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This commit is contained in:
LukasBuecherl 2022-07-25 13:28:58 -06:00
parent 1c24b1edc5
commit 8cffc3062b
3 changed files with 86 additions and 32 deletions
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113
conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/Converter.java
View file

@ -19,9 +19,11 @@ import java.io.IOException;
import java.net.URI;
import java.util.HashMap;
import java.util.HashSet;
import java.lang.reflect.Method;
import javax.xml.stream.XMLStreamException;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.SBMLDocument;
import org.sbml.jsbml.SBMLException;
import org.sbml.jsbml.SBMLWriter;
@ -110,7 +112,7 @@ public class Converter {
System.err.println("\t-tmID Set the ID of the top SBML model");
System.exit(1);
}
/**
* The main method.
@ -142,7 +144,7 @@ public class Converter {
boolean topEnvir = false; // determines if there is a topEnvironment model to be instantiated
boolean CelloModel = false; // determines if Cello-based modeling should be done
boolean PrismUnbound = true; // determines if the prism model should be bound or unbound
String compFileResult = ""; //-cf
String compareFile = ""; //-e
String mainFileResult = ""; //-mf
@ -156,7 +158,7 @@ public class Converter {
String urlVPR = ""; //The specified synbiohub repository the user wants VPR model generator to connect to.
String environment ="";
String topModelId = null;
HashSet<String> ref_sbolInputFilePath = new HashSet<String>(); //rsbol
int index = 0;
@ -428,25 +430,76 @@ public class Converter {
if(inputIsSBML && prismOut)
{
SBMLDocument inputSBMLDoc;
try
{
inputSBMLDoc = SBMLutilities.readSBML(fullInputFileName, null, null);
/*
File path = new File(fullInputFileName);
BioObservable p = null;
BioModel bioModel = BioModel.createBioModel(path.getParent(), p);
bioModel.load(fullInputFileName);
org.sbml.libsbml.SBMLReader reader = new org.sbml.libsbml.SBMLReader();
org.sbml.libsbml.SBMLDocument document = reader.readSBML(fullInputFileName);
document.setPackageRequired("comp", true);
org.sbml.libsbml.CompModelPlugin sbmlCompModel = (org.sbml.libsbml.CompModelPlugin) document.getModel().getPlugin("comp");
long numSubModels = sbmlCompModel.getNumSubmodels();
System.err.println(numSubModels);
*/
inputSBMLDoc = SBMLutilities.readSBML(fullInputFileName, null, null);
//SBML2PRISM.convertSBML2PRISM(inputSBMLDoc, fullInputFileName, PrismUnbound);
File path = new File(fullInputFileName);
BioModel bioModel = new BioModel(path.getParent());
bioModel.load(fullInputFileName);
bioModel.createCompPlugin();
System.err.println(bioModel.getListOfSubmodels());
if(bioModel.getListOfSubmodels().isEmpty())
{
SBML2PRISM.convertSBML2PRISM(inputSBMLDoc, fullInputFileName, PrismUnbound);
}else {
if (bioModel.flattenModel(true) != null) {
SBMLDocument sbml = bioModel.flattenModel(true);
SBML2PRISM.convertSBML2PRISM(sbml, fullInputFileName, PrismUnbound);
}
}
/*
if (bioModel.flattenModel(true) != null) {
SBMLDocument sbml = bioModel.flattenModel(true);
//SBMLDocument sbml = bioModel.getSBMLDocument();
//System.err.println(inputSBMLDoc.equals(inputSBMLDoc));
//System.err.println(sbml.equals(sbml));
//System.err.println(sbml.equals(sbml));
SBML2PRISM.convertSBML2PRISM(sbml, fullInputFileName, PrismUnbound);
}
}
*/
SBML2PRISM.convertSBML2PRISM(inputSBMLDoc, fullInputFileName, PrismUnbound);
/*
File path = new File(fullInputFileName);
// BioObservable p = null;
// BioModel bioModel = BioModel.createBioModel(path.getParent(), p);
BioModel bioModel = new BioModel(path.getParent());
bioModel.load(fullInputFileName);
if (bioModel.flattenModel(true) != null) {
//SBMLDocument sbml = bioModel.flattenModel(true);
SBMLDocument sbml = bioModel.getSBMLDocument();
//System.err.println(inputSBMLDoc.equals(inputSBMLDoc));
//System.err.println(sbml.equals(sbml));
//System.err.println(sbml.equals(sbml));
//SBML2PRISM.convertSBML2PRISM(sbml, fullInputFileName, PrismUnbound);
}
*/
}
catch (XMLStreamException e)
{
@ -461,7 +514,7 @@ public class Converter {
catch (BioSimException e) {
System.err.println("ERROR: Invalid SBML file");
}
}else if(inputIsSBML)
{
SBOLDocument outSBOLDoc = new SBOLDocument();
@ -546,13 +599,13 @@ public class Converter {
String circuit_name = file.getName();
circuit_name = circuit_name.replace(".xml", "");
String vpr_output = circuit_name + "_topModule";
if(!topLevelURIStr.isEmpty())
{
if (doVPR) {
TopLevel top = sbolDoc.getTopLevel(URI.create(topLevelURIStr));
SBOLDocument newSbolDoc = sbolDoc.createRecursiveCopy(top);
try {
newSbolDoc = VPRModelGenerator.generateModel(urlVPR, newSbolDoc, vpr_output);
//newSbolDoc.write("C:\\Users\\elros\\Desktop\\TestingConverter\\VPRoutput.xml");
@ -565,18 +618,18 @@ public class Converter {
e.printStackTrace();
}
//generateSBMLFromSBOL(newSbolDoc, outputDir);
for (ModuleDefinition moduleDef : newSbolDoc.getRootModuleDefinitions())
{
HashMap<String,BioModel> models = SBOL2SBML.generateModel(outputDir, moduleDef, newSbolDoc, CelloModel);
SBMLutilities.exportSBMLModels(models, outputDir, outputFileName, noOutput, sbmlOut, singleSBMLOutput);
}
}
else {
ModuleDefinition topModuleDef = sbolDoc.getModuleDefinition(URI.create(topLevelURIStr));
HashMap<String,BioModel> models = SBOL2SBML.generateModel(outputDir, topModuleDef, sbolDoc, CelloModel);
SBMLutilities.exportSBMLModels(models, outputDir, outputFileName, noOutput, sbmlOut, singleSBMLOutput);
ModuleDefinition topModuleDef = sbolDoc.getModuleDefinition(URI.create(topLevelURIStr));
HashMap<String,BioModel> models = SBOL2SBML.generateModel(outputDir, topModuleDef, sbolDoc, CelloModel);
SBMLutilities.exportSBMLModels(models, outputDir, outputFileName, noOutput, sbmlOut, singleSBMLOutput);
}
}
else
@ -594,20 +647,20 @@ public class Converter {
e.printStackTrace();
}
}
for (ModuleDefinition moduleDef : sbolDoc.getRootModuleDefinitions())
{
HashMap<String,BioModel> models = SBOL2SBML.generateModel(outputDir, moduleDef, sbolDoc, CelloModel);
SBMLutilities.exportSBMLModels(models, outputDir, outputFileName, noOutput, sbmlOut, singleSBMLOutput);
}
}
if (topModelId != null) {
SBMLDocument topModel = SBMLutilities.readSBML(vpr_output+".xml", null, null);
topModel.getModel().setId(topModelId);
SBMLWriter writer = new SBMLWriter();
try {
//SBMLutilities.removeUnusedNamespaces(sbml);
//SBMLutilities.removeUnusedNamespaces(sbml);
writer.writeSBMLToFile(topModel, outputDir + File.separator + topModelId + ".xml");
}
catch (SBMLException e) {
@ -620,26 +673,26 @@ public class Converter {
e.printStackTrace();
}
}
if (doVPR) {
if (topEnvir) {
SBMLDocument topEnvironment = SBMLutilities.readSBML(environment, null, null);
CompSBMLDocumentPlugin docPlugin = (CompSBMLDocumentPlugin) topEnvironment.getPlugin("comp");
ExternalModelDefinition exte = docPlugin.getExternalModelDefinition("TopModel");
exte.setId(vpr_output);
exte.setSource(vpr_output + ".xml");
//exte.setId("topModule");
//exte.setSource("topModule.xml");
CompModelPlugin SBMLplugin = (CompModelPlugin) topEnvironment.getModel().getPlugin("comp");
Submodel top = SBMLplugin.getSubmodel("C1");
top.setModelRef(vpr_output);
//top.setModelRef("topModule");
SBMLWriter writing = new SBMLWriter();
writing.writeSBMLToFile(topEnvironment, outputDir + File.separator + "Simulation_Environment.xml");
}
}

2
dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/parser/BioModel.java
View file

@ -6399,7 +6399,7 @@ public class BioModel extends CoreObservable{
}
}
private ArrayList<String> getListOfSubmodels() throws XMLStreamException, IOException, BioSimException {
public ArrayList<String> getListOfSubmodels() throws XMLStreamException, IOException, BioSimException { // Changed private to public (Lukas)
ArrayList<String> comps = new ArrayList<String>();
if (this.getGridEnabledFromFile(filename.replace(".gcm",".xml"))) {

3
dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/util/SBMLutilities.java
View file

@ -1968,7 +1968,8 @@ public class SBMLutilities extends CoreObservable
{
String leftStr = convertMath2PrismProperty(math.getLeftChild());
String rightStr = convertMath2PrismProperty(math.getRightChild());
return "(" + leftStr + " ^ " + rightStr + ")";
//return "(" + leftStr + " ^ " + rightStr + ")";
return "pow(" + leftStr + " , " + rightStr + ")";
}
else if (math.getType() == ASTNode.Type.RATIONAL)
{