private void initialize() throws BioclipseException {
if (dsBusinessModel == null) {
dsBusinessModel = new DSBusinessModel();
dsBusinessModel.initialize();
}
if (dsBusinessModel == null) throw new BioclipseException("Error initializing DS model.");
}
/**
* Get a list of all available tests
*
* @return
* @throws BioclipseException
*/
public List<String> getEndpoints() throws BioclipseException {
initialize();
List<String> epIDs = new ArrayList<String>();
for (Endpoint ep : dsBusinessModel.getEndpoints()) {
epIDs.add(ep.getId());
}
return epIDs;
}
/**
* Get a list of all available tests
*
* @return
* @throws BioclipseException
*/
public List<String> getTests() throws BioclipseException {
initialize();
List<String> testIDS = new ArrayList<String>();
for (IDSTest test : dsBusinessModel.getTests()) {
testIDS.add(test.getId());
}
return testIDS;
}
public IDSTest getTest(String testID) throws BioclipseException {
if (testID == null) throw new BioclipseException("Test: " + testID + " must not be null.");
initialize();
for (IDSTest test : dsBusinessModel.getTests()) {
if (testID.equals(test.getId())) return test;
}
logger.warn("Test: " + testID + " could not be found.");
throw new BioclipseException("Test: " + testID + " could not be found.");
}
public Endpoint getEndpoint(String endpointID) throws BioclipseException {
if (endpointID == null)
throw new BioclipseException("Endpoint: " + endpointID + " must not be null.");
initialize();
for (Endpoint ep : dsBusinessModel.getEndpoints()) {
if (endpointID.equals(ep.getId())) return ep;
}
logger.warn("Endpoint: " + endpointID + " could not be found.");
throw new BioclipseException("Endpoint: " + endpointID + " could not be found.");
}
public List<IDSTest> getFullTests() throws BioclipseException {
initialize();
return dsBusinessModel.getTests();
}
/**
* Removes a model. Removes extension and any files.
*
* @param model
*/
public void removeModel(IDSTest model, String pluginID) {
// Remove from DSBusinessModel
dsBusinessModel.getTests().remove(model);
for (Endpoint ep : dsBusinessModel.getEndpoints()) {
if (ep.getTests() != null) {
ep.getTests().remove(model);
logger.debug("Removed model " + model.getName() + " from EP " + ep.getName());
}
}
// Remove extensions in models.container plugin
// =============================================
File pluginXMLfile;
try {
pluginXMLfile = new File(FileUtil.getFilePath("plugin.xml", pluginID));
Builder parser = new Builder();
Document doc = parser.build(pluginXMLfile);
Element root = doc.getRootElement();
Element extension = null;
// Find extension in plugin.xml, if exists
Elements existingExtensions = root.getChildElements("extension");
if (existingExtensions != null && existingExtensions.size() > 0) {
for (int i = 0; i < existingExtensions.size(); i++) {
extension = existingExtensions.get(i);
// If exists a model with same name, remove it
Elements existingTests = extension.getChildElements("test");
if (existingTests != null && existingTests.size() > 0) {
for (int j = 0; j < existingTests.size(); j++) {
Element test = existingTests.get(j);
String testName = test.getAttribute("name").getValue();
// Remove spaces included by XML serialization
while (testName.contains(" ")) testName = testName.replace(" ", " ");
if (model.getName().equals(testName)) {
test.getParent().removeChild(test);
logger.debug("Removing existing model extension: " + model.getName());
// Also remove the files
Elements resources = test.getChildElements("resource");
for (int rescnt = 0; rescnt < resources.size(); rescnt++) {
Element resource = resources.get(rescnt);
String path = resource.getAttribute("path").getValue();
try {
File reFile = new File(FileUtil.getFilePath(path, pluginID));
if (reFile.exists()) {
logger.debug("Removing file: " + reFile);
reFile.delete();
} else logger.debug("Unable to locate file to remove: " + path);
} catch (Exception e) {
logger.error("Problems removing file: " + path);
}
}
}
}
}
}
}
// Serialize the updated plugin.xml to file
Serializer serializer = new Serializer(new FileOutputStream(pluginXMLfile));
serializer.setIndent(4);
serializer.setMaxLength(64);
serializer.write(doc);
} catch (IllegalArgumentException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
} catch (ValidityException e) {
e.printStackTrace();
} catch (ParsingException e) {
e.printStackTrace();
}
}
public List<Endpoint> getFullEndpoints() throws BioclipseException {
initialize();
return dsBusinessModel.getEndpoints();
}