def test_ecomap():
"""
test mappings between GAF codes and ECO
"""
m = EcoMap()
assert m.coderef_to_ecoclass('IEA', 'GO_REF:0000002') == 'ECO:0000256'
assert m.coderef_to_ecoclass('IEA') == 'ECO:0000501'
assert m.coderef_to_ecoclass('IEA', 'FAKE:ID') == 'ECO:0000501'
assert m.ecoclass_to_coderef('ECO:0000501') == ('IEA', None)
assert m.ecoclass_to_coderef('ECO:0000256') == ('IEA', 'GO_REF:0000002')
assert m.coderef_to_ecoclass('BADCODE', None) == None
assert m.coderef_to_ecoclass('BADCODE', 'GO_REF:xxx') == None
assert m.ecoclass_to_coderef('ECO:9999999999999999999') == (None, None)
assert m.coderef_to_ecoclass('ISO', None) == 'ECO:0000266'
class AssocFilter:
def __init__(self, filter_rule : FilterRule):
self.filter_rule = filter_rule
self.ecomap = EcoMap()
def validate_line(self, assoc):
evi_code = self.ecomap.ecoclass_to_coderef(assoc["evidence"]["type"])[0]
if evi_code in self.filter_rule.unwanted_evidence_codes:
return False
if len(self.filter_rule.unwanted_evi_code_ref_combos) > 0:
references = assoc["evidence"]["has_supporting_reference"]
for evi_ref_combo in self.filter_rule.unwanted_evi_code_ref_combos:
if evi_ref_combo[0] == evi_code and evi_ref_combo[1] in references:
return False
if len(self.filter_rule.unwanted_properties) > 0 and "annotation_properties" in assoc:
for up in self.filter_rule.unwanted_properties:
if up in assoc["annotation_properties"]:
return False
if len(self.filter_rule.required_attributes) > 0:
meets_requirement = False
for attr in self.filter_rule.required_attributes:
# a[attr] is dict
for k in attr.keys():
if assoc[k] in attr[k]:
meets_requirement = True
if not meets_requirement:
return False
return True
