Merge pull request #229 from MoTrPAC/fix-mw-validation

Fix refmet name validation

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: MotrpacBicQC
 Type: Package
 Title: QC/QA functions for the MoTrPAC community
-Version: 0.9.1
-Date: 2024-02-02
+Version: 0.9.12
+Date: 2024-02-22
 Author: MoTrPAC Bioinformatics Center
 Maintainer: David Jimenez-Morales <davidjm@stanford.edu>
 Description: R Package for the analysis of MoTrPAC datasets. 

R/metabolomics_data_dictionary.R

@@ -97,7 +97,7 @@ validate_refmetname <- function(dataf, verbose){
 
     search_api <- paste0("https://www.metabolomicsworkbench.org/rest/refmet/match/",URLencode(rn),"/name/")
     here <- jsonlite::fromJSON(search_api)
-    if(length(here) == 0){
+    if(here$refmet_name == "-"){
       if(verbose) message(paste0("      (-) `refmet_name` [`", rn, "`] not available in RefMet. Please, contact MW/BIC (Error RN1)"))
       irm <- irm + 1
       idna <- idna + 1

tests/testthat/test-refmet.R

@@ -0,0 +1,39 @@
+context("Testing validate_refmetname function")
+
+test_that("validate_refmetname handles known refmet_name correctly", {
+  # Example test data
+  test_data <- data.frame(
+    refmet_name = c("1-Methyl nicotinamide",  "11-Deoxycortisol", "This Should Fail", "I hope this as well---", "-"),
+    stringsAsFactors = FALSE
+  )
+
+  # Call the function with verbose = FALSE to suppress messages during test
+  actual_missed_ids <- validate_refmetname(test_data, verbose = FALSE)
+
+  # Check if the actual missed IDs match the expected outcome
+  expect_equal(actual_missed_ids, 3)
+})
+
+
+test_that("Successful API call returns correctly structured list with no additional elements", {
+  # Known good refmet_name that will return a successful response
+  test_refmet_name <- "11-Deoxycortisol"
+
+  # Expected elements in the response
+  expected_elements <- c("refmet_name", "formula", "exactmass", "super_class", "main_class", "sub_class")
+
+  search_api <- paste0("https://www.metabolomicsworkbench.org/rest/refmet/match/",URLencode(test_refmet_name),"/name/")
+  response <- jsonlite::fromJSON(search_api)
+
+  # Check that the response has all the expected elements
+  expect_true(all(expected_elements %in% names(response)), "Response is missing expected elements.")
+
+  # Check for no additional elements
+  expect_equal(length(names(response)), length(expected_elements), 
+               info = "Response contains additional unexpected elements.")
+
+  unexpected_elements <- setdiff(names(response), expected_elements)
+  expect_equal(unexpected_elements, character(0), 
+               info = paste("Unexpected elements in response:", paste(unexpected_elements, collapse = ", ")))
+})
+