Add changes for the Armadillo backend

DESCRIPTION

@@ -42,7 +42,6 @@ Imports:
     dplyr,
     DSMolgenisArmadillo,
     jsonlite,
-    methods,
     opalr,
     purrr,
     RcppTOML,
@@ -55,34 +54,5 @@ Imports:
 Depends: 
     R (>= 4.1.0)
 VignetteBuilder: knitr
-Collate: 
-    'ArmadilloCredentials-class.R'
-    'audit.R'
-    'audit_engine.R'
-    'dsROCrate-package.R'
-    'dsROCrate.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'
-    'utils-digest.R'
-    'utils-opal.R'
-    'utils-rocrate.R'
-    'utils-rocrateR.R'
-    'utils-safe_data.R'
-    'utils-safe_output.R'
-    'utils-safe_people.R'
-    'utils-safe_project.R'
-    'utils-safe_setting.R'
-    'utils-show.R'
-    'utils-tibble.R'
 URL: https://github.com/FederatedMethods/dsROCrate
 BugReports: https://github.com/FederatedMethods/dsROCrate/issues

NAMESPACE

@@ -1,6 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(audit,armadillo)
+S3method(audit,ArmadilloCredentials)
 S3method(audit,character)
 S3method(audit,cr8tor)
 S3method(audit,list)
@@ -30,9 +30,9 @@ S3method(flatten_safe_setting,default)
 S3method(flatten_safe_setting,rocrate)
 S3method(init,opal)
 S3method(init,rocrate)
-S3method(parse_user_profiles,armadillo)
+S3method(parse_user_profiles,ArmadilloCredentials)
 S3method(print,cr8tor_bundle)
-S3method(project_exists,armadillo)
+S3method(project_exists,ArmadilloCredentials)
 S3method(report,character)
 S3method(report,default)
 S3method(report,list)
@@ -49,7 +49,7 @@ S3method(safe_people,character)
 S3method(safe_people,default)
 S3method(safe_people,opal)
 S3method(safe_people,rocrate)
-S3method(safe_project,armadillo)
+S3method(safe_project,ArmadilloCredentials)
 S3method(safe_project,character)
 S3method(safe_project,default)
 S3method(safe_project,opal)
@@ -68,8 +68,5 @@ export(safe_output)
 export(safe_people)
 export(safe_project)
 export(safe_setting)
-exportMethods(safe_project)
-import(methods)
-importClassesFrom(DSMolgenisArmadillo,ArmadilloCredentials)
 importFrom(rocrateR,get_entity)
 importFrom(utils,write.csv)

R/audit.R

@@ -39,7 +39,7 @@ audit <- function(x, ...) {
 
 #' @rdname audit
 #' @export
-audit.armadillo <- function(x, ..., intent = NULL) {
+audit.ArmadilloCredentials <- function(x, ..., intent = NULL) {
   stop(
     "The audit for Armadillo backend is not currently implemented!",
     call. = FALSE

R/dsROCrate-package.R

@@ -2,7 +2,7 @@
 "_PACKAGE"
 
 ## usethis namespace: start
-#' @import methods
-#' @importClassesFrom DSMolgenisArmadillo ArmadilloCredentials
+# @import methods
+# @importClassesFrom DSMolgenisArmadillo ArmadilloCredentials
 ## usethis namespace: end
 NULL

R/safe_project.R

@@ -251,38 +251,27 @@ safe_project.rocrate <- function(
 }
 
 # S4 methods ----
-# Bridge method for your S4 class
-#' @method safe_project armadillo
+#' @method safe_project ArmadilloCredentials
 #' @rdname safe_project
 #' @export
-safe_project.armadillo <- function(x, ...) {
-  methods::callGeneric(x, ...)
-}
-
-#' @aliases safe_project,armadillo-method
-#' @export
-setMethod(
-  "safe_project",
-  signature(x = "armadillo"),
-  function(
-    x,
-    ...,
-    profile = "default",
-    project = NULL,
-    rocrate = rocrateR::rocrate_5s(),
-    asset_id_suffix = "#asset:",
-    project_id_suffix = "#project:",
-    path = NULL,
-    resources = NULL,
-    tables = NULL,
-    user = NULL
-  ) {
-    # check if the given `project` exists
-    project_exists(x, project = project)
+safe_project.ArmadilloCredentials <- function(
+  x,
+  ...,
+  profile = "default",
+  project = NULL,
+  rocrate = rocrateR::rocrate_5s(),
+  asset_id_suffix = "#asset:",
+  project_id_suffix = "#project:",
+  path = NULL,
+  resources = NULL,
+  tables = NULL,
+  user = NULL
+) {
+  # check if the given `project` exists
+  project_exists(x, project = project)
 
-    # retrieve details associated to `project`
-    project_details_tbl <- MolgenisArmadillo::armadillo.get_projects_info() |>
-      purrr::list_c() |>
-      tibble::as_tibble()
-  }
-)
+  # retrieve details associated to `project`
+  project_details_tbl <- MolgenisArmadillo::armadillo.get_projects_info() |>
+    purrr::list_c() |>
+    tibble::as_tibble()
+}

R/utils-connection.R

@@ -45,24 +45,13 @@ parse_user_profiles.opal <- function(x, ..., user) {
 }
 
 # S4 methods ----
-# Bridge method for your S4 class
-#' @method parse_user_profiles armadillo
+#' @method parse_user_profiles ArmadilloCredentials
 #' @rdname parse_user_profiles
 #' @export
-parse_user_profiles.armadillo <- function(x, ...) {
-  methods::callGeneric(x, ...)
+parse_user_profiles.ArmadilloCredentials <- function(x, ..., user) {
+  message("PLACEHOLDER!")
 }
 
-#' @aliases parse_user_profiles,armadillo-method
-#' @family Armadillo
-setMethod(
-  "parse_user_profiles",
-  signature(x = "armadillo"),
-  function(x, ..., user) {
-    message("PLACEHOLDER!")
-  }
-)
-
 #' Verify if project exists
 #'
 #' Wrapper for the [opalr::opal.project_exists()] and
@@ -104,19 +93,11 @@ project_exists.opal <- function(x, ..., project) {
 }
 
 # S4 methods ----
-# Bridge method for your S4 class
-#' @method project_exists armadillo
+#' @method project_exists ArmadilloCredentials
 #' @rdname project_exists
 #' @export
-project_exists.armadillo <- function(x, ...) {
-  methods::callGeneric(x, ...)
-}
-
-#' @aliases project_exists,armadillo-method
 #' @family Armadillo
-setMethod(
-  "project_exists",
-  signature(x = "armadillo"),
+project_exists.ArmadilloCredentials <-
   function(
     x,
     ...,
@@ -132,4 +113,3 @@ setMethod(
       )
     }
   }
-)

R/zzz.R

@@ -0,0 +1,3 @@
+.onLoad <- function(libname, pkgname) {
+  # methods::setOldClass("ArmadilloCredentials")
+}