Create a Debug Workflow Node

We went to create a “debug” workflow node with the same environment as any other Biokepi node and connect to it to be able to experiment/troubleshoot commands.

When Secotrec/Ketrew/OCaml Are Available

See one of the commands (depending on your setup):

secotrec-local deploy-debug-node --help
secotrec-gke deploy-debug-node --help
secotrec-aws deploy-debug-node --help

For the GKE setup see the screenshot in the PR hammerlab/secotrec#74.

While “Running-Local”

For the setup as in the “running-local” tutorial, the above commands do not work because secotrec-local is fetched without its corresponding opam/ketrew environment:

secotrec-local deploy-debug-node

gives

/tmp/run-genspiof73f45-cmd.sh: line 5: ketrew: command not found
sh: 1: ocaml: not found

So, let's configure the “launch environment” as in the tutorial:

secotrec-local biokepi-machine $epidisco_dev/biokepi_machine.ml
secotrec-local docker-compose -- exec epidisco-dev opam config exec bash
ketrew init --just-client http://kserver:8080/gui?token=dsleaijdej308098ddecja9c8jra8cjrf98r

And use this workflow script instead (cf. also this gist):

curl -L -o debug-workflow.ml \
  https://gist.github.com/smondet/731e8cc0ee61e09ff02d3723f5e388e8/raw/19a9641a1d22d473d8bca41ca1745abf9f29429a/wobi-local-deploy-debug.ml

And start the workflow:

ocaml debug-workflow.ml

Grab the ID of the container from the Ketrew UI:

Or using the TextUI from inside the container:

Then you need to exit the launch-countainer:

exit

you can now use the container ID to “join” the workflow-node:

docker exec -it 'f0fe431d-4874-5220-bbbe-8e789ea8bd67' bash

And you are now in a container, see:

 $ whoami
biokepi
 $ java -version
java version "1.8.0_131"
Java(TM) SE Runtime Environment (build 1.8.0_131-b11)
Java HotSpot(TM) 64-Bit Server VM (build 25.131-b11, mixed mode)