Merge pull request #22 from elreda/check-open-connections-in-unix

Check open connections in unix before deleting. Candidate for #5
bjcairns · Oct 9, 2019 · 54cdf46 · 54cdf46
2 parents 68c2168 + d9571bd
commit 54cdf46
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Showing 4 changed files with 14 additions and 10 deletions.
diff --git a/R/misc-functions.R b/R/misc-functions.R
@@ -9,7 +9,7 @@
 
   # Parse file name and path
   if (file == "") file <- paste0("ukb-schemas-", date_str, ".sqlite")
-  full_path <- paste0(path.expand(path), "\\", file)
+  full_path <- paste0(path.expand(path), "/", file)
 
   # If `file`` exists, session is `interactive()` and `!overwrite`, then prompt 
   # to overwrite the file
@@ -22,8 +22,18 @@
     }
     if (!isTRUE(overwrite)) 
       stop(UKBSCHEMAS_ERRORS$OVERWRITE)
-    else tryCatch(
-      file.remove(full_path),
+    else tryCatch({
+      if (.Platform$OS.type == "unix"){
+          sys_command <- paste("lsof", full_path, "| wc -l")
+          processes_using_file <- as.numeric(system(sys_command, intern = TRUE,
+                                                    ignore.stdout = TRUE,
+                                                    ignore.stderr = TRUE))
+          if (processes_using_file>1) {
+            stop(UKBSCHEMAS_ERRORS$FAILED_OVERWRITE)
+          }
+        }
+        file.remove(full_path)
+      },
       error = function(err) {
         stop(UKBSCHEMAS_ERRORS$FAILED_OVERWRITE)
       },

diff --git a/R/tidy-schemas.R b/R/tidy-schemas.R
@@ -61,7 +61,7 @@
         dplyr::mutate(.x, parent_id = NA, selectable = NA) %>%
           dplyr::mutate(type = type, value = as.character(value)) %>%
           dplyr::group_by(encoding_id) %>%
-          dplyr::mutate(code_id = row_number()) %>%
+          dplyr::mutate(code_id = dplyr::row_number()) %>%
           dplyr::ungroup()
       }
     )

diff --git a/tests/testthat/test-save-db.R b/tests/testthat/test-save-db.R
@@ -72,9 +72,6 @@ test_that("save_db() fails on overwrite = FALSE, non-interactive", {
 
 test_that("save_db() fails to overwrite when db is connected", {
 
-  # This only seems to work on Windows
-  skip_if_not(.Platform$OS.type == "windows", "Skipping test if not Windows")
-
   db_file <- test_db_file()
 
   expect_error(

diff --git a/tests/testthat/test-ukbschemas-db.R b/tests/testthat/test-ukbschemas-db.R
@@ -84,9 +84,6 @@ test_that("ukbschemas_db() fails on overwrite = FALSE, non-interactive", {
 
 test_that("ukbschemas_db() fails to overwrite when db is connected", {
 
-  # This only seems to work on Windows
-  skip_if_not(.Platform$OS.type == "windows", "Skipping test if not Windows")
-
   db_file <- test_db_file()
 
   expect_error(