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

Example 1 with Season

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

the class StudyImporterForSimons method getOrCreateSeason.

private Season getOrCreateSeason(String seasonName) {
    String seasonNameLower = seasonName.toLowerCase().trim();
    Season season = nodeFactory.findSeason(seasonNameLower);
    if (null == season) {
        season = nodeFactory.createSeason(seasonNameLower);
    }
    return season;
}

Example 2 with Season

use of org.eol.globi.domain.Season 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 + "]");
            }
        }
    }
}

Example 3 with Season

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

the class StudyImporterForWrast method getOrCreateSeason.

private Season getOrCreateSeason(String seasonName) {
    String seasonNameLower = seasonName.toLowerCase().trim();
    Season season = nodeFactory.findSeason(seasonNameLower);
    if (null == season) {
        season = nodeFactory.createSeason(seasonNameLower);
    }
    return season;
}