introducing rstudio addin for dso repro stage

CHANGELOG.md

@@ -4,6 +4,17 @@ 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).
 
+## v0.6
+
+### New Features
+
+-   Introduced the `repro` function that performs `dso repro` of a single stage with or without its dependencies
+-   Introduced the corresponding rstudio addins for the `repro` function
+
+### Fixes
+
+-   Removed ... in reload function
+
 ## v0.5.0
 
 ### New Features

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dso
 Type: Package
 Title: dso R companion package
-Version: 0.5.0
+Version: 0.6
 Author: Daniel Schreyer<[email protected]>,
     Gregor Sturm<[email protected]>,
     Thomas Schwarzl<[email protected]>
@@ -18,7 +18,8 @@ Imports:
     here,
     stringr,
     methods,
-    rlang
+    rlang,
+    rstudioapi (>= 0.11)
 RoxygenNote: 7.3.2
 Suggests:
     testthat (>= 3.0.0)

NAMESPACE

@@ -6,9 +6,12 @@ S3method(print,dsoParams)
 export(compile_config)
 export(create_stage)
 export(dsoParams)
+export(dso_repro_stage_addin)
+export(dso_repro_stage_w_dependencies_addin)
 export(init)
 export(read_params)
 export(reload)
+export(repro)
 export(safe_get)
 export(set_stage)
 export(stage_here)
@@ -21,6 +24,7 @@ importFrom(here,here)
 importFrom(here,i_am)
 importFrom(methods,show)
 importFrom(rlang,caller_env)
+importFrom(rstudioapi,viewer)
 importFrom(stringr,coll)
 importFrom(stringr,str_match_all)
 importFrom(stringr,str_replace)

R/addin.R

@@ -0,0 +1,81 @@
+#' Execute dso repro and display the result
+#'
+#' This function reproduces the current stage without its dependencies
+#' and displays the resulting report in the RStudio Viewer pane.
+#'
+#' @return None
+#' @export
+#' @importFrom glue glue
+#' @importFrom rstudioapi viewer
+#' @examples
+#' \dontrun{
+#' dso_repro_stage_addin()
+#' }
+dso_repro_stage_addin <- function() {
+  stage_path <- get_stage_path()
+  dvc_yaml_path <- file.path(stage_path, "dvc.yaml")
+
+  repro(dvc_yaml_path, single_stage = TRUE)
+
+  check_report()
+}
+
+#' Execute dso repro with dependencies and display the result
+#'
+#' This function reproduces the current stage along its dependencies
+#' and displays the resulting report in the RStudio Viewer pane.
+#'
+#' @return None
+#' @export
+#' @importFrom glue glue
+#' @importFrom rstudioapi viewer
+#' @examples
+#' \dontrun{
+#' dso_repro_stage_w_dependencies_addin()
+#' }
+dso_repro_stage_w_dependencies_addin <- function() {
+  stage_path <- get_stage_path()
+  dvc_yaml_path <- file.path(stage_path, "dvc.yaml")
+
+  repro(dvc_yaml_path, single_stage = FALSE)
+
+  check_report()
+}
+
+#' Get the current stage path
+#'
+#' This function retrieves the absolute path to the current stage.
+#' If the stage is not defined, it stops with an error message.
+#'
+#' @return The absolute path to the current stage.
+#' @noRd
+get_stage_path <- function() {
+  if (length(stage_here()) == 0) {
+    stop(glue::glue("stage_here() is not defined. Please read in your config file using read_params()."))
+  } else {
+    return(stage_here())
+  }
+}
+
+#' Check and display the report
+#'
+#' This function checks for the generated report files in the stage directory
+#' and displays the report in the RStudio Viewer pane if a single report file is found.
+#'
+#' @return None
+#' @noRd
+#' @importFrom glue glue
+#' @importFrom rstudioapi viewer
+check_report <- function() {
+  report_files <- list.files(stage_here("report"), pattern = "\\.pdf$|\\.html$", full.names = TRUE)
+
+  if (length(report_files) == 1) {
+    report_file <- report_files[1]
+    message(glue::glue("Report generated: {report_file}"))
+    message(glue::glue("Displaying report file: {report_file}"))
+    # Check the file extension and display in the viewer
+    rstudioapi::viewer(report_file)
+  } else {
+    stop(glue::glue("No report file or multiple report files were identified. Please check the report directory."))
+  }
+}

R/class-dsoParams.R

@@ -113,12 +113,11 @@ setMethod(
 
 #' @title reload function
 #' @description
-#'
-#' Generic for function reload
+#' Generic function for reloading configurations.
 #'
 #' @param object dsoParams config object
 #' @export
-setGeneric("reload", function(object,...) standardGeneric("reload"))
+setGeneric("reload", function(object) standardGeneric("reload"))
 
 
 #' @title reload dso params

R/read_params.R

@@ -14,23 +14,23 @@
 #' @importFrom yaml read_yaml
 #' @export
 read_params <- function(stage_path = NULL, return_list = FALSE) {
-  if(!is.logical(return_list))
+  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)) {
-
+  if (!is.null(stage_path)) {
     # first check for input validity
-    if(!is.character(stage_path))
+    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$stage_dir)) {
+    if (is.null(config_env$stage_dir)) {
       stop("stage_path argument missing.")
     } else {
       cat(paste("reloading from already set stage_path:", config_env$stage_dir))
@@ -41,30 +41,37 @@ read_params <- function(stage_path = NULL, return_list = FALSE) {
   tmp_config_file <- tempfile()
   tmp_err_file <- tempfile()
 
-  tryCatch({
-    output <- system2(DSO_EXEC,
-                      c("get-config",
-                        shQuote(stage_path)),
-                      stdout = tmp_config_file,
-                      stderr = tmp_err_file)
+  tryCatch(
+    {
+      output <- system2(DSO_EXEC,
+        c(
+          "get-config",
+          shQuote(stage_path)
+        ),
+        stdout = tmp_config_file,
+        stderr = tmp_err_file
+      )
 
-    stderror <- readLines(tmp_err_file)
+      stderror <- readLines(tmp_err_file)
 
-    # error handling, display only rows after first error
-    # for better readability
-    if (output != 0 || any(grepl("ERROR", stderror))) {
-      stop(
-        paste("An error occurred when executing dso get-config:\n",
-              paste(
-                stderror[which(grepl("ERROR", stderror)) : length(stderror)],
-                collapse = "\n"
-              )
+      # error handling, display only rows after first error
+      # for better readability
+      if (output != 0 || any(grepl("ERROR", stderror))) {
+        stop(
+          paste(
+            "An error occurred when executing dso get-config:\n",
+            paste(
+              stderror[which(grepl("ERROR", stderror)):length(stderror)],
+              collapse = "\n"
+            )
+          )
         )
-      )
+      }
+    },
+    error = function(e) {
+      stop("An error occurred when executing dso get-config: ", e$message)
     }
-  }, error = function(e) {
-    stop("An error occurred when executing dso get-config: ", e$message)
-  })
+  )
 
   yaml <- read_yaml(tmp_config_file)
   unlink(tmp_config_file)

R/repro.R

@@ -0,0 +1,29 @@
+#' @title Reproduce a dso stage
+#' @description
+#' Reproduce a dso stage with or without its dependencies.
+#' @details
+#' This function reproduces a stage specified by `stage_path`. If `single_stage` is set to `TRUE`,
+#' it reproduces the stage without its dependencies. Otherwise, it reproduces the current stage along with all its dependency stages.
+#' By default, the current stage will be reproduced.
+#' @param stage_path The path to a stage. Defaults to the current stage by using `stage_here()`.
+#' @param single_stage Logical flag indicating whether to reproduce only the current stage (`TRUE`) or the current stage with all dependencies (`FALSE`). Defaults to `FALSE`.
+#' @export
+repro <- function(stage_path = stage_here(), single_stage = F) {
+  if (single_stage) {
+    message(glue::glue("Reproducing the current stage with all its dependency stages."))
+    repro_cmd <- "repro"
+  } else {
+    message(glue::glue("Reproducing the current stage without dependencies."))
+    repro_cmd <- "repro -s"
+  }
+  result <- system2(
+    DSO_EXEC,
+    c(repro_cmd, shQuote(file.path(stage_path, "dvc.yaml")))
+  )
+
+  if (result != 0) {
+    stop(glue::glue("DSO {repro_cmd} failed with status: {result}"))
+  } else {
+    message("dso repro was executed successfully")
+  }
+}

inst/rstudio/addins.dcf

@@ -0,0 +1,9 @@
+Name: dso repro stage
+Description: Execute dso repro -s
+Binding: dso_repro_stage_addin
+Interactive: false
+
+Name: dso repro stage with dependencies
+Description: Execute dso repro
+Binding: dso_repro_stage_w_dependencies_addin
+Interactive: false