From eb343e2ea75c5dcc4b67dd183c8bb5acb1a49fa2 Mon Sep 17 00:00:00 2001 From: jcschaff Date: Thu, 30 May 2024 14:16:27 -0400 Subject: [PATCH] add interactive_login and jupyter notebook --- .openapi-generator-ignore | 28 +- example_latest.ipynb | 213 ++++ poetry.lock | 1789 ++++++++++++++++++++++++++- pyproject.toml | 3 + vcell_api_client/auth/__init__.py | 0 vcell_api_client/auth/auth_utils.py | 145 +++ 6 files changed, 2139 insertions(+), 39 deletions(-) create mode 100644 example_latest.ipynb create mode 100644 vcell_api_client/auth/__init__.py create mode 100644 vcell_api_client/auth/auth_utils.py diff --git a/.openapi-generator-ignore b/.openapi-generator-ignore index 7484ee5..96a94c5 100644 --- a/.openapi-generator-ignore +++ b/.openapi-generator-ignore @@ -1,23 +1,11 @@ # OpenAPI Generator Ignore # Generated by openapi-generator https://github.com/openapitools/openapi-generator -# Use this file to prevent files from being overwritten by the generator. -# The patterns follow closely to .gitignore or .dockerignore. - -# As an example, the C# client generator defines ApiClient.cs. -# You can make changes and tell OpenAPI Generator to ignore just this file by uncommenting the following line: -#ApiClient.cs - -# You can match any string of characters against a directory, file or extension with a single asterisk (*): -#foo/*/qux -# The above matches foo/bar/qux and foo/baz/qux, but not foo/bar/baz/qux - -# You can recursively match patterns against a directory, file or extension with a double asterisk (**): -#foo/**/qux -# This matches foo/bar/qux, foo/baz/qux, and foo/bar/baz/qux - -# You can also negate patterns with an exclamation (!). -# For example, you can ignore all files in a docs folder with the file extension .md: -#docs/*.md -# Then explicitly reverse the ignore rule for a single file: -#!docs/README.md +git_push.sh +requirements.txt +setup.cfg +setup.py +test-requirements.txt +.gitlab-ci.yml +.travis.yml +pyproject.toml diff --git a/example_latest.ipynb b/example_latest.ipynb new file mode 100644 index 0000000..e047e3d --- /dev/null +++ b/example_latest.ipynb @@ -0,0 +1,213 @@ +{ + "cells": [ + { + "cell_type": "code", + "source": [ + "from vcell_api_client.api_client import ApiClient, Configuration\n", + "from vcell_api_client.auth.auth_utils import login_interactive\n", + "from vcell_api_client import Publication\n", + "from vcell_api_client.api.publication_resource_api import PublicationResourceApi" + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-05-30T18:11:43.313995Z", + "start_time": "2024-05-30T18:11:43.309359Z" + } + }, + "id": "5e183b4a68315dfe", + "outputs": [], + "execution_count": 2 + }, + { + "cell_type": "markdown", + "source": [ + "# VCell API Client usage\n", + "1. as a public user (no authentication)\n", + "2. as an authenticated user (with authentication)" + ], + "metadata": { + "collapsed": false + }, + "id": "d11f5830839dbfb4" + }, + { + "cell_type": "markdown", + "source": [ + "## 1) Create anonymous API Client - access to public resources" + ], + "metadata": { + "collapsed": false + }, + "id": "524d1696c6c50b83" + }, + { + "cell_type": "code", + "source": [ + "api_url: str = \"https://vcell-dev.cam.uchc.edu\" # vcell base url\n", + "\n", + "public_client = ApiClient(configuration=Configuration(host=api_url))" + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-05-30T18:11:46.721743Z", + "start_time": "2024-05-30T18:11:46.718117Z" + } + }, + "id": "902c6d3a8dc70af", + "outputs": [], + "execution_count": 3 + }, + { + "cell_type": "markdown", + "source": [ + "### Test Publication API - without authentication\n", + "1. get publications - doesn't need authentication/authorization" + ], + "metadata": { + "collapsed": false + }, + "id": "b12dfb281d589869" + }, + { + "cell_type": "code", + "source": [ + "public_publication_api = PublicationResourceApi(public_client)\n", + "pubs: list[Publication] = public_publication_api.get_publications()\n", + "display(pubs[0])" + ], + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-05-30T18:11:50.556705Z", + "start_time": "2024-05-30T18:11:50.274764Z" + } + }, + "id": "9ba5b1ac2df17231", + "outputs": [ + { + "data": { + "text/plain": [ + "Publication(pub_key=270069811, title='K+ and pH homeostasis in plant cells is controlled by a synchronized K+ /H+ antiport at the plasma and vacuolar membrane', authors=['Li, K.', 'Grauschopf, C.', 'Hedrich, R.', 'Dreyer, I.', 'Konrad, K. R.'], year=2024, citation='New Phytol . 2024 Feb;241(4):1525-1542', pubmedid='38017688', doi='10.1111/nph.19436', endnoteid=None, url=None, wittid=-1, biomodel_refs=[BiomodelRef(bm_key=270051643, name='Li_et_al_2024_NewPhytol_Guard_Cell_Homeostats', owner_name='idreyer', owner_key=97134174, version_flag=3)], mathmodel_refs=[], var_date=datetime.date(2023, 11, 28))" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "execution_count": 4 + }, + { + "cell_type": "markdown", + "source": [ + "## 2) invoke VCell API as an authenticated user\n", + "This will open a browser window to login into VCell using Auth0. After login, the browser will redirect to the VCell webapp '/success_login'. `api_client` will be authenticated for VCell API requests. " + ], + "metadata": { + "collapsed": false + }, + "id": "6444e342beaccd4d" + }, + { + "cell_type": "code", + "id": "f56d96abf59682dd", + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-05-30T18:12:01.401238Z", + "start_time": "2024-05-30T18:11:54.267319Z" + } + }, + "source": [ + "client_id: str = 'cjoWhd7W8A8znf7Z7vizyvKJCiqTgRtf' # default client id for standalone VCell clients\n", + "issuer_url: str = 'https://dev-dzhx7i2db3x3kkvq.us.auth0.com' # Auth0 issuer url for VCell\n", + "\n", + "authenticated_client = login_interactive(api_base_url=api_url, client_id=client_id, issuer_url=issuer_url)\n", + "display(\"may loose focus to the browser window for login, switch back to this notebook after login.\")" + ], + "outputs": [ + { + "data": { + "text/plain": [ + "'may loose focus to the browser window for login, switch back to this notebook after login.'" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "execution_count": 5 + }, + { + "cell_type": "markdown", + "id": "a0e558b807038809", + "metadata": { + "collapsed": false + }, + "source": [ + "### Test Publication API\n", + "1. get publications - also doesn't need authentication/authorization" + ] + }, + { + "cell_type": "code", + "id": "8f95b36e4437ccbb", + "metadata": { + "collapsed": false, + "ExecuteTime": { + "end_time": "2024-05-30T18:12:07.915716Z", + "start_time": "2024-05-30T18:12:07.748765Z" + } + }, + "source": [ + "publication_api = PublicationResourceApi(authenticated_client)\n", + "pubs: list[Publication] = publication_api.get_publications()\n", + "display(pubs[0])" + ], + "outputs": [ + { + "data": { + "text/plain": [ + "Publication(pub_key=270069811, title='K+ and pH homeostasis in plant cells is controlled by a synchronized K+ /H+ antiport at the plasma and vacuolar membrane', authors=['Li, K.', 'Grauschopf, C.', 'Hedrich, R.', 'Dreyer, I.', 'Konrad, K. R.'], year=2024, citation='New Phytol . 2024 Feb;241(4):1525-1542', pubmedid='38017688', doi='10.1111/nph.19436', endnoteid=None, url=None, wittid=-1, biomodel_refs=[BiomodelRef(bm_key=270051643, name='Li_et_al_2024_NewPhytol_Guard_Cell_Homeostats', owner_name='idreyer', owner_key=97134174, version_flag=3)], mathmodel_refs=[], var_date=datetime.date(2023, 11, 28))" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "execution_count": 6 + }, + { + "cell_type": "code", + "id": "ed266f9194abb748", + "metadata": { + "collapsed": false + }, + "source": [], + "outputs": [], + "execution_count": null + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": 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"sha256:8b22a8f1910bfd188e596fe7fc05dcbd87e810c8a4ba010bdb3da86637398474"}, +] + [[package]] name = "zipp" version = "3.19.0" description = "Backport of pathlib-compatible object wrapper for zip files" -optional = true +optional = false python-versions = ">=3.8" files = [ {file = "zipp-3.19.0-py3-none-any.whl", hash = "sha256:96dc6ad62f1441bcaccef23b274ec471518daf4fbbc580341204936a5a3dddec"}, @@ -1879,4 +3630,4 @@ test = ["black", "flake8", "flake8-docstrings", "isort", "mypy", "pytest", "pyte [metadata] lock-version = "2.0" python-versions = ">=3.9,<4.0" -content-hash = "8b1ed3761ebb12dacbd907d7c1071d9df6744d29af75295387261f4860500b35" +content-hash = "58150c9193fcba2df6f3fba9bc2acfcd8b7a63fa06e2442c275ba4b3cc84deeb" diff --git a/pyproject.toml b/pyproject.toml index 0f3d05f..3186f30 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,6 +32,9 @@ urllib3 = ">= 1.25.3" python-dateutil = ">=2.8.2" pydantic = ">=2" typing-extensions = ">=4.7.1" +requests-oauth2client = "^1.5.1" +jupyter = "^1.0.0" + black = { version = "^21.5b2", optional = true} isort = { version = "^5.8.0", optional = true} diff --git a/vcell_api_client/auth/__init__.py b/vcell_api_client/auth/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/vcell_api_client/auth/auth_utils.py b/vcell_api_client/auth/auth_utils.py new file mode 100644 index 0000000..8912c79 --- /dev/null +++ b/vcell_api_client/auth/auth_utils.py @@ -0,0 +1,145 @@ +import socket +import webbrowser +from contextlib import closing +from http.server import HTTPServer, BaseHTTPRequestHandler +from typing import Optional +from urllib import parse + +import requests +from pydantic import BaseModel, StrictStr +from requests_oauth2client import OAuth2Client, AuthorizationRequest, AuthorizationResponse, BearerToken + +from vcell_api_client.api_client import ApiClient, Configuration + +LOGIN_SUCCESS = "/login_success" +OIDC_TEST_CALLBACK = "/oidc_test_callback" +WELL_KNOWN_CONFIG_PATH = "/.well-known/openid-configuration" + + +class AuthCodeResponse(BaseModel): + access_token: Optional[StrictStr] = None + id_token: Optional[StrictStr] = None + refresh_token: Optional[StrictStr] = None + + +class OAuthHttpServer(HTTPServer): + + def __init__(self, *args, success_redirect_url: str, **kwargs): + HTTPServer.__init__(self, *args, **kwargs) + self.authorization_code = "" + self.path = "" + self.fullpath = "" + self.success_redirect_url = success_redirect_url + + +class OAuthHttpHandler(BaseHTTPRequestHandler): + def do_GET(self): + # redirect to the login_success page + success_redirect_url: str = self.server.success_redirect_url + self.send_response(303) # Send HTTP 303 response + self.send_header("Location", success_redirect_url) # Set the Location header to the redirect URL + self.end_headers() + + # # close the window instead of showing the login_success page + # self.send_response(200) + # self.send_header("Content-Type", "text/html") + # self.end_headers() + # self.wfile.write("".encode("UTF-8")) + + parsed = parse.urlparse(self.path) + qs = parse.parse_qs(parsed.query) + self.server.path = parsed.path + self.server.authorization_code = qs["code"][0] + self.server.fullpath = self.path + + def log_message(self, format, *args): + # Override this method to suppress logging + return + +def find_free_port() -> int: + # all ports must be registered as http://localhost:/oidc_test_callback in Auth0 redirect URI. + # specific ports (ending with 111) are chosen from dynamic/private port range 49152-65535 + # to avoid conflicts with other services and be tolerated by firewalls. + # + # corresponding redirect URI registration in Auth0: + # http://localhost:51111/oidc_test_callback,http://localhost:52111/oidc_test_callback, + # http://localhost:53111/oidc_test_callback,http://localhost:54111/oidc_test_callback, + # http://localhost:55111/oidc_test_callback,http://localhost:56111/oidc_test_callback, + # http://localhost:57111/oidc_test_callback,http://localhost:58111/oidc_test_callback, + # http://localhost:59111/oidc_test_callback,http://localhost:60111/oidc_test_callback, + # http://localhost:61111/oidc_test_callback,http://localhost:62111/oidc_test_callback, + # http://localhost:63111/oidc_test_callback,http://localhost:64111/oidc_test_callback, + # http://localhost:65111/oidc_test_callback + # + # selected ports which are registered are 51111, 52111, ... 64111, 65111 + for port in range(51111, 65112, 1000): # Iterate over the range of ports + with closing(socket.socket(socket.AF_INET, socket.SOCK_STREAM)) as s: + try: + assert(type(s) == socket.socket) + s.bind(('', port)) # Try to bind to the port + except socket.error as e: + continue # If bind fails, this port is not free, so move on to the next one + return port # If bind succeeds, this port is free, so return it + raise RuntimeError('No free ports found') # If no free port is found in the range + + +def login_interactive_tokens(client_id: str, auth_url: str, token_url: str, jwks_uri: str, success_redirect_url: str) -> AuthCodeResponse: + """ + This function is used to login interactively to the VCell API. + It is used for the ApiClient class to set the access token. + :param api_base_url: The base URL of the VCell API. + :param client_id: The client ID of the VCell API OIDC auth provider. + :param auth_url: The auth URL of the VCell API IODC auth provider. + :return: An AuthCodeResponse object with access, id and refresh tokens. + """ + hostname = "localhost" + temp_http_port = find_free_port() + + with OAuthHttpServer((hostname, temp_http_port), OAuthHttpHandler, success_redirect_url=success_redirect_url) as httpd: + redirectURI = f'http://{hostname}:{temp_http_port}{OIDC_TEST_CALLBACK}' + + oauth2client = OAuth2Client( + token_endpoint=token_url, + authorization_endpoint=auth_url, + redirect_uri=redirectURI, + client_id=client_id, + jwks_uri=jwks_uri + ) + + authorization_request: AuthorizationRequest = oauth2client.authorization_request(scope="openid email profile offline_access") + + webbrowser.open(url=authorization_request.uri, new=1, autoraise=True) + + httpd.handle_request() + + authorization_response: AuthorizationResponse = authorization_request.validate_callback(httpd.fullpath) + + token: BearerToken = oauth2client.authorization_code(code=authorization_response, validate=False) + + auth_code_response: AuthCodeResponse = AuthCodeResponse(access_token=token.access_token, id_token=str(token.id_token), refresh_token=token.refresh_token) + return auth_code_response + + +def get_authorization_and_token_endpoints(issuer_url: str) -> tuple[str, str, str]: + response = requests.get(f'{issuer_url}{WELL_KNOWN_CONFIG_PATH}') + response.raise_for_status() # Raise an exception if the request was unsuccessful + data = response.json() + return data.get('authorization_endpoint'), data.get('token_endpoint'), data.get('jwks_uri') + + +def login_interactive(api_base_url: str, client_id: str, issuer_url: str) -> ApiClient: + """ + This function is used to login interactively to the VCell API. + It is used for the ApiClient class to set the access token. + :param api_base_url: The base URL of the VCell API. + :param client_id: The client ID of the VCell API OIDC auth provider. + :param issuer_url: The base URL of the VCell API OIDC auth provider. + :return: An ApiClient object with the access token set. + """ + auth_url, token_url, jwks_uri = get_authorization_and_token_endpoints(issuer_url) + auth_code_response: AuthCodeResponse = login_interactive_tokens( + client_id=client_id, auth_url=auth_url, token_url=token_url, jwks_uri=jwks_uri, success_redirect_url=api_base_url + LOGIN_SUCCESS) + id_token = auth_code_response.id_token + api_client = ApiClient(configuration=Configuration(host=api_base_url, access_token=id_token)) + api_client.set_default_header('Authorization', f'Bearer {id_token}') + return api_client