Making 'file_path' optional in config.json

Multiscale-Genomics · Nov 2, 2017 · 197e030 · 197e030
1 parent 92cde86
commit 197e030
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/apps/jsonapp.py b/apps/jsonapp.py
@@ -135,7 +135,7 @@ def _read_config(self, json_path):
 
         output_files = {}
         for output_file in configuration["output_files"]:
-            output_files[output_file["name"]] = output_file["file"]["file_path"]
+            output_files[output_file["name"]] = output_file["file"].get("file_path", None)
 
         arguments = {}
         for argument in configuration["arguments"]:
@@ -159,10 +159,10 @@ def _read_metadata(self, json_path):
             input_metadata[ID] = Metadata(
                 data_type=input_file["data_type"],
                 file_type=input_file["file_type"],
+                file_path=input_file["file_path"],
                 meta_data=input_file["meta_data"],
                 taxon_id=input_file["taxon_id"],
-                file_path=input_file.get("file_path", None),  # optional
-                sources=input_file.get("sources", []),  # optional
+                sources=input_file["sources"]
             )
         return input_metadata