Java PathAnnotation類代碼示例

import org.apache.taverna.robundle.manifest.PathAnnotation; //導入依賴的package包/類
@SuppressWarnings("deprecation")
private Collection<URI> bundleSubjects() throws IOException {
	Set<URI> subjects = new HashSet<>();
	subjects.add(bundle.getRoot().toUri());
	for (PathMetadata pathMetadata : manifest.getAggregates()) {
		subjects.add(pathMetadata.getUri());
		if (pathMetadata.getFile() != null)
			subjects.add(pathMetadata.getFile().toUri());
		if (pathMetadata.getFolder() != null)
			subjects.add(pathMetadata.getFolder().toUri());
		// subjects.add(pathMetadata.getProxy());
	}
	for (PathAnnotation a : manifest.getAnnotations())
		subjects.add(a.getUri());
	subjects.remove(null);
	return subjects;
}
 

import org.apache.taverna.robundle.manifest.PathAnnotation; //導入依賴的package包/類
/**
 * Add an aggregation to the Research Object Bundle
 * @param roBundle The bundle to add to
 * @param fileName The file name of the aggregation
 * @param manifestAnnotations The list of manifest aggregations
 * @param content The identifier for the resource containing the
 *                body of the annotation
 * @throws IOException Errors accessing the bundle
 */
private void addAggregation(Bundle roBundle,
                            List<PathAnnotation> manifestAnnotations,
                            String fileName,
                            String content) throws IOException {
    Path annotations = Bundles.getAnnotations(roBundle);
    Path packedPath = annotations.resolve(fileName);
    Bundles.setStringValue(packedPath, content);
    PathAnnotation packedFile = new PathAnnotation();
    packedFile.setContent(packedPath);
    packedFile.setAbout(roBundle.getManifest().getId());
    packedFile.generateAnnotationId();
    manifestAnnotations.add(packedFile);
}
 

import org.apache.taverna.robundle.manifest.PathAnnotation; //導入依賴的package包/類
/**
 * Generate a Research Object bundle from lobstr and check it
 */
@Test
public void generateAndSaveROBundle() throws Exception {

    // RO details
    GitDetails lobSTRdraft3RODetails = new GitDetails("https://github.com/common-workflow-language/workflows.git",
            "933bf2a1a1cce32d88f88f136275535da9df0954", "lobstr-draft3/");

    // Create new RO bundle
    Bundle bundle = roBundleService.createBundle(lobSTRdraft3, lobSTRdraft3RODetails);
    Path bundleRoot = bundle.getRoot().resolve("workflow");

    // Check bundle exists
    assertNotNull(bundle);

    // Check basic manifest metadata
    Manifest manifest = bundle.getManifest();
    assertEquals("CWL Viewer", manifest.getCreatedBy().getName());
    assertEquals("https://view.commonwl.org", manifest.getCreatedBy().getUri().toString());
    assertEquals("Mark Robinson", manifest.getAuthoredBy().get(0).getName());
    assertEquals(new URI("https://w3id.org/cwl/view/git/933bf2a1a1cce32d88f88f136275535da9df0954/workflows/lobSTR/lobSTR-workflow.cwl"),
            manifest.getId());
    assertEquals(new URI("https://w3id.org/cwl/view/git/933bf2a1a1cce32d88f88f136275535da9df0954/workflows/lobSTR/lobSTR-workflow.cwl?format=ro"),
            manifest.getRetrievedFrom());

    // Check cwl aggregation information
    assertEquals(14, manifest.getAggregates().size());
    PathMetadata cwlAggregate = manifest.getAggregation(
            bundleRoot.resolve("lobSTR-workflow.cwl"));
    // NOTE: This permalink is based on local folder structure, here in tests
    // it is slightly different but normally would not be
    assertEquals("https://w3id.org/cwl/view/git/933bf2a1a1cce32d88f88f136275535da9df0954/lobstr-draft3/lobSTR-workflow.cwl?format=raw",
            cwlAggregate.getRetrievedFrom().toString());
    assertEquals("Mark Robinson", cwlAggregate.getAuthoredBy().get(0).getName());
    assertEquals("mailto:[email protected]", cwlAggregate.getAuthoredBy().get(0).getUri().toString());
    assertNull(cwlAggregate.getAuthoredBy().get(0).getOrcid());
    assertEquals("text/x-yaml", cwlAggregate.getMediatype());
    assertEquals("https://w3id.org/cwl/draft-3", cwlAggregate.getConformsTo().toString());

    // Check visualisations exist as aggregates
    PathMetadata pngAggregate = manifest.getAggregation(bundleRoot.resolve("visualisation.png"));
    assertEquals("image/png", pngAggregate.getMediatype());
    PathMetadata svgAggregate = manifest.getAggregation(bundleRoot.resolve("visualisation.svg"));
    assertEquals("image/svg+xml", svgAggregate.getMediatype());

    // Check RDF and packed workflows exist as annotations
    List<PathAnnotation> annotations = manifest.getAnnotations();
    assertEquals(2, annotations.size());
    assertEquals(new URI("annotations/merged.cwl"), annotations.get(0).getContent());
    assertEquals(new URI("annotations/workflow.ttl"), annotations.get(1).getContent());

    // Check git2prov link is in the history
    List<Path> history = manifest.getHistory();
    assertEquals(1, history.size());
    assertEquals("http:/git2prov.org/git2prov?giturl=https:/github.com/common-workflow-language/workflows.git&serialization=PROV-JSON",
            history.get(0).toString());

    // Save and check it exists in the temporary folder
    roBundleService.saveToFile(bundle);
    File[] fileList =  roBundleFolder.getRoot().listFiles();
    assertTrue(fileList.length == 1);
    for (File ro : fileList) {
        assertTrue(ro.getName().endsWith(".zip"));
        Bundle savedBundle = Bundles.openBundle(ro.toPath());
        assertNotNull(savedBundle);
    }

}