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

Example 61 with Specimen

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

the class StudyImporterForSIAD method downloadAndImportResource.

private void downloadAndImportResource(String resource, String source) throws StudyImporterException {
    try {
        LabeledCSVParser labeledCSVParser = parserFactory.createParser(resource, "UTF-8");
        labeledCSVParser.changeDelimiter('\t');
        while (labeledCSVParser.getLine() != null) {
            String name = labeledCSVParser.getValueByLabel("name");
            String ref = labeledCSVParser.getValueByLabel("source");
            String title = "SIAD-" + ref;
            String citation = "ABRS 2009. Australian Faunal Directory. " + name + ". Australian Biological Resources StudyNode, Canberra. " + CitationUtil.createLastAccessedString(ref);
            StudyImpl study1 = new StudyImpl(title, source, null, citation);
            study1.setExternalId(ref);
            Study study = nodeFactory.getOrCreateStudy(study1);
            Specimen specimen = nodeFactory.createSpecimen(study, new TaxonImpl(name, null));
            String hostName = labeledCSVParser.getValueByLabel("host name");
            Specimen hostSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl(hostName, null));
            InteractType type = map.get(labeledCSVParser.getValueByLabel("interaction"));
            specimen.interactsWith(hostSpecimen, type);
        }
    } catch (FileNotFoundException e) {
        throw new StudyImporterException("failed to open tmp file", e);
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to map data", e);
    } catch (IOException e) {
        throw new StudyImporterException("failed to read resource [" + resource + "]", e);
    }
}

Example 62 with Specimen

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

the class StudyImporterForSPIRETest method assertSingleImport.

private void assertSingleImport(String spireHabitat, String envoId, String envoLabel) throws NodeFactoryException {
    StudyImporterForSPIRE studyImporterForSPIRE = createImporter();
    HashMap<String, String> properties = new HashMap<String, String>();
    properties.put(StudyConstant.TITLE, "the study of men eating dogs");
    properties.put(StudyImporterForSPIRE.PREY_NAME, "dog");
    properties.put(StudyImporterForSPIRE.PREDATOR_NAME, "man");
    properties.put(StudyImporterForSPIRE.LOCALITY_ORIGINAL, "something");
    properties.put(StudyImporterForSPIRE.OF_HABITAT, spireHabitat);
    studyImporterForSPIRE.importTrophicLink(properties);
    resolveNames();
    Taxon dog = taxonIndex.findTaxonByName("dog");
    assertThat(dog, is(notNullValue()));
    Taxon man = taxonIndex.findTaxonByName("man");
    assertThat(man, is(notNullValue()));
    Iterable<Relationship> specimenRels = ((NodeBacked) man).getUnderlyingNode().getRelationships(Direction.INCOMING, NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS));
    int count = 0;
    for (Relationship specimenRel : specimenRels) {
        count++;
        Specimen specimen = new SpecimenNode(specimenRel.getStartNode());
        assertThat(specimen.getSampleLocation().getLatitude(), is(1.0));
        assertThat(specimen.getSampleLocation().getLongitude(), is(2.0));
        List<Environment> environments = specimen.getSampleLocation().getEnvironments();
        assertThat(environments.size(), is(1));
        Environment environment = environments.get(0);
        assertThat(environment.getExternalId(), is(envoId));
        assertThat(environment.getName(), is(envoLabel));
    }
    assertThat(count, is(1));
}

Example 63 with Specimen

use of org.eol.globi.domain.Specimen 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 64 with Specimen

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

the class TaxonInteractionIndexerTest method indexNoNameNoMatch.

@Test
public void indexNoNameNoMatch() throws NodeFactoryException {
    Specimen human = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Homo sapiens", PropertyAndValueDictionary.NO_MATCH));
    Specimen animal = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Canis lupus", PropertyAndValueDictionary.NO_MATCH));
    human.ate(animal);
    for (int i = 0; i < 10; i++) {
        Specimen fish = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Arius felis", null));
        human.ate(fish);
    }
    assertNull(taxonIndex.findTaxonById(PropertyAndValueDictionary.NO_MATCH));
    assertNull(taxonIndex.findTaxonByName("Homo sapiens"));
    new NameResolver(getGraphDb(), new NonResolvingTaxonIndex(getGraphDb())).resolve();
    assertNotNull(taxonIndex.findTaxonByName("Homo sapiens"));
    assertNull(taxonIndex.findTaxonById(PropertyAndValueDictionary.NO_MATCH));
    assertNull(taxonIndex.findTaxonByName(PropertyAndValueDictionary.NO_NAME));
}

Example 65 with Specimen

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

the class TaxonInteractionIndexerTest method buildTaxonInterIndex.

@Test
public void buildTaxonInterIndex() throws NodeFactoryException, PropertyEnricherException {
    Specimen human = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Homo sapiens", "NCBI:9606"));
    Specimen animal = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Canis lupus", "WORMS:2"));
    human.ate(animal);
    for (int i = 0; i < 10; i++) {
        Specimen fish = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Arius felis", "WORMS:158711"));
        human.ate(fish);
    }
    assertNull(taxonIndex.findTaxonById("WORMS:2"));
    assertNull(taxonIndex.findTaxonByName("Homo sapiens"));
    new NameResolver(getGraphDb(), new NonResolvingTaxonIndex(getGraphDb())).resolve();
    new TaxonInteractionIndexer(getGraphDb()).index();
    Taxon homoSapiens = taxonIndex.findTaxonByName("Homo sapiens");
    assertNotNull(homoSapiens);
    Iterable<Relationship> rels = ((NodeBacked) homoSapiens).getUnderlyingNode().getRelationships(Direction.OUTGOING, NodeUtil.asNeo4j(InteractType.ATE));
    List<String> humanFood = new ArrayList<String>();
    List<Long> counts = new ArrayList<Long>();
    List<String> labels = new ArrayList<>();
    for (Relationship rel : rels) {
        humanFood.add((String) rel.getEndNode().getProperty("name"));
        counts.add((Long) rel.getProperty("count"));
        labels.add((String) rel.getProperty("label"));
    }
    assertThat(humanFood.size(), is(4));
    assertThat(humanFood, hasItems("Arius felis", "Canis lupus"));
    assertThat(counts, hasItems(10L, 1L));
    assertThat(labels, hasItems("eats"));
}