Example usage for com.mongodb QueryBuilder get

Introduction

In this page you can find the example usage for com.mongodb QueryBuilder get.

Prototype

public DBObject get() 

Source Link

Document

Creates a DBObject query to be used for the driver's find operations

Usage

From source file:org.opencb.cellbase.lib.db.core.ConservationMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllScoresByRegionList(List<Region> regions, QueryOptions options) {
    //TODO not finished yet
    List<Document> queries = new ArrayList<>();
    List<String> ids = new ArrayList<>(regions.size());
    List<Integer> integerChunkIds;
    for (Region region : regions) {
        integerChunkIds = new ArrayList<>();
        // positions below 1 are not allowed
        if (region.getStart() < 1) {
            region.setStart(1);//from   w w w. j a v  a 2s.c  om
        }
        if (region.getEnd() < 1) {
            region.setEnd(1);
        }

        /****/
        QueryBuilder builder;
        int regionChunkStart = getChunkId(region.getStart(), this.chunkSize);
        int regionChunkEnd = getChunkId(region.getEnd(), this.chunkSize);
        if (regionChunkStart == regionChunkEnd) {
            builder = QueryBuilder.start("_chunkIds")
                    .is(getChunkIdPrefix(region.getChromosome(), region.getStart(), chunkSize));
        } else {
            //                for (int chunkId = regionChunkStart; chunkId <= regionChunkEnd; chunkId++) {
            //                    integerChunkIds.add(chunkId);
            //                }
            //    //            QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosomeInfo()).and("chunkId").in(hunkIds);
            //                builder = QueryBuilder.start("chromosome").is(region.getChromosomeInfo()).and("chunkId").in(integerChunkIds);
            builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end")
                    .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd());
        }
        /****/

        queries.add(new Document(builder.get().toMap()));
        ids.add(region.toString());

        //            logger.debug(builder.get().toString());

    }
    List<QueryResult> queryResults = executeQueryList2(ids, queries, options);
    //        List<QueryResult> queryResults = executeQueryList(ids, queries, options);

    for (int i = 0; i < regions.size(); i++) {
        Region region = regions.get(i);
        QueryResult queryResult = queryResults.get(i);
        List<Document> list = (List<Document>) queryResult.getResult();

        Map<String, List<Float>> typeMap = new HashMap();

        //            int start = region.getStart();

        for (int j = 0; j < list.size(); j++) {
            Document chunk = list.get(j);

            if (!chunk.isEmpty()) {
                BasicDBList valuesChunk = (BasicDBList) chunk.get("values");
                if (valuesChunk != null) { // TODO: temporary patch to skip empty chunks - remove as soon as conservation is reloaded
                    String source = chunk.getString("source");
                    List<Float> valuesList;
                    if (!typeMap.containsKey(source)) {
                        valuesList = new ArrayList<>(region.getEnd() - region.getStart() + 1);
                        for (int val = 0; val < region.getEnd() - region.getStart() + 1; val++) {
                            valuesList.add(null);
                        }
                        typeMap.put(source, valuesList);
                    } else {
                        valuesList = typeMap.get(source);
                    }

                    valuesChunk = (BasicDBList) chunk.get("values");
                    int pos = 0;
                    if (region.getStart() > chunk.getInteger("start")) {
                        pos = region.getStart() - chunk.getInteger("start");
                    }

                    for (; pos < valuesChunk.size()
                            && (pos + chunk.getInteger("start") <= region.getEnd()); pos++) {
                        valuesList.set(pos + chunk.getInteger("start") - region.getStart(),
                                new Float((Double) valuesChunk.get(pos)));
                    }
                } else {
                    continue;
                }

            }

            BasicDBList resultList = new BasicDBList();
            for (Map.Entry<String, List<Float>> elem : typeMap.entrySet()) {
                for (Float value : elem.getValue()) {
                    if (value != null) {
                        resultList.add(new Score(new Double(value), elem.getKey()));
                    }
                }
            }
            if (!resultList.isEmpty()) {
                queryResult.setResult(resultList);
            } else {
                queryResult.setResult(null);
            }
        }
    }
    return queryResults;
}

---

From source file:org.opencb.cellbase.lib.db.core.GeneMongoDBAdaptor.java

License:Apache License

@Override
public QueryResult getAll(QueryOptions options) {
    QueryBuilder builder = new QueryBuilder();

    List<String> biotypes = options.getAsStringList("biotype");
    if (biotypes != null && biotypes.size() > 0) {
        BasicDBList biotypeIds = new BasicDBList();
        biotypeIds.addAll(biotypes);//from  w w  w . ja va 2 s.  co m
        builder = builder.and("biotype").in(biotypeIds);
    }

    return executeQuery("result", new Document(builder.get().toMap()), options);
}

---

From source file:org.opencb.cellbase.lib.db.core.GeneMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByIdList(List<String> idList, QueryOptions options) {
    List<Document> queries = new ArrayList<>(idList.size());
    for (String id : idList) {
        QueryBuilder builder = QueryBuilder.start("transcripts.xrefs.id").is(id);
        queries.add(new Document(builder.get().toMap()));
    }//  w  w  w.ja  va 2  s. c  o  m

    //        options = addExcludeReturnFields("transcripts", options);
    //        return executeQueryList(idList, queries, options);
    return executeQueryList2(idList, queries, options);
}

---

From source file:org.opencb.cellbase.lib.db.core.GeneMongoDBAdaptor.java

License:Apache License

@Override
public QueryResult getStatsById(String id, QueryOptions options) {

    Map<String, Object> stats = new HashMap<>();
    QueryResult queryResult = new QueryResult();
    queryResult.setId(id);//  www. ja  v  a2  s. c o m

    QueryBuilder geneBuilder = QueryBuilder.start("transcripts.xrefs.id").is(id);
    long dbTimeStart = System.currentTimeMillis();
    QueryResult geneQueryResult = executeQuery(id, new Document(geneBuilder.get().toMap()), new QueryOptions());
    // TODO: clinical variant summary is only provided for ClinVar (hardcoded below)
    QueryOptions clinicalQueryOptions = new QueryOptions("source", "clinvar");
    clinicalQueryOptions.put("include",
            "annot.consequenceTypes.soTerms,clinvarSet.referenceClinVarAssertion.clinicalSignificance.description");
    QueryResult clinicalQueryResult = clinicalDBAdaptor.getByGeneId(id, clinicalQueryOptions);
    long dbTimeEnd = System.currentTimeMillis();
    queryResult.setDbTime(Long.valueOf(dbTimeEnd - dbTimeStart).intValue());

    if (geneQueryResult.getNumResults() > 0) {
        queryResult.setNumResults(1);
        stats = setCoreGeneStats(geneQueryResult, stats);
        stats = setVariantStats(clinicalQueryResult, stats);
        queryResult.setResult(Collections.singletonList(stats));
    }

    return queryResult;
    //        gene name
    //        ensembl gene id
    //        chr
    //        start
    //        end
    //        sequence length
    //        num transcripts
    //        breakdown num transcripts by biotype
    //        num exons
    //        num drug interactions
    //        Clinical Variants {
    //            #
    //            Breakdown by clinical significance
    //            Breakdown by SO
    //        }

    //        options = addExcludeReturnFields("transcripts", options);
    //        return executeQueryList(idList, queries, options);

}

---

From source file:org.opencb.cellbase.lib.db.core.GeneMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByRegionList(List<Region> regions, QueryOptions options) {
    List<Document> queries = new ArrayList<>();

    List<Object> biotypes = options.getList("biotype", null);
    BasicDBList biotypeIds = new BasicDBList();
    if (biotypes != null && biotypes.size() > 0) {
        biotypeIds.addAll(biotypes);// w  ww.j a  v a2s  .com
    }

    List<String> ids = new ArrayList<>(regions.size());
    for (Region region : regions) {

        QueryBuilder builder = null;
        // If regions is 1 position then query can be optimize using chunks
        if (region.getStart() == region.getEnd()) {
            builder = QueryBuilder.start("_chunkIds")
                    .is(getChunkIdPrefix(region.getChromosome(), region.getStart(), geneChunkSize)).and("end")
                    .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd());
        } else {
            builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end")
                    .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd());
        }

        if (biotypeIds.size() > 0) {
            builder = builder.and("biotype").in(biotypeIds);
        }
        queries.add(new Document(builder.get().toMap()));
        ids.add(region.toString());
    }
    return executeQueryList2(ids, queries, options);
    //        return executeQueryList(ids, queries, options);
}

---

From source file:org.opencb.cellbase.lib.db.core.GenomeMongoDBAdaptor.java

License:Apache License

@Deprecated
public QueryResult speciesInfoTmp(String id, QueryOptions options) {
    // reading application.properties file

    //        String[] speciesArray = applicationProperties.getProperty("SPECIES").split(",");

    //        List<Document> queries = new ArrayList<>(1);
    //        for (String id : idList) {
    QueryBuilder builder = QueryBuilder.start("species").is(id);

    //        queries.add(builder.get());
    //        }//from w  ww . j  a  v a2  s .  co  m

    //        options = addExcludeReturnFields("transcripts", options);
    return executeQuery(id, new Document(builder.get().toMap()), options);

}

---

From source file:org.opencb.cellbase.lib.db.core.GenomeMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllSequencesByRegionList(List<Region> regions, QueryOptions options) {
    /****//* www.j  av  a  2  s.  c  o m*/
    String chunkIdSuffix = this.chunkSize / 1000 + "k";
    /****/

    List<Document> queries = new ArrayList<>();
    List<String> ids = new ArrayList<>(regions.size());
    List<String> chunkIds;
    List<Integer> integerChunkIds;
    for (Region region : regions) {
        chunkIds = new ArrayList<>();
        integerChunkIds = new ArrayList<>();
        // positions below 1 are not allowed
        if (region.getStart() < 1) {
            region.setStart(1);
        }
        if (region.getEnd() < 1) {
            region.setEnd(1);
        }

        /****/
        int regionChunkStart = getChunkId(region.getStart(), this.chunkSize);
        int regionChunkEnd = getChunkId(region.getEnd(), this.chunkSize);
        for (int chunkId = regionChunkStart; chunkId <= regionChunkEnd; chunkId++) {
            String chunkIdStr = region.getChromosome() + "_" + chunkId + "_" + chunkIdSuffix;
            chunkIds.add(chunkIdStr);
            integerChunkIds.add(chunkId);
        }
        //            QueryBuilder builder = QueryBuilder.start("sequenceName").is(region.getChromosomeInfo()).and("_chunkIds").in(chunkIds);
        QueryBuilder builder = QueryBuilder.start("_chunkIds").in(chunkIds);
        /****/
        queries.add(new Document(builder.get().toMap()));
        ids.add(region.toString());

        logger.info(new Document(builder.get().toMap()).toString());
    }

    List<QueryResult> queryResults = executeQueryList2(ids, queries, options, genomeSequenceCollection);
    for (int i = 0; i < regions.size(); i++) {
        Region region = regions.get(i);
        QueryResult queryResult = queryResults.get(i);

        List list = queryResult.getResult();
        StringBuilder sb = new StringBuilder();
        for (int j = 0; j < list.size(); j++) {
            Document chunk = (Document) list.get(j);
            sb.append(chunk.get("sequence"));
        }

        int startStr = getOffset(region.getStart());
        int endStr = getOffset(region.getStart()) + (region.getEnd() - region.getStart()) + 1;

        String subStr = "";

        if (getChunkId(region.getStart(), this.chunkSize) > 0) {
            if (sb.toString().length() > 0 && sb.toString().length() >= endStr) {
                subStr = sb.toString().substring(startStr, endStr);
            }
        } else {
            if (sb.toString().length() > 0 && sb.toString().length() + 1 >= endStr) {
                subStr = sb.toString().substring(startStr - 1, endStr - 1);
            }
        }
        logger.info("((Document)list.get(0)).getString(\"sequenceType\") = {}",
                ((Document) list.get(0)).getString("sequenceType"));
        logger.info("((Document)list.get(0)).getString(\"assembly\") = {}",
                ((Document) list.get(0)).getString("assembly"));
        GenomeSequenceFeature genomeSequenceFeature = new GenomeSequenceFeature(region.getChromosome(),
                region.getStart(), region.getEnd(), 1, ((Document) list.get(0)).getString("sequenceType"),
                ((Document) list.get(0)).getString("assembly"), subStr);

        queryResult.setResult(Arrays.asList(genomeSequenceFeature));
    }

    return queryResults;
}

---

From source file:org.opencb.cellbase.lib.db.core.ProteinMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByIdList(List<String> idList, QueryOptions options) {
    List<Document> queries = new ArrayList<>(idList.size());
    for (String id : idList) {
        QueryBuilder builder = QueryBuilder.start("name").is(id);
        queries.add(new Document(builder.get().toMap()));
    }/*ww  w  . ja v a2 s  .c o  m*/

    //        options = addExcludeReturnFields("transcripts", options);
    return executeQueryList2(idList, queries, options);
}

---

From source file:org.opencb.cellbase.lib.db.core.ProteinMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByXrefList(List<String> idList, QueryOptions options) {
    List<Document> queries = new ArrayList<>(idList.size());
    for (String id : idList) {
        QueryBuilder builder = QueryBuilder.start("dbReference.id").is(id);
        queries.add(new Document(builder.get().toMap()));
    }//from  w ww .j a  v a  2  s. co  m

    //        options = addExcludeReturnFields("transcripts", options);
    //        return executeQueryList(idList, queries, options);
    return executeQueryList2(idList, queries, options);
}

---

From source file:org.opencb.cellbase.lib.db.core.ProteinMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllFunctionPredictionByEnsemblTranscriptIdList(List<String> transcriptIdList,
        QueryOptions options) {//from  w  w  w . jav  a  2 s  .  c  o m
    List<Document> queries = new ArrayList<>(transcriptIdList.size());

    if (options.containsKey("aaPosition")) {
        if (options.containsKey("aaChange")) {
            addIncludeReturnFields(
                    "aaPositions." + options.getString("aaPosition") + "." + options.getString("aaChange"),
                    options);
        } else {
            addIncludeReturnFields("aaPositions." + options.getString("aaPosition"), options);
        }
    }

    for (String id : transcriptIdList) {
        QueryBuilder builder = QueryBuilder.start("transcriptId").is(id);
        queries.add(new Document(builder.get().toMap()));
    }

    //        options = addExcludeReturnFields("transcripts", options);
    return executeQueryList2(transcriptIdList, queries, options, proteinFunctionalPredictionCollection);
}

---

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