Initial commit

R/bibliography.R

@@ -0,0 +1,45 @@
+#'@include xmlMods.R
+#'@import XML
+#'
+NULL
+
+#' Tests if the metabarcode database has at least one bibliography reference
+#' 
+#' @export
+has.bibliography = function(barcodedb) {
+  length(getNodeSet(barcodedb,
+                    path='/obi:obimetabarcodedb/obi:bibliography',
+                    c(obi="http://metabarcoding.org/OBIMetabarcodes")))>0
+}
+
+#' @export
+add.reference.barcodedb  = function(barcodedb,bibfile,bibutils='bib2xml') {
+  
+  if (! has.bibliography(barcodedb)) {
+    # We create the bibliography node
+    
+    metabarcode = getNodeSet(barcodedb,
+                          path='/obi:obimetabarcodedb',
+                          c(obi="http://metabarcoding.org/OBIMetabarcodes"))[[1]]
+    
+    spare = sparexmltree()
+    
+    bibliography = getNodeSet(spare,
+                          path='/obi:obimetabarcodedb/obi:bibliography',
+                          c(obi="http://metabarcoding.org/OBIMetabarcodes"))[[1]]
+    
+    bibliography = xmlClone(bibliography)
+    
+    addChildren(metadata,bibliography,
+                at = NA)
+    
+
+  }
+
+  bibliography=getNodeSet(barcodedb,
+                          path='/obi:obimetabarcodedb/obi:bibliography',
+                          c(obi="http://metabarcoding.org/OBIMetabarcodes"))
+  
+  ref = bib2mods(bibfile,bibutils)
+  hidden=addChildren(bibliography[[1]],kids=ref) 
+}