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dsROCrate 0.2.1

Bug Fixes

  • Removed a duplicate, conflicting definition of as.data.frame.safe_call() (two files each defined this S3 method with different output columns; only one could ever take effect, silently). The safe-call.R version — timestamp, user, r_cmd, fx, args, session, profile — is now the sole implementation.
  • Fixed print.safe_symbol() referencing stale column/parent fields left over from before the 0.2.0 symbol-model refactor; it now correctly displays the symbol's asset, expr, and session (guarding on both NULL and NA, since these fields default to NA_character_).
  • Fixed as.data.frame.symbol_registry(), which previously iterated over the columns of the underlying tibble instead of its rows (via lapply() on a data frame), causing it to error whenever called on a non-empty registry. It also referenced non-existent parent/column fields. The method now simply returns x$symbols coerced to a data frame, which already carries the correct columns.
  • Fixed register_symbol() erroring on a brand-new, empty registry (the very first symbol registered in any session): the emptiness check compared nrow() of a plain, pre-tibble list() before checking length(), producing a zero-length logical passed to ||. The length() check is now evaluated first, so it short-circuits correctly.
  • Fixed as.data.frame.safe_call()'s args column having an unstable name and shape depending on how many arguments the underlying call had (a single-argument call collapsed the column into one named after that argument, e.g. x; multiple arguments spread into several columns instead of one). The argument list is now wrapped with I(list(...)) so it always appears as a single, reliably-named args list-column.
  • Added regression tests for safe_call()/as.data.frame.safe_call(), print.safe_symbol(), and register_symbol()/as.data.frame.symbol_registry(), none of which previously had any test coverage.

Internal Changes

  • Removed unused internal helpers: has_symbol()/has_symbol.symbol_registry() (and its S3 export) and safe_symbol_reference()/new_safe_symbol_reference(), none of which were called anywhere in the package.
  • Removed leftover commented-out code from safe_symbol() and print.safe_call().
  • Added roxygen2 documentation (@param, @returns, @keywords internal, @noRd) and explanatory comments to the internal symbol-tracking functions introduced in 0.2.0 (safe_call(), safe_symbol(), safe_reference(), symbol_registry(), and their supporting utilities), with no change in behaviour.
  • Updated spell-check WORDLIST.
  • Re-rendered vignettes to refresh example output.

dsROCrate 0.2.0

Breaking Changes

  • The audit log tibble returned via safe_output() no longer includes a table column. It has been replaced by three more granular columns: kind (whether the tracked object is a table, resource or expression), asset (the resolved table/resource name) and expr (the associated R expression, when applicable). Code that reads the table column directly will need to be updated.

New Features

  • Added a symbol registry and call-tracking system (safe_symbol(), safe_call(), safe_reference(), symbol_registry()) that replaces regex-based parsing of Opal logs, modelling assignments and aggregate function calls as objects and resolving arguments back to the symbols/tables they reference.
  • Added a generic backend abstraction layer (backend_logs(), backend_options(), backend_users(), backend_projects(), backend_sys_perms(), and others) so internal code no longer calls opalr:: directly, paving the way for additional backends.
  • Added early Armadillo backend scaffolding: check_permissions(), init(), report(), safe_data(), safe_output(), safe_people() and safe_setting() now all have ArmadilloCredentials methods, returning clear "not yet implemented" errors ahead of full support.
  • Added default S3 methods for audit(), audit_engine() and check_permissions(), giving clearer errors when an unsupported connection object is supplied.
  • Added a verbose argument to check_permissions() (opal method) to optionally print a success message when permissions are sufficient.
  • Added print.safe_call() and print.safe_symbol() methods, plus as.data.frame() methods for safe_call and symbol_registry objects, for readable inspection of the new internal tracking objects.

Improvements

  • safe_people() now determines admin/auditor status from actual system permissions and group membership, rather than a hardcoded name check against "admin"/"administrator", improving compatibility with deployments that use differently named privileged accounts.
  • Permission lookup failures during safe_people() now fall back gracefully to an empty result instead of aborting the whole audit.
  • Consolidated backend-version and connection-validation logic into the new generic backend framework, reducing duplication between Opal-specific code paths.

Documentation

  • Removed a vignette section demonstrating direct calls to internal helper functions, which have since been renamed as part of the backend abstraction work.
  • Updated documentation to reflect that init(), safe_data(), report() and related functions now accept either opal or ArmadilloCredentials connections.

Internal Changes

  • Added test coverage for audit(), audit_engine() and check_permissions(), along with a mock-connection test helper, reducing reliance on a live demo Opal server.
  • Added uuid to Imports, used to generate unique IDs for tracked symbols.
  • Bumped the testthat version requirement in Suggests from >= 3.0.0 to >= 3.1.4.

dsROCrate 0.1.0

New Features

  • Added check_permissions() support for backend connections, allowing users to verify whether a connection has sufficient privileges to run safe_* auditing functions before execution (#15).
  • Permission validation now provides actionable feedback, including guidance on how to configure Opal users and roles when required permissions are missing (#15).
  • Added Opal version validation during backend checks to ensure compatibility with APIs required for auditing and permission verification workflows (#22).

Improvements

  • Refactored backend validation into an extensible S3 framework, providing a cleaner architecture for supporting additional backends in future releases (#23).
  • Introduced a unified backend validation workflow that standardises connection, version and permission checks across auditing functions (#23).
  • Replaced use of opalr::opal.datasources() with opalr::opal.projects(), reducing the permissions required for metadata extraction and improving compatibility with auditor accounts (#21).
  • Updated auditing workflows to support Opal's Audit System role, reducing the need for administrator-level accounts when generating RO-Crates and audit reports (#20).

Bug Fixes

  • Fixed generation of orphaned permission entities in RO-Crates by excluding administrator and auditor permissions from dataset permission records where corresponding user entities are not included (#19).
  • Improved consistency between safe_data() and safe_people() permission handling (#19).

Documentation

  • Updated deployment vignette to reference the FederatedMethods-maintained DataSHIELD Docker deployment resources and repository structure (#16).
  • Updated user documentation to reflect support for Opal's Audit System role and revised permission requirements (#20).
  • Reviewed documentation for internal helper functions and adjusted visibility of internal APIs where appropriate (#17).
  • Added documentation and examples for backend permission validation workflows (#15).

Internal Changes

  • Improved separation of concerns between connection validation, backend capability checks and permission validation (#22, #23).
  • Refined internal validation infrastructure to simplify future backend integrations.
  • General maintenance, testing and documentation updates.

dsROCrate 0.0.2

  • This patch addresses an issue with the vignettes. The safe_output.opal() S3 generic now uses overwrite = TRUE to update the root (./) entity.

dsROCrate 0.0.1

  • Initial CRAN submission.
  • This version contains standard functions for auditing (audit()), reporting (report()) and extracting five safe principle components (safe_*()).
  • This version currently only supports OBiBa's Opal as the backend.