sapiopycommons 2025.7.7a580__py3-none-any.whl → 2025.7.9a582__py3-none-any.whl

sapiopycommons/eln/experiment_report_util.py

@@ -2,7 +2,7 @@ from sapiopylib.rest.ELNService import ElnManager
 from sapiopylib.rest.User import SapioUser
 from sapiopylib.rest.pojo.CustomReport import CustomReportCriteria, AbstractReportTerm, RawReportTerm
 from sapiopylib.rest.pojo.datatype.FieldDefinition import FieldType
-from sapiopylib.rest.pojo.eln.ElnExperiment import ElnExperiment, ElnExperimentQueryCriteria, ElnTemplate
+from sapiopylib.rest.pojo.eln.ElnExperiment import ElnExperiment, ElnExperimentQueryCriteria
 from sapiopylib.rest.pojo.eln.SapioELNEnums import ElnExperimentStatus, ElnBaseDataType
 from sapiopylib.rest.utils.recordmodel.PyRecordModel import PyRecordModel
 from sapiopylib.rest.utils.recordmodel.RecordModelWrapper import WrappedType
@@ -250,22 +250,17 @@ class ExperimentReportUtil:
         return {exp: list(records) for exp, records in exp_to_records.items()}
 
     @staticmethod
-    def get_experiment_options(context: UserIdentifier, experiments: list[ExperimentIdentifier | ElnTemplate]) \
+    def get_experiment_options(context: UserIdentifier, experiments: list[ExperimentIdentifier]) \
             -> dict[int, dict[str, str]]:
         """
-        Run a custom report to retrieve the experiment options for all the provided experiments or experiment templates.
-        Effectively a batched version of the get_notebook_experiment_options function of ElnManager.
+        Run a custom report to retrieve the experiment options for all the provided experiments. Effectively a batched
+        version of the get_notebook_experiment_options function of ElnManager.
 
         :param context: The current webhook context or a user object to send requests from.
-        :param experiments: The experiment/template identifiers to retrieve the experiment options for.
+        :param experiments: The experiment identifiers to retrieve the experiment options for.
         :return: A dictionary mapping the notebook experiment ID to the options for that experiment.
         """
-        exp_ids: list[int] = []
-        for exp in experiments:
-            if isinstance(exp, ElnTemplate):
-                exp_ids.append(exp.template_id)
-            else:
-                exp_ids.append(AliasUtil.to_notebook_id(exp))
+        exp_ids: list[int] = AliasUtil.to_notebook_ids(experiments)
 
         report_builder = CustomReportBuilder(NotebookExperimentOptionPseudoDef.DATA_TYPE_NAME)
         tb = report_builder.get_term_builder()

sapiopycommons/eln/plate_designer.py

@@ -167,7 +167,7 @@ class PlateDesignerEntry(ElnEntryStep):
             self._designer_elements_by_plate = {}
         self._designer_elements_by_plate.clear()
         for element in self._designer_elements:
-            plate_id: int = element.get_field_value(WellElement.PLATE_RECORD_ID__FIELD.field_name)
+            plate_id: int = element.get(WellElement.PLATE_RECORD_ID__FIELD)
             self._designer_elements_by_plate.setdefault(plate_id, []).append(element)
         return self._designer_elements
 
@@ -194,8 +194,7 @@ class PlateDesignerEntry(ElnEntryStep):
         return self._designer_elements_by_plate[plate]
 
     def create_well_element(self, sample: RecordModel, plate: RecordModel, location: PlateLocation | None = None,
-                            layer: int = 1, wrapper_type: type[WrappedType] | None = None) \
-            -> WrappedType | PyRecordModel:
+                            wrapper_type: type[WrappedType] | None = None) -> WrappedType | PyRecordModel:
         """
         Create a new plate designer well element for the input sample and plate. A record model manager store and commit
         must be called to save this new well element to the server.
@@ -204,7 +203,6 @@ class PlateDesignerEntry(ElnEntryStep):
         :param plate: The plate that the element is for. Must exist in the system (i.e. have a >0 record ID).
         :param location: The location of the well element. If not provided, the row and column position fields of the
             sample will be used.
-        :param layer: The layer that the well element is on.
         :param wrapper_type: The record model wrapper to use for the plate designer well element. If not provided, the
             returned record will be a PyRecordModel instead of a WrappedRecordModel.
         :return: The newly created PlateDesignerWellElementModel.
@@ -218,8 +216,6 @@ class PlateDesignerEntry(ElnEntryStep):
             raise SapioException("Sample record must be of type Sample.")
         if AliasUtil.to_data_type_name(plate) != "Plate":
             raise SapioException("Plate record must be of type Plate.")
-        if layer < 1:
-            raise SapioException("Layer must be greater than 0.")
 
         dt: type[WrappedType] | str = wrapper_type if wrapper_type else WellElement.DATA_TYPE_NAME
         plate_id: int = AliasUtil.to_record_id(plate)
@@ -229,7 +225,6 @@ class PlateDesignerEntry(ElnEntryStep):
             WellElement.ROW_POSITION__FIELD: location.row_pos if location else sample.get_field_value("RowPosition"),
             WellElement.COL_POSITION__FIELD: str(location.col_pos) if location else sample.get_field_value("ColPosition"),
             WellElement.SOURCE_DATA_TYPE_NAME__FIELD: "Sample",
-            WellElement.LAYER__FIELD: layer,
         }
         element = self._rec_handler.add_models_with_data(dt, [fields])[0]
 

sapiopycommons/files/file_util.py

@@ -327,13 +327,11 @@ class FileUtil:
         :param files: A dictionary of file name to file data as a string or bytes.
         :return: The bytes for a zip file containing the input files.
         """
-        with io.BytesIO() as zip_buffer:
-            with zipfile.ZipFile(zip_buffer, "w", zipfile.ZIP_DEFLATED) as zip_file:
-                for file_name, file_data in files.items():
-                    zip_file.writestr(file_name, file_data)
-            # PR-47697: Indent the getvalue call into the outer with block. Making the call outside of the with block
-            # throws an I/O exception.
-            return zip_buffer.getvalue()
+        zip_buffer: io.BytesIO = io.BytesIO()
+        with zipfile.ZipFile(zip_buffer, "w", zipfile.ZIP_DEFLATED) as zip_file:
+            for file_name, file_data in files.items():
+                zip_file.writestr(file_name, file_data)
+        return zip_buffer.getvalue()
 
     # Deprecated functions:
 

sapiopycommons/general/accession_service.py

@@ -199,7 +199,7 @@ class AccessionRequestId(AbstractAccessionServiceOperator):
 
     Properties:
         numberOfCharacters: Number of characters maximum in the request ID.
-        accessorName: This is a legacy variable from drum.getNextIdListByMapName(), which allows setting different "accessorName" from old system. We need this for compatibility patch for converting these to the new preference format.
+        accessorName: This is a legacy variable from drum.getNextIdListByMapName(), which allows setting different "accessorName" from old system. We need this for compability patch for converting these to the new preference format.
     """
     _num_of_characters: int
     _accessor_name: str
@@ -341,7 +341,7 @@ class AccessionService:
     def get_affixed_id_in_batch(self, data_type_name: str, data_field_name: str, num_ids: int, prefix: str | None,
                                 suffix: str | None, num_digits: int | None, start_num: int = 1) -> list[str]:
         """
-        Get the batch affixed IDs that are maximal in cache and contiguous for a particular datatype.datafield under a given format.
+        Get the batch affixed IDs that are maximal in cache and contiguious for a particular datatype.datafield under a given format.
         :param data_type_name: The datatype name to look for max ID
         :param data_field_name: The datafield name to look for max ID
         :param num_ids: The number of IDs to accession.

sapiopycommons/general/aliases.py

@@ -219,9 +219,7 @@ class AliasUtil:
             # noinspection PyTypeChecker
             fields: FieldMap = record.get_fields()
         else:
-            # TI-47593: Copy the record's fields by using the get() method instead of copy_to_dict() so that date
-            # macros get translated to valid field values.
-            fields: FieldMap = {f: record.fields.get(f) for f in record.fields}
+            fields: FieldMap = record.fields.copy_to_dict()
         # PR-47457: Only include the record ID if the caller requests it, since including the record ID can break
         # callbacks in certain circumstances if the record ID is negative.
         if include_record_id:

sapiopycommons/general/audit_log.py

@@ -8,7 +8,6 @@ from sapiopycommons.customreport.column_builder import ColumnBuilder
 from sapiopycommons.customreport.term_builder import TermBuilder
 from sapiopycommons.datatype.pseudo_data_types import AuditLogPseudoDef
 from sapiopycommons.general.aliases import RecordIdentifier, AliasUtil, UserIdentifier, FieldIdentifier, FieldValue
-from sapiopycommons.general.exceptions import SapioException
 
 
 class EventType(Enum):
@@ -135,9 +134,6 @@ class AuditLogUtil:
         :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.
         """
-        # PR-47701: Throw an exception if no records are provided.
-        if not records:
-            raise SapioException("No records provided. Please provide at least one record to build a report for.")
         # Build the raw report term querying for any entry with a matching record ID value to the record ID's
         # passed in.
         record_ids = AliasUtil.to_record_ids(records)
@@ -164,9 +160,6 @@ class AuditLogUtil:
         :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.
         """
-        # PR-47701: Return an empty dictionary if no records are provided.
-        if not records:
-            return {}
         # First, we must build our report criteria for running the Custom Report.
         criteria = AuditLogUtil.create_data_record_audit_log_report(records, fields)
 

sapiopycommons/general/custom_report_util.py

@@ -24,12 +24,6 @@ class CustomReportUtil:
         System reports are also known as predefined searches in the system and must be defined in the data designer for
         a specific data type. That is, saved searches created by users cannot be run using this function.
 
-        IMPORTANT NOTICE: Custom reports that are not single data type (i.e. they have terms or columns from multiple
-        data types) may not be 100% time accurate. Such reports use the system's ancestor table to retrieve the
-        relationships, and this table takes some time to update after relationships are updated, especially for more
-        populous data types. If you need 100% time accurate results to the current state of the records and
-        relationships in the database, you should query for the records directly instead of using a custom report.
-
         :param context: The current webhook context or a user object to send requests from.
         :param report_name: The name of the system report to run.
         :param filters: If provided, filter the results of the report using the given mapping of headers to values to
@@ -69,12 +63,6 @@ class CustomReportUtil:
         results. They are like advanced or predefined searches from the system, except they are constructed from
         within the webhook instead of from within the system.
 
-        IMPORTANT NOTICE: Custom reports that are not single data type (i.e. they have terms or columns from multiple
-        data types) may not be 100% time accurate. Such reports use the system's ancestor table to retrieve the
-        relationships, and this table takes some time to update after relationships are updated, especially for more
-        populous data types. If you need 100% time accurate results to the current state of the records and
-        relationships in the database, you should query for the records directly instead of using a custom report.
-
         :param context: The current webhook context or a user object to send requests from.
         :param report_criteria: The custom report criteria to run.
         :param filters: If provided, filter the results of the report using the given mapping of headers to values to

sapiopycommons/processtracking/custom_workflow_handler.py

@@ -94,9 +94,6 @@ class QueueItemHandler:
     """
     A class used for handling the display of records in custom process queues, which are controlled in the system by
     ProcessQueueItem data types.
-
-    IMPORTANT NOTICE: This is only for custom processes that make use of ProcessQueueItem records. For experiment
-    processes that use AssignedProcess records, see the ProcessTracking class.
     """
     user: SapioUser
     context: ProcessQueueContext | None
@@ -108,8 +105,7 @@ class QueueItemHandler:
         """
         self.user = AliasUtil.to_sapio_user(context)
         self.rec_handler = RecordHandler(self.user)
-        # PR-47565: Only initialize a ProcessQueueContext if the given context object has context_data.
-        if isinstance(context, SapioWebhookContext) and context.context_data:
+        if isinstance(context, SapioWebhookContext):
             self.context = ProcessQueueContext(context)
         else:
             self.context = None
@@ -264,9 +260,6 @@ class QueueItemHandler:
         Given a list of records, create process queue item records for them at the provided process and step names.
         You must store and commit using the record model manager in order for these changes to take effect.
 
-        IMPORTANT NOTICE: This is only for custom processes that make use of ProcessQueueItem records. For experiment
-        processes that use AssignedProcess records, see the ProcessTracking class.
-
         :param records: The records to create process queue items for.
         :param process: The name of the process to queue for.
         :param step: The name of the step in the above process to queue for. This is the "Workflow Name" field of the
@@ -299,9 +292,6 @@ class QueueItemHandler:
         criteria and remove them from the queue by setting the ShowInQueue field on the process queue items to false.
         You must store and commit using the record model manager in order for these changes to take effect.
 
-        IMPORTANT NOTICE: This is only for custom processes that make use of ProcessQueueItem records. For experiment
-        processes that use AssignedProcess records, see the ProcessTracking class.
-
         :param records: The records to remove from the queue.
         :param wrapper: The record model wrapper for the process queue items being updated. If not provided, the
             returned records will be PyRecordModels instead of WrappedRecordModels.

sapiopycommons/processtracking/endpoints.py

@@ -5,12 +5,6 @@ from sapiopycommons.general.aliases import RecordIdentifier, AliasUtil, Experime
 
 
 class ProcessTracking:
-    """
-    A class for calling the Foundations process tracking endpoints.
-
-    IMPORTANT NOTICE: This is only for experiment processes that make use of AssignedProcess records. For custom
-    processes that use ProcessQueueItem records, see the QueueItemHandler class.
-    """
     @staticmethod
     def assign_to_process(context: UserIdentifier, data_type: DataTypeIdentifier, records: list[RecordIdentifier],
                           process_name: str, step_number: int | None = None, branch_id: int | None = None,
@@ -20,9 +14,6 @@ class ProcessTracking:
         at that step.
         Synonymous with what occurs during request creation or when using the assign to process button.
 
-        IMPORTANT NOTICE: This is only for experiment processes that make use of AssignedProcess records. For custom
-        processes that use ProcessQueueItem records, see the QueueItemHandler class.
-
         :param context: The current webhook context or a user object to send requests from.
         :param data_type: The data type of the tracked records.
         :param records: A list of the tracked records.
@@ -55,9 +46,6 @@ class ProcessTracking:
         tracked records from "Ready for -" to "In Process -" for their current step.
         Synonymous with what occurs when starting a process step in the system.
 
-        IMPORTANT NOTICE: This is only for experiment processes that make use of AssignedProcess records. For custom
-        processes that use ProcessQueueItem records, see the QueueItemHandler class.
-
         :param context: The current webhook context or a user object to send requests from.
         :param data_type: The data type of the tracked records.
         :param records: A list of the tracked records.
@@ -85,9 +73,6 @@ class ProcessTracking:
         Moves the assigned process down to the descendant sample(s) if both samples are provided in the records list.
         Synonymous with what occurs when completing an experiment in the system.
 
-        IMPORTANT NOTICE: This is only for experiment processes that make use of AssignedProcess records. For custom
-        processes that use ProcessQueueItem records, see the QueueItemHandler class.
-
         :param context: The current webhook context or a user object to send requests from.
         :param data_type: The data type of the tracked records.
         :param records: A list of the tracked records.
@@ -111,9 +96,6 @@ class ProcessTracking:
         records must be "In Process -" for the given step.
         Synonymous with what occurs when failing a sample due to a QC failure in a process in the system.
 
-        IMPORTANT NOTICE: This is only for experiment processes that make use of AssignedProcess records. For custom
-        processes that use ProcessQueueItem records, see the QueueItemHandler class.
-
         :param context: The current webhook context or a user object to send requests from.
         :param data_type: The data type of the tracked records.
         :param records: A list of the tracked records.
@@ -140,9 +122,6 @@ class ProcessTracking:
         will move their status to "Ready for -" for the next step in the process, or "Completed -" if this was the
         last step.
 
-        IMPORTANT NOTICE: This is only for experiment processes that make use of AssignedProcess records. For custom
-        processes that use ProcessQueueItem records, see the QueueItemHandler class.
-
         :param context: The current webhook context or a user object to send requests from.
         :param data_type: The data type of the tracked records.
         :param records: A list of the tracked records.
@@ -170,9 +149,6 @@ class ProcessTracking:
         step will move their status to "Ready for -" for the next step in the process, or "Completed -" if this was the
         last step.
 
-        IMPORTANT NOTICE: This is only for experiment processes that make use of AssignedProcess records. For custom
-        processes that use ProcessQueueItem records, see the QueueItemHandler class.
-
         :param context: The current webhook context or a user object to send requests from.
         :param data_type: The data type of the tracked records.
         :param records: A list of the tracked records.
@@ -204,9 +180,6 @@ class ProcessTracking:
         Synonymous with what occurs when reprocessing records to a previous step due to QC failures in a process in the
         system.
 
-        IMPORTANT NOTICE: This is only for experiment processes that make use of AssignedProcess records. For custom
-        processes that use ProcessQueueItem records, see the QueueItemHandler class.
-
         :param context: The current webhook context or a user object to send requests from.
         :param records: A list of ReturnPoint records to reprocess to.
         """