SiLA_2_Manager

The SiLA_2_Manager is an open-source framework for laboratory automation with a modern IoT interface. It provides the user with a SiLA service management system, a scheduler, a scripting environment, a experiment planning utility, and a data handler to link service data to a database.

Installation

Read the docs for more detailed information.

Compatibility

The SiLA Manager is compatible with the SiLA2 Python repository and all SiLA servers generated with it. Follow the instructions in the SiLA2 Python repository to create your own SiLA servers or use the provided examples (HelloSiLA) to test the SiLA 2 Manager. You can also install the SiLA2 python library and codegenerator from pypi using pip. The other SiLA 2 repositories (like C# and Tecan) will be supported very soon.

Development Environment

Setting up the python environment

1. Install pipenv
   Visit: https://pypi.org/project/pipenv/
   or try using pip install pipenv

2. Install the project pipfile
   Move to the project main directory, where the pipfile is located
   Run: pipenv install
   This will install all required python packages in a virtual environment.

3. Entering the virtual environment
   Most IDE's support automatic detection of virtual environments and will start the console in this environment. For some IDE's this requires some changes in the settings menu.
   If no IDE is used you can enter the environment by entering: pipenv shell

Generating the documentation

This README contains the bare essentials to get the device manager up and running. For a more detailed description and further information read the documentation. The documentation can be generated using sphinx.

1. Run the following command from within the docs folder
   To generate a pdf (Perl and latexmk required): make latexpdf
   To generate a html-file make html

2. The file will be stored in the _build folder inside the docs folder

Setup

1. Install Docker (v2.3.0.5)
   Visit https://www.docker.com/products/docker-desktop

2. Download and start the images of PostgreSQL and redis: Run docker run --name postgres -e POSTGRES_PASSWORD=1234 -d -p 5432:5432 postgres
   Run docker run --name redis -d -p 6379:6379 redis The next time you want use the containers you can start them directly: docker start postgres docker start redis

3. Create the user-script docker image cd user_script_env docker build -t user_script .

4. Activate development mode export DEVICE_MANAGER_ENV_PRODUCTION=0 or set DEVICE_MANAGER_ENV_PRODUCTION=0 if you are on windows

5. Setup a test database:
   Run python setup_db.py from inside your pipenv environment.

6. Create Config File:
   Run python generate_config.py from inside your pipenv environment.

Starting the Backend development Server

Linux

Run ./run_backend_server.sh from inside your pipenv environment.

Windows

Run ./run_backend_server.bat from inside your pipenv environment.

Server Deployment on Ubuntu 12.04

First Install

1. Install nginx On ubuntu this can be installed with apt
   sudo apt install nginx

2. Install PostgreSQL
   sudo apt install postgresql-12
sudo apt install postgresql-client-12

3. Install Docker
   Use the official instructions

4. Install Supervisor
   sudo apt install supervisor

5. Install Redis sudo apt install redis-server

6. Install and run pipenv
   sudo apt install pipenv
mkdir .venv
pipenv sync

7. Fix protobuf installation
   Uninstall protobuf and reinstall it using the --no-binary flag.
   pipenv shell
sudo pip3 uninstall protobuf
   Check that protobuf has been uninstalled:
   pip3 list
sudo pip3 install --no-binary=:all: -t $/home/<usr>/sila2_device_manager/.venv/lib/python3.8/site-packages protobuf==3.15.0
   Check that protobuf has been reinstalled.

8. Replace some files in the sila2lib of the virtual environment
   sudo pipenv run python3.8 replace_files.py

9. Install and Enable Nginx Config
   sudo cp server-config/device-manager.conf /etc/nginx/sites-available/
sudo ln -s /etc/nginx/sites-available/device-manager.conf /etc/nginx/sites-enabled/device-manager.conf

10. Install Supervisor Config
    sudo cp server-config/device-manager-backend.supervisor.conf /etc/supervisor/conf.d
sudo cp server-config/device-manager-scheduler.supervisor.conf /etc/supervisor/conf.d

11. Create the device-manager user and group and add yourself
    sudo adduser --system --no-create-home --group --ingroup docker device-manager
sudo gpasswd -a your-user-name device-manager

12. Create www directory
    sudo mkdir /var/www/html/device-manager-frontend
chmod -R device-manager /var/www/html/device-manager-frontend
chgrp -R device-manager /var/www/html/device-manager-frontend
chmod -R 775 /var/www/html/device-manager-frontend

13. Create Backend Config Directory
    sudo mkdir /etc/device-manager/

14. Start and Enable PostgreSQL
    sudo systemctl enable postgresql.service
sudo systemctl start postgresql.service

    Fill the database with the initial values and examples
    pipenv run python setup_db.py

15. Set Postgres password
    sudo -u postgres psql postgres
\password postgres
    enter the password
    \q

16. Start and Enable Docker
    sudo systemctl enable docker.service
sudo systemctl start docker.service

17. Enable and configure Redis
    edit /etc/redis/redis.conf and change
    supervised no to supervised systemd
sudo systemctl enable redis.service
sudo systemctl start redis.service

18. Create the user-script docker image
    cd user_script_env
sudo docker build -t user_script .
cd ..

19. Deploy Backend
    sudo pipenv run ./deploy_backend.sh

20. Edit Device-Manager Configuration File
    The configuration files are located in the main directory under:
    ./server-config/device-manager.conf
./server-config/device-manager-backend.supervisor.conf
./server-config/device-manager-scheduler.supervisor.conf

21. Build and Install Frontend
    cd frontend
sudo make
sudo make install

22. Start and Enable Nginx
    sudo systemctl enable nginx.service
sudo systemctl start nginx.service

23. Start and Enable Supervisor
    sudo systemctl enable supervisor.service
sudo systemctl start supervisor.service

Deploying New Versions

To deploy a new version its often enough to repeate step 17 and 19. Then restart nginx and supervisor by using
sudo systemctl restart nginx.service
and
sudo systemctl restart supervisor.service

Server management

You can use supervisorctl to manage the backend and scheduler processes separately. The logs can be viewed under /var/log/device-manager.
To restart the backend or the scheduler service, use supervisorctl. Enter supervisorctl:
sudo supervisorctl
and run the restart command for the respective service:
restart backend:device-manager-backend-0

License

This code is licensed under the MIT License