R/methodInsertTable.R

In omopgenerics: Methods and Classes for the OMOP Common Data Model

# Copyright 2023 DARWIN EU (C)
#
# This file is part of omopgenerics
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

#' Insert a table to a cdm object.
#'
#' @param cdm A cdm reference or the source of a cdm reference.
#' @param name Name of the table to insert.
#' @param table Table to insert to the cdm.
#' @param overwrite Whether to overwrite an existent table.
#' @param temporary Whether to create a temporary table.
#'
#' @export
#'
#' @return The cdm reference.
#' library(omopgenerics)
#' library(dplyr, warn.conflicts = FALSE)
#'
#' person <- tibble(
#'   person_id = 1, gender_concept_id = 0, year_of_birth = 1990,
#'   race_concept_id = 0, ethnicity_concept_id = 0
#' )
#' observation_period <- tibble(
#'   observation_period_id = 1, person_id = 1,
#'   observation_period_start_date = as.Date("2000-01-01"),
#'   observation_period_end_date = as.Date("2023-12-31"),
#'   period_type_concept_id = 0
#' )
#' cdm <- cdmFromTables(
#'   tables = list("person" = person, "observation_period" = observation_period),
#'   cdmName = "my_example_cdm"
#' )
#'
#' x <- tibble(a = 1)
#'
#' cdm <- insertTable(cdm = cdm, name = "new_table", table = x)
#'
#' cdm$new_table
#'
insertTable <- function(cdm, name, table, overwrite = TRUE, temporary = FALSE) {
  assertCharacter(name, length = 1, minNumCharacter = 1, na = TRUE)
  assertClass(table, "data.frame")
  table <- dplyr::as_tibble(table)
  assertLogical(temporary, length = 1)
  UseMethod("insertTable")
}

#' @export
insertTable.cdm_reference <- function(cdm, name, table, overwrite = TRUE, temporary = FALSE) {
  value <- insertTable(
    cdm = cdmSource(cdm), name = name, table = table, overwrite = overwrite
  )
  attr(value, "cdm_reference") <- cdm
  if (temporary) {
    value <- value |> dplyr::compute(temporary = TRUE)
     dropTable(cdm = cdm, name = name)
  }
  cdm[[name]] <- value
  return(cdm)
}

#' @export
insertTable.local_cdm <- function(cdm, name, table, ...) {
  newCdmTable(table = table, src = cdm, name = name)
}