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.variation.MutationMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByProteinIdList(List<String> proteinIdList, QueryOptions options) {
    List<Document> queries = new ArrayList<>();
    for (String id : proteinIdList) {
        QueryBuilder builder = QueryBuilder.start("protein").is(id);
        queries.add(new Document(builder.get().toMap()));
    }/*from   ww w.  j a v  a2  s  . c om*/

    return executeQueryList2(proteinIdList, queries, options);
}

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From source file:org.opencb.cellbase.lib.db.variation.MutationMongoDBAdaptor.java

License:Apache License

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

    List<String> ids = new ArrayList<>(regions.size());
    for (Region region : regions) {
        QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("start")
                .greaterThanEquals(region.getStart()).lessThanEquals(region.getEnd());
        queries.add(new Document(builder.get().toMap()));
        ids.add(region.toString());/* ww  w  . j  ava 2 s .  c o m*/
    }

    return executeQueryList2(ids, queries, options);
}

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From source file:org.opencb.cellbase.lib.db.variation.VariantFunctionalScoreMongoDBAdaptor.java

License:Apache License

@Override
public QueryResult getByVariant(String chromosome, int position, String reference, String alternate,
        QueryOptions queryOptions) {//from w w w.j a va  2 s  .  com
    String chunkId = getChunkIdPrefix(chromosome, position,
            MongoDBCollectionConfiguration.VARIATION_FUNCTIONAL_SCORE_CHUNK_SIZE);
    QueryBuilder builder = QueryBuilder.start("_chunkIds").is(chunkId);
    //                .and("chromosome").is(chromosome)
    //                .and("start").is(position);
    //        System.out.println(chunkId);
    QueryResult result = executeQuery(chromosome + "_" + position + "_" + reference + "_" + alternate,
            new Document(builder.get().toMap()), queryOptions, mongoDBCollection);

    //        System.out.println("result = " + result);

    int offset = (position % MongoDBCollectionConfiguration.VARIATION_FUNCTIONAL_SCORE_CHUNK_SIZE) - 1;
    List<Score> scores = new ArrayList<>();
    for (Object object : result.getResult()) {
        //            System.out.println("object = " + object);
        Document dbObject = (Document) object;
        BasicDBList basicDBList = (BasicDBList) dbObject.get("values");
        Long l1 = (Long) basicDBList.get(offset);
        //            System.out.println("l1 = " + l1);
        if (dbObject.getString("source").equalsIgnoreCase("cadd_raw")) {
            float value = 0f;
            switch (alternate.toLowerCase()) {
            case "a":
                value = ((short) (l1 >> 48) - 10000) / DECIMAL_RESOLUTION;
                break;
            case "c":
                value = ((short) (l1 >> 32) - 10000) / DECIMAL_RESOLUTION;
                break;
            case "g":
                value = ((short) (l1 >> 16) - 10000) / DECIMAL_RESOLUTION;
                break;
            case "t":
                value = ((short) (l1 >> 0) - 10000) / DECIMAL_RESOLUTION;
                break;
            default:
                break;
            }
            scores.add(Score.newBuilder().setScore(value).setSource(dbObject.getString("source"))
                    .setDescription(null)
                    //                        .setDescription("")
                    .build());
        }

        if (dbObject.getString("source").equalsIgnoreCase("cadd_scaled")) {
            float value = 0f;
            switch (alternate.toLowerCase()) {
            case "a":
                value = ((short) (l1 >> 48)) / DECIMAL_RESOLUTION;
                break;
            case "c":
                value = ((short) (l1 >> 32)) / DECIMAL_RESOLUTION;
                break;
            case "g":
                value = ((short) (l1 >> 16)) / DECIMAL_RESOLUTION;
                break;
            case "t":
                value = ((short) (l1 >> 0)) / DECIMAL_RESOLUTION;
                break;
            default:
                break;
            }
            scores.add(Score.newBuilder().setScore(value).setSource(dbObject.getString("source"))
                    .setDescription(null)
                    //                        .setDescription("")
                    .build());
        }
    }

    result.setResult(scores);
    return result;
}

---

From source file:org.opencb.cellbase.lib.db.variation.VariationMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByIdList(List<String> idList, QueryOptions options) {
    List<Document> queries = new ArrayList<>();
    for (String id : idList) {
        QueryBuilder builder = QueryBuilder.start("ids").is(id);
        queries.add(new Document(builder.get().toMap()));
    }/*from  w  w  w.  j  a  va2 s. com*/
    return executeQueryList2(idList, queries, options);
}

---

From source file:org.opencb.cellbase.lib.db.variation.VariationMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByTranscriptIdList(List<String> idList, QueryOptions options) {
    List<Document> queries = new ArrayList<>();
    for (String id : idList) {
        QueryBuilder builder = QueryBuilder.start("annotation.consequenceTypes.ensemblTranscriptId").is(id);
        queries.add(new Document(builder.get().toMap()));
    }//from  ww  w. j  a v a 2s. c o m
    return executeQueryList2(idList, queries, options);
}

---

From source file:org.opencb.cellbase.lib.db.variation.VariationMongoDBAdaptor.java

License:Apache License

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

    // TODO: do not allow phenotype queries on the variation collection.
    // TODO: phenotype queries shall be answered by the clinicalMongoDBAdaptor
    String phenotype = options.getString("phenotype");
    if (phenotype != null && !phenotype.equals("")) {
        for (Region region : regions) {
            QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("start")
                    .greaterThanEquals(region.getStart()).lessThanEquals(region.getEnd());
            builder = builder.and("phenotype").is(phenotype);
            queries.add(new Document(builder.get().toMap()));
            ids.add(region.toString());//from   ww  w  . ja v  a2s. c  o  m
        }
        return executeQueryList2(ids, queries, options, mongoVariationPhenotypeDBCollection2);
    } else {
        String consequenceTypes = options.getString("consequence_type", null);
        BasicDBList consequenceTypeDBList = new BasicDBList();
        if (consequenceTypes != null && !consequenceTypes.equals("")) {
            for (String ct : consequenceTypes.split(",")) {
                consequenceTypeDBList.add(ct);
            }
        }

        for (Region region : regions) {
            // QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getSequenceName())
            // .and("end").greaterThan(region.getStart()).and("start").lessThan(region.getEnd());
            QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("start")
                    .greaterThanEquals(region.getStart()).lessThanEquals(region.getEnd());
            if (consequenceTypeDBList.size() > 0) {
                builder = builder.and("annotation.consequenceTypes.sequenceOntologyTerms.name")
                        .in(consequenceTypeDBList);
            }
            queries.add(new Document(builder.get().toMap()));
            ids.add(region.toString());
        }

        return executeQueryList2(ids, queries, options);
    }
}

---

From source file:org.opencb.cellbase.lib.db.variation.VariationMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getIdByVariantList(List<Variant> variations, QueryOptions options) {
    List<Document> queries = new ArrayList<>(variations.size());
    List<QueryResult> results;

    for (Variant variation : variations) {
        String chunkId = getChunkIdPrefix(variation.getChromosome(), variation.getStart(), variationChunkSize);
        QueryBuilder builder = QueryBuilder.start("_chunkIds").is(chunkId).and("chromosome")
                .is(variation.getChromosome()).and("start").is(variation.getStart()).and("alternate")
                .is(variation.getAlternate());
        if (variation.getReference() != null) {
            builder = builder.and("reference").is(variation.getReference());
        }//w  w w.  j  a  v  a 2s. c  o  m

        queries.add(new Document(builder.get().toMap()));
    }

    results = executeQueryList2(variations, queries, options, mongoDBCollection);

    for (QueryResult result : results) {
        List<String> idList = new LinkedList();

        BasicDBList idListObject = (BasicDBList) result.getResult();
        for (Object idObject : idListObject) {
            Document variantObject = (Document) idObject;
            // Arbitrarily selects the first one. Assuming variants in variation collection will just have one id
            idList.add(((BasicDBList) variantObject.get("ids")).get(0).toString());
        }

        //            result.setResult(Joiner.on(",").skipNulls().join(idList));
        result.setResult(idList);
    }

    return results;
}

---

From source file:org.opencb.cellbase.lib.db.variation.VariationMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByVariantList(List<Variant> variations, QueryOptions options) {
    List<Document> queries = new ArrayList<>(variations.size());
    List<QueryResult> results;

    for (Variant variation : variations) {
        String chunkId = getChunkIdPrefix(variation.getChromosome(), variation.getStart(), variationChunkSize);

        QueryBuilder builder = QueryBuilder.start("_chunkIds").is(chunkId).and("chromosome")
                .is(variation.getChromosome()).and("start").is(variation.getStart()).and("alternate")
                .is(variation.getAlternate());

        if (variation.getReference() != null) {
            builder = builder.and("reference").is(variation.getReference());
        }//from   w ww.j  a  v a 2  s  . c  o m

        queries.add(new Document(builder.get().toMap()));
    }

    results = executeQueryList2(variations, queries, options, mongoDBCollection);
    //        results = executeQueryList(variations, queries, options, mongoDBCollection);

    return results;
}

---

From source file:org.opencb.cellbase.lib.impl.ClinicalMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByGenomicVariantList(List<Variant> variantList, QueryOptions options) {
    List<Document> queries = new ArrayList<>();
    List<String> ids = new ArrayList<>(variantList.size());
    List<QueryResult> queryResultList;
    for (Variant genomicVariant : variantList) {
        QueryBuilder builder = QueryBuilder.start("chromosome").is(genomicVariant.getChromosome()).and("start")
                .is(genomicVariant.getStart()).and("alternate").is(genomicVariant.getAlternate());
        if (genomicVariant.getReference() != null) {
            builder = builder.and("reference").is(genomicVariant.getReference());
        }//from   w ww  .j av a  2 s.  c o  m
        queries.add(new Document(builder.get().toMap()));
        logger.debug(new Document(builder.get().toMap()).toJson());
        ids.add(genomicVariant.toString());
    }

    queryResultList = executeQueryList2(ids, queries, options);

    for (QueryResult queryResult : queryResultList) {
        List<Document> clinicalList = (List<Document>) queryResult.getResult();

        List<Cosmic> cosmicList = new ArrayList<>();
        List<Gwas> gwasList = new ArrayList<>();
        List<ClinVar> clinvarList = new ArrayList<>();

        for (Object clinicalObject : clinicalList) {
            Document clinical = (Document) clinicalObject;

            if (isCosmic(clinical)) {
                Cosmic cosmic = getCosmic(clinical);
                cosmicList.add(cosmic);
            } else if (isGwas(clinical)) {
                Gwas gwas = getGwas(clinical);
                gwasList.add(gwas);

            } else if (isClinvar(clinical)) {
                ClinVar clinvar = getClinvar(clinical);
                //                    if (clinvarList == null) {
                //                        clinvarList = new ArrayList<>();
                //                    }
                clinvarList.add(clinvar);
            }
        }
        //            Map<String, Object> clinicalData = new HashMap<>();
        //            if(cosmicList!=null && cosmicList.size()>0) {
        //                clinicalData.put("cosmic", cosmicList);
        //            }
        //            if(gwasList!=null && gwasList.size()>0) {
        //                clinicalData.put("gwas", gwasList);
        //            }
        //            if(clinvarList!=null && clinvarList.size()>0) {
        //                clinicalData.put("clinvar", clinvarList);
        //            }
        VariantTraitAssociation variantTraitAssociation = new VariantTraitAssociation(clinvarList, gwasList,
                cosmicList);
        if (!(variantTraitAssociation.getCosmic().isEmpty() && variantTraitAssociation.getGwas().isEmpty()
                && variantTraitAssociation.getClinvar().isEmpty())) {

            // FIXME quick solution to compile
            // queryResult.setResult(clinicalData);
            queryResult.setResult(Collections.singletonList(variantTraitAssociation));
            queryResult.setNumResults(variantTraitAssociation.getCosmic().size()
                    + variantTraitAssociation.getGwas().size() + variantTraitAssociation.getClinvar().size());
        } else {
            queryResult.setResult(null);
            queryResult.setNumResults(0);
        }
    }

    return queryResultList;
}

---

From source file:org.opencb.cellbase.lib.impl.ConservationMongoDBAdaptor.java

License:Apache License

public List<QueryResult> getAllByRegionList(List regionList, QueryOptions options) {
    //TODO not finished yet
    List<Document> queries = new ArrayList<>();
    List<String> ids = new ArrayList<>(regionList.size());
    List<String> integerChunkIds;

    List<Region> regions = regionList;
    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 a2 s. c  o  m
        }
        if (region.getEnd() < 1) {
            region.setEnd(1);
        }

        // Max region size is 10000bp
        if (region.getEnd() - region.getStart() > 10000) {
            region.setEnd(region.getStart() + 10000);
        }

        QueryBuilder builder;
        int regionChunkStart = getChunkId(region.getStart(),
                MongoDBCollectionConfiguration.CONSERVATION_CHUNK_SIZE);
        int regionChunkEnd = getChunkId(region.getEnd(),
                MongoDBCollectionConfiguration.CONSERVATION_CHUNK_SIZE);
        if (regionChunkStart == regionChunkEnd) {
            builder = QueryBuilder.start("_chunkIds").is(getChunkIdPrefix(region.getChromosome(),
                    region.getStart(), MongoDBCollectionConfiguration.CONSERVATION_CHUNK_SIZE));
        } else {
            //                for (int chunkId = regionChunkStart; chunkId <= regionChunkEnd; chunkId++) {
            ////                    integerChunkIds.add(chunkId);
            //                    integerChunkIds.add(region.getChromosomeInfo() + "_" + chunkId + "_" + this.chunkSize/1000 + "k");
            //                }
            //                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());
        }
        //            QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosomeInfo()).and("chunkId").in(hunkIds);
        /****/

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

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

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

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

        //            int start = region.getStart();

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

            //                BasicDBList valuesChunk = (BasicDBList) chunk.get("values");
            ArrayList valuesChunk = chunk.get("values", ArrayList.class);

            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++) {
                //                    System.out.println("valuesList SIZE = " + valuesList.size());
                //                    System.out.println("pos = " + pos);
                //                    System.out.println("DIV " + (chunk.getInt("start") - region.getStart()));
                //                    System.out.println("valuesChunk = " + valuesChunk.get(pos));
                //                    System.out.println("indexFinal = " + (pos + chunk.getInt("start") - region.getStart()));
                valuesList.set(pos + chunk.getInteger("start") - region.getStart(),
                        new Float((Double) valuesChunk.get(pos)));
            }
        }
        //
        BasicDBList resultList = new BasicDBList();
        //            ConservationScoreRegion conservedRegionChunk;
        GenomicScoreRegion<Float> conservedRegionChunk;
        for (Map.Entry<String, List<Float>> elem : typeMap.entrySet()) {
            //                conservedRegionChunk = new ConservationScoreRegion(region.getChromosome(), region.getStart(),
            //                        region.getEnd(), elem.getKey(), elem.getValue());
            conservedRegionChunk = new GenomicScoreRegion<>(region.getChromosome(), region.getStart(),
                    region.getEnd(), elem.getKey(), elem.getValue());
            resultList.add(conservedRegionChunk);
        }
        queryResult.setResult(resultList);
    }

    return queryResults;
}

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