def test_parse_site_residue_only():
rp = ReachProcessor(None)
text = ['serine residue', 'serine', 'a serine site']
for t in text:
residue, site = rp._parse_site_text(t)
assert (residue == 'Serine')
assert (site is None)
def test_parse_site_text():
rp = ReachProcessor(None)
text = [
'threonine 185', 'thr 185', 'thr-185', 'threonine residue 185', 'T185'
]
for t in text:
residue, site = rp._parse_site_text(t)
assert (residue == 'Threonine')
assert (site == '185')
def process_json_str(json_str, citation=None):
"""Return a ReachProcessor by processing the given REACH json string.
The output from the REACH parser is in this json format.
For more information on the format, see: https://github.com/clulab/reach
Parameters
----------
json_str : str
The json string to be processed.
citation : Optional[str]
A PubMed ID passed to be used in the evidence for the extracted INDRA
Statements. Default: None
Returns
-------
rp : ReachProcessor
A ReachProcessor containing the extracted INDRA Statements
in rp.statements.
"""
assert isinstance(json_str, basestring)
json_str = json_str.replace('frame-id', 'frame_id')
json_str = json_str.replace('argument-label', 'argument_label')
json_str = json_str.replace('object-meta', 'object_meta')
json_str = json_str.replace('doc-id', 'doc_id')
json_str = json_str.replace('is-hypothesis', 'is_hypothesis')
json_str = json_str.replace('is-negated', 'is_negated')
json_str = json_str.replace('is-direct', 'is_direct')
json_str = json_str.replace('found-by', 'found_by')
try:
json_dict = json.loads(json_str)
except ValueError:
logger.error('Could not decode JSON string.')
return None
rp = ReachProcessor(json_dict, citation)
rp.get_modifications()
rp.get_complexes()
rp.get_activation()
rp.get_translocation()
rp.get_regulate_amounts()
return rp
