Issue with text_processing/fix_headers/renameLN_LR.py

[slstaples]

Hello! I've struggled with this a bit and need some help. I can't figure out why the program listed above won't run--Aleks indicated it should work, but it gives me the following error on a PC (I am doing essentially the same task, just changing GA to GR instead of LN to LR):
Traceback (most recent call last):
File "rename_GA_GR.py", line 16, in
with open(full_name, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: 'test_files\GA\1\108_GA_1_NA_1_F_10539_UA.txt'

Thanks in advance for your help!

[markfullmer]

@slstaples , I was able to reproduce the error you're seeing on a Mac.

The reason this is happening is that part of the script is still trying to process a filename which a previous part of the script has already renamed (i.e., the file changed 108_GA_1_NA_1_F_10539_UA.txt' to 108_GR_1_NA_1_F_10539_UA.txt', so, in effect the error is correct -- the file can no longer be found, and it therefore can't complete the operation of manipulating the header (<Assignment: GA>).

Looking at the code, this can be resolved by flipping the order of operations: first manipulate the header, then rename the file. I've shown the code change in a diff below, if that's useful for reference. This order of operations change should be made to the existing rename_LN_LR.py as well as to the new script you're working on, rename_GA_GR.py.

Let me know if you have any additional questions!

diff --git a/fix_headers/renameLN_LR.py b/fix_headers/renameLN_LR.py
index a4a44bc..a728fbc 100755
--- a/fix_headers/renameLN_LR.py
+++ b/fix_headers/renameLN_LR.py
@@ -10,8 +10,6 @@ args = parser.parse_args()
 for root, dirs, files in os.walk(args.dir):
     for fileName in files:
         full_name= os.path.join(root,fileName)
-        if "_LN_" in full_name:
-            os.rename(full_name, full_name.replace("_LN_", "_LR_"))
         if ".txt" in full_name:
             with open(full_name, 'r') as f:
                 s= f.read()
@@ -20,5 +18,6 @@ for root, dirs, files in os.walk(args.dir):
                    with open(full_name, "w") as f:
                             f.write(s)
                             f.close()
-
-
+        if "_LN_" in full_name:
+            os.rename(full_name, full_name.replace("_LN_", "_LR_"))
+