Merge pull request #149 from mrc-ide/mrc-5495-writable

Make files writable when they are exported.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: orderly2
 Title: Orderly Next Generation
-Version: 1.99.19
+Version: 1.99.20
 Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"),
                     email = "[email protected]"),
              person("Robert", "Ashton", role = "aut"),

R/outpack_root.R

@@ -72,6 +72,11 @@ file_export <- function(root, id, there, here, dest, overwrite, call = NULL) {
     }
     fs::file_copy(there_full, here_full, overwrite)
   }
+
+  # Files in the archive and file store are (generally) read-only.
+  # When exporting for interactive use, it's easier on the user if we make them
+  # writable again.
+  fs::file_chmod(here_full, "u+w")
 }
 
 

tests/testthat/test-outpack-helpers.R

@@ -157,3 +157,33 @@ test_that("good error message if file not found in packet", {
       i = "For 'd.txt' did you mean 'a.txt', 'b.txt' or 'c.txt'",
       i = "Remember that all orderly paths are case sensitive"))
 })
+
+
+test_that("Can overwrite when copying files from packet", {
+  root <- create_temporary_root(use_file_store = TRUE)
+
+  id1 <- create_random_packet(root)
+  id2 <- create_random_packet(root)
+
+  # Just a bit of a sanity check. The two packets are random, so we'd expect
+  # them to have different contents.
+  expect_false(identical(
+    readRDS(file.path(root$path, "archive", "data", id1, "data.rds")),
+    readRDS(file.path(root$path, "archive", "data", id2, "data.rds"))))
+
+  dst <- temp_file()
+
+  suppressMessages(
+    orderly_copy_files(id1, files = "data.rds", dest = dst, root = root))
+
+  expect_identical(
+    readRDS(file.path(dst, "data.rds")),
+    readRDS(file.path(root$path, "archive", "data", id1, "data.rds")))
+
+  suppressMessages(
+    orderly_copy_files(id2, files = "data.rds", dest = dst, root = root))
+
+  expect_identical(
+    readRDS(file.path(dst, "data.rds")),
+    readRDS(file.path(root$path, "archive", "data", id2, "data.rds")))
+})

tests/testthat/test-outpack-packet.R

@@ -449,6 +449,23 @@ test_that("Re-adding files triggers hash", {
 })
 
 
+test_that("Can detect changes to dependencies", {
+  root <- create_temporary_root()
+  id <- create_random_packet(root, "data")
+
+  path_src <- withr::local_tempdir()
+  p <- outpack_packet_start_quietly(path_src, "next", root = root)
+
+  outpack_packet_use_dependency(p, id, "data.rds")
+  saveRDS(1:10, file.path(path_src, "data.rds"))
+
+  err <- expect_error(
+    outpack_packet_end_quietly(p),
+    "File was changed after being added")
+  expect_equal(err$body, c(x = "data.rds"))
+})
+
+
 test_that("Can ignore files from the final packet", {
   root <- create_temporary_root(path_archive = "archive", use_file_store = TRUE)
   path_src <- create_temporary_simple_src()