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Diffstat (limited to 'topics/ci-cd')
| -rw-r--r-- | topics/ci-cd/utility-scripts.gmi | 63 |
1 files changed, 63 insertions, 0 deletions
diff --git a/topics/ci-cd/utility-scripts.gmi b/topics/ci-cd/utility-scripts.gmi new file mode 100644 index 0000000..fb95526 --- /dev/null +++ b/topics/ci-cd/utility-scripts.gmi @@ -0,0 +1,63 @@ +# Utility Scripts + +Sometimes we need to run some utility scripts manually to set up certain things that do not render themselves to automation very well. + +This is especially relevant for any script that might need to interact with the SQLite database. + +This document notes some gotchas that you might run into trying to run +=> ./topics/authentication/cli_utility_scripts the utility scripts. + +## Register System Administrator + +Start by getting a shell into the CI/CD container: + +``` +sudo guix container exec <PID> /run/current-system/profile/bin/bash --login +``` + +replacing =<PID>= with the process ID of the container. + +Now stop GN3: + +``` +herd stop genenetwork3 +``` + +In a separate terminal on the *host* system, change the owner of the directory +and file: +``` +sudo chown -R fredm /export/data/genenetwork-sqlite +``` + +Now start a guix shell in the *genenetwork3* repository (on the host) and run +the utility script(s) you need to run: + +``` +$ cd /home/fredm/genenetwork3 +$ guix shell --container --network --share=/export/data/genenetwork-sqlite \ + --development --file=guix.scm +[env] $ python3 -m scripts.register_sys_admin \ + /export/data/genenetwork-sqlite/auth.db +``` + +Once you have run (all) the utility script(s) you needed to run, you can exit +the shell and restore the file user: +``` +sudo chown -R guixbuilder13 /export/data/genenetwork-sqlite +``` + +now go back to the CI/CD container shell and restart genenetwork3: +``` +herd start genenetwork3 +``` +then exit the shell. + +### Failed Attempts + +Tried +``` +mount --bind -o rw,umask=0002,gid=1000,uid=1000 \ + /home/frederick/genenetwork/local-ci-cd/data/genenetwork-sqlite \ + /home/frederick/genenetwork/ci-cd-container-dirs +``` +but the file (and mount target) retain the original permissions. |