Example 1 with BngUnitSystem
use of org.vcell.model.bngl.BngUnitSystem 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 BngUnitSystem
use of org.vcell.model.bngl.BngUnitSystem in project vcell by virtualcell.
the class BNGLUnitsPanel method getUnits.
public BngUnitSystem getUnits() {
if (getSelectedButtonText(buttonGroup) == null) {
// better to return a default than null
return new BngUnitSystem(BngUnitOrigin.DEFAULT);
}
if (getSelectedButtonText(buttonGroup).equals(concentrations)) {
double volume = Double.parseDouble(cVolumeSize.getText());
ConcUnitSystem cus = ConcUnitSystem.values()[0];
for (ConcUnitSystem s : ConcUnitSystem.values()) {
if (s.description.equals(concentrationUnitsCombo.getSelectedItem().toString())) {
cus = s;
break;
}
}
TimeUnitSystem tus = TimeUnitSystem.values()[0];
for (TimeUnitSystem s : TimeUnitSystem.values()) {
if (s.description.equals(cTimeUnitsCombo.getSelectedItem().toString())) {
tus = s;
break;
}
}
return BngUnitSystem.createAsConcentration(BngUnitOrigin.USER, volume, cus, tus);
} else {
// molecules
// we know for sure it's valid double
double volume = Double.parseDouble(mVolumeSize.getText());
VolumeUnitSystem vus = VolumeUnitSystem.values()[0];
for (VolumeUnitSystem s : VolumeUnitSystem.values()) {
if (s.description.equals(mVolumeUnitsCombo.getSelectedItem().toString())) {
vus = s;
break;
}
}
TimeUnitSystem tus = TimeUnitSystem.values()[0];
for (TimeUnitSystem s : TimeUnitSystem.values()) {
if (s.description.equals(mTimeUnitsCombo.getSelectedItem().toString())) {
tus = s;
break;
}
}
return BngUnitSystem.createAsMolecules(BngUnitOrigin.USER, volume, vus, tus);
}
}
Also used :
VolumeUnitSystem(org.vcell.model.bngl.BngUnitSystem.VolumeUnitSystem)
BngUnitSystem(org.vcell.model.bngl.BngUnitSystem)
TimeUnitSystem(org.vcell.model.bngl.BngUnitSystem.TimeUnitSystem)
ConcUnitSystem(org.vcell.model.bngl.BngUnitSystem.ConcUnitSystem)
Example 3 with BngUnitSystem
use of org.vcell.model.bngl.BngUnitSystem in project vcell by virtualcell.
the class VCMLHandler method convertVcmlToVcDocument.
public static VCDocument convertVcmlToVcDocument(File vcmlFilePath) throws Exception {
ExternalDocInfo documentInfo = new ExternalDocInfo(vcmlFilePath, true);
File file = documentInfo.getFile();
if (file != null && !file.getName().isEmpty() && file.getName().endsWith("bngl")) {
BngUnitSystem bngUnitSystem = new BngUnitSystem(BngUnitSystem.BngUnitOrigin.DEFAULT);
String fileText;
try {
fileText = BeanUtils.readBytesFromFile(file, null);
} catch (IOException e1) {
e1.printStackTrace();
return null;
}
Reader reader = documentInfo.getReader();
boolean bException = true;
while (bException) {
try {
BioModel bioModel = createDefaultBioModelDocument(bngUnitSystem);
SimulationContext ruleBasedSimContext = bioModel.addNewSimulationContext("temp NFSim app", SimulationContext.Application.RULE_BASED_STOCHASTIC);
List<SimulationContext> appList = new ArrayList<SimulationContext>();
appList.add(ruleBasedSimContext);
Model.RbmModelContainer rbmModelContainer = bioModel.getModel().getRbmModelContainer();
RbmUtils.reactionRuleLabelIndex = 0;
RbmUtils.reactionRuleNames.clear();
ASTModel astModel = RbmUtils.importBnglFile(reader);
if (astModel.hasUnitSystem()) {
bngUnitSystem = astModel.getUnitSystem();
}
if (astModel.hasCompartments()) {
Structure struct = bioModel.getModel().getStructure(0);
if (struct != null) {
bioModel.getModel().removeStructure(struct);
}
}
RbmUtils.BnglObjectConstructionVisitor constructionVisitor = null;
if (!astModel.hasMolecularDefinitions()) {
System.out.println("Molecular Definition Block missing.");
constructionVisitor = new RbmUtils.BnglObjectConstructionVisitor(bioModel.getModel(), appList, bngUnitSystem, false);
} else {
constructionVisitor = new RbmUtils.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);
// inserting <potentially> corrected DocumentInfo
fileText = panel.getText();
}
}
}
VCDocument doc = null;
XMLSource xmlSource = documentInfo.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();
// TODO: Check for all child elements
// 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);
}
return doc;
}
Also used :
Element(org.jdom.Element)
ArrayList(java.util.ArrayList)
Reader(java.io.Reader)
ExternalDocInfo(cbit.vcell.xml.ExternalDocInfo)
Structure(cbit.vcell.model.Structure)
VCDocument(org.vcell.util.document.VCDocument)
IOException(java.io.IOException)
SimulationContext(cbit.vcell.mapping.SimulationContext)
IOException(java.io.IOException)
PropertyVetoException(java.beans.PropertyVetoException)
RbmUtils(org.vcell.model.rbm.RbmUtils)
BngUnitSystem(org.vcell.model.bngl.BngUnitSystem)
BNGLDebuggerPanel(org.vcell.model.bngl.gui.BNGLDebuggerPanel)
BioModel(cbit.vcell.biomodel.BioModel)
ASTModel(org.vcell.model.bngl.ASTModel)
BioModel(cbit.vcell.biomodel.BioModel)
Model(cbit.vcell.model.Model)
File(java.io.File)
XMLSource(cbit.vcell.xml.XMLSource)
Element(org.jdom.Element)
ASTModel(org.vcell.model.bngl.ASTModel)
Example 4 with BngUnitSystem
use of org.vcell.model.bngl.BngUnitSystem in project vcell by virtualcell.
the class BNGExecutorServiceMultipass method preprocessInput.
// parse the compartmental bngl file and produce the "trick"
// where each molecule has an extra Site with the compartments as possible States
// a reserved name will be used for this Site
//
private String preprocessInput(String cBngInputString) throws ParseException, PropertyVetoException, ExpressionBindingException {
// take the cBNGL file (as string), parse it to recover the rules (we'll need them later)
// and create the bngl string with the extra, fake site for the compartments
BioModel bioModel = new BioModel(null);
bioModel.setName("BngBioModel");
model = new Model("model");
bioModel.setModel(model);
model.createFeature();
simContext = bioModel.addNewSimulationContext("BioNetGen app", SimulationContext.Application.NETWORK_DETERMINISTIC);
List<SimulationContext> appList = new ArrayList<SimulationContext>();
appList.add(simContext);
// set convention for initial conditions in generated application for seed species (concentration or count)
BngUnitSystem bngUnitSystem = new BngUnitSystem(BngUnitOrigin.DEFAULT);
InputStream is = new ByteArrayInputStream(cBngInputString.getBytes());
BufferedReader br = new BufferedReader(new InputStreamReader(is));
ASTModel astModel = RbmUtils.importBnglFile(br);
if (astModel.hasCompartments()) {
Structure struct = model.getStructure(0);
if (struct != null) {
try {
model.removeStructure(struct);
} catch (PropertyVetoException e) {
e.printStackTrace();
}
}
}
BnglObjectConstructionVisitor constructionVisitor = null;
constructionVisitor = new BnglObjectConstructionVisitor(model, appList, bngUnitSystem, true);
astModel.jjtAccept(constructionVisitor, model.getRbmModelContainer());
int numCompartments = model.getStructures().length;
if (numCompartments == 0) {
throw new RuntimeException("No structure present in the bngl file.");
} else if (numCompartments == 1) {
// for single compartment we don't need the 'trick'
compartmentMode = CompartmentMode.hide;
} else {
compartmentMode = CompartmentMode.asSite;
}
// extract all polymer observables for special treatment at the end
for (RbmObservable oo : model.getRbmModelContainer().getObservableList()) {
if (oo.getSequence() == RbmObservable.Sequence.PolymerLengthEqual) {
polymerEqualObservables.add(oo);
} else if (oo.getSequence() == RbmObservable.Sequence.PolymerLengthGreater) {
polymerGreaterObservables.add(oo);
}
}
for (RbmObservable oo : polymerEqualObservables) {
model.getRbmModelContainer().removeObservable(oo);
}
for (RbmObservable oo : polymerGreaterObservables) {
model.getRbmModelContainer().removeObservable(oo);
}
// replace all reversible rules with 2 direct rules
List<ReactionRule> newRRList = new ArrayList<>();
for (ReactionRule rr : model.getRbmModelContainer().getReactionRuleList()) {
if (rr.isReversible()) {
ReactionRule rr1 = ReactionRule.deriveDirectRule(rr);
newRRList.add(rr1);
ReactionRule rr2 = ReactionRule.deriveInverseRule(rr);
newRRList.add(rr2);
} else {
newRRList.add(rr);
}
model.getRbmModelContainer().removeReactionRule(rr);
}
// model.getRbmModelContainer().getReactionRuleList().clear();
model.getRbmModelContainer().setReactionRules(newRRList);
StringWriter bnglStringWriter = new StringWriter();
PrintWriter writer = new PrintWriter(bnglStringWriter);
writer.println(RbmNetworkGenerator.BEGIN_MODEL);
writer.println();
// RbmNetworkGenerator.writeCompartments(writer, model, null);
RbmNetworkGenerator.writeParameters(writer, model.getRbmModelContainer(), false);
RbmNetworkGenerator.writeMolecularTypes(writer, model, compartmentMode);
RbmNetworkGenerator.writeSpeciesSortedAlphabetically(writer, model, simContext, compartmentMode);
RbmNetworkGenerator.writeObservables(writer, model.getRbmModelContainer(), compartmentMode);
// RbmNetworkGenerator.writeFunctions(writer, rbmModelContainer, ignoreFunctions);
RbmNetworkGenerator.writeReactions(writer, model.getRbmModelContainer(), null, false, compartmentMode);
writer.println(RbmNetworkGenerator.END_MODEL);
writer.println();
// we parse the real numbers from the bngl file provided by the caller, the nc in the simContext has the default ones
NetworkConstraints realNC = extractNetworkConstraints(cBngInputString);
String maxStoichiometry = extractMaxStoichiometry(cBngInputString);
simContext.getNetworkConstraints().setMaxMoleculesPerSpecies(realNC.getMaxMoleculesPerSpecies());
simContext.getNetworkConstraints().setMaxIteration(realNC.getMaxIteration());
ModelParameter speciesLimitParam = model.getModelParameter(NetworkConstraints.SPECIES_LIMIT_PARAMETER);
if (speciesLimitParam != null) {
// if it's not there we are already using the default
String s = speciesLimitParam.getExpression().infix();
// extract speciesLimit
simContext.getNetworkConstraints().setSpeciesLimit((int) Float.parseFloat(s));
}
ModelParameter reactionsLimitParam = model.getModelParameter(NetworkConstraints.REACTIONS_LIMIT_PARAMETER);
if (reactionsLimitParam != null) {
String r = reactionsLimitParam.getExpression().infix();
// extract reactionsLimit
simContext.getNetworkConstraints().setReactionsLimit((int) Float.parseFloat(r));
}
simContext.getNetworkConstraints().setTestConstraints(simContext.getNetworkConstraints().getMaxIteration(), simContext.getNetworkConstraints().getMaxMoleculesPerSpecies(), simContext.getNetworkConstraints().getSpeciesLimit(), simContext.getNetworkConstraints().getReactionsLimit(), // we don't need a testMaxStoichiometryMap (I guess)
null);
// RbmNetworkGenerator.generateNetworkEx(1, simContext.getNetworkConstraints().getMaxMoleculesPerSpecies(), false, writer, model.getRbmModelContainer(), simContext, NetworkGenerationRequirements.AllowTruncatedStandardTimeout);
generateNetworkLocal(1, simContext.getNetworkConstraints().getMaxMoleculesPerSpecies(), maxStoichiometry, writer);
String sInputString = bnglStringWriter.toString();
return sInputString;
}
Also used :
InputStreamReader(java.io.InputStreamReader)
ReactionRule(cbit.vcell.model.ReactionRule)
ByteArrayInputStream(java.io.ByteArrayInputStream)
InputStream(java.io.InputStream)
RbmObservable(cbit.vcell.model.RbmObservable)
ArrayList(java.util.ArrayList)
SimulationContext(cbit.vcell.mapping.SimulationContext)
PropertyVetoException(java.beans.PropertyVetoException)
ModelParameter(cbit.vcell.model.Model.ModelParameter)
BngUnitSystem(org.vcell.model.bngl.BngUnitSystem)
BnglObjectConstructionVisitor(org.vcell.model.rbm.RbmUtils.BnglObjectConstructionVisitor)
StringWriter(java.io.StringWriter)
ByteArrayInputStream(java.io.ByteArrayInputStream)
BioModel(cbit.vcell.biomodel.BioModel)
ASTModel(org.vcell.model.bngl.ASTModel)
Model(cbit.vcell.model.Model)
BioModel(cbit.vcell.biomodel.BioModel)
BufferedReader(java.io.BufferedReader)
Structure(cbit.vcell.model.Structure)
ASTModel(org.vcell.model.bngl.ASTModel)
PrintWriter(java.io.PrintWriter)
NetworkConstraints(org.vcell.model.rbm.NetworkConstraints)
Aggregations
BngUnitSystem (org.vcell.model.bngl.BngUnitSystem)4
BioModel (cbit.vcell.biomodel.BioModel)3
SimulationContext (cbit.vcell.mapping.SimulationContext)3
Structure (cbit.vcell.model.Structure)3
PropertyVetoException (java.beans.PropertyVetoException)3
ArrayList (java.util.ArrayList)3
ASTModel (org.vcell.model.bngl.ASTModel)3
Model (cbit.vcell.model.Model)2
ExternalDocInfo (cbit.vcell.xml.ExternalDocInfo)2
XMLSource (cbit.vcell.xml.XMLSource)2
BufferedReader (java.io.BufferedReader)2
File (java.io.File)2
IOException (java.io.IOException)2
Reader (java.io.Reader)2
Element (org.jdom.Element)2
BNGLDebuggerPanel (org.vcell.model.bngl.gui.BNGLDebuggerPanel)2
BnglObjectConstructionVisitor (org.vcell.model.rbm.RbmUtils.BnglObjectConstructionVisitor)2
VCDocument (org.vcell.util.document.VCDocument)2
ImageException (cbit.image.ImageException)1
VCMetaData (cbit.vcell.biomodel.meta.VCMetaData)1
