + "^^" + STRING + " " + graphName + "\n" + prop + "tim_id " + TIMBUCTOO_NEXT + " " + prop + "propName1 " + graphName + "\n" + prop + "propName2 " + RDF_TYPE + " " + TIM_PROP_DESC + " " + graphName + "\n" + collection1 + " " + TIM_HAS_PROPERTY + " " + prop + "propName2 " + graphName + "\n" + prop + "propName2 " + TIM_PROP_ID + " 2" + "^^" + INTEGER + " " + graphName + "\n" + prop + "propName2 " + RDFS_LABEL + " propName2" + "^^" + STRING + " " + graphName + "\n" + prop + "propName1 " + TIMBUCTOO_NEXT + " " + prop + "propName2 " + graphName + "\n" + rowData + "1 " + RDF_TYPE + " " + collection1 + " " + graphName + "\n" + collection1 + " " + TIM_HAS_ROW + " " + rowData + "1 " + graphName + "\n" + rowData + "1 " + prop + "propName1" + " value1" + "^^" + STRING + " " + graphName + "\n" + rowData + "1 " + prop + "propName2" + " val2" + "^^" + STRING + " " + graphName + "\n" + rowData + "1 " + prop + "tim_id" + " {UUID}" + "^^" + STRING + " " + graphName + "\n" + rowData + "2 " + RDF_TYPE + " " + collection1 + " " + graphName + "\n" + collection1 + " " + TIM_HAS_ROW + " " + rowData + "2 " + graphName + "\n" + rowData + "2 " + prop + "propName1" + " entVal1" + "^^" + STRING + " " + graphName + "\n" + rowData + "2 " + prop + "propName2" + " entVal2" + "^^" + STRING + " " + graphName + "\n" + rowData + "2 " + prop + "tim_id" + " {UUID}" + "^^" + STRING + " " + graphName + "\n" + collection2 + " " + RDF_TYPE + " " + collection2 + "type " + graphName + "\n" + collection2 + " " + RDF_TYPE + " " + TIM_TABULAR_COLLECTION + " " + graphName + "\n" + collection2 + " " + RDFS_LABEL + " collection2" + "^^" + STRING + " " + graphName + "\n" + fileUri + " " + TIM_HASCOLLECTION + " " + collection2 + " " + graphName + "\n" + collection1 + " " + TIMBUCTOO_NEXT + " " + collection2 + " " + graphName + "\n" + prop + "tim_id " + RDF_TYPE + " " + TIM_PROP_DESC + " " + graphName + "\n" + collection2 + " " + TIM_HAS_PROPERTY + " " + prop + "tim_id " + graphName + "\n" + prop + "tim_id " + TIM_PROP_ID + " -1" + "^^" + INTEGER + " " + graphName + "\n" + prop + "tim_id " + RDFS_LABEL + " tim_id" + "^^" + STRING + " " + graphName + "\n" + prop + "prop3 " + RDF_TYPE + " " + TIM_PROP_DESC + " " + graphName + "\n" + collection2 + " " + TIM_HAS_PROPERTY + " " + prop + "prop3 " + graphName + "\n" + prop + "prop3 " + TIM_PROP_ID + " 1" + "^^" + INTEGER + " " + graphName + "\n" + prop + "prop3 " + RDFS_LABEL + " prop3" + "^^" + STRING + " " + graphName + "\n" + prop + "tim_id " + TIMBUCTOO_NEXT + " " + prop + "prop3 " + graphName + "\n" + prop + "prop4 " + RDF_TYPE + " " + TIM_PROP_DESC + " " + graphName + "\n" + collection2 + " " + TIM_HAS_PROPERTY + " " + prop + "prop4 " + graphName + "\n" + prop + "prop4 " + TIM_PROP_ID + " 2" + "^^" + INTEGER + " " + graphName + "\n" + prop + "prop4 " + RDFS_LABEL + " prop4" + "^^" + STRING + " " + graphName + "\n" + prop + "prop3 " + TIMBUCTOO_NEXT + " " + prop + "prop4 " + graphName + "\n" + rowData + "3 " + RDF_TYPE + " " + collection2 + " " + graphName + "\n" + collection2 + " " + TIM_HAS_ROW + " " + rowData + "3 " + graphName + "\n" + rowData + "3 " + prop + "prop3" + " value1" + "^^" + STRING + " " + graphName + "\n" + rowData + "3 " + prop + "prop4" + " val2" + "^^" + STRING + " " + graphName + "\n" + rowData + "3 " + prop + "tim_id" + " {UUID}" + "^^" + STRING + " " + graphName + "\n" + rowData + "4 " + RDF_TYPE + " " + collection2 + " " + graphName + "\n" + collection2 + " " + TIM_HAS_ROW + " " + rowData + "4 " + graphName + "\n" + rowData + "4 " + prop + "prop3" + " entVal1" + "^^" + STRING + " " + graphName + "\n" + rowData + "4 " + prop + "prop4" + " entVal2" + "^^" + STRING + " " + graphName + "\n" + rowData + "4 " + prop + "tim_id" + " {UUID}" + "^^" + STRING + " " + graphName + "\n", generatedRdf.replaceAll("[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}", "{UUID}"));
}

Example 8 with LogStorageFailedException

use of nl.knaw.huygens.timbuctoo.v5.filestorage.exceptions.LogStorageFailedException in project timbuctoo by HuygensING.

the class RmlRdfCreator method sendQuads.

@Override
public void sendQuads(RdfSerializer saver, DataSet dataSet, Consumer<String> status) throws LogStorageFailedException {
    RdfDataSourceFactory dataSourceFactory = dataSet.getDataSource();
    final Model model = ModelFactory.createDefaultModel();
    try {
        model.read(new ByteArrayInputStream(rdfData.getBytes(StandardCharsets.UTF_8)), null, "JSON-LD");
    } catch (Exception e) {
        throw new LogStorageFailedException(e);
    }
    final RmlMappingDocument rmlMappingDocument = rmlBuilder.fromRdf(model, dataSourceFactory::apply);
    if (rmlMappingDocument.getErrors().size() > 0) {
        throw new LogStorageFailedException("failure: " + String.join("\nfailure: ", rmlMappingDocument.getErrors()) + "\n");
    }
    // FIXME: trigger onprefix for all rml prefixes
    // FIXME: store rml and retrieve it from tripleStore when mapping
    Stream<Quad> triples = rmlMappingDocument.execute(new ReportingErrorHandler(status));
    Iterator<Quad> iterator = triples.iterator();
    while (iterator.hasNext()) {
        Quad triple = iterator.next();
        saver.onQuad(triple.getSubject().getUri().get(), triple.getPredicate().getUri().get(), triple.getObject().getContent(), triple.getObject().getLiteralType().orElse(null), triple.getObject().getLiteralLanguage().orElse(null), baseUri);
    }
}

Example 9 with LogStorageFailedException

use of nl.knaw.huygens.timbuctoo.v5.filestorage.exceptions.LogStorageFailedException in project timbuctoo by HuygensING.

the class ImportManager method generateLog.

public Future<ImportStatus> generateLog(String baseUri, String defaultGraph, RdfCreator creator) throws LogStorageFailedException {
    importStatus.start(this.getClass().getSimpleName() + ".generateLog", baseUri);
    try {
        // add to the log structure
        int[] index = new int[1];
        logListStore.updateData(logList -> {
            index[0] = logList.addEntry(LogEntry.create(baseUri, defaultGraph, creator));
            return logList;
        });
        // schedule processing
        return executorService.submit(() -> processLogsUntil(index[0]));
    } catch (IOException e) {
        importStatus.addError("Could not update logList", e);
        throw new LogStorageFailedException(e);
    }
}

Example 10 with LogStorageFailedException

use of nl.knaw.huygens.timbuctoo.v5.filestorage.exceptions.LogStorageFailedException in project timbuctoo by HuygensING.

the class DataSetMetadataMutation method get.

@Override
public Object get(DataFetchingEnvironment env) {
    DataSet dataSet = MutationHelpers.getDataSet(env, dataSetRepository::getDataSet);
    MutationHelpers.checkAdminPermissions(env, dataSet.getMetadata());
    try {
        Map md = env.getArgument("metadata");
        final String baseUri = dataSet.getMetadata().getBaseUri().endsWith("/") ? dataSet.getMetadata().getBaseUri() : dataSet.getMetadata().getBaseUri() + "/";
        addMutation(dataSet, new PredicateMutation().entity(baseUri, this.<String>parseProp(md, "title", v -> replace("http://purl.org/dc/terms/title", value(v))), this.<String>parseProp(md, "description", v -> replace("http://purl.org/dc/terms/description", value(v, MARKDOWN))), this.<String>parseProp(md, "imageUrl", v -> replace("http://xmlns.com/foaf/0.1/depiction", value(v))), this.<String>parseProp(md, "license", v -> replace("http://purl.org/dc/terms/license", subject(v))), this.<Map>parseProp(md, "owner", owner -> getOrCreate("http://purl.org/dc/terms/rightsHolder", baseUri + "rightsHolder", this.<String>parseProp(owner, "name", v -> replace("http://schema.org/name", value(v))), this.<String>parseProp(owner, "email", v -> replace("http://schema.org/email", value(v))))), this.<Map>parseProp(md, "contact", owner -> getOrCreate("http://schema.org/ContactPoint", baseUri + "ContactPoint", this.<String>parseProp(owner, "name", v -> replace("http://schema.org/name", value(v))), this.<String>parseProp(owner, "email", v -> replace("http://schema.org/email", value(v))))), this.<Map>parseProp(md, "provenanceInfo", owner -> getOrCreate("http://purl.org/dc/terms/provenance", baseUri + "Provenance", this.<String>parseProp(owner, "title", v -> replace("http://purl.org/dc/terms/title", value(v))), this.<String>parseProp(owner, "body", v -> replace("http://purl.org/dc/terms/description", value(v, MARKDOWN)))))));
        return new DataSetWithDatabase(dataSet);
    } catch (LogStorageFailedException | InterruptedException | ExecutionException e) {
        throw new RuntimeException(e);
    }
}