Example usage for com.mongodb QueryBuilder get

List of usage examples for com.mongodb QueryBuilder get

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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.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   ww w.  j  av  a 2 s  .com
        queries.add(new Document(builder.get().toMap()));
        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.db.variation.ClinicalMongoDBAdaptor.java

License:Apache License

public QueryResult getListClinvarAccessions(QueryOptions queryOptions) {
    QueryBuilder builder = QueryBuilder.start("clinvarSet.referenceClinVarAssertion.clinVarAccession.acc")
            .exists(true);/*from  www . j a va 2  s. c om*/
    queryOptions.put("include", Arrays.asList("clinvarSet.referenceClinVarAssertion.clinVarAccession.acc"));
    QueryResult queryResult = executeQuery("", new Document(builder.get().toMap()), queryOptions);
    List accInfoList = (List) queryResult.getResult();
    List<String> accList = new ArrayList<>(accInfoList.size());
    Document accInfo;
    QueryResult listAccessionsToReturn = new QueryResult();

    for (Object accInfoObject : accInfoList) {
        accInfo = (Document) accInfoObject;
        accInfo = (Document) accInfo.get("clinvarSet");
        accList.add((String) ((Document) ((Document) ((Document) 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.lib.db.variation.ClinicalMongoDBAdaptor.java

License:Apache License

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

    /**//from w  w  w  .  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);
    jsonObjectMapper.configure(MapperFeature.REQUIRE_SETTERS_FOR_GETTERS, true);
    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.getReference()).and("alternate").is(variantAnnotation.getAlternate());
        Document update = null;
        try {
            update = new Document("$set",
                    new Document("annot", JSON.parse(writer.writeValueAsString(variantAnnotation))));
            update.put("$addToSet",
                    new Document("_geneIds", new Document("$each", getGeneIds(variantAnnotation))));
        } catch (JsonProcessingException e) {
            e.printStackTrace();
        }
        //            Document update = new Document("$set", new Document("annotation",
        //                    convertVariantAnnotation(variantAnnotation)));
        mongoDBCollection.update(new Document(builder.get().toMap()), update, queryOptions);
    }

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

From source file:org.opencb.cellbase.lib.db.variation.ClinVarMongoDBAdaptor.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("referenceClinVarAssertion.clinVarAccession.acc").is(id);
        queries.add(new Document(builder.get().toMap()));
    }//from  w w w  .j  ava2 s. c o m

    return executeQueryList2(idList, queries, options);
}

From source file:org.opencb.cellbase.lib.db.variation.ClinVarMongoDBAdaptor.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) {

        // 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(new Document(builder.get().toMap()).toString());
        queries.add(new Document(builder.get().toMap()));
        ids.add(region.toString());/*from   ww  w . j  av a2 s  .com*/
    }
    return executeQueryList2(ids, queries, options);
}

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

License:Apache License

public QueryResult getListAccessions(QueryOptions queryOptions) {
    QueryBuilder builder = QueryBuilder.start();
    queryOptions.put("include", Arrays.asList("referenceClinVarAssertion.clinVarAccession.acc"));
    QueryResult queryResult = executeQuery("", new Document(builder.get().toMap()), queryOptions);
    BasicDBList accInfoList = (BasicDBList) queryResult.getResult();
    List<String> accList = new ArrayList<>(accInfoList.size());
    Document accInfo;//from   ww w.  j a va  2  s . c o  m
    QueryResult listAccessionsToReturn = new QueryResult();

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

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

    return listAccessionsToReturn;
}

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

License:Apache License

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

    List<Object> biotypes = options.getList("disease", null);
    if (biotypes != null && biotypes.size() > 0) {
        BasicDBList biotypeIds = new BasicDBList();
        biotypeIds.addAll(biotypes);/*  www  . j  a  va2 s . c  o  m*/
        builder = builder.and("primaryHistology").in(biotypeIds);
    }

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

From source file:org.opencb.cellbase.lib.db.variation.MutationMongoDBAdaptor.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("id").is(id);
        queries.add(new Document(builder.get().toMap()));
    }/*from ww w .  j  a v  a2  s  .  co m*/

    return executeQueryList2(idList, queries, options);
}

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

License:Apache License

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

    return executeQueryList2(idList, queries, options);
}

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

License:Apache License

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

    return executeQueryList2(geneNameList, queries, options);
}