sapiopycommons 2024.7.25a299__tar.gz → 2024.8.2a301__tar.gz

{sapiopycommons-2024.7.25a299 → sapiopycommons-2024.8.2a301}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2024.7.25a299
+Version: 2024.8.2a301
 Summary: Official Sapio Python API Utilities Package
 Project-URL: Homepage, https://github.com/sapiosciences
 Author-email: Jonathan Steck <jsteck@sapiosciences.com>, Yechen Qiao <yqiao@sapiosciences.com>

{sapiopycommons-2024.7.25a299 → sapiopycommons-2024.8.2a301}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "sapiopycommons"
-version='2024.07.25a299'
+version='2024.08.02a301'
 authors = [
     { name="Jonathan Steck", email="jsteck@sapiosciences.com" },
     { name="Yechen Qiao", email="yqiao@sapiosciences.com" },

{sapiopycommons-2024.7.25a299 → sapiopycommons-2024.8.2a301}/src/sapiopycommons/callbacks/callback_util.py

@@ -15,7 +15,7 @@ from sapiopylib.rest.pojo.datatype.FieldDefinition import AbstractVeloxFieldDefi
 from sapiopylib.rest.pojo.webhook.ClientCallbackRequest import OptionDialogRequest, ListDialogRequest, \
     FormEntryDialogRequest, InputDialogCriteria, TableEntryDialogRequest, ESigningRequestPojo, \
     DataRecordDialogRequest, InputSelectionRequest, FilePromptRequest, MultiFilePromptRequest, \
-    TempTableSelectionRequest
+    TempTableSelectionRequest, DisplayPopupRequest, PopupType
 from sapiopylib.rest.pojo.webhook.ClientCallbackResult import ESigningResponsePojo
 from sapiopylib.rest.pojo.webhook.WebhookContext import SapioWebhookContext
 from sapiopylib.rest.pojo.webhook.WebhookEnums import FormAccessLevel, ScanToSelectCriteria, SearchType
@@ -52,11 +52,23 @@ class CallbackUtil:
         Set the width that dialogs will appear as for those dialogs that support specifying their width.
 
         :param width_pixels: The number of pixels wide that dialogs will appear as.
-        :param width_percent: The percentage of the client's screen width that dialogs will appear as.
+        :param width_percent: The percentage (as a value between 0 and 1) of the client's screen width that dialogs
+            will appear as.
         """
         self.width_pixels = width_pixels
         self.width_percent = width_percent
-    
+
+    def toaster_popup(self, message: str, title: str = "", popup_type: PopupType = PopupType.Info) -> None:
+        """
+        Display a toaster popup in the bottom right corner of the user's screen.
+
+        :param message: The message to display in the toaster.
+        :param title: The title to display at the top of the toaster.
+        :param popup_type: The popup type to use for the toaster. This controls the color that the toaster appears with.
+            Info is blue, Success is green, Warning is yellow, and Error is red
+        """
+        self.callback.display_popup(DisplayPopupRequest(title, message, popup_type))
+
     def option_dialog(self, title: str, msg: str, options: list[str], default_option: int = 0,
                       user_can_cancel: bool = False) -> str:
         """
@@ -71,7 +83,8 @@ class CallbackUtil:
             SapioUserCancelledException is thrown.
         :return: The name of the button that the user selected.
         """
-        request = OptionDialogRequest(title, msg, options, default_option, user_can_cancel)
+        request = OptionDialogRequest(title, msg, options, default_option, user_can_cancel,
+                                      width_in_pixels=self.width_pixels, width_percentage=self.width_percent)
         response: int | None = self.callback.show_option_dialog(request)
         if response is None:
             raise SapioUserCancelledException()
@@ -111,16 +124,20 @@ class CallbackUtil:
         """
         return self.option_dialog(title, msg, ["Yes", "No"], 0 if default_yes else 1, False) == "Yes"
 
-    def list_dialog(self, title: str, options: list[str], multi_select: bool = False) -> list[str]:
+    def list_dialog(self, title: str, options: list[str], multi_select: bool = False,
+                    preselected_values: list[str] | None = None) -> list[str]:
         """
         Create a list dialog with the given options for the user to choose from.
 
         :param title: The title of the dialog.
         :param options: The list options that the user has to choose from.
         :param multi_select: Whether the user is able to select multiple options from the list.
+        :param preselected_values: A list of values that will already be selected when the list dialog is created. The
+            user can unselect these values if they want to.
         :return: The list of options that the user selected.
         """
-        request = ListDialogRequest(title, multi_select, options)
+        request = ListDialogRequest(title, multi_select, options, preselected_values,
+                                    width_in_pixels=self.width_pixels, width_percentage=self.width_percent)
         response: list[str] | None = self.callback.show_list_dialog(request)
         if response is None:
             raise SapioUserCancelledException()
@@ -163,8 +180,6 @@ class CallbackUtil:
         builder = FormBuilder(data_type, display_name, plural_display_name)
         for field_def in fields:
             field_name = field_def.data_field_name
-            if values and hasattr(field_def, "default_value"):
-                field_def.default_value = values.get(field_name)
             column: int = 0
             span: int = 4
             if column_positions and field_name in column_positions:
@@ -173,7 +188,8 @@ class CallbackUtil:
                 span = position[1]
             builder.add_field(field_def, column, span)
 
-        request = FormEntryDialogRequest(title, msg, builder.get_temporary_data_type())
+        request = FormEntryDialogRequest(title, msg, builder.get_temporary_data_type(), values,
+                                         width_in_pixels=self.width_pixels, width_percentage=self.width_percent)
         response: FieldMap | None = self.callback.show_form_entry_dialog(request)
         if response is None:
             raise SapioUserCancelledException()
@@ -215,13 +231,13 @@ class CallbackUtil:
         modifier = FieldModifier(visible=True, editable=editable)
 
         # Build the form using only those fields that are desired.
+        values: dict[str, Any] = {}
         builder = FormBuilder(data_type, type_def.display_name, type_def.plural_display_name)
         for field_name in fields:
             field_def = field_defs.get(field_name)
             if field_def is None:
                 raise SapioException(f"No field of name \"{field_name}\" in field definitions of type \"{data_type}\"")
-            if hasattr(field_def, "default_value"):
-                field_def.default_value = record.get_field_value(field_name)
+            values[field_name] = record.get_field_value(field_name)
             column: int = 0
             span: int = 4
             if column_positions and field_name in column_positions:
@@ -230,7 +246,8 @@ class CallbackUtil:
                 span = position[1]
             builder.add_field(modifier.modify_field(field_def), column, span)
 
-        request = FormEntryDialogRequest(title, msg, builder.get_temporary_data_type())
+        request = FormEntryDialogRequest(title, msg, builder.get_temporary_data_type(), values,
+                                         width_in_pixels=self.width_pixels, width_percentage=self.width_percent)
         response: FieldMap | None = self.callback.show_form_entry_dialog(request)
         if response is None:
             raise SapioUserCancelledException()
@@ -245,7 +262,8 @@ class CallbackUtil:
         :param field: The definition for a field that the user must provide input to.
         :return: The response value from the user for the given field.
         """
-        request = InputDialogCriteria(title, msg, field, self.width_pixels, self.width_percent)
+        request = InputDialogCriteria(title, msg, field,
+                                      width_in_pixels=self.width_pixels, width_percentage=self.width_percent)
         response: Any | None = self.callback.show_input_dialog(request)
         if response is None:
             raise SapioUserCancelledException()
@@ -322,6 +340,8 @@ class CallbackUtil:
                      msg: str,
                      fields: list[AbstractVeloxFieldDefinition],
                      values: list[FieldMap],
+                     group_by: str | None = None,
+                     image_data: list[bytes] | None = None,
                      *,
                      data_type: str = "Default",
                      display_name: str | None = None,
@@ -335,6 +355,10 @@ class CallbackUtil:
         :param fields: The definitions of the fields to display as table columns. Fields will be displayed in the order
             they are provided in this list.
         :param values: The values to set for each row of the table.
+        :param group_by: If provided, the created table dialog will be grouped by the field with this name by default.
+            The user may remove this grouping if they want to.
+        :param image_data: The bytes to the images that should be displayed in the rows of the table. Each element in
+            the image data list corresponds to the element at the same index in the values list.
         :param data_type: The data type name for the temporary data type that will be created for this table.
         :param display_name: The display name for the temporary data type. If not provided, defaults to the data type
             name.
@@ -356,7 +380,9 @@ class CallbackUtil:
         for field in fields:
             builder.add_field(modifier.modify_field(field))
 
-        request = TableEntryDialogRequest(title, msg, builder.get_temporary_data_type(), values)
+        request = TableEntryDialogRequest(title, msg, builder.get_temporary_data_type(), values,
+                                          record_image_data_list=image_data, group_by_field=group_by,
+                                          width_in_pixels=self.width_pixels, width_percentage=self.width_percent)
         response: list[FieldMap] | None = self.callback.show_table_entry_dialog(request)
         if response is None:
             raise SapioUserCancelledException()
@@ -367,7 +393,9 @@ class CallbackUtil:
                             msg: str,
                             fields: list[str],
                             records: list[SapioRecord],
-                            editable: bool | None = True) -> list[FieldMap]:
+                            editable: bool | None = True,
+                            group_by: str | None = None,
+                            image_data: list[bytes] | None = None) -> list[FieldMap]:
         """
         Create a table dialog where the user may input data into the fields of the table. The table is constructed from
         a given list of records of a singular type. Provided field names must match fields on the definition of the data
@@ -384,6 +412,10 @@ class CallbackUtil:
             they are provided in this list.
         :param editable: If true, all fields are displayed as editable. If false, all fields are displayed as
             uneditable. If none, only those fields that are defined as editable by the data designer will be editable.
+        :param group_by: If provided, the created table dialog will be grouped by the field with this name by default.
+            The user may remove this grouping if they want to.
+        :param image_data: The bytes to the images that should be displayed in the rows of the table. Each element in
+            the image data list corresponds to the element at the same index in the records list.
         :return: A list of dictionaries mapping the data field names of the given field definitions to the response
             value from the user for that field for each row.
         """
@@ -410,7 +442,9 @@ class CallbackUtil:
                 raise SapioException(f"No field of name \"{field_name}\" in field definitions of type \"{data_type}\"")
             builder.add_field(modifier.modify_field(field_def))
 
-        request = TableEntryDialogRequest(title, msg, builder.get_temporary_data_type(), field_map_list)
+        request = TableEntryDialogRequest(title, msg, builder.get_temporary_data_type(), field_map_list,
+                                          record_image_data_list=image_data, group_by_field=group_by,
+                                          width_in_pixels=self.width_pixels, width_percentage=self.width_percent)
         response: list[FieldMap] | None = self.callback.show_table_entry_dialog(request)
         if response is None:
             raise SapioUserCancelledException()
@@ -567,7 +601,8 @@ class CallbackUtil:
         for field in final_fields:
             builder.add_field(field)
 
-        request = TableEntryDialogRequest(title, msg, builder.get_temporary_data_type(), values)
+        request = TableEntryDialogRequest(title, msg, builder.get_temporary_data_type(), values,
+                                          width_in_pixels=self.width_pixels, width_percentage=self.width_percent)
         response: list[FieldMap] | None = self.callback.show_table_entry_dialog(request)
         if response is None:
             raise SapioUserCancelledException()
@@ -616,7 +651,8 @@ class CallbackUtil:
                 raise SapioException(f"The data type \"{data_type}\" does not have a layout by the name "
                                      f"\"{layout_name}\" in the system.")
 
-        request = DataRecordDialogRequest(title, record, layout, minimized, access_level, plugin_path_list)
+        request = DataRecordDialogRequest(title, record, layout, minimized, access_level, plugin_path_list,
+                                          width_in_pixels=self.width_pixels, width_percentage=self.width_percent)
         response: bool = self.callback.data_record_form_view_dialog(request)
         if not response:
             raise SapioUserCancelledException()
@@ -663,7 +699,7 @@ class CallbackUtil:
         return response
     
     def record_selection_dialog(self, msg: str, fields: list[str], records: list[SapioRecord],
-                                multi_select: bool = True) -> list[FieldMap]:
+                                multi_select: bool = True) -> list[SapioRecord]:
         """
         Create a record selection dialog for a list of records for the user to choose from. Provided field names must
         match fields on the definition of the data type of the given records.
@@ -676,7 +712,7 @@ class CallbackUtil:
             they are provided in this list.
         :param records: The records to display as rows in the table.
         :param multi_select: Whether the user is able to select multiple records from the list.
-        :return: A list of field maps corresponding to the chosen input records.
+        :return: A list of the selected records.
         """
         data_types: set[str] = {x.data_type_name for x in records}
         if len(data_types) > 1:
@@ -807,7 +843,8 @@ class CallbackUtil:
             for field in additional_fields:
                 builder.add_field(field)
             temp_dt = builder.get_temporary_data_type()
-        request = ESigningRequestPojo(title, msg, show_comment, temp_dt)
+        request = ESigningRequestPojo(title, msg, show_comment, temp_dt,
+                                      width_in_pixels=self.width_pixels, width_percentage=self.width_percent)
         response: ESigningResponsePojo | None = self.callback.show_esign_dialog(request)
         if response is None:
             raise SapioUserCancelledException()
@@ -906,7 +943,7 @@ class CallbackUtil:
         :param file_name: The name of the file.
         :param file_data: The data of the file, provided as either a string or as a bytes array.
         """
-        data = io.StringIO(file_data) if isinstance(file_data, str) else io.BytesIO(file_data)
+        data = io.BytesIO(file_data.encode() if isinstance(file_data, str) else file_data)
         self.callback.send_file(file_name, False, data)
 
 

{sapiopycommons-2024.7.25a299 → sapiopycommons-2024.8.2a301}/src/sapiopycommons/datatype/attachment_util.py

@@ -1,5 +1,6 @@
 import io
 
+from sapiopylib.rest.DataMgmtService import DataMgmtServer
 from sapiopylib.rest.User import SapioUser
 from sapiopylib.rest.pojo.webhook.WebhookContext import SapioWebhookContext
 from sapiopylib.rest.utils.recordmodel.RecordModelWrapper import WrappedType
@@ -12,31 +13,35 @@ from sapiopycommons.recordmodel.record_handler import RecordHandler
 # FR-46064 - Initial port of PyWebhookUtils to sapiopycommons.
 class AttachmentUtil:
     @staticmethod
-    def get_attachment_bytes(context: SapioWebhookContext, attachment: SapioRecord) -> bytes:
+    def get_attachment_bytes(context: SapioWebhookContext | SapioUser, attachment: SapioRecord) -> bytes:
         """
         Get the data bytes for the given attachment record. Makes a webservice call to retrieve the data.
 
-        :param context: The current webhook context.
+        :param context: The current webhook context or a user object to send requests from.
         :param attachment: The attachment record.
         :return: The bytes for the attachment's file data.
         """
         attachment = AliasUtil.to_data_record(attachment)
+        if isinstance(context, SapioWebhookContext):
+            dr_man = context.data_record_manager
+        else:
+            dr_man = DataMgmtServer.get_data_record_manager(context)
         with io.BytesIO() as data_sink:
             def consume_data(chunk: bytes):
                 data_sink.write(chunk)
-            context.data_record_manager.get_attachment_data(attachment, consume_data)
+            dr_man.get_attachment_data(attachment, consume_data)
             data_sink.flush()
             data_sink.seek(0)
             file_bytes = data_sink.read()
         return file_bytes
 
     @staticmethod
-    def set_attachment_bytes(context: SapioWebhookContext, attachment: SapioRecord,
+    def set_attachment_bytes(context: SapioWebhookContext | SapioUser, attachment: SapioRecord,
                              file_name: str, file_bytes: bytes) -> None:
         """
         Set the attachment data for a given attachment record. Makes a webservice call to set the data.
 
-        :param context: The current webhook context.
+        :param context: The current webhook context or a user object to send requests from.
         :param attachment: The attachment record. Must be an existing data record that is an attachment type.
         :param file_name: The name of the attachment.
         :param file_bytes: The bytes of the attachment data.
@@ -45,8 +50,12 @@ class AttachmentUtil:
             raise SapioException("Provided record cannot have its attachment data set, as it does not exist in the "
                                  "system yet.")
         attachment = AliasUtil.to_data_record(attachment)
+        if isinstance(context, SapioWebhookContext):
+            dr_man = context.data_record_manager
+        else:
+            dr_man = DataMgmtServer.get_data_record_manager(context)
         with io.BytesIO(file_bytes) as stream:
-            context.data_record_manager.set_attachment_data(attachment, file_name, stream)
+            dr_man.set_attachment_data(attachment, file_name, stream)
 
     @staticmethod
     def create_attachment(context: SapioWebhookContext | SapioUser, file_name: str, file_bytes: bytes,

{sapiopycommons-2024.7.25a299 → sapiopycommons-2024.8.2a301}/src/sapiopycommons/eln/experiment_handler.py

@@ -1,7 +1,9 @@
 import time
 from collections.abc import Mapping, Iterable
 
+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
@@ -17,7 +19,7 @@ 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 sapiopycommons.general.aliases import AliasUtil, SapioRecord
+from sapiopycommons.general.aliases import AliasUtil, SapioRecord, ExperimentIdentifier
 from sapiopycommons.general.exceptions import SapioException
 
 Step = str | ElnEntryStep
@@ -27,7 +29,8 @@ 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.
@@ -77,31 +80,57 @@ 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):
+    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.
+        """
+        if isinstance(context, SapioWebhookContext):
+            self.user = context.user
+            self.context = context
+        else:
+            self.user = context
+            self.context = None
         # 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:
+        # CR-37038 - Allow other experiment object types to be provided. Convert them all down to ElnExperiment.
+        if experiment is not None:
+            # 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 = context.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 = context.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 (context is None or 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
+        if context and context.eln_experiment == experiment:
+            experiment: ElnExperiment | None = None
 
         # 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.__protocol = ElnExperimentProtocol(experiment, self.user) if experiment else context.active_protocol
         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 = {}
@@ -263,7 +292,7 @@ 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 +609,6 @@ 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.
@@ -617,7 +644,7 @@ class ExperimentHandler:
         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)
 
@@ -641,7 +668,7 @@ 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.")
@@ -658,17 +685,6 @@ 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 update_step(self, step: Step,
                     entry_name: str | None = None,
                     related_entry_set: Iterable[int] | None = None,
@@ -956,6 +972,27 @@ 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-2024.7.25a299 → sapiopycommons-2024.8.2a301}/src/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-2024.7.25a299 → sapiopycommons-2024.8.2a301}/src/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-2024.7.25a299 → sapiopycommons-2024.8.2a301}/src/sapiopycommons/files/file_util.py

@@ -21,7 +21,8 @@ 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 +38,8 @@ 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 +52,13 @@ 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 +69,8 @@ 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 +82,8 @@ 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 +238,7 @@ 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)
 

{sapiopycommons-2024.7.25a299 → sapiopycommons-2024.8.2a301}/src/sapiopycommons/files/file_validator.py

@@ -8,7 +8,6 @@ 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
@@ -80,7 +79,7 @@ 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.

{sapiopycommons-2024.7.25a299 → sapiopycommons-2024.8.2a301}/src/sapiopycommons/general/aliases.py

@@ -50,7 +50,27 @@ class AliasUtil:
 
         :return: A list of record IDs for the input records.
         """
-        return [(x if isinstance(x, int) else x.record_id) for x in records]
+        return [(AliasUtil.to_record_id(x)) for x in records]
+
+    @staticmethod
+    def to_record_id(record: RecordIdentifier):
+        """
+        Convert a single variable that could be either an integer, DataRecord, PyRecordModel,
+        or WrappedRecordModel to just an integer (taking the record ID from the record).
+
+        :return: A record ID for the input record.
+        """
+        return record if isinstance(record, int) else record.record_id
+
+    @staticmethod
+    def to_data_type_name(record: SapioRecord) -> str:
+        """
+        Convert a single variable that could be either a Data Record, PyRecordModel, or WrappedRecordModel to the
+        data type name for that record.
+
+        :return: The data type name for the input record.
+        """
+        return record.data_type_name
 
     @staticmethod
     def to_field_map_lists(records: Iterable[SapioRecord]) -> list[FieldMap]: