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.opencga.catalog.db.mongodb.CatalogMongoProjectDBAdaptor.java

License:Apache License

@Override
public QueryResult<AclEntry> getProjectAcl(long projectId, String userId) throws CatalogDBException {
    long startTime = startQuery();
    /*/* w w w. ja  va  2 s  .  com*/
    DBObject match1 = new BasicDBObject("$match", new BasicDBObject("projects.id", projectId));
    DBObject project = new BasicDBObject("$project", BasicDBObjectBuilder
        .start("_id", false)
        .append("projects.acl", true)
        .append("projects.id", true).get());
    DBObject unwind1 = new BasicDBObject("$unwind", "$projects");
    DBObject match2 = new BasicDBObject("$match", new BasicDBObject("projects.id", projectId));
    DBObject unwind2 = new BasicDBObject("$unwind", "$projects.acl");
    DBObject match3 = new BasicDBObject("$match", new BasicDBObject("projects.acl.userId", userId));
            
    */
    Bson match1 = Aggregates.match(Filters.eq("projects.id", projectId));
    //        Bson project = Projections.fields(Projections.excludeId(), Projections.include("projects.acl", "projects.id"));
    Bson project = Aggregates.project(
            Projections.fields(Projections.excludeId(), Projections.include("projects.acl", "projects.id")));
    Bson unwind1 = Aggregates.unwind("$projects");
    Bson match2 = Aggregates.match(Filters.eq("projects.id", projectId));
    Bson unwind2 = Aggregates.unwind("$projects.acl");
    Bson match3 = Aggregates.match(Filters.eq("projects.acl.userId", userId));

    List<Bson> operations = new LinkedList<>();
    operations.add(match1);
    operations.add(project);
    operations.add(unwind1);
    operations.add(match2);
    operations.add(unwind2);
    operations.add(match3);

    QueryResult aggregate = userCollection.aggregate(operations, null);
    List<AclEntry> acls = new LinkedList<>();
    if (aggregate.getNumResults() != 0) {
        //            DBObject aclObject = (DBObject) ((DBObject) ((DBObject) aggregate.getResult().get(0)).get("projects")).get("acl");
        Document aclObject = (Document) ((Document) ((Document) aggregate.getResult().get(0)).get("projects"))
                .get("acl");
        AclEntry acl = parseObject(aclObject, AclEntry.class);
        acls.add(acl);
    }
    return endQuery("get project ACL", startTime, acls);
}

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

License:Apache License

@Override
public QueryResult setProjectAcl(long projectId, AclEntry newAcl) throws CatalogDBException {
    long startTime = startQuery();
    String userId = newAcl.getUserId();
    if (!dbAdaptorFactory.getCatalogUserDBAdaptor().userExists(userId)) {
        throw new CatalogDBException("Can not set ACL to non-existent user: " + userId);
    }/*  www. j  a v a  2  s. c o  m*/

    Document newAclObject = getMongoDBDocument(newAcl, "ACL");
    //DBObject newAclObject = getDbObject(newAcl, "ACL");

    List<AclEntry> projectAcls = getProjectAcl(projectId, userId).getResult();
    Bson query = new Document("projects.id", projectId);
    Bson push = Updates.push("projects.$.acl", newAclObject);
    if (!projectAcls.isEmpty()) { // ensure that there is no acl for that user in that project. pull
        Bson pull = Updates.pull("projects.$.acl", Filters.eq("userId", userId));
        userCollection.update(query, pull, null);
    }
    /*
    DBObject query = new BasicDBObject("projects.id", projectId);
    BasicDBObject push = new BasicDBObject("$push", new BasicDBObject("projects.$.acl", newAclObject));
    if (!projectAcls.isEmpty()) {  // ensure that there is no acl for that user in that project. pull
    DBObject pull = new BasicDBObject("$pull", new BasicDBObject("projects.$.acl", new BasicDBObject("userId", userId)));
    userCollection.update(query, pull, null);
    }
    */
    //Put study
    QueryResult pushResult = userCollection.update(query, push, null);
    return endQuery("Set project acl", startTime, pushResult);
}

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

License:Apache License

private long getDiskUsageByStudy(int studyId) {
    /*//from   w w  w.  java  2 s.  c om
    List<DBObject> operations = Arrays.<DBObject>asList(
        new BasicDBObject(
                "$match",
                new BasicDBObject(
                        PRIVATE_STUDY_ID,
                        studyId
                        //new BasicDBObject("$in",studyIds)
                )
        ),
        new BasicDBObject(
                "$group",
                BasicDBObjectBuilder
                        .start("_id", "$" + PRIVATE_STUDY_ID)
                        .append("diskUsage",
                                new BasicDBObject(
                                        "$sum",
                                        "$diskUsage"
                                )).get()
        )
    );*/
    List<Bson> operations = new ArrayList<>();
    operations.add(Aggregates.match(Filters.eq(PRIVATE_STUDY_ID, studyId)));
    operations.add(Aggregates.group("$" + PRIVATE_STUDY_ID, Accumulators.sum("diskUsage", "$diskUsage")));

    //        Bson match = Aggregates.match(Filters.eq(PRIVATE_STUDY_ID, studyId));
    //        Aggregates.group()

    QueryResult<Document> aggregate = dbAdaptorFactory.getCatalogFileDBAdaptor().getFileCollection()
            .aggregate(operations, null);
    if (aggregate.getNumResults() == 1) {
        Object diskUsage = aggregate.getResult().get(0).get("diskUsage");
        if (diskUsage instanceof Integer) {
            return ((Integer) diskUsage).longValue();
        } else if (diskUsage instanceof Long) {
            return ((Long) diskUsage);
        } else {
            return Long.parseLong(diskUsage.toString());
        }
    } else {
        return 0;
    }
}

---

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

License:Apache License

@Override
public QueryResult<Group> getGroup(long studyId, @Nullable String groupId, List<String> userIds)
        throws CatalogDBException {
    long startTime = startQuery();
    checkStudyId(studyId);// www  .  ja  v a2  s.  c o  m
    for (String userId : userIds) {
        dbAdaptorFactory.getCatalogUserDBAdaptor().checkUserExists(userId);
    }
    if (groupId != null && groupId.length() > 0 && !groupExists(studyId, groupId)) {
        throw new CatalogDBException("Group \"" + groupId + "\" does not exist in study " + studyId);
    }

    /*
    * 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("$" + QueryParams.VARIABLE_SET.key()));
    aggregation.add(Aggregates.match(Filters.eq(QueryParams.VARIABLE_SET_ID.key(), variableSetId)));
    QueryResult<VariableSet> queryResult = studyCollection.aggregate(aggregation, variableSetConverter, new QueryOptions());
    * */
    List<Bson> aggregation = new ArrayList<>();
    aggregation.add(Aggregates.match(Filters.eq(PRIVATE_ID, studyId)));
    aggregation.add(Aggregates.project(Projections.include(QueryParams.GROUPS.key())));
    aggregation.add(Aggregates.unwind("$" + QueryParams.GROUPS.key()));

    //        Document query = new Document(PRIVATE_ID, studyId);
    //        List<Bson> groupQuery = new ArrayList<>();
    if (userIds.size() > 0) {
        aggregation.add(Aggregates.match(Filters.in(QueryParams.GROUP_USER_IDS.key(), userIds)));
        //            groupQuery.add(Filters.in("userIds", userIds));
    }
    if (groupId != null && groupId.length() > 0) {
        aggregation.add(Aggregates.match(Filters.eq(QueryParams.GROUP_NAME.key(), groupId)));
        //            groupQuery.add(Filters.eq("id", groupId));
    }

    //        Bson projection = new Document(QueryParams.GROUPS.key(), new Document("$elemMatch", groupQuery));

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

    //        QueryResult<Document> queryResult = studyCollection.find(query, projection, null);
    List<Study> studies = CatalogMongoDBUtils.parseStudies(queryResult);
    List<Group> groups = new ArrayList<>();
    studies.stream().filter(study -> study.getGroups() != null)
            .forEach(study -> groups.addAll(study.getGroups()));
    return endQuery("getGroup", startTime, groups);
}

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

License:Apache License

@Deprecated
@Override//from   ww  w . j a  v  a2  s  .  com
public QueryResult<Role> getRole(long studyId, String userId, String groupId, String roleId,
        QueryOptions options) throws CatalogDBException {
    long startTime = startQuery();

    Bson query = new Document(PRIVATE_ID, studyId);
    List<Bson> roleQuery = new ArrayList<>();
    List<String> userIds = new ArrayList<>();
    if (userId != null) {
        userIds.add(userId);
    }
    if (groupId != null) {
        userIds.add(groupId);
    }
    if (userIds.size() > 0) {
        roleQuery.add(Filters.in("userIds", userIds));
    }
    if (roleId != null) {
        roleQuery.add(Filters.eq("id", roleId));
    }
    Bson projection = Projections.elemMatch(QueryParams.ROLES.key(), Filters.and(roleQuery));

    QueryResult<Document> queryResult = studyCollection.find(query, projection,
            filterOptions(options, FILTER_ROUTE_STUDIES + QueryParams.ROLES.key() + "."));
    List<Study> studies = CatalogMongoDBUtils.parseStudies(queryResult);
    List<Role> roles = new ArrayList<>(1);
    //        studies.stream().filter(study -> study.getRoles() != null).forEach(study -> {
    //            roles.addAll(study.getRoles());
    //        });
    return endQuery("getRole", startTime, roles);
}

---

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

License:Apache License

@Override
public void removeUsersFromGroup(long studyId, String groupId, List<String> members) throws CatalogDBException {
    for (String member : members) {
        dbAdaptorFactory.getCatalogUserDBAdaptor().checkUserExists(member);
    }//from w w w.java 2  s.c o  m

    Bson and = Filters.and(Filters.eq(PRIVATE_ID, studyId), Filters.eq("groups.name", groupId));
    Bson pull = Updates.pullAll("groups.$.userIds", members);
    QueryResult<UpdateResult> update = studyCollection.update(and, pull, null);
    if (update.first().getModifiedCount() != 1) {
        throw new CatalogDBException("Unable to remove members from group " + groupId);
    }
}

---

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

License:Apache License

@Override
public Long variableSetExists(long variableSetId) {
    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)));
    QueryResult<VariableSet> queryResult = studyCollection.aggregate(aggregation, variableSetConverter,
            new QueryOptions());

    return (long) queryResult.getResult().size();
}

---

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

License:Apache License

@Override
public QueryResult<VariableSet> createVariableSet(long studyId, VariableSet variableSet)
        throws CatalogDBException {
    long startTime = startQuery();

    if (variableSetExists(variableSet.getName(), studyId) > 0) {
        throw new CatalogDBException("VariableSet { name: '" + variableSet.getName() + "'} already exists.");
    }//from   www.j a v  a 2s .c  o  m

    long variableSetId = getNewId();
    variableSet.setId(variableSetId);
    Document object = getMongoDBDocument(variableSet, "VariableSet");

    Bson bsonQuery = Filters.eq(PRIVATE_ID, studyId);
    Bson update = Updates.push("variableSets", object);
    QueryResult<UpdateResult> queryResult = studyCollection.update(bsonQuery, update, null);

    if (queryResult.first().getModifiedCount() == 0) {
        throw new CatalogDBException(
                "createVariableSet: Could not create a new variable set in study " + studyId);
    }

    return endQuery("createVariableSet", startTime, getVariableSet(variableSetId, null));
}

---

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

License:Apache License

@Override
public QueryResult<VariableSet> addFieldToVariableSet(long variableSetId, Variable variable)
        throws CatalogDBException {
    long startTime = startQuery();

    checkVariableSetExists(variableSetId);
    checkVariableNotInVariableSet(variableSetId, variable.getName());

    Bson bsonQuery = Filters.eq(QueryParams.VARIABLE_SET_ID.key(), variableSetId);
    Bson update = Updates.push(QueryParams.VARIABLE_SET.key() + ".$." + VariableSetParams.VARIABLE.key(),
            getMongoDBDocument(variable, "variable"));
    QueryResult<UpdateResult> queryResult = studyCollection.update(bsonQuery, update, null);
    if (queryResult.first().getModifiedCount() == 0) {
        throw CatalogDBException.updateError("VariableSet", variableSetId);
    }/*from  w w  w.j  a  v  a  2  s.c o  m*/
    if (variable.isRequired()) {
        dbAdaptorFactory.getCatalogSampleDBAdaptor().addVariableToAnnotations(variableSetId, variable);
        dbAdaptorFactory.getCatalogCohortDBAdaptor().addVariableToAnnotations(variableSetId, variable);
        dbAdaptorFactory.getCatalogIndividualDBAdaptor().addVariableToAnnotations(variableSetId, variable);
    }
    return endQuery("Add field to variable set", startTime, getVariableSet(variableSetId, null));
}

---

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

License:Apache License

@Override
public QueryResult<VariableSet> renameFieldVariableSet(long variableSetId, String oldName, String newName)
        throws CatalogDBException {
    long startTime = startQuery();

    checkVariableSetExists(variableSetId);
    checkVariableInVariableSet(variableSetId, oldName);
    checkVariableNotInVariableSet(variableSetId, newName);

    // The field can be changed if we arrive to this point.
    // 1. we obtain the variable
    Variable variable = getVariable(variableSetId, oldName);

    // 2. we take it out from the array.
    Bson bsonQuery = Filters.eq(QueryParams.VARIABLE_SET_ID.key(), variableSetId);
    Bson update = Updates.pull(QueryParams.VARIABLE_SET.key() + ".$." + VariableSetParams.VARIABLE.key(),
            Filters.eq("name", oldName));
    QueryResult<UpdateResult> queryResult = studyCollection.update(bsonQuery, update, null);

    if (queryResult.first().getModifiedCount() == 0) {
        throw new CatalogDBException(
                "VariableSet {id: " + variableSetId + "} - Could not rename the field " + oldName);
    }//from w  w w  .  ja  va2s  .c  o  m
    if (queryResult.first().getModifiedCount() > 1) {
        throw new CatalogDBException("VariableSet {id: " + variableSetId
                + "} - An unexpected error happened when extracting the "
                + "variable from the variableSet to do the rename. Please, report this error to the OpenCGA developers.");
    }

    // 3. we change the name in the variable object and push it again in the array.
    variable.setName(newName);
    update = Updates.push(QueryParams.VARIABLE_SET.key() + ".$." + VariableSetParams.VARIABLE.key(),
            getMongoDBDocument(variable, "Variable"));
    queryResult = studyCollection.update(bsonQuery, update, null);

    if (queryResult.first().getModifiedCount() != 1) {
        throw new CatalogDBException("VariableSet {id: " + variableSetId
                + "} - A critical error happened when trying to rename one "
                + "of the variables of the variableSet object. Please, report this error to the OpenCGA developers.");
    }

    // 4. Change the field id in the annotations
    dbAdaptorFactory.getCatalogSampleDBAdaptor().renameAnnotationField(variableSetId, oldName, newName);
    dbAdaptorFactory.getCatalogCohortDBAdaptor().renameAnnotationField(variableSetId, oldName, newName);

    return endQuery("Rename field in variableSet", startTime, getVariableSet(variableSetId, null));
}

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