diff util/Reader.py @ 46:061da5d3a219 draft

planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 3160592f4119e684ab5843dd28a2e6cf11df0121-dirty

--- a/util/Reader.py	Tue May 01 21:52:46 2018 -0400
+++ b/util/Reader.py	Tue Jun 19 16:28:36 2018 -0400
@@ -120,11 +120,15 @@
         # TODO: Optimize this double loop
         for input_data in array_inputs:
             input_false_path = input_data["false_path"]
-            input_data["name"] = santitizer.sanitize_name_input(input_data["name"])
-            extensionObject = ExtensionClass(input_false_path, input_data)
-            extensionObject.generateCustomTrack()
-            datatype_dictionary.update({input_data["order_index"]: extensionObject})
-            self.logger.debug("%s object: %s has been created", ExtensionClass, input_data["name"])
+            # if the file is empty, skip the rest
+            if os.path.isfile(input_false_path) and os.path.getsize(input_false_path) > 0:
+                input_data["name"] = santitizer.sanitize_name_input(input_data["name"])
+                extensionObject = ExtensionClass(input_false_path, input_data)
+                extensionObject.generateCustomTrack()
+                datatype_dictionary.update({input_data["order_index"]: extensionObject})
+                self.logger.debug("%s object: %s has been created", ExtensionClass, input_data["name"])
+            else:
+                self.logger.info("The input file: %s is empty, skip creating the track for this data", input_data["name"])
         return datatype_dictionary