sapiopycommons 2025.2.6a420__py3-none-any.whl → 2025.2.7a424__py3-none-any.whl

sapiopycommons/files/file_validator.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-import re
 from abc import abstractmethod
 from typing import Any
 
@@ -10,9 +9,9 @@ from sapiopylib.rest.pojo.datatype.FieldDefinition import VeloxIntegerFieldDefin
     AbstractVeloxFieldDefinition
 
 from sapiopycommons.callbacks.callback_util import CallbackUtil
-from sapiopycommons.customreport.auto_pagers import QuickReportDictAutoPager
 from sapiopycommons.files.file_data_handler import FileDataHandler, FilterList
 from sapiopycommons.general.aliases import UserIdentifier, AliasUtil
+from sapiopycommons.general.custom_report_util import CustomReportUtil
 from sapiopycommons.general.exceptions import SapioUserCancelledException
 from sapiopycommons.general.time_util import TimeUtil
 
@@ -312,8 +311,8 @@ class MatchesPatternRule(ColumnRule):
     """
     pattern: str
 
-    def __init__(self, header: str, pattern: str | re.Pattern[str], *, reason: str | None = None,
-                 whitelist: FilterList = None, blacklist: FilterList = None):
+    def __init__(self, header: str, pattern: str, *, reason: str | None = None, whitelist: FilterList = None,
+                 blacklist: FilterList = None):
         """
         :param header: The header that this rule acts upon.
         :param pattern: A regex pattern.
@@ -530,7 +529,7 @@ class UniqueSystemValueRule(ColumnRule):
         # Run a quick report for all records of this type that match these field values.
         term = RawReportTerm(self.data_type_name, self.data_field_name, RawTermOperation.EQUAL_TO_OPERATOR,
                              "{" + ",".join(values) + "}")
-        results: list[dict[str, Any]] = QuickReportDictAutoPager(self.user, term).get_all_at_once()
+        results: list[dict[str, Any]] = CustomReportUtil.run_quick_report(self.user, term)
         existing_values: list[Any] = [x.get(self.data_field_name) for x in results]
         return file_handler.get_in_list(self.header, existing_values)
 
@@ -564,6 +563,6 @@ class ExistingSystemValueRule(ColumnRule):
         # Run a quick report for all records of this type that match these field values.
         term = RawReportTerm(self.data_type_name, self.data_field_name, RawTermOperation.EQUAL_TO_OPERATOR,
                              "{" + ",".join(values) + "}")
-        results: list[dict[str, Any]] = QuickReportDictAutoPager(self.user, term).get_all_at_once()
+        results: list[dict[str, Any]] = CustomReportUtil.run_quick_report(self.user, term)
         existing_values: list[Any] = [x.get(self.data_field_name) for x in results]
         return file_handler.get_not_in_list(self.header, existing_values)

sapiopycommons/flowcyto/flow_cyto.py

@@ -2,8 +2,8 @@ from __future__ import annotations
 
 from weakref import WeakValueDictionary
 
-from databind.json import dumps
 from sapiopylib.rest.User import SapioUser
+from databind.json import dumps
 
 from sapiopycommons.flowcyto.flowcyto_data import FlowJoWorkspaceInputJson, UploadFCSInputJson, \
     ComputeFlowStatisticsInputJson

sapiopycommons/general/accession_service.py

@@ -95,7 +95,7 @@ class AccessionWithPrefixSuffix(AbstractAccessionServiceOperator):
 
     @property
     def default_accessor_name(self):
-        return "PREFIX_AND_SUFFIX" + "(" + self.prefix + "," + self.suffix + ")"
+        return "PREFIX_AND_SUFFIX" + "(" + self.prefix + "," + self.suffix + ")";
 
 
 class AccessionGlobalPrefixSuffix(AbstractAccessionServiceOperator):

sapiopycommons/general/aliases.py

@@ -1,50 +1,50 @@
 from collections.abc import Iterable
-from typing import Any, TypeAlias
+from typing import Any
 
 from sapiopylib.rest.User import SapioUser
 from sapiopylib.rest.pojo.DataRecord import DataRecord
-from sapiopylib.rest.pojo.datatype.FieldDefinition import FieldType, AbstractVeloxFieldDefinition
+from sapiopylib.rest.pojo.datatype.FieldDefinition import FieldType
 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.webhook.WebhookContext import SapioWebhookContext
 from sapiopylib.rest.utils.Protocols import ElnExperimentProtocol, ElnEntryStep
-from sapiopylib.rest.utils.recordmodel.PyRecordModel import PyRecordModel, AbstractRecordModel
+from sapiopylib.rest.utils.recordmodel.PyRecordModel import PyRecordModel
 from sapiopylib.rest.utils.recordmodel.RecordModelWrapper import WrappedRecordModel, WrappedType, WrapperField
 
 from sapiopycommons.general.exceptions import SapioException
 
-FieldValue: TypeAlias = int | float | str | bool | None
+FieldValue = int | float | str | bool | None
 """Allowable values for fields in the system."""
-RecordModel: TypeAlias = PyRecordModel | AbstractRecordModel | WrappedRecordModel
+RecordModel = PyRecordModel | WrappedRecordModel
 """Different forms that a record model could take."""
-SapioRecord: TypeAlias = DataRecord | RecordModel
+SapioRecord = DataRecord | RecordModel
 """A record could be provided as either a DataRecord, PyRecordModel, or WrappedRecordModel (WrappedType)."""
-RecordIdentifier: TypeAlias = SapioRecord | int
+RecordIdentifier = SapioRecord | int
 """A RecordIdentifier is either a record type or an integer for the record's record ID."""
-DataTypeIdentifier: TypeAlias = SapioRecord | type[WrappedType] | str
+DataTypeIdentifier = SapioRecord | type[WrappedType] | str
 """A DataTypeIdentifier is either a SapioRecord, a record model wrapper type, or a string."""
-FieldIdentifier: TypeAlias = AbstractVeloxFieldDefinition | WrapperField | str | tuple[str, FieldType]
+FieldIdentifier = WrapperField | str | tuple[str, FieldType]
 """A FieldIdentifier is either wrapper field from a record model wrapper, a string, or a tuple of string
 and field type."""
-FieldIdentifierKey: TypeAlias = WrapperField | str
+FieldIdentifierKey = WrapperField | str
 """A FieldIdentifierKey is a FieldIdentifier, except it can't be a tuple, s tuples can't be used as keys in
 dictionaries.."""
-HasFieldWrappers: TypeAlias = type[WrappedType] | WrappedRecordModel
+HasFieldWrappers = type[WrappedType] | WrappedRecordModel
 """An identifier for classes that have wrapper fields."""
-ExperimentIdentifier: TypeAlias = ElnExperimentProtocol | ElnExperiment | int
+ExperimentIdentifier = ElnExperimentProtocol | ElnExperiment | int
 """An ExperimentIdentifier is either an experiment protocol, experiment, or an integer for the experiment's notebook
 ID."""
-ExperimentEntryIdentifier: TypeAlias = ElnEntryStep | ExperimentEntry | int
+ExperimentEntryIdentifier = ElnEntryStep | ExperimentEntry | int
 """An ExperimentEntryIdentifier is either an ELN entry step, experiment entry, or an integer for the entry's ID."""
-FieldMap: TypeAlias = dict[str, FieldValue]
+FieldMap = dict[str, FieldValue]
 """A field map is simply a dict of data field names to values. The purpose of aliasing this is to help distinguish
 any random dict in a webhook from one which is explicitly used for record fields."""
-FieldIdentifierMap: TypeAlias = dict[FieldIdentifierKey, FieldValue]
+FieldIdentifierMap = dict[FieldIdentifierKey, FieldValue]
 """A field identifier map is the same thing as a field map, except the keys can be field identifiers instead
 of just strings. Note that although one of the allowed field identifiers is a tuple, you can't use tuples as
 keys in a dictionary."""
-UserIdentifier: TypeAlias = SapioWebhookContext | SapioUser
+UserIdentifier = SapioWebhookContext | SapioUser
 """An identifier for classes from which a user object can be used for sending requests."""
 
 
@@ -142,25 +142,23 @@ class AliasUtil:
     @staticmethod
     def to_data_field_name(value: FieldIdentifier) -> str:
         """
-        Convert an object that can be used to identify a data field to a data field name string.
+        Convert a string or WrapperField to a data field name string.
 
-        :param value: An object that can be used to identify a data field.
+        :param value: A string or WrapperField.
         :return: A string of the data field name of the input value.
         """
         if isinstance(value, tuple):
             return value[0]
         if isinstance(value, WrapperField):
             return value.field_name
-        if isinstance(value, AbstractVeloxFieldDefinition):
-            return value.data_field_name
         return value
 
     @staticmethod
     def to_data_field_names(values: Iterable[FieldIdentifier]) -> list[str]:
         """
-        Convert an iterable of objects that can be used to identify data fields to a list of data field name strings.
+        Convert an iterable of strings or WrapperFields to a list of data field name strings.
 
-        :param values: An iterable of objects that can be used to identify a data field.
+        :param values: An iterable of strings or WrapperFields.
         :return: A list of strings of the data field names of the input values.
         """
         return [AliasUtil.to_data_field_name(x) for x in values]
@@ -206,32 +204,21 @@ class AliasUtil:
         raise SapioException(f"The wrapper of data type \"{data_type.get_wrapper_data_type_name()}\" doesn't have a "
                              f"field with the name \"{field}\",")
 
-    @staticmethod
-    def to_field_map(record: SapioRecord) -> FieldMap:
-        """
-        Convert a given record value to a field map. This includes the given RecordId of the given record.
-
-        :return: The field map for the input record.
-        """
-        if isinstance(record, DataRecord):
-            # noinspection PyTypeChecker
-            fields: FieldMap = record.get_fields()
-        else:
-            fields: FieldMap = record.fields.copy_to_dict()
-        fields["RecordId"] = AliasUtil.to_record_id(record)
-        return fields
-
     @staticmethod
     def to_field_map_lists(records: Iterable[SapioRecord]) -> list[FieldMap]:
         """
-        Convert a list of variables that could either be DataRecords, PyRecordModels, or WrappedRecordModels
-        to a list of their field maps. This includes the given RecordId of the given records.
+        Convert a list of variables that could either be DataRecords, PyRecordModels,
+        or WrappedRecordModels to a list of their field maps.
 
         :return: A list of field maps for the input records.
         """
         field_map_list: list[FieldMap] = []
         for record in records:
-            field_map_list.append(AliasUtil.to_field_map(record))
+            if isinstance(record, DataRecord):
+                # noinspection PyTypeChecker
+                field_map_list.append(record.get_fields())
+            else:
+                field_map_list.append(record.fields.copy_to_dict())
         return field_map_list
 
     @staticmethod

sapiopycommons/general/audit_log.py

@@ -3,11 +3,11 @@ from enum import Enum
 from sapiopylib.rest.User import SapioUser
 from sapiopylib.rest.pojo.CustomReport import ReportColumn, CustomReportCriteria
 
-from sapiopycommons.customreport.auto_pagers import CustomReportDictAutoPager
 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.custom_report_util import CustomReportUtil
 
 
 class EventType(Enum):
@@ -164,7 +164,7 @@ class AuditLogUtil:
         criteria = AuditLogUtil.create_data_record_audit_log_report(records, fields)
 
         # Then we must run the custom report using that criteria.
-        raw_report_data: list[dict[str, FieldValue]] = CustomReportDictAutoPager(self.user, criteria).get_all_at_once()
+        raw_report_data: list[dict[str, FieldValue]] = CustomReportUtil.run_custom_report(self.user, criteria)
 
         # This section will prepare a map matching the original RecordIdentifier by record id.
         # This is because the audit log entries will have record ids, but we want the keys in our result map

sapiopycommons/general/custom_report_util.py

@@ -1,4 +1,3 @@
-import warnings
 from collections.abc import Iterable
 
 from sapiopylib.rest.DataMgmtService import DataMgmtServer
@@ -41,7 +40,6 @@ class CustomReportUtil:
             had a Sample column with a data field name of Identifier and a Request column with the same data field name,
             then the dictionary keys for these columns would be Sample.Identifier and Request.Identifier respectively.
         """
-        warnings.warn("Deprecated in favor of the SystemReportDictAutoPager class.", DeprecationWarning)
         results: tuple = CustomReportUtil._exhaust_system_report(context, report_name, page_limit,
                                                                  page_size, page_number)
         columns: list[ReportColumn] = results[0]
@@ -84,7 +82,6 @@ class CustomReportUtil:
             had a Sample column with a data field name of Identifier and a Request column with the same data field name,
             then the dictionary keys for these columns would be Sample.Identifier and Request.Identifier respectively.
         """
-        warnings.warn("Deprecated in favor of the CustomReportDictAutoPager class.", DeprecationWarning)
         results: tuple = CustomReportUtil._exhaust_custom_report(context, report_criteria, page_limit,
                                                                  page_size, page_number)
         columns: list[ReportColumn] = results[0]
@@ -120,7 +117,6 @@ class CustomReportUtil:
         :return: The results of the report listed row by row, mapping each cell to the header it is under. The header
             values in the dicts are the data field names of the columns.
         """
-        warnings.warn("Deprecated in favor of the QuickReportDictAutoPager class.", DeprecationWarning)
         results: tuple = CustomReportUtil._exhaust_quick_report(context, report_term, page_limit,
                                                                 page_size, page_number)
         columns: list[ReportColumn] = results[0]
@@ -131,8 +127,7 @@ class CustomReportUtil:
     def get_system_report_criteria(context: UserIdentifier, report_name: str) -> CustomReport:
         """
         Retrieve a custom report from the system given the name of the report. This works by querying the system report
-        with a page number of 0 and page size of 1 to minimize the amount of data transfer needed to retrieve the
-        report's config.
+        with a page number and size of 1 to minimize the amount of data transfer needed to retrieve the report's config.
 
         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.
@@ -148,24 +143,6 @@ class CustomReportUtil:
         report_man = DataMgmtServer.get_custom_report_manager(user)
         return report_man.run_system_report_by_name(report_name, 1, 0)
 
-    @staticmethod
-    def get_quick_report_criteria(context: UserIdentifier, report_term: RawReportTerm) -> CustomReport:
-        """
-        Retrieve a quick report from the system given a report term. This works by making a quick report query
-        with a page number of 0 and page size of 1 to minimize the amount of data transfer needed to retrieve the
-        report's config.
-
-        Using this, you can add to the root term of the search to then run a new search, or provide it to client
-        callbacks or directives that take CustomReports.
-
-        :param context: The current webhook context or a user object to send requests from.
-        :param report_term: The raw report term to use for the quick report.
-        :return: The CustomReport object for the given report term.
-        """
-        user: SapioUser = AliasUtil.to_sapio_user(context)
-        report_man = DataMgmtServer.get_custom_report_manager(user)
-        return report_man.run_quick_report(report_term, 1, 0)
-
     @staticmethod
     def _exhaust_system_report(context: UserIdentifier,
                                report_name: str,

sapiopycommons/general/exceptions.py

@@ -1,20 +1,3 @@
-from enum import Enum
-
-
-class MessageDisplayType(Enum):
-    """
-    An enum representing the different ways in which a message can be displayed to the user.
-    """
-    TOASTER_SUCCESS = 0
-    TOASTER_INFO = 1
-    TOASTER_WARNING = 2
-    TOASTER_ERROR = 3
-    OK_DIALOG = 4
-    DISPLAY_INFO = 5
-    DISPLAY_WARNING = 6
-    DISPLAY_ERROR = 7
-
-
 # FR-46064 - Initial port of PyWebhookUtils to sapiopycommons.
 class SapioException(Exception):
     """
@@ -46,29 +29,7 @@ class SapioDialogTimeoutException(SapioException):
     pass
 
 
-class DisplayableException(SapioException):
-    """
-    A generic exception that promises to return a user-friendly message explaining the error that should be displayed to
-    the user. Note that it is up to whichever class that catches this exception to actually display the message.
-    """
-    msg: str
-    display_type: MessageDisplayType | None
-    title: str | None
-
-    def __init__(self, msg: str, display_type: MessageDisplayType | None = None, title: str | None = None):
-        """
-        :param msg: The message that should be displayed to the user.
-        :param display_type: The manner in which the message should be displayed. If None, then the display type should
-            be controlled by the class that catches this exception.
-        :param title: If the display type is able to have a title, this is the title that will be displayed. If None,
-            then the title should be controlled by the class that catches this exception.
-        """
-        self.msg = msg
-        self.display_type = display_type
-        self.title = title
-
-
-class SapioUserErrorException(DisplayableException):
+class SapioUserErrorException(SapioException):
     """
     An exception caused by user error (e.g. user provided a CSV when an XLSX was expected), which promises to return a
     user-friendly message explaining the error that should be displayed to the user.
@@ -78,7 +39,7 @@ class SapioUserErrorException(DisplayableException):
     pass
 
 
-class SapioCriticalErrorException(DisplayableException):
+class SapioCriticalErrorException(SapioException):
     """
     A critical exception caused by user error, which promises to return a user-friendly message explaining the error
     that should be displayed to the user.

sapiopycommons/multimodal/multimodal.py

@@ -6,7 +6,6 @@ from weakref import WeakValueDictionary
 
 from databind.json import dumps, loads
 from sapiopylib.rest.User import SapioUser
-from sapiopylib.rest.pojo.DataRecord import DataRecord
 
 from sapiopycommons.general.exceptions import SapioException
 from sapiopycommons.multimodal.multimodal_data import *

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 CustomReportRecordAutoPager(self.user, report, wrapper).get_all_at_once()
+        return self.rec_handler.query_models_by_report(wrapper, report)
 
     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 CustomReportDictAutoPager(self.user, report)]
+                                 for x in CustomReportUtil.run_custom_report(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

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-import warnings
 from collections.abc import Iterable
 from weakref import WeakValueDictionary
 
@@ -233,7 +232,7 @@ 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 {AliasUtil.to_record_id(x): x for x in self.query_models_by_id(wrapper_type, ids, page_limit, page_size)}
+        return {x.record_id: 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]:
@@ -301,7 +300,6 @@ 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)
@@ -895,14 +893,14 @@ class RecordHandler:
 
     @staticmethod
     def values_to_field_maps(field_name: FieldIdentifier, values: Iterable[FieldValue],
-                             existing_fields: list[FieldMap] | None = None) -> list[FieldMap]:
+                             existing_fields: list[FieldIdentifier] | 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.