Examples with BioModelInfo org.vcell.util.document.BioModelInfo used on opensource projects

Example 1 with BioModelInfo

use of org.vcell.util.document.BioModelInfo in project vcell by virtualcell.

the class ClientRequestManager method curateDocument.

/**
 * Insert the method's description here.
 * Creation date: (6/22/2004 10:50:34 PM)
 * @param documentInfo cbit.vcell.document.VCDocumentInfo
 */
public void curateDocument(final VCDocumentInfo documentInfo, final int curateType, final TopLevelWindowManager requester) {
    if (documentInfo != null) {
        // see if we have this open
        String documentID = documentInfo.getVersion().getVersionKey().toString();
        if (getMdiManager().haveWindow(documentID)) {
            // already open, refuse
            PopupGenerator.showErrorDialog(requester, "Selected edition is open, cannot " + CurateSpec.CURATE_TYPE_NAMES[curateType]);
            return;
        } else {
            // don't have it open, try to CURATE it
            int confirm = PopupGenerator.showComponentOKCancelDialog(requester.getComponent(), new JTextArea(CurateSpec.CURATE_TYPE_ACTIONS[curateType] + " cannot be undone without VCELL administrative assistance.\n" + CurateSpec.CURATE_TYPE_STATES[curateType] + " versions of documents cannot be deleted without VCELL administrative assistance.\n" + (curateType == CurateSpec.PUBLISH ? CurateSpec.CURATE_TYPE_STATES[curateType] + " versions of documents MUST remain publically accessible to other VCELL users.\n" : "") + "Do you want to " + CurateSpec.CURATE_TYPE_NAMES[curateType] + " document '" + documentInfo.getVersion().getName() + "'" + "\nwith version date '" + documentInfo.getVersion().getDate().toString() + "'?"), "WARNING -- " + CurateSpec.CURATE_TYPE_ACTIONS[curateType] + " operation cannot be undone");
            if (confirm == JOptionPane.OK_OPTION) {
                AsynchClientTask task1 = new AsynchClientTask(CurateSpec.CURATE_TYPE_ACTIONS[curateType] + " document...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                    @Override
                    public void run(Hashtable<String, Object> hashTable) throws Exception {
                        if (documentInfo instanceof BioModelInfo) {
                            getDocumentManager().curate(new CurateSpec((BioModelInfo) documentInfo, curateType));
                        } else if (documentInfo instanceof MathModelInfo) {
                            getDocumentManager().curate(new CurateSpec((MathModelInfo) documentInfo, curateType));
                        } else {
                            throw new RuntimeException(CurateSpec.CURATE_TYPE_ACTIONS[curateType] + " not supported for VCDocumentInfo type " + documentInfo.getClass().getName());
                        }
                    }
                };
                ClientTaskDispatcher.dispatch(requester.getComponent(), new Hashtable<String, Object>(), new AsynchClientTask[] { task1 }, false);
            } else {
                // user canceled
                return;
            }
        }
    } else {
        // nothing selected
        return;
    }
}

Example 2 with BioModelInfo

use of org.vcell.util.document.BioModelInfo in project vcell by virtualcell.

the class ClientRequestManager method accessPermissions.

public void accessPermissions(Component requester, VCDocument vcDoc) {
    VersionInfo selectedVersionInfo = null;
    switch(vcDoc.getDocumentType()) {
        case BIOMODEL_DOC:
            BioModelInfo[] bioModelInfos = getDocumentManager().getBioModelInfos();
            for (BioModelInfo bioModelInfo : bioModelInfos) {
                if (bioModelInfo.getVersion().getVersionKey().equals(vcDoc.getVersion().getVersionKey())) {
                    selectedVersionInfo = bioModelInfo;
                    break;
                }
            }
            break;
        case MATHMODEL_DOC:
            MathModelInfo[] mathModelInfos = getDocumentManager().getMathModelInfos();
            for (MathModelInfo mathModelInfo : mathModelInfos) {
                if (mathModelInfo.getVersion().getVersionKey().equals(vcDoc.getVersion().getVersionKey())) {
                    selectedVersionInfo = mathModelInfo;
                    break;
                }
            }
            break;
        case GEOMETRY_DOC:
            GeometryInfo[] geoInfos = getDocumentManager().getGeometryInfos();
            for (GeometryInfo geoInfo : geoInfos) {
                if (geoInfo.getVersion().getVersionKey().equals(vcDoc.getVersion().getVersionKey())) {
                    selectedVersionInfo = geoInfo;
                    break;
                }
            }
            break;
    }
    getMdiManager().getDatabaseWindowManager().accessPermissions(requester, selectedVersionInfo);
}

Example 3 with BioModelInfo

use of org.vcell.util.document.BioModelInfo in project vcell by virtualcell.

the class ClientRequestManager method openAfterChecking.

private void openAfterChecking(VCDocumentInfo documentInfo, final TopLevelWindowManager requester, final boolean inNewWindow) {
    final String DOCUMENT_INFO = "documentInfo";
    final String SEDML_TASK = "SedMLTask";
    final String SEDML_MODEL = "SedMLModel";
    final String BNG_UNIT_SYSTEM = "bngUnitSystem";
    /* asynchronous and not blocking any window */
    bOpening = true;
    Hashtable<String, Object> hashTable = new Hashtable<String, Object>();
    // may want to insert corrected VCDocumentInfo later if our import debugger corrects it (BNGL Debugger).
    hashTable.put(DOCUMENT_INFO, documentInfo);
    // start a thread that gets it and updates the GUI by creating a new document desktop
    String taskName = null;
    if (documentInfo instanceof ExternalDocInfo) {
        taskName = "Importing document";
        ExternalDocInfo externalDocInfo = (ExternalDocInfo) documentInfo;
        File file = externalDocInfo.getFile();
        if (file != null && !file.getName().isEmpty() && file.getName().endsWith("bngl")) {
            BngUnitSystem bngUnitSystem = new BngUnitSystem(BngUnitOrigin.DEFAULT);
            String fileText;
            String originalFileText;
            try {
                fileText = BeanUtils.readBytesFromFile(file, null);
                originalFileText = new String(fileText);
            } catch (IOException e1) {
                e1.printStackTrace();
                DialogUtils.showErrorDialog(requester.getComponent(), "<html>Error reading file " + file.getPath() + "</html>");
                return;
            }
            Reader reader = externalDocInfo.getReader();
            boolean bException = true;
            while (bException) {
                try {
                    BioModel bioModel = createDefaultBioModelDocument(bngUnitSystem);
                    boolean bStochastic = true;
                    boolean bRuleBased = true;
                    SimulationContext ruleBasedSimContext = bioModel.addNewSimulationContext("temp NFSim app", SimulationContext.Application.RULE_BASED_STOCHASTIC);
                    List<SimulationContext> appList = new ArrayList<SimulationContext>();
                    appList.add(ruleBasedSimContext);
                    RbmModelContainer rbmModelContainer = bioModel.getModel().getRbmModelContainer();
                    RbmUtils.reactionRuleLabelIndex = 0;
                    RbmUtils.reactionRuleNames.clear();
                    ASTModel astModel = RbmUtils.importBnglFile(reader);
                    // for now, hasUnitSystem() always returns false
                    if (astModel.hasUnitSystem()) {
                        bngUnitSystem = astModel.getUnitSystem();
                    }
                    if (astModel.hasCompartments()) {
                        Structure struct = bioModel.getModel().getStructure(0);
                        if (struct != null) {
                            bioModel.getModel().removeStructure(struct);
                        }
                    }
                    BnglObjectConstructionVisitor constructionVisitor = null;
                    if (!astModel.hasMolecularDefinitions()) {
                        System.out.println("Molecular Definition Block missing.");
                        constructionVisitor = new BnglObjectConstructionVisitor(bioModel.getModel(), appList, bngUnitSystem, false);
                    } else {
                        constructionVisitor = new BnglObjectConstructionVisitor(bioModel.getModel(), appList, bngUnitSystem, true);
                    }
                    astModel.jjtAccept(constructionVisitor, rbmModelContainer);
                    bException = false;
                } catch (final Exception e) {
                    e.printStackTrace(System.out);
                    BNGLDebuggerPanel panel = new BNGLDebuggerPanel(fileText, e);
                    int oKCancel = DialogUtils.showComponentOKCancelDialog(requester.getComponent(), panel, "Bngl Debugger: " + file.getName());
                    if (oKCancel == JOptionPane.CANCEL_OPTION || oKCancel == JOptionPane.DEFAULT_OPTION) {
                        throw new UserCancelException("Canceling Import");
                    }
                    // inserting <potentially> corrected DocumentInfo
                    fileText = panel.getText();
                    externalDocInfo = new ExternalDocInfo(panel.getText());
                    reader = externalDocInfo.getReader();
                    hashTable.put(DOCUMENT_INFO, externalDocInfo);
                }
            }
            if (!originalFileText.equals(fileText)) {
                // file has been modified
                String message = "Importing <b>" + file.getName() + "</b> into vCell. <br>Overwrite the file on the disk?<br>";
                message = "<html>" + message + "</html>";
                Object[] options = { "Overwrite and Import", "Import Only", "Cancel" };
                int returnCode = JOptionPane.showOptionDialog(requester.getComponent(), message, "Bngl Debugger", JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null, options, options[2]);
                if (returnCode == JOptionPane.YES_OPTION) {
                    try {
                        FileWriter fw = new FileWriter(file);
                        fw.write(fileText);
                        fw.close();
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                } else if (returnCode == JOptionPane.CANCEL_OPTION || returnCode == JOptionPane.CLOSED_OPTION) {
                    return;
                }
            }
            if (!(bngUnitSystem.getOrigin() == BngUnitOrigin.PARSER)) {
                BNGLUnitsPanel panel = new BNGLUnitsPanel(bngUnitSystem);
                int oKCancel = DialogUtils.showComponentOKCancelDialog(requester.getComponent(), panel, " Bngl Units Selector", null, false);
                if (oKCancel == JOptionPane.CANCEL_OPTION || oKCancel == JOptionPane.DEFAULT_OPTION) {
                    // TODO: or do nothing and continue with default values?
                    return;
                } else {
                    bngUnitSystem = panel.getUnits();
                }
            }
            hashTable.put(BNG_UNIT_SYSTEM, bngUnitSystem);
        } else if (file != null && !file.getName().isEmpty() && file.getName().toLowerCase().endsWith(".sedml")) {
            try {
                XMLSource xmlSource = externalDocInfo.createXMLSource();
                File sedmlFile = xmlSource.getXmlFile();
                SedML sedml = Libsedml.readDocument(sedmlFile).getSedMLModel();
                if (sedml == null || sedml.getModels().isEmpty()) {
                    return;
                }
                AbstractTask chosenTask = SEDMLChooserPanel.chooseTask(sedml, requester.getComponent(), file.getName());
                hashTable.put(SEDML_MODEL, sedml);
                hashTable.put(SEDML_TASK, chosenTask);
            } catch (Exception e) {
                e.printStackTrace();
                throw new RuntimeException("failed to read document: " + e.getMessage(), e);
            }
        } else if (file != null && !file.getName().isEmpty() && (file.getName().toLowerCase().endsWith(".sedx") || file.getName().toLowerCase().endsWith(".omex"))) {
            try {
                ArchiveComponents ac = null;
                ac = Libsedml.readSEDMLArchive(new FileInputStream(file));
                SEDMLDocument doc = ac.getSedmlDocument();
                SedML sedml = doc.getSedMLModel();
                if (sedml == null) {
                    throw new RuntimeException("Failed importing " + file.getName());
                }
                if (sedml.getModels().isEmpty()) {
                    throw new RuntimeException("Unable to find any model in " + file.getName());
                }
                AbstractTask chosenTask = SEDMLChooserPanel.chooseTask(sedml, requester.getComponent(), file.getName());
                hashTable.put(SEDML_MODEL, sedml);
                hashTable.put(SEDML_TASK, chosenTask);
            } catch (Exception e) {
                e.printStackTrace();
                throw new RuntimeException("failed to read archive: " + e.getMessage(), e);
            }
        }
    } else {
        taskName = "Loading document '" + documentInfo.getVersion().getName() + "' from database";
    }
    AsynchClientTask task0 = new AsynchClientTask(taskName, AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (!inNewWindow) {
                // request was to replace the document in an existing window
                getMdiManager().blockWindow(requester.getManagerID());
            }
        }
    };
    AsynchClientTask task1 = new AsynchClientTask(taskName, AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            VCDocument doc = null;
            VCDocumentInfo documentInfo = (VCDocumentInfo) hashTable.get(DOCUMENT_INFO);
            if (documentInfo instanceof BioModelInfo) {
                BioModelInfo bmi = (BioModelInfo) documentInfo;
                doc = getDocumentManager().getBioModel(bmi);
            } else if (documentInfo instanceof MathModelInfo) {
                MathModelInfo mmi = (MathModelInfo) documentInfo;
                doc = getDocumentManager().getMathModel(mmi);
            } else if (documentInfo instanceof GeometryInfo) {
                GeometryInfo gmi = (GeometryInfo) documentInfo;
                doc = getDocumentManager().getGeometry(gmi);
            } else if (documentInfo instanceof ExternalDocInfo) {
                ExternalDocInfo externalDocInfo = (ExternalDocInfo) documentInfo;
                File file = externalDocInfo.getFile();
                if (file != null && !file.getName().isEmpty() && (file.getName().toLowerCase().endsWith(".sedx") || file.getName().toLowerCase().endsWith(".omex"))) {
                    TranslationLogger transLogger = new TranslationLogger(requester);
                    doc = XmlHelper.sedmlToBioModel(transLogger, externalDocInfo, (SedML) hashTable.get(SEDML_MODEL), (AbstractTask) hashTable.get(SEDML_TASK));
                } else if (!externalDocInfo.isXML()) {
                    if (hashTable.containsKey(BNG_UNIT_SYSTEM)) {
                        // not XML, look for BNGL etc.
                        // we use the BngUnitSystem already created during the 1st pass
                        BngUnitSystem bngUnitSystem = (BngUnitSystem) hashTable.get(BNG_UNIT_SYSTEM);
                        BioModel bioModel = createDefaultBioModelDocument(bngUnitSystem);
                        SimulationContext ruleBasedSimContext = bioModel.addNewSimulationContext("NFSim app", SimulationContext.Application.RULE_BASED_STOCHASTIC);
                        SimulationContext odeSimContext = bioModel.addNewSimulationContext("BioNetGen app", SimulationContext.Application.NETWORK_DETERMINISTIC);
                        List<SimulationContext> appList = new ArrayList<SimulationContext>();
                        appList.add(ruleBasedSimContext);
                        appList.add(odeSimContext);
                        // set convention for initial conditions in generated application for seed species (concentration or count)
                        ruleBasedSimContext.setUsingConcentration(bngUnitSystem.isConcentration());
                        odeSimContext.setUsingConcentration(bngUnitSystem.isConcentration());
                        RbmModelContainer rbmModelContainer = bioModel.getModel().getRbmModelContainer();
                        RbmUtils.reactionRuleLabelIndex = 0;
                        RbmUtils.reactionRuleNames.clear();
                        Reader reader = externalDocInfo.getReader();
                        ASTModel astModel = RbmUtils.importBnglFile(reader);
                        if (bioModel.getModel() != null && bioModel.getModel().getVcMetaData() != null) {
                            VCMetaData vcMetaData = bioModel.getModel().getVcMetaData();
                            vcMetaData.setFreeTextAnnotation(bioModel, astModel.getProlog());
                        }
                        if (astModel.hasCompartments()) {
                            Structure struct = bioModel.getModel().getStructure(0);
                            if (struct != null) {
                                bioModel.getModel().removeStructure(struct);
                            }
                        }
                        BnglObjectConstructionVisitor constructionVisitor = null;
                        if (!astModel.hasMolecularDefinitions()) {
                            System.out.println("Molecular Definition Block missing. Extracting it from Species, Reactions, Obserbables.");
                            constructionVisitor = new BnglObjectConstructionVisitor(bioModel.getModel(), appList, bngUnitSystem, false);
                        } else {
                            constructionVisitor = new BnglObjectConstructionVisitor(bioModel.getModel(), appList, bngUnitSystem, true);
                        }
                        // we'll convert the kinetic parameters to BngUnitSystem inside the visit(ASTKineticsParameter...)
                        astModel.jjtAccept(constructionVisitor, rbmModelContainer);
                        // set the volume in the newly created application to BngUnitSystem.bnglModelVolume
                        // TODO: set the right values if we import compartments from the bngl file!
                        // if(!bngUnitSystem.isConcentration()) {
                        Expression sizeExpression = new Expression(bngUnitSystem.getVolume());
                        ruleBasedSimContext.getGeometryContext().getStructureMapping(0).getSizeParameter().setExpression(sizeExpression);
                        odeSimContext.getGeometryContext().getStructureMapping(0).getSizeParameter().setExpression(sizeExpression);
                        // }
                        // we remove the NFSim application if any seed species is clamped because NFSim doesn't know what to do with it
                        boolean bClamped = false;
                        for (SpeciesContextSpec scs : ruleBasedSimContext.getReactionContext().getSpeciesContextSpecs()) {
                            if (scs.isConstant()) {
                                bClamped = true;
                                break;
                            }
                        }
                        if (bClamped) {
                            bioModel.removeSimulationContext(ruleBasedSimContext);
                        }
                        // // TODO: DON'T delete this code
                        // // the code below is needed if we also want to create simulations, example for 1 rule based simulation
                        // // it is rule-based so it wont have to flatten, should be fast.
                        // MathMappingCallback callback = new MathMappingCallbackTaskAdapter(getClientTaskStatusSupport());
                        // NetworkGenerationRequirements networkGenerationRequirements = null; // network generation should not be executed.
                        // ruleBasedSimContext.refreshMathDescription(callback,networkGenerationRequirements);
                        // Simulation sim = ruleBasedSimContext.addNewSimulation(SimulationOwner.DEFAULT_SIM_NAME_PREFIX,callback,networkGenerationRequirements);
                        doc = bioModel;
                    }
                } else {
                    // is XML
                    try (TranslationLogger transLogger = new TranslationLogger(requester)) {
                        XMLSource xmlSource = externalDocInfo.createXMLSource();
                        org.jdom.Element rootElement = xmlSource.getXmlDoc().getRootElement();
                        String xmlType = rootElement.getName();
                        String modelXmlType = null;
                        if (xmlType.equals(XMLTags.VcmlRootNodeTag)) {
                            // For now, assuming that <vcml> element has only one child (biomodel, mathmodel or geometry).
                            // Will deal with multiple children of <vcml> Element when we get to model composition.
                            @SuppressWarnings("unchecked") List<Element> childElementList = rootElement.getChildren();
                            // assuming first child is the biomodel, mathmodel or geometry.
                            Element modelElement = childElementList.get(0);
                            modelXmlType = modelElement.getName();
                        }
                        if (xmlType.equals(XMLTags.BioModelTag) || (xmlType.equals(XMLTags.VcmlRootNodeTag) && modelXmlType.equals(XMLTags.BioModelTag))) {
                            doc = XmlHelper.XMLToBioModel(xmlSource);
                        } else if (xmlType.equals(XMLTags.MathModelTag) || (xmlType.equals(XMLTags.VcmlRootNodeTag) && modelXmlType.equals(XMLTags.MathModelTag))) {
                            doc = XmlHelper.XMLToMathModel(xmlSource);
                        } else if (xmlType.equals(XMLTags.GeometryTag) || (xmlType.equals(XMLTags.VcmlRootNodeTag) && modelXmlType.equals(XMLTags.GeometryTag))) {
                            doc = XmlHelper.XMLToGeometry(xmlSource);
                        } else if (xmlType.equals(XMLTags.SbmlRootNodeTag)) {
                            Namespace namespace = rootElement.getNamespace(XMLTags.SBML_SPATIAL_NS_PREFIX);
                            boolean bIsSpatial = (namespace == null) ? false : true;
                            doc = XmlHelper.importSBML(transLogger, xmlSource, bIsSpatial);
                        } else if (xmlType.equals(XMLTags.CellmlRootNodeTag)) {
                            if (requester instanceof BioModelWindowManager) {
                                doc = XmlHelper.importBioCellML(transLogger, xmlSource);
                            } else {
                                doc = XmlHelper.importMathCellML(transLogger, xmlSource);
                            }
                        } else if (xmlType.equals(MicroscopyXMLTags.FRAPStudyTag)) {
                            doc = VFrapXmlHelper.VFRAPToBioModel(hashTable, xmlSource, getDocumentManager(), requester);
                        } else if (xmlType.equals(XMLTags.SedMLTypeTag)) {
                            doc = XmlHelper.sedmlToBioModel(transLogger, externalDocInfo, (SedML) hashTable.get(SEDML_MODEL), (AbstractTask) hashTable.get(SEDML_TASK));
                        } else {
                            // unknown XML format
                            throw new RuntimeException("unsupported XML format, first element tag is <" + rootElement.getName() + ">");
                        }
                        if (externalDocInfo.getDefaultName() != null) {
                            doc.setName(externalDocInfo.getDefaultName());
                        }
                    }
                }
                if (doc == null) {
                    File f = externalDocInfo.getFile();
                    if (f != null) {
                        throw new RuntimeException("Unable to determine type of file " + f.getCanonicalPath());
                    }
                    throw new ProgrammingException();
                }
            }
            // create biopax objects using annotation
            if (doc instanceof BioModel) {
                BioModel bioModel = (BioModel) doc;
                try {
                    bioModel.getVCMetaData().createBioPaxObjects(bioModel);
                } catch (Exception e) {
                    e.printStackTrace();
                }
            }
            requester.prepareDocumentToLoad(doc, inNewWindow);
            hashTable.put("doc", doc);
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("Showing document", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false, false) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            try {
                Throwable exc = (Throwable) hashTable.get(ClientTaskDispatcher.TASK_ABORTED_BY_ERROR);
                if (exc == null) {
                    VCDocument doc = (VCDocument) hashTable.get("doc");
                    DocumentWindowManager windowManager = null;
                    if (inNewWindow) {
                        windowManager = createDocumentWindowManager(doc);
                        // request was to create a new top-level window with this doc
                        getMdiManager().createNewDocumentWindow(windowManager);
                    // if (windowManager instanceof BioModelWindowManager) {
                    // ((BioModelWindowManager)windowManager).preloadApps();
                    // }
                    } else {
                        // request was to replace the document in an existing window
                        windowManager = (DocumentWindowManager) requester;
                        getMdiManager().setCanonicalTitle(requester.getManagerID());
                        windowManager.resetDocument(doc);
                    }
                    hashTable.put(WIN_MGR_KEY, windowManager);
                }
            } finally {
                if (!inNewWindow) {
                    getMdiManager().unBlockWindow(requester.getManagerID());
                }
                bOpening = false;
            }
        }
    };
    AsynchClientTask task3 = new AsynchClientTask("Special Layout", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false, false) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // TODO Auto-generated method stub
            if (documentInfo instanceof ExternalDocInfo) {
                ExternalDocInfo externalDocInfo = (ExternalDocInfo) documentInfo;
                if (externalDocInfo.isBioModelsNet()) {
                    DocumentWindowManager windowManager = (DocumentWindowManager) hashTable.get(WIN_MGR_KEY);
                    if (windowManager instanceof BioModelWindowManager) {
                        ((BioModelWindowManager) windowManager).specialLayout();
                    }
                }
            }
        }
    };
    AsynchClientTask task4 = new AsynchClientTaskFunction(ClientRequestManager::setWindowFocus, "Set window focus", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false, false);
    ClientTaskDispatcher.dispatch(requester.getComponent(), hashTable, new AsynchClientTask[] { task0, task1, task2, task3, task4 }, false);
}

Example 4 with BioModelInfo

use of org.vcell.util.document.BioModelInfo 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 BioModelInfo

use of org.vcell.util.document.BioModelInfo in project vcell by virtualcell.

the class DatabaseWindowManager method compareAnotherModel.

/**
 * Comment
 */
public void compareAnotherModel() {
    // 
    if (getPanelSelection() == null) {
        PopupGenerator.showErrorDialog(this, "Error Comparing documents : First document not selected");
        return;
    }
    VCDocumentInfo thisDocumentInfo = getPanelSelection();
    // Choose the other documentInfo. Bring up the appropriate dbTreePanel depending on the type of thisDocumentInfo
    VCDocumentInfo otherDocumentInfo = null;
    try {
        otherDocumentInfo = selectDocument(thisDocumentInfo.getVCDocumentType(), this);
    } catch (Exception e) {
        if (!(e instanceof UserCancelException)) {
            e.printStackTrace();
            DialogUtils.showErrorDialog(this.getComponent(), "Error Comparing documents: " + e.getMessage());
        }
        return;
    }
    if (otherDocumentInfo == null) {
        // PopupGenerator.showErrorDialog(this, "Error Comparing documents : Second document is null ");
        return;
    }
    // Check if both document types are of the same kind. If not, throw an error.
    if (((thisDocumentInfo instanceof BioModelInfo) && !(otherDocumentInfo instanceof BioModelInfo)) || ((thisDocumentInfo instanceof MathModelInfo) && !(otherDocumentInfo instanceof MathModelInfo)) || ((thisDocumentInfo instanceof GeometryInfo) && !(otherDocumentInfo instanceof GeometryInfo))) {
        PopupGenerator.showErrorDialog(this, "Error Comparing documents : The two documents are not of the same type!");
        return;
    }
    // Now that we have both the document versions to be compared, do the comparison and display the result
    compareWithOther(otherDocumentInfo, thisDocumentInfo);
}