def test_stats_entities(collection_data: CollectionData):
c1 = BioEntity('c1', 'cn1', CHEMICAL)
g1, g2 = BioEntity('g1', 'gn1', GENE), BioEntity('g2', 'gn2', GENE)
d1 = BioEntity('d1', 'dn1', DISEASE)
collection_data.relations_db.insert_entries([
relation_entry_from_entities(c1, g1, 'expression', pmid='1',
prob=0.99),
relation_entry_from_entities(c1, g2, 'transport', pmid='2', prob=0.01),
relation_entry_from_entities(c1, g2, 'transport', pmid='3', prob=0.02),
relation_entry_from_entities(g2, d1, 'marker', pmid='4', prob=0.09)
])
task = CalculateStatsTask(collection_data)
task.execute()
stats = collection_data.stats
assert stats.chemicals == EntityGroupCounts(total=1,
relations=3,
top=[EntityIdCount('c1', 3)])
assert stats.genes == EntityGroupCounts(
total=2,
relations=4,
top=[EntityIdCount('g2', 3),
EntityIdCount('g1', 1)])
assert stats.diseases == EntityGroupCounts(total=1,
relations=1,
top=[EntityIdCount('d1', 1)])
def test_get_relation_pmid_probs_all_pmids(relations_db: ExtractedRelationsDatabase):
c1 = BioEntity('c1', 'cn1', CHEMICAL)
g1, g2 = BioEntity('g1', 'gn1', GENE), BioEntity('g2', 'gn2', GENE)
relations_db.insert_entries([
relation_entry_from_entities(c1, g1, 'expression', pmid='1', prob=0.9),
relation_entry_from_entities(c1, g1, 'expression', pmid='2', prob=0.5),
relation_entry_from_entities(c1, g2, 'transport', pmid='3', prob=1.0),
])
probs = list(relations_db.get_relation_pmid_probs(id1='c1', id2='g1', label='expression', pmids=['1', '2', '3']))
assert set(probs) == {RelationPmidProb('1', 0.9), RelationPmidProb('2', 0.5)}
def test_get_entity_pairs(relations_db: ExtractedRelationsDatabase):
c1 = BioEntity('c1', 'cn1', CHEMICAL)
g1, g2 = BioEntity('g1', 'gn1', GENE), BioEntity('g2', 'gn2', GENE)
relations_db.insert_entries([
relation_entry_from_entities(c1, g1, 'expression', pmid='1', prob=0.9),
relation_entry_from_entities(c1, g1, 'expression', pmid='2', prob=0.5),
relation_entry_from_entities(c1, g2, 'transport', pmid='3', prob=0.1)
])
pairs = list(relations_db.get_entity_pairs())
assert len(pairs) == 2
assert pairs[0] == (c1, g1)
assert pairs[1] == (c1, g2)
def test_stats_total(collection_data: CollectionData):
c1 = BioEntity('c1', 'cn1', CHEMICAL)
g1, g2 = BioEntity('g1', 'gn1', GENE), BioEntity('g2', 'gn2', GENE)
collection_data.relations_db.insert_entries([
relation_entry_from_entities(c1, g1, 'expression', pmid='1', prob=0.9),
relation_entry_from_entities(c1, g2, 'transport', pmid='2', prob=0.1)
])
task = CalculateStatsTask(collection_data)
task.execute()
stats = collection_data.stats
assert stats.total_relations == 2
assert stats.total_entities == 3
def test_merged_relations_pmid_filter(relations_db: ExtractedRelationsDatabase):
c1 = BioEntity('c1', 'cn1', CHEMICAL)
g1, g2 = BioEntity('g1', 'gn1', GENE), BioEntity('g2', 'gn2', GENE)
d1 = BioEntity('d1', 'dn1', DISEASE)
relations_db.insert_entries([
relation_entry_from_entities(c1, g1, 'expression', pmid='1', prob=0.9),
relation_entry_from_entities(c1, g1, 'expression', pmid='2', prob=0.5),
relation_entry_from_entities(g1, d1, 'marker', pmid='1', prob=0.1)
])
merged = list(relations_db.get_merged_relations(pmid='1'))
assert len(merged) == 2
assert merged[0] == MergedRelation(c1, g1, 'expression', prob=pytest.approx(0.9), pmids=['1'])
assert merged[1] == MergedRelation(g1, d1, 'marker', prob=pytest.approx(0.1), pmids=['1'])
def test_stats_r_type_counts(collection_data: CollectionData):
c1 = BioEntity('c1', 'cn1', CHEMICAL)
g1, g2 = BioEntity('g1', 'gn1', GENE), BioEntity('g2', 'gn2', GENE)
collection_data.relations_db.insert_entries([
relation_entry_from_entities(c1, g1, 'expression', pmid='1',
prob=0.99),
relation_entry_from_entities(c1, g2, 'transport', pmid='2', prob=0.01),
relation_entry_from_entities(c1, g2, 'transport', pmid='3', prob=0.02),
relation_entry_from_entities(c1, g2, 'transport', pmid='4', prob=0.09)
])
task = CalculateStatsTask(collection_data)
task.execute()
stats = collection_data.stats
assert stats.r_type_counts == [
RTypeCounts('expression', [0] * 19 + [1]),
RTypeCounts('transport', [2, 1] + [0] * 18)
]
def test_get_extracted_relations(relations_db: ExtractedRelationsDatabase):
c1 = BioEntity('c1', 'cn1', CHEMICAL)
g1, g2 = BioEntity('g1', 'gn1', GENE), BioEntity('g2', 'gn2', GENE)
relations_db.insert_entries([
relation_entry_from_entities(c1, g1, 'expression', pmid='1', prob=0.9),
relation_entry_from_entities(c1, g1, 'expression', pmid='2', prob=0.5),
relation_entry_from_entities(c1, g2, 'transport', pmid='3', prob=1.0),
])
extracted = list(relations_db.get_extracted_relations())
assert len(extracted) == 3
assert extracted[0].as_dict() == \
relation_entry_from_entities(c1, g1, 'expression', pmid='1', prob=pytest.approx(0.9)).as_dict()
assert extracted[1].as_dict() == \
relation_entry_from_entities(c1, g1, 'expression', pmid='2', prob=pytest.approx(0.5)).as_dict()
assert extracted[2].as_dict() == \
relation_entry_from_entities(c1, g2, 'transport', pmid='3', prob=pytest.approx(1.0)).as_dict()