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

Example 6 with Annotation

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

the class AnnotationTest method test_pubConstructors.

@Test
public void test_pubConstructors() throws SBOLValidationException, URISyntaxException {
    Annotation CD_annot = gRNA_b_gene.createAnnotation(new QName(prURI, "protein", "pr"), true);
    assertTrue(gRNA_b_gene.getAnnotation(CD_annot.getQName()).getBooleanValue());
    assertTrue(gRNA_b_gene.getAnnotations().size() == 1);
    assertTrue(CD_annot.isBooleanValue());
    CD_annot.setBooleanValue(false);
    assertFalse(gRNA_b_gene.getAnnotation(CD_annot.getQName()).getBooleanValue());
    gRNA_b_gene.removeAnnotation(CD_annot);
    assertTrue(gRNA_b_gene.getAnnotations().size() == 0);
    // test constructor with double
    CD_annot = gRNA_b_gene.createAnnotation(new QName(prURI, "protein", "pr"), 1.0);
    assertTrue(gRNA_b_gene.getAnnotation(CD_annot.getQName()).getDoubleValue() == 1.0);
    assertTrue(gRNA_b_gene.getAnnotations().size() == 1);
    assertTrue(CD_annot.isDoubleValue());
    CD_annot.setDoubleValue(5.0);
    assertTrue(CD_annot.getDoubleValue() == 5.0);
    gRNA_b_gene.removeAnnotation(CD_annot);
    assertTrue(gRNA_b_gene.getAnnotations().size() == 0);
    // test constructor with int
    CD_annot = gRNA_b_gene.createAnnotation(new QName(prURI, "protein", "pr"), 2);
    assertTrue(gRNA_b_gene.getAnnotation(CD_annot.getQName()).getIntegerValue() == 2);
    assertTrue(gRNA_b_gene.getAnnotations().size() == 1);
    assertTrue(CD_annot.isIntegerValue());
    CD_annot.setIntegerValue(7);
    assertTrue(CD_annot.getIntegerValue() == 7);
    gRNA_b_gene.removeAnnotation(CD_annot);
    assertTrue(gRNA_b_gene.getAnnotations().size() == 0);
    // test constructor with string
    CD_annot = gRNA_b_gene.createAnnotation(new QName(prURI, "protein", "pr"), "protein");
    assertTrue(gRNA_b_gene.getAnnotation(CD_annot.getQName()).getStringValue().equals("protein"));
    assertTrue(gRNA_b_gene.getAnnotations().size() == 1);
    assertTrue(CD_annot.isStringValue());
    CD_annot.setStringValue("notAProtein");
    assertTrue(CD_annot.getStringValue().equals("notAProtein"));
    gRNA_b_gene.removeAnnotation(CD_annot);
    assertTrue(gRNA_b_gene.getAnnotations().size() == 0);
    // test constructor with URI
    CD_annot = gRNA_b_gene.createAnnotation(new QName(prURI, "protein", "pr"), new URI("http://www.sbolstandard.org/protein"));
    assertTrue(gRNA_b_gene.getAnnotation(CD_annot.getQName()).getURIValue().equals(new URI("http://www.sbolstandard.org/protein")));
    assertTrue(gRNA_b_gene.getAnnotations().size() == 1);
    assertTrue(CD_annot.isURIValue());
    CD_annot.setURIValue(new URI("http://www.sbolstandard.org/gene"));
    assertTrue(CD_annot.getURIValue().equals(new URI("http://www.sbolstandard.org/gene")));
    gRNA_b_gene.removeAnnotation(CD_annot);
    assertTrue(gRNA_b_gene.getAnnotations().size() == 0);
}

Example 7 with Annotation

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

the class SBOLReader method parseSequenceConstraint.

private static SequenceConstraint parseSequenceConstraint(NestedDocument<QName> sequenceConstraint) throws SBOLValidationException {
    // URIcompliance.extractDisplayId(sequenceConstraint.getIdentity());
    String displayId = null;
    String name = null;
    String description = null;
    // URI.create(URIcompliance.extractPersistentId(sequenceConstraint.getIdentity()));
    URI persistentIdentity = null;
    URI restriction = null;
    URI subject = null;
    URI object = null;
    String version = null;
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    List<Annotation> annotations = new ArrayList<>();
    for (NamedProperty<QName> namedProperty : sequenceConstraint.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", sequenceConstraint.getIdentity());
            }
            persistentIdentity = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.SequenceConstraint.restriction)) {
            if (!(namedProperty.getValue() instanceof Literal) || restriction != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-11407", sequenceConstraint.getIdentity());
            }
            restriction = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.SequenceConstraint.hasSubject)) {
            if (!(namedProperty.getValue() instanceof Literal) || subject != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-11402", sequenceConstraint.getIdentity());
            }
            subject = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.SequenceConstraint.hasObject)) {
            if (!(namedProperty.getValue() instanceof Literal) || object != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-11404", sequenceConstraint.getIdentity());
            }
            object = URI.create(((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", sequenceConstraint.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", sequenceConstraint.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", sequenceConstraint.getIdentity());
            }
            description = ((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", sequenceConstraint.getIdentity());
            }
            version = ((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", sequenceConstraint.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", sequenceConstraint.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    SequenceConstraint s = new SequenceConstraint(sequenceConstraint.getIdentity(), restriction, subject, object);
    if (displayId != null)
        s.setDisplayId(displayId);
    if (name != null)
        s.setName(name);
    if (description != null)
        s.setDescription(description);
    if (persistentIdentity != null)
        s.setPersistentIdentity(persistentIdentity);
    if (version != null)
        s.setVersion(version);
    s.setWasDerivedFroms(wasDerivedFroms);
    s.setWasGeneratedBys(wasGeneratedBys);
    if (!annotations.isEmpty())
        s.setAnnotations(annotations);
    return s;
}

Example 8 with Annotation

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

the class SBOLReader method parseGenericLocation.

/**
 * @param typeGenLoc
 * @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,
 * 11002; or
 *</li>
 * <li>an SBOL validation rule violation occurred in the following constructor or methods:
 * 	<ul>
 * 		<li>{@link GenericLocation#GenericLocation(URI)},</li>
 * 		<li>{@link GenericLocation#setDisplayId(String)},</li>
 * 		<li>{@link GenericLocation#setVersion(String)},</li>
 * 		<li>{@link GenericLocation#setWasDerivedFrom(URI)}, or</li>
 * 		<li>{@link Identified#setAnnotations(List)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
private static GenericLocation parseGenericLocation(NestedDocument<QName> typeGenLoc) throws SBOLValidationException {
    // URIcompliance.extractDisplayId(typeGenLoc.getIdentity());
    String displayId = null;
    String name = null;
    String description = null;
    // URI.create(URIcompliance.extractPersistentId(typeGenLoc.getIdentity()));
    URI persistentIdentity = null;
    URI orientation = null;
    String version = null;
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    List<Annotation> annotations = new ArrayList<>();
    for (NamedProperty<QName> namedProperty : typeGenLoc.getProperties()) {
        if (namedProperty.getName().equals(Sbol2Terms.GenericLocation.orientation) || namedProperty.getName().equals(Sbol2Terms.GenericLocation.Orientation)) {
            if (!(namedProperty.getValue() instanceof Literal) || orientation != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-11002", typeGenLoc.getIdentity());
            }
            orientation = URI.create(((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", typeGenLoc.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", typeGenLoc.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", typeGenLoc.getIdentity());
            }
            description = ((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", typeGenLoc.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", typeGenLoc.getIdentity());
            }
            version = ((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", typeGenLoc.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", typeGenLoc.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    GenericLocation gl = new GenericLocation(typeGenLoc.getIdentity());
    if (displayId != null)
        gl.setDisplayId(displayId);
    if (name != null)
        gl.setName(name);
    if (description != null)
        gl.setDescription(description);
    if (orientation != null)
        try {
            gl.setOrientation(OrientationType.convertToOrientationType(orientation));
        } catch (SBOLValidationException e) {
            throw new SBOLValidationException("sbol-11002", gl);
        }
    if (persistentIdentity != null)
        gl.setPersistentIdentity(persistentIdentity);
    if (version != null)
        gl.setVersion(version);
    gl.setWasDerivedFroms(wasDerivedFroms);
    gl.setWasGeneratedBys(wasGeneratedBys);
    if (!annotations.isEmpty())
        gl.setAnnotations(annotations);
    return gl;
}

Example 9 with Annotation

use of org.sbolstandard.core2.Annotation 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;
}

Example 10 with Annotation

use of org.sbolstandard.core2.Annotation 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;
}