isamples_docker

Location to store resources needed to build iSamples Docker containers

Prerequisites

• Install docker https://docs.docker.com/engine/install/
• Configure a docker group and add your user to it https://docs.docker.com/engine/install/linux-postinstall/
• Install docker compose https://docs.docker.com/compose/install/ https://docs.docker.com/compose/cli-command/#installing-compose-v2
• Install git-lfs https://git-lfs.github.com

How to build container

First initialize the submodules so you have all the submodules pulled in correctly: git submodule init If you've already done that, make sure that you are up to date with all of the remote branches specified in .gitmodules: git submodule update --remote

Then cd up to the isb docker directory and initialize git lfs: cd .. git lfs install git lfs pull

Then cd back to the root: cd .. and run the docker build for the flavor you are interested in: docker-compose --env-file .env.opencontext -p isamples_docker_opencontext up --build

This should have brought up the containers

How to ping it to see if it's working

At this point, you should have a running iSamples in a Box container. You can manually open the docs and use the interactive UI by pinging: http://localhost:8000/docs. From there, you should be able to interactively hit the various API methods.

The Solr schema should have also been created -- check it at http://localhost:8983/solr/ and look for a collection called isb_core_records.

Manually run an import

• Find the iSB Docker container like this: docker ps
• Run bash in the iSB container like this: docker exec -it isamples_docker_isamples_inabox_1 bash
• Once inside bash, export PYTHONPATH to our container install directory (not quite sure why this is required) export PYTHONPATH=/app
• Run a db import: python scripts/opencontext_things.py --config ./isb.cfg load -m 1000
• Run a solr import once the db is done: python scripts/opencontext_things.py --config ./isb.cfg populate_isb_core_solr -m 1000

Import SQL dump into the db

• Dump the data from an existing source: pg_dump -U isb_writer -h localhost -d isb_1 > isamples.sql
• Copy the file into the container: docker ps -- get the name of the postgres container docker cp isamples.sql isamples_docker_db_1:/isamples.sql -- copy it into the container where isamples_docker_db_1 is the container name obtained from docker ps
• Run the import in the container: docker exec -it isamples_docker_db_1 bash -- open a shell psql --username=isb_writer --dbname=isb_1 -f ./isamples.sql

Manually control the containers with systemctl

• Create the service file at /etc/systemd/system/isb_opencontext.service

  [Unit]
  Description=Docker Compose iSB OpenContext Application Service
  Requires=docker.service
  After=docker.service
  
  [Service]
  Type=oneshot
  RemainAfterExit=yes
  WorkingDirectory=/home/isamples/isamples_inabox_opencontext/isamples_docker
  ExecStart=/usr/bin/docker compose --env-file .env.sesar -p isamples_docker_sesar up -d --build
  ExecStop=/usr/bin/docker compose -p isamples_docker_sesar down 
  TimeoutStartSec=0
  
  [Install]
  WantedBy=multi-user.target    
  

• Bring it up: sudo systemctl start isb_opencontext
• Shut it down: sudo systemctl stop isb_opencontext

Updating dependencies

Images are cached, so it is necessary to force a pull from the hub in order to get updates. This example updates solr to the latest:

sudo docker pull solr:latest

Then rebuild the container. The containers operated with systemd are removed on shutdown and built on startup. So after a new image is pulled, simply shutdown and start the service.

Information about an image can be found with:

sudo docker image history solr

React build output

The React build output is copied to the iSamples in a Box image and served from uvicorn at the /ui path. During development, it is helpful to run the React build by itself. You may do so like this:

docker build --target node_build .

This will create an image and you can grab the image id for the image by running docker image ls. After that you may run the image and open a shell by:

docker run image_id_
docker exec -it image_id bash

Inside the image, the build output will be located at /app/build -- you may copy that out of the image and open it in your favorite web browser if need be:

docker cp image_name:/app/build ~/Desktop/

Secrets

Docker secrets are configured using the Docker secrets feature: https://docs.docker.com/compose/compose-file/#secrets

There is a manual setup step where there needs to be a secrets directory created as a child of the docker checkout on the target machine. Currently, it is expected to contain two plaintext files called orcid_client_id and orcid_client_secret.

Setting up nginx

nginx can be configured as the front-end web server for the web serverice offered by the docker instance. These commands all require sudo.

Installation

Install nginx with:

apt update
apt dist-upgrade
apt install nginx
ufw allow "Nginx Full"

Install LetsEncrypt for certificate management:

apt install python3-certbot-nginx

Configure

Running certbot first puts in place some nginx configuration to support SSL:

certbot --nginx -d henry.cyverse.org -d isb.isample.xyz

The complete config for nginx is provided. The specific /location/ entries associate a path with the port advertised by the corresponding docker instance.

/etc/nginx/sites-enabled/default :

server {
    listen [::]:443 ssl ipv6only=on; # managed by Certbot
    listen 443 ssl; # managed by Certbot
    ssl_certificate /etc/letsencrypt/live/henry.cyverse.org/fullchain.pem; # managed by Certbot
    ssl_certificate_key /etc/letsencrypt/live/henry.cyverse.org/privkey.pem; # managed by Certbot
    include /etc/letsencrypt/options-ssl-nginx.conf; # managed by Certbot
    ssl_dhparam /etc/letsencrypt/ssl-dhparams.pem; # managed by Certbot

    root /var/www/html;
    location / {
            try_files $uri $uri/ =404;
    }

    location /opencontext/ {
        rewrite /opencontext/(.*)  /$1  break;
        proxy_set_header Host $host;
        proxy_set_header X-Real-IP $remote_addr;
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        proxy_set_header X-Forwarded-Proto $scheme;
        proxy_set_header X-Forwarded-Scheme $scheme;
        proxy_set_header X-Forwarded-Host $server_name;
        proxy_set_header Upgrade $http_upgrade;
        proxy_set_header Connection "Upgrade";
        proxy_redirect off;
        proxy_buffering off;
        proxy_http_version 1.1;
        proxy_pass http://localhost:9000;
    }

    location /geome/ {
        rewrite /geome/(.*)  /$1  break;
        proxy_set_header Host $host;
        proxy_set_header X-Real-IP $remote_addr;
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        proxy_set_header X-Forwarded-Proto $scheme;
        proxy_set_header X-Forwarded-Scheme $scheme;
        proxy_set_header X-Forwarded-Host $server_name;
        proxy_set_header Upgrade $http_upgrade;
        proxy_set_header Connection "Upgrade";
        proxy_redirect off;
        proxy_buffering off;
        proxy_http_version 1.1;
        proxy_pass http://localhost:10000;
    }
}
server {
    if ($host = isb.isample.xyz) {
        return 301 https://$host$request_uri;
    } # managed by Certbot

    if ($host = henry.cyverse.org) {
        return 301 https://$host$request_uri;
    } # managed by Certbot

        listen 80 ;
        listen [::]:80 ;
    server_name henry.cyverse.org isb.isample.xyz;
    return 404; # managed by Certbot
}

Miscellanea

Start / stop nginx:

sudo systemctl stop nginx

sudo systemctl start nginx

sudo systemctl restart nginx

Is something listening?

sudo netstat -tulpn

Is the firewall open?

sudo ufw status numbered

Renew a certificate (this should be automatic):

# test renewal with a dry run
sudo certbot renew --dry-run

# actual renewal
sudo certbot renew