forked from enviPath/enviPy
[Feature] Server pagination implementation (#243)
## Major Changes - Implement a REST style API app in epapi - Currently implements a GET method for all entity types in the browse menu (both package level and global) - Provides paginated results per default with query style filtering for reviewed vs unreviewed. - Provides new paginated templates with thin wrappers per entity types for easier maintainability - Implements e2e tests for the API ## Minor changes - Added more comprehensive gitignore to cover coverage reports and other test/node.js etc. data. - Add additional CI file for API tests that only gets triggered on API relevant changes. ## ⚠️ Currently only works with session-based authentication. Token based will be added in new PR. Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Co-authored-by: jebus <lorsbach@envipath.com> Reviewed-on: enviPath/enviPy#243 Co-authored-by: Tobias O <tobias.olenyi@envipath.com> Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
This commit is contained in:
94
.gitea/actions/setup-envipy/action.yaml
Normal file
94
.gitea/actions/setup-envipy/action.yaml
Normal file
@ -0,0 +1,94 @@
|
||||
name: 'Setup enviPy Environment'
|
||||
description: 'Shared setup for enviPy CI - installs dependencies and prepares environment'
|
||||
|
||||
inputs:
|
||||
skip-frontend:
|
||||
description: 'Skip frontend build steps (pnpm, tailwind)'
|
||||
required: false
|
||||
default: 'false'
|
||||
skip-playwright:
|
||||
description: 'Skip Playwright installation'
|
||||
required: false
|
||||
default: 'false'
|
||||
ssh-private-key:
|
||||
description: 'SSH private key for git access'
|
||||
required: true
|
||||
run-migrations:
|
||||
description: 'Run Django migrations after setup'
|
||||
required: false
|
||||
default: 'true'
|
||||
|
||||
runs:
|
||||
using: "composite"
|
||||
steps:
|
||||
- name: Install system tools via apt
|
||||
shell: bash
|
||||
run: |
|
||||
sudo apt-get update
|
||||
sudo apt-get install -y postgresql-client openjdk-11-jre-headless
|
||||
|
||||
- name: Setup ssh
|
||||
shell: bash
|
||||
run: |
|
||||
mkdir -p ~/.ssh
|
||||
echo "${{ inputs.ssh-private-key }}" > ~/.ssh/id_ed25519
|
||||
chmod 600 ~/.ssh/id_ed25519
|
||||
ssh-keyscan git.envipath.com >> ~/.ssh/known_hosts
|
||||
eval $(ssh-agent -s)
|
||||
ssh-add ~/.ssh/id_ed25519
|
||||
|
||||
- name: Install pnpm
|
||||
uses: pnpm/action-setup@v4
|
||||
with:
|
||||
version: 10
|
||||
|
||||
- name: Use Node.js
|
||||
uses: actions/setup-node@v4
|
||||
with:
|
||||
node-version: 20
|
||||
cache: "pnpm"
|
||||
|
||||
- name: Install uv
|
||||
uses: astral-sh/setup-uv@v6
|
||||
with:
|
||||
enable-cache: true
|
||||
|
||||
- name: Setup Python venv
|
||||
shell: bash
|
||||
run: |
|
||||
uv sync --locked --all-extras --dev
|
||||
|
||||
- name: Install Playwright
|
||||
if: inputs.skip-playwright == 'false'
|
||||
shell: bash
|
||||
run: |
|
||||
source .venv/bin/activate
|
||||
playwright install --with-deps
|
||||
|
||||
- name: Build Frontend
|
||||
if: inputs.skip-frontend == 'false'
|
||||
shell: bash
|
||||
run: |
|
||||
uv run python scripts/pnpm_wrapper.py install
|
||||
cat << 'EOF' > pnpm-workspace.yaml
|
||||
onlyBuiltDependencies:
|
||||
- '@parcel/watcher'
|
||||
- '@tailwindcss/oxide'
|
||||
EOF
|
||||
uv run python scripts/pnpm_wrapper.py run build
|
||||
|
||||
- name: Wait for Postgres
|
||||
shell: bash
|
||||
run: |
|
||||
until pg_isready -h postgres -U ${{ env.POSTGRES_USER }}; do
|
||||
echo "Waiting for postgres..."
|
||||
sleep 2
|
||||
done
|
||||
echo "Postgres is ready!"
|
||||
|
||||
- name: Run Django Migrations
|
||||
if: inputs.run-migrations == 'true'
|
||||
shell: bash
|
||||
run: |
|
||||
source .venv/bin/activate
|
||||
python manage.py migrate --noinput
|
||||
86
.gitea/workflows/api-ci.yaml
Normal file
86
.gitea/workflows/api-ci.yaml
Normal file
@ -0,0 +1,86 @@
|
||||
name: API CI
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||||
|
||||
on:
|
||||
pull_request:
|
||||
branches:
|
||||
- develop
|
||||
paths:
|
||||
- 'epapi/**'
|
||||
- 'epdb/models.py' # API depends on models
|
||||
- 'epdb/logic.py' # API depends on business logic
|
||||
- 'tests/fixtures/**' # API tests use fixtures
|
||||
workflow_dispatch:
|
||||
|
||||
jobs:
|
||||
api-tests:
|
||||
if: ${{ !contains(gitea.event.pull_request.title, 'WIP') }}
|
||||
runs-on: ubuntu-latest
|
||||
|
||||
services:
|
||||
postgres:
|
||||
image: postgres:16
|
||||
env:
|
||||
POSTGRES_USER: ${{ vars.POSTGRES_USER }}
|
||||
POSTGRES_PASSWORD: ${{ secrets.POSTGRES_PASSWORD }}
|
||||
POSTGRES_DB: ${{ vars.POSTGRES_DB }}
|
||||
ports:
|
||||
- ${{ vars.POSTGRES_PORT}}:5432
|
||||
options: >-
|
||||
--health-cmd="pg_isready -U postgres"
|
||||
--health-interval=10s
|
||||
--health-timeout=5s
|
||||
--health-retries=5
|
||||
|
||||
env:
|
||||
RUNNER_TOOL_CACHE: /toolcache
|
||||
EP_DATA_DIR: /opt/enviPy/
|
||||
ALLOWED_HOSTS: 127.0.0.1,localhost
|
||||
DEBUG: True
|
||||
LOG_LEVEL: INFO
|
||||
MODEL_BUILDING_ENABLED: True
|
||||
APPLICABILITY_DOMAIN_ENABLED: True
|
||||
ENVIFORMER_PRESENT: True
|
||||
ENVIFORMER_DEVICE: cpu
|
||||
FLAG_CELERY_PRESENT: False
|
||||
PLUGINS_ENABLED: True
|
||||
SERVER_URL: http://localhost:8000
|
||||
ADMIN_APPROVAL_REQUIRED: True
|
||||
REGISTRATION_MANDATORY: True
|
||||
LOG_DIR: ''
|
||||
# DB
|
||||
POSTGRES_SERVICE_NAME: postgres
|
||||
POSTGRES_DB: ${{ vars.POSTGRES_DB }}
|
||||
POSTGRES_USER: ${{ vars.POSTGRES_USER }}
|
||||
POSTGRES_PASSWORD: ${{ secrets.POSTGRES_PASSWORD }}
|
||||
POSTGRES_PORT: 5432
|
||||
# SENTRY
|
||||
SENTRY_ENABLED: False
|
||||
# MS ENTRA
|
||||
MS_ENTRA_ENABLED: False
|
||||
|
||||
steps:
|
||||
- name: Checkout repository
|
||||
uses: actions/checkout@v4
|
||||
|
||||
# Use shared setup action - skips frontend builds for API-only tests
|
||||
- name: Setup enviPy Environment
|
||||
uses: ./.gitea/actions/setup-envipy
|
||||
with:
|
||||
skip-frontend: 'true'
|
||||
skip-playwright: 'true'
|
||||
ssh-private-key: ${{ secrets.ENVIPY_CI_PRIVATE_KEY }}
|
||||
run-migrations: 'true'
|
||||
|
||||
- name: Run API tests
|
||||
run: |
|
||||
source .venv/bin/activate
|
||||
python manage.py test epapi -v 2
|
||||
|
||||
- name: Test API endpoints availability
|
||||
run: |
|
||||
source .venv/bin/activate
|
||||
python manage.py runserver 0.0.0.0:8000 &
|
||||
SERVER_PID=$!
|
||||
sleep 5
|
||||
curl -f http://localhost:8000/api/v1/docs || echo "API docs not available"
|
||||
kill $SERVER_PID
|
||||
@ -64,64 +64,17 @@ jobs:
|
||||
MS_ENTRA_ENABLED: False
|
||||
|
||||
steps:
|
||||
|
||||
- name: Checkout repository
|
||||
uses: actions/checkout@v4
|
||||
|
||||
- name: Install system tools via apt
|
||||
run: |
|
||||
sudo apt-get update
|
||||
sudo apt-get install -y postgresql-client redis-tools openjdk-11-jre-headless
|
||||
|
||||
- name: Setup ssh
|
||||
run: |
|
||||
echo "${{ secrets.ENVIPY_CI_PRIVATE_KEY }}" > ~/.ssh/id_ed25519
|
||||
chmod 600 ~/.ssh/id_ed25519
|
||||
ssh-keyscan git.envipath.com >> ~/.ssh/known_hosts
|
||||
eval $(ssh-agent -s)
|
||||
ssh-add ~/.ssh/id_ed25519
|
||||
|
||||
- name: Install pnpm
|
||||
uses: pnpm/action-setup@v4
|
||||
# Use shared setup action - includes all dependencies and migrations
|
||||
- name: Setup enviPy Environment
|
||||
uses: ./.gitea/actions/setup-envipy
|
||||
with:
|
||||
version: 10
|
||||
|
||||
- name: Use Node.js
|
||||
uses: actions/setup-node@v4
|
||||
with:
|
||||
node-version: 20
|
||||
cache: "pnpm"
|
||||
|
||||
- name: Install uv
|
||||
uses: astral-sh/setup-uv@v6
|
||||
with:
|
||||
enable-cache: true
|
||||
|
||||
- name: Setup venv
|
||||
run: |
|
||||
uv sync --locked --all-extras --dev
|
||||
source .venv/bin/activate
|
||||
playwright install --with-deps
|
||||
|
||||
- name: Run PNPM Commands
|
||||
run: |
|
||||
uv run python scripts/pnpm_wrapper.py install
|
||||
cat << 'EOF' > pnpm-workspace.yaml
|
||||
onlyBuiltDependencies:
|
||||
- '@parcel/watcher'
|
||||
- '@tailwindcss/oxide'
|
||||
EOF
|
||||
uv run python scripts/pnpm_wrapper.py run build
|
||||
|
||||
- name: Wait for services
|
||||
run: |
|
||||
until pg_isready -h postgres -U postgres; do sleep 2; done
|
||||
# until redis-cli -h redis ping; do sleep 2; done
|
||||
|
||||
- name: Run Django Migrations
|
||||
run: |
|
||||
source .venv/bin/activate
|
||||
python manage.py migrate --noinput
|
||||
skip-frontend: 'false'
|
||||
skip-playwright: 'false'
|
||||
ssh-private-key: ${{ secrets.ENVIPY_CI_PRIVATE_KEY }}
|
||||
run-migrations: 'true'
|
||||
|
||||
- name: Run frontend tests
|
||||
run: |
|
||||
|
||||
373
.gitignore
vendored
373
.gitignore
vendored
@ -1,20 +1,375 @@
|
||||
*.pyc
|
||||
|
||||
|
||||
|
||||
### Python ###
|
||||
|
||||
# Byte-compiled / optimized / DLL files
|
||||
__pycache__/
|
||||
*.py[codz]
|
||||
*$py.class
|
||||
|
||||
# C extensions
|
||||
*.so
|
||||
|
||||
# Distribution / packaging
|
||||
.Python
|
||||
build/
|
||||
develop-eggs/
|
||||
dist/
|
||||
downloads/
|
||||
eggs/
|
||||
.eggs/
|
||||
lib/
|
||||
lib64/
|
||||
parts/
|
||||
sdist/
|
||||
var/
|
||||
wheels/
|
||||
share/python-wheels/
|
||||
*.egg-info/
|
||||
.installed.cfg
|
||||
*.egg
|
||||
MANIFEST
|
||||
|
||||
# PyInstaller
|
||||
# Usually these files are written by a python script from a template
|
||||
# before PyInstaller builds the exe, so as to inject date/other infos into it.
|
||||
*.manifest
|
||||
*.spec
|
||||
|
||||
# Installer logs
|
||||
pip-log.txt
|
||||
pip-delete-this-directory.txt
|
||||
|
||||
# Unit test / coverage reports
|
||||
htmlcov/
|
||||
.tox/
|
||||
.nox/
|
||||
.coverage
|
||||
.coverage.*
|
||||
.cache
|
||||
nosetests.xml
|
||||
coverage.xml
|
||||
*.cover
|
||||
*.py.cover
|
||||
.hypothesis/
|
||||
.pytest_cache/
|
||||
cover/
|
||||
|
||||
# Translations
|
||||
*.mo
|
||||
*.pot
|
||||
|
||||
# Django stuff:
|
||||
*.log
|
||||
local_settings.py
|
||||
db.sqlite3
|
||||
.idea/
|
||||
db.sqlite3-journal
|
||||
static/admin/
|
||||
static/django_extensions/
|
||||
|
||||
# Flask stuff:
|
||||
instance/
|
||||
.webassets-cache
|
||||
|
||||
# Scrapy stuff:
|
||||
.scrapy
|
||||
|
||||
# Sphinx documentation
|
||||
docs/_build/
|
||||
|
||||
# PyBuilder
|
||||
.pybuilder/
|
||||
target/
|
||||
|
||||
# Jupyter Notebook
|
||||
.ipynb_checkpoints
|
||||
|
||||
# IPython
|
||||
profile_default/
|
||||
ipython_config.py
|
||||
|
||||
|
||||
# pdm
|
||||
# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
|
||||
# pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
|
||||
# https://pdm-project.org/en/latest/usage/project/#working-with-version-control
|
||||
# pdm.lock
|
||||
# pdm.toml
|
||||
.pdm-python
|
||||
.pdm-build/
|
||||
|
||||
# pixi
|
||||
# Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
|
||||
# pixi.lock
|
||||
# Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
|
||||
# in the .venv directory. It is recommended not to include this directory in version control.
|
||||
.pixi
|
||||
|
||||
# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
|
||||
__pypackages__/
|
||||
|
||||
# Celery stuff
|
||||
celerybeat-schedule
|
||||
celerybeat.pid
|
||||
|
||||
# Redis
|
||||
*.rdb
|
||||
*.aof
|
||||
*.pid
|
||||
|
||||
# RabbitMQ
|
||||
mnesia/
|
||||
rabbitmq/
|
||||
rabbitmq-data/
|
||||
|
||||
# ActiveMQ
|
||||
activemq-data/
|
||||
|
||||
# SageMath parsed files
|
||||
*.sage.py
|
||||
|
||||
# Environments
|
||||
.env
|
||||
.envrc
|
||||
.venv
|
||||
env/
|
||||
venv/
|
||||
ENV/
|
||||
env.bak/
|
||||
venv.bak/
|
||||
|
||||
# Spyder project settings
|
||||
.spyderproject
|
||||
.spyproject
|
||||
|
||||
# Rope project settings
|
||||
.ropeproject
|
||||
|
||||
# mkdocs documentation
|
||||
/site
|
||||
|
||||
# mypy
|
||||
.mypy_cache/
|
||||
.dmypy.json
|
||||
dmypy.json
|
||||
|
||||
# Pyre type checker
|
||||
.pyre/
|
||||
|
||||
# pytype static type analyzer
|
||||
.pytype/
|
||||
|
||||
# Cython debug symbols
|
||||
cython_debug/
|
||||
|
||||
# PyCharm
|
||||
# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
|
||||
# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
|
||||
# and can be added to the global gitignore or merged into this file. For a more nuclear
|
||||
# option (not recommended) you can uncomment the following to ignore the entire idea folder.
|
||||
.idea/
|
||||
|
||||
# Abstra
|
||||
# Abstra is an AI-powered process automation framework.
|
||||
# Ignore directories containing user credentials, local state, and settings.
|
||||
# Learn more at https://abstra.io/docs
|
||||
.abstra/
|
||||
|
||||
# Visual Studio Code
|
||||
# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
|
||||
# that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
|
||||
# and can be added to the global gitignore or merged into this file. However, if you prefer,
|
||||
# you could uncomment the following to ignore the entire vscode folder
|
||||
.vscode/
|
||||
*.code-workspace
|
||||
|
||||
# Ruff stuff:
|
||||
.ruff_cache/
|
||||
|
||||
# UV cache
|
||||
.uv-cache/
|
||||
|
||||
# PyPI configuration file
|
||||
.pypirc
|
||||
|
||||
# Marimo
|
||||
marimo/_static/
|
||||
marimo/_lsp/
|
||||
__marimo__/
|
||||
|
||||
# Streamlit
|
||||
.streamlit/secrets.toml
|
||||
|
||||
### Agents ###
|
||||
.claude/
|
||||
.codex/
|
||||
.cursor/
|
||||
.github/prompts/
|
||||
.junie/
|
||||
.windsurf/
|
||||
|
||||
AGENTS.md
|
||||
CLAUDE.md
|
||||
GEMINI.md
|
||||
.aider.*
|
||||
|
||||
### Node.js ###
|
||||
|
||||
# Logs
|
||||
logs
|
||||
*.log
|
||||
npm-debug.log*
|
||||
yarn-debug.log*
|
||||
yarn-error.log*
|
||||
lerna-debug.log*
|
||||
|
||||
# Diagnostic reports (https://nodejs.org/api/report.html)
|
||||
report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json
|
||||
|
||||
# Runtime data
|
||||
pids
|
||||
*.pid
|
||||
*.seed
|
||||
*.pid.lock
|
||||
|
||||
# Directory for instrumented libs generated by jscoverage/JSCover
|
||||
lib-cov
|
||||
|
||||
# Coverage directory used by tools like istanbul
|
||||
coverage
|
||||
*.lcov
|
||||
|
||||
# nyc test coverage
|
||||
.nyc_output
|
||||
|
||||
# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files)
|
||||
.grunt
|
||||
|
||||
# Bower dependency directory (https://bower.io/)
|
||||
bower_components
|
||||
|
||||
# node-waf configuration
|
||||
.lock-wscript
|
||||
|
||||
# Compiled binary addons (https://nodejs.org/api/addons.html)
|
||||
build/Release
|
||||
|
||||
# Dependency directories
|
||||
node_modules/
|
||||
jspm_packages/
|
||||
|
||||
# Snowpack dependency directory (https://snowpack.dev/)
|
||||
web_modules/
|
||||
|
||||
# TypeScript cache
|
||||
*.tsbuildinfo
|
||||
|
||||
# Optional npm cache directory
|
||||
.npm
|
||||
|
||||
# Optional eslint cache
|
||||
.eslintcache
|
||||
|
||||
# Optional stylelint cache
|
||||
.stylelintcache
|
||||
|
||||
# Optional REPL history
|
||||
.node_repl_history
|
||||
|
||||
# Output of 'npm pack'
|
||||
*.tgz
|
||||
|
||||
# Yarn Integrity file
|
||||
.yarn-integrity
|
||||
|
||||
# dotenv environment variable files
|
||||
.env
|
||||
.env.*
|
||||
!.env.example
|
||||
|
||||
# parcel-bundler cache (https://parceljs.org/)
|
||||
.cache
|
||||
.parcel-cache
|
||||
|
||||
# Next.js build output
|
||||
.next
|
||||
out
|
||||
|
||||
# Nuxt.js build / generate output
|
||||
.nuxt
|
||||
dist
|
||||
.output
|
||||
|
||||
# Gatsby files
|
||||
.cache/
|
||||
# Comment in the public line in if your project uses Gatsby and not Next.js
|
||||
# https://nextjs.org/blog/next-9-1#public-directory-support
|
||||
# public
|
||||
|
||||
# vuepress build output
|
||||
.vuepress/dist
|
||||
|
||||
# vuepress v2.x temp and cache directory
|
||||
.temp
|
||||
.cache
|
||||
|
||||
# Sveltekit cache directory
|
||||
.svelte-kit/
|
||||
|
||||
# vitepress build output
|
||||
**/.vitepress/dist
|
||||
|
||||
# vitepress cache directory
|
||||
**/.vitepress/cache
|
||||
|
||||
# Docusaurus cache and generated files
|
||||
.docusaurus
|
||||
|
||||
# Serverless directories
|
||||
.serverless/
|
||||
|
||||
# FuseBox cache
|
||||
.fusebox/
|
||||
|
||||
# DynamoDB Local files
|
||||
.dynamodb/
|
||||
|
||||
# Firebase cache directory
|
||||
.firebase/
|
||||
|
||||
# TernJS port file
|
||||
.tern-port
|
||||
|
||||
# Stores VSCode versions used for testing VSCode extensions
|
||||
.vscode-test
|
||||
|
||||
# yarn v3
|
||||
.pnp.*
|
||||
.yarn/*
|
||||
!.yarn/patches
|
||||
!.yarn/plugins
|
||||
!.yarn/releases
|
||||
!.yarn/sdks
|
||||
!.yarn/versions
|
||||
|
||||
# Vite files
|
||||
vite.config.js.timestamp-*
|
||||
vite.config.ts.timestamp-*
|
||||
.vite/
|
||||
|
||||
### Custom ###
|
||||
|
||||
debug.log
|
||||
scratches/
|
||||
test-results/
|
||||
|
||||
data/
|
||||
*.arff
|
||||
|
||||
.DS_Store
|
||||
|
||||
node_modules/
|
||||
# Auto generated
|
||||
static/css/output.css
|
||||
|
||||
*.code-workspace
|
||||
.vscode/
|
||||
/pnpm-workspace.yaml
|
||||
# macOS system files
|
||||
.DS_Store
|
||||
.Trashes
|
||||
._*
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
from epdb.api import router as epdb_app_router
|
||||
from epapi.v1.router import router as v1_router # Refactored API from epdb.api_v2
|
||||
from epdb.legacy_api import router as epdb_legacy_app_router
|
||||
from ninja import NinjaAPI
|
||||
|
||||
@ -8,5 +8,5 @@ api_v1 = NinjaAPI(title="API V1 Docs", urls_namespace="api-v1")
|
||||
api_legacy = NinjaAPI(title="Legacy API Docs", urls_namespace="api-legacy")
|
||||
|
||||
# Add routers
|
||||
api_v1.add_router("/", epdb_app_router)
|
||||
api_v1.add_router("/", v1_router)
|
||||
api_legacy.add_router("/", epdb_legacy_app_router)
|
||||
|
||||
@ -48,6 +48,7 @@ INSTALLED_APPS = [
|
||||
"django_extensions",
|
||||
"oauth2_provider",
|
||||
# Custom
|
||||
"epapi", # API endpoints (v1, etc.)
|
||||
"epdb",
|
||||
# "migration",
|
||||
]
|
||||
@ -198,6 +199,12 @@ if not os.path.exists(LOG_DIR):
|
||||
os.mkdir(LOG_DIR)
|
||||
|
||||
PLUGIN_DIR = os.path.join(EP_DATA_DIR, "plugins")
|
||||
|
||||
API_PAGINATION_DEFAULT_PAGE_SIZE = int(os.environ.get("API_PAGINATION_DEFAULT_PAGE_SIZE", 50))
|
||||
PAGINATION_MAX_PER_PAGE_SIZE = int(
|
||||
os.environ.get("API_PAGINATION_MAX_PAGE_SIZE", 100)
|
||||
) # Ninja override
|
||||
|
||||
if not os.path.exists(PLUGIN_DIR):
|
||||
os.mkdir(PLUGIN_DIR)
|
||||
|
||||
@ -355,6 +362,7 @@ FLAGS = {
|
||||
# -> /password_reset/done is covered as well
|
||||
LOGIN_EXEMPT_URLS = [
|
||||
"/register",
|
||||
"/api/v1/", # Let API handle its own authentication
|
||||
"/api/legacy/",
|
||||
"/o/token/",
|
||||
"/o/userinfo/",
|
||||
|
||||
0
epapi/__init__.py
Normal file
0
epapi/__init__.py
Normal file
6
epapi/apps.py
Normal file
6
epapi/apps.py
Normal file
@ -0,0 +1,6 @@
|
||||
from django.apps import AppConfig
|
||||
|
||||
|
||||
class EpapiConfig(AppConfig):
|
||||
default_auto_field = "django.db.models.BigAutoField"
|
||||
name = "epapi"
|
||||
0
epapi/migrations/__init__.py
Normal file
0
epapi/migrations/__init__.py
Normal file
1
epapi/tests/__init__.py
Normal file
1
epapi/tests/__init__.py
Normal file
@ -0,0 +1 @@
|
||||
# Tests for epapi app
|
||||
1
epapi/tests/v1/__init__.py
Normal file
1
epapi/tests/v1/__init__.py
Normal file
@ -0,0 +1 @@
|
||||
# Tests for epapi v1 API
|
||||
532
epapi/tests/v1/test_api_permissions.py
Normal file
532
epapi/tests/v1/test_api_permissions.py
Normal file
@ -0,0 +1,532 @@
|
||||
from django.test import TestCase, tag
|
||||
|
||||
from epdb.logic import GroupManager, PackageManager, UserManager
|
||||
from epdb.models import (
|
||||
Compound,
|
||||
GroupPackagePermission,
|
||||
Permission,
|
||||
UserPackagePermission,
|
||||
)
|
||||
|
||||
|
||||
@tag("api", "end2end")
|
||||
class APIPermissionTestBase(TestCase):
|
||||
"""
|
||||
Base class for API permission tests.
|
||||
|
||||
Sets up common test data:
|
||||
- user1: Owner of packages
|
||||
- user2: User with various permissions
|
||||
- user3: User with no permissions
|
||||
- reviewed_package: Public package (reviewed=True)
|
||||
- unreviewed_package_owned: Unreviewed package owned by user1
|
||||
- unreviewed_package_read: Unreviewed package with READ permission for user2
|
||||
- unreviewed_package_write: Unreviewed package with WRITE permission for user2
|
||||
- unreviewed_package_all: Unreviewed package with ALL permission for user2
|
||||
- unreviewed_package_no_access: Unreviewed package with no permissions for user2/user3
|
||||
- group_package: Unreviewed package accessible via group permission
|
||||
- test_group: Group containing user2
|
||||
"""
|
||||
|
||||
@classmethod
|
||||
def setUpTestData(cls):
|
||||
# Create users
|
||||
cls.user1 = UserManager.create_user(
|
||||
"permission-user1",
|
||||
"permission-user1@envipath.com",
|
||||
"SuperSafe",
|
||||
set_setting=False,
|
||||
add_to_group=False,
|
||||
is_active=True,
|
||||
)
|
||||
cls.user2 = UserManager.create_user(
|
||||
"permission-user2",
|
||||
"permission-user2@envipath.com",
|
||||
"SuperSafe",
|
||||
set_setting=False,
|
||||
add_to_group=False,
|
||||
is_active=True,
|
||||
)
|
||||
cls.user3 = UserManager.create_user(
|
||||
"permission-user3",
|
||||
"permission-user3@envipath.com",
|
||||
"SuperSafe",
|
||||
set_setting=False,
|
||||
add_to_group=False,
|
||||
is_active=True,
|
||||
)
|
||||
|
||||
# Delete default packages to ensure clean test data
|
||||
for user in [cls.user1, cls.user2, cls.user3]:
|
||||
default_pkg = user.default_package
|
||||
user.default_package = None
|
||||
user.save()
|
||||
if default_pkg:
|
||||
default_pkg.delete()
|
||||
|
||||
# Create reviewed package (public)
|
||||
cls.reviewed_package = PackageManager.create_package(
|
||||
cls.user1, "Reviewed Package", "Public package"
|
||||
)
|
||||
cls.reviewed_package.reviewed = True
|
||||
cls.reviewed_package.save()
|
||||
|
||||
# Create unreviewed packages with various permissions
|
||||
cls.unreviewed_package_owned = PackageManager.create_package(
|
||||
cls.user1, "User1 Owned Package", "Owned by user1"
|
||||
)
|
||||
|
||||
cls.unreviewed_package_read = PackageManager.create_package(
|
||||
cls.user1, "User2 Read Package", "User2 has READ permission"
|
||||
)
|
||||
UserPackagePermission.objects.create(
|
||||
user=cls.user2, package=cls.unreviewed_package_read, permission=Permission.READ[0]
|
||||
)
|
||||
|
||||
cls.unreviewed_package_write = PackageManager.create_package(
|
||||
cls.user1, "User2 Write Package", "User2 has WRITE permission"
|
||||
)
|
||||
UserPackagePermission.objects.create(
|
||||
user=cls.user2, package=cls.unreviewed_package_write, permission=Permission.WRITE[0]
|
||||
)
|
||||
|
||||
cls.unreviewed_package_all = PackageManager.create_package(
|
||||
cls.user1, "User2 All Package", "User2 has ALL permission"
|
||||
)
|
||||
UserPackagePermission.objects.create(
|
||||
user=cls.user2, package=cls.unreviewed_package_all, permission=Permission.ALL[0]
|
||||
)
|
||||
|
||||
cls.unreviewed_package_no_access = PackageManager.create_package(
|
||||
cls.user1, "No Access Package", "No permissions for user2/user3"
|
||||
)
|
||||
|
||||
# Create group and group package
|
||||
cls.test_group = GroupManager.create_group(
|
||||
cls.user1, "Test Group", "Group for permission testing"
|
||||
)
|
||||
cls.test_group.user_member.add(cls.user2)
|
||||
cls.test_group.save()
|
||||
|
||||
cls.group_package = PackageManager.create_package(
|
||||
cls.user1, "Group Package", "Accessible via group permission"
|
||||
)
|
||||
GroupPackagePermission.objects.create(
|
||||
group=cls.test_group, package=cls.group_package, permission=Permission.READ[0]
|
||||
)
|
||||
|
||||
# Create test compounds in each package
|
||||
cls.reviewed_compound = Compound.create(
|
||||
cls.reviewed_package, "C", "Reviewed Compound", "Test compound"
|
||||
)
|
||||
cls.owned_compound = Compound.create(
|
||||
cls.unreviewed_package_owned, "CC", "Owned Compound", "Test compound"
|
||||
)
|
||||
cls.read_compound = Compound.create(
|
||||
cls.unreviewed_package_read, "CCC", "Read Compound", "Test compound"
|
||||
)
|
||||
cls.write_compound = Compound.create(
|
||||
cls.unreviewed_package_write, "CCCC", "Write Compound", "Test compound"
|
||||
)
|
||||
cls.all_compound = Compound.create(
|
||||
cls.unreviewed_package_all, "CCCCC", "All Compound", "Test compound"
|
||||
)
|
||||
cls.no_access_compound = Compound.create(
|
||||
cls.unreviewed_package_no_access, "CCCCCC", "No Access Compound", "Test compound"
|
||||
)
|
||||
cls.group_compound = Compound.create(
|
||||
cls.group_package, "CCCCCCC", "Group Compound", "Test compound"
|
||||
)
|
||||
|
||||
|
||||
@tag("api", "end2end")
|
||||
class PackageListPermissionTest(APIPermissionTestBase):
|
||||
"""
|
||||
Test permissions for /api/v1/packages/ endpoint.
|
||||
|
||||
Special case: This endpoint allows anonymous access (auth=None)
|
||||
"""
|
||||
|
||||
ENDPOINT = "/api/v1/packages/"
|
||||
|
||||
def test_anonymous_user_sees_only_reviewed_packages(self):
|
||||
"""Anonymous users should only see reviewed packages."""
|
||||
self.client.logout()
|
||||
response = self.client.get(self.ENDPOINT)
|
||||
|
||||
self.assertEqual(response.status_code, 200)
|
||||
payload = response.json()
|
||||
|
||||
# Should only see reviewed package
|
||||
self.assertEqual(payload["total_items"], 1)
|
||||
self.assertEqual(payload["items"][0]["uuid"], str(self.reviewed_package.uuid))
|
||||
self.assertEqual(payload["items"][0]["review_status"], "reviewed")
|
||||
|
||||
def test_authenticated_user_sees_all_readable_packages(self):
|
||||
"""Authenticated users see reviewed + packages they have access to."""
|
||||
self.client.force_login(self.user2)
|
||||
response = self.client.get(self.ENDPOINT)
|
||||
|
||||
self.assertEqual(response.status_code, 200)
|
||||
payload = response.json()
|
||||
|
||||
# user2 should see:
|
||||
# - reviewed_package (public)
|
||||
# - unreviewed_package_read (READ permission)
|
||||
# - unreviewed_package_write (WRITE permission)
|
||||
# - unreviewed_package_all (ALL permission)
|
||||
# - group_package (via group membership)
|
||||
# Total: 5 packages
|
||||
self.assertEqual(payload["total_items"], 5)
|
||||
|
||||
visible_uuids = {item["uuid"] for item in payload["items"]}
|
||||
expected_uuids = {
|
||||
str(self.reviewed_package.uuid),
|
||||
str(self.unreviewed_package_read.uuid),
|
||||
str(self.unreviewed_package_write.uuid),
|
||||
str(self.unreviewed_package_all.uuid),
|
||||
str(self.group_package.uuid),
|
||||
}
|
||||
self.assertEqual(visible_uuids, expected_uuids)
|
||||
|
||||
def test_owner_sees_all_owned_packages(self):
|
||||
"""Package owner sees all packages they created."""
|
||||
self.client.force_login(self.user1)
|
||||
response = self.client.get(self.ENDPOINT)
|
||||
|
||||
self.assertEqual(response.status_code, 200)
|
||||
payload = response.json()
|
||||
|
||||
# user1 owns all packages
|
||||
# Total: 7 packages (all packages created in setUpTestData)
|
||||
self.assertEqual(payload["total_items"], 7)
|
||||
|
||||
def test_filter_by_review_status_true(self):
|
||||
"""Filter to show only reviewed packages."""
|
||||
self.client.force_login(self.user2)
|
||||
response = self.client.get(self.ENDPOINT, {"review_status": True})
|
||||
|
||||
self.assertEqual(response.status_code, 200)
|
||||
payload = response.json()
|
||||
|
||||
# Only reviewed_package
|
||||
self.assertEqual(payload["total_items"], 1)
|
||||
self.assertTrue(all(item["review_status"] == "reviewed" for item in payload["items"]))
|
||||
|
||||
def test_filter_by_review_status_false(self):
|
||||
"""Filter to show only unreviewed packages."""
|
||||
self.client.force_login(self.user2)
|
||||
response = self.client.get(self.ENDPOINT, {"review_status": False})
|
||||
|
||||
self.assertEqual(response.status_code, 200)
|
||||
payload = response.json()
|
||||
|
||||
# user2's accessible unreviewed packages: 4
|
||||
self.assertEqual(payload["total_items"], 4)
|
||||
self.assertTrue(all(item["review_status"] == "unreviewed" for item in payload["items"]))
|
||||
|
||||
def test_anonymous_filter_unreviewed_returns_empty(self):
|
||||
"""Anonymous users get no results when filtering for unreviewed."""
|
||||
self.client.logout()
|
||||
response = self.client.get(self.ENDPOINT, {"review_status": False})
|
||||
|
||||
self.assertEqual(response.status_code, 200)
|
||||
payload = response.json()
|
||||
|
||||
self.assertEqual(payload["total_items"], 0)
|
||||
|
||||
|
||||
@tag("api", "end2end")
|
||||
class GlobalCompoundListPermissionTest(APIPermissionTestBase):
|
||||
"""
|
||||
Test permissions for /api/v1/compounds/ endpoint.
|
||||
|
||||
This endpoint requires authentication.
|
||||
"""
|
||||
|
||||
ENDPOINT = "/api/v1/compounds/"
|
||||
|
||||
def test_anonymous_user_cannot_access(self):
|
||||
"""Anonymous users should get 401 Unauthorized."""
|
||||
self.client.logout()
|
||||
response = self.client.get(self.ENDPOINT)
|
||||
|
||||
self.assertEqual(response.status_code, 401)
|
||||
|
||||
def test_authenticated_user_sees_compounds_from_readable_packages(self):
|
||||
"""Authenticated users see compounds from packages they can read."""
|
||||
self.client.force_login(self.user2)
|
||||
response = self.client.get(self.ENDPOINT)
|
||||
|
||||
self.assertEqual(response.status_code, 200)
|
||||
payload = response.json()
|
||||
|
||||
# user2 should see compounds from:
|
||||
# - reviewed_package (public)
|
||||
# - unreviewed_package_read (READ permission)
|
||||
# - unreviewed_package_write (WRITE permission)
|
||||
# - unreviewed_package_all (ALL permission)
|
||||
# - group_package (via group membership)
|
||||
# Total: 5 compounds
|
||||
self.assertEqual(payload["total_items"], 5)
|
||||
|
||||
visible_uuids = {item["uuid"] for item in payload["items"]}
|
||||
expected_uuids = {
|
||||
str(self.reviewed_compound.uuid),
|
||||
str(self.read_compound.uuid),
|
||||
str(self.write_compound.uuid),
|
||||
str(self.all_compound.uuid),
|
||||
str(self.group_compound.uuid),
|
||||
}
|
||||
self.assertEqual(visible_uuids, expected_uuids)
|
||||
|
||||
def test_user_without_permission_cannot_see_compound(self):
|
||||
"""User without permission to package cannot see its compounds."""
|
||||
self.client.force_login(self.user3)
|
||||
response = self.client.get(self.ENDPOINT)
|
||||
|
||||
self.assertEqual(response.status_code, 200)
|
||||
payload = response.json()
|
||||
|
||||
# user3 should only see compounds from reviewed_package
|
||||
self.assertEqual(payload["total_items"], 1)
|
||||
self.assertEqual(payload["items"][0]["uuid"], str(self.reviewed_compound.uuid))
|
||||
|
||||
def test_owner_sees_all_compounds(self):
|
||||
"""Package owner sees all compounds they created."""
|
||||
self.client.force_login(self.user1)
|
||||
response = self.client.get(self.ENDPOINT)
|
||||
|
||||
self.assertEqual(response.status_code, 200)
|
||||
payload = response.json()
|
||||
|
||||
# user1 owns all packages, so sees all compounds
|
||||
self.assertEqual(payload["total_items"], 7)
|
||||
|
||||
def test_read_permission_allows_viewing(self):
|
||||
"""READ permission allows viewing compounds."""
|
||||
self.client.force_login(self.user2)
|
||||
response = self.client.get(self.ENDPOINT)
|
||||
|
||||
self.assertEqual(response.status_code, 200)
|
||||
payload = response.json()
|
||||
|
||||
# Check that read_compound is included
|
||||
uuids = [item["uuid"] for item in payload["items"]]
|
||||
self.assertIn(str(self.read_compound.uuid), uuids)
|
||||
|
||||
def test_write_permission_allows_viewing(self):
|
||||
"""WRITE permission also allows viewing compounds."""
|
||||
self.client.force_login(self.user2)
|
||||
response = self.client.get(self.ENDPOINT)
|
||||
|
||||
self.assertEqual(response.status_code, 200)
|
||||
payload = response.json()
|
||||
|
||||
# Check that write_compound is included
|
||||
uuids = [item["uuid"] for item in payload["items"]]
|
||||
self.assertIn(str(self.write_compound.uuid), uuids)
|
||||
|
||||
def test_all_permission_allows_viewing(self):
|
||||
"""ALL permission allows viewing compounds."""
|
||||
self.client.force_login(self.user2)
|
||||
response = self.client.get(self.ENDPOINT)
|
||||
|
||||
self.assertEqual(response.status_code, 200)
|
||||
payload = response.json()
|
||||
|
||||
# Check that all_compound is included
|
||||
uuids = [item["uuid"] for item in payload["items"]]
|
||||
self.assertIn(str(self.all_compound.uuid), uuids)
|
||||
|
||||
def test_group_permission_allows_viewing(self):
|
||||
"""Group membership grants access to group-permitted packages."""
|
||||
self.client.force_login(self.user2)
|
||||
response = self.client.get(self.ENDPOINT)
|
||||
|
||||
self.assertEqual(response.status_code, 200)
|
||||
payload = response.json()
|
||||
|
||||
# Check that group_compound is included
|
||||
uuids = [item["uuid"] for item in payload["items"]]
|
||||
self.assertIn(str(self.group_compound.uuid), uuids)
|
||||
|
||||
|
||||
@tag("api", "end2end")
|
||||
class PackageScopedCompoundListPermissionTest(APIPermissionTestBase):
|
||||
"""
|
||||
Test permissions for /api/v1/package/{uuid}/compound/ endpoint.
|
||||
|
||||
This endpoint requires authentication AND package access.
|
||||
"""
|
||||
|
||||
def test_anonymous_user_cannot_access_reviewed_package(self):
|
||||
"""Anonymous users should get 401 even for reviewed packages."""
|
||||
self.client.logout()
|
||||
endpoint = f"/api/v1/package/{self.reviewed_package.uuid}/compound/"
|
||||
response = self.client.get(endpoint)
|
||||
|
||||
self.assertEqual(response.status_code, 401)
|
||||
|
||||
def test_authenticated_user_can_access_reviewed_package(self):
|
||||
"""Authenticated users can access reviewed packages."""
|
||||
self.client.force_login(self.user3)
|
||||
endpoint = f"/api/v1/package/{self.reviewed_package.uuid}/compound/"
|
||||
response = self.client.get(endpoint)
|
||||
|
||||
self.assertEqual(response.status_code, 200)
|
||||
payload = response.json()
|
||||
|
||||
self.assertEqual(payload["total_items"], 1)
|
||||
self.assertEqual(payload["items"][0]["uuid"], str(self.reviewed_compound.uuid))
|
||||
|
||||
def test_user_can_access_package_with_read_permission(self):
|
||||
"""User with READ permission can access package-scoped endpoint."""
|
||||
self.client.force_login(self.user2)
|
||||
endpoint = f"/api/v1/package/{self.unreviewed_package_read.uuid}/compound/"
|
||||
response = self.client.get(endpoint)
|
||||
|
||||
self.assertEqual(response.status_code, 200)
|
||||
payload = response.json()
|
||||
|
||||
self.assertEqual(payload["total_items"], 1)
|
||||
self.assertEqual(payload["items"][0]["uuid"], str(self.read_compound.uuid))
|
||||
|
||||
def test_user_can_access_package_with_write_permission(self):
|
||||
"""User with WRITE permission can access package-scoped endpoint."""
|
||||
self.client.force_login(self.user2)
|
||||
endpoint = f"/api/v1/package/{self.unreviewed_package_write.uuid}/compound/"
|
||||
response = self.client.get(endpoint)
|
||||
|
||||
self.assertEqual(response.status_code, 200)
|
||||
payload = response.json()
|
||||
|
||||
self.assertEqual(payload["total_items"], 1)
|
||||
self.assertEqual(payload["items"][0]["uuid"], str(self.write_compound.uuid))
|
||||
|
||||
def test_user_can_access_package_with_all_permission(self):
|
||||
"""User with ALL permission can access package-scoped endpoint."""
|
||||
self.client.force_login(self.user2)
|
||||
endpoint = f"/api/v1/package/{self.unreviewed_package_all.uuid}/compound/"
|
||||
response = self.client.get(endpoint)
|
||||
|
||||
self.assertEqual(response.status_code, 200)
|
||||
payload = response.json()
|
||||
|
||||
self.assertEqual(payload["total_items"], 1)
|
||||
self.assertEqual(payload["items"][0]["uuid"], str(self.all_compound.uuid))
|
||||
|
||||
def test_user_cannot_access_package_without_permission(self):
|
||||
"""User without permission gets 403 Forbidden."""
|
||||
self.client.force_login(self.user2)
|
||||
endpoint = f"/api/v1/package/{self.unreviewed_package_no_access.uuid}/compound/"
|
||||
response = self.client.get(endpoint)
|
||||
|
||||
self.assertEqual(response.status_code, 403)
|
||||
|
||||
def test_nonexistent_package_returns_404(self):
|
||||
"""Request for non-existent package returns 404."""
|
||||
self.client.force_login(self.user2)
|
||||
fake_uuid = "00000000-0000-0000-0000-000000000000"
|
||||
endpoint = f"/api/v1/package/{fake_uuid}/compound/"
|
||||
response = self.client.get(endpoint)
|
||||
|
||||
self.assertEqual(response.status_code, 404)
|
||||
|
||||
def test_owner_can_access_owned_package(self):
|
||||
"""Package owner can access their package."""
|
||||
self.client.force_login(self.user1)
|
||||
endpoint = f"/api/v1/package/{self.unreviewed_package_owned.uuid}/compound/"
|
||||
response = self.client.get(endpoint)
|
||||
|
||||
self.assertEqual(response.status_code, 200)
|
||||
payload = response.json()
|
||||
|
||||
self.assertEqual(payload["total_items"], 1)
|
||||
self.assertEqual(payload["items"][0]["uuid"], str(self.owned_compound.uuid))
|
||||
|
||||
def test_group_member_can_access_group_package(self):
|
||||
"""Group member can access package via group permission."""
|
||||
self.client.force_login(self.user2)
|
||||
endpoint = f"/api/v1/package/{self.group_package.uuid}/compound/"
|
||||
response = self.client.get(endpoint)
|
||||
|
||||
self.assertEqual(response.status_code, 200)
|
||||
payload = response.json()
|
||||
|
||||
self.assertEqual(payload["total_items"], 1)
|
||||
self.assertEqual(payload["items"][0]["uuid"], str(self.group_compound.uuid))
|
||||
|
||||
def test_non_group_member_cannot_access_group_package(self):
|
||||
"""Non-group member cannot access package with only group permission."""
|
||||
self.client.force_login(self.user3)
|
||||
endpoint = f"/api/v1/package/{self.group_package.uuid}/compound/"
|
||||
response = self.client.get(endpoint)
|
||||
|
||||
self.assertEqual(response.status_code, 403)
|
||||
|
||||
|
||||
@tag("api", "end2end")
|
||||
class MultiResourcePermissionTest(APIPermissionTestBase):
|
||||
"""
|
||||
Test that permission system works consistently across all resource types.
|
||||
|
||||
Tests a sample of other endpoints to ensure permission logic is consistent.
|
||||
"""
|
||||
|
||||
def test_rules_endpoint_respects_permissions(self):
|
||||
"""Rules endpoint uses same permission logic."""
|
||||
from epdb.models import SimpleAmbitRule
|
||||
|
||||
# Create rule in no-access package
|
||||
rule = SimpleAmbitRule.create(
|
||||
self.unreviewed_package_no_access, "Test Rule", "Test", "[C:1]>>[C:1]O"
|
||||
)
|
||||
|
||||
self.client.force_login(self.user2)
|
||||
response = self.client.get("/api/v1/rules/")
|
||||
|
||||
self.assertEqual(response.status_code, 200)
|
||||
payload = response.json()
|
||||
|
||||
# user2 should not see the rule from no_access_package
|
||||
rule_uuids = [item["uuid"] for item in payload["items"]]
|
||||
self.assertNotIn(str(rule.uuid), rule_uuids)
|
||||
|
||||
def test_reactions_endpoint_respects_permissions(self):
|
||||
"""Reactions endpoint uses same permission logic."""
|
||||
from epdb.models import Reaction
|
||||
|
||||
# Create reaction in no-access package
|
||||
reaction = Reaction.create(
|
||||
self.unreviewed_package_no_access, "Test Reaction", "Test", ["C"], ["CO"]
|
||||
)
|
||||
|
||||
self.client.force_login(self.user2)
|
||||
response = self.client.get("/api/v1/reactions/")
|
||||
|
||||
self.assertEqual(response.status_code, 200)
|
||||
payload = response.json()
|
||||
|
||||
# user2 should not see the reaction from no_access_package
|
||||
reaction_uuids = [item["uuid"] for item in payload["items"]]
|
||||
self.assertNotIn(str(reaction.uuid), reaction_uuids)
|
||||
|
||||
def test_pathways_endpoint_respects_permissions(self):
|
||||
"""Pathways endpoint uses same permission logic."""
|
||||
from epdb.models import Pathway
|
||||
|
||||
# Create pathway in no-access package
|
||||
pathway = Pathway.objects.create(
|
||||
package=self.unreviewed_package_no_access, name="Test Pathway", description="Test"
|
||||
)
|
||||
|
||||
self.client.force_login(self.user2)
|
||||
response = self.client.get("/api/v1/pathways/")
|
||||
|
||||
self.assertEqual(response.status_code, 200)
|
||||
payload = response.json()
|
||||
|
||||
# user2 should not see the pathway from no_access_package
|
||||
pathway_uuids = [item["uuid"] for item in payload["items"]]
|
||||
self.assertNotIn(str(pathway.uuid), pathway_uuids)
|
||||
477
epapi/tests/v1/test_contract_get_entities.py
Normal file
477
epapi/tests/v1/test_contract_get_entities.py
Normal file
@ -0,0 +1,477 @@
|
||||
from django.test import TestCase, tag
|
||||
|
||||
from epdb.logic import PackageManager, UserManager
|
||||
from epdb.models import Compound, Reaction, Pathway, EPModel, SimpleAmbitRule, Scenario
|
||||
|
||||
|
||||
class BaseTestAPIGetPaginated:
|
||||
"""
|
||||
Mixin class for API pagination tests.
|
||||
|
||||
Subclasses must inherit from both this class and TestCase, e.g.:
|
||||
class MyTest(BaseTestAPIGetPaginated, TestCase):
|
||||
...
|
||||
|
||||
Subclasses must define:
|
||||
- resource_name: Singular name (e.g., "compound")
|
||||
- resource_name_plural: Plural name (e.g., "compounds")
|
||||
- global_endpoint: Global listing endpoint (e.g., "/api/v1/compounds/")
|
||||
- package_endpoint_template: Template for package-scoped endpoint or None
|
||||
- total_reviewed: Number of reviewed items to create
|
||||
- total_unreviewed: Number of unreviewed items to create
|
||||
- create_reviewed_resource(cls, package, idx): Factory method
|
||||
- create_unreviewed_resource(cls, package, idx): Factory method
|
||||
"""
|
||||
|
||||
# Configuration to be overridden by subclasses
|
||||
resource_name = None
|
||||
resource_name_plural = None
|
||||
global_endpoint = None
|
||||
package_endpoint_template = None
|
||||
total_reviewed = 50
|
||||
total_unreviewed = 20
|
||||
default_page_size = 50
|
||||
max_page_size = 100
|
||||
|
||||
@classmethod
|
||||
def setUpTestData(cls):
|
||||
# Create test user
|
||||
cls.user = UserManager.create_user(
|
||||
f"{cls.resource_name}-user",
|
||||
f"{cls.resource_name}-user@envipath.com",
|
||||
"SuperSafe",
|
||||
set_setting=False,
|
||||
add_to_group=False,
|
||||
is_active=True,
|
||||
)
|
||||
|
||||
# Delete the auto-created default package to ensure clean test data
|
||||
default_pkg = cls.user.default_package
|
||||
cls.user.default_package = None
|
||||
cls.user.save()
|
||||
default_pkg.delete()
|
||||
|
||||
# Create reviewed package
|
||||
cls.reviewed_package = PackageManager.create_package(
|
||||
cls.user, "Reviewed Package", f"Reviewed package for {cls.resource_name} tests"
|
||||
)
|
||||
cls.reviewed_package.reviewed = True
|
||||
cls.reviewed_package.save()
|
||||
|
||||
# Create unreviewed package
|
||||
cls.unreviewed_package = PackageManager.create_package(
|
||||
cls.user, "Draft Package", f"Unreviewed package for {cls.resource_name} tests"
|
||||
)
|
||||
|
||||
# Create reviewed resources
|
||||
for idx in range(cls.total_reviewed):
|
||||
cls.create_reviewed_resource(cls.reviewed_package, idx)
|
||||
|
||||
# Create unreviewed resources
|
||||
for idx in range(cls.total_unreviewed):
|
||||
cls.create_unreviewed_resource(cls.unreviewed_package, idx)
|
||||
|
||||
# Set up package-scoped endpoints if applicable
|
||||
if cls.package_endpoint_template:
|
||||
cls.reviewed_package_endpoint = cls.package_endpoint_template.format(
|
||||
uuid=cls.reviewed_package.uuid
|
||||
)
|
||||
cls.unreviewed_package_endpoint = cls.package_endpoint_template.format(
|
||||
uuid=cls.unreviewed_package.uuid
|
||||
)
|
||||
|
||||
@classmethod
|
||||
def create_reviewed_resource(cls, package, idx):
|
||||
"""
|
||||
Create a single reviewed resource.
|
||||
Must be implemented by subclass.
|
||||
|
||||
Args:
|
||||
package: The package to create the resource in
|
||||
idx: Index of the resource (0-based)
|
||||
"""
|
||||
raise NotImplementedError(f"{cls.__name__} must implement create_reviewed_resource()")
|
||||
|
||||
@classmethod
|
||||
def create_unreviewed_resource(cls, package, idx):
|
||||
"""
|
||||
Create a single unreviewed resource.
|
||||
Must be implemented by subclass.
|
||||
|
||||
Args:
|
||||
package: The package to create the resource in
|
||||
idx: Index of the resource (0-based)
|
||||
"""
|
||||
raise NotImplementedError(f"{cls.__name__} must implement create_unreviewed_resource()")
|
||||
|
||||
def setUp(self):
|
||||
self.client.force_login(self.user)
|
||||
|
||||
def test_requires_session_authentication(self):
|
||||
"""Test that the global endpoint requires authentication."""
|
||||
self.client.logout()
|
||||
response = self.client.get(self.global_endpoint)
|
||||
self.assertEqual(response.status_code, 401)
|
||||
|
||||
def test_global_listing_uses_default_page_size(self):
|
||||
"""Test that the global endpoint uses default pagination settings."""
|
||||
response = self.client.get(self.global_endpoint, {"review_status": True})
|
||||
self.assertEqual(response.status_code, 200)
|
||||
|
||||
payload = response.json()
|
||||
self.assertEqual(payload["page"], 1)
|
||||
self.assertEqual(payload["page_size"], self.default_page_size)
|
||||
self.assertEqual(payload["total_items"], self.total_reviewed)
|
||||
|
||||
# Verify only reviewed items are returned
|
||||
self.assertTrue(all(item["review_status"] == "reviewed" for item in payload["items"]))
|
||||
|
||||
def test_can_request_later_page(self):
|
||||
"""Test that pagination works for later pages."""
|
||||
if self.total_reviewed <= self.default_page_size:
|
||||
self.skipTest(
|
||||
f"Not enough items to test pagination "
|
||||
f"({self.total_reviewed} <= {self.default_page_size})"
|
||||
)
|
||||
|
||||
response = self.client.get(self.global_endpoint, {"page": 2})
|
||||
self.assertEqual(response.status_code, 200)
|
||||
|
||||
payload = response.json()
|
||||
self.assertEqual(payload["page"], 2)
|
||||
|
||||
# Calculate expected items on page 2
|
||||
expected_items = min(self.default_page_size, self.total_reviewed - self.default_page_size)
|
||||
self.assertEqual(len(payload["items"]), expected_items)
|
||||
|
||||
# Verify only reviewed items are returned
|
||||
self.assertTrue(all(item["review_status"] == "reviewed" for item in payload["items"]))
|
||||
|
||||
def test_page_size_is_capped(self):
|
||||
"""Test that page size is capped at the maximum."""
|
||||
if self.total_reviewed <= self.max_page_size:
|
||||
self.skipTest(
|
||||
f"Not enough items to test page size cap "
|
||||
f"({self.total_reviewed} <= {self.max_page_size})"
|
||||
)
|
||||
|
||||
response = self.client.get(self.global_endpoint, {"page_size": 150})
|
||||
self.assertEqual(response.status_code, 200)
|
||||
|
||||
payload = response.json()
|
||||
self.assertEqual(payload["page_size"], self.max_page_size)
|
||||
self.assertEqual(len(payload["items"]), self.max_page_size)
|
||||
|
||||
def test_package_endpoint_for_reviewed_package(self):
|
||||
"""Test the package-scoped endpoint for reviewed packages."""
|
||||
if not self.package_endpoint_template:
|
||||
self.skipTest("No package endpoint for this resource")
|
||||
|
||||
response = self.client.get(self.reviewed_package_endpoint)
|
||||
self.assertEqual(response.status_code, 200)
|
||||
|
||||
payload = response.json()
|
||||
self.assertEqual(payload["total_items"], self.total_reviewed)
|
||||
|
||||
# Verify only reviewed items are returned
|
||||
self.assertTrue(all(item["review_status"] == "reviewed" for item in payload["items"]))
|
||||
|
||||
def test_package_endpoint_for_unreviewed_package(self):
|
||||
"""Test the package-scoped endpoint for unreviewed packages."""
|
||||
if not self.package_endpoint_template:
|
||||
self.skipTest("No package endpoint for this resource")
|
||||
|
||||
response = self.client.get(self.unreviewed_package_endpoint)
|
||||
self.assertEqual(response.status_code, 200)
|
||||
|
||||
payload = response.json()
|
||||
self.assertEqual(payload["total_items"], self.total_unreviewed)
|
||||
|
||||
# Verify only unreviewed items are returned
|
||||
self.assertTrue(all(item["review_status"] == "unreviewed" for item in payload["items"]))
|
||||
|
||||
|
||||
@tag("api", "end2end")
|
||||
class PackagePaginationAPITest(TestCase):
|
||||
ENDPOINT = "/api/v1/packages/"
|
||||
|
||||
@classmethod
|
||||
def setUpTestData(cls):
|
||||
cls.user = UserManager.create_user(
|
||||
"package-user",
|
||||
"package-user@envipath.com",
|
||||
"SuperSafe",
|
||||
set_setting=False,
|
||||
add_to_group=False,
|
||||
is_active=True,
|
||||
)
|
||||
|
||||
# Delete the auto-created default package to ensure clean test data
|
||||
default_pkg = cls.user.default_package
|
||||
cls.user.default_package = None
|
||||
cls.user.save()
|
||||
default_pkg.delete()
|
||||
|
||||
# Create reviewed packages
|
||||
cls.total_reviewed = 25
|
||||
for idx in range(cls.total_reviewed):
|
||||
package = PackageManager.create_package(
|
||||
cls.user, f"Reviewed Package {idx:03d}", "Reviewed package for tests"
|
||||
)
|
||||
package.reviewed = True
|
||||
package.save()
|
||||
|
||||
# Create unreviewed packages
|
||||
cls.total_unreviewed = 15
|
||||
for idx in range(cls.total_unreviewed):
|
||||
PackageManager.create_package(
|
||||
cls.user, f"Draft Package {idx:03d}", "Unreviewed package for tests"
|
||||
)
|
||||
|
||||
def setUp(self):
|
||||
self.client.force_login(self.user)
|
||||
|
||||
def test_anonymous_can_access_reviewed_packages(self):
|
||||
self.client.logout()
|
||||
response = self.client.get(self.ENDPOINT)
|
||||
self.assertEqual(response.status_code, 200)
|
||||
|
||||
payload = response.json()
|
||||
# Anonymous users can only see reviewed packages
|
||||
self.assertEqual(payload["total_items"], self.total_reviewed)
|
||||
self.assertTrue(all(item["review_status"] == "reviewed" for item in payload["items"]))
|
||||
|
||||
def test_listing_uses_default_page_size(self):
|
||||
response = self.client.get(self.ENDPOINT)
|
||||
self.assertEqual(response.status_code, 200)
|
||||
|
||||
payload = response.json()
|
||||
self.assertEqual(payload["page"], 1)
|
||||
self.assertEqual(payload["page_size"], 50)
|
||||
self.assertEqual(payload["total_items"], self.total_reviewed + self.total_unreviewed)
|
||||
|
||||
def test_reviewed_filter_true(self):
|
||||
response = self.client.get(self.ENDPOINT, {"review_status": True})
|
||||
self.assertEqual(response.status_code, 200)
|
||||
|
||||
payload = response.json()
|
||||
self.assertEqual(payload["total_items"], self.total_reviewed)
|
||||
self.assertTrue(all(item["review_status"] == "reviewed" for item in payload["items"]))
|
||||
|
||||
def test_reviewed_filter_false(self):
|
||||
response = self.client.get(self.ENDPOINT, {"review_status": False})
|
||||
self.assertEqual(response.status_code, 200)
|
||||
|
||||
payload = response.json()
|
||||
self.assertEqual(payload["total_items"], self.total_unreviewed)
|
||||
self.assertTrue(all(item["review_status"] == "unreviewed" for item in payload["items"]))
|
||||
|
||||
def test_reviewed_filter_false_anonymous(self):
|
||||
self.client.logout()
|
||||
response = self.client.get(self.ENDPOINT, {"review_status": False})
|
||||
self.assertEqual(response.status_code, 200)
|
||||
|
||||
payload = response.json()
|
||||
# Anonymous users cannot access unreviewed packages
|
||||
self.assertEqual(payload["total_items"], 0)
|
||||
|
||||
|
||||
@tag("api", "end2end")
|
||||
class CompoundPaginationAPITest(BaseTestAPIGetPaginated, TestCase):
|
||||
"""Compound pagination tests using base class."""
|
||||
|
||||
resource_name = "compound"
|
||||
resource_name_plural = "compounds"
|
||||
global_endpoint = "/api/v1/compounds/"
|
||||
package_endpoint_template = "/api/v1/package/{uuid}/compound/"
|
||||
total_reviewed = 125
|
||||
total_unreviewed = 35
|
||||
|
||||
@classmethod
|
||||
def create_reviewed_resource(cls, package, idx):
|
||||
simple_smiles = ["C", "CC", "CCC", "CCCC", "CCCCC"]
|
||||
smiles = simple_smiles[idx % len(simple_smiles)] + ("O" * (idx // len(simple_smiles)))
|
||||
return Compound.create(
|
||||
package,
|
||||
smiles,
|
||||
f"Reviewed Compound {idx:03d}",
|
||||
"Compound for pagination tests",
|
||||
)
|
||||
|
||||
@classmethod
|
||||
def create_unreviewed_resource(cls, package, idx):
|
||||
simple_smiles = ["C", "CC", "CCC", "CCCC", "CCCCC"]
|
||||
smiles = simple_smiles[idx % len(simple_smiles)] + ("N" * (idx // len(simple_smiles)))
|
||||
return Compound.create(
|
||||
package,
|
||||
smiles,
|
||||
f"Draft Compound {idx:03d}",
|
||||
"Compound for pagination tests",
|
||||
)
|
||||
|
||||
|
||||
@tag("api", "end2end")
|
||||
class RulePaginationAPITest(BaseTestAPIGetPaginated, TestCase):
|
||||
"""Rule pagination tests using base class."""
|
||||
|
||||
resource_name = "rule"
|
||||
resource_name_plural = "rules"
|
||||
global_endpoint = "/api/v1/rules/"
|
||||
package_endpoint_template = "/api/v1/package/{uuid}/rule/"
|
||||
total_reviewed = 125
|
||||
total_unreviewed = 35
|
||||
|
||||
@classmethod
|
||||
def create_reviewed_resource(cls, package, idx):
|
||||
# Create unique SMIRKS by combining chain length and functional group variations
|
||||
# This ensures each idx gets a truly unique SMIRKS pattern
|
||||
carbon_chain = "C" * (idx + 1) # C, CC, CCC, ... (grows with idx)
|
||||
smirks = f"[{carbon_chain}:1]>>[{carbon_chain}:1]O"
|
||||
return SimpleAmbitRule.create(
|
||||
package,
|
||||
f"Reviewed Rule {idx:03d}",
|
||||
f"Rule {idx} for pagination tests",
|
||||
smirks,
|
||||
)
|
||||
|
||||
@classmethod
|
||||
def create_unreviewed_resource(cls, package, idx):
|
||||
# Create unique SMIRKS by varying the carbon chain length
|
||||
carbon_chain = "C" * (idx + 1) # C, CC, CCC, ... (grows with idx)
|
||||
smirks = f"[{carbon_chain}:1]>>[{carbon_chain}:1]N"
|
||||
return SimpleAmbitRule.create(
|
||||
package,
|
||||
f"Draft Rule {idx:03d}",
|
||||
f"Rule {idx} for pagination tests",
|
||||
smirks,
|
||||
)
|
||||
|
||||
|
||||
@tag("api", "end2end")
|
||||
class ReactionPaginationAPITest(BaseTestAPIGetPaginated, TestCase):
|
||||
"""Reaction pagination tests using base class."""
|
||||
|
||||
resource_name = "reaction"
|
||||
resource_name_plural = "reactions"
|
||||
global_endpoint = "/api/v1/reactions/"
|
||||
package_endpoint_template = "/api/v1/package/{uuid}/reaction/"
|
||||
total_reviewed = 125
|
||||
total_unreviewed = 35
|
||||
|
||||
@classmethod
|
||||
def create_reviewed_resource(cls, package, idx):
|
||||
# Generate unique SMILES with growing chain lengths to avoid duplicates
|
||||
# Each idx gets a unique chain length
|
||||
educt_smiles = "C" * (idx + 1) # C, CC, CCC, ... (grows with idx)
|
||||
product_smiles = educt_smiles + "O"
|
||||
return Reaction.create(
|
||||
package=package,
|
||||
name=f"Reviewed Reaction {idx:03d}",
|
||||
description="Reaction for pagination tests",
|
||||
educts=[educt_smiles],
|
||||
products=[product_smiles],
|
||||
)
|
||||
|
||||
@classmethod
|
||||
def create_unreviewed_resource(cls, package, idx):
|
||||
# Generate unique SMILES with growing chain lengths to avoid duplicates
|
||||
# Each idx gets a unique chain length
|
||||
educt_smiles = "C" * (idx + 1) # C, CC, CCC, ... (grows with idx)
|
||||
product_smiles = educt_smiles + "N"
|
||||
return Reaction.create(
|
||||
package=package,
|
||||
name=f"Draft Reaction {idx:03d}",
|
||||
description="Reaction for pagination tests",
|
||||
educts=[educt_smiles],
|
||||
products=[product_smiles],
|
||||
)
|
||||
|
||||
|
||||
@tag("api", "end2end")
|
||||
class PathwayPaginationAPITest(BaseTestAPIGetPaginated, TestCase):
|
||||
"""Pathway pagination tests using base class."""
|
||||
|
||||
resource_name = "pathway"
|
||||
resource_name_plural = "pathways"
|
||||
global_endpoint = "/api/v1/pathways/"
|
||||
package_endpoint_template = "/api/v1/package/{uuid}/pathway/"
|
||||
total_reviewed = 125
|
||||
total_unreviewed = 35
|
||||
|
||||
@classmethod
|
||||
def create_reviewed_resource(cls, package, idx):
|
||||
return Pathway.objects.create(
|
||||
package=package,
|
||||
name=f"Reviewed Pathway {idx:03d}",
|
||||
description="Pathway for pagination tests",
|
||||
)
|
||||
|
||||
@classmethod
|
||||
def create_unreviewed_resource(cls, package, idx):
|
||||
return Pathway.objects.create(
|
||||
package=package,
|
||||
name=f"Draft Pathway {idx:03d}",
|
||||
description="Pathway for pagination tests",
|
||||
)
|
||||
|
||||
|
||||
@tag("api", "end2end")
|
||||
class ModelPaginationAPITest(BaseTestAPIGetPaginated, TestCase):
|
||||
"""Model pagination tests using base class."""
|
||||
|
||||
resource_name = "model"
|
||||
resource_name_plural = "models"
|
||||
global_endpoint = "/api/v1/models/"
|
||||
package_endpoint_template = "/api/v1/package/{uuid}/model/"
|
||||
total_reviewed = 125
|
||||
total_unreviewed = 35
|
||||
|
||||
@classmethod
|
||||
def create_reviewed_resource(cls, package, idx):
|
||||
return EPModel.objects.create(
|
||||
package=package,
|
||||
name=f"Reviewed Model {idx:03d}",
|
||||
description="Model for pagination tests",
|
||||
)
|
||||
|
||||
@classmethod
|
||||
def create_unreviewed_resource(cls, package, idx):
|
||||
return EPModel.objects.create(
|
||||
package=package,
|
||||
name=f"Draft Model {idx:03d}",
|
||||
description="Model for pagination tests",
|
||||
)
|
||||
|
||||
|
||||
@tag("api", "end2end")
|
||||
class ScenarioPaginationAPITest(BaseTestAPIGetPaginated, TestCase):
|
||||
"""Scenario pagination tests using base class."""
|
||||
|
||||
resource_name = "scenario"
|
||||
resource_name_plural = "scenarios"
|
||||
global_endpoint = "/api/v1/scenarios/"
|
||||
package_endpoint_template = "/api/v1/package/{uuid}/scenario/"
|
||||
total_reviewed = 125
|
||||
total_unreviewed = 35
|
||||
|
||||
@classmethod
|
||||
def create_reviewed_resource(cls, package, idx):
|
||||
return Scenario.create(
|
||||
package,
|
||||
f"Reviewed Scenario {idx:03d}",
|
||||
"Scenario for pagination tests",
|
||||
"2025-01-01",
|
||||
"lab",
|
||||
[],
|
||||
)
|
||||
|
||||
@classmethod
|
||||
def create_unreviewed_resource(cls, package, idx):
|
||||
return Scenario.create(
|
||||
package,
|
||||
f"Draft Scenario {idx:03d}",
|
||||
"Scenario for pagination tests",
|
||||
"2025-01-01",
|
||||
"field",
|
||||
[],
|
||||
)
|
||||
0
epapi/v1/__init__.py
Normal file
0
epapi/v1/__init__.py
Normal file
8
epapi/v1/auth.py
Normal file
8
epapi/v1/auth.py
Normal file
@ -0,0 +1,8 @@
|
||||
from ninja.security import HttpBearer
|
||||
from ninja.errors import HttpError
|
||||
|
||||
|
||||
class BearerTokenAuth(HttpBearer):
|
||||
def authenticate(self, request, token):
|
||||
# FIXME: placeholder; implement it in O(1) time
|
||||
raise HttpError(401, "Invalid or expired token")
|
||||
95
epapi/v1/dal.py
Normal file
95
epapi/v1/dal.py
Normal file
@ -0,0 +1,95 @@
|
||||
from django.db.models import Model
|
||||
from epdb.logic import PackageManager
|
||||
from epdb.models import CompoundStructure, User, Package, Compound
|
||||
from uuid import UUID
|
||||
|
||||
from .errors import EPAPINotFoundError, EPAPIPermissionDeniedError
|
||||
|
||||
|
||||
def get_compound_or_error(user, compound_uuid: UUID):
|
||||
"""
|
||||
Get compound by UUID with permission check.
|
||||
"""
|
||||
try:
|
||||
compound = Compound.objects.get(uuid=compound_uuid)
|
||||
package = compound.package
|
||||
except Compound.DoesNotExist:
|
||||
raise EPAPINotFoundError(f"Compound with UUID {compound_uuid} not found")
|
||||
|
||||
# FIXME: optimize package manager to exclusively work with UUIDs
|
||||
if not user or user.is_anonymous or not PackageManager.readable(user, package):
|
||||
raise EPAPIPermissionDeniedError("Insufficient permissions to access this compound.")
|
||||
|
||||
return compound
|
||||
|
||||
|
||||
def get_package_or_error(user, package_uuid: UUID):
|
||||
"""
|
||||
Get package by UUID with permission check.
|
||||
"""
|
||||
|
||||
# FIXME: update package manager with custom exceptions to avoid manual checks here
|
||||
try:
|
||||
package = Package.objects.get(uuid=package_uuid)
|
||||
except Package.DoesNotExist:
|
||||
raise EPAPINotFoundError(f"Package with UUID {package_uuid} not found")
|
||||
|
||||
# FIXME: optimize package manager to exclusively work with UUIDs
|
||||
if not user or user.is_anonymous or not PackageManager.readable(user, package):
|
||||
raise EPAPIPermissionDeniedError("Insufficient permissions to access this package.")
|
||||
|
||||
return package
|
||||
|
||||
|
||||
def get_user_packages_qs(user: User | None):
|
||||
"""Get all packages readable by the user."""
|
||||
if not user or user.is_anonymous:
|
||||
return PackageManager.get_reviewed_packages()
|
||||
return PackageManager.get_all_readable_packages(user, include_reviewed=True)
|
||||
|
||||
|
||||
def get_user_entities_qs(model_class: Model, user: User | None):
|
||||
"""Build queryset for reviewed package entities."""
|
||||
|
||||
if not user or user.is_anonymous:
|
||||
return model_class.objects.filter(package__reviewed=True).select_related("package")
|
||||
|
||||
qs = model_class.objects.filter(
|
||||
package__in=PackageManager.get_all_readable_packages(user, include_reviewed=True)
|
||||
).select_related("package")
|
||||
return qs
|
||||
|
||||
|
||||
def get_package_scoped_entities_qs(
|
||||
model_class: Model, package_uuid: UUID, user: User | None = None
|
||||
):
|
||||
"""Build queryset for specific package entities."""
|
||||
package = get_package_or_error(user, package_uuid)
|
||||
qs = model_class.objects.filter(package=package).select_related("package")
|
||||
return qs
|
||||
|
||||
|
||||
def get_user_structures_qs(user: User | None):
|
||||
"""Build queryset for structures accessible to the user (via compound->package)."""
|
||||
|
||||
if not user or user.is_anonymous:
|
||||
return CompoundStructure.objects.filter(compound__package__reviewed=True).select_related(
|
||||
"compound__package"
|
||||
)
|
||||
|
||||
qs = CompoundStructure.objects.filter(
|
||||
compound__package__in=PackageManager.get_all_readable_packages(user, include_reviewed=True)
|
||||
).select_related("compound__package")
|
||||
return qs
|
||||
|
||||
|
||||
def get_package_compound_scoped_structure_qs(
|
||||
package_uuid: UUID, compound_uuid: UUID, user: User | None = None
|
||||
):
|
||||
"""Build queryset for specific package compound structures."""
|
||||
|
||||
get_package_or_error(user, package_uuid)
|
||||
compound = get_compound_or_error(user, compound_uuid)
|
||||
|
||||
qs = CompoundStructure.objects.filter(compound=compound).select_related("compound__package")
|
||||
return qs
|
||||
0
epapi/v1/endpoints/__init__.py
Normal file
0
epapi/v1/endpoints/__init__.py
Normal file
41
epapi/v1/endpoints/compounds.py
Normal file
41
epapi/v1/endpoints/compounds.py
Normal file
@ -0,0 +1,41 @@
|
||||
from django.conf import settings as s
|
||||
from ninja import Router
|
||||
from ninja_extra.pagination import paginate
|
||||
from uuid import UUID
|
||||
|
||||
from epdb.models import Compound
|
||||
from ..pagination import EnhancedPageNumberPagination
|
||||
from ..schemas import CompoundOutSchema, ReviewStatusFilter
|
||||
from ..dal import get_user_entities_qs, get_package_scoped_entities_qs
|
||||
|
||||
router = Router()
|
||||
|
||||
|
||||
@router.get("/compounds/", response=EnhancedPageNumberPagination.Output[CompoundOutSchema])
|
||||
@paginate(
|
||||
EnhancedPageNumberPagination,
|
||||
page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
|
||||
filter_schema=ReviewStatusFilter,
|
||||
)
|
||||
def list_all_compounds(request):
|
||||
"""
|
||||
List all compounds from reviewed packages.
|
||||
"""
|
||||
return get_user_entities_qs(Compound, request.user).order_by("name").all()
|
||||
|
||||
|
||||
@router.get(
|
||||
"/package/{uuid:package_uuid}/compound/",
|
||||
response=EnhancedPageNumberPagination.Output[CompoundOutSchema],
|
||||
)
|
||||
@paginate(
|
||||
EnhancedPageNumberPagination,
|
||||
page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
|
||||
filter_schema=ReviewStatusFilter,
|
||||
)
|
||||
def list_package_compounds(request, package_uuid: UUID):
|
||||
"""
|
||||
List all compounds for a specific package.
|
||||
"""
|
||||
user = request.user
|
||||
return get_package_scoped_entities_qs(Compound, package_uuid, user).order_by("name").all()
|
||||
41
epapi/v1/endpoints/models.py
Normal file
41
epapi/v1/endpoints/models.py
Normal file
@ -0,0 +1,41 @@
|
||||
from django.conf import settings as s
|
||||
from ninja import Router
|
||||
from ninja_extra.pagination import paginate
|
||||
from uuid import UUID
|
||||
|
||||
from epdb.models import EPModel
|
||||
from ..pagination import EnhancedPageNumberPagination
|
||||
from ..schemas import ModelOutSchema, ReviewStatusFilter
|
||||
from ..dal import get_user_entities_qs, get_package_scoped_entities_qs
|
||||
|
||||
router = Router()
|
||||
|
||||
|
||||
@router.get("/models/", response=EnhancedPageNumberPagination.Output[ModelOutSchema])
|
||||
@paginate(
|
||||
EnhancedPageNumberPagination,
|
||||
page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
|
||||
filter_schema=ReviewStatusFilter,
|
||||
)
|
||||
def list_all_models(request):
|
||||
"""
|
||||
List all models from reviewed packages.
|
||||
"""
|
||||
return get_user_entities_qs(EPModel, request.user).order_by("name").all()
|
||||
|
||||
|
||||
@router.get(
|
||||
"/package/{uuid:package_uuid}/model/",
|
||||
response=EnhancedPageNumberPagination.Output[ModelOutSchema],
|
||||
)
|
||||
@paginate(
|
||||
EnhancedPageNumberPagination,
|
||||
page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
|
||||
filter_schema=ReviewStatusFilter,
|
||||
)
|
||||
def list_package_models(request, package_uuid: UUID):
|
||||
"""
|
||||
List all models for a specific package.
|
||||
"""
|
||||
user = request.user
|
||||
return get_package_scoped_entities_qs(EPModel, package_uuid, user).order_by("name").all()
|
||||
27
epapi/v1/endpoints/packages.py
Normal file
27
epapi/v1/endpoints/packages.py
Normal file
@ -0,0 +1,27 @@
|
||||
from django.conf import settings as s
|
||||
from ninja import Router
|
||||
from ninja_extra.pagination import paginate
|
||||
import logging
|
||||
|
||||
from ..dal import get_user_packages_qs
|
||||
from ..pagination import EnhancedPageNumberPagination
|
||||
from ..schemas import PackageOutSchema, SelfReviewStatusFilter
|
||||
|
||||
router = Router()
|
||||
logger = logging.getLogger(__name__)
|
||||
|
||||
|
||||
@router.get("/packages/", response=EnhancedPageNumberPagination.Output[PackageOutSchema], auth=None)
|
||||
@paginate(
|
||||
EnhancedPageNumberPagination,
|
||||
page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
|
||||
filter_schema=SelfReviewStatusFilter,
|
||||
)
|
||||
def list_all_packages(request):
|
||||
"""
|
||||
List packages accessible to the user.
|
||||
|
||||
"""
|
||||
user = request.user
|
||||
qs = get_user_packages_qs(user)
|
||||
return qs.order_by("name").all()
|
||||
42
epapi/v1/endpoints/pathways.py
Normal file
42
epapi/v1/endpoints/pathways.py
Normal file
@ -0,0 +1,42 @@
|
||||
from django.conf import settings as s
|
||||
from ninja import Router
|
||||
from ninja_extra.pagination import paginate
|
||||
from uuid import UUID
|
||||
|
||||
from epdb.models import Pathway
|
||||
from ..pagination import EnhancedPageNumberPagination
|
||||
from ..schemas import PathwayOutSchema, ReviewStatusFilter
|
||||
from ..dal import get_user_entities_qs, get_package_scoped_entities_qs
|
||||
|
||||
router = Router()
|
||||
|
||||
|
||||
@router.get("/pathways/", response=EnhancedPageNumberPagination.Output[PathwayOutSchema])
|
||||
@paginate(
|
||||
EnhancedPageNumberPagination,
|
||||
page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
|
||||
filter_schema=ReviewStatusFilter,
|
||||
)
|
||||
def list_all_pathways(request):
|
||||
"""
|
||||
List all pathways from reviewed packages.
|
||||
"""
|
||||
user = request.user
|
||||
return get_user_entities_qs(Pathway, user).order_by("name").all()
|
||||
|
||||
|
||||
@router.get(
|
||||
"/package/{uuid:package_uuid}/pathway/",
|
||||
response=EnhancedPageNumberPagination.Output[PathwayOutSchema],
|
||||
)
|
||||
@paginate(
|
||||
EnhancedPageNumberPagination,
|
||||
page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
|
||||
filter_schema=ReviewStatusFilter,
|
||||
)
|
||||
def list_package_pathways(request, package_uuid: UUID):
|
||||
"""
|
||||
List all pathways for a specific package.
|
||||
"""
|
||||
user = request.user
|
||||
return get_package_scoped_entities_qs(Pathway, package_uuid, user).order_by("name").all()
|
||||
42
epapi/v1/endpoints/reactions.py
Normal file
42
epapi/v1/endpoints/reactions.py
Normal file
@ -0,0 +1,42 @@
|
||||
from django.conf import settings as s
|
||||
from ninja import Router
|
||||
from ninja_extra.pagination import paginate
|
||||
from uuid import UUID
|
||||
|
||||
from epdb.models import Reaction
|
||||
from ..pagination import EnhancedPageNumberPagination
|
||||
from ..schemas import ReactionOutSchema, ReviewStatusFilter
|
||||
from ..dal import get_user_entities_qs, get_package_scoped_entities_qs
|
||||
|
||||
router = Router()
|
||||
|
||||
|
||||
@router.get("/reactions/", response=EnhancedPageNumberPagination.Output[ReactionOutSchema])
|
||||
@paginate(
|
||||
EnhancedPageNumberPagination,
|
||||
page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
|
||||
filter_schema=ReviewStatusFilter,
|
||||
)
|
||||
def list_all_reactions(request):
|
||||
"""
|
||||
List all reactions from reviewed packages.
|
||||
"""
|
||||
user = request.user
|
||||
return get_user_entities_qs(Reaction, user).order_by("name").all()
|
||||
|
||||
|
||||
@router.get(
|
||||
"/package/{uuid:package_uuid}/reaction/",
|
||||
response=EnhancedPageNumberPagination.Output[ReactionOutSchema],
|
||||
)
|
||||
@paginate(
|
||||
EnhancedPageNumberPagination,
|
||||
page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
|
||||
filter_schema=ReviewStatusFilter,
|
||||
)
|
||||
def list_package_reactions(request, package_uuid: UUID):
|
||||
"""
|
||||
List all reactions for a specific package.
|
||||
"""
|
||||
user = request.user
|
||||
return get_package_scoped_entities_qs(Reaction, package_uuid, user).order_by("name").all()
|
||||
42
epapi/v1/endpoints/rules.py
Normal file
42
epapi/v1/endpoints/rules.py
Normal file
@ -0,0 +1,42 @@
|
||||
from django.conf import settings as s
|
||||
from ninja import Router
|
||||
from ninja_extra.pagination import paginate
|
||||
from uuid import UUID
|
||||
|
||||
from epdb.models import Rule
|
||||
from ..pagination import EnhancedPageNumberPagination
|
||||
from ..schemas import ReviewStatusFilter, RuleOutSchema
|
||||
from ..dal import get_user_entities_qs, get_package_scoped_entities_qs
|
||||
|
||||
router = Router()
|
||||
|
||||
|
||||
@router.get("/rules/", response=EnhancedPageNumberPagination.Output[RuleOutSchema])
|
||||
@paginate(
|
||||
EnhancedPageNumberPagination,
|
||||
page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
|
||||
filter_schema=ReviewStatusFilter,
|
||||
)
|
||||
def list_all_rules(request):
|
||||
"""
|
||||
List all rules from reviewed packages.
|
||||
"""
|
||||
user = request.user
|
||||
return get_user_entities_qs(Rule, user).order_by("name").all()
|
||||
|
||||
|
||||
@router.get(
|
||||
"/package/{uuid:package_uuid}/rule/",
|
||||
response=EnhancedPageNumberPagination.Output[RuleOutSchema],
|
||||
)
|
||||
@paginate(
|
||||
EnhancedPageNumberPagination,
|
||||
page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
|
||||
filter_schema=ReviewStatusFilter,
|
||||
)
|
||||
def list_package_rules(request, package_uuid: UUID):
|
||||
"""
|
||||
List all rules for a specific package.
|
||||
"""
|
||||
user = request.user
|
||||
return get_package_scoped_entities_qs(Rule, package_uuid, user).order_by("name").all()
|
||||
36
epapi/v1/endpoints/scenarios.py
Normal file
36
epapi/v1/endpoints/scenarios.py
Normal file
@ -0,0 +1,36 @@
|
||||
from django.conf import settings as s
|
||||
from ninja import Router
|
||||
from ninja_extra.pagination import paginate
|
||||
from uuid import UUID
|
||||
|
||||
from epdb.models import Scenario
|
||||
from ..pagination import EnhancedPageNumberPagination
|
||||
from ..schemas import ReviewStatusFilter, ScenarioOutSchema
|
||||
from ..dal import get_user_entities_qs, get_package_scoped_entities_qs
|
||||
|
||||
router = Router()
|
||||
|
||||
|
||||
@router.get("/scenarios/", response=EnhancedPageNumberPagination.Output[ScenarioOutSchema])
|
||||
@paginate(
|
||||
EnhancedPageNumberPagination,
|
||||
page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
|
||||
filter_schema=ReviewStatusFilter,
|
||||
)
|
||||
def list_all_scenarios(request):
|
||||
user = request.user
|
||||
return get_user_entities_qs(Scenario, user).order_by("name").all()
|
||||
|
||||
|
||||
@router.get(
|
||||
"/package/{uuid:package_uuid}/scenario/",
|
||||
response=EnhancedPageNumberPagination.Output[ScenarioOutSchema],
|
||||
)
|
||||
@paginate(
|
||||
EnhancedPageNumberPagination,
|
||||
page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
|
||||
filter_schema=ReviewStatusFilter,
|
||||
)
|
||||
def list_package_scenarios(request, package_uuid: UUID):
|
||||
user = request.user
|
||||
return get_package_scoped_entities_qs(Scenario, package_uuid, user).order_by("name").all()
|
||||
50
epapi/v1/endpoints/structure.py
Normal file
50
epapi/v1/endpoints/structure.py
Normal file
@ -0,0 +1,50 @@
|
||||
from django.conf import settings as s
|
||||
from ninja import Router
|
||||
from ninja_extra.pagination import paginate
|
||||
from uuid import UUID
|
||||
|
||||
from ..pagination import EnhancedPageNumberPagination
|
||||
from ..schemas import CompoundStructureOutSchema, StructureReviewStatusFilter
|
||||
from ..dal import (
|
||||
get_user_structures_qs,
|
||||
get_package_compound_scoped_structure_qs,
|
||||
)
|
||||
|
||||
router = Router()
|
||||
|
||||
|
||||
@router.get(
|
||||
"/structures/", response=EnhancedPageNumberPagination.Output[CompoundStructureOutSchema]
|
||||
)
|
||||
@paginate(
|
||||
EnhancedPageNumberPagination,
|
||||
page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
|
||||
filter_schema=StructureReviewStatusFilter,
|
||||
)
|
||||
def list_all_structures(request):
|
||||
"""
|
||||
List all structures from all packages.
|
||||
"""
|
||||
user = request.user
|
||||
return get_user_structures_qs(user).order_by("name").all()
|
||||
|
||||
|
||||
@router.get(
|
||||
"/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}/structure/",
|
||||
response=EnhancedPageNumberPagination.Output[CompoundStructureOutSchema],
|
||||
)
|
||||
@paginate(
|
||||
EnhancedPageNumberPagination,
|
||||
page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
|
||||
filter_schema=StructureReviewStatusFilter,
|
||||
)
|
||||
def list_package_structures(request, package_uuid: UUID, compound_uuid: UUID):
|
||||
"""
|
||||
List all structures for a specific package and compound.
|
||||
"""
|
||||
user = request.user
|
||||
return (
|
||||
get_package_compound_scoped_structure_qs(package_uuid, compound_uuid, user)
|
||||
.order_by("name")
|
||||
.all()
|
||||
)
|
||||
28
epapi/v1/errors.py
Normal file
28
epapi/v1/errors.py
Normal file
@ -0,0 +1,28 @@
|
||||
from ninja.errors import HttpError
|
||||
|
||||
|
||||
class EPAPIError(HttpError):
|
||||
status_code: int = 500
|
||||
|
||||
def __init__(self, message: str) -> None:
|
||||
super().__init__(status_code=self.status_code, message=message)
|
||||
|
||||
@classmethod
|
||||
def from_exception(cls, exc: Exception):
|
||||
return cls(message=str(exc))
|
||||
|
||||
|
||||
class EPAPIUnauthorizedError(EPAPIError):
|
||||
status_code = 401
|
||||
|
||||
|
||||
class EPAPIPermissionDeniedError(EPAPIError):
|
||||
status_code = 403
|
||||
|
||||
|
||||
class EPAPINotFoundError(EPAPIError):
|
||||
status_code = 404
|
||||
|
||||
|
||||
class EPAPIValidationError(EPAPIError):
|
||||
status_code = 422
|
||||
60
epapi/v1/pagination.py
Normal file
60
epapi/v1/pagination.py
Normal file
@ -0,0 +1,60 @@
|
||||
import math
|
||||
from typing import Any, Generic, List, TypeVar
|
||||
|
||||
from django.db.models import QuerySet
|
||||
from ninja import Schema
|
||||
from ninja.pagination import PageNumberPagination
|
||||
|
||||
T = TypeVar("T")
|
||||
|
||||
|
||||
class EnhancedPageNumberPagination(PageNumberPagination):
|
||||
class Output(Schema, Generic[T]):
|
||||
items: List[T]
|
||||
page: int
|
||||
page_size: int
|
||||
total_items: int
|
||||
total_pages: int
|
||||
|
||||
def paginate_queryset(
|
||||
self,
|
||||
queryset: QuerySet,
|
||||
pagination: PageNumberPagination.Input,
|
||||
**params: Any,
|
||||
) -> Any:
|
||||
page_size = self._get_page_size(pagination.page_size)
|
||||
offset = (pagination.page - 1) * page_size
|
||||
total_items = self._items_count(queryset)
|
||||
total_pages = math.ceil(total_items / page_size) if page_size > 0 else 0
|
||||
|
||||
return {
|
||||
"items": queryset[offset : offset + page_size],
|
||||
"page": pagination.page,
|
||||
"page_size": page_size,
|
||||
"total_items": total_items,
|
||||
"total_pages": total_pages,
|
||||
}
|
||||
|
||||
async def apaginate_queryset(
|
||||
self,
|
||||
queryset: QuerySet,
|
||||
pagination: PageNumberPagination.Input,
|
||||
**params: Any,
|
||||
) -> Any:
|
||||
page_size = self._get_page_size(pagination.page_size)
|
||||
offset = (pagination.page - 1) * page_size
|
||||
total_items = await self._aitems_count(queryset)
|
||||
total_pages = math.ceil(total_items / page_size) if page_size > 0 else 0
|
||||
|
||||
if isinstance(queryset, QuerySet):
|
||||
items = [obj async for obj in queryset[offset : offset + page_size]]
|
||||
else:
|
||||
items = queryset[offset : offset + page_size]
|
||||
|
||||
return {
|
||||
"items": items,
|
||||
"page": pagination.page,
|
||||
"page_size": page_size,
|
||||
"total_items": total_items,
|
||||
"total_pages": total_pages,
|
||||
}
|
||||
22
epapi/v1/router.py
Normal file
22
epapi/v1/router.py
Normal file
@ -0,0 +1,22 @@
|
||||
from ninja import Router
|
||||
from ninja.security import SessionAuth
|
||||
from .auth import BearerTokenAuth
|
||||
from .endpoints import packages, scenarios, compounds, rules, reactions, pathways, models, structure
|
||||
|
||||
# Main router with authentication
|
||||
router = Router(
|
||||
auth=[
|
||||
SessionAuth(),
|
||||
BearerTokenAuth(),
|
||||
]
|
||||
)
|
||||
|
||||
# Include all endpoint routers
|
||||
router.add_router("", packages.router)
|
||||
router.add_router("", scenarios.router)
|
||||
router.add_router("", compounds.router)
|
||||
router.add_router("", rules.router)
|
||||
router.add_router("", reactions.router)
|
||||
router.add_router("", pathways.router)
|
||||
router.add_router("", models.router)
|
||||
router.add_router("", structure.router)
|
||||
104
epapi/v1/schemas.py
Normal file
104
epapi/v1/schemas.py
Normal file
@ -0,0 +1,104 @@
|
||||
from ninja import FilterSchema, FilterLookup, Schema
|
||||
from typing import Annotated, Optional
|
||||
from uuid import UUID
|
||||
|
||||
|
||||
# Filter schema for query parameters
|
||||
class ReviewStatusFilter(FilterSchema):
|
||||
"""Filter schema for review_status query parameter."""
|
||||
|
||||
review_status: Annotated[Optional[bool], FilterLookup("package__reviewed")] = None
|
||||
|
||||
|
||||
class SelfReviewStatusFilter(FilterSchema):
|
||||
"""Filter schema for review_status query parameter on self-reviewed entities."""
|
||||
|
||||
review_status: Annotated[Optional[bool], FilterLookup("reviewed")] = None
|
||||
|
||||
|
||||
class StructureReviewStatusFilter(FilterSchema):
|
||||
"""Filter schema for review_status on structures (via compound->package)."""
|
||||
|
||||
review_status: Annotated[Optional[bool], FilterLookup("compound__package__reviewed")] = None
|
||||
|
||||
|
||||
# Base schema for all package-scoped entities
|
||||
class PackageEntityOutSchema(Schema):
|
||||
"""Base schema for entities belonging to a package."""
|
||||
|
||||
uuid: UUID
|
||||
url: str = ""
|
||||
name: str
|
||||
description: str
|
||||
review_status: str = ""
|
||||
package: str = ""
|
||||
|
||||
@staticmethod
|
||||
def resolve_url(obj):
|
||||
return obj.url
|
||||
|
||||
@staticmethod
|
||||
def resolve_package(obj):
|
||||
return obj.package.url
|
||||
|
||||
@staticmethod
|
||||
def resolve_review_status(obj):
|
||||
return "reviewed" if obj.package.reviewed else "unreviewed"
|
||||
|
||||
|
||||
# All package-scoped entities inherit from base
|
||||
class ScenarioOutSchema(PackageEntityOutSchema):
|
||||
pass
|
||||
|
||||
|
||||
class CompoundOutSchema(PackageEntityOutSchema):
|
||||
pass
|
||||
|
||||
|
||||
class RuleOutSchema(PackageEntityOutSchema):
|
||||
pass
|
||||
|
||||
|
||||
class ReactionOutSchema(PackageEntityOutSchema):
|
||||
pass
|
||||
|
||||
|
||||
class PathwayOutSchema(PackageEntityOutSchema):
|
||||
pass
|
||||
|
||||
|
||||
class ModelOutSchema(PackageEntityOutSchema):
|
||||
pass
|
||||
|
||||
|
||||
class CompoundStructureOutSchema(PackageEntityOutSchema):
|
||||
compound: str = ""
|
||||
|
||||
@staticmethod
|
||||
def resolve_compound(obj):
|
||||
return obj.compound.url
|
||||
|
||||
@staticmethod
|
||||
def resolve_package(obj):
|
||||
return obj.compound.package.url
|
||||
|
||||
@staticmethod
|
||||
def resolve_review_status(obj):
|
||||
return "reviewed" if obj.compound.package.reviewed else "unreviewed"
|
||||
|
||||
|
||||
# Package is special (no package FK)
|
||||
class PackageOutSchema(Schema):
|
||||
uuid: UUID
|
||||
url: str = ""
|
||||
name: str
|
||||
description: str
|
||||
review_status: str = ""
|
||||
|
||||
@staticmethod
|
||||
def resolve_url(obj):
|
||||
return obj.url
|
||||
|
||||
@staticmethod
|
||||
def resolve_review_status(obj):
|
||||
return "reviewed" if obj.reviewed else "unreviewed"
|
||||
@ -444,6 +444,7 @@ class PackageManager(object):
|
||||
if PackageManager.readable(user, p):
|
||||
return p
|
||||
else:
|
||||
# FIXME: use custom exception to be translatable to 403 in API
|
||||
raise ValueError(
|
||||
"Insufficient permissions to access Package with ID {}".format(package_id)
|
||||
)
|
||||
|
||||
251
epdb/views.py
251
epdb/views.py
@ -474,20 +474,15 @@ def packages(request):
|
||||
if request.method == "GET":
|
||||
context = get_base_context(request)
|
||||
context["title"] = "enviPath - Packages"
|
||||
|
||||
context["object_type"] = "package"
|
||||
context["meta"]["current_package"] = context["meta"]["user"].default_package
|
||||
context["meta"]["can_edit"] = True
|
||||
|
||||
reviewed_package_qs = Package.objects.filter(reviewed=True).order_by("created")
|
||||
unreviewed_package_qs = PackageManager.get_all_readable_packages(current_user).order_by(
|
||||
"name"
|
||||
)
|
||||
# Context for paginated template
|
||||
context["entity_type"] = "package"
|
||||
context["api_endpoint"] = "/api/v1/packages/"
|
||||
context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
|
||||
context["list_title"] = "packages"
|
||||
|
||||
context["reviewed_objects"] = reviewed_package_qs
|
||||
context["unreviewed_objects"] = unreviewed_package_qs
|
||||
|
||||
return render(request, "collections/objects_list.html", context)
|
||||
return render(request, "collections/packages_paginated.html", context)
|
||||
|
||||
elif request.method == "POST":
|
||||
if hidden := request.POST.get("hidden", None):
|
||||
@ -533,29 +528,16 @@ def compounds(request):
|
||||
if request.method == "GET":
|
||||
context = get_base_context(request)
|
||||
context["title"] = "enviPath - Compounds"
|
||||
|
||||
context["object_type"] = "compound"
|
||||
context["meta"]["current_package"] = context["meta"]["user"].default_package
|
||||
|
||||
reviewed_compound_qs = Compound.objects.none()
|
||||
# Context for paginated template
|
||||
context["entity_type"] = "compound"
|
||||
context["api_endpoint"] = "/api/v1/compounds/"
|
||||
context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
|
||||
context["list_mode"] = "tabbed"
|
||||
context["list_title"] = "compounds"
|
||||
|
||||
for p in PackageManager.get_reviewed_packages():
|
||||
reviewed_compound_qs |= Compound.objects.filter(package=p)
|
||||
|
||||
reviewed_compound_qs = reviewed_compound_qs.order_by("name")
|
||||
|
||||
if request.GET.get("all"):
|
||||
return JsonResponse(
|
||||
{
|
||||
"objects": [
|
||||
{"name": pw.name, "url": pw.url, "reviewed": True}
|
||||
for pw in reviewed_compound_qs
|
||||
]
|
||||
}
|
||||
)
|
||||
|
||||
context["reviewed_objects"] = reviewed_compound_qs
|
||||
return render(request, "collections/objects_list.html", context)
|
||||
return render(request, "collections/compounds_paginated.html", context)
|
||||
|
||||
elif request.method == "POST":
|
||||
# delegate to default package
|
||||
@ -571,32 +553,19 @@ def rules(request):
|
||||
if request.method == "GET":
|
||||
context = get_base_context(request)
|
||||
context["title"] = "enviPath - Rules"
|
||||
|
||||
context["object_type"] = "rule"
|
||||
context["meta"]["current_package"] = context["meta"]["user"].default_package
|
||||
context["breadcrumbs"] = [
|
||||
{"Home": s.SERVER_URL},
|
||||
{"Rule": s.SERVER_URL + "/rule"},
|
||||
]
|
||||
reviewed_rule_qs = Rule.objects.none()
|
||||
|
||||
for p in PackageManager.get_reviewed_packages():
|
||||
reviewed_rule_qs |= Rule.objects.filter(package=p)
|
||||
# Context for paginated template
|
||||
context["entity_type"] = "rule"
|
||||
context["api_endpoint"] = "/api/v1/rules/"
|
||||
context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
|
||||
context["list_title"] = "rules"
|
||||
|
||||
reviewed_rule_qs = reviewed_rule_qs.order_by("name")
|
||||
|
||||
if request.GET.get("all"):
|
||||
return JsonResponse(
|
||||
{
|
||||
"objects": [
|
||||
{"name": pw.name, "url": pw.url, "reviewed": True}
|
||||
for pw in reviewed_rule_qs
|
||||
]
|
||||
}
|
||||
)
|
||||
|
||||
context["reviewed_objects"] = reviewed_rule_qs
|
||||
return render(request, "collections/objects_list.html", context)
|
||||
return render(request, "collections/rules_paginated.html", context)
|
||||
|
||||
elif request.method == "POST":
|
||||
# delegate to default package
|
||||
@ -612,32 +581,19 @@ def reactions(request):
|
||||
if request.method == "GET":
|
||||
context = get_base_context(request)
|
||||
context["title"] = "enviPath - Reactions"
|
||||
|
||||
context["object_type"] = "reaction"
|
||||
context["meta"]["current_package"] = context["meta"]["user"].default_package
|
||||
context["breadcrumbs"] = [
|
||||
{"Home": s.SERVER_URL},
|
||||
{"Reaction": s.SERVER_URL + "/reaction"},
|
||||
]
|
||||
reviewed_reaction_qs = Reaction.objects.none()
|
||||
|
||||
for p in PackageManager.get_reviewed_packages():
|
||||
reviewed_reaction_qs |= Reaction.objects.filter(package=p).order_by("name")
|
||||
# Context for paginated template
|
||||
context["entity_type"] = "reaction"
|
||||
context["api_endpoint"] = "/api/v1/reactions/"
|
||||
context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
|
||||
context["list_title"] = "reactions"
|
||||
|
||||
reviewed_reaction_qs = reviewed_reaction_qs.order_by("name")
|
||||
|
||||
if request.GET.get("all"):
|
||||
return JsonResponse(
|
||||
{
|
||||
"objects": [
|
||||
{"name": pw.name, "url": pw.url, "reviewed": True}
|
||||
for pw in reviewed_reaction_qs
|
||||
]
|
||||
}
|
||||
)
|
||||
|
||||
context["reviewed_objects"] = reviewed_reaction_qs
|
||||
return render(request, "collections/objects_list.html", context)
|
||||
return render(request, "collections/reactions_paginated.html", context)
|
||||
|
||||
elif request.method == "POST":
|
||||
# delegate to default package
|
||||
@ -653,33 +609,19 @@ def pathways(request):
|
||||
if request.method == "GET":
|
||||
context = get_base_context(request)
|
||||
context["title"] = "enviPath - Pathways"
|
||||
|
||||
context["object_type"] = "pathway"
|
||||
context["meta"]["current_package"] = context["meta"]["user"].default_package
|
||||
context["breadcrumbs"] = [
|
||||
{"Home": s.SERVER_URL},
|
||||
{"Pathway": s.SERVER_URL + "/pathway"},
|
||||
]
|
||||
|
||||
reviewed_pathway_qs = Pathway.objects.none()
|
||||
# Context for paginated template
|
||||
context["entity_type"] = "pathway"
|
||||
context["api_endpoint"] = "/api/v1/pathways/"
|
||||
context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
|
||||
context["list_title"] = "pathways"
|
||||
|
||||
for p in PackageManager.get_reviewed_packages():
|
||||
reviewed_pathway_qs |= Pathway.objects.filter(package=p).order_by("name")
|
||||
|
||||
reviewed_pathway_qs = reviewed_pathway_qs.order_by("name")
|
||||
|
||||
if request.GET.get("all"):
|
||||
return JsonResponse(
|
||||
{
|
||||
"objects": [
|
||||
{"name": pw.name, "url": pw.url, "reviewed": True}
|
||||
for pw in reviewed_pathway_qs
|
||||
]
|
||||
}
|
||||
)
|
||||
|
||||
context["reviewed_objects"] = reviewed_pathway_qs
|
||||
return render(request, "collections/objects_list.html", context)
|
||||
return render(request, "collections/pathways_paginated.html", context)
|
||||
|
||||
elif request.method == "POST":
|
||||
# delegate to default package
|
||||
@ -703,25 +645,13 @@ def scenarios(request):
|
||||
{"Scenario": s.SERVER_URL + "/scenario"},
|
||||
]
|
||||
|
||||
reviewed_scenario_qs = Scenario.objects.none()
|
||||
# Context for paginated template
|
||||
context["entity_type"] = "scenario"
|
||||
context["api_endpoint"] = "/api/v1/scenarios/"
|
||||
context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
|
||||
context["list_title"] = "scenarios"
|
||||
|
||||
for p in PackageManager.get_reviewed_packages():
|
||||
reviewed_scenario_qs |= Scenario.objects.filter(package=p).order_by("name")
|
||||
|
||||
reviewed_scenario_qs = reviewed_scenario_qs.order_by("name")
|
||||
|
||||
if request.GET.get("all"):
|
||||
return JsonResponse(
|
||||
{
|
||||
"objects": [
|
||||
{"name": s.name, "url": s.url, "reviewed": True}
|
||||
for s in reviewed_scenario_qs
|
||||
]
|
||||
}
|
||||
)
|
||||
|
||||
context["reviewed_objects"] = reviewed_scenario_qs
|
||||
return render(request, "collections/objects_list.html", context)
|
||||
return render(request, "collections/scenarios_paginated.html", context)
|
||||
|
||||
elif request.method == "POST":
|
||||
# delegate to default package
|
||||
@ -736,42 +666,28 @@ def models(request):
|
||||
if request.method == "GET":
|
||||
context = get_base_context(request)
|
||||
context["title"] = "enviPath - Models"
|
||||
|
||||
context["object_type"] = "model"
|
||||
context["meta"]["current_package"] = context["meta"]["user"].default_package
|
||||
context["breadcrumbs"] = [
|
||||
{"Home": s.SERVER_URL},
|
||||
{"Model": s.SERVER_URL + "/model"},
|
||||
]
|
||||
|
||||
# Keep model_types for potential modal/action use
|
||||
context["model_types"] = {
|
||||
"ML Relative Reasoning": "ml-relative-reasoning",
|
||||
"Rule Based Relative Reasoning": "rule-based-relative-reasoning",
|
||||
"EnviFormer": "enviformer",
|
||||
}
|
||||
|
||||
for k, v in s.CLASSIFIER_PLUGINS.items():
|
||||
context["model_types"][v.display()] = k
|
||||
|
||||
reviewed_model_qs = EPModel.objects.none()
|
||||
# Context for paginated template
|
||||
context["entity_type"] = "model"
|
||||
context["api_endpoint"] = "/api/v1/models/"
|
||||
context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
|
||||
context["list_title"] = "models"
|
||||
|
||||
for p in PackageManager.get_reviewed_packages():
|
||||
reviewed_model_qs |= EPModel.objects.filter(package=p).order_by("name")
|
||||
|
||||
reviewed_model_qs = reviewed_model_qs.order_by("name")
|
||||
|
||||
if request.GET.get("all"):
|
||||
return JsonResponse(
|
||||
{
|
||||
"objects": [
|
||||
{"name": pw.name, "url": pw.url, "reviewed": True}
|
||||
for pw in reviewed_model_qs
|
||||
]
|
||||
}
|
||||
)
|
||||
|
||||
context["reviewed_objects"] = reviewed_model_qs
|
||||
return render(request, "collections/objects_list.html", context)
|
||||
return render(request, "collections/models_paginated.html", context)
|
||||
|
||||
elif request.method == "POST":
|
||||
current_user = _anonymous_or_real(request)
|
||||
@ -848,6 +764,10 @@ def package_models(request, package_uuid):
|
||||
context["meta"]["current_package"] = current_package
|
||||
context["object_type"] = "model"
|
||||
context["breadcrumbs"] = breadcrumbs(current_package, "model")
|
||||
context["entity_type"] = "model"
|
||||
context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/model/"
|
||||
context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
|
||||
context["list_title"] = "models"
|
||||
|
||||
reviewed_model_qs = EPModel.objects.none()
|
||||
unreviewed_model_qs = EPModel.objects.none()
|
||||
@ -869,9 +789,6 @@ def package_models(request, package_uuid):
|
||||
}
|
||||
)
|
||||
|
||||
context["reviewed_objects"] = reviewed_model_qs
|
||||
context["unreviewed_objects"] = unreviewed_model_qs
|
||||
|
||||
context["model_types"] = {
|
||||
"ML Relative Reasoning": "mlrr",
|
||||
"Rule Based Relative Reasoning": "rbrr",
|
||||
@ -884,7 +801,7 @@ def package_models(request, package_uuid):
|
||||
for k, v in s.CLASSIFIER_PLUGINS.items():
|
||||
context["model_types"][v.display()] = k
|
||||
|
||||
return render(request, "collections/objects_list.html", context)
|
||||
return render(request, "collections/models_paginated.html", context)
|
||||
|
||||
elif request.method == "POST":
|
||||
log_post_params(request)
|
||||
@ -1242,6 +1159,11 @@ def package_compounds(request, package_uuid):
|
||||
context["meta"]["current_package"] = current_package
|
||||
context["object_type"] = "compound"
|
||||
context["breadcrumbs"] = breadcrumbs(current_package, "compound")
|
||||
context["entity_type"] = "compound"
|
||||
context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/compound/"
|
||||
context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
|
||||
context["list_mode"] = "tabbed"
|
||||
context["list_title"] = "compounds"
|
||||
|
||||
reviewed_compound_qs = Compound.objects.none()
|
||||
unreviewed_compound_qs = Compound.objects.none()
|
||||
@ -1267,10 +1189,7 @@ def package_compounds(request, package_uuid):
|
||||
}
|
||||
)
|
||||
|
||||
context["reviewed_objects"] = reviewed_compound_qs
|
||||
context["unreviewed_objects"] = unreviewed_compound_qs
|
||||
|
||||
return render(request, "collections/objects_list.html", context)
|
||||
return render(request, "collections/compounds_paginated.html", context)
|
||||
|
||||
elif request.method == "POST":
|
||||
compound_name = request.POST.get("compound-name")
|
||||
@ -1389,19 +1308,17 @@ def package_compound_structures(request, package_uuid, compound_uuid):
|
||||
context["breadcrumbs"] = breadcrumbs(
|
||||
current_package, "compound", current_compound, "structure"
|
||||
)
|
||||
context["entity_type"] = "structure"
|
||||
context["page_title"] = f"{current_compound.name} - Structures"
|
||||
context["api_endpoint"] = (
|
||||
f"/api/v1/package/{current_package.uuid}/compound/{current_compound.uuid}/structure/"
|
||||
)
|
||||
context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
|
||||
context["compound"] = current_compound
|
||||
context["list_mode"] = "combined"
|
||||
context["list_title"] = "structures"
|
||||
|
||||
reviewed_compound_structure_qs = CompoundStructure.objects.none()
|
||||
unreviewed_compound_structure_qs = CompoundStructure.objects.none()
|
||||
|
||||
if current_package.reviewed:
|
||||
reviewed_compound_structure_qs = current_compound.structures.order_by("name")
|
||||
else:
|
||||
unreviewed_compound_structure_qs = current_compound.structures.order_by("name")
|
||||
|
||||
context["reviewed_objects"] = reviewed_compound_structure_qs
|
||||
context["unreviewed_objects"] = unreviewed_compound_structure_qs
|
||||
|
||||
return render(request, "collections/objects_list.html", context)
|
||||
return render(request, "collections/structures_paginated.html", context)
|
||||
|
||||
elif request.method == "POST":
|
||||
structure_name = request.POST.get("structure-name")
|
||||
@ -1548,6 +1465,10 @@ def package_rules(request, package_uuid):
|
||||
context["meta"]["current_package"] = current_package
|
||||
context["object_type"] = "rule"
|
||||
context["breadcrumbs"] = breadcrumbs(current_package, "rule")
|
||||
context["entity_type"] = "rule"
|
||||
context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/rule/"
|
||||
context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
|
||||
context["list_title"] = "rules"
|
||||
|
||||
reviewed_rule_qs = Rule.objects.none()
|
||||
unreviewed_rule_qs = Rule.objects.none()
|
||||
@ -1569,10 +1490,7 @@ def package_rules(request, package_uuid):
|
||||
}
|
||||
)
|
||||
|
||||
context["reviewed_objects"] = reviewed_rule_qs
|
||||
context["unreviewed_objects"] = unreviewed_rule_qs
|
||||
|
||||
return render(request, "collections/objects_list.html", context)
|
||||
return render(request, "collections/rules_paginated.html", context)
|
||||
|
||||
elif request.method == "POST":
|
||||
log_post_params(request)
|
||||
@ -1750,11 +1668,15 @@ def package_reactions(request, package_uuid):
|
||||
|
||||
if request.method == "GET":
|
||||
context = get_base_context(request)
|
||||
context["title"] = f"enviPath - {current_package.name} - {current_package.name} - Reactions"
|
||||
context["title"] = f"enviPath - {current_package.name} - Reactions"
|
||||
|
||||
context["meta"]["current_package"] = current_package
|
||||
context["object_type"] = "reaction"
|
||||
context["breadcrumbs"] = breadcrumbs(current_package, "reaction")
|
||||
context["entity_type"] = "reaction"
|
||||
context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/reaction/"
|
||||
context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
|
||||
context["list_title"] = "reactions"
|
||||
|
||||
reviewed_reaction_qs = Reaction.objects.none()
|
||||
unreviewed_reaction_qs = Reaction.objects.none()
|
||||
@ -1780,10 +1702,7 @@ def package_reactions(request, package_uuid):
|
||||
}
|
||||
)
|
||||
|
||||
context["reviewed_objects"] = reviewed_reaction_qs
|
||||
context["unreviewed_objects"] = unreviewed_reaction_qs
|
||||
|
||||
return render(request, "collections/objects_list.html", context)
|
||||
return render(request, "collections/reactions_paginated.html", context)
|
||||
|
||||
elif request.method == "POST":
|
||||
reaction_name = request.POST.get("reaction-name")
|
||||
@ -1902,6 +1821,10 @@ def package_pathways(request, package_uuid):
|
||||
context["meta"]["current_package"] = current_package
|
||||
context["object_type"] = "pathway"
|
||||
context["breadcrumbs"] = breadcrumbs(current_package, "pathway")
|
||||
context["entity_type"] = "pathway"
|
||||
context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/pathway/"
|
||||
context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
|
||||
context["list_title"] = "pathways"
|
||||
|
||||
reviewed_pathway_qs = Pathway.objects.none()
|
||||
unreviewed_pathway_qs = Pathway.objects.none()
|
||||
@ -1925,10 +1848,7 @@ def package_pathways(request, package_uuid):
|
||||
}
|
||||
)
|
||||
|
||||
context["reviewed_objects"] = reviewed_pathway_qs
|
||||
context["unreviewed_objects"] = unreviewed_pathway_qs
|
||||
|
||||
return render(request, "collections/objects_list.html", context)
|
||||
return render(request, "collections/pathways_paginated.html", context)
|
||||
|
||||
elif request.method == "POST":
|
||||
log_post_params(request)
|
||||
@ -2465,6 +2385,10 @@ def package_scenarios(request, package_uuid):
|
||||
context["meta"]["current_package"] = current_package
|
||||
context["object_type"] = "scenario"
|
||||
context["breadcrumbs"] = breadcrumbs(current_package, "scenario")
|
||||
context["entity_type"] = "scenario"
|
||||
context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/scenario/"
|
||||
context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
|
||||
context["list_title"] = "scenarios"
|
||||
|
||||
reviewed_scenario_qs = Scenario.objects.none()
|
||||
unreviewed_scenario_qs = Scenario.objects.none()
|
||||
@ -2490,9 +2414,6 @@ def package_scenarios(request, package_uuid):
|
||||
}
|
||||
)
|
||||
|
||||
context["reviewed_objects"] = reviewed_scenario_qs
|
||||
context["unreviewed_objects"] = unreviewed_scenario_qs
|
||||
|
||||
from envipy_additional_information import (
|
||||
SEDIMENT_ADDITIONAL_INFORMATION,
|
||||
SLUDGE_ADDITIONAL_INFORMATION,
|
||||
@ -2527,7 +2448,7 @@ def package_scenarios(request, package_uuid):
|
||||
context["soil_additional_information"] = SOIL_ADDITIONAL_INFORMATION
|
||||
context["sediment_additional_information"] = SEDIMENT_ADDITIONAL_INFORMATION
|
||||
|
||||
return render(request, "collections/objects_list.html", context)
|
||||
return render(request, "collections/scenarios_paginated.html", context)
|
||||
elif request.method == "POST":
|
||||
log_post_params(request)
|
||||
|
||||
|
||||
@ -9,7 +9,8 @@ dependencies = [
|
||||
"django>=5.2.1",
|
||||
"django-extensions>=4.1",
|
||||
"django-model-utils>=5.0.0",
|
||||
"django-ninja>=1.4.1",
|
||||
"django-ninja>=1.4.5",
|
||||
"django-ninja-extra>=0.30.6",
|
||||
"django-oauth-toolkit>=3.0.1",
|
||||
"django-polymorphic>=4.1.0",
|
||||
"enviformer",
|
||||
@ -47,6 +48,7 @@ dev = [
|
||||
"ruff>=0.13.3",
|
||||
"pytest-playwright>=0.7.1",
|
||||
"pytest-django>=4.11.1",
|
||||
"pytest-cov>=7.0.0",
|
||||
]
|
||||
|
||||
[tool.ruff]
|
||||
@ -121,3 +123,22 @@ collectstatic = { cmd = "uv run python manage.py collectstatic --noinput", help
|
||||
] }
|
||||
|
||||
frontend-test-setup = { cmd = "playwright install", help = "Install the browsers required for frontend testing" }
|
||||
|
||||
[tool.pytest.ini_options]
|
||||
addopts = "--verbose --capture=no --durations=10"
|
||||
testpaths = ["tests", "*/tests"]
|
||||
pythonpath = ["."]
|
||||
norecursedirs = [
|
||||
"env",
|
||||
"venv",
|
||||
"envipy-plugins",
|
||||
"envipy-additional-information",
|
||||
"envipy-ambit",
|
||||
"enviformer",
|
||||
]
|
||||
markers = [
|
||||
"api: API tests",
|
||||
"frontend: Frontend tests",
|
||||
"end2end: End-to-end tests",
|
||||
"slow: Slow tests",
|
||||
]
|
||||
|
||||
@ -36,24 +36,17 @@
|
||||
@import "./daisyui-theme.css";
|
||||
|
||||
/* Loading Spinner - Benzene Ring */
|
||||
.loading-spinner {
|
||||
.benzene-spinner {
|
||||
display: flex;
|
||||
justify-content: center;
|
||||
align-items: center;
|
||||
padding: 2rem;
|
||||
}
|
||||
|
||||
.loading-spinner svg {
|
||||
.benzene-spinner svg {
|
||||
width: 48px;
|
||||
height: 48px;
|
||||
animation: spin 2s linear infinite;
|
||||
}
|
||||
|
||||
.loading-spinner .hexagon,
|
||||
.loading-spinner .double-bonds {
|
||||
fill: none;
|
||||
stroke: currentColor;
|
||||
stroke-width: 2;
|
||||
animation: spin 3s linear infinite;
|
||||
}
|
||||
|
||||
@keyframes spin {
|
||||
|
||||
@ -5,31 +5,26 @@
|
||||
*/
|
||||
|
||||
document.addEventListener('alpine:init', () => {
|
||||
Alpine.data('paginatedList', (initialItems = [], options = {}) => ({
|
||||
allItems: initialItems,
|
||||
filteredItems: [],
|
||||
Alpine.data('remotePaginatedList', (options = {}) => ({
|
||||
items: [],
|
||||
currentPage: 1,
|
||||
totalPages: 0,
|
||||
totalItems: 0,
|
||||
perPage: options.perPage || 50,
|
||||
searchQuery: '',
|
||||
endpoint: options.endpoint || '',
|
||||
isReviewed: options.isReviewed || false,
|
||||
instanceId: options.instanceId || Math.random().toString(36).substring(2, 9),
|
||||
isLoading: false,
|
||||
error: null,
|
||||
|
||||
init() {
|
||||
this.filteredItems = this.allItems;
|
||||
},
|
||||
|
||||
get totalPages() {
|
||||
return Math.ceil(this.filteredItems.length / this.perPage);
|
||||
if (this.endpoint) {
|
||||
this.fetchPage(1);
|
||||
}
|
||||
},
|
||||
|
||||
get paginatedItems() {
|
||||
const start = (this.currentPage - 1) * this.perPage;
|
||||
const end = start + this.perPage;
|
||||
return this.filteredItems.slice(start, end);
|
||||
},
|
||||
|
||||
get totalItems() {
|
||||
return this.filteredItems.length;
|
||||
return this.items;
|
||||
},
|
||||
|
||||
get showingStart() {
|
||||
@ -38,36 +33,65 @@ document.addEventListener('alpine:init', () => {
|
||||
},
|
||||
|
||||
get showingEnd() {
|
||||
return Math.min(this.currentPage * this.perPage, this.totalItems);
|
||||
if (this.totalItems === 0) return 0;
|
||||
return Math.min((this.currentPage - 1) * this.perPage + this.items.length, this.totalItems);
|
||||
},
|
||||
|
||||
search(query) {
|
||||
this.searchQuery = query.toLowerCase();
|
||||
if (this.searchQuery === '') {
|
||||
this.filteredItems = this.allItems;
|
||||
} else {
|
||||
this.filteredItems = this.allItems.filter(item =>
|
||||
item.name.toLowerCase().includes(this.searchQuery)
|
||||
);
|
||||
async fetchPage(page) {
|
||||
if (!this.endpoint) {
|
||||
return;
|
||||
}
|
||||
|
||||
this.isLoading = true;
|
||||
this.error = null;
|
||||
|
||||
try {
|
||||
const url = new URL(this.endpoint, window.location.origin);
|
||||
// Preserve existing query parameters and add pagination params
|
||||
url.searchParams.set('page', page.toString());
|
||||
url.searchParams.set('page_size', this.perPage.toString());
|
||||
|
||||
const response = await fetch(url.toString(), {
|
||||
headers: { Accept: 'application/json' },
|
||||
credentials: 'same-origin'
|
||||
});
|
||||
|
||||
if (!response.ok) {
|
||||
throw new Error(`Failed to load ${this.endpoint} (status ${response.status})`);
|
||||
}
|
||||
|
||||
const data = await response.json();
|
||||
this.items = data.items || [];
|
||||
this.totalItems = data.total_items || 0;
|
||||
this.totalPages = data.total_pages || 0;
|
||||
this.currentPage = data.page || page;
|
||||
this.perPage = data.page_size || this.perPage;
|
||||
|
||||
// Dispatch event for parent components (e.g., tab count updates)
|
||||
this.$dispatch('items-loaded', { totalItems: this.totalItems });
|
||||
} catch (err) {
|
||||
console.error(err);
|
||||
this.error = `Unable to load ${this.endpoint}. Please try again.`;
|
||||
} finally {
|
||||
this.isLoading = false;
|
||||
}
|
||||
this.currentPage = 1;
|
||||
},
|
||||
|
||||
nextPage() {
|
||||
if (this.currentPage < this.totalPages) {
|
||||
this.currentPage++;
|
||||
this.fetchPage(this.currentPage + 1);
|
||||
}
|
||||
},
|
||||
|
||||
prevPage() {
|
||||
if (this.currentPage > 1) {
|
||||
this.currentPage--;
|
||||
this.fetchPage(this.currentPage - 1);
|
||||
}
|
||||
},
|
||||
|
||||
goToPage(page) {
|
||||
if (page >= 1 && page <= this.totalPages) {
|
||||
this.currentPage = page;
|
||||
this.fetchPage(page);
|
||||
}
|
||||
},
|
||||
|
||||
@ -76,54 +100,43 @@ document.addEventListener('alpine:init', () => {
|
||||
const total = this.totalPages;
|
||||
const current = this.currentPage;
|
||||
|
||||
// Handle empty case
|
||||
if (total === 0) {
|
||||
return pages;
|
||||
}
|
||||
|
||||
if (total <= 7) {
|
||||
// Show all pages if 7 or fewer
|
||||
for (let i = 1; i <= total; i++) {
|
||||
pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` });
|
||||
}
|
||||
} else {
|
||||
// More than 7 pages - show first, last, and sliding window around current
|
||||
// Always show first page
|
||||
pages.push({ page: 1, isEllipsis: false, key: `${this.instanceId}-page-1` });
|
||||
|
||||
// Determine the start and end of the middle range
|
||||
let rangeStart, rangeEnd;
|
||||
let rangeStart;
|
||||
let rangeEnd;
|
||||
|
||||
if (current <= 4) {
|
||||
// Near the beginning: show pages 2-5
|
||||
rangeStart = 2;
|
||||
rangeEnd = 5;
|
||||
} else if (current >= total - 3) {
|
||||
// Near the end: show last 4 pages before the last page
|
||||
rangeStart = total - 4;
|
||||
rangeEnd = total - 1;
|
||||
} else {
|
||||
// In the middle: show current page and one on each side
|
||||
rangeStart = current - 1;
|
||||
rangeEnd = current + 1;
|
||||
}
|
||||
|
||||
// Add ellipsis before range if there's a gap
|
||||
if (rangeStart > 2) {
|
||||
pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-start` });
|
||||
}
|
||||
|
||||
// Add pages in the range
|
||||
for (let i = rangeStart; i <= rangeEnd; i++) {
|
||||
pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` });
|
||||
}
|
||||
|
||||
// Add ellipsis after range if there's a gap
|
||||
if (rangeEnd < total - 1) {
|
||||
pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-end` });
|
||||
}
|
||||
|
||||
// Always show last page
|
||||
pages.push({ page: total, isEllipsis: false, key: `${this.instanceId}-page-${total}` });
|
||||
}
|
||||
|
||||
|
||||
@ -1,10 +0,0 @@
|
||||
{% if meta.can_edit %}
|
||||
<li>
|
||||
<a
|
||||
role="button"
|
||||
onclick="document.getElementById('new_compound_modal').showModal(); return false;"
|
||||
>
|
||||
<span class="glyphicon glyphicon-plus"></span> New Compound</a
|
||||
>
|
||||
</li>
|
||||
{% endif %}
|
||||
@ -1,10 +0,0 @@
|
||||
{% if meta.can_edit %}
|
||||
<li>
|
||||
<a
|
||||
role="button"
|
||||
onclick="document.getElementById('new_compound_structure_modal').showModal(); return false;"
|
||||
>
|
||||
<span class="glyphicon glyphicon-plus"></span> New Compound Structure</a
|
||||
>
|
||||
</li>
|
||||
{% endif %}
|
||||
@ -1,10 +0,0 @@
|
||||
{% if meta.can_edit and meta.enabled_features.MODEL_BUILDING %}
|
||||
<li>
|
||||
<a
|
||||
role="button"
|
||||
onclick="document.getElementById('new_model_modal').showModal(); return false;"
|
||||
>
|
||||
<span class="glyphicon glyphicon-plus"></span> New Model</a
|
||||
>
|
||||
</li>
|
||||
{% endif %}
|
||||
@ -1,25 +0,0 @@
|
||||
<li>
|
||||
<a
|
||||
role="button"
|
||||
onclick="document.getElementById('new_package_modal').showModal(); return false;"
|
||||
>
|
||||
<span class="glyphicon glyphicon-plus"></span> New Package</a
|
||||
>
|
||||
</li>
|
||||
<li>
|
||||
<a
|
||||
role="button"
|
||||
onclick="document.getElementById('import_package_modal').showModal(); return false;"
|
||||
>
|
||||
<span class="glyphicon glyphicon-import"></span> Import Package from JSON</a
|
||||
>
|
||||
</li>
|
||||
<li>
|
||||
<a
|
||||
role="button"
|
||||
onclick="document.getElementById('import_legacy_package_modal').showModal(); return false;"
|
||||
>
|
||||
<span class="glyphicon glyphicon-import"></span> Import Package from legacy
|
||||
JSON</a
|
||||
>
|
||||
</li>
|
||||
@ -1,9 +0,0 @@
|
||||
{% if meta.can_edit %}
|
||||
<li>
|
||||
<a
|
||||
href="{% if meta.current_package %}{{ meta.current_package.url }}/predict{% else %}{{ meta.server_url }}/predict{% endif %}"
|
||||
>
|
||||
<span class="glyphicon glyphicon-plus"></span> New Pathway</a
|
||||
>
|
||||
</li>
|
||||
{% endif %}
|
||||
@ -1,10 +0,0 @@
|
||||
{% if meta.can_edit %}
|
||||
<li>
|
||||
<a
|
||||
role="button"
|
||||
onclick="document.getElementById('new_reaction_modal').showModal(); return false;"
|
||||
>
|
||||
<span class="glyphicon glyphicon-plus"></span> New Reaction</a
|
||||
>
|
||||
</li>
|
||||
{% endif %}
|
||||
@ -1,10 +0,0 @@
|
||||
{% if meta.can_edit %}
|
||||
<li>
|
||||
<a
|
||||
role="button"
|
||||
onclick="document.getElementById('new_rule_modal').showModal(); return false;"
|
||||
>
|
||||
<span class="glyphicon glyphicon-plus"></span> New Rule</a
|
||||
>
|
||||
</li>
|
||||
{% endif %}
|
||||
@ -1,10 +0,0 @@
|
||||
{% if meta.can_edit %}
|
||||
<li>
|
||||
<a
|
||||
role="button"
|
||||
onclick="document.getElementById('new_scenario_modal').showModal(); return false;"
|
||||
>
|
||||
<span class="glyphicon glyphicon-plus"></span> New Scenario</a
|
||||
>
|
||||
</li>
|
||||
{% endif %}
|
||||
98
templates/collections/_paginated_list_partial.html
Normal file
98
templates/collections/_paginated_list_partial.html
Normal file
@ -0,0 +1,98 @@
|
||||
{# Partial for paginated list content - expects to be inside a remotePaginatedList Alpine.js context #}
|
||||
{# Variables: empty_text (string), show_review_badge (bool), always_show_badge (bool) #}
|
||||
|
||||
{# Loading state #}
|
||||
<div x-show="isLoading">{% include "components/loading-spinner.html" %}</div>
|
||||
|
||||
{# Error state #}
|
||||
<div
|
||||
x-show="!isLoading && error"
|
||||
class="alert alert-error/50 text-sm"
|
||||
x-text="error"
|
||||
></div>
|
||||
|
||||
{# Content #}
|
||||
<template x-if="!isLoading && !error">
|
||||
<div>
|
||||
{# Empty state #}
|
||||
<div
|
||||
x-show="totalItems === 0"
|
||||
class="text-base-content/70 py-8 text-center"
|
||||
>
|
||||
<p>No {{ empty_text|default:"items" }} found.</p>
|
||||
</div>
|
||||
|
||||
{# Items list #}
|
||||
<ul class="menu bg-base-100 rounded-box w-full" x-show="totalItems > 0">
|
||||
<template x-for="obj in paginatedItems" :key="obj.url">
|
||||
<li>
|
||||
<a :href="obj.url" class="hover:bg-base-200">
|
||||
<span x-text="obj.name"></span>
|
||||
{% if show_review_badge %}
|
||||
<span
|
||||
class="tooltip tooltip-left ml-auto"
|
||||
data-tip="Reviewed"
|
||||
{% if not always_show_badge %}
|
||||
x-show="obj.review_status === 'reviewed'"
|
||||
{% endif %}
|
||||
>
|
||||
<svg
|
||||
xmlns="http://www.w3.org/2000/svg"
|
||||
width="24"
|
||||
height="24"
|
||||
viewBox="0 0 24 24"
|
||||
fill="none"
|
||||
stroke="currentColor"
|
||||
stroke-width="2"
|
||||
stroke-linecap="round"
|
||||
stroke-linejoin="round"
|
||||
class="lucide lucide-check-icon lucide-check"
|
||||
>
|
||||
<path d="M20 6 9 17l-5-5" />
|
||||
</svg>
|
||||
</span>
|
||||
{% endif %}
|
||||
</a>
|
||||
</li>
|
||||
</template>
|
||||
</ul>
|
||||
|
||||
{# Pagination controls #}
|
||||
<div
|
||||
x-show="totalPages > 1"
|
||||
class="mt-4 flex items-center justify-between px-2"
|
||||
>
|
||||
<span class="text-base-content/70 text-sm">
|
||||
Showing <span x-text="showingStart"></span>-<span
|
||||
x-text="showingEnd"
|
||||
></span>
|
||||
of <span x-text="totalItems"></span>
|
||||
</span>
|
||||
<div class="join">
|
||||
<button
|
||||
class="join-item btn btn-sm"
|
||||
:disabled="currentPage === 1"
|
||||
@click="prevPage()"
|
||||
>
|
||||
«
|
||||
</button>
|
||||
<template x-for="item in pageNumbers" :key="item.key">
|
||||
<button
|
||||
class="join-item btn btn-sm"
|
||||
:class="{ 'btn-active': item.page === currentPage }"
|
||||
:disabled="item.isEllipsis"
|
||||
@click="!item.isEllipsis && goToPage(item.page)"
|
||||
x-text="item.page"
|
||||
></button>
|
||||
</template>
|
||||
<button
|
||||
class="join-item btn btn-sm"
|
||||
:disabled="currentPage === totalPages"
|
||||
@click="nextPage()"
|
||||
>
|
||||
»
|
||||
</button>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</template>
|
||||
33
templates/collections/compounds_paginated.html
Normal file
33
templates/collections/compounds_paginated.html
Normal file
@ -0,0 +1,33 @@
|
||||
{% extends "collections/paginated_base.html" %}
|
||||
|
||||
{% block page_title %}Compounds{% endblock %}
|
||||
|
||||
{% block action_button %}
|
||||
{% if meta.can_edit %}
|
||||
<button
|
||||
type="button"
|
||||
class="btn btn-primary btn-sm"
|
||||
onclick="document.getElementById('new_compound_modal').showModal(); return false;"
|
||||
>
|
||||
New Compound
|
||||
</button>
|
||||
{% endif %}
|
||||
{% endblock action_button %}
|
||||
|
||||
{% block action_modals %}
|
||||
{% include "modals/collections/new_compound_modal.html" %}
|
||||
{% endblock action_modals %}
|
||||
|
||||
{% block description %}
|
||||
<p>
|
||||
A compound stores the structure of a molecule and can include
|
||||
meta-information.
|
||||
</p>
|
||||
<a
|
||||
target="_blank"
|
||||
href="https://wiki.envipath.org/index.php/compounds"
|
||||
class="link link-primary"
|
||||
>
|
||||
Learn more >>
|
||||
</a>
|
||||
{% endblock description %}
|
||||
32
templates/collections/models_paginated.html
Normal file
32
templates/collections/models_paginated.html
Normal file
@ -0,0 +1,32 @@
|
||||
{% extends "collections/paginated_base.html" %}
|
||||
|
||||
{% block page_title %}Models{% endblock %}
|
||||
|
||||
{% block action_button %}
|
||||
{% if meta.can_edit and meta.enabled_features.MODEL_BUILDING %}
|
||||
<button
|
||||
type="button"
|
||||
class="btn btn-primary btn-sm"
|
||||
onclick="document.getElementById('new_model_modal').showModal(); return false;"
|
||||
>
|
||||
New Model
|
||||
</button>
|
||||
{% endif %}
|
||||
{% endblock action_button %}
|
||||
|
||||
{% block action_modals %}
|
||||
{% if meta.enabled_features.MODEL_BUILDING %}
|
||||
{% include "modals/collections/new_model_modal.html" %}
|
||||
{% endif %}
|
||||
{% endblock action_modals %}
|
||||
|
||||
{% block description %}
|
||||
<p>A model applies machine learning to limit the combinatorial explosion.</p>
|
||||
<a
|
||||
target="_blank"
|
||||
href="https://wiki.envipath.org/index.php/relative_reasoning"
|
||||
class="link link-primary"
|
||||
>
|
||||
Learn more >>
|
||||
</a>
|
||||
{% endblock description %}
|
||||
@ -5,6 +5,7 @@
|
||||
{# Serialize objects data for Alpine pagination #}
|
||||
{# prettier-ignore-start #}
|
||||
{# FIXME: This is a hack to get the objects data into the JavaScript code. #}
|
||||
{% if object_type != 'scenario' %}
|
||||
<script>
|
||||
window.reviewedObjects = [
|
||||
{% for obj in reviewed_objects %}
|
||||
@ -17,9 +18,9 @@
|
||||
{% endfor %}
|
||||
];
|
||||
</script>
|
||||
{% endif %}
|
||||
{# prettier-ignore-end #}
|
||||
|
||||
{% if object_type != 'package' %}
|
||||
<div class="px-8 py-4">
|
||||
<input
|
||||
type="text"
|
||||
@ -28,35 +29,12 @@
|
||||
placeholder="Search by name"
|
||||
/>
|
||||
</div>
|
||||
{% endif %}
|
||||
|
||||
{% block action_modals %}
|
||||
{% if object_type == 'package' %}
|
||||
{% include "modals/collections/new_package_modal.html" %}
|
||||
{% include "modals/collections/import_package_modal.html" %}
|
||||
{% include "modals/collections/import_legacy_package_modal.html" %}
|
||||
{% elif object_type == 'compound' %}
|
||||
{% include "modals/collections/new_compound_modal.html" %}
|
||||
{% elif object_type == 'rule' %}
|
||||
{% include "modals/collections/new_rule_modal.html" %}
|
||||
{% elif object_type == 'reaction' %}
|
||||
{% include "modals/collections/new_reaction_modal.html" %}
|
||||
{% elif object_type == 'pathway' %}
|
||||
{# {% include "modals/collections/new_pathway_modal.html" %} #}
|
||||
{% elif object_type == 'node' %}
|
||||
{% if object_type == 'node' %}
|
||||
{% include "modals/collections/new_node_modal.html" %}
|
||||
{% elif object_type == 'edge' %}
|
||||
{% include "modals/collections/new_edge_modal.html" %}
|
||||
{% elif object_type == 'scenario' %}
|
||||
{% include "modals/collections/new_scenario_modal.html" %}
|
||||
{% elif object_type == 'model' %}
|
||||
{% include "modals/collections/new_model_modal.html" %}
|
||||
{% elif object_type == 'setting' %}
|
||||
{#{% include "modals/collections/new_setting_modal.html" %}#}
|
||||
{% elif object_type == 'user' %}
|
||||
<div></div>
|
||||
{% elif object_type == 'group' %}
|
||||
{% include "modals/collections/new_group_modal.html" %}
|
||||
{% endif %}
|
||||
{% endblock action_modals %}
|
||||
|
||||
@ -66,32 +44,10 @@
|
||||
<div class="card-body px-0 py-4">
|
||||
<div class="flex items-center justify-between">
|
||||
<h2 class="card-title text-2xl">
|
||||
{% if object_type == 'package' %}
|
||||
Packages
|
||||
{% elif object_type == 'compound' %}
|
||||
Compounds
|
||||
{% elif object_type == 'structure' %}
|
||||
Compound structures
|
||||
{% elif object_type == 'rule' %}
|
||||
Rules
|
||||
{% elif object_type == 'reaction' %}
|
||||
Reactions
|
||||
{% elif object_type == 'pathway' %}
|
||||
Pathways
|
||||
{% elif object_type == 'node' %}
|
||||
{% if object_type == 'node' %}
|
||||
Nodes
|
||||
{% elif object_type == 'edge' %}
|
||||
Edges
|
||||
{% elif object_type == 'scenario' %}
|
||||
Scenarios
|
||||
{% elif object_type == 'model' %}
|
||||
Model
|
||||
{% elif object_type == 'setting' %}
|
||||
Settings
|
||||
{% elif object_type == 'user' %}
|
||||
Users
|
||||
{% elif object_type == 'group' %}
|
||||
Groups
|
||||
{% endif %}
|
||||
</h2>
|
||||
<div id="actionsButton" class="dropdown dropdown-end hidden">
|
||||
@ -119,103 +75,17 @@
|
||||
class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
|
||||
>
|
||||
{% block actions %}
|
||||
{% if object_type == 'package' %}
|
||||
{% include "actions/collections/package.html" %}
|
||||
{% elif object_type == 'compound' %}
|
||||
{% include "actions/collections/compound.html" %}
|
||||
{% elif object_type == 'structure' %}
|
||||
{% include "actions/collections/compound_structure.html" %}
|
||||
{% elif object_type == 'rule' %}
|
||||
{% include "actions/collections/rule.html" %}
|
||||
{% elif object_type == 'reaction' %}
|
||||
{% include "actions/collections/reaction.html" %}
|
||||
{% elif object_type == 'setting' %}
|
||||
{% include "actions/collections/setting.html" %}
|
||||
{% elif object_type == 'scenario' %}
|
||||
{% include "actions/collections/scenario.html" %}
|
||||
{% elif object_type == 'model' %}
|
||||
{% include "actions/collections/model.html" %}
|
||||
{% elif object_type == 'pathway' %}
|
||||
{% include "actions/collections/pathway.html" %}
|
||||
{% elif object_type == 'node' %}
|
||||
{% if object_type == 'node' %}
|
||||
{% include "actions/collections/node.html" %}
|
||||
{% elif object_type == 'edge' %}
|
||||
{% include "actions/collections/edge.html" %}
|
||||
{% elif object_type == 'group' %}
|
||||
{% include "actions/collections/group.html" %}
|
||||
{% endif %}
|
||||
{% endblock %}
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
<div class="mt-2">
|
||||
<!-- Set Text above links -->
|
||||
{% if object_type == 'package' %}
|
||||
<p>
|
||||
A package contains pathways, rules, etc. and can reflect specific
|
||||
experimental conditions.
|
||||
<a
|
||||
target="_blank"
|
||||
href="https://wiki.envipath.org/index.php/packages"
|
||||
class="link link-primary"
|
||||
>Learn more >></a
|
||||
>
|
||||
</p>
|
||||
{% elif object_type == 'compound' %}
|
||||
<p>
|
||||
A compound stores the structure of a molecule and can include
|
||||
meta-information.
|
||||
<a
|
||||
target="_blank"
|
||||
href="https://wiki.envipath.org/index.php/compounds"
|
||||
class="link link-primary"
|
||||
>Learn more >></a
|
||||
>
|
||||
</p>
|
||||
{% elif object_type == 'structure' %}
|
||||
<p>
|
||||
The structures stored in this compound
|
||||
<a
|
||||
target="_blank"
|
||||
href="https://wiki.envipath.org/index.php/compounds"
|
||||
class="link link-primary"
|
||||
>Learn more >></a
|
||||
>
|
||||
</p>
|
||||
{% elif object_type == 'rule' %}
|
||||
<p>
|
||||
A rule describes a biotransformation reaction template that is
|
||||
defined as SMIRKS.
|
||||
<a
|
||||
target="_blank"
|
||||
href="https://wiki.envipath.org/index.php/Rules"
|
||||
class="link link-primary"
|
||||
>Learn more >></a
|
||||
>
|
||||
</p>
|
||||
{% elif object_type == 'reaction' %}
|
||||
<p>
|
||||
A reaction is a specific biotransformation from educt compounds to
|
||||
product compounds.
|
||||
<a
|
||||
target="_blank"
|
||||
href="https://wiki.envipath.org/index.php/reactions"
|
||||
class="link link-primary"
|
||||
>Learn more >></a
|
||||
>
|
||||
</p>
|
||||
{% elif object_type == 'pathway' %}
|
||||
<p>
|
||||
A pathway displays the (predicted) biodegradation of a compound as
|
||||
graph.
|
||||
<a
|
||||
target="_blank"
|
||||
href="https://wiki.envipath.org/index.php/pathways"
|
||||
class="link link-primary"
|
||||
>Learn more >></a
|
||||
>
|
||||
</p>
|
||||
{% elif object_type == 'node' %}
|
||||
{% if object_type == 'node' %}
|
||||
<p>
|
||||
Nodes represent the (predicted) compounds in a graph.
|
||||
<a
|
||||
@ -227,7 +97,7 @@
|
||||
</p>
|
||||
{% elif object_type == 'edge' %}
|
||||
<p>
|
||||
Edges represent the links between Nodes in a graph
|
||||
Edges represent the links between nodes in a graph.
|
||||
<a
|
||||
target="_blank"
|
||||
href="https://wiki.envipath.org/index.php/edges"
|
||||
@ -235,70 +105,15 @@
|
||||
>Learn more >></a
|
||||
>
|
||||
</p>
|
||||
{% elif object_type == 'scenario' %}
|
||||
<p>
|
||||
A scenario contains meta-information that can be attached to other
|
||||
data (compounds, rules, ..).
|
||||
<a
|
||||
target="_blank"
|
||||
href="https://wiki.envipath.org/index.php/scenarios"
|
||||
class="link link-primary"
|
||||
>Learn more >></a
|
||||
>
|
||||
</p>
|
||||
{% elif object_type == 'model' %}
|
||||
<p>
|
||||
A model applies machine learning to limit the combinatorial
|
||||
explosion.
|
||||
<a
|
||||
target="_blank"
|
||||
href="https://wiki.envipath.org/index.php/relative_reasoning"
|
||||
class="link link-primary"
|
||||
>Learn more >></a
|
||||
>
|
||||
</p>
|
||||
{% elif object_type == 'setting' %}
|
||||
<p>
|
||||
A setting includes configuration parameters for pathway
|
||||
predictions.
|
||||
<a
|
||||
target="_blank"
|
||||
href="https://wiki.envipath.org/index.php/settings"
|
||||
class="link link-primary"
|
||||
>Learn more >></a
|
||||
>
|
||||
</p>
|
||||
{% elif object_type == 'user' %}
|
||||
<p>
|
||||
Register now to create own packages and to submit and manage your
|
||||
data.
|
||||
<a
|
||||
target="_blank"
|
||||
href="https://wiki.envipath.org/index.php/users"
|
||||
class="link link-primary"
|
||||
>Learn more >></a
|
||||
>
|
||||
</p>
|
||||
{% elif object_type == 'group' %}
|
||||
<p>
|
||||
Users can team up in groups to share packages.
|
||||
<a
|
||||
target="_blank"
|
||||
href="https://wiki.envipath.org/index.php/groups"
|
||||
class="link link-primary"
|
||||
>Learn more >></a
|
||||
>
|
||||
</p>
|
||||
{% endif %}
|
||||
|
||||
<!-- If theres nothing to show extend the text above -->
|
||||
{% if reviewed_objects and unreviewed_objects %}
|
||||
{% if reviewed_objects|length == 0 and unreviewed_objects|length == 0 %}
|
||||
<p class="mt-4">
|
||||
Nothing found. There are two possible reasons: <br /><br />1.
|
||||
There is no content yet.<br />2. You have no reading
|
||||
permissions.<br /><br />Please be sure you have at least reading
|
||||
permissions.
|
||||
Nothing found. There are two possible reasons:<br /><br />
|
||||
1. There is no content yet.<br />
|
||||
2. You have no reading permissions.<br /><br />
|
||||
Please ensure you have at least reading permissions.
|
||||
</p>
|
||||
{% endif %}
|
||||
{% endif %}
|
||||
@ -306,7 +121,7 @@
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<!-- Lists Container - Full Width with Reviewed on Right -->
|
||||
<!-- Lists Container -->
|
||||
<div class="w-full">
|
||||
{% if reviewed_objects %}
|
||||
{% if reviewed_objects|length > 0 %}
|
||||
@ -404,7 +219,7 @@
|
||||
>
|
||||
<input
|
||||
type="checkbox"
|
||||
{% if reviewed_objects|length == 0 or object_type == 'package' %}checked{% endif %}
|
||||
{% if reviewed_objects|length == 0 %}checked{% endif %}
|
||||
/>
|
||||
<div class="collapse-title text-xl font-medium">
|
||||
Unreviewed
|
||||
@ -466,31 +281,6 @@
|
||||
</div>
|
||||
{% endif %}
|
||||
</div>
|
||||
|
||||
{% if objects %}
|
||||
<!-- Unreviewable objects such as User / Group / Setting -->
|
||||
<div class="card bg-base-100">
|
||||
<div class="card-body">
|
||||
<ul class="menu bg-base-200 rounded-box w-full">
|
||||
{% for obj in objects %}
|
||||
{% if object_type == 'user' %}
|
||||
<li>
|
||||
<a href="{{ obj.url }}" class="hover:bg-base-300"
|
||||
>{{ obj.username }}</a
|
||||
>
|
||||
</li>
|
||||
{% else %}
|
||||
<li>
|
||||
<a href="{{ obj.url }}" class="hover:bg-base-300"
|
||||
>{{ obj.name }}</a
|
||||
>
|
||||
</li>
|
||||
{% endif %}
|
||||
{% endfor %}
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
{% endif %}
|
||||
</div>
|
||||
|
||||
<script>
|
||||
|
||||
95
templates/collections/packages_paginated.html
Normal file
95
templates/collections/packages_paginated.html
Normal file
@ -0,0 +1,95 @@
|
||||
{% extends "collections/paginated_base.html" %}
|
||||
|
||||
{% block page_title %}Packages{% endblock %}
|
||||
|
||||
{% block action_button %}
|
||||
{% if meta.can_edit %}
|
||||
<div class="flex items-center gap-2">
|
||||
<button
|
||||
type="button"
|
||||
class="btn btn-primary btn-sm"
|
||||
id="new-package-button"
|
||||
onclick="document.getElementById('new_package_modal').showModal(); return false;"
|
||||
>
|
||||
<svg
|
||||
xmlns="http://www.w3.org/2000/svg"
|
||||
width="24"
|
||||
height="24"
|
||||
viewBox="0 0 24 24"
|
||||
fill="none"
|
||||
stroke="currentColor"
|
||||
stroke-width="2"
|
||||
stroke-linecap="round"
|
||||
stroke-linejoin="round"
|
||||
class="lucide lucide-folder-plus-icon lucide-folder-plus"
|
||||
>
|
||||
<path d="M12 10v6" />
|
||||
<path d="M9 13h6" />
|
||||
<path
|
||||
d="M20 20a2 2 0 0 0 2-2V8a2 2 0 0 0-2-2h-7.9a2 2 0 0 1-1.69-.9L9.6 3.9A2 2 0 0 0 7.93 3H4a2 2 0 0 0-2 2v13a2 2 0 0 0 2 2Z"
|
||||
/>
|
||||
</svg>
|
||||
</button>
|
||||
<div class="dropdown dropdown-end">
|
||||
<div tabindex="0" role="button" class="btn btn-sm">
|
||||
Import
|
||||
<svg
|
||||
xmlns="http://www.w3.org/2000/svg"
|
||||
width="16"
|
||||
height="16"
|
||||
viewBox="0 0 24 24"
|
||||
fill="none"
|
||||
stroke="currentColor"
|
||||
stroke-width="2"
|
||||
stroke-linecap="round"
|
||||
stroke-linejoin="round"
|
||||
class="lucide lucide-chevron-down ml-1"
|
||||
>
|
||||
<path d="m6 9 6 6 6-6" />
|
||||
</svg>
|
||||
</div>
|
||||
<ul
|
||||
tabindex="-1"
|
||||
class="dropdown-content menu bg-base-100 rounded-box z-50 w-56 p-2"
|
||||
>
|
||||
<li>
|
||||
<a
|
||||
role="button"
|
||||
onclick="document.getElementById('import_package_modal').showModal(); return false;"
|
||||
>
|
||||
Import Package from JSON
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a
|
||||
role="button"
|
||||
onclick="document.getElementById('import_legacy_package_modal').showModal(); return false;"
|
||||
>
|
||||
Import Package from legacy JSON
|
||||
</a>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
{% endif %}
|
||||
{% endblock action_button %}
|
||||
|
||||
{% block action_modals %}
|
||||
{% include "modals/collections/new_package_modal.html" %}
|
||||
{% include "modals/collections/import_package_modal.html" %}
|
||||
{% include "modals/collections/import_legacy_package_modal.html" %}
|
||||
{% endblock action_modals %}
|
||||
|
||||
{% block description %}
|
||||
<p>
|
||||
A package contains pathways, rules, etc. and can reflect specific
|
||||
experimental conditions.
|
||||
</p>
|
||||
<a
|
||||
target="_blank"
|
||||
href="https://wiki.envipath.org/index.php/packages"
|
||||
class="link link-primary"
|
||||
>
|
||||
Learn more >>
|
||||
</a>
|
||||
{% endblock description %}
|
||||
134
templates/collections/paginated_base.html
Normal file
134
templates/collections/paginated_base.html
Normal file
@ -0,0 +1,134 @@
|
||||
{% extends "framework_modern.html" %}
|
||||
{% load static %}
|
||||
|
||||
{# List title for empty text - defaults to "items", should be overridden by child templates #}
|
||||
{% block list_title %}items{% endblock %}
|
||||
|
||||
{% block content %}
|
||||
{% block action_modals %}
|
||||
{% endblock action_modals %}
|
||||
|
||||
<div class="px-8 py-4">
|
||||
<!-- Header Section -->
|
||||
<div class="card bg-base-100">
|
||||
<div class="card-body px-0 py-4">
|
||||
<div class="flex items-center justify-between">
|
||||
<h2 class="card-title text-2xl">
|
||||
{% block page_title %}{{ page_title|default:"Items" }}{% endblock %}
|
||||
</h2>
|
||||
{% block action_button %}
|
||||
{# Can be overridden by including action buttons for entity type #}
|
||||
{% endblock %}
|
||||
</div>
|
||||
<div class="mt-2">
|
||||
{% block description %}
|
||||
{% endblock %}
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
{% if list_mode == "combined" %}
|
||||
{# ===== COMBINED MODE: Single list without tabs ===== #}
|
||||
<div
|
||||
class="mt-6 w-full"
|
||||
x-data="remotePaginatedList({
|
||||
endpoint: '{{ api_endpoint }}',
|
||||
instanceId: '{{ entity_type }}_combined',
|
||||
perPage: {{ per_page|default:50 }}
|
||||
})"
|
||||
>
|
||||
{% include "collections/_paginated_list_partial.html" with empty_text=list_title|default:"items" show_review_badge=True %}
|
||||
</div>
|
||||
{% else %}
|
||||
{# ===== TABBED MODE: Reviewed/Unreviewed tabs (default) ===== #}
|
||||
<div
|
||||
class="mt-6 w-full"
|
||||
x-data="{
|
||||
activeTab: 'reviewed',
|
||||
reviewedCount: 0,
|
||||
unreviewedCount: 0,
|
||||
reviewedLoaded: false,
|
||||
unreviewedLoaded: false,
|
||||
updateTabSelection() {
|
||||
// Only auto-select unreviewed tab if both have loaded and there are no reviewed items
|
||||
if (this.reviewedLoaded && this.unreviewedLoaded && this.reviewedCount === 0 && this.unreviewedCount > 0) {
|
||||
this.activeTab = 'unreviewed';
|
||||
}
|
||||
}
|
||||
}"
|
||||
>
|
||||
{# No items found message #}
|
||||
<div
|
||||
x-show="reviewedCount === 0 && unreviewedCount === 0"
|
||||
class="text-base-content/70 py-8 text-center"
|
||||
>
|
||||
<p>No items found.</p>
|
||||
</div>
|
||||
|
||||
{# Tabs Navigation #}
|
||||
<div
|
||||
role="tablist"
|
||||
class="tabs tabs-border"
|
||||
x-show="reviewedCount > 0 || unreviewedCount > 0"
|
||||
>
|
||||
<button
|
||||
role="tab"
|
||||
class="tab"
|
||||
:class="{ 'tab-active': activeTab === 'reviewed' }"
|
||||
@click="activeTab = 'reviewed'"
|
||||
x-show="reviewedCount > 0"
|
||||
>
|
||||
Reviewed
|
||||
<span
|
||||
class="badge badge-xs badge-dash badge-info mb-2 ml-2"
|
||||
x-text="reviewedCount"
|
||||
></span>
|
||||
</button>
|
||||
<button
|
||||
role="tab"
|
||||
class="tab"
|
||||
:class="{ 'tab-active': activeTab === 'unreviewed' }"
|
||||
@click="activeTab = 'unreviewed'"
|
||||
x-show="unreviewedCount > 0"
|
||||
>
|
||||
Unreviewed
|
||||
<span
|
||||
class="badge badge-xs badge-dash badge-info mb-2 ml-2"
|
||||
x-text="unreviewedCount"
|
||||
></span>
|
||||
</button>
|
||||
</div>
|
||||
|
||||
{# Reviewed Tab Content #}
|
||||
<div
|
||||
class="mt-6"
|
||||
x-show="activeTab === 'reviewed' && (reviewedCount > 0 || unreviewedCount > 0)"
|
||||
x-data="remotePaginatedList({
|
||||
endpoint: '{{ api_endpoint }}?review_status=true',
|
||||
instanceId: '{{ entity_type }}_reviewed',
|
||||
isReviewed: true,
|
||||
perPage: {{ per_page|default:50 }}
|
||||
})"
|
||||
@items-loaded="reviewedCount = totalItems; reviewedLoaded = true; updateTabSelection()"
|
||||
>
|
||||
{% include "collections/_paginated_list_partial.html" with empty_text="reviewed "|add:list_title|default:"items" show_review_badge=True always_show_badge=True %}
|
||||
</div>
|
||||
|
||||
{# Unreviewed Tab Content #}
|
||||
<div
|
||||
class="mt-6"
|
||||
x-show="activeTab === 'unreviewed' && (reviewedCount > 0 || unreviewedCount > 0)"
|
||||
x-data="remotePaginatedList({
|
||||
endpoint: '{{ api_endpoint }}?review_status=false',
|
||||
instanceId: '{{ entity_type }}_unreviewed',
|
||||
isReviewed: false,
|
||||
perPage: {{ per_page|default:50 }}
|
||||
})"
|
||||
@items-loaded="unreviewedCount = totalItems; unreviewedLoaded = true; updateTabSelection()"
|
||||
>
|
||||
{% include "collections/_paginated_list_partial.html" with empty_text="unreviewed "|add:list_title|default:"items" %}
|
||||
</div>
|
||||
</div>
|
||||
{% endif %}
|
||||
</div>
|
||||
{% endblock content %}
|
||||
29
templates/collections/pathways_paginated.html
Normal file
29
templates/collections/pathways_paginated.html
Normal file
@ -0,0 +1,29 @@
|
||||
{% extends "collections/paginated_base.html" %}
|
||||
|
||||
{% block page_title %}Pathways{% endblock %}
|
||||
|
||||
{% block action_button %}
|
||||
{% if meta.can_edit %}
|
||||
<div class="flex items-center gap-2">
|
||||
<a
|
||||
class="btn btn-primary btn-sm"
|
||||
href="{% if meta.current_package %}{{ meta.current_package.url }}/predict{% else %}/predict{% endif %}"
|
||||
>
|
||||
New Pathway
|
||||
</a>
|
||||
</div>
|
||||
{% endif %}
|
||||
{% endblock action_button %}
|
||||
|
||||
{% block description %}
|
||||
<p>
|
||||
A pathway displays the (predicted) biodegradation of a compound as graph.
|
||||
</p>
|
||||
<a
|
||||
target="_blank"
|
||||
href="https://wiki.envipath.org/index.php/pathways"
|
||||
class="link link-primary"
|
||||
>
|
||||
Learn more >>
|
||||
</a>
|
||||
{% endblock description %}
|
||||
33
templates/collections/reactions_paginated.html
Normal file
33
templates/collections/reactions_paginated.html
Normal file
@ -0,0 +1,33 @@
|
||||
{% extends "collections/paginated_base.html" %}
|
||||
|
||||
{% block page_title %}Reactions{% endblock %}
|
||||
|
||||
{% block action_button %}
|
||||
{% if meta.can_edit %}
|
||||
<button
|
||||
type="button"
|
||||
class="btn btn-primary btn-sm"
|
||||
onclick="document.getElementById('new_reaction_modal').showModal(); return false;"
|
||||
>
|
||||
New Reaction
|
||||
</button>
|
||||
{% endif %}
|
||||
{% endblock action_button %}
|
||||
|
||||
{% block action_modals %}
|
||||
{% include "modals/collections/new_reaction_modal.html" %}
|
||||
{% endblock action_modals %}
|
||||
|
||||
{% block description %}
|
||||
<p>
|
||||
A reaction is a specific biotransformation from educt compounds to product
|
||||
compounds.
|
||||
</p>
|
||||
<a
|
||||
target="_blank"
|
||||
href="https://wiki.envipath.org/index.php/reactions"
|
||||
class="link link-primary"
|
||||
>
|
||||
Learn more >>
|
||||
</a>
|
||||
{% endblock description %}
|
||||
33
templates/collections/rules_paginated.html
Normal file
33
templates/collections/rules_paginated.html
Normal file
@ -0,0 +1,33 @@
|
||||
{% extends "collections/paginated_base.html" %}
|
||||
|
||||
{% block page_title %}Rules{% endblock %}
|
||||
|
||||
{% block action_button %}
|
||||
{% if meta.can_edit %}
|
||||
<button
|
||||
type="button"
|
||||
class="btn btn-primary btn-sm"
|
||||
onclick="document.getElementById('new_rule_modal').showModal(); return false;"
|
||||
>
|
||||
New Rule
|
||||
</button>
|
||||
{% endif %}
|
||||
{% endblock action_button %}
|
||||
|
||||
{% block action_modals %}
|
||||
{% include "modals/collections/new_rule_modal.html" %}
|
||||
{% endblock action_modals %}
|
||||
|
||||
{% block description %}
|
||||
<p>
|
||||
A rule describes a biotransformation reaction template that is defined as
|
||||
SMIRKS.
|
||||
</p>
|
||||
<a
|
||||
target="_blank"
|
||||
href="https://wiki.envipath.org/index.php/Rules"
|
||||
class="link link-primary"
|
||||
>
|
||||
Learn more >>
|
||||
</a>
|
||||
{% endblock description %}
|
||||
33
templates/collections/scenarios_paginated.html
Normal file
33
templates/collections/scenarios_paginated.html
Normal file
@ -0,0 +1,33 @@
|
||||
{% extends "collections/paginated_base.html" %}
|
||||
|
||||
{% block page_title %}Scenarios{% endblock %}
|
||||
|
||||
{% block action_button %}
|
||||
{% if meta.can_edit %}
|
||||
<button
|
||||
type="button"
|
||||
class="btn btn-primary btn-sm"
|
||||
onclick="document.getElementById('new_scenario_modal').showModal(); return false;"
|
||||
>
|
||||
New Scenario
|
||||
</button>
|
||||
{% endif %}
|
||||
{% endblock action_button %}
|
||||
|
||||
{% block action_modals %}
|
||||
{% include "modals/collections/new_scenario_modal.html" %}
|
||||
{% endblock action_modals %}
|
||||
|
||||
{% block description %}
|
||||
<p>
|
||||
A scenario contains meta-information that can be attached to other data
|
||||
(compounds, rules, ..).
|
||||
</p>
|
||||
<a
|
||||
target="_blank"
|
||||
href="https://wiki.envipath.org/index.php/scenarios"
|
||||
class="link link-primary"
|
||||
>
|
||||
Learn more >>
|
||||
</a>
|
||||
{% endblock description %}
|
||||
30
templates/collections/structures_paginated.html
Normal file
30
templates/collections/structures_paginated.html
Normal file
@ -0,0 +1,30 @@
|
||||
{% extends "collections/paginated_base.html" %}
|
||||
|
||||
{% block page_title %}{{ page_title|default:"Structures" }}{% endblock %}
|
||||
|
||||
{% block action_button %}
|
||||
{% if meta.can_edit %}
|
||||
<button
|
||||
type="button"
|
||||
class="btn btn-primary btn-sm"
|
||||
onclick="document.getElementById('new_compound_structure_modal').showModal(); return false;"
|
||||
>
|
||||
New Structure
|
||||
</button>
|
||||
{% endif %}
|
||||
{% endblock action_button %}
|
||||
|
||||
{% block action_modals %}
|
||||
{# FIXME: New Compound Structure Modal #}
|
||||
{% endblock action_modals %}
|
||||
|
||||
{% block description %}
|
||||
<p>The structures stored in this compound.</p>
|
||||
<a
|
||||
target="_blank"
|
||||
href="https://wiki.envipath.org/index.php/compounds"
|
||||
class="link link-primary"
|
||||
>
|
||||
Learn more >>
|
||||
</a>
|
||||
{% endblock description %}
|
||||
11
templates/components/loading-spinner.html
Normal file
11
templates/components/loading-spinner.html
Normal file
@ -0,0 +1,11 @@
|
||||
<div class="benzene-spinner">
|
||||
<svg viewBox="0 0 1000 1000" xmlns="http://www.w3.org/2000/svg">
|
||||
<path
|
||||
class="hexagon"
|
||||
d="m 758.78924,684.71562 0.65313,-363.85 33.725,0.066 -0.65313,363.85001 z M 201.52187,362.53368 512.50834,173.66181 530.01077,202.48506 219.03091,391.35694 z M 510.83924,841.63056 199.3448,653.59653 216.77465,624.72049 528.2691,812.76111 z M 500,975 85.905556,742.30278 l 0,-474.94722 L 500,24.999998 914.09445,257.64444 l 0,475.00001 z M 124.90833,722.45834 500,936.15556 880.26389,713.69722 l 0,-436.15555 L 500,63.949998 124.90833,286.40833 z"
|
||||
fill="black"
|
||||
stroke="black"
|
||||
stroke-width="2"
|
||||
/>
|
||||
</svg>
|
||||
</div>
|
||||
@ -68,7 +68,7 @@
|
||||
{% endif %}
|
||||
</head>
|
||||
<body class="bg-base-300 min-h-screen">
|
||||
{% include "includes/navbar.html" %}
|
||||
{% include "components/navbar.html" %}
|
||||
|
||||
{# Main Content Area #}
|
||||
<main class="w-full">
|
||||
@ -128,7 +128,7 @@
|
||||
{% endblock main_content %}
|
||||
</main>
|
||||
|
||||
{% include "includes/footer.html" %}
|
||||
{% include "components/footer.html" %}
|
||||
|
||||
{# Floating Help Tab #}
|
||||
{% if not public_mode %}
|
||||
|
||||
@ -37,7 +37,6 @@ class TestPackagePage(EnviPyStaticLiveServerTestCase):
|
||||
# Find number of current pathways by extracting it from pathway button
|
||||
num_pathways = int(re.search(r"Pathways \((\d+)\)", pathway_button.inner_text()).group(1))
|
||||
pathway_button.click()
|
||||
page.get_by_role("button", name="Actions").click()
|
||||
page.get_by_role("link", name="New Pathway").click()
|
||||
# Check that the predict page 'in [package_name]' text shows the current package
|
||||
expect(page.get_by_role("strong").get_by_text("test package")).to_be_visible()
|
||||
@ -59,8 +58,7 @@ class TestPackagePage(EnviPyStaticLiveServerTestCase):
|
||||
"""Make a new empty package with name 'test package'"""
|
||||
page.get_by_role("button", name="Browse").click()
|
||||
page.get_by_role("link", name="Package", exact=True).click()
|
||||
page.get_by_role("button", name="Actions").click()
|
||||
page.get_by_role("button", name="New Package").click()
|
||||
page.locator("#new-package-button").click()
|
||||
page.get_by_role("textbox", name="Name").click()
|
||||
page.get_by_role("textbox", name="Name").fill("test package")
|
||||
page.get_by_role("textbox", name="Description").click()
|
||||
|
||||
136
uv.lock
generated
136
uv.lock
generated
@ -1,5 +1,5 @@
|
||||
version = 1
|
||||
revision = 2
|
||||
revision = 3
|
||||
requires-python = ">=3.12"
|
||||
resolution-markers = [
|
||||
"sys_platform == 'linux' or sys_platform == 'win32'",
|
||||
@ -368,6 +368,89 @@ wheels = [
|
||||
{ url = "https://files.pythonhosted.org/packages/d1/d6/3965ed04c63042e047cb6a3e6ed1a63a35087b6a609aa3a15ed8ac56c221/colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6", size = 25335, upload-time = "2022-10-25T02:36:20.889Z" },
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "contextlib2"
|
||||
version = "21.6.0"
|
||||
source = { registry = "https://pypi.org/simple" }
|
||||
sdist = { url = "https://files.pythonhosted.org/packages/c7/13/37ea7805ae3057992e96ecb1cffa2fa35c2ef4498543b846f90dd2348d8f/contextlib2-21.6.0.tar.gz", hash = "sha256:ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869", size = 43795, upload-time = "2021-06-27T06:54:40.841Z" }
|
||||
wheels = [
|
||||
{ url = "https://files.pythonhosted.org/packages/76/56/6d6872f79d14c0cb02f1646cbb4592eef935857c0951a105874b7b62a0c3/contextlib2-21.6.0-py2.py3-none-any.whl", hash = "sha256:3fbdb64466afd23abaf6c977627b75b6139a5a3e8ce38405c5b413aed7a0471f", size = 13277, upload-time = "2021-06-27T06:54:20.972Z" },
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "coverage"
|
||||
version = "7.12.0"
|
||||
source = { registry = "https://pypi.org/simple" }
|
||||
sdist = { url = "https://files.pythonhosted.org/packages/89/26/4a96807b193b011588099c3b5c89fbb05294e5b90e71018e065465f34eb6/coverage-7.12.0.tar.gz", hash = "sha256:fc11e0a4e372cb5f282f16ef90d4a585034050ccda536451901abfb19a57f40c", size = 819341, upload-time = "2025-11-18T13:34:20.766Z" }
|
||||
wheels = [
|
||||
{ url = "https://files.pythonhosted.org/packages/02/bf/638c0427c0f0d47638242e2438127f3c8ee3cfc06c7fdeb16778ed47f836/coverage-7.12.0-cp312-cp312-macosx_10_13_x86_64.whl", hash = "sha256:29644c928772c78512b48e14156b81255000dcfd4817574ff69def189bcb3647", size = 217704, upload-time = "2025-11-18T13:32:28.906Z" },
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||||
{ url = "https://files.pythonhosted.org/packages/08/e1/706fae6692a66c2d6b871a608bbde0da6281903fa0e9f53a39ed441da36a/coverage-7.12.0-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:8638cbb002eaa5d7c8d04da667813ce1067080b9a91099801a0053086e52b736", size = 218064, upload-time = "2025-11-18T13:32:30.161Z" },
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||||
{ url = "https://files.pythonhosted.org/packages/a9/8b/eb0231d0540f8af3ffda39720ff43cb91926489d01524e68f60e961366e4/coverage-7.12.0-cp312-cp312-manylinux1_i686.manylinux_2_28_i686.manylinux_2_5_i686.whl", hash = "sha256:083631eeff5eb9992c923e14b810a179798bb598e6a0dd60586819fc23be6e60", size = 249560, upload-time = "2025-11-18T13:32:31.835Z" },
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||||
{ url = "https://files.pythonhosted.org/packages/e9/a1/67fb52af642e974d159b5b379e4d4c59d0ebe1288677fbd04bbffe665a82/coverage-7.12.0-cp312-cp312-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl", hash = "sha256:99d5415c73ca12d558e07776bd957c4222c687b9f1d26fa0e1b57e3598bdcde8", size = 252318, upload-time = "2025-11-18T13:32:33.178Z" },
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||||
{ url = "https://files.pythonhosted.org/packages/41/e5/38228f31b2c7665ebf9bdfdddd7a184d56450755c7e43ac721c11a4b8dab/coverage-7.12.0-cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:e949ebf60c717c3df63adb4a1a366c096c8d7fd8472608cd09359e1bd48ef59f", size = 253403, upload-time = "2025-11-18T13:32:34.45Z" },
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||||
{ url = "https://files.pythonhosted.org/packages/ec/4b/df78e4c8188f9960684267c5a4897836f3f0f20a20c51606ee778a1d9749/coverage-7.12.0-cp312-cp312-manylinux_2_31_riscv64.manylinux_2_39_riscv64.whl", hash = "sha256:6d907ddccbca819afa2cd014bc69983b146cca2735a0b1e6259b2a6c10be1e70", size = 249984, upload-time = "2025-11-18T13:32:35.747Z" },
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||||
{ url = "https://files.pythonhosted.org/packages/ba/51/bb163933d195a345c6f63eab9e55743413d064c291b6220df754075c2769/coverage-7.12.0-cp312-cp312-musllinux_1_2_aarch64.whl", hash = "sha256:b1518ecbad4e6173f4c6e6c4a46e49555ea5679bf3feda5edb1b935c7c44e8a0", size = 251339, upload-time = "2025-11-18T13:32:37.352Z" },
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||||
{ url = "https://files.pythonhosted.org/packages/15/40/c9b29cdb8412c837cdcbc2cfa054547dd83affe6cbbd4ce4fdb92b6ba7d1/coverage-7.12.0-cp312-cp312-musllinux_1_2_i686.whl", hash = "sha256:51777647a749abdf6f6fd8c7cffab12de68ab93aab15efc72fbbb83036c2a068", size = 249489, upload-time = "2025-11-18T13:32:39.212Z" },
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||||
{ url = "https://files.pythonhosted.org/packages/c8/da/b3131e20ba07a0de4437a50ef3b47840dfabf9293675b0cd5c2c7f66dd61/coverage-7.12.0-cp312-cp312-musllinux_1_2_riscv64.whl", hash = "sha256:42435d46d6461a3b305cdfcad7cdd3248787771f53fe18305548cba474e6523b", size = 249070, upload-time = "2025-11-18T13:32:40.598Z" },
|
||||
{ url = "https://files.pythonhosted.org/packages/70/81/b653329b5f6302c08d683ceff6785bc60a34be9ae92a5c7b63ee7ee7acec/coverage-7.12.0-cp312-cp312-musllinux_1_2_x86_64.whl", hash = "sha256:5bcead88c8423e1855e64b8057d0544e33e4080b95b240c2a355334bb7ced937", size = 250929, upload-time = "2025-11-18T13:32:42.915Z" },
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||||
{ url = "https://files.pythonhosted.org/packages/a3/00/250ac3bca9f252a5fb1338b5ad01331ebb7b40223f72bef5b1b2cb03aa64/coverage-7.12.0-cp312-cp312-win32.whl", hash = "sha256:dcbb630ab034e86d2a0f79aefd2be07e583202f41e037602d438c80044957baa", size = 220241, upload-time = "2025-11-18T13:32:44.665Z" },
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||||
{ url = "https://files.pythonhosted.org/packages/64/1c/77e79e76d37ce83302f6c21980b45e09f8aa4551965213a10e62d71ce0ab/coverage-7.12.0-cp312-cp312-win_amd64.whl", hash = "sha256:2fd8354ed5d69775ac42986a691fbf68b4084278710cee9d7c3eaa0c28fa982a", size = 221051, upload-time = "2025-11-18T13:32:46.008Z" },
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||||
{ url = "https://files.pythonhosted.org/packages/31/f5/641b8a25baae564f9e52cac0e2667b123de961985709a004e287ee7663cc/coverage-7.12.0-cp312-cp312-win_arm64.whl", hash = "sha256:737c3814903be30695b2de20d22bcc5428fdae305c61ba44cdc8b3252984c49c", size = 219692, upload-time = "2025-11-18T13:32:47.372Z" },
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||||
{ url = "https://files.pythonhosted.org/packages/b8/14/771700b4048774e48d2c54ed0c674273702713c9ee7acdfede40c2666747/coverage-7.12.0-cp313-cp313-macosx_10_13_x86_64.whl", hash = "sha256:47324fffca8d8eae7e185b5bb20c14645f23350f870c1649003618ea91a78941", size = 217725, upload-time = "2025-11-18T13:32:49.22Z" },
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||||
{ url = "https://files.pythonhosted.org/packages/17/a7/3aa4144d3bcb719bf67b22d2d51c2d577bf801498c13cb08f64173e80497/coverage-7.12.0-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:ccf3b2ede91decd2fb53ec73c1f949c3e034129d1e0b07798ff1d02ea0c8fa4a", size = 218098, upload-time = "2025-11-18T13:32:50.78Z" },
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||||
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||||
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||||
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||||
@ -473,15 +556,31 @@ wheels = [
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wheels = [
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{ url = "https://files.pythonhosted.org/packages/e6/51/86968a38f074a56a675d72d470dce9405c9ddb53856c1686ca5e2ba44f81/django_ninja-1.5.0-py3-none-any.whl", hash = "sha256:e305fc42588406a202d4479263b501813ec863a3a4e11cb091fb905ecdf9bc62", size = 2428939, upload-time = "2025-11-13T17:57:59.967Z" },
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[[package]]
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wheels = [
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[[package]]
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@ -562,6 +661,7 @@ dependencies = [
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{ name = "django-extensions" },
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{ name = "django-model-utils" },
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{ name = "django-ninja" },
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{ name = "django-ninja-extra" },
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{ name = "django-oauth-toolkit" },
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{ name = "django-polymorphic" },
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{ name = "enviformer" },
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@ -589,6 +689,7 @@ dev = [
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{ name = "django-stubs" },
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{ name = "poethepoet" },
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{ name = "pre-commit" },
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{ name = "pytest-cov" },
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{ name = "pytest-django" },
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{ name = "pytest-playwright" },
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{ name = "ruff" },
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@ -604,7 +705,8 @@ requires-dist = [
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{ name = "django-model-utils", specifier = ">=5.0.0" },
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{ name = "django-ninja", specifier = ">=1.4.1" },
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@ -621,6 +723,7 @@ requires-dist = [
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{ name = "pytest-django", marker = "extra == 'dev'", specifier = ">=4.11.1" },
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{ name = "pytest-playwright", marker = "extra == 'dev'", specifier = ">=0.7.1" },
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{ name = "python-dotenv", specifier = ">=1.1.0" },
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@ -858,6 +961,15 @@ wheels = [
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[[package]]
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Reference in New Issue
Block a user