Examples with GeometryInfo cbit.vcell.geometry.GeometryInfo used on opensource projects

Example 6 with GeometryInfo

use of cbit.vcell.geometry.GeometryInfo 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, boolean bGrantSupportPermissions) {
    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));
            if (bGrantSupportPermissions) {
                getAclEditor().grantVCellSupportPermissions();
            }
            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, false);
                        }
                    }
                }
            }
        }
    };
    ClientTaskDispatcher.dispatch(requester, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
}

Example 7 with GeometryInfo

use of cbit.vcell.geometry.GeometryInfo 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);
}

Example 8 with GeometryInfo

use of cbit.vcell.geometry.GeometryInfo in project vcell by virtualcell.

the class ClientRequestManager method accessPermissionsEx.

public void accessPermissionsEx(Component requester, VCDocument vcDoc, boolean bGrantSupportPermissions) {
    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, true);
}

Example 9 with GeometryInfo

use of cbit.vcell.geometry.GeometryInfo 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 10 with GeometryInfo

use of cbit.vcell.geometry.GeometryInfo in project vcell by virtualcell.

the class RuleBasedTest method main.

public static void main(String[] args) {
    try {
        PropertyLoader.loadProperties();
    } catch (Exception e) {
        e.printStackTrace();
    }
    final int numTrials = 40;
    VCDatabaseVisitor vcDatabaseVisitor = new VCDatabaseVisitor() {

        @Override
        public void visitMathModel(MathModel mathModel, PrintStream logFilePrintStream) {
            throw new IllegalArgumentException("Not Implemented");
        }

        @Override
        public void visitGeometry(Geometry geometry, PrintStream logFilePrintStream) {
            throw new IllegalArgumentException("Not Implemented");
        }

        @Override
        public void visitBioModel(BioModel bioModel, PrintStream logFilePrintStream) {
            SimulationContext[] simulationContexts = bioModel.getSimulationContexts();
            for (SimulationContext simContext : simulationContexts) {
                if ((simContext.getApplicationType() == Application.NETWORK_STOCHASTIC) && simContext.getGeometry().getDimension() == 0) {
                    File baseDirectory = createDirFile(simContext);
                    try {
                        checkNonspatialStochasticSimContext(simContext, baseDirectory, numTrials);
                    } catch (Exception e) {
                        e.printStackTrace();
                        if (!e.getMessage().contains("Only Mass Action Kinetics supported ")) {
                            writeMessageTofile(baseDirectory, e.getMessage());
                        }
                    }
                }
            }
        }

        @Override
        public boolean filterMathModel(MathModelInfo mathModelInfo) {
            return false;
        }

        @Override
        public boolean filterGeometry(GeometryInfo geometryInfo) {
            return false;
        }

        @Override
        public boolean filterBioModel(BioModelInfo bioModelInfo) {
            return // bioModelInfo.getVersion().getName().equals("model");
            bioModelInfo.getVersion().getName().equals("simpleModel_Network_orig");
        }
    };
    String currentUserID = "schaff";
    String[] allUsers = new String[] { /*-all*/
    currentUserID, "-" };
    VCDatabaseScanner.scanBioModels(allUsers, vcDatabaseVisitor, false);
}