/**
* 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 void runTest(
String testID,
IMolecule mol,
IReturner<List<? extends ITestResult>> returner,
IProgressMonitor monitor)
throws BioclipseException {
ICDKManager cdk = net.bioclipse.cdk.business.Activator.getDefault().getJavaCDKManager();
IDSTest test = getTest(testID);
List<? extends ITestResult> ret = null;
try {
// Preprocess the molecule
ICDKMolecule cdkmol = cdk.asCDKMolecule(mol);
// Clone the mol
IAtomContainer clonedAC = null;
try {
clonedAC = (IAtomContainer) cdkmol.getAtomContainer().clone();
} catch (CloneNotSupportedException e) {
logger.error("Could not clone mol: " + cdkmol);
return;
}
ICDKMolecule clonedMol = new CDKMolecule(clonedAC);
ret = test.runWarningTest(clonedMol, monitor);
} catch (Exception e) {
// in case of error...
LogUtils.debugTrace(logger, e);
ITestResult er = new SimpleResult("Error: " + e.getMessage(), ITestResult.ERROR);
er.setDetailedMessage(e.getMessage());
List<ITestResult> trlist = new ArrayList<ITestResult>();
trlist.add(er);
monitor.done();
returner.completeReturn(trlist);
return;
}
monitor.done();
returner.completeReturn(ret);
}
/**
* 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();
}
}
/**
* Run all tests in an EndPoint in a job.
*
* @param endpointID
* @param mol
* @param returner
* @param monitor
* @throws BioclipseException
*/
public void runEndpoint(
String endpointID,
IMolecule mol,
IReturner<Map<String, List<? extends ITestResult>>> returner,
IProgressMonitor monitor)
throws BioclipseException {
getEndpoint(endpointID);
// Set up result container
Map<String, List<? extends ITestResult>> ret =
new HashMap<String, List<? extends ITestResult>>();
// Get manager interface, we want to use the AOP
IDSManager ds = Activator.getDefault().getJavaManager();
Map<String, BioclipseJob<List<ITestResult>>> jobs =
new HashMap<String, BioclipseJob<List<ITestResult>>>();
// This is done in abstractDSTest + ds.runTest
// ICDKManager cdk = net.bioclipse.cdk.business.Activator.getDefault().getJavaCDKManager();
// //Preprocess the molecule
// ICDKMolecule cdkmol = cdk.asCDKMolecule(mol);
//
// try {
// cdkmol = cdk.removeExplicitHydrogens(cdkmol);
// cdkmol=cdk.perceiveAromaticity(cdkmol);
// cdkmol=cdk.addImplicitHydrogens(cdkmol);
// } catch (InvocationTargetException e1) {
// throw new BioclipseException("Could not preprocess molecule: " + e1.getMessage());
// }
// Loop over all tests in this endpoint and run them
for (IDSTest test : getEndpoint(endpointID).getTests()) {
// //Clone the mol
// IAtomContainer clonedAC=null;
// try {
// clonedAC = (IAtomContainer) cdkmol.getAtomContainer().clone();
// } catch (CloneNotSupportedException e) {
// //Should not happen
// logger.error("Could not clone mol: " + cdkmol);
// continue;
// }
// ICDKMolecule clonedMol=new CDKMolecule(clonedAC);
// Start up a job with the test
BioclipseJob<List<ITestResult>> job =
ds.runTest(
test.getId(), mol, new BioclipseJobUpdateHook<List<ITestResult>>(test.getName()));
jobs.put(test.getId(), job);
job.schedule();
}
// Join all jobs, wait for them to end
for (String testID : jobs.keySet()) {
try {
BioclipseJob<List<ITestResult>> job = jobs.get(testID);
logger.debug("Waiting for test: " + testID);
job.join();
logger.debug(" - Test: " + testID + " finished.");
List<ITestResult> testres = job.getReturnValue();
ret.put(testID, testres);
} catch (InterruptedException e) {
throw new BioclipseException("Job interrupted");
}
}
monitor.done();
returner.completeReturn(ret);
}
