diff --git a/conversion/pom.xml b/conversion/pom.xml index 355f2027b..39eaa18c4 100644 --- a/conversion/pom.xml +++ b/conversion/pom.xml @@ -71,7 +71,7 @@ org.virtualparts virtualparts-data - 2.0.10-SNAPSHOT + 2.0.12-SNAPSHOT diff --git a/conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/Converter.java b/conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/Converter.java index 86dba3c80..5e98960d8 100644 --- a/conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/Converter.java +++ b/conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/Converter.java @@ -17,6 +17,7 @@ import java.io.File; import java.io.FileNotFoundException; import java.io.IOException; import java.net.URI; +import java.util.HashMap; import java.util.HashSet; import java.util.List; @@ -443,7 +444,7 @@ public class Converter { if(!topLevelURIStr.isEmpty()) { ModuleDefinition topModuleDef = sbolDoc.getModuleDefinition(URI.create(topLevelURIStr)); - List models = SBOL2SBML.generateModel(outputDir, topModuleDef, sbolDoc); + HashMap models = SBOL2SBML.generateModel(outputDir, topModuleDef, sbolDoc); SBMLutilities.exportSBMLModels(models, outputDir, outputFileName, noOutput, sbmlOut, singleSBMLOutput); } else @@ -451,7 +452,7 @@ public class Converter { //No ModuleDefinition URI provided so loop over all rootModuleDefinition for (ModuleDefinition moduleDef : sbolDoc.getRootModuleDefinitions()) { - List models = SBOL2SBML.generateModel(outputDir, moduleDef, sbolDoc); + HashMap models = SBOL2SBML.generateModel(outputDir, moduleDef, sbolDoc); SBMLutilities.exportSBMLModels(models, outputDir, outputFileName, noOutput, sbmlOut, singleSBMLOutput); } } diff --git a/conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/SBOL2SBML.java b/conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/SBOL2SBML.java index e1e57aff1..2b08b4246 100644 --- a/conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/SBOL2SBML.java +++ b/conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/SBOL2SBML.java @@ -105,23 +105,26 @@ public class SBOL2SBML { * @throws BioSimException - if something is wrong with the SBML model. * @throws SBOLValidationException */ - public static List generateModel(String projectDirectory, ModuleDefinition moduleDef, SBOLDocument sbolDoc) throws XMLStreamException, IOException, BioSimException, SBOLValidationException { + public static HashMap generateModel(String projectDirectory, ModuleDefinition moduleDef, SBOLDocument sbolDoc) throws XMLStreamException, IOException, BioSimException, SBOLValidationException { - List models = new LinkedList(); + HashMap models = new HashMap(); BioModel targetModel = new BioModel(projectDirectory); targetModel.createSBMLDocument(getDisplayID(moduleDef), false, false); - org.sbolstandard.core2.Model sbolModel = sbolDoc.createModel(getDisplayID(moduleDef)+"_model", "1", - URI.create("file:" + getDisplayID(moduleDef) + ".xml"), - EDAMOntology.SBML, SystemsBiologyOntology.DISCRETE_FRAMEWORK); - moduleDef.addModel(sbolModel); - + if (sbolDoc.getModel(getDisplayID(moduleDef)+"_model", "1")==null) { + org.sbolstandard.core2.Model sbolModel = sbolDoc.createModel(getDisplayID(moduleDef)+"_model", "1", + URI.create("file:" + getDisplayID(moduleDef) + ".xml"), + EDAMOntology.SBML, SystemsBiologyOntology.DISCRETE_FRAMEWORK); + moduleDef.addModel(sbolModel); + } + // Annotate SBML model with SBOL module definition Model sbmlModel = targetModel.getSBMLDocument().getModel(); SBOLAnnotation modelAnno = new SBOLAnnotation(sbmlModel.getMetaId(), moduleDef.getClass().getSimpleName(), moduleDef.getIdentity()); AnnotationUtility.setSBOLAnnotation(sbmlModel, modelAnno); + // TODO: add moduleDef flattening here for (FunctionalComponent comp : moduleDef.getFunctionalComponents()) { if (isSpeciesComponent(comp, sbolDoc)) { generateSpecies(comp, sbolDoc, targetModel); @@ -130,7 +133,7 @@ public class SBOL2SBML { } else if (isOutputComponent(comp)){ generateOutputPort(comp, targetModel); } - } else if (isPromoterComponent(comp, sbolDoc)) { + } else if (isPromoterComponent(moduleDef, comp, sbolDoc)) { generatePromoterSpecies(comp, sbolDoc, targetModel); if (isInputComponent(comp)) { generateInputPort(comp, targetModel); @@ -242,7 +245,7 @@ public class SBOL2SBML { } for (FunctionalComponent promoter : moduleDef.getFunctionalComponents()) { - if (isPromoterComponent(promoter, sbolDoc)) { + if (isPromoterComponent(moduleDef, promoter, sbolDoc)) { if (!promoterToActivators.containsKey(promoter)) promoterToActivators.put(promoter, new LinkedList()); if (!promoterToRepressors.containsKey(promoter)) @@ -270,14 +273,18 @@ public class SBOL2SBML { BioModel subTargetModel = new BioModel(projectDirectory); if (subTargetModel.load(projectDirectory + File.separator + getDisplayID(subModuleDef) + ".xml")) { generateSubModel(projectDirectory, subModule, moduleDef, sbolDoc, subTargetModel, targetModel); + } if ((subTargetModel=models.get(getDisplayID(subModuleDef)))!=null) { + generateSubModel(projectDirectory, subModule, moduleDef, sbolDoc, subTargetModel, targetModel); } else { - List subModels = generateSubModel(projectDirectory, subModule, moduleDef, sbolDoc, targetModel); - models.addAll(subModels); + HashMap subModels = generateSubModel(projectDirectory, subModule, moduleDef, sbolDoc, targetModel); + for (String key : subModels.keySet()) { + models.put(key,subModels.get(key)); + } } } - models.add(targetModel); + models.put(getDisplayID(moduleDef),targetModel); return models; } @@ -330,12 +337,12 @@ public class SBOL2SBML { * @throws BioSimException - if something is wrong the with SBML model. * @throws SBOLValidationException */ - private static List generateSubModel(String projectDirectory, Module subModule, ModuleDefinition moduleDef, SBOLDocument sbolDoc, + private static HashMap generateSubModel(String projectDirectory, Module subModule, ModuleDefinition moduleDef, SBOLDocument sbolDoc, BioModel targetModel) throws XMLStreamException, IOException, BioSimException, SBOLValidationException { ModuleDefinition subModuleDef = sbolDoc.getModuleDefinition(subModule.getDefinitionURI()); //convert each submodules into its own SBML model stored in their own .xml file. - List subModels = generateModel(projectDirectory, subModuleDef, sbolDoc); - BioModel subTargetModel = subModels.get(subModels.size()-1); + HashMap subModels = generateModel(projectDirectory, subModuleDef, sbolDoc); + BioModel subTargetModel = subModels.get(getDisplayID(subModuleDef)); //Perform replacement and replacedBy with each subModules to its referenced ModuleDefinition. generateSubModel(projectDirectory, subModule, moduleDef, sbolDoc, subTargetModel, targetModel); @@ -461,14 +468,15 @@ public class SBOL2SBML { * @param targetModel - The SBML model to store the SBML promoter species created from the conversion. */ private static void generatePromoterSpecies(FunctionalComponent promoter, SBOLDocument sbolDoc, BioModel targetModel) { - + // Count promoters int promoterCnt = 0; if (promoter.getDefinition() != null) { ComponentDefinition tuCD = promoter.getDefinition(); for (Component comp : tuCD.getComponents()) { if (comp.getDefinition() != null) { - if (comp.getDefinition().getRoles().contains(SequenceOntology.PROMOTER)) { + if (comp.getDefinition().getRoles().contains(SequenceOntology.PROMOTER)|| + comp.getDefinition().getRoles().contains(SequenceOntology.OPERATOR)) { promoterCnt++; } } @@ -499,9 +507,11 @@ public class SBOL2SBML { } } - targetModel.createPromoter(promoterId, -1, -1, true, false, null); + if (targetModel.getSBMLDocument().getModel().getSpecies(promoterId)==null) { + targetModel.createPromoter(promoterId, -1, -1, true, false, null); + } Species sbmlPromoter = targetModel.getSBMLDocument().getModel().getSpecies(promoterId); - + // Annotate SBML promoter species with SBOL component and component definition ComponentDefinition compDef = sbolDoc.getComponentDefinition(promoter.getDefinitionURI()); if (compDef!=null) { @@ -601,7 +611,7 @@ public class SBOL2SBML { boolean onPort = (complexSpecies.getDirection().equals(DirectionType.IN) || complexSpecies.getDirection().equals(DirectionType.OUT)); Reaction complexFormationRxn = targetModel.createComplexReaction(getDisplayID(complexSpecies), null, onPort); - complexFormationRxn.setId(getDisplayID(complexFormation)); + //complexFormationRxn.setId(getDisplayID(complexFormation)); SBMLutilities.setDefaultMetaID(targetModel.getSBMLDocument(), complexFormationRxn, 1); // Annotate SBML complex formation reaction with SBOL interaction @@ -665,7 +675,8 @@ public class SBOL2SBML { ComponentDefinition tuCD = promoter.getDefinition(); for (Component comp : tuCD.getComponents()) { if (comp.getDefinition() != null) { - if (comp.getDefinition().getRoles().contains(SequenceOntology.PROMOTER)) { + if (comp.getDefinition().getRoles().contains(SequenceOntology.PROMOTER)|| + comp.getDefinition().getRoles().contains(SequenceOntology.OPERATOR)) { promoterCnt++; } } @@ -1014,6 +1025,8 @@ public class SBOL2SBML { * @return True if the given FunctionalComponent is a valid output SBML component. False otherwise. */ private static boolean isOutputComponent(FunctionalComponent comp) { + // TODO: hack to avoid mapping promoters + if (comp.getDefinition().getTypes().contains(ComponentDefinition.DNA)) return false; return comp.getDirection().equals(DirectionType.OUT) || comp.getDirection().equals(DirectionType.INOUT); } @@ -1093,10 +1106,25 @@ public class SBOL2SBML { * @param sbolDoc - The SBOL Document to check if the given FunctionalComponent exist. * @return True if the given FunctionalComponent is a valid promoter. False otherwise. */ - private static boolean isPromoterComponent(FunctionalComponent comp, SBOLDocument sbolDoc) { + private static boolean isPromoterComponent(ModuleDefinition moduleDef, + FunctionalComponent comp, SBOLDocument sbolDoc) { ComponentDefinition compDef = sbolDoc.getComponentDefinition(comp.getDefinitionURI()); if (compDef==null) return false; - return isPromoterDefinition(compDef); + + // TODO: hack to avoid adding promoters with no interactions + if (isPromoterDefinition(compDef)) { + boolean foundParticipation = false; + for (Interaction interaction : moduleDef.getInteractions()) { + for (Participation participation : interaction.getParticipations()) { + if (participation.getParticipant().equals(comp)) { + foundParticipation = true; + break; + } + } + } + return foundParticipation; + } + return false; } /** @@ -1292,7 +1320,7 @@ public class SBOL2SBML { for (Participation partici : interact.getParticipations()) { FunctionalComponent comp = moduleDef.getFunctionalComponent(partici.getParticipantURI()); if ((partici.containsRole(SystemsBiologyOntology.PROMOTER)|| - partici.containsRole(SystemsBiologyOntology.TEMPLATE)) && isPromoterComponent(comp, sbolDoc)) + partici.containsRole(SystemsBiologyOntology.TEMPLATE)) && isPromoterComponent(moduleDef, comp, sbolDoc)) hasPromoter = true; else if (partici.containsRole(SystemsBiologyOntology.PRODUCT) && (isProteinComponent(comp, sbolDoc)||isRNAComponent(comp, sbolDoc))) @@ -1325,7 +1353,7 @@ public class SBOL2SBML { for (Participation partici : interact.getParticipations()) { FunctionalComponent comp = moduleDef.getFunctionalComponent(partici.getParticipantURI()); if ((partici.containsRole(SystemsBiologyOntology.PROMOTER)|| - partici.containsRole(SystemsBiologyOntology.STIMULATED)) && isPromoterComponent(comp, sbolDoc)) + partici.containsRole(SystemsBiologyOntology.STIMULATED)) && isPromoterComponent(moduleDef, comp, sbolDoc)) hasActivated = true; else if (partici.containsRole(SystemsBiologyOntology.STIMULATOR) /*&& isTFComponent(comp, sbolDoc)*/) hasActivator = true; @@ -1354,7 +1382,7 @@ public class SBOL2SBML { for (Participation partici : interact.getParticipations()) { FunctionalComponent comp = moduleDef.getFunctionalComponent(partici.getParticipantURI()); if ((partici.containsRole(SystemsBiologyOntology.PROMOTER) || - partici.containsRole(SystemsBiologyOntology.INHIBITED)) && isPromoterComponent(comp, sbolDoc)) + partici.containsRole(SystemsBiologyOntology.INHIBITED)) && isPromoterComponent(moduleDef, comp, sbolDoc)) hasRepressed = true; else if (partici.containsRole(SystemsBiologyOntology.INHIBITOR) ) hasRepressor = true; @@ -1439,8 +1467,8 @@ public class SBOL2SBML { if(uri!=null){ ModuleDefinition topModuleDef= sbolDoc.getModuleDefinition(URI.create(uri)); - List models = SBOL2SBML.generateModel(outputDir, topModuleDef, sbolDoc); - for (BioModel model : models) + HashMap models = SBOL2SBML.generateModel(outputDir, topModuleDef, sbolDoc); + for (BioModel model : models.values()) { model.save(outputDir + File.separator + model.getSBMLDocument().getModel().getId() + ".xml"); } @@ -1449,8 +1477,8 @@ public class SBOL2SBML { //No ModuleDefinition URI provided so loop over all rootModuleDefinition for (ModuleDefinition moduleDef : sbolDoc.getRootModuleDefinitions()) { - List models = SBOL2SBML.generateModel(outputDir, moduleDef, sbolDoc); - for (BioModel model : models) + HashMap models = SBOL2SBML.generateModel(outputDir, moduleDef, sbolDoc); + for (BioModel model : models.values()) { model.save(outputDir + File.separator + model.getSBMLDocument().getModel().getId() + ".xml"); } diff --git a/conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/VPRModelGenerator.java b/conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/VPRModelGenerator.java index ce8b0009b..89ea66515 100644 --- a/conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/VPRModelGenerator.java +++ b/conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/VPRModelGenerator.java @@ -67,7 +67,7 @@ public class VPRModelGenerator { collectionURI = collectionURI.substring(0, collectionURI.lastIndexOf('/')); String collectionId = collectionURI.substring(collectionURI.lastIndexOf('/')+1); collectionURI = collectionURI + '/' + collectionId + "_collection/" + cd.getVersion(); - if (!collections.contains(collectionURI)) { + if (!collections.contains(URI.create(collectionURI))) { collections.add(URI.create(collectionURI)); } } @@ -80,11 +80,11 @@ public class VPRModelGenerator { if(!rootModuleID.isEmpty() && rootModuleID != null) { - interactionAdder = new SBOLInteractionAdder_GeneCentric(URI.create(endpoint), rootModuleID, params); + interactionAdder = new SBOLInteractionAdder_GeneCentric(URI.create(endpoint), rootModuleID, params, true); } else { - interactionAdder = new SBOLInteractionAdder_GeneCentric(URI.create(endpoint), "TopModule", params); + interactionAdder = new SBOLInteractionAdder_GeneCentric(URI.create(endpoint), "TopModule", params, true); } interactionAdder.addInteractions(generatedModel); return generatedModel; diff --git a/dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/util/SBMLutilities.java b/dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/util/SBMLutilities.java index 4bc67337b..45a558779 100644 --- a/dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/util/SBMLutilities.java +++ b/dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/util/SBMLutilities.java @@ -145,7 +145,7 @@ public class SBMLutilities extends CoreObservable * @throws IOException Unable to write file to SBML. * @throws BioSimException - if sbml model is invalid. */ - public static void exportSBMLModels(List models, String outputDir, String outputFileName, + public static void exportSBMLModels(HashMap models, String outputDir, String outputFileName, boolean noOutput, boolean sbmlOut, boolean singleSBMLOutput) throws SBMLException, XMLStreamException, IOException, BioSimException { // Note: Since SBOL2SBML converter encase the result of SBML model in BioModels, the last biomodel @@ -216,11 +216,11 @@ public class SBMLutilities extends CoreObservable * @throws IOException Unable to write file to SBML. * @throws BioSimException - if sbml model is invalid. */ - public static ArrayList exportMultSBMLFile(List models, String outputDir) throws XMLStreamException, IOException, BioSimException + public static ArrayList exportMultSBMLFile(HashMap models, String outputDir) throws XMLStreamException, IOException, BioSimException { ArrayList submodels = new ArrayList(); //Multiple SBML output - for (BioModel model : models) + for (BioModel model : models.values()) { String filename = model.getSBMLDocument().getModel().getId() + ".xml"; model.save(outputDir + File.separator + filename); diff --git a/gui/jcs_swap/.gitignore b/gui/jcs_swap/.gitignore new file mode 100644 index 000000000..41e9b607b --- /dev/null +++ b/gui/jcs_swap/.gitignore @@ -0,0 +1,4 @@ +/default.data +/default.key +/testCache1.data +/testCache1.key diff --git a/gui/src/main/java/edu/utah/ece/async/ibiosim/gui/Gui.java b/gui/src/main/java/edu/utah/ece/async/ibiosim/gui/Gui.java index 74f9bc84e..2a848dee4 100644 --- a/gui/src/main/java/edu/utah/ece/async/ibiosim/gui/Gui.java +++ b/gui/src/main/java/edu/utah/ece/async/ibiosim/gui/Gui.java @@ -6177,10 +6177,10 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot try { for (ModuleDefinition moduleDef : inputSBOLDoc.getRootModuleDefinitions()) { if (moduleDef.getModels().size()==0) { - List models; + HashMap models; try { models = SBOL2SBML.generateModel(root, moduleDef, inputSBOLDoc); - for (BioModel model : models) { + for (BioModel model : models.values()) { if (overwrite(root + File.separator + model.getSBMLDocument().getModel().getId() + ".xml", model.getSBMLDocument().getModel().getId() + ".xml")) { model.save(root + File.separator + model.getSBMLDocument().getModel().getId() + ".xml"); diff --git a/gui/src/main/java/edu/utah/ece/async/ibiosim/gui/synthesisView/SynthesisView.java b/gui/src/main/java/edu/utah/ece/async/ibiosim/gui/synthesisView/SynthesisView.java index 7e1a167ec..21079322a 100644 --- a/gui/src/main/java/edu/utah/ece/async/ibiosim/gui/synthesisView/SynthesisView.java +++ b/gui/src/main/java/edu/utah/ece/async/ibiosim/gui/synthesisView/SynthesisView.java @@ -586,7 +586,7 @@ public class SynthesisView extends JTabbedPane implements ActionListener, Runnab List solutionFileIDs = new ArrayList(); for (ModuleDefinition moduleDef : solution.getRootModuleDefinitions()) { - List models = SBOL2SBML.generateModel(solution_dir, moduleDef, solution); + HashMap models = SBOL2SBML.generateModel(solution_dir, moduleDef, solution); solutionFileIDs.addAll(SBMLutilities.exportMultSBMLFile(models, solution_dir)); } return solutionFileIDs;