fix documentation and linking issues from #306

.github/workflows/R-CMD-check.yaml

@@ -29,21 +29,21 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: rcmdcheck
 
-      - uses: r-lib/actions/check-r-package@v1
+      - uses: r-lib/actions/check-r-package@v2
 
       - name: Show testthat output
         if: always()
@@ -52,7 +52,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@main
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dataone
-Version: 2.2.2
-Date: 2022-06-08
+Version: 2.3.0
+Date: 2025-10-08
 Title: R Interface to the DataONE REST API
 Authors@R: c( person("Matthew B.", "Jones", role = c("aut","cre"), email = "jones@nceas.ucsb.edu", comment=c(ORCID = "0000-0003-0077-4738")), 
   person("Peter", "Slaughter", role = "aut", email = "slaughter@nceas.ucsb.edu", comment=c(ORCID = "0000-0002-2192-403X")),
@@ -62,4 +62,5 @@ Collate:
     'dataone-package.R'
 Encoding: UTF-8
 VignetteBuilder: knitr
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.3
+Roxygen: list(markdown = TRUE)

R/AbstractTableDescriber.R

@@ -30,13 +30,13 @@
 #' For example, the EMLParser registers itself as a handler for eml v2.0.0 - v2.1.1
 #' with the following.
 #' 
-#' \code{
+#' `
 #' if (!exists("tableDescriber.registry")) tableDescriber.registry <- list()
 #' tableDescriber.registry[[ "eml://ecoinformatics.org/eml-2.0.0" ]] <- "EMLParser"
 #' tableDescriber.registry[[ "eml://ecoinformatics.org/eml-2.0.1" ]] <- "EMLParser"
 #' tableDescriber.registry[[ "eml://ecoinformatics.org/eml-2.1.0" ]] <- "EMLParser"
 #' tableDescriber.registry[[ "eml://ecoinformatics.org/eml-2.1.1" ]] <- "EMLParser"
-#' }
+#' `
 #' 
 #' Note that the key in the list is the DataONE formatIdentifier that can be 
 #' found at "https://cn.dataone.org/cn/v2/formats".
@@ -195,7 +195,7 @@ setGeneric("data.tableAttributeOrientation", function(x, index, ...) {
 #' @param index - the index of the table within the document
 #' @param ... Additional parameters
 #' @return the number of lines to skip
-#' @seealso \code{help(read.table)}
+#' @seealso `help(read.table)`
 #' @author rnahf
 #' @export
 setGeneric("data.tableSkipLinesHeader", function(x, index, ...) {

R/AuthenticationManager.R

@@ -29,41 +29,37 @@
 #' updating objects on DataONE nodes and reserving identifiers might fail if your 
 #' authorization credentials are missing or expired.
 #' 
-#' DataONE version 1.0 identifies you using CILogon-provided x509 certificates. DataONE has 
-#' partnered with CILogon to provide a widely-accessible certificate issuing mechanism 
-#' that allows DataONE users to use existing trusted institutional and public accounts.
-#' 
-#' DataONE version 2.0 provides an addition authentication mechanism known as
-#' authentication tokens. For information about tokens and instructions for generating
+#' DataONE version 2.0 provides an authentication mechanism known using JWT
+#' Bearer tokens. For information about tokens and instructions for generating
 #' a token for use with the dataone R package, view the overview document by
-#' entering the command: \code{'vignette("dataone-overview")'}. DataONE authentication
-#' tokens can be obtained by signing in to your DataONE account at https://search.dataone.org.
+#' entering the command: `'vignette("v01-dataone-overview")'`. DataONE authentication
+#' tokens can be obtained by signing in to your DataONE account at https://search.dataone.org
+#' and copying the token from your profile settings.
+#' 
+#' Additionally, DataONE API version 1.0 identifies you using CILogon-provided x509 certificates. 
+#' DataONE partnered with CILogon to provide a widely-accessible certificate issuing mechanism 
+#' that allows DataONE users to use existing trusted institutional and public accounts, but this method
+#' is deprecated and generally users should use JWT Bearer tokens as described above.
 #' 
-#' CILogon recognizes many identity providers, including many universities as well as
-#' Google, so most times users new to DataONE can get certificates using one
-#' of their existing accounts. For more information about the CILogon service, see 
-#' \url{https://cilogon.org/?skin=DataONE} .
-#' @slot obscured Value of type \code{"character"} Is authentication disabled (obscured)?
+#' @slot obscured Value of type `"character"` Is authentication disabled (obscured)?
 #' @rdname AuthenticationManager-class
 #' @aliases AuthenticationManager-class
 #' @section Methods:
-#' \itemize{
-#'  \item{\code{\link{AuthenticationManager}}}{: Create an AuthenticationManager object.}
-#'  \item{\code{\link{isAuthValid}}}{: Verify authentication for a member node.}
-#'  \item{\code{\link{getToken}}}{: Get the value of the DataONE Authentication Token, if one exists.}
-#'  \item{\code{\link{getCert}}}{: Get the DataONE X.509 Certificate location.}
-#'  \item{\code{\link{getAuthMethod}}}{: Get the current valid authentication mechanism.}
-#'  \item{\code{\link{getAuthSubject}}}{: Get the authentication subject.}
-#'  \item{\code{\link{getAuthExpires}}}{: Get the expiration date of the current authentication method.}
-#'  \item{\code{\link{isAuthExpired}}}{: Check if the currently valid authentication method has reached the expiration time.}
-#'  \item{\code{\link{obscureAuth}}}{: Temporarily disable DataONE authentication.}
-#'  \item{\code{\link{restoreAuth}}}{: Restore authentication (after being disabled with \code{obscureAuth}).}
-#'  \item{\code{\link{showAuth}}}{: Display all authentication information.}
-#'  \item{\code{\link{getTokenInfo}}}{: Display all authentication token information.}
-#'  \item{\code{\link{getCertInfo}}}{: Display all X.509 certificate information.}
+#' * [AuthenticationManager()]: Create an AuthenticationManager object
+#' * [isAuthValid()]: Verify authentication for a member node
+#' * [getToken()]: Get the value of the DataONE Authentication Token, if one exists
+#' * [getCert()]: Get the DataONE X.509 Certificate location
+#' * [getAuthMethod()]: Get the current valid authentication mechanism
+#' * [getAuthSubject()]: Get the authentication subject
+#' * [getAuthExpires()]: Get the expiration date of the current authentication method
+#' * [isAuthExpired()]: Check if the currently valid authentication method has reached the expiration time
+#' * [obscureAuth()]: Temporarily disable DataONE authentication
+#' * [restoreAuth()]: Restore authentication (after being disabled with `obscureAuth`)
+#' * [showAuth()]: Display all authentication information
+#' * [getTokenInfo()]: Display all authentication token information
+#' * [getCertInfo()]: Display all X.509 certificate information
 #'  
-#' }
-#' @seealso \code{\link{dataone}}{ package description.}
+#' @seealso [dataone()] package description.
 #' @import base64enc
 #' @importFrom jsonlite fromJSON
 #' @include D1Node.R
@@ -99,7 +95,7 @@ setMethod("AuthenticationManager", signature=character(), function() {
 #' via the R options facility, it will be used i.e. available via getOption("dataone_token").  However, 
 #' authentication tokens can only be used for DataONE v2 or higher nodes. X.509 certificates can be used 
 #' with DataONE v1 or higher nodes. 
-#' See the \emph{"dataone"} vignette \emph{"dataone-overview"} for more information on authentication.
+#' See the *"dataone"* vignette *"v01-dataone-overview"* for more information on authentication.
 #' @param .Object An AuthenticationManager instance
 #' @param node The node object (MNode or CNode) that authentication is being checked for.
 #' @param ... additional parameters
@@ -181,8 +177,8 @@ setGeneric("getAuthMethod", function(.Object, ...) {
 })
 
 #' @rdname getAuthMethod
-#' @details The current authentication method being used, either an authentication token or an X.509 certificate. The \code{'node'}
-#' argument is used to determine the authentication mechanism that is appropriate for the specified \code{'node'}.
+#' @details The current authentication method being used, either an authentication token or an X.509 certificate. The `'node'`
+#' argument is used to determine the authentication mechanism that is appropriate for the specified `'node'`.
 #' For example, authentication tokens are supported on DataONE nodes that use the DataONE V2.0 API or higher, so if the 
 #' node uses the V1 API, then only an X.509 certificate can be used.
 #' @param node A D1Node instance to determine the authentication method for.
@@ -203,8 +199,8 @@ setGeneric("getAuthSubject", function(.Object, ...) {
 
 #' @rdname getAuthSubject
 #' @details The authenticated user, aka 'subject' is retrieved from the authentication mechanism
-#' currently being used, either an authentication token or an X.509 certificate. The \code{'node'}
-#' argument is used to determine the authentication mechanism that is appropriate for the specified \code{'node'}.
+#' currently being used, either an authentication token or an X.509 certificate. The `'node'`
+#' argument is used to determine the authentication mechanism that is appropriate for the specified `'node'`.
 #' For example, authentication tokens are supported on DataONE nodes that use the DataONE V2.0 API or higher, so if the 
 #' node uses the V1 API, then only an X.509 certificate can be used.
 #' @param node A D1Node instance
@@ -248,10 +244,10 @@ setMethod("isAuthExpired", signature("AuthenticationManager"), function(.Object,
 })
 
 #' Temporarily disable DataONE authentication.
-#' @description Calling \code{obscureAuth} temporarily disables authentication so that
+#' @description Calling `obscureAuth` temporarily disables authentication so that
 #' @details This method is intended to be used for authentication testing.
-#' \code{isAuthValid} will return FALSE. Authentication can be re-enabled by calling
-#' \code{restoreAuth}.
+#' `isAuthValid` will return FALSE. Authentication can be re-enabled by calling
+#' `restoreAuth`.
 #' @rdname obscureAuth
 #' @aliases obscureAuth
 #' @param .Object An AuthenticationManager instance
@@ -266,7 +262,7 @@ setMethod("obscureAuth", signature("AuthenticationManager"), function(.Object) {
     return(.Object)
 })
 
-#' Restore authentication (after being disabled with \code{obscureAuth}).
+#' Restore authentication (after being disabled with `obscureAuth`).
 #' @rdname restoreAuth
 #' @aliases restoreAuth
 #' @param .Object An AuthenticationManager instance
@@ -315,7 +311,7 @@ parseAuthToken <- function(authToken) {
 #' Evaluate DataONE authentication.
 #' @description A valid DataONE authentication method is looked for and all
 #' authentication information is retrieved from it.
-#' @details If the node specified in the \code{'node'} parameter is a DataONE v2 node
+#' @details If the node specified in the `'node'` parameter is a DataONE v2 node
 #' or higher, then an authentication token is checked if one exists. If it is readable
 #' and not expired, then information for the token is returned. If a valid token does
 #' not exist, then the X.509 certificate is checked, if it exists. If it is valid