added warning message with all taxa ids which are not in the local da…

…tabase (#131) Co-authored-by: Pavel Vychyk <pavel@wks10.izn-ffm.intern>
BIONF · Dec 17, 2024 · f27f1fc · f27f1fc
1 parent 4491303
commit f27f1fc
Showing 1 changed file with 12 additions and 0 deletions.
diff --git a/R/createTaxonomyMatrix.R b/R/createTaxonomyMatrix.R
@@ -118,8 +118,20 @@ getTaxonomyInfo <- function(inputTaxa = NULL, currentNCBIinfo = NULL) {
     tmp <- list()
     outList <- list()
     k <- 1
+    missingTaxa <- setdiff(inputTaxa, currentNCBIinfo$ncbiID)
+    if (length(missingTaxa) > 0) {
+    	warning(
+    		cat(length(missingTaxa), 
+    		    "id(s) missed in currentNCBIinfo, check taxon database: ",
+    	             paste(missingTaxa, collapse = ", ")
+    	            )
+    	)
+    }
     for (refID in inputTaxa) {
         # get info for this taxon
+        if (refID %in% missingTaxa) {
+	    next
+        }
         refEntry <- currentNCBIinfo[currentNCBIinfo$ncbiID == refID, ]
         lastID <- refEntry$parentID
         inputTaxaInfo <- refEntry