From 13919b0b61ca7c7204222a988673929a96fd52db Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sun, 3 Dec 2023 09:48:09 -0600 Subject: Rename --- topics/CI-CD/utility-scripts.gmi | 63 ---------------------------------------- topics/ci-cd/utility-scripts.gmi | 63 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 63 insertions(+), 63 deletions(-) delete mode 100644 topics/CI-CD/utility-scripts.gmi create mode 100644 topics/ci-cd/utility-scripts.gmi diff --git a/topics/CI-CD/utility-scripts.gmi b/topics/CI-CD/utility-scripts.gmi deleted file mode 100644 index fb95526..0000000 --- a/topics/CI-CD/utility-scripts.gmi +++ /dev/null @@ -1,63 +0,0 @@ -# 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 /run/current-system/profile/bin/bash --login -``` - -replacing == 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. 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 /run/current-system/profile/bin/bash --login +``` + +replacing == 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. -- cgit v1.2.3