use of cbit.vcell.geometry.GeometryInfo in project vcell by virtualcell.
the class ClientRequestManager method deleteDocument.
/**
* Insert the method's description here.
* Creation date: (6/22/2004 10:50:34 PM)
* @param documentInfo cbit.vcell.document.VCDocumentInfo
*/
public void deleteDocument(final VCDocumentInfo documentInfo, 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 delete");
return;
} else {
// don't have it open, try to delete it
String confirm = PopupGenerator.showWarningDialog(requester, getUserPreferences(), UserMessage.warn_deleteDocument, documentInfo.getVersion().getName());
if (confirm.equals(UserMessage.OPTION_DELETE)) {
AsynchClientTask task1 = new AsynchClientTask("Deleting document...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
if (documentInfo instanceof BioModelInfo) {
getDocumentManager().delete((BioModelInfo) documentInfo);
} else if (documentInfo instanceof MathModelInfo) {
getDocumentManager().delete((MathModelInfo) documentInfo);
} else if (documentInfo instanceof GeometryInfo) {
getDocumentManager().delete((GeometryInfo) documentInfo);
} else {
throw new RuntimeException("delete 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;
}
}
use of cbit.vcell.geometry.GeometryInfo in project vcell by virtualcell.
the class DbDriver method getVCInfoContainer.
/**
* Insert the method's description here.
* Creation date: (9/24/2003 12:54:32 PM)
* @return cbit.vcell.modeldb.VCInfoContainer
*/
public static VCInfoContainer getVCInfoContainer(User user, Connection con, DatabaseSyntax dbSyntax) throws SQLException, DataAccessException {
VCInfoContainer results = null;
//
VCImageInfo[] vcImageInfos = null;
GeometryInfo[] geometryInfos = null;
MathModelInfo[] mathModelInfos = null;
BioModelInfo[] bioModelInfos = null;
//
StringBuffer sql = null;
String special = null;
ResultSet rset = null;
boolean enableSpecial = true;
boolean enableDistinct = true;
Statement stmt = con.createStatement();
try {
//
// BioModelInfos
//
{
double beginTime = System.currentTimeMillis();
special = " ORDER BY " + BioModelTable.table.name.getQualifiedColName() + "," + BioModelTable.table.versionBranchID.getQualifiedColName() + "," + BioModelTable.table.versionDate.getQualifiedColName();
sql = new StringBuffer(BioModelTable.table.getInfoSQL(user, null, (enableSpecial ? special : null), dbSyntax));
sql.insert(7, Table.SQL_GLOBAL_HINT);
rset = stmt.executeQuery(sql.toString());
ArrayList<BioModelInfo> tempInfos = new ArrayList<BioModelInfo>();
Set<String> distinctV = new HashSet<String>();
while (rset.next()) {
BioModelInfo versionInfo = (BioModelInfo) BioModelTable.table.getInfo(rset, con, dbSyntax);
if (!distinctV.contains(versionInfo.getVersion().getVersionKey().toString())) {
tempInfos.add(versionInfo);
distinctV.add(versionInfo.getVersion().getVersionKey().toString());
}
}
rset.close();
if (tempInfos.size() > 0) {
bioModelInfos = new BioModelInfo[tempInfos.size()];
tempInfos.toArray(bioModelInfos);
}
if (lg.isInfoEnabled()) {
lg.info("BioModelInfo Time=" + (((double) System.currentTimeMillis() - beginTime) / (double) 1000));
}
}
//
// MathModelInfos
//
{
double beginTime = System.currentTimeMillis();
special = " ORDER BY " + MathModelTable.table.name.getQualifiedColName() + "," + MathModelTable.table.versionBranchID.getQualifiedColName() + "," + MathModelTable.table.versionDate.getQualifiedColName();
sql = new StringBuffer(MathModelTable.table.getInfoSQL(user, null, (enableSpecial ? special : null), dbSyntax));
sql.insert(7, Table.SQL_GLOBAL_HINT);
rset = stmt.executeQuery(sql.toString());
ArrayList<MathModelInfo> tempInfos = new ArrayList<MathModelInfo>();
Set<String> distinctV = new HashSet<String>();
while (rset.next()) {
MathModelInfo versionInfo = (MathModelInfo) MathModelTable.table.getInfo(rset, con, dbSyntax);
if (!distinctV.contains(versionInfo.getVersion().getVersionKey().toString())) {
tempInfos.add(versionInfo);
distinctV.add(versionInfo.getVersion().getVersionKey().toString());
}
}
rset.close();
if (tempInfos.size() > 0) {
mathModelInfos = new MathModelInfo[tempInfos.size()];
tempInfos.toArray(mathModelInfos);
}
if (lg.isInfoEnabled()) {
lg.info("MathModelInfo Time=" + (((double) System.currentTimeMillis() - beginTime) / (double) 1000));
}
}
//
// VCImageInfos
//
{
double beginTime = System.currentTimeMillis();
special = " ORDER BY " + ImageTable.table.name.getQualifiedColName() + "," + ImageTable.table.versionBranchID.getQualifiedColName() + "," + ImageTable.table.versionDate.getQualifiedColName();
sql = new StringBuffer(ImageTable.table.getInfoSQL(user, null, (enableSpecial ? special : null), true, dbSyntax));
sql.insert(7, Table.SQL_GLOBAL_HINT);
rset = stmt.executeQuery(sql.toString());
ArrayList<VCImageInfo> tempInfos = new ArrayList<VCImageInfo>();
Set<String> distinctV = new HashSet<String>();
while (rset.next()) {
VCImageInfo versionInfo = (VCImageInfo) ImageTable.table.getInfo(rset, con, dbSyntax);
if (!distinctV.contains(versionInfo.getVersion().getVersionKey().toString())) {
tempInfos.add(versionInfo);
distinctV.add(versionInfo.getVersion().getVersionKey().toString());
}
}
rset.close();
if (tempInfos.size() > 0) {
vcImageInfos = new VCImageInfo[tempInfos.size()];
tempInfos.toArray(vcImageInfos);
}
if (lg.isInfoEnabled()) {
lg.info("ImageInfo Time=" + (((double) System.currentTimeMillis() - beginTime) / (double) 1000));
}
}
//
// GeometeryInfos
//
{
double beginTime = System.currentTimeMillis();
special = " ORDER BY " + GeometryTable.table.name.getQualifiedColName() + "," + GeometryTable.table.versionBranchID.getQualifiedColName() + "," + GeometryTable.table.versionDate.getQualifiedColName();
sql = new StringBuffer(GeometryTable.table.getInfoSQL(user, null, (enableSpecial ? special : null), true, dbSyntax));
sql.insert(7, Table.SQL_GLOBAL_HINT + (enableDistinct ? "DISTINCT " : ""));
rset = stmt.executeQuery(sql.toString());
ArrayList<GeometryInfo> tempInfos = new ArrayList<GeometryInfo>();
Set<String> distinctV = new HashSet<String>();
while (rset.next()) {
GeometryInfo versionInfo = (GeometryInfo) GeometryTable.table.getInfo(rset, con);
if (!distinctV.contains(versionInfo.getVersion().getVersionKey().toString())) {
tempInfos.add(versionInfo);
distinctV.add(versionInfo.getVersion().getVersionKey().toString());
}
}
rset.close();
if (tempInfos.size() > 0) {
geometryInfos = new GeometryInfo[tempInfos.size()];
tempInfos.toArray(geometryInfos);
}
if (lg.isInfoEnabled()) {
lg.info("GeometryInfo Time=" + (((double) System.currentTimeMillis() - beginTime) / (double) 1000));
}
}
} finally {
if (stmt != null) {
stmt.close();
}
}
results = new VCInfoContainer(user, vcImageInfos, geometryInfos, mathModelInfos, bioModelInfos);
return results;
}
use of cbit.vcell.geometry.GeometryInfo in project vcell by virtualcell.
the class StandaloneRuleBasedTest method main.
public static void main(String[] args) {
try {
PropertyLoader.loadProperties();
} catch (Exception e) {
e.printStackTrace();
}
final int numTrials = 40;
// 30 seconds
final long bngTimeoutDurationMS = 30000;
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, bngTimeoutDurationMS);
} catch (Exception e) {
e.printStackTrace();
if (!e.getMessage().contains("Only Mass Action Kinetics supported ")) {
StochtestFileUtils.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);
}
use of cbit.vcell.geometry.GeometryInfo in project vcell by virtualcell.
the class ClientRequestManager method getGeometryFromDocumentSelection.
public Geometry getGeometryFromDocumentSelection(Component parentComponent, VCDocumentInfo vcDocumentInfo, boolean bClearVersion) throws Exception, UserCancelException {
Geometry geom = null;
if (vcDocumentInfo.getVersionType().equals(VersionableType.BioModelMetaData)) /* documentType == VCDocument.BIOMODEL_DOC */
{
BioModelInfo bioModelInfo = getDocumentManager().getBioModelInfo(vcDocumentInfo.getVersion().getVersionKey());
BioModelChildSummary bioModelChildSummary = bioModelInfo.getBioModelChildSummary();
if (bioModelChildSummary != null && bioModelChildSummary.getSimulationContextNames() != null) {
Vector<Integer> spatialV = new Vector<Integer>();
for (int i = 0; i < bioModelChildSummary.getSimulationContextNames().length; i++) {
if (bioModelChildSummary.getGeometryDimensions()[i] > 0) {
spatialV.add(i);
}
}
if (spatialV.size() > 0) {
String[] columnNames = new String[] { "Application", "Geometry", "Dimension" };
String[][] rowData = new String[spatialV.size()][3];
for (int i = 0; i < spatialV.size(); i++) {
rowData[i][0] = bioModelChildSummary.getSimulationContextNames()[spatialV.elementAt(i)];
rowData[i][1] = bioModelChildSummary.getGeometryNames()[spatialV.elementAt(i)];
rowData[i][2] = bioModelChildSummary.getGeometryDimensions()[spatialV.elementAt(i)] + "";
}
int[] selection = DialogUtils.showComponentOKCancelTableList(JOptionPane.getFrameForComponent(parentComponent), "Select Geometry", columnNames, rowData, ListSelectionModel.SINGLE_SELECTION);
ModelGeometryOPResults modelGeometryOPResults = (ModelGeometryOPResults) getDocumentManager().getSessionManager().getUserMetaDbServer().doTestSuiteOP(new ModelGeometryOP((BioModelInfo) vcDocumentInfo, rowData[selection[0]][0]));
geom = getDocumentManager().getGeometry(modelGeometryOPResults.getGeometryKey());
// BioModel bioModel = getDocumentManager().getBioModel((BioModelInfo)vcDocumentInfo);
// for (int i = 0; i < bioModel.getSimulationContexts().length; i++) {
// if(bioModel.getSimulationContexts()[i].getName().equals(rowData[selection[0]][0])){
// geom = bioModel.getSimulationContexts()[i].getGeometry();
// break;
// }
// }
} else {
throw new Exception("BioModel '" + bioModelInfo.getVersion().getName() + "' contains no spatial geometries.");
}
} else {
throw new Exception("BioModel '" + bioModelInfo.getVersion().getName() + "' contains no spatial geometries.");
}
} else if (vcDocumentInfo.getVersionType().equals(VersionableType.MathModelMetaData)) /* documentType == VCDocument.MATHMODEL_DOC */
{
MathModelInfo mathModelInfo = getDocumentManager().getMathModelInfo(vcDocumentInfo.getVersion().getVersionKey());
MathModelChildSummary mathModelChildSummary = mathModelInfo.getMathModelChildSummary();
if (mathModelChildSummary != null) {
if (mathModelChildSummary.getGeometryDimension() > 0) {
ModelGeometryOPResults modelGeometryOPResults = (ModelGeometryOPResults) getDocumentManager().getSessionManager().getUserMetaDbServer().doTestSuiteOP(new ModelGeometryOP((MathModelInfo) vcDocumentInfo));
geom = getDocumentManager().getGeometry(modelGeometryOPResults.getGeometryKey());
// MathModel mathModel = getDocumentManager().getMathModel(mathModelInfo);
// geom = mathModel.getMathDescription().getGeometry();
} else {
throw new Exception("MathModel '" + mathModelInfo.getVersion().getName() + "' contains no spatial geometry.");
}
} else {
throw new Exception("MathModel '" + mathModelInfo.getVersion().getName() + "' contains no spatial geometry.");
}
} else if (vcDocumentInfo.getVersionType().equals(VersionableType.Geometry)) {
geom = getDocumentManager().getGeometry((GeometryInfo) vcDocumentInfo);
if (geom.getDimension() == 0) {
throw new Exception("Error, Only spatial geometries allowed (dimension > 0).");
}
} else {
throw new IllegalArgumentException("Error selecting geometry from document type " + vcDocumentInfo.getVersionType() + ". Must be BioModel,MathModel or Geometry.");
}
if (geom == null) {
throw new Exception("error selecting geometry");
}
if (bClearVersion) {
geom.clearVersion();
}
return geom;
}
use of cbit.vcell.geometry.GeometryInfo in project vcell by virtualcell.
the class DatabaseWindowManager method compareLatestEdition.
/**
* Comment
*/
public void compareLatestEdition() {
//
if (getPanelSelection() == null) {
PopupGenerator.showErrorDialog(this, "Error Comparing documents : No first document selected");
return;
}
VCDocumentInfo thisDocumentInfo = getPanelSelection();
//
// Get the latest version of the documentInfo
//
VCDocumentInfo[] documentVersionsList = null;
try {
documentVersionsList = getDocumentVersionDates(thisDocumentInfo);
} catch (DataAccessException e) {
PopupGenerator.showErrorDialog(this, "Error accessing second document!");
}
if (documentVersionsList == null || documentVersionsList.length == 0) {
PopupGenerator.showErrorDialog(this, "Error Comparing documents : Not Enough Versions to Compare!");
return;
}
//
// Obtaining the latest version of the current documentInfo
//
VCDocumentInfo latestDocumentInfo = documentVersionsList[documentVersionsList.length - 1];
for (int i = 0; i < documentVersionsList.length; i++) {
if (documentVersionsList[i].getVersion().getDate().after(latestDocumentInfo.getVersion().getDate())) {
latestDocumentInfo = documentVersionsList[i];
}
}
if (thisDocumentInfo.getVersion().getDate().after(latestDocumentInfo.getVersion().getDate())) {
PopupGenerator.showErrorDialog(this, "Current Version is the latest! Choose another Version or Model to compare!");
return;
}
// Check if both document types are of the same kind. If not, throw an error.
if (((thisDocumentInfo instanceof BioModelInfo) && !(latestDocumentInfo instanceof BioModelInfo)) || ((thisDocumentInfo instanceof MathModelInfo) && !(latestDocumentInfo instanceof MathModelInfo)) || ((thisDocumentInfo instanceof GeometryInfo) && !(latestDocumentInfo 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(latestDocumentInfo, thisDocumentInfo);
}
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