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wattos

Archival copy of the restraints-grid servlet code by Jurgen Doreleijers, plus a Docker Compose deployment of the NMR Restraints Grid (NRG) servlet that fronts it.

  • wattos_orig.tar.gz — original SVN checkout from Google Code
  • wattos/ — Java source tree (Ant-based), plus the exploded webapp under wattos/NRG/ that Tomcat serves directly. Compiled classes and runtime jars under NRG/WEB-INF/ are tracked in git, so a fresh checkout starts up without a build step.
  • initdb/ — SQL bootstrap scripts run on first MySQL startup (01_createdb.sql + wattos_load.sql)
  • dbfs/ — block files and seed CSVs bind-mounted into the DB
  • tomcat/ — Tomcat server.xml mounted into the Tomcat container
  • mysql/ — legacy pre-compose deployment artefacts (no longer used)
  • scripts/rebuild.sh — incremental single-file Java rebuild for quick edits (Ant alternative for one-off changes)

wattos

Wattos was originally on Google Code; its commit history was lost when Google Code shut down. It was imported into git from a local working copy in 2019, a decade after it was written.

Quick start (fresh checkout)

You don't need a JDK or Ant locally — the deployed webapp ships with its compiled classes and runtime jars under wattos/NRG/WEB-INF/. Docker is the only prerequisite.

git clone <this repo>
cd wattos                     # the deployment root (contains docker-compose.yml)
docker compose up -d          # starts wattos-mysql and wattos-tomcat
                              # initdb seeds the DB on first start (~30s)

# Smoke test:
curl -s -o /dev/null -w '%{http_code}\n' \
    http://127.0.0.1:8080/NRG/MRGridServlet
# → 200

That's it. The landing page is at http://127.0.0.1:8080/NRG/MRGridServlet and works straight out of git because NRG/WEB-INF/classes/Wattos/**/*.class and NRG/WEB-INF/lib/*.jar are checked in. For local-path dev (rather than the production paths the docker-compose.yml defaults point at), copy .env.example to .env and set the bind-mount vars — see Configuration below.

Running with Docker Compose

docker compose up -d brings up two containers on a wattos-network bridge:

  • wattos-mysql — mysql:8 (8.4 LTS). On first start it runs everything in initdb/ (schema + data load); subsequent starts reuse the named volume wattos_mysql-data. The MySQL 5.7 query cache is gone in 8.0+, so warm-page caching now happens application-side (see Tomcat below).
  • wattos-tomcat — tomcat:11-jdk21-temurin (Tomcat 11 on Temurin JDK 21). The exploded webapp at wattos/NRG/ is bind-mounted into the container as /usr/local/tomcat/webapps/NRG/, so jar and class changes show up as ordinary git diffs. Only port 8080 is published, on 127.0.0.1. JVM heap is set to -Xmx768m to leave room for the in-process response cache (256 MB Caffeine LRU in MRGridServlet, replacing the old MySQL query cache — landing page goes from ~2.5s cold to ~2 ms warm).

Configuration

Bind-mount sources and the mysql user: are parameterised via ${VAR:-default} in docker-compose.yml. Defaults are the production absolute paths under /projects/BMRB/public/wattos/..., so the live server keeps working with no .env file.

For local development, copy .env.example to .env (gitignored) and set INITDB_DIR, DBFS_DIR, HTML_DIR, RUNTIME_PROPS, NRG_DIR, PDB_DIR, MYSQL_USER to match your checkout.

Common operations

# Bring everything up (or apply compose changes after a git pull)
docker compose up -d

# Restart just Tomcat (e.g. after rebuilding Java sources)
docker compose restart wattos-tomcat

# Wipe the DB volume and re-run initdb (~30s on prod hardware)
docker compose down -v && docker compose up -d

# Smoke test the servlet
curl -s -o /dev/null -w '%{http_code}\n' \
    http://127.0.0.1:8080/NRG/MRGridServlet

The servlet's only mapping is Wattos.Servlet.MRGridServlet → /MRGridServlet (see wattos/NRG/WEB-INF/web.xml).

Rebuilding after Java source changes

You need a JDK (≥17) and Ant only when modifying .java sources. Two flows, both writing back into wattos/NRG/WEB-INF/classes/ so a Tomcat restart picks up the new bytecode:

Ant (recommended for clean rebuilds of the servlet): the build file lives one level down from the deployment root, in the Java project dir:

cd wattos                        # the inner wattos/ — sibling to docker-compose.yml
ant -f buildEclipse.xml          # default install-servlet — compile +
                                 # copy classes into NRG/WEB-INF/classes/
cd ..                            # back to deployment root
docker compose restart wattos-tomcat

install-servlet compiles the servlet closure (Wattos/{Servlet,Episode_II,Database,Common,Utils,Star,Soup}/) against the runtime jars already in NRG/WEB-INF/lib/ and the servlet-api.jar inside the running Tomcat container (auto-cached at /tmp/wattos-servlet-api.jar). No internet access needed for this target. Other useful targets:

  • ant compile-servlet — just build/Wattos/, no copy step
  • ant jar-servlet — package lib/Wattos.jar from the closure
  • ant clean-servlet — wipe build/

scripts/rebuild.sh (faster for one-file edits): run from the deployment root,

./scripts/rebuild.sh wattos/src/Wattos/Servlet/MRGridServlet.java
./scripts/rebuild.sh wattos/src/Wattos/Episode_II/SQL_*.java
docker compose restart wattos-tomcat

Same classpath as ant install-servlet, but compiles only the named files instead of the whole closure. Skips the rest, which is faster for single-source iteration.

Full-tree build (CLI + servlet, including the Swing GUI bits): from the inner wattos/ (same as Ant above),

ant -f buildEclipse.xml jar      # auto-runs fetch-deps if lib/ is empty
ant -f buildEclipse.xml test     # runs the JUnit suite

fetch-deps populates wattos/lib/ by mirroring NRG/WEB-INF/lib/*.jar and pulling the build-time-only deps (itext, jfreechart, swing-layout, junit, hamcrest, …) from Maven Central; the downloads are gitignored. Currently 24/33 tests pass — the 9 failures are pre-existing data / network rot, not infrastructure.

Both jar and class files under NRG/WEB-INF/ are tracked in git, so any rebuild shows up as an ordinary diff.

Reverse proxy

nginx fronts the container with stock proxy_pass:

location /NRG/ {
    proxy_pass http://127.0.0.1:8080/NRG/;
}

AJP is no longer used (the connector was removed when the unmaintained nginx_ajp_module was retired). If AJP ever needs to come back, add a <Connector protocol="AJP/1.3" .../> to tomcat/server.xml with a secret="..." attribute (Tomcat 9.0.31+ rejects AJP without one).

For an Apache front-end, the equivalent is:

<Proxy *>
    Require all granted
</Proxy>

ProxyPass        /NRG/ http://127.0.0.1:8080/NRG/
ProxyPassReverse /NRG/ http://127.0.0.1:8080/NRG/

RedirectMatch permanent ^/$        /NRG/MRGridServlet
RedirectMatch permanent ^/NRG(/*)$ /NRG/MRGridServlet

Volumes / bind mounts

DB filesystem (mounted at /wattos/ in both containers):

  • dbfs/bfiles/ — block files served by the servlet
  • dbfs/entry.csv, mrblock.csv, mrfile.csv — seed data loaded by initdb/wattos_load.sql on first DB start
  • html/molgrap/ — molecular-graphics images

Servlet-only:

  • /pdb/data/structures — wwPDB structures archive (point at any directory if you don't have a local mirror)

Paths are still hardcoded in the SQL scripts and in wattos.runtime.properties* (/wattos/dbfs, /pdb/data/structures, /wattos/html/molgrap/...), so the bind-mount targets above are not freely renameable.