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.IndividualMongoDBAdaptor.java

License:Apache License

private QueryResult<Individual> remove(int id, boolean force) throws CatalogDBException {
    long startTime = startQuery();
    checkId(id);//from   w w  w.jav a2  s.co m
    QueryResult<Individual> individual = get(id, new QueryOptions());
    Bson bson = Filters.eq(QueryParams.ID.key(), id);
    QueryResult<DeleteResult> remove = individualCollection.remove(bson, null);
    return endQuery("Delete individual", startTime, individual);
}

---

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

License:Apache License

public long getNewAutoIncrementId(String field) { //, MongoDBCollection metaCollection
    //        QueryResult<BasicDBObject> result = metaCollection.findAndModify(
    //                new BasicDBObject("_id", CatalogMongoDBAdaptor.METADATA_OBJECT_ID),  //Query
    //                new BasicDBObject(field, true),  //Fields
    //                null,
    //                new BasicDBObject("$inc", new BasicDBObject(field, 1)), //Update
    //                new QueryOptions("returnNew", true),
    //                BasicDBObject.class
    //        );/*w  ww.j av a  2  s  .c o m*/

    Bson query = Filters.eq(PRIVATE_ID, MongoDBAdaptorFactory.METADATA_OBJECT_ID);
    Document projection = new Document(field, true);
    Bson inc = Updates.inc(field, 1L);
    QueryOptions queryOptions = new QueryOptions("returnNew", true);
    QueryResult<Document> result = metaCollection.findAndUpdate(query, projection, null, inc, queryOptions);
    //        return (int) Float.parseFloat(result.getResult().get(0).get(field).toString());
    return result.getResult().get(0).getLong(field);
}

---

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

License:Apache License

@Override
public QueryResult<StudyAclEntry> getDaemonAcl(List<String> members) throws CatalogDBException {
    long startTime = startQuery();

    Bson match = Aggregates.match(Filters.eq(PRIVATE_ID, "METADATA"));
    Bson unwind = Aggregates.unwind("$" + CohortDBAdaptor.QueryParams.ACL.key());
    Bson match2 = Aggregates.match(Filters.in(CohortDBAdaptor.QueryParams.ACL_MEMBER.key(), members));
    Bson project = Aggregates.project(//from   ww w .ja  v a 2s.  c  om
            Projections.include(CohortDBAdaptor.QueryParams.ID.key(), CohortDBAdaptor.QueryParams.ACL.key()));

    QueryResult<Document> aggregate = metaCollection.aggregate(Arrays.asList(match, unwind, match2, project),
            null);
    StudyAclEntry result = null;
    if (aggregate.getNumResults() == 1) {
        result = parseObject(((Document) aggregate.getResult().get(0).get("acl")), StudyAclEntry.class);
    }
    return endQuery("get daemon Acl", startTime, Arrays.asList(result));
}

---

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

License:Apache License

@Deprecated
static long getNewAutoIncrementId(String field, MongoDBCollection metaCollection) {
    //        QueryResult<BasicDBObject> result = metaCollection.findAndModify(
    //                new BasicDBObject("_id", CatalogMongoDBAdaptor.METADATA_OBJECT_ID),  //Query
    //                new BasicDBObject(field, true),  //Fields
    //                null,
    //                new BasicDBObject("$inc", new BasicDBObject(field, 1)), //Update
    //                new QueryOptions("returnNew", true),
    //                BasicDBObject.class
    //        );//from  www  .j av  a  2  s .  co m

    Bson query = Filters.eq("_id", MongoDBAdaptorFactory.METADATA_OBJECT_ID);
    Document projection = new Document(field, true);
    Bson inc = Updates.inc(field, 1);
    QueryOptions queryOptions = new QueryOptions("returnNew", true);
    QueryResult<Document> result = metaCollection.findAndUpdate(query, projection, null, inc, queryOptions);
    //        return (int) Float.parseFloat(result.getResult().get(0).get(field).toString());
    return result.getResult().get(0).getInteger(field);
}

---

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

License:Apache License

static QueryResult<Document> getAcl(long id, List<String> members, MongoDBCollection collection, Logger logger)
        throws CatalogDBException {
    List<Bson> aggregation = new ArrayList<>();
    aggregation.add(Aggregates.match(Filters.eq(PRIVATE_ID, id)));
    aggregation.add(Aggregates.project(/*from   w w w .  j a v  a  2s  .  c  o m*/
            Projections.include(FileDBAdaptor.QueryParams.ID.key(), FileDBAdaptor.QueryParams.ACL.key())));
    aggregation.add(Aggregates.unwind("$" + FileDBAdaptor.QueryParams.ACL.key()));

    List<Bson> filters = new ArrayList<>();
    if (members != null && members.size() > 0) {
        filters.add(Filters.in(FileDBAdaptor.QueryParams.ACL_MEMBER.key(), members));
    }

    if (filters.size() > 0) {
        Bson filter = filters.size() == 1 ? filters.get(0) : Filters.and(filters);
        aggregation.add(Aggregates.match(filter));
    }

    for (Bson bson : aggregation) {
        logger.debug("Get Acl: {}",
                bson.toBsonDocument(Document.class, com.mongodb.MongoClient.getDefaultCodecRegistry()));
    }

    return collection.aggregate(aggregation, null);
}

---

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

License:Apache License

public static void addAnnotationQueryFilter(String optionKey, Query query, Map<String, Variable> variableMap,
        List<Bson> annotationSetFilter) throws CatalogDBException {
    // Annotation Filter
    final String sepOr = ",";

    String annotationKey;/* w ww.  ja  v  a2s  . com*/
    if (optionKey.startsWith("annotation.")) {
        annotationKey = optionKey.substring("annotation.".length());
    } else {
        throw new CatalogDBException(
                "Wrong annotation query. Expects: {\"annotation.<variable>\" , <operator><value> } ");
    }
    String annotationValue = query.getString(optionKey);

    final String variableId;
    final String route;
    if (annotationKey.contains(".")) {
        String[] variableIdRoute = annotationKey.split("\\.", 2);
        variableId = variableIdRoute[0];
        route = "." + variableIdRoute[1];
    } else {
        variableId = annotationKey;
        route = "";
    }
    String[] values = annotationValue.split(sepOr);

    QueryParam.Type type = QueryParam.Type.TEXT;

    if (variableMap != null) {
        Variable variable = variableMap.get(variableId);
        if (variable == null) {
            throw new CatalogDBException("Variable \"" + variableId + "\" not found in variableSet ");
        }
        Variable.VariableType variableType = variable.getType();
        if (variable.getType() == Variable.VariableType.OBJECT) {
            String[] routes = route.split("\\.");
            for (String r : routes) {
                if (variable.getType() != Variable.VariableType.OBJECT) {
                    throw new CatalogDBException("Unable to query variable " + annotationKey);
                }
                if (variable.getVariableSet() != null) {
                    Map<String, Variable> subVariableMap = variable.getVariableSet().stream()
                            .collect(Collectors.toMap(Variable::getName, Function.<Variable>identity()));
                    if (subVariableMap.containsKey(r)) {
                        variable = subVariableMap.get(r);
                        variableType = variable.getType();
                    }
                } else {
                    variableType = Variable.VariableType.TEXT;
                    break;
                }
            }
        }
        if (variableType == Variable.VariableType.BOOLEAN) {
            type = QueryParam.Type.BOOLEAN;

        } else if (variableType == Variable.VariableType.NUMERIC) {
            type = QueryParam.Type.DECIMAL;
        }
    }

    List<Bson> valueList = addCompQueryFilter(type, "value" + route, Arrays.asList(values), new ArrayList<>());
    annotationSetFilter.add(
            Filters.elemMatch("annotations", Filters.and(Filters.eq("name", variableId), valueList.get(0))));
}

---

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

License:Apache License

@Override
public QueryResult<Project> insert(Project project, String userId, QueryOptions options)
        throws CatalogDBException {
    long startTime = startQuery();

    List<Study> studies = project.getStudies();
    if (studies == null) {
        studies = Collections.emptyList();
    }//from ww w.  j  a va 2 s.  c  om
    project.setStudies(Collections.<Study>emptyList());

    // Check if project.alias already exists.
    //        DBObject countQuery = BasicDBObjectBuilder
    //                .start("id", userId)
    //                .append("projects.alias", project.getAlias())
    //                .get();
    Bson countQuery = Filters.and(Filters.eq("id", userId), Filters.eq("projects.alias", project.getAlias()));
    QueryResult<Long> count = userCollection.count(countQuery);
    if (count.getResult().get(0) != 0) {
        throw new CatalogDBException(
                "Project {alias:\"" + project.getAlias() + "\"} already exists in this user");
    }
    //        if(getProjectId(userId, project.getAlias()) >= 0){
    //            throw new CatalogManagerException( "Project {alias:\"" + project.getAlias() + "\"} already exists in this user");
    //        }

    //Generate json
    //        int projectId = CatalogMongoDBUtils.getNewAutoIncrementId(metaCollection);
    long projectId = dbAdaptorFactory.getCatalogMetaDBAdaptor().getNewAutoIncrementId();
    project.setId(projectId);
    //        DBObject query = new BasicDBObject("id", userId);
    //        query.put("projects.alias", new BasicDBObject("$ne", project.getAlias()));
    Bson query = Filters.and(Filters.eq("id", userId), Filters.ne("projects.alias", project.getAlias()));

    Document projectDocument = projectConverter.convertToStorageType(project);
    //        DBObject update = new BasicDBObject("$push", new BasicDBObject("projects", projectDBObject));
    Bson update = Updates.push("projects", projectDocument);

    //Update object
    //        QueryResult<WriteResult> queryResult = userCollection.update(query, update, null);
    QueryResult<UpdateResult> queryResult = userCollection.update(query, update, null);

    if (queryResult.getResult().get(0).getModifiedCount() == 0) { // Check if the project has been inserted
        throw new CatalogDBException(
                "Project {alias:\"" + project.getAlias() + "\"} already exists in this user");
    }

    String errorMsg = "";
    for (Study study : studies) {
        String studyErrorMsg = dbAdaptorFactory.getCatalogStudyDBAdaptor()
                .insert(project.getId(), study, options).getErrorMsg();
        if (studyErrorMsg != null && !studyErrorMsg.isEmpty()) {
            errorMsg += ", " + study.getAlias() + ":" + studyErrorMsg;
        }
    }
    List<Project> result = get(project.getId(), null).getResult();
    return endQuery("Create Project", startTime, result, errorMsg, null);
}

---

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

License:Apache License

@Override
public QueryResult renameAlias(long projectId, String newProjectAlias) throws CatalogDBException {
    long startTime = startQuery();
    //        String projectOwner = getProjectOwner(projectId);
    ////  w w  w  .j av  a 2s  .  c o m
    //        int collisionProjectId = getProjectId(projectOwner, newProjectAlias);
    //        if (collisionProjectId != -1) {
    //            throw new CatalogManagerException("Couldn't rename project alias, alias already used in the same user");
    //        }

    QueryResult<Project> projectResult = get(projectId, null); // if projectId doesn't exist, an exception is raised
    Project project = projectResult.getResult().get(0);

    //String oldAlias = project.getAlias();
    project.setAlias(newProjectAlias);

    /*
    DBObject query = BasicDBObjectBuilder
        .start("projects.id", projectId)
        .append("projects.alias", new BasicDBObject("$ne", newProjectAlias))    // check that any other project in the user has
        // the new name
        .get();
    DBObject update = new BasicDBObject("$set",
        new BasicDBObject("projects.$.alias", newProjectAlias));
    */
    Bson query = Filters.and(Filters.eq("projects.id", projectId),
            Filters.ne("projects.alias", newProjectAlias));
    Bson update = Updates.set("projects.$.alias", newProjectAlias);

    QueryResult<UpdateResult> result = userCollection.update(query, update, null);
    if (result.getResult().get(0).getModifiedCount() == 0) { //Check if the the study has been inserted
        throw new CatalogDBException("Project {alias:\"" + newProjectAlias + "\"} already exists");
    }
    return endQuery("rename project alias", startTime, result);
}

---

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   ww w  . ja  va2 s . 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   ww w.  jav  a  2  s .c  o m*/
        return result.getResult().get(0).get("id").toString();
    }
}

---

• «
• 1
• 2
• 3
• 4
• 5
• 6
• 7
• 8
• 9
• 10
• 11
• 12
• 13
• 14
• 15
• 16
• 17
• 18
• 19
• 20
• 21
• 22
• 23
• 24
• 25
• 26
• 27
• »