Examples with ClientTaskStatusSupport org.vcell.util.ClientTaskStatusSupport used on opensource projects

Example 1 with ClientTaskStatusSupport

use of org.vcell.util.ClientTaskStatusSupport in project vcell by virtualcell.

the class TFGenerateReport method run.

/**
 * Insert the method's description here.
 * Creation date: (11/17/2004 2:08:09 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
public void run(Hashtable<String, Object> hashTable) throws Exception {
    ClientTaskStatusSupport pp = getClientTaskStatusSupport();
    String report = (String) hashTable.get(TFRefresh.TF_REPORT);
    if (report == null) {
        report = "";
    }
    // tfwm.updateSimRunningStatus(pp);
    if (tcrit != null && tcn != null) {
        if (userDefinedRegrRef != null) {
            report += tfwm.generateTestCaseReport(tcn, tcrit, pp, userDefinedRegrRef);
        } else {
            report += tfwm.generateTestCaseReport(tcn, tcrit, pp, null);
        }
    } else if (tcn != null) {
        report += tfwm.generateTestCaseReport(tcn, null, pp, null);
    } else if (tsin != null) {
        report += tfwm.generateTestSuiteReport(tsin, pp);
    }
    if (report != null && report.length() > 0) {
        hashTable.put(TFRefresh.TF_REPORT, report);
    }
}

Example 2 with ClientTaskStatusSupport

use of org.vcell.util.ClientTaskStatusSupport in project vcell by virtualcell.

the class TFRunSims method run.

/**
 * Insert the method's description here.
 * Creation date: (11/17/2004 2:08:09 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
public void run(Hashtable<String, Object> hashTable) {
    ClientTaskStatusSupport pp = getClientTaskStatusSupport();
    String errors = (String) hashTable.get(TFRefresh.TF_ERRORS);
    if (errors == null) {
        errors = "";
    }
    String error = "";
    if (tcrit != null) {
        error = tfwm.startSimulations(new TestCriteriaNew[] { tcrit }, pp);
    } else if (tcn != null) {
        error = tfwm.startSimulations(tcn.getTestCriterias(), pp);
    } else if (tsin != null) {
        error = tfwm.startTestSuiteSimulations(tsin, pp);
    }
    errors += (error == null ? "" : error);
    if (errors != null && errors.length() > 0) {
        hashTable.put(TFRefresh.TF_ERRORS, errors);
    }
}

Example 3 with ClientTaskStatusSupport

use of org.vcell.util.ClientTaskStatusSupport in project vcell by virtualcell.

the class BioModelsNetJPanel method searchImport.

private void searchImport() {
    AsynchClientTask searchTask = new AsynchClientTask("Search BioModels", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Hashtable<String, String> vcellCompatibleBioModels_ID_Name_Hash = readVCellCompatibleBioModels_ID_Name_Hash();
            ClientTaskStatusSupport clientTaskStatusSupport = getClientTaskStatusSupport();
            // clientTaskStatusSupport.setProgress(0);
            clientTaskStatusSupport.setMessage("Initializing BioModels Search...");
            BioModelsWebServicesServiceLocator bioModelsWebServicesServiceLocator = new BioModelsWebServicesServiceLocator();
            BioModelsWebServices bioModelsWebServices = bioModelsWebServicesServiceLocator.getBioModelsWebServices();
            // clientTaskStatusSupport.setProgress(10);
            clientTaskStatusSupport.setMessage("Executing BioModels Search...");
            TreeSet<String> modelIDsMergedSearch = new TreeSet<String>();
            boolean bHasModelEntryID = modelEntryIDTextField.getText() != null && modelEntryIDTextField.getText().length() > 0;
            if (bHasModelEntryID) {
                clientTaskStatusSupport.setMessage("Executing BioModels Search (Model ID matches)...");
                // String[] modelIDsAll = bioModelsWebServices.getAllModelsId();
                String[] modelIDsAll = vcellCompatibleBioModels_ID_Name_Hash.keySet().toArray(new String[0]);
                for (int i = 0; i < modelIDsAll.length; i++) {
                    if (modelIDsAll[i].toUpperCase().indexOf(modelEntryIDTextField.getText().toUpperCase()) != -1) {
                        modelIDsMergedSearch.add(modelIDsAll[i]);
                    }
                }
            }
            boolean bHasModelName = modelNameTextField.getText() != null && modelNameTextField.getText().length() > 0;
            if (bHasModelName) {
                clientTaskStatusSupport.setMessage("Executing BioModels Search (Model Name matches)...");
                TreeSet<String> modelIDsByNameSet = new TreeSet<String>();
                // String[] modelIDsByName = bioModelsWebServices.getModelsIdByName(modelNameTextField.getText());
                String[] modelIDsAll = vcellCompatibleBioModels_ID_Name_Hash.keySet().toArray(new String[0]);
                for (int i = 0; i < modelIDsAll.length; i++) {
                    if (vcellCompatibleBioModels_ID_Name_Hash.get(modelIDsAll[i]).toUpperCase().indexOf(modelNameTextField.getText().toUpperCase()) != -1) {
                        modelIDsByNameSet.add(modelIDsAll[i]);
                    }
                }
                // }
                if (bHasModelEntryID) {
                    // intersection
                    modelIDsMergedSearch.retainAll(modelIDsByNameSet);
                } else {
                    modelIDsMergedSearch = modelIDsByNameSet;
                }
            }
            boolean bHasModelPublication = publicationTextField.getText() != null && publicationTextField.getText().length() > 0;
            if (bHasModelPublication) {
                clientTaskStatusSupport.setMessage("Executing BioModels Search (Publication matches)...");
                TreeSet<String> modelIDsByPublicationSet = new TreeSet<String>();
                String[] modelIDsbyPublication = bioModelsWebServices.getModelsIdByPublication(publicationTextField.getText());
                for (int i = 0; i < modelIDsbyPublication.length; i++) {
                    modelIDsByPublicationSet.add(modelIDsbyPublication[i]);
                }
                if (bHasModelEntryID || bHasModelName) {
                    // intersection
                    modelIDsMergedSearch.retainAll(modelIDsByPublicationSet);
                } else {
                    modelIDsMergedSearch = modelIDsByPublicationSet;
                }
            }
            if (!(bHasModelEntryID || bHasModelName || bHasModelPublication)) {
                // Get all models
                // modelIDsMergedSearch.addAll(Arrays.asList(bioModelsWebServices.getAllModelsId()));
                modelIDsMergedSearch.addAll(Arrays.asList(vcellCompatibleBioModels_ID_Name_Hash.keySet().toArray(new String[0])));
            }
            // clientTaskStatusSupport.setProgress(COLLECTION_PROGRESS);
            if (modelIDsMergedSearch.size() > 0) {
                // Intersect with supported BioModel IDs
                modelIDsMergedSearch.retainAll(Arrays.asList(vcellCompatibleBioModels_ID_Name_Hash.keySet().toArray(new String[0])));
                clientTaskStatusSupport.setMessage("Found " + modelIDsMergedSearch.size() + " VCell compatible BioModels");
                String[] modelIDMergedSearchArr = modelIDsMergedSearch.toArray(new String[0]);
                TreeMap<String, String> model_ID_Name_Map = new TreeMap<String, String>();
                String nameNotfound = "NameNotFound_0";
                for (int i = 0; i < modelIDMergedSearchArr.length; i++) {
                    if (clientTaskStatusSupport.isInterrupted()) {
                        // DialogUtils.showWarningDialog(BioModelsNetJPanel.this, "Search Cancelled");
                        throw UserCancelException.CANCEL_GENERIC;
                    }
                    try {
                        // clientTaskStatusSupport.setMessage("Retrieving "+modelIDMergedSearchArr[i]+" "+(i+1)+" of "+modelIDMergedSearchArr.length);
                        // String modelName = bioModelsWebServices.getModelNameById(modelIDMergedSearchArr[i]);
                        String modelName = vcellCompatibleBioModels_ID_Name_Hash.get(modelIDMergedSearchArr[i]);
                        // Assume model names are unique
                        model_ID_Name_Map.put(modelName, modelIDMergedSearchArr[i]);
                    } catch (Exception e) {
                        // For some reason Web Service API sometimes throws java.util.NoSuchElementException
                        // if id exists but name can't be found.
                        e.printStackTrace();
                        model_ID_Name_Map.put(nameNotfound, modelIDMergedSearchArr[i]);
                        nameNotfound = TokenMangler.getNextEnumeratedToken(nameNotfound);
                    }
                }
                // Make name,id rowdata for tablelist to allow user selection
                String[] sortedModelNames = model_ID_Name_Map.keySet().toArray(new String[0]);
                final String[][] rowData = new String[sortedModelNames.length][2];
                for (int i = 0; i < sortedModelNames.length; i++) {
                    rowData[i][0] = sortedModelNames[i];
                    rowData[i][1] = model_ID_Name_Map.get(sortedModelNames[i]);
                }
                // Allow user to select model for opening
                final String importNow = "Import";
                final String cancel = "Cancel";
                DialogUtils.TableListResult result = DialogUtils.showComponentOptionsTableList(BioModelsNetJPanel.this, "Select a BioModel to import", new String[] { "Model Names", "BioModels Entry ID" }, rowData, ListSelectionModel.SINGLE_SELECTION, null, new String[] { importNow, cancel }, importNow, new Comparator<Object>() {

                    public int compare(Object o1, Object o2) {
                        if (o1 instanceof String && o2 instanceof String) {
                            return ((String) o1).compareTo((String) o2);
                        }
                        throw new RuntimeException("row data should only be String");
                    }
                });
                if (result.selectedOption != null && result.selectedOption.equals(importNow)) {
                    // Close Dialog showing "this" panel so ProgressPopup not obscured during openDocument
                    SwingUtilities.invokeAndWait(new Runnable() {

                        public void run() {
                            disposeParentDialog();
                        }
                    });
                    closeClientTaskStatusSupport(clientTaskStatusSupport);
                    // Download and open (in new window) SBML document selected by user
                    String bioModelSBML = bioModelsWebServices.getModelSBMLById(rowData[result.selectedTableRows[0]][1]);
                    final ExternalDocInfo externalDocInfo = new ExternalDocInfo(bioModelSBML, sortedModelNames[result.selectedTableRows[0]]);
                    new Thread(new Runnable() {

                        public void run() {
                            documentWindow.getTopLevelWindowManager().getRequestManager().openDocument(externalDocInfo, documentWindow.getTopLevelWindowManager(), true);
                        }
                    }).start();
                }
            } else {
                closeClientTaskStatusSupport(clientTaskStatusSupport);
                DialogUtils.showWarningDialog(BioModelsNetJPanel.this, "No BioModels found matching current search criteria.");
                throw UserCancelException.CANCEL_GENERIC;
            }
        }
    };
    ClientTaskDispatcher.dispatch(BioModelsNetJPanel.this, new Hashtable<String, Object>(), new AsynchClientTask[] { searchTask }, true, true, null, true);
}

Example 4 with ClientTaskStatusSupport

use of org.vcell.util.ClientTaskStatusSupport in project vcell by virtualcell.

the class BioformatsImageDatasetReader method runpb.

// mkdir bioformatsJarTempDir
// cd bioformatsJarTempDir
// ls -1 /home/vcell/workspace_biofthrift/vcell-bioformats/target/dependency/* | xargs -n 1 jar xf
// ls -1 /home/vcell/workspace_biofthrift/vcell-bioformats/target/vcell-bioformats-0.0.4.jar | xargs -n 1 jar xf
// rm -rf META-INF
// mkdir META-INF
// echo -e "Manifest-Version: 1.0\nMain-Class: org.vcell.bioformats.BioFormatsImageDatasetReaderFrm\n"
// jar cf mynewbiof.jar .
private String runpb(ArrayList<String> cmdList, ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    // DEBUGGING CODE
    // final Exception[] excHolder = new Exception[1];
    // System.out.println("\n--cmd begin--");
    // Arrays.stream(cmdList.toArray()).map(s->s+" ").forEach(System.out::print);
    // System.out.println("\n--cmd end--");
    // final PrintStream origstdout = System.out;
    // ByteArrayOutputStream baos = new ByteArrayOutputStream();
    // PrintStream newps = new PrintStream(baos) {
    // @Override
    // public void println(String x) {
    // try {
    // baos.write(x.getBytes());
    // origstdout.println(x.substring(0, Math.min(x.length()-1, 400)));
    // detectException(x);
    // detectMessage(clientTaskStatusSupport, x);
    // }catch (Exception e) {
    // excHolder[0] = e;
    // }
    // }
    // };
    // try {
    // System.setOut(newps);
    // BioFormatsImageDatasetReaderFrm.main(cmdList.toArray(new String[0]));
    // String output = baos.toString();
    // if(excHolder[0] != null) {
    // throw excHolder[0];
    // }
    // output = output.substring(output.indexOf(BIOF_XML_START_DELIM)+BIOF_XML_START_DELIM.length()+1, output.indexOf(BIOF_XML_END_DELIM));
    // if(true) {return output;}
    // }finally {
    // System.setOut(origstdout);
    // }
    cmdList.add(0, ResourceUtil.getVCellJava());
    cmdList.add(1, "-jar");
    cmdList.add(2, // new File("/home/vcell/workspace_biofthrift/vcell-bioformats/target/vcell-bioformats-0.0.4.jar").getAbsolutePath()+":"+
    ResourceUtil.getBioFormatsExecutableJarFile().getAbsolutePath());
    // cmdList.add(3,"org.vcell.bioformats.BioFormatsImageDatasetReaderFrm");//Main class name in vcell-bioformats project
    ProcessBuilder pb = new ProcessBuilder(cmdList);
    // out and err in one stream
    pb.redirectErrorStream(true);
    System.out.println("\n--cmd begin--");
    Arrays.stream(pb.command().toArray()).map(s -> s + " ").forEach(System.out::print);
    System.out.println("\n--cmd end--");
    final Process p = pb.start();
    BufferedReader br = new BufferedReader(new InputStreamReader(p.getInputStream()));
    String line;
    StringBuffer sb = new StringBuffer();
    while ((line = br.readLine()) != null) {
        sb.append(line);
        detectMessage(clientTaskStatusSupport, line);
        detectException(line);
    }
    p.waitFor(5, TimeUnit.SECONDS);
    return sb.substring(sb.indexOf(BIOF_XML_START_DELIM) + BIOF_XML_START_DELIM.length(), sb.indexOf(BIOF_XML_END_DELIM));
}

Example 5 with ClientTaskStatusSupport

use of org.vcell.util.ClientTaskStatusSupport in project vcell by virtualcell.

the class WorkflowJGraphProxy method workflowRun.

public void workflowRun() throws Exception {
    ClientTaskStatusSupport progress = new ClientTaskStatusSupport() {

        String message = "";

        int progress = 0;

        @Override
        public void setProgress(int progress) {
            this.progress = progress;
        }

        @Override
        public void setMessage(String message) {
            this.message = message;
        }

        @Override
        public boolean isInterrupted() {
            return false;
        }

        @Override
        public int getProgress() {
            return progress;
        }

        @Override
        public void addProgressDialogListener(ProgressDialogListener progressDialogListener) {
        }
    };
    context.getWorkflow().compute(context, progress);
}