feat: Tests for invalid data in GTFS dataset

conftest.py

@@ -28,6 +28,12 @@ def pytest_addoption(parser):
         default=False,
         help="run expensive tests",
     )
+    parser.addoption(
+        "--sanitycheck",
+        action="store_true",
+        default=False,
+        help="run sanity checks",
+    )
 
 
 def pytest_configure(config):
@@ -39,6 +45,10 @@ def pytest_configure(config):
     config.addinivalue_line(
         "markers", "runexpensive: mark test to run expensive tests"
     )
+    config.addinivalue_line(
+        "markers",
+        "sanitycheck: mark test to run checks in dependencies' code.",
+    )
 
 
 def pytest_collection_modifyitems(config, items):  # noqa:C901
@@ -47,6 +57,7 @@ def pytest_collection_modifyitems(config, items):  # noqa:C901
         config.getoption("--runsetup")
         & config.getoption("--runinteg")
         & config.getoption("--runexpensive")
+        & config.getoption("--sanitycheck")
     ):
         # do full test suite when all flags are given
         return
@@ -75,3 +86,12 @@ def pytest_collection_modifyitems(config, items):  # noqa:C901
         for item in items:
             if "runexpensive" in item.keywords:
                 item.add_marker(skip_runexpensive)
+
+    # do not add sanitycheck marks when the sanitycheck flag is given
+    if not config.getoption("--sanitycheck"):
+        skip_sanitycheck = pytest.mark.skip(
+            reason="need --sanitycheck option to run"
+        )
+        for item in items:
+            if "sanitycheck" in item.keywords:
+                item.add_marker(skip_sanitycheck)

notebooks/gtfs/check_unmatched_id_warnings.py

@@ -46,8 +46,8 @@
         feed.trips,
         pd.DataFrame(
             {
-                "service_id": [101],
-                "route_id": [20304],
+                "service_id": ["101023"],
+                "route_id": ["2030445"],
                 "trip_id": ["VJbedb4cfd0673348e017d42435abbdff3ddacbf89"],
                 "trip_headsign": ["Newport"],
                 "block_id": [np.nan],
@@ -70,8 +70,7 @@
         feed.routes,
         pd.DataFrame(
             {
-                "service_id": [101],
-                "route_id": [20304],
+                "route_id": ["20304"],
                 "agency_id": ["OL5060"],
                 "route_short_name": ["X145"],
                 "route_long_name": [np.nan],
@@ -91,3 +90,5 @@
 # the pipeline and therefore the user will be made aware. It is also flagged
 # as an error which means that 'the GTFS is violated'
 # (https://mrcagney.github.io/gtfs_kit_docs/).
+
+# %%

tests/gtfs/test_validation.py

@@ -117,6 +117,148 @@ def test_is_valid(self, gtfs_fixture):
             found_cols == exp_cols
         ).all(), f"Expected columns {exp_cols}. Found: {found_cols}"
 
+    @pytest.mark.sanitycheck
+    def test_trips_unmatched_ids(self, gtfs_fixture):
+        """Tests to evaluate gtfs-klt's reaction to invalid IDs in trips.
+
+        Parameters
+        ----------
+        gtfs_fixture : GtfsInstance
+            a GtfsInstance test fixure
+
+        """
+        feed = gtfs_fixture.feed
+
+        # add row to tripas table with invald trip_id, route_id, service_id
+        feed.trips = pd.concat(
+            [
+                feed.trips,
+                pd.DataFrame(
+                    {
+                        "service_id": ["101023"],
+                        "route_id": ["2030445"],
+                        "trip_id": [
+                            "VJbedb4cfd0673348e017d42435abbdff3ddacbf89"
+                        ],
+                        "trip_headsign": ["Newport"],
+                        "block_id": [np.nan],
+                        "shape_id": [
+                            "RPSPc4c99ac6aff7e4648cbbef785f88427a48efa80f"
+                        ],
+                        "wheelchair_accessible": [0],
+                        "trip_direction_name": [np.nan],
+                        "vehicle_journey_code": ["VJ109"],
+                    }
+                ),
+            ],
+            axis=0,
+        )
+
+        # assert different errors/warnings haave been raised
+        new_valid = feed.validate()
+        assert (
+            len(new_valid[new_valid.message == "Undefined route_id"]) == 1
+        ), "gtfs-kit failed to recognise invalid route_id"
+        assert (
+            len(new_valid[new_valid.message == "Undefined service_id"]) == 1
+        ), "gtfs-kit failed to recognise invalid service_id"
+        assert (
+            len(new_valid[new_valid.message == "Trip has no stop times"]) == 1
+        ), "gtfs-kit failed to recognise invalid service_id"
+        assert len(new_valid) == 10, "Validation table not expected size"
+
+    @pytest.mark.sanitycheck
+    def test_routes_unmatched_ids(self, gtfs_fixture):
+        """Tests to evaluate gtfs-klt's reaction to invalid IDs in routes.
+
+        Parameters
+        ----------
+        gtfs_fixture : GtfsInstance
+            a GtfsInstance test fixure
+
+        """
+        feed = gtfs_fixture.feed
+
+        # add row to tripas table with invald trip_id, route_id, service_id
+        feed.routes = pd.concat(
+            [
+                feed.routes,
+                pd.DataFrame(
+                    {
+                        "route_id": ["20304"],
+                        "agency_id": ["OL5060"],
+                        "route_short_name": ["X145"],
+                        "route_long_name": [np.nan],
+                        "route_type": [200],
+                    }
+                ),
+            ],
+            axis=0,
+        )
+
+        # assert different errors/warnings haave been raised
+        new_valid = feed.validate()
+        assert (
+            len(new_valid[new_valid.message == "Undefined agency_id"]) == 1
+        ), "gtfs-kit failed to recognise invalid agency_id"
+        assert (
+            len(new_valid[new_valid.message == "Route has no trips"]) == 1
+        ), "gtfs-kit failed to recognise that there are routes with no trips"
+        assert len(new_valid) == 9, "Validation table not expected size"
+
+    @pytest.mark.sanitycheck
+    def test_unmatched_service_id_behaviour(self, gtfs_fixture):
+        """Tests to evaluate gtfs-klt's reaction to invalid IDs in calendar.
+
+        Parameters
+        ----------
+        gtfs_fixture : GtfsInstance
+            a GtfsInstance test fixure
+
+        Notes
+        -----
+        'gtfs-kit' does not care about unmatched service IDs in the calendar
+        table. The Calendar table can have data with any service_id as long as
+        the datatypes are string. However, gtfs_kit will state an error if the
+        calendar table contains duplicate service_ids.
+
+        """
+        feed = gtfs_fixture.feed
+        original_error_count = len(feed.validate())
+
+        # introduce a dummy row with a non matching service_id
+        feed.calendar = pd.concat(
+            [
+                feed.calendar,
+                pd.DataFrame(
+                    {
+                        "service_id": ["1018872"],
+                        "monday": [0],
+                        "tuesday": [0],
+                        "wednesday": [0],
+                        "thursday": [0],
+                        "friday": [0],
+                        "saturday": [0],
+                        "sunday": [0],
+                        "start_date": ["20200104"],
+                        "end_date": ["20230301"],
+                    }
+                ),
+            ],
+            axis=0,
+        )
+        new_error_count = len(feed.validate())
+        assert (
+            new_error_count == original_error_count
+        ), "Unrecognised error in validaation table"
+
+        # drop a row from the calendar table
+        feed.calendar.drop(3, inplace=True)
+        new_valid = feed.validate()
+        assert (
+            len(new_valid[new_valid.message == "Undefined service_id"]) == 1
+        ), "gtfs-kit failed to identify missing service_id"
+
     def test_print_alerts_defence(self, gtfs_fixture):
         """Check defensive behaviour of print_alerts()."""
         with pytest.raises(