Fix parse_ml_filename() misparsing year/country-stratified filenames

R/merge_ml_results.R

@@ -21,6 +21,7 @@
 #'
 #' @examples
 #' parse_ml_filename("Csp_drug_AMX_genes_binary_42_top_features.tsv")
+#' parse_ml_filename("Csp_drug_year_AMX_2010-2015_genes_binary_year_42_performance.tsv")
 #'
 #' @export
 parse_ml_filename <- function(filename) {
@@ -63,25 +64,30 @@ parse_ml_filename <- function(filename) {
     # Case A: drug_class
     if (xs[i + 1] == "class") {
       out$drug_label <- "drug_class"
-      out$drug_or_class <- xs[i + 2]
-      i <- i + 3
+      i <- i + 2
     }
     # Case B: simple drug
     else {
       out$drug_label <- "drug"
-      out$drug_or_class <- xs[i + 1]
-      i <- i + 2
+      i <- i + 1
     }
   } else {
     stop("ERROR: expected 'drug' token after species")
   }
 
   # ---------------------------
-  # 4. Stratified?
+  # 4. Stratified? (the strat label, if present, comes before the
+  # drug/drug_class value, e.g. "..._drug_year_AMX_2010-2015_...")
   # ---------------------------
   if (i <= length(xs) && xs[i] %in% c("year", "country")) {
     out$strat_label <- xs[i]
     i <- i + 1
+  }
+
+  out$drug_or_class <- xs[i]
+  i <- i + 1
+
+  if (!is.na(out$strat_label)) {
     out$strat_value <- xs[i]
     i <- i + 1
   }

tests/testthat/test-merge-ml-results.R

@@ -0,0 +1,61 @@
+# Unit tests for parse_ml_filename() in merge_ml_results.R.
+
+test_that("parse_ml_filename parses an unstratified drug filename", {
+  out <- parse_ml_filename("Csp_drug_AMX_genes_binary_42_top_features.tsv")
+
+  expect_false(out$shuffled)
+  expect_equal(out$species, "Csp")
+  expect_equal(out$drug_label, "drug")
+  expect_equal(out$drug_or_class, "AMX")
+  expect_true(is.na(out$strat_label))
+  expect_true(is.na(out$strat_value))
+  expect_equal(out$feature_type, "genes")
+  expect_equal(out$feature_subtype, "binary")
+  expect_equal(out$seed, 42L)
+})
+
+test_that("parse_ml_filename parses an unstratified drug_class filename", {
+  out <- parse_ml_filename("Csp_drug_class_AMINOGLYCOSIDES_genes_binary_42_performance.tsv")
+
+  expect_equal(out$drug_label, "drug_class")
+  expect_equal(out$drug_or_class, "AMINOGLYCOSIDES")
+  expect_true(is.na(out$strat_label))
+  expect_equal(out$seed, 42L)
+})
+
+test_that("parse_ml_filename detects a shuffled run", {
+  out <- parse_ml_filename("shuffled_Csp_drug_AMX_genes_binary_42_top_features.tsv")
+
+  expect_true(out$shuffled)
+  expect_equal(out$drug_or_class, "AMX")
+})
+
+test_that("parse_ml_filename parses a year-stratified drug filename", {
+  # The strat label sits between "drug" and the drug value in the actual
+  # filenames written by the matrix-generation code, e.g.
+  # "<species>_drug_year_<drug>_<year_range>_...".
+  out <- parse_ml_filename(
+    "Csp_drug_year_AMX_2010-2015_genes_binary_year_42_performance.tsv"
+  )
+
+  expect_equal(out$species, "Csp")
+  expect_equal(out$drug_label, "drug")
+  expect_equal(out$drug_or_class, "AMX")
+  expect_equal(out$strat_label, "year")
+  expect_equal(out$strat_value, "2010-2015")
+  expect_equal(out$feature_type, "genes")
+  expect_equal(out$feature_subtype, "binary")
+  expect_equal(out$seed, 42L)
+})
+
+test_that("parse_ml_filename parses a country-stratified drug_class filename", {
+  out <- parse_ml_filename(
+    "Csp_drug_class_country_AMINOGLYCOSIDES_USA_genes_binary_country_7_top_features.tsv"
+  )
+
+  expect_equal(out$drug_label, "drug_class")
+  expect_equal(out$drug_or_class, "AMINOGLYCOSIDES")
+  expect_equal(out$strat_label, "country")
+  expect_equal(out$strat_value, "USA")
+  expect_equal(out$seed, 7L)
+})