Example usage for com.mongodb QueryBuilder or

List of usage examples for com.mongodb QueryBuilder or

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Introduction

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

Prototype

@SuppressWarnings("unchecked")
public QueryBuilder or(final DBObject... ors)

Source Link

Document

Equivalent to an $or operand

Usage

From source file:org.opencb.opencga.storage.mongodb.variant.adaptors.VariantMongoDBAdaptor.java

License:Apache License

private <T> QueryBuilder addQueryFilter(String key, String value, final QueryBuilder builder, QueryOperation op,
        Function<String, T> map) {
    QueryOperation operation = checkOperator(value);
    QueryBuilder auxBuilder;/*ww  w . java2s . co m*/
    if (op == QueryOperation.OR) {
        auxBuilder = QueryBuilder.start();
    } else {
        auxBuilder = builder;
    }

    if (operation == null) {
        if (value.startsWith("!")) {
            T mapped = map.apply(value.substring(1));
            if (mapped instanceof Collection) {
                auxBuilder.and(key).notIn(mapped);
            } else {
                auxBuilder.and(key).notEquals(mapped);
            }
        } else {
            T mapped = map.apply(value);
            if (mapped instanceof Collection) {
                auxBuilder.and(key).in(mapped);
            } else {
                auxBuilder.and(key).is(mapped);
            }
        }
    } else if (operation == QueryOperation.OR) {
        String[] array = value.split(OR);
        List list = new ArrayList(array.length);
        for (String elem : array) {
            if (elem.startsWith("!")) {
                throw new VariantQueryException(
                        "Unable to use negate (!) operator in OR sequences (<it_1>(,<it_n>)*)");
            } else {
                T mapped = map.apply(elem);
                if (mapped instanceof Collection) {
                    list.addAll(((Collection) mapped));
                } else {
                    list.add(mapped);
                }
            }
        }
        auxBuilder.and(key).in(list);
    } else {
        //Split in two lists: positive and negative
        String[] array = value.split(AND);
        List listIs = new ArrayList(array.length);
        List listNotIs = new ArrayList(array.length);

        for (String elem : array) {
            if (elem.startsWith("!")) {
                T mapped = map.apply(elem.substring(1));
                if (mapped instanceof Collection) {
                    listNotIs.addAll(((Collection) mapped));
                } else {
                    listNotIs.add(mapped);
                }
            } else {
                T mapped = map.apply(elem);
                if (mapped instanceof Collection) {
                    listIs.addAll(((Collection) mapped));
                } else {
                    listIs.add(mapped);
                }
            }
        }

        if (!listIs.isEmpty()) { //Can not use method "is" because it will be overwritten with the "notEquals" or "notIn" method
            auxBuilder.and(key).all(listIs);
        }
        if (listNotIs.size() == 1) {
            auxBuilder.and(key).notEquals(listNotIs.get(0));
        } else if (listNotIs.size() > 1) {
            auxBuilder.and(key).notIn(listNotIs);
        }

    }

    if (op == QueryOperation.OR) {
        builder.or(auxBuilder.get());
    }
    return builder;
}

From source file:org.opencb.opencga.storage.mongodb.variant.adaptors.VariantMongoDBAdaptor.java

License:Apache License

/**
 * Accept a list of comparative filters separated with "," or ";" with the expression:
 * {OPERATION}{VALUE}, where the accepted operations are: <, <=, >, >=, =, ==, !=, ~=.
 *
 * @param key/*from   w w w  .  j a  v  a  2  s  .  c  o  m*/
 * @param value
 * @param builder
 * @param extendKey
 * @return
 */
private QueryBuilder addCompListQueryFilter(String key, String value, QueryBuilder builder, boolean extendKey) {
    QueryOperation op = checkOperator(value);
    List<String> values = splitValue(value, op);

    QueryBuilder compBuilder;
    if (op == QueryOperation.OR) {
        compBuilder = QueryBuilder.start();
    } else {
        compBuilder = builder;
    }

    for (String elem : values) {
        addCompQueryFilter(key, elem, compBuilder, extendKey);
    }

    if (op == QueryOperation.OR) {
        builder.or(compBuilder.get());
    }
    return builder;
}

From source file:org.opencb.opencga.storage.mongodb.variant.adaptors.VariantMongoDBAdaptor.java

License:Apache License

/**
 * Accept filters separated with "," or ";" with the expression:
 * [{STUDY}:]{COHORT}{OPERATION}{VALUE}.
 * Where STUDY is optional if defaultStudyConfiguration is provided
 *
 * @param key                       Stats field to filter
 * @param values                    Values to parse
 * @param builder                   QueryBuilder
 * @param defaultStudyConfiguration/*  www. j  ava 2s .  c  o m*/
 */
private void addStatsFilterList(String key, String values, QueryBuilder builder,
        StudyConfiguration defaultStudyConfiguration) {
    QueryOperation op = checkOperator(values);
    List<String> valuesList = splitValue(values, op);
    List<DBObject> statsQueries = new LinkedList<>();
    for (String value : valuesList) {
        statsQueries.add(addStatsFilter(key, value, new QueryBuilder(), defaultStudyConfiguration).get());
    }

    if (!statsQueries.isEmpty()) {
        if (op == QueryOperation.OR) {
            builder.or(statsQueries.toArray(new DBObject[statsQueries.size()]));
        } else {
            builder.and(statsQueries.toArray(new DBObject[statsQueries.size()]));
        }
    }
}

From source file:org.opencb.opencga.storage.mongodb.variant.adaptors.VariantMongoDBAdaptor.java

License:Apache License

private QueryBuilder getRegionFilter(List<Region> regions, QueryBuilder builder) {
    if (regions != null && !regions.isEmpty()) {
        DBObject[] objects = new DBObject[regions.size()];
        int i = 0;
        for (Region region : regions) {
            DBObject regionObject = new BasicDBObject();
            //                if (region.getEnd() - region.getStart() < 1000000) {
            //                    List<String> chunkIds = getChunkIds(region);
            //                    regionObject.put(DocumentToVariantConverter.AT_FIELD + '.' + DocumentToVariantConverter
            //                            .CHUNK_IDS_FIELD,
            //                            new Document("$in", chunkIds));
            //                } else {
            //                    regionObject.put(DocumentToVariantConverter.CHROMOSOME_FIELD, region.getChromosome());
            //                }

            int end = region.getEnd();
            if (end < Integer.MAX_VALUE) { // Avoid overflow
                end++;/*from w  ww .ja v a 2s  .c  o m*/
            }
            regionObject
                    .put("_id",
                            new Document()
                                    .append("$gte",
                                            VariantStringIdConverter.buildId(region.getChromosome(),
                                                    region.getStart()))
                                    .append("$lt",
                                            VariantStringIdConverter.buildId(region.getChromosome(), end)));

            objects[i] = regionObject;
            i++;
        }
        builder.or(objects);
    }
    return builder;
}

From source file:org.opencb.opencga.storage.mongodb.variant.VariantMongoDBAdaptor.java

License:Apache License

private QueryBuilder parseQuery(Query query, QueryBuilder builder) {
    if (query != null) {

        /** VARIANT PARAMS **/

        if (query.containsKey(VariantQueryParams.REGION.key())
                && !query.getString(VariantQueryParams.REGION.key()).isEmpty()) {
            List<String> stringList = query.getAsStringList(VariantQueryParams.REGION.key());
            List<Region> regions = new ArrayList<>(stringList.size());
            for (String reg : stringList) {
                Region region = Region.parseRegion(reg);
                regions.add(region);/*  www.j a v a 2 s.co m*/
            }
            getRegionFilter(regions, builder);
        }

        if (query.getString(VariantQueryParams.ID.key()) != null
                && !query.getString(VariantQueryParams.ID.key()).isEmpty()) {
            List<String> ids = query.getAsStringList(VariantQueryParams.ID.key());
            addQueryListFilter(
                    DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.XREFS_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.XREF_ID_FIELD,
                    ids, builder, QueryOperation.OR);
            addQueryListFilter(DBObjectToVariantConverter.IDS_FIELD, ids, builder, QueryOperation.OR);
        }

        if (query.containsKey(VariantQueryParams.GENE.key())) {
            List<String> xrefs = query.getAsStringList(VariantQueryParams.GENE.key());
            addQueryListFilter(
                    DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.XREFS_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.XREF_ID_FIELD,
                    xrefs, builder, QueryOperation.OR);
        }

        if (query.containsKey(VariantQueryParams.REFERENCE.key())
                && query.getString(VariantQueryParams.REFERENCE.key()) != null) {
            addQueryStringFilter(DBObjectToVariantConverter.REFERENCE_FIELD,
                    query.getString(VariantQueryParams.REFERENCE.key()), builder);
        }

        if (query.containsKey(VariantQueryParams.ALTERNATE.key())
                && query.getString(VariantQueryParams.ALTERNATE.key()) != null) {
            addQueryStringFilter(DBObjectToVariantConverter.ALTERNATE_FIELD,
                    query.getString(VariantQueryParams.ALTERNATE.key()), builder);
        }

        if (query.containsKey(VariantQueryParams.TYPE.key())
                && !query.getString(VariantQueryParams.TYPE.key()).isEmpty()) {
            addQueryStringFilter(DBObjectToVariantConverter.TYPE_FIELD,
                    query.getString(VariantQueryParams.TYPE.key()), builder);
        }

        /** ANNOTATION PARAMS **/

        if (query.containsKey(VariantQueryParams.ANNOTATION_EXISTS.key())) {
            builder.and(DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                    + DBObjectToVariantAnnotationConverter.ANNOT_ID_FIELD);
            builder.exists(query.getBoolean(VariantQueryParams.ANNOTATION_EXISTS.key()));
        }

        if (query.containsKey(VariantQueryParams.ANNOT_XREF.key())) {
            List<String> xrefs = query.getAsStringList(VariantQueryParams.ANNOT_XREF.key());
            addQueryListFilter(
                    DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.XREFS_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.XREF_ID_FIELD,
                    xrefs, builder, QueryOperation.AND);
        }

        if (query.containsKey(VariantQueryParams.ANNOT_CONSEQUENCE_TYPE.key())) {
            List<String> cts = new ArrayList<>(
                    query.getAsStringList(VariantQueryParams.ANNOT_CONSEQUENCE_TYPE.key()));
            List<Integer> ctsInteger = new ArrayList<>(cts.size());
            for (Iterator<String> iterator = cts.iterator(); iterator.hasNext();) {
                String ct = iterator.next();
                if (ct.startsWith("SO:")) {
                    ct = ct.substring(3);
                }
                try {
                    ctsInteger.add(Integer.parseInt(ct));
                } catch (NumberFormatException e) {
                    logger.error("Error parsing integer ", e);
                    iterator.remove(); //Remove the malformed query params.
                }
            }
            query.put(VariantQueryParams.ANNOT_CONSEQUENCE_TYPE.key(), cts);
            addQueryListFilter(
                    DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.CONSEQUENCE_TYPE_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.SO_ACCESSION_FIELD,
                    ctsInteger, builder, QueryOperation.AND);
        }

        if (query.containsKey(VariantQueryParams.ANNOT_BIOTYPE.key())) {
            List<String> biotypes = query.getAsStringList(VariantQueryParams.ANNOT_BIOTYPE.key());
            addQueryListFilter(
                    DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.CONSEQUENCE_TYPE_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.BIOTYPE_FIELD,
                    biotypes, builder, QueryOperation.AND);
        }

        if (query.containsKey(VariantQueryParams.POLYPHEN.key())) {
            addCompQueryFilter(
                    DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.CONSEQUENCE_TYPE_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.POLYPHEN_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.SCORE_SCORE_FIELD,
                    query.getString(VariantQueryParams.POLYPHEN.key()), builder);
        }

        if (query.containsKey(VariantQueryParams.SIFT.key())) {
            System.out.println(query.getString(VariantQueryParams.SIFT.key()));
            addCompQueryFilter(
                    DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.CONSEQUENCE_TYPE_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.SIFT_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.SCORE_SCORE_FIELD,
                    query.getString(VariantQueryParams.SIFT.key()), builder);
        }

        if (query.containsKey(VariantQueryParams.PROTEIN_SUBSTITUTION.key())) {
            List<String> list = new ArrayList<>(
                    query.getAsStringList(VariantQueryParams.PROTEIN_SUBSTITUTION.key()));
            addScoreFilter(
                    DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.CONSEQUENCE_TYPE_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.PROTEIN_SUBSTITUTION_SCORE_FIELD,
                    list, builder);
            query.put(VariantQueryParams.PROTEIN_SUBSTITUTION.key(), list); //Replace the QueryOption without the malformed query params
        }

        if (query.containsKey(VariantQueryParams.CONSERVATION.key())) {
            List<String> list = new ArrayList<>(query.getAsStringList(VariantQueryParams.CONSERVATION.key()));
            addScoreFilter(DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                    + DBObjectToVariantAnnotationConverter.CONSERVED_REGION_SCORE_FIELD, list, builder);
            query.put(VariantQueryParams.CONSERVATION.key(), list);
        }

        if (query.containsKey(VariantQueryParams.ALTERNATE_FREQUENCY.key())) {
            List<String> list = new ArrayList<>(
                    query.getAsStringList(VariantQueryParams.ALTERNATE_FREQUENCY.key()));
            addFrequencyFilter(
                    DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.POPULATION_FREQUENCIES_FIELD,
                    DBObjectToVariantAnnotationConverter.POPULATION_FREQUENCY_ALTERNATE_FREQUENCY_FIELD, list,
                    builder); // Same method addFrequencyFilter is used for reference and allele frequencies. Need to provide the field (reference/alternate) where to check the frequency
        }

        if (query.containsKey(VariantQueryParams.REFERENCE_FREQUENCY.key())) {
            List<String> list = new ArrayList<>(
                    query.getAsStringList(VariantQueryParams.REFERENCE_FREQUENCY.key()));
            addFrequencyFilter(
                    DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.POPULATION_FREQUENCIES_FIELD,
                    DBObjectToVariantAnnotationConverter.POPULATION_FREQUENCY_REFERENCE_FREQUENCY_FIELD, list,
                    builder); // Same method addFrequencyFilter is used for reference and allele frequencies. Need to provide the field (reference/alternate) where to check the frequency
        }

        /** STATS PARAMS **/

        if (query.get(VariantQueryParams.STATS_MAF.key()) != null
                && !query.getString(VariantQueryParams.STATS_MAF.key()).isEmpty()) {
            addCompQueryFilter(
                    DBObjectToVariantConverter.STATS_FIELD + "." + DBObjectToVariantStatsConverter.MAF_FIELD,
                    query.getString(VariantQueryParams.STATS_MAF.key()), builder);
        }

        if (query.get(VariantQueryParams.STATS_MGF.key()) != null
                && !query.getString(VariantQueryParams.STATS_MGF.key()).isEmpty()) {
            addCompQueryFilter(
                    DBObjectToVariantConverter.STATS_FIELD + "." + DBObjectToVariantStatsConverter.MGF_FIELD,
                    query.getString(VariantQueryParams.STATS_MGF.key()), builder);
        }

        if (query.get(VariantQueryParams.MISSING_ALLELES.key()) != null
                && !query.getString(VariantQueryParams.MISSING_ALLELES.key()).isEmpty()) {
            addCompQueryFilter(
                    DBObjectToVariantConverter.STATS_FIELD + "."
                            + DBObjectToVariantStatsConverter.MISSALLELE_FIELD,
                    query.getString(VariantQueryParams.MISSING_ALLELES.key()), builder);
        }

        if (query.get(VariantQueryParams.MISSING_GENOTYPES.key()) != null
                && !query.getString(VariantQueryParams.MISSING_GENOTYPES.key()).isEmpty()) {
            addCompQueryFilter(
                    DBObjectToVariantConverter.STATS_FIELD + "."
                            + DBObjectToVariantStatsConverter.MISSGENOTYPE_FIELD,
                    query.getString(VariantQueryParams.MISSING_GENOTYPES.key()), builder);
        }

        if (query.get("numgt") != null && !query.getString("numgt").isEmpty()) {
            for (String numgt : query.getAsStringList("numgt")) {
                String[] split = numgt.split(":");
                addCompQueryFilter(
                        DBObjectToVariantConverter.STATS_FIELD + "."
                                + DBObjectToVariantStatsConverter.NUMGT_FIELD + "." + split[0],
                        split[1], builder);
            }
        }

        /** STUDIES **/
        QueryBuilder studyBuilder = QueryBuilder.start();

        if (query.containsKey(VariantQueryParams.STUDIES.key())) { // && !options.getList("studies").isEmpty() && !options.getListAs("studies", String.class).get(0).isEmpty()) {
            List<Integer> studyIds = getStudyIds(query.getAsList(VariantQueryParams.STUDIES.key()), null);
            addQueryListFilter(DBObjectToVariantSourceEntryConverter.STUDYID_FIELD, studyIds, studyBuilder,
                    QueryOperation.AND);
        }

        if (query.containsKey(VariantQueryParams.FILES.key())) { // && !options.getList("files").isEmpty() && !options.getListAs("files", String.class).get(0).isEmpty()) {
            addQueryListFilter(
                    DBObjectToVariantSourceEntryConverter.FILES_FIELD + "."
                            + DBObjectToVariantSourceEntryConverter.FILEID_FIELD,
                    query.getAsIntegerList(VariantQueryParams.FILES.key()), studyBuilder, QueryOperation.AND);
        }

        if (query.containsKey(VariantQueryParams.GENOTYPE.key())) {
            String sampleGenotypesCSV = query.getString(VariantQueryParams.GENOTYPE.key());

            //                String AND = ",";
            //                String OR = ";";
            //                String IS = ":";

            //                String AND = "AND";
            //                String OR = "OR";
            //                String IS = ":";

            String AND = ";";
            String OR = ",";
            String IS = ":";

            // we may need to know the study type
            //                studyConfigurationManager.getStudyConfiguration(1, null).getResult().get(0).

            String[] sampleGenotypesArray = sampleGenotypesCSV.split(AND);
            System.out.println("sampleGenotypesArray = " + Arrays.toString(sampleGenotypesArray));

            for (String sampleGenotypes : sampleGenotypesArray) {
                String[] sampleGenotype = sampleGenotypes.split(IS);
                if (sampleGenotype.length != 2) {
                    continue;
                }
                int sample = Integer.parseInt(sampleGenotype[0]);
                String[] genotypes = sampleGenotype[1].split(OR);
                QueryBuilder genotypesBuilder = QueryBuilder.start();
                for (String genotype : genotypes) {
                    if ("0/0".equals(genotype) || "0|0".equals(genotype)) {
                        QueryBuilder andBuilder = QueryBuilder.start();
                        List<String> otherGenotypes = Arrays.asList("0/1", "1/0", "1/1", "-1/-1", "0|1", "1|0",
                                "1|1", "-1|-1", "0|2", "2|0", "2|1", "1|2", "2|2", "0/2", "2/0", "2/1", "1/2",
                                "2/2", DBObjectToSamplesConverter.UNKNOWN_GENOTYPE);
                        for (String otherGenotype : otherGenotypes) {
                            andBuilder.and(new BasicDBObject(
                                    DBObjectToVariantSourceEntryConverter.GENOTYPES_FIELD + "." + otherGenotype,
                                    new BasicDBObject("$not", new BasicDBObject("$elemMatch",
                                            new BasicDBObject("$eq", sample)))));
                        }
                        genotypesBuilder.or(andBuilder.get());
                    } else {
                        String s = DBObjectToVariantSourceEntryConverter.GENOTYPES_FIELD + "."
                                + DBObjectToSamplesConverter.genotypeToStorageType(genotype);
                        //or [ {"samp.0|0" : { $elemMatch : { $eq : <sampleId> } } } ]
                        genotypesBuilder.or(new BasicDBObject(s,
                                new BasicDBObject("$elemMatch", new BasicDBObject("$eq", sample))));
                    }
                }
                studyBuilder.and(genotypesBuilder.get());
            }
        }

        // If Study Query is used then we add a elemMatch query
        DBObject studyQuery = studyBuilder.get();
        if (studyQuery.keySet().size() != 0) {
            builder.and(DBObjectToVariantConverter.STUDIES_FIELD).elemMatch(studyQuery);
        }
    }

    logger.debug("Find = " + builder.get());
    return builder;
}

From source file:org.opencb.opencga.storage.mongodb.variant.VariantMongoDBAdaptor.java

License:Apache License

private QueryBuilder addQueryListFilter(String key, List<?> values, QueryBuilder builder, QueryOperation op) {
    if (values != null)
        if (values.size() == 1) {
            if (op == QueryOperation.AND) {
                builder.and(key).is(values.get(0));
            } else {
                builder.or(QueryBuilder.start(key).is(values.get(0)).get());
            }/*from   w  ww. j  av a  2  s .  c  o m*/
        } else if (!values.isEmpty()) {
            if (op == QueryOperation.AND) {
                builder.and(key).in(values);
            } else {
                builder.or(QueryBuilder.start(key).in(values).get());
            }
        }
    return builder;
}

From source file:org.opencb.opencga.storage.mongodb.variant.VariantMongoDBAdaptor.java

License:Apache License

private QueryBuilder getRegionFilter(List<Region> regions, QueryBuilder builder) {
    if (regions != null && !regions.isEmpty()) {
        DBObject[] objects = new DBObject[regions.size()];
        int i = 0;
        for (Region region : regions) {
            if (region.getEnd() - region.getStart() < 1000000) {
                List<String> chunkIds = getChunkIds(region);
                DBObject regionObject = new BasicDBObject("_at.chunkIds", new BasicDBObject("$in", chunkIds))
                        .append(DBObjectToVariantConverter.START_FIELD,
                                new BasicDBObject("$lte", region.getEnd()))
                        .append(DBObjectToVariantConverter.END_FIELD,
                                new BasicDBObject("$gte", region.getStart()));
                objects[i] = regionObject;
            } else {
                DBObject regionObject = new BasicDBObject(DBObjectToVariantConverter.CHROMOSOME_FIELD,
                        region.getChromosome())
                                .append(DBObjectToVariantConverter.START_FIELD,
                                        new BasicDBObject("$lte", region.getEnd()))
                                .append(DBObjectToVariantConverter.END_FIELD,
                                        new BasicDBObject("$gte", region.getStart()));
                objects[i] = regionObject;
            }//from   w  ww.j  av  a  2 s  .c o m
            i++;
        }
        builder.or(objects);
    }
    return builder;
}

From source file:org.opencb.opencga.storage.mongodb.variant.VariantMongoDBAdaptor.java

License:Apache License

@Deprecated
private QueryBuilder parseQueryOptions(QueryOptions options, QueryBuilder builder) {
    if (options != null) {

        if (options.containsKey("sort")) {
            if (options.getBoolean("sort")) {
                options.put("sort", new BasicDBObject(DBObjectToVariantConverter.CHROMOSOME_FIELD, 1)
                        .append(DBObjectToVariantConverter.START_FIELD, 1));
            } else {
                options.remove("sort");
            }//from w  w w  .ja v  a  2 s.co  m
        }

        /** GENOMIC REGION **/

        if (options.containsKey(VariantQueryParams.REGION.key())
                && !options.getString(VariantQueryParams.REGION.key()).isEmpty()) {
            List<String> stringList = options.getAsStringList(VariantQueryParams.REGION.key());
            List<Region> regions = new ArrayList<>(stringList.size());
            for (String reg : stringList) {
                Region region = Region.parseRegion(reg);
                regions.add(region);
            }
            getRegionFilter(regions, builder);
        }

        //            if (options.containsKey(VariantQueryParams.CHROMOSOME.key())) {
        //                List<String> chromosome = options.getAsStringList(VariantQueryParams.CHROMOSOME.key());
        //                addQueryListFilter(DBObjectToVariantConverter.CHROMOSOME_FIELD, chromosome, builder, QueryOperation.OR);
        //            }

        if (options.containsKey(VariantQueryParams.GENE.key())) {
            List<String> xrefs = options.getAsStringList(VariantQueryParams.GENE.key());
            addQueryListFilter(
                    DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.XREFS_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.XREF_ID_FIELD,
                    xrefs, builder, QueryOperation.OR);
        }

        if (options.getString(VariantQueryParams.ID.key()) != null
                && !options.getString(VariantQueryParams.ID.key()).isEmpty()) { //) && !options.getString("id").isEmpty()) {
            List<String> ids = options.getAsStringList(VariantQueryParams.ID.key());
            addQueryListFilter(
                    DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.XREFS_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.XREF_ID_FIELD,
                    ids, builder, QueryOperation.OR);
            addQueryListFilter(DBObjectToVariantConverter.IDS_FIELD, ids, builder, QueryOperation.OR);
        }

        /** VARIANT **/

        if (options.containsKey(VariantQueryParams.TYPE.key())) { // && !options.getString("type").isEmpty()) {
            addQueryStringFilter(DBObjectToVariantConverter.TYPE_FIELD,
                    options.getString(VariantQueryParams.TYPE.key()), builder);
        }

        if (options.containsKey(VariantQueryParams.REFERENCE.key())
                && options.getString(VariantQueryParams.REFERENCE.key()) != null) {
            addQueryStringFilter(DBObjectToVariantConverter.REFERENCE_FIELD,
                    options.getString(VariantQueryParams.REFERENCE.key()), builder);
        }

        if (options.containsKey(VariantQueryParams.ALTERNATE.key())
                && options.getString(VariantQueryParams.ALTERNATE.key()) != null) {
            addQueryStringFilter(DBObjectToVariantConverter.ALTERNATE_FIELD,
                    options.getString(VariantQueryParams.ALTERNATE.key()), builder);
        }

        /** ANNOTATION **/

        if (options.containsKey(VariantQueryParams.ANNOTATION_EXISTS.key())) {
            builder.and(DBObjectToVariantConverter.ANNOTATION_FIELD)
                    .exists(options.getBoolean(VariantQueryParams.ANNOTATION_EXISTS.key()));
        }

        if (options.containsKey(VariantQueryParams.ANNOT_XREF.key())) {
            List<String> xrefs = options.getAsStringList(VariantQueryParams.ANNOT_XREF.key());
            addQueryListFilter(
                    DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.XREFS_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.XREF_ID_FIELD,
                    xrefs, builder, QueryOperation.AND);
        }

        if (options.containsKey(VariantQueryParams.ANNOT_CONSEQUENCE_TYPE.key())) {
            List<String> cts = new ArrayList<>(
                    options.getAsStringList(VariantQueryParams.ANNOT_CONSEQUENCE_TYPE.key()));
            List<Integer> ctsInteger = new ArrayList<>(cts.size());
            for (Iterator<String> iterator = cts.iterator(); iterator.hasNext();) {
                String ct = iterator.next();
                if (ct.startsWith("SO:")) {
                    ct = ct.substring(3);
                }
                try {
                    ctsInteger.add(Integer.parseInt(ct));
                } catch (NumberFormatException e) {
                    logger.error("Error parsing integer ", e);
                    iterator.remove(); //Remove the malformed query params.
                }
            }
            options.put(VariantQueryParams.ANNOT_CONSEQUENCE_TYPE.key(), cts); //Replace the QueryOption without the malformed query params
            addQueryListFilter(
                    DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.CONSEQUENCE_TYPE_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.SO_ACCESSION_FIELD,
                    ctsInteger, builder, QueryOperation.AND);
        }

        if (options.containsKey(VariantQueryParams.ANNOT_BIOTYPE.key())) {
            List<String> biotypes = options.getAsStringList(VariantQueryParams.ANNOT_BIOTYPE.key());
            addQueryListFilter(
                    DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.CONSEQUENCE_TYPE_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.BIOTYPE_FIELD,
                    biotypes, builder, QueryOperation.AND);
        }

        if (options.containsKey(VariantQueryParams.POLYPHEN.key())) {
            addCompQueryFilter(
                    DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.CONSEQUENCE_TYPE_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.POLYPHEN_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.SCORE_SCORE_FIELD,
                    options.getString(VariantQueryParams.POLYPHEN.key()), builder);
        }

        if (options.containsKey(VariantQueryParams.SIFT.key())) {
            addCompQueryFilter(
                    DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.CONSEQUENCE_TYPE_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.SIFT_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.SCORE_SCORE_FIELD,
                    options.getString(VariantQueryParams.SIFT.key()), builder);
        }

        if (options.containsKey(VariantQueryParams.PROTEIN_SUBSTITUTION.key())) {
            List<String> list = new ArrayList<>(
                    options.getAsStringList(VariantQueryParams.PROTEIN_SUBSTITUTION.key()));
            addScoreFilter(
                    DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.CONSEQUENCE_TYPE_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.PROTEIN_SUBSTITUTION_SCORE_FIELD,
                    list, builder);
            options.put(VariantQueryParams.PROTEIN_SUBSTITUTION.key(), list); //Replace the QueryOption without the malformed query params
        }

        if (options.containsKey(VariantQueryParams.CONSERVATION.key())) {
            List<String> list = new ArrayList<>(options.getAsStringList(VariantQueryParams.CONSERVATION.key()));
            addScoreFilter(DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                    + DBObjectToVariantAnnotationConverter.CONSERVED_REGION_SCORE_FIELD, list, builder);
            options.put(VariantQueryParams.CONSERVATION.key(), list); //Replace the QueryOption without the malformed query params
        }

        if (options.containsKey(VariantQueryParams.ALTERNATE_FREQUENCY.key())) {
            List<String> list = new ArrayList<>(
                    options.getAsStringList(VariantQueryParams.ALTERNATE_FREQUENCY.key()));
            addFrequencyFilter(
                    DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.POPULATION_FREQUENCIES_FIELD,
                    DBObjectToVariantAnnotationConverter.POPULATION_FREQUENCY_ALTERNATE_FREQUENCY_FIELD, list,
                    builder); // Same method addFrequencyFilter is used for reference and allele frequencies. Need to provide the field (reference/alternate) where to check the frequency
        }

        if (options.containsKey(VariantQueryParams.REFERENCE_FREQUENCY.key())) {
            List<String> list = new ArrayList<>(
                    options.getAsStringList(VariantQueryParams.REFERENCE_FREQUENCY.key()));
            addFrequencyFilter(
                    DBObjectToVariantConverter.ANNOTATION_FIELD + "."
                            + DBObjectToVariantAnnotationConverter.POPULATION_FREQUENCIES_FIELD,
                    DBObjectToVariantAnnotationConverter.POPULATION_FREQUENCY_REFERENCE_FREQUENCY_FIELD, list,
                    builder); // Same method addFrequencyFilter is used for reference and allele frequencies. Need to provide the field (reference/alternate) where to check the frequency
        }

        /** STATS **/

        if (options.get(VariantQueryParams.STATS_MAF.key()) != null
                && !options.getString(VariantQueryParams.STATS_MAF.key()).isEmpty()) {
            addCompQueryFilter(
                    DBObjectToVariantConverter.STATS_FIELD + "." + DBObjectToVariantStatsConverter.MAF_FIELD,
                    options.getString(VariantQueryParams.STATS_MAF.key()), builder);
        }

        if (options.get(VariantQueryParams.STATS_MGF.key()) != null
                && !options.getString(VariantQueryParams.STATS_MGF.key()).isEmpty()) {
            addCompQueryFilter(
                    DBObjectToVariantConverter.STATS_FIELD + "." + DBObjectToVariantStatsConverter.MGF_FIELD,
                    options.getString(VariantQueryParams.STATS_MGF.key()), builder);
        }

        if (options.get(VariantQueryParams.MISSING_ALLELES.key()) != null
                && !options.getString(VariantQueryParams.MISSING_ALLELES.key()).isEmpty()) {
            addCompQueryFilter(
                    DBObjectToVariantConverter.STATS_FIELD + "."
                            + DBObjectToVariantStatsConverter.MISSALLELE_FIELD,
                    options.getString(VariantQueryParams.MISSING_ALLELES.key()), builder);
        }

        if (options.get(VariantQueryParams.MISSING_GENOTYPES.key()) != null
                && !options.getString(VariantQueryParams.MISSING_GENOTYPES.key()).isEmpty()) {
            addCompQueryFilter(
                    DBObjectToVariantConverter.STATS_FIELD + "."
                            + DBObjectToVariantStatsConverter.MISSGENOTYPE_FIELD,
                    options.getString(VariantQueryParams.MISSING_GENOTYPES.key()), builder);
        }

        if (options.get("numgt") != null && !options.getString("numgt").isEmpty()) {
            for (String numgt : options.getAsStringList("numgt")) {
                String[] split = numgt.split(":");
                addCompQueryFilter(
                        DBObjectToVariantConverter.STATS_FIELD + "."
                                + DBObjectToVariantStatsConverter.NUMGT_FIELD + "." + split[0],
                        split[1], builder);
            }
        }

        //            if (options.get("freqgt") != null && !options.getString("freqgt").isEmpty()) {
        //                for (String freqgt : getStringList(options.get("freqgt"))) {
        //                    String[] split = freqgt.split(":");
        //                    addCompQueryFilter(
        //                            DBObjectToVariantSourceEntryConverter.STATS_FIELD + "." + DBObjectToVariantStatsConverter.FREQGT_FIELD + "." + split[0],
        //                            split[1], builder);
        //                }
        //            }

        /** FILES **/
        QueryBuilder fileBuilder = QueryBuilder.start();

        if (options.containsKey(VariantQueryParams.STUDIES.key())) { // && !options.getList("studies").isEmpty() && !options.getListAs("studies", String.class).get(0).isEmpty()) {
            addQueryListFilter(DBObjectToVariantSourceEntryConverter.STUDYID_FIELD,
                    options.getAsIntegerList(VariantQueryParams.STUDIES.key()), fileBuilder,
                    QueryOperation.AND);
        }

        if (options.containsKey(VariantQueryParams.FILES.key())) { // && !options.getList("files").isEmpty() && !options.getListAs("files", String.class).get(0).isEmpty()) {
            addQueryListFilter(
                    DBObjectToVariantSourceEntryConverter.FILES_FIELD + "."
                            + DBObjectToVariantSourceEntryConverter.FILEID_FIELD,
                    options.getAsIntegerList(VariantQueryParams.FILES.key()), fileBuilder, QueryOperation.AND);
        }

        if (options.containsKey(VariantQueryParams.GENOTYPE.key())) {
            String sampleGenotypesCSV = options.getString(VariantQueryParams.GENOTYPE.key());

            //                String AND = ",";
            //                String OR = ";";
            //                String IS = ":";

            //                String AND = "AND";
            //                String OR = "OR";
            //                String IS = ":";

            String AND = ";";
            String OR = ",";
            String IS = ":";

            String[] sampleGenotypesArray = sampleGenotypesCSV.split(AND);
            for (String sampleGenotypes : sampleGenotypesArray) {
                String[] sampleGenotype = sampleGenotypes.split(IS);
                if (sampleGenotype.length != 2) {
                    continue;
                }
                int sample = Integer.parseInt(sampleGenotype[0]);
                String[] genotypes = sampleGenotype[1].split(OR);
                QueryBuilder genotypesBuilder = QueryBuilder.start();
                for (String genotype : genotypes) {
                    String s = DBObjectToVariantSourceEntryConverter.GENOTYPES_FIELD + "."
                            + DBObjectToSamplesConverter.genotypeToStorageType(genotype);
                    //or [ {"samp.0|0" : { $elemMatch : { $eq : <sampleId> } } } ]
                    genotypesBuilder.or(new BasicDBObject(s,
                            new BasicDBObject("$elemMatch", new BasicDBObject("$eq", sample))));
                }
                fileBuilder.and(genotypesBuilder.get());
            }
        }

        DBObject fileQuery = fileBuilder.get();
        if (fileQuery.keySet().size() != 0) {
            builder.and(DBObjectToVariantConverter.STUDIES_FIELD).elemMatch(fileQuery);
        }
    }

    logger.debug("Find = " + builder.get());
    return builder;
}

From source file:org.wrml.contrib.runtime.service.mongo.MongoService.java

License:Apache License

private DBObject createMongoQuery(final SearchCriteria searchCriteria) {

    QueryBuilder queryBuilder = null;/*from w w  w  .  j  a  va 2  s  .com*/

    final List<SearchCriterion> and = searchCriteria.getAnd();
    if (and != null && !and.isEmpty()) {

        queryBuilder = new QueryBuilder();

        for (final SearchCriterion searchCriterion : and) {

            final String referenceSlot = searchCriterion.getReferenceSlot();
            queryBuilder.and(referenceSlot);
            addQueryCriterion(searchCriterion, queryBuilder);

        }

    }

    final List<SearchCriterion> or = searchCriteria.getOr();
    if (or != null && !or.isEmpty()) {

        final DBObject[] orQueryCriterionArray = new DBObject[or.size()];
        for (int i = 0; i < or.size(); i++) {
            final SearchCriterion searchCriterion = or.get(i);
            final String referenceSlot = searchCriterion.getReferenceSlot();
            final QueryBuilder orQueryCriterionBuilder = QueryBuilder.start(referenceSlot);
            addQueryCriterion(searchCriterion, orQueryCriterionBuilder);
            orQueryCriterionArray[i] = orQueryCriterionBuilder.get();
        }

        final QueryBuilder orQueryBuilder = new QueryBuilder();
        orQueryBuilder.or(orQueryCriterionArray);

        if (queryBuilder != null) {
            // AND the OR clause together with the AND query
            queryBuilder.and(orQueryBuilder.get());
        } else {
            queryBuilder = orQueryBuilder;
        }
    }

    if (queryBuilder == null) {
        return null;
    }

    final DBObject mongoQuery = queryBuilder.get();
    return mongoQuery;
}