sapiopycommons 2024.7.24a298__py3-none-any.whl → 2024.7.29a300__py3-none-any.whl

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/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/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/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_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/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/general/aliases.py

@@ -50,7 +50,17 @@ 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_field_map_lists(records: Iterable[SapioRecord]) -> list[FieldMap]:

sapiopycommons/general/audit_log.py

@@ -0,0 +1,200 @@
+from enum import Enum
+from typing import Any
+
+from sapiopylib.rest.DataRecordManagerService import DataRecordManager
+from sapiopylib.rest.User import SapioUser
+from sapiopylib.rest.pojo.CustomReport import ReportColumn, RawReportTerm, CustomReportCriteria, RawTermOperation, \
+    CompositeReportTerm, CompositeTermOperation
+from sapiopylib.rest.pojo.datatype.FieldDefinition import FieldType
+from sapiopylib.rest.pojo.webhook.WebhookContext import SapioWebhookContext
+
+from sapiopycommons.src.sapiopycommons.general.aliases import RecordIdentifier, AliasUtil
+from sapiopycommons.src.sapiopycommons.general.custom_report_util import CustomReportUtil
+
+EVENTTYPE_COLUMN = "EVENTTYPE"
+TIMESTAMP_COLUMN = "TIMESTAMP"
+DATATYPENAME_COLUMN = "DATATYPENAME"
+RECORDID_COLUMN = "RECORDID"
+DESCRIPTION_COLUMN = "DESCRIPTION"
+USERNAME_COLUMN = "USERNAME"
+USERCOMMENT_COLUMN = "USERCOMMENT"
+RECORDNAME_COLUMN = "RECORDNAME"
+DATAFIELDNAME_COLUMN = "DATAFIELDNAME"
+ORIGINALVALUE_COLUMN = "ORIGINALVALUE"
+NEWVALUE_COLUMN = "NEWVALUE"
+
+
+class EventType(Enum):
+    """An enum to represent the possible event type values with the event type column in the audit log table."""
+    ADD = 0
+    DELETE = 1
+    MODIFY = 2
+    INFO = 3
+    ERROR = 4
+    WARNING = 5
+    IMPORT = 6
+    GENERATE = 7
+    EXPORT = 8
+    ADDREF = 9
+    REMOVEREF = 10
+    ESIGNATURE = 11
+    ROLEASSIGNMENT = 12
+
+
+class AuditLogEntry:
+
+    __event_type: EventType
+    __date: int
+    __data_type_name: str
+    __record_id: int
+    __description: str
+    __users_login_name: str
+    __comment: str
+    __data_record_name: str
+    __data_field_name: str
+    __original_value: str
+    __new_value: str
+
+    @property
+    def event_type(self) -> EventType:
+        return self.__event_type
+
+    @property
+    def date(self) -> int:
+        return self.__date
+
+    @property
+    def data_type_name(self) -> str:
+        return self.__data_type_name
+
+    @property
+    def record_id(self) -> int:
+        return self.__record_id
+
+    @property
+    def description(self) -> str:
+        return self.__description
+
+    @property
+    def users_login_name(self) -> str:
+        return self.__users_login_name
+
+    @property
+    def comment(self) -> str:
+        return self.__comment
+
+    @property
+    def data_record_name(self) -> str:
+        return self.__data_record_name
+
+    @property
+    def data_field_name(self) -> str:
+        return self.__data_field_name
+
+    @property
+    def original_value(self) -> str:
+        return self.__original_value
+
+    @property
+    def new_value(self) -> str:
+        return self.__new_value
+
+    def __init__(self, report_row: dict[str, Any]):
+        self.__event_type = EventType((report_row[EVENTTYPE_COLUMN]))
+        self.__date = report_row[TIMESTAMP_COLUMN]
+        self.__data_type_name = report_row[DATATYPENAME_COLUMN]
+        self.__record_id = report_row[RECORDID_COLUMN]
+        self.__description = report_row[DESCRIPTION_COLUMN]
+        self.__users_login_name = report_row[USERNAME_COLUMN]
+        self.__comment = report_row[USERCOMMENT_COLUMN]
+        self.__data_record_name = report_row[RECORDNAME_COLUMN]
+        self.__data_field_name = report_row[DATAFIELDNAME_COLUMN]
+        self.__original_value = report_row[ORIGINALVALUE_COLUMN]
+        self.__new_value = report_row[NEWVALUE_COLUMN]
+
+
+class AuditLog:
+    AUDIT_LOG_PSEUDO_DATATYPE: str = "AUDITLOG"
+    EVENT_TYPE: ReportColumn = ReportColumn(AUDIT_LOG_PSEUDO_DATATYPE, EVENTTYPE_COLUMN, FieldType.ENUM)
+    DATE: ReportColumn = ReportColumn(AUDIT_LOG_PSEUDO_DATATYPE, TIMESTAMP_COLUMN, FieldType.DATE)
+    DATA_TYPE_NAME: ReportColumn = ReportColumn(AUDIT_LOG_PSEUDO_DATATYPE, DATATYPENAME_COLUMN, FieldType.STRING)
+    RECORD_ID: ReportColumn = ReportColumn(AUDIT_LOG_PSEUDO_DATATYPE, RECORDID_COLUMN, FieldType.LONG)
+    DESCRIPTION: ReportColumn = ReportColumn(AUDIT_LOG_PSEUDO_DATATYPE, DESCRIPTION_COLUMN, FieldType.STRING)
+    USERS_LOGIN_NAME: ReportColumn = ReportColumn(AUDIT_LOG_PSEUDO_DATATYPE, USERNAME_COLUMN, FieldType.STRING)
+    COMMENT: ReportColumn = ReportColumn(AUDIT_LOG_PSEUDO_DATATYPE, USERCOMMENT_COLUMN, FieldType.STRING)
+    DATA_RECORD_NAME: ReportColumn = ReportColumn(AUDIT_LOG_PSEUDO_DATATYPE, RECORDNAME_COLUMN, FieldType.STRING)
+    DATA_FIELD_NAME: ReportColumn = ReportColumn(AUDIT_LOG_PSEUDO_DATATYPE, DATAFIELDNAME_COLUMN, FieldType.STRING)
+    ORIGINAL_VALUE: ReportColumn = ReportColumn(AUDIT_LOG_PSEUDO_DATATYPE, ORIGINALVALUE_COLUMN, FieldType.STRING)
+    NEW_VALUE: ReportColumn = ReportColumn(AUDIT_LOG_PSEUDO_DATATYPE, NEWVALUE_COLUMN, FieldType.STRING)
+
+    AUDIT_LOG_COLUMNS = [EVENT_TYPE, DATE, DATA_TYPE_NAME, RECORD_ID, DESCRIPTION, USERS_LOGIN_NAME, COMMENT,
+                         DATA_RECORD_NAME, DATA_FIELD_NAME, ORIGINAL_VALUE, NEW_VALUE]
+    user: SapioUser
+
+    def __init__(self, context: SapioWebhookContext | SapioUser):
+        self.user = context if isinstance(context, SapioUser) else context.user
+
+    @staticmethod
+    def create_data_record_audit_log_report(records: list[RecordIdentifier], fields: list[str] | None = None) -> CustomReportCriteria:
+        """
+        This method creates a CustomReportCriteria object for running an audit log query based on data records.
+
+        Creates a CustomReportCriteria object with a query term based on the record ids/records passed into the method.
+        Optionally, the fields parameter can be populated to limit the search to particular fields. If the fields
+        parameter is not populated, the search will include results for all field changes.
+
+        :param records: The DataRecords, RecordModels, or record ids to base the search on.
+        :param fields: The data field names to include changes for.
+        :return: The constructed CustomReportCriteria object, which can be used to run a report on the audit log.
+        """
+        # We need to compile the record ids from these record identifiers as "str" variables, so they can be
+        # concatenated.
+        record_ids = AliasUtil.to_record_ids(records)
+        id_strs = [str(id_int) for id_int in record_ids]
+
+        # Next we'll build the raw report term querying for any entry with a matching record id value to the record ID's
+        # passed in
+        root_term = RawReportTerm(AuditLog.AUDIT_LOG_PSEUDO_DATATYPE, RECORDID_COLUMN,
+                                  RawTermOperation.EQUAL_TO_OPERATOR, "{" + ",".join(id_strs) + "}")
+
+        # If the user passed in any specific fields, then we should limit the query to those fields.
+        if fields:
+            field_term = RawReportTerm(AuditLog.AUDIT_LOG_PSEUDO_DATATYPE, DATAFIELDNAME_COLUMN,
+                                       RawTermOperation.EQUAL_TO_OPERATOR, "{" + ",".join(fields) + "}")
+            root_term = CompositeReportTerm(root_term, CompositeTermOperation.AND_OPERATOR, field_term)
+
+        return CustomReportCriteria(AuditLog.AUDIT_LOG_COLUMNS, root_term)
+
+    def run_data_record_audit_log_report(self, records: list[RecordIdentifier], fields: list[str] | None = None) -> dict[RecordIdentifier, list[AuditLogEntry]]:
+        """
+        This method runs a custom report for changes made to the given data records using the audit log.
+        See "create_data_record_audit_log_report" for more details about the data record audit log report.
+
+        :param records: The DataRecords, RecordModels, or record ids to base the search on.
+        :param fields: The data field names to include changes for.
+        :return: A dictionary where the keys are the record identifiers passed in, and the values are a list of
+            AuditLogEntry objects which match the record id value of those records.
+        """
+        # First, we must build our report criteria for running the Custom Report.
+        criteria = AuditLog.create_data_record_audit_log_report(records, fields)
+
+        # Then we must run the custom report using that criteria.
+        raw_report_data: list[dict[str, Any]] = CustomReportUtil.run_custom_report(self.user, criteria)
+
+        # This section will prepare a map matching the original RecordIdentifier by record id.
+        # This is because the audit log entries will have record ids, but we want the keys in our result map
+        # to match the record identifiers that the user passed in, for convenience.
+        record_identifier_mapping: dict[int, RecordIdentifier] = dict()
+        for record in records:
+            record_id = AliasUtil.to_record_id(record)
+            record_identifier_mapping[record_id] = record
+
+        # Finally, we compile our audit data into a map where the keys are the record identifiers passed in,
+        # and the value is a list of applicable audit log entries.
+        final_audit_data: dict[RecordIdentifier, list[AuditLogEntry]] = dict()
+        for audit_entry_data in raw_report_data:
+            audit_entry: AuditLogEntry = AuditLogEntry(audit_entry_data)
+            identifier: RecordIdentifier = record_identifier_mapping.get(audit_entry.record_id)
+            final_audit_data.setdefault(identifier, []).append(audit_entry)
+
+        return final_audit_data

sapiopycommons/recordmodel/record_handler.py

@@ -7,6 +7,7 @@ from sapiopylib.rest.pojo.CustomReport import CustomReportCriteria, RawReportTer
 from sapiopylib.rest.pojo.DataRecord import DataRecord
 from sapiopylib.rest.pojo.DataRecordPaging import DataRecordPojoPageCriteria
 from sapiopylib.rest.pojo.datatype.FieldDefinition import FieldType
+from sapiopylib.rest.pojo.eln.SapioELNEnums import ElnBaseDataType
 from sapiopylib.rest.pojo.webhook.WebhookContext import SapioWebhookContext
 from sapiopylib.rest.utils.autopaging import QueryDataRecordsAutoPager, QueryDataRecordByIdListAutoPager, \
     QueryAllRecordsOfTypeAutoPager
@@ -16,6 +17,7 @@ from sapiopylib.rest.utils.recordmodel.RecordModelManager import RecordModelMana
 from sapiopylib.rest.utils.recordmodel.RecordModelWrapper import WrappedType, WrappedRecordModel
 from sapiopylib.rest.utils.recordmodel.RelationshipPath import RelationshipPath, RelationshipNode, \
     RelationshipNodeType
+from sapiopylib.rest.utils.recordmodel.ancestry import RecordModelAncestorManager
 
 from sapiopycommons.general.aliases import RecordModel, SapioRecord, FieldMap
 from sapiopycommons.general.custom_report_util import CustomReportUtil
@@ -32,6 +34,7 @@ class RecordHandler:
     rec_man: RecordModelManager
     inst_man: RecordModelInstanceManager
     rel_man: RecordModelRelationshipManager
+    an_man: RecordModelAncestorManager
 
     def __init__(self, context: SapioWebhookContext | SapioUser):
         """
@@ -42,6 +45,7 @@ class RecordHandler:
         self.rec_man = RecordModelManager(self.user)
         self.inst_man = self.rec_man.instance_manager
         self.rel_man = self.rec_man.relationship_manager
+        self.an_man = RecordModelAncestorManager(self.rec_man)
 
     def wrap_model(self, record: DataRecord, wrapper_type: type[WrappedType]) -> WrappedType:
         """
@@ -51,6 +55,7 @@ class RecordHandler:
         :param wrapper_type: The record model wrapper to use.
         :return: The record model for the input.
         """
+        self.__verify_data_type([record], wrapper_type)
         return self.inst_man.add_existing_record_of_type(record, wrapper_type)
 
     def wrap_models(self, records: Iterable[DataRecord], wrapper_type: type[WrappedType]) -> list[WrappedType]:
@@ -61,6 +66,7 @@ class RecordHandler:
         :param wrapper_type: The record model wrapper to use.
         :return: The record models for the input.
         """
+        self.__verify_data_type(records, wrapper_type)
         return self.inst_man.add_existing_records_of_type(list(records), wrapper_type)
 
     def query_models(self, wrapper_type: type[WrappedType], field: str, value_list: Iterable[Any],
@@ -831,8 +837,6 @@ class RecordHandler:
         path, if any. The hierarchy must be linear (1:1 relationship between data types at every step) and the
         relationship path must already be loaded.
 
-        Currently, the relationship path may only contain parent/child nodes.
-
         :param models: A list of record models.
         :param path: The relationship path to follow.
         :param wrapper_type: The record model wrapper to use.
@@ -843,15 +847,44 @@ class RecordHandler:
         # PR-46832: Update path traversal to account for changes to RelationshipPath in Sapiopylib.
         path: list[RelationshipNode] = path.path
         for model in models:
-            current: PyRecordModel = model if isinstance(model, PyRecordModel) else model.backing_model
+            current: PyRecordModel | None = model if isinstance(model, PyRecordModel) else model.backing_model
             for node in path:
-                direction = node.direction
+                data_type: str = node.data_type_name
+                direction: RelationshipNodeType = node.direction
                 if current is None:
                     break
                 if direction == RelationshipNodeType.CHILD:
-                    current = current.get_child_of_type(node.data_type_name)
+                    current = current.get_child_of_type(data_type)
                 elif direction == RelationshipNodeType.PARENT:
-                    current = current.get_parent_of_type(node.data_type_name)
+                    current = current.get_parent_of_type(data_type)
+                elif direction == RelationshipNodeType.ANCESTOR:
+                    ancestors: list[PyRecordModel] = list(self.an_man.get_ancestors_of_type(current, data_type))
+                    if not ancestors:
+                        current = None
+                    elif len(ancestors) > 1:
+                        raise SapioException(f"Hierarchy contains multiple ancestors of type {data_type}.")
+                    else:
+                        current = ancestors[0]
+                elif direction == RelationshipNodeType.DESCENDANT:
+                    descendants: list[PyRecordModel] = list(self.an_man.get_descendant_of_type(current, data_type))
+                    if not descendants:
+                        current = None
+                    elif len(descendants) > 1:
+                        raise SapioException(f"Hierarchy contains multiple descendants of type {data_type}.")
+                    else:
+                        current = descendants[0]
+                elif direction == RelationshipNodeType.FORWARD_SIDE_LINK:
+                    current = current.get_forward_side_link(node.data_field_name)
+                elif direction == RelationshipNodeType.REVERSE_SIDE_LINK:
+                    field_name: str = node.data_field_name
+                    reverse_links: list[PyRecordModel] = current.get_reverse_side_link(field_name, data_type)
+                    if not reverse_links:
+                        current = None
+                    elif len(reverse_links) > 1:
+                        raise SapioException(f"Hierarchy contains multiple reverse links of type {data_type} on field "
+                                             f"{field_name}.")
+                    else:
+                        current = reverse_links[0]
                 else:
                     raise SapioException("Unsupported path direction.")
             ret_dict.update({model: self.inst_man.wrap(current, wrapper_type) if current else None})
@@ -864,8 +897,6 @@ class RecordHandler:
         path, if any. The hierarchy may be non-linear (1:Many relationships between data types are allowed) and the
         relationship path must already be loaded.
 
-        Currently, the relationship path may only contain parent/child nodes.
-
         :param models: A list of record models.
         :param path: The relationship path to follow.
         :param wrapper_type: The record model wrapper to use.
@@ -880,14 +911,23 @@ class RecordHandler:
             next_search: set[PyRecordModel] = set()
             # Exhaust the records at each step in the path, then use those records for the next step.
             for node in path:
-                direction = node.direction
+                data_type: str = node.data_type_name
+                direction: RelationshipNodeType = node.direction
                 if len(current_search) == 0:
                     break
                 for search in current_search:
                     if direction == RelationshipNodeType.CHILD:
-                        next_search.update(search.get_children_of_type(node.data_type_name))
+                        next_search.update(search.get_children_of_type(data_type))
                     elif direction == RelationshipNodeType.PARENT:
-                        next_search.update(search.get_parents_of_type(node.data_type_name))
+                        next_search.update(search.get_parents_of_type(data_type))
+                    elif direction == RelationshipNodeType.ANCESTOR:
+                        next_search.update(self.an_man.get_ancestors_of_type(search, data_type))
+                    elif direction == RelationshipNodeType.DESCENDANT:
+                        next_search.update(self.an_man.get_descendant_of_type(search, data_type))
+                    elif direction == RelationshipNodeType.FORWARD_SIDE_LINK:
+                        next_search.add(search.get_forward_side_link(node.data_field_name))
+                    elif direction == RelationshipNodeType.REVERSE_SIDE_LINK:
+                        next_search.update(search.get_reverse_side_link(node.data_field_name, data_type))
                     else:
                         raise SapioException("Unsupported path direction.")
                 current_search = next_search
@@ -908,8 +948,6 @@ class RecordHandler:
         relationships (e.g. a sample which is aliquoted to a number of samples, then those aliquots are pooled back
         together into a single sample).
 
-        Currently, the relationship path may only contain parent/child nodes.
-
         :param models: A list of record models.
         :param path: The relationship path to follow.
         :param wrapper_type: The record model wrapper to use.
@@ -922,13 +960,22 @@ class RecordHandler:
         for model in models:
             current: list[PyRecordModel] = [model if isinstance(model, PyRecordModel) else model.backing_model]
             for node in path:
-                direction = node.direction
+                data_type: str = node.data_type_name
+                direction: RelationshipNodeType = node.direction
                 if len(current) == 0:
                     break
                 if direction == RelationshipNodeType.CHILD:
-                    current = current[0].get_children_of_type(node.data_type_name)
+                    current = current[0].get_children_of_type(data_type)
                 elif direction == RelationshipNodeType.PARENT:
-                    current = current[0].get_parents_of_type(node.data_type_name)
+                    current = current[0].get_parents_of_type(data_type)
+                elif direction == RelationshipNodeType.ANCESTOR:
+                    current = list(self.an_man.get_ancestors_of_type(current[0], data_type))
+                elif direction == RelationshipNodeType.DESCENDANT:
+                    current = list(self.an_man.get_descendant_of_type(current[0], data_type))
+                elif direction == RelationshipNodeType.FORWARD_SIDE_LINK:
+                    current = [current[0].get_forward_side_link(node.data_field_name)]
+                elif direction == RelationshipNodeType.REVERSE_SIDE_LINK:
+                    current = current[0].get_reverse_side_link(node.data_field_name, data_type)
                 else:
                     raise SapioException("Unsupported path direction.")
             ret_dict.update({model: self.inst_man.wrap(current[0], wrapper_type) if current else None})
@@ -959,3 +1006,18 @@ class RecordHandler:
                                          f"encountered in system that matches all provided identifiers.")
                 unique_record = result
         return unique_record
+
+    @staticmethod
+    def __verify_data_type(records: Iterable[DataRecord], wrapper_type: type[WrappedType]) -> None:
+        """
+        Throw an exception if the data type of the given records and wrapper don't match.
+        """
+        model_type: str = wrapper_type.get_wrapper_data_type_name()
+        for record in records:
+            record_type: str = record.data_type_name
+            # Account for ELN data type records.
+            if ElnBaseDataType.is_eln_type(record_type):
+                record_type = ElnBaseDataType.get_base_type(record_type).data_type_name
+            if record_type != model_type:
+                raise SapioException(f"Data record of type {record_type} cannot be wrapped by the record model wrapper "
+                                     f"of type {model_type}")

sapiopycommons/rules/eln_rule_handler.py

@@ -1,5 +1,5 @@
 from sapiopylib.rest.pojo.DataRecord import DataRecord
-from sapiopylib.rest.pojo.webhook.VeloxRules import VeloxRuleType, VeloxRuleParser
+from sapiopylib.rest.pojo.eln.SapioELNEnums import ElnBaseDataType
 from sapiopylib.rest.pojo.webhook.WebhookContext import SapioWebhookContext
 from sapiopylib.rest.utils.recordmodel.RecordModelManager import RecordModelManager, RecordModelInstanceManager
 from sapiopylib.rest.utils.recordmodel.RecordModelWrapper import WrappedType
@@ -12,7 +12,6 @@ from sapiopycommons.general.exceptions import SapioException
 class ElnRuleHandler:
     """
     A class which helps with the parsing and navigation of the ELN rule result map of a webhook context.
-    TODO: Add functionality around the VeloxRuleType of the rule results.
     """
     __context: SapioWebhookContext
     """The context that this handler is working from."""
@@ -64,13 +63,8 @@ class ElnRuleHandler:
                         # Get the data type of this record. If this is an ELN type, ignore the digits.
                         data_type: str = record.data_type_name
                         # PR-46331: Ensure that all ELN types are converted to their base data type name.
-                        # TODO: Use ElnBaseDataType.is_eln_type when it is no longer bugged in sapiopylib.
-                        if data_type.startswith("ELNExperiment_"):
-                            data_type = "ELNExperiment"
-                        elif data_type.startswith("ELNExperimentDetail_"):
-                            data_type = "ELNExperimentDetail"
-                        elif data_type.startswith("ELNSampleDetail_"):
-                            data_type = "ELNSampleDetail"
+                        if ElnBaseDataType.is_eln_type(data_type):
+                            data_type = ElnBaseDataType.get_base_type(data_type).data_type_name
                         # Update the list of records of this type that exist so far globally.
                         self.__records.setdefault(data_type, set()).add(record)
                         # Do the same for the list of records of this type for this specific entry.
@@ -85,19 +79,9 @@ class ElnRuleHandler:
             entry_dict: dict[str, dict[int, FieldMap]] = {}
             for record_result in entry_results:
                 for result in record_result.velox_type_rule_field_map_result_list:
-                    # TODO: sapiopylib currently has a bug where this velox_type_pojo variable is stored as a dict instead
-                    #  of as the intended VeloxRuleType object. Parse that dict as a VeloxRuleType before use.
-                    velox_type: VeloxRuleType | dict = result.velox_type_pojo
-                    if isinstance(velox_type, dict):
-                        velox_type: VeloxRuleType = VeloxRuleParser.parse_velox_rule_type(velox_type)
-                    data_type: str = velox_type.data_type_name
-                    # TODO: Use ElnBaseDataType.is_eln_type when it is no longer bugged in sapiopylib.
-                    if data_type.startswith("ELNExperiment_"):
-                        data_type = "ELNExperiment"
-                    elif data_type.startswith("ELNExperimentDetail_"):
-                        data_type = "ELNExperimentDetail"
-                    elif data_type.startswith("ELNSampleDetail_"):
-                        data_type = "ELNSampleDetail"
+                    data_type: str = result.velox_type_pojo.data_type_name
+                    if ElnBaseDataType.is_eln_type(data_type):
+                        data_type = ElnBaseDataType.get_base_type(data_type).data_type_name
                     for field_map in result.field_map_list:
                         rec_id: int = field_map.get("RecordId")
                         self.__field_maps.setdefault(data_type, {}).update({rec_id: field_map})

sapiopycommons/rules/on_save_rule_handler.py

@@ -1,5 +1,5 @@
 from sapiopylib.rest.pojo.DataRecord import DataRecord
-from sapiopylib.rest.pojo.webhook.VeloxRules import VeloxRuleType, VeloxRuleParser
+from sapiopylib.rest.pojo.eln.SapioELNEnums import ElnBaseDataType
 from sapiopylib.rest.pojo.webhook.WebhookContext import SapioWebhookContext
 from sapiopylib.rest.utils.recordmodel.RecordModelManager import RecordModelManager, RecordModelInstanceManager
 from sapiopylib.rest.utils.recordmodel.RecordModelWrapper import WrappedType
@@ -12,7 +12,6 @@ from sapiopycommons.general.exceptions import SapioException
 class OnSaveRuleHandler:
     """
     A class which helps with the parsing and navigation of the on save rule result map of a webhook context.
-    TODO: Add functionality around the VeloxRuleType of the rule results.
     """
     __context: SapioWebhookContext
     """The context that this handler is working from."""
@@ -51,9 +50,6 @@ class OnSaveRuleHandler:
         self.__base_id_to_records = {}
         # Each record ID in the context has a list of results for that record.
         for record_id, rule_results in self.__context.velox_on_save_result_map.items():
-            # TODO: Record IDs are currently being stored in the map as strings instead of ints. This can be removed
-            #  once sapiopylib is fixed.
-            record_id = int(record_id)
             # Keep track of the records for this specific record ID.
             id_dict: dict[str, set[DataRecord]] = {}
             # The list of results for a record consist of a list of data records and a VeloxType that specifies
@@ -64,13 +60,8 @@ class OnSaveRuleHandler:
                     # Get the data type of this record. If this is an ELN type, ignore the digits.
                     data_type: str = record.data_type_name
                     # PR-46331: Ensure that all ELN types are converted to their base data type name.
-                    # TODO: Use ElnBaseDataType.is_eln_type when it is no longer bugged in sapiopylib.
-                    if data_type.startswith("ELNExperiment_"):
-                        data_type = "ELNExperiment"
-                    elif data_type.startswith("ELNExperimentDetail_"):
-                        data_type = "ELNExperimentDetail"
-                    elif data_type.startswith("ELNSampleDetail_"):
-                        data_type = "ELNSampleDetail"
+                    if ElnBaseDataType.is_eln_type(data_type):
+                        data_type = ElnBaseDataType.get_base_type(data_type).data_type_name
                     # Update the list of records of this type that exist so far globally.
                     self.__records.setdefault(data_type, set()).add(record)
                     # Do the same for the list of records of this type that relate to this record ID.
@@ -82,24 +73,11 @@ class OnSaveRuleHandler:
         self.__base_id_to_field_maps = {}
         # Repeat the same thing for the field map results.
         for record_id, rule_results in self.__context.velox_on_save_field_map_result_map.items():
-            # TODO: Record IDs are currently being stored in the map as strings instead of ints. This can be removed
-            #  once sapiopylib is fixed.
-            record_id = int(record_id)
             id_dict: dict[str, dict[int, FieldMap]] = {}
             for record_result in rule_results:
-                # TODO: sapiopylib currently has a bug where this velox_type_pojo variable is stored as a dict instead
-                #  of as the intended VeloxRuleType object. Parse that dict as a VeloxRuleType before use.
-                velox_type: VeloxRuleType | dict = record_result.velox_type_pojo
-                if isinstance(velox_type, dict):
-                    velox_type: VeloxRuleType = VeloxRuleParser.parse_velox_rule_type(velox_type)
-                data_type: str = velox_type.data_type_name
-                # TODO: Use ElnBaseDataType.is_eln_type when it is no longer bugged in sapiopylib.
-                if data_type.startswith("ELNExperiment_"):
-                    data_type = "ELNExperiment"
-                elif data_type.startswith("ELNExperimentDetail_"):
-                    data_type = "ELNExperimentDetail"
-                elif data_type.startswith("ELNSampleDetail_"):
-                    data_type = "ELNSampleDetail"
+                data_type: str = record_result.velox_type_pojo.data_type_name
+                if ElnBaseDataType.is_eln_type(data_type):
+                    data_type = ElnBaseDataType.get_base_type(data_type).data_type_name
                 for field_map in record_result.field_map_list:
                     rec_id: int = field_map.get("RecordId")
                     self.__field_maps.setdefault(data_type, {}).update({rec_id: field_map})

{sapiopycommons-2024.7.24a298.dist-info → sapiopycommons-2024.7.29a300.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2024.7.24a298
+Version: 2024.7.29a300
 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-2024.7.24a298.dist-info → sapiopycommons-2024.7.29a300.dist-info}/RECORD

@@ -1,26 +1,27 @@
 sapiopycommons/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/callbacks/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/callbacks/callback_util.py,sha256=caeIWCHvK33jDs3TRskpJv0kDe7W8NPK4MyJPjgztwo,58012
+sapiopycommons/callbacks/callback_util.py,sha256=YdaN1iNnJ51EauvKfEOAUwahu1dt_YVvr4Zia29g9qc,61123
 sapiopycommons/chem/IndigoMolecules.py,sha256=QqFDi9CKERj6sn_ZwVcS2xZq4imlkaTeCrpq1iNcEJA,1992
 sapiopycommons/chem/Molecules.py,sha256=t80IsQBPJ9mwE8ZxnWomAGrZDhdsOuPvLaTPb_N6jGU,8639
 sapiopycommons/chem/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/datatype/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/datatype/attachment_util.py,sha256=YlnMprj5IGBbAZDLG2khS1P7JIYTw_NYfpJAfRZfP3M,3219
+sapiopycommons/datatype/attachment_util.py,sha256=23JQ4avSmBBJdCv95LVj31x8rUCclzB_DYFBijH0NII,3708
 sapiopycommons/eln/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/eln/experiment_handler.py,sha256=v1pG4qtZb8OSNWfKtFo6NjnEkReqnu5R9i_hqWh_xxg,57198
+sapiopycommons/eln/experiment_handler.py,sha256=RspUDmPmBQIG7l7q_luFP8yeRljdU3E64066NH5CtdI,59817
 sapiopycommons/eln/experiment_report_util.py,sha256=FTLw-6SLAMeoWTOO-qhGROE9g54pZdyoQJIhiIzlwGw,7848
 sapiopycommons/eln/plate_designer.py,sha256=FYJfhhNq8hdfuXgDYOYHy6g0m2zNwQXZWF_MTPzElDg,7184
 sapiopycommons/files/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/files/complex_data_loader.py,sha256=XSJOl676mIklJo78v07-70u1b015a5DI4sqZPI3C-Tw,1475
-sapiopycommons/files/file_bridge.py,sha256=GI3-gWFzcL0q0c8jKOxTevbzJqtUpiElmkXfTnMsaOo,6224
+sapiopycommons/files/complex_data_loader.py,sha256=8jgYF5iGDD6Abw8JRWLYxUWVwj4s4pH5HylyxEGFZSU,1471
+sapiopycommons/files/file_bridge.py,sha256=njx_5Z3tvQUNW4mPazQerL8lopLAFStIByHWHJ7m5ug,6220
 sapiopycommons/files/file_bridge_handler.py,sha256=MU2wZR4VY606yx6Bnv8-LzG3mGCeuXeRBn914WNRFCo,13601
 sapiopycommons/files/file_data_handler.py,sha256=3-guAdhJdeJWAFq1a27ijspkO7uMMZ6CapMCD_6o4jA,36746
-sapiopycommons/files/file_util.py,sha256=44mzhn3M_QltoncBB-ooX7_yO6u5k-XU_bzUXHGxUiw,26299
-sapiopycommons/files/file_validator.py,sha256=BhXB2XnoNEzdBXuwul1s2RNoj-3ZoiMmephUCU_0o3Y,28113
+sapiopycommons/files/file_util.py,sha256=ronTlJimQ6ttJN6Y9qfAzEWoeWnDoUbohkdObNK5mJQ,27042
+sapiopycommons/files/file_validator.py,sha256=EqPCXfVCiilgnOb2G-yZg8XWeDqYp9iVCg8AaWznvf4,28040
 sapiopycommons/files/file_writer.py,sha256=5u_iZXTQvuUU7ceHZr8Q001_tvgJhOqBwAnB_pxcAbQ,16027
 sapiopycommons/general/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/general/accession_service.py,sha256=HYgyOsH_UaoRnoury-c2yTW8SeG4OtjLemdpCzoV4R8,13484
-sapiopycommons/general/aliases.py,sha256=i6af5o2oVFGNcyk7GkvTWXQs0H9xTbFKc_GIah8NKVU,3594
+sapiopycommons/general/aliases.py,sha256=vP2Fl0YEzm8z6Qe9e-SUWWAopKzK_qdvdQ9mVewg9Oc,3976
+sapiopycommons/general/audit_log.py,sha256=LNpBCpZ5mz47-HzHel8PUz1TYGCnxTY6dnerZu-cwOo,9076
 sapiopycommons/general/custom_report_util.py,sha256=cLgIR5Fn3M9uyAtgfTYRv3JRk2SKNevnsb_R5zidSYs,15557
 sapiopycommons/general/exceptions.py,sha256=DOlLKnpCatxQF-lVCToa8ryJgusWLvip6N_1ALN00QE,1679
 sapiopycommons/general/popup_util.py,sha256=-mN5IgYPrLrOEHJ4CHPi2rec4_WAN6X0yMxHwD5h3Bs,30126
@@ -31,13 +32,13 @@ sapiopycommons/multimodal/multimodal_data.py,sha256=zqgYHO-ULaPKV0POFWZVY9N-Sfm1
 sapiopycommons/processtracking/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/processtracking/endpoints.py,sha256=g5h_uCVByqacYm9zWAz8TyAdRsGfaO2o0b5RSJdOaSA,10926
 sapiopycommons/recordmodel/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/recordmodel/record_handler.py,sha256=AyK1H3x-g1eu1Mt9XD1h57yRrZp_TJjZlEaQ2kPP4Dc,54432
+sapiopycommons/recordmodel/record_handler.py,sha256=qqsHeGNyqQeFKuZ4U2v2MD278AlH4n1HMvSTOY0hbyo,58636
 sapiopycommons/rules/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/rules/eln_rule_handler.py,sha256=qfkBZtck0KK1i9s9Xe2UZqkzQOgPCzDxRkhxE8Si1xk,10671
-sapiopycommons/rules/on_save_rule_handler.py,sha256=JY9F30IcHwFVdgPAMQtTYuRastV1jeezhVktyrzNASU,10763
+sapiopycommons/rules/eln_rule_handler.py,sha256=rz9E1PQLShCZM09JafMl_ylUqBbMs-et0FsOG41tQL0,9480
+sapiopycommons/rules/on_save_rule_handler.py,sha256=I06HwsNvulyU0avSXOU0itBDAmiOxsyW8KGk_gH0FHc,9238
 sapiopycommons/webhook/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/webhook/webhook_handlers.py,sha256=ibpBY3Sk3Eij919bIdW0awzlogYoQSWYDDOg--NwsQE,13431
-sapiopycommons-2024.7.24a298.dist-info/METADATA,sha256=RGnkahp9FWKycBSI9dfrZg1n-5CkU7aZM8laJZsc0fM,3176
-sapiopycommons-2024.7.24a298.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
-sapiopycommons-2024.7.24a298.dist-info/licenses/LICENSE,sha256=HyVuytGSiAUQ6ErWBHTqt1iSGHhLmlC8fO7jTCuR8dU,16725
-sapiopycommons-2024.7.24a298.dist-info/RECORD,,
+sapiopycommons-2024.7.29a300.dist-info/METADATA,sha256=fuvVIkg01kxr3N8oqN-QG_zsljp-OfhiUn4zDgLEGH4,3176
+sapiopycommons-2024.7.29a300.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
+sapiopycommons-2024.7.29a300.dist-info/licenses/LICENSE,sha256=HyVuytGSiAUQ6ErWBHTqt1iSGHhLmlC8fO7jTCuR8dU,16725
+sapiopycommons-2024.7.29a300.dist-info/RECORD,,