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

Example 56 with StudyImpl

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

the class StudyImporterForCruaud 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("cruaud", SOURCE, "http://dx.doi.org/10.1093/sysbio/sys068", null));
        while (dataParser.getLine() != null) {
            if (importFilter.shouldImportRecord((long) dataParser.getLastLineNumber())) {
                try {
                    String parasiteName = StringUtils.trim(dataParser.getValueByLabel("Family and Species"));
                    String hostName = StringUtils.trim(dataParser.getValueByLabel("Natural host Ficus species"));
                    hostName = StringUtils.replace(hostName, "F.", "Ficus");
                    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);
                        String samplingLocation = StringUtils.trim(dataParser.getValueByLabel("Sampling location"));
                        if (getGeoNamesService().hasTermForLocale(samplingLocation)) {
                            LatLng pointForLocality = getGeoNamesService().findLatLng(samplingLocation);
                            if (pointForLocality == null) {
                                LOG.warn("no location associated with locality [" + samplingLocation + "]");
                            } else {
                                Location location = nodeFactory.getOrCreateLocation(new LocationImpl(pointForLocality.getLat(), pointForLocality.getLng(), null, null));
                                parasite.caughtIn(location);
                                host.caughtIn(location);
                            }
                        } else {
                            LOG.warn("no location associated with locality [" + samplingLocation + "]");
                        }
                    }
                } catch (NodeFactoryException | NumberFormatException e) {
                    throw new StudyImporterException("failed to import line [" + (dataParser.lastLineNumber() + 1) + "]", e);
                }
            }
        }
    } catch (IOException e) {
        throw new StudyImporterException("problem importing [" + RESOURCE_PATH + "]", e);
    }
}

Example 57 with StudyImpl

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

the class StudyImporterForGemina method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    String studyResource = "gemina_search_2008-01-03.txt";
    try {
        String source = "Schriml, L. M., Arze, C., Nadendla, S., Ganapathy, A., Felix, V., Mahurkar, A., … Hall, N. (2009). GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database. Nucleic Acids Research, 38(Database), D754–D764. doi:10.1093/nar/gkp832";
        Study study = nodeFactory.getOrCreateStudy(new StudyImpl(source, source, "doi:10.1093/nar/gkp832", source));
        LabeledCSVParser parser = parserFactory.createParser(studyResource, "UTF-8");
        parser.changeDelimiter('\t');
        String[] line;
        while ((line = parser.getLine()) != null) {
            if (line.length > 7) {
                String pathogenId = parser.getValueByLabel("Pathogen Taxonomy");
                String pathogenExternalId = StringUtils.isBlank(pathogenId) ? null : TaxonomyProvider.NCBI.getIdPrefix() + pathogenId;
                Specimen pathogen = nodeFactory.createSpecimen(study, new TaxonImpl(parser.getValueByLabel("Pathogen"), pathogenExternalId));
                String hostId = line[7];
                String hostReservoirExternalId = StringUtils.isBlank(hostId) ? null : TaxonomyProvider.NCBI.getIdPrefix() + hostId;
                Specimen host = nodeFactory.createSpecimen(study, new TaxonImpl(parser.getValueByLabel("Host/Reservoir"), hostReservoirExternalId));
                pathogen.interactsWith(host, InteractType.PATHOGEN_OF);
            }
        }
    } catch (IOException | NodeFactoryException e) {
        throw new StudyImporterException("failed to import [" + studyResource + "]", e);
    }
}

Example 58 with StudyImpl

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

the class StudyImporterForGoMexSI2 method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    Study study = nodeFactory.getOrCreateStudy(new StudyImpl("GoMexSI", GOMEXI_SOURCE_DESCRIPTION, null, ExternalIdUtil.toCitation("James D. Simons", "<a href=\"http://www.ingentaconnect.com/content/umrsmas/bullmar/2013/00000089/00000001/art00009\">Building a Fisheries Trophic Interaction Database for Management and Modeling Research in the Gulf of Mexico Large Marine Ecosystem.</a>", null)));
    final Map<String, Map<String, String>> predatorIdToPredatorNames = new HashMap<String, Map<String, String>>();
    final Map<String, List<Map<String, String>>> predatorIdToPreyNames = new HashMap<String, List<Map<String, String>>>();
    Map<String, Study> referenceIdToStudy = new HashMap<String, Study>();
    addSpecimen(getPredatorResourcePath(), "PRED_", new ParseEventHandler() {

        @Override
        public void onSpecimen(String predatorUID, Map<String, String> properties) {
            predatorIdToPredatorNames.put(predatorUID, properties);
        }
    });
    addSpecimen(getPreyResourcePath(), "PREY_", new ParseEventHandler() {

        @Override
        public void onSpecimen(String predatorUID, Map<String, String> properties) {
            List<Map<String, String>> preyList = predatorIdToPreyNames.get(predatorUID);
            if (preyList == null) {
                preyList = new ArrayList<Map<String, String>>();
                predatorIdToPreyNames.put(predatorUID, preyList);
            }
            preyList.add(properties);
        }
    });
    addReferences(referenceIdToStudy);
    addObservations(predatorIdToPredatorNames, referenceIdToStudy, predatorIdToPreyNames, study);
}

Example 59 with StudyImpl

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

the class StudyImporterForGoMexSI2 method addNewStudy.

private void addNewStudy(Map<String, Study> referenceIdToStudy, String referenceResource, LabeledCSVParser parser, String refId, String contributors) throws StudyImporterException {
    Study study;
    String refTag = getMandatoryValue(referenceResource, parser, "REF_TAG");
    String externalId = getMandatoryValue(referenceResource, parser, "GAME_ID");
    String description = getMandatoryValue(referenceResource, parser, "TITLE_REF");
    String publicationYear = getMandatoryValue(referenceResource, parser, "YEAR_PUB");
    study = nodeFactory.getOrCreateStudy(new StudyImpl(refTag, getSourceCitation(), null, ExternalIdUtil.toCitation(contributors, description, publicationYear)));
    if (StringUtils.isNotBlank(externalId)) {
        study.setExternalId(ExternalIdUtil.urlForExternalId(TaxonomyProvider.ID_PREFIX_GAME + externalId));
    }
    referenceIdToStudy.put(refId, study);
}

Example 60 with StudyImpl

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

the class NodeFactoryWithDatasetContextTest method createStudy.

@Test
public void createStudy() {
    NodeFactory factory = Mockito.mock(NodeFactory.class);
    DatasetImpl dataset = new DatasetImpl("some/namespace", URI.create("some:uri"));
    NodeFactoryWithDatasetContext factoryWithDS = new NodeFactoryWithDatasetContext(factory, dataset);
    StudyImpl study = new StudyImpl("some title", "some source", "some doi", "some citation");
    study.setExternalId("some:id");
    factoryWithDS.createStudy(study);
    ArgumentCaptor<Study> argument = ArgumentCaptor.forClass(Study.class);
    verify(factory).createStudy(argument.capture());
    assertEquals("globi:some/namespace", argument.getValue().getSourceId());
    assertEquals("some title", argument.getValue().getTitle());
    assertEquals("some citation", argument.getValue().getCitation());
    assertEquals("some doi", argument.getValue().getDOI());
    assertEquals("some:id", argument.getValue().getExternalId());
}