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

Example 31 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 32 with AsynchClientTask

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

the class DocumentWindowManager method openGeometryDocumentWindow.

/**
 * Insert the method's description here.
 * Creation date: (1/21/2006 10:45:13 AM)
 */
public void openGeometryDocumentWindow(final Geometry geom) {
    AsynchClientTask task1 = new AsynchClientTask("opening geometry", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            try {
                GeometryInfo geomInfo = getRequestManager().getDocumentManager().getGeometryInfo(geom.getVersion().getVersionKey());
                hashTable.put("geomInfo", geomInfo);
            } catch (ObjectNotFoundException e) {
                if (getVCDocument().getVersion() != null && !getVCDocument().getVersion().getOwner().equals(getRequestManager().getDocumentManager().getUser())) {
                    throw new RuntimeException("Opening a geometry document window for '" + geom.getName() + "' from\n" + "Model '" + getVCDocument().getName() + "' owned by user (" + getVCDocument().getVersion().getOwner().getName() + ")\n" + "FAILED because user (" + getRequestManager().getDocumentManager().getUser().getName() + ") does not have permission.\n" + "Save Model '" + getVCDocument().getName() + "' to your account to have full access to the geometry.");
                } else {
                    throw e;
                }
            }
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("opening geometry", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            GeometryInfo geomInfo = (GeometryInfo) hashTable.get("geomInfo");
            getRequestManager().openDocument(geomInfo, DocumentWindowManager.this, true);
        }
    };
    ClientTaskDispatcher.dispatch(this.getComponent(), new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
}

Example 33 with AsynchClientTask

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

the class MathModelWindowManager method actionPerformed.

/**
 * Invoked when an action occurs.
 */
public void actionPerformed(java.awt.event.ActionEvent e) {
    String actionCommand = e.getActionCommand();
    final Object source = e.getSource();
    if (source instanceof GeometryViewer && actionCommand.equals(GuiConstants.ACTIONCMD_CREATE_GEOMETRY) || actionCommand.equals(GuiConstants.ACTIONCMD_EDITCURRENTSPATIAL_GEOMETRY)) {
        AsynchClientTask geomRegionsTask = new AsynchClientTask("Update Geometric regions", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                Geometry newGeom = (Geometry) hashTable.get("doc");
                ClientRequestManager.continueAfterMathModelGeomChangeWarning(MathModelWindowManager.this, newGeom);
                newGeom.precomputeAll(new GeometryThumbnailImageFactoryAWT());
            }
        };
        AsynchClientTask applyGeomTask = new AsynchClientTask("Apply Geometry", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                Geometry newGeom = (Geometry) hashTable.get("doc");
                if (newGeom.getName() == null) {
                    newGeom.setName(getMathModel().getName() + "_" + BeanUtils.generateDateTimeString());
                }
                ((MathModel) getVCDocument()).getMathDescription().setGeometry(newGeom);
            }
        };
        createGeometry(getMathModel().getMathDescription().getGeometry(), new AsynchClientTask[] { /*editSelectTask,*/
        geomRegionsTask, applyGeomTask }, TopLevelWindowManager.DEFAULT_CREATEGEOM_SELECT_DIALOG_TITLE, TopLevelWindowManager.APPLY_GEOMETRY_BUTTON_TEXT, (actionCommand.equals(GuiConstants.ACTIONCMD_EDITCURRENTSPATIAL_GEOMETRY) ? new DocumentWindowManager.GeometrySelectionInfo() : null));
    }
    if (source instanceof GeometryViewer && actionCommand.equals(GuiConstants.ACTIONCMD_CHANGE_GEOMETRY)) {
        getRequestManager().changeGeometry(this, null);
    }
}

Example 34 with AsynchClientTask

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

the class PdeTimePlotMultipleVariablesPanel method showTimePlot.

public void showTimePlot() {
    if ((plotChangeTimer = ClientTaskDispatcher.getBlockingTimer(this, multiTimePlotHelper.getPdeDatacontext(), null, plotChangeTimer, new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e2) {
            showTimePlot();
        }
    }, "PdeTimePlotMultipleVariablesPanel update...")) != null) {
        return;
    }
    VariableType varType = multiTimePlotHelper.getVariableType();
    Object[] selectedValues = variableJList.getSelectedValues();
    DataIdentifier[] selectedDataIdentifiers = new DataIdentifier[selectedValues.length];
    System.arraycopy(selectedValues, 0, selectedDataIdentifiers, 0, selectedValues.length);
    if (selectedDataIdentifiers.length > 1) {
        for (DataIdentifier selectedDataIdentifier : selectedDataIdentifiers) {
            if (!selectedDataIdentifier.getVariableType().getVariableDomain().equals(varType.getVariableDomain())) {
                PopupGenerator.showErrorDialog(this, "Please choose VOLUME variables or MEMBRANE variables only");
                variableJList.clearSelection();
                variableJList.setSelectedValue(multiTimePlotHelper.getPdeDatacontext().getVariableName(), true);
                return;
            }
        }
    }
    try {
        final int numSelectedVariables = selectedDataIdentifiers.length;
        final int numSelectedSpatialPoints = pointVector.size();
        int[][] indices = new int[numSelectedVariables][numSelectedSpatialPoints];
        // 
        for (int i = 0; i < numSelectedSpatialPoints; i++) {
            for (int v = 0; v < numSelectedVariables; v++) {
                if (selectedDataIdentifiers[v].getVariableType().equals(varType)) {
                    if (varType.equals(VariableType.VOLUME) || varType.equals(VariableType.VOLUME_REGION) || varType.equals(VariableType.POSTPROCESSING)) {
                        SpatialSelectionVolume ssv = (SpatialSelectionVolume) pointVector.get(i);
                        indices[v][i] = ssv.getIndex(0);
                    } else if (varType.equals(VariableType.MEMBRANE) || varType.equals(VariableType.MEMBRANE_REGION)) {
                        SpatialSelectionMembrane ssm = (SpatialSelectionMembrane) pointVector.get(i);
                        indices[v][i] = ssm.getIndex(0);
                    }
                } else {
                    if (varType.equals(VariableType.VOLUME) || varType.equals(VariableType.VOLUME_REGION) || varType.equals(VariableType.POSTPROCESSING)) {
                        SpatialSelectionVolume ssv = (SpatialSelectionVolume) pointVector2.get(i);
                        indices[v][i] = ssv.getIndex(0);
                    } else if (varType.equals(VariableType.MEMBRANE) || varType.equals(VariableType.MEMBRANE_REGION)) {
                        SpatialSelectionMembrane ssm = (SpatialSelectionMembrane) pointVector2.get(i);
                        indices[v][i] = ssm.getIndex(0);
                    }
                }
            }
        }
        final String[] selectedVarNames = new String[numSelectedVariables];
        for (int i = 0; i < selectedVarNames.length; i++) {
            selectedVarNames[i] = selectedDataIdentifiers[i].getName();
        }
        final double[] timePoints = multiTimePlotHelper.getPdeDatacontext().getTimePoints();
        TimeSeriesJobSpec tsjs = new TimeSeriesJobSpec(selectedVarNames, indices, null, timePoints[0], 1, timePoints[timePoints.length - 1], VCDataJobID.createVCDataJobID(multiTimePlotHelper.getUser(), true));
        if (!tsjs.getVcDataJobID().isBackgroundTask()) {
            throw new RuntimeException("Use getTimeSeries(...) if not a background job");
        }
        Hashtable<String, Object> hash = new Hashtable<String, Object>();
        hash.put(PDEDataViewer.StringKey_timeSeriesJobSpec, tsjs);
        AsynchClientTask task1 = new PDEDataViewer.TimeSeriesDataRetrievalTask("Retrieving Data", multiTimePlotHelper, multiTimePlotHelper.getPdeDatacontext());
        AsynchClientTask task2 = new AsynchClientTask("showing time plot", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                TSJobResultsNoStats tsJobResultsNoStats = (TSJobResultsNoStats) hashTable.get(PDEDataViewer.StringKey_timeSeriesJobResults);
                int plotCount = numSelectedVariables * numSelectedSpatialPoints;
                SymbolTableEntry[] symbolTableEntries = new SymbolTableEntry[plotCount];
                String[] plotNames = new String[plotCount];
                double[][] plotDatas = new double[1 + plotCount][];
                plotDatas[0] = timePoints;
                int plotIndex = 0;
                for (int v = 0; v < numSelectedVariables; v++) {
                    String varName = selectedVarNames[v];
                    double[][] data = tsJobResultsNoStats.getTimesAndValuesForVariable(varName);
                    for (int i = 1; i < data.length; i++) {
                        symbolTableEntries[plotIndex] = multiTimePlotHelper.getsimulation().getMathDescription().getEntry(varName);
                        plotNames[plotIndex] = varName + " at P[" + (i - 1) + "]";
                        plotDatas[plotIndex + 1] = data[i];
                        plotIndex++;
                    }
                }
                Plot2D plot2D = new SingleXPlot2D(symbolTableEntries, multiTimePlotHelper.getDataSymbolMetadataResolver(), ReservedVariable.TIME.getName(), plotNames, plotDatas, new String[] { "Time Plot", ReservedVariable.TIME.getName(), "" });
                plotPane.setPlot2D(plot2D);
            }
        };
        ClientTaskDispatcher.dispatch(this, hash, new AsynchClientTask[] { task1, task2 }, false, true, true, null, false);
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}

Example 35 with AsynchClientTask

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

the class DBReactionWizardPanel method searchUserReactions.

/**
 * Insert the method's description here.
 * Creation date: (7/12/2003 2:45:44 PM)
 */
private void searchUserReactions(final ReactionQuerySpec reactionQuerySpec) {
    if (getDocumentManager() != null) {
        final DocumentManager docManager = getDocumentManager();
        final JList jlist = getReactionsJList();
        // 
        final String RXSTRING_VALUE_KEY = "rxString";
        // 
        AsynchClientTask searchReactions = new AsynchClientTask("searching reactions", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            public void run(Hashtable<String, Object> hash) {
                try {
                    mapRXStringtoRXIDs.clear();
                    // 
                    ReactionDescription[] dbrd = docManager.getUserReactionDescriptions(reactionQuerySpec);
                    // 
                    if (dbrd != null && !(getStructure() instanceof Membrane)) {
                        Vector<ReactionDescription> noflux = new Vector<ReactionDescription>();
                        for (int i = 0; i < dbrd.length; i += 1) {
                            if (!dbrd[i].isFluxReaction()) {
                                noflux.add(dbrd[i]);
                            }
                        }
                        if (noflux.size() > 0) {
                            dbrd = new ReactionDescription[noflux.size()];
                            noflux.copyInto(dbrd);
                        }
                    }
                    // 
                    String[] dbrdS = null;
                    if (dbrd != null) {
                        // if(mapRXStringtoRXIDs == null){mapRXStringtoRXIDs = new java.util.Hashtable();}
                        for (int i = 0; i < dbrd.length; i += 1) {
                            String rxString = dbrd[i].toString();
                            if (!mapRXStringtoRXIDs.containsKey(rxString)) {
                                mapRXStringtoRXIDs.put(rxString, new Vector<String>());
                            }
                            mapRXStringtoRXIDs.get(rxString).add(dbrd[i].getVCellRXID().toString());
                            mapRXIDtoBMIDs.put(dbrd[i].getVCellRXID(), dbrd[i].getVCellBioModelID());
                            mapRXIDtoStructRefIDs.put(dbrd[i].getVCellRXID(), dbrd[i].getVCellStructRef());
                        }
                        dbrdS = (String[]) mapRXStringtoRXIDs.keySet().toArray(new String[0]);
                    }
                    // 
                    if (dbrd != null && dbrd.length > 0) {
                        hash.put(RXSTRING_VALUE_KEY, dbrdS);
                    }
                } catch (DataAccessException e) {
                    PopupGenerator.showErrorDialog(DBReactionWizardPanel.this, e.getMessage());
                }
            }
        };
        // 
        AsynchClientTask updateRXList = new AsynchClientTask("updateRXList", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            public void run(Hashtable<String, Object> hash) {
                String[] dbrdS = (String[]) hash.get(RXSTRING_VALUE_KEY);
                if (dbrdS != null) {
                    jlist.setListData(dbrdS);
                } else {
                    jlist.setListData(new String[0]);
                }
                afterSearchConfigure();
            }
        };
        // 
        Hashtable<String, Object> hashTemp = new Hashtable<String, Object>();
        ClientTaskDispatcher.dispatch(this, hashTemp, new AsynchClientTask[] { searchReactions, updateRXList }, false);
    }
}