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Minor fixes for parse/handling paths #23

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Minor fixes for parse/handling paths #23

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d62b5b8
fix return on bad parse to be None, None
alistairewj Feb 20, 2019
38ef8fa
fix os.expanduser not handling pathlib2 path properly
alistairewj Feb 20, 2019
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3 changes: 3 additions & 0 deletions negbio/pipeline/parse.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,9 @@ def __init__(self, model_dir=None):
logging.debug("downloading GENIA+PubMed model if necessary ...")
model_dir = ModelFetcher.download_and_install_model(
'GENIA+PubMed', os.path.join(tempfile.gettempdir(), 'models'))
elif 'pathlib' in str(type(model_dir)):
# avoid python 2/3 compatibility issues with os/pathlib2
model_dir = str(model_dir)
self.model_dir = os.path.expanduser(model_dir)

logging.debug('loading model %s ...' % self.model_dir)
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2 changes: 1 addition & 1 deletion negbio/pipeline/ptb2ud.py
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Expand Up @@ -174,7 +174,7 @@ def convert_dg(dependency_graph, text, offset, ann_index=0, rel_index=0, has_lem
if index == -1:
logging.debug('Cannot convert parse tree to dependency graph at %d\n%d\n%s',
start, offset, str(dependency_graph))
return
return None, None

ann = bioc.BioCAnnotation()
ann.id = 'T{}'.format(ann_index)
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