Add SVN compatibility

NAMESPACE

@@ -1,11 +1,13 @@
 # Generated by roxygen2: do not edit by hand
 
-export(demoRepo)
+export(demoRepoGit)
+export(demoRepoSVN)
 export(diffQced)
-export(gitLog)
 export(logAccept)
 export(logAssign)
 export(logCreate)
 export(logPending)
 export(logSummary)
-export(with_demoRepo)
+export(vcsLastCommit)
+export(with_demoRepoGit)
+export(with_demoRepoSVN)

R/demoRepo-content.R

@@ -0,0 +1,51 @@
+#' @keywords internal
+demoRepo_content1 <- function() {
+  writeLines("Version: 1.0", con = "temp.Rproj")
+
+  # Add scripts to the repo
+  fs::dir_create("script/pk", recurse = TRUE)
+  fs::dir_create("deliv/figure")
+  fs::dir_create("deliv/table")
+
+  writeLines(
+    c(
+      "library(tidyverse)",
+      'src_abc <- mrgda::read_src_dir(here::here("data", "source", "STUDY-ABC"))',
+      "derived <- list(sl = list(),tv = list())",
+      'dm_0 <- src_abc$dm %>% filter(ACTARM != "Screen Failure")',
+      "derived$sl$dm <- dm_0"
+    ),
+    "script/data-assembly.R"
+  )
+
+  writeLines(
+    c(
+      "library(tidyverse)",
+      "studies <- list()",
+      'studies$pk_abc <- readr::read_rds(here::here("data", "derived", "studies", "pk-abc.rds"))',
+      "pk_0 <- bind_rows(studies) %>% arrange(USUBJID, DATETIME)",
+      'pk_1 <- pk_0 %>% mrgda::assign_id(., "USUBJID")',
+      "pk_out <- pk_1"
+    ),
+    "script/combine-da.R"
+  )
+
+  writeLines(
+    c(
+      'pk_spec <- yspec::load_spec(here::here("script", "script/examp-yaml.yaml"))'
+    ),
+    "script/pk/load-spec.R"
+  )
+
+  writeLines(c('This is the first version of the txt file'),
+             "script/examp-txt.txt")
+
+  writeLines(c("This is the first version of the yaml file"),
+             "script/examp-yaml.yaml")
+
+  writeLines(c("This is the first version of the yml file"),
+             "pkgr.yml")
+
+  # Create QC log
+  logCreate()
+}

R/demoRepo.R → R/demoRepoGit.R

@@ -13,10 +13,10 @@
 #' 
 #' @param clean Logical indicating if the temporary directory should be deleted after use
 #' 
-#' @usage demoRepo(clean = TRUE)
+#' @usage demoRepoGit(clean = TRUE)
 #'
 #' @export
-demoRepo <- function(clean = TRUE) {
+demoRepoGit <- function(clean = TRUE) {
 
   repoInitPath <- withr::local_tempdir(
     "qctools-demo-",
@@ -28,49 +28,7 @@ demoRepo <- function(clean = TRUE) {
 
   withr::local_dir(repoInitPath)
 
-  writeLines("Version: 1.0", con = "temp.Rproj")
-
-  # Add scripts to the repo
-  fs::dir_create("script/pk", recurse = TRUE)
-
-  writeLines(
-    c(
-      "library(tidyverse)",
-      'src_abc <- mrgda::read_src_dir(here::here("data", "source", "STUDY-ABC"))',
-      "derived <- list(sl = list(),tv = list())",
-      'dm_0 <- src_abc$dm %>% filter(ACTARM != "Screen Failure")',
-      "derived$sl$dm <- dm_0"
-    ),
-    "script/data-assembly.R"
-  )
-
-  writeLines(
-    c(
-      "library(tidyverse)",
-      "studies <- list()",
-      'studies$pk_abc <- readr::read_rds(here::here("data", "derived", "studies", "pk-abc.rds"))',
-      "pk_0 <- bind_rows(studies) %>% arrange(USUBJID, DATETIME)",
-      'pk_1 <- pk_0 %>% mrgda::assign_id(., "USUBJID")',
-      "pk_out <- pk_1"
-    ),
-    "script/combine-da.R"
-  )
-
-  writeLines(
-    c(
-      'pk_spec <- yspec::load_spec(here::here("script", "script/examp-yaml.yaml"))'
-    ),
-    "script/pk/load-spec.R"
-  )
-
-  writeLines(c('This is the first version of the txt file'),
-             "script/examp-txt.txt")
-
-  writeLines(c("This is the first version of the yaml file"),
-             "script/examp-yaml.yaml")
-
-  # Create QC log
-  logCreate()
+  demoRepo_content1()
 
   processx::run("git", c("add", "."))
   processx::run("git", c("commit", "-m", "'initial commit'", "--quiet"))
@@ -133,11 +91,11 @@ demoRepo <- function(clean = TRUE) {
   repoInitPath
 }
 
-#' @rdname demoRepo
+#' @rdname demoRepoGit
 #' 
 #' @param code Executable code to run 
 #' @export
-with_demoRepo <- function(code, clean = TRUE) {
-  repo <- demoRepo(clean)
+with_demoRepoGit <- function(code, clean = TRUE) {
+  repo <- demoRepoGit(clean)
   withr::with_dir(repo, code)
 }

R/demoRepoSVN.R

@@ -0,0 +1,105 @@
+#' Create Demo SVN Repo
+#' 
+#' @description 
+#' Create a SVN repo with files checked in and a QC log. The purpose of this 
+#' demo repo is for the user to become familiar with using review functions. 
+#' 
+#' The files checked into the repo are at various stages in terms of their QC
+#' status. This function returns the path to the repo, so that the user can set
+#' their working directory to it.
+#'
+#' This demo repo is created under the R session `/tmp/` directory, so a new one
+#' will need to be generated whenever the user restarts R.
+#' 
+#' @param clean Logical indicating if the temporary directory should be deleted after use
+#' 
+#' @usage demoRepoSVN(clean = TRUE)
+#'
+#' @export
+demoRepoSVN <- function(clean = TRUE) {
+
+  repoInitPath <- withr::local_tempdir(
+    "qctools-demo-svn-",
+    clean = clean, 
+    .local_envir = parent.frame()
+  )
+
+  processx::run("svnadmin", c("create", repoInitPath))
+  repoDir <- file.path(repoInitPath, "svn-proj-123")
+
+  processx::run("svn", c("co", paste0("file://", repoInitPath), repoDir, "-q"))
+
+  withr::local_dir(repoDir)
+
+  demoRepo_content1()
+
+  # Check everything into SVN
+  processx::run("svn", c("add", "--force", "."))
+  processx::run("svn", c("commit", "-m", "'initial commit'", "-q", "-q"))
+
+  logAssign("script/data-assembly.R")
+  logAssign("script/pk/load-spec.R")
+  logAssign("script/combine-da.R")
+  logAssign("script/examp-txt.txt")
+
+  processx::run("svn", c("add", "--force", "."))
+  processx::run("svn", c("commit", "-m", "'logAssign scripts ready for QC'", "-q", "-q"))
+
+  logAccept("script/data-assembly.R")
+  logAccept("script/pk/load-spec.R")
+  logAccept("script/combine-da.R")
+
+  # Check in updates to QC log
+  processx::run("svn", c("add", "--force", "."))
+  processx::run("svn", c("commit", "-m", "'logAccept scripts ready for QC'", "-q", "-q"))
+
+  # Make edits to QCed file
+  writeLines(
+    c('pk_spec <- yspec::load_spec(here::here("script", "examp-yaml.yaml"))'),
+    "script/pk/load-spec.R"
+  )
+
+  processx::run("svn", c("add", "--force", "."))
+  processx::run("svn", c("commit", "-m", "'modify load-spec script'", "-q", "-q"))
+
+  writeLines(
+    c(
+      "library(tidyverse)",
+      'source(here::here("script", "data-assembly", "da-functions.R"))',
+      'src_abc <- mrgda::read_src_dir(here::here("data", "source", "STUDY-ABC"))',
+      "derived <- list(sl = list(),tv = list())",
+      'dm_0 <- src_abc$dm %>% filter(ACTARM != "Screen Failure")',
+      "derived$sl$dm <- dm_0",
+      'pk_0 <- src_abc$pc %>% filter(PCTEST == "TEST OF INTEREST")',
+      "derived$tv$pc <- pk_0",
+      'ex_1 <- src_abc$ex %>% filter(EXTRT == "DRUG OF INTEREST")',
+      "derived$tv$dosing <- ex_1"
+    ),
+    "script/data-assembly.R"
+  )
+
+  processx::run("svn", c("add", "--force", "."))
+  processx::run("svn", c("commit", "-m", "'modify data-assembly'", "-q", "-q"))
+
+  writeLines(
+    c("The following tasks are suggested to gain familiarity with the review package:",
+      '- run `diffQced()` on "script/pk/load-spec.R" and "script/data-assembly.R"',
+      '- run `renderQCSummary()`',
+      '- use `logAssign()` to add "script/examp-txt.txt" to the QC log',
+      '- run `logPending()` to see what scripts are in need of QC',
+      '- use `logAccept()` to sign off on any scripts with pending QC'),
+    "README.md"
+  )
+
+  repoDir
+
+}
+
+#' @rdname demoRepoSVN
+#' 
+#' @param code Executable code to run 
+#' @export
+with_demoRepoSVN <- function(code, clean = TRUE) {
+  repo <- demoRepoSVN(clean)
+  withr::with_dir(repo, code)
+}

R/diffQced.R

@@ -8,13 +8,15 @@
 #' @param file file path from working directory
 #' 
 #' @examples 
-#' with_demoRepo({
+#' with_demoRepoGit({
 #'   diffQced("script/data-assembly.R")
 #' })
 #' 
 #' @export
 diffQced <- function(file) {
 
+  vcs <- get_vcs()
+
   # Modify file to correct path format
   file_abs <- fs::path_abs(path = file)
 
@@ -32,28 +34,25 @@ diffQced <- function(file) {
   if (length(log_file) == 0) {
     stop(paste0(file, " not in QC log"), call. = FALSE)
   }
-  
-  version_new <- gitLog(file)[["last_commit"]]
+
+  version_new <- vcsLastCommit(file)[["last_commit"]]
   version_qc <- log_file[length(log_file)]
 
   if (version_new == version_qc) {
     stop("File is up to date with QC", call. = FALSE)
   }
 
-  # Prepend "./" so that 'git cat-file' interprets the path relative to the
-  # working directory rather than the top-level directory of the Git repo.
-  commit_file_new <- paste0(version_new, ":./", file_rel)
-  commit_file_qc <- paste0(version_qc, ":./", file_rel)
-
   tempfile_new <- file.path(tempdir(), paste0("new-", basename(file_rel)))
   tempfile_qc <- file.path(tempdir(), paste0("qced-", basename(file_rel)))
 
-  processx::run(
-    "git", c("cat-file", "blob", commit_file_new),
-    stdout = tempfile_new, wd = logDir())
-  processx::run(
-    "git", c("cat-file", "blob", commit_file_qc),
-    stdout = tempfile_qc, wd = logDir())
+  vcsExport(
+    .file = file_rel,
+    .vcs = vcs,
+    .version_new = version_new,
+    .version_qc = version_qc,
+    .temp_new = tempfile_new,
+    .temp_qc = tempfile_qc
+    )
 
   diffobj::diffFile(
     target = tempfile_qc,

R/get-vcs.R

@@ -0,0 +1,22 @@
+#' @keywords internal
+get_vcs <- function() {
+
+  svnCheck <- tryCatch(processx::run("svn", c("info"), 
+                                     wd = logDir(),
+                                     error_on_status = FALSE))
+
+  if (svnCheck$status == 0) {
+    return("svn")
+  } 
+
+  gitCheck <- tryCatch(processx::run("git", c("log"), 
+                                     wd = logDir(),
+                                     error_on_status = FALSE))
+
+  if (gitCheck$status == 0) {
+    return("git")
+  } 
+
+  stop(logDir(), " is not a git or svn repository")
+
+}

R/logAccept.R

@@ -8,19 +8,19 @@
 #' @param file character file path (either the absolute or relative file path from the QC log)
 #' 
 #' @examples 
-#' with_demoRepo({
+#' with_demoRepoGit({
 #'   logAccept(file = "script/data-assembly.R")
 #' })
 #' 
 #' @export
 logAccept <- function(file){
 
-  git_commit <- gitLog(file)
+  version <- vcsLastCommit(file)
 
   logEdit(
     .file = file,
     .reviewer = Sys.info()[["user"]],
-    .commit = git_commit$last_commit
+    .commit = version$last_commit
   )
 
 }

R/logAssign.R

@@ -12,7 +12,7 @@
 #' @param reviewer specify a specific person to review the file (defaults to "anyone")
 #' 
 #' @examples 
-#' with_demoRepo({
+#' with_demoRepoGit({
 #'   logAssign(
 #'     file = "script/examp-yaml.yaml", 
 #'     reviewer = "person1")

R/logCreate.R

@@ -5,7 +5,7 @@
 #' created in the directory where the RStudio project file (`*.Rproj`) exists.
 #' 
 #' @examples 
-#' with_demoRepo({
+#' with_demoRepoGit({
 #'   file.remove("QClog.csv")
 #'   logCreate()
 #' })