#####################################################################
## This program is distributed in the hope that it will be useful, ##
## but WITHOUT ANY WARRANTY; without even the implied warranty of ##
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ##
## GNU General Public License for more details. ##
#####################################################################
#' @name Register/update annotation
#' @rdname rgstr_funcs
#' @title Functions for registering & updating annotation information
#'
#' @description
#' These functions are used to register and update the chemical and assay
#' annotation information.
#'
#' @param what Character of length 1, the name of the ID to register or update
#' @param flds Named list, the other fields and their values
#' @param id Integer, the ID value(s) to update
#'
#'
#' @details
#' These functions are used to populate the gtox database with the necessary
#' annotation information to complete the processing. As shown in the package
#' vignette, the package requires some information about the samples and assays
#' before data can be loaded into the gtox database.
#'
#' Depending on what is being registered, different information is required.
#' The following table lists the fields that can be registered/updated by these
#' functions, and the minimal fields required for registering a new ID. (The
#' database table affected is in parentheses.)
#'
#' \itemize{
#' \item asid (assay_source): assay_source_name
#' \item aid (assay): asid, assay_name, assay_footprint
#' \item acid (assay_component): aid, assay_component_name
#' \item aeid (assay_component_endpoint): acid, assay_component_endpoint_name,
#' normalized_data_type
#' \item spid (sample): spid, chid
#' \item chid (chemical): chid, casn
#' \item clib (chemical_library): chid, clib
#' \item *vehicle (vehicle): vehicle_name
#' \item *waid (assay_plate_well): apid, spid, rowi, coli, wllt, vhid, conc
#' \item *apid (assay_plate): aid
#' }
#'
#' Note: The functions accept the abbreviated forms of the names, ie. "aenm"
#' rather than the full "assay_component_endpoint_name." More information about
#' the registration process and all of the fields is available in the vignette.
#' * indicate PMI-specific fields.
#'
#' @examples
#'
#' ## Store the current config settings, so they can be reloaded at the end
#' ## of the examples
#' conf_store <- gtoxConfList()
#' gtoxConfDefault()
#'
#' ## Load current ASID information
#' gtoxLoadAsid()
#'
#' ## Register a new assay source
#' gtoxRegister(what = "asid", flds = list(asnm = "example_asid",
#' asph = "example_phase"))
#'
#' ## Show the newly registered ASID
#' gtoxLoadAsid(add.fld = "assay_source_desc")
#'
#' ## Notice that the newly created ASID does not have an assay_source_desc.
#' ## The field could have been defined during the registration process, but
#' ## can also be updated using gtoxUpdate
#' i1 <- gtoxLoadAsid()[asnm == "example_asid", asid]
#' gtoxUpdate(what = "asid",
#' id = i1,
#' flds = list(assay_source_desc = "example asid description"))
#' gtoxLoadAsid(add.fld = "assay_source_desc")
#'
#' ## Remove the created ASID. Note: Manually deleting primary keys can cause
#' ## serious database problems and should not generally be done.
#' gtoxSendQuery(paste0("DELETE FROM assay_source WHERE asid = ", i1, ";"))
#'
#' ## Reset configuration
#' options(conf_store)
#'
#' @return None
#'
NULL
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