Example 1 with ProgrammingException
use of org.vcell.util.ProgrammingException 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_MODELS = "SedMLModels";
final String BNG_UNIT_SYSTEM = "bngUnitSystem";
final String BMDB_DEFAULT_APPLICATION = "Deterministic";
/* 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);
hashTable.put("isBMDB", false);
hashTable.put("isSEDML", false);
// 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());
List<SedML> sedmls = new ArrayList<>();
sedmls.add(sedml);
hashTable.put(SEDML_MODELS, sedmls);
// 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));
List<SEDMLDocument> docs = ac.getSedmlDocuments();
List<SedML> sedmls = new ArrayList<>();
for (SEDMLDocument doc : docs) {
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());
}
sedmls.add(sedml);
}
// AbstractTask chosenTask = SEDMLChooserPanel.chooseTask(sedml, requester.getComponent(),
// file.getName());
hashTable.put(SEDML_MODELS, sedmls);
// 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;
List<VCDocument> docs = new ArrayList<>();
boolean isBMDB = false;
boolean isSEDML = false;
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);
// iterate through one or more SEDML objects
List<SedML> sedmls = (List<SedML>) hashTable.get(SEDML_MODELS);
for (SedML sedml : sedmls) {
// default to import all tasks
List<VCDocument> vcdocs = XmlHelper.sedmlToBioModel(transLogger, externalDocInfo, sedml, null, null, false);
for (VCDocument vcdoc : vcdocs) {
docs.add(vcdoc);
}
}
// treat the same since OMEX is just and archive with SED-ML file(s)
isSEDML = true;
} 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,
Element modelElement = childElementList.get(0);
// mathmodel or geometry.
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);
isBMDB = externalDocInfo.isBioModelsNet();
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)) {
// we know it is a single SedML since it is an actual XML source
List<SedML> sedmls = (List<SedML>) hashTable.get(SEDML_MODELS);
SedML sedml = sedmls.get(0);
// default to import all tasks
docs = XmlHelper.sedmlToBioModel(transLogger, externalDocInfo, sedml, null, externalDocInfo.getFile().getAbsolutePath(), false);
isSEDML = true;
} 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 && docs == 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("isBMDB", isBMDB);
hashTable.put("isSEDML", isSEDML);
if (!isSEDML) {
hashTable.put("doc", doc);
} else {
hashTable.put("docs", docs);
}
}
};
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) {
boolean isSEDML = (boolean) hashTable.get("isSEDML");
if (isSEDML) {
List<VCDocument> docs = (List<VCDocument>) hashTable.get("docs");
List<DocumentWindowManager> windowManagers = new ArrayList<DocumentWindowManager>();
for (VCDocument doc : docs) {
DocumentWindowManager windowManager = createDocumentWindowManager(doc);
getMdiManager().createNewDocumentWindow(windowManager);
windowManagers.add(windowManager);
}
hashTable.put("managers", windowManagers);
hashTable.put("docs", docs);
} else {
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);
} 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);
hashTable.put("doc", doc);
}
}
} catch (Exception ex) {
ex.printStackTrace();
// TODO: check why getMdiManager().createNewDocumentWindow(windowManager) fails sometimes
} 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 {
if (documentInfo instanceof ExternalDocInfo) {
ExternalDocInfo externalDocInfo = (ExternalDocInfo) documentInfo;
boolean isSEDML = (boolean) hashTable.get("isSEDML");
if (externalDocInfo.isBioModelsNet() || externalDocInfo.isFromXmlFile() || !isSEDML) {
DocumentWindowManager windowManager = (DocumentWindowManager) hashTable.get(WIN_MGR_KEY);
if (windowManager instanceof BioModelWindowManager) {
((BioModelWindowManager) windowManager).specialLayout();
}
}
if (isSEDML) {
List<DocumentWindowManager> windowManagers = (List<DocumentWindowManager>) hashTable.get("managers");
if (windowManagers != null) {
for (DocumentWindowManager manager : windowManagers) {
((BioModelWindowManager) manager).specialLayout();
}
}
}
}
}
};
AsynchClientTask task4 = new AsynchClientTaskFunction(ClientRequestManager::setWindowFocus, "Set window focus", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false, false);
AsynchClientTask task6 = new AsynchClientTask("Renaming, please wait...", // TASKTYPE_NONSWING_BLOCKING
AsynchClientTask.TASKTYPE_NONSWING_BLOCKING, // TASKTYPE_NONSWING_BLOCKING
false, // TASKTYPE_NONSWING_BLOCKING
false) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
VCDocument doc = (VCDocument) hashTable.get("doc");
if (!(doc instanceof BioModel)) {
return;
}
boolean isBMDB = (boolean) hashTable.get("isBMDB");
if (documentInfo instanceof ExternalDocInfo) {
if (isBMDB) {
idToNameConversion(doc);
}
}
if (isBMDB) {
BioModel bioModel = (BioModel) doc;
SimulationContext simulationContext = bioModel.getSimulationContext(0);
simulationContext.setName(BMDB_DEFAULT_APPLICATION);
MathMappingCallback callback = new MathMappingCallback() {
@Override
public void setProgressFraction(float fractionDone) {
}
@Override
public void setMessage(String message) {
}
@Override
public boolean isInterrupted() {
return false;
}
};
MathMapping mathMapping = simulationContext.createNewMathMapping(callback, NetworkGenerationRequirements.ComputeFullNoTimeout);
MathDescription mathDesc = null;
try {
mathDesc = mathMapping.getMathDescription(callback);
simulationContext.setMathDescription(mathDesc);
Simulation sim = new Simulation(mathDesc);
sim.setName(simulationContext.getBioModel().getFreeSimulationName());
simulationContext.addSimulation(sim);
bioModel.refreshDependencies();
} catch (MappingException | MathException | MatrixException | ExpressionException | ModelException e1) {
e1.printStackTrace();
}
hashTable.put("doc", doc);
}
}
};
ClientTaskDispatcher.dispatch(requester.getComponent(), hashTable, new AsynchClientTask[] { task0, task1, task6, task2, task3, task4 }, false);
}
Also used :
SetMathDescription(cbit.vcell.client.task.SetMathDescription)
MathDescription(cbit.vcell.math.MathDescription)
ArrayList(java.util.ArrayList)
UserCancelException(org.vcell.util.UserCancelException)
SpeciesContextSpec(cbit.vcell.mapping.SpeciesContextSpec)
ExpressionException(cbit.vcell.parser.ExpressionException)
MappingException(cbit.vcell.mapping.MappingException)
SedML(org.jlibsedml.SedML)
ExternalDocInfo(cbit.vcell.xml.ExternalDocInfo)
AsynchClientTaskFunction(cbit.vcell.client.task.AsynchClientTaskFunction)
MatrixException(cbit.vcell.matrix.MatrixException)
VCMetaData(cbit.vcell.biomodel.meta.VCMetaData)
BnglObjectConstructionVisitor(org.vcell.model.rbm.RbmUtils.BnglObjectConstructionVisitor)
RbmModelContainer(cbit.vcell.model.Model.RbmModelContainer)
GeometryInfo(cbit.vcell.geometry.GeometryInfo)
ArrayList(java.util.ArrayList)
List(java.util.List)
VCDocument(org.vcell.util.document.VCDocument)
MathMappingCallback(cbit.vcell.mapping.SimulationContext.MathMappingCallback)
ModelException(cbit.vcell.model.ModelException)
FileInputStream(java.io.FileInputStream)
Namespace(org.jdom.Namespace)
BngUnitSystem(org.vcell.model.bngl.BngUnitSystem)
BNGLDebuggerPanel(org.vcell.model.bngl.gui.BNGLDebuggerPanel)
SEDMLDocument(org.jlibsedml.SEDMLDocument)
MathMapping(cbit.vcell.mapping.MathMapping)
CSGObject(cbit.vcell.geometry.CSGObject)
ChooseFile(cbit.vcell.client.task.ChooseFile)
File(java.io.File)
AsynchClientTask(cbit.vcell.client.task.AsynchClientTask)
FileWriter(java.io.FileWriter)
Element(org.jdom.Element)
StlReader(cbit.vcell.geometry.surface.StlReader)
FileReader(java.io.FileReader)
ImageDatasetReader(org.vcell.vcellij.ImageDatasetReader)
Reader(java.io.Reader)
BufferedReader(java.io.BufferedReader)
ArchiveComponents(org.jlibsedml.ArchiveComponents)
ProgrammingException(org.vcell.util.ProgrammingException)
Structure(cbit.vcell.model.Structure)
Hashtable(java.util.Hashtable)
BNGLUnitsPanel(org.vcell.model.bngl.gui.BNGLUnitsPanel)
BioModelInfo(org.vcell.util.document.BioModelInfo)
IOException(java.io.IOException)
MathModelInfo(org.vcell.util.document.MathModelInfo)
SimulationContext(cbit.vcell.mapping.SimulationContext)
ProgrammingException(org.vcell.util.ProgrammingException)
MatrixException(cbit.vcell.matrix.MatrixException)
GeometryException(cbit.vcell.geometry.GeometryException)
IOException(java.io.IOException)
DataAccessException(org.vcell.util.DataAccessException)
MappingException(cbit.vcell.mapping.MappingException)
PropertyVetoException(java.beans.PropertyVetoException)
ImageException(cbit.image.ImageException)
UtilCancelException(org.vcell.util.UtilCancelException)
ModelException(cbit.vcell.model.ModelException)
DataFormatException(java.util.zip.DataFormatException)
ExpressionException(cbit.vcell.parser.ExpressionException)
MathException(cbit.vcell.math.MathException)
UserCancelException(org.vcell.util.UserCancelException)
Simulation(cbit.vcell.solver.Simulation)
VCDocumentInfo(org.vcell.util.document.VCDocumentInfo)
Expression(cbit.vcell.parser.Expression)
MathException(cbit.vcell.math.MathException)
BioModel(cbit.vcell.biomodel.BioModel)
XMLSource(cbit.vcell.xml.XMLSource)
Element(org.jdom.Element)
ASTModel(org.vcell.model.bngl.ASTModel)
Example 2 with ProgrammingException
use of org.vcell.util.ProgrammingException in project vcell by virtualcell.
the class ChildWindowManager method findChildWindowManager.
/**
* @param component not null
* @return ChildWindowManager
* @throws ProgrammingException if unable to find ChildWindowManager
*/
public static ChildWindowManager findChildWindowManager(Component component) {
ManagedChild mc = LWNamespace.findOwnerOfType(ManagedChild.class, component);
if (mc != null) {
return mc.getChildWindowManager();
}
if (LG.isDebugEnabled()) {
LG.debug(ExecutionTrace.justClassName(component) + " does not have ManagedChild parent");
}
TopLevelWindow dw = LWNamespace.findOwnerOfType(TopLevelWindow.class, component);
if (dw != null) {
return dw.getChildWindowManager();
}
throw new ProgrammingException("ChildWindowManager.findChildWindowManager(Component) could not find a ChildWindowManager for component: " + component.getName() + " which is a " + component.getClass().getCanonicalName());
}
Also used :
ProgrammingException(org.vcell.util.ProgrammingException)
TopLevelWindow(cbit.vcell.client.desktop.TopLevelWindow)
Example 3 with ProgrammingException
use of org.vcell.util.ProgrammingException in project vcell by virtualcell.
the class SbmlExtensionFilter method askUser.
@Override
public void askUser(ChooseContext c) throws UserCancelException {
BioModel bioModel = c.chosenContext.getBioModel();
JFrame currentWindow = c.currentWindow;
selectedSimWOSBE = null;
selectedSimContext = c.chosenContext;
// get user choice of structure and its size and computes absolute sizes of compartments using the StructureSizeSolver.
Structure[] structures = bioModel.getModel().getStructures();
// get the nonspatial simulationContexts corresponding to names in applicableAppNameList
// This is needed in ApplnSelectionAndStructureSizeInputPanel
String strucName = null;
double structSize = 1.0;
int structSelection = -1;
int option = JOptionPane.CANCEL_OPTION;
ApplnSelectionAndStructureSizeInputPanel applnStructInputPanel = null;
while (structSelection < 0) {
applnStructInputPanel = new ApplnSelectionAndStructureSizeInputPanel();
applnStructInputPanel.setSimContext(c.chosenContext);
applnStructInputPanel.setStructures(structures);
if (applnStructInputPanel.isNeedStructureSizes()) {
applnStructInputPanel.setPreferredSize(new java.awt.Dimension(350, 400));
applnStructInputPanel.setMaximumSize(new java.awt.Dimension(350, 400));
option = DialogUtils.showComponentOKCancelDialog(currentWindow, applnStructInputPanel, "Specify Structure Size to Export:");
structSelection = applnStructInputPanel.getStructSelectionIndex();
if (option == JOptionPane.CANCEL_OPTION || option == JOptionPane.CLOSED_OPTION) {
break;
} else if (option == JOptionPane.OK_OPTION && structSelection < 0) {
DialogUtils.showErrorDialog(currentWindow, "Please select a structure and set its size");
}
} else {
// adapt to legacy logic ...
structSelection = 0;
option = JOptionPane.OK_OPTION;
}
}
if (option == JOptionPane.OK_OPTION) {
applnStructInputPanel.applyStructureNameAndSizeValues();
strucName = applnStructInputPanel.getSelectedStructureName();
selectedSimContext = applnStructInputPanel.getSelectedSimContext();
GeometryContext geoContext = selectedSimContext.getGeometryContext();
if (!isSpatial) {
// calculate structure Sizes only if appln is not spatial
structSize = applnStructInputPanel.getStructureSize();
// Invoke StructureSizeEvaluator to compute absolute sizes of compartments if all sizes are not set
if ((geoContext.isAllSizeSpecifiedNull() && geoContext.isAllVolFracAndSurfVolSpecifiedNull()) || ((strucName == null || structSize <= 0.0) && (geoContext.isAllSizeSpecifiedNull() && geoContext.isAllVolFracAndSurfVolSpecified())) || (!geoContext.isAllSizeSpecifiedPositive() && geoContext.isAllVolFracAndSurfVolSpecifiedNull()) || (!geoContext.isAllSizeSpecifiedPositive() && !geoContext.isAllVolFracAndSurfVolSpecified()) || (geoContext.isAllSizeSpecifiedNull() && !geoContext.isAllVolFracAndSurfVolSpecified())) {
DialogUtils.showErrorDialog(currentWindow, "Cannot export to SBML without compartment sizes being set. This can be automatically " + " computed if the absolute size of at least one compartment and the relative sizes (Surface-to-volume-ratio/Volume-fraction) " + " of all compartments are known. Sufficient information is not available to perform this computation." + "\n\nThis can be fixed by going back to the application '" + selectedSimContext.getName() + "' and setting structure sizes in the 'StructureMapping' tab.");
throw UserCancelException.CANCEL_XML_TRANSLATION;
}
if (!geoContext.isAllSizeSpecifiedPositive() && geoContext.isAllVolFracAndSurfVolSpecified()) {
Structure chosenStructure = selectedSimContext.getModel().getStructure(strucName);
StructureMapping chosenStructMapping = selectedSimContext.getGeometryContext().getStructureMapping(chosenStructure);
try {
StructureSizeSolver.updateAbsoluteStructureSizes(selectedSimContext, chosenStructure, structSize, chosenStructMapping.getSizeParameter().getUnitDefinition());
} catch (Exception e) {
throw new ProgrammingException("exception updating sizes", e);
}
}
} else {
if (!geoContext.isAllUnitSizeParameterSetForSpatial()) {
DialogUtils.showErrorDialog(currentWindow, "Cannot export to SBML without compartment size ratios being set." + "\n\nThis can be fixed by going back to the application '" + selectedSimContext.getName() + "' and setting structure" + " size ratios in the 'StructureMapping' tab.");
throw UserCancelException.CANCEL_XML_TRANSLATION;
}
}
// Select simulation whose overrides need to be exported
// If simContext doesn't have simulations, don't pop up simulationSelectionPanel
Simulation[] sims = bioModel.getSimulations(selectedSimContext);
// display only those simulations that have overrides in the simulationSelectionPanel.
Vector<Simulation> orSims = new Vector<Simulation>();
for (int s = 0; (sims != null) && (s < sims.length); s++) {
if (sims[s].getMathOverrides().hasOverrides()) {
orSims.addElement(sims[s]);
}
}
Simulation[] overriddenSims = orSims.toArray(new Simulation[orSims.size()]);
if (overriddenSims.length > 0) {
SimulationSelectionPanel simSelectionPanel = new SimulationSelectionPanel();
simSelectionPanel.setPreferredSize(new java.awt.Dimension(600, 400));
simSelectionPanel.setMaximumSize(new java.awt.Dimension(600, 400));
simSelectionPanel.setSimulations(overriddenSims);
int simOption = DialogUtils.showComponentOKCancelDialog(currentWindow, simSelectionPanel, "Select Simulation whose overrides should be exported:");
if (simOption == JOptionPane.OK_OPTION) {
selectedSimWOSBE = simSelectionPanel.getSelectedSimulation();
// if (chosenSimulation != null) {
// CARRY hashTable.put("selectedSimulation", chosenSimulation);
// }
} else if (simOption == JOptionPane.CANCEL_OPTION || simOption == JOptionPane.CLOSED_OPTION) {
// Hence canceling the entire export to SBML operation.
throw UserCancelException.CANCEL_XML_TRANSLATION;
}
}
} else if (option == JOptionPane.CANCEL_OPTION || option == JOptionPane.CLOSED_OPTION) {
// Hence canceling the entire export to SBML operation.
throw UserCancelException.CANCEL_XML_TRANSLATION;
}
if (selectedSimWOSBE != null) {
String selectedFileName = c.filename;
// rename file to contain exported simulation.
String ext = FilenameUtils.getExtension(selectedFileName);
String base = FilenameUtils.getBaseName(selectedFileName);
String path = FilenameUtils.getPath(selectedFileName);
base += "_" + TokenMangler.mangleToSName(selectedSimWOSBE.getName());
selectedFileName = path + base + ext;
c.selectedFile.renameTo(new File(selectedFileName));
}
}
Also used :
SimulationSelectionPanel(org.vcell.sbml.gui.SimulationSelectionPanel)
StructureMapping(cbit.vcell.mapping.StructureMapping)
ProgrammingException(org.vcell.util.ProgrammingException)
UserCancelException(org.vcell.util.UserCancelException)
Simulation(cbit.vcell.solver.Simulation)
JFrame(javax.swing.JFrame)
ApplnSelectionAndStructureSizeInputPanel(org.vcell.sbml.gui.ApplnSelectionAndStructureSizeInputPanel)
BioModel(cbit.vcell.biomodel.BioModel)
GeometryContext(cbit.vcell.mapping.GeometryContext)
ProgrammingException(org.vcell.util.ProgrammingException)
Structure(cbit.vcell.model.Structure)
Vector(java.util.Vector)
File(java.io.File)
Example 4 with ProgrammingException
use of org.vcell.util.ProgrammingException in project vcell by virtualcell.
the class ClientTaskDispatcher method runTask.
/**
* call currentTask.run(hash) with log4j logging; check for required keys
* @param currentTask not null
* @param hash not null
* @param taskList current set of tasks being dispatched
* @throws Exception
*/
private static void runTask(AsynchClientTask currentTask, Hashtable<String, Object> hash, Collection<AsynchClientTask> taskList) throws Exception {
if (lg.isDebugEnabled()) {
String msg = "Thread " + Thread.currentThread().getName() + " calling task " + currentTask.getTaskName();
if (lg.isDebugEnabled()) {
Object obj = hash.get(STACK_TRACE_ARRAY);
StackTraceElement[] ste = BeanUtils.downcast(StackTraceElement[].class, obj);
if (ste != null) {
msg += '\n' + StringUtils.join(ste, '\n');
}
lg.debug(msg);
} else {
lg.debug(msg);
}
}
// check required elements present
StringBuilder sb = null;
for (KeyInfo requiredKey : currentTask.requiredKeys()) {
Object obj = hash.get(requiredKey.name);
if (obj == null) {
if (sb == null)
sb = initStringBuilder(currentTask);
sb.append("Missing required key " + requiredKey.name + '\n');
continue;
}
Class<?> foundClass = obj.getClass();
if (!requiredKey.clzz.isAssignableFrom(foundClass)) {
if (sb == null)
sb = initStringBuilder(currentTask);
sb.append("key " + requiredKey.name + " type " + foundClass.getName() + " not of required type " + requiredKey.clzz.getName());
sb.append('\n');
}
}
if (sb == null) {
// no problems found
currentTask.run(hash);
return;
}
sb.append("Prior tasks\n");
for (AsynchClientTask pt : taskList) {
if (pt == currentTask) {
break;
}
sb.append('\t' + pt.getTaskName() + '\n');
}
hash.put(HASH_DATA_ERROR, HASH_DATA_ERROR);
throw new ProgrammingException(sb.toString());
}
Also used :
KeyInfo(cbit.vcell.client.task.AsynchClientTask.KeyInfo)
EventObject(java.util.EventObject)
ProgrammingException(org.vcell.util.ProgrammingException)
Example 5 with ProgrammingException
use of org.vcell.util.ProgrammingException in project vcell by virtualcell.
the class ClientTaskDispatcher method setFinalWindow.
/**
* set final window in hash
* @param hash non null
* @param fWindow non null
* @throws ProgrammingException if more than one set in the same hash
* @see AsynchClientTask#setFinalWindow(Hashtable, cbit.vcell.client.ChildWindowManager.ChildWindow)
* @see AsynchClientTask#setFinalWindow(Hashtable, java.awt.Container)
*/
// package
static void setFinalWindow(Hashtable<String, Object> hash, FinalWindow fWindow) {
if (!hash.contains(FINAL_WINDOW)) {
hash.put(FINAL_WINDOW, fWindow);
return;
}
Object existing = hash.get(FINAL_WINDOW);
final String def = "null";
String e = ClassUtils.getShortClassName(existing, def);
String n = ClassUtils.getShortClassName(fWindow, def);
throw new ProgrammingException("duplicate final windows" + e + " and " + n);
}
Also used :
EventObject(java.util.EventObject)
ProgrammingException(org.vcell.util.ProgrammingException)
Aggregations
ProgrammingException (org.vcell.util.ProgrammingException)10
BioModel (cbit.vcell.biomodel.BioModel)2
Structure (cbit.vcell.model.Structure)2
ExpressionException (cbit.vcell.parser.ExpressionException)2
Simulation (cbit.vcell.solver.Simulation)2
File (java.io.File)2
EventObject (java.util.EventObject)2
UserCancelException (org.vcell.util.UserCancelException)2
ImageException (cbit.image.ImageException)1
VCMetaData (cbit.vcell.biomodel.meta.VCMetaData)1
ChildWindow (cbit.vcell.client.ChildWindowManager.ChildWindow)1
TopLevelWindow (cbit.vcell.client.desktop.TopLevelWindow)1
AsynchClientTask (cbit.vcell.client.task.AsynchClientTask)1
KeyInfo (cbit.vcell.client.task.AsynchClientTask.KeyInfo)1
AsynchClientTaskFunction (cbit.vcell.client.task.AsynchClientTaskFunction)1
ChooseFile (cbit.vcell.client.task.ChooseFile)1
SetMathDescription (cbit.vcell.client.task.SetMathDescription)1
CSGObject (cbit.vcell.geometry.CSGObject)1
GeometryException (cbit.vcell.geometry.GeometryException)1
GeometryInfo (cbit.vcell.geometry.GeometryInfo)1
