sapiopycommons 2025.3.10a455__py3-none-any.whl → 2025.3.21a458__py3-none-any.whl

sapiopycommons/processtracking/custom_workflow_handler.py

@@ -5,10 +5,10 @@ from sapiopylib.rest.pojo.CustomReport import CustomReportCriteria
 from sapiopylib.rest.pojo.webhook.WebhookContext import SapioWebhookContext
 from sapiopylib.rest.utils.recordmodel.RecordModelWrapper import WrappedType
 
+from sapiopycommons.customreport.auto_pagers import CustomReportDictAutoPager, CustomReportRecordAutoPager
 from sapiopycommons.customreport.custom_report_builder import CustomReportBuilder
 from sapiopycommons.datatype.data_fields import ProcessQueueItemFields, SystemFields, ProcessWorkflowTrackingFields
 from sapiopycommons.general.aliases import UserIdentifier, AliasUtil, SapioRecord
-from sapiopycommons.general.custom_report_util import CustomReportUtil
 from sapiopycommons.general.exceptions import SapioException
 from sapiopycommons.general.time_util import TimeUtil
 from sapiopycommons.recordmodel.record_handler import RecordHandler
@@ -185,7 +185,7 @@ class QueueItemHandler:
         :return: A list of every queue item in the system that matches the search criteria.
         """
         report = self.build_queue_item_report(criteria)
-        return self.rec_handler.query_models_by_report(wrapper, report)
+        return CustomReportRecordAutoPager(self.user, report, wrapper).get_all_at_once()
 
     def get_records_from_item_report(self, wrapper: type[WrappedType],
                                      criteria: QueueItemReportCriteria = QueueItemReportCriteria()) -> list[WrappedType]:
@@ -203,7 +203,7 @@ class QueueItemHandler:
         criteria.not_data_type_names = None
         report = self.build_queue_item_report(criteria)
         record_ids: list[int] = [x[ProcessQueueItemFields.DATA_RECORD_ID__FIELD.field_name]
-                                 for x in CustomReportUtil.run_custom_report(self.user, report)]
+                                 for x in CustomReportDictAutoPager(self.user, report)]
         return self.rec_handler.query_models_by_id(wrapper, record_ids)
 
     def get_queue_items_for_records(self, records: Iterable[SapioRecord], wrapper: type[WrappedType],

sapiopycommons/recordmodel/record_handler.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import warnings
 from collections.abc import Iterable
 from weakref import WeakValueDictionary
 
@@ -232,7 +233,7 @@ class RecordHandler:
         :param page_size: The size of the pages to query. If None, the page size may be limited by the platform.
         :return: The record models for the queried records mapped in a dictionary by their record ID.
         """
-        return {x.record_id: x for x in self.query_models_by_id(wrapper_type, ids, page_limit, page_size)}
+        return {AliasUtil.to_record_id(x): x for x in self.query_models_by_id(wrapper_type, ids, page_limit, page_size)}
 
     def query_all_models(self, wrapper_type: type[WrappedType], page_limit: int | None = None,
                          page_size: int | None = None) -> list[WrappedType]:
@@ -300,6 +301,7 @@ class RecordHandler:
             not None, in which case it overwrites the given report's value. Note that the number of the first page is 0.
         :return: The record models for the queried records that matched the given report.
         """
+        warnings.warn("Deprecated in favor of the [System/Custom/Quick]ReportRecordAutoPager classes.", DeprecationWarning)
         if isinstance(report_name, str):
             results: list[dict[str, FieldValue]] = CustomReportUtil.run_system_report(self.user, report_name, filters,
                                                                                       page_limit, page_size, page_number)
@@ -893,14 +895,14 @@ class RecordHandler:
 
     @staticmethod
     def values_to_field_maps(field_name: FieldIdentifier, values: Iterable[FieldValue],
-                             existing_fields: list[FieldIdentifier] | None = None) -> list[FieldMap]:
+                             existing_fields: list[FieldMap] | None = None) -> list[FieldMap]:
         """
         Add a list of values for a specific field to a list of dictionaries pairing each value to that field name.
 
         :param field_name: The name of the field that the values are from.
         :param values: A list of field values.
         :param existing_fields: An optional existing fields map list to add the new values to. Values are added in the
-          list in the same order that they appear. If no existing fields are provided, returns a new fields map list.
+            list in the same order that they appear. If no existing fields are provided, returns a new fields map list.
         :return: A fields map list that contains the given values mapped by the given field name.
         """
         # Update the existing fields map list if one is given.

sapiopycommons/samples/aliquot.py

@@ -0,0 +1,48 @@
+from sapiopycommons.general.aliases import SapioRecord
+from sapiopylib.rest.User import SapioUser
+from sapiopylib.rest.utils.MultiMap import SetMultimap
+
+# FR-47421 Added module
+
+def create_aliquot_for_samples(parent_sample_to_num_aliquots_map: dict[SapioRecord, int], user: SapioUser) -> SetMultimap[SapioRecord, int]:
+    """"
+    Ask server to create aliquot records for provided sample parent records.
+    :param parent_sample_to_num_aliquots_map: The dictionary containing (parent sample record) -> (number of aliquots to create) mapping.
+    :return: The dictionary containing (parent sample record) -> (list of new aliquot record ids) mapping.
+    """
+    # throw error if at least one record id is blank
+    has_negative_record_ids = any([record.record_id < 0 for record in parent_sample_to_num_aliquots_map.keys()])
+    if has_negative_record_ids:
+        raise ValueError("At least one record requested for aliquot has a negative record ID. "
+                         "You should have stored record model changes first.")
+    has_blank_record_ids = any([record.record_id is None for record in parent_sample_to_num_aliquots_map.keys()])
+    if has_blank_record_ids:
+        raise ValueError("At least one record requested for aliquot does not currently have a record ID.")
+    record_id_to_sapio_record_map = {record.record_id: record for record in parent_sample_to_num_aliquots_map.keys()}
+    parent_record_id_to_num_aliquots_map = {record.record_id: num_aliquots for record, num_aliquots in parent_sample_to_num_aliquots_map.items()}
+    aliquot_result: SetMultimap[int, int] = create_aliquot_for_samples_record_ids(parent_record_id_to_num_aliquots_map, user)
+    ret: SetMultimap[SapioRecord, int] = SetMultimap()
+    for parent_record_id in aliquot_result.keys():
+        parent_record = record_id_to_sapio_record_map[parent_record_id]
+        for aliquot_record_id in aliquot_result.get(parent_record_id):
+            ret.put(parent_record, aliquot_record_id)
+    return ret
+
+
+def create_aliquot_for_samples_record_ids(parent_record_id_to_num_aliquots_map: dict[int, int], user: SapioUser) -> SetMultimap[int, int]:
+    """
+    Ask the server to create aliquot records for the provided sample record IDs.
+    :param sample_record_id_list: The dictionary containing (parent sample record id) -> (number of aliquots to create) mapping.
+    :return: The dictionary containing (parent sample record id) -> (list of new aliquot record ids) mapping.
+    """
+    if not parent_record_id_to_num_aliquots_map:
+        return SetMultimap()
+    endpoint_path = 'sample/aliquot'
+    response = user.plugin_put(endpoint_path, payload=parent_record_id_to_num_aliquots_map)
+    user.raise_for_status(response)
+    response_map: dict[int, list[int]] = response.json()
+    ret: SetMultimap[int, int] = SetMultimap()
+    for parent_record_id, aliquot_record_ids in response_map.items():
+        for aliquot_record_id in aliquot_record_ids:
+            ret.put(int(parent_record_id), int(aliquot_record_id))
+    return ret