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.mongodb.db.regulatory.TfbsMongoDBAdaptor.java

License:Apache License

/**
 * PARTICULAR METHODS FOR TFBS CLASS/* w ww  .j  a  v a  2  s.c om*/
 */
@Override
public List<QueryResult> getAllByIdList(List<String> idList, QueryOptions options) {
    List<DBObject> queries = new ArrayList<>();
    for (String id : idList) {
        QueryBuilder builder = QueryBuilder.start("name").is(id).and("featureType").is("TF_binding_site_motif");
        //            System.out.println("Query: " + builder.get());
        queries.add(builder.get());
    }
    options = addExcludeReturnFields("chunkIds", options);
    return executeQueryList2(idList, queries, options);
}

From source file:org.opencb.cellbase.mongodb.db.systems.ProteinProteinInteractionMongoDBAdaptor.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("xrefs.id").is(id);
        queries.add(builder.get());
    }// w w  w. j  a v a  2s .c om
    //        options = addExcludeReturnFields("transcripts", options);
    return executeQueryList2(idList, queries, options);
}

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

License:Apache License

@Override
public List<QueryResult> getAllEffectsByVariantList(List<GenomicVariant> variants, QueryOptions options) {
    List<QueryResult> queryResults = new ArrayList<>(variants.size());
    List<DBObject> queries = new ArrayList<>(variants.size());
    for (GenomicVariant genomicVariant : variants) {
        QueryBuilder builder = QueryBuilder.start("chromosome").is(genomicVariant.getChromosome()).and("start")
                .lessThanEquals(genomicVariant.getPosition()).and("end")
                .greaterThanEquals(genomicVariant.getPosition());
        queries.add(builder.get());
    }//from w w  w.  j  ava2 s .  c o  m

    options = addExcludeReturnFields("transcripts.xrefs", options);

    BasicDBObject returnFields = getReturnFields(options);
    BasicDBList list = executeFind(queries.get(0), returnFields, options, db.getCollection("core"));
    long dbTimeStart, dbTimeEnd;

    GenomicVariantEffectPredictor genomicVariantEffectPredictor = new GenomicVariantEffectPredictor();
    //            List<Gene> genes = jsonObjectMapper.readValue(list.toString(), new TypeReference<List<Gene>>() { });
    List<Gene> genes = new ArrayList<>();
    dbTimeStart = System.currentTimeMillis();
    List<GenomicVariantEffect> a = genomicVariantEffectPredictor.getAllEffectsByVariant(variants.get(0), genes,
            null);
    dbTimeEnd = System.currentTimeMillis();

    QueryResult queryResult = new QueryResult();
    queryResult.setDbTime(Long.valueOf(dbTimeEnd - dbTimeStart).intValue());
    queryResult.setNumResults(list.size());
    queryResult.setResult(a);

    queryResults.add(queryResult);

    return queryResults;
}

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

License:Apache License

@Override
public QueryResult getAllClinvar(QueryOptions options) {
    //        options.addToListOption("include", "clinvarSet");
    //        options.addToListOption("include", "chromosome");
    //        options.addToListOption("include", "start");
    //        options.addToListOption("include", "end");
    //        options.addToListOption("include", "reference");
    //        options.addToListOption("include", "alternate");
    //        options.addToListOption("include", "annot");
    QueryBuilder builder = QueryBuilder.start();

    builder = addClinvarFilters(builder, options);

    //        List<DBObject> pipeline = new ArrayList<>();
    //        pipeline = addClinvarAggregationFilters(pipeline, options);
    //        DBObject fields = new BasicDBObject();
    //        fields.put("clinvarSet", 1);
    //        fields.put("chromosome", 1);
    //        fields.put("start", 1);
    //        fields.put("end", 1);
    //        fields.put("reference", 1);
    //        fields.put("alternate", 1);
    //        fields.put("annot", 1);
    //        pipeline.add(new BasicDBObject("$project", fields));

    //        return executeAggregation2("", pipeline, options);
    return executeQuery("result", builder.get(), options);
    //        return prepareClinvarQueryResultList(Collections.singletonList(executeQuery("result", builder.get(), options))).get(0);
}

From source file:org.opencb.cellbase.mongodb.db.variation.ClinicalMongoDBAdaptor.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) {

        QueryBuilder 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());//w ww  .j  a v a  2  s.c om
    }
    return executeQueryList2(ids, queries, options);
}

From source file:org.opencb.cellbase.mongodb.db.variation.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  ww  . j a  va2 s  .  co m*/
        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 = new ArrayList<>();
        List<Gwas> gwasList = new ArrayList<>();
        List<Clinvar> clinvarList = new ArrayList<>();

        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<>();
        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);
        }
        if (!clinicalData.isEmpty()) {
            // FIXME quick solution to compile
            //            queryResult.setResult(clinicalData);
            queryResult.setResult(Arrays.asList(clinicalData));
            queryResult.setNumResults(cosmicList.size() + clinvarList.size() + gwasList.size());
        } else {
            queryResult.setResult(null);
            queryResult.setNumResults(0);
        }
    }

    return queryResultList;
}

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

License:Apache License

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

    /**/* w ww  . j  av a 2 s .c  om*/
     * 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.getAlternateAllele());
        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)));
        mongoDBCollection.update(builder.get(), update, queryOptions);
    }

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

From source file:org.opencb.cellbase.mongodb.db.variation.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());
    }/* w w w  . ja  v  a2  s  . c  o m*/

    return executeQueryList2(idList, queries, options);
}

From source file:org.opencb.cellbase.mongodb.db.variation.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  ww  . j  a v  a  2 s .  c  o m
        ids.add(region.toString());
    }
    return executeQueryList2(ids, queries, options);
}

From source file:org.opencb.cellbase.mongodb.db.variation.MutationMongoDBAdaptor.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("id").is(id);
        queries.add(builder.get());
    }/*w w w  . j  a va2s.c o  m*/

    return executeQueryList2(idList, queries, options);
}