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

Example 1 with AsynchClientTask

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

the class PDEDataViewer method sendImageJDomain.

private void sendImageJDomain() {
    try {
        if (getPdeDataContext().getDataIdentifier().getVariableType().getType() != VariableType.VOLUME.getType()) {
            DialogUtils.showErrorDialog(this, "Domain info for " + getPdeDataContext().getDataIdentifier().getVariableType() + " not yet implemented for ImageJ");
            return;
        }
        final ImageJHelper.ListenAndCancel listenAndCancel = new ImageJHelper.ListenAndCancel();
        AsynchClientTask sendDataTask = new AsynchClientTask("Sending domain Data...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                ImageJHelper.sendVolumeDomain(PDEDataViewer.this, getPdeDataContext(), getPdeDataContext().getCartesianMesh().getISize(), getClientTaskStatusSupport(), listenAndCancel, "Volume domains '" + getSimulationModelInfo().getContextName() + "':'" + getSimulation().getName() + "'", getSimulationModelInfo());
            }
        };
        ClientTaskDispatcher.dispatch(PDEDataViewer.this, new Hashtable<>(), new AsynchClientTask[] { sendDataTask }, true, false, true, listenAndCancel, false);
    } catch (Exception e) {
        handleException(e);
    }
}

Example 2 with AsynchClientTask

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

the class ClientRequestManager method changeGeometry0.

private void changeGeometry0(final TopLevelWindowManager requester, final SimulationContext simContext) {
    AsynchClientTask selectDocumentTypeTask = createSelectDocTask(requester);
    AsynchClientTask selectLoadGeomTask = createSelectLoadGeomTask(requester);
    AsynchClientTask processGeometryTask = new AsynchClientTask("Processing geometry...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Geometry newGeometry = (Geometry) hashTable.get(GEOMETRY_KEY);
            if (requester instanceof MathModelWindowManager) {
                // User can cancel here
                continueAfterMathModelGeomChangeWarning((MathModelWindowManager) requester, newGeometry);
            }
            if (newGeometry.getDimension() > 0 && newGeometry.getGeometrySurfaceDescription().getGeometricRegions() == null) {
                newGeometry.getGeometrySurfaceDescription().updateAll();
            }
        }
    };
    AsynchClientTask setNewGeometryTask = new AsynchClientTask("Setting new Geometry...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Geometry newGeometry = (Geometry) hashTable.get(GEOMETRY_KEY);
            if (newGeometry != null) {
                if (requester instanceof BioModelWindowManager) {
                    simContext.setGeometry(newGeometry);
                } else if (requester instanceof MathModelWindowManager) {
                    MathModel mathModel = (MathModel) ((MathModelWindowManager) requester).getVCDocument();
                    mathModel.getMathDescription().setGeometry(newGeometry);
                }
            }
        }
    };
    Hashtable<String, Object> hashTable = new Hashtable<String, Object>();
    ClientTaskDispatcher.dispatch(requester.getComponent(), hashTable, new AsynchClientTask[] { selectDocumentTypeTask, selectLoadGeomTask, processGeometryTask, setNewGeometryTask }, false);
}

Example 3 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 4 with AsynchClientTask

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

the class DatabaseWindowManager method accessPermissions.

/**
 * Insert the method's description here.
 * Creation date: (5/14/2004 5:35:55 PM)
 */
public void accessPermissions(final Component requester, final VersionInfo selectedVersionInfo) {
    final GroupAccess groupAccess = selectedVersionInfo.getVersion().getGroupAccess();
    final DocumentManager docManager = getRequestManager().getDocumentManager();
    AsynchClientTask task1 = new AsynchClientTask("show dialog", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            getAclEditor().clearACLList();
            getAclEditor().setACLState(new ACLEditor.ACLState(groupAccess));
            Object choice = showAccessPermissionDialog(getAclEditor(), requester);
            if (choice != null) {
                hashTable.put("choice", choice);
            }
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("access permission", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Object choice = hashTable.get("choice");
            if (choice != null && choice.equals("OK")) {
                ACLEditor.ACLState aclState = getAclEditor().getACLState();
                if (aclState != null) {
                    if (aclState.isAccessPrivate() || (aclState.getAccessList() != null && aclState.getAccessList().length == 0)) {
                        VersionInfo vInfo = null;
                        if (selectedVersionInfo instanceof BioModelInfo) {
                            vInfo = docManager.setGroupPrivate((BioModelInfo) selectedVersionInfo);
                        } else if (selectedVersionInfo instanceof MathModelInfo) {
                            vInfo = docManager.setGroupPrivate((MathModelInfo) selectedVersionInfo);
                        } else if (selectedVersionInfo instanceof GeometryInfo) {
                            vInfo = docManager.setGroupPrivate((GeometryInfo) selectedVersionInfo);
                        } else if (selectedVersionInfo instanceof VCImageInfo) {
                            vInfo = docManager.setGroupPrivate((VCImageInfo) selectedVersionInfo);
                        }
                    } else if (aclState.isAccessPublic()) {
                        VersionInfo vInfo = null;
                        if (selectedVersionInfo instanceof BioModelInfo) {
                            vInfo = docManager.setGroupPublic((BioModelInfo) selectedVersionInfo);
                        } else if (selectedVersionInfo instanceof MathModelInfo) {
                            vInfo = docManager.setGroupPublic((MathModelInfo) selectedVersionInfo);
                        } else if (selectedVersionInfo instanceof GeometryInfo) {
                            vInfo = docManager.setGroupPublic((GeometryInfo) selectedVersionInfo);
                        } else if (selectedVersionInfo instanceof VCImageInfo) {
                            vInfo = docManager.setGroupPublic((VCImageInfo) selectedVersionInfo);
                        }
                    } else {
                        String[] aclUserNames = aclState.getAccessList();
                        String[] originalGroupAccesNames = new String[0];
                        // Turn User[] into String[]
                        if (groupAccess instanceof GroupAccessSome) {
                            GroupAccessSome gas = (GroupAccessSome) groupAccess;
                            User[] originalUsers = gas.getNormalGroupMembers();
                            for (int i = 0; i < originalUsers.length; i += 1) {
                                originalGroupAccesNames = (String[]) BeanUtils.addElement(originalGroupAccesNames, originalUsers[i].getName());
                            }
                        }
                        // Determine users needing adding
                        String[] needToAddUsers = new String[0];
                        for (int i = 0; i < aclUserNames.length; i += 1) {
                            if (!BeanUtils.arrayContains(originalGroupAccesNames, aclUserNames[i])) {
                                System.out.println("Added user=" + aclUserNames[i]);
                                needToAddUsers = (String[]) BeanUtils.addElement(needToAddUsers, aclUserNames[i]);
                            }
                        }
                        // Determine users needing removing
                        String[] needToRemoveUsers = new String[0];
                        for (int i = 0; i < originalGroupAccesNames.length; i += 1) {
                            if (!BeanUtils.arrayContains(aclUserNames, originalGroupAccesNames[i])) {
                                System.out.println("Removed user=" + originalGroupAccesNames[i]);
                                needToRemoveUsers = (String[]) BeanUtils.addElement(needToRemoveUsers, originalGroupAccesNames[i]);
                            }
                        }
                        VersionInfo vInfo = null;
                        String errorNames = "";
                        // Add Users to Group Access List
                        for (int i = 0; i < needToAddUsers.length; i++) {
                            try {
                                if (selectedVersionInfo instanceof BioModelInfo) {
                                    vInfo = docManager.addUserToGroup((BioModelInfo) selectedVersionInfo, needToAddUsers[i]);
                                } else if (selectedVersionInfo instanceof MathModelInfo) {
                                    vInfo = docManager.addUserToGroup((MathModelInfo) selectedVersionInfo, needToAddUsers[i]);
                                } else if (selectedVersionInfo instanceof GeometryInfo) {
                                    vInfo = docManager.addUserToGroup((GeometryInfo) selectedVersionInfo, needToAddUsers[i]);
                                } else if (selectedVersionInfo instanceof VCImageInfo) {
                                    vInfo = docManager.addUserToGroup((VCImageInfo) selectedVersionInfo, needToAddUsers[i]);
                                }
                            } catch (ObjectNotFoundException e) {
                                errorNames += "Error changing permissions.\n" + selectedVersionInfo.getVersionType().getTypeName() + " \"" + selectedVersionInfo.getVersion().getName() + "\" edition (" + selectedVersionInfo.getVersion().getDate() + ")\nnot found, " + "your model list may be out of date, please go to menu Server->Reconnect to refresh the model list" + "\n";
                                break;
                            } catch (DataAccessException e) {
                                errorNames += "Error adding user '" + needToAddUsers[i] + "' : " + e.getMessage() + "\n";
                            }
                        }
                        // Remove users from Group Access List
                        for (int i = 0; i < needToRemoveUsers.length; i++) {
                            try {
                                if (selectedVersionInfo instanceof BioModelInfo) {
                                    vInfo = docManager.removeUserFromGroup((BioModelInfo) selectedVersionInfo, needToRemoveUsers[i]);
                                } else if (selectedVersionInfo instanceof MathModelInfo) {
                                    vInfo = docManager.removeUserFromGroup((MathModelInfo) selectedVersionInfo, needToRemoveUsers[i]);
                                } else if (selectedVersionInfo instanceof GeometryInfo) {
                                    vInfo = docManager.removeUserFromGroup((GeometryInfo) selectedVersionInfo, needToRemoveUsers[i]);
                                } else if (selectedVersionInfo instanceof VCImageInfo) {
                                    vInfo = docManager.removeUserFromGroup((VCImageInfo) selectedVersionInfo, needToRemoveUsers[i]);
                                }
                            } catch (DataAccessException e) {
                                errorNames += "Error Removing user '" + needToRemoveUsers[i] + "'\n  -----" + e.getMessage() + "\n";
                            }
                        }
                        if (errorNames.length() > 0) {
                            if (DatabaseWindowManager.this.getComponent() != null) {
                                PopupGenerator.showErrorDialog(DatabaseWindowManager.this, errorNames);
                            } else {
                                DialogUtils.showErrorDialog(requester, errorNames);
                            }
                            accessPermissions(requester, selectedVersionInfo);
                        }
                    }
                }
            }
        }
    };
    ClientTaskDispatcher.dispatch(requester, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
}

Example 5 with AsynchClientTask

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

the class DBReactionWizardPanel method applySelectedReactionElements.

/**
 * Comment
 */
private void applySelectedReactionElements() {
    AsynchClientTask getRXSourceModelTask = new AsynchClientTask("Get RX source model", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // Get the complete original model the user selected reaction is from
            Model fromModel = getDocumentManager().getBioModel(resolvedReaction.getVCellBioModelID()).getModel();
            // find the user selected ReactionStep in the original model
            ReactionStep fromRXStep = null;
            ReactionStep[] rxArr = fromModel.getReactionSteps();
            for (int i = 0; i < rxArr.length; i++) {
                if (rxArr[i].getKey().equals(resolvedReaction.getVCellRXID())) {
                    fromRXStep = rxArr[i];
                    break;
                }
            }
            // Create user assignment preferences
            BioCartoonTool.UserResolvedRxElements userResolvedRxElements = new BioCartoonTool.UserResolvedRxElements();
            userResolvedRxElements.fromSpeciesContextArr = new SpeciesContext[resolvedReaction.elementCount()];
            userResolvedRxElements.toSpeciesArr = new Species[resolvedReaction.elementCount()];
            userResolvedRxElements.toStructureArr = new Structure[resolvedReaction.elementCount()];
            StringBuffer warningsSB = new StringBuffer();
            for (int i = 0; i < resolvedReaction.elementCount(); i++) {
                System.out.println(resolvedReaction.getOrigSpeciesContextName(i));
                userResolvedRxElements.fromSpeciesContextArr[i] = fromModel.getSpeciesContext(resolvedReaction.getOrigSpeciesContextName(i));
                userResolvedRxElements.toSpeciesArr[i] = (speciesAssignmentJCB[i].getSelectedItem() instanceof Species ? (Species) speciesAssignmentJCB[i].getSelectedItem() : null);
                userResolvedRxElements.toStructureArr[i] = (Structure) structureAssignmentJCB[i].getSelectedItem();
                if (userResolvedRxElements.toSpeciesArr[i] != null) {
                    SpeciesContext fromSpeciesContext = userResolvedRxElements.fromSpeciesContextArr[i];
                    Species toSpecies = userResolvedRxElements.toSpeciesArr[i];
                    if (fromSpeciesContext.getSpecies().getDBSpecies() != null && !Compare.isEqualOrNull(toSpecies.getDBSpecies(), fromSpeciesContext.getSpecies().getDBSpecies())) {
                        warningsSB.append((warningsSB.length() > 0 ? "\n" : "") + "'" + fromSpeciesContext.getSpecies().getCommonName() + "' formal(" + (fromSpeciesContext.getSpecies().getDBSpecies() != null ? fromSpeciesContext.getSpecies().getDBSpecies().getPreferredName() : "null") + ")" + "\nwill be re-assigned to\n" + "'" + toSpecies.getCommonName() + "' formal(" + (toSpecies.getDBSpecies() != null ? toSpecies.getDBSpecies().getPreferredName() : "null") + ")");
                    }
                }
            }
            if (warningsSB.length() > 0) {
                final String proceed = "Add reaction anyway";
                final String cancel = "Cancel";
                String result = DialogUtils.showWarningDialog(DBReactionWizardPanel.this, "A user choice selected under 'Assign to Model species' will force re-assignment of " + "the formal reference for one of the species in the reaction.\n" + warningsSB, new String[] { proceed, cancel }, cancel);
                if (result.equals(cancel)) {
                    throw UserCancelException.CANCEL_GENERIC;
                }
            }
            hashTable.put("fromRXStep", fromRXStep);
            hashTable.put("userResolvedRxElements", userResolvedRxElements);
        }
    };
    AsynchClientTask pasteReactionTask = new AsynchClientTask("Paste reaction", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // TODO Auto-generated method stub
            Model pasteToModel = DBReactionWizardPanel.this.getModel();
            Structure pasteToStructure = DBReactionWizardPanel.this.getStructure();
            BioCartoonTool.pasteReactionSteps(DBReactionWizardPanel.this, new ReactionStep[] { (ReactionStep) hashTable.get("fromRXStep") }, pasteToModel, pasteToStructure, false, (UserResolvedRxElements) hashTable.get("userResolvedRxElements"), rxPasteInterface);
            closeParent();
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { getRXSourceModelTask, pasteReactionTask }, false, false, null, true);
}