Merge pull request #54 from bento-platform/develop

Version 2.1.0

.github/workflows/lint.yml

@@ -9,7 +9,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v1
-      - name: Install dependencies
-        run: pip install -r requirements.txt
+      - uses: actions/setup-python@v2
+        name: Set up Python
+        with:
+          python-version: 3.9
+      - name: Install flake8
+        run: python -m pip install flake8
       - name: Run linter
         run: flake8 ./bento_lib ./tests

.github/workflows/test.yml

@@ -3,6 +3,7 @@ on:
   push:
     branches:
       - master
+      - develop
   pull_request:
 jobs:
   test:
@@ -22,10 +23,14 @@ jobs:
           --health-retries 5
     steps:
       - uses: actions/checkout@v1
+      - uses: actions/setup-python@v2
+        name: Set up Python
+        with:
+          python-version: ${{ matrix.python-version }}
       - name: Install dependencies
-        run: pip install -r requirements.txt
+        run: python -m pip install -r requirements.txt
       - name: Test
-        run: pytest -svv --cov=bento_lib --cov-branch
+        run: mkdir -p tmp && pytest -svv --cov=bento_lib --cov-branch
         env:
           TEST_REDIS_HOST: localhost
           TEST_REDIS_PORT: 6379
@@ -38,5 +43,9 @@ jobs:
         python-version: [ 3.6, 3.9 ]
     steps:
       - uses: actions/checkout@v1
+      - uses: actions/setup-python@v2
+        name: Set up Python
+        with:
+          python-version: ${{ matrix.python-version }}
       - name: Install bento_lib
-        run: pip install .[flask,django]
+        run: python -m pip install .

bento_lib/package.cfg

@@ -1,5 +1,5 @@
 [package]
 name = bento_lib
-version = 2.0.0
+version = 2.1.0
 authors = David Lougheed
 author_emails = [email protected]

bento_lib/search/data_structure.py

@@ -18,6 +18,17 @@
 ArrayLengthData = Tuple[str, int, Tuple["ArrayLengthData", ...]]
 
 
+def _icontains(lhs: str, rhs: str):
+    """
+    Same as the "contains" operator, except with case-folded (i.e. case
+    insensitive) arguments.
+    :param lhs: The LHS for the operation.
+    :param rhs: The RHS for the operation.
+    :return: The result of the icontains operation.
+    """
+    return contains(lhs.casefold(), rhs.casefold())
+
+
 def _validate_data_structure_against_schema(data_structure: QueryableStructure, schema: JSONSchema):
     """
     Validates a queryable data structure of some type against a JSON schema. This is an important validation step,
@@ -434,6 +445,7 @@ def _resolve(resolve: Tuple[q.Literal, ...], resolving_ds: QueryableStructure, _
     q.FUNCTION_GE: _binary_op(ge),
 
     q.FUNCTION_CO: _binary_op(contains),
+    q.FUNCTION_ICO: _binary_op(_icontains),
 
     q.FUNCTION_RESOLVE: _resolve
 }

bento_lib/search/operations.py

@@ -6,6 +6,7 @@
     "SEARCH_OP_GE",
 
     "SEARCH_OP_CO",
+    "SEARCH_OP_ICO",
 
     "SEARCH_OPERATIONS",
 ]
@@ -18,6 +19,7 @@
 SEARCH_OP_GE = "ge"
 
 SEARCH_OP_CO = "co"
+SEARCH_OP_ICO = "ico"
 
 SEARCH_OPERATIONS = (
     SEARCH_OP_EQ,
@@ -26,4 +28,5 @@
     SEARCH_OP_GT,
     SEARCH_OP_GE,
     SEARCH_OP_CO,
+    SEARCH_OP_ICO,
 )

bento_lib/search/postgres.py

@@ -329,11 +329,17 @@ def _resolve(args: q.Args, params: tuple, schema: JSONSchema, _internal: bool =
                                    sql.Identifier(f_id) if f_id is not None else sql.SQL("*")), params
 
 
-def _contains(args: q.Args, params: tuple, schema: JSONSchema, internal: bool = False) -> SQLComposableWithParams:
+# TODO rename the function ?
+def _contains(op: str, args: q.Args, params: tuple, schema: JSONSchema, internal: bool = False, )\
+        -> SQLComposableWithParams:
     lhs_sql, lhs_params = search_ast_to_psycopg2_expr(args[0], params, schema, internal)
     rhs_sql, rhs_params = search_ast_to_psycopg2_expr(q.Expression(fn=q.FUNCTION_HELPER_WC, args=[args[1]]), params,
                                                       schema, internal)
-    return sql.SQL("({}) LIKE ({})").format(lhs_sql, rhs_sql), params + lhs_params + rhs_params
+    return sql.SQL("({}) {} ({})").format(lhs_sql, sql.SQL(op), rhs_sql), params + lhs_params + rhs_params
+
+
+def _contains_op(op) -> Callable[[q.Args, tuple, JSONSchema, bool], SQLComposableWithParams]:
+    return lambda args, params, schema, internal: _contains(op, args, params, schema, internal)
 
 
 POSTGRES_SEARCH_LANGUAGE_FUNCTIONS: Dict[
@@ -350,7 +356,8 @@ def _contains(args: q.Args, params: tuple, schema: JSONSchema, internal: bool =
     q.FUNCTION_GT: _binary_op(">"),
     q.FUNCTION_GE: _binary_op(">="),
 
-    q.FUNCTION_CO: _contains,
+    q.FUNCTION_CO: _contains_op("LIKE"),
+    q.FUNCTION_ICO: _contains_op("ILIKE"),
 
     q.FUNCTION_RESOLVE: _resolve,
 

bento_lib/search/queries.py

@@ -7,7 +7,8 @@
     SEARCH_OP_EQ,
     SEARCH_OP_GT,
     SEARCH_OP_GE,
-    SEARCH_OP_CO
+    SEARCH_OP_CO,
+    SEARCH_OP_ICO
 )
 
 
@@ -21,6 +22,7 @@
     "FUNCTION_GT",
     "FUNCTION_GE",
     "FUNCTION_CO",
+    "FUNCTION_ICO",
     "FUNCTION_RESOLVE",
     "FUNCTION_HELPER_WC",
 
@@ -56,6 +58,7 @@
 FUNCTION_GE = "#ge"
 
 FUNCTION_CO = "#co"
+FUNCTION_ICO = "#ico"
 
 FUNCTION_RESOLVE = "#resolve"
 
@@ -71,6 +74,7 @@
     FUNCTION_GT,
     FUNCTION_GE,
     FUNCTION_CO,
+    FUNCTION_ICO,
     FUNCTION_RESOLVE,
     FUNCTION_HELPER_WC,
 )
@@ -87,6 +91,7 @@
     FUNCTION_GT: BINARY_RANGE,
     FUNCTION_GE: BINARY_RANGE,
     FUNCTION_CO: BINARY_RANGE,
+    FUNCTION_ICO: BINARY_RANGE,
     FUNCTION_RESOLVE: (0, None),
     FUNCTION_HELPER_WC: (1, 1),
 }
@@ -100,6 +105,7 @@
     FUNCTION_GE: SEARCH_OP_GE,
 
     FUNCTION_CO: SEARCH_OP_CO,
+    FUNCTION_ICO: SEARCH_OP_ICO,
 }
 
 

requirements.txt

@@ -13,7 +13,7 @@ filelock==3.0.12
 flake8==3.9.0
 Flask==1.1.2
 idna==2.10
-importlib-metadata==3.7.3
+importlib-metadata==3.9.1
 iniconfig==1.1.1
 itsdangerous==1.1.0
 Jinja2==2.11.3
@@ -26,7 +26,7 @@ pluggy==0.13.1
 psycopg2-binary==2.8.6
 py==1.10.0
 pycodestyle==2.7.0
-pyflakes==2.3.0
+pyflakes==2.3.1
 pyparsing==2.4.7
 pyrsistent==0.17.3
 pytest==6.2.2
@@ -36,7 +36,7 @@ python-dateutil==2.8.1
 pytz==2021.1
 redis==3.5.3
 requests==2.25.1
-responses==0.13.1
+responses==0.13.2
 six==1.15.0
 sqlparse==0.4.1
 toml==0.10.2

tests/test_search.py

@@ -50,7 +50,13 @@
                                             "queryable": "all"
                                         }
                                     },
-                                    "label": {"type": "string"}
+                                    "label": {
+                                        "type": "string",
+                                        "search": {
+                                            "operations": [operations.SEARCH_OP_ICO],
+                                            "queryable": "all"
+                                        }
+                                    }
                                 },
                                 "search": {
                                     "database": {
@@ -390,6 +396,7 @@
     [queries.FUNCTION_GT, 5, 6],
     [queries.FUNCTION_GE, 5, 6],
     [queries.FUNCTION_CO, "hello", "h"],
+    [queries.FUNCTION_ICO, "LABEL", "label"],
     [queries.FUNCTION_RESOLVE, "biosamples", "[item]", "procedure", "code", "id"],
 )
 
@@ -411,6 +418,7 @@
     [queries.FUNCTION_GT, 5],
     [queries.FUNCTION_GE, 5],
     [queries.FUNCTION_CO, "hello"],
+    [queries.FUNCTION_ICO, "LABEL"],
     *TEST_INVALID_FUNCTIONS
 )
 
@@ -474,6 +482,8 @@
     ["#eq", ["#resolve", "test_op_3", "[item]", "[item]"], 8]
 ]
 
+TEST_QUERY_24 = ["#ico", ["#resolve", "biosamples", "[item]", "procedure", "code", "label"], "label"]
+
 TEST_LARGE_QUERY_1 = [
     "#and",
     ["#eq",
@@ -625,6 +635,7 @@
     (TEST_QUERY_21, False, True, 27, 1),  # Accessing 3 elements in test_op_2, plus 9 in test_op_3 (non-flattened)
     (TEST_QUERY_22, False, True,  9, 9),  # Accessing 9 in test_op_3 and checking them against itself
     (TEST_QUERY_23, False, True, 27, 1),  # test_op_3: 9, test_op_1: 3
+    (TEST_QUERY_24,  False, True,  2, 2),
 )
 
 # Query, Internal, Exception
@@ -679,6 +690,7 @@
     (TEST_QUERY_21, False, ()),
     (TEST_QUERY_22, False, ()),
     (TEST_QUERY_23, False, (6, 8)),
+    (TEST_QUERY_24, True, ("%label%",)),
 )
 
 PG_INVALID_EXPRESSIONS = (