fix dataset descriptions

openproblems-bio · Nov 29, 2024 · e87140d · e87140d
1 parent 25905ec
commit e87140d
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Showing 4 changed files with 80 additions and 71 deletions.
diff --git a/results/_include/_baseline_descriptions.qmd b/results/_include/_baseline_descriptions.qmd
@@ -9,25 +9,28 @@ lines <- pmap_chr(baselines, function(method_name, method_summary, method_descri
   references_doi <- pluck(rest, "references_doi", .default = NULL)
   references_bibtex <- pluck(rest, "references_bibtex", .default = NULL)
 
-  if ("paper_reference" %in% names(rest)) {
-    ref <- split_cite_fun(rest$paper_reference)
-  } else {
-    bibs <- c()
-    if (!is.null(references_doi) && !is.na(references_doi)) {
-      bibs <- get_bibtex_from_doi(references_doi)
-    }
-    if (!is.null(references_bibtex) && !is.na(references_bibtex)) {
-      bibs <- c(bibs, references_bibtex)
-    }
-    # Write new entries to library.bib
-    write_library(bibs)
-    # Get bibtex references
-    if (!is.null(bibs)) {
-      ref <- get_bibtex_entries(bibs)
+  ref <-
+    if ("paper_reference" %in% names(rest)) {
+      split_cite_fun(rest$paper_reference)
+    } else {
+      bibs <- c()
+      if (!is.null(references_doi) && !is.na(references_doi)) {
+        bibs <- get_bibtex_from_doi(references_doi)
+      }
+      if (!is.null(references_bibtex) && !is.na(references_bibtex)) {
+        bibs <- c(bibs, references_bibtex)
+      }
+      # Write new entries to library.bib
+      write_library(bibs)
+      # Get bibtex references
+      if (!is.null(bibs)) {
+        get_bibtex_entries(bibs)
+      } else {
+        ""
+      }
     } else {
-      ref <- ""
+      ""
     }
-  }
 
   if (ref != "") ref <- paste0(" ", ref)
 

diff --git a/results/_include/_dataset_descriptions.qmd b/results/_include/_dataset_descriptions.qmd
@@ -8,32 +8,34 @@ lines <- pmap_chr(dataset_info, function(dataset_id, dataset_name, dataset_summa
   date_created <- pluck(rest, "date_created", .default = NULL)
   file_size <- pluck(rest, "file_size", .default = NULL)
 
-  if (grep("^[a-zA-Z0-9]+[0-9]{4}[a-z]+$",data_reference) && !grepl("^@",data_reference)) {
-    ref <- split_cite_fun(data_reference)
-  } else {
-    bibs <- convert_to_bibtex(data_reference)
-    # Write new entries to library.bib
-    write_library(bibs)
-    ref <- get_bibtex_entries(bibs)
-  }
+  ref <-
+    if (grepl("^[a-zA-Z0-9]+[0-9]{4}[a-z]+$", data_reference) && !grepl("^@", data_reference)) {
+      split_cite_fun(data_reference)
+    } else {
+      bibs <- convert_to_bibtex(data_reference)
+      # Write new entries to library.bib
+      write_library(bibs)
+      get_bibtex_entries(bibs)
+    }
 
   if (ref != "") ref <- paste0(" ", ref)
   
-  dataset_link <- if (!is.null(source_dataset_id) && dir.exists(paste0("../../datasets/", source_dataset_id))) {
-    glue::glue("../../datasets/{source_dataset_id}")
-  } else if (dir.exists(paste0("../../datasets/", dataset_id))) {
-    glue::glue("../../datasets/{dataset_id}")
-  } else {
-    NULL
-  }
+  dataset_link <-
+    if (!is.null(source_dataset_id) && dir.exists(paste0("../../datasets/", source_dataset_id))) {
+      glue::glue("../../datasets/{source_dataset_id}")
+    } else if (dir.exists(paste0("../../datasets/", dataset_id))) {
+      glue::glue("../../datasets/{dataset_id}")
+    } else {
+      NULL
+    }
 
   # 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
+      structure(file_size, class = "object_size"),
+      units = "auto",
+      standard = "IEC",
+      digits = 2
     )
   }
 

diff --git a/results/_include/_method_descriptions.qmd b/results/_include/_method_descriptions.qmd
@@ -8,25 +8,27 @@ lines <- pmap_chr(method_info %>% filter(!is_baseline), function(method_name, me
   code_version <- pluck(rest, "code_version", .default = NULL)
   references_doi <- pluck(rest, "references_doi", .default = NULL)
   references_bibtex <- pluck(rest, "references_bibtex", .default = NULL)
-  if ("paper_reference" %in% names(rest)) {
-    ref <- split_cite_fun(rest$paper_reference)
-  } else {
-    bibs <- c()
-    if (!is.null(references_doi) && !is.na(references_doi)) {
-      bibs <- get_bibtex_from_doi(references_doi)
-    }
-    if (!is.null(references_bibtex) && !is.na(references_bibtex)) {
-      bibs <- c(bibs, references_bibtex)
-    }
-    # Write new entries to library.bib
-    write_library(bibs)
-    # Get bibtex references
-    if (!is.null(bibs)) {
-      ref <- get_bibtex_entries(bibs)
+
+  ref <-
+    if ("paper_reference" %in% names(rest)) {
+      split_cite_fun(rest$paper_reference)
     } else {
-      ref <- ""
+      bibs <- c()
+      if (!is.null(references_doi) && !is.na(references_doi)) {
+        bibs <- get_bibtex_from_doi(references_doi)
+      }
+      if (!is.null(references_bibtex) && !is.na(references_bibtex)) {
+        bibs <- c(bibs, references_bibtex)
+      }
+      # Write new entries to library.bib
+      write_library(bibs)
+      # Get bibtex references
+      if (!is.null(bibs)) {
+        get_bibtex_entries(bibs)
+      } else {
+        ""
+      }
     }
-  }
 
   if (ref != "") ref <- paste0(" ", ref)
   

diff --git a/results/_include/_metric_descriptions.qmd b/results/_include/_metric_descriptions.qmd
@@ -6,26 +6,28 @@ lines <- pmap_chr(metric_info, function(metric_name, metric_summary, metric_desc
   code_version <- pluck(rest, "code_version", .default = NULL)
   references_doi <- pluck(rest, "references_doi", .default = NULL)
   references_bibtex <- pluck(rest, "references_bibtex", .default = NULL)
-  if ("paper_reference" %in% names(rest)) {
-    ref <- split_cite_fun(rest$paper_reference)
-  } else {
-    bibs <- c()
-    if (!is.null(references_doi) && !is.na(references_doi)) {
-      bibs <- get_bibtex_from_doi(references_doi)
-    }
-    if (!is.null(references_bibtex) && !is.na(references_bibtex)) {
-      bibs <- c(bibs, references_bibtex)
-    }
-    # Write new entries to library.bib
-    write_library(bibs)
-
-    # Get bibtex references
-    if (!is.null(bibs)) {
-      ref <- get_bibtex_entries(bibs)
+  
+  ref <-
+    if ("paper_reference" %in% names(rest)) {
+      split_cite_fun(rest$paper_reference)
     } else {
-      ref <- ""
+      bibs <- c()
+      if (!is.null(references_doi) && !is.na(references_doi)) {
+        bibs <- get_bibtex_from_doi(references_doi)
+      }
+      if (!is.null(references_bibtex) && !is.na(references_bibtex)) {
+        bibs <- c(bibs, references_bibtex)
+      }
+      # Write new entries to library.bib
+      write_library(bibs)
+
+      # Get bibtex references
+      if (!is.null(bibs)) {
+        get_bibtex_entries(bibs)
+      } else {
+        ""
+      }
     }
-  }
 
   if (ref != "") ref <- paste0(" ", ref)