Release 1 (#66)

Co-authored-by: Xander Bil <[email protected]>
Co-authored-by: driesaster <[email protected]>
Co-authored-by: Xander Bil <[email protected]>
Co-authored-by: miboelae <[email protected]>
Co-authored-by: Michaël Boelaert <[email protected]>
Co-authored-by: Marieke <[email protected]>

.github/workflows/lint.yml

@@ -1,4 +1,4 @@
-name: Lint
+name: Code Style
 
 on:
   push:
@@ -43,4 +43,62 @@ jobs:
 
       - name: Run Backend linter
         run: autopep8 -rd --exit-code backend
+
+  pytest:
+    name: Unit Testing
+    runs-on: self-hosted
+    env:
+      DATABASE_URI: "${{ secrets.POSTGRES_CONNECTION }}"
+      FRONTEND_URL: "https://localhost:8080"
+      CAS_SERVER_URL: "https://login.ugent.be"
+      SECRET_KEY: "test" 
+      ALGORITHM: "HS256" 
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.12
+    - name: Install dependencies
+      working-directory: backend
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+    - name: Initialize Database
+      working-directory: backend
+      run: |
+        alembic upgrade head
+    - name: Test with pytest
+      working-directory: backend
+      run: |
+        pip install pytest pytest-cov pytest-html pytest-sugar pytest-json-report
+        py.test -v --cov --html=../reports/pytest/report.html
+    - name: Archive pytest coverage results
+      uses: actions/upload-artifact@v1
+      with:
+        name: pytest-coverage-report
+        path: reports/pytest/
+    - name: clean up alembic
+      working-directory: backend
+      if: always()
+      run: alembic downgrade base
+  pyright:
+    name: Pyright
+    runs-on: self-hosted
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.12
+    - name: Install dependencies
+      working-directory: backend
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install pyright
 
+    - name: run pyright
+      working-directory: backend
+      run: |
+        pyright

.gitignore

@@ -0,0 +1,2 @@
+.coverage
+**/reports/

backend/.flake8

@@ -2,3 +2,4 @@
 extend-ignore = E203
 exclude = .git,__pycache__,venv
 indent-size = 4
+max-line-length = 88

backend/.gitignore

@@ -1,2 +1,7 @@
 __pycache__
 *venv*
+
+*.db
+config.yml
+.env
+.coverage

backend/README.md

@@ -1,23 +1,26 @@
-## Run the backend api
+# Backend API
 
-### Setup
+## Running the API
 
-#### In this directy execute the following command to create a python environment:
+### Setup
 
 ```sh
+# Create a python virtual environment
 python -m venv venv
-```
-
-#### Activate the environment:
-
-```sh
+# Activate the environment
 source venv/bin/activate
+# Install dependencies
+pip install -r requirements.txt
 ```
 
-#### Install the dependencies:
+#### Create a `.env` file with following content
 
-```sh
-pip install -r requirements.txt
+```yml
+FRONTEND_URL="https://localhost:8080"
+CAS_SERVER_URL="https://login.ugent.be"
+DATABASE_URI="database connection string: postgresql://..., see discord..."
+SECRET_KEY="<secret key to sign JWT tokens>" # e.g. generate with `openssl rand -hex 32`
+ALGORITHM="HS256" # algorithm used to sign JWT tokens
 ```
 
 ### Usage
@@ -34,10 +37,36 @@ source venv/bin/activate
 ./run.sh
 ```
 
-It will start a local development server on port `8000`
+This will start a local development server on port `5173`
+
+## The API
+
+## Login
+
+Authentication happens with the use of CAS. The client can ask where it can find
+the CAS server with the `/api/authority` endpoint. A ticket then can be obtained
+via `<authority>?service=<redirect_url>`. The CAS server will redirect to
+`<redirect_url>?ticket=<ticket>` after authentication. Once the client is
+authenticated, further authorization happens with [JWT](https://jwt.io/). To
+obtain this token, a `POST` request has to be made to `/api/token/`, with the
+CAS ticket `<ticket>` and the `<redirect_url>`. The redirect url is needed to
+verify the ticket. If the ticket is valid, a webtoken will be returned. To
+authorize each request, add the token in the `Authorization` header.
+
+## Developing
 
 #### To format the python code in place to conform to PEP 8 style:
 
 ```sh
 autopep8 -ri .
 ```
+
+## Testing
+
+You can add tests by creating `test_*` files and `test_*` functions under `tests` directory.
+
+### Run the tests (in the virtual environment):
+
+```sh
+pytest -v
+```

backend/alembic.ini

@@ -0,0 +1,113 @@
+# A generic, single database configuration.
+
+[alembic]
+# path to migration scripts
+script_location = alembic
+
+# template used to generate migration file names; The default value is %%(rev)s_%%(slug)s
+# Uncomment the line below if you want the files to be prepended with date and time
+# see https://alembic.sqlalchemy.org/en/latest/tutorial.html#editing-the-ini-file
+# for all available tokens
+# file_template = %%(year)d_%%(month).2d_%%(day).2d_%%(hour).2d%%(minute).2d-%%(rev)s_%%(slug)s
+
+# sys.path path, will be prepended to sys.path if present.
+# defaults to the current working directory.
+prepend_sys_path = .
+
+# timezone to use when rendering the date within the migration file
+# as well as the filename.
+# If specified, requires the python>=3.9 or backports.zoneinfo library.
+# Any required deps can installed by adding `alembic[tz]` to the pip requirements
+# string value is passed to ZoneInfo()
+# leave blank for localtime
+# timezone =
+
+# max length of characters to apply to the
+# "slug" field
+# truncate_slug_length = 40
+
+# set to 'true' to run the environment during
+# the 'revision' command, regardless of autogenerate
+# revision_environment = false
+
+# set to 'true' to allow .pyc and .pyo files without
+# a source .py file to be detected as revisions in the
+# versions/ directory
+# sourceless = false
+
+# version location specification; This defaults
+# to alembic/versions.  When using multiple version
+# directories, initial revisions must be specified with --version-path.
+# The path separator used here should be the separator specified by "version_path_separator" below.
+# version_locations = %(here)s/bar:%(here)s/bat:alembic/versions
+
+# version path separator; As mentioned above, this is the character used to split
+# version_locations. The default within new alembic.ini files is "os", which uses os.pathsep.
+# If this key is omitted entirely, it falls back to the legacy behavior of splitting on spaces and/or commas.
+# Valid values for version_path_separator are:
+#
+# version_path_separator = :
+# version_path_separator = ;
+# version_path_separator = space
+version_path_separator = os  # Use os.pathsep. Default configuration used for new projects.
+
+# set to 'true' to search source files recursively
+# in each "version_locations" directory
+# new in Alembic version 1.10
+# recursive_version_locations = false
+
+# the output encoding used when revision files
+# are written from script.py.mako
+# output_encoding = utf-8
+
+[post_write_hooks]
+# post_write_hooks defines scripts or Python functions that are run
+# on newly generated revision scripts.  See the documentation for further
+# detail and examples
+
+# format using "black" - use the console_scripts runner, against the "black" entrypoint
+# hooks = black
+# black.type = console_scripts
+# black.entrypoint = black
+# black.options = -l 79 REVISION_SCRIPT_FILENAME
+
+# lint with attempts to fix using "ruff" - use the exec runner, execute a binary
+# hooks = ruff
+# ruff.type = exec
+# ruff.executable = %(here)s/.venv/bin/ruff
+# ruff.options = --fix REVISION_SCRIPT_FILENAME
+
+# Logging configuration
+[loggers]
+keys = root,sqlalchemy,alembic
+
+[handlers]
+keys = console
+
+[formatters]
+keys = generic
+
+[logger_root]
+level = WARN
+handlers = console
+qualname =
+
+[logger_sqlalchemy]
+level = WARN
+handlers =
+qualname = sqlalchemy.engine
+
+[logger_alembic]
+level = INFO
+handlers =
+qualname = alembic
+
+[handler_console]
+class = StreamHandler
+args = (sys.stderr,)
+level = NOTSET
+formatter = generic
+
+[formatter_generic]
+format = %(levelname)-5.5s [%(name)s] %(message)s
+datefmt = %H:%M:%S

backend/alembic/README

@@ -0,0 +1 @@
+Generic single-database configuration.

backend/alembic/env.py

@@ -0,0 +1,102 @@
+from src.user.models import Base as UserBase
+from src.subject.models import Base as SubjectBase
+from src.project.models import Base as ProjectBase
+from src.group.models import Base as GroupBase
+from src.submission.models import Base as SubmissionBase
+import os
+import sys
+from logging.config import fileConfig
+
+from sqlalchemy import engine_from_config
+from sqlalchemy import pool
+from sqlalchemy import MetaData
+
+from alembic import context
+from src import config as c
+
+
+# Calculate the path based on the location of the env.py file
+d = os.path.dirname
+parent_dir = d(d(os.path.abspath(__file__)))
+sys.path.append(parent_dir)
+
+# Import the Base from each of your model submodules
+
+# this is the Alembic Config object, which provides
+# access to the values within the .ini file in use.
+config = context.config
+
+# Interpret the config file for Python logging.
+# This line sets up loggers basically.
+if config.config_file_name is not None:
+    fileConfig(config.config_file_name)
+
+config.set_main_option('sqlalchemy.url', c.CONFIG.database_uri)
+
+# add your model's MetaData object here
+# for 'autogenerate' support
+# from myapp import mymodel
+# target_metadata = mymodel.Base.metadata
+combined_metadata = MetaData()
+for base in [ProjectBase, SubjectBase, UserBase, GroupBase, SubmissionBase]:
+    for table in base.metadata.tables.values():
+        combined_metadata._add_table(table.name, table.schema, table)
+
+target_metadata = combined_metadata
+
+# other values from the config, defined by the needs of env.py,
+# can be acquired:
+# my_important_option = config.get_main_option("my_important_option")
+# ... etc.
+
+
+def run_migrations_offline() -> None:
+    """Run migrations in 'offline' mode.
+
+    This configures the context with just a URL
+    and not an Engine, though an Engine is acceptable
+    here as well.  By skipping the Engine creation
+    we don't even need a DBAPI to be available.
+
+    Calls to context.execute() here emit the given string to the
+    script output.
+
+    """
+    url = config.get_main_option("sqlalchemy.url")
+    context.configure(
+        url=url,
+        target_metadata=target_metadata,
+        literal_binds=True,
+        dialect_opts={"paramstyle": "named"},
+    )
+
+    with context.begin_transaction():
+        context.run_migrations()
+
+
+def run_migrations_online() -> None:
+    """Run migrations in 'online' mode.
+
+    In this scenario we need to create an Engine
+    and associate a connection with the context.
+
+    """
+    connectable = engine_from_config(
+        config.get_section(config.config_ini_section, {}),
+        prefix="sqlalchemy.",
+        poolclass=pool.NullPool,
+    )
+
+    with connectable.connect() as connection:
+        context.configure(
+            connection=connection, target_metadata=target_metadata
+        )
+
+        with context.begin_transaction():
+            context.run_migrations()
+
+
+if context.is_offline_mode():
+    run_migrations_offline()
+else:
+    run_migrations_online()