protected void transformXML(File[] files) {
int number = 0;
try {
SAXBuilder builder = new SAXBuilder();
for (int f = 0; f < files.length; f++) {
int fn = f + 1;
// split by treatment
Document doc = builder.build(files[f]);
Element root = doc.getRootElement();
List<Element> treatments =
XPath.selectNodes(root, "/tax:taxonx/tax:taxonxBody/tax:treatment");
// detach all but one treatments from doc
ArrayList<Element> saved = new ArrayList<Element>();
for (int t = 1; t < treatments.size(); t++) {
Element e = treatments.get(t);
doc.removeContent(e);
e.detach();
saved.add(e);
}
// now doc is a template to create other treatment files
// root.detach();
formatDescription(
(Element) XPath.selectSingleNode(root, "/tax:taxonx/tax:taxonxBody/tax:treatment"),
".//tax:div[@type='description']",
".//tax:p",
fn,
0);
root.detach();
writeTreatment2Transformed(root, fn, 0);
listener.info((number++) + "", fn + "_0.xml"); // list the file on GUI here
getDescriptionFrom(root, fn, 0);
// replace treatement in doc with a new treatment in saved
Iterator<Element> it = saved.iterator();
int count = 1;
while (it.hasNext()) {
Element e = it.next();
Element body = root.getChild("taxonxBody", root.getNamespace());
Element treatment =
(Element) XPath.selectSingleNode(root, "/tax:taxonx/tax:taxonxBody/tax:treatment");
// in treatment/div[@type="description"], replace <tax:p> tag with <description
// pid="1.txtp436_1.txt">
int index = body.indexOf(treatment);
e = formatDescription(e, ".//tax:div[@type='description']", ".//tax:p", fn, count);
body.setContent(index, e);
// write each treatment as a file in the target/transfromed folder
// write description text in the target/description folder
root.detach();
writeTreatment2Transformed(root, fn, count);
listener.info((number++) + "", fn + "_" + count + ".xml"); // list the file on GUI here
getDescriptionFrom(root, fn, count);
count++;
}
}
} catch (Exception e) {
e.printStackTrace();
LOGGER.error("Type4Transformer : error.", e);
}
}
/**
* Used for editing : swaps 2 elements.
*
* @param el1
* @param el2
* @throws Exception
*/
protected void swapElements(Element el1, Element el2) throws Exception {
Element parent = el1.getParentElement();
if (parent == null) {
throw new IllegalArgumentException("No parent element for swapping");
}
int index1 = parent.indexOf(el1);
if (index1 == -1) {
throw new IllegalArgumentException("Element 1 not found for swapping");
}
int index2 = parent.indexOf(el2);
if (index2 == -1) {
throw new IllegalArgumentException("Element 2 not found for swapping");
}
Element el1Spare = (Element) el1.clone();
parent.setContent(index1, (Element) el2.clone());
parent.setContent(index2, el1Spare);
}
private void doit()
throws JDOMException, IOException, SAXException, ParserConfigurationException,
TransformerConfigurationException, TransformerException {
Document CATALOG_DOCUMENT = FileIO.readDocumentFromLocalFile(CATALOG_FILE);
List l =
XPath.newInstance(
"//resource[contains(@type,'exmaralda') and descendant::exmaralda-coma[@type='local']]")
.selectNodes(CATALOG_DOCUMENT);
for (Object o : l) {
Element resourceElement = (Element) o;
Element comaCorpusElement =
(Element)
XPath.newInstance("descendant::exmaralda-coma[@type='local']")
.selectSingleNode(resourceElement);
String url = comaCorpusElement.getAttributeValue("url").substring(7);
System.out.println("Processing " + url);
COMACorpus comaCorpus = new COMACorpus();
comaCorpus.readCorpus(new File(url), true);
// resourceElement.removeChildren("annotation");
HashSet<String> annotationNames = comaCorpus.getAnnotationNames();
for (String annotationName : annotationNames) {
if (XPath.newInstance("descendant::annotation[@category='" + annotationName + "']")
.selectSingleNode(resourceElement)
== null) {
Element annotationElement = new Element("annotation");
annotationElement.setAttribute("category", annotationName);
int index =
resourceElement.indexOf(
(Element)
XPath.newInstance("descendant::short-description[last()]")
.selectSingleNode(resourceElement));
resourceElement.addContent(index + 1, annotationElement);
}
}
FileIO.writeDocumentToLocalFile(CATALOG_FILE, CATALOG_DOCUMENT);
}
}
/**
* For Ajax Editing : removes an element from a metadata ([del] link).
*
* @param dbms
* @param session
* @param id
* @param ref
* @param parentRef
* @return
* @throws Exception
*/
public synchronized Element deleteElementEmbedded(
Dbms dbms, UserSession session, String id, String ref, String parentRef) throws Exception {
String schema = dataManager.getMetadataSchema(dbms, id);
// --- get metadata from session
Element md = getMetadataFromSession(session, id);
// --- locate the geonet:info element and clone for later re-use
Element info = (Element) (md.getChild(Edit.RootChild.INFO, Edit.NAMESPACE)).clone();
md.removeChild(Edit.RootChild.INFO, Edit.NAMESPACE);
// --- get element to remove
EditLib editLib = dataManager.getEditLib();
Element el = editLib.findElement(md, ref);
if (el == null) throw new IllegalStateException(MSG_ELEMENT_NOT_FOUND_AT_REF + ref);
String uName = el.getName();
Namespace ns = el.getNamespace();
Element parent = el.getParentElement();
Element result = null;
if (parent != null) {
int me = parent.indexOf(el);
// --- check and see whether the element to be deleted is the last one of its kind
Filter elFilter = new ElementFilter(uName, ns);
if (parent.getContent(elFilter).size() == 1) {
// --- get geonet child element with attribute name = unqualified name
Filter chFilter = new ElementFilter(Edit.RootChild.CHILD, Edit.NAMESPACE);
List children = parent.getContent(chFilter);
for (int i = 0; i < children.size(); i++) {
Element ch = (Element) children.get(i);
String name = ch.getAttributeValue("name");
if (name != null && name.equals(uName)) {
result = (Element) ch.clone();
break;
}
}
// -- now delete the element as requested
parent.removeContent(me);
// --- existing geonet child element not present so create it and insert it
// --- where the last element was deleted
if (result == null) {
result = editLib.createElement(schema, el, parent);
parent.addContent(me, result);
}
result.setAttribute(Edit.ChildElem.Attr.PARENT, parentRef);
result.addContent(info);
}
// --- if not the last one then just delete it
else {
parent.removeContent(me);
}
} else {
throw new IllegalStateException("Element at ref = " + ref + " doesn't have a parent");
}
// if we don't need a child then create a geonet:null element
if (result == null) {
result = new Element(Edit.RootChild.NULL, Edit.NAMESPACE);
result.addContent(info);
}
// --- reattach the info element to the metadata
md.addContent((Element) info.clone());
// --- store the metadata in the session again
setMetadataIntoSession(session, (Element) md.clone(), id);
return result;
}
/**
* Add content before or after an element.
*
* @param sibling an element with a parent.
* @param toAdd the content to add alongside <code>sibling</code>.
* @param after <code>true</code> to add it after <code>sibling</code>.
*/
public static void insertSiblings(
final Element sibling, final Collection<? extends Content> toAdd, final boolean after) {
final Element parentElement = sibling.getParentElement();
final int index = parentElement.indexOf(sibling);
parentElement.addContent(after ? index + 1 : index, toAdd);
}