Merge remote-tracking branch 'origin/main' into feature/task_batch_in…

…tegration/update_results
openproblems-bio · Jan 23, 2025 · 6b81d51 · 6b81d51
2 parents d9ee7ba + e2a0162
commit 6b81d51
Showing 3 changed files with 27 additions and 13 deletions.
diff --git a/.github/workflows/quarto_netlify.yml b/.github/workflows/quarto_netlify.yml
@@ -66,6 +66,12 @@ jobs:
       - name: Render with Quarto
         shell: bash -l {0}  
         run: |
+          # touch results/*/library.bib files
+          for task in results/*; do
+            touch "$task/library.bib"
+          done
+
+          # render
           quarto render --profile evaluate_code
       
       ## push actions

diff --git a/results/_generate_task_pages.py b/results/_generate_task_pages.py
@@ -43,3 +43,8 @@
     print(f"Write to {index_qmd}", flush=True)
     with index_qmd.open("w", encoding ="utf-8") as f:
         f.write(content)
+
+    library = task_info_file.parent.parent / "library.bib"
+    if not library.exists():
+        print(f"Create {library}", flush=True)
+        library.write_text("")
diff --git a/results/_include/_dataset_descriptions.qmd b/results/_include/_dataset_descriptions.qmd
@@ -30,27 +30,30 @@ lines <- pmap_chr(dataset_info, function(dataset_id, dataset_name, dataset_summa
     }
 
   # Make file_size human readable
-  if (!is.null(file_size)) {
-    file_size_str <- format(
-      structure(file_size, class = "object_size"),
-      units = "auto",
-      standard = "IEC",
-      digits = 2
-    )
-  }
+  file_size_str <-
+    if (is.na(file_size) || is.null(file_size)) {
+      NULL
+    } else {
+      format(
+        structure(file_size, class = "object_size"),
+        units = "auto",
+        standard = "IEC",
+        digits = 2
+      )
+    }
 
   dataset_meta <- tribble(
     ~icon, ~value,
     "bi bi-link-45deg", if(!is.null(dataset_link)) paste0("[Source dataset](", dataset_link, ")") else NULL,
     "bi bi-box-arrow-up-right", if(!is.null(data_url)) paste0("[Data source](", data_url, ")") else NULL,
     "bi bi-calendar", if(!is.null(date_created)) paste0(date_created) else NULL,
-    "bi bi-file-earmark-text", if(!is.null(file_size)) file_size_str else NULL,
+    "bi bi-file-earmark-text", file_size_str,
     ) %>% filter(!sapply(value, is.null))
   
   meta_list <- paste(
-      paste0("<i class=\"", dataset_meta$icon, "\"></i> ", dataset_meta$value),
-      collapse = " · "
-    )
+    paste0("<i class=\"", dataset_meta$icon, "\"></i> ", dataset_meta$value),
+    collapse = " · "
+  )
   
   summ <- (dataset_summary %|% "Missing 'dataset_summary'") %>% str_replace_all("\\n", " ") %>% str_replace_all("\\. *$", "")
   
@@ -65,4 +68,4 @@ lines <- pmap_chr(dataset_info, function(dataset_id, dataset_name, dataset_summa
   |"))
 })
 knitr::asis_output(paste(lines, collapse = "\n"))
-```
+ ```