Now I found an error, will take a look later:

Traceback (most recent call last):
File "plos_corpus.py", line 1060, in
main()
File "plos_corpus.py", line 1042, in main
dois_needed_list = get_dois_needed_list()
File "plos_corpus.py", line 316, in get_dois_needed_list
local_article_list = [filename_to_doi(article) for article in listdir_nohidden(directory, '.xml')]
File "plos_corpus.py", line 316, in
local_article_list = [filename_to_doi(article) for article in listdir_nohidden(directory, '.xml')]
File "plos_corpus.py", line 130, in filename_to_doi
return doi
UnboundLocalError: local variable 'doi' referenced before assignment

The problem is in the method filename_to_doi(). When the flow doesn't enter in any of the 3 if, this error is occurs. I will print out the filename that is being processed to see which one trigger this.

This guy is the culprit:
allofplos_xml/journal.pone.correction.dc398db7-e121-4bce-82d1-feac6d9bc68f.xml

I found that the REGEX was targeted to newarticledir but the file is in the corpusdir.
Will try by removing the dir in the validate_file function. BTW, what is validating is the file name, not the file, so I will rename it accordingly.

Pushed some changes, what is left: url_to_path(), change this method because annot_prefix is not 'plos.correction.' anymore

Hi @sbassi, if you read the PR, my changes were designed to change the annotation files to a new structure. The reason your file failed is because it's the old structure: journal.p[journal code].correction, whereas now it's plos.correction, which does not require discovering the journal name. Would you please revert your changes? Thanks!

I don't get it, if it is now plos.correction, why do we have a file called journal.pone.correction.dc398db7-e121-4bce-82d1-feac6d9bc68f.xml?

'annotation' DOI files deleted, redownloaded onto allofplos server, zip file recreated!