Merge pull request #13 from Bioprotocols/development

Alpha Release Candidate

.gitignore

@@ -1,14 +1,55 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST__pycache__/
+*.py[cod]
+*$py.class
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
 **/__pycache__/**
-pamled/media/**/
-pamled/pamled_editor/static/**
-pamled/pamled_editor/templates/**
+pamled/editor/static/**
+pamled/editor/templates/**
 **/.vscode
-pamled/db.sqlite3
-pamled/pamled_editor/client/.editorconfig
 pamled/.env
 **/node_modules
-**/package-lock.json
 **/.editorconfig
 pamled/general.log
 general.log
-pamled/pamled_editor/migrations
+backend/pamled_editor/migrations
+backend/api/migrations
+backend/editor/migrations
+backend/accounts/migrations
+backend/media/
+oso

Pipfile

@@ -0,0 +1,28 @@
+[[source]]
+url = "https://pypi.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[dev-packages]
+pylint = "*"
+
+[packages]
+Django = "==3.2.9"
+django-cors-headers = "*"
+djangorestframework = "*"
+django-oso = "*"
+jsonfield = "*"
+python-decouple = "*"
+pypaml = {git = "https://github.com/Bioprotocols/paml.git"}
+
+# Keep black at version under 22 because:
+# There are incompatible versions in the resolved dependencies:
+# - click<8,>=7.0 (from transcriptic==9.5.0)
+# - click>=8.0.0 (from black==22.1.0)
+black = "<22"
+
+[requires]
+python_version = "3.9"
+
+[pipenv]
+allow_prereleases = true

README.md

@@ -1,37 +1,124 @@
-# Instructions for running the PAML Editor in Development
-- Install [node.js](https://nodejs.org/en/download/)
-- Clone this repository (`/` is the root of the cloned repository, below)
-- Set the secret key in `/pamled/.env`:
+# **Introduction**
+
+The PAML Editor (PAMLED) is a web application that supports the authoring and sharing of PAML protocols.  PAMLED consists of two components: `frontend` and `backend`.  The frontend is a React-based server for handling the graphical interface.   The backend is a Django REST server that handles persistent storage (protocols, user accounts, and primitives), and access to the pyPAML library.
+
+# **User Guide**
+
+See the user guide at: [User Guide](frontend/web/src/USERGUIDE.md)
+
+# **Running the PAML Editor in Development**
+
+## **Pre-requisites**
+- Backend <a name="backend-deps"></a>
+    - [Python 3.9](https://www.python.org/downloads/release/python-390/)
+    - [Pipenv](https://pipenv.pypa.io/en/latest/install/)
+- Frontend <a name="frontend-deps"></a>
+    - [Node & Npm](https://nodejs.org/en/download/)
+
+
+## **Backend Instructions**
+---
+
+1. On your development system install [backend dependencies](#backend-deps)
+
+2. Get PAMLED:
+```bash
+git clone https://github.com/Bioprotocols/pamled.git
 ```
-# in /
-python -c "import secrets; print(f'SECRET_KEY=\"{secrets.token_urlsafe()}\"')"  > pamled/.env
+
+3. Initialize the pamled pipenv environment:
+```bash
+cd pamled
+pipenv install
+pipenv shell
 ```
-- Create a python environment:
+
+4. Set the secret key in `backend/.env`:
+ ```bash
+ python -c "import secrets; print(f'SECRET_KEY=\"{secrets.token_urlsafe()}\"')"  > backend/.env
+ ```
+
+5. Initialize the backend
+```bash
+# from within the pipenv shell
+cd backend
+python manage.py makemigrations accounts editor
+python manage.py migrate
+
+# optionally create a admin user
+python manage.py createsuperuser
 ```
-virutalenv env
-source /env/bin/activate
-pip install -r requirements.txt
-```
-- Install the client dependencies
-```
-# in /pamled/pamled_editor/client
-npm install
-```
-- Generate the client Vue templates and copy into the Django server static files
+
+6. Start the backend
+```bash
+# from within the pipenv shell, in backend/
+python manage.py runserver
 ```
-cd /pamled/pamled_editor/client
-npm run build -- --mode staging
+
+The backend server should now be running. You will see some output in the terminal like this:
 ```
-- Optionally run the front end Vue server with the Vue CLI
+Performing system checks...
+
+System check identified no issues (0 silenced).
+January 24, 2022 - 18:52:36
+Django version 3.2.9, using settings 'pamled.settings'
+Starting development server at http://127.0.0.1:8000/
+Quit the server with CONTROL-C.
 ```
-# in /pamled/pamled_editor/client
-npm run serve
+
+## **Frontend Instructions**
+---
+
+1. On your development system install:
+- [node & npm](https://nodejs.org/en/download/)
+
+2. Initialize the frontend
+```bash
+# while in backend/ from above
+cd ../frontend/web
+npm install
 ```
-- Run the Django server
+
+3. Start the frontend
+```bash
+# while in frontend/web/
+npm run start
 ```
-# in /pamled
-pip install django
-python manage.py makemigrations # If you modify any of the django models
-python manage.py migrate # setup the database
-python manage.py runserver
-```
+
+If npm does not open a browser automatically then you can connect to the frontend at `http://localhost:3000` from your preferred browser.
+
+4. Once connected you should be greeted by a login page. If you made a superuser account then you can login with that. Otherwise you can navigate to the sign up page and register a new account with your development database.
+
+5. Once logged in you will see the editor.
+
+
+## **Development using Visual Studio Code**
+---
+For those familiar with VSCode the backand and frontend instructions have mostly been encapsulated within a VSCode workspace. See the `pamled.code-workspace` in the root of the repo.
+
+**Note** that this workspace does still require `pipenv` and `npm` to be installed.
+
+## **Tasks**
+
+The workspace provides a set of tasks available via command palette (`Ctrl+Shift+P`) under `Tasks: Run Task`.
+
+These make initialization of the backend and frontend a bit easier to manage.
+> ### Tasks:
+> - Make Migrations
+> - Migrate
+> - Create Superuser
+> - Nuke DB & Migrations
+
+## **Launchers**
+
+It also provides a set of launch commands available from the `Run and Debug` panel (`Ctrl+Shift+D`).
+
+These make it easier to launch all of the editor parts at once.
+>### Launchers
+>- Django
+>- React
+>- Firefox
+>- Chrome
+>### Compound Launchers
+>- Django & React & Firefox
+>- Django & React & Chrome

backend/.gitignore

@@ -0,0 +1,2 @@
+.env
+db.sqlite3

backend/accounts/admin.py

@@ -0,0 +1,26 @@
+from django.contrib import admin
+from django.contrib.auth.admin import UserAdmin as DjangoUserAdmin
+from django.utils.translation import gettext_lazy as _
+
+from .models import User
+
+@admin.register(User)
+class UserAdmin(DjangoUserAdmin):
+    """Define admin model for custom User model with no email field."""
+
+    fieldsets = (
+        (None, {'fields': ('email', 'password')}),
+        (_('Personal info'), {'fields': ('first_name', 'last_name')}),
+        (_('Permissions'), {'fields': ('is_active', 'is_staff', 'is_superuser',
+                                       'groups', 'user_permissions')}),
+        (_('Important dates'), {'fields': ('last_login', 'date_joined')}),
+    )
+    add_fieldsets = (
+        (None, {
+            'classes': ('wide',),
+            'fields': ('email', 'password1', 'password2'),
+        }),
+    )
+    list_display = ('email', 'first_name', 'last_name', 'is_staff')
+    search_fields = ('email', 'first_name', 'last_name')
+    ordering = ('email',)

pamled/pamled_editor/apps.py → backend/accounts/apps.py

@@ -1,6 +1,6 @@
 from django.apps import AppConfig
 
 
-class PamledEditorConfig(AppConfig):
+class AccountsConfig(AppConfig):
     default_auto_field = 'django.db.models.BigAutoField'
-    name = 'pamled_editor'
+    name = 'accounts'

backend/accounts/models.py

@@ -0,0 +1,47 @@
+from django.db import models
+from django.contrib.auth.models import AbstractUser, BaseUserManager
+from django.utils.translation import gettext_lazy as _
+
+class UserManager(BaseUserManager):
+    """Define a model manager for User model with no username field."""
+
+    use_in_migrations = True
+
+    def _create_user(self, email, password, **extra_fields):
+        """Create and save a User with the given email and password."""
+        if not email:
+            raise ValueError('The given email must be set')
+        email = self.normalize_email(email)
+        user = self.model(email=email, **extra_fields)
+        user.set_password(password)
+        user.save(using=self._db)
+        return user
+
+    def create_user(self, email, password=None, **extra_fields):
+        """Create and save a regular User with the given email and password."""
+        extra_fields.setdefault('is_staff', False)
+        extra_fields.setdefault('is_superuser', False)
+        return self._create_user(email, password, **extra_fields)
+
+    def create_superuser(self, email, password, **extra_fields):
+        """Create and save a SuperUser with the given email and password."""
+        extra_fields.setdefault('is_staff', True)
+        extra_fields.setdefault('is_superuser', True)
+
+        if extra_fields.get('is_staff') is not True:
+            raise ValueError('Superuser must have is_staff=True.')
+        if extra_fields.get('is_superuser') is not True:
+            raise ValueError('Superuser must have is_superuser=True.')
+
+        return self._create_user(email, password, **extra_fields)
+
+class User(AbstractUser):
+    """User model."""
+
+    username = None
+    email = models.EmailField(_('email address'), unique=True)
+
+    USERNAME_FIELD = 'email'
+    REQUIRED_FIELDS = []
+
+    objects = UserManager()

backend/accounts/policy/authorization.polar

@@ -0,0 +1,11 @@
+allow(user: accounts::User, _action, _resource) if
+    user.is_staff;
+
+allow(user: accounts::User, "GET", resource) if
+    user_owns_protocol(user, resource);
+
+allow(user: accounts::User, "DELETE", resource) if
+    user_owns_protocol(user, resource);
+
+user_owns_protocol(user: accounts::User, resource: editor::Protocol) if
+    resource in editor::Protocol.objects.filter(owner: user);

backend/accounts/tests.py

@@ -0,0 +1,3 @@
+from django.test import TestCase
+
+# Create your tests here.

backend/accounts/urls.py

@@ -0,0 +1,12 @@
+from django.urls import path
+
+from . import views
+
+urlpatterns = [
+    path('csrf/', views.get_csrf, name='api-accounts-csrf'),
+    path('signup/', views.signup_view, name='api-accounts-signup'),
+    path('login/', views.login_view, name='api-accounts-login'),
+    path('logout/', views.logout_view, name='api-accounts-logout'),
+    path('session/', views.SessionView.as_view(), name='api-accounts-session'),
+    path('whoami/', views.WhoAmIView.as_view(), name='api-accounts-whoami'),
+]