Examples with NestedDocument org.sbolstandard.core.datatree.NestedDocument used on opensource projects

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Example 1 with NestedDocument

use of org.sbolstandard.core.datatree.NestedDocument in project libSBOLj by SynBioDex.

the class SBOLReader method parseCombinatorialDerivation.

/**
 * @param SBOLDoc
 * @param topLevel
 * @param nested
 * @return
 */
@SuppressWarnings("unchecked")
private static CombinatorialDerivation parseCombinatorialDerivation(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;
    URI template = null;
    StrategyType strategy = null;
    String version = null;
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    Set<URI> attachments = new HashSet<>();
    Set<VariableComponent> variableComponents = new HashSet<>();
    List<Annotation> annotations = new ArrayList<>();
    for (NamedProperty<QName> namedProperty : topLevel.getProperties()) {
        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.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.CombinatorialDerivation.template)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-12904", topLevel.getIdentity());
                }
                template = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
            } else if (namedProperty.getValue() instanceof IdentifiableDocument) {
                if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.ComponentDefinition.ComponentDefinition)) {
                    ComponentDefinition cd = parseComponentDefinition(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue(), nested);
                    template = cd.getIdentity();
                } else {
                    throw new SBOLValidationException("sbol-12904", topLevel.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-12904", topLevel.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.CombinatorialDerivation.strategy)) {
            if (!(namedProperty.getValue() instanceof Literal) || strategy != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-12902", topLevel.getIdentity());
            }
            String strategyTypeStr = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
            try {
                strategy = StrategyType.convertToStrategyType(URI.create(strategyTypeStr));
            } catch (SBOLValidationException e) {
                throw new SBOLValidationException("sbol-12902", topLevel.getIdentity());
            }
        } 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.CombinatorialDerivation.hasVariableComponent)) {
            if (namedProperty.getValue() instanceof NestedDocument) {
                NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
                if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.VariableComponent.VariableComponent)) {
                    throw new SBOLValidationException("sbol-12906", topLevel.getIdentity());
                }
                variableComponents.add(parseVariableComponent(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.VariableComponent.VariableComponent)) {
                    throw new SBOLValidationException("sbol-12906", topLevel.getIdentity());
                }
                variableComponents.add(parseVariableComponent(SBOLDoc, nested.get(uri), nested));
            }
        } 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));
        }
    }
    CombinatorialDerivation c = new CombinatorialDerivation(topLevel.getIdentity(), template);
    if (strategy != null)
        c.setStrategy(strategy);
    if (displayId != null)
        c.setDisplayId(displayId);
    if (persistentIdentity != null)
        c.setPersistentIdentity(persistentIdentity);
    if (name != null)
        c.setName(name);
    if (!variableComponents.isEmpty())
        c.setVariableComponents(variableComponents);
    if (description != null)
        c.setDescription(description);
    if (!annotations.isEmpty())
        c.setAnnotations(annotations);
    if (version != null)
        c.setVersion(version);
    c.setWasDerivedFroms(wasDerivedFroms);
    c.setWasGeneratedBys(wasGeneratedBys);
    c.setAttachments(attachments);
    CombinatorialDerivation oldC = SBOLDoc.getCombinatorialDerivation(topLevel.getIdentity());
    if (oldC == null) {
        SBOLDoc.addCombinatorialDerivation(c);
    } else {
        if (!c.equals(oldC)) {
            throw new SBOLValidationException("sbol-10202", c);
        }
    }
    return c;
}
Also used : StringifyQName(org.sbolstandard.core.io.json.StringifyQName) QName(javax.xml.namespace.QName) ArrayList(java.util.ArrayList) URIcompliance.createCompliantURI(org.sbolstandard.core2.URIcompliance.createCompliantURI) URI(java.net.URI) NestedDocument(org.sbolstandard.core.datatree.NestedDocument) IdentifiableDocument(org.sbolstandard.core.datatree.IdentifiableDocument) Literal(org.sbolstandard.core.datatree.Literal) HashSet(java.util.HashSet)

Example 2 with NestedDocument

use of org.sbolstandard.core.datatree.NestedDocument 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;
}
Also used : StringifyQName(org.sbolstandard.core.io.json.StringifyQName) QName(javax.xml.namespace.QName) ArrayList(java.util.ArrayList) URIcompliance.createCompliantURI(org.sbolstandard.core2.URIcompliance.createCompliantURI) URI(java.net.URI) NestedDocument(org.sbolstandard.core.datatree.NestedDocument) IdentifiableDocument(org.sbolstandard.core.datatree.IdentifiableDocument) Literal(org.sbolstandard.core.datatree.Literal) HashSet(java.util.HashSet)

Example 3 with NestedDocument

use of org.sbolstandard.core.datatree.NestedDocument 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;
}
Also used : StringifyQName(org.sbolstandard.core.io.json.StringifyQName) QName(javax.xml.namespace.QName) ArrayList(java.util.ArrayList) URIcompliance.createCompliantURI(org.sbolstandard.core2.URIcompliance.createCompliantURI) URI(java.net.URI) NestedDocument(org.sbolstandard.core.datatree.NestedDocument) IdentifiableDocument(org.sbolstandard.core.datatree.IdentifiableDocument) Literal(org.sbolstandard.core.datatree.Literal) HashSet(java.util.HashSet)

Example 4 with NestedDocument

use of org.sbolstandard.core.datatree.NestedDocument in project libSBOLj by SynBioDex.

the class SBOLReader method parseActivity.

@SuppressWarnings("unchecked")
private static Activity parseActivity(SBOLDocument SBOLDoc, IdentifiableDocument<QName> topLevel, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
    String displayId = null;
    String name = null;
    String description = null;
    URI persistentIdentity = null;
    String version = null;
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    Set<URI> attachments = new HashSet<>();
    DateTime startedAtTime = null;
    DateTime endedAtTime = null;
    Set<URI> wasInformedBys = new HashSet<>();
    Set<Association> qualifiedAssociations = new HashSet<>();
    Set<Usage> qualifiedUsages = 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.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 if (namedProperty.getName().equals(Sbol2Terms.Activity.startedAtTime)) {
            if (!(namedProperty.getValue() instanceof Literal) || startedAtTime != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-12402", topLevel.getIdentity());
            }
            DateTimeFormatter fmt = ISODateTimeFormat.dateTime();
            try {
                startedAtTime = fmt.parseDateTime(((Literal<QName>) namedProperty.getValue()).getValue().toString());
            } catch (IllegalArgumentException e) {
                throw new SBOLValidationException("sbol-12402", topLevel.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Activity.endedAtTime)) {
            if (!(namedProperty.getValue() instanceof Literal) || endedAtTime != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-12403", topLevel.getIdentity());
            }
            DateTimeFormatter fmt = ISODateTimeFormat.dateTime();
            try {
                endedAtTime = fmt.parseDateTime(((Literal<QName>) namedProperty.getValue()).getValue().toString());
            } catch (IllegalArgumentException e) {
                throw new SBOLValidationException("sbol-12403", topLevel.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Activity.wasInformedBy)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-12406", topLevel.getIdentity());
                }
                wasInformedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else if (namedProperty.getValue() instanceof IdentifiableDocument) {
                if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.Activity.Activity)) {
                    Activity activity = parseActivity(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue(), nested);
                    wasInformedBys.add(activity.getIdentity());
                } else {
                    throw new SBOLValidationException("sbol-12406", topLevel.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-12406", topLevel.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Activity.qualifiedAssociation)) {
            if (namedProperty.getValue() instanceof NestedDocument) {
                NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
                if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.Association.Association)) {
                    throw new SBOLValidationException("sbol-12404", topLevel.getIdentity());
                }
                qualifiedAssociations.add(parseAssociation(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.Association.Association)) {
                    throw new SBOLValidationException("sbol-12404", topLevel.getIdentity());
                }
                qualifiedAssociations.add(parseAssociation(SBOLDoc, nestedDocument, nested));
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Activity.qualifiedUsage)) {
            if (namedProperty.getValue() instanceof NestedDocument) {
                NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
                if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.Usage.Usage)) {
                    throw new SBOLValidationException("sbol-12405", topLevel.getIdentity());
                }
                qualifiedUsages.add(parseUsage(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.Usage.Usage)) {
                    throw new SBOLValidationException("sbol-12405", topLevel.getIdentity());
                }
                qualifiedUsages.add(parseUsage(SBOLDoc, nestedDocument, nested));
            }
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    // GenericTopLevel t = SBOLDoc.createGenericTopLevel(topLevel.getIdentity(), topLevel.getType());
    Activity t = new Activity(topLevel.getIdentity());
    if (persistentIdentity != null)
        t.setPersistentIdentity(persistentIdentity);
    if (version != null)
        t.setVersion(version);
    if (displayId != null)
        t.setDisplayId(displayId);
    if (name != null)
        t.setName(name);
    if (description != null)
        t.setDescription(description);
    t.setWasDerivedFroms(wasDerivedFroms);
    t.setWasGeneratedBys(wasGeneratedBys);
    if (!annotations.isEmpty())
        t.setAnnotations(annotations);
    if (startedAtTime != null)
        t.setStartedAtTime(startedAtTime);
    if (endedAtTime != null)
        t.setEndedAtTime(endedAtTime);
    if (!qualifiedAssociations.isEmpty())
        t.setAssociations(qualifiedAssociations);
    if (!qualifiedUsages.isEmpty())
        t.setUsages(qualifiedUsages);
    if (!wasInformedBys.isEmpty())
        t.setWasInformedBys(wasInformedBys);
    if (!attachments.isEmpty())
        t.setAttachments(attachments);
    Activity oldA = SBOLDoc.getActivity(topLevel.getIdentity());
    if (oldA == null) {
        SBOLDoc.addActivity(t);
    } else {
        if (!t.equals(oldA)) {
            throw new SBOLValidationException("sbol-10202", t);
        }
    }
    return t;
}
Also used : StringifyQName(org.sbolstandard.core.io.json.StringifyQName) QName(javax.xml.namespace.QName) ArrayList(java.util.ArrayList) URIcompliance.createCompliantURI(org.sbolstandard.core2.URIcompliance.createCompliantURI) URI(java.net.URI) NestedDocument(org.sbolstandard.core.datatree.NestedDocument) DateTime(org.joda.time.DateTime) IdentifiableDocument(org.sbolstandard.core.datatree.IdentifiableDocument) Literal(org.sbolstandard.core.datatree.Literal) DateTimeFormatter(org.joda.time.format.DateTimeFormatter) HashSet(java.util.HashSet)

Example 5 with NestedDocument

use of org.sbolstandard.core.datatree.NestedDocument in project libSBOLj by SynBioDex.

the class SBOLReader method parseSequenceAnnotationV1.

/**
 * @param SBOLDoc
 * @param sequenceAnnotation
 * @param precedePairs
 * @param parentURI
 * @param sa_num
 * @param instantiatedComponents
 * @return
 * @throws SBOLValidationException if either of the following conditions is satisfied:
 * <ul>
 * <li>if an SBOL validation rule violation occurred in any of the following constructors or methods:
 * 	<ul>
 * 		<li>{@link URIcompliance#createCompliantURI(String, String, String)}, </li>
 * 		<li>{@link #parseDnaComponentV1(SBOLDocument, IdentifiableDocument)}, </li>
 * 		<li>{@link Range#Range(URI, int, int)}, </li>
 * 		<li>{@link Range#setDisplayId(String)}, </li>
 * 		<li>{@link Range#setVersion(String)}, </li>
 * 		<li>{@link GenericLocation#GenericLocation(URI)}, </li>
 * 		<li>{@link SequenceAnnotation#SequenceAnnotation(URI, Set)}, </li>
 * 		<li>{@link SequenceAnnotation#setDisplayId(String)}, </li>
 * 		<li>{@link SequenceAnnotation#setVersion(String)}, </li>
 * 		<li>{@link SequenceAnnotation#setWasDerivedFrom(URI)}, </li>
 * 		<li>{@link SequenceAnnotation#setComponent(URI)}, or </li>
 * 		<li>{@link SequenceAnnotation#setAnnotations(List)}; or</li>
 * 	</ul>
 * </li>
 * <li>the following SBOL validation rule was violated: 11002.</li>
 * </ul>
 * @throws SBOLConversionException
 */
private static SequenceAnnotation parseSequenceAnnotationV1(SBOLDocument SBOLDoc, NestedDocument<QName> sequenceAnnotation, List<SBOLPair> precedePairs, String parentURI, int sa_num, Set<String> instantiatedComponents) throws SBOLValidationException, SBOLConversionException {
    Integer start = null;
    Integer end = null;
    String strand = null;
    URI componentURI = null;
    URI identity = sequenceAnnotation.getIdentity();
    String persIdentity = sequenceAnnotation.getIdentity().toString();
    List<Annotation> annotations = new ArrayList<>();
    if (URIPrefix != null) {
        persIdentity = createCompliantURI(parentURI, "annotation" + sa_num, "").toString();
        identity = createCompliantURI(parentURI, "annotation" + sa_num, version);
    }
    if (!sequenceAnnotation.getType().equals(Sbol1Terms.SequenceAnnotations.SequenceAnnotation)) {
        throw new SBOLConversionException("QName has to be" + Sbol1Terms.SequenceAnnotations.SequenceAnnotation.toString());
    }
    for (NamedProperty<QName> namedProperty : sequenceAnnotation.getProperties()) {
        if (namedProperty.getName().equals(Sbol1Terms.SequenceAnnotations.bioStart)) {
            if (!(namedProperty.getValue() instanceof Literal) || start != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-11102", sequenceAnnotation.getIdentity());
            }
            String temp = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
            start = Integer.parseInt(temp);
        } else if (namedProperty.getName().equals(Sbol1Terms.SequenceAnnotations.bioEnd)) {
            if (!(namedProperty.getValue() instanceof Literal) || end != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-11103", sequenceAnnotation.getIdentity());
            }
            String temp2 = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
            end = Integer.parseInt(temp2);
        } else if (namedProperty.getName().equals(Sbol1Terms.SequenceAnnotations.strand)) {
            if (!(namedProperty.getValue() instanceof Literal) || strand != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-11002", sequenceAnnotation.getIdentity());
            }
            strand = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol1Terms.SequenceAnnotations.subComponent)) {
            if (componentURI != null) {
                throw new SBOLValidationException("sbol-10904", sequenceAnnotation.getIdentity());
            }
            if (namedProperty.getValue() instanceof NestedDocument) {
                componentURI = parseDnaComponentV1(SBOLDoc, (NestedDocument<QName>) namedProperty.getValue()).getIdentity();
            } else {
                if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                    throw new SBOLValidationException("sbol-10904", sequenceAnnotation.getIdentity());
                }
                componentURI = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
            }
        } else if (namedProperty.getName().equals(Sbol1Terms.SequenceAnnotations.precedes)) {
            URI left = sequenceAnnotation.getIdentity();
            URI right = null;
            if (namedProperty.getValue() instanceof NestedDocument) {
                // TODO: need to check if ++sa_num here okay
                right = parseSequenceAnnotationV1(SBOLDoc, (NestedDocument<QName>) namedProperty.getValue(), precedePairs, parentURI, ++sa_num, instantiatedComponents).getIdentity();
            } else {
                if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                    throw new SBOLValidationException("sbol-11404", sequenceAnnotation.getIdentity());
                }
                right = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
            }
            SBOLPair pair = new SBOLPair(left, right);
            precedePairs.add(pair);
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    String componentDisplayId = URIcompliance.extractDisplayId(componentURI);
    String displayId = "annotation" + sa_num;
    if (compliant && componentDisplayId != null && !instantiatedComponents.contains(componentDisplayId)) {
        identity = createCompliantURI(parentURI, componentDisplayId + "_annotation", version);
        persIdentity = createCompliantURI(parentURI, componentDisplayId + "_annotation", "").toString();
        displayId = componentDisplayId + "_annotation";
    }
    // Note: Do not create a seqAnnotation if Location is empty
    Location location = null;
    if (// create SequenceAnnotation & Component
    start != null && end != null) {
        URI range_identity = createCompliantURI(persIdentity, "range", version);
        location = new Range(range_identity, start, end);
        if (!persIdentity.equals("")) {
            location.setPersistentIdentity(createCompliantURI(persIdentity, "range", ""));
            location.setDisplayId("range");
            location.setVersion(version);
        }
        if (strand != null) {
            if (strand.equals("+")) {
                location.setOrientation(OrientationType.INLINE);
            } else if (strand.equals("-")) {
                location.setOrientation(OrientationType.REVERSECOMPLEMENT);
            }
        }
    } else {
        URI dummyGenericLoc_id = createCompliantURI(persIdentity, "genericLocation", version);
        location = new GenericLocation(dummyGenericLoc_id);
        if (!persIdentity.equals("")) {
            location.setPersistentIdentity(createCompliantURI(persIdentity, "genericLocation", ""));
            location.setDisplayId("genericLocation");
            location.setVersion(version);
        }
        if (strand != null) {
            if (strand.equals("+")) {
                location.setOrientation(OrientationType.INLINE);
            } else if (strand.equals("-")) {
                location.setOrientation(OrientationType.REVERSECOMPLEMENT);
            }
        }
    }
    Set<Location> locations = new HashSet<>();
    locations.add(location);
    SequenceAnnotation s = new SequenceAnnotation(identity, locations);
    if (!persIdentity.equals("")) {
        s.setPersistentIdentity(URI.create(persIdentity));
        s.setDisplayId(displayId);
        s.setVersion(version);
    }
    if (identity != sequenceAnnotation.getIdentity())
        s.addWasDerivedFrom(sequenceAnnotation.getIdentity());
    if (componentURI != null)
        s.setComponent(componentURI);
    if (!annotations.isEmpty())
        s.setAnnotations(annotations);
    return s;
}
Also used : StringifyQName(org.sbolstandard.core.io.json.StringifyQName) QName(javax.xml.namespace.QName) ArrayList(java.util.ArrayList) URIcompliance.createCompliantURI(org.sbolstandard.core2.URIcompliance.createCompliantURI) URI(java.net.URI) NestedDocument(org.sbolstandard.core.datatree.NestedDocument) Literal(org.sbolstandard.core.datatree.Literal) HashSet(java.util.HashSet)

Aggregations

URI (java.net.URI)16 ArrayList (java.util.ArrayList)16 NestedDocument (org.sbolstandard.core.datatree.NestedDocument)16 QName (javax.xml.namespace.QName)15 StringifyQName (org.sbolstandard.core.io.json.StringifyQName)15 HashSet (java.util.HashSet)13 Literal (org.sbolstandard.core.datatree.Literal)13 URIcompliance.createCompliantURI (org.sbolstandard.core2.URIcompliance.createCompliantURI)13 IdentifiableDocument (org.sbolstandard.core.datatree.IdentifiableDocument)9 NamedProperty (org.sbolstandard.core.datatree.Datatree.NamedProperty)3 NestedDocument (org.sbolstandard.core.datatree.Datatree.NestedDocument)3 NamedProperty (org.sbolstandard.core.datatree.NamedProperty)3 HashMap (java.util.HashMap)1 Set (java.util.Set)1 DateTime (org.joda.time.DateTime)1 DateTimeFormatter (org.joda.time.format.DateTimeFormatter)1
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