add interactive_login and jupyter notebook

virtualcell · May 30, 2024 · eb343e2 · eb343e2
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diff --git 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
@@ -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": "3.12.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}