sapiopycommons 2025.6.11a561__py3-none-any.whl → 2025.6.18a563__py3-none-any.whl

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

@@ -327,10 +327,10 @@ 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)
+        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

@@ -7,7 +7,6 @@ from sapiopylib.rest.pojo.datatype.FieldDefinition import FieldType, AbstractVel
 from sapiopylib.rest.pojo.eln.ElnExperiment import ElnExperiment
 from sapiopylib.rest.pojo.eln.ExperimentEntry import ExperimentEntry
 from sapiopylib.rest.pojo.eln.SapioELNEnums import ElnBaseDataType
-from sapiopylib.rest.pojo.eln.eln_headings import ElnExperimentTab
 from sapiopylib.rest.pojo.webhook.WebhookContext import SapioWebhookContext
 from sapiopylib.rest.utils.Protocols import ElnExperimentProtocol, ElnEntryStep
 from sapiopylib.rest.utils.recordmodel.PyRecordModel import PyRecordModel, AbstractRecordModel
@@ -220,9 +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/processtracking/custom_workflow_handler.py

@@ -105,8 +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