Ensure citation html builder accepts dois with doi: prefix

R/detail_dataset.R

@@ -38,9 +38,11 @@ build_dataset_details_view <- function(result) {
         )
       )
 
+      permalink_url <- dataset_accession_url(as.character(ds$accession_code %|||% ""))
       header_rows <- add_permalink_button_to_last_row(
         header_rows,
-        ds$ds_code
+        ds$ds_code,
+        copy_url = permalink_url
       )
 
       htmltools::div(htmltools::tagList(header_rows))
@@ -103,8 +105,8 @@ build_dataset_details_view <- function(result) {
     }),
 
     dataset_citation = shiny::renderUI({
-      citation_html <- build_dataset_citation_text(ds, author_name, start_year)
-      citation_text <- xml2::xml_text(xml2::read_html(as.character(citation_html)))
+      citation_html <- build_dataset_citation_html(ds, author_name, start_year)
+      citation_text <- xml2::xml_text(xml2::read_html(paste0("<div>", as.character(citation_html), "</div>")))
       copy_icon <- load_svg_icon(
         "copy",
         style = "width:13px;height:13px;vertical-align:-0.1em;flex-shrink:0;"
@@ -151,26 +153,55 @@ parse_dataset_author_label <- function(owner_label) {
 }
 
 
-#' Build Dataset Citation Text (HTML)
+#' Extract Clean DOI from Accession Code
+#'
+#' Returns the bare DOI (without any "doi:" prefix) when `raw_accession`
+#' matches the DOI pattern, or NULL otherwise.
+#' @noRd
+extract_clean_doi <- function(raw_accession) {
+  if (grepl("^(doi:)?10\\.\\d{4,9}/", raw_accession)) {
+    sub("^doi:", "", raw_accession)
+  } else {
+    NULL
+  }
+}
+
+#' Resolve Dataset Accession Code to a Canonical URL
+#'
+#' Returns the best persistent URL for a dataset accession code:
+#' - DOI accession  -> `https://doi.org/<doi>`
+#' - VegBank legacy -> `https://identifiers.org/vegbank:<accession>`
+#' - Unrecognised   -> NULL (caller falls back to https://vegbank.org/cite)
+#' @noRd
+dataset_accession_url <- function(raw_accession) {
+  clean_doi <- extract_clean_doi(raw_accession)
+  if (!is.null(clean_doi)) {
+    return(paste0("https://doi.org/", clean_doi))
+  }
+  if (grepl("^VB\\.ds\\.\\d+\\.", raw_accession)) {
+    return(paste0("https://identifiers.org/vegbank:", raw_accession))
+  }
+  NULL
+}
+
+#' Build Dataset Citation HTML
 #'
 #' Returns the HTML-formatted citation string for a VegBank dataset.
 #' @noRd
-build_dataset_citation_text <- function(ds, author_name, start_year) {
+build_dataset_citation_html <- function(ds, author_name, start_year) {
   safe_author_html <- htmltools::htmlEscape(as.character(author_name %|||% "Unknown Author"))
   safe_name_html   <- htmltools::htmlEscape(as.character(ds$name %|||% "Unnamed Dataset"))
   raw_accession <- as.character(ds$accession_code %|||% "Unspecified")
 
-  is_doi <- grepl("^10\\.\\d{4,9}/", raw_accession)
+  url        <- dataset_accession_url(raw_accession)
+  clean_doi  <- extract_clean_doi(raw_accession)
   is_vegbank <- grepl("^VB\\.ds\\.\\d+\\.", raw_accession)
-  if (is_doi) {
-    display <- paste0("doi:", raw_accession)
-    url <- paste0("https://doi.org/", raw_accession)
+  if (!is.null(clean_doi)) {
+    display <- paste0("doi:", clean_doi)
   } else if (is_vegbank) {
     display <- paste0("vegbank:", raw_accession)
-    url <- paste0("https://identifiers.org/vegbank:", raw_accession)
   } else {
     display <- raw_accession
-    url <- NULL
   }
 
   if (!is.null(url)) {

R/detail_helpers.R

@@ -418,20 +418,23 @@ create_detail_link <- function(input_id, code_value, display_text) {
 
 #' Create Copy permalink Link Button
 #'
-#' Renders a minimal inline button that copies `vegbank.org/cite/<vb_code>` to
-#' the clipboard. The click behavior is implemented in `vegbank_app.js`.
+#' Renders a minimal inline button that copies a URL to the clipboard.
+#' By default the URL is `https://vegbank.org/cite/<vb_code>`; pass
+#' `copy_url` to override (e.g., a DOI URL for datasets with a DOI accession).
+#' The click behavior is implemented in `vegbank_app.js`.
 #'
 #' @param vb_code VegBank code (e.g., "ob.1234", "cc.567", "ds.987")
 #' @param label Button label text (defaults to "Copy permalink")
+#' @param copy_url Optional URL string to copy instead of the default cite URL
 #' @return An htmltools button tag, or NULL when vb_code is missing
 #' @noRd
-create_permalink_button <- function(vb_code, label = "Copy permalink") {
+create_permalink_button <- function(vb_code, label = "Copy permalink", copy_url = NULL) {
   if (is.null(vb_code) || length(vb_code) == 0 || is.na(vb_code) || !nzchar(trimws(as.character(vb_code)))) {
     return(NULL)
   }
 
   code <- trimws(as.character(vb_code)[1])
-  copy_text <- paste0("vegbank.org/cite/", code)
+  copy_text <- if (!is.null(copy_url)) copy_url else paste0("https://vegbank.org/cite/", code)
   copy_icon <- load_svg_icon(
     "copy",
     style = "width:13px;height:13px;vertical-align:-0.1em;flex-shrink:0;"
@@ -457,16 +460,17 @@ create_permalink_button <- function(vb_code, label = "Copy permalink") {
 #'
 #' @param rows List of htmltools tag elements (for header rows)
 #' @param vb_code VegBank code used for the permalink /cite URL
+#' @param copy_url Optional URL string passed through to `create_permalink_button`
 #' @return A list of header row tags with the last row wrapped in
 #'   `div.vb-copy-inline-row` when a copy button can be created
 #' @noRd
-add_permalink_button_to_last_row <- function(rows, vb_code) {
+add_permalink_button_to_last_row <- function(rows, vb_code, copy_url = NULL) {
   rows <- Filter(Negate(is.null), rows)
   if (length(rows) == 0) {
     return(rows)
   }
 
-  copy_button <- create_permalink_button(vb_code)
+  copy_button <- create_permalink_button(vb_code, copy_url = copy_url)
   if (is.null(copy_button)) {
     return(rows)
   }

inst/shiny/www/vegbank_styles.css

@@ -415,12 +415,14 @@ table.dataTable tbody tr.selected-entity:hover,
   position: fixed;
   top: var(--navbar-height);
   height: calc(100vh - var(--navbar-height));
+  height: calc(100dvh - var(--navbar-height));
   overflow-y: auto;
   background: #fff;
   border-left: 1px solid rgba(40, 70, 94, 0.15);
   box-shadow: -4px 0 20px rgba(0, 0, 0, 0.12), -2px 0 8px rgba(0, 0, 0, 0.08);
   z-index: 1050;
   padding: 0 20px 0;
+  padding: 0 20px env(safe-area-inset-bottom);
   transition: right 0.35s cubic-bezier(0.4, 0, 0.2, 1);
 }
 

tests/testthat/test_detail_concept.R

@@ -57,7 +57,7 @@ test_that("build_comm_concept_details_view header includes copy permalink button
 
   expect_true(grepl("vb-copy-permalink", html, fixed = TRUE))
   expect_true(grepl("Copy permalink", html, fixed = TRUE))
-  expect_true(grepl("vegbank.org/cite/cc.47882", html, fixed = TRUE))
+  expect_true(grepl("https://vegbank.org/cite/cc.47882", html, fixed = TRUE))
 })
 
 test_that("build_plant_concept_details_view handles valid data", {

tests/testthat/test_detail_dataset.R

@@ -19,10 +19,10 @@ test_that("parse_dataset_author_label handles NULL / NA / empty", {
   expect_equal(parse_dataset_author_label("   "),        "Unknown Author")
 })
 
-# ==== build_dataset_citation_text() ====
+# ==== build_dataset_citation_html() ====
 
-test_that("build_dataset_citation_text builds correct citation — start only", {
-  text <- build_dataset_citation_text(
+test_that("build_dataset_citation_html builds correct citation — start only", {
+  text <- build_dataset_citation_html(
     mock_dataset_ds201120,
     author_name = "Kyle Palmquist",
     start_year  = "2017"
@@ -35,10 +35,10 @@ test_that("build_dataset_citation_text builds correct citation — start only",
   expect_true(grepl("VB.ds.201120.DWLFOT", text, fixed = TRUE))
 })
 
-test_that("build_dataset_citation_text sanitizes dataset name", {
+test_that("build_dataset_citation_html sanitizes dataset name", {
   ds_xss <- mock_dataset_ds201120
   ds_xss$name <- '<script>alert("xss")</script>'
-  text <- build_dataset_citation_text(
+  text <- build_dataset_citation_html(
     ds_xss,
     author_name = "Kyle Palmquist",
     start_year  = "2017"
@@ -87,15 +87,38 @@ test_that("build_dataset_details_view header contains ds_code and name", {
   expect_true(grepl("unnamed dataset", html2, fixed = TRUE))
 })
 
-test_that("build_dataset_details_view header includes copy permalink button", {
+test_that("build_dataset_details_view header includes copy permalink button — VegBank accession uses identifiers.org", {
   mock_session <- shiny::MockShinySession$new()
 
   details <- build_dataset_details_view(mock_dataset_ds201120)
   html <- htmltools::renderTags(details$dataset_header(shinysession = mock_session))$html
 
   expect_true(grepl("vb-copy-permalink", html, fixed = TRUE))
   expect_true(grepl("Copy permalink", html, fixed = TRUE))
-  expect_true(grepl("vegbank.org/cite/ds.201120", html, fixed = TRUE))
+  expect_true(grepl("https://identifiers.org/vegbank:VB.ds.201120.DWLFOT", html, fixed = TRUE))
+  expect_false(grepl("vegbank.org/cite", html, fixed = TRUE))
+})
+
+test_that("build_dataset_details_view header uses identifiers.org permalink for unnamed VegBank dataset", {
+  mock_session <- shiny::MockShinySession$new()
+
+  details <- build_dataset_details_view(mock_dataset_ds201398)
+  html <- htmltools::renderTags(details$dataset_header(shinysession = mock_session))$html
+
+  expect_true(grepl("vb-copy-permalink", html, fixed = TRUE))
+  expect_true(grepl("https://identifiers.org/vegbank:VB.ds.201398.UNNAMEDDATASET", html, fixed = TRUE))
+  expect_false(grepl("vegbank.org/cite", html, fixed = TRUE))
+})
+
+test_that("build_dataset_details_view header uses doi.org permalink for DOI accession", {
+  mock_session <- shiny::MockShinySession$new()
+
+  details <- build_dataset_details_view(mock_dataset_ds201910)
+  html <- htmltools::renderTags(details$dataset_header(shinysession = mock_session))$html
+
+  expect_true(grepl("vb-copy-permalink", html, fixed = TRUE))
+  expect_true(grepl("https://doi.org/10.5072/FK26D61D4V", html, fixed = TRUE))
+  expect_false(grepl("vegbank.org/cite", html, fixed = TRUE))
 })
 
 test_that("build_dataset_details_view details card contains accession, author, plot count link", {
@@ -168,10 +191,10 @@ test_that("build_dataset_details_view details plot count link has correct ds_cod
   expect_true(grepl("obs-count-link", html, fixed = TRUE))
 })
 
-# ==== build_dataset_citation_text() accession/DOI link rendering ====
+# ==== build_dataset_citation_html() accession/DOI link rendering ====
 
-test_that("build_dataset_citation_text renders VegBank accession as correct link and label", {
-  tag <- build_dataset_citation_text(
+test_that("build_dataset_citation_html renders VegBank accession as correct link and label", {
+  tag <- build_dataset_citation_html(
     mock_dataset_ds201120,
     author_name = "Kyle Palmquist",
     start_year  = "2017"
@@ -181,8 +204,8 @@ test_that("build_dataset_citation_text renders VegBank accession as correct link
   expect_true(grepl("href=\"https://identifiers.org/vegbank:VB.ds.201120.DWLFOT\"", html, fixed = TRUE))
 })
 
-test_that("build_dataset_citation_text renders DOI as correct link and label", {
-  tag <- build_dataset_citation_text(
+test_that("build_dataset_citation_html renders DOI as correct link and label", {
+  tag <- build_dataset_citation_html(
     mock_dataset_ds201910,
     author_name = "Rushirah Nenuji",
     start_year  = "2026"
@@ -191,3 +214,12 @@ test_that("build_dataset_citation_text renders DOI as correct link and label", {
   expect_true(grepl(">doi:10.5072/FK26D61D4V<", html, fixed = TRUE))
   expect_true(grepl("href=\"https://doi.org/10.5072/FK26D61D4V\"", html, fixed = TRUE))
 })
+
+test_that("build_dataset_citation_html renders doi:-prefixed accession as link", {
+  ds <- mock_dataset_ds201910
+  ds$accession_code <- "doi:10.82902/J17P4J"
+  tag <- build_dataset_citation_html(ds, author_name = "Matthew Jones", start_year = "2026")
+  html <- as.character(tag)
+  expect_true(grepl(">doi:10.82902/J17P4J<", html, fixed = TRUE))
+  expect_true(grepl("href=\"https://doi.org/10.82902/J17P4J\"", html, fixed = TRUE))
+})

tests/testthat/test_detail_helpers.R

@@ -276,7 +276,7 @@ test_that("create_permalink_button builds a copy control with cite URL", {
   expect_true(grepl("vb-copy-permalink", html, fixed = TRUE))
   expect_true(grepl("Copy permalink", html, fixed = TRUE))
   expect_false(grepl("Copy permalink link", html, fixed = TRUE))
-  expect_true(grepl("vegbank.org/cite/ob.2948", html, fixed = TRUE))
+  expect_true(grepl("https://vegbank.org/cite/ob.2948", html, fixed = TRUE))
 })
 
 test_that("create_permalink_button returns NULL for missing vb_code", {

tests/testthat/test_detail_plot.R

@@ -275,7 +275,7 @@ test_that("build_plot_obs_details_view header includes copy permalink button", {
 
   expect_true(grepl("vb-copy-permalink", html, fixed = TRUE))
   expect_true(grepl("Copy permalink", html, fixed = TRUE))
-  expect_true(grepl("vegbank.org/cite/ob.2948", html, fixed = TRUE))
+  expect_true(grepl("https://vegbank.org/cite/ob.2948", html, fixed = TRUE))
 })
 
 test_that("normalize_plot_obs_result only uses first row of multi-row input", {