Merge pull request #52 from CBIIT/3.1.0

Merge 3.1.0 hotfix

Author: vshand11

src/process_manifest.py

@@ -83,8 +83,8 @@ def process_manifest_file(log, configs, has_file_id, file_infos, manifest_rows,
 # This method will create a new manifest file with the file id column added to the pre-manifest.
 def add_file_id(file_id_name, file_name_name, final_manifest_path, file_infos, manifest_rows, manifest_columns, omit_prefix):
     output = []
-    for file in file_infos:
-        row = [row for row in manifest_rows if row[file_name_name] == file["fileName"]][0]
+    for row in manifest_rows:
+        file = [file for file in file_infos if file["fileName"] == row[file_name_name]][0]
         file[FILE_ID_DEFAULT] = file[FILE_ID_DEFAULT] if omit_prefix == False else file[FILE_ID_DEFAULT].replace(DCF_PREFIX, "")
         row[file_id_name] = file[FILE_ID_DEFAULT]
         output.append(row.values())