{
 "cells": [
  {
   "cell_type": "code",
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/schaff/Documents/workspace/vcell/python-restclient/.venv/lib/python3.12/site-packages/pydantic/_internal/_fields.py:151: UserWarning: Field \"model_key\" has conflict with protected namespace \"model_\".\n",
      "\n",
      "You may be able to resolve this warning by setting `model_config['protected_namespaces'] = ()`.\n",
      "  warnings.warn(\n"
     ]
    }
   ],
   "source": [
    "from vcell_client.api_client import ApiClient, Configuration\n",
    "from vcell_client.auth.auth_utils import login_interactive\n",
    "from vcell_client import Publication\n",
    "from vcell_client.api.publication_resource_api import PublicationResourceApi"
   ],
   "metadata": {
    "collapsed": false,
    "ExecuteTime": {
     "end_time": "2024-05-01T21:12:53.063024Z",
     "start_time": "2024-05-01T21:12:52.850129Z"
    }
   },
   "id": "5e183b4a68315dfe",
   "execution_count": 1
  },
  {
   "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",
   "outputs": [],
   "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": "2024-05-01T21:13:12.872880Z",
     "start_time": "2024-05-01T21:13:12.870503Z"
    }
   },
   "id": "902c6d3a8dc70af",
   "execution_count": 2
  },
  {
   "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",
   "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"
    }
   ],
   "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": "2024-05-01T21:13:15.493227Z",
     "start_time": "2024-05-01T21:13:15.190372Z"
    }
   },
   "id": "9ba5b1ac2df17231",
   "execution_count": 3
  },
  {
   "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",
   "execution_count": 6,
   "id": "f56d96abf59682dd",
   "metadata": {
    "collapsed": false,
    "ExecuteTime": {
     "end_time": "2024-05-01T21:14:26.398587Z",
     "start_time": "2024-05-01T21:14:25.485352Z"
    }
   },
   "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"
    }
   ],
   "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.\")"
   ]
  },
  {
   "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",
   "execution_count": 7,
   "id": "8f95b36e4437ccbb",
   "metadata": {
    "collapsed": false,
    "ExecuteTime": {
     "end_time": "2024-05-01T21:14:34.427704Z",
     "start_time": "2024-05-01T21:14:34.148156Z"
    }
   },
   "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"
    }
   ],
   "source": [
    "publication_api = PublicationResourceApi(authenticated_client)\n",
    "pubs: list[Publication] = publication_api.get_publications()\n",
    "display(pubs[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ed266f9194abb748",
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": []
  }
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