示例#1
0
  /**
   * 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();
    }
  }
示例#2
0
  /**
   * 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);
  }