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

Example 11 with InteractType

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

the class ReportGenerator method countInteractionsAndTaxa.

private void countInteractionsAndTaxa(Iterable<Relationship> specimens, Set<Long> ids, Counter interactionCounter, Set<Long> idsNoMatch) {
    for (Relationship specimen : specimens) {
        Iterable<Relationship> relationships = specimen.getEndNode().getRelationships();
        for (Relationship relationship : relationships) {
            InteractType[] types = InteractType.values();
            for (InteractType type : types) {
                if (relationship.isType(NodeUtil.asNeo4j(type)) && !relationship.hasProperty(PropertyAndValueDictionary.INVERTED)) {
                    interactionCounter.count();
                    break;
                }
            }
        }
        Relationship classifiedAs = specimen.getEndNode().getSingleRelationship(NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS), Direction.OUTGOING);
        if (classifiedAs != null) {
            Node taxonNode = classifiedAs.getEndNode();
            ids.add(taxonNode.getId());
            if (!TaxonUtil.isResolved(new TaxonNode(taxonNode))) {
                idsNoMatch.add(taxonNode.getId());
            }
        }
    }
}

Example 12 with InteractType

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

the class StudyImporterForVertNetTest method parseAssOcc.

protected Map<String, InteractType> parseAssOcc(String str) {
    Map<String, InteractType> mapping = new TreeMap<String, InteractType>() {

        {
            put("ate", InteractType.ATE);
            put("eaten by", InteractType.EATEN_BY);
            put("parasite of", InteractType.PARASITE_OF);
        }
    };
    String[] occurrences = StringUtils.split(str, ";");
    Map<String, InteractType> assoc = new TreeMap<String, InteractType>();
    for (String occurrence : occurrences) {
        int index = StringUtils.indexOf(occurrence, ")");
        if (index > 0) {
            String association = StringUtils.substring(StringUtils.trim(StringUtils.substring(occurrence, 0, index)), 1);
            String rest = StringUtils.substring(occurrence, index + 1);
            InteractType interactType = mapping.get(association);
            if (interactType != null) {
                String trim = StringUtils.trim(rest);
                int nsIndex = StringUtils.indexOf(trim, "http://arctos.database.museum/guid/");
                String strip = nsIndex < 0 ? trim : StringUtils.substring(trim, nsIndex, trim.length());
                String ns = StringUtils.replace(strip, "institutional catalog number ", "http://arctos.database.museum/guid/");
                assoc.put(StringUtils.replace(ns, " ", ":"), interactType);
            }
        }
    }
    return assoc;
}

Example 13 with InteractType

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

the class StudyImporterForBrose method addInteractionForConsumer.

private void addInteractionForConsumer(LabeledCSVParser parser, Study localStudy, String predatorName) throws NodeFactoryException, StudyImporterException {
    Location location = null;
    String locationString = parser.getValueByLabel("Geographic location");
    LatLng latLng = LOC_MAP.get(StringUtils.trim(locationString));
    if (latLng == null) {
        getLogger().warn(localStudy, "failed to find location for [" + locationString + "]");
    } else {
        location = nodeFactory.getOrCreateLocation(new LocationImpl(latLng.getLat(), latLng.getLng(), null, null));
        String habitat = StringUtils.join(parser.getValueByLabel("General habitat"), " ", parser.getValueByLabel("Specific habitat"));
        String habitatId = "BROSE:" + habitat.replaceAll("\\W", "_");
        nodeFactory.getOrCreateEnvironments(location, habitatId, habitat);
    }
    Specimen consumer = nodeFactory.createSpecimen(localStudy, new TaxonImpl(predatorName, null));
    consumer.caughtIn(location);
    addLifeStage(parser, consumer, "Lifestage consumer");
    String name = getName(parser, "Taxonomy resource", "Common name(s) resource");
    if (StringUtils.isBlank(name) || StringUtils.length(name) < 2) {
        String message = "found (near) empty prey name on line [" + parser.lastLineNumber() + "] + [" + name + "]";
        LOG.warn(message);
        getLogger().warn(localStudy, message);
    } else {
        Specimen resource = nodeFactory.createSpecimen(localStudy, new TaxonImpl(name, null));
        resource.caughtIn(location);
        addLifeStage(parser, resource, "Lifestage - resource");
        String interactionType = parser.getValueByLabel("Type of feeding interaction");
        Map<String, InteractType> typeMapping = new HashMap<String, InteractType>() {

            {
                put("predacious", InteractType.PREYS_UPON);
                put("predator", InteractType.PREYS_UPON);
                put("herbivorous", InteractType.ATE);
                put("parasitoid", InteractType.PARASITE_OF);
                put("parasitic", InteractType.PARASITE_OF);
                put("bacterivorous", InteractType.ATE);
                put("omnivore", InteractType.ATE);
                put("detritivorous", InteractType.ATE);
                put("pathogen", InteractType.PATHOGEN_OF);
            }
        };
        InteractType interactType = typeMapping.get(interactionType);
        if (interactType == null) {
            throw new StudyImporterException("found unsupported interaction type [" + interactionType + "]");
        }
        consumer.interactsWith(resource, interactType);
    }
}

Example 14 with InteractType

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

the class StudyImporterForSeltmann method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    final String archiveURL = DatasetUtil.getNamedResourceURI(getDataset(), "archive");
    if (org.apache.commons.lang.StringUtils.isBlank(archiveURL)) {
        throw new StudyImporterException("failed to import [" + getDataset().getNamespace() + "]: no [archiveURL] specified");
    }
    DB db = DBMaker.newMemoryDirectDB().compressionEnable().transactionDisable().make();
    final HTreeMap<String, Map<String, String>> assocMap = db.createHashMap("assocMap").make();
    try {
        InputStream inputStream = DatasetUtil.getNamedResourceStream(getDataset(), "archive");
        ZipInputStream zipInputStream = new ZipInputStream(inputStream);
        ZipEntry entry;
        File assocTempFile = null;
        File occTempFile = null;
        while ((entry = zipInputStream.getNextEntry()) != null) {
            if (entry.getName().matches("(^|(.*/))associatedTaxa.tsv$")) {
                assocTempFile = FileUtils.saveToTmpFile(zipInputStream, entry);
            } else if (entry.getName().matches("(^|(.*/))occurrences.tsv$")) {
                occTempFile = FileUtils.saveToTmpFile(zipInputStream, entry);
            } else {
                IOUtils.copy(zipInputStream, new NullOutputStream());
            }
        }
        IOUtils.closeQuietly(zipInputStream);
        if (assocTempFile == null) {
            throw new StudyImporterException("failed to find expected [associatedTaxa.tsv] resource");
        }
        if (occTempFile == null) {
            throw new StudyImporterException("failed to find expected [occurrences.tsv] resource");
        }
        BufferedReader assocReader = FileUtils.getUncompressedBufferedReader(new FileInputStream(assocTempFile), CharsetConstant.UTF8);
        LabeledCSVParser parser = CSVTSVUtil.createLabeledCSVParser(assocReader);
        parser.changeDelimiter('\t');
        while (parser.getLine() != null) {
            Map<String, String> prop = new HashMap<String, String>();
            addKeyValue(parser, prop, "dwc:coreid");
            addKeyValue(parser, prop, "dwc:basisOfRecord");
            addKeyValue(parser, prop, FIELD_IDIGBIO_RECORD_ID);
            addKeyValue(parser, prop, FIELD_ASSOCIATED_GENUS);
            addKeyValue(parser, prop, FIELD_ASSOCIATED_SPECIFIC_EPITHET);
            addKeyValue(parser, prop, FIELD_ASSOCIATED_SCIENTIFIC_NAME);
            addKeyValue(parser, prop, "dwc:basisOfRecord");
            addKeyValue(parser, prop, "aec:associatedRelationshipTerm");
            addKeyValue(parser, prop, "aec:associatedRelationshipURI");
            addKeyValue(parser, prop, "aec:associatedLocationOnHost");
            addKeyValue(parser, prop, "aec:associatedEmergenceVerbatimDate");
            String coreId = parser.getValueByLabel("dwc:coreid");
            if (StringUtils.isBlank(coreId)) {
                LOG.warn("no coreid for line [" + parser.getLastLineNumber() + 1 + "]");
            } else {
                assocMap.put(coreId, prop);
            }
        }
        LabeledCSVParser occurrence = CSVTSVUtil.createLabeledCSVParser(new FileInputStream(occTempFile));
        occurrence.changeDelimiter('\t');
        while (occurrence.getLine() != null) {
            String references = occurrence.getValueByLabel("dcterms:references");
            Study study = nodeFactory.getOrCreateStudy(new StudyImpl("seltmann" + references, CitationUtil.sourceCitationLastAccessed(this.getDataset(), references), null, references));
            String recordId = occurrence.getValueByLabel(FIELD_IDIGBIO_RECORD_ID);
            Map<String, String> assoc = assocMap.get(recordId);
            if (assoc != null) {
                String targetName = getTargetNameFromAssocMap(assoc);
                String sourceName = occurrence.getValueByLabel("scientificName");
                String eventDate = occurrence.getValueByLabel("eventDate");
                Date date = null;
                if (StringUtils.equals(eventDate, "0000-00-00")) {
                    getLogger().warn(study, "found suspicious event date [" + eventDate + "]" + getLineMsg(occurrence));
                } else if (StringUtils.isBlank(eventDate)) {
                    getLogger().warn(study, "found suspicious event date [" + eventDate + "]" + getLineMsg(occurrence));
                } else {
                    DateTimeFormatter fmtDateTime1 = DateTimeFormat.forPattern("yyyy-MM-dd").withZoneUTC();
                    String dateString = eventDate.split("/")[0];
                    try {
                        date = fmtDateTime1.parseDateTime(dateString).toDate();
                    } catch (IllegalArgumentException e) {
                        getLogger().warn(study, "invalid date [" + dateString + "] " + getLineMsg(occurrence));
                    }
                }
                if (StringUtils.isBlank(sourceName)) {
                    getLogger().warn(study, "found blank source taxon name" + getLineMsg(occurrence));
                }
                if (StringUtils.isBlank(targetName)) {
                    getLogger().warn(study, "found blank associated target taxon name" + getLineMsg(occurrence));
                }
                InteractType interactType = parseInteractType(occurrence, assoc);
                if (interactType != null && StringUtils.isNotBlank(sourceName) && StringUtils.isNotBlank(targetName)) {
                    try {
                        createInteraction(occurrence, study, assoc, targetName, sourceName, date, interactType);
                    } catch (NodeFactoryException ex) {
                        String message = "failed to import interaction because of [" + ex.getMessage() + "]" + getLineMsg(occurrence);
                        LOG.warn(message);
                        getLogger().warn(study, message);
                    }
                }
            }
        }
    } catch (IOException | NodeFactoryException e) {
        throw new StudyImporterException(e);
    }
    db.close();
}

Example 15 with InteractType

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

the class StudyImporterForSIAD method downloadAndImportResource.

private void downloadAndImportResource(String resource, String source) throws StudyImporterException {
    try {
        LabeledCSVParser labeledCSVParser = parserFactory.createParser(resource, "UTF-8");
        labeledCSVParser.changeDelimiter('\t');
        while (labeledCSVParser.getLine() != null) {
            String name = labeledCSVParser.getValueByLabel("name");
            String ref = labeledCSVParser.getValueByLabel("source");
            String title = "SIAD-" + ref;
            String citation = "ABRS 2009. Australian Faunal Directory. " + name + ". Australian Biological Resources StudyNode, Canberra. " + CitationUtil.createLastAccessedString(ref);
            StudyImpl study1 = new StudyImpl(title, source, null, citation);
            study1.setExternalId(ref);
            Study study = nodeFactory.getOrCreateStudy(study1);
            Specimen specimen = nodeFactory.createSpecimen(study, new TaxonImpl(name, null));
            String hostName = labeledCSVParser.getValueByLabel("host name");
            Specimen hostSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl(hostName, null));
            InteractType type = map.get(labeledCSVParser.getValueByLabel("interaction"));
            specimen.interactsWith(hostSpecimen, type);
        }
    } catch (FileNotFoundException e) {
        throw new StudyImporterException("failed to open tmp file", e);
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to map data", e);
    } catch (IOException e) {
        throw new StudyImporterException("failed to read resource [" + resource + "]", e);
    }
}