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

Introduction

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

Prototype

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

Source Link

Document

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

Usage

From source file:com.exorath.exodata.impl.IExoDocument.java

License:Apache License

@Override
public Observable<UpdateResult> push(String key, Object value) {
    return update(Updates.push(key, value), true);
}

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

License:Apache License

@Override
public QueryResult<ObjectMap> addAdminSession(Session session) throws CatalogDBException {
    long startTime = startQuery();

    Bson query = new Document(PRIVATE_ID, "METADATA");
    Bson updates = Updates.push("admin.sessions",
            new Document("$each", Arrays.asList(getMongoDBDocument(session, "Session"))).append("$slice", -5));
    QueryResult<UpdateResult> update = metaCollection.update(query, updates, null);

    if (update.first().getModifiedCount() == 0) {
        throw new CatalogDBException("An internal error occurred when logging the admin");
    }/*  w  w  w  . j a  va 2  s.  c  om*/

    ObjectMap resultObjectMap = new ObjectMap();
    resultObjectMap.put("sessionId", session.getId());
    resultObjectMap.put("userId", "admin");
    return endQuery("Login", startTime, Collections.singletonList(resultObjectMap));
}

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

License:Apache License

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

    List<Study> studies = project.getStudies();
    if (studies == null) {
        studies = Collections.emptyList();
    }//from   w w  w .ja  v a  2s  . c o  m
    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()
                .createStudy(project.getId(), study, options).getErrorMsg();
        if (studyErrorMsg != null && !studyErrorMsg.isEmpty()) {
            errorMsg += ", " + study.getAlias() + ":" + studyErrorMsg;
        }
    }
    List<Project> result = getProject(project.getId(), null).getResult();
    return endQuery("Create Project", startTime, result, errorMsg, null);
}

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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);
    }//from  w w  w . j a  v a 2  s  . com

    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

@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.");
    }/*w ww .java 2 s  .co 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));
}

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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  ww .j  av  a2 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));
}

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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  www. ja v  a 2s.  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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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();
    }//w  w  w  .j a v  a 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);
}

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

License:Apache License

@Override
@Deprecated/*from w  w w . jav a  2 s .c o m*/
public QueryResult<AnnotationSet> annotate(long sampleId, AnnotationSet annotationSet, boolean overwrite)
        throws CatalogDBException {
    long startTime = startQuery();

    /*QueryResult<Long> count = sampleCollection.count(
        new BasicDBObject("annotationSets.id", annotationSet.getId()).append(PRIVATE_ID, sampleId));*/
    QueryResult<Long> count = sampleCollection
            .count(new Document("annotationSets.name", annotationSet.getName()).append(PRIVATE_ID, sampleId));
    if (overwrite) {
        if (count.getResult().get(0) == 0) {
            throw CatalogDBException.idNotFound("AnnotationSet", annotationSet.getName());
        }
    } else {
        if (count.getResult().get(0) > 0) {
            throw CatalogDBException.alreadyExists("AnnotationSet", "name", annotationSet.getName());
        }
    }

    /*DBObject object = getDbObject(annotationSet, "AnnotationSet");
            
    DBObject query = new BasicDBObject(PRIVATE_ID, sampleId);*/
    Document object = getMongoDBDocument(annotationSet, "AnnotationSet");

    Bson query = new Document(PRIVATE_ID, sampleId);
    if (overwrite) {
        ((Document) query).put("annotationSets.name", annotationSet.getName());
    } else {
        ((Document) query).put("annotationSets.name", new Document("$ne", annotationSet.getName()));
    }

    /*
    DBObject update;
    if (overwrite) {
    update = new BasicDBObject("$set", new BasicDBObject("annotationSets.$", object));
    } else {
    update = new BasicDBObject("$push", new BasicDBObject("annotationSets", object));
    }
    */

    Bson update;
    if (overwrite) {
        update = Updates.set("annotationSets.$", object);
    } else {
        update = Updates.push("annotationSets", object);
    }

    QueryResult<UpdateResult> queryResult = sampleCollection.update(query, update, null);

    if (queryResult.first().getModifiedCount() != 1) {
        throw CatalogDBException.alreadyExists("AnnotationSet", "name", annotationSet.getName());
    }

    return endQuery("", startTime, Collections.singletonList(annotationSet));
}

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

License:Apache License

@Override
public QueryResult<ObjectMap> addSession(String userId, Session session) throws CatalogDBException {
    long startTime = startQuery();

    Bson query = new Document(QueryParams.ID.key(), userId);
    Bson updates = Updates.push("sessions",
            new Document("$each", Arrays.asList(getMongoDBDocument(session, "Session"))));
    //                        .append("$slice", -50));
    QueryResult<UpdateResult> update = userCollection.update(query, updates, null);

    if (update.first().getModifiedCount() == 0) {
        throw new CatalogDBException("An internal error occurred when logging the user" + userId);
    }//from w w  w  . j  ava 2 s.c o m

    ObjectMap resultObjectMap = new ObjectMap();
    resultObjectMap.put("sessionId", session.getId());
    resultObjectMap.put("userId", userId);
    return endQuery("Login", startTime, Collections.singletonList(resultObjectMap));
}

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