def test_sort_group_by_agent_pair_custom_function():
stmts = _get_sort_corpus()
ha = HtmlAssembler(stmts,
sort_by=lambda d: 4 * d['trips'] + 2 * d['reach'] + 2 *
d['medscan'] + d['sparser'] - d['isi'])
json_model = ha.make_json_model(grouping_level='agent-pair')
assert list(json_model.keys()) == ['Fez-Baz', 'Bar-Baz', 'Fez-Bar']
ha.make_model(grouping_level='agent-pair')
def test_sort_group_by_statement_sort_by_none():
stmts = _get_sort_corpus()
ha = HtmlAssembler(stmts, sort_by=None)
json_model = ha.make_json_model(grouping_level='statement')
statements = \
json_model['all-statements']['stmts_formatted'][0]['stmt_info_list']
got_h_list = [int(s['hash']) for s in statements]
inp_h_list = [s.get_hash() for s in stmts]
assert got_h_list == inp_h_list
def test_sort_group_by_relation():
ha = HtmlAssembler(_get_sort_corpus())
# Test ordering, grouping by relation.
json_model = ha.make_json_model(grouping_level='relation')
assert list(json_model.keys()) == ['all-relations']
relations = json_model['all-relations']['stmts_formatted']
assert len(relations) == 5, len(relations)
# Make sure the HTML assembles.
model = ha.make_model(grouping_level='relation')
with open('test_relation.html', 'w') as f:
f.write(model)
def test_sort_group_by_statement():
ha = HtmlAssembler(_get_sort_corpus())
# Test ordering and grouping by statement.
json_model = ha.make_json_model(grouping_level='statement')
assert list(json_model.keys()) == ['all-statements']
assert len(json_model['all-statements']['stmts_formatted']) == 1
statements = \
json_model['all-statements']['stmts_formatted'][0]['stmt_info_list']
assert len(statements) == 6
assert [len(s['evidence']) for s in statements] == [4, 3, 2, 2, 1, 1]
# Make sure the html assembly works.
ha.make_model(grouping_level='statement')
def test_sort_group_by_statement_custom_function():
stmts = _get_sort_corpus()
ha = HtmlAssembler(stmts,
sort_by=lambda d: 4 * d['trips'] + 2 * d['reach'] + 2 *
d['medscan'] + d['sparser'] - d['isi'])
json_model = ha.make_json_model(grouping_level='statement')
statements = \
json_model['all-statements']['stmts_formatted'][0]['stmt_info_list']
assert len(statements) == len(stmts)
exp_order = [
'6106301533612997', '-17995265549545446', '34182032179844940',
'32266861591785935', '-30059881887512900', '-5998595995539618'
]
assert [s['hash'] for s in statements] == exp_order
ha.make_model(grouping_level='statement')
def test_sort_group_by_agent_custom_ordering():
stmts = _get_sort_corpus()
custom_values = [0.1, 0.2, 0.15, 0.6, 0.3, 0.8]
val_dict = {s.get_hash(): v for v, s in zip(custom_values, stmts)}
custom_stat = StmtStat('value', val_dict, float, AveAggregator)
ha = HtmlAssembler(stmts, sort_by='value', custom_stats=[custom_stat])
json_model = ha.make_json_model(grouping_level='agent-pair')
assert len(json_model.keys()) == 4
# This result was slightly counter-intuitive, but recall that averages will
# mean a grouping with the conversion will always have a lower value than
# the conversion itself, so it makes sense for it to come out on top.
assert list(json_model.keys()) == [
'Fez-Far-Faz-Bar-Baz', 'Fez-Bar', 'Bar-Baz', 'Fez-Baz'
]
ha.make_model(grouping_level='agent-pair')
def test_sort_group_by_statement_custom_ordering():
stmts = _get_sort_corpus()
custom_values = [0.1, 0.2, 0.15, 0.6, 0.3, 0.8]
val_dict = {s.get_hash(): v for v, s in zip(custom_values, stmts)}
custom_stat = StmtStat('value', val_dict, float, AveAggregator)
ha = HtmlAssembler(stmts, sort_by='value', custom_stats=[custom_stat])
json_model = ha.make_json_model(grouping_level='statement')
statements = \
json_model['all-statements']['stmts_formatted'][0]['stmt_info_list']
got_h_list = [int(s['hash']) for s in statements]
exp_h_list = sorted((h for h in val_dict.keys()),
key=lambda h: val_dict[h],
reverse=True)
assert got_h_list == exp_h_list
ha.make_model(grouping_level='statement')
def test_sort_group_by_relation_custom_function():
stmts = _get_sort_corpus()
ha = HtmlAssembler(stmts,
sort_by=lambda d: 4 * d['trips'] + 2 * d['reach'] + 2 *
d['medscan'] + d['sparser'] - d['isi'])
json_model = ha.make_json_model(grouping_level='relation')
relations = json_model['all-relations']['stmts_formatted']
assert len(relations) == 5, len(relations)
relation_names = [rel['short_name'] for rel in relations]
exp_rel_names = [
'<b>Bar</b> phosphorylates <b>Baz</b>.',
'<b>Fez</b> inhibits <b>Baz</b>.',
'<b>Bar</b> binds <b>Baz</b> and <b>Fez</b>.',
'<b>Fez</b> decreases the amount of <b>Baz</b>.',
'<b>Fez</b> catalyzes the conversion of <b>Far</b> and <b>Faz</b> into '
'<b>Bar</b> and <b>Baz</b>.'
]
assert relation_names == exp_rel_names, relation_names
ha.make_model(grouping_level='relation')
def test_sort_default():
ha = HtmlAssembler(_get_sort_corpus())
# Test the ordering of the statements in the default mode of make_json_model
json_model = ha.make_json_model()
assert list(json_model.keys()) == ['Fez-Baz', 'Bar-Baz', 'Fez-Bar']
exp_stmt_counts = {'Fez-Baz': 4, 'Bar-Baz': 2, 'Fez-Bar': 2}
assert all(
len(json_model[k]['stmts_formatted']) == n
for k, n in exp_stmt_counts.items())
ev_counts = {
k: sum(
len(s['evidence']) for r in m['stmts_formatted']
for s in r['stmt_info_list'])
for k, m in json_model.items()
}
assert ev_counts == {'Fez-Baz': 8, 'Bar-Baz': 7, 'Fez-Bar': 3}, ev_counts
# Check to make sure the HTML assembler runs.
model = ha.make_model()
with open('test_agent_pair.html', 'w') as f:
f.write(model)
def test_sort_group_by_relation_custom_ordering():
stmts = _get_sort_corpus()
custom_values = [0.1, 0.2, 0.15, 0.6, 0.3, 0.8]
val_dict = {s.get_hash(): v for v, s in zip(custom_values, stmts)}
custom_stat = StmtStat('value', val_dict, float, AveAggregator)
ha = HtmlAssembler(stmts, sort_by='value', custom_stats=[custom_stat])
json_model = ha.make_json_model(grouping_level='relation')
assert list(json_model.keys()) == ['all-relations']
relations = json_model['all-relations']['stmts_formatted']
assert len(relations) == 5, len(relations)
relation_names = [rel['short_name'] for rel in relations]
exp_relation_names = [
'<b>Fez</b> catalyzes the conversion of <b>Far</b> and <b>Faz</b> into '
'<b>Bar</b> and <b>Baz</b>.', '<b>Bar</b> phosphorylates <b>Baz</b>.',
'<b>Fez</b> decreases the amount of <b>Baz</b>.',
'<b>Bar</b> binds <b>Baz</b> and <b>Fez</b>.',
'<b>Fez</b> inhibits <b>Baz</b>.'
]
assert relation_names == exp_relation_names
ha.make_model(grouping_level='relation')
