diff XSeekerPreparator.R @ 6:207e36770d18 draft

" master branch Updating"

--- a/XSeekerPreparator.R	Wed Jan 20 09:17:48 2021 +0000
+++ b/XSeekerPreparator.R	Wed Jan 20 17:47:51 2021 +0000
@@ -1,7 +1,7 @@
 
 
 TOOL_NAME <- "XSeekerPreparator"
-VERSION <- "1.1.2"
+VERSION <- "1.1.3"
 
 OUTPUT_SPECIFIC_TOOL <- "XSeeker_Galaxy"
 
@@ -551,12 +551,24 @@
 }
 
 find_grouping_var <- function(var_meta) {
-    for (grouping_var in c(".", "Bio")) {
-        if (!is.null(rdata$variableMetadata[[grouping_var]])) {
-            return (grouping_var)
+    known_colnames = c(
+        "name", "namecustom", "mz", "mzmin", "mzmax",
+        "rt", "rtmin", "rtmax", "npeaks", "isotopes", "adduct", "pcgroup"
+    )
+    col_names <- colnames(var_meta)
+    classes = list()
+    for (name in col_names) {
+        if (!(name %in% known_colnames)) {
+            classes[[length(classes)+1]] = name
         }
     }
-    return (NULL)
+    if (length(classes) > 1) {
+        stop(sprintf("Only one class expected in the variable metadata. Found %d .", length(classes)))
+    }
+    if (length(classes) === 0) {
+        stop("Could not find any class column in your variableMetadata.")
+    }
+    return (classes[[1]])
 }
 
 add_sample_to_database <- function(orm, env, context, smol_xcms_set) {