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

Example 51 with Specimen

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

the class StudyImporterForAkin method addSpecimen.

private Specimen addSpecimen(Study study, LabeledCSVParser parser, String[] header, String[] line) throws StudyImporterException, NodeFactoryException {
    Specimen specimen = null;
    int speciesIndex = findIndexForColumnWithNameThrowOnMissing("Fish Species", header);
    String speciesName = line[speciesIndex];
    if (StringUtils.isNotBlank(speciesName)) {
        specimen = nodeFactory.createSpecimen(study, new TaxonImpl(speciesName, null));
        addSpecimenLength(parser, header, line, specimen, study);
        addStomachVolume(parser, header, line, specimen, study);
        addCollectionDate(study, parser, header, line, specimen);
    } else {
        getLogger().warn(study, "found blank species name on line [" + parser.lastLineNumber() + "]");
    }
    return specimen;
}

Example 52 with Specimen

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

the class StudyImporterForAkin method parseLine.

private void parseLine(String[][] siteInfos, String studyResource, Study study, LabeledCSVParser parser, String[] header, String[] line) throws NodeFactoryException, IOException {
    try {
        Specimen specimen = addSpecimen(study, parser, header, line);
        if (specimen != null) {
            Location location = parseLocation(findSiteInfo(header, line, siteInfos, parser));
            specimen.caughtIn(location);
            addPrey(study, parser, header, line, specimen, location);
        }
    } catch (StudyImporterException ex) {
        getLogger().warn(study, "[" + studyResource + "]:" + ex.getMessage());
    }
}

Example 53 with Specimen

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

the class StudyImporterForBioInfo method createSpecimen.

private Specimen createSpecimen(LabeledCSVParser parser, Study study, Map<String, Taxon> taxonMap, String nbnId, String bioTaxonId) throws StudyImporterException {
    Specimen specimen = null;
    if (StringUtils.isBlank(nbnId)) {
        try {
            Taxon taxon = taxonMap.get(bioTaxonId);
            if (taxon == null) {
                getLogger().warn(study, "empty/no taxon name for bioinfo taxon id [" + bioTaxonId + "] on line [" + parser.lastLineNumber() + 1 + "]");
            } else {
                specimen = nodeFactory.createSpecimen(study, new TaxonImpl(taxon.getName(), TaxonomyProvider.BIO_INFO + "taxon:" + bioTaxonId));
                setSpecimenExternalId(parser, specimen);
            }
        } catch (NodeFactoryException e) {
            throw new StudyImporterException("failed to create taxon with scientific name [" + bioTaxonId + "]", e);
        }
    } else {
        specimen = createSpecimen(study, parser, nbnId);
    }
    return specimen;
}

Example 54 with Specimen

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

the class StudyImporterForSeltmann method createInteraction.

protected void createInteraction(LabeledCSVParser occurrence, Study study, Map<String, String> assoc, String targetName, String sourceName, Date date, InteractType interactType) throws StudyImporterException {
    Specimen source = nodeFactory.createSpecimen(study, new TaxonImpl(sourceName, null));
    Specimen target = nodeFactory.createSpecimen(study, new TaxonImpl(targetName, null));
    source.interactsWith(target, interactType);
    String sourceBasisOfRecord = occurrence.getValueByLabel("basisOfRecord");
    source.setBasisOfRecord(nodeFactory.getOrCreateBasisOfRecord(sourceBasisOfRecord, sourceBasisOfRecord));
    final String recordId = occurrence.getValueByLabel(FIELD_IDIGBIO_RECORD_ID);
    source.setProperty(FIELD_IDIGBIO_RECORD_ID, recordId);
    source.setExternalId(recordId);
    source.setProperty(FIELD_OCCURRENCE_ID, occurrence.getValueByLabel(FIELD_OCCURRENCE_ID));
    source.setProperty(FIELD_CATALOG_NUMBER, occurrence.getValueByLabel(FIELD_CATALOG_NUMBER));
    String targetBasisOfRecord = assoc.get("dwc:basisOfRecord");
    target.setBasisOfRecord(nodeFactory.getOrCreateBasisOfRecord(targetBasisOfRecord, targetBasisOfRecord));
    final String assocRecordId = assoc.get(FIELD_IDIGBIO_RECORD_ID);
    target.setProperty(FIELD_IDIGBIO_RECORD_ID, assocRecordId);
    target.setExternalId(assocRecordId);
    nodeFactory.setUnixEpochProperty(source, date);
    nodeFactory.setUnixEpochProperty(target, date);
    String latitude = occurrence.getValueByLabel("decimalLatitude");
    String longitude = occurrence.getValueByLabel("decimalLongitude");
    if (StringUtils.isNotBlank(latitude) && StringUtils.isNotBlank(longitude)) {
        Location loc = nodeFactory.getOrCreateLocation(new LocationImpl(Double.parseDouble(latitude), Double.parseDouble(longitude), null, null));
        source.caughtIn(loc);
    }
}

Example 55 with Specimen

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

the class StudyImporterForRoopnarine method importTrophicInteractions.

private List<Specimen> importTrophicInteractions(String trophicGuildLookup, Map<Integer, List<String>> trophicGuildNumberToSpeciesMap, String studyResource, Study study, Location location) throws StudyImporterException {
    try {
        LabeledCSVParser parser = parserFactory.createParser(studyResource, CharsetConstant.UTF8);
        List<Specimen> predatorSpecimen = new ArrayList<Specimen>();
        while (parser.getLine() != null) {
            List<String> preyTaxonList = importPreyList(trophicGuildNumberToSpeciesMap, parser, study);
            if (preyTaxonList.size() > 0) {
                predatorSpecimen.addAll(importPredatorSpecimen(trophicGuildLookup, trophicGuildNumberToSpeciesMap, parser, preyTaxonList, study, location));
            }
        }
        return predatorSpecimen;
    } catch (IOException e) {
        throw new StudyImporterException("failed to read trophic guild lookup [" + trophicGuildLookup + "]", e);
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to import trophic links [" + studyResource + "]", e);
    } catch (StudyImporterException e) {
        throw new StudyImporterException("failed to import trophic links from resource [" + studyResource + "]", e);
    }
}