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

Example 1 with InteractType

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

the class StudyImporterForJSONLD method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    Model model;
    try {
        model = buildModel();
    } catch (IOException e) {
        throw new StudyImporterException("failed to import [" + getResourceURI() + "]", e);
    }
    Query query;
    try {
        query = QueryFactory.create(IOUtils.toString(new DatasetLocal().getResource("find-jsonld-interactions.rq"), CharsetConstant.UTF8));
    } catch (IOException e) {
        throw new StudyImporterException("failed to find sparql query", e);
    }
    QueryExecution exec = QueryExecutionFactory.create(query, model);
    try {
        ResultSet results = exec.execSelect();
        while (results.hasNext()) {
            QuerySolution solution = results.nextSolution();
            String subj = solution.get("subj").asResource().getURI();
            String creationDate = solution.get("creationDate").asLiteral().getString();
            String authorURI = solution.get("author").toString();
            String author;
            try {
                author = nodeFactory.getAuthorResolver().findFullName(authorURI);
            } catch (IOException e) {
                throw new StudyImporterException("failed to resolve author URI [" + authorURI + "]");
            }
            final String source1 = author + ". " + new DateTime(parseDate(creationDate)).getYear() + ". " + CitationUtil.createLastAccessedString(getResourceURI().toString());
            Study study = nodeFactory.getOrCreateStudy(new StudyImpl(getResourceURI() + subj, source1, null, subj));
            study.setExternalId(subj);
            Specimen source = createSpecimen(solution, study, "subjTaxon");
            Specimen target = createSpecimen(solution, study, "targetTaxon");
            String interactType = solution.get("p").asResource().getLocalName();
            InteractType interactType1 = InteractType.typeOf(StringUtils.replace(interactType, "RO_", "RO:"));
            if (interactType1 == null) {
                throw new StudyImporterException("failed to map interaction type [" + interactType + "]");
            }
            String collTime = solution.get("collTime").asLiteral().getString();
            Date date = parseDate(collTime);
            nodeFactory.setUnixEpochProperty(source, date);
            nodeFactory.setUnixEpochProperty(target, date);
            Location loc = nodeFactory.getOrCreateLocation(new LocationImpl(solution.get("collLat").asLiteral().getDouble(), solution.get("collLng").asLiteral().getDouble(), null, null));
            target.caughtIn(loc);
            source.caughtIn(loc);
            source.interactsWith(target, interactType1);
        }
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to import jsonld data in [" + getResourceURI() + "]", e);
    } finally {
        exec.close();
    }
}

Example 2 with InteractType

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

the class StudyImporterForWebOfLife method parseInteractionType.

public InteractType parseInteractionType(LabeledCSVParser parser) throws StudyImporterException {
    final String interactionTypeString = parser.getValueByLabel("Type of interactions");
    final Map<String, InteractType> interactionTypeMap = new HashMap<String, InteractType>() {

        {
            put("Pollination", InteractType.POLLINATED_BY);
            put("Seed Dispersal", InteractType.HAS_DISPERAL_VECTOR);
            put("Host-Parasite", InteractType.HAS_PARASITE);
            put("Plant-Herbivore", InteractType.EATEN_BY);
        }
    };
    final InteractType interactType1 = interactionTypeMap.get(interactionTypeString);
    if (interactType1 == null) {
        LOG.warn("found unsupported interaction type [" + interactionTypeString + "]");
    }
    return interactType1 == null ? InteractType.INTERACTS_WITH : interactType1;
}

Example 3 with InteractType

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

the class StudyImporterForSeltmann method parseInteractType.

private InteractType parseInteractType(LabeledCSVParser occurrence, Map<String, String> assoc) throws StudyImporterException {
    String interactionURI = assoc.get("aec:associatedRelationshipURI");
    InteractType interactType;
    if (StringUtils.isBlank(interactionURI)) {
        interactType = InteractType.INTERACTS_WITH;
    } else {
        final Map<String, InteractType> assocInteractMap = new HashMap<String, InteractType>() {

            {
                // interaction types that could probably be more specific (e.g. found inside, found on, emerged from)
                put("http://purl.obolibrary.org/obo/RO_0002220", InteractType.INTERACTS_WITH);
                put("http://purl.obolibrary.org/obo/RO_0001025", InteractType.INTERACTS_WITH);
                put("http://eol.org/schema/terms/emergedFrom", InteractType.INTERACTS_WITH);
            }
        };
        interactType = InteractType.typeOf(interactionURI);
        interactType = interactType == null ? assocInteractMap.get(interactionURI) : interactType;
        if (interactType == null) {
            throw new StudyImporterException("found unsupported interactionURI: [" + interactionURI + "] related to" + getLineMsg(occurrence));
        }
    }
    return interactType;
}

Example 4 with InteractType

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

the class StudyImporterForINaturalistTest method loadInteractionMap.

@Test
public void loadInteractionMap() throws IOException {
    String resourceName = StudyImporterForINaturalist.TYPE_MAP_URI_DEFAULT;
    LabeledCSVParser labeledCSVParser = importer.parserFactory.createParser(resourceName, CharsetConstant.UTF8);
    Map<Integer, InteractType> typeMap = StudyImporterForINaturalist.buildTypeMap(resourceName, labeledCSVParser);
    assertThat(typeMap.get(13), is(InteractType.ATE));
    assertThat(typeMap.get(1685), is(InteractType.ATE));
    assertThat(typeMap.get(839), is(InteractType.PREYS_UPON));
}

Example 5 with InteractType

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

the class StudyImporterForINaturalistTest method importTestResponseWithTaxonId.

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

        {
        }
    }, new HashMap<Integer, InteractType>() {

        {
            put(47, InteractType.HAS_HOST);
        }
    });
    resolveNames();
    assertThat(NodeUtil.findAllStudies(getGraphDb()).size(), is(10));
    Study anotherStudy = nodeFactory.findStudy("INAT:2366807");
    assertThat(anotherStudy, is(notNullValue()));
    assertThat(anotherStudy.getExternalId(), is("https://www.inaturalist.org/observations/2366807"));
    assertThat(taxonIndex.findTaxonById("GBIF:2959023"), is(nullValue()));
    assertThat(taxonIndex.findTaxonById("GBIF:7246356"), is(nullValue()));
    assertThat(taxonIndex.findTaxonById("INAT_TAXON:406089"), is(notNullValue()));
    assertThat(taxonIndex.findTaxonById("INAT_TAXON:480390"), is(notNullValue()));
}