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

Example 1 with DataSource

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

the class GraphElementManipulation method oneToManyCollapse.

/**
 * Creates a one-to-many collapsed concept by creating collapsed concept of
 * a source to all targets. Source concept is NOT deleted by this method.
 *
 * @param graph
 * @param source
 * @param targets
 */
public static final Set<ONDEXConcept> oneToManyCollapse(ONDEXGraph graph, ONDEXConcept source, Collection<ONDEXConcept> targets) {
    boolean createNewTarget = false;
    Set<ONDEXConcept> result = new HashSet<ONDEXConcept>();
    System.err.println("Targets number:" + targets.size());
    for (ONDEXConcept target : targets) {
        System.err.println(target.getOfType());
        ConceptClass newClass = target.getOfType();
        Set<ConceptClass> set = new HashSet<ConceptClass>();
        set.add(newClass);
        set.add(source.getOfType());
        if (set.size() > 1) {
            createNewTarget = true;
            newClass = getCompoundConceptClass(graph, set);
        }
        DataSource newDataSource = target.getElementOf();
        Set<DataSource> allDataSources = new HashSet<DataSource>();
        allDataSources.add(newDataSource);
        allDataSources.add(source.getElementOf());
        if (allDataSources.size() > 1) {
            createNewTarget = true;
            newDataSource = getCompoundDataSource(graph, allDataSources);
        }
        ONDEXConcept realTarget = target;
        if (createNewTarget) {
            realTarget = copyConcept(graph, target, newClass, newDataSource);
            copyRelations(graph, target, realTarget);
            graph.deleteConcept(target.getId());
        }
        copyConceptData(graph, source, realTarget);
        copyRelations(graph, source, realTarget);
        result.add(realTarget);
    }
    return result;
}

Example 2 with DataSource

use of net.sourceforge.ondex.core.DataSource 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 3 with DataSource

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

the class DefaultAccessionMapper method map.

@Override
public ConceptAccession map(S src, ONDEXConcept concept, ONDEXGraph graph) {
    String accession = this.getAccessionValueMapper().map(src, graph);
    if (accession == null)
        return null;
    DataSource dataSrc = Optional.ofNullable(this.getDataSourceMapper()).map(m -> m.map(src, graph)).orElseThrow(() -> new NullPointerException(this.getClass().getName() + " needs a data source mapper"));
    boolean isAmbiguous = Optional.ofNullable(this.getAmbiguityMapper()).map(m -> m.map(src, graph)).map(Boolean.TRUE::equals).orElseThrow(() -> new NullPointerException(this.getClass().getName() + " needs an ambiguity mapper"));
    return CachedGraphWrapper.getInstance(graph).getAccession(accession, dataSrc, isAmbiguous, concept);
}

Example 4 with DataSource

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

the class AbstractONDEXGraphMetaDataTest method testGetDataSource.

/**
 * Test method for
 * {@link net.sourceforge.ondex.core.ONDEXGraphMetaData#getDataSource(java.lang.String)}
 * .
 */
@Test
public void testGetDataSource() {
    testCreateDataSource();
    DataSource _dataSource = omd.getDataSource("dataSource");
    assertEquals("not matching", _dataSource, dataSource);
    assertEquals("wrong id", _dataSource.getId(), dataSource.getId());
    assertEquals("wrong fullname", _dataSource.getFullname(), dataSource.getFullname());
    assertEquals("wrong description", _dataSource.getDescription(), dataSource.getDescription());
    DataSource _dataSource2 = omd.getDataSource("dataSource2");
    assertEquals("not matching", _dataSource2, dataSource2);
    assertEquals("wrong id", _dataSource2.getId(), dataSource2.getId());
    assertEquals("wrong fullname", _dataSource2.getFullname(), dataSource2.getFullname());
    assertEquals("wrong description", _dataSource2.getDescription(), dataSource2.getDescription());
    DataSource _dataSource3 = omd.getDataSource("dataSource3");
    assertEquals("not matching", _dataSource3, dataSource3);
    assertEquals("wrong id", _dataSource3.getId(), dataSource3.getId());
    assertEquals("wrong fullname", _dataSource3.getFullname(), dataSource3.getFullname());
    assertEquals("wrong description", _dataSource3.getDescription(), dataSource3.getDescription());
}

Example 5 with DataSource

use of net.sourceforge.ondex.core.DataSource 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);
}