Examples with JaxbAlignmentReader eu.esdihumboldt.hale.common.align.io.impl.JaxbAlignmentReader used on opensource projects

Example 1 with JaxbAlignmentReader

use of eu.esdihumboldt.hale.common.align.io.impl.JaxbAlignmentReader in project hale by halestudio.

the class AppSchemaFileWriterTest method loadTestProject.

@BeforeClass
public static void loadTestProject() {
    try {
        URL archiveLocation = AppSchemaFileWriterTest.class.getResource(PROJECT_LOCATION);
        ArchiveProjectReader projectReader = new ArchiveProjectReader();
        projectReader.setSource(new DefaultInputSupplier(archiveLocation.toURI()));
        IOReport report = projectReader.execute(new LogProgressIndicator());
        if (!report.isSuccess()) {
            throw new RuntimeException("project reader execution failed");
        }
        tempDir = projectReader.getTemporaryFiles().iterator().next();
        project = projectReader.getProject();
        assertNotNull(project);
        sourceSchemaSpace = new DefaultSchemaSpace();
        targetSchemaSpace = new DefaultSchemaSpace();
        // load schemas
        List<IOConfiguration> resources = project.getResources();
        for (IOConfiguration resource : resources) {
            String actionId = resource.getActionId();
            String providerId = resource.getProviderId();
            // get provider
            IOProvider provider = null;
            IOProviderDescriptor descriptor = IOProviderExtension.getInstance().getFactory(providerId);
            if (descriptor == null) {
                throw new RuntimeException("Could not load I/O provider with ID: " + resource.getProviderId());
            }
            provider = descriptor.createExtensionObject();
            provider.loadConfiguration(resource.getProviderConfiguration());
            prepareProvider(provider, project, tempDir.toURI());
            IOReport providerReport = provider.execute(new LogProgressIndicator());
            if (!providerReport.isSuccess()) {
                throw new RuntimeException("I/O provider execution failed");
            }
            // TODO: could (should?) be done by an advisor
            if (provider instanceof SchemaReader) {
                Schema schema = ((SchemaReader) provider).getSchema();
                if (actionId.equals(SchemaIO.ACTION_LOAD_SOURCE_SCHEMA)) {
                    sourceSchemaSpace.addSchema(schema);
                } else if (actionId.equals(SchemaIO.ACTION_LOAD_TARGET_SCHEMA)) {
                    targetSchemaSpace.addSchema(schema);
                }
            }
        }
        // load alignment
        List<ProjectFileInfo> projectFiles = project.getProjectFiles();
        for (ProjectFileInfo projectFile : projectFiles) {
            if (projectFile.getName().equals(AlignmentIO.PROJECT_FILE_ALIGNMENT)) {
                AlignmentReader alignReader = new JaxbAlignmentReader();
                alignReader.setSource(new DefaultInputSupplier(projectFile.getLocation()));
                alignReader.setSourceSchema(sourceSchemaSpace);
                alignReader.setTargetSchema(targetSchemaSpace);
                alignReader.setPathUpdater(new PathUpdate(null, null));
                IOReport alignReport = alignReader.execute(new LogProgressIndicator());
                if (!alignReport.isSuccess()) {
                    throw new RuntimeException("alignment reader execution failed");
                }
                alignment = alignReader.getAlignment();
                assertNotNull(alignment);
                break;
            }
        }
    } catch (Exception e) {
        log.error("Exception occurred", e);
        fail("Test project could not be loaded: " + e.getMessage());
    }
}

Example 2 with JaxbAlignmentReader

use of eu.esdihumboldt.hale.common.align.io.impl.JaxbAlignmentReader in project hale by halestudio.

the class AppSchemaIsolatedWorkspacesMappingTest method init.

@BeforeClass
public static void init() throws Exception {
    TestUtil.startConversionService();
    sourceSchemaSpace = new DefaultSchemaSpace();
    targetSchemaSpace = new DefaultSchemaSpace();
    Schema source = loadSchema(new HaleSchemaReader(), SOURCE_SCHEMA_PATH);
    assertNotNull(source);
    sourceSchemaSpace.addSchema(source);
    Schema target = loadSchema(new XmlSchemaReader(), TARGET_SCHEMA_STATIONS_PATH);
    assertNotNull(target);
    targetSchemaSpace.addSchema(target);
    // make sure MeasurementsType is included in the mapping relevant types
    List<TypeDefinition> mappingRelevantTypes = new ArrayList<>();
    mappingRelevantTypes.add(targetSchemaSpace.getType(MEASUREMENTS_QNAME));
    targetSchemaSpace.toggleMappingRelevant(mappingRelevantTypes);
    assertEquals(3, targetSchemaSpace.getMappingRelevantTypes().size());
    alignment = loadAlignment(new JaxbAlignmentReader(), ALIGNMENT_PATH);
    assertNotNull(alignment);
}