Refactor resistance summary calculation

Updated resistance summary calculation to read from the database and include a count of resistant classes.

Author: AbhirupaGhosh

R/data_processing.R

@@ -1370,15 +1370,18 @@ cleanMetaData <- function(duckdb_path, path, ref_file_path = "data_raw/") {
     dplyr::filter(genome_drug.resistant_phenotype %in% c("Resistant", "Susceptible")) |>
     DBI::dbWriteTable(conn = con, name = "filtered_metadata", overwrite = TRUE)
 
-  resistance_summary <- dplyr::tbl(con, "filtered_metadata") |>
-    tibble::as_tibble() |>
-    dplyr::filter(genome_drug.resistant_phenotype == "Resistant") |>
-    dplyr::group_by(genome.genome_id) |>
-    dplyr::summarise(
-      num_resistant_classes = dplyr::n_distinct(drug_class),
-      resistant_classes = paste(unique(class_abbr), collapse = "_")
-    )
-
+   resistance_summary <- DBI::dbReadTable(con, "filtered_metadata") |>
+  dplyr::filter(genome_drug.resistant_phenotype == "Resistant") |>
+  dplyr::group_by(genome.genome_id) |>
+  dplyr::summarise(
+    resistant_classes = paste(sort(unique(class_abbr)), collapse = "_"),
+    .groups = "drop"
+  ) |>
+  dplyr::collect() |>
+  dplyr::mutate(
+    num_resistant_classes = stringr::str_count(resistant_classes, "_") + 1
+  ) 
+  
   year_breaks <- seq(1980, 2026, by = 5)
   dplyr::tbl(con, "filtered_metadata") |>
     tibble::as_tibble() |>