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

Example 31 with Study

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

the class StudyImporterForGoMexSI2 method addObservations.

private void addObservations(Map<String, Map<String, String>> predatorIdToPredatorSpecimen, Map<String, Study> refIdToStudyMap, Map<String, List<Map<String, String>>> predatorUIToPreyLists, Study metaStudy) throws StudyImporterException {
    String locationResource = getLocationsResourcePath();
    try {
        TermLookupService cmecsService = new CMECSService();
        LabeledCSVParser parser = parserFactory.createParser(locationResource, CharsetConstant.UTF8);
        while (parser.getLine() != null) {
            String refId = getMandatoryValue(locationResource, parser, "DATA_ID");
            if (!refIdToStudyMap.containsKey(refId)) {
                getLogger().warn(metaStudy, "failed to find study for ref id [" + refId + "] on related to observation location in [" + locationResource + ":" + parser.getLastLineNumber() + "]");
            } else {
                Study study = refIdToStudyMap.get(refId);
                String specimenId = getMandatoryValue(locationResource, parser, "PRED_ID");
                Location location = parseLocation(locationResource, parser);
                Location locationNode = nodeFactory.getOrCreateLocation(location);
                enrichLocation(metaStudy, locationResource, cmecsService, parser, locationNode);
                String predatorId = refId + specimenId;
                Map<String, String> predatorProperties = predatorIdToPredatorSpecimen.get(predatorId);
                if (predatorProperties == null) {
                    getLogger().warn(study, "failed to lookup predator [" + refId + ":" + specimenId + "] for location at [" + locationResource + ":" + (parser.getLastLineNumber() + 1) + "]");
                } else {
                    addObservation(predatorUIToPreyLists, parser, study, locationNode, predatorId, predatorProperties);
                }
            }
        }
    } catch (IOException e) {
        throw new StudyImporterException("failed to open resource [" + locationResource + "]", e);
    }
}

Example 32 with Study

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

the class NodeFactoryWithDatasetContextTest method getOrCreateStudy.

@Test
public void getOrCreateStudy() throws NodeFactoryException {
    NodeFactory factory = Mockito.mock(NodeFactory.class);
    Dataset dataset = new DatasetImpl("some/namespace", URI.create("some:uri"));
    NodeFactoryWithDatasetContext factoryWithDS = new NodeFactoryWithDatasetContext(factory, dataset);
    factoryWithDS.getOrCreateStudy(new StudyImpl("some title"));
    ArgumentCaptor<Study> argument = ArgumentCaptor.forClass(Study.class);
    verify(factory).getOrCreateStudy(argument.capture());
    assertEquals("globi:some/namespace", argument.getValue().getSourceId());
    assertEquals("some title", argument.getValue().getTitle());
}

Example 33 with Study

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

the class GraphExporterImpl method exportDataOntology.

private void exportDataOntology(List<Study> studies, String baseDir) throws StudyImporterException {
    try {
        ExporterRDF studyExporter = new ExporterRDF();
        OutputStreamWriter writer = openStream(baseDir + "globi.nq.gz");
        int total = studies.size();
        int count = 1;
        for (Study study : studies) {
            studyExporter.exportStudy(study, writer, true);
            if (count % 50 == 0) {
                LOG.info("added triples for [" + count + "] of [" + total + "] studies...");
            }
            count++;
        }
        LOG.info("adding triples for [" + total + "] of [" + total + "] studies.");
        LOG.info("writing nquads archive...");
        closeStream(baseDir + "globi.nq.gz", writer);
    } catch (IOException e) {
        throw new StudyImporterException("failed to export as owl", e);
    }
}

Example 34 with Study

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

the class GraphExporterImpl method exportNames.

private void exportNames(List<Study> studies, String baseDir, StudyExporter exporter, String filename) throws StudyImporterException {
    try {
        String filePath = baseDir + filename;
        OutputStreamWriter writer = openStream(filePath);
        for (Study study : studies) {
            boolean includeHeader = studies.indexOf(study) == 0;
            exporter.exportStudy(study, writer, includeHeader);
        }
        closeStream(filePath, writer);
    } catch (IOException e) {
        throw new StudyImporterException("failed to export unmatched source taxa", e);
    }
}

Example 35 with Study

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

the class ExporterSiteMapForNames method export.

@Override
public void export(GraphDatabaseService graphDatabase, String baseDir) throws StudyImporterException {
    Set<String> names = new HashSet<String>();
    names.add("Homo sapiens");
    // just do it once
    final List<Study> allStudies = NodeUtil.findAllStudies(graphDatabase);
    for (Study allStudy : allStudies) {
        final Iterable<Relationship> specimens = NodeUtil.getSpecimens(allStudy);
        for (Relationship specimen : specimens) {
            final Iterable<Relationship> relationships = specimen.getEndNode().getRelationships(Direction.OUTGOING, NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS));
            if (relationships.iterator().hasNext()) {
                final Node endNode = relationships.iterator().next().getEndNode();
                final TaxonNode taxonNode = new TaxonNode(endNode);
                names.add(taxonNode.getName());
            }
        }
    }
    final String queryParamName = "interactionType=interactsWith&sourceTaxon=";
    final String siteMapLocation = "https://depot.globalbioticinteractions.org/snapshot/target/data/sitemap/names/";
    SiteMapUtils.generateSiteMap(names, baseDir, queryParamName, siteMapLocation);
}