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

Example 31 with SBOLDocument

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

the class SBOLReader method parseAgent.

@SuppressWarnings("unchecked")
private static Agent parseAgent(SBOLDocument SBOLDoc, IdentifiableDocument<QName> topLevel) 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<>();
    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 {
            annotations.add(new Annotation(namedProperty));
        }
    }
    Agent t = new Agent(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);
    t.setAttachments(attachments);
    if (!annotations.isEmpty())
        t.setAnnotations(annotations);
    Agent oldA = SBOLDoc.getAgent(topLevel.getIdentity());
    if (oldA == null) {
        SBOLDoc.addAgent(t);
    } else {
        if (!t.equals(oldA)) {
            throw new SBOLValidationException("sbol-10202", t);
        }
    }
    return t;
}

Example 32 with SBOLDocument

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

the class SBOLReader method parseModule.

/**
 * @param module
 * @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, 11604, 11702; or
 *</li>
 * <li>an SBOL validation rule violation occurred in the following constructor or methods:
 * 	<ul>
 * 		<li>{@link #parseMapsTo(NestedDocument, boolean)},</li>
 * 		<li>{@link Module#Module(URI, URI)},</li>
 * 		<li>{@link Module#setDisplayId(String)},</li>
 * 		<li>{@link Module#setVersion(String)},</li>
 * 		<li>{@link Module#setWasDerivedFrom(URI)},</li>
 * 		<li>{@link Identified#setAnnotations(List)}, or</li>
 * 		<li>{@link Module#setMapsTos(Set)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
@SuppressWarnings("unchecked")
private static Module parseModule(SBOLDocument SBOLDoc, NestedDocument<QName> module, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
    // URIcompliance.extractDisplayId(module.getIdentity());
    String displayId = null;
    String name = null;
    String description = null;
    // URI.create(URIcompliance.extractPersistentId(module.getIdentity()));
    URI persistentIdentity = null;
    String version = null;
    URI definitionURI = null;
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    Set<MapsTo> mappings = new HashSet<>();
    List<Annotation> annotations = new ArrayList<>();
    for (NamedProperty<QName> namedProperty : module.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", module.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", module.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", module.getIdentity());
            }
            displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Module.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-11706", module.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-11706", module.getIdentity());
                }
                mappings.add(parseMapsTo(nested.get(uri), false));
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Module.hasMapping)) {
            System.err.println("Warning: tag should be sbol:mapTo, not sbol:mapping.");
            if (namedProperty.getValue() instanceof NestedDocument) {
                mappings.add(parseMapsTo(((NestedDocument<QName>) namedProperty.getValue()), true));
            } else {
                URI uri = (URI) ((Literal<QName>) namedProperty.getValue()).getValue();
                mappings.add(parseMapsTo(nested.get(uri), true));
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Module.hasDefinition)) {
            if (definitionURI != null) {
                throw new SBOLValidationException("sbol-11702", module.getIdentity());
            }
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-11702", module.getIdentity());
                }
                definitionURI = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
            } else if (namedProperty.getValue() instanceof IdentifiableDocument) {
                if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.ModuleDefinition.ModuleDefinition)) {
                    ModuleDefinition moduleDefinition = parseModuleDefinition(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue(), nested);
                    definitionURI = moduleDefinition.getIdentity();
                } else {
                    throw new SBOLValidationException("sbol-11702", module.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-11702", module.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", module.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", module.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", module.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", module.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    Module submodule = new Module(module.getIdentity(), definitionURI);
    if (persistentIdentity != null)
        submodule.setPersistentIdentity(persistentIdentity);
    if (version != null)
        submodule.setVersion(version);
    if (displayId != null)
        submodule.setDisplayId(displayId);
    if (!mappings.isEmpty())
        submodule.setMapsTos(mappings);
    if (name != null)
        submodule.setName(name);
    if (description != null)
        submodule.setDescription(description);
    submodule.setWasDerivedFroms(wasDerivedFroms);
    submodule.setWasGeneratedBys(wasGeneratedBys);
    if (!annotations.isEmpty())
        submodule.setAnnotations(annotations);
    return submodule;
}

Example 33 with SBOLDocument

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

the class SBOLReader method parseComponent.

/**
 * @param component
 * @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, 10519, 10602, 10607; or
 *</li>
 * <li>an SBOL validation rule violation occurred in the following constructor or methods:
 * 	<ul>
 * 		<li>{@link #parseMapsTo(NestedDocument, boolean)},</li>
 * 		<li>{@link Component#Component(URI, AccessType, URI)},</li>
 * 		<li>{@link Component#setVersion(String)},</li>
 * 		<li>{@link Component#setDisplayId(String)},</li>
 * 		<li>{@link Component#setAccess(AccessType)},</li>
 * 		<li>{@link Component#setMapsTos(Set)},</li>
 * 		<li>{@link Component#setDefinition(URI)},</li>
 * 		<li>{@link Component#setWasDerivedFrom(URI)}, or</li>
 * 		<li>{@link Identified#setAnnotations(List)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
@SuppressWarnings("unchecked")
private static Component parseComponent(SBOLDocument SBOLDoc, NestedDocument<QName> component, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
    // URIcompliance.extractDisplayId(component.getIdentity());
    String displayId = null;
    String name = null;
    String description = null;
    // URI.create(URIcompliance.extractPersistentId(component.getIdentity()));
    URI persistentIdentity = null;
    String version = null;
    URI subComponentURI = null;
    AccessType access = null;
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    Set<URI> roles = new HashSet<>();
    URI roleIntegration = null;
    List<Annotation> annotations = new ArrayList<>();
    Set<MapsTo> mapsTo = new HashSet<>();
    for (NamedProperty<QName> namedProperty : component.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", component.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", component.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", component.getIdentity());
            }
            displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Component.roles)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10702", component.getIdentity());
            }
            roles.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.Component.roleIntegration)) {
            if (!(namedProperty.getValue() instanceof Literal) || roleIntegration != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10708", component.getIdentity());
            }
            roleIntegration = URI.create(((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", component.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", component.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Module.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", component.getIdentity());
                }
                mapsTo.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", component.getIdentity());
                }
                mapsTo.add(parseMapsTo(nested.get(uri), false));
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.ComponentInstance.hasComponentDefinition)) {
            if (subComponentURI != null) {
                throw new SBOLValidationException("sbol-10602", component.getIdentity());
            }
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-10602", component.getIdentity());
                }
                subComponentURI = 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);
                    subComponentURI = componentDefinition.getIdentity();
                } else {
                    throw new SBOLValidationException("sbol-10602", component.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-10602", component.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", component.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", component.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", component.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", component.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    Component c = new Component(component.getIdentity(), access, subComponentURI);
    if (persistentIdentity != null)
        c.setPersistentIdentity(persistentIdentity);
    if (version != null)
        c.setVersion(version);
    if (displayId != null)
        c.setDisplayId(displayId);
    if (access != null)
        c.setAccess(access);
    if (roleIntegration != null)
        try {
            c.setRoleIntegration(RoleIntegrationType.convertToRoleIntegrationType(roleIntegration));
        } catch (SBOLValidationException e) {
            throw new SBOLValidationException("sbol-10708", c);
        }
    if (!roles.isEmpty())
        c.setRoles(roles);
    if (!mapsTo.isEmpty())
        c.setMapsTos(mapsTo);
    if (subComponentURI != null)
        c.setDefinition(subComponentURI);
    if (name != null)
        c.setName(name);
    if (description != null)
        c.setDescription(description);
    c.setWasDerivedFroms(wasDerivedFroms);
    c.setWasGeneratedBys(wasGeneratedBys);
    if (!annotations.isEmpty())
        c.setAnnotations(annotations);
    return c;
}

Example 34 with SBOLDocument

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

the class SBOLReader method parseDnaSequenceV1.

/**
 * @param SBOLDoc
 * @param topLevel
 * @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, String, boolean)},</li>
 * 		<li>{@link Sequence#Sequence(URI, String, URI)},</li>
 * 		<li>{@link Sequence#setVersion(String)},</li>
 * 		<li>{@link Sequence#setWasDerivedFrom(URI)},</li>
 * 		<li>{@link Sequence#setDisplayId(String)},</li>
 * 		<li>{@link Identified#setAnnotations(List)},</li>
 * 		<li>{@link Sequence#setIdentity(URI)}, or </li>
 * 		<li>{@link SBOLDocument#addSequence(Sequence)}; or</li>
 * 	</ul>
 * </li>
 * <li>any of the following SBOL validation rules was violated: 10202, 10204, 10212, 10213.</li>
 * </ul>
 */
private static Sequence parseDnaSequenceV1(SBOLDocument SBOLDoc, IdentifiableDocument<QName> topLevel) throws SBOLValidationException {
    String elements = null;
    String displayId = null;
    String name = null;
    String description = null;
    URI identity = topLevel.getIdentity();
    URI persistentIdentity = topLevel.getIdentity();
    URI encoding = Sequence.IUPAC_DNA;
    List<Annotation> annotations = new ArrayList<>();
    if (URIPrefix != null) {
        displayId = URIcompliance.findDisplayId(topLevel.getIdentity().toString());
        identity = createCompliantURI(URIPrefix, TopLevel.SEQUENCE, displayId, version, typesInURI);
        persistentIdentity = createCompliantURI(URIPrefix, TopLevel.SEQUENCE, displayId, "", typesInURI);
    }
    for (NamedProperty<QName> namedProperty : topLevel.getProperties()) {
        if (namedProperty.getName().equals(Sbol1Terms.DNASequence.nucleotides)) {
            elements = ((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();
            if (URIPrefix != null) {
                identity = createCompliantURI(URIPrefix, TopLevel.SEQUENCE, displayId, version, typesInURI);
            }
        } 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 {
            annotations.add(new Annotation(namedProperty));
        }
    }
    Sequence sequence = new Sequence(identity, elements, encoding);
    if (persistentIdentity != null) {
        sequence.setPersistentIdentity(persistentIdentity);
        sequence.setVersion(version);
    }
    if (identity != topLevel.getIdentity())
        sequence.addWasDerivedFrom(topLevel.getIdentity());
    if (displayId != null)
        sequence.setDisplayId(displayId);
    if (name != null)
        sequence.setName(name);
    if (description != null)
        sequence.setDescription(description);
    if (!annotations.isEmpty())
        sequence.setAnnotations(annotations);
    Sequence oldS = SBOLDoc.getSequence(identity);
    if (oldS == null) {
        SBOLDoc.addSequence(sequence);
    } else if (sequence.getWasDerivedFroms().size() > 0 && oldS.getWasDerivedFroms().size() > 0 && !sequence.getWasDerivedFroms().equals(oldS.getWasDerivedFroms())) {
        URI wasDerivedFrom = (URI) sequence.getWasDerivedFroms().toArray()[0];
        Set<TopLevel> topLevels = SBOLDoc.getByWasDerivedFrom(wasDerivedFrom);
        for (TopLevel top : topLevels) {
            if (top instanceof Sequence) {
                return (Sequence) top;
            }
        }
        do {
            displayId = displayId + "_";
            identity = createCompliantURI(URIPrefix, TopLevel.SEQUENCE, displayId, version, typesInURI);
            persistentIdentity = createCompliantURI(URIPrefix, TopLevel.SEQUENCE, displayId, "", typesInURI);
        } while (SBOLDoc.getSequence(identity) != null);
        sequence.setIdentity(identity);
        sequence.setDisplayId(displayId);
        sequence.setPersistentIdentity(persistentIdentity);
        SBOLDoc.addSequence(sequence);
    } else if (dropObjectsWithDuplicateURIs) {
        return oldS;
    } else {
        if (!sequence.equals(oldS)) {
            throw new SBOLValidationException("sbol-10202", sequence);
        }
    }
    return sequence;
}

Example 35 with SBOLDocument

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

the class SBOLReader method parseCollection.

/**
 * @param SBOLDoc
 * @param topLevel
 * @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, 12102; or</li>
 * <li>an SBOL validation rule violation occurred in the following constructor or methods:
 * 	<ul>
 * 		<li>{@link Collection#Collection(URI)}, </li>
 * 		<li>{@link Collection#setDisplayId(String)}, </li>
 * 		<li>{@link Collection#setVersion(String)}, </li>
 * 		<li>{@link Collection#setMembers(Set)}, </li>
 * 		<li>{@link Collection#setWasDerivedFrom(URI)}, </li>
 * 		<li>{@link Identified#setAnnotations(List)}, or</li>
 * 		<li>{@link SBOLDocument#addCollection(Collection)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
@SuppressWarnings({ "rawtypes", "unchecked" })
private static Collection parseCollection(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> members = 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.Collection.hasMembers)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-12102", topLevel.getIdentity());
                }
                members.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else if (namedProperty.getValue() instanceof NestedDocument) {
                if (((IdentifiableDocument) namedProperty).getType().equals(Sbol2Terms.Collection.Collection))
                    parseCollection(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.ModuleDefinition.ModuleDefinition))
                    parseModuleDefinition(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Model.Model))
                    parseModel(SBOLDoc, (IdentifiableDocument) namedProperty);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Sequence.Sequence))
                    parseSequence(SBOLDoc, (IdentifiableDocument) namedProperty);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.ComponentDefinition.ComponentDefinition))
                    parseComponentDefinition(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.CombinatorialDerivation.CombinatorialDerivation))
                    parseCombinatorialDerivation(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Implementation.Implementation))
                    parseImplementation(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Attachment.Attachment))
                    parseAttachment(SBOLDoc, (IdentifiableDocument) namedProperty);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Activity.Activity))
                    parseActivity(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Agent.Agent))
                    parseAgent(SBOLDoc, (IdentifiableDocument) namedProperty);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Plan.Plan))
                    parsePlan(SBOLDoc, (IdentifiableDocument) namedProperty);
                else
                    parseGenericTopLevel(SBOLDoc, (IdentifiableDocument) namedProperty);
            } else {
                throw new SBOLValidationException("sbol-12102", 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));
        }
    }
    Collection c = new Collection(topLevel.getIdentity());
    if (displayId != null)
        c.setDisplayId(displayId);
    if (version != null)
        c.setVersion(version);
    if (persistentIdentity != null)
        c.setPersistentIdentity(persistentIdentity);
    if (!members.isEmpty())
        c.setMembers(members);
    if (name != null)
        c.setName(name);
    if (description != null)
        c.setDescription(description);
    c.setWasDerivedFroms(wasDerivedFroms);
    c.setWasGeneratedBys(wasGeneratedBys);
    c.setAttachments(attachments);
    if (!annotations.isEmpty())
        c.setAnnotations(annotations);
    Collection oldC = SBOLDoc.getCollection(topLevel.getIdentity());
    if (oldC == null) {
        SBOLDoc.addCollection(c);
    } else {
        if (!c.equals(oldC)) {
            throw new SBOLValidationException("sbol-10202", c);
        }
    }
    return c;
}