Examples with FunctionalComponent org.sbolstandard.core2.FunctionalComponent used on opensource projects

Example 1 with FunctionalComponent

use of org.sbolstandard.core2.FunctionalComponent in project libSBOLj by SynBioDex.

the class ModuleDefinitionOutput method createInverter.

private static void createInverter(SBOLDocument document, ModuleDefinition moduleDef, ComponentDefinition promoter, ComponentDefinition TF) throws Exception {
    FunctionalComponent laciInverterModuleDef_promoter = moduleDef.createFunctionalComponent("promoter", AccessType.PUBLIC, promoter.getIdentity(), DirectionType.INOUT);
    FunctionalComponent laciInverterModuleDef_TF = moduleDef.createFunctionalComponent("TF", AccessType.PUBLIC, TF.getIdentity(), DirectionType.INOUT);
    Interaction interaction = moduleDef.createInteraction("LacI_pLacI", new HashSet<URI>(Arrays.asList(toURI(Terms.interactionTypes.transcriptionalRepression))));
    Participation participation = interaction.createParticipation(promoter.getDisplayId(), laciInverterModuleDef_promoter.getIdentity(), toURI(Terms.participantRoles.promoter));
    Participation participation2 = interaction.createParticipation(TF.getDisplayId(), laciInverterModuleDef_TF.getIdentity(), toURI(Terms.participantRoles.inhibitor));
}

Example 2 with FunctionalComponent

use of org.sbolstandard.core2.FunctionalComponent 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 FunctionalComponent

use of org.sbolstandard.core2.FunctionalComponent in project libSBOLj by SynBioDex.

the class SBOLReader method parseFunctionalComponent.

/**
 * @param functionalComponent
 * @param nested
 * @return
 * @throws SBOLValidationException if either of the following conditions is satisfied:
 * <ul>
 * <li>any of the following SBOL validation rules was violated:
 * 10203, 10204, 10206, 10208, 10212, 10213, 10602, 10607, 11606, 11802; or
 * </li>
 * <li>an SBOL validation rule violation occurred in the following constructor or methods:
 * 	<ul>
 * 		<li>{@link #parseMapsTo(NestedDocument, boolean)},</li>
 * 		<li>{@link FunctionalComponent#FunctionalComponent(URI, AccessType, URI, DirectionType)},</li>
 * 		<li>{@link FunctionalComponent#setDisplayId(String)},</li>
 * 		<li>{@link FunctionalComponent#setVersion(String)},</li>
 * 		<li>{@link FunctionalComponent#setWasDerivedFrom(URI)},</li>
 * 		<li>{@link FunctionalComponent#setMapsTos(Set)}, or</li>
 * 		<li>{@link Identified#setAnnotations(List)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
@SuppressWarnings("unchecked")
private static FunctionalComponent parseFunctionalComponent(SBOLDocument SBOLDoc, NestedDocument<QName> functionalComponent, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
    // URIcompliance.extractDisplayId(functionalComponent.getIdentity());
    String displayId = null;
    String name = null;
    String description = null;
    // URI.create(URIcompliance.extractPersistentId(functionalComponent.getIdentity()));
    URI persistentIdentity = null;
    String version = null;
    AccessType access = null;
    DirectionType direction = null;
    URI functionalComponentURI = null;
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    List<Annotation> annotations = new ArrayList<>();
    Set<MapsTo> mappings = new HashSet<>();
    for (NamedProperty<QName> namedProperty : functionalComponent.getProperties()) {
        if (namedProperty.getName().equals(Sbol2Terms.Identified.persistentIdentity)) {
            if (!(namedProperty.getValue() instanceof Literal) || persistentIdentity != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10203", functionalComponent.getIdentity());
            }
            persistentIdentity = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.version)) {
            if (!(namedProperty.getValue() instanceof Literal) || version != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10206", functionalComponent.getIdentity());
            }
            version = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.displayId)) {
            if (!(namedProperty.getValue() instanceof Literal) || displayId != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10204", functionalComponent.getIdentity());
            }
            displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.ComponentInstance.access)) {
            if (!(namedProperty.getValue() instanceof Literal) || access != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10607", functionalComponent.getIdentity());
            }
            String accessTypeStr = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
            if (accessTypeStr.startsWith("http://www.sbolstandard.org/")) {
                System.err.println("Warning: namespace for access types should be http://sbols.org/v2#");
                accessTypeStr = accessTypeStr.replace("http://www.sbolstandard.org/", "http://sbols.org/v2#");
            }
            try {
                access = AccessType.convertToAccessType(URI.create(accessTypeStr));
            } catch (SBOLValidationException e) {
                throw new SBOLValidationException("sbol-10607", functionalComponent.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.FunctionalComponent.direction)) {
            if (!(namedProperty.getValue() instanceof Literal) || direction != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-11802", functionalComponent.getIdentity());
            }
            String directionTypeStr = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
            if (directionTypeStr.startsWith("http://www.sbolstandard.org/")) {
                System.err.println("Warning: namespace for direction types should be http://sbols.org/v2#");
                directionTypeStr = directionTypeStr.replace("http://www.sbolstandard.org/", "http://sbols.org/v2#");
                directionTypeStr = directionTypeStr.replace("input", "in");
                directionTypeStr = directionTypeStr.replace("output", "out");
            }
            try {
                direction = DirectionType.convertToDirectionType(URI.create(directionTypeStr));
            } catch (SBOLValidationException e) {
                throw new SBOLValidationException("sbol-11802", functionalComponent.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.ComponentInstance.hasMapsTo)) {
            if (namedProperty.getValue() instanceof NestedDocument) {
                NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
                if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.MapsTo.MapsTo)) {
                    throw new SBOLValidationException("sbol-10606", functionalComponent.getIdentity());
                }
                mappings.add(parseMapsTo(((NestedDocument<QName>) namedProperty.getValue()), false));
            } else {
                URI uri = (URI) ((Literal<QName>) namedProperty.getValue()).getValue();
                NestedDocument<QName> nestedDocument = nested.get(uri);
                if (nestedDocument == null || nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.MapsTo.MapsTo)) {
                    throw new SBOLValidationException("sbol-10606", functionalComponent.getIdentity());
                }
                mappings.add(parseMapsTo(nested.get(uri), false));
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.ComponentInstance.hasComponentDefinition)) {
            if (functionalComponentURI != null) {
                throw new SBOLValidationException("sbol-10602", functionalComponent.getIdentity());
            }
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-10602", functionalComponent.getIdentity());
                }
                functionalComponentURI = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
            } else if (namedProperty.getValue() instanceof IdentifiableDocument) {
                if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.ComponentDefinition.ComponentDefinition)) {
                    ComponentDefinition componentDefinition = parseComponentDefinition(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue(), nested);
                    functionalComponentURI = componentDefinition.getIdentity();
                } else {
                    throw new SBOLValidationException("sbol-10602", functionalComponent.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-10602", functionalComponent.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.title)) {
            if (!(namedProperty.getValue() instanceof Literal) || name != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10212", functionalComponent.getIdentity());
            }
            name = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.description)) {
            if (!(namedProperty.getValue() instanceof Literal) || description != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10213", functionalComponent.getIdentity());
            }
            description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.wasDerivedFrom)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10208", functionalComponent.getIdentity());
            }
            wasDerivedFroms.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.wasGeneratedBy)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10221", functionalComponent.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    FunctionalComponent fc = new FunctionalComponent(functionalComponent.getIdentity(), access, functionalComponentURI, direction);
    if (persistentIdentity != null)
        fc.setPersistentIdentity(persistentIdentity);
    if (version != null)
        fc.setVersion(version);
    if (displayId != null)
        fc.setDisplayId(displayId);
    if (!mappings.isEmpty())
        fc.setMapsTos(mappings);
    if (name != null)
        fc.setName(name);
    if (description != null)
        fc.setDescription(description);
    fc.setWasDerivedFroms(wasDerivedFroms);
    fc.setWasGeneratedBys(wasGeneratedBys);
    if (!annotations.isEmpty())
        fc.setAnnotations(annotations);
    return fc;
}

Example 4 with FunctionalComponent

use of org.sbolstandard.core2.FunctionalComponent in project libSBOLj by SynBioDex.

the class SBOLReader method parseModuleDefinition.

/**
 * @param SBOLDoc
 * @param topLevel
 * @param nested
 * @return
 *
 * @throws SBOLValidationException if either of the following conditions is satisfied:
 * <ul>
 * <li>any of the following SBOL validation rules was violated:
 * 10202, 10203, 10204, 10206, 10208, 10212, 10213, 11602, 11607 or</li>
 * <li>an SBOL validation rule violation occurred in the following constructor or methods:
 * 	<ul>
 * 		<li>{@link #parseModule(NestedDocument, Map)},</li>
 * 		<li>{@link #parseInteraction(NestedDocument, Map)},</li>
 * 		<li>{@link #parseFunctionalComponent(NestedDocument, Map)},</li>
 * 		<li>{@link ModuleDefinition#ModuleDefinition(URI)}, </li>
 * 		<li>{@link ModuleDefinition#setDisplayId(String)}, </li>
 * 		<li>{@link ModuleDefinition#setVersion(String)}, </li>
 * 		<li>{@link ModuleDefinition#setFunctionalComponents(Set)}, </li>
 * 		<li>{@link ModuleDefinition#setInteractions(Set)}, </li>
 * 		<li>{@link ModuleDefinition#setModels(Set)}, </li>
 * 		<li>{@link ModuleDefinition#setModules(Set)}, </li>
 * 		<li>{@link ModuleDefinition#setWasDerivedFrom(URI)}, </li>
 * 		<li>{@link ModuleDefinition#setAnnotations(List)}, or</li>
 * 		<li>{@link SBOLDocument#addModuleDefinition(ModuleDefinition)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
@SuppressWarnings("unchecked")
private static ModuleDefinition parseModuleDefinition(SBOLDocument SBOLDoc, IdentifiableDocument<QName> topLevel, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
    // URIcompliance.extractDisplayId(topLevel.getIdentity());
    String displayId = null;
    String name = null;
    String description = null;
    // URI.create(URIcompliance.extractPersistentId(topLevel.getIdentity()));
    URI persistentIdentity = null;
    String version = null;
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    Set<URI> attachments = new HashSet<>();
    Set<URI> roles = new HashSet<>();
    Set<URI> models = new HashSet<>();
    Set<FunctionalComponent> functionalComponents = new HashSet<>();
    Set<Interaction> interactions = new HashSet<>();
    Set<Module> subModules = new HashSet<>();
    List<Annotation> annotations = new ArrayList<>();
    for (NamedProperty<QName> namedProperty : topLevel.getProperties()) {
        if (namedProperty.getName().equals(Sbol2Terms.Identified.persistentIdentity)) {
            if (!(namedProperty.getValue() instanceof Literal) || persistentIdentity != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10203", topLevel.getIdentity());
            }
            persistentIdentity = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.version)) {
            if (!(namedProperty.getValue() instanceof Literal) || version != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10206", topLevel.getIdentity());
            }
            version = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.displayId)) {
            if (!(namedProperty.getValue() instanceof Literal) || displayId != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10204", topLevel.getIdentity());
            }
            displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.ModuleDefinition.roles)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-11602", topLevel.getIdentity());
            }
            roles.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.ModuleDefinition.hasModule) || namedProperty.getName().equals(Sbol2Terms.ModuleDefinition.hasSubModule)) {
            if (namedProperty.getValue() instanceof NestedDocument) {
                NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
                if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.Module.Module)) {
                    throw new SBOLValidationException("sbol-11604", topLevel.getIdentity());
                }
                subModules.add(parseModule(SBOLDoc, ((NestedDocument<QName>) namedProperty.getValue()), nested));
            } else {
                URI uri = (URI) ((Literal<QName>) namedProperty.getValue()).getValue();
                NestedDocument<QName> nestedDocument = nested.get(uri);
                if (nestedDocument == null || nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.Module.Module)) {
                    throw new SBOLValidationException("sbol-11604", topLevel.getIdentity());
                }
                subModules.add(parseModule(SBOLDoc, nested.get(uri), nested));
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.ModuleDefinition.hasInteractions)) {
            if (namedProperty.getValue() instanceof NestedDocument) {
                NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
                if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.Interaction.Interaction)) {
                    throw new SBOLValidationException("sbol-11605", topLevel.getIdentity());
                }
                interactions.add(parseInteraction((NestedDocument<QName>) namedProperty.getValue(), nested));
            } else {
                URI uri = (URI) ((Literal<QName>) namedProperty.getValue()).getValue();
                NestedDocument<QName> nestedDocument = nested.get(uri);
                if (nestedDocument == null || nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.Interaction.Interaction)) {
                    throw new SBOLValidationException("sbol-11605", topLevel.getIdentity());
                }
                interactions.add(parseInteraction(nested.get(uri), nested));
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.ModuleDefinition.hasfunctionalComponent) || namedProperty.getName().equals(Sbol2Terms.ComponentDefinition.hasComponent)) {
            if (namedProperty.getValue() instanceof NestedDocument) {
                NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
                if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.FunctionalComponent.FunctionalComponent)) {
                    throw new SBOLValidationException("sbol-11606", topLevel.getIdentity());
                }
                functionalComponents.add(parseFunctionalComponent(SBOLDoc, (NestedDocument<QName>) namedProperty.getValue(), nested));
            } else {
                URI uri = (URI) ((Literal<QName>) namedProperty.getValue()).getValue();
                NestedDocument<QName> nestedDocument = nested.get(uri);
                if (nestedDocument == null || nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.FunctionalComponent.FunctionalComponent)) {
                    throw new SBOLValidationException("sbol-11606", topLevel.getIdentity());
                }
                functionalComponents.add(parseFunctionalComponent(SBOLDoc, nested.get(uri), nested));
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.ModuleDefinition.hasModels)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-11607", topLevel.getIdentity());
                }
                models.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else if (namedProperty.getValue() instanceof IdentifiableDocument) {
                if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.Model.Model)) {
                    Model model = parseModel(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue());
                    models.add(model.getIdentity());
                } else {
                    throw new SBOLValidationException("sbol-11607", topLevel.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-11607", topLevel.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.title)) {
            if (!(namedProperty.getValue() instanceof Literal) || name != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10212", topLevel.getIdentity());
            }
            name = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.description)) {
            if (!(namedProperty.getValue() instanceof Literal) || description != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10213", topLevel.getIdentity());
            }
            description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.wasDerivedFrom)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10208", topLevel.getIdentity());
            }
            wasDerivedFroms.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.wasGeneratedBy)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10221", topLevel.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.TopLevel.hasAttachment)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-XXXXX", topLevel.getIdentity());
                }
                attachments.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else if (namedProperty.getValue() instanceof IdentifiableDocument) {
                if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.Attachment.Attachment)) {
                    Attachment attachment = parseAttachment(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue());
                    attachments.add(attachment.getIdentity());
                } else {
                    throw new SBOLValidationException("sbol-XXXXX", topLevel.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-XXXXX", topLevel.getIdentity());
            }
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    // ModuleDefinition moduleDefinition = SBOLDoc.createModuleDefinition(topLevel.getIdentity());
    ModuleDefinition moduleDefinition = new ModuleDefinition(topLevel.getIdentity());
    if (!roles.isEmpty())
        moduleDefinition.setRoles(roles);
    if (persistentIdentity != null)
        moduleDefinition.setPersistentIdentity(persistentIdentity);
    if (version != null)
        moduleDefinition.setVersion(version);
    if (displayId != null)
        moduleDefinition.setDisplayId(displayId);
    if (!functionalComponents.isEmpty())
        moduleDefinition.setFunctionalComponents(functionalComponents);
    if (!interactions.isEmpty())
        moduleDefinition.setInteractions(interactions);
    if (!models.isEmpty())
        moduleDefinition.setModels(models);
    if (!subModules.isEmpty())
        moduleDefinition.setModules(subModules);
    if (name != null)
        moduleDefinition.setName(name);
    if (description != null)
        moduleDefinition.setDescription(description);
    moduleDefinition.setWasDerivedFroms(wasDerivedFroms);
    moduleDefinition.setWasGeneratedBys(wasGeneratedBys);
    moduleDefinition.setAttachments(attachments);
    if (!annotations.isEmpty())
        moduleDefinition.setAnnotations(annotations);
    ModuleDefinition oldM = SBOLDoc.getModuleDefinition(topLevel.getIdentity());
    if (oldM == null) {
        SBOLDoc.addModuleDefinition(moduleDefinition);
    } else {
        if (!moduleDefinition.equals(oldM)) {
            throw new SBOLValidationException("sbol-10202", moduleDefinition);
        }
    }
    return moduleDefinition;
}

Example 5 with FunctionalComponent

use of org.sbolstandard.core2.FunctionalComponent in project libSBOLj by SynBioDex.

the class SBOLDocument method updateReferences.

// TODO: need to update persistentIdentities too
private void updateReferences(HashMap<URI, URI> uriMap) throws SBOLValidationException {
    for (TopLevel topLevel : getTopLevels()) {
        for (URI wasDerivedFrom : topLevel.getWasDerivedFroms()) {
            if (uriMap.get(wasDerivedFrom) != null) {
                topLevel.removeWasDerivedFrom(wasDerivedFrom);
                topLevel.addWasDerivedFrom(uriMap.get(wasDerivedFrom));
            }
        }
        for (URI wasGeneratedBy : topLevel.getWasGeneratedBys()) {
            if (uriMap.get(wasGeneratedBy) != null) {
                topLevel.removeWasGeneratedBy(wasGeneratedBy);
                topLevel.addWasGeneratedBy(uriMap.get(wasGeneratedBy));
            }
        }
        for (URI attachmentURI : topLevel.getAttachmentURIs()) {
            if (uriMap.get(attachmentURI) != null) {
                topLevel.removeAttachment(attachmentURI);
                topLevel.addAttachment(uriMap.get(attachmentURI));
            }
        }
    }
    for (Collection collection : getCollections()) {
        for (URI memberURI : collection.getMemberURIs()) {
            if (uriMap.get(memberURI) != null) {
                collection.removeMember(memberURI);
                collection.addMember(uriMap.get(memberURI));
            }
        }
        updateReferences(collection, uriMap);
    }
    for (ComponentDefinition componentDefinition : getComponentDefinitions()) {
        updateReferences(componentDefinition, uriMap);
        for (Component component : componentDefinition.getComponents()) {
            if (uriMap.get(component.getDefinitionURI()) != null) {
                component.setDefinition(uriMap.get(component.getDefinitionURI()));
                for (MapsTo mapsTo : component.getMapsTos()) {
                    ComponentDefinition cd = getComponentDefinition(component.getDefinitionURI());
                    if (cd != null) {
                        String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
                        URI newURI = URIcompliance.createCompliantURI(cd.getPersistentIdentity().toString(), displayId, cd.getVersion());
                        mapsTo.setRemote(newURI);
                    }
                }
            }
            updateReferences(component, uriMap);
            for (MapsTo mapsTo : component.getMapsTos()) {
                updateReferences(mapsTo, uriMap);
            }
        }
        for (SequenceAnnotation sa : componentDefinition.getSequenceAnnotations()) {
            for (Location loc : sa.getLocations()) {
                updateReferences(loc, uriMap);
            }
            updateReferences(sa, uriMap);
        }
        for (SequenceConstraint sc : componentDefinition.getSequenceConstraints()) {
            updateReferences(sc, uriMap);
        }
        for (URI sequenceURI : componentDefinition.getSequenceURIs()) {
            if (uriMap.get(sequenceURI) != null) {
                componentDefinition.removeSequence(sequenceURI);
                componentDefinition.addSequence(uriMap.get(sequenceURI));
            }
        }
    }
    for (ModuleDefinition moduleDefinition : getModuleDefinitions()) {
        updateReferences(moduleDefinition, uriMap);
        for (FunctionalComponent functionalComponent : moduleDefinition.getFunctionalComponents()) {
            if (uriMap.get(functionalComponent.getDefinitionURI()) != null) {
                functionalComponent.setDefinition(uriMap.get(functionalComponent.getDefinitionURI()));
                for (MapsTo mapsTo : functionalComponent.getMapsTos()) {
                    ComponentDefinition cd = getComponentDefinition(functionalComponent.getDefinitionURI());
                    if (cd != null) {
                        String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
                        URI newURI = URIcompliance.createCompliantURI(cd.getPersistentIdentity().toString(), displayId, cd.getVersion());
                        mapsTo.setRemote(newURI);
                    }
                }
            }
            updateReferences(functionalComponent, uriMap);
            for (MapsTo mapsTo : functionalComponent.getMapsTos()) {
                updateReferences(mapsTo, uriMap);
            }
        }
        for (Module module : moduleDefinition.getModules()) {
            if (uriMap.get(module.getDefinitionURI()) != null) {
                module.setDefinition(uriMap.get(module.getDefinitionURI()));
                for (MapsTo mapsTo : module.getMapsTos()) {
                    ModuleDefinition md = getModuleDefinition(module.getDefinitionURI());
                    if (md != null) {
                        String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
                        URI newURI = URIcompliance.createCompliantURI(md.getPersistentIdentity().toString(), displayId, md.getVersion());
                        mapsTo.setRemote(newURI);
                    }
                }
            }
            updateReferences(module, uriMap);
            for (MapsTo mapsTo : module.getMapsTos()) {
                updateReferences(mapsTo, uriMap);
            }
        }
        for (Interaction interaction : moduleDefinition.getInteractions()) {
            updateReferences(interaction, uriMap);
            for (Participation participation : interaction.getParticipations()) {
                updateReferences(participation, uriMap);
            }
        }
        for (URI modelURI : moduleDefinition.getModelURIs()) {
            if (uriMap.get(modelURI) != null) {
                moduleDefinition.removeModel(modelURI);
                moduleDefinition.addModel(uriMap.get(modelURI));
            }
        }
    }
    for (Model model : getModels()) {
        updateReferences(model, uriMap);
    }
    for (Sequence sequence : getSequences()) {
        updateReferences(sequence, uriMap);
    }
    for (Attachment attachment : getAttachments()) {
        updateReferences(attachment, uriMap);
    }
    for (Implementation implementation : getImplementations()) {
        if (implementation.isSetBuilt()) {
            URI built = implementation.getBuiltURI();
            if (uriMap.get(built) != null) {
                implementation.setBuilt(uriMap.get(built));
            }
        }
        updateReferences(implementation, uriMap);
    }
    for (GenericTopLevel genericTopLevel : getGenericTopLevels()) {
        updateReferences(genericTopLevel, uriMap);
    }
    for (CombinatorialDerivation combinatorialDerivation : getCombinatorialDerivations()) {
        updateReferences(combinatorialDerivation, uriMap);
        if (uriMap.get(combinatorialDerivation.getTemplateURI()) != null) {
            combinatorialDerivation.setTemplate(uriMap.get(combinatorialDerivation.getTemplateURI()));
            ComponentDefinition cd = getComponentDefinition(combinatorialDerivation.getTemplateURI());
            if (cd != null) {
                for (VariableComponent variableComponent : combinatorialDerivation.getVariableComponents()) {
                    String displayId = URIcompliance.extractDisplayId(variableComponent.getVariableURI());
                    URI newURI = URIcompliance.createCompliantURI(cd.getPersistentIdentity().toString(), displayId, cd.getVersion());
                    variableComponent.setVariable(newURI);
                }
            }
        }
        for (VariableComponent variableComponent : combinatorialDerivation.getVariableComponents()) {
            updateReferences(variableComponent, uriMap);
        }
    }
    for (Activity activity : getActivities()) {
        updateReferences(activity, uriMap);
        for (Association association : activity.getAssociations()) {
            if (uriMap.get(association.getAgentURI()) != null) {
                association.setAgent(uriMap.get(association.getAgentURI()));
            }
            if (uriMap.get(association.getPlanURI()) != null) {
                association.setPlan(uriMap.get(association.getPlanURI()));
            }
            updateReferences(association, uriMap);
        }
        for (Usage usage : activity.getUsages()) {
            if (uriMap.get(usage.getEntityURI()) != null) {
                usage.setEntity(uriMap.get(usage.getEntityURI()));
            }
            updateReferences(usage, uriMap);
        }
    }
    for (Agent agent : getAgents()) {
        updateReferences(agent, uriMap);
    }
    for (Plan plan : getPlans()) {
        updateReferences(plan, uriMap);
    }
}