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

Example 46 with StudyImpl

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

the class StudyImporterForStrona method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    LabeledCSVParser dataParser;
    try {
        dataParser = parserFactory.createParser(RESOURCE_PATH, CharsetConstant.UTF8);
    } catch (IOException e) {
        throw new StudyImporterException("failed to read resource [" + RESOURCE_PATH + "]", e);
    }
    try {
        Study study = nodeFactory.getOrCreateStudy(new StudyImpl("strona2013", SOURCE + " . " + CitationUtil.createLastAccessedString(RESOURCE_PATH), "http://dx.doi.org/10.1890/12-1419.1", SOURCE));
        while (dataParser.getLine() != null) {
            if (importFilter.shouldImportRecord((long) dataParser.getLastLineNumber())) {
                try {
                    String parasiteName = StringUtils.trim(dataParser.getValueByLabel("P_SP"));
                    String hostName = StringUtils.trim(dataParser.getValueByLabel("H_SP"));
                    if (areNamesAvailable(parasiteName, hostName)) {
                        Specimen parasite = nodeFactory.createSpecimen(study, new TaxonImpl(parasiteName, null));
                        Specimen host = nodeFactory.createSpecimen(study, new TaxonImpl(hostName, null));
                        parasite.interactsWith(host, InteractType.PARASITE_OF);
                    }
                } catch (NodeFactoryException | NumberFormatException e) {
                    throw new StudyImporterException("failed to import line [" + (dataParser.lastLineNumber() + 1) + "]", e);
                }
            }
        }
    } catch (IOException | NodeFactoryException e) {
        throw new StudyImporterException("problem importing [" + RESOURCE_PATH + "]", e);
    }
}

Example 47 with StudyImpl

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

the class StudyImporterForSimons method importStudy.

private Study importStudy(ParserFactory parserFactory, String studyResource) throws StudyImporterException {
    Study study = nodeFactory.getOrCreateStudy(new StudyImpl("Simons 1997", StudyImporterForGoMexSI2.GOMEXI_SOURCE_DESCRIPTION, null, ExternalIdUtil.toCitation("James D. Simons", "Food habits and trophic structure of the demersal fish assemblages on the Mississippi-Alabama continental shelf.", "1997")));
    try {
        LabeledCSVParser csvParser = parserFactory.createParser(studyResource, CharsetConstant.UTF8);
        Map<String, String> columnMapper = COLUMN_MAPPER;
        LengthParser parser = new LengthRangeParserImpl(columnMapper.get(LENGTH_RANGE_IN_MM));
        while (csvParser.getLine() != null) {
            addNextRecordToStudy(csvParser, study, COLUMN_MAPPER, parser);
        }
    } catch (IOException e) {
        throw new StudyImporterException("failed to createTaxon study [" + studyResource + "]", e);
    }
    return study;
}

Example 48 with StudyImpl

use of org.eol.globi.domain.StudyImpl 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 49 with StudyImpl

use of org.eol.globi.domain.StudyImpl 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 50 with StudyImpl

use of org.eol.globi.domain.StudyImpl 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"));
}