Create ansible config for deploying Explorer and NeoDB

.gitignore

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+files/SANBI_Wildcard*
+files/sanbidev-combat-tb-explorer*

README.md

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+=== Deploy COMBAT-TB-Explorer and NeoDB
+
+Ansible roles and configuration to deploy [COMBAT TB Explorer and NeoDB](https://academic.oup.com/bioinformatics/article/36/3/982/5554700).
+
+This depends on these files (need to be put in the files/ folder) which are not included in the repository:
+1. The SANBI wildcard SSL certificate (SANBI\_Wildcard.all.pem and SANBI\_Wildcard.key)
+2. The source code downloaded from [Bitbucket](https://bitbucket.org/sanbidev/combat-tb-explorer/src/master/) using the Download repository option
+
+

files/combine.py

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+#!/usr/bin/env python3
+
+import argparse
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Combine files and ensure that each file used terminates with a line break')
+    parser.add_argument('output_file', type=argparse.FileType('w'))
+    parser.add_argument('input_filenames', nargs='+')
+    args = parser.parse_args()
+    output = args.output_file
+    for filename in args.input_filenames:
+        text = open(filename).read()
+        if text[-1] != '\n':
+            text += '\n'
+        output.write(text)
+    output.close()

hosts

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+explorer.sanbi.ac.za ansible_user=ubuntu

playbook.yml

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+---
+- hosts: all
+  become: true
+  vars:
+    container_count: 4
+    default_container_name: docker
+    default_container_image: ubuntu
+    default_container_command: sleep 1
+  roles:
+    - docker
+    - role: explorer
+      tags:
+        - explorer

roles/docker/handlers/main.yml

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+- name: Restart Docker
+  service:
+    name: docker
+    state: restarted

roles/docker/tasks/main.yml

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+---
+- name: Install aptitude
+  ansible.builtin.apt:
+    name: aptitude
+    state: latest
+    update_cache: true
+
+- name: Install required system packages
+  ansible.builtin.apt:
+    pkg:
+      - apt-transport-https
+      - ca-certificates
+      - curl
+      - software-properties-common
+      - python3-pip
+      - virtualenv
+      - python3-setuptools
+    state: latest
+    update_cache: true
+
+- name: Add Docker GPG apt Key
+  ansible.builtin.apt_key:
+    url: https://download.docker.com/linux/ubuntu/gpg
+    state: present
+
+- name: Add Docker Repository
+  ansible.builtin.apt_repository:
+    repo: deb https://download.docker.com/linux/ubuntu jammy stable
+    state: present
+
+- name: Update apt and install docker-ce
+  ansible.builtin.apt:
+    name: docker-ce
+    state: latest
+    update_cache: true
+
+- name: Install Docker Module for Python
+  ansible.builtin.pip:
+    name: docker
+
+- name: Configure MTU for Docker
+  ansible.builtin.copy: 
+    dest: /etc/docker/daemon.json
+    owner: root
+    group: root
+    content: |
+      {
+        "mtu": {{docker_mtu|default("1450")}}
+      }
+  notify:
+    - Restart Docker
+
+- name: Add ansible_user to docker group
+  ansible.builtin.user:
+    name: '{{ ansible_user }}'
+    groups: docker
+    append: yes
+

roles/docker/vars/main.yml

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+docker_mtu: 1450

roles/explorer/tasks/main.yml

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+---
+- name: Install unzip
+  ansible.builtin.package:
+    name: unzip
+    state: present
+
+- name: Unpack Explorer code
+  ansible.builtin.unarchive:
+    copy: true
+    src: "{{explorer_src}}"
+    dest: "/home/{{ansible_user}}"
+    owner: "{{ansible_user}}"
+    creates: "/home/{{ansible_user}}/{{explorer_src|replace('.zip','')}}" 
+
+- name: Rename Explorer code
+  ansible.builtin.file:
+    src: "/home/{{ansible_user}}/{{explorer_src|replace('.zip', '')}}"
+    path: "/home/{{ansible_user}}/explorer_src"
+    state: link
+
+- name: Copy SSL cert in place
+  ansible.builtin.copy:
+    src: "{{item}}"
+    dest: "/home/{{ansible_user}}/explorer_src/docker-svc/nginx"
+  loop:
+    - SANBI_Wildcard.all.pem
+    - SANBI_Wildcard.key
+
+- name: Install jq
+  ansible.builtin.package:
+    name: jq
+    state: present
+
+- name: Save IP address
+  ansible.builtin.shell:
+    cmd: "ip --json a |jq -r '.[1]|.addr_info[0].local'"
+  register: host_ip
+
+- name: Fix hostname of explorer
+  ansible.builtin.lineinfile:
+    path: "/home/{{ansible_user}}/explorer_src/docker-compose-prod.yml"
+    line: "    extra_hosts: [\"explorer.sanbi.ac.za:{{host_ip.stdout_lines[0]}}\"]"
+    search_string: "    extra_hosts: [\"explorer.sanbi.ac.za"
+    state: present
+
+- name: Install docker-compose Python module
+  ansible.builtin.pip:
+    name: docker-compose
+    state: present
+
+- name: Start Explorer
+  community.docker.docker_compose:
+    project_src: "/home/{{ansible_user}}/explorer_src"
+    files:
+      - docker-compose-prod.yml
+    state: present
+
+- name: Install systemd unit for explorer
+  ansible.builtin.template:
+    src: docker-compose-app.service.j2
+    dest: /etc/systemd/system/docker-compose-app.service
+    owner: root
+    group: root
+    mode: 0644
+
+- name: Enable systemd unit for explorer
+  ansible.builtin.systemd: 
+    name: docker-compose-app
+    daemon_reload: true
+    enabled: true
+    state: started

roles/explorer/vars/main.yml

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+explorer_src: sanbidev-combat-tb-explorer-f53458ddf00a.zip

templates/docker-compose-app.service.j2

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+# /etc/systemd/system/docker-compose-app.service
+
+[Unit]
+Description=Docker Compose Application Service
+Requires=docker.service
+After=docker.service
+StartLimitIntervalSec=60
+
+[Service]
+WorkingDirectory=/home/{{ansible_user}}/explorer_src
+ExecStart=/usr/bin/docker compose up
+ExecStop=/usr/bin/docker compose down
+TimeoutStartSec=0
+Restart=on-failure
+StartLimitBurst=3
+
+[Install]
+WantedBy=multi-user.target