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

Example 56 with Specimen

use of org.eol.globi.domain.Specimen 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 57 with Specimen

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

the class StudyImporterForWrast method addNextRecordToStudy.

private void addNextRecordToStudy(LabeledCSVParser csvParser, Study study, Map<String, String> columnToNormalizedTermMapper, LengthParser lengthParser) throws StudyImporterException {
    String seasonName = csvParser.getValueByLabel(columnToNormalizedTermMapper.get(SEASON));
    String preyItem = csvParser.getValueByLabel(columnToNormalizedTermMapper.get(PREY_SPECIES));
    if (preyItem == null) {
        getLogger().warn(study, "no prey name for line [" + csvParser.getLastLineNumber() + "]");
    } else {
        Specimen prey = createAndClassifySpecimen(preyItem, study);
        String habitat = csvParser.getValueByLabel(COLUMN_MAPPER.get(HABITAT));
        String site = csvParser.getValueByLabel(COLUMN_MAPPER.get(SITE));
        String region = csvParser.getValueByLabel(COLUMN_MAPPER.get(REGION));
        String sampleLocationId = createLocationId(habitat, region, site);
        Map<String, LatLng> averageLocations = getLocationMap();
        LatLng latLng1 = averageLocations.get(sampleLocationId);
        if (latLng1 == null) {
            throw new StudyImporterException("no location information for [" + sampleLocationId + "] on line [" + csvParser.getLastLineNumber() + "] found in [" + averageLocations + "]");
        }
        if (depthMap == null) {
            depthMap = createDepthMap(study);
        }
        Double depth = depthMap.get(createDepthId(seasonName, region, site, habitat));
        Double altitude = depth == null ? null : -depth;
        if (depth == null) {
            getLogger().warn(study, createMsgPrefix(csvParser) + " failed to find depth for habitat, region, site and season: [" + createDepthId(seasonName, region, site, habitat) + "], skipping entry");
        }
        Location sampleLocation;
        try {
            sampleLocation = nodeFactory.getOrCreateLocation(new LocationImpl(latLng1.getLat(), latLng1.getLng(), altitude, null));
        } catch (NodeFactoryException e) {
            throw new StudyImporterException("failed to create location", e);
        }
        prey.caughtIn(sampleLocation);
        prey.caughtDuring(getOrCreateSeason(seasonName));
        String speciesName = csvParser.getValueByLabel(columnToNormalizedTermMapper.get(PREDATOR_SPECIES));
        String predatorId = csvParser.getValueByLabel(columnToNormalizedTermMapper.get(PREDATOR_SPECIMEN_ID));
        Map<String, Specimen> predatorMap = getPredatorSpecimenMap();
        Specimen predator = predatorMap.get(predatorId);
        if (predator == null) {
            predator = addPredatorSpecimen(csvParser, study, lengthParser, seasonName, sampleLocation, speciesName, predatorId, predatorMap);
        }
        predator.ate(prey);
        Date date = parseCollectionDate(csvParser, study);
        try {
            nodeFactory.setUnixEpochProperty(predator, date);
            nodeFactory.setUnixEpochProperty(prey, date);
        } catch (NodeFactoryException e) {
            throw new StudyImporterException("specimen not associated to study", e);
        }
    }
}

Example 58 with Specimen

use of org.eol.globi.domain.Specimen 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 59 with Specimen

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

the class StudyImporterForSimons method addNextRecordToStudy.

private void addNextRecordToStudy(LabeledCSVParser csvParser, Study study, Map<String, String> columnToNormalizedTermMapper, LengthParser lengthParser) throws StudyImporterException {
    String seasonName = csvParser.getValueByLabel(columnToNormalizedTermMapper.get(SEASON));
    Specimen prey = createAndClassifySpecimen(csvParser.getValueByLabel(columnToNormalizedTermMapper.get(PREY_SPECIES)), study);
    Location sampleLocation = getOrCreateSampleLocation(csvParser, columnToNormalizedTermMapper);
    prey.caughtIn(sampleLocation);
    prey.caughtDuring(getOrCreateSeason(seasonName));
    String speciesName = csvParser.getValueByLabel(columnToNormalizedTermMapper.get(PREDATOR_SPECIES));
    // see https://github.com/jhpoelen/gomexsi/issues/41
    String occurrenceId = csvParser.getValueByLabel("spcode") + csvParser.getValueByLabel("sizecl") + csvParser.getValueByLabel("cruise") + csvParser.getValueByLabel("stcode");
    Map<String, Specimen> predatorMap = getPredatorSpecimenMap();
    Specimen predator = predatorMap.get(occurrenceId);
    if (predator == null) {
        predator = createAndClassifySpecimen(speciesName, study);
        predator.setLengthInMm(lengthParser.parseLengthInMm(csvParser));
        predator.caughtDuring(getOrCreateSeason(seasonName));
        predator.caughtIn(sampleLocation);
        predatorMap.put(occurrenceId, predator);
    }
    predator.ate(prey);
}

Example 60 with Specimen

use of org.eol.globi.domain.Specimen 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);
            }
        }
    }
}