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

Example 16 with InteractType

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

the class StudyImporterForVertNetTest method parseAssociatedOccurrences2.

@Ignore
@Test
public void parseAssociatedOccurrences2() throws IOException {
    ObjectMapper mapper = new ObjectMapper();
    JsonNode jsonNode1 = mapper.readTree(IOUtils.toString(new GZIPInputStream(getClass().getResourceAsStream("vertnet/response_associated_occurrences.json.gz"))));
    JsonNode recs = jsonNode1.get("recs");
    StringWriter linkOs = new StringWriter();
    CSVPrint linkPrinter = CSVTSVUtil.createCSVPrint(linkOs);
    linkPrinter.print(new String[] { "source", "interaction_type", "target" });
    linkPrinter.setAutoFlush(true);
    StringWriter nodeOs = new StringWriter();
    CSVPrint nodePrinter = CSVTSVUtil.createCSVPrint(nodeOs);
    String[] nodeFields = { "individualid", "decimallongitude", "decimallatitude", "year", "month", "day", "basisofrecord", "scientificname", "dataset_citation" };
    nodePrinter.print(nodeFields);
    nodePrinter.setAutoFlush(true);
    for (JsonNode rec : recs) {
        String specimenId = getOrNull(rec, "individualid");
        String associatedOcc = getOrNull(rec, "associatedoccurrences");
        if (StringUtils.isNotBlank(specimenId) && StringUtils.isNotBlank(associatedOcc)) {
            Map<String, InteractType> associatedoccurrences = parseAssOcc(associatedOcc);
            for (Map.Entry<String, InteractType> entry : associatedoccurrences.entrySet()) {
                linkPrinter.println();
                linkPrinter.print(specimenId);
                linkPrinter.print(entry.getValue().toString());
                linkPrinter.print(entry.getKey());
            }
            nodePrinter.println();
            for (String field : nodeFields) {
                String value = getOrNull(rec, field);
                nodePrinter.print(StringUtils.isBlank(value) ? "" : value);
            }
        }
    }
    linkPrinter.flush();
    linkPrinter.close();
    assertThat(linkOs.toString(), is("source,interaction_type,target" + "\nhttp://arctos.database.museum/guid/CUMV:Amph:16004,EATEN_BY,http://arctos.database.museum/guid/CUMV:Rept:4988" + "\nhttp://arctos.database.museum/guid/DMNS:Bird:34623,ATE,http://arctos.database.museum/guid/DMNS:Mamm:13142" + "\nhttp://arctos.database.museum/guid/DMNS:Bird:34623,ATE,http://arctos.database.museum/guid/DMNS:Mamm:13143" + "\nhttp://arctos.database.museum/guid/DMNS:Bird:34728,ATE,DZTM::Denver:Zoology:Tissue:Mammal:2285" + "\nhttp://arctos.database.museum/guid/DMNS:Bird:34728,ATE,http://arctos.database.museum/guid/DMNS:Mamm:13685"));
    assertThat(nodeOs.toString(), is("individualid,decimallongitude,decimallatitude,year,month,day,basisofrecord,scientificname,dataset_citation" + "\nindividualID,180,-90,2014,10,10,basisOfRecord,scientificName,test citation" + "\nhttp://arctos.database.museum/guid/CUMV:Amph:16004,-76.45442,42.4566,1953,09,27,PreservedSpecimen,Rana sylvatica," + "\nhttp://arctos.database.museum/guid/DMNS:Bird:21686,-106.434158,38.709448,1940,07,27,PreservedSpecimen,Lagopus leucurus,Denver Museum of Nature & Science Bird Collection" + "\nhttp://arctos.database.museum/guid/DMNS:Bird:21688,-106.434158,38.709448,1940,07,27,PreservedSpecimen,Lagopus leucurus,Denver Museum of Nature & Science Bird Collection" + "\nhttp://arctos.database.museum/guid/DMNS:Bird:21689,-106.434158,38.709448,1940,07,27,PreservedSpecimen,Lagopus leucurus,Denver Museum of Nature & Science Bird Collection" + "\nhttp://arctos.database.museum/guid/DMNS:Bird:26722,-105.02222,39.38528,1943,06,24,PreservedSpecimen,Chordeiles minor,Denver Museum of Nature & Science Bird Collection" + "\nhttp://arctos.database.museum/guid/DMNS:Bird:26724,-105.02222,39.38528,1943,06,24,PreservedSpecimen,Chordeiles minor,Denver Museum of Nature & Science Bird Collection" + "\nhttp://arctos.database.museum/guid/DMNS:Bird:34623,-104.738965,39.461082,2012,04,30,PreservedSpecimen,Asio otus,Denver Museum of Nature & Science Bird Collection" + "\nhttp://arctos.database.museum/guid/DMNS:Bird:34728,-105.096498,40.454918,2012,08,10,PreservedSpecimen,Buteo swainsoni,Denver Museum of Nature & Science Bird Collection"));
}

Example 17 with InteractType

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

the class StudyImporterForHechinger method addLink.

private void addLink(Study study, Map<Integer, Term> stageForNode, Map<Integer, String> taxonForNode, LabeledCSVParser links, Location location) throws StudyImporterException, NodeFactoryException {
    Integer consumerNodeID = Integer.parseInt(links.getValueByLabel("ConsumerNodeID"));
    Integer resourceNodeID = Integer.parseInt(links.getValueByLabel("ResourceNodeID"));
    String linkType = links.getValueByLabel("LinkType");
    InteractType interactType = interactionMapping.get(StringUtils.trim(StringUtils.lowerCase(linkType)));
    if (interactType == null) {
        throw new StudyImporterException("failed to map interaction type [" + linkType + "] in line [" + links.lastLineNumber() + "]");
    }
    Specimen consumer = nodeFactory.createSpecimen(study, new TaxonImpl(taxonForNode.get(consumerNodeID), null));
    consumer.setLifeStage(stageForNode.get(consumerNodeID));
    consumer.setExternalId(getNamespace() + ":NodeID:" + consumerNodeID);
    consumer.caughtIn(location);
    String resourceName = taxonForNode.get(resourceNodeID);
    Specimen resource = nodeFactory.createSpecimen(study, new TaxonImpl(resourceName, null));
    resource.setLifeStage(stageForNode.get(resourceNodeID));
    resource.setExternalId(getNamespace() + ":NodeID:" + resourceNodeID);
    resource.caughtIn(location);
    consumer.interactsWith(resource, interactType);
}

Example 18 with InteractType

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

the class InteractionListenerImpl method expand.

private List<Map<String, String>> expand(Map<String, String> properties, String associatedTaxa) {
    List<Map<String, String>> expandedList;
    expandedList = new ArrayList<>();
    String[] associatedPairs = associatedTaxa.split("\\|");
    for (String associatedPair : associatedPairs) {
        String[] typeAndTarget = associatedPair.split(":");
        if (typeAndTarget.length > 1) {
            String typeName = typeAndTarget[0];
            String targetTaxon = typeAndTarget[1];
            HashMap<String, String> expanded = new HashMap<>(properties);
            expanded.put(TARGET_TAXON_NAME, StringUtils.trim(targetTaxon));
            expanded.put(INTERACTION_TYPE_NAME, StringUtils.trim(typeName));
            InteractType interactType = StudyImporterForMetaTable.generateInteractionType(expanded);
            if (interactType != null) {
                expanded.put(INTERACTION_TYPE_NAME, interactType.getLabel());
                expanded.put(INTERACTION_TYPE_ID, interactType.getIRI());
            } else {
                getLogger().warn(studyFromLink(expanded), "unsupported interaction type for name [" + typeName + "]");
            }
            expandedList.add(expanded);
        }
    }
    return expandedList;
}

Example 19 with InteractType

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

the class StudyImporterForKelpForest method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    try {
        String source = "Beas-Luna, R., Novak, M., Carr, M. H., Tinker, M. T., Black, A., Caselle, J. E., … Iles, A. (2014). An Online Database for Informing Ecological Network Models: http://kelpforest.ucsc.edu. PLoS ONE, 9(10), e109356. doi:10.1371/journal.pone.0109356";
        Study study = nodeFactory.getOrCreateStudy(new StudyImpl(source, source, "doi:10.1371/journal.pone.0109356", source));
        LabeledCSVParser parser = parserFactory.createParser(NODES, "UTF-8");
        String[] line;
        Map<String, Long> nameToId = new HashMap<String, Long>();
        while ((line = parser.getLine()) != null) {
            if (line.length > 2) {
                String name = parser.getValueByLabel("working_name");
                String itisId = parser.getValueByLabel("itis_id");
                Long id = StringUtils.isBlank(itisId) ? null : Long.parseLong(itisId);
                id = (id != null && id > 0L) ? id : null;
                nameToId.put(name, id);
            }
        }
        Map<String, InteractType> typeToType = new HashMap<String, InteractType>() {

            {
                put("trophic", InteractType.ATE);
                put("parasitic", InteractType.PARASITE_OF);
            }
        };
        parser = parserFactory.createParser(LINKS, "UTF-8");
        while ((line = parser.getLine()) != null) {
            if (line.length > 2) {
                String interactionType = parser.getValueByLabel("type");
                InteractType interactType = typeToType.get(interactionType);
                if (null == interactType) {
                    LOG.warn("ignoring type [" + interactionType + "] on line: [" + (parser.getLastLineNumber() + 1) + "]");
                } else {
                    Specimen sourceSpecimen = createSpecimen(parser, nameToId, "node_1_working_name", "node1_stage", study);
                    Specimen targetSpecimen = createSpecimen(parser, nameToId, "node_2_working_name", "node2_stage", study);
                    sourceSpecimen.interactsWith(targetSpecimen, interactType);
                }
            }
        }
    } catch (IOException | NodeFactoryException e) {
        throw new StudyImporterException("failed to import", e);
    }
}

Example 20 with InteractType

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

the class StudyImporterForINaturalist method retrieveDataParseResults.

private int retrieveDataParseResults() throws StudyImporterException {
    List<Integer> typesIgnored;
    try {
        typesIgnored = buildTypesIgnored(parserFactory.createParser(getTypeIgnoredURI(), CharsetConstant.UTF8));
    } catch (IOException e) {
        throw new StudyImporterException("failed to load ignored interaction types from [" + getTypeIgnoredURI() + "]");
    }
    Map<Integer, InteractType> typeMap;
    try {
        LabeledCSVParser labeledCSVParser = parserFactory.createParser(getTypeMapURI(), CharsetConstant.UTF8);
        typeMap = buildTypeMap(getTypeMapURI(), labeledCSVParser);
    } catch (IOException e) {
        throw new StudyImporterException("failed to load interaction mapping from [" + getTypeMapURI() + "]");
    }
    int totalInteractions = 0;
    int previousResultCount = 0;
    int pageNumber = 1;
    do {
        String uri = INATURALIST_URL + "/observation_field_values.json?type=taxon&page=" + pageNumber + "&per_page=100&quality_grade=research";
        try {
            previousResultCount = parseJSON(getDataset().getResource(uri), typesIgnored, typeMap);
            pageNumber++;
            totalInteractions += previousResultCount;
        } catch (IOException | StudyImporterException e) {
            throw new StudyImporterException("failed to import iNaturalist at [" + uri + "]", e);
        }
    } while (previousResultCount > 0);
    return totalInteractions;
}