papyri-docker

Dockerized papyri.info stack.

Clone with:

git clone --recurse-submodules https://github.com/dcthree/papyri-docker

Running

First, you need to obtain a GitHub Personal Access Token with package registry permissions (see "Creating a personal access token"), and set it as the environment variable GITHUB_TOKEN for the docker compose process. You'll also need to set the environment variable GITHUB_USERNAME to your GitHub username. There are a variety of ways you can set these environment variables, including using an unversioned .env file in the directory where you've cloned this repository. These environment variables must be available for the navigator container to successfully build packages.

Then, from this repository's directory:

1. docker compose build
2. docker compose up -d
3. Watch logs in a separate terminal in the same directory: docker compose logs -f -t
4. If all is successful, you should be able to access the running copy once httpd comes up at: http://127.0.0.1:8000

Gotchas

• Disk Space: after bringing up a complete stack, my docker system df shows 40GB of images, 1GB of containers, and 26GB of volumes (67GB total). You may need to increase the default disk allocation if you're running e.g. Docker for Mac.
• Network Port: if another service is already bound to port 8000, httpd will fail to come up. If this happens, you can just stop the other service and run docker compose up -d again.
• Memory: I have 16GB of RAM, 1GB of swap, and 6 VCPUs allocated to Docker. Bringing this up makes my system quite slow...
• Exeption Logging: to see full Rails logs from the sosol container in Docker logs, set RAILS_LOG_TO_STDOUT=true
• Initial Indexing: if something goes wrong with the indexing process, you may need to use docker compose up -d --force-recreate when re-trying.
• Docker Compose Timeout: the default Docker Compose HTTP timeout of 60 seconds can sometimes cause problems with docker compose up/docker compose stop, due to the delay in responsiveness of some services. If you run into this, prefix the commands with e.g. COMPOSE_HTTP_TIMEOUT=10000.
• GitHub Maven Package Registry Auth: if you get a 401 Unauthorized error from trying to build dispatch.war or sync.war when you run docker compose up navigator, you may have an invalid GitHub Personal Access Token (basic) due to token expiration or invalid scope. Try using a new token following the instructions above.
• Want to start over from scratch?: run docker compose down -v.

Structure

• httpd: Apache 2.2 server, proxies the Navigator, Editor, XSugar, and Fuseki
  • indexer: container that runs the indexing process using the below services
    • navigator: the main "Papyrological Navigator" server
    • fuseki: Apache Jena Fuseki 1.x SPARQL Server (aka "Numbers Server")
    • tomcat-pn: Tomcat server runing "dispatch" and "sync" servlets
    • solr: Tomcat server running Apache Solr for search
  • sosol: Puma server serving the Rails Editor (aka "SoSOL") application
    • xsugar: container that runs XSugar, an XML transformer used by sosol
  • postgres: PostgreSQL 13 server, shared by sosol, and tomcat-pn
  • repo_clone: shared Git checkout of the large main idp.data repository, shared by navigator, fuseki, tomcat-pn, sosol, & httpd

The papyri.info "Top Level Data Flow" diagram may help with understanding:

Service Startup Order

Services get started in the following order:

• ppostgres: no service/startup dependencies
• fuseki: no service/startup dependencies
• xsugar: no service/startup dependencies
• repo_clone: no service/startup dependencies, clones canonical
• navigator: once canonical is cloned and fuseki is up, sets config for solr, builds WAR files for tomcat-pn, runs "mapping" which loads data into fuseki
• solr: once solr config (/opt/solr/server/solr/solr.xml.lock) is in place, written by navigator
• indexer: once fuseki and solr are up and mapping is done, runs "indexing" which loads data into solr
• tomcat-pn: once WAR files are built by navigator and "mapping" is done
• sosol: once canonical is cloned and mysql is available, though some functionality depends on fuseki (as well as "mapping" from navigator) and xsugar
• httpd: once /srv/data/papyri.info/git/navigator/pn-config/pi.conf is in place and the proxied services sosol, xsugar, tomcat-pn, fuseki, and solr are available, Apache is started up as httpd

Service startup order is important, and the current docker-compose.yml uses several strategies to control it:

1. wait-for-it.sh used to wait for network service availability; indexer uses it to wait for solr startup, sosol uses it to wait for mysql startup
2. lockfiles on shared volumes are used to enforce processes that only need to run once only running once; these lockfiles are also sometimes used as a wait signal for containers that need the process to finish before they can run (these busy-wait until the lockfile exists)

Some containers also use links and depends_on clauses, but these are no longer relied upon to enforce startup order.

Servers vs. Processes

You may note that we have some containers which run as continuous servers, and others which are containerized processes for building artifacts needed by those servers. Categorizing them may be useful:

Servers:

• http
• fuseki
• solr
• sosol
• tomcat-pn
• mysql
• xsugar

Processes:

• repo_clone
• navigator
• indexer