R.Admin-methods.R Maven / Gradle / Ivy

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# WARNING: AUTOGENERATED CODE
#
#    This code was generated by a tool.
#    
#    Manual changes to this file may cause unexpected behavior in your application.
#    Manual changes to this file will be overwritten if the code is regenerated.


# ##############################################################################
#' AdminClient methods
#' @include AllClasses.R
#' @include AllGenerics.R
#' @include commons.R

#' @description This function implements the OpenCGA calls for managing Admin.

#' The following table summarises the available *actions* for this client:
#'
#' | endpointName | Endpoint WS | parameters accepted |
#' | -- | :-- | --: |
#' | groupByAudit | /{apiVersion}/admin/audit/groupBy | count, limit, fields[*], entity[*], action, before, after, date |
#' | installCatalog | /{apiVersion}/admin/catalog/install | body[*] |
#' | jwtCatalog | /{apiVersion}/admin/catalog/jwt | organization, body[*] |
#' | createUsers | /{apiVersion}/admin/users/create | body[*] |
#' | importUsers | /{apiVersion}/admin/users/import | organization, body[*] |
#' | permissionsUsers | /{apiVersion}/admin/users/permissions | study, entryIds, permissions, category |
#' | searchUsers | /{apiVersion}/admin/users/search | include, exclude, limit, skip, count, organization, user, authenticationId |
#' | syncUsers | /{apiVersion}/admin/users/sync | organization, body[*] |
#' | usersUpdateGroups | /{apiVersion}/admin/users/{user}/groups/update | organization, user[*], action, body[*] |
#'
#' @md
#' @seealso \url{http://docs.opencb.org/display/opencga/Using+OpenCGA} and the RESTful API documentation
#' \url{http://bioinfo.hpc.cam.ac.uk/opencga-prod/webservices/}
#' [*]: Required parameter
#' @export

setMethod("adminClient", "OpencgaR", function(OpencgaR, user, endpointName, params=NULL, ...) {
    switch(endpointName,

        #' @section Endpoint /{apiVersion}/admin/audit/groupBy:
        #' Group by operation.
        #' @param count Count the number of elements matching the group.
        #' @param limit Maximum number of documents (groups) to be returned.
        #' @param fields Comma separated list of fields by which to group by.
        #' @param entity Entity to be grouped by. Allowed values: ['AUDIT NOTE ORGANIZATION USER PROJECT STUDY FILE SAMPLE JOB INDIVIDUAL COHORT DISEASE_PANEL FAMILY CLINICAL_ANALYSIS INTERPRETATION VARIANT ALIGNMENT CLINICAL EXPRESSION RGA FUNCTIONAL']
        #' @param action Action performed.
        #' @param before Object before update.
        #' @param after Object after update.
        #' @param date Date <,<=,>,>=(Format: yyyyMMddHHmmss) and yyyyMMddHHmmss-yyyyMMddHHmmss.
        groupByAudit=fetchOpenCGA(object=OpencgaR, category="admin", categoryId=NULL, subcategory="audit",
                subcategoryId=NULL, action="groupBy", params=params, httpMethod="GET",
                as.queryParam=c("fields","entity"), ...),

        #' @section Endpoint /{apiVersion}/admin/catalog/install:
        #' Install OpenCGA database.
        #' @param data JSON containing the mandatory parameters.
        installCatalog=fetchOpenCGA(object=OpencgaR, category="admin", categoryId=NULL, subcategory="catalog",
                subcategoryId=NULL, action="install", params=params, httpMethod="POST", as.queryParam=NULL, ...),

        #' @section Endpoint /{apiVersion}/admin/catalog/jwt:
        #' Change JWT secret key.
        #' @param organization Organization id.
        #' @param data JSON containing the parameters.
        jwtCatalog=fetchOpenCGA(object=OpencgaR, category="admin", categoryId=NULL, subcategory="catalog",
                subcategoryId=NULL, action="jwt", params=params, httpMethod="POST", as.queryParam=NULL, ...),

        #' @section Endpoint /{apiVersion}/admin/users/create:
        #' Create a new user.
        #' @param data JSON containing the parameters.
        createUsers=fetchOpenCGA(object=OpencgaR, category="admin", categoryId=NULL, subcategory="users",
                subcategoryId=NULL, action="create", params=params, httpMethod="POST", as.queryParam=NULL, ...),

        #' @section Endpoint /{apiVersion}/admin/users/import:
        #' Import users or a group of users from LDAP or AAD.
        #' @param organization Organization id.
        #' @param data JSON containing the parameters.
        importUsers=fetchOpenCGA(object=OpencgaR, category="admin", categoryId=NULL, subcategory="users",
                subcategoryId=NULL, action="import", params=params, httpMethod="POST", as.queryParam=NULL, ...),

        #' @section Endpoint /{apiVersion}/admin/users/permissions:
        #' User permissions.
        #' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
        #' @param entryIds Comma separated list of entry ids.
        #' @param permissions Comma separated list of permissions to be retrieved.
        #' @param category Category corresponding to the id's provided.
        permissionsUsers=fetchOpenCGA(object=OpencgaR, category="admin", categoryId=NULL, subcategory="users",
                subcategoryId=NULL, action="permissions", params=params, httpMethod="GET", as.queryParam=NULL, ...),

        #' @section Endpoint /{apiVersion}/admin/users/search:
        #' User search method.
        #' @param include Fields included in the response, whole JSON path must be provided.
        #' @param exclude Fields excluded in the response, whole JSON path must be provided.
        #' @param limit Number of results to be returned.
        #' @param skip Number of results to skip.
        #' @param count Get the total number of results matching the query. Deactivated by default.
        #' @param organization Organization id.
        #' @param user User ID.
        #' @param authenticationId Authentication origin ID.
        searchUsers=fetchOpenCGA(object=OpencgaR, category="admin", categoryId=NULL, subcategory="users",
                subcategoryId=NULL, action="search", params=params, httpMethod="GET", as.queryParam=NULL, ...),

        #' @section Endpoint /{apiVersion}/admin/users/sync:
        #' Synchronise a group of users from an authentication origin with a group in a study from catalog.
        #' @param organization Organization id.
        #' @param data JSON containing the parameters.
        syncUsers=fetchOpenCGA(object=OpencgaR, category="admin", categoryId=NULL, subcategory="users",
                subcategoryId=NULL, action="sync", params=params, httpMethod="POST", as.queryParam=NULL, ...),

        #' @section Endpoint /{apiVersion}/admin/users/{user}/groups/update:
        #' Add or remove users from existing groups.
        #' @param organization Organization id.
        #' @param user User ID.
        #' @param action Action to be performed: ADD or REMOVE user to/from groups. Allowed values: ['ADD REMOVE']
        #' @param data JSON containing the parameters.
        usersUpdateGroups=fetchOpenCGA(object=OpencgaR, category="admin/users", categoryId=user, subcategory="groups",
                subcategoryId=NULL, action="update", params=params, httpMethod="POST", as.queryParam=NULL, ...),
    )
})