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

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Example 26 with Location

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

the class StudyImporterForAkin method parseLine.

private void parseLine(String[][] siteInfos, String studyResource, Study study, LabeledCSVParser parser, String[] header, String[] line) throws NodeFactoryException, IOException {
    try {
        Specimen specimen = addSpecimen(study, parser, header, line);
        if (specimen != null) {
            Location location = parseLocation(findSiteInfo(header, line, siteInfos, parser));
            specimen.caughtIn(location);
            addPrey(study, parser, header, line, specimen, location);
        }
    } catch (StudyImporterException ex) {
        getLogger().warn(study, "[" + studyResource + "]:" + ex.getMessage());
    }
}
Also used : Specimen(org.eol.globi.domain.Specimen) Location(org.eol.globi.domain.Location)

Example 27 with Location

use of org.eol.globi.domain.Location 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);
    }
}
Also used : Specimen(org.eol.globi.domain.Specimen) TaxonImpl(org.eol.globi.domain.TaxonImpl) LocationImpl(org.eol.globi.domain.LocationImpl) Location(org.eol.globi.domain.Location)

Example 28 with Location

use of org.eol.globi.domain.Location 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);
        }
    }
}
Also used : Specimen(org.eol.globi.domain.Specimen) LocationImpl(org.eol.globi.domain.LocationImpl) LatLng(org.eol.globi.geo.LatLng) Date(java.util.Date) Location(org.eol.globi.domain.Location)

Example 29 with Location

use of org.eol.globi.domain.Location 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);
}
Also used : Specimen(org.eol.globi.domain.Specimen) Location(org.eol.globi.domain.Location)

Example 30 with Location

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

the class StudyImporterForWrastTest method createAndPopulateStudyFromLavacaBay.

@Test
public void createAndPopulateStudyFromLavacaBay() throws StudyImporterException, ParseException {
    String csvString = "\"Month\",\"Day\",\"Year\",\"Region\",\"Season\",\"Habitat\",\"Site\",\"Family\",\"Predator Species\",\"TL (mm)\",\"Prey Item Species\",\"Prey item\",\"Number\",\"Condition Index\",\"Volume\",\"Percent Content\",\"Prey Item Trophic Level\",\"Notes\",\"Call #\"\n";
    csvString += "7,24,2001,\"Lower\",\"Fall\",\"Marsh\",1,\"Sciaenidae\",\"Sciaenops ocellatus\",420,\"Acrididae spp. \",\"Acrididae \",1,\"III\",0.4,3.2520325203,2.5,,1\n";
    csvString += "7,25,2001,\"Lower\",\"Spring\",\"Non-Veg \",1,\"Ariidae\",\"Arius felis\",176,\"Aegathoa oculata \",\"Aegathoa oculata\",4,\"I\",0.01,3.3333333333,2.1,,2\n";
    csvString += "7,26,2001,\"Upper\",\"Spring\",\"Reef\",2,\"Depth\",\"Missing depth\",176,\"Aegathoa oculata \",\"Aegathoa oculata\",4,\"I\",0.01,3.3333333333,2.1,,2\n";
    Map<String, String> contentMap = new HashMap<String, String>();
    String locationString = "\"Location\",\"Latitude\",\"Longitude\",,\"Region\",\"Habitat\",\"Site\"\n" + "\"LM1\",28.595267,-96.477033,,\"Lower\",\"Marsh edge\",1\n" + "\"LSG1\",28.596233,-96.476483,,\"Lower\",\"Marsh edge\",1\n" + "\"LM2\",28.593150,-96.474633,,\"Lower\",\"Marsh edge\",2\n" + "\"LSG2\",28.594833,-96.473967,,\"Lower\",\"Marsh edge\",2\n" + "\"LNV1A\",28.608417,-96.475517,,\"Lower\",\"Non-Veg \",1\n" + "\"LNV1B\",28.607217,-96.474500,,\"Lower\",\"Non-Veg \",1\n" + "\"LNV2A\",28.592400,-96.483033,,\"Lower\",\"Non-Veg \",2\n" + "\"LNV2B\",28.590883,-96.484133,,\"Lower\",\"Non-Veg \",2\n" + "\"UR2B\",28.656483,-96.597217,,\"Upper\",\"Reef\",2";
    String envString = "\"Date\",\"Season\",\"Upper/Lower\",\"Habitat\",\"Site\",\"Air Temp (ºC)\",\"Wind Chill (ºC)\",\"Relative Humidity (%)\",\"Heat Index (ºC)\",\"Dew Point (ºC)\",\"Max Wind intensity (mph)\",\"Ave Wind intensity (mph)\",\"Wind Direction\",\"Cloud Cover (%)\",\"Rain?\",\"Depth (m)\",\"Temp (ºC) Surface\",\"Temp (ºC) Bottom\",\"Mean Temp Surface/Bottom\",\"pH Surface\",\"pH Bottom\",\"Mean pH Surface/Bottom\",\"DO (mg/L) Surface\",\"DO (mg/L) Bottom\",\"Mean DO Surface/Bottom\",\"Sal (o/oo) Surface\",\"Sal (o/oo) Bottom\",\"Mean Sal Surface/Bottom\",\"Secchi (m)\"\n" + "7/24/2006,\"Summer\",\"L\",\"R\",1,\"81.3 (F)\",\"81.5 (F)\",71.8,\"86.2 (F)\",\"70.6 (F)\",8.5,8.1,\"SE\",75,\"Yes\",1.9,30.79,30.34,30.565,8.11,8.13,8.12,5.16,4.8,4.98,22.8,23.07,22.935,0.4\n" + "7/24/2006,\"Summer\",\"L\",\"R\",2,\"81.3 (F)\",\"81.5 (F)\",71.8,\"86.2 (F)\",\"70.6 (F)\",8.5,8.1,\"SE\",75,\"Yes\",2.1,31.07,30.14,30.605,8.11,8.1,8.105,5.14,4.64,4.89,23.37,23.84,23.605,0.48\n" + "10/26/2006,\"Fall\",\"L\",\"M\",1,26.8,26.5,78,30,22.4,17.9,15,\"S \",95,\"No\",0.8,25.57,,25.57,8.29,,8.29,8.32,,8.32,21.26,,21.26,\"Bottom\"\n" + "10/26/2006,\"Fall\",\"L\",\"M\",2,26.8,26.5,78,30,22.4,17.9,15,\"S \",95,\"No\",0.4,25.84,,25.84,8.32,,8.32,8.21,,8.21,21.47,,21.47,\"Bottom\"\n" + "10/26/2006,\"Fall\",\"L\",\"SG\",1,26.8,26.5,78,30,22.4,17.9,15,\"S \",95,\"No\",0.8,25.57,,25.57,8.29,,8.29,8.32,,8.32,21.26,,21.26,\"Bottom\"\n" + "4/27/2007,\"Spring\",\"L\",\"R\",1,22.4,22.3,75,23.1,18.1,10.4,9.1,\"NW\",98,\"No\",1.6,23.43,23.39,23.41,,,,7.31,7.09,7.2,14.64,14.64,14.64,0.32\n" + "4/27/2007,\"Spring\",\"L\",\"R\",2,22.4,22.3,75,23.1,18.1,10.4,9.1,\"NW\",98,\"No\",2,23.77,23.77,23.77,,,,7.01,6.82,6.915,15.04,15.04,15.04,0.38\n" + "4/27/2007,\"Spring\",\"L\",\"NV\",1,22.4,22.3,75,23.1,18.1,10.4,9.1,\"NW\",98,\"No\",2,23.85,23.85,23.85,,,,6.96,6.81,6.885,14.65,14.65,14.65,0.48\n" + "4/27/2007,\"Spring\",\"L\",\"NV\",2,22.4,22.3,75,23.1,18.1,10.4,9.1,\"NW\",98,\"No\",1.8,23.78,23.78,23.78,,,,6.87,6.65,6.76,15.11,15.18,15.145,0.45";
    contentMap.put(StudyImporterForWrast.LAVACA_BAY_LOCATIONS, locationString);
    contentMap.put(StudyImporterForWrast.LAVACA_BAY_DATA_SOURCE, csvString);
    contentMap.put(StudyImporterForWrast.LAVACA_BAY_ENVIRONMENTAL, envString);
    StudyImporterForWrast importer = new StudyImporterForWrast(new TestParserFactory(contentMap), nodeFactory);
    importStudy(importer);
    Study study = getStudySingleton(getGraphDb());
    int specimenCount = 0;
    for (Relationship specimen : NodeUtil.getSpecimens(study)) {
        specimenCount++;
    }
    assertThat(specimenCount, is(5));
    assertNotNull(taxonIndex.findTaxonByName("Sciaenops ocellatus"));
    assertNotNull(taxonIndex.findTaxonByName("Arius felis"));
    assertNotNull(taxonIndex.findTaxonByName("Aegathoa oculata"));
    assertNotNull(nodeFactory.findSeason("spring"));
    assertNotNull(nodeFactory.findSeason("fall"));
    Study foundStudy = nodeFactory.findStudy("Wrast 2008");
    assertNotNull(foundStudy);
    for (Relationship rel : NodeUtil.getSpecimens(study)) {
        Date unixEpochProperty = nodeFactory.getUnixEpochProperty(new SpecimenNode(rel.getEndNode()));
        SimpleDateFormat simpleDateFormat = StudyImporterForWrast.getSimpleDateFormat();
        Date endDate = simpleDateFormat.parse("7/27/2001");
        Date startDate = simpleDateFormat.parse("7/23/2001");
        assertThat(unixEpochProperty.before(endDate), is(true));
        assertThat(unixEpochProperty.after(startDate), is(true));
        Specimen specimen = new SpecimenNode(rel.getEndNode());
        for (Relationship ateRel : NodeUtil.getStomachContents(specimen)) {
            TaxonNode taxon = new TaxonNode(rel.getEndNode().getSingleRelationship(NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS), Direction.OUTGOING).getEndNode());
            String scientificName = taxon.getName();
            if ("Sciaenops ocellatus".equals(scientificName)) {
                Location location = specimen.getSampleLocation();
                assertThat(location, is(not(nullValue())));
                assertThat(location.getLatitude(), is((28.595267 + 28.596233) / 2.0));
                assertThat(location.getLongitude(), is((-96.477033 - 96.476483) / 2.0));
                assertThat(location.getAltitude(), is(-0.8));
                Iterable<Relationship> stomachContents = NodeUtil.getStomachContents(specimen);
                int count = 0;
                for (Relationship containsRel : stomachContents) {
                    Node endNode = containsRel.getEndNode().getSingleRelationship(NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS), Direction.OUTGOING).getEndNode();
                    Object name = endNode.getProperty("name");
                    String name1 = (String) name;
                    assertThat(name1.replaceAll("\\W", ""), is("Acrididae"));
                    count++;
                }
                assertEquals(1, count);
                Season season = specimen.getSeason();
                assertEquals("fall", season.getTitle());
                assertEquals(420.0d, specimen.getLengthInMm());
            } else if ("Arius felis".equals(scientificName)) {
                Location location = specimen.getSampleLocation();
                assertThat(location, is(not(nullValue())));
                assertThat(location.getLatitude(), is((28.608417 + 28.607217) / 2.0));
                assertThat(location.getLongitude(), is((-96.475517 - 96.474500) / 2.0));
                assertThat(location.getAltitude(), is(-2.0d));
                Iterable<Relationship> stomachContents = NodeUtil.getStomachContents(specimen);
                int count = 0;
                for (Relationship containsRel : stomachContents) {
                    Object name = containsRel.getEndNode().getSingleRelationship(NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS), Direction.OUTGOING).getEndNode().getProperty("name");
                    assertEquals("Aegathoa oculata", name);
                    count++;
                }
                assertEquals(2, count);
                Season season = specimen.getSeason();
                assertEquals("spring", season.getTitle());
                assertEquals(176.0d, specimen.getLengthInMm());
            } else if ("Missing depth".equals(scientificName)) {
                Location location = specimen.getSampleLocation();
                assertThat(location, is(not(nullValue())));
                assertThat(location.getAltitude(), is(nullValue()));
            } else {
                fail("unexpected scientificName of predator [" + scientificName + "]");
            }
        }
    }
}
Also used : Study(org.eol.globi.domain.Study) TaxonNode(org.eol.globi.domain.TaxonNode) HashMap(java.util.HashMap) Node(org.neo4j.graphdb.Node) SpecimenNode(org.eol.globi.domain.SpecimenNode) TaxonNode(org.eol.globi.domain.TaxonNode) SpecimenNode(org.eol.globi.domain.SpecimenNode) Date(java.util.Date) Specimen(org.eol.globi.domain.Specimen) Relationship(org.neo4j.graphdb.Relationship) Season(org.eol.globi.domain.Season) SimpleDateFormat(java.text.SimpleDateFormat) Location(org.eol.globi.domain.Location) Test(org.junit.Test)

Aggregations

Location (org.eol.globi.domain.Location)44 LocationImpl (org.eol.globi.domain.LocationImpl)32 Specimen (org.eol.globi.domain.Specimen)31 Study (org.eol.globi.domain.Study)24 StudyImpl (org.eol.globi.domain.StudyImpl)16 TaxonImpl (org.eol.globi.domain.TaxonImpl)16 Date (java.util.Date)14 IOException (java.io.IOException)13 LabeledCSVParser (com.Ostermiller.util.LabeledCSVParser)12 HashMap (java.util.HashMap)8 LatLng (org.eol.globi.geo.LatLng)8 TermImpl (org.eol.globi.domain.TermImpl)6 Test (org.junit.Test)6 Relationship (org.neo4j.graphdb.Relationship)6 SpecimenNode (org.eol.globi.domain.SpecimenNode)5 ArrayList (java.util.ArrayList)4 Taxon (org.eol.globi.domain.Taxon)4 Node (org.neo4j.graphdb.Node)3 List (java.util.List)2 Map (java.util.Map)2
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