chore: set up FOCA

.cruft.json

@@ -8,7 +8,7 @@
       "author_email": "[email protected]",
       "development_status": "1 - Planning",
       "short_description": "File handler utilizing TUS and MinIO with DRS-Filer integration.",
-      "project_name": "tus-storagehandler",
+      "project_name": "tus_storagehandler",
       "project_slug": "tus_storagehandler",
       "github_username": "elixir-cloud-aai",
       "python_version": "3.11",

.github/ISSUE_TEMPLATE/general-purpose.md

@@ -46,4 +46,4 @@ bug in -->
 - Operating System and version (desktop or mobile):
 - Link to your project:
 
-[issue-tracker]: https://github.com/elixir-cloud-aai/tus-storagehandler/issues
+[issue-tracker]: https://github.com/elixir-cloud-aai/tus_storagehandler/issues

.github/workflows/run-application.yaml

@@ -0,0 +1,48 @@
+---
+name: Run Application
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+
+      - name: Install Poetry
+        run: |
+          curl -sSL https://install.python-poetry.org | python3 -
+          echo "$HOME/.local/bin" >> $GITHUB_PATH
+
+      - name: Activate environment and install dependencies
+        run: |
+          make v
+          source .venv/bin/activate
+          make i
+
+      - name: Start server in the background
+        run: |
+          tus_storagehandler &
+          echo $! > server.pid
+
+      - name: Run tests
+        run: |
+          poetry run pytest tests/test_integration
+
+      - name: Stop server
+        run: |
+          kill $(cat server.pid) || true
+...

.markdownlint.yaml

@@ -65,7 +65,7 @@ MD037: true  # Spaces inside emphasis markers
 MD038: true  # Spaces inside code span elements
 MD039: true  # Spaces inside link elements
 MD040: true  # Fenced code blocks should have a language specified
-MD041: false # First line need not be h1
+MD041: false  # First line need not be h1
 MD046: true  # Code block style
 MD047: true  # Files should end with a single newline character
 MD048: true  # Code fence style

README.md

@@ -18,53 +18,76 @@ File handler utilizing TUS and MinIO with DRS-Filer integration.
 - [Basic Usage](#basic-usage)
 - [Installation](#installation)
 - [Development](#development)
+- [Environment Variables](#environment-variables)
 - [Contributing](#contributing)
 - [Code of Conduct](#code-of-conduct)
 - [Versioning](#versioning)
 - [License](#license)
 - [Contact](#contact)
 
 ## Synopsis
-This application provides endpoints for uploading, downloading, and listing files in a MinIO bucket, with TUS protocol support for uploads, and CORS enabled for cross-origin requests.
+
+This application provides endpoints for uploading, downloading, and listing
+files in a MinIO bucket, with TUS protocol support for uploads, and CORS enabled
+for cross-origin requests.
 
 ## Basic Usage
 
 ## Installation
 
 ### Prerequisites
 
-This flask application requires a running instance of [minio](https://min.io/download)
+This Flask application requires a running instance of
+[MinIO](https://min.io/download).
 
-Run the minio instance by executing the following command in the location where minio is installed
+Run the MinIO instance by executing the following command in the location where
+MinIO is installed:
 
 ```sh
 minio server /data --console-address ":9001"
 ```
 
 ### Install Dependencies using Poetry
 
-1. **Download the required dependencies**
+1. **Clone the Repository**
+
+   To get started, first, clone the repository using the following command:
+
+   ```sh
+   git clone https://github.com/elixir-cloud-aai/tus-storagehandler.git
+   ```
+
+1. **Navigate to the package folder**
+
+   Navigate to the folder `tus_storagehandler`:
+
+   ```sh
+   cd tus_storagehandler
+   ```
 
-   Navigate to the folder `tus_storagehandler`.
+1. **Install Poetry**
 
-2. **Install Poetry**
+   If you haven't already, install Poetry by following the instructions on the
+   [Poetry website](https://python-poetry.org/docs/#installation).
 
-   If you haven't already, install Poetry by following the instructions on the [Poetry website](https://python-poetry.org/docs/#installation).
+1. **Create and Activate a Virtual Environment (optional)**
 
-3. **Create and Activate a Virtual Environment (optional)**
+   Poetry automatically creates and manages a virtual environment for your
+   project. You can activate it using:
 
-   Poetry automatically creates and manages a virtual environment for your project. You can activate it using:
    ```sh
    poetry shell
    ```
 
-4. **Install Dependencies**
+1. **Install Dependencies**
+
+   Run the following command to install the dependencies defined in the
+   `pyproject.toml` file:
 
-   Run the following command to install the dependencies defined in the `pyproject.toml` file:
    ```sh
    poetry install
    ```
-  
+
 ## Development
 
 For ease of use, certain scripts have been abbreviated in `Makefile`, make sure
@@ -157,6 +180,16 @@ make u
 > **Note**: This is not the complete list of commands, run `make` to find out if
 > more have been added.
 
+## Environment Variables
+
+<!-- markdownlint-disable line-length -->
+
+| **Environment Variable** | **Description** | **Usage** | **Error Handling** |
+|--|--|--|--| 
+| `CSH_FOCA_CONFIG_PATH` | Specifies the path to the configuration file for the FOCA app. | The FOCA app uses this environment variable to locate the configuration file. If not set, it defaults to `dev`. | If the configuration file is not found at the specified or default path, a `FileNotFoundError` will be raised. |
+
+<!-- markdownlint-enable line-length -->
+
 ## Contributing
 
 This project is a community effort and lives off _your_ contributions, be it in

deployment/config.yaml

@@ -0,0 +1,42 @@
+---
+server:
+    host: '0.0.0.0'
+    port: 8080
+    debug: false
+    environment: development
+    testing: false
+    use_reloader: true
+
+security:
+    auth:
+        required: true
+        add_key_to_claims: true
+        allow_expired: false
+        audience: null
+        claim_identity: sub
+        claim_issuer: iss
+        algorithms:
+            - RS256
+        validation_methods:
+            - userinfo
+            - public_key
+        validation_checks: all
+
+api:
+    specs:
+        - path: tus_storagehandler/api/specs/specs.yaml
+          append: null
+          add_operation_fields:
+              x-openapi-router-controller: tus_storagehandler.api.elixircloud.csh.controllers
+          connexion:
+              strict_validation: true
+              validate_responses: false
+              options:
+                  swagger_ui: true
+                  serve_spec: true
+
+exceptions:
+    required_members: [['message'], ['code']]
+    status_member: ['code']
+    exceptions: tus_storagehandler.exceptions.exceptions
+...

docs/source/pages/tus_storagehandler.api.elixircloud.csh.rst

@@ -0,0 +1,21 @@
+tus\_storagehandler.api.elixircloud.csh package
+===============================================
+
+Submodules
+----------
+
+tus\_storagehandler.api.elixircloud.csh.controllers module
+----------------------------------------------------------
+
+.. automodule:: tus_storagehandler.api.elixircloud.csh.controllers
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tus_storagehandler.api.elixircloud.csh
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pages/tus_storagehandler.api.elixircloud.rst

@@ -0,0 +1,18 @@
+tus\_storagehandler.api.elixircloud package
+===========================================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tus_storagehandler.api.elixircloud.csh
+
+Module contents
+---------------
+
+.. automodule:: tus_storagehandler.api.elixircloud
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pages/tus_storagehandler.api.rst

@@ -0,0 +1,18 @@
+tus\_storagehandler.api package
+===============================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tus_storagehandler.api.elixircloud
+
+Module contents
+---------------
+
+.. automodule:: tus_storagehandler.api
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/pages/tus_storagehandler.rst

@@ -1,13 +1,29 @@
 tus\_storagehandler package
 ===========================
 
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   tus_storagehandler.api
+
 Submodules
 ----------
 
-tus\_storagehandler.main module
--------------------------------
+tus\_storagehandler.app module
+------------------------------
+
+.. automodule:: tus_storagehandler.app
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+tus\_storagehandler.exceptions module
+-------------------------------------
 
-.. automodule:: tus_storagehandler.main
+.. automodule:: tus_storagehandler.exceptions
    :members:
    :undoc-members:
    :show-inheritance: