Example usage for com.mongodb.client.model Projections include

List of usage examples for com.mongodb.client.model Projections include

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Introduction

In this page you can find the example usage for com.mongodb.client.model Projections include.

Prototype

public static Bson include(final List<String> fieldNames)

Source Link

Document

Creates a projection that includes all of the given fields.

Usage

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

License:Apache License

/**
 * The method will return the variable object given variableSetId and the variableId.
 * @param variableSetId Id of the variableSet.
 * @param variableId Id of the variable inside the variableSet.
 * @return the variable object.//w w w . ja  v  a  2 s.c o  m
 */
private Variable getVariable(long variableSetId, String variableId) throws CatalogDBException {
    List<Bson> aggregation = new ArrayList<>();
    aggregation.add(Aggregates.match(Filters.elemMatch(QueryParams.VARIABLE_SET.key(),
            Filters.eq(VariableSetParams.ID.key(), variableSetId))));
    aggregation.add(Aggregates.project(Projections.include(QueryParams.VARIABLE_SET.key())));
    aggregation.add(Aggregates.unwind("$" + QueryParams.VARIABLE_SET.key()));
    aggregation.add(Aggregates.match(Filters.eq(QueryParams.VARIABLE_SET_ID.key(), variableSetId)));
    aggregation.add(
            Aggregates.unwind("$" + QueryParams.VARIABLE_SET.key() + "." + VariableSetParams.VARIABLE.key()));
    aggregation.add(Aggregates.match(Filters
            .eq(QueryParams.VARIABLE_SET.key() + "." + VariableSetParams.VARIABLE_NAME.key(), variableId)));

    QueryResult<Document> queryResult = studyCollection.aggregate(aggregation, new QueryOptions());

    Document variableSetDocument = (Document) queryResult.first().get(QueryParams.VARIABLE_SET.key());
    VariableSet variableSet = variableSetConverter.convertToDataModelType(variableSetDocument);
    Iterator<Variable> iterator = variableSet.getVariables().iterator();
    if (iterator.hasNext()) {
        return iterator.next();
    } else {
        // This error should never be raised.
        throw new CatalogDBException(
                "VariableSet {id: " + variableSetId + "} - Could not obtain variable object.");
    }
}

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

License:Apache License

@Override
public QueryResult<VariableSet> getAllVariableSets(long studyId, QueryOptions options)
        throws CatalogDBException {

    long startTime = startQuery();

    List<Bson> mongoQueryList = new LinkedList<>();

    for (Map.Entry<String, Object> entry : options.entrySet()) {
        String key = entry.getKey().split("\\.")[0];
        try {/*from   ww w .  j a  va 2  s .  c o  m*/
            if (isDataStoreOption(key) || isOtherKnownOption(key)) {
                continue; //Exclude DataStore options
            }
            CatalogStudyDBAdaptor.VariableSetParams option = CatalogStudyDBAdaptor.VariableSetParams
                    .getParam(key) != null ? CatalogStudyDBAdaptor.VariableSetParams.getParam(key)
                            : CatalogStudyDBAdaptor.VariableSetParams.getParam(entry.getKey());
            switch (option) {
            case STUDY_ID:
                addCompQueryFilter(option, option.name(), PRIVATE_ID, options, mongoQueryList);
                break;
            default:
                String optionsKey = "variableSets." + entry.getKey().replaceFirst(option.name(), option.key());
                addCompQueryFilter(option, entry.getKey(), optionsKey, options, mongoQueryList);
                break;
            }
        } catch (IllegalArgumentException e) {
            throw new CatalogDBException(e);
        }
    }

    /*
    QueryResult<DBObject> queryResult = studyCollection.aggregate(Arrays.<DBObject>asList(
        new BasicDBObject("$match", new BasicDBObject(PRIVATE_ID, studyId)),
        new BasicDBObject("$project", new BasicDBObject("variableSets", 1)),
        new BasicDBObject("$unwind", "$variableSets"),
        new BasicDBObject("$match", new BasicDBObject("$and", mongoQueryList))
    ), filterOptions(options, FILTER_ROUTE_STUDIES));
    */

    List<Bson> aggregation = new ArrayList<>();
    aggregation.add(Aggregates.match(Filters.eq(PRIVATE_ID, studyId)));
    aggregation.add(Aggregates.project(Projections.include("variableSets")));
    aggregation.add(Aggregates.unwind("$variableSets"));
    if (mongoQueryList.size() > 0) {
        aggregation.add(Aggregates.match(Filters.and(mongoQueryList)));
    }

    QueryResult<Document> queryResult = studyCollection.aggregate(aggregation,
            filterOptions(options, FILTER_ROUTE_STUDIES));

    List<VariableSet> variableSets = parseObjects(queryResult, Study.class).stream()
            .map(study -> study.getVariableSets().get(0)).collect(Collectors.toList());

    return endQuery("", startTime, variableSets);
}

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

License:Apache License

@Override
public long getStudyIdByVariableSetId(long variableSetId) throws CatalogDBException {
    //        DBObject query = new BasicDBObject("variableSets.id", variableSetId);
    Bson query = Filters.eq("variableSets.id", variableSetId);
    Bson projection = Projections.include("id");

    //        QueryResult<DBObject> queryResult = studyCollection.find(query, new BasicDBObject("id", true), null);
    QueryResult<Document> queryResult = studyCollection.find(query, projection, null);

    if (!queryResult.getResult().isEmpty()) {
        Object id = queryResult.getResult().get(0).get("id");
        return id instanceof Number ? ((Number) id).intValue() : (int) Double.parseDouble(id.toString());
    } else {//from w  w w. j  a  v  a2s  .c o  m
        throw CatalogDBException.idNotFound("VariableSet", variableSetId);
    }
}

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

License:Apache License

protected QueryResult rank(MongoDBCollection collection, Bson query, List<String> groupByField, String idField,
        int numResults, boolean asc) {

    if (groupByField == null || groupByField.isEmpty()) {
        return new QueryResult();
    }//  w w  w  .ja  v a  2 s .  c o  m

    if (groupByField.size() == 1) {
        // if only one field then we call to simple rank
        return rank(collection, query, groupByField.get(0), idField, numResults, asc);
    } else {
        Bson match = Aggregates.match(query);

        // add all group-by fields to the projection together with the aggregation field name
        List<String> groupByFields = new ArrayList<>(groupByField);
        groupByFields.add(idField);
        Bson project = Aggregates.project(Projections.include(groupByFields));

        // _id document creation to have the multiple id
        Document id = new Document();
        for (String s : groupByField) {
            id.append(s, "$" + s);
        }
        Bson group = Aggregates.group(id, Accumulators.sum("count", 1));
        Bson sort;
        if (asc) {
            sort = Aggregates.sort(Sorts.ascending("count"));
        } else {
            sort = Aggregates.sort(Sorts.descending("count"));
        }
        Bson limit = Aggregates.limit(numResults);

        return collection.aggregate(Arrays.asList(match, project, group, sort, limit), new QueryOptions());
    }
}

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

License:Apache License

protected QueryResult groupBy(MongoDBCollection collection, Bson query, List<String> groupByField,
        String idField, QueryOptions options) {
    if (groupByField == null || groupByField.isEmpty()) {
        return new QueryResult();
    }//from w  ww.  j  av  a  2 s  .  c om

    List<String> groupByFields = new ArrayList<>(groupByField);
    //        if (groupByField.size() == 1) {
    //            // if only one field then we call to simple groupBy
    //            return groupBy(collection, query, groupByField.get(0), idField, options);
    //        } else {
    Bson match = Aggregates.match(query);

    // add all group-by fields to the projection together with the aggregation field name
    List<String> includeGroupByFields = new ArrayList<>(groupByField);
    includeGroupByFields.add(idField);
    List<Bson> projections = new ArrayList<>();
    addDateProjection(projections, includeGroupByFields, groupByFields);
    projections.add(Projections.include(includeGroupByFields));
    Bson project = Aggregates.project(Projections.fields(projections));
    //            Bson project = Aggregates.project(Projections.include(groupByFields));

    // _id document creation to have the multiple id
    Document id = new Document();
    for (String s : groupByFields) {
        id.append(s, "$" + s);
    }
    Bson group;
    if (options.getBoolean("count", false)) {
        group = Aggregates.group(id, Accumulators.sum("count", 1));
    } else {
        group = Aggregates.group(id, Accumulators.addToSet("features", "$" + idField));
    }
    return collection.aggregate(Arrays.asList(match, project, group), options);
    //        }
}

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

License:Apache License

@Override
public long getId(String userId, String projectAlias) throws CatalogDBException {
    QueryResult<Document> queryResult = userCollection.find(
            new BsonDocument("projects.alias", new BsonString(projectAlias)).append("id",
                    new BsonString(userId)),
            Projections.fields(Projections.include("projects.id"),
                    Projections.elemMatch("projects", Filters.eq("alias", projectAlias))),
            null);//from www.  ja v a2s  . c o  m
    /*
            QueryResult<DBObject> queryResult = userCollection.find(
        BasicDBObjectBuilder
                .start("projects.alias", projectAlias)
                .append("id", userId).get(),
        BasicDBObjectBuilder.start("projects.id", true)
                .append("projects", new BasicDBObject("$elemMatch", new BasicDBObject("alias", projectAlias))).get(),
        null
            );*/
    User user = parseUser(queryResult);
    if (user == null || user.getProjects().isEmpty()) {
        return -1;
    } else {
        return user.getProjects().get(0).getId();
    }
}

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

License:Apache License

@Override
public String getOwnerId(long projectId) throws CatalogDBException {
    //        DBObject query = new BasicDBObject("projects.id", projectId);
    Bson query = Filters.eq("projects.id", projectId);

    //        DBObject projection = new BasicDBObject("id", "true");
    Bson projection = Projections.include("id");

    //        QueryResult<DBObject> result = userCollection.find(query, projection, null);
    QueryResult<Document> result = userCollection.find(query, projection, null);

    if (result.getResult().isEmpty()) {
        throw CatalogDBException.idNotFound("Project", projectId);
    } else {//from w  w w  .  jav  a 2  s. c  om
        return result.getResult().get(0).get("id").toString();
    }
}

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

License:Apache License

@Override
public QueryResult<Project> get(Query query, QueryOptions options) throws CatalogDBException {
    long startTime = startQuery();
    if (!query.containsKey(QueryParams.STATUS_NAME.key())) {
        query.append(QueryParams.STATUS_NAME.key(), "!=" + Status.TRASHED + ";!=" + Status.DELETED);
    }//from   w  w  w  . ja v  a 2 s.c om
    List<Bson> aggregates = new ArrayList<>();

    aggregates.add(Aggregates.unwind("$projects"));
    aggregates.add(Aggregates.match(parseQuery(query)));

    // Check include
    if (options != null && options.get(QueryOptions.INCLUDE) != null) {
        List<String> includeList = new ArrayList<>();
        List<String> optionsAsStringList = options.getAsStringList(QueryOptions.INCLUDE);
        includeList.addAll(optionsAsStringList.stream().collect(Collectors.toList()));
        if (!includeList.contains(QueryParams.ID.key())) {
            includeList.add(QueryParams.ID.key());
        }

        // Check if they start with projects.
        for (int i = 0; i < includeList.size(); i++) {
            if (!includeList.get(i).startsWith("projects.")) {
                String param = "projects." + includeList.get(i);
                includeList.set(i, param);
            }
        }
        if (includeList.size() > 0) {
            aggregates.add(Aggregates.project(Projections.include(includeList)));
        }
    }

    QueryResult<Project> projectQueryResult = userCollection.aggregate(aggregates, projectConverter, options);

    if (options == null || !options.containsKey(QueryOptions.EXCLUDE)
            || !options.getAsStringList(QueryOptions.EXCLUDE).contains("projects.studies")) {
        for (Project project : projectQueryResult.getResult()) {
            Query studyQuery = new Query(StudyDBAdaptor.QueryParams.PROJECT_ID.key(), project.getId());
            try {
                QueryResult<Study> studyQueryResult = dbAdaptorFactory.getCatalogStudyDBAdaptor()
                        .get(studyQuery, options);
                project.setStudies(studyQueryResult.getResult());
            } catch (CatalogDBException e) {
                e.printStackTrace();
            }
        }
    }

    return endQuery("Get project", startTime, projectQueryResult.getResult());
}

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

License:Apache License

@Override
public QueryResult nativeGet(Query query, QueryOptions options) throws CatalogDBException {
    if (!query.containsKey(QueryParams.STATUS_NAME.key())) {
        query.append(QueryParams.STATUS_NAME.key(), "!=" + Status.TRASHED + ";!=" + Status.DELETED);
    }//from  w  ww. j a  v a  2 s  .  c  om
    List<Bson> aggregates = new ArrayList<>();
    aggregates.add(Aggregates.match(parseQuery(query)));
    aggregates.add(Aggregates.unwind("$projects"));

    // Check include & excludes
    if (options != null && options.get(QueryOptions.INCLUDE) != null) {
        List<String> includeList = new ArrayList<>();
        List<String> optionsAsStringList = options.getAsStringList(QueryOptions.INCLUDE);
        includeList.addAll(optionsAsStringList.stream().collect(Collectors.toList()));

        if (includeList.size() > 0) {
            aggregates.add(Aggregates.project(Projections.include(includeList)));
        }
    }

    QueryResult<Document> projectQueryResult = userCollection.aggregate(aggregates, options);
    ArrayList<Document> returnedProjectList = new ArrayList<>();

    for (Document user : projectQueryResult.getResult()) {
        Document project = (Document) user.get("projects");
        Query studyQuery = new Query(StudyDBAdaptor.QueryParams.PROJECT_ID.key(), project.get("id"));
        QueryResult studyQueryResult = dbAdaptorFactory.getCatalogStudyDBAdaptor().nativeGet(studyQuery,
                options);
        project.remove("studies");
        project.append("studies", studyQueryResult.getResult());
        returnedProjectList.add(project);
    }

    projectQueryResult.setResult(returnedProjectList);

    return projectQueryResult;

}

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

License:Apache License

@Override
public long getStudyId(long sampleId) throws CatalogDBException {
    /*DBObject query = new BasicDBObject(PRIVATE_ID, sampleId);
    BasicDBObject projection = new BasicDBObject(PRIVATE_STUDY_ID, true);
    QueryResult<DBObject> queryResult = sampleCollection.find(query, projection, null);*/
    Bson query = new Document(PRIVATE_ID, sampleId);
    Bson projection = Projections.include(PRIVATE_STUDY_ID);
    QueryResult<Document> queryResult = sampleCollection.find(query, projection, null);

    if (!queryResult.getResult().isEmpty()) {
        Object studyId = queryResult.getResult().get(0).get(PRIVATE_STUDY_ID);
        return studyId instanceof Number ? ((Number) studyId).longValue() : Long.parseLong(studyId.toString());
    } else {/*from   www .j  a  v a 2  s.com*/
        throw CatalogDBException.idNotFound("Sample", sampleId);
    }
}