updated new documents index management

dna_add.sh

@@ -96,30 +96,18 @@ then
 	exit 1
 fi
 
-#get list of current documents in the container
-doc_list=$(find "$container_path"/* -maxdepth 0 -type d -printf "%f\n")
-
-#if none, new document of index 0
-if [ -z "$doc_list" ]; then
-	doc_index=0
-else
-#else index equals to max index +1
-	max_index=$(echo "${doc_list[*]}" | sort -nr | head -n1)
-	doc_index=$((max_index+1))
-fi
+# add a new document in the xml file and get its new index
+doc_index=$(add_document "$container_path")
 
 stored_document_path="$container_path"/$doc_index
  
 mkdir -p "$stored_document_path"
 
-add_document "$container_path" $doc_index
+#----Source Encoding----#
 
 # get the fragment length from the container options
 frag_length=$(get_container_param $container_path "frag_length")
 
-
-#----Source Encoding----#
-
 assembly_type=$(get_container_param $container_path "assembly_type")
 
 source_encoding_script="$project_dir"/source_encoding/source_encoding.py

metadata_manager.sh

@@ -71,21 +71,34 @@ set_container_param() {
 add_document() {
 	#add a new document to the container
 	#$1 container path
-	#$2 document index
 	
 	#save operation in logs
-	log_metadata_call "$1" add_document "$2"
+	log_metadata_call "$1" add_document
+	
+	#define the new document index
+	index_list=$(xmlstarlet sel -t -v "/container_metadata/documents/document/@id" "$1"/$meta_file_name)
+	#if existing index list is none, new document has index 0
+	if [ -z "$index_list" ]; then
+		doc_index="0"
+	else
+		#max existing index +1
+		doc_index=$(($(echo "${index_list[*]}" | sort -nr | head -n1)+1))
+	fi
 	
 	#add a document then add the attribute 'index' for all documents wo attribute (should only be the added one)
 	xmlstarlet edit -L -s "/container_metadata/documents" --type elem --name document \
-		--insert  "/container_metadata/documents/document[not(@id)]" --type attr --name id --value "$2" \
+		--insert  "/container_metadata/documents/document[not(@id)]" --type attr --name id --value $doc_index \
 		"$1"/$meta_file_name
+	
 	#add the creation date
-	add_doc_param $1 $2 "creation_date" "$(date)"
+	add_doc_param $1 $doc_index "creation_date" "$(date)"
 	
 	#----Update number of documents----#
 	number_doc=$(get_container_param "$1" "number_of_documents")
 	set_container_param "$1" "number_of_documents" $((number_doc+1))
+	
+	#return the index of the new document
+	echo $doc_index
 }
 
 
@@ -150,4 +163,3 @@ get_all_doc_param() {
 
 
 
-