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

Example 41 with TaxonImpl

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

the class LinkerTermMatcherTest method exactMatchExcludeStrains.

@Test
@Ignore
public // see https://github.com/GlobalNamesArchitecture/gnparser/issues/291
void exactMatchExcludeStrains() throws NodeFactoryException, PropertyEnricherException {
    taxonIndex.getOrCreateTaxon(new TaxonImpl("Phytophthora infestans", null));
    new LinkerTermMatcher(getGraphDb()).link();
    Collection<String> ids = LinkerTestUtil.assertHasOther("Phytophthora infestans", 6, taxonIndex, RelTypes.SAME_AS);
    assertThat(ids, hasItem("NCBI:4787"));
    assertThat(ids, not(hasItem("NCBI:403677")));
}

Example 42 with TaxonImpl

use of org.eol.globi.domain.TaxonImpl 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 43 with TaxonImpl

use of org.eol.globi.domain.TaxonImpl 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 44 with TaxonImpl

use of org.eol.globi.domain.TaxonImpl 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
    }
}

Example 45 with TaxonImpl

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

the class StudyImporterForBell method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    for (String resource : RESOURCE) {
        LabeledCSVParser parser = null;
        try {
            parser = parserFactory.createParser(resource, "UTF-8");
            while (parser.getLine() != null) {
                String sourceCitation = "Bell, K. C., Matek, D., Demboski, J. R., & Cook, J. A. (2015). Expanded Host Range of Sucking Lice and Pinworms of Western North American Chipmunks. Comparative Parasitology, 82(2), 312–321. doi:10.1654/4756.1 . Data provided by Kayce C. Bell.";
                String guid = parser.getValueByLabel("GUID");
                String externalId = "http://arctos.database.museum/guid/" + guid;
                String description = null;
                String collectionId = null;
                for (String key : REFS.keySet()) {
                    if (guid.startsWith(key)) {
                        description = REFS.get(key);
                        collectionId = key;
                        break;
                    }
                }
                if (StringUtils.isBlank(description)) {
                    LOG.warn("missing collectionId [" + guid + "] in file [" + resource + "] on line [" + parser.lastLineNumber() + "]");
                    description = sourceCitation;
                    collectionId = "";
                }
                Study study = nodeFactory.getOrCreateStudy(new StudyImpl("bell-" + collectionId, sourceCitation, "http://dx.doi.org/10.1654/4756.1", ExternalIdUtil.toCitation(null, sourceCitation + " " + description, null)));
                String genus = parser.getValueByLabel("Genus");
                String species = parser.getValueByLabel("Species");
                String parasiteName = StringUtils.join(new String[] { StringUtils.trim(genus), StringUtils.trim(species) }, " ");
                Specimen parasite = nodeFactory.createSpecimen(study, new TaxonImpl(parasiteName, null));
                parasite.setExternalId(externalId);
                Location location = getLocation(parser, parasite);
                parasite.caughtIn(location);
                String scientificName = parser.getValueByLabel("SCIENTIFIC_NAME");
                String hostName = StringUtils.trim(scientificName);
                Specimen host = nodeFactory.createSpecimen(study, new TaxonImpl(hostName, null));
                host.caughtIn(location);
                host.setExternalId(externalId);
                parasite.interactsWith(host, InteractType.PARASITE_OF);
                Date date = parseDate(parser);
                nodeFactory.setUnixEpochProperty(parasite, date);
                nodeFactory.setUnixEpochProperty(host, date);
            }
        } catch (Throwable e) {
            throw new StudyImporterException(getErrorMessage(resource, parser), e);
        }
    }
}