def _get_translocation_target(node_modifier_data):
# First check if there is a translocation modifier
if node_modifier_data is None or node_modifier_data == {}:
return None
modifier = node_modifier_data.get(pc.MODIFIER)
if modifier is None or modifier != pc.TRANSLOCATION:
return None
# Next, make sure there is information on the translocation target
transloc_data = node_modifier_data.get(pc.EFFECT)
if transloc_data is None:
return None
to_loc_info = transloc_data.get(pc.TO_LOC)
if not to_loc_info:
return None
to_loc_ns = to_loc_info.get('namespace')
to_loc_name = to_loc_info.get('name')
# Only use GO Cellular Component location names
if to_loc_ns not in ('GO', 'GOCC', 'GOCCID') or not to_loc_name:
return None
return go_client.get_valid_location(to_loc_name)
def test_get_valid_location():
assert go_client.get_valid_location('0001669') == 'acrosomal vesicle'
assert go_client.get_valid_location('GO:0001669') == 'acrosomal vesicle'
assert go_client.get_valid_location('acrosomal vesicle') == \
'acrosomal vesicle'
assert go_client.get_valid_location('acrosome') == 'acrosomal vesicle'
def fix_json_stmt(json_stmt):
# Step 1: fix JSON directly to reduce errors when deserializing
# 1.1 Fix statement type issues
# Change to IncreaseAmount
if json_stmt['type'] == 'GeneTranscriptExpress':
json_stmt['type'] = 'IncreaseAmount'
stmt_type = json_stmt['type']
stmt_class = get_statement_by_name(stmt_type)
# 1.2 - Check for string agents.
for ag_key in stmt_class._agent_order:
json_stmt[ag_key] = fix_json_agent(json_stmt.get(ag_key))
# 1.3 - Fix other misc things that are statement type specific
if stmt_type in mod_class_names:
position = json_stmt.get('position')
residue = json_stmt.get('residue')
if isinstance(position, list):
if len(position) != 1:
logger.error('Invalid position: %s' % position)
else:
json_stmt['position'] = position[0]
if isinstance(residue, list):
if len(residue) != 1:
logger.error('Invalid residue: %s' % residue)
elif not isinstance(residue[0], str):
logger.error('Invalid residue: %s' % residue)
else:
json_stmt['residue'] = residue[0]
elif isinstance(residue, bool):
json_stmt['residue'] = None
elif stmt_type in ('Activation', 'Inhibition'):
obj_activity = json_stmt.get('obj_activity')
if isinstance(obj_activity, list):
if len(obj_activity) != 1:
logger.error('Invalid object activity: %s' % obj_activity)
else:
json_stmt['obj_activity'] = obj_activity[0]
obj = json_stmt.get('obj')
if isinstance(obj, (list, str)):
raise InvalidAgent
elif stmt_type == 'Translocation':
# Fix locations if possible
for loc_param in ('from_location', 'to_location'):
loc = json_stmt.get(loc_param)
if loc:
# Some invalid locations are produced very often and can be
# silently skipped
if loc in known_invalid_locations:
loc = None
else:
loc = go_client.get_valid_location(loc)
if not loc:
loc = None
else:
loc = None
json_stmt[loc_param] = loc
# Skip Translocation with both locations None
if (json_stmt.get('from_location') is None
and json_stmt.get('to_location') is None):
raise TranslocationWithoutLocations
elif stmt_type == 'IncreaseAmount':
# Skip if there is no subject
subj = json_stmt.get('subj')
if not subj:
raise MissingSubj
# 1.4 - Fix evidence
evs = json_stmt.get('evidence')
if evs and isinstance(evs, list):
ev = evs[0]
text = ev.get('text')
if not isinstance(text, str) or not text:
raise MissingEvidenceText
pmid = ev.get('pmid')
if isinstance(pmid, str) and pmid.startswith('PMID'):
json_stmt['evidence'][0]['pmid'] = \
json_stmt['evidence'][0]['pmid'][4:]
else:
raise InvalidEvidence
return json_stmt
