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https://github.com/beak-insights/felicity-lims.git
synced 2025-02-21 07:22:53 +08:00
added automata script
This commit is contained in:
Aurthur Musendame
parent
38fd5affc9
commit
470d7146b2
2 changed files with 169 additions and 0 deletions
78
bin/Make
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78
bin/Make
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# Variables
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CONDA_INSTALLER_URL=https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
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REPO_URL=https://github.com/beak-insights/felicity-lims/
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INSTALL_DIR=/home/felicity/felicity-lims
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CONDA_DIR=/home/felicity/miniconda3
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ENV_NAME=felicity
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PYTHON_VERSION=3.12
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help: ## Show this help.
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u/egrep -h '(\s##\s|^##\s)' $(MAKEFILE_LIST) | egrep -v '^--' | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[32m %-35s\033[0m %s\n", $$1, $$2}'
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# Default target
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all: install-dependencies create-user clone-repo install-miniconda setup-env install-node setup-pnpm setup-db install-webapp setup-supervisor
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# Install dependencies
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install-dependencies:
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sudo apt-get update
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sudo apt-get install -y git libcairo2-dev pkg-config python3-dev gcc g++ postgresql postgresql-contrib
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# Create user 'felicity' with password 'felicity'
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create-user:
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sudo adduser --disabled-password --gecos "" felicity
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echo "felicity:felicity" | sudo chpasswd
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# Clone the repository
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clone-repo: create-user
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sudo -u felicity git clone $(REPO_URL) $(INSTALL_DIR)
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# Download and install Miniconda
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install-miniconda:
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wget $(CONDA_INSTALLER_URL) -O Miniconda.sh
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bash Miniconda.sh -b -p $(CONDA_DIR)
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rm Miniconda.sh
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# Create and activate the 'felicity' environment
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setup-env: install-miniconda
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sudo -u felicity $(CONDA_DIR)/bin/conda create -n $(ENV_NAME) python=$(PYTHON_VERSION) -y
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# Install Node.js 18 and PNPM
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install-node:
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curl -fsSL https://deb.nodesource.com/setup_18.x | sudo -E bash -
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sudo apt-get install -y nodejs
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setup-pnpm: install-node
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npm install -g pnpm
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# Set up PostgreSQL
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setup-db: install-dependencies
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sudo systemctl start postgresql
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sudo systemctl enable postgresql
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sudo -u postgres psql -c "CREATE USER felicity WITH PASSWORD 'felicity';"
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sudo -u postgres psql -c "CREATE DATABASE felicity_lims OWNER felicity;"
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sudo -u postgres psql -d felicity_lims -c "GRANT ALL PRIVILEGES ON SCHEMA public TO felicity;"
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# Install webapp dependencies and build the project
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install-webapp: clone-repo setup-env setup-pnpm
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cd $(INSTALL_DIR) && sudo -u felicity $(CONDA_DIR)/envs/$(ENV_NAME)/bin/pnpm i
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cd $(INSTALL_DIR) && sudo -u felicity $(CONDA_DIR)/envs/$(ENV_NAME)/bin/pnpm standalone:build
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# Set up Supervisor
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setup-supervisor:
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sudo apt-get install -y supervisor
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@echo "[program:felicity_lims]" | sudo tee /etc/supervisor/conf.d/felicity_lims.conf
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@echo "command=$(CONDA_DIR)/envs/$(ENV_NAME)/bin/python $(INSTALL_DIR)/path/to/felicity_script.py" | sudo tee -a /etc/supervisor/conf.d/felicity_lims.conf
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@echo "autostart=true" | sudo tee -a /etc/supervisor/conf.d/felicity_lims.conf
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@echo "autorestart=true" | sudo tee -a /etc/supervisor/conf.d/felicity_lims.conf
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@echo "stderr_logfile=/var/log/felicity_lims.err.log" | sudo tee -a /etc/supervisor/conf.d/felicity_lims.conf
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@echo "stdout_logfile=/var/log/felicity_lims.out.log" | sudo tee -a /etc/supervisor/conf.d/felicity_lims.conf
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sudo supervisorctl reread
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sudo supervisorctl update
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# Clean up
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clean:
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rm -rf $(INSTALL_DIR)
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sudo deluser felicity --remove-home
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sudo apt-get remove --purge -y git libcairo2-dev pkg-config python3-dev gcc g++ postgresql postgresql-contrib nodejs supervisor
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sudo apt-get autoremove -y
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sudo apt-get clean
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91
bin/felicity.sh
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91
bin/felicity.sh
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#!/bin/bash
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# Update package lists
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sudo apt-get update
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# Install required packages
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sudo apt-get install -y git libcairo2-dev pkg-config python3-dev gcc g++
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# Create user 'felicity' with password 'felicity'
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sudo adduser --disabled-password --gecos "" felicity
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echo "felicity:felicity" | sudo chpasswd
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# Switch to the 'felicity' user
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sudo -u felicity
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# Install PostgreSQL
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sudo apt-get install -y postgresql postgresql-contrib
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# Start PostgreSQL service
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sudo systemctl start postgresql
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sudo systemctl enable postgresql
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# Create PostgreSQL user 'felicity' with password 'felicity'
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sudo -u postgres psql -c "CREATE USER felicity WITH PASSWORD 'felicity';"
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# Create a database for 'felicity'
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sudo -u postgres psql -c "CREATE DATABASE felicity_lims OWNER felicity;"
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# Grant all privileges on the 'public' schema to the 'felicity' user
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sudo -u postgres psql -d felicity_lims -c "GRANT ALL PRIVILEGES ON SCHEMA public TO felicity;"
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# Download and install Miniconda
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wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
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bash Miniconda3-latest-Linux-x86_64.sh -b
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# Initialize Miniconda
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export PATH="/home/felicity/miniconda3/bin:\$PATH"
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source /home/felicity/miniconda3/bin/activate
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# Create and activate the 'felicity' environment with Python 3.12
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conda create -n felicity python=3.12 -y
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conda activate felicity
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# Install Node.js 18 and PNPM
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curl -fsSL https://deb.nodesource.com/setup_18.x | sudo -E bash -
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sudo apt-get install -y nodejs
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npm install -g pnpm
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# Clone the repository
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# shellcheck disable=SC2164
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cd /home/felicity
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git clone https://github.com/beak-insights/felicity-lims.git
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# Change directory to the cloned repository
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# shellcheck disable=SC2164
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cd /home/felicity/felicity-lims
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# install requirements
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pip install -r requirements.txt
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# Set up PostgreSQL
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pnpm db:al:upgrade
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# Install webapp dependencies
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pnpm i
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# Build webapp and set up Felicity to serve static files
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pnpm standalone:build
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# Install Supervisor
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sudo apt-get install -y supervisor
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# Create Supervisor configuration file
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cat <<EOF | sudo tee /etc/supervisor/conf.d/felicity_lims.conf
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[program:felicity_lims]
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command=/home/felicity/miniconda3/envs/felicity/bin/python /home/felicity/felicity-lims
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autostart=true
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autorestart=true
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stderr_logfile=/var/log/felicity_lims.err.log
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stdout_logfile=/var/log/felicity_lims.out.log
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EOF
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# Update Supervisor
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sudo supervisorctl reread
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sudo supervisorctl update
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# Check Supervisor status
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sudo systemctl status supervisor
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# Check program status
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sudo supervisorctl status
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