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 It has been replaced by three more granular columns: kind (whether the tracked object is a table, resource or expression), asset (the resolved table/resource name) and expr (the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.

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.

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.

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.

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.

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).

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).

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).

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).

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.

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

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.