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

Example 71 with TaxonImpl

use of org.eol.globi.domain.TaxonImpl 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 72 with TaxonImpl

use of org.eol.globi.domain.TaxonImpl 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 73 with TaxonImpl

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

the class StudyImporterForRoopnarine method importPredatorSpecimen.

private List<Specimen> importPredatorSpecimen(String trophicGuildLookup, Map<Integer, List<String>> trophicGuildNumberToSpeciesMap, LabeledCSVParser parser, List<String> preyTaxonList, Study study, Location location) throws StudyImporterException {
    Integer predatorGuildNumber = parseGuildNumber(trophicGuildLookup, parser);
    List<Specimen> predatorSpecimenList = new ArrayList<Specimen>();
    List<String> predatorTaxaList = trophicGuildNumberToSpeciesMap.get(predatorGuildNumber);
    if (predatorTaxaList == null) {
        throw new StudyImporterException("no species available for guild number [" + predatorGuildNumber + "]");
    }
    for (String predatorTaxa : predatorTaxaList) {
        // TODO - here's where the specimen model doesn't fit nicely - need a way to distinguish inferred relationships from direct observations
        if (StringUtils.isBlank(predatorTaxa)) {
            getLogger().info(study, "found blank predator name on line [" + parser.lastLineNumber() + "]");
        } else {
            Specimen predatorSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl(predatorTaxa, null));
            predatorSpecimen.caughtIn(location);
            predatorSpecimenList.add(predatorSpecimen);
            for (String preyTaxonName : preyTaxonList) {
                if (StringUtils.isBlank(preyTaxonName)) {
                    getLogger().info(study, "found blank prey name for predator [" + predatorTaxa + "] on line [" + parser.lastLineNumber() + "]");
                } else {
                    Specimen preySpecimen = nodeFactory.createSpecimen(study, new TaxonImpl(preyTaxonName, null));
                    preySpecimen.caughtIn(location);
                    predatorSpecimen.ate(preySpecimen);
                }
            }
        }
    }
    return predatorSpecimenList;
}

Example 74 with TaxonImpl

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

the class StudyImporterForStrona method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    LabeledCSVParser dataParser;
    try {
        dataParser = parserFactory.createParser(RESOURCE_PATH, CharsetConstant.UTF8);
    } catch (IOException e) {
        throw new StudyImporterException("failed to read resource [" + RESOURCE_PATH + "]", e);
    }
    try {
        Study study = nodeFactory.getOrCreateStudy(new StudyImpl("strona2013", SOURCE + " . " + CitationUtil.createLastAccessedString(RESOURCE_PATH), "http://dx.doi.org/10.1890/12-1419.1", SOURCE));
        while (dataParser.getLine() != null) {
            if (importFilter.shouldImportRecord((long) dataParser.getLastLineNumber())) {
                try {
                    String parasiteName = StringUtils.trim(dataParser.getValueByLabel("P_SP"));
                    String hostName = StringUtils.trim(dataParser.getValueByLabel("H_SP"));
                    if (areNamesAvailable(parasiteName, hostName)) {
                        Specimen parasite = nodeFactory.createSpecimen(study, new TaxonImpl(parasiteName, null));
                        Specimen host = nodeFactory.createSpecimen(study, new TaxonImpl(hostName, null));
                        parasite.interactsWith(host, InteractType.PARASITE_OF);
                    }
                } catch (NodeFactoryException | NumberFormatException e) {
                    throw new StudyImporterException("failed to import line [" + (dataParser.lastLineNumber() + 1) + "]", e);
                }
            }
        }
    } catch (IOException | NodeFactoryException e) {
        throw new StudyImporterException("problem importing [" + RESOURCE_PATH + "]", e);
    }
}

Example 75 with TaxonImpl

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

the class StudyImporterForWebOfLife method importNetwork.

public void importNetwork(InteractType interactType1, Location networkLocation, Study study, File file) throws IOException, NodeFactoryException {
    LabeledCSVParser interactions = CSVTSVUtil.createLabeledCSVParser(new FileInputStream(file));
    final String[] targetLabels = interactions.getLabels();
    List<String> targetTaxonNames = new ArrayList<String>();
    List<String> ignoredLabels = Arrays.asList("number of hosts sampled", "");
    for (String targetLabel : targetLabels) {
        String trimmedLabel = StringUtils.trim(targetLabel);
        if (StringUtils.isNotBlank(targetLabel) || !ignoredLabels.contains(trimmedLabel)) {
            targetTaxonNames.add(targetLabel);
        }
    }
    String[] line;
    while ((line = interactions.getLine()) != null) {
        String sourceTaxonName = line[0];
        final Specimen sourceSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl(sourceTaxonName, null));
        sourceSpecimen.caughtIn(networkLocation);
        for (String targetTaxonName : targetTaxonNames) {
            final String valueByLabel = StringUtils.trim(interactions.getValueByLabel(targetTaxonName));
            if (StringUtils.isNotBlank(valueByLabel) && !StringUtils.equals("0", valueByLabel)) {
                final Specimen targetSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl(targetTaxonName, null));
                targetSpecimen.caughtIn(networkLocation);
                sourceSpecimen.interactsWith(targetSpecimen, interactType1);
            }
        }
    }
}