sapiopycommons 2024.3.19a157__py3-none-any.whl → 2025.1.17a402__py3-none-any.whl

sapiopycommons/webhook/webservice_handlers.py

@@ -0,0 +1,317 @@
+import sys
+import traceback
+from abc import abstractmethod, ABC
+from base64 import b64decode
+from logging import Logger
+from typing import Any
+
+from flask import request, Response, Request
+from sapiopylib.rest.DataRecordManagerService import DataRecordManager
+from sapiopylib.rest.User import SapioUser
+from sapiopylib.rest.WebhookService import AbstractWebhookHandler
+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 werkzeug.datastructures import Headers
+from werkzeug.datastructures.structures import MultiDict
+from werkzeug.exceptions import UnsupportedMediaType, BadRequest
+
+from sapiopycommons.general.exceptions import SapioException
+from sapiopycommons.recordmodel.record_handler import RecordHandler
+
+
+class SapioWebserviceException(Exception):
+    """
+    An exception to be thrown by webservice classes when responding to a request with an error.
+    """
+    msg: str
+    code: int
+
+    def __init__(self, msg: str, code: int = 500):
+        """
+        :param msg: The message to return in the webservice response.
+        :param code: The status code to return in the webservice response.
+        """
+        self.msg = msg
+        self.code = code
+
+
+class SapioWebserviceResult:
+    """
+    A result to be returned by AbstractWebserviceHandler endpoints, for sending information back to the caller.
+    """
+    message: str
+    is_error: bool
+    status_code: int
+    payload: dict[str, Any]
+
+    def __init__(self, message: str = "Success", status_code: int = 200, is_error: bool = False,
+                 payload: dict[str, Any] | None = None):
+        """
+        :param message: A message to return to the sender describing what happened.
+        :param status_code: An HTTP status code to return to the sender.
+        :param is_error: Whether the webservice had an error during processing.
+        :param payload: A payload of additional information to return to the sender.
+        """
+        self.message = message
+        self.status_code = status_code
+        self.is_error = is_error
+        self.payload = payload
+        if payload is None:
+            self.payload = {}
+
+    def to_json(self) -> dict[str, Any]:
+        return {"message": self.message,
+                "statusCode": self.status_code,
+                "isError": self.is_error,
+                "payload": self.payload}
+
+    def to_result(self) -> tuple[dict[str, Any], int]:
+        return self.to_json(), self.status_code
+
+
+WebserviceResponse = SapioWebserviceResult | Response | tuple[dict[str, Any] | int]
+
+
+class AbstractWebserviceHandler(AbstractWebhookHandler):
+    """
+    A base class for constructing POST webservice endpoints on your webhook server. These are endpoints that can be
+    communicated with by external sources without needing to format the request in the webhook context format that
+    normal webhook handlers expect.
+
+    Since this extends AbstractWebhookHandler, you can still register endpoints from this class in the same way you
+    would normal webhook endpoints.
+    """
+    request: Request
+
+    def post(self) -> Response | tuple[dict[str, Any], int]:
+        """
+        Internal method to be executed to translate incoming POST requests.
+        """
+        # noinspection PyBroadException
+        try:
+            self.request = request
+            try:
+                raw_json = request.json
+                headers = request.headers
+                params = request.args
+            except UnsupportedMediaType as e:
+                return SapioWebserviceResult(str(e), 415, True).to_json(), 415
+            except BadRequest as e:
+                return SapioWebserviceResult(str(e), 400, True).to_json(), 400
+            ret_val: WebserviceResponse = self.run(raw_json, headers, params)
+            if isinstance(ret_val, SapioWebserviceResult):
+                return ret_val.to_result()
+            return ret_val
+        except Exception:
+            print('Error occurred while running webservice custom logic. See traceback.', file=sys.stderr)
+            traceback.print_exc()
+            return SapioWebserviceResult("Unexpected error occurred.", 500, True).to_json(), 500
+
+    # noinspection PyMethodOverriding
+    @abstractmethod
+    def run(self, payload: Any, headers: Headers, params: MultiDict[str, str]) -> WebserviceResponse:
+        """
+        The execution details for this endpoint.
+
+        :param payload: The JSON payload from the request. Usually a dictionary of strings to Any.
+        :param headers: The headers from the request. Can be used like a dictionary.
+        :param params: The URL parameters from the request.
+        :return: A response object to send back to the requester.
+        """
+        pass
+
+    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.
+
+        :param headers: The headers of the webservice request.
+        :return: A SapioUser object used to make requests to a Sapio server as authorized by the headers.
+        """
+        # Get the system URL from the headers.
+        if "System-URL" not in headers:
+            raise SapioWebserviceException("No \"System-URL\" provided in headers.", 400)
+        url: str = headers.get("System-URL")
+        if not url.endswith("/webservice/api"):
+            raise SapioWebserviceException(f"\"System-URL\" must be a webservice API URL for the target system: {url}", 400)
+
+        # Get the login credentials from the headers.
+        auth: str = headers.get("Authorization")
+        if auth and auth.startswith("Basic "):
+            credentials: list[str] = b64decode(auth.split("Basic ")[1]).decode().split(":")
+            user = self.basic_auth(url, credentials[0], credentials[1])
+        elif auth and auth.startswith("Bearer "):
+            user = self.bearer_token_auth(url, auth.split("Bearer ")[1])
+        elif "X-API-TOKEN" in headers:
+            user = self.api_token_auth(url, headers.get("X-API-TOKEN"))
+        else:
+            raise SapioWebserviceException(f"Unrecognized Authorization method.", 400)
+        # Make a simple webservice call to confirm that the credentials are valid.
+        try:
+            # noinspection PyStatementEffect
+            user.session_additional_data
+        except Exception:
+            if "Unauthorized (javax.ws.rs.NotAuthorizedException: Incorrect username or password.)" in traceback.format_exc():
+                raise SapioWebserviceException("Unauthorized. Incorrect username or password.", 401)
+            else:
+                raise SapioWebserviceException("System-URL is invalid or user cannot be authenticated.", 401)
+        return user
+
+    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)
+
+
+class CommonsWebserviceHandler(AbstractWebserviceHandler, ABC):
+    """
+    A subclass of AbstractWebservicePostHandler that provides additional quality of life features, including
+    authentication of a SapioUser from the request headers, initialization of various commonly used managers, and more.
+    """
+    logger: Logger
+
+    user: SapioUser | None
+
+    dr_man: DataRecordManager
+    rec_man: RecordModelManager
+    inst_man: RecordModelInstanceManager
+    rel_man: RecordModelRelationshipManager
+    an_man: RecordModelAncestorManager
+
+    dt_cache: DataTypeCacheManager
+    rec_handler: RecordHandler
+
+    def run(self, payload: Any, headers: Headers, params: MultiDict[str, str]) -> WebserviceResponse:
+        try:
+            self.initialize(headers)
+            result = self.execute(self.user, payload, headers, params)
+            if result is None:
+                raise SapioException("Your execute function returned a None result! Don't forget your return statement!")
+            return result
+        except SapioWebserviceException as e:
+            return self.handle_webservice_exception(e)
+        except Exception as e:
+            return self.handle_unexpected_exception(e)
+
+    def initialize(self, headers: Headers) -> None:
+        """
+        A function that can be optionally overridden by your classes to initialize additional instance variables,
+        or set up whatever else you wish to set up before the execute function is ran. Default behavior initializes a
+        SapioUser and various manager classes to make requests from.
+        """
+        self.user = None
+        self.user = self.authenticate_user(headers)
+
+        self.logger = self.user.logger
+
+        self.dr_man = DataRecordManager(self.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(self.user)
+
+    @abstractmethod
+    def execute(self, user: SapioUser, payload: Any, headers: Headers, params: MultiDict[str, str]) \
+            -> SapioWebserviceResult:
+        """
+        The execution details for this endpoint.
+
+        :param user: The SapioUser object authenticated from the request headers.
+        :param payload: The JSON payload from the request. Usually a dictionary of strings to Any.
+        :param headers: The headers from the request. Can be used like a dictionary.
+        :param params: The URL parameters from the request.
+        :return: A response object to send back to the requester.
+        """
+        pass
+
+    def handle_webservice_exception(self, e: SapioWebserviceException) -> WebserviceResponse:
+        """
+        Handle a generic exception which isn't one of the handled Sapio exceptions.
+
+        Default behavior returns a webservice result with the message and error code of the webservice exception.
+        Additionally, the stack trace of the exception that was thrown is logged to the webhook server.
+
+        :param e: The exception that was raised.
+        :return: A webservice result to return to the requester.
+        """
+        result: WebserviceResponse | None = self.handle_any_exception(e)
+        if result is not None:
+            return result
+        msg: str = traceback.format_exc()
+        self.log_error(msg)
+        return SapioWebserviceResult(e.msg, e.code, True)
+
+    def handle_unexpected_exception(self, e: Exception) -> WebserviceResponse:
+        """
+        Handle a generic exception which isn't one of the handled Sapio exceptions.
+
+        Default behavior returns a 500 code result with a generic error message informing the user to contact Sapio
+        support. Additionally, the stack trace of the exception that was thrown is logged to the webhook server.
+
+        :param e: The exception that was raised.
+        :return: A webservice result to return to the requester.
+        """
+        result: SapioWebserviceResult | None = self.handle_any_exception(e)
+        if result is not None:
+            return result
+        msg: str = traceback.format_exc()
+        self.log_error(msg)
+        return SapioWebserviceResult("Unexpected error occurred during webservice execution. "
+                                     "Please contact Sapio support.", 500, True)
+
+    # noinspection PyMethodMayBeStatic,PyUnusedLocal
+    def handle_any_exception(self, e: Exception) -> WebserviceResponse | None:
+        """
+        An exception handler which runs regardless of the type of exception that was raised. Can be used to "rollback"
+        the client if an error occurs. Default behavior does nothing and returns None.
+
+        :param e: The exception that was raised.
+        :return: An optional response to the caller. 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. If 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 webhook server log. Log destination is stdout.
+        """
+        # If there's no user, then there's no logger.
+        if self.user:
+            self.logger.info(msg)
+
+    def log_error(self, msg: str) -> None:
+        """
+        Write an error message to the webhook server log. Log destination is stderr.
+        """
+        # If there's no user, then there's no logger.
+        if self.user:
+            self.logger.error(msg)

{sapiopycommons-2024.3.19a157.dist-info → sapiopycommons-2025.1.17a402.dist-info}/METADATA

@@ -1,11 +1,10 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2024.3.19a157
+Version: 2025.1.17a402
 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-Expression: MPL-2.0
-License-File: LICENSE
+License: MPL-2.0
 Keywords: eln,lims,rest,sapio
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Developers
@@ -17,7 +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
 
 
@@ -50,6 +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-2025.1.17a402.dist-info/RECORD

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{sapiopycommons-2024.3.19a157.dist-info → sapiopycommons-2025.1.17a402.dist-info}/WHEEL

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