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

Example 1 with Term

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

the class StudyImporterForKelpForest method createSpecimen.

protected Specimen createSpecimen(LabeledCSVParser parser, Map<String, Long> nameToId, String nameLabel, String stageLabel, Study study) throws NodeFactoryException {
    String sourceName = parser.getValueByLabel(nameLabel);
    Long id = nameToId.get(sourceName);
    String taxonExternalId = id == null ? null : TaxonomyProvider.ID_PREFIX_ITIS + id;
    Specimen sourceSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl(sourceName, taxonExternalId));
    String sourceLifeStage = parser.getValueByLabel(stageLabel);
    Term orCreateLifeStage = nodeFactory.getOrCreateLifeStage("KELP:" + sourceLifeStage, sourceLifeStage);
    sourceSpecimen.setLifeStage(orCreateLifeStage);
    return sourceSpecimen;
}

Example 2 with Term

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

the class StudyImporterForSPIRE method addLifeStage.

private void addLifeStage(Specimen specimen, String name) throws NodeFactoryException {
    Term terms;
    terms = nodeFactory.getOrCreateLifeStage("SPIRE:" + name, name);
    specimen.setLifeStage(terms);
}

Example 3 with Term

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

the class StudyImporterForHurlbert method importInteraction.

protected void importInteraction(Set<String> regions, Set<String> locales, Set<String> habitats, Record record, Study study, String preyTaxonName, String predatorName) throws StudyImporterException {
    try {
        Taxon predatorTaxon = new TaxonImpl(predatorName);
        Specimen predatorSpecimen = nodeFactory.createSpecimen(study, predatorTaxon);
        setBasisOfRecordAsLiterature(predatorSpecimen);
        Taxon preyTaxon = new TaxonImpl(preyTaxonName);
        String preyNameId = StringUtils.trim(columnValueOrNull(record, "Prey_Name_ITIS_ID"));
        if (NumberUtils.isDigits(preyNameId)) {
            preyTaxon.setExternalId(TaxonomyProvider.ITIS.getIdPrefix() + preyNameId);
        }
        Specimen preySpecimen = nodeFactory.createSpecimen(study, preyTaxon);
        setBasisOfRecordAsLiterature(preySpecimen);
        String preyStage = StringUtils.trim(columnValueOrNull(record, "Prey_Stage"));
        if (StringUtils.isNotBlank(preyStage)) {
            Term lifeStage = nodeFactory.getOrCreateLifeStage("HULBERT:" + StringUtils.replace(preyStage, " ", "_"), preyStage);
            preySpecimen.setLifeStage(lifeStage);
        }
        String preyPart = StringUtils.trim(columnValueOrNull(record, "Prey_Part"));
        if (StringUtils.isNotBlank(preyPart)) {
            Term term = nodeFactory.getOrCreateBodyPart("HULBERT:" + StringUtils.replace(preyPart, " ", "_"), preyPart);
            preySpecimen.setBodyPart(term);
        }
        Date date = addCollectionDate(record, study);
        nodeFactory.setUnixEpochProperty(predatorSpecimen, date);
        nodeFactory.setUnixEpochProperty(preySpecimen, date);
        LocationImpl location = new LocationImpl(null, null, null, null);
        String longitude = columnValueOrNull(record, "Longitude_dd");
        String latitude = columnValueOrNull(record, "Latitude_dd");
        if (NumberUtils.isNumber(latitude) && NumberUtils.isNumber(longitude)) {
            try {
                LatLng latLng = LocationUtil.parseLatLng(latitude, longitude);
                String altitude = columnValueOrNull(record, "Altitude_mean_m");
                Double altitudeD = NumberUtils.isNumber(altitude) ? Double.parseDouble(altitude) : null;
                location = new LocationImpl(latLng.getLat(), latLng.getLng(), altitudeD, null);
            } catch (InvalidLocationException e) {
                getLogger().warn(study, "found invalid (lat,lng) pair: (" + latitude + "," + longitude + ")");
            }
        }
        String locationRegion = columnValueOrNull(record, "Location_Region");
        String locationSpecific = columnValueOrNull(record, "Location_Specific");
        location.setLocality(StringUtils.join(Arrays.asList(locationRegion, locationSpecific), ":"));
        Location locationNode = nodeFactory.getOrCreateLocation(location);
        String habitat_type = columnValueOrNull(record, "Habitat_type");
        List<Term> habitatList = Arrays.stream(StringUtils.split(StringUtils.defaultIfBlank(habitat_type, ""), ";")).map(StringUtils::trim).map(habitat -> new TermImpl(idForHabitat(habitat), habitat)).collect(Collectors.toList());
        nodeFactory.addEnvironmentToLocation(locationNode, habitatList);
        preySpecimen.caughtIn(locationNode);
        predatorSpecimen.caughtIn(locationNode);
        predatorSpecimen.ate(preySpecimen);
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to create interaction between [" + predatorName + "] and [" + preyTaxonName + "]", e);
    }
}

Example 4 with Term

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

the class StudyImporterForHechinger method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    Study study = createStudy();
    try {
        LabeledCSVParser nodes = parserFactory.createParser(getNodesResourceName(), CharsetConstant.UTF8);
        nodes.changeDelimiter(getDelimiter());
        Map<Integer, Term> stageForNode = new HashMap<>();
        Map<Integer, String> taxonForNode = new HashMap<Integer, String>();
        while (nodes.getLine() != null) {
            Integer nodeId = getNodeId(nodes);
            if (nodeId != null) {
                String name = parseMostGranularTaxonName(nodes);
                if (StringUtils.isBlank(name)) {
                    name = nodes.getValueByLabel("WorkingName");
                    if (StringUtils.isBlank(name)) {
                        getLogger().warn(study, "failed to find name for node on line [" + nodes.lastLineNumber() + "]");
                    }
                }
                if (StringUtils.isNotBlank(name)) {
                    try {
                        taxonForNode.put(nodeId, name);
                        String stage = nodes.getValueByLabel("Stage");
                        stageForNode.put(nodeId, nodeFactory.getOrCreateLifeStage(getNamespace() + ":" + stage, stage));
                    } catch (NodeFactoryException e) {
                        throw new StudyImporterException("failed to reader line [" + nodes.lastLineNumber() + "]", e);
                    }
                }
            }
        }
        LabeledCSVParser links = parserFactory.createParser(getLinksResourceName(), CharsetConstant.UTF8);
        links.changeDelimiter(getDelimiter());
        while (links.getLine() != null) {
            List<Location> locations = new ArrayList<>();
            if (getLocation() != null) {
                Location loc = nodeFactory.getOrCreateLocation(new LocationImpl(getLocation().getLat(), getLocation().getLng(), null, null));
                if (loc != null) {
                    locations.add(loc);
                }
            }
            if (StringUtils.equals("1", links.getValueByLabel("PresentAtCSM"))) {
                locations.add(nodeFactory.getOrCreateLocation(new LocationImpl(34.403511, -119.537873, null, null)));
            }
            if (StringUtils.equals("1", links.getValueByLabel("PresentAtEPB"))) {
                locations.add(nodeFactory.getOrCreateLocation(new LocationImpl(31.748606, -116.626854, null, null)));
            }
            if (StringUtils.equals("1", links.getValueByLabel("PresentAtBSQ"))) {
                locations.add(nodeFactory.getOrCreateLocation(new LocationImpl(30.378207, -115.938835, null, null)));
            }
            for (Location location : locations) {
                addLink(study, stageForNode, taxonForNode, links, location);
            }
        }
    } catch (IOException | NodeFactoryException e) {
        throw new StudyImporterException("failed import study", e);
    }
}

Example 5 with Term

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

the class StudyImporterForGoMexSI2 method addPhysiologicalState.

private void addPhysiologicalState(Map<String, String> properties, Specimen specimen) throws StudyImporterException {
    try {
        String name = properties.get(SpecimenConstant.PHYSIOLOGICAL_STATE_LABEL);
        Term term = nodeFactory.getOrCreatePhysiologicalState(GOMEXSI_NAMESPACE + name, name);
        specimen.setPhysiologicalState(term);
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to map life stage", e);
    }
}