Advanced validation and cleaning

src/assess_gtfs/cleaners.py

@@ -3,8 +3,18 @@
 from typing import Union
 
 import numpy as np
+from gtfs_kit.cleaners import clean_ids as clean_ids_gk
+from gtfs_kit.cleaners import (
+    clean_route_short_names as clean_route_short_names_gk,
+)
+from gtfs_kit.cleaners import clean_times as clean_times_gk
+from gtfs_kit.cleaners import drop_zombies as drop_zombies_gk
 
-from assess_gtfs.utils.defence import _check_iterable, _gtfs_defence
+from assess_gtfs.utils.defence import (
+    _check_iterable,
+    _gtfs_defence,
+    _type_defence,
+)
 
 
 def drop_trips(gtfs, trip_id: Union[str, list, np.ndarray]) -> None:
@@ -175,3 +185,63 @@ def clean_multiple_stop_fast_travel_warnings(
         ~gtfs.multiple_stops_invalid["trip_id"].isin(trip_ids)
     ]
     return None
+
+
+def core_cleaners(
+    gtfs,
+    clean_ids: bool = True,
+    clean_times: bool = True,
+    clean_route_short_names: bool = True,
+    drop_zombies: bool = True,
+) -> None:
+    """Clean the gtfs with the core cleaners of gtfs-kit.
+
+    The source code for the cleaners, along with detailed descriptions of the
+    cleaning they are performing can be found here:
+    https://github.com/mrcagney/gtfs_kit/blob/master/gtfs_kit/cleaners.py
+
+    All credit for these cleaners goes to the creators of the gtfs_kit package.
+    HOMEPAGE:  https://github.com/mrcagney/gtfs_kit
+
+    Parameters
+    ----------
+    gtfs : GtfsInstance
+        The gtfs to clean
+    clean_ids : bool, optional
+        Whether or not to use clean_ids, by default True
+    clean_times : bool, optional
+        Whether or not to use clean_times, by default True
+    clean_route_short_names : bool, optional
+        Whether or not to use clean_route_short_names, by default True
+    drop_zombies : bool, optional
+        Whether or not to use drop_zombies, by default True
+
+    Returns
+    -------
+    None
+
+    """
+    # defences
+    _gtfs_defence(gtfs, "gtfs")
+    _type_defence(clean_ids, "clean_ids", bool)
+    _type_defence(clean_times, "clean_times", bool)
+    _type_defence(clean_route_short_names, "clean_route_short_names", bool)
+    _type_defence(drop_zombies, "drop_zombies", bool)
+    # cleaning
+    if clean_ids:
+        clean_ids_gk(gtfs.feed)
+    if clean_times:
+        clean_times_gk(gtfs.feed)
+    if clean_route_short_names:
+        clean_route_short_names_gk(gtfs.feed)
+    if drop_zombies:
+        try:
+            drop_zombies_gk(gtfs.feed)
+        except KeyError:
+            warnings.warn(
+                UserWarning(
+                    "The drop_zombies cleaner was unable to operate on "
+                    "clean_feed as the trips table has no shape_id column"
+                )
+            )
+    return None

src/assess_gtfs/gtfs_utils.py

@@ -475,3 +475,36 @@ def convert_pandas_to_plotly(
     if return_html:
         return fig.to_html(full_html=False)
     return fig
+
+
+def _function_pipeline(
+    gtfs, func_map: dict, operations: Union[dict, type[None]]
+) -> None:
+    """Iterate through and act on a functional pipeline."""
+    _gtfs_defence(gtfs, "gtfs")
+    _type_defence(func_map, "func_map", dict)
+    _type_defence(operations, "operations", (dict, type(None)))
+    if operations:
+        for key in operations.keys():
+            if key not in func_map.keys():
+                raise KeyError(
+                    f"'{key}' function passed to 'operations' is not a "
+                    "known operation. Known operation include: "
+                    f"{func_map.keys()}"
+                )
+        for operation in operations:
+            # check value is dict or none (for kwargs)
+            _type_defence(
+                operations[operation],
+                f"operations[{operation}]",
+                (dict, type(None)),
+            )
+            operations[operation] = (
+                {} if operations[operation] is None else operations[operation]
+            )
+            func_map[operation](gtfs=gtfs, **operations[operation])
+    # if no operations passed, carry out all operations
+    else:
+        for operation in func_map:
+            func_map[operation](gtfs=gtfs)
+    return None

src/assess_gtfs/multi_validation.py

@@ -160,12 +160,12 @@ def save_feeds(
             inst.save(path, overwrite=overwrite)
         return None
 
-    def clean_feeds(self, clean_kwargs: Union[dict, None] = None) -> None:
+    def clean_feeds(self, cleansers: Union[dict, None] = None) -> None:
         """Clean each of the feeds in the MultiGtfsInstance.
 
         Parameters
         ----------
-        clean_kwargs : Union[dict, None], optional
+        cleansers : Union[dict, None], optional
             The kwargs to pass to GtfsInstance.clean_feed() for each Gtfs in
             the MultiGtfsInstance, by default None
 
@@ -175,28 +175,26 @@ def clean_feeds(self, clean_kwargs: Union[dict, None] = None) -> None:
 
         """
         # defences
-        _type_defence(clean_kwargs, "clean_kwargs", (dict, type(None)))
-        if isinstance(clean_kwargs, type(None)):
-            clean_kwargs = {}
+        _type_defence(cleansers, "cleansers", (dict, type(None)))
+        if isinstance(cleansers, type(None)):
+            cleansers = {}
         # clean GTFS instances
         progress = tqdm(
             zip(self.paths, self.instances), total=len(self.instances)
         )
         for path, inst in progress:
             progress.set_description(f"Cleaning GTFS from path {path}")
-            inst.clean_feed(**clean_kwargs)
+            inst.clean_feed(cleansers=cleansers)
         return None
 
-    def is_valid(
-        self, validation_kwargs: Union[dict, None] = None
-    ) -> pd.DataFrame:
+    def is_valid(self, validators: Union[dict, None] = None) -> pd.DataFrame:
         """Validate each of the feeds in the MultiGtfsInstance.
 
         Parameters
         ----------
-        validation_kwargs : Union[dict, None], optional
-            The kwargs to pass to GtfsInstance.is_valid() for each Gtfs in
-            the MultiGtfsInstance, by default None
+        validators : Union[dict, None], optional
+            The kwargs to pass to GtfsInstance.is_valid(validators) for each
+            Gtfs in the MultiGtfsInstance, by default None
 
         Returns
         -------
@@ -206,18 +204,16 @@ def is_valid(
 
         """
         # defences
-        _type_defence(
-            validation_kwargs, "validation_kwargs", (dict, type(None))
-        )
-        if isinstance(validation_kwargs, type(None)):
-            validation_kwargs = {}
+        _type_defence(validators, "validators", (dict, type(None)))
+        if isinstance(validators, type(None)):
+            validators = {}
         # clean GTFS instances
         progress = tqdm(
             zip(self.paths, self.instances), total=len(self.instances)
         )
         for path, inst in progress:
             progress.set_description(f"Validating GTFS from path {path}")
-            inst.is_valid(**validation_kwargs)
+            inst.is_valid(validators=validators)
 
         # concat all validation tables into one
         tables = []

src/assess_gtfs/validation.py

@@ -18,12 +18,10 @@
 from plotly.graph_objects import Figure as PlotlyFigure
 from pretty_html_table import build_table
 
+import assess_gtfs.cleaners as cleaners
+import assess_gtfs.validators as gtfs_validators
 from assess_gtfs.calendar import create_calendar_from_dates
-from assess_gtfs.cleaners import (
-    clean_consecutive_stop_fast_travel_warnings,
-    clean_multiple_stop_fast_travel_warnings,
-)
-from assess_gtfs.gtfs_utils import filter_gtfs
+from assess_gtfs.gtfs_utils import _function_pipeline, filter_gtfs
 from assess_gtfs.report.report_utils import TemplateHTML, _set_up_report_dir
 from assess_gtfs.routes import (
     get_saved_route_type_lookup,
@@ -40,10 +38,29 @@
     _is_expected_filetype,
     _type_defence,
 )
-from assess_gtfs.validators import (
-    validate_travel_between_consecutive_stops,
-    validate_travel_over_multiple_stops,
-)
+
+# THESE MAPPINGS CAN NOT BE MOVED TO CONSTANTS AS THEY INTRODUCE DEPENDENCY
+# ISSUES.
+# TODO: Update these once further cleaners/validators are merged
+CLEAN_FEED_FUNCTION_MAP = {
+    "core_cleaners": cleaners.core_cleaners,
+    "clean_consecutive_stop_fast_travel_warnings": (
+        cleaners.clean_consecutive_stop_fast_travel_warnings
+    ),
+    "clean_multiple_stop_fast_travel_warnings": (
+        cleaners.clean_multiple_stop_fast_travel_warnings
+    ),
+}
+
+VALIDATE_FEED_FUNC_MAP = {
+    "core_validation": gtfs_validators.core_validation,
+    "validate_travel_between_consecutive_stops": (
+        gtfs_validators.validate_travel_between_consecutive_stops
+    ),
+    "validate_travel_over_multiple_stops": (
+        gtfs_validators.validate_travel_over_multiple_stops
+    ),
+}
 
 
 def _get_intermediate_dates(
@@ -313,26 +330,28 @@ def get_gtfs_files(self) -> list:
         self.file_list = file_list
         return self.file_list
 
-    def is_valid(self, far_stops: bool = False) -> pd.DataFrame:
+    def is_valid(self, validators: dict = None) -> pd.DataFrame:
         """Check a feed is valid with `gtfs_kit`.
 
         Parameters
         ----------
-        far_stops : bool, optional
-            Whether or not to perform validation for far stops (both
-            between consecutive stops and over multiple stops), by default
-            False.
+        validators : dict, optional
+            A dictionary of function name to kwargs mappings.
 
         Returns
         -------
         pd.core.frame.DataFrame
             Table of errors, warnings & their descriptions.
 
         """
-        self.validity_df = self.feed.validate()
-        if far_stops:
-            validate_travel_between_consecutive_stops(self)
-            validate_travel_over_multiple_stops(self)
+        _type_defence(validators, "validators", (dict, type(None)))
+        # create validity df
+        self.validity_df = pd.DataFrame(
+            columns=["type", "message", "table", "rows"]
+        )
+        _function_pipeline(
+            gtfs=self, func_map=VALIDATE_FEED_FUNC_MAP, operations=validators
+        )
         return self.validity_df
 
     def print_alerts(self, alert_type: str = "error") -> None:
@@ -383,36 +402,27 @@ def print_alerts(self, alert_type: str = "error") -> None:
 
         return None
 
-    def clean_feed(
-        self, validate: bool = False, fast_travel: bool = False
-    ) -> None:
-        """Attempt to clean feed using `gtfs_kit`.
+    def clean_feed(self, cleansers: dict = None) -> None:
+        """Clean the gtfs feed.
 
         Parameters
         ----------
-        validate: bool, optional
-            Whether or not to validate the dataframe before cleaning, by
-            default False.
-        fast_travel: bool, optional
-            Whether or not to clean warnings related to fast travel, by default
-            False.
+        cleansers : dict, optional
+            A mapping of cleansing functions and kwargs, by default None
+
+        Returns
+        -------
+        None
 
         """
-        _type_defence(fast_travel, "fast_travel", bool)
-        _type_defence(validate, "valiidate", bool)
-        if validate:
-            self.is_valid(far_stops=fast_travel)
-        try:
-            # In cases where shape_id is missing, keyerror is raised.
-            # https://developers.google.com/transit/gtfs/reference#shapestxt
-            # shows that shapes.txt is optional file.
-            self.feed = self.feed.clean()
-            if fast_travel:
-                clean_consecutive_stop_fast_travel_warnings(self)
-                clean_multiple_stop_fast_travel_warnings(self)
-        except KeyError:
-            # TODO: Issue 74 - Improve this to clean feed when KeyError raised
-            print("KeyError. Feed was not cleaned.")
+        # DEV NOTE: Opting not to allow for validation in clean_feed().
+        #           .is_valid() should be used before hand.
+        # DEV NOTE 2: Use of param name 'cleansers' is to avoid conflicts
+        _type_defence(cleansers, "cleansers", (dict, type(None)))
+        _function_pipeline(
+            gtfs=self, func_map=CLEAN_FEED_FUNCTION_MAP, operations=cleansers
+        )
+        return None
 
     def _produce_stops_map(
         self, what_geoms: str, is_filtered: bool, crs: Union[int, str]
@@ -1386,7 +1396,7 @@ def html_report(
         report_dir: Union[str, pathlib.Path] = "outputs",
         overwrite: bool = False,
         summary_type: str = "mean",
-        extended_validation: bool = False,
+        extended_validation: bool = True,
         clean_feed: bool = True,
     ) -> None:
         """Generate a HTML report describing the GTFS data.
@@ -1403,7 +1413,7 @@ def html_report(
             default "mean"
         extended_validation : bool, optional
             Whether or not to create extended reports for gtfs validation
-            errors/warnings, by default False
+            errors/warnings, by default True
         clean_feed : bool, optional
             Whether or not to clean the feed before validating, by default True
 
@@ -1431,10 +1441,11 @@ def html_report(
         date = datetime.datetime.strftime(datetime.datetime.now(), "%d-%m-%Y")
 
         # feed evaluation
+        self.is_valid()
         if clean_feed:
-            self.clean_feed(validate=True, fast_travel=True)
-        # re-validate to clean any newly raised errors/warnings
-        validation_dataframe = self.is_valid(far_stops=True)
+            self.clean_feed()
+            # re-validate to clean any newly raised errors/warnings
+            validation_dataframe = self.is_valid()
 
         # create extended reports if requested
         if extended_validation:

src/assess_gtfs/validators.py

@@ -264,3 +264,13 @@ def validate_travel_over_multiple_stops(gtfs: "GtfsInstance") -> None:
         )
 
     return far_stops_df
+
+
+def core_validation(gtfs: "GtfsInstance"):
+    """Carry out the main validators of gtfs-kit."""
+    _gtfs_defence(gtfs, "gtfs")
+    validation_df = gtfs.feed.validate()
+    gtfs.validity_df = pd.concat(
+        [validation_df, gtfs.validity_df], axis=0
+    ).reset_index(drop=True)
+    #