Merge pull request #222 from vimc/vimc-3702

vimc-3702: Backup before rebuild

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: orderly
 Title: Lightweight Reproducible Reporting
-Version: 1.1.30
+Version: 1.1.31
 Description: Order, create and store reports from R.  By defining a
     lightweight interface around the inputs and outputs of an
     analysis, a lot of the repetitive work for reproducible research

NEWS.md

@@ -1,3 +1,7 @@
+# orderly 1.1.31
+
+* `orderly::orderly_rebuild()` creates a dated backup of the database before running, allowing this potentially destructive operation to be recovered from (VIMC-3702)
+
 # orderly 1.1.28
 
 * `orderly::orderly_develop_clean()` no longer deletes artefacts that are re-exported from sources (VIMC-3671, reported by @cewalters)

R/db.R

@@ -184,6 +184,7 @@ orderly_rebuild <- function(root = NULL, locate = TRUE, verbose = TRUE,
   }
 
   if (!if_schema_changed || report_db_needs_rebuild(config)) {
+    orderly_backup(config, suffix = paste0(".", iso_time_str(Sys.time())))
     orderly_log("rebuild", "db")
     report_db_rebuild(config, verbose)
     invisible(TRUE)
@@ -202,12 +203,12 @@ orderly_rebuild <- function(root = NULL, locate = TRUE, verbose = TRUE,
 ## > backup may be performed on a live source database without
 ## > preventing other database connections from reading or writing to
 ## > the source database while the backup is underway.
-orderly_backup <- function(config = NULL, locate = TRUE) {
+orderly_backup <- function(config = NULL, locate = TRUE, suffix = NULL) {
   config <- orderly_config_get(config, locate)
   if (config$destination$driver[[1]] == "RSQLite") {
     curr <- orderly_db_args(config$destination, config)$args$dbname
 
-    dest <- path_db_backup(config$root, curr)
+    dest <- path_db_backup(config$root, curr, suffix)
     dir.create(dirname(dest), FALSE, TRUE)
 
     prefix <- paste0(config$root, "/")

R/paths.R

@@ -63,8 +63,13 @@ path_changelog_txt <- function(path, type) {
 }
 
 
-path_db_backup <- function(root, file) {
-  file.path(root, "backup", "db", basename(file), fsep = "/")
+path_db_backup <- function(root, file, suffix = NULL) {
+  if (is.null(suffix)) {
+    filename <- basename(file)
+  } else {
+    filename <- paste0(basename(file), suffix)
+  }
+  file.path(root, "backup", "db", filename, fsep = "/")
 }
 
 

tests/testthat/test-db.R

@@ -456,3 +456,32 @@ test_that("db includes elapsed time", {
   expect_equal(d$elapsed,
                readRDS(path_orderly_run_rds(p))$meta$elapsed)
 })
+
+
+test_that("rebuild nonempty database with backup", {
+  skip_on_cran_windows()
+  path <- prepare_orderly_example("minimal")
+  id <- orderly_run("example", root = path, echo = FALSE)
+  orderly_commit(id, root = path)
+
+  con <- orderly_db("destination", path)
+  DBI::dbExecute(con, "UPDATE report_version SET published = 1")
+  DBI::dbDisconnect(con)
+
+  orderly_rebuild(path)
+
+  files <- dir(file.path(path, "backup/db"))
+  expect_equal(length(files), 1)
+  expect_match(files, "^orderly\\.sqlite\\.[0-9]{8}-[0-9]{6}$")
+
+  con1 <- orderly_db("destination", path)
+  con2 <- DBI::dbConnect(RSQLite::SQLite(),
+                         dbname = file.path(path, "backup/db", files))
+  expect_equal(
+    DBI::dbReadTable(con1, "report_version")$published, 0)
+  expect_equal(
+    DBI::dbReadTable(con2, "report_version")$published, 1)
+
+  DBI::dbDisconnect(con1)
+  DBI::dbDisconnect(con2)
+})