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

Example 1 with XMLMockObjects

use of ome.specification.XMLMockObjects 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 XMLMockObjects

use of ome.specification.XMLMockObjects 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 XMLMockObjects

use of ome.specification.XMLMockObjects 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 XMLMockObjects

use of ome.specification.XMLMockObjects 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);
        }
    }
}

Example 5 with XMLMockObjects

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

the class FakeReader method populateSPW.

private int populateSPW(MetadataStore store, int screens, int plates, int rows, int cols, int fields, int acqs, boolean withMicrobeam) {
    final XMLMockObjects xml = new XMLMockObjects();
    OME ome = null;
    if (screens == 0) {
        ome = xml.createPopulatedPlate(plates, rows, cols, fields, acqs, withMicrobeam);
    } else {
        ome = xml.createPopulatedScreen(screens, plates, rows, cols, fields, acqs, withMicrobeam);
    }
    if (withMicrobeam)
        roiCount = roiCount + plates;
    ;
    getOmeXmlMetadata().setRoot(new OMEXMLMetadataRoot(ome));
    // copy populated SPW metadata into destination MetadataStore
    getOmeXmlService().convertMetadata(omeXmlMetadata, store);
    domains = new String[] { FormatTools.HCS_DOMAIN };
    return ome.sizeOfImageList();
}