fix dataset references

results/_include/_dataset_descriptions.qmd

@@ -1,7 +1,10 @@
 ```{r dataset_description}
 #| echo: false
 lines <- pmap_chr(dataset_info, function(dataset_name, dataset_summary, dataset_description, data_reference, ...) {
-  ref <- split_cite_fun(data_reference)
+  bibs <- convert_to_bibtex(data_reference)
+  # Write new entries to library.bib
+  write_library(bibs)
+  ref <- get_bibtex_entries(bibs)
   rest <- list(...)
   source_dataset_id <- if ("source_dataset_id" %in% names(rest)) rest$source_dataset_id else NULL
   dataset_link <- if (!is.null(source_dataset_id) && dir.exists(paste0("../../datasets/", source_dataset_id))) {
@@ -19,7 +22,7 @@ lines <- pmap_chr(dataset_info, function(dataset_name, dataset_summary, dataset_
   strip_margin(glue::glue("
   |### {dataset_link}
   |
-  |{summ}{ref}.
+  |{summ} {ref}.
   |
   |{dataset_description %|% ''}
   |"))

results/_include/_load_data.qmd

@@ -3,6 +3,7 @@
 ```{r setup}
 #| include: false
 #| error: true
+#| echo: true
 
 library(tidyverse)
 library(funkyheatmap)
@@ -52,6 +53,31 @@ split_cite_fun <- function(keys) {
   paste0("[@", paste(refs, collapse = "; @"), "]")
 }
 
+
+convert_to_bibtex <- function(refs) {
+
+  bibtexhandle <- curl::new_handle()
+  curl::handle_setheaders(bibtexhandle, "accept" = "application/x-bibtex")
+
+  bibs <- map(refs, function(ref) {
+    if (grepl("^@", ref)) {
+      # text is already a bibtex, update citation key
+      ref
+    } else {
+      url <- paste0("https://doi.org/", ref)
+      res <- curl::curl_fetch_memory(url, handle = bibtexhandle)
+      if (res$status_code != 200) {
+        cli::cli_alert_warning(paste0("Error processing doi '", ref, "'"))
+        ""
+      } else {
+        rawToChar(res$content)
+      }
+    }
+  })
+  return(unlist(bibs))
+}
+
+
 get_bibtex_from_doi <- function(dois) {
   if (is.null(dois)) return("")
 

results/_include/_results_table.qmd

@@ -15,7 +15,7 @@ mean_na_zero <- function(x) {
 }
 
 res_tib1 <- res_tib0 %>% 
-  group_by(method_id, method_name, paper_reference, code_url) %>%
+  group_by(method_id, method_name, code_url) %>%
   summarise_if(is.numeric, mean_na_zero) %>%
   ungroup() %>%
   mutate(