QueryBuilder: Implementation of contains Filter Operator applied to JSON Fields for SQLite backend

.gitignore

@@ -43,3 +43,6 @@ pplot_out/
 
 # docker
 docker-bake.override.json
+
+# benchmark
+.benchmarks/

src/aiida/storage/sqlite_zip/orm.py

@@ -285,8 +285,7 @@
             return case((type_filter, casted_entity.ilike(value, escape='\\')), else_=False)
 
         if operator == 'contains':
-            # to-do, see: https://github.com/sqlalchemy/sqlalchemy/discussions/7836
-            raise NotImplementedError('The operator `contains` is not implemented for SQLite-based storage plugins.')
+            return func.json_contains(database_entity, json.dumps(value))
 
         if operator == 'has_key':
             return (

src/aiida/storage/sqlite_zip/utils.py

@@ -48,12 +48,44 @@
     cursor.close()
 
 
+def _contains(lhs: Union[dict, list], rhs: Union[dict, list]):
+    if isinstance(lhs, dict) and isinstance(rhs, dict):
+        for key in rhs:
+            if key not in lhs or not _contains(lhs[key], rhs[key]):
+                return False
+        return True
+
+    elif isinstance(lhs, list) and isinstance(rhs, list):
+        for item in rhs:
+            if not any(_contains(e, item) for e in lhs):
+                return False
+        return True
+    else:
+        return lhs == rhs
+
+
+def _json_contains(lhs: Union[str, bytes, bytearray, dict, list], rhs: Union[str, bytes, bytearray, dict, list]):
+    try:
+        if isinstance(lhs, (str, bytes, bytearray)):
+            lhs = json.loads(lhs)
+        if isinstance(rhs, (str, bytes, bytearray)):
+            rhs = json.loads(rhs)
+    except json.JSONDecodeError:
+        return 0
+    return int(_contains(lhs, rhs))
+
+
+def register_json_contains(dbapi_connection, _):
+    dbapi_connection.create_function('json_contains', 2, _json_contains)
+
+
 def create_sqla_engine(path: Union[str, Path], *, enforce_foreign_keys: bool = True, **kwargs) -> Engine:
     """Create a new engine instance."""
     engine = create_engine(f'sqlite:///{path}', json_serializer=json.dumps, json_deserializer=json.loads, **kwargs)
     event.listen(engine, 'connect', sqlite_case_sensitive_like)
     if enforce_foreign_keys:
         event.listen(engine, 'connect', sqlite_enforce_foreign_keys)
+    event.listen(engine, 'connect', register_json_contains)
     return engine
 
 

tests/benchmark/test_json_contains.py

@@ -0,0 +1,138 @@
+import random
+import string
+
+import pytest
+
+from aiida import orm
+from aiida.orm.querybuilder import QueryBuilder
+
+GROUP_NAME = 'json-contains'
+
+
+COMPLEX_JSON_DEPTH_RANGE = [2**i for i in range(4)]
+COMPLEX_JSON_BREADTH_RANGE = [2**i for i in range(4)]
+LARGE_TABLE_SIZE_RANGE = [2**i for i in range(1, 11)]
+
+
+def gen_json(depth: int, breadth: int):
+    def gen_str(n: int, with_digits: bool = True):
+        population = string.ascii_letters
+        if with_digits:
+            population += string.digits
+        return ''.join(random.choices(population, k=n))
+
+    if depth == 0:  # random primitive value
+        # real numbers are not included as their equivalence is tricky
+        return random.choice(
+            [
+                random.randint(-114, 514),  # integers
+                gen_str(6),  # strings
+                random.choice([True, False]),  # booleans
+                None,  # nulls
+            ]
+        )
+
+    else:
+        gen_dict = random.choice([True, False])
+        data = [gen_json(depth - 1, breadth) for _ in range(breadth)]
+        if gen_dict:
+            keys = set()
+            while len(keys) < breadth:
+                keys.add(gen_str(6, False))
+            data = dict(zip(list(keys), data))
+        return data
+
+
+def extract_component(data, p: float = -1):
+    if random.random() < p:
+        return data
+
+    if isinstance(data, dict) and data:
+        key = random.choice(list(data.keys()))
+        return {key: extract_component(data[key])}
+    elif isinstance(data, list) and data:
+        element = random.choice(data)
+        return [extract_component(element)]
+    else:
+        return data
+
+
+@pytest.mark.benchmark(group=GROUP_NAME)
+@pytest.mark.parametrize('depth', [1, 2, 4, 8])
+@pytest.mark.parametrize('breadth', [1, 2, 4])
+@pytest.mark.usefixtures('aiida_profile_clean')
+def test_deep_json(benchmark, depth, breadth):
+    lhs = gen_json(depth, breadth)
+    rhs = extract_component(lhs, p=1.0 / depth)
+    assert 0 == len(QueryBuilder().append(orm.Dict).all())
+
+    orm.Dict(
+        {
+            'id': f'{depth}-{breadth}',
+            'data': lhs,
+        }
+    ).store()
+    qb = QueryBuilder().append(
+        orm.Dict,
+        filters={
+            'attributes.data': {'contains': rhs},
+        },
+        project=['attributes.id'],
+    )
+    qb.all()
+    result = benchmark(qb.all)
+    assert len(result) == 1
+
+
+@pytest.mark.benchmark(group=GROUP_NAME)
+@pytest.mark.parametrize('depth', [2])
+@pytest.mark.parametrize('breadth', [1, 10, 100])
+@pytest.mark.usefixtures('aiida_profile_clean')
+def test_wide_json(benchmark, depth, breadth):
+    lhs = gen_json(depth, breadth)
+    rhs = extract_component(lhs, p=1.0 / depth)
+    assert 0 == len(QueryBuilder().append(orm.Dict).all())
+
+    orm.Dict(
+        {
+            'id': f'{depth}-{breadth}',
+            'data': lhs,
+        }
+    ).store()
+    qb = QueryBuilder().append(
+        orm.Dict,
+        filters={
+            'attributes.data': {'contains': rhs},
+        },
+        project=['attributes.id'],
+    )
+    qb.all()
+    result = benchmark(qb.all)
+    assert len(result) == 1
+
+
+@pytest.mark.benchmark(group=GROUP_NAME)
+@pytest.mark.parametrize('num_entries', LARGE_TABLE_SIZE_RANGE)
+@pytest.mark.usefixtures('aiida_profile_clean')
+def test_large_table(benchmark, num_entries):
+    data = gen_json(2, 10)
+    rhs = extract_component(data)
+    assert 0 == len(QueryBuilder().append(orm.Dict).all())
+
+    for i in range(num_entries):
+        orm.Dict(
+            {
+                'id': f'N={num_entries}, i={i}',
+                'data': data,
+            }
+        ).store()
+    qb = QueryBuilder().append(
+        orm.Dict,
+        filters={
+            'attributes.data': {'contains': rhs},
+        },
+        project=['attributes.id'],
+    )
+    qb.all()
+    result = benchmark(qb.all)
+    assert len(result) == num_entries