sapiopycommons 2024.11.11a364__py3-none-any.whl → 2024.11.18a366__py3-none-any.whl

sapiopycommons/webhook/webhook_handlers.py

@@ -4,16 +4,25 @@ from logging import Logger
 
 from sapiopylib.rest.DataMgmtService import DataMgmtServer
 from sapiopylib.rest.DataRecordManagerService import DataRecordManager
+from sapiopylib.rest.User import SapioUser
 from sapiopylib.rest.WebhookService import AbstractWebhookHandler
+from sapiopylib.rest.pojo.Message import VeloxLogMessage, VeloxLogLevel
 from sapiopylib.rest.pojo.webhook.WebhookContext import SapioWebhookContext
 from sapiopylib.rest.pojo.webhook.WebhookEnums import WebhookEndpointType
 from sapiopylib.rest.pojo.webhook.WebhookResult import SapioWebhookResult
+from sapiopylib.rest.utils.DataTypeCacheManager import DataTypeCacheManager
 from sapiopylib.rest.utils.recordmodel.RecordModelManager import RecordModelManager, RecordModelInstanceManager, \
     RecordModelRelationshipManager
 from sapiopylib.rest.utils.recordmodel.ancestry import RecordModelAncestorManager
 
+from sapiopycommons.callbacks.callback_util import CallbackUtil
+from sapiopycommons.eln.experiment_handler import ExperimentHandler
 from sapiopycommons.general.exceptions import SapioUserErrorException, SapioCriticalErrorException, \
-    SapioUserCancelledException
+    SapioUserCancelledException, SapioException, SapioDialogTimeoutException
+from sapiopycommons.general.sapio_links import SapioNavigationLinker
+from sapiopycommons.recordmodel.record_handler import RecordHandler
+from sapiopycommons.rules.eln_rule_handler import ElnRuleHandler
+from sapiopycommons.rules.on_save_rule_handler import OnSaveRuleHandler
 
 
 # FR-46064 - Initial port of PyWebhookUtils to sapiopycommons.
@@ -25,6 +34,7 @@ class CommonsWebhookHandler(AbstractWebhookHandler):
     """
     logger: Logger
 
+    user: SapioUser
     context: SapioWebhookContext
 
     dr_man: DataRecordManager
@@ -34,29 +44,64 @@ class CommonsWebhookHandler(AbstractWebhookHandler):
     # FR-46329: Add the ancestor manager to CommonsWebhookHandler.
     an_man: RecordModelAncestorManager
 
+    dt_cache: DataTypeCacheManager
+    rec_handler: RecordHandler
+    callback: CallbackUtil
+    exp_handler: ExperimentHandler | None
+    rule_handler: OnSaveRuleHandler | ElnRuleHandler | None
+
     def run(self, context: SapioWebhookContext) -> SapioWebhookResult:
+        self.user = context.user
         self.context = context
-        self.logger = context.user.logger
+
+        self.logger = self.user.logger
 
         self.dr_man = context.data_record_manager
-        self.rec_man = RecordModelManager(context.user)
+        self.rec_man = RecordModelManager(self.user)
         self.inst_man = self.rec_man.instance_manager
         self.rel_man = self.rec_man.relationship_manager
         self.an_man = RecordModelAncestorManager(self.rec_man)
 
+        self.dt_cache = DataTypeCacheManager(self.user)
+        self.rec_handler = RecordHandler(context)
+        self.callback = CallbackUtil(context)
+        if context.eln_experiment is not None:
+            self.exp_handler = ExperimentHandler(context)
+        else:
+            self.exp_handler = None
+        if self.is_on_save_rule():
+            self.rule_handler = OnSaveRuleHandler(context)
+        elif self.is_eln_rule():
+            self.rule_handler = ElnRuleHandler(context)
+        else:
+            self.rule_handler = None
+
         # Wrap the execution of each webhook in a try/catch. If an exception occurs, handle any special sapiopycommons
         # exceptions. Otherwise, return a generic message stating that an error occurred.
         try:
-            return self.execute(context)
+            self.initialize(context)
+            result = self.execute(context)
+            if result is None:
+                raise SapioException("Your execute function returned a None result! Don't forget your return statement!")
+            return result
         except SapioUserErrorException as e:
             return self.handle_user_error_exception(e)
         except SapioCriticalErrorException as e:
             return self.handle_critical_error_exception(e)
         except SapioUserCancelledException as e:
             return self.handle_user_cancelled_exception(e)
+        except SapioDialogTimeoutException as e:
+            return self.handle_dialog_timeout_exception(e)
         except Exception as e:
             return self.handle_unexpected_exception(e)
 
+    def initialize(self, context: SapioWebhookContext) -> None:
+        """
+        A function that can be optionally overridden by your webhooks to initialize additional instance variables,
+        or set up whatever else you wish to set up before the execute function is ran. Default behavior does nothing.
+        """
+        pass
+
     @abstractmethod
     def execute(self, context: SapioWebhookContext) -> SapioWebhookResult:
         """
@@ -68,11 +113,12 @@ class CommonsWebhookHandler(AbstractWebhookHandler):
     # the run method and into their own functions.
     def handle_user_error_exception(self, e: SapioUserErrorException) -> SapioWebhookResult:
         """
-        Handle a SapioUserErrorException. Default behavior returns the error message as display text in a webhook
-        result.
+        Handle a SapioUserErrorException.
+
+        Default behavior returns a false result and the error message as display text in a webhook result.
 
         :param e: The exception that was raised.
-        :return: A SapioWebhookResult reporting the exception to the user.
+        :return: A SapioWebhookResult to end the webhook session with.
         """
         result: SapioWebhookResult | None = self.handle_any_exception(e)
         if result is not None:
@@ -82,45 +128,83 @@ class CommonsWebhookHandler(AbstractWebhookHandler):
 
     def handle_critical_error_exception(self, e: SapioCriticalErrorException) -> SapioWebhookResult:
         """
-        Handle a SapioCriticalErrorException. Default behavior makes a display_error client callback.
+        Handle a SapioCriticalErrorException.
+
+        Default behavior makes a display_error client callback with the error message and returns a false result.
 
         :param e: The exception that was raised.
-        :return: A SapioWebhookResult reporting the exception to the user.
+        :return: A SapioWebhookResult to end the webhook session with.
         """
         result: SapioWebhookResult | None = self.handle_any_exception(e)
         if result is not None:
             return result
         self.log_error(traceback.format_exc())
-        DataMgmtServer.get_client_callback(self.context.user).display_error(e.args[0])
+        # This error can be thrown by endpoints that can't send client callbacks. If that happens, fall back onto
+        # sending display text instead.
+        if self.can_send_client_callback():
+            self.callback.display_error(e.args[0])
+        else:
+            return SapioWebhookResult(False, e.args[0])
         return SapioWebhookResult(False)
 
-    def handle_unexpected_exception(self, e: Exception) -> SapioWebhookResult:
+    def handle_user_cancelled_exception(self, e: SapioUserCancelledException) -> SapioWebhookResult:
         """
-        Handle a generic exception which isn't a SapioUserErrorException or SapioCriticalErrorException. Default
-        behavior returns a generic error message as display text informing the user to contact Sapio support.
+        Handle a SapioUserCancelledException.
+
+        Default behavior simply ends the webhook session with a true result (since the user cancelling is a valid
+        action).
 
         :param e: The exception that was raised.
-        :return: A SapioWebhookResult reporting the exception to the user.
+        :return: A SapioWebhookResult to end the webhook session with.
         """
         result: SapioWebhookResult | None = self.handle_any_exception(e)
         if result is not None:
             return result
-        self.log_error(traceback.format_exc())
-        return SapioWebhookResult(False, display_text="Unexpected error occurred during webhook execution. "
-                                                      "Please contact Sapio support.")
+        return SapioWebhookResult(True)
 
-    def handle_user_cancelled_exception(self, e: SapioUserCancelledException) -> SapioWebhookResult:
+    def handle_dialog_timeout_exception(self, e: SapioDialogTimeoutException) -> SapioWebhookResult:
         """
-        Handle a SapioUserCancelledException. Default behavior returns "User Cancelled" as display text in a webhook
-        result.
+        Handle a SapioDialogTimeoutException.
+
+        Default behavior displays an OK popup notifying the user that the dialog has timed out and returns a false
+        webhook result.
+
+        :param e: The exception that was raised.
+        :return: A SapioWebhookResult to end the webhook session with.
+        """
+        result: SapioWebhookResult | None = self.handle_any_exception(e)
+        if result is not None:
+            return result
+        # This dialog could time out too! Ignore it if it does.
+        # No need to check can_send_client_callback() here, as this exception should only be thrown by endpoints that
+        # are capable of sending callbacks.
+        try:
+            self.callback.ok_dialog("Notice", "You have remained idle for too long and this dialog has timed out. "
+                                              "Close and re-initiate it to continue.")
+        except SapioDialogTimeoutException:
+            pass
+        return SapioWebhookResult(False)
+
+    def handle_unexpected_exception(self, e: Exception) -> SapioWebhookResult:
+        """
+        Handle a generic exception which isn't one of the handled Sapio exceptions.
+
+        Default behavior returns a false webhook result with a generic error message as display text informing the user
+        to contact Sapio support. Additionally, the stace trace of the exception that was thrown is logged to the
+        execution log for the webhook call in the system.
 
         :param e: The exception that was raised.
-        :return: A SapioWebhookResult with display text saying the user cancelled the request.
+        :return: A SapioWebhookResult to end the webhook session with.
         """
         result: SapioWebhookResult | None = self.handle_any_exception(e)
         if result is not None:
             return result
-        return SapioWebhookResult(False, display_text="User cancelled.")
+        msg: str = traceback.format_exc()
+        self.log_error(msg)
+        # FR-47079: Also log all unexpected exception messages to the webhook execution log within the platform.
+        self.log_error_to_webhook_execution_log(msg)
+        return SapioWebhookResult(False, display_text="Unexpected error occurred during webhook execution. "
+                                                      "Please contact Sapio support.")
 
     # noinspection PyMethodMayBeStatic,PyUnusedLocal
     def handle_any_exception(self, e: Exception) -> SapioWebhookResult | None:
@@ -130,38 +214,65 @@ class CommonsWebhookHandler(AbstractWebhookHandler):
 
         :param e: The exception that was raised.
         :return: An optional SapioWebhookResult. May return a custom message to the client that wouldn't have been
-            sent by one of the normal exception handlers, or may return None if no result needs returned.
+            sent by one of the normal exception handlers, or may return None if no result needs returned. It a result is
+            returned, then the default behavior of other exception handlers is skipped.
         """
         return None
 
     def log_info(self, msg: str) -> None:
         """
-        Write an info message to the log. Log destination is stdout. This message will be prepended with the user's
-        username and the experiment ID of the experiment they are in, if any.
+        Write an info message to the webhook server log. Log destination is stdout. This message will be prepended with
+        the user's username and the experiment ID of the experiment they are in, if any.
         """
-        exp_id = None
-        if self.context.eln_experiment is not None:
-            exp_id = self.context.eln_experiment.notebook_experiment_id
-        # CR-46333: Add the user's group to the logging message.
-        user = self.context.user
-        username = user.username
-        group_name = user.session_additional_data.current_group_name
-        self.logger.info(f"(User: {username}, Group: {group_name}, Experiment: {exp_id}):\n{msg}")
+        self.logger.info(self._format_log(msg, "log_info call"))
 
     def log_error(self, msg: str) -> None:
         """
-        Write an error message to the log. Log destination is stderr. This message will be prepended with the user's
-        username and the experiment ID of the experiment they are in, if any.
+        Write an error message to the webhook server log. Log destination is stderr. This message will be prepended with
+        the user's username and the experiment ID of the experiment they are in, if any.
+        """
+        # PR-46209: Use logger.error instead of logger.info when logging errors.
+        self.logger.error(self._format_log(msg, "log_error call"))
+
+    def log_error_to_webhook_execution_log(self, msg: str) -> None:
+        """
+        Write an error message to the platform's webhook execution log. This can be reviewed by navigating to the
+        webhook configuration where the webhook that called this function is defined and clicking the "View Log"
+        button. From there, select one of the rows for the webhook executions and click "Download Log" from the right
+        side table.
         """
-        exp_id = None
+        messenger = DataMgmtServer.get_messenger(self.user)
+        messenger.log_message(VeloxLogMessage(message=self._format_log(msg, "Error occurred during webhook execution."),
+                                              log_level=VeloxLogLevel.ERROR,
+                                              originating_class=self.__class__.__name__))
+
+    def _format_log(self, msg: str, prefix: str | None = None) -> str:
+        """
+        Given a message to log, populate it with some metadata about this particular webhook execution, including
+        the group of the user and the invocation type of the webhook call.
+        """
+        # If we're able to, provide a link to the location that the error occurred at.
+        navigator = SapioNavigationLinker(self.context)
         if self.context.eln_experiment is not None:
-            exp_id = self.context.eln_experiment.notebook_experiment_id
+            link = navigator.experiment(self.context.eln_experiment)
+        elif self.context.data_record and not self.context.data_record_list:
+            link = navigator.data_record(self.context.data_record)
+        elif self.context.base_data_record:
+            link = navigator.data_record(self.context.base_data_record)
+        else:
+            link = None
+
+        message: str = ""
+        if prefix:
+            message += prefix + "\n"
+        message += f"Webhook invocation type: {self.context.end_point_type.display_name}\n"
+        message += f"Username: {self.user.username}\n"
         # CR-46333: Add the user's group to the logging message.
-        user = self.context.user
-        username = user.username
-        group_name = user.session_additional_data.current_group_name
-        # PR-46209: Use logger.error instead of logger.info when logging errors.
-        self.logger.error(f"(User: {username}, Group: {group_name}, Experiment: {exp_id}):\n{msg}")
+        message += f"User group: {self.user.session_additional_data.current_group_name}\n"
+        if link:
+            message += f"User location: {link}\n"
+        message += msg
+        return message
 
     def is_main_toolbar(self) -> bool:
         """
@@ -237,3 +348,51 @@ class CommonsWebhookHandler(AbstractWebhookHandler):
         :return: True if this endpoint was invoked as a scheduled action.
         """
         return self.context.end_point_type == WebhookEndpointType.SCHEDULEDPLUGIN
+
+    def is_action_button_field(self) -> bool:
+        """
+        :return: True if this endpoint was invoked as an action button field.
+        """
+        return self.context.end_point_type == WebhookEndpointType.ACTIONDATAFIELD
+
+    def is_action_text_field(self) -> bool:
+        """
+        :return: True if this endpoint was invoked as an action text field.
+        """
+        return self.context.end_point_type == WebhookEndpointType.ACTION_TEXT_FIELD
+
+    def is_custom(self) -> bool:
+        """
+        :return: True if this endpoint was invoked from a custom point, such as a custom queue.
+        """
+        return self.context.end_point_type == WebhookEndpointType.CUSTOM
+
+    def is_calendar_event_click_handler(self) -> bool:
+        """
+        :return: True if this endpoint was invoked from a calendar event click handler.
+        """
+        return self.context.end_point_type == WebhookEndpointType.CALENDAR_EVENT_CLICK_HANDLER
+
+    def is_eln_menu_grabber(self) -> bool:
+        """
+        :return: True if this endpoint was invoked as a notebook entry grabber.
+        """
+        return self.context.end_point_type == WebhookEndpointType.NOTEBOOKEXPERIMENTGRABBER
+
+    def is_conversation_bot(self) -> bool:
+        """
+        :return: True if this endpoint was invoked as from a conversation bot.
+        """
+        return self.context.end_point_type == WebhookEndpointType.CONVERSATION_BOT
+
+    def is_multi_data_type_table_toolbar(self) -> bool:
+        """
+        :return: True if this endpoint was invoked as a multi data type table toolbar button.
+        """
+        return self.context.end_point_type == WebhookEndpointType.REPORTTOOLBAR
+
+    def can_send_client_callback(self) -> bool:
+        """
+        :return: Whether client callbacks and directives can be sent from this webhook's endpoint type.
+        """
+        return self.context.is_client_callback_available

sapiopycommons/webhook/webservice_handlers.py

@@ -0,0 +1,67 @@
+import sys
+import traceback
+from abc import abstractmethod
+from typing import Any
+
+from flask import request
+from sapiopylib.rest.User import SapioUser
+from sapiopylib.rest.WebhookService import AbstractWebhookHandler
+from sapiopylib.rest.pojo.webhook.WebhookResult import SapioWebhookResult
+
+
+class AbstractWebserviceHandler(AbstractWebhookHandler):
+    """
+    A base class for constructing "webservice" endpoints on your webhook server. These are endpoints that can be
+    communicated with by external sources without needing to format the payload JSON in the webhook context format that
+    webhook handlers expect.
+
+    The entire payload JSON is sent to the run method of this class. It is up to the run method to determine how
+    this JSON should be parsed. In order to communicate with a Sapio system, a SapioUser object must be able to be
+    defined using the payload. Functions have been provided for constructing users with various authentication methods.
+
+    Since this extends AbstractWebhookHandler, you can still register endpoints from this class in the same way you
+    would normal webhook endpoints.
+    """
+    def post(self) -> dict[str, Any]:
+        """
+        Internal method to be executed to translate incoming requests.
+        """
+        # noinspection PyBroadException
+        try:
+            return self.run(request.json).to_json()
+        except Exception:
+            print('Error occurred while running webservice custom logic. See traceback.', file=sys.stderr)
+            traceback.print_exc()
+            return SapioWebhookResult(False, display_text="Error occurred during webservice execution.").to_json()
+
+    @abstractmethod
+    def run(self, payload: dict[str, Any]) -> SapioWebhookResult:
+        pass
+
+    def basic_auth(self, url: str, username: str, password: str) -> SapioUser:
+        """
+        :param url: The URL of the Sapio system that requests from this user will be sent to.
+            Must end in /webservice/api
+        :param username: The username to authenticate requests with.
+        :param password: The password to authenticate requests with.
+        :return: A SapioUser that will authenticate requests using basic auth.
+        """
+        return SapioUser(url, self.verify_sapio_cert, self.client_timeout_seconds, username=username, password=password)
+
+    def api_token_auth(self, url: str, api_token: str) -> SapioUser:
+        """
+        :param url: The URL of the Sapio system that requests from this user will be sent to.
+            Must end in /webservice/api
+        :param api_token: The API token to authenticate requests with.
+        :return: A SapioUser that will authenticate requests using an API token.
+        """
+        return SapioUser(url, self.verify_sapio_cert, self.client_timeout_seconds, api_token=api_token)
+
+    def bearer_token_auth(self, url: str, bearer_token: str) -> SapioUser:
+        """
+        :param url: The URL of the Sapio system that requests from this user will be sent to.
+            Must end in /webservice/api
+        :param bearer_token: The bearer token to authenticate requests with.
+        :return: A SapioUser that will authenticate requests using a bearer token.
+        """
+        return SapioUser(url, self.verify_sapio_cert, self.client_timeout_seconds, bearer_token=bearer_token)

{sapiopycommons-2024.11.11a364.dist-info → sapiopycommons-2024.11.18a366.dist-info}/METADATA

@@ -1,9 +1,10 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2024.11.11a364
+Version: 2024.11.18a366
 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>
+License: MPL-2.0
 Keywords: eln,lims,rest,sapio
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Developers
@@ -15,7 +16,8 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Requires-Python: >=3.10
-Requires-Dist: sapiopylib>=2023.12.13.174
+Requires-Dist: databind>=4.5
+Requires-Dist: sapiopylib>=2024.5.24.210
 Description-Content-Type: text/markdown
 
 
@@ -48,6 +50,7 @@ This license does not provide any rights to use any other copyrighted artifacts
 ## Dependencies
 The following dependencies are required for this package:
 - [sapiopylib - The official Sapio Informatics Platform Python API package.](https://pypi.org/project/sapiopylib/)
+- [databind - Databind is a library inspired by jackson-databind to de-/serialize Python dataclasses.](https://pypi.org/project/databind/)
 
 ## Getting Help
 If you have a support contract with Sapio Sciences, please use our [technical support channels](https://sapio-sciences.atlassian.net/servicedesk/customer/portals).

sapiopycommons-2024.11.18a366.dist-info/RECORD

@@ -0,0 +1,59 @@
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+sapiopycommons/callbacks/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+sapiopycommons/callbacks/callback_util.py,sha256=nb6cXK8yFq96gtG0Z2NiK-qdNaRh88bavUH-ZoBjh18,67953
+sapiopycommons/callbacks/field_builder.py,sha256=8n0jcbMgtMUHjie4C1-IkpAuHz4zBxbZtWpr4y0kABU,36868
+sapiopycommons/chem/IndigoMolecules.py,sha256=3f-aig3AJkKJhRmhlQ0cI-5G8oeaQk_3foJTDZCvoko,2040
+sapiopycommons/chem/Molecules.py,sha256=SQKnqdZnhYj_6HGtEZmE_1DormonRR1-nBAQ__z4gms,11485
+sapiopycommons/chem/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+sapiopycommons/customreport/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+sapiopycommons/customreport/column_builder.py,sha256=0RO53e9rKPZ07C--KcepN6_tpRw_FxF3O9vdG0ilKG8,3014
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+sapiopycommons/customreport/term_builder.py,sha256=oVsr7iFPnug2TrZUCcAMhyps-b62kDodPcBxyQeneUY,16763
+sapiopycommons/datatype/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+sapiopycommons/datatype/attachment_util.py,sha256=_l2swuP8noIGAl4bwzBUEhr6YlN_OVZl3-gi1XqFHYA,3364
+sapiopycommons/datatype/data_fields.py,sha256=g8Ib6LH8ikNu9AzeVJs8Z2qS8A-cplACeFU7vYguNEY,4063
+sapiopycommons/datatype/pseudo_data_types.py,sha256=Fe75Rnq5evyeJM1nC0sLkLGKAC74g2-GEeTdMeId80o,27649
+sapiopycommons/eln/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+sapiopycommons/eln/experiment_handler.py,sha256=VJPBQSP_4QmhSGDCRDOb5neOjGM6sZ9krvJEmDkpVV8,69282
+sapiopycommons/eln/experiment_report_util.py,sha256=9wWV6oEdKtfn2rI5V0BtmuW9OJlGFd9U07FIf889Gjw,37679
+sapiopycommons/eln/plate_designer.py,sha256=FYJfhhNq8hdfuXgDYOYHy6g0m2zNwQXZWF_MTPzElDg,7184
+sapiopycommons/files/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+sapiopycommons/files/complex_data_loader.py,sha256=T39veNhvYl6j_uZjIIJ8Mk5Aa7otR5RB-g8XlAdkksA,1421
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