Examples with RdfSerializer nl.knaw.huygens.timbuctoo.v5.rdfio.RdfSerializer used on opensource projects

Example 1 with RdfSerializer

use of nl.knaw.huygens.timbuctoo.v5.rdfio.RdfSerializer in project timbuctoo by HuygensING.

the class TabularRdfCreator method sendQuads.

@Override
public void sendQuads(RdfSerializer saver, DataSet dataSet, Consumer<String> statusConsumer) throws LogStorageFailedException {
    try (CachedFile file = dataSet.getImportManager().getFile(fileToken)) {
        final RawUploadRdfSaver rawUploadRdfSaver = new RawUploadRdfSaver(dataSet.getMetadata(), file.getFile().getName(), file.getMimeType(), saver, fileName, Clock.systemUTC());
        loader.loadData(Lists.newArrayList(tuple(fileName, file.getFile())), new Importer(new StateMachine<>(rawUploadRdfSaver), new ResultReporter(statusConsumer)));
    } catch (Exception e) {
        throw new LogStorageFailedException(e);
    }
}

Example 2 with RdfSerializer

use of nl.knaw.huygens.timbuctoo.v5.rdfio.RdfSerializer in project timbuctoo by HuygensING.

the class ImportManager method processLogsUntil.

private synchronized ImportStatus processLogsUntil(int maxIndex) {
    importStatus.start(this.getClass().getSimpleName() + ".processLogs", null);
    ListIterator<LogEntry> unprocessed = logListStore.getData().getUnprocessed();
    boolean dataWasAdded = false;
    while (unprocessed.hasNext() && unprocessed.nextIndex() <= maxIndex) {
        int index = unprocessed.nextIndex();
        LogEntry entry = unprocessed.next();
        importStatus.startEntry(entry);
        if (entry.getLogToken().isPresent()) {
            // logToken
            String logToken = entry.getLogToken().get();
            try (CachedLog log = logStorage.getLog(logToken)) {
                final Stopwatch stopwatch = Stopwatch.createStarted();
                for (RdfProcessor processor : subscribedProcessors) {
                    if (processor.getCurrentVersion() <= index) {
                        String msg = "******* " + processor.getClass().getSimpleName() + " Started importing full log...";
                        LOG.info(msg);
                        importStatus.setStatus(msg);
                        RdfParser rdfParser = serializerFactory.makeRdfParser(log);
                        processor.start(index);
                        rdfParser.importRdf(log, entry.getBaseUri(), entry.getDefaultGraph(), processor);
                        processor.commit();
                    }
                }
                long elapsedTime = stopwatch.elapsed(TimeUnit.SECONDS);
                String msg = "Finished importing. Total import took " + elapsedTime + " seconds.";
                LOG.info(msg);
                importStatus.setStatus(msg);
                dataWasAdded = true;
            } catch (Exception e) {
                LOG.error("Processing log failed", e);
                importStatus.addError("Processing log failed", e);
            }
            // Update the log, even after RdfProcessingFailedException | IOException
            try {
                logListStore.updateData(logList -> {
                    logList.markAsProcessed(index);
                    return logList;
                });
            } catch (IOException e) {
                LOG.error("Updating the log failed", e);
                importStatus.addError("Updating log failed", e);
            }
        } else {
            // no logToken
            RdfCreator creator = entry.getRdfCreator().get();
            String token = "";
            MediaType mediaType;
            Optional<Charset> charset;
            File tempFile = null;
            try {
                tempFile = File.createTempFile("log_to_generate", "nq");
                try (OutputStream stream = new GZIPOutputStream(new FileOutputStream(tempFile))) {
                    if (creator instanceof PlainRdfCreator) {
                        try (RdfSerializer serializer = serializerFactory.makeRdfSerializer(stream)) {
                            mediaType = serializer.getMediaType();
                            charset = Optional.of(serializer.getCharset());
                            ((PlainRdfCreator) creator).sendQuads(serializer, dataSet, importStatus::setStatus);
                        } catch (Exception e) {
                            LOG.error("Log generation failed", e);
                            importStatus.addError("Log generation failed", e);
                            break;
                        }
                    } else {
                        try (RdfPatchSerializer srlzr = serializerFactory.makeRdfPatchSerializer(stream, entry.getBaseUri())) {
                            mediaType = srlzr.getMediaType();
                            charset = Optional.of(srlzr.getCharset());
                            ((PatchRdfCreator) creator).sendQuads(srlzr, importStatus::setStatus, dataSet);
                        } catch (Exception e) {
                            LOG.error("Log generation failed", e);
                            importStatus.addError("Log generation failed", e);
                            break;
                        }
                    }
                }
                try (InputStream inputStream = new GZIPInputStream(new FileInputStream(tempFile))) {
                    token = logStorage.saveLog(inputStream, "log_generated_by_" + creator.getClass().getSimpleName(), mediaType, charset);
                }
                LogEntry entryWithLog;
                entryWithLog = LogEntry.addLogToEntry(entry, token);
                unprocessed.set(entryWithLog);
                token = "";
                // move back to process this item again
                unprocessed.previous();
            } catch (Exception e) {
                if (token.isEmpty()) {
                    LOG.error("Log processing failed", e);
                } else {
                    LOG.error("Log processing failed. Log created but not added to the list!", e);
                }
                importStatus.addError("Log processing failed", e);
                break;
            } finally {
                if (tempFile != null) {
                    tempFile.delete();
                }
            }
        }
        // end else with no condition
        importStatus.finishEntry();
    }
    // end main while loop
    if (dataWasAdded) {
        webhooks.run();
    }
    importStatus.finishList();
    // update log.json
    try {
        logListStore.updateData(Function.identity());
    } catch (IOException e) {
        LOG.error("Updating the log failed", e);
        importStatus.addError("Updating log failed", e);
    }
    return importStatus;
}

Example 3 with RdfSerializer

use of nl.knaw.huygens.timbuctoo.v5.rdfio.RdfSerializer in project timbuctoo by HuygensING.

the class BdbRmlDataSourceStoreTest method itWorks.

@Test
public void itWorks() throws Exception {
    BdbNonPersistentEnvironmentCreator dbCreator = new BdbNonPersistentEnvironmentCreator();
    DataSetMetaData dataSetMetadata = new BasicDataSetMetaData("userid", "datasetid", "http://timbuctoo.huygens.knaw.nl/v5/userid/datasetid", "http://example.org/prefix/", false, false);
    final RmlDataSourceStore rmlDataSourceStore = new BdbRmlDataSourceStore(dbCreator.getDatabase("userid", "datasetid", "rmlSource", true, TupleBinding.getPrimitiveBinding(String.class), TupleBinding.getPrimitiveBinding(String.class), new StringStringIsCleanHandler()), new ImportStatus(new LogList()));
    RdfSerializer rdfSerializer = new RmlDataSourceRdfSerializer(rmlDataSourceStore);
    RawUploadRdfSaver rawUploadRdfSaver = new RawUploadRdfSaver(dataSetMetadata, "fileName", APPLICATION_OCTET_STREAM_TYPE, rdfSerializer, "origFileName", Clock.systemUTC());
    final String inputCol1 = rawUploadRdfSaver.addCollection("collection1");
    ImportPropertyDescriptions importPropertyDescriptions = new ImportPropertyDescriptions();
    importPropertyDescriptions.getOrCreate(1).setPropertyName("propName1");
    importPropertyDescriptions.getOrCreate(2).setPropertyName("propName2");
    rawUploadRdfSaver.addPropertyDescriptions(inputCol1, importPropertyDescriptions);
    rawUploadRdfSaver.addEntity(inputCol1, ImmutableMap.of("propName1", "value1", "propName2", "val2"));
    rawUploadRdfSaver.addEntity(inputCol1, ImmutableMap.of("propName1", "entVal1", "propName2", "entVal2"));
    final String inputCol2 = rawUploadRdfSaver.addCollection("collection2");
    ImportPropertyDescriptions importPropertyDescriptions1 = new ImportPropertyDescriptions();
    importPropertyDescriptions1.getOrCreate(1).setPropertyName("prop3");
    importPropertyDescriptions1.getOrCreate(2).setPropertyName("prop4");
    rawUploadRdfSaver.addPropertyDescriptions(inputCol2, importPropertyDescriptions1);
    rawUploadRdfSaver.addEntity(inputCol2, ImmutableMap.of("prop3", "value1", "prop4", "val2"));
    rawUploadRdfSaver.addEntity(inputCol2, ImmutableMap.of("prop3", "entVal1", "prop4", "entVal2"));
    rdfSerializer.close();
    RdfDataSource rdfDataSource = new RdfDataSource(rmlDataSourceStore, inputCol1, new JexlRowFactory(ImmutableMap.of(), new HashMapBasedJoinHandler()));
    RdfDataSource rdfDataSource2 = new RdfDataSource(rmlDataSourceStore, inputCol2, new JexlRowFactory(ImmutableMap.of(), new HashMapBasedJoinHandler()));
    final List<String> collection1;
    final List<String> collection2;
    try (Stream<Row> stream = rdfDataSource.getRows(new ThrowingErrorHandler())) {
        collection1 = stream.map(x -> x.getRawValue("propName1") + ":" + x.getRawValue("propName2")).collect(toList());
    }
    try (Stream<Row> stream = rdfDataSource2.getRows(new ThrowingErrorHandler())) {
        collection2 = stream.map(x -> x.getRawValue("prop3") + ":" + x.getRawValue("prop4")).collect(toList());
    }
    assertThat(collection1, contains("value1:val2", "entVal1:entVal2"));
    assertThat(collection2, contains("value1:val2", "entVal1:entVal2"));
    dbCreator.close();
}

Example 4 with RdfSerializer

use of nl.knaw.huygens.timbuctoo.v5.rdfio.RdfSerializer 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 5 with RdfSerializer

use of nl.knaw.huygens.timbuctoo.v5.rdfio.RdfSerializer 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);
    }
}