/**
* 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.");
}
/**
* 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);
}