Streamline package

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: dsROCrate
-Title: 'DataSHIELD' RO-Crate Wrapper Functions
+Title: 'DataSHIELD' RO-Crate Governance Functions
 Version: 0.0.1
 Authors@R: c(
     person(given = "Roberto",
@@ -26,7 +26,6 @@ License: MIT + file LICENSE
 Suggests: 
     dsBaseClient,
     DSI,
-    DSMolgenisArmadillo,
     DSOpal,
     knitr,
     MolgenisArmadillo,
@@ -41,6 +40,7 @@ RoxygenNote: 7.3.3
 Imports: 
     digest,
     dplyr,
+    DSMolgenisArmadillo,
     jsonlite,
     methods,
     purrr,
@@ -53,22 +53,24 @@ Imports:
     yaml
 Depends: 
     R (>= 4.1.0)
+Remotes:
+    ResearchObject/ro-crate-r
 VignetteBuilder: knitr
 Collate: 
     'ArmadilloCredentials-class.R'
-    'audit_cr8tor.R'
-    'audit_safe_people.R'
-    'audit_safe_project.R'
-    'audit_study.R'
+    'audit.R'
+    'audit_engine.R'
     'dsROCrate-package.R'
     'dsROCrate.R'
-    'rocrate_report.R'
+    'print.R'
+    'report.R'
     'safe_data.R'
     'safe_output.R'
     'safe_people.R'
     'safe_project.R'
     'safe_setting.R'
     'utils-armadillo.R'
+    'utils-audit.R'
     'utils-connection.R'
     'utils-cr8tor.R'
     'utils-date.R'

NAMESPACE

@@ -1,12 +1,13 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(audit_safe_people,default)
-S3method(audit_safe_people,opal)
-S3method(audit_safe_project,default)
-S3method(audit_safe_project,opal)
-S3method(audit_study,default)
-S3method(audit_study,list)
-S3method(audit_study,opal)
+S3method(audit,armadillo)
+S3method(audit,character)
+S3method(audit,cr8tor)
+S3method(audit,list)
+S3method(audit,opal)
+S3method(audit,rocrate)
+S3method(audit_engine,cr8tor)
+S3method(audit_engine,opal)
 S3method(extract_safe_data,opal)
 S3method(extract_safe_data,rocrate)
 S3method(extract_safe_output,opal)
@@ -29,10 +30,11 @@ S3method(flatten_safe_setting,default)
 S3method(flatten_safe_setting,rocrate)
 S3method(init,opal)
 S3method(init,rocrate)
-S3method(rocrate_report,character)
-S3method(rocrate_report,default)
-S3method(rocrate_report,list)
-S3method(rocrate_report,rocrate)
+S3method(print,cr8tor_bundle)
+S3method(report,character)
+S3method(report,default)
+S3method(report,list)
+S3method(report,rocrate)
 S3method(safe_data,character)
 S3method(safe_data,default)
 S3method(safe_data,opal)
@@ -55,13 +57,9 @@ S3method(safe_setting,default)
 S3method(safe_setting,opal)
 S3method(safe_setting,rocrate)
 export(armadillo_login)
-export(audit_cr8tor)
-export(audit_safe_people)
-export(audit_safe_project)
-export(audit_study)
+export(audit)
 export(init)
-export(load_cr8tor_bundle)
-export(rocrate_report)
+export(report)
 export(safe_data)
 export(safe_output)
 export(safe_people)

R/audit.R

@@ -0,0 +1,148 @@
+#' Create an audit RO-Crate
+#'
+#' Create an audit RO-Crate following the 5 Safes Principles.
+#'
+#' This function handles various audit types, which will be dispatched based on
+#' the input object. If the input object is
+#'
+#' \itemize{
+#'     \item a _connection_ to a DataSHIELD server (e.g., OBiBa's Opal):
+#'.    generates an RO-Crate object with deployment details, including outputs.
+#'     \item a _path_ pointing to
+#'     \itemize{
+#'         \item **a `cr8tor` archive / governance bundle**: generates an
+#'         RO-Crate object with pre-deployment governance details.
+#'         \item **an RO-Crate object**: generates an RO-Crate object with
+#'         clearly defined 5 Safes elements.
+#'     }
+#'     \item an _RO-Crate_ object: generates an RO-Crate object with clearly
+#'     defined 5 Safes elements.
+#' }
+#' @param x Object to be audited. This can be
+#'     \itemize{
+#'         \item a _connection_ to a DataSHIELD server (e.g., OBiBa's Opal).
+#'         \item a _path_ pointing to an RO-Crate OR a `cr8tor` archive /
+#'.        governance bundle.
+#'         \item an _RO-Crate_ object.
+#'     }
+#'     Alternatively, a list of any of the above.
+#' @param ... Additional arguments.
+#' @param intent Additional object with governance bundle/specification of the
+#'     intent of a project. It takes the same types as `x`.
+#' @inheritParams audit_engine
+#'
+#' @returns RO-Crate with audit details.
+#' @export
+audit <- function(x, ...) {
+  UseMethod("audit")
+}
+
+#' @rdname audit
+#' @export
+audit.armadillo <- function(x, ..., intent = NULL) {
+  # <PLACEHOLDER>
+}
+
+#' @rdname audit
+#' @export
+audit.character <- function(x, ..., intent = NULL) {
+  # verify if the given path exists, if not, return an error message
+  if (!file.exists(x)) {
+    stop("The given file does not exist!", call. = FALSE)
+  }
+
+  # attempt loading a `cr8tor` bundle
+  x_obj <- tryCatch(
+    load_cr8tor_bundle(x, ...),
+    error = function(e) NULL
+  )
+  # alternatively, attempt loading an RO-Crate
+  if (is.null(x_obj)) {
+    x_obj <- tryCatch(
+      rocrateR::load_rocrate(x, ...),
+      error = function(e) NULL
+    )
+  }
+
+  if (is.null(x_obj)) {
+    stop(
+      "The given path does not point to a valid `cr8tor` archive nor an `rocrate",
+      call. = FALSE
+    )
+  }
+
+  # attempt auditing intent
+  intent_lst <- audit_intent(intent, ...)
+
+  # call next method
+  main_audit <- audit(x_obj, intent_lst$main_audit_args)
+
+  # return list
+  if (is.null(intent_lst$intent_audit)) {
+    return(main_audit)
+  }
+  list(intent = intent_lst$intent_audit, deployment = main_audit)
+}
+
+#' @rdname audit
+#' @export
+audit.cr8tor <- function(x, ..., intent = NULL) {
+  # attempt auditing intent
+  intent_lst <- audit_intent(intent, ..., excluded_args = "path")
+
+  # audit_engine(x, exclude_args(..., "path"), intent = intent)
+
+  # call next method
+  main_audit <- audit_engine(x, intent_lst$main_audit_args)
+
+  # return list
+  if (is.null(intent_lst$intent_audit)) {
+    return(main_audit)
+  }
+  list(intent = intent_lst$intent_audit, deployment = main_audit)
+}
+
+#' @rdname audit
+#' @export
+audit.list <- function(x, ..., intent = NULL) {
+  purrr::map(x, audit, ..., intent = intent)
+}
+
+#' @rdname audit
+#' @export
+audit.opal <- function(
+  x,
+  ...,
+  intent = NULL,
+  project = NULL,
+  user = NULL,
+  logs_from = -Inf,
+  logs_to = Inf,
+  path = NULL
+) {
+  # attempt auditing intent
+  intent_lst <- audit_intent(intent, ...)
+
+  # call next method
+  main_audit <- audit_engine(
+    x,
+    project = c(intent_lst$main_audit_args$project, project),
+    user = c(intent_lst$main_audit_args$user, user),
+    logs_from = logs_from,
+    logs_to = logs_to,
+    path = path,
+    intent_lst$main_audit_args
+  )
+
+  # return list
+  if (is.null(intent_lst$intent_audit)) {
+    return(main_audit)
+  }
+  list(intent = intent_lst$intent_audit, deployment = main_audit)
+}
+
+#' @rdname audit
+#' @export
+audit.rocrate <- function(x, ..., intent = NULL) {
+  # <PLACEHOLDER>
+}