From 0145afece7ae647d2bb7d12efe471248bb1132be Mon Sep 17 00:00:00 2001
From: Pavel Vychyk <pavel@wks10.izn-ffm.intern>
Date: Tue, 10 Dec 2024 11:58:07 +0100
Subject: [PATCH] added warning message with all taxa ids which are not in the
 local database

---
 R/createTaxonomyMatrix.R | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/R/createTaxonomyMatrix.R b/R/createTaxonomyMatrix.R
index 347d293d..58d04b4d 100644
--- a/R/createTaxonomyMatrix.R
+++ b/R/createTaxonomyMatrix.R
@@ -117,8 +117,20 @@ 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