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Add a new instrument

Each instrument is identified by a unique <INSTRUMENT_ID>, which should be lowercase and contain only letters and numbers but is otherwise arbitrary (e.g. "newinst1"). Note that some parts of the system rely on convention, so make sure to use exactly <INSTRUMENT_ID> (case-sensitive!) in the below steps.

  1. On the instrument, create a folder named Backup (capital B!) in the folder where the acquired files are saved.

  2. Add the following block to the end of the instruments section in envs/alphakraken.${ENV}.yaml (mind the correct indentation!):

   <INSTRUMENT_ID>:
    type: <INSTRUMENT_TYPE>
    username: <username for instrument>
    mount_src: //<ip address of instrument>/<INSTRUMENT_ID>
    mount_target: instruments/<INSTRUMENT_ID>

Here, <INSTRUMENT_TYPE> is one of the keys defined in the InstrumentKeys class (thermo, bruker, sciex) and determines what output is expected from the instrument: thermo -> one .raw file, bruker -> one .d folder, sciex -> one .wiff file plus more files with the same stem.

  1. In docker-compose.yaml, add a new worker service, by copying an existing one and adapting it like:
  airflow-worker-<INSTRUMENT_ID>:
    <<: *airflow-worker
    command: celery worker -q kraken_queue_<INSTRUMENT_ID>
    # there might be additional keys here, just copy them
    volumes:
      - ${MOUNTS_PATH:?error}/airflow_logs:/opt/airflow/logs:rw
      - ${MOUNTS_PATH:?error}/output:/opt/airflow/mounts/output:ro
      - ${MOUNTS_PATH:?error}/instruments/<INSTRUMENT_ID>:/opt/airflow/mounts/instruments/<INSTRUMENT_ID>:ro
      - ${MOUNTS_PATH:?error}/backup/<INSTRUMENT_ID>:/opt/airflow/mounts/backup/<INSTRUMENT_ID>:rw

Make sure to replace each instance of <INSTRUMENT_ID> with the correct instrument ID and to not accidentally drop the ro and rw flags as they limit file access rights.

  1. Transfer the changes in 2. and 3. to all AlphaKraken PCs/VMs.

  2. On the PC hosting the workers execute

./mount.sh <INSTRUMENT_ID> mount

to mount the instrument folder. If you want to create a persistent mount, additionally use

./mount.sh <INSTRUMENT_ID> fstab

and copy the resulting entry to /etc/fstab and set the correct password.

  1. Start the new container
./compose.sh up airflow-worker-<INSTRUMENT_ID> -d

  1. Restart all relevant infrastructure containers (scheduler, file_mover and file_remover) with the --build flag.

  2. Open the airflow UI and unpause the new *.<INSTRUMENT_ID> DAGs. It might be wise to do this one after another, (instrument_watcher -> acquisition_handler -> acquisition_processor.) and to check the logs for errors before starting the next one.