sapiopycommons 2025.4.10a478__tar.gz → 2025.4.11a479__tar.gz

{sapiopycommons-2025.4.10a478 → sapiopycommons-2025.4.11a479}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2025.4.10a478
+Version: 2025.4.11a479
 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-2025.4.10a478 → sapiopycommons-2025.4.11a479}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "sapiopycommons"
-version='2025.04.10a478'
+version='2025.04.11a479'
 authors = [
     { name="Jonathan Steck", email="jsteck@sapiosciences.com" },
     { name="Yechen Qiao", email="yqiao@sapiosciences.com" },

{sapiopycommons-2025.4.10a478 → sapiopycommons-2025.4.11a479}/src/sapiopycommons/callbacks/callback_util.py

@@ -38,6 +38,7 @@ from sapiopycommons.general.aliases import FieldMap, SapioRecord, AliasUtil, Rec
 from sapiopycommons.general.custom_report_util import CustomReportUtil
 from sapiopycommons.general.exceptions import SapioUserCancelledException, SapioException, SapioUserErrorException, \
     SapioDialogTimeoutException
+from sapiopycommons.general.time_util import TimeUtil
 from sapiopycommons.recordmodel.record_handler import RecordHandler
 
 DataTypeLayoutIdentifier: TypeAlias = DataTypeLayout | str | None
@@ -682,7 +683,8 @@ class CallbackUtil:
                             default_modifier: FieldModifier | None = None,
                             field_modifiers: dict[FieldIdentifier, FieldModifier] | None = None,
                             group_by: FieldIdentifier | None = None,
-                            image_data: Iterable[bytes] | None = None) -> list[FieldMap]:
+                            image_data: Iterable[bytes] | None = None,
+                            index_field: str | 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.
@@ -712,6 +714,12 @@ class CallbackUtil:
             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.
+        :param index_field: If provided, the returned field maps will contain a field with this name that is equal to
+            the record ID of the record at the same index in the records list. This can be used to map the results
+            back to the original records. This is used instead of using a RecordId field, as the RecordId field has
+            special behavior in the system that can cause issues if the given records are uncommitted record models
+            with negative record IDs, meaning we don't want to have a RecordId field in the field maps provided to the
+            system.
         :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.
         """
@@ -723,7 +731,10 @@ class CallbackUtil:
         if not records:
             raise SapioException("No records provided.")
         data_type: str = AliasUtil.to_singular_data_type_name(records)
-        field_map_list: list[FieldMap] = AliasUtil.to_field_map_list(records)
+        if index_field is not None:
+            field_map_list: list[FieldMap] = self.__get_indexed_field_maps(records, index_field)
+        else:
+            field_map_list: list[FieldMap] = AliasUtil.to_field_map_list(records)
 
         # Convert the group_by parameter to a field name.
         if group_by is not None:
@@ -793,13 +804,17 @@ class CallbackUtil:
         :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.
         """
+        # Index the records with a field name that is the current time in milliseconds. This is done to avoid
+        # collisions with any existing field names.
+        index_field: str = f"_{TimeUtil.now_in_millis()}"
         results: list[FieldMap] = self.record_table_dialog(title, msg, fields, records,
                                                            default_modifier=default_modifier,
                                                            field_modifiers=field_modifiers,
-                                                           group_by=group_by, image_data=image_data)
+                                                           group_by=group_by, image_data=image_data,
+                                                           index_field=index_field)
         records_by_id: dict[int, SapioRecord] = self.rec_handler.map_by_id(records)
         for result in results:
-            records_by_id[result["RecordId"]].set_field_values(result)
+            records_by_id[result[index_field]].set_field_values(result)
 
     def create_record_table_dialog(self,
                                    title: str,
@@ -873,7 +888,8 @@ class CallbackUtil:
                                field_modifiers: dict[FieldIdentifier, FieldModifier] | None = None,
                                column_positions: dict[str, tuple[int, int]] | None = None,
                                group_by: FieldIdentifier | None = None,
-                               image_data: Iterable[bytes] | None = None) -> list[FieldMap]:
+                               image_data: Iterable[bytes] | None = None,
+                               index_field: str | None = None) -> list[FieldMap]:
         """
         Create a dialog where the user may input data into the specified fields. The dialog is constructed from
         a given list of records of a singular type.
@@ -909,6 +925,12 @@ class CallbackUtil:
         :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. Only used if the
             adaptive dialog becomes a table.
+        :param index_field: If provided, the returned field maps will contain a field with this name that is equal to
+            the record ID of the record at the same index in the records list. This can be used to map the results
+            back to the original records. This is used instead of using a RecordId field, as the RecordId field has
+            special behavior in the system that can cause issues if the given records are uncommitted record models
+            with negative record IDs, meaning we don't want to have a RecordId field in the field maps provided to the
+            system. Only used if the adaptive dialog becomes a table.
         :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. Even if a form was displayed, the field values will still
             be returned in a list.
@@ -921,7 +943,7 @@ class CallbackUtil:
                                             default_modifier=default_modifier, field_modifiers=field_modifiers)]
         return self.record_table_dialog(title, msg, fields, records,
                                         default_modifier=default_modifier, field_modifiers=field_modifiers,
-                                        group_by=group_by, image_data=image_data)
+                                        group_by=group_by, image_data=image_data, index_field=index_field)
 
     def set_record_adaptive_dialog(self,
                                    title: str,
@@ -1685,6 +1707,27 @@ class CallbackUtil:
         with io.BytesIO(FileUtil.zip_files(files)) as data:
             self.callback.send_file(zip_name, False, data)
 
+    @staticmethod
+    def __get_indexed_field_maps(records: Iterable[SapioRecord], index_field: str) -> list[FieldMap]:
+        """
+        For dialogs that accept multiple records, we may want to be able to match the returned results back to the
+        records that they're for. In this case, we need to add an index to each record so that we can match them back
+        to the original records. We can't use the RecordId field, as new record models have negative record IDs that
+        cause the callback dialogs to bug out if the RecordId field is present and negative.
+
+        :param records: The records to return indexed field maps of.
+        :param index_field: The name of the field to use as the index. Make sure that this field doesn't exist on the
+            records, as then it will overwrite the existing value.
+        :return: A list of field maps for the records, with an index field added to each. The value of the index on
+            each field map is the record's record ID (even if it's a record model with a negative ID).
+        """
+        ret_val: list[FieldMap] = []
+        for record in records:
+            field_map: FieldMap = AliasUtil.to_field_map(record)
+            field_map[index_field] = AliasUtil.to_record_id(record)
+            ret_val.append(field_map)
+        return ret_val
+
     @staticmethod
     def __temp_dt_from_field_defs(data_type: DataTypeIdentifier, display_name: str | None,
                                   plural_display_name: str | None, fields: Iterable[AbstractVeloxFieldDefinition],

{sapiopycommons-2025.4.10a478 → sapiopycommons-2025.4.11a479}/src/sapiopycommons/eln/experiment_step_factory.py

@@ -38,12 +38,12 @@ from sapiopylib.rest.utils.plates.PlatingUtils import PlatingOrder
 class ExperimentStepFactory:
     user: SapioUser
     _exp_handler: ExperimentHandler
-    
+
     _exp_id: int
 
     _eln_man: ElnManager
     _exp_cache: ExperimentCacheManager
-    
+
     def __init__(self, exp_handler: ExperimentHandler):
         self.user = exp_handler.user
         self._exp_handler = exp_handler
@@ -198,7 +198,8 @@ class ExperimentStepFactory:
                     elif isinstance(field_set, str):
                         field_sets.add(self._exp_cache.get_field_set(field_set).field_set_id)
                 entry_criteria.field_set_id_list = list(field_sets)
-            entry_criteria.field_definition_list = criteria.field_definitions
+            if criteria.field_definitions:
+                entry_criteria.field_definition_list = list(criteria.field_definitions)
             if criteria.predefined_field_names:
                 if entry_criteria.field_definition_list is None:
                     entry_criteria.field_definition_list = []
@@ -323,7 +324,8 @@ class ExperimentStepFactory:
                     elif isinstance(field_set, str):
                         field_sets.add(self._exp_cache.get_field_set(field_set).field_set_id)
                 entry_criteria.field_set_id_list = list(field_sets)
-            entry_criteria.field_definition_list = list(criteria.field_definitions)
+            if criteria.field_definitions:
+                entry_criteria.field_definition_list = list(criteria.field_definitions)
             if criteria.predefined_field_names:
                 if entry_criteria.field_definition_list is None:
                     entry_criteria.field_definition_list = []

{sapiopycommons-2025.4.10a478 → sapiopycommons-2025.4.11a479}/src/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(WellElement.PLATE_RECORD_ID__FIELD)
+            plate_id: int = element.get(WellElement.PLATE_RECORD_ID__FIELD.field_name)
             self._designer_elements_by_plate.setdefault(plate_id, []).append(element)
         return self._designer_elements
 
@@ -194,7 +194,8 @@ class PlateDesignerEntry(ElnEntryStep):
         return self._designer_elements_by_plate[plate]
 
     def create_well_element(self, sample: RecordModel, plate: RecordModel, location: PlateLocation | None = None,
-                            wrapper_type: type[WrappedType] | None = None) -> WrappedType | PyRecordModel:
+                            layer: int = 1, 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.
@@ -203,6 +204,7 @@ 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.
@@ -216,6 +218,8 @@ 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)
@@ -225,6 +229,7 @@ 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-2025.4.10a478 → sapiopycommons-2025.4.11a479}/src/sapiopycommons/eln/step_creation.py

@@ -59,8 +59,8 @@ class StepCreation:
         self.is_removable = None
         self.is_renamable = None
         self.is_static_view = None
-        self._related_entry_set = None
-        self._dependency_set = None
+        self.related_entry_set = None
+        self.dependency_set = None
         self.requires_grabber_plugin = False
         self.entry_singleton_id = None
         self.is_hidden = None