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

Example 21 with InteractType

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

the class StudyImporterForINaturalist method buildTypeMap.

public static Map<Integer, InteractType> buildTypeMap(String resource, LabeledCSVParser labeledCSVParser) throws IOException {
    LabeledCSVParser parser = labeledCSVParser;
    Map<Integer, InteractType> typeMap = new TreeMap<Integer, InteractType>();
    while (parser.getLine() != null) {
        String inatIdString = parser.getValueByLabel("observation_field_id");
        Integer inatId = null;
        String prefix = PREFIX_OBSERVATION_FIELD;
        if (StringUtils.startsWith(inatIdString, prefix)) {
            inatId = Integer.parseInt(inatIdString.replace(prefix, ""));
        }
        if (inatId == null) {
            LOG.warn("failed to map observation field id [" + inatIdString + "] in line [" + resource + ":" + parser.lastLineNumber() + "]");
        } else {
            String interactionTypeId = parser.getValueByLabel("interaction_type_id");
            InteractType interactType = InteractType.typeOf(interactionTypeId);
            if (interactType == null) {
                LOG.warn("failed to map interaction type [" + interactionTypeId + "] in line [" + resource + ":" + parser.lastLineNumber() + "]");
            } else {
                typeMap.put(inatId, interactType);
            }
        }
    }
    return typeMap;
}

Example 22 with InteractType

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

the class TaxonInteractionIndexer method createTaxonInteractions.

public void createTaxonInteractions(Map<Fun.Tuple3<Long, String, Long>, Long> taxonInteractions) {
    StopWatch watchForEntireRun = new StopWatch();
    watchForEntireRun.start();
    long count = 0;
    Transaction tx = null;
    for (Fun.Tuple3<Long, String, Long> uniqueTaxonInteraction : taxonInteractions.keySet()) {
        if (count % 1000 == 0) {
            finalizeTx(tx);
            tx = graphService.beginTx();
        }
        final Node sourceTaxon = graphService.getNodeById(uniqueTaxonInteraction.a);
        final Node targetTaxon = graphService.getNodeById(uniqueTaxonInteraction.c);
        if (sourceTaxon != null && targetTaxon != null) {
            final InteractType relType = InteractType.valueOf(uniqueTaxonInteraction.b);
            final Long interactionCount = taxonInteractions.get(uniqueTaxonInteraction);
            createInteraction(sourceTaxon, targetTaxon, relType, false, interactionCount);
            createInteraction(targetTaxon, sourceTaxon, InteractType.inverseOf(relType), true, interactionCount);
        }
        count++;
    }
    finalizeTx(tx);
    watchForEntireRun.stop();
    LOG.info("created [" + count + "] taxon interactions in " + getProgressMsg(count, watchForEntireRun.getTime()));
}

Example 23 with InteractType

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

the class StudyImporterForINaturalistTest method importTestResponse.

@Test
public void importTestResponse() throws IOException, StudyImporterException {
    importer.parseJSON(getClass().getResourceAsStream("inaturalist/sample_inaturalist_response.json"), new ArrayList<Integer>() {

        {
            add(47);
        }
    }, new HashMap<Integer, InteractType>() {

        {
            put(13, InteractType.ATE);
        }
    });
    resolveNames();
    assertThat(NodeUtil.findAllStudies(getGraphDb()).size(), is(22));
    Study anotherStudy = nodeFactory.findStudy("INAT:831");
    assertThat(anotherStudy, is(notNullValue()));
    assertThat(anotherStudy.getCitation(), containsString("Ken-ichi Ueda. 2008. Argiope eating Orthoptera. iNaturalist.org. Accessed at <https://www.inaturalist.org/observations/831> on "));
    assertThat(anotherStudy.getExternalId(), is("https://www.inaturalist.org/observations/831"));
    anotherStudy = nodeFactory.findStudy("INAT:97380");
    assertThat(anotherStudy, is(notNullValue()));
    assertThat(anotherStudy.getCitation(), containsString("annetanne. 2012. Misumena vatia eating Eristalis nemorum."));
    assertThat(anotherStudy.getExternalId(), is("https://www.inaturalist.org/observations/97380"));
    Taxon sourceTaxonNode = taxonIndex.findTaxonByName("Arenaria interpres");
    assertThat(sourceTaxonNode, is(not(nullValue())));
    Iterable<Relationship> relationships = ((NodeBacked) sourceTaxonNode).getUnderlyingNode().getRelationships(Direction.INCOMING, NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS));
    for (Relationship relationship : relationships) {
        Node sourceSpecimen = relationship.getStartNode();
        assertThat(new SpecimenNode(sourceSpecimen).getBasisOfRecord().getName(), is("HumanObservation"));
        assertThat(new SpecimenNode(sourceSpecimen).getBasisOfRecord().getId(), is("TEST:HumanObservation"));
        assertThat(new SpecimenNode(sourceSpecimen).getExternalId(), containsString(TaxonomyProvider.ID_PREFIX_INATURALIST));
        Relationship ateRel = sourceSpecimen.getSingleRelationship(NodeUtil.asNeo4j(InteractType.ATE), Direction.OUTGOING);
        Node preySpecimen = ateRel.getEndNode();
        assertThat(preySpecimen, is(not(nullValue())));
        Relationship preyClassification = preySpecimen.getSingleRelationship(NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS), Direction.OUTGOING);
        String actualPreyName = (String) preyClassification.getEndNode().getProperty("name");
        assertThat(actualPreyName, is("Crepidula fornicata"));
        Relationship locationRel = sourceSpecimen.getSingleRelationship(NodeUtil.asNeo4j(RelTypes.COLLECTED_AT), Direction.OUTGOING);
        assertThat((Double) locationRel.getEndNode().getProperty("latitude"), is(41.249813));
        assertThat((Double) locationRel.getEndNode().getProperty("longitude"), is(-72.542556));
        Relationship collectedRel = sourceSpecimen.getSingleRelationship(NodeUtil.asNeo4j(RelTypes.COLLECTED), Direction.INCOMING);
        assertThat((Long) collectedRel.getProperty(SpecimenConstant.DATE_IN_UNIX_EPOCH), is(any(Long.class)));
    }
}