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{
"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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