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Example 1 with StudyImpl

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

the class StudyImporterForJSONLD method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    Model model;
    try {
        model = buildModel();
    } catch (IOException e) {
        throw new StudyImporterException("failed to import [" + getResourceURI() + "]", e);
    }
    Query query;
    try {
        query = QueryFactory.create(IOUtils.toString(new DatasetLocal().getResource("find-jsonld-interactions.rq"), CharsetConstant.UTF8));
    } catch (IOException e) {
        throw new StudyImporterException("failed to find sparql query", e);
    }
    QueryExecution exec = QueryExecutionFactory.create(query, model);
    try {
        ResultSet results = exec.execSelect();
        while (results.hasNext()) {
            QuerySolution solution = results.nextSolution();
            String subj = solution.get("subj").asResource().getURI();
            String creationDate = solution.get("creationDate").asLiteral().getString();
            String authorURI = solution.get("author").toString();
            String author;
            try {
                author = nodeFactory.getAuthorResolver().findFullName(authorURI);
            } catch (IOException e) {
                throw new StudyImporterException("failed to resolve author URI [" + authorURI + "]");
            }
            final String source1 = author + ". " + new DateTime(parseDate(creationDate)).getYear() + ". " + CitationUtil.createLastAccessedString(getResourceURI().toString());
            Study study = nodeFactory.getOrCreateStudy(new StudyImpl(getResourceURI() + subj, source1, null, subj));
            study.setExternalId(subj);
            Specimen source = createSpecimen(solution, study, "subjTaxon");
            Specimen target = createSpecimen(solution, study, "targetTaxon");
            String interactType = solution.get("p").asResource().getLocalName();
            InteractType interactType1 = InteractType.typeOf(StringUtils.replace(interactType, "RO_", "RO:"));
            if (interactType1 == null) {
                throw new StudyImporterException("failed to map interaction type [" + interactType + "]");
            }
            String collTime = solution.get("collTime").asLiteral().getString();
            Date date = parseDate(collTime);
            nodeFactory.setUnixEpochProperty(source, date);
            nodeFactory.setUnixEpochProperty(target, date);
            Location loc = nodeFactory.getOrCreateLocation(new LocationImpl(solution.get("collLat").asLiteral().getDouble(), solution.get("collLng").asLiteral().getDouble(), null, null));
            target.caughtIn(loc);
            source.caughtIn(loc);
            source.interactsWith(target, interactType1);
        }
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to import jsonld data in [" + getResourceURI() + "]", e);
    } finally {
        exec.close();
    }
}
Also used : InteractType(org.eol.globi.domain.InteractType) Study(org.eol.globi.domain.Study) Query(com.hp.hpl.jena.query.Query) StudyImpl(org.eol.globi.domain.StudyImpl) IOException(java.io.IOException) DatasetLocal(org.eol.globi.service.DatasetLocal) QueryExecution(com.hp.hpl.jena.query.QueryExecution) DateTime(org.joda.time.DateTime) Date(java.util.Date) Specimen(org.eol.globi.domain.Specimen) QuerySolution(com.hp.hpl.jena.query.QuerySolution) Model(com.hp.hpl.jena.rdf.model.Model) ResultSet(com.hp.hpl.jena.query.ResultSet) LocationImpl(org.eol.globi.domain.LocationImpl) Location(org.eol.globi.domain.Location)

Example 2 with StudyImpl

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

the class StudyImporterForINaturalist method importInteraction.

private void importInteraction(Taxon targetTaxon, long observationId, String interactionDataType, InteractType interactionTypeId, JsonNode observation, Taxon sourceTaxon, String interactionTypeName) throws StudyImporterException, NodeFactoryException {
    Date observationDate = getObservationDate(observation);
    StringBuilder citation = buildCitation(observation, interactionTypeName, targetTaxon.getName(), sourceTaxon.getName(), observationDate);
    String url = ExternalIdUtil.urlForExternalId(TaxonomyProvider.ID_PREFIX_INATURALIST + observationId);
    citation.append(CitationUtil.createLastAccessedString(url));
    StudyImpl study1 = new StudyImpl(TaxonomyProvider.ID_PREFIX_INATURALIST + observationId, getSourceString(), null, citation.toString());
    study1.setExternalId(url);
    Study study = nodeFactory.getOrCreateStudy(study1);
    createAssociation(observationId, interactionDataType, interactionTypeId, observation, targetTaxon, sourceTaxon, study, observationDate);
}
Also used : Study(org.eol.globi.domain.Study) StudyImpl(org.eol.globi.domain.StudyImpl) Date(java.util.Date)

Example 3 with StudyImpl

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

the class StudyImporterForRobledo method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    String description = "García-Robledo C, Erickson DL, Staines CL, Erwin TL, Kress WJ. Tropical Plant–Herbivore Networks: Reconstructing Species Interactions Using DNA Barcodes Heil M, editor. PLoS ONE [Internet]. 2013 January 8;8(1):e52967. Available from: http://dx.doi.org/10.1371/journal.pone.0052967";
    String doi = "http://dx.doi.org/10.1371/journal.pone.0052967";
    Study study1 = new StudyImpl("García-Robledo et al 2013", description, doi, description);
    Study study = nodeFactory.getOrCreateStudy(study1);
    Map<String, String> abrLookup = buildPlantLookup();
    // spatial location from: http://www.ots.ac.cr/index.php?option=com_content&task=view&id=163&Itemid=348
    Double latitude = LocationUtil.parseDegrees("10°26'N");
    Double longitude = LocationUtil.parseDegrees("83°59'W");
    Location location;
    try {
        location = nodeFactory.getOrCreateLocation(new LocationImpl(latitude, longitude, 35.0, null));
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to create location", e);
    }
    // TODO: need to map date range of collections
    String studyResource = "robledo/table_s1_extract.csv";
    try {
        LabeledCSVParser parser = parserFactory.createParser(studyResource, CharsetConstant.UTF8);
        while (parser.getLine() != null) {
            String beetleName = parser.getValueByLabel("Herbivore species");
            String beetleScientificName = completeBeetleName(beetleName);
            Specimen predator = nodeFactory.createSpecimen(study, new TaxonImpl(beetleScientificName, null));
            predator.caughtIn(location);
            for (String plantAbbreviation : abrLookup.keySet()) {
                String plantScientificName = abrLookup.get(plantAbbreviation);
                String valueByLabel = parser.getValueByLabel(plantAbbreviation);
                try {
                    int interactionCode = Integer.parseInt(valueByLabel);
                    if (interactionCode > 0) {
                        Specimen plant = nodeFactory.createSpecimen(study, new TaxonImpl(plantScientificName, null));
                        plant.caughtIn(location);
                        predator.ate(plant);
                    }
                } catch (NumberFormatException ex) {
                    getLogger().warn(study, "malformed or no value [" + valueByLabel + "] found for [" + plantScientificName + "(" + plantAbbreviation + ")" + "] and beetle [" + beetleScientificName + "] could be found in [" + studyResource + ":" + parser.lastLineNumber() + "]");
                }
            }
        }
    } catch (IOException e) {
        throw new StudyImporterException("problem reading [" + studyResource + "]", e);
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("cannot create specimens from [" + studyResource + "]", e);
    }
}
Also used : Study(org.eol.globi.domain.Study) TaxonImpl(org.eol.globi.domain.TaxonImpl) StudyImpl(org.eol.globi.domain.StudyImpl) LabeledCSVParser(com.Ostermiller.util.LabeledCSVParser) IOException(java.io.IOException) Specimen(org.eol.globi.domain.Specimen) LocationImpl(org.eol.globi.domain.LocationImpl) Location(org.eol.globi.domain.Location)

Example 4 with StudyImpl

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

the class StudyImporterForWebOfLife method importNetworks.

public void importNetworks(String archiveURL, String sourceCitation) throws StudyImporterException {
    try {
        InputStream inputStream = getDataset().getResource(archiveURL);
        ZipInputStream zipInputStream = new ZipInputStream(inputStream);
        ZipEntry entry;
        File referencesTempFile = null;
        Map<String, File> networkTempFileMap = new HashMap<String, File>();
        while ((entry = zipInputStream.getNextEntry()) != null) {
            if (entry.getName().matches("(^|(.*/))references\\.csv$")) {
                referencesTempFile = FileUtils.saveToTmpFile(zipInputStream, entry);
            } else if (entry.getName().matches(".*\\.csv$")) {
                networkTempFileMap.put(entry.getName().replace(".csv", ""), FileUtils.saveToTmpFile(zipInputStream, entry));
            } else {
                IOUtils.copy(zipInputStream, new NullOutputStream());
            }
        }
        IOUtils.closeQuietly(zipInputStream);
        if (referencesTempFile == null) {
            throw new StudyImporterException("failed to find expected [references.csv] resource in [" + archiveURL + "]");
        }
        if (networkTempFileMap.size() == 0) {
            throw new StudyImporterException("failed to find expected network csv files");
        }
        BufferedReader assocReader = FileUtils.getUncompressedBufferedReader(new FileInputStream(referencesTempFile), CharsetConstant.UTF8);
        LabeledCSVParser parser = CSVTSVUtil.createLabeledCSVParser(assocReader);
        while (parser.getLine() != null) {
            final String citation = parser.getValueByLabel("Reference");
            if (StringUtils.isBlank(citation)) {
                throw new StudyImporterException("found missing reference");
            }
            final String networkId = parser.getValueByLabel("ID");
            if (!networkTempFileMap.containsKey(networkId)) {
                throw new StudyImporterException("found network id [" + networkId + "], but no associated data.");
            }
            final Study study = nodeFactory.getOrCreateStudy(new StudyImpl("bascompte:" + citation, sourceCitation, null, citation));
            importNetwork(parseInteractionType(parser), parseLocation(parser), study, networkTempFileMap.get(networkId));
        }
    } catch (IOException e) {
        throw new StudyImporterException(e);
    } catch (NodeFactoryException e) {
        throw new StudyImporterException(e);
    }
}
Also used : Study(org.eol.globi.domain.Study) HashMap(java.util.HashMap) ZipInputStream(java.util.zip.ZipInputStream) FileInputStream(java.io.FileInputStream) InputStream(java.io.InputStream) ZipEntry(java.util.zip.ZipEntry) StudyImpl(org.eol.globi.domain.StudyImpl) LabeledCSVParser(com.Ostermiller.util.LabeledCSVParser) IOException(java.io.IOException) FileInputStream(java.io.FileInputStream) ZipInputStream(java.util.zip.ZipInputStream) BufferedReader(java.io.BufferedReader) File(java.io.File) NullOutputStream(org.apache.commons.io.output.NullOutputStream)

Example 5 with StudyImpl

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

the class StudyImporterForRoopnarine method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    String suffix = ".csv";
    String prefix = "roopnarine/857470.item.";
    String trophicGuildLookup = prefix + 4 + suffix;
    final Map<Integer, List<String>> trophicGuildNumberToSpeciesMap = buildGuildLookup(trophicGuildLookup);
    Map<String, LatLng> resourceLocation = resourceLocationMap(suffix, prefix);
    Study study = nodeFactory.getOrCreateStudy(new StudyImpl("Roopnarine et al 2013", "Roopnarine, P.D. & Hertog, R., 2013. Detailed Food Web Networks of Three Greater Antillean Coral Reef Systems: The Cayman Islands, Cuba, and Jamaica. DatasetImpl Papers in Ecology, 2013, pp.1–9. Available at: http://dx.doi.org/10.7167/2013/857470.", "http://dx.doi.org/10.7167/2013/857470", null));
    for (Map.Entry<String, LatLng> resourceLatLngEntry : resourceLocation.entrySet()) {
        LatLng latLng = resourceLatLngEntry.getValue();
        Location location;
        try {
            location = nodeFactory.getOrCreateLocation(new LocationImpl(latLng.getLat(), latLng.getLng(), 0.0, null));
        } catch (NodeFactoryException e) {
            throw new StudyImporterException("failed to create location", e);
        }
        String studyResource = resourceLatLngEntry.getKey();
        getLogger().info(study, "import of [" + studyResource + "] started...");
        List<Specimen> predatorSpecimen = importTrophicInteractions(trophicGuildLookup, trophicGuildNumberToSpeciesMap, studyResource, study, location);
        getLogger().info(study, "import of [" + studyResource + "] done.");
    }
}
Also used : Study(org.eol.globi.domain.Study) StudyImpl(org.eol.globi.domain.StudyImpl) Specimen(org.eol.globi.domain.Specimen) LocationImpl(org.eol.globi.domain.LocationImpl) ArrayList(java.util.ArrayList) List(java.util.List) LatLng(org.eol.globi.geo.LatLng) HashMap(java.util.HashMap) Map(java.util.Map) Location(org.eol.globi.domain.Location)

Aggregations

StudyImpl (org.eol.globi.domain.StudyImpl)82 Study (org.eol.globi.domain.Study)60 Test (org.junit.Test)40 Specimen (org.eol.globi.domain.Specimen)33 TaxonImpl (org.eol.globi.domain.TaxonImpl)33 IOException (java.io.IOException)20 LabeledCSVParser (com.Ostermiller.util.LabeledCSVParser)17 Location (org.eol.globi.domain.Location)15 StringWriter (java.io.StringWriter)12 LocationImpl (org.eol.globi.domain.LocationImpl)12 Date (java.util.Date)9 HashMap (java.util.HashMap)9 Taxon (org.eol.globi.domain.Taxon)9 StudyNode (org.eol.globi.domain.StudyNode)7 Node (org.neo4j.graphdb.Node)7 File (java.io.File)6 TermImpl (org.eol.globi.domain.TermImpl)6 DatasetImpl (org.eol.globi.service.DatasetImpl)6 InteractType (org.eol.globi.domain.InteractType)5 NonResolvingTaxonIndex (org.eol.globi.taxon.NonResolvingTaxonIndex)5