sapiopycommons 2024.8.15a304__py3-none-any.whl → 2024.8.19a305__py3-none-any.whl

sapiopycommons/eln/experiment_handler.py

@@ -1,7 +1,12 @@
+from __future__ import annotations
+
 import time
 from collections.abc import Mapping, Iterable
+from weakref import WeakValueDictionary
 
+from sapiopylib.rest.DataMgmtService import DataMgmtServer
 from sapiopylib.rest.ELNService import ElnManager
+from sapiopylib.rest.User import SapioUser
 from sapiopylib.rest.pojo.DataRecord import DataRecord
 from sapiopylib.rest.pojo.eln.ElnExperiment import ElnExperiment, TemplateExperimentQueryPojo, ElnTemplate, \
     InitializeNotebookExperimentPojo, ElnExperimentUpdateCriteria
@@ -16,8 +21,9 @@ from sapiopylib.rest.utils.Protocols import ElnEntryStep, ElnExperimentProtocol
 from sapiopylib.rest.utils.recordmodel.PyRecordModel import PyRecordModel
 from sapiopylib.rest.utils.recordmodel.RecordModelManager import RecordModelInstanceManager, RecordModelManager
 from sapiopylib.rest.utils.recordmodel.RecordModelWrapper import WrappedType
+from sapiopylib.rest.utils.recordmodel.properties import Child
 
-from sapiopycommons.general.aliases import AliasUtil, SapioRecord
+from sapiopycommons.general.aliases import AliasUtil, SapioRecord, ExperimentIdentifier, RecordModel
 from sapiopycommons.general.exceptions import SapioException
 
 Step = str | ElnEntryStep
@@ -27,7 +33,8 @@ itself."""
 
 # FR-46064 - Initial port of PyWebhookUtils to sapiopycommons.
 class ExperimentHandler:
-    context: SapioWebhookContext
+    user: SapioUser
+    context: SapioWebhookContext | None
     """The context that this handler is working from."""
 
     # Basic experiment info from the context.
@@ -77,45 +84,107 @@ class ExperimentHandler:
                                     ElnExperimentStatus.Canceled]
     """The set of statuses that an ELN experiment could have and be considered locked."""
 
-    def __init__(self, context: SapioWebhookContext, experiment: ElnExperiment | None = None):
+    __instances: WeakValueDictionary[str, ExperimentHandler] = WeakValueDictionary()
+    __initialized: bool
+
+    def __new__(cls, context: SapioWebhookContext | SapioUser,
+                experiment: ExperimentIdentifier | SapioRecord | None = None):
+        """
+        :param context: The current webhook context or a user object to send requests from.
+        :param experiment: If an experiment is provided that is separate from the experiment that is in the context,
+            that experiment will be used by this ExperimentHandler instead. An experiment can be provided in various
+            forms, including an ElnExperiment, ElnExperimentProtocol, an experiment record, or a notebook experiment ID.
+        """
+        param_results = cls.__parse_params(context, experiment)
+        user = param_results[0]
+        experiment = param_results[2]
+        key = f"{user.__hash__()}:{experiment.notebook_experiment_id}"
+        obj = cls.__instances.get(key)
+        if not obj:
+            obj = object.__new__(cls)
+            obj.__initialized = False
+            cls.__instances[key] = obj
+        return obj
+
+    def __init__(self, context: SapioWebhookContext | SapioUser,
+                 experiment: ExperimentIdentifier | SapioRecord | None = None):
         """
         Initialization will throw an exception if there is no ELN Experiment in the provided context and no experiment
         is provided.
 
-        :param context: The current webhook context.
+        :param context: The current webhook context or a user object to send requests from.
         :param experiment: If an experiment is provided that is separate from the experiment that is in the context,
-            that experiment will be used by this ExperimentHandler instead.
+            that experiment will be used by this ExperimentHandler instead. An experiment can be provided in various
+            forms, including an ElnExperiment, ElnExperimentProtocol, an experiment record, or a notebook experiment ID.
         """
-        # FR-46495 - Allow the init function of ExperimentHandler to take in an ElnExperiment that is separate from the
-        # context.
-        if context.eln_experiment is None and experiment is None:
-            raise SapioException("Cannot initialize ExperimentHandler. No ELN Experiment in the context.")
-        if context.eln_experiment == experiment:
-            experiment = None
-        self.context = context
+        param_results = self.__parse_params(context, experiment)
+        self.user = param_results[0]
+        self.context = param_results[1]
+        experiment = param_results[2]
 
         # Get the basic information about this experiment that already exists in the context and is often used.
-        self.__eln_exp = experiment if experiment else context.eln_experiment
-        self.__protocol = ElnExperimentProtocol(experiment, context.user) if experiment else context.active_protocol
+        self.__eln_exp = experiment
+        self.__protocol = ElnExperimentProtocol(experiment, self.user)
         self.__exp_id = self.__protocol.get_id()
 
         # Grab various managers that may be used.
-        self.__eln_man = context.eln_manager
-        self.__inst_man = RecordModelManager(context.user).instance_manager
+        self.__eln_man = DataMgmtServer.get_eln_manager(self.user)
+        self.__inst_man = RecordModelManager(self.user).instance_manager
 
         # Create empty caches to fill when necessary.
         self.__steps = {}
         self.__step_options = {}
         # CR-46330: Cache any experiment entry information that might already exist in the context.
         self.__queried_all_steps = False
-        # We can only trust the entries in the context if no experiment was given as an input parameter.
-        if experiment is None:
-            if context.experiment_entry is not None:
-                self.__steps.update({context.active_step.get_name(): context.active_step})
-            if context.experiment_entry_list is not None:
-                for entry in context.experiment_entry_list:
+        # We can only trust the entries in the context if the experiment that this handler is for is the same as the
+        # one from the context.
+        if self.context is not None and self.context.eln_experiment == experiment:
+            if self.context.experiment_entry is not None:
+                self.__steps.update({self.context.active_step.get_name(): self.context.active_step})
+            if self.context.experiment_entry_list is not None:
+                for entry in self.context.experiment_entry_list:
                     self.__steps.update({entry.entry_name: ElnEntryStep(self.__protocol, entry)})
 
+    @staticmethod
+    def __parse_params(context: SapioWebhookContext | SapioUser,
+                       experiment: ExperimentIdentifier | SapioRecord | None = None) \
+            -> tuple[SapioUser, SapioWebhookContext | None, ElnExperiment]:
+        if isinstance(context, SapioWebhookContext):
+            user = context.user
+            context = context
+        else:
+            user = context
+            context = None
+        if context is not None and context.eln_experiment is not None and experiment is None:
+            experiment = context.eln_experiment
+        # FR-46495 - Allow the init function of ExperimentHandler to take in an ElnExperiment that is separate from the
+        # context.
+        # CR-37038 - Allow other experiment object types to be provided. Convert them all down to ElnExperiment.
+        if (context is None or context.eln_experiment is None) and experiment is not None:
+            eln_manager = DataMgmtServer.get_eln_manager(user)
+            # If this object is already an ElnExperiment, do nothing.
+            if isinstance(experiment, ElnExperiment):
+                pass
+            # If this object is an ElnExperimentProtocol, then we can get the ElnExperiment from the object.
+            elif isinstance(experiment, ElnExperimentProtocol):
+                experiment: ElnExperiment = experiment.eln_experiment
+            # If this object is an integer, assume it is a notebook ID that we can query the system with.
+            elif isinstance(experiment, int):
+                notebook_id: int = experiment
+                experiment: ElnExperiment = eln_manager.get_eln_experiment_by_id(notebook_id)
+                if not experiment:
+                    raise SapioException(f"No experiment with notebook ID {notebook_id} located in the system.")
+            # If this object is a record, assume it is an experiment record that we can query the system with.
+            else:
+                record_id: int = AliasUtil.to_record_ids([experiment])[0]
+                experiment: ElnExperiment = eln_manager.get_eln_experiment_by_record_id(record_id)
+                if not experiment:
+                    raise SapioException(f"No experiment with record ID {record_id} located in the system.")
+        if experiment is None:
+            raise SapioException("Cannot initialize ExperimentHandler. No ELN Experiment found in the provided parameters.")
+
+        return user, context, experiment
+
     # FR-46495: Split the creation of the experiment in launch_experiment into a create_experiment function.
     @staticmethod
     def create_experiment(context: SapioWebhookContext,
@@ -263,7 +332,7 @@ class ExperimentHandler:
         :return: The data record for this experiment. None if it has no record.
         """
         if not hasattr(self, "_ExperimentHandler__exp_record"):
-            drm = self.context.data_record_manager
+            drm = DataMgmtServer.get_data_record_manager(self.user)
             dt = self.__eln_exp.experiment_data_type_name
             results = drm.query_data_records_by_id(dt, [self.__eln_exp.experiment_record_id]).result_list
             # PR-46504: Set the exp_record to None if there are no results.
@@ -580,8 +649,6 @@ class ExperimentHandler:
         step.set_records(AliasUtil.to_data_records(records))
 
     # FR-46496 - Provide alias of set_step_records for use with form entries.
-    # TODO: Provide a similar aliased function for attachment entries once sapiopylib allows setting multiple
-    #  attachments to an attachment step.
     def set_form_record(self, step: Step, record: SapioRecord) -> None:
         """
         Sets the record for a form entry.
@@ -599,7 +666,8 @@ class ExperimentHandler:
         self.set_step_records(step, [record])
 
     # FR-46496 - Provide functions for adding and removing rows from an ELN data type entry.
-    def add_eln_rows(self, step: Step, count: int) -> list[PyRecordModel]:
+    def add_eln_rows(self, step: Step, count: int, wrapper_type: type[WrappedType] | None = None) \
+            -> list[PyRecordModel | WrappedType]:
         """
         Add rows to an ELNExperimentDetail or ELNSampleDetail table entry. The rows will not appear in the system
         until a record manager store and commit has occurred.
@@ -611,15 +679,37 @@ class ExperimentHandler:
             The step may be provided as either a string for the name of the step or an ElnEntryStep.
             If given a name, throws an exception if no step of the given name exists in the experiment.
         :param count: The number of new rows to add to the entry.
+        :param wrapper_type: Optionally wrap the ELN data type in a record model wrapper. If not provided, returns
+            an unwrapped PyRecordModel.
         :return: A list of the newly created rows.
         """
         step = self.__to_eln_step(step)
         if step.eln_entry.entry_type != ElnEntryType.Table:
             raise SapioException("The provided step is not a table entry.")
         dt: str = step.get_data_type_names()[0]
-        if not self.__is_eln_type(dt):
+        if not ElnBaseDataType.is_eln_type(dt):
             raise SapioException("The provided step is not an ELN data type entry.")
-        return self.__inst_man.add_new_records(dt, count)
+        records: list[PyRecordModel] = self.__inst_man.add_new_records(dt, count)
+        if wrapper_type:
+            return self.__inst_man.wrap_list(records, wrapper_type)
+        return records
+
+    def add_eln_row(self, step: Step, wrapper_type: type[WrappedType] | None = None) -> PyRecordModel | WrappedType:
+        """
+        Add a row to an ELNExperimentDetail or ELNSampleDetail table entry. The row will not appear in the system
+        until a record manager store and commit has occurred.
+
+        If no step functions have been called before and a step is being searched for by name, queries for the
+        list of steps in the experiment and caches them.
+
+        :param step:
+            The step may be provided as either a string for the name of the step or an ElnEntryStep.
+            If given a name, throws an exception if no step of the given name exists in the experiment.
+        :param wrapper_type: Optionally wrap the ELN data type in a record model wrapper. If not provided, returns
+            an unwrapped PyRecordModel.
+        :return: The newly created row.
+        """
+        return self.add_eln_rows(step, 1, wrapper_type)[0]
 
     def remove_eln_rows(self, step: Step, records: list[SapioRecord]) -> None:
         """
@@ -641,7 +731,7 @@ class ExperimentHandler:
         """
         step = self.__to_eln_step(step)
         dt: str = step.get_data_type_names()[0]
-        if not self.__is_eln_type(dt):
+        if not ElnBaseDataType.is_eln_type(dt):
             raise SapioException("The provided step is not an ELN data type entry.")
         if any([x.data_type_name != dt for x in records]):
             raise SapioException("Not all of the provided records match the data type of the step.")
@@ -658,16 +748,59 @@ class ExperimentHandler:
             for record in record_models:
                 record.delete()
 
-    # TODO: Remove and use the function of the same name in ElnBaseDataType in the future. Currently this function is
-    #  bugged in sapiopylib and is comparing against base_type.name instead of base_type.value.
-    @staticmethod
-    def __is_eln_type(data_type: str):
-        if data_type is None or not data_type:
-            return False
-        for base_type in ElnBaseDataType:
-            if data_type.lower().startswith(base_type.value.lower()):
-                return True
-        return False
+    def remove_eln_row(self, step: Step, record: SapioRecord) -> None:
+        """
+        Remove a row from an ELNExperimentDetail or ELNSampleDetail table entry. ELN data type table entries display all
+        records in the system that match the entry's data type. This means that removing rows from an ELN data type
+        table entry is equivalent to deleting the records for the rows.
+
+        The row will not be deleted in the system until a record manager store and commit has occurred.
+
+        If no step functions have been called before and a step is being searched for by name, queries for the
+        list of steps in the experiment and caches them.
+
+        :param step:
+            The step may be provided as either a string for the name of the step or an ElnEntryStep.
+            If given a name, throws an exception if no step of the given name exists in the experiment.
+        :param record:
+            The record to remove from the given step.
+            The record may be provided as either a DataRecord, PyRecordModel, or WrappedRecordModel.
+        """
+        self.remove_eln_row(step, [record])
+
+    def add_sample_details(self, step: Step, samples: list[RecordModel], wrapper_type: type[WrappedType]) \
+            -> list[PyRecordModel | WrappedType]:
+        """
+        Add sample details to a sample details entry while relating them to the input sample records.
+
+        :param step:
+            The step may be provided as either a string for the name of the step or an ElnEntryStep.
+            If given a name, throws an exception if no step of the given name exists in the experiment.
+        :param samples: The sample records to add the sample details to.
+        :param wrapper_type: Optionally wrap the sample details in a record model wrapper. If not provided, returns
+            an unwrapped PyRecordModel.
+        :return: The newly created sample details. The indices of the samples in the input list match the index of the
+            sample details in this list that they are related to.
+        """
+        step = self.__to_eln_step(step)
+        if step.eln_entry.entry_type != ElnEntryType.Table:
+            raise SapioException("The provided step is not a table entry.")
+        dt: str = step.get_data_type_names()[0]
+        if not ElnBaseDataType.is_eln_type(dt) or ElnBaseDataType.get_base_type(dt) != ElnBaseDataType.SAMPLE_DETAIL:
+            raise SapioException("The provided step is not an ELNSampleDetail entry.")
+        records: list[PyRecordModel] = []
+        for sample in samples:
+            if sample.data_type_name != "Sample":
+                raise SapioException(f"Received a {sample.data_type_name} record when Sample records were expected.")
+            detail: PyRecordModel = sample.add(Child.of_type_name(dt))
+            detail.set_field_values({
+                "SampleId": sample.get_field_value("SampleId"),
+                "OtherSampleId": sample.get_field_value("OtherSampleId")
+            })
+            records.append(detail)
+        if wrapper_type:
+            return self.__inst_man.wrap_list(records, wrapper_type)
+        return records
 
     def update_step(self, step: Step,
                     entry_name: str | None = None,
@@ -956,6 +1089,27 @@ class ExperimentHandler:
             step.unlock_step()
             step.eln_entry.entry_status = ExperimentEntryStatus.UnlockedChangesRequired
 
+    def disable_step(self, step: Step) -> None:
+        """
+        Set the status of the input step to Disabled. This is the state that entries are in when they are waiting for
+        entries that they are dependent upon to be submitted before they can be enabled. If you have unsubmitted an
+        entry and want its dependent entries to be locked again, then you would use this to set their status to
+        disabled.
+
+        Makes a webservice call to update the step. Checks if the step is already unlocked, and does nothing if so.
+
+        If no step functions have been called before and a step is being searched for by name, queries for the
+        list of steps in the experiment and caches them.
+
+        :param step:
+            The step to disable.
+            The step may be provided as either a string for the name of the step or an ElnEntryStep.
+            If given a name, throws an exception if no step of the given name exists in the experiment.
+        """
+        step = self.__to_eln_step(step)
+        if step.eln_entry.entry_status in self.__ENTRY_LOCKED_STATUSES:
+            self.update_step(step, entry_status=ExperimentEntryStatus.Disabled)
+
     def step_is_submitted(self, step: Step) -> bool:
         """
         Determine if the input step has already been submitted.

sapiopycommons/files/complex_data_loader.py

@@ -23,7 +23,7 @@ class CDL:
             "fileName": file_name
         }
         user: SapioUser = context if isinstance(context, SapioUser) else context.user
-        with io.StringIO(file_data) if isinstance(file_data, str) else io.BytesIO(file_data) as data_stream:
+        with io.BytesIO(file_data.encode() if isinstance(file_data, str) else file_data) as data_stream:
             response = user.post_data_stream(sub_path, params=params, data_stream=data_stream)
         user.raise_for_status(response)
         # The response content is returned as bytes for a comma separated string of record IDs.

sapiopycommons/files/file_bridge.py

@@ -54,7 +54,7 @@ class FileBridge:
             'Filepath': f"bridge://{bridge_name}/{file_path}"
         }
         user: SapioUser = context if isinstance(context, SapioUser) else context.user
-        with io.StringIO(file_data) if isinstance(file_data, str) else io.BytesIO(file_data) as data_stream:
+        with io.BytesIO(file_data.encode() if isinstance(file_data, str) else file_data) as data_stream:
             response = user.post_data_stream(sub_path, params=params, data_stream=data_stream)
         user.raise_for_status(response)
 

sapiopycommons/files/file_bridge_handler.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 from abc import abstractmethod, ABC
+from weakref import WeakValueDictionary
 
 from sapiopycommons.files.file_bridge import FileBridge
 from sapiopylib.rest.User import SapioUser
@@ -23,12 +24,32 @@ class FileBridgeHandler:
     __directories: dict[str, Directory]
     """A cache of directory file paths to Directory objects."""
 
+    __instances: WeakValueDictionary[str, FileBridgeHandler] = WeakValueDictionary()
+    __initialized: bool
+
+    def __new__(cls, context: SapioWebhookContext | SapioUser, bridge_name: str):
+        """
+        :param context: The current webhook context or a user object to send requests from.
+        """
+        user = context if isinstance(context, SapioUser) else context.user
+        key = f"{user.__hash__()}:{bridge_name}"
+        obj = cls.__instances.get(key)
+        if not obj:
+            obj = object.__new__(cls)
+            obj.__initialized = False
+            cls.__instances[key] = obj
+        return obj
+
     def __init__(self, context: SapioWebhookContext | SapioUser, bridge_name: str):
         """
         :param context: The current webhook context or a user object to send requests from.
         :param bridge_name: The name of the bridge to communicate with. This is the "connection name" in the
             file bridge configurations.
         """
+        if self.__initialized:
+            return
+        self.__initialized = True
+
         self.user = context if isinstance(context, SapioUser) else context.user
         self.__bridge = bridge_name
         self.__file_cache = {}

sapiopycommons/files/file_util.py

@@ -1,4 +1,6 @@
 import io
+import warnings
+import zipfile
 
 import pandas
 from numpy import dtype
@@ -21,7 +23,8 @@ class FileUtil:
     """
     @staticmethod
     def tokenize_csv(file_bytes: bytes, required_headers: list[str] | None = None, header_row_index: int | None = 0,
-                     seperator: str = ",", *, encoding: str | None = None) -> tuple[list[dict[str, str]], list[list[str]]]:
+                     seperator: str = ",", *, encoding: str | None = None, exception_on_empty: bool = True) \
+            -> tuple[list[dict[str, str]], list[list[str]]]:
         """
         Tokenize a CSV file. The provided file must be uniform. That is, if row 1 has 10 cells, all the rows in the file
         must have 10 cells. Otherwise, the Pandas parser throws a tokenizer exception.
@@ -37,6 +40,8 @@ class FileUtil:
         :param encoding: The encoding used to read the given file bytes. If not provided, uses utf-8. If your file
             contains a non-utf-8 character, then a UnicodeDecodeError will be thrown. If this happens, consider using
             ISO-8859-1 as the encoding.
+        :param exception_on_empty: Throw a user error exception if the provided file bytes result in an empty list in
+            the first element of the returned tuple.
         :return: The CSV parsed into a list of dicts where each dict is a row, mapping the headers to the cells for
             that row. Also returns a list of each row above the headers (the metadata), parsed into a list of each cell.
             If the header row index is 0 or None, this list will be empty.
@@ -49,11 +54,13 @@ class FileUtil:
         metadata: list[list[str]] = FileUtil.data_frame_to_lists(file_metadata)
         # Parse the data from the file body into a list of dicts.
         rows: list[dict[str, str]] = FileUtil.data_frame_to_dicts(file_body, required_headers, header_row_index)
+        if exception_on_empty and not rows:
+            raise SapioUserErrorException("The provided file contains no rows of information below the headers.")
         return rows, metadata
 
     @staticmethod
-    def tokenize_xlsx(file_bytes: bytes, required_headers: list[str] | None = None, header_row_index: int | None = 0) \
-            -> tuple[list[dict[str, str]], list[list[str]]]:
+    def tokenize_xlsx(file_bytes: bytes, required_headers: list[str] | None = None, header_row_index: int | None = 0,
+                      *, exception_on_empty: bool = True) -> tuple[list[dict[str, str]], list[list[str]]]:
         """
         Tokenize an XLSX file row by row.
 
@@ -64,6 +71,8 @@ class FileUtil:
             row is returned in the metadata list. If input is None, then no row is considered to be the header row,
             meaning that required headers are also ignored if any are provided. By default, the first row (0th index)
             is assumed to be the header row.
+        :param exception_on_empty: Throw a user error exception if the provided file bytes result in an empty list in
+            the first element of the returned tuple.
         :return: The XLSX parsed into a list of dicts where each dict is a row, mapping the headers to the cells for
             that row. Also returns a list of each row above the headers (the metadata), parsed into a list of each cell.
             If the header row index is 0 or None, this list will be empty.
@@ -75,6 +84,8 @@ class FileUtil:
         metadata: list[list[str]] = FileUtil.data_frame_to_lists(file_metadata)
         # Parse the data from the file body into a list of dicts.
         rows: list[dict[str, str]] = FileUtil.data_frame_to_dicts(file_body, required_headers, header_row_index)
+        if exception_on_empty and not rows:
+            raise SapioUserErrorException("The provided file contains no rows of information below the headers.")
         return rows, metadata
 
     @staticmethod
@@ -229,7 +240,7 @@ class FileUtil:
         :param file_data: The CSV file to be converted.
         :return: The bytes of the CSV file converted to an XLSX file.
         """
-        with (io.BytesIO(file_data) if isinstance(file_data, bytes) else io.StringIO(file_data)) as csv:
+        with (io.BytesIO(file_data.encode() if isinstance(file_data, str) else file_data)) as csv:
             # Setting header to false makes pandas read the CSV as-is.
             data_frame = pandas.read_csv(csv, sep=",", header=None)
 
@@ -273,6 +284,20 @@ class FileUtil:
             file_bytes: bytes = buffer.getvalue()
         return file_bytes
 
+    @staticmethod
+    def zip_files(files: dict[str, str | bytes]) -> bytes:
+        """
+        Create a zip file for a collection of files.
+
+        :param files: A dictionary of file name to file data as a string or bytes.
+        :return: The bytes for a zip file containing the input files.
+        """
+        zip_buffer: io.BytesIO = io.BytesIO()
+        with zipfile.ZipFile(zip_buffer, "w", zipfile.ZIP_DEFLATED) as zip_file:
+            for file_name, file_data in files.items():
+                zip_file.writestr(file_name, file_data)
+        return zip_buffer.getvalue()
+
     # Deprecated functions:
 
     # FR-46097 - Add write file request shorthand functions to FileUtil.
@@ -290,6 +315,8 @@ class FileUtil:
         :param request_context: Context that will be returned to the webhook server in the client callback result.
         :return: A SapioWebhookResult with the write request as its client callback request.
         """
+        warnings.warn("FileUtil.write_file is deprecated as of 24.5+. Use CallbackUtil.write_file instead.",
+                      DeprecationWarning)
         return SapioWebhookResult(True, client_callback_request=WriteFileRequest(file_bytes, file_name,
                                                                                  request_context))
 
@@ -306,6 +333,8 @@ class FileUtil:
         :param request_context: Context that will be returned to the webhook server in the client callback result.
         :return: A SapioWebhookResult with the write request as its client callback request.
         """
+        warnings.warn("FileUtil.write_files is deprecated as of 24.5+. Use CallbackUtil.write_file instead.",
+                      DeprecationWarning)
         return SapioWebhookResult(True, client_callback_request=MultiFileRequest(files, request_context))
 
     @staticmethod
@@ -333,6 +362,8 @@ class FileUtil:
             1 - The file name of the requested file if the user provided one.
             2 - The file bytes of the requested file if the user provided one.
         """
+        warnings.warn("FileUtil.request_file is deprecated as of 24.5+. Use CallbackUtil.request_file instead.",
+                      DeprecationWarning)
         client_callback = context.client_callback_result
         result_context: str | None = client_callback.callback_context_data if client_callback else None
         # If the user cancels, terminate the interaction.
@@ -385,6 +416,8 @@ class FileUtil:
             May also contain a result that will terminate the client interaction if the user canceled the prompt.
             1 - A dictionary that maps the file names to the file bytes for each provided file.
         """
+        warnings.warn("FileUtil.request_files is deprecated as of 24.5+. Use CallbackUtil.request_files instead.",
+                      DeprecationWarning)
         client_callback = context.client_callback_result
         result_context: str | None = client_callback.callback_context_data if client_callback else None
         # If the user cancels, terminate the interaction.
@@ -427,7 +460,7 @@ class FileUtil:
         if len(allowed_extensions) != 0:
             matches: bool = False
             for ext in allowed_extensions:
-                if file_path.endswith("." + ext):
+                if file_path.endswith("." + ext.lstrip(".")):
                     matches = True
                     break
             if matches is False:

sapiopycommons/files/file_validator.py

@@ -8,11 +8,11 @@ from sapiopylib.rest.pojo.CustomReport import RawReportTerm, RawTermOperation
 from sapiopylib.rest.pojo.datatype.FieldDefinition import VeloxIntegerFieldDefinition, VeloxStringFieldDefinition, \
     AbstractVeloxFieldDefinition
 from sapiopylib.rest.pojo.webhook.WebhookContext import SapioWebhookContext
-from sapiopylib.rest.pojo.webhook.WebhookResult import SapioWebhookResult
 
 from sapiopycommons.callbacks.callback_util import CallbackUtil
 from sapiopycommons.files.file_data_handler import FileDataHandler, FilterList
 from sapiopycommons.general.custom_report_util import CustomReportUtil
+from sapiopycommons.general.exceptions import SapioUserCancelledException
 from sapiopycommons.general.time_util import TimeUtil
 
 
@@ -80,10 +80,10 @@ class FileValidator:
 
         return failed_rows
 
-    def build_violation_report(self, context: SapioWebhookResult | SapioUser,
+    def build_violation_report(self, context: SapioWebhookContext | SapioUser,
                                rule_violations: dict[int, list[ValidationRule]]) -> None:
         """
-        Build a simple report of any rule violations in the file to display to the user as a table dialog.
+        Display a simple report of any rule violations in the file to the user as a table dialog.
 
         :param context: The current webhook context or a user object to send requests from.
         :param rule_violations: A dict of rule violations generated by a call to validate_file.
@@ -121,9 +121,24 @@ class FileValidator:
                         "Reason": violation.reason[:2000]
                     })
 
-        callback_util = CallbackUtil(context)
-        callback_util.table_dialog("Errors", "The following rule violations were encountered in the provided file.",
-                                   columns, rows)
+        callback = CallbackUtil(context)
+        callback.table_dialog("Errors", "The following rule violations were encountered in the provided file.",
+                              columns, rows)
+
+    def validate_and_report_errors(self, context: SapioWebhookContext | SapioUser) -> None:
+        """
+        Validate the file. If any rule violations are found, display a simple report of any rule violations in the file
+        to the user as a table dialog and throw a SapioUserCancelled exception after the user acknowledges the dialog
+        to end the webhook interaction.
+
+        Shorthand for calling validate_file() and then build_violation_report() if there are any errors.
+
+        :param context: The current webhook context or a user object to send requests from.
+        """
+        violations = self.validate_file()
+        if violations:
+            self.build_violation_report(context, violations)
+            raise SapioUserCancelledException()
 
 
 class ValidationRule: