Examples with XMLWriter ome.specification.XMLWriter used on opensource projects

Example 1 with XMLWriter

use of ome.specification.XMLWriter in project bioformats by openmicroscopy.

the class SchemaCurrent_TO_2010_06_Test method testDowngradeTo201006ImageNoMetadata.

/**
 * Tests the XSLT used to downgrade from current schema to 2010-06.
 * An XML file with an image is created and the stylesheet is applied.
 * @throws Exception Thrown if an error occurred.
 */
@Test(enabled = false)
public void testDowngradeTo201006ImageNoMetadata() throws Exception {
    File inFile = File.createTempFile("testDowngradeTo201006ImageNoMetadata", "." + OME_XML_FORMAT);
    files.add(inFile);
    File middleFileA = File.createTempFile("testDowngradeTo201006ImageNoMetadataMiddleA", "." + OME_XML_FORMAT);
    files.add(middleFileA);
    File outputFile = File.createTempFile("testDowngradeTo201006ImageNoMetadataOutput", "." + OME_XML_FORMAT);
    files.add(outputFile);
    XMLMockObjects xml = new XMLMockObjects();
    XMLWriter writer = new XMLWriter();
    writer.writeFile(inFile, xml.createImage(), true);
    // Dump out file for debuging
    // File fCheckIn  = new File("/Users/andrew/Desktop/wibble1.xml");
    // writer.writeFile(fCheckIn , xml.getRoot(), true);
    transformFileWithStream(inFile, middleFileA, STYLESHEET_A);
    transformFileWithStream(middleFileA, outputFile, STYLESHEET_B);
    Document doc = anOmeValidator.parseFileWithStreamArray(outputFile, schemaArray);
    Assert.assertNotNull(doc);
    // Should only have one root node i.e. OME node
    NodeList list = doc.getChildNodes();
    Assert.assertEquals(list.getLength(), 1);
    Node root = list.item(0);
    Assert.assertEquals(root.getNodeName(), XMLWriter.OME_TAG);
    // now analyse the root node
    list = root.getChildNodes();
    String name;
    Node n;
    Document docSrc = anOmeValidator.parseFile(inFile, null);
    Node rootSrc = docSrc.getChildNodes().item(0);
    Node imageNode = null;
    NodeList listSrc = rootSrc.getChildNodes();
    for (int i = 0; i < listSrc.getLength(); i++) {
        n = listSrc.item(i);
        name = n.getNodeName();
        if (name != null) {
            if (name.contains(XMLWriter.IMAGE_TAG))
                imageNode = n;
        }
    }
    for (int i = 0; i < list.getLength(); i++) {
        n = list.item(i);
        name = n.getNodeName();
        if (name != null) {
            // TODO: add other node
            if (name.contains(XMLWriter.IMAGE_TAG) && imageNode != null)
                checkImageNode(n, imageNode);
        }
    }
}

Example 2 with XMLWriter

use of ome.specification.XMLWriter in project bioformats by openmicroscopy.

the class SchemaCurrent_TO_2003_FC_Test method testDowngradeTo2003FCImageNoMetadata.

/**
 * Tests the XSLT used to downgrade from current schema to 2003-FC.
 * An XML file with an image is created and the stylesheet is applied.
 * @throws Exception Thrown if an error occurred.
 */
@Test(enabled = false)
public void testDowngradeTo2003FCImageNoMetadata() throws Exception {
    File inFile = File.createTempFile("testDowngradeTo2003FCImageNoMetadata", "." + OME_XML_FORMAT);
    files.add(inFile);
    File middleFileA = File.createTempFile("testDowngradeTo2003FCImageNoMetadataMiddleA", "." + OME_XML_FORMAT);
    files.add(middleFileA);
    File middleFileB = File.createTempFile("testDowngradeTo2003FCImageNoMetadataMiddleB", "." + OME_XML_FORMAT);
    files.add(middleFileB);
    File outputFile = File.createTempFile("testDowngradeTo2003FCImageNoMetadataOutput", "." + OME_XML_FORMAT);
    files.add(outputFile);
    XMLMockObjects xml = new XMLMockObjects();
    XMLWriter writer = new XMLWriter();
    writer.writeFile(inFile, xml.createImage(), true);
    transformFileWithStream(inFile, middleFileA, STYLESHEET_A);
    transformFileWithStream(middleFileA, middleFileB, STYLESHEET_B);
    transformFileWithStream(middleFileB, outputFile, STYLESHEET_C);
    Document doc = anOmeValidator.parseFileWithStreamArray(outputFile, schemaArray);
    Assert.assertNotNull(doc);
    // Should only have one root node i.e. OME node
    NodeList list = doc.getChildNodes();
    Assert.assertEquals(list.getLength(), 1);
    Node root = list.item(0);
    Assert.assertEquals(root.getNodeName(), XMLWriter.OME_TAG);
    // now analyse the root node
    list = root.getChildNodes();
    String name;
    Node n;
    Document docSrc = anOmeValidator.parseFile(inFile, null);
    Node rootSrc = docSrc.getChildNodes().item(0);
    Node imageNode = null;
    NodeList listSrc = rootSrc.getChildNodes();
    for (int i = 0; i < listSrc.getLength(); i++) {
        n = listSrc.item(i);
        name = n.getNodeName();
        if (name != null) {
            if (name.contains(XMLWriter.IMAGE_TAG))
                imageNode = n;
        }
    }
    for (int i = 0; i < list.getLength(); i++) {
        n = list.item(i);
        name = n.getNodeName();
        if (name != null) {
            // TODO: add other node
            if (name.contains(XMLWriter.IMAGE_TAG) && imageNode != null)
                checkImageNode(n, imageNode);
        }
    }
}

Example 3 with XMLWriter

use of ome.specification.XMLWriter in project bioformats by openmicroscopy.

the class Schema_Transform_Test method createImageFile.

/**
 * Generates an <code>OME-XML</code> file.
 *
 * @param index The type of image to import. One of the constants defined
 *              by this class.
 * @return The image file.
 * @throws Exception Thrown if an error occurred.
 */
private File createImageFile(int index) throws Exception {
    // First create an image
    File f = File.createTempFile("tempFileName", "." + OME_XML);
    XMLMockObjects xml = new XMLMockObjects();
    XMLWriter writer = new XMLWriter();
    if (index == IMAGE_ROI) {
        writer.writeFile(f, xml.createImageWithROI(), true);
    } else if (index == IMAGE_ANNOTATED_DATA) {
        writer.writeFile(f, xml.createImageWithAnnotatedAcquisitionData(), true);
    } else {
        writer.writeFile(f, xml.createImageWithAcquisitionData(), true);
    }
    return f;
}

Example 4 with XMLWriter

use of ome.specification.XMLWriter in project bioformats by openmicroscopy.

the class SchemaCurrent_TO_2008_02_Test method testDowngradeTo200802ImageNoMetadata.

/**
 * Tests the XSLT used to downgrade from current schema to 2008-02.
 * An XML file with an image is created and the stylesheet is applied.
 * @throws Exception Thrown if an error occurred.
 */
@Test(enabled = false)
public void testDowngradeTo200802ImageNoMetadata() throws Exception {
    File inFile = File.createTempFile("testDowngradeTo200802ImageNoMetadata", "." + OME_XML_FORMAT);
    files.add(inFile);
    File middleFileA = File.createTempFile("testDowngradeTo200802ImageNoMetadataMiddleA", "." + OME_XML_FORMAT);
    files.add(middleFileA);
    File middleFileB = File.createTempFile("testDowngradeTo200802ImageNoMetadataMiddleB", "." + OME_XML_FORMAT);
    files.add(middleFileB);
    File outputFile = File.createTempFile("testDowngradeTo200802ImageNoMetadataOutput", "." + OME_XML_FORMAT);
    files.add(outputFile);
    XMLMockObjects xml = new XMLMockObjects();
    XMLWriter writer = new XMLWriter();
    writer.writeFile(inFile, xml.createImage(), true);
    transformFileWithStream(inFile, middleFileA, STYLESHEET_A);
    transformFileWithStream(middleFileA, middleFileB, STYLESHEET_B);
    transformFileWithStream(middleFileB, outputFile, STYLESHEET_C);
    Document doc = anOmeValidator.parseFileWithStreamArray(outputFile, schemaArray);
    Assert.assertNotNull(doc);
    // Should only have one root node i.e. OME node
    NodeList list = doc.getChildNodes();
    Assert.assertEquals(list.getLength(), 1);
    Node root = list.item(0);
    Assert.assertEquals(root.getNodeName(), XMLWriter.OME_TAG);
    // now analyse the root node
    list = root.getChildNodes();
    String name;
    Node n;
    Document docSrc = anOmeValidator.parseFile(inFile, null);
    Node rootSrc = docSrc.getChildNodes().item(0);
    Node imageNode = null;
    NodeList listSrc = rootSrc.getChildNodes();
    for (int i = 0; i < listSrc.getLength(); i++) {
        n = listSrc.item(i);
        name = n.getNodeName();
        if (name != null) {
            if (name.contains(XMLWriter.IMAGE_TAG))
                imageNode = n;
        }
    }
    for (int i = 0; i < list.getLength(); i++) {
        n = list.item(i);
        name = n.getNodeName();
        if (name != null) {
            // TODO: add other node
            if (name.contains(XMLWriter.IMAGE_TAG) && imageNode != null)
                checkImageNode(n, imageNode);
        }
    }
}