Examples with OriginalMetadataAnnotation loci.formats.meta.OriginalMetadataAnnotation used on opensource projects

Example 1 with OriginalMetadataAnnotation

use of loci.formats.meta.OriginalMetadataAnnotation in project bioformats by openmicroscopy.

the class OMEXMLServiceImpl method populateOriginalMetadata.

/**
 * @see OMEXMLService#populateOriginalMetadata(loci.formats.ome.OMEXMLMetadata, Hashtable)
 */
@Override
public void populateOriginalMetadata(OMEXMLMetadata omexmlMeta, Hashtable<String, Object> metadata) {
    omexmlMeta.resolveReferences();
    if (metadata.size() == 0) {
        return;
    }
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexmlMeta.getRoot();
    StructuredAnnotations annotations = root.getStructuredAnnotations();
    if (annotations == null)
        annotations = new StructuredAnnotations();
    int annotationIndex = annotations.sizeOfXMLAnnotationList();
    if (annotationIndex > 0) {
        String lastAnnotationID = omexmlMeta.getXMLAnnotationID(annotationIndex - 1);
        String lastIndex = lastAnnotationID.substring(lastAnnotationID.lastIndexOf(":") + 1);
        try {
            int index = Integer.parseInt(lastIndex);
            while (index >= annotationIndex) {
                annotationIndex++;
            }
        } catch (NumberFormatException e) {
        }
    }
    for (String key : metadata.keySet()) {
        OriginalMetadataAnnotation annotation = new OriginalMetadataAnnotation();
        annotation.setID(MetadataTools.createLSID("Annotation", annotationIndex));
        annotation.setKeyValue(key, metadata.get(key).toString());
        annotations.addXMLAnnotation(annotation);
        annotationIndex++;
    }
    root.setStructuredAnnotations(annotations);
    omexmlMeta.setRoot(root);
}

Example 2 with OriginalMetadataAnnotation

use of loci.formats.meta.OriginalMetadataAnnotation in project bioformats by openmicroscopy.

the class OMEXMLServiceImpl method populateOriginalMetadata.

/**
 * @see OMEXMLService#populateOriginalMetadata(loci.formats.ome.OMEXMLMetadata, java.lang.String, java.lang.String)
 */
@Override
public void populateOriginalMetadata(OMEXMLMetadata omexmlMeta, String key, String value) {
    omexmlMeta.resolveReferences();
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexmlMeta.getRoot();
    StructuredAnnotations annotations = root.getStructuredAnnotations();
    if (annotations == null)
        annotations = new StructuredAnnotations();
    int annotationIndex = annotations.sizeOfXMLAnnotationList();
    if (annotationIndex > 0) {
        String lastAnnotationID = omexmlMeta.getXMLAnnotationID(annotationIndex - 1);
        String lastIndex = lastAnnotationID.substring(lastAnnotationID.lastIndexOf(":") + 1);
        try {
            int index = Integer.parseInt(lastIndex);
            while (index >= annotationIndex) {
                annotationIndex++;
            }
        } catch (NumberFormatException e) {
        }
    }
    OriginalMetadataAnnotation annotation = new OriginalMetadataAnnotation();
    annotation.setID(MetadataTools.createLSID("Annotation", annotationIndex));
    annotation.setKeyValue(key, value);
    annotations.addXMLAnnotation(annotation);
    root.setStructuredAnnotations(annotations);
    omexmlMeta.setRoot(root);
}

Example 3 with OriginalMetadataAnnotation

use of loci.formats.meta.OriginalMetadataAnnotation in project bioformats by openmicroscopy.

the class OMEXMLServiceImpl method getOriginalMetadata.

/**
 * @see OMEXMLService#getOriginalMetadata(loci.formats.ome.OMEXMLMetadata)
 */
@Override
public Hashtable getOriginalMetadata(OMEXMLMetadata omexmlMeta) {
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexmlMeta.getRoot();
    StructuredAnnotations annotations = root.getStructuredAnnotations();
    if (annotations == null) {
        return null;
    }
    Hashtable metadata = new Hashtable();
    for (int i = 0; i < annotations.sizeOfXMLAnnotationList(); i++) {
        XMLAnnotation annotation = annotations.getXMLAnnotation(i);
        if (annotation instanceof OriginalMetadataAnnotation) {
            OriginalMetadataAnnotation original = (OriginalMetadataAnnotation) annotation;
            metadata.put(original.getKey(), original.getValueForKey());
            continue;
        }
        String xml = annotation.getValue();
        try {
            Document annotationRoot = XMLTools.parseDOM(xml);
            NodeList metadataNodes = annotationRoot.getElementsByTagName("OriginalMetadata");
            for (int meta = 0; meta < metadataNodes.getLength(); meta++) {
                Element metadataNode = (Element) metadataNodes.item(meta);
                NodeList keys = metadataNode.getElementsByTagName("Key");
                NodeList values = metadataNode.getElementsByTagName("Value");
                for (int q = 0; q < keys.getLength(); q++) {
                    Node key = keys.item(q);
                    Node value = values.item(q);
                    metadata.put(key.getTextContent(), value.getTextContent());
                }
            }
            if (metadataNodes.getLength() == 0) {
                metadataNodes = annotationRoot.getDocumentElement().getChildNodes();
                for (int meta = 0; meta < metadataNodes.getLength(); meta++) {
                    // com.sun.org.apache.xerces.internal.dom.DeferredCommentImpl.
                    if (metadataNodes.item(meta) instanceof Element) {
                        Element node = (Element) metadataNodes.item(meta);
                        String name = node.getNodeName();
                        NamedNodeMap attrs = node.getAttributes();
                        Node value = attrs.getNamedItem("Value");
                        if (value != null) {
                            metadata.put(name, value.getNodeValue());
                        }
                    }
                }
            }
        } catch (ParserConfigurationException e) {
            LOGGER.debug("Failed to parse OriginalMetadata", e);
        } catch (SAXException e) {
            LOGGER.debug("Failed to parse OriginalMetadata", e);
        } catch (IOException e) {
            LOGGER.debug("Failed to parse OriginalMetadata", e);
        }
    }
    return metadata;
}

Example 4 with OriginalMetadataAnnotation

use of loci.formats.meta.OriginalMetadataAnnotation in project bioformats by openmicroscopy.

the class OMEXMLServiceTest method testOriginalMetadata.

@Test
public void testOriginalMetadata() throws ServiceException {
    OMEXMLMetadata metadata = service.createOMEXMLMetadata();
    service.populateOriginalMetadata(metadata, "testKey", "testValue");
    Hashtable metadataTable = service.getOriginalMetadata(metadata);
    assertEquals(metadataTable.size(), 1);
    assertTrue("testValue".equals(metadataTable.get("testKey")));
    OME root = (OME) metadata.getRoot();
    StructuredAnnotations annotations = root.getStructuredAnnotations();
    assertEquals(annotations.sizeOfXMLAnnotationList(), 1);
    XMLAnnotation xmlAnn = annotations.getXMLAnnotation(0);
    String txt = "<OriginalMetadata><Key>testKey</Key><Value>testValue</Value></OriginalMetadata>";
    assertEquals(txt, xmlAnn.getValue());
    OriginalMetadataAnnotation omAnn = (OriginalMetadataAnnotation) xmlAnn;
    assertEquals("testValue", omAnn.getValueForKey());
}