sapiopycommons 2025.7.17a612__py3-none-any.whl → 2025.7.18a614__py3-none-any.whl

sapiopycommons/rules/eln_rule_handler.py

@@ -126,16 +126,12 @@ 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.
@@ -154,7 +150,7 @@ 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. This can also occur under certain circumstances if the records are HVDTs.
+        record due to ACL.
 
         :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
@@ -174,9 +170,6 @@ 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

@@ -122,16 +122,12 @@ 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.
@@ -150,7 +146,7 @@ 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. This can also occur under certain circumstances if the records are HVDTs.
+        record due to ACL.
 
         :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
@@ -170,9 +166,6 @@ 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

@@ -7,6 +7,7 @@ import traceback
 from abc import abstractmethod
 from logging import Logger
 
+from sapiopylib.rest import UserManagerService, GroupManagerService, MessengerService
 from sapiopylib.rest.AccessionService import AccessionManager
 from sapiopylib.rest.CustomReportService import CustomReportManager
 from sapiopylib.rest.DashboardManager import DashboardManager
@@ -15,13 +16,10 @@ from sapiopylib.rest.DataRecordManagerService import DataRecordManager
 from sapiopylib.rest.DataService import DataManager
 from sapiopylib.rest.DataTypeService import DataTypeManager
 from sapiopylib.rest.ELNService import ElnManager
-from sapiopylib.rest.GroupManagerService import VeloxGroupManager
-from sapiopylib.rest.MessengerService import SapioMessenger
 from sapiopylib.rest.PicklistService import PickListManager
 from sapiopylib.rest.ReportManager import ReportManager
 from sapiopylib.rest.SesssionManagerService import SessionManager
 from sapiopylib.rest.User import SapioUser
-from sapiopylib.rest.UserManagerService import VeloxUserManager
 from sapiopylib.rest.WebhookService import AbstractWebhookHandler
 from sapiopylib.rest.pojo.Message import VeloxLogMessage, VeloxLogLevel
 from sapiopylib.rest.pojo.webhook.ClientCallbackRequest import PopupType
@@ -87,9 +85,9 @@ class CommonsWebhookHandler(AbstractWebhookHandler):
     """A class for making requests to the data type webservice endpoints."""
     eln_man: ElnManager
     """A class for making requests to the ELN management webservice endpoints."""
-    group_man: VeloxGroupManager
+    group_man: GroupManagerService
     """A class for making requests to the group management webservice endpoints."""
-    messenger: SapioMessenger
+    messenger: MessengerService
     """A class for making requests to the message webservice endpoints."""
     list_man: PickListManager
     """A class for making requests to the pick list webservice endpoints."""
@@ -97,7 +95,7 @@ class CommonsWebhookHandler(AbstractWebhookHandler):
     """A class for making requests to the report webservice endpoints."""
     session_man: SessionManager
     """A class for making requests to the session management webservice endpoints."""
-    user_man: VeloxUserManager
+    user_man: UserManagerService
     """A class for making requests to the user management webservice endpoints."""
 
     rec_man: RecordModelManager
@@ -222,9 +220,6 @@ 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, Mapping
+from typing import Any
 
 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: Mapping[str, str]) -> SapioUser:
+    def authenticate_user(self, headers: dict[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-2025.7.17a612.dist-info → sapiopycommons-2025.7.18a614.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2025.7.17a612
+Version: 2025.7.18a614
 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>=2025.4.17.264
+Requires-Dist: sapiopylib>=2024.5.24.210
 Description-Content-Type: text/markdown
 
 

sapiopycommons-2025.7.18a614.dist-info/RECORD

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sapiopycommons/eln/experiment_cache.py

@@ -1,188 +0,0 @@
-from __future__ import annotations
-
-from weakref import WeakValueDictionary
-
-from sapiopylib.rest.ELNService import ElnManager
-from sapiopylib.rest.User import SapioUser
-from sapiopylib.rest.pojo.datatype.FieldDefinition import AbstractVeloxFieldDefinition
-from sapiopylib.rest.pojo.eln.ElnExperiment import ElnTemplate, TemplateExperimentQuery
-from sapiopylib.rest.pojo.eln.SapioELNEnums import ElnBaseDataType
-from sapiopylib.rest.pojo.eln.field_set import ElnFieldSetInfo
-from sapiopylib.rest.pojo.eln.protocol_template import ProtocolTemplateInfo, ProtocolTemplateQuery
-
-from sapiopycommons.general.aliases import UserIdentifier, AliasUtil
-from sapiopycommons.general.exceptions import SapioException
-
-
-# FR-47530: Created a class that caches experiment template and predefined field information.
-class ExperimentCacheManager:
-    """
-    A class to manage the caching of experiment-related information.
-    """
-    user: SapioUser
-    eln_man: ElnManager
-
-    _templates: list[ElnTemplate]
-    """A list of experiment templates. Only cached when first accessed."""
-    _protocols: list[ProtocolTemplateInfo]
-    """A list of protocol templates. Only cached when first accessed."""
-    _field_sets: dict[str, ElnFieldSetInfo]
-    """A dictionary of field set name to field set. Only cached when first accessed."""
-    _field_set_fields: dict[int, list[AbstractVeloxFieldDefinition]]
-    """A dictionary of field set ID to field definitions. Only cached when first accessed."""
-    _predefined_fields: dict[str, dict[str, AbstractVeloxFieldDefinition]]
-    """A dictionary of ELN data type name to predefined field definitions. Only cached when first accessed."""
-
-    __instances: WeakValueDictionary[SapioUser, ExperimentCacheManager] = WeakValueDictionary()
-    __initialized: bool
-
-    def __new__(cls, context: UserIdentifier):
-        """
-        :param context: The current webhook context or a user object to send requests from.
-        """
-        user = AliasUtil.to_sapio_user(context)
-        obj = cls.__instances.get(user)
-        if not obj:
-            obj = object.__new__(cls)
-            obj.__initialized = False
-            cls.__instances[user] = obj
-        return obj
-
-    def __init__(self, context: UserIdentifier):
-        """
-        :param context: The current webhook context or a user object to send requests from.
-        """
-        if self.__initialized:
-            return
-        self.__initialized = True
-
-        self.user = AliasUtil.to_sapio_user(context)
-        self.eln_man = ElnManager(self.user)
-
-        self._field_set_fields = {}
-        self._predefined_fields = {}
-
-    def get_experiment_template(self, name: str, active: bool = True, version: int | None = None,
-                                first_match: bool = False, public: bool | None = True) -> ElnTemplate:
-        """
-        Get the experiment template with the given information.
-
-        :param name: The name of the template.
-        :param active: Whether the template is marked as active.
-        :param version: The version of the template to get. If None, the latest version will be returned.
-        :param first_match: If true, returns the first match found. If false, raises an exception.
-        :param public: Whether the template is public. If true, only pubic templates will be queried. If false, only
-            private templates will be queried. If None, both public and private templates will be queried. Non-public
-            templates do not have a version number, so this will always fail if public is false and a version number is
-            provided.
-        :return: The experiment template with the given information.
-        """
-        if not hasattr(self, "_templates"):
-            query = TemplateExperimentQuery()
-            query.active_templates_only = False
-            query.latest_version_only = False
-            self._templates = self.eln_man.get_template_experiment_list(query)
-        return self._find_template(self._templates, name, active, version, first_match, public)
-
-
-    def get_protocol_template(self, name: str, active: bool = True, version: int | None = None,
-                              first_match: bool = False, public: bool | None = True) -> ProtocolTemplateInfo:
-        """
-        Get the protocol template with the given information. Will throw an exception if multiple templates match
-        the given information.
-
-        :param name: The name of the template.
-        :param active: Whether the template is marked as active.
-        :param version: The version of the template to get. If None, the latest version will be returned.
-        :param first_match: If true, returns the first match found. If false, raises an exception.
-        :param public: Whether the template is public. If true, only pubic templates will be queried. If false, only
-            private templates will be queried. If None, both public and private templates will be queried. Non-public
-            templates do not have a version number, so this will always fail if public is false and a version number is
-            provided.
-        :return: The protocol template with the given information.
-        """
-        if not hasattr(self, "_protocols"):
-            query = ProtocolTemplateQuery()
-            query.active_templates_only = False
-            query.latest_version_only = False
-            self._protocols = self.eln_man.get_protocol_template_info_list(query)
-        return self._find_template(self._protocols, name, active, version, first_match, public)
-
-    @staticmethod
-    def _find_template(templates: list[ElnTemplate] | list[ProtocolTemplateInfo], name: str, active: bool,
-                       version: int, first_match: bool, public: bool | None) -> ElnTemplate | ProtocolTemplateInfo:
-        """
-        Find the experiment or protocol template with the given information.
-        """
-        matches = []
-        for template in templates:
-            if template.template_name != name:
-                continue
-            if template.active != active:
-                continue
-            if version is not None and template.template_version != version:
-                continue
-            if public is True and template.template_version is None:
-                continue
-            if public is False and template.template_version is not None:
-                continue
-            matches.append(template)
-        if not matches:
-            raise SapioException(f"No template with the name \"{name}\"" +
-                                 ("" if version is None else f" and the version {version}") +
-                                 f" found.")
-        # Only filter for the max version number if any of the matches actually have a version number.
-        versioned_matches = [x for x in matches if x.template_version is not None]
-        if version is None and versioned_matches:
-            return max(versioned_matches, key=lambda x: x.template_version)
-        if len(matches) > 1 and not first_match:
-            raise SapioException(f"Multiple templates with the name \"{name}\" found. Consider setting first_match to "
-                                 f"true, or restrict your search criteria further.")
-        return matches[0]
-
-    def get_predefined_field(self, field_name: str, data_type: ElnBaseDataType) -> AbstractVeloxFieldDefinition:
-        """
-        Get the predefined field of the given name for the given ELN data type.
-
-        :param field_name: The name of the field.
-        :param data_type: The ELN data type of the field.
-        :return: The predefined field of the given name for the given ELN data type.
-        """
-        return self.get_predefined_fields(data_type)[field_name]
-
-    def get_predefined_fields(self, data_type: ElnBaseDataType) -> dict[str, AbstractVeloxFieldDefinition]:
-        """
-        Get the predefined fields for the given ELN data type.
-
-        :param data_type: The ELN data type to get the predefined fields for.
-        :return: A dictionary of field name to field definition for the given ELN data type.
-        """
-        if data_type.data_type_name not in self._predefined_fields:
-            fields: list[AbstractVeloxFieldDefinition] = self.eln_man.get_predefined_fields(data_type)
-            self._predefined_fields[data_type.data_type_name] = {x.data_field_name: x for x in fields}
-        return self._predefined_fields[data_type.data_type_name]
-
-    def get_field_set(self, name: str) -> ElnFieldSetInfo:
-        """
-        Get the field set with the given name.
-
-        :param name: The name of the field set.
-        :return: The field set with the given name.
-        """
-        if not hasattr(self, "_field_sets"):
-            self._field_sets = {x.field_set_name: x for x in self.eln_man.get_field_set_info_list()}
-        return self._field_sets[name]
-
-    def get_field_set_fields(self, field_set: ElnFieldSetInfo | int) -> list[AbstractVeloxFieldDefinition]:
-        """
-        Get the fields of the given field set.
-
-        :param field_set: The field set to get the fields from. Can be either an ElnFieldSetInfo object or an integer
-            for the set ID.
-        :return: The fields of the given field set.
-        """
-        field_set: int = field_set if isinstance(field_set, int) else field_set.field_set_id
-        if field_set in self._field_set_fields:
-            return self._field_set_fields[field_set]
-        self._field_set_fields[field_set] = self.eln_man.get_predefined_fields_from_field_set_id(field_set)
-        return self._field_set_fields[field_set]