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

Example 1 with Specimen

use of org.eol.globi.domain.Specimen 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 Specimen

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

the class StudyImporterForINaturalist method getSourceSpecimen.

private Specimen getSourceSpecimen(long observationId, String interactionDataType, Taxon sourceTaxon, Study study) throws StudyImporterException, NodeFactoryException {
    if (!"taxon".equals(interactionDataType)) {
        throw new StudyImporterException("expected [taxon] as observation_type datatype, but found [" + interactionDataType + "]");
    }
    Specimen sourceSpecimen = nodeFactory.createSpecimen(study, sourceTaxon);
    sourceSpecimen.setExternalId(TaxonomyProvider.ID_PREFIX_INATURALIST + observationId);
    return sourceSpecimen;
}

Example 3 with Specimen

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

the class StudyImporterForKelpForest method createSpecimen.

protected Specimen createSpecimen(LabeledCSVParser parser, Map<String, Long> nameToId, String nameLabel, String stageLabel, Study study) throws NodeFactoryException {
    String sourceName = parser.getValueByLabel(nameLabel);
    Long id = nameToId.get(sourceName);
    String taxonExternalId = id == null ? null : TaxonomyProvider.ID_PREFIX_ITIS + id;
    Specimen sourceSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl(sourceName, taxonExternalId));
    String sourceLifeStage = parser.getValueByLabel(stageLabel);
    Term orCreateLifeStage = nodeFactory.getOrCreateLifeStage("KELP:" + sourceLifeStage, sourceLifeStage);
    sourceSpecimen.setLifeStage(orCreateLifeStage);
    return sourceSpecimen;
}

Example 4 with Specimen

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

the class StudyImporterForRobledo method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    String description = "García-Robledo C, Erickson DL, Staines CL, Erwin TL, Kress WJ. Tropical Plant–Herbivore Networks: Reconstructing Species Interactions Using DNA Barcodes Heil M, editor. PLoS ONE [Internet]. 2013 January 8;8(1):e52967. Available from: http://dx.doi.org/10.1371/journal.pone.0052967";
    String doi = "http://dx.doi.org/10.1371/journal.pone.0052967";
    Study study1 = new StudyImpl("García-Robledo et al 2013", description, doi, description);
    Study study = nodeFactory.getOrCreateStudy(study1);
    Map<String, String> abrLookup = buildPlantLookup();
    // spatial location from: http://www.ots.ac.cr/index.php?option=com_content&task=view&id=163&Itemid=348
    Double latitude = LocationUtil.parseDegrees("10°26'N");
    Double longitude = LocationUtil.parseDegrees("83°59'W");
    Location location;
    try {
        location = nodeFactory.getOrCreateLocation(new LocationImpl(latitude, longitude, 35.0, null));
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to create location", e);
    }
    // TODO: need to map date range of collections
    String studyResource = "robledo/table_s1_extract.csv";
    try {
        LabeledCSVParser parser = parserFactory.createParser(studyResource, CharsetConstant.UTF8);
        while (parser.getLine() != null) {
            String beetleName = parser.getValueByLabel("Herbivore species");
            String beetleScientificName = completeBeetleName(beetleName);
            Specimen predator = nodeFactory.createSpecimen(study, new TaxonImpl(beetleScientificName, null));
            predator.caughtIn(location);
            for (String plantAbbreviation : abrLookup.keySet()) {
                String plantScientificName = abrLookup.get(plantAbbreviation);
                String valueByLabel = parser.getValueByLabel(plantAbbreviation);
                try {
                    int interactionCode = Integer.parseInt(valueByLabel);
                    if (interactionCode > 0) {
                        Specimen plant = nodeFactory.createSpecimen(study, new TaxonImpl(plantScientificName, null));
                        plant.caughtIn(location);
                        predator.ate(plant);
                    }
                } catch (NumberFormatException ex) {
                    getLogger().warn(study, "malformed or no value [" + valueByLabel + "] found for [" + plantScientificName + "(" + plantAbbreviation + ")" + "] and beetle [" + beetleScientificName + "] could be found in [" + studyResource + ":" + parser.lastLineNumber() + "]");
                }
            }
        }
    } catch (IOException e) {
        throw new StudyImporterException("problem reading [" + studyResource + "]", e);
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("cannot create specimens from [" + studyResource + "]", e);
    }
}

Example 5 with Specimen

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

the class StudyImporterForRaymond method getSpecimen.

private Specimen getSpecimen(LabeledCSVParser dietParser, String nameLabel, String lifeStageLabel, Study study) throws NodeFactoryException {
    String predatorName = dietParser.getValueByLabel(nameLabel);
    Specimen predator = nodeFactory.createSpecimen(study, new TaxonImpl(predatorName, null));
    String predatorLifeStage = dietParser.getValueByLabel(lifeStageLabel);
    predator.setLifeStage(nodeFactory.getOrCreateLifeStage("RAYMOND:" + predatorLifeStage, predatorLifeStage));
    return predator;
}