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 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_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 test_parse_site_residue_only():
text = ['serine residue', 'serine', 'a serine site', 's', 'ser']
assert unicode_strs(text)
for t in text:
residue, site = ReachProcessor._parse_site_text(t)
assert unicode_strs((residue, site))
assert (residue == 'S')
assert (site is None)
def test_parse_site_residue_only():
text = ['serine residue', 'serine', 'a serine site', 's', 'ser']
assert unicode_strs(text)
for t in text:
residue, site = ReachProcessor._parse_site_text(t)
assert unicode_strs((residue, site))
assert(residue == 'S')
assert(site is None)
def test_parse_site_text():
text = ['threonine 185', 'thr 185', 'thr-185',
'threonine residue 185', 'T185']
assert unicode_strs(text)
for t in text:
residue, site = ReachProcessor._parse_site_text(t)
assert(residue == 'T')
assert(site == '185')
assert unicode_strs((residue, site))
def test_parse_site_text():
text = [
'threonine 185', 'thr 185', 'thr-185', 'threonine residue 185', 'T185'
]
assert unicode_strs(text)
for t in text:
residue, site = ReachProcessor._parse_site_text(t)
assert (residue == 'T')
assert (site == '185')
assert unicode_strs((residue, site))
def test_valid_name():
assert(ReachProcessor._get_valid_name('') == '')
assert(ReachProcessor._get_valid_name('a') == 'a')
assert(ReachProcessor._get_valid_name('Name123') == 'Name123')
assert(ReachProcessor._get_valid_name('<>#~!,./][;-') == '____________')
assert(ReachProcessor._get_valid_name('PI3 Kinase') == 'PI3_Kinase')
assert(ReachProcessor._get_valid_name('14-3-3') == 'p14_3_3')
def test_valid_name():
assert (ReachProcessor._get_valid_name('') == '')
assert (ReachProcessor._get_valid_name('a') == 'a')
assert (ReachProcessor._get_valid_name('Name123') == 'Name123')
assert (ReachProcessor._get_valid_name('<>#~!,./][;-') == '____________')
assert (ReachProcessor._get_valid_name('PI3 Kinase') == 'PI3_Kinase')
assert (ReachProcessor._get_valid_name('14-3-3') == 'p14_3_3')
def test_parse_site_text_other_aa():
t = 'A431'
residue, site = ReachProcessor._parse_site_text(t)
assert(residue == 'A')
assert(site == '431')
assert(unicode_strs((residue, site)))
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
def test_parse_site_text_number_first():
t = '293T'
residue, site = ReachProcessor._parse_site_text(t)
assert(residue == 'T')
assert(site == '293')
assert(unicode_strs((residue, site)))
def test_parse_site_text_number():
t = '135'
residue, site = ReachProcessor._parse_site_text(t)
assert(residue is None)
assert(site == '135')
assert(unicode_strs(site))
def test_parse_site_text_number():
t = '135'
residue, site = ReachProcessor._parse_site_text(t)
assert (residue is None)
assert (site == '135')
assert (unicode_strs(site))
def test_parse_site_text_number_first():
t = '293T'
residue, site = ReachProcessor._parse_site_text(t)
assert (residue == 'T')
assert (site == '293')
assert (unicode_strs((residue, site)))
def test_parse_site_text_other_aa():
t = 'A431'
residue, site = ReachProcessor._parse_site_text(t)
assert (residue == 'A')
assert (site == '431')
assert (unicode_strs((residue, site)))