Examples with DocumentManager cbit.vcell.clientdb.DocumentManager used on opensource projects

Example 26 with DocumentManager

use of cbit.vcell.clientdb.DocumentManager in project vcell by virtualcell.

the class SaveDocument method run.

/**
 * Insert the method's description here.
 * Creation date: (5/31/2004 6:04:14 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
public void run(Hashtable<String, Object> hashTable) throws java.lang.Exception {
    long l1 = System.currentTimeMillis();
    DocumentWindowManager documentWindowManager = (DocumentWindowManager) hashTable.get(CommonTask.DOCUMENT_WINDOW_MANAGER.name);
    VCDocument currentDocument = documentWindowManager.getVCDocument();
    DocumentManager documentManager = (DocumentManager) hashTable.get(CommonTask.DOCUMENT_MANAGER.name);
    RequestManager requestManager = (RequestManager) hashTable.get("requestManager");
    boolean bAsNew = hashTable.containsKey("newName");
    String newName = bAsNew ? (String) hashTable.get("newName") : null;
    Simulation[] simulationsToRun = (Simulation[]) hashTable.get("simulations");
    String[] independentSims = null;
    if (simulationsToRun != null && simulationsToRun.length > 0) {
        independentSims = new String[simulationsToRun.length];
        for (int i = 0; i < simulationsToRun.length; i++) {
            independentSims[i] = simulationsToRun[i].getName();
        }
    }
    VCDocument savedDocument = null;
    switch(currentDocument.getDocumentType()) {
        case BIOMODEL_DOC:
            {
                if (bAsNew) {
                    // Substitute Field Func Names-----
                    VersionableTypeVersion originalVersionableTypeVersion = null;
                    if (currentDocument.getVersion() != null) {
                        // From Opened...
                        originalVersionableTypeVersion = new VersionableTypeVersion(VersionableType.BioModelMetaData, currentDocument.getVersion());
                    }
                    documentManager.substituteFieldFuncNames((BioModel) currentDocument, originalVersionableTypeVersion);
                    // --------------------------------
                    savedDocument = documentManager.saveAsNew((BioModel) currentDocument, newName, independentSims);
                } else {
                    savedDocument = documentManager.save((BioModel) currentDocument, independentSims);
                }
                break;
            }
        case MATHMODEL_DOC:
            {
                if (bAsNew) {
                    // Substitute Field Func Names-----
                    VersionableTypeVersion originalVersionableTypeVersion = ((MathModelWindowManager) documentWindowManager).getCopyFromBioModelAppVersionableTypeVersion();
                    if (originalVersionableTypeVersion == null && currentDocument.getVersion() != null) {
                        // From Opened...
                        originalVersionableTypeVersion = new VersionableTypeVersion(VersionableType.MathModelMetaData, currentDocument.getVersion());
                    }
                    documentManager.substituteFieldFuncNames((MathModel) currentDocument, originalVersionableTypeVersion);
                    // --------------------------------
                    savedDocument = documentManager.saveAsNew((MathModel) currentDocument, newName, independentSims);
                } else {
                    savedDocument = documentManager.save((MathModel) currentDocument, independentSims);
                }
                break;
            }
        case GEOMETRY_DOC:
            {
                if (bAsNew) {
                    savedDocument = documentManager.saveAsNew((Geometry) currentDocument, newName);
                } else {
                    savedDocument = documentManager.save((Geometry) currentDocument);
                }
                break;
            }
        default:
            {
                throw new RuntimeException("unexpected document type " + currentDocument.getDocumentType().name());
            }
    }
    documentWindowManager.prepareDocumentToLoad(savedDocument, false);
    hashTable.put(SaveDocument.DOC_KEY, savedDocument);
    // generate PerformanceMonitorEvent
    long l2 = System.currentTimeMillis();
    double duration = ((double) (l2 - l1)) / 1000;
// requestManager.getAsynchMessageManager().reportPerformanceMonitorEvent(
// new PerformanceMonitorEvent(
// this, documentManager.getUser(), new PerformanceData(
// "SaveDocument.run()",
// MessageEvent.SAVING_STAT,
// new PerformanceDataEntry[] {
// new PerformanceDataEntry("document saved", savedDocument.getName()),
// new PerformanceDataEntry("remote call duration", Double.toString(duration))
// }
// )
// )
// );
}

Example 27 with DocumentManager

use of cbit.vcell.clientdb.DocumentManager in project vcell by virtualcell.

the class FieldDataGUIPanel method addNewExternalData.

public static AsynchClientTask[] addNewExternalData(final Component requester, final FieldDataGUIPanel fieldDataGUIPanel, final boolean isFromSimulation) {
    final RequestManager clientRequestManager = fieldDataGUIPanel.fieldDataWindowManager.getLocalRequestManager();
    AsynchClientTask task1 = new AsynchClientTask("creating field data", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FieldDataFileOperationSpec fdos = (FieldDataFileOperationSpec) hashTable.get("fdos");
            String initialExtDataName = (String) hashTable.get("initFDName");
            fdos.specEDI = null;
            FieldDataInfoPanel fdip = new FieldDataInfoPanel();
            fdip.setSimulationMode(isFromSimulation);
            fdip.initISize(fdos.isize);
            fdip.initIOrigin(fdos.origin);
            fdip.initIExtent(fdos.extent);
            fdip.initTimes(fdos.times);
            fdip.initNames(TokenMangler.fixTokenStrict(initialExtDataName), fdos.varNames);
            fdip.setAnnotation(fdos.annotation);
            FieldDataFileOperationSpec userDefinedFDOS = new FieldDataFileOperationSpec();
            while (true) {
                int choice = PopupGenerator.showComponentOKCancelDialog(requester, fdip, "Create new field data");
                if (choice == JOptionPane.OK_OPTION) {
                    // Check values
                    try {
                        userDefinedFDOS.extent = fdip.getExtent();
                    } catch (Exception e) {
                        PopupGenerator.showErrorDialog(requester, "Problem with Extent values. Please re-enter.\n" + e.getMessage() + "\nTry Again.", e);
                        continue;
                    }
                    try {
                        userDefinedFDOS.origin = fdip.getOrigin();
                    } catch (Exception e) {
                        PopupGenerator.showErrorDialog(requester, "Problem with Origin values. Please re-enter.\n" + e.getMessage() + "\nTry Again.", e);
                        continue;
                    }
                    try {
                        userDefinedFDOS.varNames = fdip.getVariableNames();
                    } catch (Exception e) {
                        PopupGenerator.showErrorDialog(requester, "Problem with Variable names. Please re-enter.\n" + e.getMessage() + "\nTry Again.", e);
                        continue;
                    }
                    userDefinedFDOS.annotation = fdip.getAnnotation();
                    userDefinedFDOS.times = fdip.getTimes();
                    try {
                        if (fdip.getFieldName() == null || fdip.getFieldName().length() == 0 || !fdip.getFieldName().equals(TokenMangler.fixTokenStrict(fdip.getFieldName()))) {
                            throw new Exception("Field Data names can contain only letters,digits and underscores");
                        }
                        // Check to see if this name is already used
                        DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) fieldDataGUIPanel.getJTree1().getModel().getRoot();
                        for (int i = 0; i < rootNode.getChildCount(); i += 1) {
                            ExternalDataIdentifier extDataID = ((FieldDataMainList) ((DefaultMutableTreeNode) rootNode.getChildAt(i)).getUserObject()).externalDataIdentifier;
                            if (fdip.getFieldName().equals(extDataID.getName())) {
                                throw new Exception("New Field Data name " + fdip.getFieldName() + " already used.");
                            }
                        }
                    } catch (Exception e) {
                        PopupGenerator.showErrorDialog(requester, "Error saving Field Data Name to Database. Try again.\n" + e.getMessage(), e);
                        continue;
                    }
                    hashTable.put("userDefinedFDOS", userDefinedFDOS);
                    hashTable.put("fieldName", fdip.getFieldName());
                    break;
                } else {
                    throw UserCancelException.CANCEL_GENERIC;
                }
            }
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("saving field data", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // Add to Server Disk
            // save Database
            FieldDataFileOperationSpec tempFDOS = (FieldDataFileOperationSpec) hashTable.get("userDefinedFDOS");
            String fieldName = (String) hashTable.get("fieldName");
            FieldDataFileOperationSpec fdos = (FieldDataFileOperationSpec) hashTable.get("fdos");
            DocumentManager documentManager = clientRequestManager.getDocumentManager();
            FieldDataDBOperationSpec newExtDataIDSpec = FieldDataDBOperationSpec.createSaveNewExtDataIDSpec(documentManager.getUser(), fieldName, tempFDOS.annotation);
            tempFDOS.specEDI = documentManager.fieldDataDBOperation(newExtDataIDSpec).extDataID;
            fdos.specEDI = tempFDOS.specEDI;
            fdos.annotation = tempFDOS.annotation;
            try {
                if (!isFromSimulation) {
                    fdos.extent = tempFDOS.extent;
                    fdos.origin = tempFDOS.origin;
                    fdos.varNames = tempFDOS.varNames;
                    fdos.times = tempFDOS.times;
                    // 
                    // Subvolumes and Regions NOT implemented now
                    // 
                    fdos.cartesianMesh = CartesianMesh.createSimpleCartesianMesh(fdos.origin, fdos.extent, fdos.isize, new RegionImage(new // empty regions
                    VCImageUncompressed(// empty regions
                    null, // empty regions
                    new byte[fdos.isize.getXYZ()], fdos.extent, fdos.isize.getX(), fdos.isize.getY(), fdos.isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
                }
                // Add to Server Disk
                documentManager.fieldDataFileOperation(fdos);
            } catch (Exception e) {
                try {
                    // try to cleanup new ExtDataID
                    documentManager.fieldDataDBOperation(FieldDataDBOperationSpec.createDeleteExtDataIDSpec(fdos.specEDI));
                } catch (Exception e2) {
                // ignore
                }
                fdos.specEDI = null;
                throw e;
            }
        }
    };
    AsynchClientTask task3 = new AsynchClientTask("refreshing field data", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FieldDataFileOperationSpec fdos = (FieldDataFileOperationSpec) hashTable.get("fdos");
            DefaultMutableTreeNode root = ((DefaultMutableTreeNode) fieldDataGUIPanel.getJTree1().getModel().getRoot());
            if (root.getChildCount() == 0) {
                fieldDataGUIPanel.updateJTree(clientRequestManager);
            } else {
                int alphabeticalIndex = -1;
                for (int i = 0; i < root.getChildCount(); i += 1) {
                    if ((((FieldDataMainList) ((DefaultMutableTreeNode) root.getChildAt(i)).getUserObject())).externalDataIdentifier.getName().compareToIgnoreCase(fdos.specEDI.getName()) > 0) {
                        alphabeticalIndex = i;
                        break;
                    }
                }
                if (alphabeticalIndex == -1) {
                    alphabeticalIndex = root.getChildCount();
                }
                DefaultMutableTreeNode mainNode = new DefaultMutableTreeNode(new FieldDataMainList(fdos.specEDI, fdos.annotation));
                mainNode.add(new DefaultMutableTreeNode(new FieldDataVarMainList()));
                ((DefaultTreeModel) fieldDataGUIPanel.getJTree1().getModel()).insertNodeInto(mainNode, root, alphabeticalIndex);
            }
        }
    };
    return new AsynchClientTask[] { task1, task2, task3 };
}

Example 28 with DocumentManager

use of cbit.vcell.clientdb.DocumentManager in project vcell by virtualcell.

the class FieldDataGUIPanel method updateJTree.

public void updateJTree(final RequestManager clientRequestManager) {
    if (clientRequestManager == null) {
        DefaultMutableTreeNode emptyNode = new DefaultMutableTreeNode("No Info Available");
        getJTree1().setModel(new DefaultTreeModel(emptyNode));
    } else {
        DefaultMutableTreeNode startupNode = new DefaultMutableTreeNode("Gathering Field Data Information... (Please wait)");
        getJTree1().setModel(new DefaultTreeModel(startupNode));
        AsynchClientTask gatherInfo = new AsynchClientTask("gatherInfo", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                try {
                    DocumentManager documentManager = clientRequestManager.getDocumentManager();
                    FieldDataDBOperationSpec fdos = FieldDataDBOperationSpec.createGetExtDataIDsSpec(documentManager.getUser());
                    FieldDataDBOperationResults fieldDataDBOperationResults = documentManager.fieldDataDBOperation(fdos);
                    ExternalDataIdentifier[] externalDataIdentifierArr = fieldDataDBOperationResults.extDataIDArr;
                    String[] extDataAnnotArr = fieldDataDBOperationResults.extDataAnnotArr;
                    TreeMap<ExternalDataIdentifier, String> sortedExtDataIDTreeMap = new TreeMap<ExternalDataIdentifier, String>(new Comparator<ExternalDataIdentifier>() {

                        public int compare(ExternalDataIdentifier o1, ExternalDataIdentifier o2) {
                            return o1.getName().compareToIgnoreCase(o2.getName());
                        }
                    });
                    for (int i = 0; i < externalDataIdentifierArr.length; i += 1) {
                        sortedExtDataIDTreeMap.put(externalDataIdentifierArr[i], extDataAnnotArr[i]);
                    }
                    DefaultMutableTreeNode rootNode = new DefaultMutableTreeNode(new InitializedRootNode("Field Data Info" + (externalDataIdentifierArr.length == 0 ? " (None Defined)" : "")));
                    Iterator<Entry<ExternalDataIdentifier, String>> sortIter = sortedExtDataIDTreeMap.entrySet().iterator();
                    while (sortIter.hasNext()) {
                        Entry<ExternalDataIdentifier, String> entry = sortIter.next();
                        DefaultMutableTreeNode mainNode = new DefaultMutableTreeNode(new FieldDataMainList(entry.getKey(), entry.getValue()));
                        mainNode.add(new DefaultMutableTreeNode(new FieldDataVarMainList()));
                        rootNode.add(mainNode);
                    }
                    hashTable.put("rootNode", rootNode);
                } catch (Exception e) {
                    DefaultMutableTreeNode errorNode = new DefaultMutableTreeNode("Error Getting Field Data Information");
                    hashTable.put("rootNode", errorNode);
                    throw e;
                }
            }
        };
        AsynchClientTask updateTree = new AsynchClientTask("updateTree", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                DefaultMutableTreeNode rootNode = (DefaultMutableTreeNode) hashTable.get("rootNode");
                getJTree1().setModel(new DefaultTreeModel(rootNode));
            }
        };
        ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { gatherInfo, updateTree });
    }
}

Example 29 with DocumentManager

use of cbit.vcell.clientdb.DocumentManager in project vcell by virtualcell.

the class GeometryMetaDataPanel method setDocumentManager.

/**
 * Sets the documentManager property (cbit.vcell.clientdb.DocumentManager) value.
 * @param documentManager The new value for the property.
 * @see #getDocumentManager
 */
public void setDocumentManager(DocumentManager documentManager) {
    DocumentManager oldValue = fieldDocumentManager;
    fieldDocumentManager = documentManager;
    firePropertyChange(CommonTask.DOCUMENT_MANAGER.name, oldValue, documentManager);
}

Example 30 with DocumentManager

use of cbit.vcell.clientdb.DocumentManager in project vcell by virtualcell.

the class ImageDbTreeModel method setDocumentManager.

/**
 * Sets the documentManager property (cbit.vcell.clientdb.DocumentManager) value.
 * @param documentManager The new value for the property.
 * @see #getDocumentManager
 */
public void setDocumentManager(DocumentManager documentManager) {
    DocumentManager oldValue = fieldDocumentManager;
    fieldDocumentManager = documentManager;
    if (oldValue != null) {
        oldValue.removeDatabaseListener(this);
    }
    if (documentManager != null) {
        documentManager.addDatabaseListener(this);
    }
    firePropertyChange(CommonTask.DOCUMENT_MANAGER.name, oldValue, documentManager);
    if (documentManager != oldValue) {
        refreshTree();
    }
}