added fix for set_unique_cl_names_dt

R/standardize_MAE.R

@@ -324,19 +324,33 @@ set_unique_cl_names_dt <- function(col_data, sep = " ") {
   clid <- get_env_identifiers("cellline")
 
   if (!is.null(col_data[[cellline_name]])) {
-    duplicated_ids <- col_data[[cellline_name]][duplicated(col_data[[cellline_name]])]
+    if (data.table::is.data.table(col_data)) {
+      # for data.table check multiple columns; and update cl names only if adding clid suffix can make them different
+      unique_col_names <- c(unlist(get_default_identifiers()[
+        c("cellline_name", "drug_name", "drug_name2",
+          "concentration2", "duration", "data_source")
+      ]), "normalization_type")
+      unique_col_names <- intersect(unique_col_names, names(col_data))
+      duplicated_ids <- col_data[[cellline_name]][duplicated(col_data, by = unique_col_names)]
+      unique_col_names_clid <- c(unique_col_names, get_default_identifiers()$cellline)
+      duplicated_ids_with_clid <- col_data[[cellline_name]][duplicated(col_data, by = unique_col_names_clid)]
+      duplicated_ids <- setdiff(duplicated_ids, duplicated_ids_with_clid)
+    } else {
+      duplicated_ids <- col_data[[cellline_name]][duplicated(col_data[[cellline_name]])]
+    }
+
     if (length(duplicated_ids) > 0) {
-      for (dup_id in unique(duplicated_ids)) {
-        dup_indices <- which(col_data[[cellline_name]] == dup_id)
-        col_data[[cellline_name]][dup_indices] <- 
-          paste0(
-            col_data[[cellline_name]][dup_indices],
-            sep,
-            "(", 
-            col_data[[clid]][dup_indices], 
-            ")"
-          )
-      }
+     for (dup_id in unique(duplicated_ids)) {
+      dup_indices <- which(col_data[[cellline_name]] == dup_id)
+      col_data[[cellline_name]][dup_indices] <- 
+        paste0(
+          col_data[[cellline_name]][dup_indices],
+          sep,
+          "(", 
+          col_data[[clid]][dup_indices], 
+          ")"
+        )
+      } 
     }
   }