Rock 2/Opal 5 Docker Installation missing dsBase

Support Developer support
1

Hi,

Recently we have tried upgrading to the lovely Opal 5. We created a docker-compose.yml file just like Opal 4.

The installation succeeded, but unfortunately I soon discovered that dsBase was not installed on Rock. resourcer succeeded, just for the record. :slight_smile:

services:
  opal:
    image: obiba/opal:5.1.2
    ports:
      - "8880:8080"
    depends_on:
      - rock
      - mongo
      - mysqldata
    environment:
      #- JAVA_OPTS=-Xms1G -Xmx8G -XX:+UseG1GC
      - OPAL_ADMINISTRATOR_PASSWORD=REDACTED
      - MONGO_HOST=mongo
      - MONGO_PORT=27017
      - MYSQLDATA_HOST=mysqldata
      - MYSQLDATA_DATABASE=dts_db
      - MYSQLDATA_USER=dts_dm
      - MYSQLDATA_PASSWORD=REDACTED
      - ROCK_HOSTS=rock:8085
    volumes:
      - /some/path/opal:/srv
  mongo:
    image: mongo:6.0
  mysqldata:
    image: mysql
    environment:
      - MYSQL_DATABASE=dts_db
      - MYSQL_USER=dts_db
      - MYSQL_PASSWORD=REDACTED
      - MYSQL_RANDOM_ROOT_PASSWORD=yes
  rock:
    image: obiba/rock:2

I also chatted with @swheater during today’s DataSHIELD drop-in. it’s hard to determine the root cause on this one, but I have also had it repeat with 2 other colleagues so there is some issue here.

2

I am getting the error message:

Connecting to localhost (localhost)|127.0.0.1|:8443… connected. ERROR: cannot verify localhost’s certificate, issued by ‘C=,ST=,L=,O=localhost,OU=Opal,CN=localhost’: Self-signed certificate encountered.

Investigating… Stuart

3

Hi,

The obiba/rock image does not contain dsBase. Use datashield/rock-base instead (which is based on obiba/rock).

Regards
Yannick

1 Like
4

I see. Then is it maybe a good idea to update the Opal Installation Documentation (and elsewhere) which suggest obiba/rock instead?

5

If you can specify the packages you would require I can create (and test) a profile, like “margin-gypsum”

1 Like
6

@yannick @swheater this docker convention is a bit new to me, actually. I know about profiles but I thought they were only for the demo site. It’s great news if we can install based on specific needs.

So for any given DataSHIELD/Rock profile, should the name be added as a suffix to the rock image? i.e. https://hub.docker.com/r/datashield/rock-margin-gypsum for margin-gypsum Profile | DataSHIELD Community Wiki ?

7

The current name scheme for packages are make to two parts: platform (for example: lemon, margin, …) which indicates version of R, Rock, Bioconductor, …, and "packages (for example, xenon, donkey) which indicates the analysis packages, and versions it contains. Stuart

1 Like