Merge pull request #8 from microbiomeDB/treeSE

allow collections list to have no ancestor ids for all collections
microbiomeDB · Jun 5, 2024 · 905e3f1 · 905e3f1
2 parents 62c0f66 + cba987a
commit 905e3f1
Show file tree

Hide file tree

Showing 2 changed files with 13 additions and 7 deletions.
diff --git a/R/class-Collections.R b/R/class-Collections.R
@@ -81,11 +81,18 @@ check_collections <- function(object) {
         return(TRUE)
     }
 
-    # check that at least one ancestorIdColumn is shared between collections
+    # check that at least one ancestorIdColumn is shared between collections, or there are no ancestors
     firstCollectionAncestorIds <- object[[1]]@ancestorIdColumns
-    if (!all(sapply(object, function(x) any(x@ancestorIdColumns %in% firstCollectionAncestorIds)))) {
-        msg <- "at least one ancestorIdColumn must be shared between collections"
-        errors <- c(errors, msg)
+    if (!!length(firstCollectionAncestorIds)) {
+        if (!all(sapply(object, function(x) any(x@ancestorIdColumns %in% firstCollectionAncestorIds)))) {
+            msg <- "at least one ancestorIdColumn must be shared between collections"
+            errors <- c(errors, msg)
+        }
+    } else {
+        if (any(sapply(object, function(x) !!length(x@ancestorIdColumns)))) {
+            msg <- "at least one ancestorIdColumn must be shared between collections"
+            errors <- c(errors, msg)
+        }
     }
 
     if (length(errors) == 0) {

diff --git a/R/internal-utils.R b/R/internal-utils.R
@@ -136,9 +136,8 @@ getCollectionName <- function(collectionId, dataSourceName, ontology = NULL) {
         # w columns like `iri` and `label`
         collectionLabel <- unique(ontology$label[ontology$iri == collectionId])
     	if (collectionLabel %in% c('Kingdom','Phylum','Class','Order','Family','Genus','Species')) {
-          collectionLabel <- unique(paste(collectionLabel, paste0("(", ontology$parentlabel[ontology$iri == collectionId], ")")))
-	}
-	print(collectionLabel)
+            collectionLabel <- unique(paste(collectionLabel, paste0("(", ontology$parentlabel[ontology$iri == collectionId], ")")))
+	    }
 
         if (length(collectionLabel) == 1) {
             return(paste(dataSourceName, collectionLabel))