Examples with TaxonNode org.eol.globi.domain.TaxonNode used on opensource projects

Example 1 with TaxonNode

use of org.eol.globi.domain.TaxonNode in project eol-globi-data by jhpoelen.

the class LinkerTermMatcher method link.

@Override
public void link() {
    Index<Node> taxons = graphDb.index().forNodes("taxons");
    IndexHits<Node> hits = taxons.query("*:*");
    final Map<Long, TaxonNode> nodeMap = new HashMap<Long, TaxonNode>();
    int counter = 1;
    for (Node hit : hits) {
        if (counter % BATCH_SIZE == 0) {
            handleBatch(graphDb, termMatcher, nodeMap, counter);
        }
        TaxonNode node = new TaxonNode(hit);
        nodeMap.put(node.getNodeID(), node);
        counter++;
    }
    handleBatch(graphDb, termMatcher, nodeMap, counter);
}

Example 2 with TaxonNode

use of org.eol.globi.domain.TaxonNode in project eol-globi-data by jhpoelen.

the class LinkerTermMatcher method handleBatch.

private void handleBatch(final GraphDatabaseService graphDb, TermMatcher termMatcher, final Map<Long, TaxonNode> nodeMap, int counter) {
    StopWatch stopWatch = new StopWatch();
    stopWatch.start();
    String msgPrefix = "batch #" + counter / BATCH_SIZE;
    LOG.info(msgPrefix + " preparing...");
    List<String> nodeIdAndNames = new ArrayList<String>();
    for (Map.Entry<Long, TaxonNode> entry : nodeMap.entrySet()) {
        String name = entry.getKey() + "|" + entry.getValue().getName();
        nodeIdAndNames.add(name);
    }
    try {
        if (nodeIdAndNames.size() > 0) {
            termMatcher.findTermsForNames(nodeIdAndNames, new TermMatchListener() {

                @Override
                public void foundTaxonForName(Long nodeId, String name, Taxon taxon, NameType relType) {
                    TaxonNode taxonNode = nodeMap.get(nodeId);
                    if (taxonNode != null && NameType.NONE != relType && !TaxonUtil.likelyHomonym(taxon, taxonNode)) {
                        NodeUtil.connectTaxa(taxon, taxonNode, graphDb, RelTypes.forType(relType));
                    }
                }
            });
        }
    } catch (PropertyEnricherException ex) {
        LOG.error(msgPrefix + " problem matching terms", ex);
    }
    stopWatch.stop();
    LOG.info(msgPrefix + " completed in [" + stopWatch.getTime() + "] ms (" + (1.0 * stopWatch.getTime() / BATCH_SIZE) + " ms/name )");
    nodeMap.clear();
}

Example 3 with TaxonNode

use of org.eol.globi.domain.TaxonNode in project eol-globi-data by jhpoelen.

the class LinkerTrustyNanoPubs method generateOrganisms.

public static void generateOrganisms(StringBuilder builder, InteractionNode interaction) {
    Collection<Specimen> participants = interaction.getParticipants();
    Map<Long, Integer> nodeIdParticipantMap = new TreeMap<>();
    int participantNumber = 0;
    for (Specimen participant : participants) {
        builder.append(String.format("\n    obo:RO_0000057 :Organism_%d ", participantNumber));
        builder.append(participants.size() - 1 == participantNumber ? "." : ";");
        nodeIdParticipantMap.put(((NodeBacked) participant).getNodeID(), participantNumber);
        participantNumber++;
    }
    participantNumber = 0;
    for (Specimen participant : participants) {
        Iterable<Relationship> classification = NodeUtil.getClassifications(participant);
        if (classification != null && classification.iterator().hasNext()) {
            TaxonNode taxonNode = new TaxonNode(classification.iterator().next().getEndNode());
            String ncbiTaxonId = resolveNCBITaxonId(taxonNode);
            if (StringUtils.isNotBlank(ncbiTaxonId)) {
                builder.append(String.format("\n  :Organism_%d a NCBITaxon:%s ", participantNumber, ncbiTaxonId));
                Iterable<Relationship> interactRel = ((NodeBacked) participant).getUnderlyingNode().getRelationships(Direction.OUTGOING, NodeUtil.asNeo4j(InteractType.values()));
                for (Relationship relationship : interactRel) {
                    if (!relationship.hasProperty(PropertyAndValueDictionary.INVERTED)) {
                        if (relationship.hasProperty(PropertyAndValueDictionary.IRI)) {
                            String interactIRI = relationship.getProperty(PropertyAndValueDictionary.IRI).toString();
                            if (StringUtils.isNotBlank(interactIRI)) {
                                builder.append(";\n");
                                builder.append(String.format("    <%s> :Organism_%d ", interactIRI, nodeIdParticipantMap.get(relationship.getEndNode().getId())));
                            }
                        }
                    }
                }
                builder.append(".");
                participantNumber++;
            }
        }
    }
}

Example 4 with TaxonNode

use of org.eol.globi.domain.TaxonNode in project eol-globi-data by jhpoelen.

the class NonResolvingTaxonIndex method findTaxonByKey.

private TaxonNode findTaxonByKey(String key, String value) {
    TaxonNode firstMatchingTaxon = null;
    if (StringUtils.isNotBlank(value)) {
        String query = key + ":\"" + QueryParser.escape(value) + "\"";
        IndexHits<Node> matchingTaxa = taxons.query(query);
        Node matchingTaxon;
        if (matchingTaxa.hasNext()) {
            matchingTaxon = matchingTaxa.next();
            if (matchingTaxon != null) {
                firstMatchingTaxon = new TaxonNode(matchingTaxon);
            }
        }
        matchingTaxa.close();
    }
    return firstMatchingTaxon;
}

Example 5 with TaxonNode

use of org.eol.globi.domain.TaxonNode in project eol-globi-data by jhpoelen.

the class LinkerTaxonIndex method link.

public void link() {
    Index<Node> taxons = graphDb.index().forNodes("taxons");
    Index<Node> ids = graphDb.index().forNodes(INDEX_TAXON_NAMES_AND_IDS, MapUtil.stringMap(IndexManager.PROVIDER, "lucene", "type", "fulltext"));
    TaxonFuzzySearchIndex fuzzySearchIndex = new TaxonFuzzySearchIndex(graphDb);
    IndexHits<Node> hits = taxons.query("*:*");
    for (Node hit : hits) {
        List<String> taxonIds = new ArrayList<>();
        List<String> taxonPathIdsAndNames = new ArrayList<>();
        TaxonNode taxonNode = new TaxonNode(hit);
        addTaxonId(taxonIds, taxonNode);
        addPathIdAndNames(taxonPathIdsAndNames, taxonNode);
        addToFuzzyIndex(graphDb, fuzzySearchIndex, hit, taxonNode);
        Iterable<Relationship> rels = hit.getRelationships(Direction.OUTGOING, NodeUtil.asNeo4j(RelTypes.SAME_AS));
        for (Relationship rel : rels) {
            TaxonNode sameAsTaxon = new TaxonNode(rel.getEndNode());
            addTaxonId(taxonIds, sameAsTaxon);
            addPathIdAndNames(taxonPathIdsAndNames, sameAsTaxon);
            addToFuzzyIndex(graphDb, fuzzySearchIndex, hit, sameAsTaxon);
        }
        Transaction tx = graphDb.beginTx();
        try {
            taxonPathIdsAndNames.addAll(taxonIds);
            String aggregateIds = StringUtils.join(taxonPathIdsAndNames, CharsetConstant.SEPARATOR);
            ids.add(hit, PropertyAndValueDictionary.PATH, aggregateIds);
            hit.setProperty(PropertyAndValueDictionary.EXTERNAL_IDS, aggregateIds);
            String aggregateTaxonIds = StringUtils.join(taxonIds, CharsetConstant.SEPARATOR);
            hit.setProperty(PropertyAndValueDictionary.NAME_IDS, aggregateTaxonIds);
            tx.success();
        } finally {
            tx.finish();
        }
    }
    hits.close();
}