Example usage for org.apache.commons.collections.keyvalue MultiKey MultiKey

Introduction

In this page you can find the example usage for org.apache.commons.collections.keyvalue MultiKey MultiKey.

Prototype

public MultiKey(Object key1, Object key2, Object key3) 

Source Link

Document

Constructor taking three keys.

Usage

From source file:org.intermine.bio.dataconversion.TreefamConverter.java

private String getGene(String geneId, String symbol, String type, String taxonId) throws ObjectStoreException {
    String identifierType = (StringUtils.isNotEmpty(type) ? type : DEFAULT_IDENTIFIER_TYPE);

    String resolvedGenePid = null;
    // test if id has been resolved
    if (resolvedIds.containsKey(new MultiKey(taxonId, geneId, symbol))) {
        resolvedGenePid = resolvedIds.get(new MultiKey(taxonId, geneId, symbol));
    } else {/*from w w  w  . j av a2s  .co  m*/
        resolvedGenePid = resolveGene(taxonId, geneId, symbol);
    }

    if (resolvedGenePid == null) {
        return null;
    }
    String refId = identifiersToGenes.get(resolvedGenePid);
    if (refId == null) {
        Item gene = createItem("Gene");
        gene.setAttribute(DEFAULT_IDENTIFIER_TYPE, resolvedGenePid);

        if (!identifierType.equals(DEFAULT_IDENTIFIER_TYPE)) {
            if ("crossReferences".equals(identifierType)) {
                gene.addToCollection(identifierType,
                        createCrossReference(gene.getIdentifier(), geneId, DATA_SOURCE_NAME, true));
            } else {
                gene.setAttribute(identifierType, geneId);
            }
        }

        gene.setReference("organism", getOrganism(taxonId));
        refId = gene.getIdentifier();
        identifiersToGenes.put(resolvedGenePid, refId);
        store(gene);
    }
    return refId;
}

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From source file:org.intermine.bio.dataconversion.TreefamConverter.java

private String resolveGene(String taxonId, String identifier, String symbol) {
    if (rslv == null || !rslv.hasTaxon(taxonId)) {
        // no id resolver available, so return the original identifier
        LOG.info("ID resolver not used for taxon ID " + taxonId);
        return identifier;
    }// w  w  w.  j  av a 2 s  .co  m

    String resolvedId = rslv.resolveIds(taxonId, Arrays.asList(identifier, symbol));

    if (resolvedId != null) {
        LOG.info("RESOLVER: failed to resolve gene to one identifier, ignoring gene: " + identifier
                + " for taxon ID " + taxonId);
    }

    resolvedIds.put(new MultiKey(taxonId, identifier, symbol), resolvedId);
    return resolvedId;
}

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From source file:org.intermine.bio.web.displayer.FriendlyMineLinkGenerator.java

/**
 * Generate a list of genes and orthologues for remote mines.
 *
 * 1. Query local mine for orthologues for genes given.
 * 2. if orthologue found query remote mine for genes
 * 3. if orthologue not found query remote mine for orthologues
 *
 * @param olm LinkManager/*from ww  w . j a  va  2 s. co m*/
 * @param organismShortName organism.shortName, eg. C. elegans
 * @param primaryIdentifier identifier for gene
 * @param mineName name of mine to query
 * @return map from mine to organism-->genes
 */
public Collection<JSONObject> getLinks(FriendlyMineManager olm, String mineName, String organismShortName,
        String primaryIdentifier) {

    if (StringUtils.isEmpty(mineName) || StringUtils.isEmpty(organismShortName)
            || StringUtils.isEmpty(primaryIdentifier)) {
        return null;
    }

    // FIXME temporarily ignoring lists with more than one organism
    if (organismShortName.contains(",")) {
        return null;
    }

    MultiKey key = new MultiKey(mineName, primaryIdentifier, organismShortName);
    Collection<JSONObject> cachedResults = olm.getLink(key);
    if (cachedResults != null && !debug) {
        return cachedResults;
    }

    Mine mine = olm.getMine(mineName);
    if (mine == null || mine.getReleaseVersion() == null) {
        LOG.info(mineName + " seems to be dead");
        return null;
    }

    Model model = olm.getInterMineAPI().getModel();

    Map<String, Set<String[]>> genes = new HashMap<String, Set<String[]>>();
    try {
        // query for homologues in remote mine
        PathQuery q = getHomologueQuery(model, organismShortName, primaryIdentifier);
        Map<String, Set<String[]>> results = runQuery(mine, q, organismShortName);
        if (results != null && !results.isEmpty()) {
            genes.putAll(results);
        } else {
            // no luck, query local mine
            Map<String, Set<String>> localHomologues = getLocalHomologues(olm, organismShortName,
                    primaryIdentifier);
            for (String remoteMineOrganism : mine.getDefaultValues()) {
                Set<String> matchingHomologues = localHomologues.get(remoteMineOrganism);
                if (matchingHomologues != null && !matchingHomologues.isEmpty()) {
                    String identifiers = StringUtil.join(matchingHomologues, ",");
                    // query remote mine for genes found in local mine
                    q = getGeneQuery(model, remoteMineOrganism, identifiers);
                    results = runQuery(mine, q, remoteMineOrganism);
                    if (results != null && !results.isEmpty()) {
                        genes.putAll(results);
                    }
                }
            }
        }
        q = getGeneQuery(model, organismShortName, primaryIdentifier);
        results = runQuery(mine, q, organismShortName);
        if (results != null && !results.isEmpty()) {
            genes.putAll(results);
        }
    } catch (Exception e) {
        LOG.warn("error generating friendly mine links", e);
        return null;
    }
    Collection<JSONObject> results = resultsToJSON(key, genes);
    olm.addLink(key, results);
    return results;
}

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From source file:org.kuali.student.r2.core.room.service.decorators.RoomServiceCacheDecorator.java

@Override
public List<RoomInfo> getRoomsByBuildingAndRoomCode(@WebParam(name = "buildingCode") String buildingCode,
        @WebParam(name = "roomCode") String roomCode, @WebParam(name = "contextInfo") ContextInfo contextInfo)
        throws DoesNotExistException, InvalidParameterException, MissingParameterException,
        OperationFailedException, PermissionDeniedException {
    MultiKey cacheKey = new MultiKey(BUILDING_ROOM_CODE_CACHE_PREFIX, buildingCode, roomCode);

    Element cachedResult = cacheManager.getCache(buildingRoomCodeCache).get(cacheKey);
    List<RoomInfo> result = null;
    if (cachedResult == null) {
        result = getNextDecorator().getRoomsByBuildingAndRoomCode(buildingCode, roomCode, contextInfo);
        cacheManager.getCache(buildingRoomCodeCache).put(new Element(cacheKey, result));
    } else {/*from   www .j a v a  2s.  co m*/
        result = (List<RoomInfo>) cachedResult.getValue();
    }

    return result;
}

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