Examples with AsynchClientTask cbit.vcell.client.task.AsynchClientTask used on opensource projects

Example 21 with AsynchClientTask

use of cbit.vcell.client.task.AsynchClientTask in project vcell by virtualcell.

the class ClientRequestManager method runSimulations.

public void runSimulations(final ClientSimManager clientSimManager, final Simulation[] simulations) {
    DocumentWindowManager documentWindowManager = clientSimManager.getDocumentWindowManager();
    /*	run some quick checks to see if we need to do a SaveAs */
    boolean needSaveAs = false;
    if (documentWindowManager.getVCDocument().getVersion() == null) {
        // never saved
        needSaveAs = true;
    } else if (!documentWindowManager.getVCDocument().getVersion().getOwner().compareEqual(getDocumentManager().getUser())) {
        // not the owner
        // keep the user informed this time
        String choice = PopupGenerator.showWarningDialog(documentWindowManager, getUserPreferences(), UserMessage.warn_SaveNotOwner, null);
        if (choice.equals(UserMessage.OPTION_SAVE_AS_NEW)) {
            needSaveAs = true;
        } else {
            // user canceled, just show existing document
            getMdiManager().showWindow(documentWindowManager.getManagerID());
            throw new UserCancelException("user canceled");
        }
    }
    // Before running the simulation, check if all the sizes of structures are set
    if (simulations != null && simulations.length > 0) {
        VCDocument vcd = documentWindowManager.getVCDocument();
        if (vcd instanceof BioModel) {
            String stochChkMsg = null;
            // we want to check when there is stochastic application if the rate laws set in model can be automatically transformed.
            for (int i = 0; i < simulations.length; i++) {
                if (simulations[i].getMathDescription().isNonSpatialStoch() || simulations[i].getMathDescription().isSpatialStoch() || simulations[i].getMathDescription().isSpatialHybrid()) {
                    if (stochChkMsg == null) {
                        stochChkMsg = ((BioModel) vcd).getModel().isValidForStochApp();
                    }
                    if (!(stochChkMsg.equals(""))) {
                        DialogUtils.showErrorDialog(documentWindowManager.getComponent(), "Problem in simulation: " + simulations[i].getName() + ".\n" + stochChkMsg);
                        throw new RuntimeException("Problem in simulation: " + simulations[i].getName() + "\n" + stochChkMsg);
                    }
                }
            }
        }
    }
    // 
    for (int i = 0; simulations != null && i < simulations.length; i++) {
        if (simulations[i].getSimulationVersion() != null && simulations[i].getSimulationVersion().getParentSimulationReference() != null) {
            simulations[i].clearVersion();
        }
    }
    /* now start the dirty work */
    /* block document window */
    JFrame currentDocumentWindow = getMdiManager().blockWindow(documentWindowManager.getManagerID());
    /* prepare hashtable for tasks */
    Hashtable<String, Object> hash = new Hashtable<String, Object>();
    hash.put("mdiManager", getMdiManager());
    hash.put(DocumentManager.IDENT, getDocumentManager());
    hash.put(CommonTask.DOCUMENT_WINDOW_MANAGER.name, documentWindowManager);
    hash.put("currentDocumentWindow", currentDocumentWindow);
    hash.put("clientSimManager", clientSimManager);
    hash.put("simulations", simulations);
    hash.put("jobManager", getClientServerManager().getJobManager());
    hash.put("requestManager", this);
    /* create tasks */
    AsynchClientTask[] tasks = null;
    if (needSaveAs) {
        // check document consistency first
        AsynchClientTask documentValid = new DocumentValidTask();
        AsynchClientTask setMathDescription = new SetMathDescription();
        // get a new name
        AsynchClientTask newName = new NewName();
        // save it
        AsynchClientTask saveDocument = new SaveDocument();
        // clean up
        AsynchClientTask finishSave = new FinishSave();
        // run the simulations
        AsynchClientTask runSims = new RunSims();
        // assemble array
        tasks = new AsynchClientTask[] { documentValid, setMathDescription, newName, saveDocument, finishSave, runSims };
    } else {
        // check document consistency first
        AsynchClientTask documentValid = new DocumentValidTask();
        AsynchClientTask setMathDescription = new SetMathDescription();
        // check if unchanged document
        AsynchClientTask checkUnchanged = new CheckUnchanged(true);
        // save it
        AsynchClientTask saveDocument = new SaveDocument();
        // check for lost results
        AsynchClientTask checkBeforeDelete = new CheckBeforeDelete();
        // delete old document
        AsynchClientTask deleteOldDocument = new DeleteOldDocument();
        // clean up
        AsynchClientTask finishSave = new FinishSave();
        // run the simulations
        AsynchClientTask runSims = new RunSims();
        // assemble array
        tasks = new AsynchClientTask[] { documentValid, setMathDescription, checkUnchanged, saveDocument, checkBeforeDelete, deleteOldDocument, finishSave, runSims };
    }
    /* run the tasks */
    ClientTaskDispatcher.dispatch(currentDocumentWindow, hash, tasks, true);
}

Example 22 with AsynchClientTask

use of cbit.vcell.client.task.AsynchClientTask in project vcell by virtualcell.

the class BioModelEditorPathwayCommonsPanel method search.

public void search() {
    String text = searchTextField.getText();
    if (text == null || text.length() == 0) {
        return;
    }
    text = text.trim();
    if (text.length() == 0) {
        return;
    }
    final String searchText = text;
    searchTextList.add(searchText);
    searchTextField.setAutoCompletionWords(searchTextList);
    AsynchClientTask task1 = new AsynchClientTask("searching", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            URL url = new URL(defaultBaseURL + "?" + PathwayCommonsKeyword.cmd + "=" + PathwayCommonsKeyword.search + "&" + PathwayCommonsKeyword.version + "=" + PathwayCommonsVersion.v2.name + "&" + PathwayCommonsKeyword.q + "=" + URLEncoder.encode(searchText, "UTF-8") + "&" + PathwayCommonsKeyword.maxHits + "=" + 14 + "&" + PathwayCommonsKeyword.output + "=" + PathwayCommonsKeyword.xml);
            System.out.println(url);
            String responseContent = BeanUtils.downloadBytes(url, getClientTaskStatusSupport());
            Document document = DOMUtil.parse(responseContent);
            Element errorElement = DOMUtil.firstChildElement(document, "error");
            if (errorElement != null) {
                // String xml = DOMUtil.firstChildContent(document, "error");
                throw new RuntimeException(errorElement.getTextContent());
            }
            Element searchResponse = DOMUtil.firstChildElement(document, "search_response");
            if (searchResponse != null) {
                // String xml = DOMUtil.firstChildContent(document, "search_response");
                // System.out.println(xml);
                hashTable.put("searchResponse", searchResponse);
            }
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("showing", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Element searchResponse = (Element) hashTable.get("searchResponse");
            if (searchResponse != null) {
                responseTreeModel.addSearchResponse(searchText, searchResponse);
            }
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 }, false, true, null);
}

Example 23 with AsynchClientTask

use of cbit.vcell.client.task.AsynchClientTask in project vcell by virtualcell.

the class BioModelEditorSabioPanel method treeSelectionChanged.

public void treeSelectionChanged() {
    System.out.println("treeSelectionChanged");
    final SBEntity kineticLaw = computeSelectedKineticLaw();
    if (kineticLaw == null) {
        return;
    }
    String kineticLawID = kineticLaw.getID();
    final String kls = new String("kineticLaw");
    if (!kineticLawID.contains(kls)) {
        return;
    }
    kineticLawID = kineticLawID.substring(kineticLawID.lastIndexOf(kls) + kls.length());
    command = "EntryID:" + kineticLawID;
    AsynchClientTask task1 = new AsynchClientTask("Importing Kinetic Laws", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(final Hashtable<String, Object> hashTable) throws Exception {
            final URL url = new URL("http://sabiork.h-its.org/sabioRestWebServices/searchKineticLaws/biopax?q=" + command);
            // final URL url = new URL("http://sabiork.h-its.org/sabioRestWebServices/searchKineticLaws/biopax?q=EntryID:33107");
            System.out.println(url.toString());
            String ERROR_CODE_TAG = "error_code";
            Document jdomDocument = XmlUtil.getJDOMDocument(url, getClientTaskStatusSupport());
            Element rootElement = jdomDocument.getRootElement();
            String errorCode = rootElement.getChildText(ERROR_CODE_TAG);
            if (errorCode != null) {
                throw new RuntimeException("Failed to access " + url + " \n\nPlease try again.");
            }
            PathwayModel pathwayModel = PathwayIOUtil.extractPathwayFromJDOM(jdomDocument, new RDFXMLContext(), getClientTaskStatusSupport());
            PathwayData pathwayData = new PathwayData("Sabio Kinetic Laws", pathwayModel);
            hashTable.put("pathwayData", pathwayData);
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("showing", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            PathwayData pathwayData = (PathwayData) hashTable.get("pathwayData");
            if (pathwayData != null) {
                setSelectedObjects(new Object[] { pathwayData });
            }
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 }, true, true, null);
}

Example 24 with AsynchClientTask

use of cbit.vcell.client.task.AsynchClientTask in project vcell by virtualcell.

the class BioModelEditorSabioPanel method populateKineticLawsTree.

public void populateKineticLawsTree() {
    // String category1 = (String)categoryList1.getSelectedItem();
    String category1 = "AnyRole";
    String category2 = (String) categoryList2.getSelectedItem();
    String entity1 = entityName1.getText();
    String entity2 = entityName2.getText();
    // http://sabiork.h-its.org/sabioRestWebServices/searchKineticLaws/biopax?q=%28Pathway:JAK-STAT%20AND%20CellularLocation:cytosol%29
    command = "";
    if (entity1.isEmpty() && entity2.isEmpty()) {
        DialogUtils.showWarningDialog(this, "No search criteria specified.");
        return;
    }
    if (!entity1.isEmpty() && entity2.isEmpty()) {
        command += category1 + ":" + entity1;
    } else if (entity1.isEmpty() && !entity2.isEmpty()) {
        command += category2 + ":" + entity2;
    } else {
        // both entities present
        command += "%28" + category1 + ":" + entity1 + "%20AND%20" + category2 + ":" + entity2 + "%29";
    }
    AsynchClientTask task1 = new AsynchClientTask("Importing Kinetic Laws", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(final Hashtable<String, Object> hashTable) throws Exception {
            final URL url = new URL("http://sabiork.h-its.org/sabioRestWebServices/searchKineticLaws/biopax?q=" + command);
            System.out.println(url.toString());
            String ERROR_CODE_TAG = "error_code";
            Document jdomDocument = XmlUtil.getJDOMDocument(url, getClientTaskStatusSupport());
            Element rootElement = jdomDocument.getRootElement();
            String errorCode = rootElement.getChildText(ERROR_CODE_TAG);
            if (errorCode != null) {
                throw new RuntimeException("Failed to access " + url + " \n\nPlease try again.");
            }
            PathwayModel pathwayModel = PathwayIOUtil.extractPathwayFromJDOM(jdomDocument, new RDFXMLContext(), getClientTaskStatusSupport());
            PathwayData pathwayData = new PathwayData("Sabio Kinetic Laws", pathwayModel);
            hashTable.put("pathwayData", pathwayData);
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("showing", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            PathwayData pathwayData = (PathwayData) hashTable.get("pathwayData");
            if (pathwayData != null) {
                responseTreeModel.addSearchResponse("text", pathwayData);
            }
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 }, true, true, null);
}

Example 25 with AsynchClientTask

use of cbit.vcell.client.task.AsynchClientTask in project vcell by virtualcell.

the class BioPaxObjectPropertiesPanel method lookupFormalName.

private void lookupFormalName(final int tableRow) {
    final String FORMAL_NAMES_KEY = "FORMAL_NAMES_KEY";
    final Entity entity = (Entity) BioPaxObjectPropertiesPanel.this.bioPaxObject;
    AsynchClientTask initLookupTask = new AsynchClientTask("init lookup...", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (!lookupContains(entity)) {
                lookupAdd(entity);
            }
            refreshInterface();
        }
    };
    AsynchClientTask lookupTask = new AsynchClientTask("looking...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING, false) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ArrayList<Xref> xrefArrList = entity.getxRef();
            ArrayList<String> formalNames = AnnotationMapping.getNameRef(xrefArrList, null);
            if (formalNames != null && formalNames.size() > 0) {
                hashTable.put(FORMAL_NAMES_KEY, formalNames);
            }
        }
    };
    AsynchClientTask finishLookupTask = new AsynchClientTask("init lookup...", AsynchClientTask.TASKTYPE_SWING_NONBLOCKING, false) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            try {
                ArrayList<String> formalNames = (ArrayList<String>) hashTable.get(FORMAL_NAMES_KEY);
                if (formalNames != null) {
                    entity.setFormalNames(formalNames);
                } else if (entity.getxRef() != null && entity.getxRef().size() > 0) {
                    String str = "";
                    for (int i = 0; i < ((Entity) BioPaxObjectPropertiesPanel.this.bioPaxObject).getxRef().size(); i++) {
                        str += (i > 0 ? "\n" : "") + entity.getxRef().get(i).getDb() + ":" + entity.getxRef().get(i).getId();
                    }
                    throw new Exception("Formal name lookup not yet implemented using:\n" + str);
                } else {
                    throw new Exception("No cross-references available to lookup formal name for " + entity.getName().get(0));
                }
            } finally {
                lookupRemove(entity);
                refreshInterface();
                table.setRowSelectionInterval(tableRow, tableRow);
            }
        }
    };
    ClientTaskDispatcher.dispatch(null, new Hashtable<String, Object>(), new AsynchClientTask[] { initLookupTask, lookupTask, finishLookupTask }, null, false, false, false, null, false);
}