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

Search in sources :

Example 16 with IdentifiableDocument

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

the class SBOLReader method parseAttachment.

@SuppressWarnings("unchecked")
private static Attachment parseAttachment(SBOLDocument SBOLDoc, IdentifiableDocument<QName> topLevel) 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;
    URI source = null;
    URI format = null;
    Long size = null;
    String hash = 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.Attachment.source)) {
            if (!(namedProperty.getValue() instanceof Literal) || source != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-13202", topLevel.getIdentity());
            }
            source = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.Attachment.format)) {
            if (!(namedProperty.getValue() instanceof Literal) || format != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-13204", topLevel.getIdentity());
            }
            format = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.Attachment.size)) {
            if (!(namedProperty.getValue() instanceof Literal) || size != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-13207", topLevel.getIdentity());
            }
            size = Long.valueOf(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.Attachment.hash)) {
            if (!(namedProperty.getValue() instanceof Literal) || hash != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-13208", topLevel.getIdentity());
            }
            hash = ((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));
        }
    }
    Attachment a = new Attachment(topLevel.getIdentity(), source);
    if (persistentIdentity != null)
        a.setPersistentIdentity(persistentIdentity);
    if (version != null)
        a.setVersion(version);
    if (displayId != null)
        a.setDisplayId(displayId);
    if (name != null)
        a.setName(name);
    if (description != null)
        a.setDescription(description);
    a.setWasDerivedFroms(wasDerivedFroms);
    a.setWasGeneratedBys(wasGeneratedBys);
    a.setAttachments(attachments);
    if (!annotations.isEmpty())
        a.setAnnotations(annotations);
    if (format != null)
        a.setFormat(format);
    if (size != null)
        a.setSize(size);
    if (hash != null)
        a.setHash(hash);
    Attachment oldA = SBOLDoc.getAttachment(topLevel.getIdentity());
    if (oldA == null) {
        SBOLDoc.addAttachment(a);
    } else {
        if (!a.equals(oldA)) {
            throw new SBOLValidationException("sbol-10202", a);
        }
    }
    return a;
}
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) IdentifiableDocument(org.sbolstandard.core.datatree.IdentifiableDocument) Literal(org.sbolstandard.core.datatree.Literal) HashSet(java.util.HashSet)

Example 17 with IdentifiableDocument

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

the class SBOLReader method parseModel.

/**
 * @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, 10502, 10504, 10508; or</li>
 * <li>an SBOL validation rule violation occurred in the following constructor or methods:
 * 	<ul>
 * 		<li>{@link Model#Model(URI, URI, URI, URI)}, </li>
 * 		<li>{@link Model#setDisplayId(String)}, </li>
 * 		<li>{@link Model#setVersion(String)}, </li>
 * 		<li>{@link Model#setWasDerivedFrom(URI)}, </li>
 * 		<li>{@link Identified#setAnnotations(List)}, or</li>
 * 		<li>{@link SBOLDocument#addModel(Model)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
@SuppressWarnings("unchecked")
private static Model parseModel(SBOLDocument SBOLDoc, IdentifiableDocument<QName> topLevel) 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;
    URI source = null;
    URI language = null;
    URI framework = 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.Model.source)) {
            if (!(namedProperty.getValue() instanceof Literal) || source != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10502", topLevel.getIdentity());
            }
            source = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.Model.language)) {
            if (!(namedProperty.getValue() instanceof Literal) || language != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10504", topLevel.getIdentity());
            }
            language = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.Model.framework)) {
            if (!(namedProperty.getValue() instanceof Literal) || framework != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10508", topLevel.getIdentity());
            }
            framework = URI.create(((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));
        }
    }
    // Model m = SBOLDoc.createModel(topLevel.getIdentity(), source, language, framework);
    Model m = new Model(topLevel.getIdentity(), source, language, framework);
    if (persistentIdentity != null)
        m.setPersistentIdentity(persistentIdentity);
    if (version != null)
        m.setVersion(version);
    if (displayId != null)
        m.setDisplayId(displayId);
    if (name != null)
        m.setName(name);
    if (description != null)
        m.setDescription(description);
    m.setWasDerivedFroms(wasDerivedFroms);
    m.setWasGeneratedBys(wasGeneratedBys);
    m.setAttachments(attachments);
    if (!annotations.isEmpty())
        m.setAnnotations(annotations);
    Model oldM = SBOLDoc.getModel(topLevel.getIdentity());
    if (oldM == null) {
        SBOLDoc.addModel(m);
    } else {
        if (!m.equals(oldM)) {
            throw new SBOLValidationException("sbol-10202", m);
        }
    }
    return m;
}
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) IdentifiableDocument(org.sbolstandard.core.datatree.IdentifiableDocument) Literal(org.sbolstandard.core.datatree.Literal) HashSet(java.util.HashSet)

Aggregations

URI (java.net.URI)17 ArrayList (java.util.ArrayList)17 HashSet (java.util.HashSet)17 QName (javax.xml.namespace.QName)17 IdentifiableDocument (org.sbolstandard.core.datatree.IdentifiableDocument)17 Literal (org.sbolstandard.core.datatree.Literal)17 StringifyQName (org.sbolstandard.core.io.json.StringifyQName)17 URIcompliance.createCompliantURI (org.sbolstandard.core2.URIcompliance.createCompliantURI)17 NestedDocument (org.sbolstandard.core.datatree.NestedDocument)9 HashMap (java.util.HashMap)1 Set (java.util.Set)1 DateTime (org.joda.time.DateTime)1 DateTimeFormatter (org.joda.time.format.DateTimeFormatter)1
About Me
UseOf

Java Tutorials :

Simple Java RabbitMQ Example with Spring
Simple Springboot JPA Eclipeslink Example
Simple SpringBoot JPA Hibernate Example
Jackson JSON @JsonIgnore and @JsonIgnoreProperties Examples
Java Infinite recursion (StackOverflowError) Jackson solutions
Simple Java Jackson Serialize Objects to JSON and convert them back To Object
ElasticSearch 5 - Upload files using Java API in binary field Example
Java JAXB marshall unmarshall Examples from String and Stream
Java 8 forEach List and Map examples
ElasticSearch 5 Java API SearchRequestBuilder examples
Java ElasticSearch 5 examples with node index and mapping - running local
Convert String to int or Integer Java 8
Java 9 in action - JShell - Ubuntu
Java - removing invalid characters from a file name
Hello world!? or Hello Tutorial