negbio_pipeline parse fails silently about negbio HOT 4 CLOSED

I think I have catched the exception and skipped the sentence (https://github.com/ncbi-nlp/NegBio/blob/master/negbio/pipeline/parse.py#L58)

from negbio.

Yes, but sometimes when you try to parse an empty sentence something breaks badly and bllip doesn't just raise an exception but crashes entirely.

I had to introduce this hack to make it work:

for passage in document.passages:
    for sentence in passage.sentences:     
        if sentence.text.isspace():
             continue

        try:
            text = sentence.text
            tree = self.parse(text)
            sentence.infons['parse tree'] = str(tree)
        except:
            logging.exception('Cannot parse sentence: {}'.format(sentence.offset))

from negbio.

I think it is a good way to handle it. Bllip parser is not maintained by us.

from negbio.

Fixed in #20

from negbio.