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

Example 6 with InteractType

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

the class InteractionListenerImpl method importValidLink.

private void importValidLink(Map<String, String> link) throws StudyImporterException, IOException {
    Study study = nodeFactory.getOrCreateStudy(studyFromLink(link));
    Specimen source = createSpecimen(link, study, SOURCE_TAXON_NAME, SOURCE_TAXON_ID, SOURCE_BODY_PART_NAME, SOURCE_BODY_PART_ID);
    Specimen target = createSpecimen(link, study, TARGET_TAXON_NAME, TARGET_TAXON_ID, TARGET_BODY_PART_NAME, TARGET_BODY_PART_ID);
    String interactionTypeId = link.get(INTERACTION_TYPE_ID);
    InteractType type = InteractType.typeOf(interactionTypeId);
    source.interactsWith(target, type, getOrCreateLocation(study, link));
}

Example 7 with InteractType

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

the class StudyImporterForINaturalist method parseSingleInteractions.

private void parseSingleInteractions(JsonNode jsonNode, List<Integer> typesIgnored, Map<Integer, InteractType> typeMap) throws NodeFactoryException, StudyImporterException, IOException {
    Taxon targetTaxon = null;
    Taxon sourceTaxon = null;
    if (jsonNode.has("taxon") && jsonNode.has("observation")) {
        targetTaxon = parseTaxon(jsonNode.get("taxon"));
        JsonNode observation = jsonNode.get("observation");
        if (jsonNode.has("taxon")) {
            sourceTaxon = parseTaxon(observation.get("taxon"));
        }
    }
    long observationId = jsonNode.get("observation_id").getLongValue();
    if (targetTaxon == null) {
        LOG.debug("skipping interaction with missing target taxon name for observation [" + observationId + "]");
    } else if (sourceTaxon == null) {
        LOG.warn("cannot create interaction with missing source taxon name for observation with id [" + observationId + "]");
    } else {
        JsonNode observationField = jsonNode.get("observation_field");
        String interactionDataType = observationField.get("datatype").getTextValue();
        String interactionTypeName = observationField.get("name").getTextValue();
        Integer interactionTypeId = observationField.get("id").getIntValue();
        if (typesIgnored.contains(interactionTypeId)) {
            LOG.debug("ignoring taxon observation field type [" + interactionTypeName + "] with id [" + interactionTypeId + "] for observation with id [" + observationId + "]");
        } else {
            InteractType interactType = typeMap.get(interactionTypeId);
            if (interactType == null) {
                unsupportedInteractionTypes.put(observationId, interactionTypeName + ",https://www.inaturalist.org/observation_fields/" + interactionTypeId);
                LOG.debug("no interaction type associated with observation field type [" + interactionTypeName + "] with id [" + interactionTypeId + "] for observation with id [" + observationId + "]");
            } else {
                handleObservation(jsonNode, targetTaxon, observationId, interactionDataType, interactType, interactionTypeName, sourceTaxon);
            }
        }
    }
}

Example 8 with InteractType

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

the class TableInteractionListenerProxy method newLink.

@Override
public void newLink(final Map<String, String> properties) throws StudyImporterException {
    final HashMap<String, String> enrichedProperties = new HashMap<String, String>() {

        {
            putAll(properties);
            put(StudyImporterForTSV.STUDY_SOURCE_CITATION, dataSourceCitation);
            final String referenceCitation = StringUtils.isBlank(properties.get(StudyImporterForTSV.REFERENCE_CITATION)) ? StudyImporterForMetaTable.generateReferenceCitation(properties) : properties.get(StudyImporterForTSV.REFERENCE_CITATION);
            put(StudyImporterForTSV.REFERENCE_ID, dataSourceCitation + referenceCitation);
            put(StudyImporterForTSV.REFERENCE_CITATION, StringUtils.isBlank(referenceCitation) ? dataSourceCitation : referenceCitation);
            if (!properties.containsKey(StudyImporterForTSV.SOURCE_TAXON_NAME)) {
                put(StudyImporterForTSV.SOURCE_TAXON_NAME, StudyImporterForMetaTable.generateSourceTaxonName(properties));
            }
            if (!properties.containsKey(StudyImporterForTSV.TARGET_TAXON_NAME)) {
                put(StudyImporterForTSV.TARGET_TAXON_NAME, StudyImporterForMetaTable.generateTargetTaxonName(properties));
            }
        }
    };
    InteractType type = StudyImporterForMetaTable.generateInteractionType(enrichedProperties);
    StudyImporterForMetaTable.setInteractionType(enrichedProperties, type);
    interactionListener.newLink(enrichedProperties);
}

Example 9 with InteractType

use of org.eol.globi.domain.InteractType 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 10 with InteractType

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

the class StudyImporterForBioInfo method createRelations.

protected void createRelations(LabeledCSVParser parser, Map<String, String> refMap, Map<String, Taxon> taxonMap) throws StudyImporterException {
    try {
        long count = 1;
        while (parser.getLine() != null) {
            if (importFilter.shouldImportRecord(count)) {
                String refIds = parser.getValueByLabel("list of reference ids");
                if (StringUtils.isNotBlank(refIds)) {
                    String[] ids = StringUtils.split(refIds, ";");
                    for (String id : ids) {
                        String trimmedId = StringUtils.trim(id);
                        Study study = createStudy(trimmedId, refMap.get(trimmedId));
                        String relationship = parser.getValueByLabel("relationship");
                        if (StringUtils.isBlank(relationship)) {
                            getLogger().warn(study, "no relationship for record on line [" + (parser.lastLineNumber() + 1) + "]");
                        }
                        InteractType interactType = INTERACTION_MAPPING.get(relationship);
                        if (null == interactType) {
                            getLogger().warn(study, "no mapping found for relationship [" + relationship + "] for record on line [" + (parser.lastLineNumber() + 1) + "]");
                        } else {
                            importInteraction(parser, study, interactType, taxonMap);
                        }
                    }
                }
            }
            count++;
        }
    } catch (IOException e1) {
        throw new StudyImporterException("problem reading trophic relations data", e1);
    }
}