Examples with EvidenceType net.sourceforge.ondex.core.EvidenceType used on opensource projects

Example 1 with EvidenceType

use of net.sourceforge.ondex.core.EvidenceType in project knetbuilder by Rothamsted.

the class ControledVocabularyHelper method createEvidence.

/**
 * Get evidence type
 *
 * @param graph
 * @param type
 * @return
 */
public static EvidenceType createEvidence(final ONDEXGraph graph, final String type) {
    final ONDEXGraphMetaData meta = graph.getMetaData();
    EvidenceType evidence = meta.getEvidenceType(type);
    if (evidence == null)
        evidence = meta.getFactory().createEvidenceType(type);
    return evidence;
}

Example 2 with EvidenceType

use of net.sourceforge.ondex.core.EvidenceType in project knetbuilder by Rothamsted.

the class GraphElementManipulation method copyConcept.

/**
 * Creates a copy of a concept and provides an opportunity to select a new
 * concept class and new DataSource.
 *
 * @param graph
 *            - graph
 * @param c
 *            - original concept that will be copied
 * @param newCC
 *            - new concept class that the copy will have
 * @param newDataSource
 *            - new DataSource that the copy will have
 * @return concept that was created
 */
public static ONDEXConcept copyConcept(ONDEXGraph graph, ONDEXConcept c, ConceptClass newCC, DataSource newDataSource) {
    EvidenceType der = ControledVocabularyHelper.createEvidence(graph, "Derived_copy");
    ONDEXConcept nc = graph.getFactory().createConcept(c.getPID(), newDataSource, newCC, der);
    copyConceptData(graph, c, nc);
    nc.removeEvidenceType(der);
    return nc;
}

Example 3 with EvidenceType

use of net.sourceforge.ondex.core.EvidenceType in project knetbuilder by Rothamsted.

the class GraphElementManipulation method conceptToCluster.

/**
 * Swaps hub concept for a cluster where every concept is connected to every
 * other concept by relation of specified type set. Use only with
 * non-directional relation types
 *
 * @param c
 *            - hub concept
 * @param clusterRel
 *            - relation type set to use in the cluster
 * @param graph
 *            - graph
 * @param rtss
 *            - relation type set() that define the cluster
 * @throws AccessDeniedException
 * @throws NullValueException
 */
public static void conceptToCluster(ONDEXConcept c, RelationType clusterRel, ONDEXGraph graph, RelationType... rtss) throws NullValueException, AccessDeniedException {
    Set<RelationType> ts = new HashSet<RelationType>(Arrays.asList(rtss));
    List<ONDEXConcept> cluster = new ArrayList<ONDEXConcept>();
    for (ONDEXRelation r : graph.getRelationsOfConcept(c)) {
        if (ts.contains(r.getOfType())) {
            if (c.equals(r.getFromConcept()) && c.equals(r.getToConcept()))
                continue;
            if (c.equals(r.getFromConcept()))
                cluster.add(r.getToConcept());
            else if (c.equals(r.getToConcept()))
                cluster.add(r.getFromConcept());
        }
    }
    Collection<EvidenceType> evidence = new ArrayList<EvidenceType>();
    for (EvidenceType et : c.getEvidence()) evidence.add(et);
    for (int i = 0; i < cluster.size(); i++) {
        for (int j = i + 1; j < cluster.size(); j++) {
            graph.createRelation(cluster.get(i), cluster.get(j), clusterRel, evidence);
        }
    }
    graph.deleteConcept(c.getId());
}

Example 4 with EvidenceType

use of net.sourceforge.ondex.core.EvidenceType in project knetbuilder by Rothamsted.

the class ONDEXGraphCloner method cloneConcept.

/**
 * Clones a concept from the original graph to the new graph
 *
 * @param conceptToClone
 *            the concept to clone in the original graph
 * @return the new Concept
 */
public ONDEXConcept cloneConcept(ONDEXConcept conceptToClone) {
    if (!metaDataHasBeenCloned) {
        cloneMetaData();
    }
    if (old2newConceptIds.containsKey(conceptToClone.getId())) {
        // " already cloned returning previously cloned concept");
        return newGraph.getConcept(old2newConceptIds.get(conceptToClone.getId()));
    }
    ONDEXGraphMetaData nomd = newGraph.getMetaData();
    String pid = conceptToClone.getPID();
    String desc = conceptToClone.getDescription();
    String anno = conceptToClone.getAnnotation();
    ArrayList<EvidenceType> ets = new ArrayList<EvidenceType>();
    for (EvidenceType evidence : conceptToClone.getEvidence()) {
        ets.add(nomd.getEvidenceType(evidence.getId()));
    }
    DataSource dataSource = conceptToClone.getElementOf();
    DataSource newDataSource = nomd.getDataSource(dataSource.getId());
    ConceptClass cc = conceptToClone.getOfType();
    ConceptClass newCC = nomd.getConceptClass(cc.getId());
    ONDEXConcept newConcept = newGraph.createConcept(pid, anno, desc, newDataSource, newCC, ets);
    // required to prevent StackOverflow when adding itself as tag
    old2newConceptIds.put(conceptToClone.getId(), newConcept.getId());
    for (ONDEXConcept tag : conceptToClone.getTags()) {
        ONDEXConcept newTag;
        if (old2newConceptIds.containsKey(tag.getId())) {
            // check if
            // tag
            // concept
            // exists
            int cid = old2newConceptIds.get(tag.getId());
            newTag = newGraph.getConcept(cid);
        } else {
            // recursive
            newTag = cloneConcept(tag);
        }
        newConcept.addTag(newTag);
    }
    for (Attribute attribute : conceptToClone.getAttributes()) {
        AttributeName att = attribute.getOfType();
        AttributeName newAtt = nomd.getAttributeName(att.getId());
        newConcept.createAttribute(newAtt, attribute.getValue(), attribute.isDoIndex());
    }
    for (ConceptName name : conceptToClone.getConceptNames()) {
        newConcept.createConceptName(name.getName(), name.isPreferred());
    }
    for (ConceptAccession acc : conceptToClone.getConceptAccessions()) {
        dataSource = acc.getElementOf();
        newDataSource = nomd.getDataSource(dataSource.getId());
        newConcept.createConceptAccession(acc.getAccession(), newDataSource, acc.isAmbiguous());
    }
    return newConcept;
}

Example 5 with EvidenceType

use of net.sourceforge.ondex.core.EvidenceType in project knetbuilder by Rothamsted.

the class DefaultHandler method addPublicationXref.

/**
 * For publications create a separate concept and relationship.
 *
 * @param c
 *            ONDEXConcept with publication
 * @param pub
 *            publicationXref used
 * @throws Exception
 */
private void addPublicationXref(ONDEXConcept c, publicationXref pub) throws Exception {
    // publication gets default data source
    DataSource elementOf = graph.getMetaData().getDataSource(Parser.cvToUse);
    if (elementOf == null)
        throw new DataSourceMissingException(Parser.cvToUse + " is missing.");
    // reused for relation
    EvidenceType evidence = graph.getMetaData().getEvidenceType(etIMPD);
    if (evidence == null)
        throw new EvidenceTypeMissingException(etIMPD + " is missing.");
    // get corresponding concept
    String rdfid = pub.getUri();
    if (!rdf2Concept.containsKey(rdfid)) {
        // create publication concept
        ConceptClass ofType = graph.getMetaData().getConceptClass(ccPublication);
        if (ofType == null)
            throw new ConceptClassMissingException(ccPublication + " is missing.");
        // add concept to global map
        ONDEXConcept pubC = graph.getFactory().createConcept(rdfid, elementOf, ofType, evidence);
        rdf2Concept.put(rdfid, pubC);
        // PubMed id is non-ambiguous for a publication
        if (pub.getID() != null)
            pubC.createConceptAccession(pub.getID(), elementOf, false);
        // add year of publication
        if (pub.getYEAR() > 0) {
            AttributeName yearAN = graph.getMetaData().getAttributeName(anYEAR);
            if (yearAN == null)
                throw new AttributeNameMissingException(anYEAR + " is missing.");
            pubC.createAttribute(yearAN, pub.getYEAR(), false);
        }
        // add journal reference
        AttributeName journalAN = graph.getMetaData().getAttributeName(anJOURNAL);
        if (journalAN == null)
            throw new AttributeNameMissingException(anJOURNAL + " is missing.");
        StringBuffer source = new StringBuffer();
        for (String s : pub.getSOURCE()) {
            source.append(s);
            source.append("\n");
        }
        if (source.length() > 0) {
            pubC.createAttribute(journalAN, source.toString(), true);
            pubC.createConceptName(source.toString(), true);
        }
        // add title of publication
        if (pub.getTITLE() != null) {
            AttributeName titleAN = graph.getMetaData().getAttributeName(anTITLE);
            if (titleAN == null)
                throw new AttributeNameMissingException(anTITLE + " is missing.");
            pubC.createAttribute(titleAN, pub.getTITLE(), true);
            pubC.createConceptName(pub.getTITLE(), false);
        }
        // add authors as list
        AttributeName authorsAN = graph.getMetaData().getAttributeName(anAUTHORS);
        if (authorsAN == null)
            throw new AttributeNameMissingException(anAUTHORS + " is missing.");
        StringBuffer authors = new StringBuffer();
        for (String s : pub.getAUTHORS()) {
            authors.append(s);
            authors.append("; ");
        }
        if (authors.length() > 0)
            pubC.createAttribute(authorsAN, authors.toString(), true);
        // add possible URL of publication, only first one
        if (pub.getURL() != null) {
            AttributeName urlAN = graph.getMetaData().getAttributeName(anURL);
            if (urlAN == null)
                throw new AttributeNameMissingException(anURL + " is missing.");
            Iterator<String> it = pub.getURL().iterator();
            if (it.hasNext())
                pubC.createAttribute(urlAN, it.next(), false);
        }
    }
    // create relation between concept and publication
    RelationType ofType = graph.getMetaData().getRelationType(rtPublishedIn);
    ONDEXConcept pubC = rdf2Concept.get(rdfid);
    graph.getFactory().createRelation(c, pubC, ofType, evidence);
}