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

Example 31 with Specimen

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

the class NameResolverTest method iNaturalistTaxon.

@Test
public void iNaturalistTaxon() throws NodeFactoryException {
    Specimen someOtherOrganism = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Blaus bla", "INAT_TAXON:58831"));
    Specimen someOtherOrganism2 = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Redus rha", "INAT_TAXON:126777"));
    someOtherOrganism.ate(someOtherOrganism2);
    final NameResolver nameResolver = new NameResolver(getGraphDb(), new NonResolvingTaxonIndex(getGraphDb()));
    nameResolver.setBatchSize(1L);
    nameResolver.resolve();
    Taxon resolvedTaxon = taxonIndex.findTaxonById("INAT_TAXON:58831");
    assertThat(resolvedTaxon, is(notNullValue()));
    assertThat(resolvedTaxon.getExternalId(), is("INAT_TAXON:58831"));
    assertThat(resolvedTaxon.getName(), is("Blaus bla"));
    Taxon resolvedTaxon2 = taxonIndex.findTaxonByName("Blaus bla");
    assertThat(resolvedTaxon2, is(notNullValue()));
    assertThat(resolvedTaxon2.getExternalId(), is("INAT_TAXON:58831"));
}

Example 32 with Specimen

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

the class ReportGeneratorTest method createStudy.

protected Study createStudy(Study study1) throws NodeFactoryException {
    Study study = nodeFactory.getOrCreateStudy(study1);
    Specimen monkey = nodeFactory.createSpecimen(study, new TaxonImpl("Monkey"));
    monkey.ate(nodeFactory.createSpecimen(study, new TaxonImpl("Banana")));
    monkey.ate(nodeFactory.createSpecimen(study, new TaxonImpl("Banana")));
    monkey.ate(nodeFactory.createSpecimen(study, new TaxonImpl("Banana")));
    TaxonImpl apple = new TaxonImpl("Apple", "some:id");
    apple.setPath("some | path");
    monkey.ate(nodeFactory.createSpecimen(study, apple));
    return study;
}

Example 33 with Specimen

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

the class StudyImporterForCoetzer method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    if (org.apache.commons.lang.StringUtils.isBlank(getResourceArchiveURI())) {
        throw new StudyImporterException("failed to import [" + getDataset().getNamespace() + "]: no [archiveURL] specified");
    }
    DB db = DBMaker.newMemoryDirectDB().compressionEnable().transactionDisable().make();
    final HTreeMap<Integer, String> taxonMap = db.createHashMap("taxonMap").make();
    final HTreeMap<Integer, String> refMap = db.createHashMap("refMap").make();
    try {
        InputStream inputStream = DatasetUtil.getNamedResourceStream(getDataset(), "archive");
        ZipInputStream zipInputStream = new ZipInputStream(inputStream);
        ZipEntry entry;
        File taxonTempFile = null;
        File assocTempFile = null;
        File referencesTempFile = null;
        File distributionTempFile = null;
        while ((entry = zipInputStream.getNextEntry()) != null) {
            if (entry.getName().matches("(^|(.*/))taxon.txt$")) {
                taxonTempFile = FileUtils.saveToTmpFile(zipInputStream, entry);
            } else if (entry.getName().matches("(^|(.*/))description.txt$")) {
                assocTempFile = FileUtils.saveToTmpFile(zipInputStream, entry);
            } else if (entry.getName().matches("(^|(.*/))references.txt$")) {
                referencesTempFile = FileUtils.saveToTmpFile(zipInputStream, entry);
            } else if (entry.getName().matches("(^|(.*/))distribution.txt$")) {
                distributionTempFile = FileUtils.saveToTmpFile(zipInputStream, entry);
            } else {
                IOUtils.copy(zipInputStream, new NullOutputStream());
            }
        }
        IOUtils.closeQuietly(zipInputStream);
        if (taxonTempFile == null) {
            throw new StudyImporterException("failed to find expected [taxon.txt] resource");
        }
        if (assocTempFile == null) {
            throw new StudyImporterException("failed to find expected [description.txt] resource");
        }
        if (referencesTempFile == null) {
            throw new StudyImporterException("failed to find expected [references.txt] resource");
        }
        if (distributionTempFile == null) {
            throw new StudyImporterException("failed to find expected [distribution.txt] resource");
        }
        BufferedReader assocReader = FileUtils.getUncompressedBufferedReader(new FileInputStream(taxonTempFile), CharsetConstant.UTF8);
        LabeledCSVParser parser = CSVTSVUtil.createLabeledCSVParser(assocReader);
        parser.changeDelimiter('\t');
        String[] line;
        while ((line = parser.getLine()) != null) {
            taxonMap.put(Integer.parseInt(line[0]), nameFor(line));
        }
        LabeledCSVParser refs = CSVTSVUtil.createLabeledCSVParser(new FileInputStream(referencesTempFile));
        refs.changeDelimiter('\t');
        String[] refsLine;
        while ((refsLine = refs.getLine()) != null) {
            refMap.put(Integer.parseInt(refsLine[0]), refsLine[1]);
        }
        LabeledCSVParser assoc = CSVTSVUtil.createLabeledCSVParser(new FileInputStream(assocTempFile));
        assoc.changeDelimiter('\t');
        final Map<String, InteractType> interactTypeMap = new HashMap<String, InteractType>() {

            {
                put("Visits flowers of", InteractType.VISITS_FLOWERS_OF);
                put("Host of", InteractType.VISITS_FLOWERS_OF);
                put("Parasite of", InteractType.PARASITE_OF);
                put("Nests in", InteractType.INTERACTS_WITH);
            }
        };
        String[] assocLine;
        while ((assocLine = assoc.getLine()) != null) {
            final Integer taxonId = Integer.parseInt(assocLine[0]);
            final String[] parts = assocLine[2].split(":");
            if (parts.length > 1) {
                String interactionString = parts[0];
                String[] targetTaxonNames = parts[1].split(",");
                for (String targetTaxonName : targetTaxonNames) {
                    final String reference = refMap.get(taxonId);
                    final String sourceTaxonName = taxonMap.get(taxonId);
                    if (StringUtils.isNotBlank(reference) && StringUtils.isNotBlank(sourceTaxonName)) {
                        final Study study = nodeFactory.getOrCreateStudy(new StudyImpl(getSourceCitation() + reference, getSourceCitationLastAccessed(), null, reference));
                        final Specimen source = nodeFactory.createSpecimen(study, new TaxonImpl(StringUtils.trim(sourceTaxonName), null));
                        final Specimen target = nodeFactory.createSpecimen(study, new TaxonImpl(StringUtils.trim(targetTaxonName), null));
                        final InteractType relType = interactTypeMap.get(interactionString);
                        if (relType == null) {
                            throw new StudyImporterException("found unsupported interaction type [" + interactionString + "]");
                        }
                        source.interactsWith(target, relType);
                    }
                }
            }
        }
    } catch (IOException | NodeFactoryException e) {
        throw new StudyImporterException(e);
    }
    db.close();
}

Example 34 with Specimen

use of org.eol.globi.domain.Specimen 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 35 with Specimen

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

the class StudyImporterForCook method addParasites.

private void addParasites(LabeledCSVParser parser, Study study, Location sampleLocation, Specimen host, Date collectionDate, String isoCol) throws NodeFactoryException {
    try {
        String valueByLabel = parser.getValueByLabel(isoCol);
        boolean parasiteDetected = !"0".equals(valueByLabel);
        boolean lengthAvailable = parasiteDetected && !"NA".equals(valueByLabel);
        if (parasiteDetected) {
            Specimen parasite = nodeFactory.createSpecimen(study, new TaxonImpl("Cymothoa excisa", null));
            parasite.caughtIn(sampleLocation);
            if (lengthAvailable) {
                double parasiteLengthCm = Double.parseDouble(valueByLabel);
                parasite.setLengthInMm(parasiteLengthCm * 10.0);
            }
            parasite.interactsWith(host, InteractType.PARASITE_OF);
            nodeFactory.setUnixEpochProperty(parasite, collectionDate);
        }
    } catch (NumberFormatException ex) {
    // ignore
    }
}