# Source code for propertyestimator.workflow.schemas

    """
    A collection of schemas which represent elements of a property calculation workflow.
    """
    import re

    from propertyestimator.utils.quantities import EstimatedQuantity
    from propertyestimator.utils.serialization import TypedBaseModel
    from propertyestimator.workflow.decorators import UNDEFINED, protocol_input
    from propertyestimator.workflow.plugins import available_protocols
    from propertyestimator.workflow.typing import is_type_subclass_of_type
    from propertyestimator.workflow.utils import ProtocolPath, ReplicatorValue

    class ProtocolSchema(TypedBaseModel):
        """A json serializable representation of a workflow protocol.
        """

        def __init__(self):
            """Constructs a new ProtocolSchema object.
            """
            self.id = None
            self.type = None

            self.inputs = {}

        def __getstate__(self):

            return {"id": self.id, "type": self.type, "inputs": self.inputs}

        def __setstate__(self, state):

            self.id = state["id"]
            self.type = state["type"]

            self.inputs = state["inputs"]

    class ProtocolGroupSchema(ProtocolSchema):
        """A json serializable representation of a workflow protocol
        group.
        """

        def __init__(self):
            """Constructs a new ProtocolGroupSchema object.
            """
            super().__init__()

            self.grouped_protocol_schemas = []

        def __getstate__(self):

            state = super(ProtocolGroupSchema, self).__getstate__()
            state.update({"grouped_protocol_schemas": self.grouped_protocol_schemas})

            return state

        def __setstate__(self, state):

            super(ProtocolGroupSchema, self).__setstate__(state)
            self.grouped_protocol_schemas = state["grouped_protocol_schemas"]

    class ProtocolReplicator(TypedBaseModel):
        """A protocol replicator contains the information necessary to replicate
        parts of a property estimation workflow.

        Any protocol whose id includes `$(replicator.id)` (where `replicator.id` is the
        id of a replicator) will be cloned for each value present in `template_values`.
        Protocols that are being replicated will also have any ReplicatorValue inputs replaced
        with the actual value taken from `template_values`.

        When the protocol is replicated, the `$(replicator.id)` placeholder in the protocol
        id will be replaced an integer which corresponds to the index of a value in the
        `template_values` array.

        Any protocols which take input from a replicated protocol will be updated to
        instead take a list of value, populated by the outputs of the replicated
        protocols.

        Notes
        -----
            * The `template_values` property must be a list of either constant values,
              or `ProtocolPath` objects which take their value from the `global` scope.
            * If children of replicated protocols are also flagged as to be replicated,
              they will only have their ids changed to match the index of the parent
              protocol, as opposed to being fully replicated.
        """

        @property
        def placeholder_id(self):
            """The string which protocols to be replicated should include in
            their ids."""
            return f"$({self.id})"

        def __init__(self, replicator_id=""):
            """Constructs a new ProtocolReplicator object.

            Parameters
            ----------
            replicator_id: str
                The id of this replicator.
            """
            self.id = replicator_id
            self.template_values = None

        def __getstate__(self):

            return {"id": self.id, "template_values": self.template_values}

        def __setstate__(self, state):

            self.id = state["id"]
            self.template_values = state["template_values"]

        def apply(
            self, protocols, template_values=None, template_index=-1, template_value=None
        ):
            """Applies this replicator to the provided set of protocols and any of
            their children.

            This protocol should be followed by a call to `update_references`
            to ensure that all protocols which take their input from a replicated
            protocol get correctly updated.

            Parameters
            ----------
            protocols: dict of str and BaseProtocol
                The protocols to apply the replicator to.
            template_values: list of Any
                A list of the values which will be inserted
                into the newly replicated protocols.

                This parameter is mutually exclusive with
                `template_index` and `template_value`
            template_index: int, optional
                A specific value which should be used for any
                protocols flagged as to be replicated by this
                replicator. This option is mainly used when
                replicating children of an already replicated
                protocol.

                This parameter is mutually exclusive with
                `template_values` and must be set along with
                a `template_value`.
            template_value: Any, optional
                A specific index which should be used for any
                protocols flagged as to be replicated by this
                replicator. This option is mainly used when
                replicating children of an already replicated
                protocol.

                This parameter is mutually exclusive with
                `template_values` and must be set along with
                a `template_index`.

            Returns
            -------
            dict of str and BaseProtocol
                The replicated protocols.
            dict of ProtocolPath and list of tuple of ProtocolPath and int
                A dictionary of references to all of the protocols which have
                been replicated, with keys of original protocol ids. Each value
                is comprised of a list of the replicated protocol ids, and their
                index into the `template_values` array.
            """

            if (
                template_values is not None
                and (template_index >= 0 or template_value is not None)
            ) or (
                template_values is None and (template_index < 0 or template_value is None)
            ):

                raise ValueError(
                    f"Either the template values array must be set, or a specific "
                    f"template index and value must be passed."
                )

            replicated_protocols = {}
            replicated_protocol_map = {}

            for protocol_id, protocol in protocols.items():

                should_replicate = self.placeholder_id in protocol_id

                # If this protocol should not be directly replicated then try and
                # replicate any child protocols...
                if not should_replicate:

                    replicated_protocols[protocol_id] = protocol

                    if template_index is not None and template_index >= 0:
                        # Make sure to include children of replicated protocols in the
                        # map to ensure correct behaviour when updating children of replicated
                        # protocols which have the replicator id in their name, and take input
                        # from another child protocol which doesn't have the replicator id in
                        # its name.
                        if ProtocolPath("", protocol_id) not in replicated_protocol_map:
                            replicated_protocol_map[ProtocolPath("", protocol_id)] = []

                        replicated_protocol_map[ProtocolPath("", protocol_id)].append(
                            (ProtocolPath("", protocol_id), template_index)
                        )

                    self._apply_to_protocol_children(
                        protocol,
                        replicated_protocol_map,
                        template_values,
                        template_index,
                        template_value,
                    )

                    continue

                # ..otherwise, we need to replicate this protocol.
                replicated_protocols.update(
                    self._apply_to_protocol(
                        protocol,
                        replicated_protocol_map,
                        template_values,
                        template_index,
                        template_value,
                    )
                )

            return replicated_protocols, replicated_protocol_map

        def _apply_to_protocol(
            self,
            protocol,
            replicated_protocol_map,
            template_values=None,
            template_index=-1,
            template_value=None,
        ):

            replicated_protocol_map[ProtocolPath("", protocol.id)] = []
            replicated_protocols = {}

            template_values_dict = {template_index: template_value}

            if template_values is not None:

                template_values_dict = {
                    index: template_value
                    for index, template_value in enumerate(template_values)
                }

            for index, template_value in template_values_dict.items():

                protocol_schema = protocol.schema
                protocol_schema.id = protocol_schema.id.replace(
                    self.placeholder_id, str(index)
                )

                replicated_protocol = available_protocols[protocol_schema.type](
                    protocol_schema.id
                )
                replicated_protocol.schema = protocol_schema

                replicated_protocol_map[ProtocolPath("", protocol.id)].append(
                    (ProtocolPath("", replicated_protocol.id), index)
                )

                # Pass the template values to any inputs which require them.
                for required_input in replicated_protocol.required_inputs:

                    input_value = replicated_protocol.get_value(required_input)

                    if not isinstance(input_value, ReplicatorValue):
                        continue

                    elif input_value.replicator_id != self.id:

                        input_value.replicator_id = input_value.replicator_id.replace(
                            self.placeholder_id, str(index)
                        )
                        continue

                    replicated_protocol.set_value(required_input, template_value)

                self._apply_to_protocol_children(
                    replicated_protocol,
                    replicated_protocol_map,
                    None,
                    index,
                    template_value,
                )

                replicated_protocols[replicated_protocol.id] = replicated_protocol

            return replicated_protocols

        def _apply_to_protocol_children(
            self,
            protocol,
            replicated_protocol_map,
            template_values=None,
            template_index=-1,
            template_value=None,
        ):

            replicated_child_ids = protocol.apply_replicator(
                self, template_values, template_index, template_value
            )

            # Append the id of this protocols to any replicated child protocols.
            for child_id, replicated_ids in replicated_child_ids.items():

                child_id.prepend_protocol_id(protocol.id)

                for replicated_id, _ in replicated_ids:
                    replicated_id.prepend_protocol_id(protocol.id)

                replicated_protocol_map.update(replicated_child_ids)

        def update_references(self, protocols, replication_map, template_values):
            """Redirects the input references of protocols to the replicated
            versions.

            Parameters
            ----------
            protocols: dict of str and BaseProtocol
                The protocols which have had this replicator applied
                to them.
            replication_map: dict of ProtocolPath and list of tuple of ProtocolPath and int
                A dictionary of references to all of the protocols which have
                been replicated, with keys of original protocol ids. Each value
                is comprised of a list of the replicated protocol ids, and their
                index into the `template_values` array.
            template_values: List of Any
                A list of the values which will be inserted
                into the newly replicated protocols.
            """

            inverse_replication_map = {}

            for original_id, replicated_ids in replication_map.items():
                for replicated_id, index in replicated_ids:
                    inverse_replication_map[replicated_id] = (original_id, index)

            for protocol_id, protocol in protocols.items():

                # Look at each of the protocols inputs and see if its value is either a ProtocolPath,
                # or a list of ProtocolPath's.
                for required_input in protocol.required_inputs:

                    all_value_references = protocol.get_value_references(required_input)
                    replicated_value_references = {}

                    for source_path, value_reference in all_value_references.items():

                        if self.placeholder_id not in value_reference.full_path:
                            continue

                        replicated_value_references[source_path] = value_reference

                    # If this protocol does not take input from one of the replicated protocols,
                    # then we are done.
                    if len(replicated_value_references) == 0:
                        continue

                    for source_path, value_reference in replicated_value_references.items():

                        full_source_path = ProtocolPath.from_string(source_path.full_path)
                        full_source_path.prepend_protocol_id(protocol_id)

                        # If the protocol was not itself replicated by this replicator, its value
                        # is set to a list containing references to all newly replicated protocols.
                        # Otherwise, the value will be set to a reference to just the protocol which
                        # was replicated using the same index.
                        value_source = [
                            ProtocolPath.from_string(
                                value_reference.full_path.replace(
                                    self.placeholder_id, str(index)
                                )
                            )
                            for index in range(len(template_values))
                        ]

                        for replicated_id, map_tuple in inverse_replication_map.items():

                            original_id, replicated_index = map_tuple

                            if (
                                full_source_path.protocol_path
                                != replicated_id.protocol_path
                            ):
                                continue

                            value_source = ProtocolPath.from_string(
                                value_reference.full_path.replace(
                                    self.placeholder_id, str(replicated_index)
                                )
                            )

                            break

                        # Replace the input value with a list of ProtocolPath's that point to
                        # the newly generated protocols.
                        protocol.set_value(source_path, value_source)

    class WorkflowOutputToStore:
        """An object which describes which data should be cached
        after a workflow has finished executing, and from which
        completed protocols should the data be collected from.

        A `WorkflowOutputToStore` maps to the `BaseStoredData`
        stored data class.

        Attributes
        ----------
        substance: ProtocolPath
            A reference to the composition of the collected data.
        """

        def __init__(self):
            """Constructs a new WorkflowOutputToStore object."""

            self.substance = None

        def __getstate__(self):

            return_value = {"substance": self.substance}
            return return_value

        def __setstate__(self, state):
            self.substance = state["substance"]

    class WorkflowSimulationDataToStore(WorkflowOutputToStore):
        """An object which describes which data should be cached
        after a workflow has finished executing, and from which
        completed protocols should the data be collected from.

        A `WorkflowSimulationDataToStore` maps to the creation of
        a `StoredSimulationData` stored data class.

        Attributes
        ----------
        coordinate_file_path: ProtocolPath
            A reference to the file path of a coordinate file which encodes
            the topology of the system.
        trajectory_file_path: ProtocolPath
            A reference to the file path of a .dcd trajectory file containing
            configurations generated by the simulation.
        statistics_file_path: ProtocolPath
            A reference to the file path of of a `StatisticsArray` csv file,
            containing statistics generated by the simulation.
        statistical_inefficiency: ProtocolPath
            A reference to the statistical inefficiency of the collected data.
        total_number_of_molecules: ProtocolPath
            A reference to the total number of molecules in the system.
        """

        def __init__(self):
            """Constructs a new WorkflowSimulationDataToStore object."""

            super().__init__()

            self.total_number_of_molecules = None

            self.trajectory_file_path = None
            self.coordinate_file_path = None

            self.statistics_file_path = None
            self.statistical_inefficiency = None

        def __getstate__(self):
            return_value = super(WorkflowSimulationDataToStore, self).__getstate__()

            return_value.update(
                {
                    "total_number_of_molecules": self.total_number_of_molecules,
                    "trajectory_file_path": self.trajectory_file_path,
                    "coordinate_file_path": self.coordinate_file_path,
                    "statistics_file_path": self.statistics_file_path,
                    "statistical_inefficiency": self.statistical_inefficiency,
                }
            )

            return return_value

        def __setstate__(self, state):

            super(WorkflowSimulationDataToStore, self).__setstate__(state)

            self.total_number_of_molecules = state["total_number_of_molecules"]

            self.trajectory_file_path = state["trajectory_file_path"]
            self.coordinate_file_path = state["coordinate_file_path"]

            self.statistics_file_path = state["statistics_file_path"]
            self.statistical_inefficiency = state["statistical_inefficiency"]

    class WorkflowDataCollectionToStore(WorkflowOutputToStore):
        """An object which describes which data should be cached
        after a workflow has finished executing, and from which
        completed protocols should the data be collected from.

        A `WorkflowDataCollectionToStore` maps to the creation of
        a `StoredDataCollection` stored data class.

        Attributes
        ----------
        data: dict of str and WorkflowSimulationDataToStore
            A dictionary of stored simulation data objects which
            have been given a unique key.
        """

        def __init__(self):
            """Constructs a new WorkflowDataCollectionToStore object."""

            super().__init__()
            self.data = {}

        def __getstate__(self):

            return_value = super(WorkflowDataCollectionToStore, self).__getstate__()

            return_value.update({"data": self.data})

            return return_value

        def __setstate__(self, state):

            super(WorkflowDataCollectionToStore, self).__setstate__(state)
            self.data = state["data"]

    class WorkflowSchema(TypedBaseModel):
        """Outlines the workflow which should be followed when calculating
        a certain property.
        """

        def __init__(self, property_type=None):
            """Constructs a new WorkflowSchema object.

            Parameters
            ----------
            property_type: str
                The type of property which this workflow aims to estimate.
            """
            self.property_type = property_type
            self.id = None

            self.protocols = {}
            self.replicators = []

            self.final_value_source = None
            self.gradients_sources = []

            self.outputs_to_store = {}

        def __getstate__(self):

            return {
                "property_type": self.property_type,
                "id": self.id,
                "protocols": self.protocols,
                "replicators": self.replicators,
                "final_value_source": self.final_value_source,
                "gradients_sources": self.gradients_sources,
                "outputs_to_store": self.outputs_to_store,
            }

        def __setstate__(self, state):

            self.property_type = state["property_type"]
            self.id = state["id"]

            self.protocols = state["protocols"]
            self.replicators = state["replicators"]

            self.final_value_source = state["final_value_source"]
            self.gradients_sources = state["gradients_sources"]

            self.outputs_to_store = state["outputs_to_store"]

        def _find_protocols_to_be_replicated(self, replicator, protocols=None):
            """Finds all protocols which have been flagged to be replicated
            by a specified replicator.

            Parameters
            ----------
            replicator: ProtocolReplicator
                The replicator of interest.
            protocols: dict of str and ProtocolSchema or list of ProtocolSchema, optional
                The protocols to search through. If None, then
                all protocols in this schema will be searched.

            Returns
            -------
            list of str
                The ids of the protocols to be replicated by the specified replicator
            """

            if protocols is None:
                protocols = self.protocols

            if isinstance(protocols, list):
                protocols = {protocol.id: protocol for protocol in protocols}

            protocols_to_replicate = []

            for protocol_id, protocol in protocols.items():

                if protocol_id.find(replicator.placeholder_id) >= 0:
                    protocols_to_replicate.append(protocol_id)

                # Search through any children
                if not isinstance(protocol, ProtocolGroupSchema):
                    continue

                protocols_to_replicate.extend(
                    self._find_protocols_to_be_replicated(
                        replicator, protocol.grouped_protocol_schemas
                    )
                )

            return protocols_to_replicate

        def _get_unreplicated_path(self, protocol_path):
            """Checks to see if the protocol pointed to by this path will only
            exist after a replicator has been applied, and if so, returns a
            path to the unreplicated protocol.

            Parameters
            ----------
            protocol_path: ProtocolPath
                The path to convert to an unreplicated path.

            Returns
            -------
            ProtocolPath
                The path which should point to only unreplicated protocols
            """

            full_unreplicated_path = str(protocol_path.full_path)

            for replicator in self.replicators:

                if replicator.placeholder_id in full_unreplicated_path:
                    continue

                protocols_to_replicate = self._find_protocols_to_be_replicated(replicator)

                for protocol_id in protocols_to_replicate:

                    match_pattern = re.escape(
                        protocol_id.replace(replicator.placeholder_id, r"\d+")
                    )
                    match_pattern = match_pattern.replace(re.escape(r"\d+"), r"\d+")

                    full_unreplicated_path = re.sub(
                        match_pattern, protocol_id, full_unreplicated_path
                    )

            return ProtocolPath.from_string(full_unreplicated_path)

        @staticmethod
        def _get_unnested_protocol_path(protocol_path):
            """Returns a protocol path whose nested property name
            has been truncated to only include the top level name,
            e.g:

            `some_protocol_id.value.uncertainty` would be truncated to `some_protocol_id.value`

            and

            `some_protocol_id.value[1]` would be truncated to `some_protocol_id.value`

            Parameters
            ----------
            protocol_path: ProtocolPath
                The path to truncate.

            Returns
            -------
            ProtocolPath
                The truncated path.
            """
            property_name, protocol_ids = ProtocolPath.to_components(
                protocol_path.full_path
            )

            # Remove any nested property names from the path
            if protocol_path.property_name.find(".") >= 0:
                property_name = property_name.split(".")[0]

            # Remove any array indices from the path
            if protocol_path.property_name.find("[") >= 0:
                property_name = property_name.split("[")[0]

            return ProtocolPath(property_name, *protocol_ids)

        def replace_protocol_types(self, protocol_replacements, protocol_group_schema=None):
            """Replaces protocols with given types with other protocols
            of specified replacements. This is useful when replacing
            the default protocols with custom ones, or swapping out base
            protocols with actual implementations

            Warnings
            --------
            This method is NOT fully implemented and is likely to fail in
            all but a few specific cases. This method should be used with
            extreme caution.

            Parameters
            ----------
            protocol_replacements: dict of str and str, None
                A dictionary with keys of the types of protocols which should be replaced
                with those protocols named by the values.
            protocol_group_schema: ProtocolGroupSchema
                The protocol group to apply the replacements to. This
                is mainly used when applying this method recursively.
            """

            if protocol_replacements is None:
                return

            if protocol_group_schema is None:
                protocol_schemas = self.protocols
            else:
                protocol_schemas = protocol_group_schema.grouped_protocol_schemas

            for protocol_schema_key in protocol_schemas:

                protocol_schema = protocol_schemas[protocol_schema_key]

                if protocol_schema.type not in protocol_replacements:
                    continue

                protocol = available_protocols[protocol_schema.type](protocol_schema.id)
                protocol.schema = protocol_schema

                new_protocol = available_protocols[
                    protocol_replacements[protocol_schema.type]
                ](protocol_schema.id)

                for input_path in new_protocol.required_inputs:

                    if input_path not in protocol.required_inputs:
                        continue

                    value = protocol.get_value(input_path)
                    new_protocol.set_value(input_path, value)

                protocol_schemas[protocol_schema_key] = new_protocol.schema

                if isinstance(protocol_schemas[protocol_schema_key], ProtocolGroupSchema):
                    self.replace_protocol_types(
                        protocol_replacements, protocol_schemas[protocol_schema_key]
                    )

        def _validate_replicators(self):

            for replicator in self.replicators:

                assert replicator.id is not None and len(replicator.id) > 0

                # if len(replicator.protocols_to_replicate) == 0:
                #     raise ValueError('A replicator does not have any protocols to replicate.')

                if not isinstance(replicator.template_values, list) and not isinstance(
                    replicator.template_values, ProtocolPath
                ):

                    raise ValueError(
                        "The template values of a replicator must either be "
                        "a list of values, or a reference to a list of values."
                    )

                if isinstance(replicator.template_values, list):

                    for template_value in replicator.template_values:

                        if not isinstance(template_value, ProtocolPath):
                            continue

                        if template_value.start_protocol not in self.protocols:
                            raise ValueError(
                                "The value source {} does not exist.".format(template_value)
                            )

                elif isinstance(replicator.template_values, ProtocolPath):

                    if not replicator.template_values.is_global:
                        raise ValueError(
                            "Template values must either be a constant, or come from the global "
                            "scope."
                        )

                if (
                    self.final_value_source is not None
                    and self.final_value_source.protocol_path.find(
                        replicator.placeholder_id
                    )
                    >= 0
                ):

                    raise ValueError(
                        "The final value source cannot come from"
                        "a protocol which is being replicated."
                    )

        def _validate_final_value(self):

            if self.final_value_source is None:
                return

            if self.final_value_source.start_protocol not in self.protocols:
                raise ValueError(
                    "The value source {} does not exist.".format(self.final_value_source)
                )

            protocol_schema = self.protocols[self.final_value_source.start_protocol]

            protocol_object = available_protocols[protocol_schema.type](protocol_schema.id)
            protocol_object.schema = protocol_schema

            protocol_object.get_value(self.final_value_source)

            attribute_type = protocol_object.get_class_attribute(
                self.final_value_source
            ).type_hint
            assert is_type_subclass_of_type(attribute_type, EstimatedQuantity)

        def _validate_gradients(self):

            from propertyestimator.properties import ParameterGradient

            for gradient_source in self.gradients_sources:

                if gradient_source.start_protocol not in self.protocols:
                    raise ValueError(
                        "The gradient source {} does not exist.".format(gradient_source)
                    )

                protocol_schema = self.protocols[gradient_source.start_protocol]

                protocol_object = available_protocols[protocol_schema.type](
                    protocol_schema.id
                )
                protocol_object.schema = protocol_schema

                protocol_object.get_value(gradient_source)

                attribute_type = protocol_object.get_class_attribute(
                    gradient_source
                ).type_hint
                assert is_type_subclass_of_type(attribute_type, ParameterGradient)

        def _validate_output_to_store(self, output_to_store):
            """Validates that the references of a particular output to store
            are valid.

            Parameters
            ----------
            output_to_store: WorkflowOutputToStore
                The output to store to validate.
            """

            if not isinstance(output_to_store, WorkflowOutputToStore):

                raise ValueError(
                    "Only `WorkflowOutputToStore` derived objects are allowed "
                    "in the outputs_to_store dictionary at this time."
                )

            attributes_to_check = ["substance"]

            if isinstance(output_to_store, WorkflowSimulationDataToStore):

                attributes_to_check.extend(
                    [
                        "total_number_of_molecules",
                        "trajectory_file_path",
                        "coordinate_file_path",
                        "statistics_file_path",
                        "statistical_inefficiency",
                    ]
                )

            for attribute_name in attributes_to_check:

                attribute_value = getattr(output_to_store, attribute_name)

                if isinstance(attribute_value, ReplicatorValue):

                    if len(self.replicators) == 0:

                        raise ValueError(
                            "An output to store is trying to take its value from a "
                            "replicator, while this schema has no replicators."
                        )

                    elif (
                        len(
                            [
                                replicator
                                for replicator in self.replicators
                                if attribute_value.replicator_id == replicator.id
                            ]
                        )
                        == 0
                    ):

                        raise ValueError(
                            "An output to store is trying to take its value from a "
                            "replicator {} which does not exist.".format(
                                attribute_value.replicator_id
                            )
                        )

                if (
                    not isinstance(attribute_value, ProtocolPath)
                    or attribute_value.is_global
                ):
                    continue

                if attribute_value.start_protocol not in self.protocols:
                    raise ValueError(
                        "The value source {} does not exist.".format(attribute_value)
                    )

                protocol_schema = self.protocols[attribute_value.start_protocol]

                protocol_object = available_protocols[protocol_schema.type](
                    protocol_schema.id
                )
                protocol_object.schema = protocol_schema

                protocol_object.get_value(attribute_value)

        def _validate_outputs_to_store(self):
            """Validates that the references to the outputs to store
            are valid.
            """

            for output_label in self.outputs_to_store:

                output_to_store = self.outputs_to_store[output_label]

                self._validate_output_to_store(output_to_store)

                if isinstance(output_to_store, WorkflowDataCollectionToStore):

                    for inner_output_to_store in output_to_store.data.values():
                        self._validate_output_to_store(inner_output_to_store)

        def validate_interfaces(self):
            """Validates the flow of the data between protocols, ensuring
            that inputs and outputs correctly match up.
            """

            self._validate_final_value()
            self._validate_gradients()
            self._validate_replicators()
            self._validate_outputs_to_store()

            for protocol_id in self.protocols:

                protocol_schema = self.protocols[protocol_id]

                protocol_object = available_protocols[protocol_schema.type](
                    protocol_schema.id
                )
                protocol_object.schema = protocol_schema

                for input_path in protocol_object.required_inputs:

                    input_value = protocol_object.get_value(input_path)
                    input_attribute = protocol_object.get_class_attribute(input_path)

                    if not isinstance(input_attribute, protocol_input):
                        continue

                    is_optional = input_attribute.optional

                    if input_value == UNDEFINED and is_optional is False:

                        raise Exception(
                            "The {} required input of protocol {} in the {} schema was "
                            "not set.".format(input_path, protocol_id, self.id)
                        )

                for input_path in protocol_object.required_inputs:

                    value_references = protocol_object.get_value_references(input_path)

                    for source_path, value_reference in value_references.items():

                        if value_reference.is_global:
                            # We handle global input validation separately
                            continue

                        value_reference = self._get_unreplicated_path(value_reference)

                        # Make sure the other protocol whose output we are interested
                        # in actually exists.
                        if value_reference.start_protocol not in self.protocols:

                            raise Exception(
                                f"The {protocol_object.id} protocol of the {self.id} schema "
                                f"tries to take input from a non-existent "
                                f"protocol: {value_reference.full_path}"
                            )

                        other_protocol_schema = self.protocols[
                            value_reference.start_protocol
                        ]

                        other_protocol_object = available_protocols[
                            other_protocol_schema.type
                        ](other_protocol_schema.id)
                        other_protocol_object.schema = other_protocol_schema

                        unnested_value_reference = self._get_unnested_protocol_path(
                            value_reference
                        )
                        unnested_source_path = self._get_unnested_protocol_path(source_path)

                        # Make sure the other protocol has the output referenced
                        # by this input.
                        other_protocol_object.get_value(unnested_value_reference)

                        # Do a very rudimentary type check between the input and
                        # output types. This is not currently possible for nested
                        # or indexed properties, or outputs of replicated protocols.
                        if (
                            value_reference.full_path != unnested_value_reference.full_path
                            or source_path.full_path != unnested_source_path.full_path
                        ):

                            continue

                        is_replicated_reference = False

                        for replicator in self.replicators:

                            if (
                                replicator.placeholder_id in protocol_id
                                and replicator.placeholder_id
                                in value_reference.protocol_path
                            ) or (
                                replicator.placeholder_id not in protocol_id
                                and replicator.placeholder_id
                                not in value_reference.protocol_path
                            ):

                                continue

                            is_replicated_reference = True
                            break

                        if is_replicated_reference:
                            continue

                        expected_input_type = protocol_object.get_class_attribute(
                            unnested_source_path
                        ).type_hint
                        expected_output_type = other_protocol_object.get_class_attribute(
                            unnested_value_reference
                        ).type_hint

                        if expected_input_type is None or expected_output_type is None:
                            continue

                        if not is_type_subclass_of_type(
                            expected_output_type, expected_input_type
                        ):

                            raise Exception(
                                f"The output type ({expected_output_type}) of {value_reference} does not "
                                f"match the requested input type ({expected_input_type}) of {source_path}"
                            )