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Merge pull request #1 from virtualcell/vcell-api-client
add vcell api client
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‎.github/workflows/main.yml

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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
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python-version: ["3.9", "3.10", "3.11", "3.12"]
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fail-fast: false
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defaults:
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run:

‎.gitignore

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.idea/
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test_output_1/
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.python-version
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**/.DS_Store

‎.pre-commit-config.yaml

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hooks:
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- id: ruff
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args: [--exit-non-zero-on-fix]
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exclude: 'pyvcell/api/.*\.py'
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- id: ruff-format
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- repo: https://github.com/pre-commit/mirrors-prettier

‎Makefile

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@echo "🚀 Static type checking: Running mypy"
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@poetry run mypy
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@echo "🚀 Checking for obsolete dependencies: Running deptry"
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@poetry run deptry .
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@poetry run deptry --exclude .venv .
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.PHONY: test
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test: ## Test the code with pytest

‎docs/modules.md

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::: pyvcell.foo
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# Modules
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## pyvcell
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::: pyvcell
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handler: python
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options:
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show_root_heading: true
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show_source: true
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show_signature_annotations: true

‎examples/vcell_publications.ipynb

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{
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"cells": [
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{
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"cell_type": "code",
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"source": [
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"from pyvcell.api.vcell_client import ApiClient, Configuration, PublicationResourceApi\n",
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"from pyvcell.api.vcell_client.auth.auth_utils import login_interactive\n",
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"from pyvcell.api.vcell_client.models import Publication"
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],
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-01-23T07:43:37.703710Z",
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"start_time": "2025-01-23T07:43:37.701027Z"
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}
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},
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"id": "5e183b4a68315dfe",
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"outputs": [],
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"execution_count": 2
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},
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{
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"cell_type": "markdown",
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"source": [
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"# VCell API Client usage\n",
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"1. as a public user (no authentication)\n",
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"2. as an authenticated user (with authentication)"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "d11f5830839dbfb4"
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},
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{
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"cell_type": "markdown",
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"source": [
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"## 1) Create anonymous API Client - access to public resources"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "524d1696c6c50b83"
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},
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{
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"cell_type": "code",
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"source": [
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"api_url: str = \"https://vcell-dev.cam.uchc.edu\" # vcell base url\n",
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"\n",
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"public_client = ApiClient(configuration=Configuration(host=api_url))"
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],
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-01-23T07:43:37.725514Z",
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"start_time": "2025-01-23T07:43:37.723335Z"
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}
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},
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"id": "902c6d3a8dc70af",
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"outputs": [],
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"execution_count": 3
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},
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{
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"cell_type": "markdown",
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"source": [
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"### Test Publication API - without authentication\n",
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"1. get publications - doesn't need authentication/authorization"
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],
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"metadata": {
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"collapsed": false
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},
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"id": "b12dfb281d589869"
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},
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{
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"cell_type": "code",
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"source": [
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"public_publication_api = PublicationResourceApi(public_client)\n",
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"pubs: list[Publication] = public_publication_api.get_publications()\n",
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"display(pubs[0])"
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],
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-01-23T07:43:38.028844Z",
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"start_time": "2025-01-23T07:43:37.735773Z"
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}
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},
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"id": "9ba5b1ac2df17231",
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"outputs": [
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{
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"data": {
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"text/plain": [
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"Publication(pub_key=279906235, title='A continuum model of mechanosensation based on contractility kit assembly', authors=['Dolgitzer', ' D.', ' Plaza-Rodríguez', ' A. I.', ' Iglesias', ' M. A.', ' Jacob', ' M. A. C.', ' Todd', ' B.', ' Robinson', ' D. N.', ' & Iglesias', ' P. A.'], year=2024, citation='Biophys J. 2024 Nov 8:S0006-3495(24)00708-2', pubmedid='39521955', doi='https://doi.org/10.1016/j.bpj.2024.10.020', endnoteid=0, url='url', wittid=0, biomodel_refs=[BiomodelRef(bm_key=279851639, name='Dolgitzer 2025 A Continuum Model of Mechanosensation Based on Contractility Kit Assembly', owner_name='Dolgitzer', owner_key=259537152, version_flag=3)], mathmodel_refs=[], var_date=datetime.date(2024, 11, 26))"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"execution_count": 4
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},
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{
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"cell_type": "markdown",
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"source": [
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"## 2) invoke VCell API as an authenticated user\n",
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"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. "
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],
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"metadata": {
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"collapsed": false
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},
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"id": "6444e342beaccd4d"
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},
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{
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"cell_type": "code",
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"id": "f56d96abf59682dd",
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-01-23T07:43:46.823079Z",
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"start_time": "2025-01-23T07:43:38.037782Z"
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}
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},
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"source": [
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"client_id: str = 'cjoWhd7W8A8znf7Z7vizyvKJCiqTgRtf' # default client id for standalone VCell clients\n",
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"issuer_url: str = 'https://dev-dzhx7i2db3x3kkvq.us.auth0.com' # Auth0 issuer url for VCell\n",
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"\n",
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"authenticated_client = login_interactive(api_base_url=api_url, client_id=client_id, issuer_url=issuer_url)\n",
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"display(\"may loose focus to the browser window for login, switch back to this notebook after login.\")"
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],
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"outputs": [
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{
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"data": {
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"text/plain": [
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"'may loose focus to the browser window for login, switch back to this notebook after login.'"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"execution_count": 5
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},
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{
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"cell_type": "markdown",
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"id": "a0e558b807038809",
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"metadata": {
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"collapsed": false
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},
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"source": [
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"### Test Publication API\n",
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"1. get publications - also doesn't need authentication/authorization"
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]
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},
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{
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"cell_type": "code",
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"id": "8f95b36e4437ccbb",
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-01-23T07:43:47.020349Z",
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"start_time": "2025-01-23T07:43:46.852654Z"
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}
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},
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"source": [
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"publication_api = PublicationResourceApi(authenticated_client)\n",
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"pubs: list[Publication] = publication_api.get_publications()\n",
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"display(pubs[0])"
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],
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"outputs": [
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{
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"data": {
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"text/plain": [
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"Publication(pub_key=279906235, title='A continuum model of mechanosensation based on contractility kit assembly', authors=['Dolgitzer', ' D.', ' Plaza-Rodríguez', ' A. I.', ' Iglesias', ' M. A.', ' Jacob', ' M. A. C.', ' Todd', ' B.', ' Robinson', ' D. N.', ' & Iglesias', ' P. A.'], year=2024, citation='Biophys J. 2024 Nov 8:S0006-3495(24)00708-2', pubmedid='39521955', doi='https://doi.org/10.1016/j.bpj.2024.10.020', endnoteid=0, url='url', wittid=0, biomodel_refs=[BiomodelRef(bm_key=279851639, name='Dolgitzer 2025 A Continuum Model of Mechanosensation Based on Contractility Kit Assembly', owner_name='Dolgitzer', owner_key=259537152, version_flag=3)], mathmodel_refs=[], var_date=datetime.date(2024, 11, 26))"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"execution_count": 6
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},
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{
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"cell_type": "code",
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"id": "ed266f9194abb748",
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-01-23T07:43:47.026801Z",
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"start_time": "2025-01-23T07:43:47.025477Z"
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}
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},
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"source": [],
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"outputs": [],
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"execution_count": null
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.12.2"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

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