sapiopycommons 2025.7.2a578__py3-none-any.whl → 2025.7.2a579__py3-none-any.whl

sapiopycommons/rules/eln_rule_handler.py

@@ -126,12 +126,16 @@ class ElnRuleHandler:
         """
         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.
@@ -150,7 +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
@@ -170,6 +174,9 @@ class ElnRuleHandler:
         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 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.

sapiopycommons/rules/on_save_rule_handler.py

@@ -122,12 +122,16 @@ class OnSaveRuleHandler:
         """
         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.
@@ -146,7 +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
@@ -166,6 +170,9 @@ class OnSaveRuleHandler:
         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 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.

sapiopycommons/webhook/webhook_handlers.py

@@ -220,6 +220,9 @@ class CommonsWebhookHandler(AbstractWebhookHandler):
         else:
             self.custom_context = None
 
+        # CR-47526: Set the dialog timeout to 1 hour by default. This can be overridden by the webhook.
+        self.callback.set_dialog_timeout(3600)
+
         # Set the default display types, titles, and messages for each type of exception that can display a message.
         self.default_user_error_display_type = MessageDisplayType.TOASTER_WARNING
         self.default_critical_error_display_type = MessageDisplayType.DISPLAY_ERROR

sapiopycommons/webhook/webservice_handlers.py

@@ -3,7 +3,7 @@ import traceback
 from abc import abstractmethod, ABC
 from base64 import b64decode
 from logging import Logger
-from typing import Any
+from typing import Any, Mapping
 
 from flask import request, Response, Request
 from sapiopylib.rest.DataRecordManagerService import DataRecordManager
@@ -122,7 +122,7 @@ class AbstractWebserviceHandler(AbstractWebhookHandler):
         """
         pass
 
-    def authenticate_user(self, headers: dict[str, str]) -> SapioUser:
+    def authenticate_user(self, headers: Mapping[str, str]) -> SapioUser:
         """
         Authenticate a user for making requests to a Sapio server using the provided headers. If no user can be
         authenticated, then an exception will be thrown.

{sapiopycommons-2025.7.2a578.dist-info → sapiopycommons-2025.7.2a579.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2025.7.2a578
+Version: 2025.7.2a579
 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>
@@ -17,7 +17,7 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Requires-Python: >=3.10
 Requires-Dist: databind>=4.5
-Requires-Dist: sapiopylib>=2024.5.24.210
+Requires-Dist: sapiopylib>=2025.4.17.264
 Description-Content-Type: text/markdown
 
 

sapiopycommons-2025.7.2a579.dist-info/RECORD

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sapiopycommons/ai/api/fielddefinitions/proto/fields_pb2.py

@@ -1,43 +0,0 @@
-# -*- coding: utf-8 -*-
-# Generated by the protocol buffer compiler.  DO NOT EDIT!
-# NO CHECKED-IN PROTOBUF GENCODE
-# source: sapiopycommons/ai/api/fielddefinitions/proto/fields.proto
-# Protobuf Python Version: 5.29.0
-"""Generated protocol buffer code."""
-from google.protobuf import descriptor as _descriptor
-from google.protobuf import descriptor_pool as _descriptor_pool
-from google.protobuf import runtime_version as _runtime_version
-from google.protobuf import symbol_database as _symbol_database
-from google.protobuf.internal import builder as _builder
-_runtime_version.ValidateProtobufRuntimeVersion(
-    _runtime_version.Domain.PUBLIC,
-    5,
-    29,
-    0,
-    '',
-    'sapiopycommons/ai/api/fielddefinitions/proto/fields.proto'
-)
-# @@protoc_insertion_point(imports)
-
-_sym_db = _symbol_database.Default()
-
-
-
-
-DESCRIPTOR = _descriptor_pool.Default().AddSerializedFile(b'\n9sapiopycommons/ai/api/fielddefinitions/proto/fields.proto\"s\n\rFieldValuePbo\x12\x16\n\x0cstring_value\x18\x0f \x01(\tH\x00\x12\x13\n\tint_value\x18\x0e \x01(\x03H\x00\x12\x16\n\x0c\x64ouble_value\x18\r \x01(\x01H\x00\x12\x14\n\nbool_value\x18\x0c \x01(\x08H\x00\x42\x07\n\x05\x66ield\"\x80\x01\n\x10\x46ieldValueMapPbo\x12-\n\x06\x66ields\x18\x01 \x03(\x0b\x32\x1d.FieldValueMapPbo.FieldsEntry\x1a=\n\x0b\x46ieldsEntry\x12\x0b\n\x03key\x18\x01 \x01(\t\x12\x1d\n\x05value\x18\x02 \x01(\x0b\x32\x0e.FieldValuePbo:\x02\x38\x01\x42(\n$com.velox.api.fielddefinitions.protoP\x01\x62\x06proto3')
-
-_globals = globals()
-_builder.BuildMessageAndEnumDescriptors(DESCRIPTOR, _globals)
-_builder.BuildTopDescriptorsAndMessages(DESCRIPTOR, 'sapiopycommons.ai.api.fielddefinitions.proto.fields_pb2', _globals)
-if not _descriptor._USE_C_DESCRIPTORS:
-  _globals['DESCRIPTOR']._loaded_options = None
-  _globals['DESCRIPTOR']._serialized_options = b'\n$com.velox.api.fielddefinitions.protoP\001'
-  _globals['_FIELDVALUEMAPPBO_FIELDSENTRY']._loaded_options = None
-  _globals['_FIELDVALUEMAPPBO_FIELDSENTRY']._serialized_options = b'8\001'
-  _globals['_FIELDVALUEPBO']._serialized_start=61
-  _globals['_FIELDVALUEPBO']._serialized_end=176
-  _globals['_FIELDVALUEMAPPBO']._serialized_start=179
-  _globals['_FIELDVALUEMAPPBO']._serialized_end=307
-  _globals['_FIELDVALUEMAPPBO_FIELDSENTRY']._serialized_start=246
-  _globals['_FIELDVALUEMAPPBO_FIELDSENTRY']._serialized_end=307
-# @@protoc_insertion_point(module_scope)

sapiopycommons/ai/api/fielddefinitions/proto/fields_pb2.pyi

@@ -1,31 +0,0 @@
-from google.protobuf.internal import containers as _containers
-from google.protobuf import descriptor as _descriptor
-from google.protobuf import message as _message
-from typing import ClassVar as _ClassVar, Mapping as _Mapping, Optional as _Optional, Union as _Union
-
-DESCRIPTOR: _descriptor.FileDescriptor
-
-class FieldValuePbo(_message.Message):
-    __slots__ = ("string_value", "int_value", "double_value", "bool_value")
-    STRING_VALUE_FIELD_NUMBER: _ClassVar[int]
-    INT_VALUE_FIELD_NUMBER: _ClassVar[int]
-    DOUBLE_VALUE_FIELD_NUMBER: _ClassVar[int]
-    BOOL_VALUE_FIELD_NUMBER: _ClassVar[int]
-    string_value: str
-    int_value: int
-    double_value: float
-    bool_value: bool
-    def __init__(self, string_value: _Optional[str] = ..., int_value: _Optional[int] = ..., double_value: _Optional[float] = ..., bool_value: bool = ...) -> None: ...
-
-class FieldValueMapPbo(_message.Message):
-    __slots__ = ("fields",)
-    class FieldsEntry(_message.Message):
-        __slots__ = ("key", "value")
-        KEY_FIELD_NUMBER: _ClassVar[int]
-        VALUE_FIELD_NUMBER: _ClassVar[int]
-        key: str
-        value: FieldValuePbo
-        def __init__(self, key: _Optional[str] = ..., value: _Optional[_Union[FieldValuePbo, _Mapping]] = ...) -> None: ...
-    FIELDS_FIELD_NUMBER: _ClassVar[int]
-    fields: _containers.MessageMap[str, FieldValuePbo]
-    def __init__(self, fields: _Optional[_Mapping[str, FieldValuePbo]] = ...) -> None: ...

sapiopycommons/ai/api/fielddefinitions/proto/fields_pb2_grpc.py

@@ -1,24 +0,0 @@
-# Generated by the gRPC Python protocol compiler plugin. DO NOT EDIT!
-"""Client and server classes corresponding to protobuf-defined services."""
-import grpc
-import warnings
-
-
-GRPC_GENERATED_VERSION = '1.70.0'
-GRPC_VERSION = grpc.__version__
-_version_not_supported = False
-
-try:
-    from grpc._utilities import first_version_is_lower
-    _version_not_supported = first_version_is_lower(GRPC_VERSION, GRPC_GENERATED_VERSION)
-except ImportError:
-    _version_not_supported = True
-
-if _version_not_supported:
-    raise RuntimeError(
-        f'The grpc package installed is at version {GRPC_VERSION},'
-        + f' but the generated code in sapiopycommons/ai/api/fielddefinitions/proto/fields_pb2_grpc.py depends on'
-        + f' grpcio>={GRPC_GENERATED_VERSION}.'
-        + f' Please upgrade your grpc module to grpcio>={GRPC_GENERATED_VERSION}'
-        + f' or downgrade your generated code using grpcio-tools<={GRPC_VERSION}.'
-    )

sapiopycommons/ai/api/fielddefinitions/proto/velox_field_def_pb2.py

@@ -1,123 +0,0 @@
-# -*- coding: utf-8 -*-
-# Generated by the protocol buffer compiler.  DO NOT EDIT!
-# NO CHECKED-IN PROTOBUF GENCODE
-# source: sapiopycommons/ai/api/fielddefinitions/proto/velox_field_def.proto
-# Protobuf Python Version: 5.29.0
-"""Generated protocol buffer code."""
-from google.protobuf import descriptor as _descriptor
-from google.protobuf import descriptor_pool as _descriptor_pool
-from google.protobuf import runtime_version as _runtime_version
-from google.protobuf import symbol_database as _symbol_database
-from google.protobuf.internal import builder as _builder
-_runtime_version.ValidateProtobufRuntimeVersion(
-    _runtime_version.Domain.PUBLIC,
-    5,
-    29,
-    0,
-    '',
-    'sapiopycommons/ai/api/fielddefinitions/proto/velox_field_def.proto'
-)
-# @@protoc_insertion_point(imports)
-
-_sym_db = _symbol_database.Default()
-
-
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-
-_globals = globals()
-_builder.BuildMessageAndEnumDescriptors(DESCRIPTOR, _globals)
-_builder.BuildTopDescriptorsAndMessages(DESCRIPTOR, 'sapiopycommons.ai.api.fielddefinitions.proto.velox_field_def_pb2', _globals)
-if not _descriptor._USE_C_DESCRIPTORS:
-  _globals['DESCRIPTOR']._loaded_options = None
-  _globals['DESCRIPTOR']._serialized_options = b'\n$com.velox.api.fielddefinitions.protoP\001'
-  _globals['_SELECTIONPROPERTIESPBO_COLORMAPPINGENTRY']._loaded_options = None
-  _globals['_SELECTIONPROPERTIESPBO_COLORMAPPINGENTRY']._serialized_options = b'8\001'
-  _globals['_SELECTIONPROPERTIESPBO_PROCESSDETAILMAPENTRY']._loaded_options = None
-  _globals['_SELECTIONPROPERTIESPBO_PROCESSDETAILMAPENTRY']._serialized_options = b'8\001'
-  _globals['_PICKLISTPROPERTIESPBO_COLORMAPPINGENTRY']._loaded_options = None
-  _globals['_PICKLISTPROPERTIESPBO_COLORMAPPINGENTRY']._serialized_options = b'8\001'
-  _globals['_PICKLISTPROPERTIESPBO_PROCESSDETAILMAPENTRY']._loaded_options = None
-  _globals['_PICKLISTPROPERTIESPBO_PROCESSDETAILMAPENTRY']._serialized_options = b'8\001'
-  _globals['_ENUMPROPERTIESPBO_COLORMAPPINGENTRY']._loaded_options = None
-  _globals['_ENUMPROPERTIESPBO_COLORMAPPINGENTRY']._serialized_options = b'8\001'
-  _globals['_FIELDTYPEPBO']._serialized_start=7309
-  _globals['_FIELDTYPEPBO']._serialized_end=7646
-  _globals['_SORTDIRECTIONPBO']._serialized_start=7649
-  _globals['_SORTDIRECTIONPBO']._serialized_end=7785
-  _globals['_FONTSIZEPBO']._serialized_start=7787
-  _globals['_FONTSIZEPBO']._serialized_end=7891
-  _globals['_TEXTDECORATIONPBO']._serialized_start=7894
-  _globals['_TEXTDECORATIONPBO']._serialized_end=8038
-  _globals['_STRINGFORMATPBO']._serialized_start=8040
-  _globals['_STRINGFORMATPBO']._serialized_end=8138
-  _globals['_DOUBLEFORMATPBO']._serialized_start=8140
-  _globals['_DOUBLEFORMATPBO']._serialized_end=8246
-  _globals['_FIELDVALIDATORPBO']._serialized_start=70
-  _globals['_FIELDVALIDATORPBO']._serialized_end=138
-  _globals['_COLORRANGEPBO']._serialized_start=140
-  _globals['_COLORRANGEPBO']._serialized_end=208
-  _globals['_BOOLEANDEPENDENTFIELDENTRYPBO']._serialized_start=210
-  _globals['_BOOLEANDEPENDENTFIELDENTRYPBO']._serialized_end=285
-  _globals['_SELECTIONDEPENDENTFIELDENTRYPBO']._serialized_start=287
-  _globals['_SELECTIONDEPENDENTFIELDENTRYPBO']._serialized_end=364
-  _globals['_ENUMDEPENDENTFIELDENTRYPBO']._serialized_start=366
-  _globals['_ENUMDEPENDENTFIELDENTRYPBO']._serialized_end=438
-  _globals['_PROCESSDETAILENTRYPBO']._serialized_start=440
-  _globals['_PROCESSDETAILENTRYPBO']._serialized_end=484
-  _globals['_BOOLEANPROPERTIESPBO']._serialized_start=487
-  _globals['_BOOLEANPROPERTIESPBO']._serialized_end=676
-  _globals['_DATEPROPERTIESPBO']._serialized_start=678
-  _globals['_DATEPROPERTIESPBO']._serialized_end=793
-  _globals['_DOUBLEPROPERTIESPBO']._serialized_start=796
-  _globals['_DOUBLEPROPERTIESPBO']._serialized_end=1117
-  _globals['_INTEGERPROPERTIESPBO']._serialized_start=1120
-  _globals['_INTEGERPROPERTIESPBO']._serialized_end=1482
-  _globals['_LONGPROPERTIESPBO']._serialized_start=1485
-  _globals['_LONGPROPERTIESPBO']._serialized_end=1844
-  _globals['_SHORTPROPERTIESPBO']._serialized_start=1847
-  _globals['_SHORTPROPERTIESPBO']._serialized_end=2207
-  _globals['_SELECTIONPROPERTIESPBO']._serialized_start=2210
-  _globals['_SELECTIONPROPERTIESPBO']._serialized_end=2945
-  _globals['_SELECTIONPROPERTIESPBO_COLORMAPPINGENTRY']._serialized_start=2793
-  _globals['_SELECTIONPROPERTIESPBO_COLORMAPPINGENTRY']._serialized_end=2844
-  _globals['_SELECTIONPROPERTIESPBO_PROCESSDETAILMAPENTRY']._serialized_start=2846
-  _globals['_SELECTIONPROPERTIESPBO_PROCESSDETAILMAPENTRY']._serialized_end=2925
-  _globals['_STRINGPROPERTIESPBO']._serialized_start=2948
-  _globals['_STRINGPROPERTIESPBO']._serialized_end=3299
-  _globals['_SIDELINKPROPERTIESPBO']._serialized_start=3302
-  _globals['_SIDELINKPROPERTIESPBO']._serialized_end=3511
-  _globals['_PICKLISTPROPERTIESPBO']._serialized_start=3514
-  _globals['_PICKLISTPROPERTIESPBO']._serialized_end=4138
-  _globals['_PICKLISTPROPERTIESPBO_COLORMAPPINGENTRY']._serialized_start=2793
-  _globals['_PICKLISTPROPERTIESPBO_COLORMAPPINGENTRY']._serialized_end=2844
-  _globals['_PICKLISTPROPERTIESPBO_PROCESSDETAILMAPENTRY']._serialized_start=2846
-  _globals['_PICKLISTPROPERTIESPBO_PROCESSDETAILMAPENTRY']._serialized_end=2925
-  _globals['_PARENTLINKPROPERTIESPBO']._serialized_start=4140
-  _globals['_PARENTLINKPROPERTIESPBO']._serialized_end=4188
-  _globals['_MULTIPARENTPROPERTIESPBO']._serialized_start=4190
-  _globals['_MULTIPARENTPROPERTIESPBO']._serialized_end=4216
-  _globals['_IDENTIFIERPROPERTIESPBO']._serialized_start=4218
-  _globals['_IDENTIFIERPROPERTIESPBO']._serialized_end=4266
-  _globals['_FILEBLOBPROPERTIESPBO']._serialized_start=4268
-  _globals['_FILEBLOBPROPERTIESPBO']._serialized_end=4291
-  _globals['_ENUMPROPERTIESPBO']._serialized_start=4294
-  _globals['_ENUMPROPERTIESPBO']._serialized_end=4608
-  _globals['_ENUMPROPERTIESPBO_COLORMAPPINGENTRY']._serialized_start=2793
-  _globals['_ENUMPROPERTIESPBO_COLORMAPPINGENTRY']._serialized_end=2844
-  _globals['_DATERANGEPROPERTIESPBO']._serialized_start=4610
-  _globals['_DATERANGEPROPERTIESPBO']._serialized_end=4728
-  _globals['_CHILDLINKPROPERTIESPBO']._serialized_start=4730
-  _globals['_CHILDLINKPROPERTIESPBO']._serialized_end=4800
-  _globals['_ACTIONSTRINGPROPERTIESPBO']._serialized_start=4803
-  _globals['_ACTIONSTRINGPROPERTIESPBO']._serialized_end=5033
-  _globals['_ACTIONPROPERTIESPBO']._serialized_start=5036
-  _globals['_ACTIONPROPERTIESPBO']._serialized_end=5170
-  _globals['_ACCESSIONPROPERTIESPBO']._serialized_start=5173
-  _globals['_ACCESSIONPROPERTIESPBO']._serialized_end=5413
-  _globals['_VELOXFIELDDEFPBO']._serialized_start=5416
-  _globals['_VELOXFIELDDEFPBO']._serialized_end=7236
-  _globals['_VELOXFIELDDEFLISTPBO']._serialized_start=7238
-  _globals['_VELOXFIELDDEFLISTPBO']._serialized_end=7306
-# @@protoc_insertion_point(module_scope)