sapiopycommons 2025.4.9a150__py3-none-any.whl → 2025.4.9a476__py3-none-any.whl

sapiopycommons/rules/eln_rule_handler.py

@@ -6,11 +6,12 @@ from sapiopylib.rest.User import SapioUser
 from sapiopylib.rest.pojo.DataRecord import DataRecord
 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.PyRecordModel import PyRecordModel
 from sapiopylib.rest.utils.recordmodel.RecordModelWrapper import WrappedType
 
 from sapiopycommons.general.aliases import FieldMap, AliasUtil, DataTypeIdentifier
 from sapiopycommons.general.exceptions import SapioException
+from sapiopycommons.recordmodel.record_handler import RecordHandler
 
 
 # FR-46064 - Initial port of PyWebhookUtils to sapiopycommons.
@@ -18,23 +19,23 @@ class ElnRuleHandler:
     """
     A class which helps with the parsing and navigation of the ELN rule result map of a webhook context.
     """
-    __context: SapioWebhookContext
+    _context: SapioWebhookContext
     """The context that this handler is working from."""
 
-    __inst_man: RecordModelInstanceManager
-    """The record model instance manager, used for wrapping the data records as record models."""
+    _rec_handler: RecordHandler
+    """The record handler, used for wrapping the data records as record models."""
 
     # Reformatted and cached version of the Velox ELN rule result map for easier handling.
-    __records: dict[str, set[DataRecord]]
+    _records: dict[str, set[DataRecord]]
     """A mapping of data type to the set of data records from the context that match that data type."""
-    __entry_to_records: dict[str, dict[str, set[DataRecord]]]
+    _entry_to_records: dict[str, dict[str, set[DataRecord]]]
     """A mapping of entry name to the sets of data records for that entry, each set of records being mapped by its
     data type."""
-    __field_maps: dict[str, dict[int, FieldMap]]
+    _field_maps: dict[str, dict[int, FieldMap]]
     """A mapping of data type to the field maps from the context that match that data type. In order to prevent
     duplicate field maps, each field map is in a dict keyed by the RecordId field in the field map, since field maps
     are just dictionaries and dictionaries aren't hashable and therefore can't go in a set."""
-    __entry_to_field_maps: dict[str, dict[str, dict[int, FieldMap]]]
+    _entry_to_field_maps: dict[str, dict[str, dict[int, FieldMap]]]
     """A mapping of entry name to the lists of field maps for that entry, each grouping of field maps being mapped by
     its data type."""
 
@@ -59,8 +60,8 @@ class ElnRuleHandler:
 
         if context.velox_eln_rule_result_map is None:
             raise SapioException("No Velox ELN rule result map in context for ElnRuleHandler to parse.")
-        self.__context = context
-        self.__inst_man = RecordModelManager(context.user).instance_manager
+        self._context = context
+        self._rec_handler = RecordHandler(context)
         self.__cache_records()
 
     def __cache_records(self) -> None:
@@ -70,10 +71,10 @@ class ElnRuleHandler:
         from to another dict that maps the data types to the records of that type.
         Doesn't cache any relationship info from the VeloxRuleType of the rule results.
         """
-        self.__records = {}
-        self.__entry_to_records = {}
+        self._records = {}
+        self._entry_to_records = {}
         # Each entry in the context has a list of results for that entry.
-        for entry, entry_results in self.__context.velox_eln_rule_result_map.items():
+        for entry, entry_results in self._context.velox_eln_rule_result_map.items():
             # Keep track of the records for this specific entry.
             entry_dict: dict[str, set[DataRecord]] = {}
             # Entry results consist of a record ID of the record in the entry and a list of results tied to that record.
@@ -89,16 +90,16 @@ class ElnRuleHandler:
                         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)
+                        self._records.setdefault(data_type, set()).add(record)
                         # Do the same for the list of records of this type for this specific entry.
                         entry_dict.setdefault(data_type, set()).add(record)
             # Update the records for this entry.
-            self.__entry_to_records.update({entry: entry_dict})
+            self._entry_to_records.update({entry: entry_dict})
 
-        self.__field_maps = {}
-        self.__entry_to_field_maps = {}
+        self._field_maps = {}
+        self._entry_to_field_maps = {}
         # Repeat the same thing for the field map results.
-        for entry, entry_results in self.__context.velox_eln_rule_field_map_result_map.items():
+        for entry, entry_results in self._context.velox_eln_rule_field_map_result_map.items():
             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:
@@ -107,37 +108,41 @@ class ElnRuleHandler:
                         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})
+                        self._field_maps.setdefault(data_type, {}).update({rec_id: field_map})
                         entry_dict.setdefault(data_type, {}).update({rec_id: field_map})
-            self.__entry_to_field_maps.update({entry: entry_dict})
+            self._entry_to_field_maps.update({entry: entry_dict})
 
     def get_entry_names(self) -> list[str]:
         """
         :return: A list of the entry names that may be used with the get_records and get_models functions. These are the
             entries from the experiment that the records in the rule context originate from.
         """
-        return list(self.__entry_to_records.keys())
+        return list(self._entry_to_records.keys())
 
     def get_field_maps_entry_names(self) -> list[str]:
         """
         :return: A list of the entry names that may be used with the get_field_maps function. These are the
             entries from the experiment that the field maps in the rule context originate from.
         """
-        return list(self.__entry_to_field_maps.keys())
+        return list(self._entry_to_field_maps.keys())
 
+    # CR-47529: Add info about HVDT behavior to the docstring of these functions.
     def get_records(self, data_type: DataTypeIdentifier, entry: str | None = None) -> list[DataRecord]:
         """
         Get records from the cached context with the given data type. Capable of being filtered to searching within
         the context of an entry name. If the given data type or entry does not exist in the context,
         returns an empty list.
 
+        Note that if you are attempting to retrieve record that are high volume data types and are receiving nothing,
+        the HVDTs may have been sent as field maps. Consider using the get_field_maps function if this occurs.
+
         :param data_type: The data type of the records to return.
         :param entry: The name of the entry to grab the records from. If None, returns the records that match the data
             type from every entry. If an entry is provided, but it does not exist in the context, returns an empty list.
         :return: The records from the context that match the input parameters.
         """
         data_type: str = AliasUtil.to_data_type_name(data_type)
-        records: dict[str, set[DataRecord]] = self.__entry_to_records.get(entry, {}) if entry else self.__records
+        records: dict[str, set[DataRecord]] = self._entry_to_records.get(entry, {}) if entry else self._records
         return list(records.get(data_type, []))
 
     # FR-46701: Add functions to the rule handlers for accessing the field maps of inaccessible records in the context.
@@ -149,7 +154,7 @@ class ElnRuleHandler:
 
         Field maps will only exist in the context if the data record that the fields are from is no longer accessible
         to the user. This can occur because the data record was deleted, or because the user does not have access to the
-        record due to ACL.
+        record due to ACL. This can also occur under certain circumstances if the records are HVDTs.
 
         :param data_type: The data type of the field maps to return.
         :param entry: The name of the entry to grab the field maps from. If None, returns the field maps that match the
@@ -158,19 +163,25 @@ class ElnRuleHandler:
         :return: The field maps from the context that match the input parameters.
         """
         data_type: str = AliasUtil.to_data_type_name(data_type)
-        field_maps: dict[str, dict[int, FieldMap]] = self.__entry_to_field_maps.get(entry, {}) if entry else self.__field_maps
+        field_maps: dict[str, dict[int, FieldMap]] = self._entry_to_field_maps.get(entry, {}) if entry else self._field_maps
         return list(field_maps.get(data_type, {}).values())
 
-    def get_models(self, wrapper_type: type[WrappedType], entry: str | None = None) -> list[WrappedType]:
+    # CR-47491: Support providing a data type name string to receive PyRecordModels instead of requiring a WrapperType.
+    def get_models(self, wrapper_type: type[WrappedType] | str, entry: str | None = None) \
+            -> list[WrappedType] | list[PyRecordModel]:
         """
         Get record models from the cached context with the given data type. Capable of being filtered to searching
         within the context of an entry name. If the given data type or entry does not exist in the context,
         returns an empty list.
 
-        :param wrapper_type: The record model wrapper to use.
+        Note that if you are attempting to retrieve record that are high volume data types and are receiving nothing,
+        the HVDTs may have been sent as field maps. Consider using the get_field_maps function if this occurs.
+
+        :param wrapper_type: The record model wrapper or data type name of the record to get from the context.
         :param entry: The name of the entry to grab the records from. If None, returns the records that match the data
             type from every entry. If an entry is provided, but it does not exist in the context, returns an empty list.
-        :return: The record models from the context that match the input parameters.
+        :return: The record models from the context that match the input parameters. If a data type name was used
+            instead of a model wrapper, then the returned records will be PyRecordModels instead of WrappedRecordModels.
         """
-        dt: str = wrapper_type.get_wrapper_data_type_name()
-        return self.__inst_man.add_existing_records_of_type(self.get_records(dt, entry), wrapper_type)
+        dt: str = AliasUtil.to_data_type_name(wrapper_type)
+        return self._rec_handler.wrap_models(self.get_records(dt, entry), wrapper_type)

sapiopycommons/rules/on_save_rule_handler.py

@@ -6,11 +6,12 @@ from sapiopylib.rest.User import SapioUser
 from sapiopylib.rest.pojo.DataRecord import DataRecord
 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.PyRecordModel import PyRecordModel
 from sapiopylib.rest.utils.recordmodel.RecordModelWrapper import WrappedType
 
 from sapiopycommons.general.aliases import FieldMap, DataTypeIdentifier, AliasUtil
 from sapiopycommons.general.exceptions import SapioException
+from sapiopycommons.recordmodel.record_handler import RecordHandler
 
 
 # FR-46064 - Initial port of PyWebhookUtils to sapiopycommons.
@@ -18,23 +19,23 @@ class OnSaveRuleHandler:
     """
     A class which helps with the parsing and navigation of the on save rule result map of a webhook context.
     """
-    __context: SapioWebhookContext
+    _context: SapioWebhookContext
     """The context that this handler is working from."""
 
-    __inst_man: RecordModelInstanceManager
-    """The record model instance manager, used for wrapping the data records as record models."""
+    _rec_handler: RecordHandler
+    """The record handler, used for wrapping the data records as record models."""
 
     # Reformatted and cached version of the Velox on save rule result map for easier handling.
-    __records: dict[str, set[DataRecord]]
+    _records: dict[str, set[DataRecord]]
     """A mapping of data type to the set of data records from the context that match that data type."""
-    __base_id_to_records: dict[int, dict[str, set[DataRecord]]]
+    _base_id_to_records: dict[int, dict[str, set[DataRecord]]]
     """A mapping of record IDs of records in the context.data_record_list to the sets of data records related to that
     record, each set of records being mapped by its data type."""
-    __field_maps: dict[str, dict[int, FieldMap]]
+    _field_maps: dict[str, dict[int, FieldMap]]
     """A mapping of data type to the field maps from the context that match that data type. In order to prevent
     duplicate field maps, each field map is in a dict keyed by the RecordId field in the field map, since field maps
     are just dictionaries and dictionaries aren't hashable and therefore can't go in a set."""
-    __base_id_to_field_maps: dict[int, dict[str, dict[int, FieldMap]]]
+    _base_id_to_field_maps: dict[int, dict[str, dict[int, FieldMap]]]
     """A mapping of record IDs of records in the context.data_record_list to the field maps related to that
     record, each grouping of field maps being mapped by its data type."""
 
@@ -59,8 +60,8 @@ class OnSaveRuleHandler:
 
         if context.velox_on_save_result_map is None:
             raise SapioException("No Velox on save rule result map in context for OnSaveRuleHandler to parse.")
-        self.__context = context
-        self.__inst_man = RecordModelManager(context.user).instance_manager
+        self._context = context
+        self._rec_handler = RecordHandler(context)
         self.__cache_records()
 
     def __cache_records(self) -> None:
@@ -69,10 +70,10 @@ class OnSaveRuleHandler:
         each record to a set of all records of that data type. The other cache maps the record ID that the records relate
         to with another dict that maps the data types to the records of that type. Doesn't cache any relationship info.
         """
-        self.__records = {}
-        self.__base_id_to_records = {}
+        self._records = {}
+        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():
+        for record_id, rule_results in self._context.velox_on_save_result_map.items():
             # 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
@@ -86,16 +87,16 @@ class OnSaveRuleHandler:
                     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)
+                    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.
                     id_dict.setdefault(data_type, set()).add(record)
             # Update the related records for this record ID.
-            self.__base_id_to_records.update({record_id: id_dict})
+            self._base_id_to_records.update({record_id: id_dict})
 
-        self.__field_maps = {}
-        self.__base_id_to_field_maps = {}
+        self._field_maps = {}
+        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():
+        for record_id, rule_results in self._context.velox_on_save_field_map_result_map.items():
             id_dict: dict[str, dict[int, FieldMap]] = {}
             for record_result in rule_results:
                 data_type: str = record_result.velox_type_pojo.data_type_name
@@ -103,37 +104,41 @@ class OnSaveRuleHandler:
                     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})
+                    self._field_maps.setdefault(data_type, {}).update({rec_id: field_map})
                     id_dict.setdefault(data_type, {}).update({rec_id: field_map})
-            self.__base_id_to_field_maps.update({record_id: id_dict})
+            self._base_id_to_field_maps.update({record_id: id_dict})
 
     def get_base_record_ids(self) -> list[int]:
         """
         :return: A list of the record IDs that may be used with the get_records and get_models functions. These are the
             record IDs to the records that caused the rule to trigger.
         """
-        return list(self.__base_id_to_records.keys())
+        return list(self._base_id_to_records.keys())
 
     def get_field_maps_base_record_ids(self) -> list[int]:
         """
         :return: A list of the record IDs that may be used with the get_field_maps function. These are the
             record IDs to the records that caused the rule to trigger.
         """
-        return list(self.__base_id_to_field_maps.keys())
+        return list(self._base_id_to_field_maps.keys())
 
+    # CR-47529: Add info about HVDT behavior to the docstring of these functions.
     def get_records(self, data_type: DataTypeIdentifier, record_id: int | None = None) -> list[DataRecord]:
         """
         Get records from the cached context with the given data type. Capable of being filtered to searching within
         the context of a record ID. If the given data type or record ID does not exist in the context,
         returns an empty list.
 
+        Note that if you are attempting to retrieve record that are high volume data types and are receiving nothing,
+        the HVDTs may have been sent as field maps. Consider using the get_field_maps function if this occurs.
+
         :param data_type: The data type of the records to return.
         :param record_id: The record ID of the base record to search from. If None, returns the records that match the
             data type from every ID. If an ID is provided, but it does not exist in the context, returns an empty list.
         :return: The records from the context that match the input parameters.
         """
         data_type: str = AliasUtil.to_data_type_name(data_type)
-        records: dict[str, set[DataRecord]] = self.__base_id_to_records.get(record_id, {}) if record_id else self.__records
+        records: dict[str, set[DataRecord]] = self._base_id_to_records.get(record_id, {}) if record_id else self._records
         return list(records.get(data_type, []))
 
     # FR-46701: Add functions to the rule handlers for accessing the field maps of inaccessible records in the context.
@@ -145,7 +150,7 @@ class OnSaveRuleHandler:
 
         Field maps will only exist in the context if the data record that the fields are from is no longer accessible
         to the user. This can occur because the data record was deleted, or because the user does not have access to the
-        record due to ACL.
+        record due to ACL. This can also occur under certain circumstances if the records are HVDTs.
 
         :param data_type: The data type of the field maps to return.
         :param record_id: The record ID of the base record to search from. If None, returns the field maps that match
@@ -154,19 +159,25 @@ class OnSaveRuleHandler:
         :return: The field maps from the context that match the input parameters.
         """
         data_type: str = AliasUtil.to_data_type_name(data_type)
-        field_maps: dict[str, dict[int, FieldMap]] = self.__base_id_to_field_maps.get(record_id, {}) if record_id else self.__field_maps
+        field_maps: dict[str, dict[int, FieldMap]] = self._base_id_to_field_maps.get(record_id, {}) if record_id else self._field_maps
         return list(field_maps.get(data_type, {}).values())
 
-    def get_models(self, wrapper_type: type[WrappedType], record_id: int | None = None) -> list[WrappedType]:
+    # CR-47491: Support providing a data type name string to receive PyRecordModels instead of requiring a WrapperType.
+    def get_models(self, wrapper_type: type[WrappedType] | str, record_id: int | None = None) \
+            -> list[WrappedType] | list[PyRecordModel]:
         """
         Get records from the cached context with the given data type. Capable of being filtered to searching within
         the context of a record ID. If the given data type or record ID does not exist in the context,
         returns an empty list.
 
-        :param wrapper_type: The record model wrapper to use.
+        Note that if you are attempting to retrieve record that are high volume data types and are receiving nothing,
+        the HVDTs may have been sent as field maps. Consider using the get_field_maps function if this occurs.
+
+        :param wrapper_type: The record model wrapper or data type name of the record to get from the context.
         :param record_id: The record ID of the base record to search from. If None, returns the records that match the
             data type from ID. If an ID is provided, but it does not exist in the context, returns an empty list.
-        :return: The record models from the context that match the input parameters.
+        :return: The record models from the context that match the input parameters. If a data type name was used
+            instead of a model wrapper, then the returned records will be PyRecordModels instead of WrappedRecordModels.
         """
-        dt: str = wrapper_type.get_wrapper_data_type_name()
-        return self.__inst_man.add_existing_records_of_type(self.get_records(dt, record_id), wrapper_type)
+        dt: str = AliasUtil.to_data_type_name(wrapper_type)
+        return self._rec_handler.wrap_models(self.get_records(dt, record_id), wrapper_type)

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