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

Example 46 with Specimen

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

the class StudyImporterForBaremore method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    Study study;
    try {
        LabeledCSVParser parser = parserFactory.createParser(DATA_SOURCE, CharsetConstant.UTF8);
        String[] line;
        study = nodeFactory.getOrCreateStudy(new StudyImpl("Baremore 2010", StudyImporterForGoMexSI2.GOMEXI_SOURCE_DESCRIPTION, "doi:10.3354/ab00214", ExternalIdUtil.toCitation("Ivy E. Baremore", "Prey Selection By The Atlantic Angel Shark Squatina Dumeril In The Northeastern Gulf Of Mexico.", "2010")));
        Location collectionLocation = nodeFactory.getOrCreateLocation(new LocationImpl(29.219302, -87.06665, null, null));
        Map<Integer, Specimen> specimenMap = new HashMap<Integer, Specimen>();
        while ((line = parser.getLine()) != null) {
            Integer sharkId = Integer.parseInt(line[0]);
            String collectionDateString = line[1];
            if (isBlank(collectionDateString)) {
                getLogger().warn(study, "line [" + parser.getLastLineNumber() + "] in [" + DATA_SOURCE + "]: missing collection date");
            } else {
                Specimen predatorSpecimen = specimenMap.get(sharkId);
                if (predatorSpecimen == null) {
                    predatorSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl("Squatina dumeril", null));
                    predatorSpecimen.caughtIn(collectionLocation);
                    addLifeStage(parser, predatorSpecimen);
                    addCollectionDate(collectionDateString, predatorSpecimen);
                }
                specimenMap.put(sharkId, predatorSpecimen);
                String totalLengthInCm = line[3];
                try {
                    Double lengthInMm = Double.parseDouble(totalLengthInCm) * 10.0;
                    predatorSpecimen.setLengthInMm(lengthInMm);
                } catch (NumberFormatException ex) {
                    throw new StudyImporterException("failed to parse length [" + totalLengthInCm);
                }
                String preySpeciesDescription = line[7];
                if (StringUtils.isBlank(preySpeciesDescription)) {
                    getLogger().info(study, "found blank prey species description [" + preySpeciesDescription + "] on line [" + parser.lastLineNumber() + "]");
                } else {
                    Specimen preySpecimen = nodeFactory.createSpecimen(study, new TaxonImpl(preySpeciesDescription, null));
                    preySpecimen.caughtIn(collectionLocation);
                    predatorSpecimen.ate(preySpecimen);
                    nodeFactory.setUnixEpochProperty(preySpecimen, nodeFactory.getUnixEpochProperty(predatorSpecimen));
                }
            }
        }
    } catch (IOException e) {
        throw new StudyImporterException("failed to parse labels", e);
    }
}

Example 47 with Specimen

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

the class StudyImporterForAkin method addPrey.

private void addPrey(Study study, LabeledCSVParser parser, String[] header, String[] line, Specimen specimen, Location location) throws StudyImporterException {
    int firstPreyIndex = findIndexForColumnWithNameThrowOnMissing("Detritus", header);
    for (int i = firstPreyIndex; i < line.length; i++) {
        String preySpeciesName = header[i];
        if (StringUtils.isNotBlank(preySpeciesName)) {
            String preyVolumeString = line[i];
            try {
                if (StringUtils.isNotBlank(preyVolumeString)) {
                    double volume = Double.parseDouble(preyVolumeString);
                    if (volume > 0) {
                        Specimen prey = nodeFactory.createSpecimen(study, new TaxonImpl(preySpeciesName, null));
                        prey.setLifeStage(parseLifeStage(nodeFactory.getTermLookupService(), preySpeciesName));
                        prey.setVolumeInMilliLiter(volume);
                        prey.caughtIn(location);
                        specimen.ate(prey);
                    }
                }
            } catch (NumberFormatException ex) {
                throw new StudyImporterException("failed to parse volume of prey [" + preySpeciesName + "] in stomach [" + preyVolumeString + "] on line [" + parser.getLastLineNumber() + "]");
            } catch (TermLookupServiceException e) {
                throw new StudyImporterException("failed to parse life stage of prey [" + preySpeciesName + "] in stomach [" + preyVolumeString + "] on line [" + parser.getLastLineNumber() + "]");
            }
        }
    }
}

Example 48 with Specimen

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

the class StudyImporterForBlewett method parsePredatorPreyInteraction.

private void parsePredatorPreyInteraction(Study study, Map<String, Location> locationMap, Map<String, Date> collectionTimeMap) throws IOException, NodeFactoryException, TermLookupServiceException {
    LabeledCSVParser parser = parserFactory.createParser("blewett/SnookDietData2000_02_Charlotte_Harbor_FL_Blewett_numeric_abundance.csv", CharsetConstant.UTF8);
    String[] header = parser.getLabels();
    String[] line;
    while ((line = parser.getLine()) != null) {
        if (line.length < 2) {
            break;
        }
        Specimen predatorSpecimen = addPredator(study, parser, line);
        List<Specimen> specimen = addPreyForPredator(header, line, study);
        for (Specimen prey : specimen) {
            predatorSpecimen.ate(prey);
        }
        String collectionCode = parser.getValueByLabel(COLLECTION_NO);
        if (collectionCode != null) {
            specimen.add(predatorSpecimen);
            setLocationAndDate(locationMap, collectionTimeMap, specimen, collectionCode);
        }
    }
}

Example 49 with Specimen

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

the class StudyImporterForBarnes method addInteractionForPredator.

private void addInteractionForPredator(LabeledCSVParser parser, Study localStudy, String predatorName) throws NodeFactoryException, StudyImporterException {
    Specimen predator = nodeFactory.createSpecimen(localStudy, new TaxonImpl(predatorName, null));
    addLifeStage(parser, predator);
    Double latitude = LocationUtil.parseDegrees(parser.getValueByLabel("Latitude"));
    Double longitude = LocationUtil.parseDegrees(parser.getValueByLabel("Longitude"));
    String depth = parser.getValueByLabel("Depth");
    Double altitudeInMeters = -1.0 * Double.parseDouble(depth);
    Location location = nodeFactory.getOrCreateLocation(new LocationImpl(latitude, longitude, altitudeInMeters, null));
    predator.caughtIn(location);
    String preyName = parser.getValueByLabel("Prey");
    if (StringUtils.isBlank(preyName)) {
        getLogger().warn(localStudy, "found empty prey name on line [" + parser.lastLineNumber() + "]");
    } else {
        Specimen prey = nodeFactory.createSpecimen(localStudy, new TaxonImpl(preyName, null));
        prey.caughtIn(location);
        predator.ate(prey);
    }
}

Example 50 with Specimen

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

the class StudyImporterForBioInfo method importInteraction.

private void importInteraction(LabeledCSVParser parser, Study study, InteractType interactType, Map<String, Taxon> taxonMap) throws StudyImporterException {
    String passiveId = parser.getValueByLabel("passive NBN Code");
    String activeId = parser.getValueByLabel("active NBN Code");
    Specimen donorSpecimen = createSpecimen(parser, study, taxonMap, passiveId, parser.getValueByLabel("my passive taxon id"));
    Specimen recipientSpecimen = createSpecimen(parser, study, taxonMap, activeId, parser.getValueByLabel("my active taxon id"));
    if (donorSpecimen != null && recipientSpecimen != null) {
        addLifeStage(parser, donorSpecimen, "stage of passive taxon", study);
        addBodyPart(parser, donorSpecimen, "part of passive taxon", study);
        addLifeStage(parser, recipientSpecimen, "stage of active taxon", study);
        addBodyPart(parser, donorSpecimen, "part of active taxon", study);
        recipientSpecimen.interactsWith(donorSpecimen, interactType);
    }
}