tests

Author: Adafede

R/parse_cli_params.R

@@ -440,8 +440,8 @@ parse_cli_params <- function(arguments, parameters) {
     if (!is.null(arguments$force)) {
       parameters$options$force <- as.logical(arguments$force)
     }
-    if (!is.null(arguments$nit_rule)) {
-      parameters$options$nitrogen_rule <- as.logical(arguments$nit_rule)
+    if (!is.null(arguments$nit_rul)) {
+      parameters$options$nitrogen_rule <- as.logical(arguments$nit_rul)
     }
     if (!is.null(arguments$summarise)) {
       parameters$options$summarise <- as.logical(arguments$summarise)

R/prepare_params.R

@@ -187,11 +187,10 @@ prepare_params <- function(params_small = get_params(step = "prepare_params"),
   if (!is.null(org_tax)) {
     if (org_tax == "") {
       org_tax <- NULL
+    } else {
+      fil_met_raw <- NULL
     }
   }
-  if (!is.null(org_tax)) {
-    fil_met_raw <- NULL
-  }
 
   log_debug(x = "Changing params")
   switch(step,

codemeta.json

@@ -513,7 +513,7 @@
     "SystemRequirements": null
   },
   "keywords": ["metaboliteannotation", "chemotaxonomy", "scoringsystem", "naturalproducts", "computationalmetabolomics", "taxonomicdistance", "specializedmetabolome"],
-  "fileSize": "2850.662KB",
+  "fileSize": "2840.261KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

tests/testthat/test_functions.R

@@ -17,7 +17,10 @@ testthat::test_that("Test functions", {
   ## Prepare config for a single step only
   prepare_params(step = "weight_annotations")
   ## For all steps
-  prepare_params()
+  params$organisms$taxon <- ""
+  prepare_params(params_small = params)
+  params$organisms$taxon <- "Gentiana lutea"
+  prepare_params(params_small = params)
   prepare_params(step = "annotate_masses")
   prepare_params(step = "annotate_spectra")
   prepare_params(step = "create_components")
@@ -293,6 +296,8 @@ testthat::test_that("Test functions", {
   )
   #### Classical
   prepare_libraries_spectra()
+  #### Again
+  prepare_libraries_spectra()
 
   ## for msp reading test
   import_spectra(dir(system.file("extdata", package = "MsBackendMsp"), full.names = TRUE, pattern = "msp$")[1L])
@@ -641,6 +646,11 @@ testthat::test_that("Test functions", {
   arguments$nit_rul <- "x"
   arguments$summarise <- "x"
 
+  # Useless
+  keep_peaks(x = 0, prop = 0)
+  normalize_peaks()
+  remove_above_precursor()
+
   parse_cli_params(
     arguments = arguments,
     parameters = params