Merge pull request #1620 from bigomics/mo-samples-from-pgx

feat: retain common samples on pgx multiomics upload

Author: ESCRI11

components/board.upload/R/upload_module_preview_counts.R

@@ -385,6 +385,7 @@ upload_table_preview_counts_server <- function(id,
       }
 
       # Load data once and cache both data frames and column names
+      samples_cache <- list()
       data_cache <- list()
       col_lists <- list()
       file_names <- character()
@@ -403,6 +404,7 @@ upload_table_preview_counts_server <- function(id,
           } else {
             df <- pgx_data$counts
           }
+          samples_cache[[i]] <- pgx_data$samples
           data_cache[[i]] <- df
           col_lists[[i]] <- colnames(df)
           file_names[i] <- dataset
@@ -481,6 +483,16 @@ upload_table_preview_counts_server <- function(id,
         df <- df[, common_cols, drop = FALSE]
         combined_df <- rbind(combined_df, df)
       }
+
+      # Combine samples_cache by intersecting rownames (only for pgx multi-omics upload)
+      if (length(samples_cache) > 0) {
+        # Find common rownames in all sample files (no prefixing!)
+        rownames_list <- lapply(samples_cache, rownames)
+        common_rows <- Reduce(intersect, rownames_list)
+        combined_samples <- samples_cache[[1]][common_rows, , drop = FALSE]
+        uploaded$samples.csv <- combined_samples
+      }
+
       uploaded$counts.csv <- combined_df
     })