Example usage for com.mongodb QueryBuilder start

List of usage examples for com.mongodb QueryBuilder start

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Introduction

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

Prototype

public static QueryBuilder start(final String key)

Source Link

Document

Creates a new query with a document key

Usage

From source file:org.opencb.cellbase.mongodb.db.ClinicalMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByGenomicVariantList(List<GenomicVariant> variantList, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>();
    List<String> ids = new ArrayList<>(variantList.size());
    List<QueryResult> queryResultList;
    for (GenomicVariant genomicVariant : variantList) {
        QueryBuilder builder = QueryBuilder.start("chromosome").is(genomicVariant.getChromosome()).and("start")
                .is(genomicVariant.getPosition()).and("alternate").is(genomicVariant.getAlternative());
        if (genomicVariant.getReference() != null) {
            builder = builder.and("reference").is(genomicVariant.getReference());
        }//from   w w  w  . jav  a 2  s.c om
        queries.add(builder.get());
        ids.add(genomicVariant.toString());
    }

    queryResultList = executeQueryList2(ids, queries, options);

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

        List<Cosmic> cosmicList = null;
        List<Gwas> gwasList = null;
        List<Clinvar> clinvarList = null;

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

            if (isCosmic(clinical)) {
                Cosmic cosmic = getCosmic(clinical);
                if (cosmicList == null) {
                    cosmicList = new ArrayList<>();
                }
                cosmicList.add(cosmic);
            } else if (isGwas(clinical)) {
                Gwas gwas = getGwas(clinical);
                if (gwasList == null) {
                    gwasList = new ArrayList<>();
                }
                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<>();
        clinicalData.put("Cosmic", cosmicList);
        clinicalData.put("Gwas", gwasList);
        clinicalData.put("Clinvar", clinvarList);
        // FIXME quick solution to compile
        //            queryResult.setResult(clinicalData);
        queryResult.setResult(Arrays.asList(clinicalData));
        queryResult.setNumResults(1);
    }

    return queryResultList;
}

From source file:org.opencb.cellbase.mongodb.db.ClinicalMongoDBAdaptor.java

License:Apache License

public QueryResult getListClinvarAccessions(QueryOptions queryOptions) {
    QueryBuilder builder = QueryBuilder.start("clinvarSet.referenceClinVarAssertion.clinVarAccession.acc")
            .exists(true);/*from w  w w .  j a v a2  s.c  o m*/
    queryOptions.put("include", Arrays.asList("clinvarSet.referenceClinVarAssertion.clinVarAccession.acc"));
    QueryResult queryResult = executeQuery("", builder.get(), queryOptions);
    List accInfoList = (List) queryResult.getResult();
    List<String> accList = new ArrayList<>(accInfoList.size());
    BasicDBObject accInfo;
    QueryResult listAccessionsToReturn = new QueryResult();

    for (Object accInfoObject : accInfoList) {
        accInfo = (BasicDBObject) accInfoObject;
        accInfo = (BasicDBObject) accInfo.get("clinvarSet");
        accList.add((String) ((BasicDBObject) ((BasicDBObject) ((BasicDBObject) accInfo
                .get("referenceClinVarAssertion"))).get("clinVarAccession")).get("acc"));
    }

    // setting listAccessionsToReturn fields
    listAccessionsToReturn.setId(queryResult.getId());
    listAccessionsToReturn.setDbTime(queryResult.getDbTime());
    listAccessionsToReturn.setNumResults(queryResult.getNumResults());
    listAccessionsToReturn.setNumTotalResults(queryResult.getNumTotalResults());
    listAccessionsToReturn.setResult(accList);

    return listAccessionsToReturn;
}

From source file:org.opencb.cellbase.mongodb.db.ClinicalMongoDBAdaptor.java

License:Apache License

public QueryResult updateAnnotations(List<VariantAnnotation> variantAnnotations, QueryOptions queryOptions) {

    /**/*w w  w .  ja v a  2s  .  c  o  m*/
     * Multiple documents may contain the same annotation
     */
    queryOptions.put("multi", true);

    /**
     * Prepare jackson to generate json strings
     */
    ObjectMapper jsonObjectMapper = new ObjectMapper();
    jsonObjectMapper.configure(SerializationFeature.WRITE_NULL_MAP_VALUES, false);
    jsonObjectMapper.setSerializationInclusion(JsonInclude.Include.NON_NULL);
    ObjectWriter writer = jsonObjectMapper.writer();

    long start = System.nanoTime();
    for (VariantAnnotation variantAnnotation : variantAnnotations) {
        QueryBuilder builder = QueryBuilder.start("chromosome").is(variantAnnotation.getChromosome())
                .and("start").is(variantAnnotation.getStart()).and("reference")
                .is(variantAnnotation.getReferenceAllele()).and("alternate")
                .is(variantAnnotation.getAlternativeAllele());
        DBObject update = null;
        try {
            update = new BasicDBObject("$set",
                    new BasicDBObject("annot", JSON.parse(writer.writeValueAsString(variantAnnotation))));
        } catch (JsonProcessingException e) {
            e.printStackTrace();
        }
        //            DBObject update = new BasicDBObject("$set", new BasicDBObject("annotation",
        //                    convertVariantAnnotation(variantAnnotation)));
        mongoDBCollection2.update(builder.get(), update, queryOptions);
    }

    return new QueryResult<>("", ((int) (System.nanoTime() - start)), 1, 1, "", "", new ArrayList());
}

From source file:org.opencb.cellbase.mongodb.db.ClinVarMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByIdList(List<String> idList, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>(idList.size());
    for (String id : idList) {
        QueryBuilder builder = QueryBuilder.start("referenceClinVarAssertion.clinVarAccession.acc").is(id);
        queries.add(builder.get());/*from   w  ww  .j a v a2s  . c o  m*/
    }

    return executeQueryList(idList, queries, options);
}

From source file:org.opencb.cellbase.mongodb.db.ClinVarMongoDBAdaptor.java

License:Apache License

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

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

        // If regions is 1 position then query can be optimize using chunks
        QueryBuilder builder = QueryBuilder
                .start("referenceClinVarAssertion.measureSet.measure.measureRelationship.sequenceLocation.chr")
                .is(region.getChromosome())
                .and("referenceClinVarAssertion.measureSet.measure.measureRelationship.sequenceLocation.stop")
                .greaterThanEquals(region.getStart())
                .and("referenceClinVarAssertion.measureSet.measure.measureRelationship.sequenceLocation.start")
                .lessThanEquals(region.getEnd());
        System.out.println(builder.get().toString());
        queries.add(builder.get());/*from  w w  w. j av a 2  s.co m*/
        ids.add(region.toString());
    }
    return executeQueryList(ids, queries, options);
}

From source file:org.opencb.cellbase.mongodb.db.ConservationMongoDBAdaptor.java

License:Apache License

@Deprecated
@Override/*from   w w  w .  jav a 2s  . c om*/
public List<QueryResult> getAllByRegionList(List<Region> regions, QueryOptions options) {
    //TODO not finished yet
    List<DBObject> queries = new ArrayList<>();
    List<String> ids = new ArrayList<>(regions.size());
    List<String> integerChunkIds;
    for (Region region : regions) {
        integerChunkIds = new ArrayList<>();
        // positions below 1 are not allowed
        if (region.getStart() < 1) {
            region.setStart(1);
        }
        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(), this.chunkSize));
        } else {
            //                for (int chunkId = regionChunkStart; chunkId <= regionChunkEnd; chunkId++) {
            ////                    integerChunkIds.add(chunkId);
            //                    integerChunkIds.add(region.getChromosome() + "_" + chunkId + "_" + this.chunkSize/1000 + "k");
            //                }
            //                builder = QueryBuilder.start("chromosome").is(region.getChromosome()).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.getChromosome()).and("chunkId").in(hunkIds);
        /****/

        queries.add(builder.get());
        ids.add(region.toString());

        logger.info(builder.get().toString());
    }

    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);
        BasicDBList list = (BasicDBList) queryResult.getResult();

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

        //            int start = region.getStart();

        for (int j = 0; j < list.size(); j++) {
            BasicDBObject chunk = (BasicDBObject) list.get(j);
            String type = chunk.getString("type");
            List<Float> valuesList;
            if (!typeMap.containsKey(type)) {
                valuesList = new ArrayList<>(region.getEnd() - region.getStart() + 1);
                for (int val = 0; val < region.getEnd() - region.getStart() + 1; val++) {
                    valuesList.add(null);
                }
                typeMap.put(type, valuesList);
            } else {
                valuesList = typeMap.get(type);
            }

            BasicDBList valuesChunk = (BasicDBList) chunk.get("values");

            int pos = 0;
            if (region.getStart() > chunk.getInt("start")) {
                pos = region.getStart() - chunk.getInt("start");
            }

            for (; pos < valuesChunk.size() && (pos + chunk.getInt("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.getInt("start") - region.getStart(),
                        new Float((Double) valuesChunk.get(pos)));
            }
        }
        //
        BasicDBList resultList = new BasicDBList();
        ConservedRegionFeature conservedRegionChunk;
        for (Map.Entry<String, List<Float>> elem : typeMap.entrySet()) {
            conservedRegionChunk = new ConservedRegionFeature(region.getChromosome(), region.getStart(),
                    region.getEnd(), elem.getKey(), elem.getValue());
            resultList.add(conservedRegionChunk);
        }
        queryResult.setResult(resultList);
    }

    return queryResults;
}

From source file:org.opencb.cellbase.mongodb.db.ConservationMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllScoresByRegionList(List<Region> regions, QueryOptions options) {
    //TODO not finished yet
    List<DBObject> 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);//  w  w  w  .j a va2 s  .  c  o m
        }
        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.getChromosome()).and("chunkId").in(hunkIds);
            //                builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("chunkId").in(integerChunkIds);
            builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end")
                    .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd());
        }
        /****/

        queries.add(builder.get());
        ids.add(region.toString());

        logger.info(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<BasicDBObject> list = (List<BasicDBObject>) queryResult.getResult();

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

        //            int start = region.getStart();

        for (int j = 0; j < list.size(); j++) {
            BasicDBObject chunk = (BasicDBObject) list.get(j);
            String type = chunk.getString("type");
            List<Float> valuesList;
            if (!typeMap.containsKey(type)) {
                valuesList = new ArrayList<>(region.getEnd() - region.getStart() + 1);
                for (int val = 0; val < region.getEnd() - region.getStart() + 1; val++) {
                    valuesList.add(null);
                }
                typeMap.put(type, valuesList);
            } else {
                valuesList = typeMap.get(type);
            }

            BasicDBList valuesChunk = (BasicDBList) chunk.get("values");

            int pos = 0;
            if (region.getStart() > chunk.getInt("start")) {
                pos = region.getStart() - chunk.getInt("start");
            }

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

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

    return queryResults;
}

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

License:Apache License

@Deprecated
@Override//  w w w  . j a  v  a 2  s  . co  m
public List<QueryResult> getAllByRegionList(List<Region> regions, QueryOptions options) {
    //TODO not finished yet
    List<DBObject> queries = new ArrayList<>();
    List<String> ids = new ArrayList<>(regions.size());
    List<String> integerChunkIds;
    for (Region region : regions) {
        integerChunkIds = new ArrayList<>();
        // positions below 1 are not allowed
        if (region.getStart() < 1) {
            region.setStart(1);
        }
        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(), this.chunkSize);
        int regionChunkEnd = getChunkId(region.getEnd(), this.chunkSize);
        if (regionChunkStart == regionChunkEnd) {
            builder = QueryBuilder.start("_chunkIds")
                    .is(getChunkIdPrefix(region.getChromosome(), region.getStart(), this.chunkSize));
        } else {
            //                for (int chunkId = regionChunkStart; chunkId <= regionChunkEnd; chunkId++) {
            ////                    integerChunkIds.add(chunkId);
            //                    integerChunkIds.add(region.getChromosome() + "_" + chunkId + "_" + this.chunkSize/1000 + "k");
            //                }
            //                builder = QueryBuilder.start("chromosome").is(region.getChromosome()).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.getChromosome()).and("chunkId").in(hunkIds);
        /****/

        queries.add(builder.get());
        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++) {
            BasicDBObject chunk = (BasicDBObject) list.get(j);
            String type = chunk.getString("type");
            List<Float> valuesList;
            if (!typeMap.containsKey(type)) {
                valuesList = new ArrayList<>(region.getEnd() - region.getStart() + 1);
                for (int val = 0; val < region.getEnd() - region.getStart() + 1; val++) {
                    valuesList.add(null);
                }
                typeMap.put(type, valuesList);
            } else {
                valuesList = typeMap.get(type);
            }

            BasicDBList valuesChunk = (BasicDBList) chunk.get("values");

            int pos = 0;
            if (region.getStart() > chunk.getInt("start")) {
                pos = region.getStart() - chunk.getInt("start");
            }

            for (; pos < valuesChunk.size() && (pos + chunk.getInt("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.getInt("start") - region.getStart(),
                        new Float((Double) valuesChunk.get(pos)));
            }
        }
        //
        BasicDBList resultList = new BasicDBList();
        ConservedRegionFeature conservedRegionChunk;
        for (Map.Entry<String, List<Float>> elem : typeMap.entrySet()) {
            conservedRegionChunk = new ConservedRegionFeature(region.getChromosome(), region.getStart(),
                    region.getEnd(), elem.getKey(), elem.getValue());
            resultList.add(conservedRegionChunk);
        }
        queryResult.setResult(resultList);
    }

    return queryResults;
}

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

License:Apache License

@Override
public List<QueryResult> getAllScoresByRegionList(List<Region> regions, QueryOptions options) {
    //TODO not finished yet
    List<DBObject> 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 ww  .  j a va2 s  .  c  o  m*/
        }
        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.getChromosome()).and("chunkId").in(hunkIds);
            //                builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("chunkId").in(integerChunkIds);
            builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("end")
                    .greaterThanEquals(region.getStart()).and("start").lessThanEquals(region.getEnd());
        }
        /****/

        queries.add(builder.get());
        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<BasicDBObject> list = (List<BasicDBObject>) queryResult.getResult();

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

        //            int start = region.getStart();

        for (int j = 0; j < list.size(); j++) {
            BasicDBObject chunk = (BasicDBObject) list.get(j);
            String type = chunk.getString("type");
            List<Float> valuesList;
            if (!typeMap.containsKey(type)) {
                valuesList = new ArrayList<>(region.getEnd() - region.getStart() + 1);
                for (int val = 0; val < region.getEnd() - region.getStart() + 1; val++) {
                    valuesList.add(null);
                }
                typeMap.put(type, valuesList);
            } else {
                valuesList = typeMap.get(type);
            }

            BasicDBList valuesChunk = (BasicDBList) chunk.get("values");

            int pos = 0;
            if (region.getStart() > chunk.getInt("start")) {
                pos = region.getStart() - chunk.getInt("start");
            }

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

        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.mongodb.db.core.GeneMongoDBAdaptor.java

License:Apache License

@Override
public List<QueryResult> getAllByIdList(List<String> idList, QueryOptions options) {
    //      QueryBuilder builder = QueryBuilder.start("transcripts.xrefs.id").in(idList);

    List<DBObject> queries = new ArrayList<>(idList.size());
    for (String id : idList) {
        QueryBuilder builder = QueryBuilder.start("transcripts.xrefs.id").is(id);
        queries.add(builder.get());//from www . j  ava  2  s. co  m
    }

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