Examples with InstanceCollection eu.esdihumboldt.hale.common.instance.model.InstanceCollection used on opensource projects

Example 1 with InstanceCollection

use of eu.esdihumboldt.hale.common.instance.model.InstanceCollection in project hale by halestudio.

the class PartitioningWFSWriter method execute.

@Override
protected IOReport execute(final ProgressIndicator progress, final IOReporter reporter) throws IOProviderConfigurationException, IOException {
    progress.begin("Upload to WFS-T", IProgressMonitor.UNKNOWN);
    try {
        progress.setCurrentTask("Partitioning data");
        // create the partitioner
        InstanceCollectionPartitioner partitioner = StreamGmlWriter.getPartitioner(this, reporter);
        // partition the graph
        int threshold = getParameter(PARAM_INSTANCES_THRESHOLD).as(Integer.class, DEFAULT_INSTANCES_THRESHOLD);
        try (ResourceIterator<InstanceCollection> parts = partitioner.partition(getInstances(), threshold, reporter)) {
            if (partitioner.requiresImmediateConsumption()) {
                // handle all parts right here, one after another
                int partCount = 0;
                boolean failed = false;
                if (parts.hasNext()) {
                    while (parts.hasNext() && !progress.isCanceled()) {
                        partCount++;
                        SubtaskProgressIndicator partitionProgress = new SubtaskProgressIndicator(progress);
                        partitionProgress.begin("Assembling part " + partCount, ProgressIndicator.UNKNOWN);
                        InstanceCollection part = parts.next();
                        partitionProgress.end();
                        progress.setCurrentTask("Upload part " + partCount + ((part.hasSize()) ? (" (" + part.size() + " instances)") : ("")));
                        IOReport report = uploadInstances(part, reporter, new SubtaskProgressIndicator(progress));
                        if (!report.isSuccess()) {
                            failed = true;
                            reporter.error("Upload of part {0} - {1}", partCount, report.getSummary());
                        } else {
                            reporter.info("Upload of part {0} - {1}", partCount, report.getSummary());
                        }
                    }
                    reporter.setSuccess(!failed && reporter.getErrors().isEmpty());
                    if (!reporter.isSuccess()) {
                        reporter.setSummary("Errors during upload to WFS-T, please see the report.");
                    } else {
                        reporter.setSummary("Successfully uploaded data via WFS-T");
                    }
                } else {
                    reporter.setSuccess(false);
                    reporter.setSummary("Partitioning yielded no instances to upload");
                }
            } else {
                // can start requests with separate thread (potentially
                // threads, but tests with WFSes show that this usually is
                // too much to handle for the service)
                int partCount = 0;
                final AtomicBoolean failed = new AtomicBoolean();
                if (parts.hasNext()) {
                    ExecutorService requestThread = Executors.newSingleThreadExecutor();
                    while (parts.hasNext() && !progress.isCanceled()) {
                        partCount++;
                        SubtaskProgressIndicator partitionProgress = new SubtaskProgressIndicator(// only used for first
                        progress);
                        // partitioning
                        if (partCount == 1)
                            partitionProgress.begin("Assembling part " + partCount, ProgressIndicator.UNKNOWN);
                        // not
                        final InstanceCollection part = parts.next();
                        // safe
                        if (partCount == 1)
                            partitionProgress.end();
                        progress.setCurrentTask("Upload part " + partCount + ((part.hasSize()) ? (" (" + part.size() + " instances)") : ("")));
                        final int currentPart = partCount;
                        requestThread.submit(new Runnable() {

                            @Override
                            public void run() {
                                try {
                                    IOReport report = uploadInstances(part, reporter, new SubtaskProgressIndicator(progress));
                                    if (!report.isSuccess()) {
                                        failed.set(true);
                                        reporter.error(new IOMessageImpl("Upload of part " + currentPart + " - " + report.getSummary(), null));
                                    } else {
                                        reporter.info(new IOMessageImpl("Upload of part " + currentPart + " - " + report.getSummary(), null));
                                    }
                                } catch (Exception e) {
                                    failed.set(true);
                                    reporter.error(new IOMessageImpl("Upload of part " + currentPart + " failed", e));
                                }
                            }
                        });
                    }
                    // wait for requests completion
                    requestThread.shutdown();
                    if (!requestThread.awaitTermination(24, TimeUnit.HOURS)) {
                        reporter.error(new IOMessageImpl("Timeout reached waiting for completion of WFS requests", null));
                    }
                    reporter.setSuccess(!failed.get() && reporter.getErrors().isEmpty());
                    if (!reporter.isSuccess()) {
                        reporter.setSummary("Errors during upload to WFS-T, please see the report.");
                    } else {
                        reporter.setSummary("Successfully uploaded data via WFS-T");
                    }
                } else {
                    reporter.setSuccess(false);
                    reporter.setSummary("Partitioning yielded no instances to upload");
                }
            }
        }
    } catch (Exception e) {
        reporter.error(new IOMessageImpl("Error during attempt to upload to WFS-T", e));
        reporter.setSuccess(false);
    } finally {
        progress.end();
    }
    return reporter;
}

Example 2 with InstanceCollection

use of eu.esdihumboldt.hale.common.instance.model.InstanceCollection in project hale by halestudio.

the class XLSInstanceIOTest method test.

/**
 * Exports the instances created by
 * {@link XLSInstanceWriterTestExamples#createInstanceCollection} into a
 * temporary XLS file by executing {@link XLSInstanceWriter#execute}.
 * Afterwards, the schema is read by {@link XLSSchemaReader} and the
 * instances are loaded by {@link XLSInstanceReader}. Each of the imported
 * instances are compared with the original instances. In addtion, a
 * different set of instances is compared with the imported instances.
 */
@Test
public void test() {
    // set instances to xls instance writer
    XLSInstanceWriter writer = new XLSInstanceWriter();
    InstanceCollection instances = XLSInstanceWriterTestExamples.createInstanceCollection();
    IContentType contentType = HalePlatform.getContentTypeManager().getContentType("eu.esdihumboldt.hale.io.xls.xls");
    writer.setParameter(InstanceTableIOConstants.SOLVE_NESTED_PROPERTIES, Value.of(false));
    File tempDir = Files.createTempDir();
    File tempFile = new File(tempDir, "data.xls");
    writer.setInstances(instances);
    try {
        // write instances to a temporary XLS file
        writer.setTarget(new FileIOSupplier(tempFile));
        writer.setContentType(contentType);
        IOReport report = writer.execute(null);
        assertTrue(report.isSuccess());
    } catch (IOProviderConfigurationException | IOException e) {
        fail("Execution of xls instance writer failed.");
    }
    // read the schema from the temporary XLS file
    XLSSchemaReader schemaReader = new XLSSchemaReader();
    schemaReader.setContentType(contentType);
    schemaReader.setSource(new FileIOSupplier(tempFile));
    schemaReader.setParameter(CommonSchemaConstants.PARAM_TYPENAME, Value.of("ItemType"));
    schemaReader.setParameter(InstanceTableIOConstants.SOLVE_NESTED_PROPERTIES, Value.of(false));
    schemaReader.setParameter(InstanceTableIOConstants.SHEET_INDEX, Value.of(0));
    try {
        IOReport report = schemaReader.execute(null);
        assertTrue(report.isSuccess());
    } catch (IOProviderConfigurationException | IOException e1) {
        fail("Execution of schema reader failed.");
    }
    Schema schema = schemaReader.getSchema();
    // read the instances form the temporary XLS file
    XLSInstanceReader reader = new XLSInstanceReader();
    reader.setSourceSchema(schema);
    reader.setParameter(CommonSchemaConstants.PARAM_SKIP_FIRST_LINE, Value.of(true));
    reader.setParameter(CommonSchemaConstants.PARAM_TYPENAME, Value.of("ItemType"));
    reader.setParameter(InstanceTableIOConstants.SOLVE_NESTED_PROPERTIES, Value.of(false));
    // read sheet with index 0 since there is only one sheet
    reader.setParameter(InstanceTableIOConstants.SHEET_INDEX, Value.of(0));
    reader.setContentType(contentType);
    reader.setSource(new FileIOSupplier(tempFile));
    try {
        IOReport report = reader.execute(null);
        assertTrue(report.isSuccess());
    } catch (IOProviderConfigurationException | IOException e) {
        fail("Execution of xls instance reader failed.");
    }
    // compare size of instance collection
    InstanceCollection inst = reader.getInstances();
    assertEquals(4, inst.size());
    // check if instance collection contains current instance
    Iterator<Instance> instanceIt = inst.iterator();
    while (instanceIt.hasNext()) {
        Instance instance = instanceIt.next();
        assertTrue(contains(instances.iterator(), instance));
    }
    // other instance should be contained in the imported instances
    InstanceCollection falseInstances = XLSInstanceWriterTestExamples.createFalseTestInstanceCollection();
    instanceIt = inst.iterator();
    while (instanceIt.hasNext()) {
        Instance instance = instanceIt.next();
        assertFalse(contains(falseInstances.iterator(), instance));
    }
    // delete file and temporary directory
    tempFile.delete();
    tempDir.delete();
}

Example 3 with InstanceCollection

use of eu.esdihumboldt.hale.common.instance.model.InstanceCollection in project hale by halestudio.

the class XLSReaderTest method testPropertyType.

/**
 * Test - check declaration of properties' datatype.
 *
 * @throws Exception , if an error occurs
 */
@Test
public void testPropertyType() throws Exception {
    Schema schema = readXLSSchema("/data/simpleOneSheet.xls", 0, typeName, "java.lang.Integer,java.lang.String,java.lang.String");
    // Test property datatype
    TypeDefinition schemaType = schema.getType(QName.valueOf(typeName));
    Binding binding = schemaType.getChildren().iterator().next().asProperty().getPropertyType().getConstraint(Binding.class);
    assertTrue("The type is not an Integer.", binding.getBinding().equals(Integer.class));
    // ### Instance
    InstanceCollection instances = readXLSInstances("/data/simpleOneSheet.xls", 0, typeName, true, schema);
    assertTrue(instances.hasSize());
    assertEquals(numberOfInstances, instances.size());
    // Check the values of the first (type) instance
    Instance instance = instances.iterator().next();
    Object[] value = instance.getProperty(QName.valueOf(properties[0]));
    assertEquals(Integer.valueOf(dataFirstColumn[0]), value[0]);
    assertTrue(value[0] instanceof Integer);
}

Example 4 with InstanceCollection

use of eu.esdihumboldt.hale.common.instance.model.InstanceCollection in project hale by halestudio.

the class XLSReaderTest method testReadBlankCells.

/**
 * Test - read xls file and data. Check handled blank cells.
 *
 * @throws Exception , if an error occurs
 */
@Test
public void testReadBlankCells() throws Exception {
    // read schema ###
    Schema schema = readXLSSchema("/data/blankEntries.xls", 0, typeName, "java.lang.String,java.lang.String,java.lang.String");
    // read instances ###
    InstanceCollection instances = readXLSInstances("/data/blankEntries.xls", 0, typeName, true, schema);
    // Number of instances should be the same
    assertTrue(instances.hasSize());
    assertEquals(numberOfInstances, instances.size());
    // Check blank property of first type
    Instance instance = instances.iterator().next();
    Object[] value;
    value = instance.getProperty(QName.valueOf(properties[1]));
    // There should be no value, therefore the length of the value-array has
    // to be
    // 0
    assertEquals(0, value.length);
    // check other values to be correct
    value = instance.getProperty(QName.valueOf(properties[0]));
    assertEquals(dataFirstColumn[0], value[0]);
    value = instance.getProperty(QName.valueOf(properties[2]));
    assertEquals(dataFirstColumn[2], value[0]);
}

Example 5 with InstanceCollection

use of eu.esdihumboldt.hale.common.instance.model.InstanceCollection in project hale by halestudio.

the class XLSReaderTest method testReadSameFileDiffSheet.

/**
 * Test - read a sample xls schema and data from same file and different
 * sheets. Check skip first
 *
 * @throws Exception , if an error occurs
 */
@Test
public void testReadSameFileDiffSheet() throws Exception {
    String sourceLocation = "/data/simpleTwoSheet.xls";
    Schema schema = readXLSSchema(sourceLocation, 0, typeName, "java.lang.String,java.lang.String,java.lang.String");
    TypeDefinition schemaType = schema.getType(QName.valueOf(typeName));
    // Check every property for their existence
    for (String propertyName : properties) {
        assertEquals(propertyName, schemaType.getChild(QName.valueOf(propertyName)).getDisplayName());
    }
    // Instance Read ###
    InstanceCollection instances = readXLSInstances(sourceLocation, 1, typeName, false, schema);
    assertTrue(instances.hasSize());
    assertEquals(numberOfInstances, instances.size());
    // get Type to check property definition (schema and instance
    // combination)
    TypeDefinition type = instances.iterator().next().getDefinition();
    ChildDefinition<?> child = null;
    assertEquals(typeName, type.getDisplayName());
    for (int i = 0; i < properties.length; i++) {
        child = type.getChild(QName.valueOf(properties[i]));
        assertEquals(properties[i], child.getDisplayName());
    }
    // Check the values of the first (type) instance
    Instance instance = instances.iterator().next();
    Object[] value;
    for (int i = 0; i < dataFirstColumn.length; i++) {
        value = instance.getProperty(QName.valueOf(properties[i]));
        assertEquals(dataFirstColumn[i], value[0]);
        assertTrue(value[0] instanceof String);
    }
}