elifesciences / bot-lax-adaptor Goto Github PK

$ ./scrape-article.sh article-xml/articles/elife-12215-v1.xml 
ERROR - 2017-09-27 17:18:52,266 - failed to render doc 'https://raw.githubusercontent.com/elifesciences/elife-article-xml/f0dd69e8d0976e68868ced40de0b7140c040e250/articles/elife-12215-v1.xml' with error: ('Author missing required competingInterests', {'version': 1, 'msid': u'12215'}) -- {}
Traceback (most recent call last):
  File "/usr/lib64/python2.7/logging/__init__.py", line 861, in emit
    msg = self.format(record)
  File "/usr/lib64/python2.7/logging/__init__.py", line 734, in format
    return fmt.format(record)
  File "/home/luke/dev/python/bot-lax-adaptor/src/conf.py", line 84, in format
    record.__dict__['extra'] = utils.json_dumps(unknown_fields)
  File "/home/luke/dev/python/bot-lax-adaptor/src/utils.py", line 121, in json_dumps
    return json.dumps(obj, default=datetime_handler, **kwargs)
  File "/usr/lib64/python2.7/json/__init__.py", line 251, in dumps
    sort_keys=sort_keys, **kw).encode(obj)
  File "/usr/lib64/python2.7/json/encoder.py", line 207, in encode
    chunks = self.iterencode(o, _one_shot=True)
  File "/usr/lib64/python2.7/json/encoder.py", line 270, in iterencode
    return _iterencode(o, 0)
  File "/home/luke/dev/python/bot-lax-adaptor/src/utils.py", line 120, in datetime_handler
    raise TypeError('Object of type %s with value of %s is not JSON serializable' % (type(obj), repr(obj)))
TypeError: Object of type <type 'file'> with value of <open file 'article-xml/articles/elife-12215-v1.xml', mode 'r' at 0x7f7c0dad9390> is not JSON serializable
Logged from file main.py, line 659
Traceback (most recent call last):
  File "src/main.py", line 671, in <module>
    print main(doc, args)
  File "src/main.py", line 650, in main
    article_json = render_single(doc, **ctx)
  File "src/main.py", line 612, in render_single
    article_data = postprocess(render(description, [soup], ctx)[0], ctx)
  File "src/main.py", line 486, in postprocess
    partial(manual_overrides, ctx),
  File "/home/luke/dev/python/bot-lax-adaptor/venv/lib/python2.7/site-packages/et3/render.py", line 21, in doall
    item = do(item, seg, ctx)
  File "/home/luke/dev/python/bot-lax-adaptor/venv/lib/python2.7/site-packages/et3/render.py", line 13, in do
    return segment(item)
  File "src/main.py", line 428, in check_authors
    raise ValueError("Author missing required competingInterests", context)
ValueError: ('Author missing required competingInterests', {'version': 1, 'msid': u'12215'})

File: ...isbnlib/_ext.py", line 20, in mask
    return msk(isbn, separator)
 File: ...isbnlib/_msk.py", line 25, in msk
    ib = canonical(isbn)
File: ...isbnlib/_core.py", line 143, in canonical
    numb = [c for c in isbnlike if c in '0123456789Xx']
TypeError: 'NoneType' object is not iterable