def test_errors_gaf():
config = assocparser.AssocParserConfig(ecomap=EcoMap())
p = GafParser(config=config)
assocs = p.parse(open("tests/resources/errors.gaf", "r"), skipheader=True)
msgs = p.report.messages
print(json.dumps(p.report.to_report_json(), indent=4))
# print("MESSAGES: {}".format(len(msgs)))
n_invalid_idspace = 0
for m in msgs:
print("MESSAGE: {}".format(m))
if m['type'] == assocparser.Report.INVALID_IDSPACE:
n_invalid_idspace += 1
assert len(msgs) == 13
assert n_invalid_idspace == 1
assert len(assocs) == 2
w = GafWriter()
w.write(assocs)
for a in assocs:
if a.object_extensions != []:
# our test file has no ORs, so in DNF this is always the first
xs = a.object_extensions[0].elements
print(xs)
for x in xs:
print('X: {}'.format(x))
# ensure that invalid expressions have been eliminated
assert x.relation == association.Curie("BFO", "0000050")
assert x.term == association.Curie.from_str('X:1')
assert len(xs) == 1
def test_errors_gaf():
config = assocparser.AssocParserConfig(ecomap=EcoMap())
p = GafParser(config=config)
assocs = p.parse(open("tests/resources/errors.gaf", "r"), skipheader=True)
msgs = p.report.messages
print(json.dumps(p.report.to_report_json(), indent=4))
# print("MESSAGES: {}".format(len(msgs)))
n_invalid_idspace = 0
for m in msgs:
print("MESSAGE: {}".format(m))
if m['type'] == assocparser.Report.INVALID_IDSPACE:
n_invalid_idspace += 1
assert len(msgs) == 16
assert n_invalid_idspace == 1
assert len(assocs) == 5
w = GafWriter()
w.write(assocs)
for a in assocs:
if a['object_extensions'] != {}:
# our test file has no ORs, so in DNF this is always the first
xs = a['object_extensions']['union_of'][0]['intersection_of']
for x in xs:
print('X: {}'.format(x))
# ensure that invalid expressions have been eliminated
assert x['property'] == 'foo'
assert x['filler'] == 'X:1'
assert len(xs) == 1
def test_errors_gaf():
p = GafParser()
p.config.ecomap = EcoMap()
assocs = p.parse(open("tests/resources/errors.gaf", "r"))
msgs = p.report.messages
print("MESSAGES: {}".format(len(msgs)))
for m in msgs:
print("MESSAGE: {}".format(m))
assert len(msgs) == 15
# we expect 4
assert len(assocs) == 7
from ontobio.io import GafWriter
w = GafWriter()
w.write(assocs)
for a in assocs:
if 'object_extensions' in a:
# our test file has no ORs, so in DNF this is always the first
xs = a['object_extensions']['union_of'][0]['intersection_of']
for x in xs:
print('X: {}'.format(x))
# ensure that invalid expressions have been eliminated
assert x['property'] == 'foo'
assert x['filler'] == 'X:1'
assert len(xs) == 1
def test_errors_gaf():
p = GafParser()
p.config.ecomap = EcoMap()
assocs = p.parse(open("tests/resources/errors.gaf", "r"))
msgs = p.report.messages
print("MESSAGES: {}".format(len(msgs)))
for m in msgs:
print("MESSAGE: {}".format(m))
assert len(msgs) == 15
# we expect 4
assert len(assocs) == 7
from ontobio.io import GafWriter
w = GafWriter()
w.write(assocs)
xs = [x for a in assocs for x in a.get('object_extensions', [])]
for x in xs:
print('X: {}'.format(x))
# ensure that invalid expressions have been eliminated
assert x['property'] == 'foo'
assert x['filler'] == 'X:1'
assert len(xs) == 3