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

Example 36 with Specimen

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

the class StudyImporterForBell method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    for (String resource : RESOURCE) {
        LabeledCSVParser parser = null;
        try {
            parser = parserFactory.createParser(resource, "UTF-8");
            while (parser.getLine() != null) {
                String sourceCitation = "Bell, K. C., Matek, D., Demboski, J. R., & Cook, J. A. (2015). Expanded Host Range of Sucking Lice and Pinworms of Western North American Chipmunks. Comparative Parasitology, 82(2), 312–321. doi:10.1654/4756.1 . Data provided by Kayce C. Bell.";
                String guid = parser.getValueByLabel("GUID");
                String externalId = "http://arctos.database.museum/guid/" + guid;
                String description = null;
                String collectionId = null;
                for (String key : REFS.keySet()) {
                    if (guid.startsWith(key)) {
                        description = REFS.get(key);
                        collectionId = key;
                        break;
                    }
                }
                if (StringUtils.isBlank(description)) {
                    LOG.warn("missing collectionId [" + guid + "] in file [" + resource + "] on line [" + parser.lastLineNumber() + "]");
                    description = sourceCitation;
                    collectionId = "";
                }
                Study study = nodeFactory.getOrCreateStudy(new StudyImpl("bell-" + collectionId, sourceCitation, "http://dx.doi.org/10.1654/4756.1", ExternalIdUtil.toCitation(null, sourceCitation + " " + description, null)));
                String genus = parser.getValueByLabel("Genus");
                String species = parser.getValueByLabel("Species");
                String parasiteName = StringUtils.join(new String[] { StringUtils.trim(genus), StringUtils.trim(species) }, " ");
                Specimen parasite = nodeFactory.createSpecimen(study, new TaxonImpl(parasiteName, null));
                parasite.setExternalId(externalId);
                Location location = getLocation(parser, parasite);
                parasite.caughtIn(location);
                String scientificName = parser.getValueByLabel("SCIENTIFIC_NAME");
                String hostName = StringUtils.trim(scientificName);
                Specimen host = nodeFactory.createSpecimen(study, new TaxonImpl(hostName, null));
                host.caughtIn(location);
                host.setExternalId(externalId);
                parasite.interactsWith(host, InteractType.PARASITE_OF);
                Date date = parseDate(parser);
                nodeFactory.setUnixEpochProperty(parasite, date);
                nodeFactory.setUnixEpochProperty(host, date);
            }
        } catch (Throwable e) {
            throw new StudyImporterException(getErrorMessage(resource, parser), e);
        }
    }
}

Example 37 with Specimen

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

the class StudyImporterForBioInfo method createSpecimen.

private Specimen createSpecimen(Study study, LabeledCSVParser labeledCSVParser, String externalId) throws StudyImporterException {
    try {
        Specimen specimen = nodeFactory.createSpecimen(study, new TaxonImpl(null, TaxonomyProvider.NBN.getIdPrefix() + externalId));
        setSpecimenExternalId(labeledCSVParser, specimen);
        return specimen;
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to create taxon with scientific name [" + externalId + "]", e);
    }
}

Example 38 with Specimen

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

the class StudyImporterForByrnes method addInteractionForPredator.

private void addInteractionForPredator(LabeledCSVParser parser, Study localStudy, String predatorName) throws NodeFactoryException, StudyImporterException {
    Specimen predator = nodeFactory.createSpecimen(localStudy, new TaxonImpl(predatorName, null));
    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));
        String feedingLink = parser.getValueByLabel("Feeding Link?");
        if (StringUtils.equals("1", StringUtils.trim(feedingLink))) {
            predator.ate(prey);
        } else {
            predator.interactsWith(prey, InteractType.INTERACTS_WITH);
        }
    }
}

Example 39 with Specimen

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

the class StudyImporterForBlewett method setLocationAndDate.

private void setLocationAndDate(Map<String, Location> locationMap, Map<String, Date> collectionTimeMap, List<Specimen> items, String collectionCode) throws NodeFactoryException {
    String collectionCodeTrim = collectionCode.trim();
    Location location = locationMap.get(collectionCodeTrim);
    if (location != null) {
        for (Specimen item : items) {
            item.caughtIn(location);
        }
    }
    Date collectionDatetime = collectionTimeMap.get(collectionCodeTrim);
    if (collectionDatetime != null) {
        for (Specimen item : items) {
            nodeFactory.setUnixEpochProperty(item, collectionDatetime);
        }
    }
}

Example 40 with Specimen

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

the class StudyImporterForBlewett method addPredator.

private Specimen addPredator(Study study, LabeledCSVParser parser, String[] line) throws NodeFactoryException, TermLookupServiceException {
    Specimen predatorSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl("Centropomus undecimalis", null));
    predatorSpecimen.setLifeStage(nodeFactory.getTermLookupService().lookupTermByName("adult"));
    try {
        String length = parser.getValueByLabel("Standard Length");
        predatorSpecimen.setLengthInMm(Double.parseDouble(length));
    } catch (NumberFormatException ex) {
        getLogger().warn(study, "found malformed length in line:" + parser.lastLineNumber() + " [" + StringUtils.join(line, ",") + "]");
    }
    return predatorSpecimen;
}