def test_databases_only():
# Check sources not in provided sources are excluded from generated template
ag_a = Agent('A')
ag_b = Agent('B')
evidences = []
colors = []
not_in_html = []
for source_type, info in DEFAULT_SOURCE_COLORS:
for n, source in enumerate(info['sources']):
# Only get 4 first sources for each type
if n < 4 and source_type == 'databases':
ev = Evidence(source_api=source,
text=f'Evidence from {source}')
evidences.append(ev)
colors.append(info['sources'][source])
else:
not_in_html.append(source)
stmt = Activation(ag_a, ag_b, evidence=evidences)
ha = HtmlAssembler(statements=[stmt])
ha.save_model('./temp_no_show_db_only.html', show_only_available=True)
with open('./temp_no_show_db_only.html') as fh:
no_show_html = fh.read()
assert all(color in no_show_html for color in colors)
badge_class = 'class="badge badge-source source-{src}"'
assert all(
badge_class.format(src=src) not in no_show_html for src in not_in_html)
def test_influence():
c2 = Concept('food insecurity',
db_refs={'WM': [('wm/food_insecurity', 1.0)]})
c1 = Concept('floods', db_refs={'WM': [('wm/floods', 1.0)]})
c3 = Concept('x', db_refs={})
stmt = Influence(Event(c1), Event(c2))
stmt2 = Influence(Event(c1), Event(c3))
ha = HtmlAssembler([stmt, stmt2])
ha.make_model()
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_assembler():
stmt = make_stmt()
ha = HtmlAssembler([stmt])
result = ha.make_model()
assert isinstance(result, str)
# Read from the template file and make sure the beginning and end of the
# content matches
loader = IndraHTMLLoader()
template, _, _ = loader.get_source(None, 'indra/indra_template.html')
assert result.startswith(template[0:100])
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_assembler():
stmt = make_stmt()
ha = HtmlAssembler([stmt])
result = ha.make_model()
assert isinstance(result, str)
# Read from the template file and make sure the beginning and end of the
# content matches
with open(template_path, 'rt') as f:
template = f.read().strip()
assert result.startswith(template[0:100])
assert result.strip().endswith(template[-10:])
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_complex():
stmt = Complex([Agent('BRAF'), Agent('RAF1')])
ha = HtmlAssembler([stmt])
ha.make_model()
# Complex with more than two members
stmt = Complex([Agent('BRAF'), Agent('RAF1'), Agent('YWAH')])
ha = HtmlAssembler([stmt])
ha.make_model()
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_active_form():
stmt = ActiveForm(Agent('MAPK1', mods=[ModCondition('phosphorylation')]),
'kinase', True)
ha = HtmlAssembler([stmt])
ha.make_model()
# Case when it's not active
stmt = ActiveForm(Agent('MAPK1', mods=[ModCondition('phosphorylation')]),
'activity', False)
ha = HtmlAssembler([stmt])
ha.make_model()
def test_custom_colors_in_html():
ag_a = Agent('A')
ag_b = Agent('B')
custom_sources: SourceInfo = {
"src_a": {
"name": "Src A",
"link": "https://example.com/src_a",
"type": "reader",
"domain": "general",
"default_style": {
"color": "white",
"background-color": "blue"
}
},
"src_b": {
"name": "Src B",
"link": "https://example.com/src_b",
"type": "database",
"domain": "general",
"default_style": {
"color": "black",
"background-color": "#bebada"
}
},
}
evidences = []
colors = []
sources = []
for source, source_info in custom_sources.items():
sources.append(source)
ev = Evidence(source_api=source, text=f'Evidence from {source}')
evidences.append(ev)
colors.append(source_info['default_style']['background-color'])
stmt = Activation(ag_a, ag_b, evidence=evidences)
ha = HtmlAssembler(statements=[stmt], custom_sources=custom_sources)
ha.save_model('./temp_custom_colors_simple.html')
with open('./temp_custom_colors_simple.html') as fh:
simple_html = fh.read()
ha = HtmlAssembler(statements=[stmt], custom_sources=custom_sources)
ha.save_model('./temp_not_simple.html', simple=False)
with open('./temp_custom_colors_simple.html') as fh:
not_simple_html = fh.read()
# Check if style rule appears
assert all(color in simple_html for color in colors)
# Test if badge appears
badge_str = 'class="badge badge-source source-{src}"'
assert all(badge_str.format(src=src) in simple_html for src in sources)
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_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_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')
def test_format_evidence_text():
stmt = make_stmt()
ev_list = HtmlAssembler._format_evidence_text(stmt)
assert len(ev_list) == 1
ev = ev_list[0]
assert isinstance(ev, dict)
assert set(ev.keys()) == {
'source_api', 'text_refs', 'text', 'source_hash', 'pmid'
}
assert ev['source_api'] == 'test'
assert ev['text_refs']['PMID'] == '1234567'
assert ev['text'] == (
'We noticed that the '
'<span class="badge badge-subject">Src kinase</span> '
'was able to phosphorylate '
'<span class="badge badge-object">'
'Ras proteins</span>.'), ev['text']
def test_colors_in_html():
ag_a = Agent('A')
ag_b = Agent('B')
evidences = []
colors = []
for source_type, info in DEFAULT_SOURCE_COLORS:
for source in info['sources']:
ev = Evidence(source_api=source, text=f'Evidence from {source}')
evidences.append(ev)
colors.append(info['sources'][source])
stmt = Activation(ag_a, ag_b, evidence=evidences)
ha = HtmlAssembler(statements=[stmt])
ha.save_model('./temp_simple.html')
ha = HtmlAssembler(statements=[stmt])
ha.save_model('./temp_not_simple.html', simple=False)
with open('./temp_simple.html') as fh:
simple_html = fh.read()
with open('./temp_not_simple.html') as fh:
not_simple_html = fh.read()
assert all(color in simple_html for color in colors)
assert all(color in not_simple_html for color in colors)
def test_translocation():
stmt = Translocation(Agent('FOXO3A'), None, 'nucleus')
ha = HtmlAssembler([stmt])
ha.make_model()
def test_dephosphorylation():
stmt = Dephosphorylation(Agent('DUSP6'), Agent('MAPK1'), 'T', '185')
ha = HtmlAssembler([stmt])
ha.make_model()
def test_inhibition():
stmt = Inhibition(Agent('DUSP4'), Agent('MAPK1'))
ha = HtmlAssembler([stmt])
ha.make_model()
def test_activation():
stmt = Activation(Agent('MAP2K1'), Agent('MAPK1'), 'kinase')
ha = HtmlAssembler([stmt])
ha.make_model()
def test_gef():
stmt = Gef(Agent('SOS1'), Agent('KRAS'))
ha = HtmlAssembler([stmt])
ha.make_model()
def test_gap():
stmt = Gap(Agent('RASA1'), Agent('KRAS'))
ha = HtmlAssembler([stmt])
ha.make_model()
def test_migration():
stmt = Migration(Concept('migration'))
ha = HtmlAssembler([stmt])
ha.make_model()
def test_event():
stmt = Event(Concept('a'))
ha = HtmlAssembler([stmt])
ha.make_model()
def test_association():
stmt = Association([Event(Concept('a')), Event(Concept('b'))])
ha = HtmlAssembler([stmt])
ha.make_model()
def test_assembler():
stmt = make_stmt()
ha = HtmlAssembler([stmt])
result = ha.make_model()
assert isinstance(result, str)
# Read from the template file and make sure the beginning and end of the
# content matches
template, _, _ = loader.get_source(None, 'indra/template.html')
assert result.startswith(template[0:100])
# Make sure assembler works with other parameters provided
stmt2 = make_bad_stmt()
ha = HtmlAssembler(source_counts={
stmt.get_hash(): {
'test': 1
},
stmt2.get_hash(): {
'test': 1
}
},
ev_counts={
stmt.get_hash(): 1,
stmt2.get_hash(): 1
},
db_rest_url='test.db.url')
ha.add_statements([stmt, stmt2])
result = ha.make_model(grouping_level='agent-pair')
assert isinstance(result, str)
result = ha.make_model(grouping_level='statement')
assert isinstance(result, str)
# Test belief badges
result = ha.make_model(grouping_level='statement', show_belief=True)
assert isinstance(result, str)
assert '<small\n' \
' class="badge badge-pill badge-belief"\n' \
' title="Belief score for this statement">1.0</small>' in result
result = ha.make_model(grouping_level='statement', show_belief=False)
assert isinstance(result, str)
assert '<small\n' \
' class="badge badge-pill badge-belief"\n' \
' title="Belief score for this statement">1</small>' \
not in result
# Test if source URL exists
assert 'http://www.causalbionet.com/' in result
# Make sure warning can be appended
ha.append_warning('warning')
assert ('\t<span style="color:red;">(CAUTION: warning occurred when '
'creating this page.)</span>' in ha.model)
# Make sure model is created before saving
ha = HtmlAssembler([stmt])
assert not ha.model
ha.save_model('tempfile.html')
assert ha.model
def test_decrease_amount():
stmt = DecreaseAmount(Agent('TP53'), Agent('MDM2'))
ha = HtmlAssembler([stmt])
ha.make_model()
