From 72ea59b617809396f1174f7b96877c9f00a453ae Mon Sep 17 00:00:00 2001
From: Lukas Gessl <lukas.gessl@stud.uni-regensburg.de>
Date: Mon, 11 Dec 2023 16:02:33 +0000
Subject: [PATCH] write and test prepend_to_save_dir()

---
 NAMESPACE                       |  1 +
 R/data_spec.R                   | 22 ++++++++++++++++++++++
 man/prepend_to_save_dir.Rd      | 23 +++++++++++++++++++++++
 tests/testthat/test-data_spec.R | 10 ++++++++++
 4 files changed, 56 insertions(+)
 create mode 100644 man/prepend_to_save_dir.Rd
 create mode 100644 tests/testthat/test-data_spec.R

diff --git a/NAMESPACE b/NAMESPACE
index f54667e..879a585 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -10,6 +10,7 @@ export(mock_data_from_existing)
 export(prepare)
 export(prepare_and_fit)
 export(prepare_and_predict)
+export(prepend_to_save_dir)
 export(qc_prepare)
 export(qc_preprocess)
 export(read)
diff --git a/R/data_spec.R b/R/data_spec.R
index daeb44c..4aeabc8 100644
--- a/R/data_spec.R
+++ b/R/data_spec.R
@@ -86,4 +86,26 @@ DataSpec <- function(
         gene_id_col = gene_id_col
     )
     return(data_spec)
+}
+
+
+#' @title To every `ModelSpec` in a list of `ModelSpec`s, prepend a fixed directory to the
+#' `save_dir` attribute
+#' @description Often one specifies the models in general, for all data sets. If you fit the 
+#' models to a specific data set (say `"mock"`), you might want to prepend a fixed directory 
+#' like `"results/mock"` to the `save_dir` attribute of all `ModelSpec`s in the list.
+#' @param model_spec_list list of `ModelSpec`s.
+#' @param dir string. The directory to prepend to the `save_dir` attribute of all 
+#' `ModelSpec`s in `model_spec_list`.
+#' @return A list of `ModelSpec`s, with `dir` prepended to the `save_dir` attribute.
+#' @export
+prepend_to_save_dir <- function(
+    model_spec_list, 
+    dir
+){
+    stopifnot(is.character(dir))
+    for(i in seq_along(model_spec_list)){
+        model_spec_list[[i]]$save_dir <- file.path(dir, model_spec_list[[i]]$save_dir)
+    }
+    return(model_spec_list)
 }
\ No newline at end of file
diff --git a/man/prepend_to_save_dir.Rd b/man/prepend_to_save_dir.Rd
new file mode 100644
index 0000000..a771409
--- /dev/null
+++ b/man/prepend_to_save_dir.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_spec.R
+\name{prepend_to_save_dir}
+\alias{prepend_to_save_dir}
+\title{To every \code{ModelSpec} in a list of \code{ModelSpec}s, prepend a fixed directory to the
+\code{save_dir} attribute}
+\usage{
+prepend_to_save_dir(model_spec_list, dir)
+}
+\arguments{
+\item{model_spec_list}{list of \code{ModelSpec}s.}
+
+\item{dir}{string. The directory to prepend to the \code{save_dir} attribute of all
+\code{ModelSpec}s in \code{model_spec_list}.}
+}
+\value{
+A list of \code{ModelSpec}s, with \code{dir} prepended to the \code{save_dir} attribute.
+}
+\description{
+Often one specifies the models in general, for all data sets. If you fit the
+models to a specific data set (say \code{"mock"}), you might want to prepend a fixed directory
+like \code{"results/mock"} to the \code{save_dir} attribute of all \code{ModelSpec}s in the list.
+}
diff --git a/tests/testthat/test-data_spec.R b/tests/testthat/test-data_spec.R
new file mode 100644
index 0000000..aafdf2f
--- /dev/null
+++ b/tests/testthat/test-data_spec.R
@@ -0,0 +1,10 @@
+test_that("prepend_to_save_dir() works", {
+
+  model_spec_list = list(
+    ModelSpec("mock1", fitter = zeroSum::zeroSum, save_dir = "mock1"),
+    ModelSpec("mock2", fitter = zeroSum::zeroSum, save_dir = "mock2")
+  )
+  expect_silent(new_msl <- prepend_to_save_dir(model_spec_list, "prepend_me"))
+  expect_equal(new_msl[[1]]$save_dir, "prepend_me/mock1")
+  expect_equal(new_msl[[2]]$save_dir, "prepend_me/mock2")
+})