dsROCrate 0.2.3

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dsROCrate
 Title: 'DataSHIELD' RO-Crate Governance Functions
-Version: 0.2.2
+Version: 0.2.3
 Authors@R: c(
     person(given = "Roberto",
            family = "Villegas-Diaz",
@@ -59,4 +59,4 @@ Depends:
 VignetteBuilder: knitr
 URL: https://github.com/FederatedMethods/dsROCrate
 BugReports: https://github.com/FederatedMethods/dsROCrate/issues
-Config/roxygen2/version: 8.0.0
+Config/roxygen2/version: 8.1.0

NEWS.md

@@ -1,3 +1,30 @@
+# dsROCrate 0.2.3
+
+## New Features
+
+* `safe_output()` now preserves Opal 6.0 `RESOLVE` operations independently of `ASSIGN` operations, including the resolved symbol and source table/resource for provenance. `RESOLVE` entries are retained even when no matching `ASSIGN` follows (e.g., a failed resolution). This is only enabled when the server reports Opal >= 6.0.
+* Every entry in the audit log tibble returned via `safe_output()` (and written to the `_mappings.csv` file) now has a unique `id` (UUID), and the tibble gains a `column` field recording the column referenced by a function call argument (e.g. `D$LAB_TSC`), where applicable.
+
+## Improvements
+
+* Function-call arguments supplied as R expressions (e.g. `D$LAB_TSC`) are now resolved back to the single registered symbol they reference, along with the referenced column. Expressions that reference several symbols, or none that are registered, are returned unchanged.
+* Audit log entries are now ordered by their original log-entry order and then timestamp, and operation IDs are regenerated as UUIDs.
+* Symbol IDs generated by `safe_symbol()` are now plain UUIDs, without the previous `"symbol-"` prefix.
+
+## Bug fixes
+
+* Fixed `safe_output()` failing when an audit session contains no `ASSIGN` operations: an empty, correctly typed symbols table is now used.
+* Fixed `safe_output()` failing when no function calls could be reconstructed from the logs: an empty, correctly typed calls table is now used.
+* `safe_output()` no longer injects a placeholder row (`ds_profile = "-999999"`) into the parsed logs; a zero-row typed tibble is used to guarantee the `ds_profile` column exists instead.
+* Fixed `resolve_dependencies()` failing on an empty symbol registry, and `resolve_provenance()` failing when given an `NA` symbol ID. Both now return an empty tibble.
+* `validate_backend_version()` (opal method) no longer emits warnings from `utils::compareVersion()`.
+
+## Internal Changes
+
+* Added tests covering `safe_output()` with `RESOLVE` and `ASSIGN` operations, and `RESOLVE` operations without `ASSIGN`; updated `as.data.frame.safe_call()` test for the new `id` column.
+* Declared additional local bindings in `safe_output()` to silence `R CMD check` notes about undefined global variables.
+* Updated roxygen2 documentation for `enrich_argument()` and `safe_call()`; regenerated with roxygen2 8.1.0.
+
 # dsROCrate 0.2.2
 
 ## Bug fixes

R/backend-opal.R

@@ -110,7 +110,7 @@ is_audit_con.opal <- function(x, ...) {
 
 #' @export
 validate_backend_version.opal <- function(x, ..., minimum = "5.7.2") {
-  if (utils::compareVersion(x$version, minimum) < 0) {
+  if (suppressWarnings(utils::compareVersion(x$version, minimum)) < 0) {
     stop(
       sprintf(
         "Opal >= %s is required, but server version is %s.",

R/safe-call-utils.R

@@ -5,7 +5,8 @@
 #' @param timestamp Timestamp to map the symbol details.
 #' @param session String with session ID.
 #'
-#' @returns `safe_reference` object.
+#' @returns `safe_reference` object, or the original argument when no
+#'   registered symbol can be resolved.
 #' @keywords internal
 #'
 #' @noRd
@@ -14,20 +15,50 @@ enrich_argument <- function(arg, registry, timestamp, session) {
     return(arg)
   }
 
+  # attempt solving the argument as a direct symbol reference
   symbol <- resolve_symbol(
     registry,
     symbol = arg,
     timestamp = timestamp,
     session = session
   )
 
+  if (!is.null(symbol)) {
+    return(safe_reference(symbol = symbol$symbol, symbol_id = symbol$id))
+  }
+
+  # if the argument isn't itself a symbol, try interpreting it as an R expr.
+  refs <- tryCatch(
+    find_symbols(arg),
+    error = function(e) NULL
+  )
+
+  if (is.null(refs) || !length(refs)) {
+    return(arg)
+  }
+
+  # if multiple symbols are found, return original obkect
+  if (length(refs) != 1L) {
+    return(arg)
+  }
+
+  ref <- refs[[1]]
+
+  symbol <- resolve_symbol(
+    registry,
+    symbol = ref$symbol,
+    timestamp = timestamp,
+    session = session
+  )
+
   if (is.null(symbol)) {
     return(arg)
   }
 
   safe_reference(
     symbol = symbol$symbol,
-    symbol_id = symbol$id
+    symbol_id = symbol$id,
+    column = ref$column
   )
 }
 

R/safe-call.R

@@ -1,6 +1,7 @@
 #' @export
 as.data.frame.safe_call <- function(x, ...) {
   data.frame(
+    id = x$id,
     timestamp = format(x$created_at, '%Y-%m-%dT%H:%M:%S'),
     user = x$user,
     r_cmd = x$original,
@@ -19,6 +20,7 @@ as.data.frame.safe_call <- function(x, ...) {
 #' @param namespace Function's namespace.
 #' @param fx Function's name.
 #' @param args List with arguments.
+#' @param id Unique call ID.
 #' @param ... Additional arguments.
 #'
 #' @returns New `safe_call` object.
@@ -31,6 +33,7 @@ new_safe_call <- function(
   namespace,
   fx,
   args,
+  id = uuid::UUIDgenerate(),
   ...
 ) {
   stopifnot(is.character(original))
@@ -39,6 +42,7 @@ new_safe_call <- function(
 
   structure(
     list(
+      id = id,
       original = original,
       package = package,
       namespace = namespace,

R/safe-symbol-utils.R

@@ -70,7 +70,7 @@ resolve_dependencies <- function(expr, registry) {
   # find symbols for the given expression
   refs <- find_symbols(expr)
 
-  if (is.null(refs)) {
+  if (is.null(refs) || !length(registry$symbols)) {
     return(tibble::tibble())
   }
 
@@ -102,7 +102,7 @@ resolve_provenance <- function(symbol_id, registry, visited = character()) {
   # local bindings
   id <- NULL
 
-  if (symbol_id %in% visited) {
+  if (symbol_id %in% visited || is.na(symbol_id)) {
     return(tibble::tibble())
   }
 

R/safe-symbol.R

@@ -48,7 +48,7 @@ new_safe_symbol <- function(
   session = NA_character_,
   action = NA_character_,
   metadata = list(),
-  id = paste0("symbol-", uuid::UUIDgenerate())
+  id = uuid::UUIDgenerate()
 ) {
   stopifnot(is.character(symbol))
   stopifnot(length(symbol) == 1)