Merge remote-tracking branch 'origin/main' into feature/no-ref/add-in…

…fo-to-method

CHANGELOG.md

@@ -12,12 +12,18 @@
 
 * Update base images documentation (PR #342).
 
-* Add foundation models benchmark page (PR #354)
+* Add foundation models benchmark page (PR #354).
+
+* Add url to benchmark datasets to dataset page (PR #362).
+
+* Change "n x m" to "n cells × m genes" on dataset info (PR #362).
 
 ## BUG FIXES
 
 * Fix error in summary figure when not all method info ids are present in the results (PR #330).
 
+* Fix "used in" section in dataset pages (PR #362).
+
 # openproblems.bio v2.3.6
 
 ## NEW CONTENT

datasets/_include/_index_template.qmd

@@ -122,7 +122,7 @@ metadata <- tribble(
   "Reference", "bi bi-file-earmark-text", paste0("@", uns$dataset_reference),
   "Size", "bi bi-cloud-download", file_size_str,
   "Created", "bi bi-calendar", uns$date_created,
-  "Dimensions", "bi bi-box", shape_str
+  "Dimensions", "bi bi-box", glue::glue("{shape[[1]]} cells × {shape[[2]]} genes")
 )
 metadata_lines <- paste0(
   "<i class=\"", metadata$icon, "\"></i> ", substitute_underscores(metadata$value), "  \n"
@@ -169,7 +169,8 @@ cat("#### Used in\n\n")
 if (nrow(related_tasks) == 0) {
   cat("No related benchmarks found.\n")
 } else {
-  links <- paste0("* [", related_tasks$task_name, "](/results/", related_tasks$task_id, ")  ")
+  task_id <- gsub("task_", "", related_tasks$task_id)
+  links <- paste0("* [", related_tasks$task_name, "](/results/", task_id, ")  ")
   cat(paste(links, collapse = "\n"))
 }
 

results/_include/_dataset_descriptions.qmd

@@ -2,10 +2,22 @@
 #| echo: false
 lines <- pmap_chr(dataset_info, function(dataset_name, dataset_summary, dataset_description, data_reference, ...) {
   ref <- split_cite_fun(data_reference)
+  rest <- list(...)
+  source_dataset_id <- if ("source_dataset_id" %in% names(rest)) rest$source_dataset_id else NULL
+  dataset_link <- if (!is.null(source_dataset_id) && dir.exists(paste0("../../datasets/", source_dataset_id))) {
+    glue::glue("[{dataset_name}](/datasets/{source_dataset_id})")
+  } else if ("scPerturb" %in% dataset_name) {
+    dataset_name
+  } else if (dir.exists(paste0("../../datasets/", rest$dataset_id))) {
+    glue::glue("[{dataset_name}](/datasets/{rest$dataset_id})")
+  } else {
+    dataset_name
+  }
   if (ref != "") ref <- paste0(" ", ref)
   summ <- (dataset_summary %|% "Missing 'dataset_summary'") %>% str_replace_all("\\n", " ") %>% str_replace_all("\\. *$", "")
+  
   strip_margin(glue::glue("
-  |### {dataset_name}
+  |### {dataset_link}
   |
   |{summ}{ref}.
   |