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

Example 16 with LocationImpl

use of org.eol.globi.domain.LocationImpl 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 17 with LocationImpl

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

Example 18 with LocationImpl

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

the class StudyImporterForBell method getLocation.

protected Location getLocation(LabeledCSVParser parser, Specimen parasite) throws NodeFactoryException {
    String latitude = parser.getValueByLabel("DEC_LAT");
    String longitude = parser.getValueByLabel("DEC_LONG");
    Location location = null;
    if (StringUtils.isNotBlank(latitude) && StringUtils.isNotBlank(longitude)) {
        location = nodeFactory.getOrCreateLocation(new LocationImpl(Double.parseDouble(latitude), Double.parseDouble(longitude), null, null));
    }
    return location;
}

Example 19 with LocationImpl

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

the class StudyImporterForSzoboszlaiIT method importAll.

@Test
public void importAll() throws StudyImporterException, IOException {
    JsonNode config = new ObjectMapper().readTree("{ \"citation\": \"Szoboszlai AI, Thayer JA, Wood SA, Sydeman WJ, Koehn LE (2015) Data from: Forage species in predator diets: synthesis of data from the California Current. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.nv5d2\",\n" + "  \"doi\": \"http://dx.doi.org/10.5061/dryad.nv5d2\",\n" + "  \"format\": \"szoboszlai\",\n" + "  \"resources\": {\n" + "    \"links\": \"http://datadryad.org/bitstream/handle/10255/dryad.94536/CCPDDlinkdata_v1.csv\",\n" + "    \"shapes\": \"http://datadryad.org/bitstream/handle/10255/dryad.94535/CCPDDlocationdata_v1.zip\"\n" + "  }\n" + "}");
    DatasetImpl dataset = new DatasetImpl("someRepo", URI.create("http://example.com"));
    dataset.setConfig(config);
    ParserFactory parserFactory = new ParserFactoryForDataset(dataset);
    StudyImporterForSzoboszlai importer = new StudyImporterForSzoboszlai(parserFactory, nodeFactory);
    importer.setDataset(dataset);
    importStudy(importer);
    List<Study> allStudies = NodeUtil.findAllStudies(getGraphDb());
    assertThat(allStudies.size(), is(not(0)));
    Study firstStudy = allStudies.get(0);
    Iterable<Relationship> specimens = NodeUtil.getSpecimens(firstStudy);
    for (Relationship specimen : specimens) {
        Specimen specimenNode = new SpecimenNode(specimen.getEndNode());
        Location sampleLocation = specimenNode.getSampleLocation();
        assertThat(sampleLocation, is(notNullValue()));
        assertThat(sampleLocation.getLatitude(), is(notNullValue()));
        assertThat(sampleLocation.getLongitude(), is(notNullValue()));
    }
    assertThat(taxonIndex.findTaxonByName("Thunnus thynnus"), is(notNullValue()));
    assertThat(nodeFactory.findLocation(new LocationImpl(34.00824202376044, -120.72716166720323, null, null)), is(notNullValue()));
}

Example 20 with LocationImpl

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

the class StudyImporterForBrose method addInteractionForConsumer.

private void addInteractionForConsumer(LabeledCSVParser parser, Study localStudy, String predatorName) throws NodeFactoryException, StudyImporterException {
    Location location = null;
    String locationString = parser.getValueByLabel("Geographic location");
    LatLng latLng = LOC_MAP.get(StringUtils.trim(locationString));
    if (latLng == null) {
        getLogger().warn(localStudy, "failed to find location for [" + locationString + "]");
    } else {
        location = nodeFactory.getOrCreateLocation(new LocationImpl(latLng.getLat(), latLng.getLng(), null, null));
        String habitat = StringUtils.join(parser.getValueByLabel("General habitat"), " ", parser.getValueByLabel("Specific habitat"));
        String habitatId = "BROSE:" + habitat.replaceAll("\\W", "_");
        nodeFactory.getOrCreateEnvironments(location, habitatId, habitat);
    }
    Specimen consumer = nodeFactory.createSpecimen(localStudy, new TaxonImpl(predatorName, null));
    consumer.caughtIn(location);
    addLifeStage(parser, consumer, "Lifestage consumer");
    String name = getName(parser, "Taxonomy resource", "Common name(s) resource");
    if (StringUtils.isBlank(name) || StringUtils.length(name) < 2) {
        String message = "found (near) empty prey name on line [" + parser.lastLineNumber() + "] + [" + name + "]";
        LOG.warn(message);
        getLogger().warn(localStudy, message);
    } else {
        Specimen resource = nodeFactory.createSpecimen(localStudy, new TaxonImpl(name, null));
        resource.caughtIn(location);
        addLifeStage(parser, resource, "Lifestage - resource");
        String interactionType = parser.getValueByLabel("Type of feeding interaction");
        Map<String, InteractType> typeMapping = new HashMap<String, InteractType>() {

            {
                put("predacious", InteractType.PREYS_UPON);
                put("predator", InteractType.PREYS_UPON);
                put("herbivorous", InteractType.ATE);
                put("parasitoid", InteractType.PARASITE_OF);
                put("parasitic", InteractType.PARASITE_OF);
                put("bacterivorous", InteractType.ATE);
                put("omnivore", InteractType.ATE);
                put("detritivorous", InteractType.ATE);
                put("pathogen", InteractType.PATHOGEN_OF);
            }
        };
        InteractType interactType = typeMapping.get(interactionType);
        if (interactType == null) {
            throw new StudyImporterException("found unsupported interaction type [" + interactionType + "]");
        }
        consumer.interactsWith(resource, interactType);
    }
}