"""
Keeps the older BaseController security and fetching methods and also
defines a base ModelManager, ModelSerializer, and ModelDeserializer.

ModelManagers are used for operations on models that occur outside the scope of
a single model object, such as:

- object creation
- object lookup
- interactions between 2+ objects of different model classes

(Since these were to replace model Mixins from
web/framework/base/controller.py the rule of thumb used there also generally
has been applied here: if it uses the trans or sa_session, put it in a manager
and not the model.)

ModelSerializers allow flexible conversion of model objects to dictionaries.
They control what keys are sent, how values are simplified, can remap keys,
and allow both predefined and user controlled key sets.

ModelDeserializers control how a model validates and process an incoming
attribute change to a model object.
"""

# TODO: it may be there's a better way to combine the above three classes
#   such as: a single flat class, serializers being singletons in the manager, etc.
#   instead of the three separate classes. With no 'apparent' perfect scheme
#   I'm opting to just keep them separate.
import builtins
import datetime
import logging
import re
from collections.abc import Callable
from functools import partial
from typing import (
    Any,
    Generic,
    NamedTuple,
    Optional,
    TYPE_CHECKING,
    TypeVar,
    Union,
)

import sqlalchemy
from sqlalchemy.orm import Query
from sqlalchemy.orm.scoping import scoped_session
from typing_extensions import Protocol

from galaxy import (
    exceptions,
    model,
)
from galaxy.model import tool_shed_install
from galaxy.model.base import check_database_connection
from galaxy.schema import ValueFilterQueryParams
from galaxy.schema.storage_cleaner import (
    CleanableItemsSummary,
    StorageItemsCleanupResult,
    StoredItem,
    StoredItemOrderBy,
)
from galaxy.security.idencoding import IdEncodingHelper
from galaxy.structured_app import (
    BasicSharedApp,
    MinimalManagerApp,
)

if TYPE_CHECKING:
    from galaxy.managers.context import ProvidesAppContext

log = logging.getLogger(__name__)


class ParsedFilter(NamedTuple):
    filter_type: str  # orm_function, function, or orm
    filter: Any
    case_insensitive: bool = False


parsed_filter = ParsedFilter
OrmFilterParserType = Union[None, dict[str, Any], Callable]
OrmFilterParsersType = dict[str, OrmFilterParserType]
FunctionFilterParserType = dict[str, Any]
FunctionFilterParsersType = dict[str, Any]


# ==== accessors from base/controller.py
def security_check(trans, item, check_ownership=False, check_accessible=False):
    """
    Security checks for an item: checks if (a) user owns item or (b) item
    is accessible to user. This is a generic method for dealing with objects
    uniformly from the older controller mixin code - however whenever possible
    the managers for a particular model should be used to perform security
    checks.
    """

    # all items are accessible to an admin
    if trans.user_is_admin:
        return item

    # Verify ownership: there is a current user and that user is the same as the item's
    if check_ownership:
        if not trans.user:
            raise exceptions.ItemOwnershipException("Must be logged in to manage Galaxy items", type="error")
        if item.user != trans.user:
            raise exceptions.ItemOwnershipException(
                f"{item.__class__.__name__} is not owned by the current user", type="error"
            )
        # no need to check accessibility if we're the owner
        return item

    # Verify accessible:
    #   if it's part of a lib - can they access via security
    #   if it's something else (sharable) have they been added to the item's users_shared_with_dot_users
    if check_accessible:
        if type(item) in (
            model.LibraryFolder,
            model.LibraryDatasetDatasetAssociation,
            model.LibraryDataset,
        ):
            if not trans.app.security_agent.can_access_library_item(trans.get_current_user_roles(), item, trans.user):
                raise exceptions.ItemAccessibilityException(
                    f"{item.__class__.__name__} is not accessible to the current user", type="error"
                )
        else:
            if (
                (item.user != trans.user)
                and (not item.importable)
                and (trans.user not in item.users_shared_with_dot_users)
            ):
                raise exceptions.ItemAccessibilityException(
                    f"{item.__class__.__name__} is not accessible to the current user", type="error"
                )
    return item


def get_class(class_name):
    """
    Returns the class object that a string denotes. Without this method, we'd have
    to do eval(<class_name>).
    """
    if class_name == "ToolShedRepository":
        item_class = tool_shed_install.ToolShedRepository
    else:
        if not hasattr(model, class_name):
            raise exceptions.MessageException(f"Item class '{class_name}' not available.")
        item_class = getattr(model, class_name)
    return item_class


def decode_id(app: BasicSharedApp, id: Any, kind: Optional[str] = None) -> int:
    # note: use str - occasionally a fully numeric id will be placed in post body and parsed as int via JSON
    #   resulting in error for valid id
    return decode_with_security(app.security, id, kind=kind)


def decode_with_security(security: IdEncodingHelper, id: Any, kind: Optional[str] = None):
    return security.decode_id(str(id), kind=kind)


def encode_with_security(security: IdEncodingHelper, id: Any, kind: Optional[str] = None):
    return security.encode_id(id, kind=kind)


def get_object(
    trans: "ProvidesAppContext",
    id,
    class_name,
    check_ownership: bool = False,
    check_accessible: bool = False,
    deleted: Union[bool, None] = None,
):
    """
    Convenience method to get a model object with the specified checks. This is
    a generic method for dealing with objects uniformly from the older
    controller mixin code - however whenever possible the managers for a
    particular model should be used to load objects.
    """
    decoded_id = id if isinstance(id, int) else decode_id(trans.app, id)
    try:
        item_class = get_class(class_name)
        assert item_class is not None
        item = trans.sa_session.get(item_class, decoded_id)
        assert item is not None
    except Exception:
        log.warning(f"Invalid {class_name} id ( {id} ) specified.")
        raise exceptions.MessageException(f"Invalid {class_name} id ( {id} ) specified", type="error")

    if check_ownership or check_accessible:
        security_check(trans, item, check_ownership, check_accessible)
    if deleted is True and not item.deleted:
        raise exceptions.ItemDeletionException(
            f'{class_name} "{getattr(item, "name", id)}" is not deleted', type="warning"
        )
    elif deleted is False and item.deleted:
        raise exceptions.ItemDeletionException(f'{class_name} "{getattr(item, "name", id)}" is deleted', type="warning")
    return item


# =============================================================================
U = TypeVar("U", bound=model._HasTable)


# -----------------------------------------------------------------------------
class ModelManager(Generic[U]):
    """
    Base class for all model/resource managers.

    Provides common queries and CRUD operations as a (hopefully) light layer
    over the ORM.
    """

    model_class: type[U]
    foreign_key_name: str
    app: BasicSharedApp

    def __init__(self, app: BasicSharedApp):
        self.app = app

    def session(self) -> scoped_session:
        return self.app.model.context

    def _session_setattr(self, item: model.Base, attr: str, val: Any, flush: bool = True):
        setattr(item, attr, val)

        self.session().add(item)
        if flush:
            session = self.session()
            session.commit()
        return item

    # .... query foundation wrapper
    def query(
        self,
        eagerloads: bool = True,
        filters=None,
        order_by=None,
        limit: Optional[int] = None,
        offset: Optional[int] = None,
    ) -> Query:
        """
        Return a basic query from model_class, filters, order_by, and limit and offset.

        Set eagerloads to False to disable them for this query.
        """
        query = self.session().query(self.model_class)
        # joined table loading
        if eagerloads is False:
            query = query.enable_eagerloads(False)
        return self._filter_and_order_query(query, filters=filters, order_by=order_by, limit=limit, offset=offset)

    def _filter_and_order_query(
        self, query: Query, filters=None, order_by=None, limit: Optional[int] = None, offset: Optional[int] = None
    ) -> Query:
        # TODO: not a lot of functional cohesion here
        query = self._apply_orm_filters(query, filters)
        query = self._apply_order_by(query, order_by)
        query = self._apply_orm_limit_offset(query, limit, offset)
        return query

    # .... filters
    def _apply_orm_filters(self, query: Query, filters) -> Query:
        """
        Add any filters to the given query.
        """
        if filters is None:
            return query

        if not isinstance(filters, list):
            filters = [filters]
        # note: implicit AND
        for filter in filters:
            query = query.filter(filter)
        return query

    # .... order, limit, and offset
    def _apply_order_by(self, query: Query, order_by) -> Query:
        """
        Return the query after adding the order_by clauses.

        Use the manager's default_order_by if order_by is None.
        """
        if order_by is None:
            return query.order_by(*self._default_order_by())

        if isinstance(order_by, (list, tuple)):
            return query.order_by(*order_by)
        return query.order_by(order_by)

    def _default_order_by(self):
        """
        Returns a tuple of columns for the default order when getting multiple models.
        """
        return (self.model_class.__table__.c.create_time,)

    def _apply_orm_limit_offset(self, query: Query, limit: Optional[int], offset: Optional[int]) -> Query:
        """
        Return the query after applying the given limit and offset (if not None).
        """
        if limit is not None:
            query = query.limit(limit)
        if offset is not None:
            query = query.offset(offset)
        return query

    # .... query resolution
    def one(self, **kwargs) -> U:
        """
        Sends kwargs to build the query and returns one and only one model.
        """
        query = self.query(**kwargs)
        return self._one_with_recast_errors(query)

    def _one_with_recast_errors(self, query: Query) -> U:
        """
        Call sqlalchemy's one and recast errors to serializable errors if any.

        :raises exceptions.ObjectNotFound: if no model is found
        :raises exceptions.InconsistentDatabase: if more than one model is found
        """
        check_database_connection(self.session())
        # overridden to raise serializable errors
        try:
            return query.one()
        except sqlalchemy.exc.NoResultFound:
            raise exceptions.ObjectNotFound(f"{self.model_class.__name__} not found")
        except sqlalchemy.exc.MultipleResultsFound:
            raise exceptions.InconsistentDatabase(f"found more than one {self.model_class.__name__}")

    # NOTE: at this layer, all ids are expected to be decoded and in int form
    def by_id(self, id: int) -> U:
        """
        Gets a model by primary id.
        """
        id_filter = self.model_class.__table__.c.id == id
        return self.one(filters=id_filter)

    # .... multirow queries
    def list(self, filters=None, order_by=None, limit=None, offset=None, **kwargs):
        """
        Returns all objects matching the given filters
        """
        # list becomes a way of applying both filters generated in the orm (such as .user ==)
        # and functional filters that aren't currently possible using the orm (such as instance calculated values
        # or annotations/tags). List splits those two filters and applies limits/offsets
        # only after functional filters (if any) using python.
        self._handle_filters_case_sensitivity(filters)
        orm_filters, fn_filters = self._split_filters(filters)
        if not fn_filters:
            # if no fn_filtering required, we can use the 'all orm' version with limit offset
            return self._orm_list(filters=orm_filters, order_by=order_by, limit=limit, offset=offset, **kwargs)

        # fn filters will change the number of items returnable by limit/offset - remove them here from the orm query
        query = self.query(filters=orm_filters, order_by=order_by, limit=None, offset=None, **kwargs)
        items = query.all()

        # apply limit, offset after SQL filtering
        items = self._apply_fn_filters_gen(items, fn_filters)
        return list(self._apply_fn_limit_offset_gen(items, limit, offset))

    def count(self, filters=None, **kwargs) -> int:
        """
        Returns the number of objects matching the given filters.

        If the filters include functional filters, this function will raise an exception as they might cause
        performance issues.
        """
        self._handle_filters_case_sensitivity(filters)
        orm_filters, fn_filters = self._split_filters(filters)
        if fn_filters:
            raise exceptions.RequestParameterInvalidException("Counting with functional filters is not supported.")

        query = self.query(filters=orm_filters, **kwargs)
        return query.count()

    def _handle_filters_case_sensitivity(self, filters):
        """Modifies the filters to make them case insensitive if needed."""
        if filters is None:
            return  # No filters to handle
        iterable_filters = filters if isinstance(filters, list) else [filters]
        for item in iterable_filters:
            # If the filter has the case_insensitive attribute set to True this means that the filter
            # is a parsed orm filter and that it needs to compare the column with a lower case version of the value.
            is_case_insensitive = getattr(item, "case_insensitive", False)
            if is_case_insensitive and isinstance(item.filter, sqlalchemy.sql.elements.BinaryExpression):
                item.filter.left = sqlalchemy.func.lower(item.filter.left)

    def _split_filters(self, filters):
        """
        Splits `filters` into a tuple of two lists:
            a list of filters to be added to the SQL query
        and a list of functional filters to be applied after the SQL query.
        """
        orm_filters: list = []
        fn_filters: list = []
        if filters is None:
            return (orm_filters, fn_filters)
        if not isinstance(filters, list):
            filters = [filters]
        for filter_ in filters:
            if not hasattr(filter_, "filter_type"):
                orm_filters.append(filter_)
            elif filter_.filter_type == "function":
                fn_filters.append(filter_.filter)
            elif filter_.filter_type == "orm_function":
                orm_filters.append(filter_.filter(self.model_class))
            else:
                orm_filters.append(filter_.filter)
        return (orm_filters, fn_filters)

    def _orm_list(self, query: Optional[Query] = None, **kwargs) -> builtins.list[U]:
        """
        Sends kwargs to build the query return all models found.
        """
        query = query or self.query(**kwargs)
        return query.all()

    def _apply_fn_filters_gen(self, items, filters):
        """
        If all the filter functions in `filters` return True for an item in `items`,
        yield that item.
        """
        # cpu-expensive
        for item in items:
            filter_results = [f(item) for f in filters]
            if all(filter_results):
                yield item

    def _apply_fn_limit_offset_gen(self, items, limit, offset):
        """
        Iterate over `items` and begin yielding items after
        `offset` number of items and stop when we've yielded
        `limit` number of items.
        """
        # change negative limit, offset to None
        if limit is not None and limit < 0:
            limit = None
        if offset is not None and offset < 0:
            offset = None

        yielded = 0
        for i, item in enumerate(items):
            if offset is not None and i < offset:
                continue
            if limit is not None and yielded >= limit:
                break
            yield item
            yielded += 1

    def by_ids(self, ids, filters=None, **kwargs):
        """
        Returns an in-order list of models with the matching ids in `ids`.
        """
        if not ids:
            return []
        ids_filter = parsed_filter("orm", self.model_class.__table__.c.id.in_(ids))
        found = self.list(filters=combine_lists(ids_filter, filters), **kwargs)
        # TODO: this does not order by the original 'ids' array

        # ...could use get (supposedly since found are in the session, the db won't be hit twice)
        # return map( self.session().query( self.model_class ).get, ids )

        # ...could implement own version here - slow?
        return self._order_items_by_id(ids, found)

    def _order_items_by_id(self, ids, items):
        """
        Given a list of (unique) ids and a list of items having an 'id' attribute,
        return items that have the given ids in that order.

        If an id in ids is not found or if an item in items doesn't have a given
        id, they will not be in the returned list.
        """
        ID_ATTR_NAME = "id"
        # TODO:?? aside from sqlalx.get mentioned above, I haven't seen an in-SQL way
        #   to make this happen. This may not be the most efficient way either.
        # NOTE: that this isn't sorting by id - this is matching the order in items to the order in ids
        # move items list into dict by id
        item_dict = {}
        for item in items:
            item_id = getattr(item, ID_ATTR_NAME, None)
            if item_id:
                item_dict[item_id] = item
        # pull from map in order of ids
        in_order = []
        for id in ids:
            if id in item_dict:
                in_order.append(item_dict[id])
        return in_order

    def create(self, flush: bool = True, *args: Any, **kwargs: Any) -> U:
        """Generically create a new model."""
        # override in subclasses
        item = self.model_class(*args, **kwargs)
        self.session().add(item)
        if flush:
            session = self.session()
            session.commit()
        return item

    def copy(self, item, **kwargs) -> U:
        """
        Clone or copy an item.
        """
        raise exceptions.NotImplemented("Abstract method")

    def update(self, item: U, new_values: dict[str, Any], flush: bool = True, **kwargs) -> U:
        """
        Given a dictionary of new values, update `item` and return it.

        ..note: NO validation or deserialization occurs here.
        """
        for key, value in new_values.items():
            if hasattr(item, key):
                setattr(item, key, value)
        session = self.session()
        session.add(item)
        if flush:
            session.commit()
        return item

    def associate(self, associate_with, item, foreign_key_name=None):
        """
        Generically associate `item` with `associate_with` based on `foreign_key_name`.
        """
        foreign_key_name = foreign_key_name or self.foreign_key_name
        setattr(associate_with, foreign_key_name, item)
        return item

    def _foreign_key(self, associated_model_class, foreign_key_name=None):
        foreign_key_name = foreign_key_name or self.foreign_key_name
        return getattr(associated_model_class, foreign_key_name)

    def query_associated(self, associated_model_class, item, foreign_key_name=None):
        """
        Generically query other items that have been associated with this `item`.
        """
        foreign_key = self._foreign_key(associated_model_class, foreign_key_name=foreign_key_name)
        return self.session().query(associated_model_class).filter(foreign_key == item)

    # a rename of sql DELETE to differentiate from the Galaxy notion of mark_as_deleted
    # def destroy( self, item, **kwargs ):
    #    return item


T = TypeVar("T")


# ---- code for classes that use one *main* model manager
# TODO: this may become unecessary if we can access managers some other way (class var, app, etc.)
class HasAModelManager(Generic[T]):
    """
    Mixin used where serializers, deserializers, filter parsers, etc.
    need some functionality around the model they're mainly concerned with
    and would perform that functionality with a manager.
    """

    #: the class used to create this serializer's generically accessible model_manager
    model_manager_class: type[
        T
    ]  # ideally this would be Type[ModelManager] but HistoryContentsManager cannot be a ModelManager
    # examples where this doesn't really work are ConfigurationSerializer (no manager)
    # and contents (2 managers)
    app: MinimalManagerApp

    def __init__(self, app: MinimalManagerApp, manager=None, **kwargs):
        self._manager = manager
        self.app = app

    @property
    def manager(self) -> T:
        """Return an appropriate manager if it exists, instantiate if not."""
        # PRECONDITION: assumes self.app is assigned elsewhere
        if not self._manager:
            # TODO: pass this serializer to it
            self._manager = self.app[self.model_manager_class]
            # this will error for unset model_manager_class'es
        return self._manager


# ==== SERIALIZERS/to_dict,from_dict
class ModelSerializingError(exceptions.InternalServerError):
    """Thrown when request model values can't be serialized"""


class ModelDeserializingError(exceptions.ObjectAttributeInvalidException):
    """Thrown when an incoming value isn't usable by the model
    (bad type, out of range, etc.)
    """


class SkipAttribute(Exception):
    """
    Raise this inside a serializer to prevent the returned dictionary from having
    a the associated key or value for this attribute.
    """


class Serializer(Protocol):
    def __call__(self, item: Any, key: str, **context) -> Any: ...


# TODO: eventually all urls should be generated by the url builder and this can be safely removed.
# Using it for now to identify in which contexts the url builder is not available
def url_for_not_available(*args, **kwargs):
    args_str = [str(arg) for arg in args]
    raise NotImplementedError(f"url_for is not available in this context - args: {args_str} ")


class ModelSerializer(HasAModelManager[T]):
    """
    Turns models into JSONable dicts.

    Maintains a map of requestable keys and the Callable() serializer functions
    that should be called for those keys.
    E.g. { 'x' : lambda item, key: item.x, ... }

    Note: if a key to serialize is not listed in the Serializer.serializable_keyset
    or serializers, it will not be returned.

    To serialize call:
        my_serializer = MySerializer( app )
        ...
        keys_to_serialize = [ 'id', 'name', 'attr1', 'attr2', ... ]
        item_dict = MySerializer.serialize( my_item, keys_to_serialize )
    """

    default_view: Optional[str]
    views: dict[str, list[str]]

    def __init__(self, app: MinimalManagerApp, **kwargs):
        """
        Set up serializer map, any additional serializable keys, and views here.
        """
        super().__init__(app, **kwargs)

        # a list of valid serializable keys that can use the default (string) serializer
        #   this allows us to: 'mention' the key without adding the default serializer
        # TODO: we may want to eventually error if a key is requested
        #   that is in neither serializable_keyset or serializers
        self.serializable_keyset: set[str] = set()
        # a map of dictionary keys to the functions (often lambdas) that create the values for those keys
        self.serializers: dict[str, Serializer] = {}
        # add subclass serializers defined there
        self.add_serializers()
        # update the keyset by the serializers (removing the responsibility from subclasses)
        self.serializable_keyset.update(self.serializers.keys())

        # views are collections of serializable attributes (a named array of keys)
        #   inspired by model.dict_{view}_visible_keys
        self.views = {}
        self.default_view = None

    @staticmethod
    def url_for(*args, context=None, **kwargs):
        trans = context and context.get("trans")
        url_for = trans and trans.url_builder or url_for_not_available
        return url_for(*args, **kwargs)

    def add_serializers(self):
        """
        Register a map of attribute keys -> serializing functions that will serialize
        the attribute.
        """
        self.serializers.update(
            {
                "id": self.serialize_id,
                "create_time": self.serialize_date,
                "update_time": self.serialize_date,
            }
        )

    def add_view(self, view_name, key_list, include_keys_from=None):
        """
        Add the list of serializable attributes `key_list` to the serializer's
        view dictionary under the key `view_name`.

        If `include_keys_from` is a proper view name, extend `key_list` by
        the list in that view.
        """
        key_list = list(set(key_list + self.views.get(include_keys_from, [])))
        self.views[view_name] = key_list
        self.serializable_keyset.update(key_list)
        return key_list

    def serialize(self, item, keys, **context):
        """
        Serialize the model `item` to a dictionary.

        Given model `item` and the list `keys`, create and return a dictionary
        built from each key in `keys` that also exists in `serializers` and
        values of calling the keyed/named serializers on item.
        """
        # TODO: constrain context to current_user/whos_asking when that's all we need (trans)
        returned = {}
        for key in keys:
            # check both serializers and serializable keys
            if key in self.serializers:
                try:
                    returned[key] = self.serializers[key](item, key, **context)
                except SkipAttribute:
                    # don't add this key if the serializer threw this
                    pass
            elif key in self.serializable_keyset:
                returned[key] = self.default_serializer(item, key, **context)
            # ignore bad/unreg keys
        return returned

    def skip(self, msg="skipped"):
        """
        To be called from inside a serializer to skip it.

        Handy for config checks, information hiding, etc.
        """
        raise SkipAttribute(msg)

    def _remap_from(self, original_key):
        if original_key in self.serializers:
            return self.serializers[original_key]
        if original_key in self.serializable_keyset:
            return lambda i, k, **c: self.default_serializer(i, original_key, **c)
        raise KeyError(f"serializer not found for remap: {original_key}")

    def default_serializer(self, item, key, **context):
        """
        Serialize the `item`'s attribute named `key`.
        """
        # TODO:?? point of change but not really necessary?
        return getattr(item, key)

    # serializers for common galaxy objects
    def serialize_date(self, item: Any, key: str, **context):
        """
        Serialize a date attribute of `item`.
        """
        date = getattr(item, key)
        return date.isoformat() if date is not None else None

    def serialize_id(self, item: Any, key: str, encode_id=True, **context):
        """
        Serialize an id attribute of `item`.
        """
        id = getattr(item, key)
        # Note: it may not be best to encode the id at this layer
        return self.app.security.encode_id(id) if id is not None and encode_id else id

    def serialize_type_id(self, item: Any, key: str, **context):
        """
        Serialize an type-id for `item`.
        """
        TYPE_ID_SEP = "-"
        type_id = getattr(item, key)
        if type_id is None:
            return None
        split = type_id.split(TYPE_ID_SEP, 1)
        # Note: it may not be best to encode the id at this layer
        return TYPE_ID_SEP.join((split[0], self.app.security.encode_id(split[1])))

    # serializing to a view where a view is a predefied list of keys to serialize
    def serialize_to_view(self, item, view=None, keys=None, default_view=None, **context):
        """
        Use a predefined list of keys (the string `view`) and any additional keys
        listed in `keys`.

        The combinations can be:
            `view` only: return those keys listed in the named view
            `keys` only: return those keys listed
            no `view` or `keys`: use the `default_view` if any
            `view` and `keys`: combine both into one list of keys
        """

        # TODO: default view + view makes no sense outside the API.index context - move default view there
        all_keys = []
        keys = keys or []
        # chose explicit over concise here
        if view:
            if keys:
                all_keys = self._view_to_keys(view) + keys
            else:
                all_keys = self._view_to_keys(view)
        else:
            if keys:
                all_keys = keys
            else:
                all_keys = self._view_to_keys(default_view)

        return self.serialize(item, all_keys, **context)

    def _view_to_keys(self, view=None):
        """
        Converts a known view into a list of keys.

        :raises RequestParameterInvalidException: if the view is not listed in `self.views`.
        """
        if view is None:
            view = self.default_view
        if view not in self.views:
            raise exceptions.RequestParameterInvalidException(
                f"unknown view - {view}", view=view, available_views=self.views
            )
        return self.views[view][:]


class ModelValidator:
    """
    An object that inspects a dictionary (generally meant to be a set of
    new/updated values for the model) and raises an error if a value is
    not acceptable.
    """

    @staticmethod
    def matches_type(key: str, val: Any, types: Union[type, tuple[Union[type, tuple[Any, ...]], ...]]):
        """
        Check `val` against the type (or tuple of types) in `types`.

        :raises exceptions.RequestParameterInvalidException: if not an instance.
        """
        if not isinstance(val, types):
            msg = f"must be a type: {types}"
            raise exceptions.RequestParameterInvalidException(msg, key=key, val=val)
        return val

    # validators for primitives and compounds of primitives
    @staticmethod
    def basestring(key: str, val: Any) -> str:
        return ModelValidator.matches_type(key, val, (str,))

    @staticmethod
    def bool(key: str, val: Any) -> bool:
        return ModelValidator.matches_type(key, val, bool)

    @staticmethod
    def nullable_basestring(key: str, val: Any) -> str:
        """
        Must be a basestring or None.
        """
        return ModelValidator.matches_type(key, val, ((str,), type(None)))

    @staticmethod
    def int_range(key: str, val: Any, min: Optional[int] = None, max: Optional[int] = None) -> int:
        """
        Must be a int between min and max.
        """
        val_ = ModelValidator.matches_type(key, val, int)
        if min is not None and val_ < min:
            raise exceptions.RequestParameterInvalidException("less than minimum", key=key, val=val_, min=min)
        if max is not None and val_ > max:
            raise exceptions.RequestParameterInvalidException("greater than maximum", key=key, val=val_, max=max)
        return val_

    @staticmethod
    def basestring_list(key: str, val: Any) -> list[str]:
        """
        Must be a list of basestrings.
        """
        # TODO: Here's where compound types start becoming a nightmare. Any more or more complex
        #   and should find a different way.
        val_ = ModelValidator.matches_type(key, val, list)
        return [ModelValidator.basestring(key, elem) for elem in val_]

    # validators for Galaxy
    @staticmethod
    def genome_build(key: str, val: Any) -> str:
        """
        Must be a valid base_string.

        Note: no checking against installation's ref list is done as many
        data sources consider this an open field.
        """
        # TODO: is this correct?
        if val is None:
            return "?"
        # currently, data source sites like UCSC are able to set the genome build to non-local build names
        # afterwards, attempting to validate the whole model will choke here
        # for genome_build_shortname, longname in self.app.genome_builds.get_genome_build_names( trans=trans ):
        #     if val == genome_build_shortname:
        #         return val
        # raise exceptions.RequestParameterInvalidException( "invalid reference", key=key, val=val )
        # IOW: fallback to string validation
        return ModelValidator.basestring(key, val)

    # def slug( self, item, key, val ):
    #    """validate slug"""
    #    pass


class Deserializer(Protocol):
    def __call__(self, item: Any, key: Any, val: Any, **kwargs) -> Any: ...


class ModelDeserializer(HasAModelManager[T]):
    """
    An object that converts an incoming serialized dict into values that can be
    directly assigned to an item's attributes and assigns them.
    """

    validate = ModelValidator()
    app: MinimalManagerApp

    # TODO:?? a larger question is: which should be first? Deserialize then validate - or - validate then deserialize?

    def __init__(self, app: MinimalManagerApp, **kwargs):
        """
        Set up deserializers and validator.
        """
        super().__init__(app, **kwargs)

        self.deserializers: dict[str, Deserializer] = {}
        self.deserializable_keyset: set[str] = set()
        self.add_deserializers()

    def add_deserializers(self):
        """
        Register a map of attribute keys -> functions that will deserialize data
        into attributes to be assigned to the item.
        """
        # to be overridden in subclasses

    def deserialize(self, item, data, flush=True, **context):
        """
        Convert an incoming serialized dict into values that can be
        directly assigned to an item's attributes and assign them
        """
        # TODO: constrain context to current_user/whos_asking when that's all we need (trans)
        sa_session = self.app.model.context
        new_dict = {}
        for key, val in data.items():
            if key in self.deserializers:
                new_dict[key] = self.deserializers[key](item, key, val, **context)
            # !important: don't error on unreg. keys -- many clients will add weird ass keys onto the model

        # TODO:?? add and flush here or in manager?
        if flush and len(new_dict):
            sa_session.add(item)
            sa_session.commit()

        return new_dict

    # ... common deserializers for primitives
    def default_deserializer(self, item, key, val, **context):
        """
        If the incoming `val` is different than the `item` value change it
        and, in either case, return the value.
        """
        # TODO: sets the item attribute to value (this may not work in all instances)

        # only do the following if val == getattr( item, key )
        if hasattr(item, key) and getattr(item, key) != val:
            setattr(item, key, val)
        return val

    def deserialize_basestring(self, item, key, val, convert_none_to_empty=False, **context):
        val = "" if (convert_none_to_empty and val is None) else self.validate.basestring(key, val)
        return self.default_deserializer(item, key, val, **context)

    def deserialize_bool(self, item, key, val, **context):
        val = self.validate.bool(key, val)
        return self.default_deserializer(item, key, val, **context)

    def deserialize_int(self, item, key, val, min=None, max=None, **context):
        val = self.validate.int_range(key, val, min, max)
        return self.default_deserializer(item, key, val, **context)

    # def deserialize_date( self, item, key, val ):
    #    #TODO: parse isoformat date into date object

    # ... common deserializers for Galaxy
    def deserialize_genome_build(self, item, key, val, **context):
        """
        Make sure `val` is a valid dbkey and assign it.
        """
        val = self.validate.genome_build(key, val)
        return self.default_deserializer(item, key, val, **context)


# ==== Building query filters based on model data
class ModelFilterParser(HasAModelManager):
    """
    Converts string tuples (partially converted query string params) of
    attr, op, val into either:

    - ORM based filters (filters that can be applied by the ORM at the SQL
      level) or
    - functional filters (filters that use derived values or values not
      within the SQL tables)

    These filters can then be applied to queries.

    This abstraction allows 'smarter' application of limit and offset at either the
    SQL level or the generator/list level based on the presence of functional
    filters. In other words, if no functional filters are present, limit and offset
    may be applied at the SQL level. If functional filters are present, limit and
    offset need to applied at the list level.

    These might be safely be replaced in the future by creating SQLAlchemy
    hybrid properties or more thoroughly mapping derived values.
    """

    # ??: this class kindof 'lives' in both the world of the controllers/param-parsing and to models/orm
    # (as the model informs how the filter params are parsed)
    # I have no great idea where this 'belongs', so it's here for now

    model_class: type[model._HasTable]
    parsed_filter = parsed_filter
    orm_filter_parsers: OrmFilterParsersType
    fn_filter_parsers: FunctionFilterParsersType

    def __init__(self, app: MinimalManagerApp, **kwargs):
        """
        Set up serializer map, any additional serializable keys, and views here.
        """
        super().__init__(app, **kwargs)

        #: regex for testing/dicing iso8601 date strings, with optional time and ms, but allowing only UTC timezone
        self.date_string_re = re.compile(
            r"^(\d{4}\-\d{2}\-\d{2})[T| ]{0,1}(\d{2}:\d{2}:\d{2}(?:\.\d{1,6}){0,1}){0,1}Z{0,1}$"
        )

        # dictionary containing parsing data for ORM/SQLAlchemy-based filters
        # ..note: although kind of a pain in the ass and verbose, opt-in/allowlisting allows more control
        #   over potentially expensive queries
        self.orm_filter_parsers = {}

        #: dictionary containing parsing data for functional filters - applied after a query is made
        self.fn_filter_parsers = {}

        # set up both of the above
        self._add_parsers()

    def _add_parsers(self):
        """
        Set up, extend, or alter `orm_filter_parsers` and `fn_filter_parsers`.
        """
        # note: these are the default filters for all models
        self.orm_filter_parsers.update(
            {
                # (prob.) applicable to all models
                "id": {"op": ("in")},
                "encoded_id": {"column": "id", "op": ("in"), "val": self.parse_id_list},
                # dates can be directly passed through the orm into a filter (no need to parse into datetime object)
                "extension": {"op": ("eq", "like", "in"), "val": {"in": lambda v: v.split(",")}},
                "create_time": {"op": ("le", "ge", "lt", "gt"), "val": self.parse_date},
                "update_time": {"op": ("le", "ge", "lt", "gt"), "val": self.parse_date},
            }
        )

    def build_filter_params(
        self,
        query_params: ValueFilterQueryParams,
        filter_attr_key: str = "q",
        filter_value_key: str = "qv",
        attr_op_split_char: str = "-",
    ) -> list[tuple[str, str, str]]:
        """
        Builds a list of tuples containing filtering information in the form of (attribute, operator, value).
        """
        DEFAULT_OP = "eq"
        qdict = query_params.model_dump(exclude_defaults=True)
        if filter_attr_key not in qdict:
            return []
        # precondition: attrs/value pairs are in-order in the qstring
        attrs = qdict.get(filter_attr_key)
        if not isinstance(attrs, list):
            attrs = [attrs]
        # ops are strings placed after the attr strings and separated by a split char (e.g. 'create_time-lt')
        # ops are optional and default to 'eq'
        reparsed_attrs = []
        ops = []
        for attr in attrs:
            op = DEFAULT_OP
            if attr_op_split_char in attr:
                # note: only split the last (e.g. q=community-tags-in&qv=rna yields ( 'community-tags', 'in', 'rna' )
                attr, op = attr.rsplit(attr_op_split_char, 1)
            ops.append(op)
            reparsed_attrs.append(attr)
        attrs = reparsed_attrs

        values = qdict.get(filter_value_key, [])
        if not isinstance(values, list):
            values = [values]
        # TODO: it may be more helpful to the consumer if we error on incomplete 3-tuples
        #   (instead of relying on zip to shorten)
        return list(zip(attrs, ops, values))

    def parse_query_filters(self, query_filters: ValueFilterQueryParams):
        """Convenience function to parse a ValueFilterQueryParams object into a collection of filtering criteria."""
        filter_params = self.build_filter_params(query_filters)
        return self.parse_filters(filter_params)

    def parse_filters(self, filter_tuple_list):
        """
        Parse string 3-tuples (attr, op, val) into orm or functional filters.
        """
        # TODO: allow defining the default filter op in this class (and not 'eq' in base/controller.py)
        parsed = []
        for attr, op, val in filter_tuple_list:
            filter_ = self.parse_filter(attr, op, val)
            parsed.append(filter_)
        return parsed

    def parse_filter(self, attr, op, val):
        """
        Attempt to parse filter as a custom/fn filter, then an orm filter, and
        if neither work - raise an error.

        :raises exceptions.RequestParameterInvalidException: if no functional or orm
            filter can be parsed.
        """
        try:
            # check for a custom filter
            fn_filter = self._parse_fn_filter(attr, op, val)
            if fn_filter is not None:
                return fn_filter

            # if no custom filter found, try to make an ORM filter
            # note: have to use explicit is None here, bool( sqlalx.filter ) == False
            orm_filter = self._parse_orm_filter(attr, op, val)
            if orm_filter is not None:
                return orm_filter

        # by convention, assume most val parsers raise ValueError
        except ValueError as val_err:
            raise exceptions.RequestParameterInvalidException(
                "unparsable value for filter", column=attr, operation=op, value=val, ValueError=str(val_err)
            )

        # if neither of the above work, raise an error with how-to info
        # TODO: send back all valid filter keys in exception for added user help
        raise exceptions.RequestParameterInvalidException("bad filter", column=attr, operation=op)

    # ---- fn filters
    def _parse_fn_filter(self, attr, op, val):
        """
        Attempt to parse a non-ORM filter function.
        """
        # fn_filter_parsers is a dict: fn_filter_parsers[attr] = {"opname1": opfn1, "opname2": opfn2, etc. }

        # attr, op is a nested dictionary pointing to the filter fn
        attr_map = self.fn_filter_parsers.get(attr, None)
        if not attr_map:
            return None
        allowed_ops = attr_map["op"]
        # allowed ops is a map here, op => fn
        filter_fn = allowed_ops.get(op, None)
        if not filter_fn:
            return None
        # parse the val from string using the 'val' parser if present (otherwise, leave as string)
        if val_parser := attr_map.get("val", None):
            val = val_parser(val)

        # curry/partial and fold the val in there now
        return self.parsed_filter(filter_type="function", filter=lambda i: filter_fn(i, val))

    # ---- ORM filters
    def _parse_orm_filter(self, attr, op, val) -> Optional[ParsedFilter]:
        """
        Attempt to parse a ORM-based filter.

        Using SQLAlchemy, this would yield a sql.elements.BinaryExpression.
        """
        # orm_filter_parsers is a dict: orm_filter_parsers[attr] = <column map>
        column_map = self.orm_filter_parsers.get(attr, None)
        if not column_map:
            # no column mapping (not allowlisted)
            return None
        if callable(column_map):
            return self.parsed_filter(filter_type="orm_function", filter=column_map(attr, op, val))
        # attr must be an allowlisted column by attr name or by key passed in column_map
        # note: column_map[ 'column' ] takes precedence
        if "column" in column_map:
            attr = column_map["column"]
        column = self.model_class.__table__.columns.get(attr)
        if column is None:
            # could be a property (hybrid_property, etc.) - assume we can make a filter from it
            column = getattr(self.model_class, attr)
        if column is None:
            # no orm column
            return None

        # op must be allowlisted: contained in the list orm_filter_list[ attr ][ 'op' ]
        allowed_ops = column_map["op"]
        if op not in allowed_ops:
            return None

        converted_op = self._convert_op_string_to_fn(column, op)
        if not converted_op:
            return None

        # parse the val from string using the 'val' parser if present (otherwise, leave as string)
        val_parser = column_map.get("val")
        # val_parser can be a dictionary indexed by the operations, in case different functions
        # need to be called depending on the operation
        if isinstance(val_parser, dict):
            val_parser = val_parser.get(op)
        if val_parser:
            val = val_parser(val)
        if op == "contains":
            # Do we want to make this configurable ?
            val = val.lower()

        orm_filter = converted_op(val)
        return self.parsed_filter(filter_type="orm", filter=orm_filter, case_insensitive=op == "contains")

    #: these are the easier/shorter string equivalents to the python operator fn names that need '__' around them
    UNDERSCORED_OPS = ("lt", "le", "eq", "ne", "ge", "gt")

    def _convert_op_string_to_fn(self, column, op_string):
        """
        Convert the query string filter op shorthand into actual ORM usable
        function names, then return the ORM function.
        """
        # correct op_string to usable function key
        fn_name = op_string
        if op_string in self.UNDERSCORED_OPS:
            fn_name = f"__{op_string}__"
        elif op_string == "in":
            fn_name = "in_"

        # get the column fn using the op_string and error if not a callable attr
        # TODO: special case 'not in' - or disallow?
        op_fn = getattr(column, fn_name, None)
        if not op_fn or not callable(op_fn):
            return None
        if op_string == "contains":
            op_fn = partial(op_fn, autoescape=True)
        return op_fn

    # ---- preset fn_filters: dictionaries of standard filter ops for standard datatypes
    def string_standard_ops(self, key):
        return {
            "op": {
                "eq": lambda i, v: v == getattr(i, key),
                "contains": lambda i, v: v in partial(getattr(i, key), autoescape=True),  # type: ignore[operator]
            }
        }

    # --- more parsers! yay!
    # TODO: These should go somewhere central - we've got ~6 parser modules/sections now
    def parse_id_list(self, id_list_string, sep=","):
        """
        Split `id_list_string` at `sep` and decode as ids.
        """
        # TODO: move id decoding out
        id_list = [self.app.security.decode_id(id_) for id_ in id_list_string.split(sep)]
        return id_list

    def parse_int_list(self, int_list_string, sep=","):
        """
        Split `int_list_string` at `sep` and parse as ints.
        """
        # TODO: move id decoding out
        int_list = [int(v) for v in int_list_string.split(sep)]
        return int_list

    def parse_date(self, date_string):
        """
        Reformats a string containing either seconds from epoch or an iso8601 formated
        date string into a new date string usable within a filter query.

        Seconds from epoch can be a floating point value as well (i.e containing ms).
        """
        # assume it's epoch if no date separator is present
        try:
            epoch = float(date_string)
            datetime_obj = datetime.datetime.fromtimestamp(epoch)
            return datetime_obj.isoformat(sep=" ")
        except ValueError:
            pass

        if match := self.date_string_re.match(date_string):
            date_string = " ".join(group for group in match.groups() if group)
            return date_string
        raise ValueError("datetime strings must be in the ISO 8601 format and in the UTC")

    def contains_non_orm_filter(self, filters: list[ParsedFilter]) -> bool:
        """Whether the list of filters contains any non-orm filter."""
        return any(filter.filter_type == "function" for filter in filters)


def parse_bool(bool_string: Union[str, bool]) -> bool:
    """
    Parse a boolean from a string.
    """
    # Be strict here to remove complexity of options (but allow already parsed).
    if bool_string in ("True", "true", True):
        return True
    if bool_string in ("False", "false", False):
        return False
    raise ValueError(f"invalid boolean: {bool_string}")


def raise_filter_err(attr, op, val, msg):
    raise exceptions.RequestParameterInvalidException(msg, column=attr, operation=op, val=val)


class SortableManager:
    """A manager interface for parsing order_by strings into actual 'order by' queries."""

    def parse_order_by(self, order_by_string, default=None):
        """Return an ORM compatible order_by clause using the given string (i.e.: 'name-dsc,create_time').
        This must be implemented by the manager."""
        raise NotImplementedError


class StorageCleanerManager(Protocol):
    """
    Interface for monitoring storage usage and managing deletion/purging of objects that consume user's storage space.
    """

    # TODO: refactor this interface to be more generic and allow for more types of cleanable items

    sort_map: dict[StoredItemOrderBy, Any]

    def get_discarded_summary(self, user: model.User) -> CleanableItemsSummary:
        """Returns information with the total storage space taken by discarded items for the given user.

        Discarded items are those that are deleted but not purged yet.
        """
        raise NotImplementedError

    def get_discarded(
        self,
        user: model.User,
        offset: Optional[int],
        limit: Optional[int],
        order: Optional[StoredItemOrderBy],
    ) -> list[StoredItem]:
        """Returns a paginated list of items deleted by the given user that are not yet purged."""
        raise NotImplementedError

    def get_archived_summary(self, user: model.User) -> CleanableItemsSummary:
        """Returns information with the total storage space taken by archived items for the given user.

        Archived items are those that are not currently active. Some archived items may be purged already, but
        this method does not return information about those.
        """
        raise NotImplementedError

    def get_archived(
        self,
        user: model.User,
        offset: Optional[int],
        limit: Optional[int],
        order: Optional[StoredItemOrderBy],
    ) -> list[StoredItem]:
        """Returns a paginated list of items archived by the given user that are not yet purged."""
        raise NotImplementedError

    def cleanup_items(self, user: model.User, item_ids: set[int]) -> StorageItemsCleanupResult:
        """Purges the given list of items by ID. The items must be owned by the user."""
        raise NotImplementedError


def combine_lists(listA: Any, listB: Any) -> list:
    """
    Combine two lists into a single list.

    Arguments can be None, non-lists, or lists. If an argument is None, it will
    not be included in the returned list. If both arguments are None, an empty
    list will be returned.
    """

    def make_list(item):
        # Check for None explicitly: __bool__ may be overwritten.
        if item is None:
            return []
        elif isinstance(item, list):
            return item
        else:
            return [item]

    return make_list(listA) + make_list(listB)
