manual-data-retrieval.md

These are some examples for manual downloads (just for reference). It is assumed that you already have the PEP-services Singularity image (instructions) and that you have the credentials set up (see readme).

Also see the PEP cli documentation for using the pepcli command.

Run an interactive shell in the pep-services Singularity container

singularity shell \
  -B ~/pepclient/config:/config:ro \
  -B ~/pepclient/secrets:/secrets:ro \
  -B ~/pepclient/working:/data \
  --pwd /data \
  pep-services.sif

Just for the record, the equivalent docker command is

docker run \
  --volume ~/pepclient/config:/config:ro \
  --volume ~/pepclient/secrets:/secrets:ro \
  --volume ~/pepclient/working:/data \
  -w /data \
  -it gitlabregistry.pep.cs.ru.nl/pep/core/prod/pep-services:latest bash

Execute pepcli

Make sure you are in /data (it needs to be a writable directory?) and execute any pepcli command with /app/pepcli

/app/pepcli \
  --client-working-directory /config \
  --oauth-token /secrets/oauth.json \
  query column-access > columns.txt

The downloaded data will be in the directory that you mounted at /data.

Execute pepcli without starting shell

singularity exec \
  -B ~/pepclient/config:/config:ro \
  -B ~/pepclient/secrets:/secrets:ro \
  -B ~/pepclient/working:/data \
  --pwd /data \
  pep-services.sif \
  /app/pepcli --client-working-directory /config --oauth-token /secrets/oauth.json query column-access > columns.txt