Example usage for com.mongodb.client.model Updates set

Introduction

In this page you can find the example usage for com.mongodb.client.model Updates set.

Prototype

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

Source Link

Document

Creates an update that sets the value of the field with the given name to the given value.

Usage

From source file:org.opencb.opencga.catalog.db.mongodb.UserMongoDBAdaptor.java

License:Apache License

@Override
public QueryResult resetPassword(String userId, String email, String newCryptPass) throws CatalogDBException {
    long startTime = startQuery();

    //        BasicDBObject query = new BasicDBObject("id", userId);
    //        query.put("email", email);
    Query query = new Query(QueryParams.ID.key(), userId);
    query.append(QueryParams.EMAIL.key(), email);
    Bson bson = parseQuery(query);//  w  w  w.j  av a 2s. c  om

    //        BasicDBObject fields = new BasicDBObject("password", newCryptPass);
    //        BasicDBObject action = new BasicDBObject("$set", fields);
    Bson set = Updates.set("password", new Document("password", newCryptPass));

    //        QueryResult<WriteResult> update = userCollection.update(query, action, null);
    QueryResult<UpdateResult> update = userCollection.update(bson, set, null);
    if (update.getResult().get(0).getModifiedCount() == 0) { //0 query matches.
        throw new CatalogDBException("Bad user or email");
    }
    return endQuery("Reset Password", startTime, Arrays.asList("Password successfully changed"));
}

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

License:Apache License

@Override
public QueryResult updateCustomAnnotations(Query query, String name, AdditionalAttribute attribute,
        QueryOptions options) {/*from  w  w w. jav a 2 s . c  o  m*/
    Document queryDocument = parseQuery(query);
    Document updateDocument = DocumentToVariantAnnotationConverter.convertToStorageType(attribute);
    return variantsCollection.update(queryDocument,
            Updates.set(DocumentToVariantConverter.CUSTOM_ANNOTATION_FIELD + "." + name, updateDocument),
            new QueryOptions(MULTI, true));
}

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

License:Apache License

@Override
public QueryResult updateSourceStats(VariantSourceStats variantSourceStats,
        StudyConfiguration studyConfiguration, QueryOptions queryOptions) {
    MongoDBCollection coll = db.getCollection(collectionName);

    VariantSource source = new VariantSource(new VariantFileMetadata());
    source.setStats(variantSourceStats.getFileStats());
    Document globalStats = variantSourceConverter.convertToStorageType(source).get("stats", Document.class);

    Bson query = parseQuery(new Query(VariantSourceQueryParam.STUDY_ID.key(), variantSourceStats.getStudyId())
            .append(VariantSourceQueryParam.FILE_ID.key(), variantSourceStats.getFileId()));
    Bson update = Updates.set("stats", globalStats);

    return coll.update(query, update, null);
}

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From source file:org.trade.core.persistence.local.mongo.MongoPersistence.java

License:Apache License

@Override
public void storeBinaryData(byte[] data, String collectionName, String identifier) throws Exception {
    MongoClient client = new MongoClient(new MongoClientURI(this.mongoUrl));
    MongoDatabase db = client.getDatabase(this.dbName);

    MongoCollection<Document> collection = db.getCollection(collectionName);
    Document doc = collection.find(Filters.eq(IDENTIFIER_FIELD, identifier)).limit(1).first();

    if (data == null) {
        // We assume that if the value is set to null, we should delete also the corresponding database entry
        if (doc != null) {
            collection.deleteOne(Filters.eq(IDENTIFIER_FIELD, identifier));
        }//from w  ww .j a  v  a  2  s . c  o m
    } else {
        // Check if the document already exists and update it
        if (doc != null) {
            collection.updateOne(Filters.eq(IDENTIFIER_FIELD, identifier),
                    Updates.combine(Updates.set(DATA_FIELD, data), Updates.currentDate("lastModified")));
        } else {
            Document document = new Document(IDENTIFIER_FIELD, identifier).append(DATA_FIELD, data)
                    .append("lastModified", new Date());
            collection.insertOne(document);
        }
    }

    client.close();
}

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From source file:uk.ac.ebi.eva.dbmigration.mongodb.ExtractAnnotationFromVariant.java

License:Apache License

private UpdateOneModel<Document> buildUpdateDocument(Document variantDocument) {
    Document annotationSubdocument = (Document) variantDocument.get(ANNOT_FIELD);
    Assert.notNull(annotationSubdocument, "Logic error");

    Set<Integer> soSet = computeSoSet(annotationSubdocument);
    Set<String> xrefSet = computeXrefSet(annotationSubdocument);
    List<Double> sift = computeMinAndMaxScore(annotationSubdocument, SIFT_FIELD);
    List<Double> polyphen = computeMinAndMaxScore(annotationSubdocument, POLYPHEN_FIELD);

    Document newAnnotationSubdocument = new Document()
            .append(VEP_VERSION_FIELD, databaseParameters.getVepVersion())
            .append(CACHE_VERSION_FIELD, databaseParameters.getVepCacheVersion());

    if (!soSet.isEmpty()) {
        newAnnotationSubdocument.append(SO_FIELD, soSet);
    }//from   w w  w. j  a  v a2  s . c o m
    if (!xrefSet.isEmpty()) {
        newAnnotationSubdocument.append(XREFS_FIELD, xrefSet);
    }
    if (!sift.isEmpty()) {
        newAnnotationSubdocument.append(SIFT_FIELD, sift);
    }
    if (!polyphen.isEmpty()) {
        newAnnotationSubdocument.append(POLYPHEN_FIELD, polyphen);
    }

    List<Document> newAnnotationArray = Collections.singletonList(newAnnotationSubdocument);

    Document query = new Document(ID_FIELD, variantDocument.get(ID_FIELD));
    Bson update = Updates.set(ANNOT_FIELD, newAnnotationArray);
    return new UpdateOneModel<>(query, update);
}

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