Implementation of reload function (#18)

* added reload function for dsoParams

* version bump

* added export

* implementation of setMethod for reload

* fixed error check and added additional explanation

* err stage_dir/ stage_path

* fixed stage_path after reload

* updated readme

* pre-commit autofixes

* Update CHANGELOG.md

version bump

* Update DESCRIPTION

version bump to 0.5.0

* description update

* pre-commit autofixes

---------

Co-authored-by: Tom Schwarzl <[email protected]>
Co-authored-by: tschwarzl <[email protected]>

CHANGELOG.md

@@ -4,8 +4,16 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v0.5.0
+
+### New Features
+
+-   Introduced `reload()` function for dsoParams
+
 ## v0.4.4
 
+### Improvements
+
 -   Improved error handling for `read_params()`
 
 ## v0.4.3

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dso
 Type: Package
 Title: dso R companion package
-Version: 0.4.4
+Version: 0.5.0
 Author: Daniel Schreyer<[email protected]>,
     Gregor Sturm<[email protected]>,
     Thomas Schwarzl<[email protected]>

NAMESPACE

@@ -8,11 +8,13 @@ export(create_stage)
 export(dsoParams)
 export(init)
 export(read_params)
+export(reload)
 export(safe_get)
 export(set_stage)
 export(stage_here)
 exportClasses(dsoParams)
 exportMethods(as.list)
+exportMethods(reload)
 exportMethods(show)
 importFrom(glue,glue)
 importFrom(here,here)

R/class-dsoParams.R

@@ -109,3 +109,30 @@ setMethod(
     })
   }
 )
+
+
+#' @title reload function
+#' @description
+#'
+#' Generic for function reload
+#'
+#' @param object dsoParams config object
+#' @export
+setGeneric("reload", function(object,...) standardGeneric("reload"))
+
+
+#' @title reload dso params
+#' @description
+#' reloads the current dsoParams config into object
+#'
+#' @param object dsoParams object
+#' @export
+setMethod("reload", "dsoParams", function(object) {
+  if (!inherits(object, "dsoParams")) {
+    stop("The object is not of class 'dsoParams'")
+  }
+
+  object <<- read_params()
+
+  invisible(object)
+})

R/read_params.R

@@ -7,14 +7,37 @@
 #' is any subdirectory of the project root). The function recompiles params.in.yaml to params.yaml on-the-fly
 #' to ensure that up-to-date params are always loaded.
 #'
-#' @param stage_path relative path to stage directory from project root
+#' @param stage_path relative path to stage directory from project root, when NULL, already set stage path will be taken from the config_environment
 #' @param return_list returns a list if TRUE, by default it return `dsoParams` class which is a list with secure access
 #'
 #' @return parameters as list of list as `dsoParams` or conventional list when `return_list` is set.
 #' @importFrom yaml read_yaml
 #' @export
-read_params <- function(stage_path, return_list = FALSE) {
-  stage_path <- set_stage(stage_path)
+read_params <- function(stage_path = NULL, return_list = FALSE) {
+  if(!is.logical(return_list))
+    stop("Argument return_list needs to be logical.")
+
+  # if stage_path argument was path, set stage from that argument
+  if(!is.null(stage_path)) {
+
+    # first check for input validity
+    if(!is.character(stage_path))
+      stop("stage_path argument must be a character string or NULL to reload the config")
+
+    # then set stage path
+    stage_path <- set_stage(stage_path)
+
+  } else {
+    # stage_path argument is null, therefore not set. Check if stage_dir
+    # has been already set in config_env, if yes reload, if not, stop with error
+    if(is.null(config_env$stage_dir)) {
+      stop("stage_path argument missing.")
+    } else {
+      cat(paste("reloading from already set stage_path:", config_env$stage_dir))
+      stage_path <- config_env$stage_dir
+    }
+  }
+
   tmp_config_file <- tempfile()
   tmp_err_file <- tempfile()
 

README.md

@@ -3,8 +3,9 @@
 The purpose of this package is to provide access to files and configuration organized in a dso project. It provides two main functions:
 
 -   `read_params(stage_path)` loads the configuration for the specified stage into an `dsoParams` R object which can be accessed like a list. The stage name must be relative to the project root. This function works independent of the current working directory, as long as you are in any subdirectory of the project.
+-   `reload(object)` reloads the config loaded by read_params. Usage: `reload(params)`
 -   `stage_here(rel_path)` is inspired by [here()](https://here.r-lib.org/). While `here()` resolves paths that are relative to the project root `stage_here()` resolves paths that are relative to the stage specified in `read_params`.
--   `safe_get(params$samplesheet)` is a helper function assuring that a nested list call does not return NULL if accessed incorrectly. ' safe_get() will produce an error and point to the incorrectly accessed slot.
+-   `safe_get()` is a helper function assuring that a nested list call does not return NULL if accessed incorrectly. ' safe_get() will produce an error and point to the incorrectly accessed slot.
 
 Additionally, `dso-r` provides an R interface to some of the most important CLI commands of `dso`.