Examples with org.hl7.fhir.dstu3.model org.hl7.fhir.dstu3.model used on opensource projects

Example 1 with org.hl7.fhir.dstu3.model

use of org.hl7.fhir.dstu3.model in project libSBOLj by SynBioDex.

the class ModelOutput method main.

public static void main(String[] args) throws Exception {
    SBOLDocument document = new SBOLDocument();
    document.setTypesInURIs(false);
    document.setDefaultURIprefix("http://www.sbolstandard.org/examples/");
    Model model = document.createModel("pIKE_Toggle_1", "", URI.create("http://virtualparts.org/part/pIKE_Toggle_1"), URI.create("http://identifiers.org/edam/format_2585"), SystemsBiologyOntology.CONTINUOUS_FRAMEWORK);
    model.setName("pIKE_Toggle_1 toggle switch");
    SBOLWriter.write(document, (System.out));
}

Example 2 with org.hl7.fhir.dstu3.model

use of org.hl7.fhir.dstu3.model in project libSBOLj by SynBioDex.

the class ModuleDefinitionOutput method main.

public static void main(String[] args) throws Exception {
    SBOLDocument document = new SBOLDocument();
    setDefaultNameSpace(document, pr.getNamespaceURI());
    ComponentDefinition gfp = createComponenDefinition(document, pr.withLocalPart("BBa_E0040"), "gfp", Terms.biopaxTerms.DnaRegion, Terms.soTerms.CDS, "gfp coding sequence");
    ComponentDefinition tetR = createComponenDefinition(document, pr.withLocalPart("BBa_C0040"), "tetR", Terms.biopaxTerms.DnaRegion, Terms.soTerms.CDS, "tetR coding sequence");
    ComponentDefinition lacI = createComponenDefinition(document, pr.withLocalPart("BBa_C0012"), "lacI", Terms.biopaxTerms.DnaRegion, Terms.soTerms.CDS, "lacI coding sequence");
    ComponentDefinition placI = createComponenDefinition(document, pr.withLocalPart("BBa_R0010"), "pLacI", Terms.biopaxTerms.DnaRegion, Terms.soTerms.promoter, "pLacI promoter");
    ComponentDefinition ptetR = createComponenDefinition(document, pr.withLocalPart("BBa_R0040"), "pTetR", Terms.biopaxTerms.DnaRegion, Terms.soTerms.promoter, "pTet promoter");
    ComponentDefinition rbslacI = createComponenDefinition(document, pr.withLocalPart("BBa_J61101"), "BBa_J61101 RBS", Terms.biopaxTerms.DnaRegion, Terms.soTerms.RBS, "RBS1");
    ComponentDefinition rbstetR = createComponenDefinition(document, pr.withLocalPart("BBa_J61120"), "BBa_J61101 RBS", Terms.biopaxTerms.DnaRegion, Terms.soTerms.RBS, "RBS2");
    ComponentDefinition rbsgfp = createComponenDefinition(document, pr.withLocalPart("BBa_J61130"), "BBa_J61101 RBS", Terms.biopaxTerms.DnaRegion, Terms.soTerms.RBS, "RBS2");
    setDefaultNameSpace(document, uniprot.getNamespaceURI());
    ComponentDefinition GFP = createComponenDefinition(document, uniprot.withLocalPart("P42212"), "GFP", Terms.biopaxTerms.Protein, Terms.sboTerms.product, "GFP protein");
    ComponentDefinition TetR = createComponenDefinition(document, uniprot.withLocalPart("Q6QR72"), "TetR", Terms.biopaxTerms.Protein, Terms.sboTerms.inhibitor, "TetR protein");
    ComponentDefinition LacI = createComponenDefinition(document, uniprot.withLocalPart("P03023"), "LacI", Terms.biopaxTerms.Protein, Terms.sboTerms.inhibitor, "LacI protein");
    setDefaultNameSpace(document, pr.getNamespaceURI());
    ComponentDefinition lacITerminator = createComponenDefinition(document, pr.withLocalPart("ECK120029600"), "ECK120029600", Terms.biopaxTerms.DnaRegion, Terms.soTerms.terminator, "Terminator1");
    ComponentDefinition tetRTerminator = createComponenDefinition(document, pr.withLocalPart("ECK120033736"), "ECK120033736", Terms.biopaxTerms.DnaRegion, Terms.soTerms.terminator, "Terminator2");
    setDefaultNameSpace(document, vpr.getNamespaceURI());
    ComponentDefinition tetRInverter = createComponenDefinition(document, vpr.withLocalPart("pIKELeftCassette_1"), "TetR Inverter", Terms.biopaxTerms.DnaRegion, Terms.soTerms.engineeredGene, "TetR Inverter");
    ComponentDefinition lacIInverter = createComponenDefinition(document, vpr.withLocalPart("pIKERightCassette_1"), "LacI Inverter", Terms.biopaxTerms.DnaRegion, Terms.soTerms.engineeredGene, "LacI Inverter");
    ComponentDefinition toggleSwitch = createComponenDefinition(document, vpr.withLocalPart("pIKE_Toggle_1"), "LacI/TetR Toggle Switch", Terms.biopaxTerms.DnaRegion, Terms.soTerms.engineeredGene, "LacI/TetR Toggle Switch");
    // tetR inverter sequences
    addPRSequence(document, ptetR, "tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac");
    addPRSequence(document, rbslacI, "aaagacaggacc");
    addPRSequence(document, lacI, "atggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagacagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcaggctgcaaacgacgaaaactacgctttagtagcttaataa");
    addPRSequence(document, lacITerminator, "ttcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaa");
    // lacI inverter sequences
    addPRSequence(document, placI, "tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac");
    addPRSequence(document, rbstetR, "aaagacaggacc");
    addPRSequence(document, tetR, "atgtccagattagataaaagtaaagtgattaacagcgcattagagctgcttaatgaggtcggaatcgaaggtttaacaacccgtaaactcgcccagaagctaggtgtagagcagcctacattgtattggcatgtaaaaaataagcgggctttgctcgacgccttagccattgagatgttagataggcaccatactcacttttgccctttagaaggggaaagctggcaagattttttacgtaataacgctaaaagttttagatgtgctttactaagtcatcgcgatggagcaaaagtacatttaggtacacggcctacagaaaaacagtatgaaactctcgaaaatcaattagcctttttatgccaacaaggtttttcactagagaatgcattatatgcactcagcgctgtggggcattttactttaggttgcgtattggaagatcaagagcatcaagtcgctaaagaagaaagggaaacacctactactgatagtatgccgccattattacgacaagctatcgaattatttgatcaccaaggtgcagagccagccttcttattcggccttgaattgatcatatgcggattagaaaaacaacttaaatgtgaaagtgggtccgctgcaaacgacgaaaactacgctttagtagcttaataa");
    addPRSequence(document, rbsgfp, "aaagaaacgaca");
    addPRSequence(document, gfp, "atgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataataa");
    addPRSequence(document, tetRTerminator, "ttcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaa");
    addSubComponents(document, tetRInverter, ptetR, rbslacI, lacI, lacITerminator);
    addSubComponents(document, lacIInverter, placI, rbstetR, tetR, rbsgfp, gfp, tetRTerminator);
    addSubComponents(document, toggleSwitch, tetRInverter, lacIInverter);
    setDefaultNameSpace(document, example.getNamespaceURI());
    ModuleDefinition laciInverterModuleDef = document.createModuleDefinition("laci_inverter");
    laciInverterModuleDef.addRole(Terms.moduleRoles.inverter);
    ModuleDefinition tetRInverterModuleDef = document.createModuleDefinition("tetr_inverter");
    tetRInverterModuleDef.addRole(Terms.moduleRoles.inverter);
    createInverter(document, laciInverterModuleDef, placI, LacI);
    createInverter(document, tetRInverterModuleDef, ptetR, TetR);
    ModuleDefinition toggleSwitchModuleDef = document.createModuleDefinition("toggle_switch");
    toggleSwitchModuleDef.addRole(toURI(example.withLocalPart("module_role/toggle_switch")));
    FunctionalComponent toggleSwitchModuleDef_TetR = toggleSwitchModuleDef.createFunctionalComponent("TetR", AccessType.PUBLIC, TetR.getIdentity(), DirectionType.INOUT);
    FunctionalComponent toggleSwitchModuleDef_LacI = toggleSwitchModuleDef.createFunctionalComponent("LacI", AccessType.PUBLIC, LacI.getIdentity(), DirectionType.INOUT);
    Module lacInverterSubModule = toggleSwitchModuleDef.createModule("laci_inverter", laciInverterModuleDef.getIdentity());
    lacInverterSubModule.createMapsTo("LacI_mapping", RefinementType.USEREMOTE, toggleSwitchModuleDef_LacI.getIdentity(), laciInverterModuleDef.getFunctionalComponent("TF").getIdentity());
    Module tetRInverterSubModule = toggleSwitchModuleDef.createModule("tetr_inverter", tetRInverterModuleDef.getIdentity());
    tetRInverterSubModule.createMapsTo("TetR_mapping", RefinementType.USEREMOTE, toggleSwitchModuleDef_TetR.getIdentity(), tetRInverterModuleDef.getFunctionalComponent("TF").getIdentity());
    Model model = document.createModel("toogleswitch", URI.create("http://virtualparts.org/part/pIKE_Toggle_1"), EDAMOntology.SBML, SystemsBiologyOntology.CONTINUOUS_FRAMEWORK);
    toggleSwitchModuleDef.addModel(model.getIdentity());
    SBOLWriter.write(document, (System.out));
}

Example 3 with org.hl7.fhir.dstu3.model

use of org.hl7.fhir.dstu3.model in project libSBOLj by SynBioDex.

the class ModuleDefinitionTest method test_modelMethods.

@Test
public void test_modelMethods() throws SBOLValidationException {
    Model model = doc.createModel("pIKE_Toggle_1", "1.0", URI.create("http://virtualparts.org/part/pIKE_Toggle_1"), URI.create("http://identifiers.org/edam/format_2585"), SystemsBiologyOntology.CONTINUOUS_FRAMEWORK);
    assertTrue(geneticToggleSwitch.addModel("pIKE_Toggle_1"));
    assertTrue(doc.getModuleDefinition("geneticToggleSwitch", "").getModels().contains(model));
    assertTrue(geneticToggleSwitch.removeModel(model.getPersistentIdentity()));
    assertTrue(geneticToggleSwitch.addModel("pIKE_Toggle_1", "1.0"));
    assertTrue(doc.getModuleDefinition("geneticToggleSwitch", "").getModels().contains(model));
    assertTrue(geneticToggleSwitch.containsModel(model.getIdentity()));
}

Example 4 with org.hl7.fhir.dstu3.model

use of org.hl7.fhir.dstu3.model in project bmoth by hhu-stups.

the class Issue73Test method testSatPredicateWithoutModel.

@Test
public void testSatPredicateWithoutModel() throws IOException {
    String formula = "1 < 2";
    BoolExpr constraint = translatePredicate(formula, z3Context);
    SolutionFinder finder = new SolutionFinder(z3Solver, z3Context);
    Set<Model> solutions = finder.findSolutions(constraint, 20);
    assertEquals(0, solutions.size());
}

Example 5 with org.hl7.fhir.dstu3.model

use of org.hl7.fhir.dstu3.model in project Dat3M by hernanponcedeleon.

the class Porthos method main.

public static void main(String[] args) throws Z3Exception, IOException {
    List<String> MCMs = Arrays.asList("sc", "tso", "pso", "rmo", "alpha", "power", "arm");
    Options options = new Options();
    Option sourceOpt = new Option("s", "source", true, "source MCM");
    sourceOpt.setRequired(true);
    options.addOption(sourceOpt);
    Option targetOpt = new Option("t", "target", true, "target MCM");
    targetOpt.setRequired(true);
    options.addOption(targetOpt);
    Option inputOpt = new Option("i", "input", true, "input file path");
    inputOpt.setRequired(true);
    options.addOption(inputOpt);
    options.addOption("state", false, "PORTHOS performs state portability");
    options.addOption(Option.builder("draw").hasArg().desc("If a buf is found, it outputs a graph \\path_to_file.dot").build());
    options.addOption(Option.builder("rels").hasArgs().desc("Relations to be drawn in the graph").build());
    options.addOption(Option.builder("unroll").hasArg().desc("Unrolling steps").build());
    CommandLineParser parserCmd = new DefaultParser();
    HelpFormatter formatter = new HelpFormatter();
    CommandLine cmd;
    try {
        cmd = parserCmd.parse(options, args);
    } catch (ParseException e) {
        System.out.println(e.getMessage());
        formatter.printHelp("PORTHOS", options);
        System.exit(1);
        return;
    }
    String source = cmd.getOptionValue("source");
    if (!MCMs.stream().anyMatch(mcms -> mcms.trim().equals(source))) {
        System.out.println("Unrecognized source");
        System.exit(0);
        return;
    }
    String target = cmd.getOptionValue("target");
    if (!MCMs.stream().anyMatch(mcms -> mcms.trim().equals(target))) {
        System.out.println("Unrecognized target");
        System.exit(0);
        return;
    }
    String inputFilePath = cmd.getOptionValue("input");
    if (!inputFilePath.endsWith("pts") && !inputFilePath.endsWith("litmus")) {
        System.out.println("Unrecognized program format");
        System.exit(0);
        return;
    }
    File file = new File(inputFilePath);
    boolean statePortability = cmd.hasOption("state");
    String[] rels = new String[100];
    if (cmd.hasOption("rels")) {
        rels = cmd.getOptionValues("rels");
    }
    String program = FileUtils.readFileToString(file, "UTF-8");
    ANTLRInputStream input = new ANTLRInputStream(program);
    Program p = new Program(inputFilePath);
    if (inputFilePath.endsWith("litmus")) {
        LitmusLexer lexer = new LitmusLexer(input);
        CommonTokenStream tokens = new CommonTokenStream(lexer);
        LitmusParser parser = new LitmusParser(tokens);
        p = parser.program(inputFilePath).p;
    }
    if (inputFilePath.endsWith("pts")) {
        PorthosLexer lexer = new PorthosLexer(input);
        CommonTokenStream tokens = new CommonTokenStream(lexer);
        PorthosParser parser = new PorthosParser(tokens);
        p = parser.program(inputFilePath).p;
    }
    int steps = 1;
    if (cmd.hasOption("unroll")) {
        steps = Integer.parseInt(cmd.getOptionValue("unroll"));
    }
    p.initialize(steps);
    Program pSource = p.clone();
    Program pTarget = p.clone();
    pSource.compile(source, false, true);
    Integer startEId = Collections.max(pSource.getEvents().stream().filter(e -> e instanceof Init).map(e -> e.getEId()).collect(Collectors.toSet())) + 1;
    pTarget.compile(target, false, true, startEId);
    Context ctx = new Context();
    ctx.setPrintMode(Z3_ast_print_mode.Z3_PRINT_SMTLIB_FULL);
    Solver s = ctx.mkSolver();
    Solver s2 = ctx.mkSolver();
    BoolExpr sourceDF = pSource.encodeDF(ctx);
    BoolExpr sourceCF = pSource.encodeCF(ctx);
    BoolExpr sourceDF_RF = pSource.encodeDF_RF(ctx);
    BoolExpr sourceDomain = Domain.encode(pSource, ctx);
    BoolExpr sourceMM = pSource.encodeMM(ctx, source);
    s.add(pTarget.encodeDF(ctx));
    s.add(pTarget.encodeCF(ctx));
    s.add(pTarget.encodeDF_RF(ctx));
    s.add(Domain.encode(pTarget, ctx));
    s.add(pTarget.encodeMM(ctx, target));
    s.add(pTarget.encodeConsistent(ctx, target));
    s.add(sourceDF);
    s.add(sourceCF);
    s.add(sourceDF_RF);
    s.add(sourceDomain);
    s.add(sourceMM);
    s.add(pSource.encodeInconsistent(ctx, source));
    s.add(encodeCommonExecutions(pTarget, pSource, ctx));
    s2.add(sourceDF);
    s2.add(sourceCF);
    s2.add(sourceDF_RF);
    s2.add(sourceDomain);
    s2.add(sourceMM);
    s2.add(pSource.encodeConsistent(ctx, source));
    if (!statePortability) {
        if (s.check() == Status.SATISFIABLE) {
            System.out.println("The program is not portable");
            // System.out.println("       0");
            if (cmd.hasOption("draw")) {
                String outputPath = cmd.getOptionValue("draw");
                Utils.drawGraph(p, pSource, pTarget, ctx, s.getModel(), outputPath, rels);
            }
            return;
        } else {
            System.out.println("The program is portable");
            // System.out.println("       1");
            return;
        }
    }
    int iterations = 0;
    Status lastCheck = Status.SATISFIABLE;
    Set<Expr> visited = new HashSet<Expr>();
    while (lastCheck == Status.SATISFIABLE) {
        lastCheck = s.check();
        if (lastCheck == Status.SATISFIABLE) {
            iterations = iterations + 1;
            Model model = s.getModel();
            s2.push();
            BoolExpr reachedState = encodeReachedState(pTarget, model, ctx);
            visited.add(reachedState);
            assert (iterations == visited.size());
            s2.add(reachedState);
            if (s2.check() == Status.UNSATISFIABLE) {
                System.out.println("The program is not state-portable");
                System.out.println("Iterations: " + iterations);
                // System.out.println("       0");
                return;
            } else {
                s2.pop();
                s.add(ctx.mkNot(reachedState));
            }
        } else {
            System.out.println("The program is state-portable");
            System.out.println("Iterations: " + iterations);
            // System.out.println("       1");
            return;
        }
    }
}