Example usage for com.mongodb.client.model Filters and

Introduction

In this page you can find the example usage for com.mongodb.client.model Filters and.

Prototype

public static Bson and(final Bson... filters) 

Source Link

Document

Creates a filter that performs a logical AND of the provided list of filters.

Usage

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

License:Apache License

private Bson parseQuery(Query query) {
    List<Bson> andBsonList = new ArrayList<>();

    createRegionQuery(query, ConservationDBAdaptor.QueryParams.REGION.key(), andBsonList);

    if (andBsonList.size() > 0) {
        return Filters.and(andBsonList);
    } else {//from www. j a v a2  s.co m
        return new Document();
    }
}

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

License:Apache License

private Bson parseQuery(Query query) {
    List<Bson> andBsonList = new ArrayList<>();

    createRegionQuery(query, QueryParams.REGION.key(), MongoDBCollectionConfiguration.GENE_CHUNK_SIZE,
            andBsonList);/* w  w  w  .  j av a2s  . c  o  m*/

    createOrQuery(query, QueryParams.ID.key(), "id", andBsonList);
    createOrQuery(query, QueryParams.NAME.key(), "name", andBsonList);
    createOrQuery(query, QueryParams.BIOTYPE.key(), "biotype", andBsonList);
    createOrQuery(query, QueryParams.XREFS.key(), "transcripts.xrefs.id", andBsonList);

    createOrQuery(query, QueryParams.TRANSCRIPT_ID.key(), "transcripts.id", andBsonList);
    createOrQuery(query, QueryParams.TRANSCRIPT_NAME.key(), "transcripts.name", andBsonList);
    createOrQuery(query, QueryParams.TRANSCRIPT_BIOTYPE.key(), "transcripts.biotype", andBsonList);

    createOrQuery(query, QueryParams.TFBS_NAME.key(), "transcripts.tfbs.name", andBsonList);
    createOrQuery(query, QueryParams.ANNOTATION_DISEASE_ID.key(), "annotation.diseases.id", andBsonList);
    createOrQuery(query, QueryParams.ANNOTATION_DISEASE_NAME.key(), "annotation.diseases.name", andBsonList);
    createOrQuery(query, QueryParams.ANNOTATION_EXPRESSION_GENE.key(), "annotation.expression.geneName",
            andBsonList);
    createOrQuery(query, QueryParams.ANNOTATION_EXPRESSION_TISSUE.key(), "annotation.expression.factorValue",
            andBsonList);
    createOrQuery(query, QueryParams.ANNOTATION_DRUGS_NAME.key(), "annotation.drugs.drugName", andBsonList);
    createOrQuery(query, QueryParams.ANNOTATION_DRUGS_GENE.key(), "annotation.drugs.geneName", andBsonList);

    if (andBsonList.size() > 0) {
        return Filters.and(andBsonList);
    } else {
        return new Document();
    }
}

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

License:Apache License

private Bson parseQuery(Query query) {
    List<Bson> andBsonList = new ArrayList<>();

    createRegionQuery(query, GenomeDBAdaptor.QueryParams.REGION.key(),
            MongoDBCollectionConfiguration.GENOME_SEQUENCE_CHUNK_SIZE, andBsonList);

    if (andBsonList.size() > 0) {
        return Filters.and(andBsonList);
    } else {//ww w.  j  av  a  2  s  .c o m
        return new Document();
    }
}

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

License:Apache License

private Bson parseQuery(Query query) {
    List<Bson> andBsonList = new ArrayList<>();

    createOrQuery(query, QueryParams.ACCESSION.key(), "accession", andBsonList);
    createOrQuery(query, QueryParams.NAME.key(), "name", andBsonList);
    createOrQuery(query, QueryParams.GENE.key(), "gene.name.value", andBsonList);
    createOrQuery(query, QueryParams.XREFS.key(), "dbReference.id", andBsonList);
    createOrQuery(query, QueryParams.KEYWORD.key(), "keyword.value", andBsonList);
    createOrQuery(query, QueryParams.FEATURE_ID.key(), "feature.id", andBsonList);
    createOrQuery(query, QueryParams.FEATURE_TYPE.key(), "feature.type", andBsonList);

    if (andBsonList.size() > 0) {
        return Filters.and(andBsonList);
    } else {//w w w . j  av a2 s  . c  o m
        return new Document();
    }
}

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

License:Apache License

private Bson parseQuery(Query query) {
    List<Bson> andBsonList = new ArrayList<>();

    createOrQuery(query, ProteinProteinInteractionDBAdaptor.QueryParams.INTERACTOR_A_ID.key(), "interactorA.id",
            andBsonList);/*from  w w w .  ja  v a2 s .  com*/
    createOrQuery(query, ProteinProteinInteractionDBAdaptor.QueryParams.INTERACTOR_B_ID.key(), "interactorB.id",
            andBsonList);
    createOrQuery(query, ProteinProteinInteractionDBAdaptor.QueryParams.INTERACTOR_A_XREFS.key(),
            "interactorA.xrefs", andBsonList);
    createOrQuery(query, ProteinProteinInteractionDBAdaptor.QueryParams.INTERACTOR_B_XREFS.key(),
            "interactorB.xrefs", andBsonList);
    createOrQuery(query, ProteinProteinInteractionDBAdaptor.QueryParams.XREFs.key(), "xrefs.id", andBsonList);
    createOrQuery(query, ProteinProteinInteractionDBAdaptor.QueryParams.TYPE_PSIMI.key(), "type.name",
            andBsonList);
    createOrQuery(query, ProteinProteinInteractionDBAdaptor.QueryParams.TYPE_NAME.key(), "type.name",
            andBsonList);
    createOrQuery(query, ProteinProteinInteractionDBAdaptor.QueryParams.DETECTION_METHOD_NAME.key(),
            "detectionMethod.name", andBsonList);

    if (andBsonList.size() > 0) {
        return Filters.and(andBsonList);
    } else {
        return new Document();
    }
}

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

License:Apache License

private Bson parseQuery(Query query) {
    List<Bson> andBsonList = new ArrayList<>();
    createRegionQuery(query, QueryParams.REGION.key(),
            MongoDBCollectionConfiguration.REGULATORY_REGION_CHUNK_SIZE, andBsonList);

    createOrQuery(query, QueryParams.NAME.key(), "name", andBsonList);
    createOrQuery(query, QueryParams.FEATURE_TYPE.key(), "featureType", andBsonList);
    createOrQuery(query, QueryParams.FEATURE_CLASS.key(), "featureClass", andBsonList);
    createOrQuery(query, QueryParams.CELL_TYPES.key(), "cellTypes", andBsonList);
    createOrQuery(query, QueryParams.SCORE.key(), "score", andBsonList);

    if (andBsonList.size() > 0) {
        return Filters.and(andBsonList);
    } else {//  w w  w. j a  va  2  s  . co  m
        return new Document();
    }
}

---

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

License:Apache License

private Bson parseQuery(Query query) {
    List<Bson> andBsonList = new ArrayList<>();

    createRegionQuery(query, VariantMongoDBAdaptor.QueryParams.REGION.key(),
            MongoDBCollectionConfiguration.VARIATION_CHUNK_SIZE, andBsonList);
    createOrQuery(query, VariantMongoDBAdaptor.QueryParams.ID.key(), "id", andBsonList);
    createOrQuery(query, QueryParams.CHROMOSOME.key(), "chromosome", andBsonList);
    createImprecisePositionQuery(query, QueryParams.CI_START_LEFT.key(), QueryParams.CI_START_RIGHT.key(),
            "sv.ciStartLeft", "sv.ciStartRight", andBsonList);
    createImprecisePositionQuery(query, QueryParams.CI_END_LEFT.key(), QueryParams.CI_END_RIGHT.key(),
            "sv.ciEndLeft", "sv.ciEndRight", andBsonList);
    createOrQuery(query, QueryParams.START.key(), "start", andBsonList, QueryValueType.INTEGER);
    //        createOrQuery(query, QueryParams.REFERENCE.key(), "reference", andBsonList);
    if (query.containsKey(QueryParams.REFERENCE.key())) {
        createOrQuery(query.getAsStringList(QueryParams.REFERENCE.key()), "reference", andBsonList);
    }/* ww w .j  ava 2s.  c  o  m*/
    if (query.containsKey(QueryParams.ALTERNATE.key())) {
        createOrQuery(query.getAsStringList(QueryParams.ALTERNATE.key()), "alternate", andBsonList);
    }
    //        createOrQuery(query, QueryParams.ALTERNATE.key(), "alternate", andBsonList);
    createOrQuery(query, VariantMongoDBAdaptor.QueryParams.CONSEQUENCE_TYPE.key(),
            "annotation.consequenceTypes.sequenceOntologyTerms.name", andBsonList);
    //        createOrQuery(query, VariantMongoDBAdaptor.QueryParams.GENE.key(), "annotation.consequenceTypes.ensemblGeneId",
    //                andBsonList);
    createGeneOrQuery(query, VariantMongoDBAdaptor.QueryParams.GENE.key(), andBsonList);

    //        createOrQuery(query, VariantMongoDBAdaptor.QueryParams.XREFS.key(), "transcripts.xrefs.id", andBsonList);

    if (andBsonList.size() > 0) {
        return Filters.and(andBsonList);
    } else {
        return new Document();
    }
}

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

License:Apache License

private Bson parseQuery(Query query) {
    List<Bson> andBsonList = new ArrayList<>();
    createOrQuery(query, XRefDBAdaptor.QueryParams.ID.key(), "transcripts.xrefs.id", andBsonList);
    createOrQuery(query, XRefDBAdaptor.QueryParams.DBNAME.key(), "transcripts.xrefs.dbName", andBsonList);

    if (andBsonList.size() > 0) {
        return Filters.and(andBsonList);
    } else {//from  w  w  w.ja  v  a 2  s.  c  o  m
        return new Document();
    }
}

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

License:Apache License

private Bson parseQuery(Query query) {
    logger.info("Parsing query...");
    Bson filtersBson = null;/* w  ww.  jav a  2 s.  c o m*/

    // No filtering parameters mean all records
    if (query.size() > 0) {
        Bson commonFiltersBson = getCommonFilters(query);
        Set<String> sourceContent = query.getAsStringList(QueryParams.SOURCE.key()) != null
                ? new HashSet<>(query.getAsStringList(QueryParams.SOURCE.key()))
                : null;
        List<Bson> sourceSpecificFilterList = new ArrayList<>();
        getClinvarFilters(query, sourceContent, sourceSpecificFilterList);
        getCosmicFilters(query, sourceContent, sourceSpecificFilterList);
        getGwasFilters(query, sourceContent, sourceSpecificFilterList);

        if (sourceSpecificFilterList.size() > 0 && commonFiltersBson != null) {
            List<Bson> filtersBsonList = new ArrayList<>();
            filtersBsonList.add(commonFiltersBson);
            filtersBsonList.add(Filters.or(sourceSpecificFilterList));
            filtersBson = Filters.and(filtersBsonList);
        } else if (commonFiltersBson != null) {
            filtersBson = commonFiltersBson;
        } else if (sourceSpecificFilterList.size() > 0) {
            filtersBson = Filters.or(sourceSpecificFilterList);
        }
    }

    if (filtersBson != null) {
        return filtersBson;
    } else {
        return new Document();
    }
}

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From source file:org.opencb.cellbase.mongodb.impl.GeneMongoDBAdaptor.java

License:Apache License

private Bson parseQuery(Query query) {
    List<Bson> andBsonList = new ArrayList<>();

    createRegionQuery(query, QueryParams.REGION.key(), MongoDBCollectionConfiguration.GENE_CHUNK_SIZE,
            andBsonList);/*from  w w w .j a v a 2s.  co  m*/

    createOrQuery(query, QueryParams.ID.key(), "id", andBsonList);
    createOrQuery(query, QueryParams.NAME.key(), "name", andBsonList);
    createOrQuery(query, QueryParams.BIOTYPE.key(), "biotype", andBsonList);
    createOrQuery(query, QueryParams.XREFS.key(), "transcripts.xrefs.id", andBsonList);

    createOrQuery(query, QueryParams.TRANSCRIPT_ID.key(), "transcripts.id", andBsonList);
    createOrQuery(query, QueryParams.TRANSCRIPT_NAME.key(), "transcripts.name", andBsonList);
    createOrQuery(query, QueryParams.TRANSCRIPT_BIOTYPE.key(), "transcripts.biotype", andBsonList);

    createOrQuery(query, QueryParams.TFBS_NAME.key(), "transcripts.tfbs.name", andBsonList);
    createOrQuery(query, QueryParams.ANNOTATION_DISEASE_ID.key(), "annotation.diseases.id", andBsonList);
    createOrQuery(query, QueryParams.ANNOTATION_DISEASE_NAME.key(), "annotation.diseases.name", andBsonList);
    createOrQuery(query, QueryParams.ANNOTATION_EXPRESSION_GENE.key(), "annotation.expression.gene",
            andBsonList);
    createOrQuery(query, QueryParams.ANNOTATION_EXPRESSION_TISSUE.key(), "annotation.expression.tissue",
            andBsonList);
    createOrQuery(query, QueryParams.ANNOTATION_DRUGS_NAME.key(), "annotation.drugs.name", andBsonList);
    createOrQuery(query, QueryParams.ANNOTATION_DRUGS_GENE.key(), "annotation.drugs.gene", andBsonList);

    if (andBsonList.size() > 0) {
        return Filters.and(andBsonList);
    } else {
        return new Document();
    }
}

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