Refactoring parameters

taxonomicallyinformedannotation · Nov 16, 2023 · 6488c31 · 6488c31
1 parent d462745
commit 6488c31
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Showing 29 changed files with 1,157 additions and 1,313 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -2,6 +2,7 @@
 
 # timaR 2.9.1
 
+* Expose all parameters (#107, #108)
 * Fix for Zenodo API
 
 # timaR 2.9.0

diff --git a/R/get_params.R b/R/get_params.R
@@ -20,16 +20,25 @@ get_params <- function(step) {
     list.files(path = file.path(paths$inst$scripts$docopt)) |>
     stringi::stri_replace_all_fixed(pattern = ".txt", replacement = "")
 
+  default_path <-
+    if (step == "prepare_params") {
+      file.path(paths$params$prepare_params)
+    } else {
+      if (step == "prepare_params_advanced") {
+        file.path(paths$params$prepare_params_advanced)
+      } else {
+        file.path(paths$params$default$path, paste0(step, ".yaml"))
+      }
+    }
+
+  # for advanced parameters to work
+  step <- step |>
+    gsub(pattern = "_advanced", replacement = "", fixed = TRUE)
+
   stopifnot("Your step does not exist." = step %in% steps)
 
   doc_path <-
     file.path(paths$inst$scripts$docopt, paste0(step, ".txt"))
-  default_path <-
-    if (step != "prepare_params") {
-      file.path(paths$params$default$path, paste0(step, ".yaml"))
-    } else {
-      file.path(paths$params$prepare_params)
-    }
 
   user_path <-
     file.path(paths$params$user$path, paste0(step, ".yaml"))

diff --git a/R/load_yaml_files.R b/R/load_yaml_files.R
@@ -17,7 +17,8 @@ load_yaml_files <- function(paths = parse_yaml_paths()) {
       pattern = ".yaml",
       full.names = TRUE
     ),
-    parse_yaml_paths()$params$prepare_params
+    parse_yaml_paths()$params$prepare_params,
+    parse_yaml_paths()$params$prepare_params_advanced
   )
   ## -1 because of params.yaml
 
@@ -28,7 +29,8 @@ load_yaml_files <- function(paths = parse_yaml_paths()) {
         pattern = ".yaml",
         full.names = TRUE
       ),
-      parse_yaml_paths()$params$prepare_params
+      parse_yaml_paths()$params$prepare_params,
+      parse_yaml_paths()$params$prepare_params_advanced
     )
   }
 

diff --git a/R/parse_cli_params.R b/R/parse_cli_params.R
@@ -12,9 +12,6 @@
 #' @examples NULL
 parse_cli_params <- function(arguments, parameters) {
   if (exists("arguments")) {
-    if (!is.null(arguments$ann_can_ini)) {
-      parameters$annotations$candidates$initial <- as.numeric(arguments$ann_can_ini)
-    }
     if (!is.null(arguments$ann_can_fin)) {
       parameters$annotations$candidates$final <- as.numeric(arguments$ann_can_fin)
     }
@@ -79,9 +76,9 @@ parse_cli_params <- function(arguments, parameters) {
     if (!is.null(arguments$fil_fea_pre)) {
       parameters$files$features$prepared <- as.character(arguments$fil_fea_pre)
     }
-    if (!is.null(arguments$fil_lib_add_pro)) {
+    if (!is.null(arguments$fil_lib_add_pre)) {
       parameters$files$libraries$adducts$prepared <-
-        as.character(arguments$fil_lib_add_pro)
+        as.character(arguments$fil_lib_add_pre)
     }
     if (!is.null(arguments$fil_lib_sop_raw_clo)) {
       parameters$files$libraries$sop$raw$closed <-
@@ -91,39 +88,55 @@ parse_cli_params <- function(arguments, parameters) {
       parameters$files$libraries$sop$raw$lotus <-
         as.character(arguments$fil_lib_sop_raw_lot)
     }
-    if (!is.null(arguments$fil_lib_sop_pro)) {
+    if (!is.null(arguments$fil_lib_sop_pre)) {
       parameters$files$libraries$sop$prepared <-
-        as.character(arguments$fil_lib_sop_pro)
+        as.character(arguments$fil_lib_sop_pre)
+    }
+    if (!is.null(arguments$fil_lib_spe_exp_neg)) {
+      parameters$files$libraries$spectral$exp$neg <-
+        as.character(arguments$fil_lib_spe_exp_neg)
+    }
+    if (!is.null(arguments$fil_lib_spe_exp_pos)) {
+      parameters$files$libraries$spectral$exp$pos <-
+        as.character(arguments$fil_lib_spe_exp_pos)
+    }
+    if (!is.null(arguments$fil_lib_spe_exp_raw)) {
+      parameters$files$libraries$spectral$exp$raw <-
+        as.character(arguments$fil_lib_spe_exp_raw)
     }
-    if (!is.null(arguments$fil_lib_spe_neg)) {
-      parameters$files$libraries$spectral$neg <-
-        as.character(arguments$fil_lib_spe_neg)
+    if (!is.null(arguments$fil_lib_spe_is_neg)) {
+      parameters$files$libraries$spectral$is$neg <-
+        as.character(arguments$fil_lib_spe_is_neg)
     }
-    if (!is.null(arguments$fil_lib_spe_pos)) {
-      parameters$files$libraries$spectral$pos <-
-        as.character(arguments$fil_lib_spe_pos)
+    if (!is.null(arguments$fil_lib_spe_is_pos)) {
+      parameters$files$libraries$spectral$is$pos <-
+        as.character(arguments$fil_lib_spe_is_pos)
     }
-    if (!is.null(arguments$fil_lib_spe_raw)) {
-      parameters$files$libraries$spectral$raw <-
-        as.character(arguments$fil_lib_spe_raw)
+    if (!is.null(arguments$fil_lib_spe_is_raw)) {
+      parameters$files$libraries$spectral$is$raw <-
+        as.character(arguments$fil_lib_spe_is_raw)
     }
     if (!is.null(arguments$fil_net_spe_edg_raw)) {
       parameters$files$networks$spectral$edges$raw <-
         as.character(arguments$fil_net_spe_edg_raw)
     }
-    if (!is.null(arguments$fil_net_spe_edg_pro)) {
+    if (!is.null(arguments$fil_net_spe_edg_pre)) {
       parameters$files$networks$spectral$edges$prepared <-
-        as.character(arguments$fil_net_spe_edg_pro)
+        as.character(arguments$fil_net_spe_edg_pre)
     }
     if (!is.null(arguments$fil_net_spe_com_raw)) {
       parameters$files$networks$spectral$components$raw <-
         as.character(arguments$fil_net_spe_com_raw)
     }
-    if (!is.null(arguments$fil_tax_raw)) {
-      parameters$files$taxa$raw <- as.character(arguments$fil_tax_raw)
+    if (!is.null(arguments$fil_net_spe_com_pre)) {
+      parameters$files$networks$spectral$components$prepared <-
+        as.character(arguments$fil_net_spe_com_pre)
     }
-    if (!is.null(arguments$fil_tax_pro)) {
-      parameters$files$taxa$prepared <- as.character(arguments$fil_tax_pro)
+    if (!is.null(arguments$fil_met_raw)) {
+      parameters$files$metadata$raw <- as.character(arguments$fil_met_raw)
+    }
+    if (!is.null(arguments$fil_met_pre)) {
+      parameters$files$metadata$prepared <- as.character(arguments$fil_met_pre)
     }
     if (!is.null(arguments$fil_spe_raw)) {
       parameters$files$spectral$raw <- as.character(arguments$fil_spe_raw)
@@ -183,6 +196,9 @@ parse_cli_params <- function(arguments, parameters) {
     if (!is.null(arguments$names_filename)) {
       parameters$names$filename <- as.character(arguments$names_filename)
     }
+    if (!is.null(arguments$names_inchikey)) {
+      parameters$names$inchikey <- as.character(arguments$names_inchikey)
+    }
     if (!is.null(arguments$names_mgf_ce)) {
       parameters$names$mgf$collision_energy <- as.character(arguments$names_mgf_ce)
     }
@@ -245,6 +261,9 @@ parse_cli_params <- function(arguments, parameters) {
     if (!is.null(arguments$names_rt)) {
       parameters$names$rt <- as.character(arguments$names_rt)
     }
+    if (!is.null(arguments$names_smiles)) {
+      parameters$names$smiles <- as.character(arguments$names_smiles)
+    }
     if (!is.null(arguments$names_source)) {
       parameters$names$source <- as.character(arguments$names_source)
     }