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

Introduction

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

Prototype

public static <TItem> Bson eq(final String fieldName, @Nullable final TItem value) 

Source Link

Document

Creates a filter that matches all documents where the value of the field name equals the specified value.

Usage

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

License:Apache License

private void getClinvarFilters(Query query, Set<String> sourceContent, List<Bson> sourceBson) {
    List<Bson> andBsonList = new ArrayList<>();

    if (sourceContent != null && sourceContent.contains("clinvar")) {
        andBsonList.add(Filters.eq("source", "clinvar"));
    }/*  w  w w. j  a v a  2 s.c o  m*/

    createOrQuery(query, QueryParams.CLINVARRCV.key(),
            "clinvarSet.referenceClinVarAssertion.clinVarAccession.acc", andBsonList);
    createClinvarRsQuery(query, andBsonList);
    createClinvarTypeQuery(query, andBsonList);
    createClinvarReviewQuery(query, andBsonList);
    createClinvarClinicalSignificanceQuery(query, andBsonList);

    if (andBsonList.size() == 1) {
        sourceBson.add(andBsonList.get(0));
    } else if (andBsonList.size() > 0) {
        sourceBson.add(Filters.and(andBsonList));
    }
}

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

License:Apache License

private void createClinvarRsQuery(Query query, List<Bson> andBsonList) {
    if (query != null && query.getString(QueryParams.CLINVARRS.key()) != null
            && !query.getString(QueryParams.CLINVARRS.key()).isEmpty()) {
        List<String> queryList = query.getAsStringList(QueryParams.CLINVARRS.key());
        if (queryList.size() == 1) {
            andBsonList.add(Filters.eq("clinvarSet.referenceClinVarAssertion.measureSet.measure.xref.id",
                    queryList.get(0).substring(2)));
            andBsonList/*from w  w  w.ja  v  a  2  s  . c  om*/
                    .add(Filters.eq("clinvarSet.referenceClinVarAssertion.measureSet.measure.xref.type", "rs"));
        } else {
            List<Bson> orBsonList = new ArrayList<>(queryList.size());
            for (String queryItem : queryList) {
                List<Bson> innerAndBsonList = new ArrayList<>();
                innerAndBsonList
                        .add(Filters.eq("clinvarSet.referenceClinVarAssertion.measureSet.measure.xref.id",
                                queryList.get(0).substring(2)));
                innerAndBsonList.add(
                        Filters.eq("clinvarSet.referenceClinVarAssertion.measureSet.measure.xref.type", "rs"));
                orBsonList.add(Filters.and(innerAndBsonList));
            }
            andBsonList.add(Filters.or(orBsonList));
        }
    }
}

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

License:Apache License

@Override
public QueryResult getRegulatoryElements(Query query, QueryOptions queryOptions) {
    Bson bson = parseQuery(query);//  w w  w . j  av a2 s.  c o m
    QueryResult<Document> queryResult = null;
    QueryResult<Document> gene = mongoDBCollection.find(bson,
            new QueryOptions(MongoDBCollection.INCLUDE, "chromosome,start,end"));
    if (gene != null) {
        MongoDBCollection regulatoryRegionCollection = mongoDataStore.getCollection("regulatory_region");
        for (Document document : gene.getResult()) {
            //                String region = document.getString("chromosome") + ":"
            //                        + document.getInteger("start", 1) + "-" + document.getInteger("end", Integer.MAX_VALUE);
            //                query.put(RegulationDBAdaptor.QueryParams.REGION.key(), region);
            Bson eq = Filters.eq("chromosome", document.getString("chromosome"));
            Bson lte = Filters.lte("start", document.getInteger("end", Integer.MAX_VALUE));
            Bson gte = Filters.gte("end", document.getInteger("start", 1));
            queryResult = regulatoryRegionCollection.find(Filters.and(eq, lte, gte), queryOptions);
        }
    }
    return queryResult;
}

---

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

License:Apache License

protected void createRegionQuery(Query query, String queryParam, List<Bson> andBsonList) {
    if (query != null && query.getString(queryParam) != null && !query.getString(queryParam).isEmpty()) {
        List<Region> regions = Region.parseRegions(query.getString(queryParam));
        if (regions != null && regions.size() > 0) {
            // if there is only one region we add the AND filter directly to the andBsonList passed
            if (regions.size() == 1) {
                Bson chromosome = Filters.eq("chromosome", regions.get(0).getChromosome());
                Bson start = Filters.lte("start", regions.get(0).getEnd());
                Bson end = Filters.gte("end", regions.get(0).getStart());
                andBsonList.add(Filters.and(chromosome, start, end));
            } else {
                // when multiple regions then we create and OR list before add it to andBsonList
                List<Bson> orRegionBsonList = new ArrayList<>(regions.size());
                for (Region region : regions) {
                    Bson chromosome = Filters.eq("chromosome", region.getChromosome());
                    Bson start = Filters.lte("start", region.getEnd());
                    Bson end = Filters.gte("end", region.getStart());
                    orRegionBsonList.add(Filters.and(chromosome, start, end));
                }//from   w w w  . j  av a 2  s . c om
                andBsonList.add(Filters.or(orRegionBsonList));
            }
        } else {
            logger.warn("Region query no created, region object is null or empty.");
        }
    }
}

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

License:Apache License

protected <T> void createOrQuery(List<T> queryValues, String mongoDbField, List<Bson> andBsonList) {
    if (queryValues.size() == 1) {
        andBsonList.add(Filters.eq(mongoDbField, queryValues.get(0)));
    } else {//from ww  w  .j  av a2 s  . c  om
        List<Bson> orBsonList = new ArrayList<>(queryValues.size());
        for (T queryItem : queryValues) {
            orBsonList.add(Filters.eq(mongoDbField, queryItem));
        }
        andBsonList.add(Filters.or(orBsonList));
    }
}

---

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

License:Apache License

@Override
public QueryResult<Score> getSubstitutionScores(Query query, QueryOptions options) {
    QueryResult result = null;//from   w  w  w  .  j a  v  a2 s .  c  o m

    // Ensembl transcript id is needed for this collection
    if (query.getString("transcript") != null) {
        Bson transcript = Filters.eq("transcriptId", query.getString("transcript"));

        int position = -1;
        String aaShortName = null;
        // If position and aa change are provided we create a 'projection' to return only the required data from the database
        if (query.get("position") != null && !query.getString("position").isEmpty()
                && query.getInt("position", 0) != 0) {
            position = query.getInt("position");
            String projectionString = "aaPositions." + position;

            // If aa change is provided we only return that information
            if (query.getString("aa") != null && !query.getString("aa").isEmpty()) {
                aaShortName = aaShortNameMap.get(query.getString("aa").toUpperCase());
                projectionString += "." + aaShortName;
            }

            // Projection is used to minimize the returned data
            Bson positionProjection = Projections.include(projectionString);
            result = proteinSubstitutionMongoDBCollection.find(transcript, positionProjection, options);
        } else {
            // Return the whole transcript data
            result = proteinSubstitutionMongoDBCollection.find(transcript, options);
        }

        if (result != null && !result.getResult().isEmpty()) {
            Document document = (Document) result.getResult().get(0);
            Document aaPositionsDocument = (Document) document.get("aaPositions");

            // Position or aa change were not provided, returning whole transcript data
            if (position == -1 || aaShortName == null) {
                // Return only the inner Document, not the whole document projected
                result.setResult(Collections.singletonList(aaPositionsDocument));
                // Position and aa were provided, return only corresponding Score objects
            } else {
                List<Score> scoreList = null;
                if (result.getNumResults() == 1 && aaPositionsDocument != null) {
                    scoreList = new ArrayList<>(NUM_PROTEIN_SUBSTITUTION_SCORE_METHODS);
                    Document positionDocument = (Document) aaPositionsDocument.get(Integer.toString(position));
                    Document aaDocument = (Document) positionDocument.get(aaShortName);
                    //                        Document proteinSubstitutionScores = (Document) result.getResult().get(0);
                    if (aaDocument.get("ss") != null) {
                        scoreList.add(new Score(Double.parseDouble("" + aaDocument.get("ss")), "sift",
                                VariantAnnotationUtils.SIFT_DESCRIPTIONS.get(aaDocument.get("se"))));
                    }
                    if (aaDocument.get("ps") != null) {
                        scoreList.add(new Score(Double.parseDouble("" + aaDocument.get("ps")), "polyphen",
                                VariantAnnotationUtils.POLYPHEN_DESCRIPTIONS.get(aaDocument.get("pe"))));
                    }
                }
                result.setResult(scoreList);
                //                    result.setResult(Collections.singletonList(scoreList));
            }
            //            // Return empty QueryResult if the query did not return any result
            //            } else {
            //                return result;
        }
    }
    // Return null if no transcript id is provided
    return result;

}

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

License:Apache License

private Bson getGeneQuery(String geneId) {
    //        List<Bson> orBsonList = new ArrayList<>(3);
    //        orBsonList.add(Filters.eq("annotation.consequenceTypes.geneName", geneId));
    //        orBsonList.add(Filters.eq("annotation.consequenceTypes.ensemblGeneId", geneId));
    //        orBsonList.add(Filters.eq("annotation.consequenceTypes.ensemblTranscriptId", geneId));

    // For some reason Mongo does not deal properly with OR queries and indexes. It is extremely slow to perform
    // the commented query above. On the contrary this query below provides instant results
    if (geneId.startsWith(ENSEMBL_GENE_ID_PATTERN)) {
        return Filters.eq("annotation.consequenceTypes.ensemblGeneId", geneId);
    } else if (geneId.startsWith(ENSEMBL_TRANSCRIPT_ID_PATTERN)) {
        return Filters.eq("annotation.consequenceTypes.ensemblTranscriptId", geneId);
    } else {/*from  w w  w .  j  a va  2 s  . c o  m*/
        return Filters.eq("annotation.consequenceTypes.geneName", geneId);
    }
}

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

License:Apache License

private void getCosmicFilters(Query query, Set<String> sourceContent, List<Bson> sourceBson) {
    // If only clinvar-specific filters are provided it must be avoided to include the source=cosmic condition since
    // sourceBson is going to be an OR list
    if (!(query.containsKey(QueryParams.CLINVARRCV.key()) || query.containsKey(QueryParams.CLINVARCLINSIG.key())
            || query.containsKey(QueryParams.CLINVARREVIEW.key())
            || query.containsKey(QueryParams.CLINVARTYPE.key())
            || query.containsKey(QueryParams.CLINVARRS.key()))) {
        if (sourceContent != null && sourceContent.contains("cosmic")) {
            sourceBson.add(Filters.eq("source", "cosmic"));
        }/*from w w  w .  jav a  2  s  . c o  m*/
    }
}

---

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

License:Apache License

protected void createOrQuery(List<String> queryValues, String mongoDbField, List<Bson> andBsonList) {
    if (queryValues.size() == 1) {
        andBsonList.add(Filters.eq(mongoDbField, queryValues.get(0)));
    } else {/*from   w ww  .  j a va  2 s.co m*/
        List<Bson> orBsonList = new ArrayList<>(queryValues.size());
        for (String queryItem : queryValues) {
            orBsonList.add(Filters.eq(mongoDbField, queryItem));
        }
        andBsonList.add(Filters.or(orBsonList));
    }
}

---

From source file:org.opencb.commons.datastore.mongodb.MongoDBQueryUtils.java

License:Apache License

public static <T> Bson createFilter(String mongoDbField, T queryValue, ComparisonOperator comparator) {
    Bson filter = null;// w w w  .  jav a2 s.  com

    if (queryValue != null) {
        if (queryValue instanceof String) {
            switch (comparator) {
            case EQUALS:
                filter = Filters.eq(mongoDbField, queryValue);
                break;
            case NOT_EQUALS:
                filter = Filters.ne(mongoDbField, queryValue);
                break;
            case EQUAL_IGNORE_CASE:
                filter = Filters.regex(mongoDbField, queryValue.toString(), "i");
                break;
            case STARTS_WITH:
                filter = Filters.regex(mongoDbField, "^" + queryValue + "*");
                break;
            case ENDS_WITH:
                filter = Filters.regex(mongoDbField, "*" + queryValue + "$");
                break;
            case REGEX:
                filter = Filters.regex(mongoDbField, queryValue.toString());
                break;
            case TEXT:
                filter = Filters.text(String.valueOf(queryValue));
                break;
            default:
                break;
            }
        } else {
            switch (comparator) {
            case EQUALS:
                filter = Filters.eq(mongoDbField, queryValue);
                break;
            case NOT_EQUALS:
                filter = Filters.ne(mongoDbField, queryValue);
                break;
            case GREATER_THAN:
                filter = Filters.gt(mongoDbField, queryValue);
                break;
            case GREATER_THAN_EQUAL:
                filter = Filters.gte(mongoDbField, queryValue);
                break;
            case LESS_THAN:
                filter = Filters.lt(mongoDbField, queryValue);
                break;
            case LESS_THAN_EQUAL:
                filter = Filters.lte(mongoDbField, queryValue);
                break;
            default:
                break;
            }
        }
    }
    return filter;
}

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