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

Example 11 with Location

use of org.eol.globi.domain.Location 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 12 with Location

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

the class StudyImporterForGoMexSI2 method addObservations.

private void addObservations(Map<String, Map<String, String>> predatorIdToPredatorSpecimen, Map<String, Study> refIdToStudyMap, Map<String, List<Map<String, String>>> predatorUIToPreyLists, Study metaStudy) throws StudyImporterException {
    String locationResource = getLocationsResourcePath();
    try {
        TermLookupService cmecsService = new CMECSService();
        LabeledCSVParser parser = parserFactory.createParser(locationResource, CharsetConstant.UTF8);
        while (parser.getLine() != null) {
            String refId = getMandatoryValue(locationResource, parser, "DATA_ID");
            if (!refIdToStudyMap.containsKey(refId)) {
                getLogger().warn(metaStudy, "failed to find study for ref id [" + refId + "] on related to observation location in [" + locationResource + ":" + parser.getLastLineNumber() + "]");
            } else {
                Study study = refIdToStudyMap.get(refId);
                String specimenId = getMandatoryValue(locationResource, parser, "PRED_ID");
                Location location = parseLocation(locationResource, parser);
                Location locationNode = nodeFactory.getOrCreateLocation(location);
                enrichLocation(metaStudy, locationResource, cmecsService, parser, locationNode);
                String predatorId = refId + specimenId;
                Map<String, String> predatorProperties = predatorIdToPredatorSpecimen.get(predatorId);
                if (predatorProperties == null) {
                    getLogger().warn(study, "failed to lookup predator [" + refId + ":" + specimenId + "] for location at [" + locationResource + ":" + (parser.getLastLineNumber() + 1) + "]");
                } else {
                    addObservation(predatorUIToPreyLists, parser, study, locationNode, predatorId, predatorProperties);
                }
            }
        }
    } catch (IOException e) {
        throw new StudyImporterException("failed to open resource [" + locationResource + "]", e);
    }
}

Example 13 with Location

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

the class StudyImporterForINaturalist method createAssociation.

private Specimen createAssociation(long observationId, String interactionDataType, InteractType interactType, JsonNode observation, Taxon targetTaxon, Taxon sourceTaxonName, Study study, Date observationDate) throws StudyImporterException, NodeFactoryException {
    Specimen sourceSpecimen = getSourceSpecimen(observationId, interactionDataType, sourceTaxonName, study);
    setBasisOfRecord(sourceSpecimen);
    Specimen targetSpecimen = nodeFactory.createSpecimen(study, targetTaxon);
    setBasisOfRecord(targetSpecimen);
    sourceSpecimen.interactsWith(targetSpecimen, interactType);
    setCollectionDate(sourceSpecimen, targetSpecimen, observationDate);
    setCollectionDate(sourceSpecimen, sourceSpecimen, observationDate);
    Location location = parseLocation(observation);
    sourceSpecimen.caughtIn(location);
    targetSpecimen.caughtIn(location);
    return sourceSpecimen;
}

Example 14 with Location

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

the class ExporterOccurrencesTest method createTestData.

private void createTestData(Double length) throws NodeFactoryException, ParseException {
    Study myStudy = nodeFactory.createStudy(new StudyImpl("myStudy", null, null, null));
    Specimen specimen = nodeFactory.createSpecimen(myStudy, new TaxonImpl("Homo sapiens", "EOL:327955"));
    specimen.setStomachVolumeInMilliLiter(666.0);
    specimen.setLifeStage(new TermImpl("GLOBI:JUVENILE", "JUVENILE"));
    specimen.setPhysiologicalState(new TermImpl("GLOBI:DIGESTATE", "DIGESTATE"));
    specimen.setBodyPart(new TermImpl("GLOBI:BONE", "BONE"));
    nodeFactory.setUnixEpochProperty(specimen, ExportTestUtil.utcTestDate());
    if (null != length) {
        specimen.setLengthInMm(length);
    }
    Location location = nodeFactory.getOrCreateLocation(new LocationImpl(12.0, -1.0, -60.0, null));
    specimen.caughtIn(location);
    Specimen wolf1 = eatWolf(specimen, myStudy);
    wolf1.caughtIn(location);
    Specimen wolf2 = eatWolf(specimen, myStudy);
    wolf2.caughtIn(location);
}

Example 15 with Location

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

the class StudyImporterForCook method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    LabeledCSVParser parser;
    try {
        parser = parserFactory.createParser(DATASET_RESOURCE_NAME, CharsetConstant.UTF8);
    } catch (IOException e) {
        throw new StudyImporterException("failed to read resource", e);
    }
    String citation = "Cook CW. The Early Life History and Reproductive Biology of Cymothoa excisa, a Marine Isopod Parasitizing Atlantic Croaker, (Micropogonias undulatus), along the Texas Coast. 2012. Master Thesis. Available from http://repositories.lib.utexas.edu/handle/2152/ETD-UT-2012-08-6285.";
    StudyImpl study1 = new StudyImpl("Cook 2012", "Data provided by Colt W. Cook. Also available from  http://repositories.lib.utexas.edu/handle/2152/ETD-UT-2012-08-6285.", null, citation);
    study1.setExternalId("http://repositories.lib.utexas.edu/handle/2152/ETD-UT-2012-08-6285");
    Study study = nodeFactory.getOrCreateStudy(study1);
    try {
        Double latitude = LocationUtil.parseDegrees("27º51'N");
        Double longitude = LocationUtil.parseDegrees("97º8'W");
        Location sampleLocation = nodeFactory.getOrCreateLocation(new LocationImpl(latitude, longitude, -3.0, null));
        try {
            while (parser.getLine() != null) {
                Specimen host = nodeFactory.createSpecimen(study, new TaxonImpl("Micropogonias undulatus", null));
                host.setLengthInMm(Double.parseDouble(parser.getValueByLabel("Fish Length")) * 10.0);
                String dateString = parser.getValueByLabel("Date");
                Date collectionDate = DateUtil.parsePatternUTC(dateString, "MM/dd/yyyy").toDate();
                nodeFactory.setUnixEpochProperty(host, collectionDate);
                host.caughtIn(sampleLocation);
                String[] isoCols = { "Iso 1", "Iso 2", "Iso 3", "Iso 4 ", "Iso 5" };
                for (String isoCol : isoCols) {
                    addParasites(parser, study, sampleLocation, host, collectionDate, isoCol);
                }
            }
        } catch (IOException e) {
            throw new StudyImporterException("failed to parse [" + DATASET_RESOURCE_NAME + "]", e);
        } catch (IllegalArgumentException e) {
            throw new StudyImporterException("failed to parse date", e);
        }
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to create host and parasite taxons", e);
    }
}