From 26348f72599ed9d12f2e6a14fd0a48695cbb2c1a Mon Sep 17 00:00:00 2001
From: Yilong Zhang <elong0527@gmail.com>
Date: Tue, 24 Oct 2023 23:14:07 +0000
Subject: [PATCH] create meta_inherit function

---
 R/meta_inherit.R                              | 58 +++++++++++++++++++
 man/meta_inherit.Rd                           | 29 ++++++++++
 man/meta_run.Rd                               |  2 +-
 .../test-independent-testing-meta_inherit.R   | 18 ++++++
 4 files changed, 106 insertions(+), 1 deletion(-)
 create mode 100644 R/meta_inherit.R
 create mode 100644 man/meta_inherit.Rd
 create mode 100644 tests/testthat/test-independent-testing-meta_inherit.R

diff --git a/R/meta_inherit.R b/R/meta_inherit.R
new file mode 100644
index 0000000..4429744
--- /dev/null
+++ b/R/meta_inherit.R
@@ -0,0 +1,58 @@
+# Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+# All rights reserved.
+#
+# This file is part of the metalite program.
+#
+# metalite is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# 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.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+#' Inherit meta information by keywords
+#'
+#' @param meta A `meta_adam` object.
+#' @param meta_inherit A `meta_adam` object to be inherit.
+#' @param name A vector of keywords from `meta_inherit` to `meta_adam`.
+#' @param overwrite A logical value to force mapping update.
+#'
+#' @return A metadata object with population defined.
+#'
+#' @examples
+#' meta_adam(population = r2rtf::r2rtf_adsl,
+#'           observation = r2rtf::r2rtf_adae) |>
+#'   meta_inherit(meta_example(), c("apat", "wk12", "ae_summary"))
+#'
+#' @export
+meta_inherit <- function(
+    meta,
+    inherit,
+    name,
+    overwrite = FALSE
+){
+
+  mapping <- list()
+  for(i in seq_along(name)){
+    x <- collect_adam_mapping(inherit, name[i])
+    if(is.null(x)){
+      stop(name[i],": keyword is not defined in the `inherit` meta information")
+    }else{
+      mapping[[i]] <- x
+    }
+  }
+
+  for(i in seq_along(mapping)){
+    if(is.null(collect_adam_mapping(meta, name[[i]])) | overwrite){
+      meta[[mapping[[i]][[".location"]]]][[name[[i]]]] <- mapping[[i]]
+    }
+  }
+
+  meta
+}
\ No newline at end of file
diff --git a/man/meta_inherit.Rd b/man/meta_inherit.Rd
new file mode 100644
index 0000000..8fa87c0
--- /dev/null
+++ b/man/meta_inherit.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/meta_inherit.R
+\name{meta_inherit}
+\alias{meta_inherit}
+\title{Inherit meta information by keywords}
+\usage{
+meta_inherit(meta, inherit, name, overwrite = FALSE)
+}
+\arguments{
+\item{meta}{A \code{meta_adam} object.}
+
+\item{name}{A vector of keywords from \code{meta_inherit} to \code{meta_adam}.}
+
+\item{overwrite}{A logical value to force mapping update.}
+
+\item{meta_inherit}{A \code{meta_adam} object to be inherit.}
+}
+\value{
+A metadata object with population defined.
+}
+\description{
+Inherit meta information by keywords
+}
+\examples{
+meta_adam(population = r2rtf::r2rtf_adsl,
+          observation = r2rtf::r2rtf_adae) |>
+  meta_inherit(meta_example(), c("apat", "wk12", "ae_summary"))
+
+}
diff --git a/man/meta_run.Rd b/man/meta_run.Rd
index d82f35f..3e567e3 100644
--- a/man/meta_run.Rd
+++ b/man/meta_run.Rd
@@ -20,7 +20,7 @@ Executed analysis based on the analysis plan.
 Execute analysis based on the analysis plan
 }
 \examples{
-if(interactive()){
+if (interactive()) {
   meta <- meta_example()
   ae_summary <- function(...) {
     "results of ae_summary"
diff --git a/tests/testthat/test-independent-testing-meta_inherit.R b/tests/testthat/test-independent-testing-meta_inherit.R
new file mode 100644
index 0000000..9860f3e
--- /dev/null
+++ b/tests/testthat/test-independent-testing-meta_inherit.R
@@ -0,0 +1,18 @@
+
+test_that("Inherit keywords", {
+  x <- meta_adam(population = r2rtf::r2rtf_adsl,
+                     observation = r2rtf::r2rtf_adae) |>
+    meta_inherit(meta_example(), c("apat", "wk12", "ae_summary"))
+
+  expect_equal(names(x$population), "apat")
+  expect_equal(names(x$observation), "wk12")
+  expect_equal(names(x$analysis), "ae_summary")
+})
+
+test_that("Wrong key words", {
+  expect_error(
+    meta_adam(population = r2rtf::r2rtf_adsl,
+              observation = r2rtf::r2rtf_adae) |>
+      meta_inherit(meta_example(), c("apat", "wk12", "ae_ser"))
+  )
+})