#+STARTUP: content #+TITLE: Building Uploader Container (2024-03-21) #+AUTHOR: Frederick Muriuki Muriithi #+OPTIONS: ^:{} * Log Fix the [[https://git.genenetwork.org/gn-uploader/commit/?id=3958ce457f621f1b75fa8843ba859d8e6015a6c7][channel introduction documentation]] on =gn-uploader= On =tux02= do: #+BEGIN_SRC shell $ guix pull -p ~/opt/guix -C channels.scm #+END_SRC where =channels.scm= has the following content #+BEGIN_SRC scheme (list (channel (name 'guix-bioinformatics) (url "https://git.genenetwork.org/guix-bioinformatics/") (branch "master")) (channel (name 'guix-forge) (url "https://git.systemreboot.net/guix-forge/") (branch "main") (introduction (make-channel-introduction "0432e37b20dd678a02efee21adf0b9525a670310" (openpgp-fingerprint "7F73 0343 F2F0 9F3C 77BF 79D3 2E25 EE8B 6180 2BB3")))) (channel (name 'guix-past) (url "https://gitlab.inria.fr/guix-hpc/guix-past") (introduction (make-channel-introduction "0c119db2ea86a389769f4d2b9c6f5c41c027e336" (openpgp-fingerprint "3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5")))) (channel (name 'gn-auth) (url "https://git.genenetwork.org/gn-auth") (branch "main")) (channel (name 'gn-uploader) (url "https://git.genenetwork.org/gn-uploader") (branch "main") (introduction (make-channel-introduction "93c77842315d304abbfc27d78d98b7d42da32a61" (openpgp-fingerprint "F370 F409 854B 90E3 52F3 AB01 362B 0BB8 B81D 5A42"))))) #+END_SRC Pull was successful! After that, we get the following on =tux02=: #+BEGIN_SRC shell $ ~/opt/guix/bin/guix describe --format=channels hint: Consider installing the `glibc-locales' package and defining `GUIX_LOCPATH', along these lines: guix install glibc-locales export GUIX_LOCPATH="$HOME/.guix-profile/lib/locale" See the "Application Setup" section in the manual, for more info. (list (channel (name 'gn-uploader) (url "https://git.genenetwork.org/gn-uploader") (branch "main") (commit "3958ce457f621f1b75fa8843ba859d8e6015a6c7") (introduction (make-channel-introduction "93c77842315d304abbfc27d78d98b7d42da32a61" (openpgp-fingerprint "F370 F409 854B 90E3 52F3 AB01 362B 0BB8 B81D 5A42")))) (channel (name 'gn-auth) (url "https://git.genenetwork.org/gn-auth") (branch "main") (commit "ade6c76208bd45c24cdd0e73bf3570e6a2bfa131")) (channel (name 'guix-forge) (url "https://git.systemreboot.net/guix-forge/") (branch "main") (commit "6c622a67051c22eeefe37eedb17d427fbb70c99b") (introduction (make-channel-introduction "0432e37b20dd678a02efee21adf0b9525a670310" (openpgp-fingerprint "7F73 0343 F2F0 9F3C 77BF 79D3 2E25 EE8B 6180 2BB3")))) (channel (name 'guix-bioinformatics) (url "https://git.genenetwork.org/guix-bioinformatics/") (branch "master") (commit "2fdbf2445e5293ba9a12b154c58774e73dfeabe5")) (channel (name 'guix) (url "https://git.savannah.gnu.org/git/guix.git") (branch "master") (commit "b0b988c41c9e0e591274495a1b2d6f27fcdae15a") (introduction (make-channel-introduction "9edb3f66fd807b096b48283debdcddccfea34bad" (openpgp-fingerprint "BBB0 2DDF 2CEA F6A8 0D1D E643 A2A0 6DF2 A33A 54FA")))) (channel (name 'guix-past) (url "https://gitlab.inria.fr/guix-hpc/guix-past") (branch "master") (commit "921f845dc0dec9f052dcda479a15e787f9fd5b0a") (introduction (make-channel-introduction "0c119db2ea86a389769f4d2b9c6f5c41c027e336" (openpgp-fingerprint "3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5"))))) #+END_SRC Now, build the container: #+BEGIN_SRC shell env PATH="/home/fredm/opt/guix/bin:${PATH}" ./uploader-deploy.sh ︙ successfully built /gnu/store/0fwp30li4ngfmradkiyc81cdmapm04bf-gn-uploader-0.0.1-a4ed5d82.drv ︙ /gnu/store/4rfwx4d376kbql9y31cfldf3prcfrvx2-run-container ︙ #+END_SRC Restart the container #+BEGIN_SRC shell $ sudo systemctl stop genenetwork-uploader-container.service $ sudo systemctl start genenetwork-uploader-container.service $ sudo systemctl status genenetwork-uploader-container.service #+END_SRC Check logs in =/export2/guix-containers/genenetwork/uploader/var/log/gunicorn-genenetwork2.log= Still getting: #+BEGIN_EXAMPLE ︙ 2024-03-21 02:18:29 from gn2.wqflask.oauth2.checks import user_logged_in 2024-03-21 02:18:29 File "/gnu/store/2qhgkf5j649kv57nw4lzsbwlnb1790vq-profile/lib/python3.10/site-packages/gn2/wqflask/oauth2/checks.py", line 10, i n 2024-03-21 02:18:29 from .client import authserver_uri, oauth2_clientid, oauth2_clientsecret 2024-03-21 02:18:29 ImportError: cannot import name 'authserver_uri' from partially initialized module 'gn2.wqflask.oauth2.client' (most likely due to a circular import) (/gnu/store/2qhgkf5j649kv57nw4lzsbwlnb1790vq-profile/lib/python3.10/site-packages/gn2/wqflask/oauth2/client.py) 2024-03-21 02:18:29 [2024-03-21 02:18:29 +0000] [9] [INFO] Worker exiting (pid: 9) ︙ #+END_EXAMPLE When we verify where this comes from: #+BEGIN_SRC shell $ ls -l /gnu/store/2qhgkf5j649kv57nw4lzsbwlnb1790vq-profile/lib/python3.10/site-packages/ | grep gn2 lrwxrwxrwx 1 root root 104 Dec 31 1969 gn2 -> /gnu/store/vfa2zdla7ixbb2l5i7k6xnlh5d1rshz9-genenetwork2-3.11-4.1e81c74/lib/python3.10/site-packages/gn2 #+END_SRC We see that the code being run is from [[https://github.com/genenetwork/genenetwork2/commit/1e81c74ee8752ad2913b4e610ba7575638755385][GeneNetwork2: commit 1e81c74]] from 05^{th} March 2024. In [[https://git.genenetwork.org/guix-bioinformatics/tree/gn/packages/genenetwork.scm?id=2fdbf2445e5293ba9a12b154c58774e73dfeabe5#n190][=guix-bioinformatics=, however]], we have specified a newer [[https://github.com/genenetwork/genenetwork2/commit/b9e04ad79e0039edba25d58f8bc03e4d2a17583b][commit b9e04ad7]] from 07^{th} March 2024. Stop uploader service and delete logs: #+BEGIN_SRC shell $ sudo systemctl stop genenetwork-uploader-container.service $ sudo rm -fv /export2/guix-containers/genenetwork/uploader/var/log/gunicorn-g* removed '/export2/guix-containers/genenetwork/uploader/var/log/gunicorn-genenetwork2.log' removed '/export2/guix-containers/genenetwork/uploader/var/log/gunicorn-genenetwork3.log' removed '/export2/guix-containers/genenetwork/uploader/var/log/gunicorn-gn-auth.log' removed '/export2/guix-containers/genenetwork/uploader/var/log/gunicorn-gn-uploader.log' $ ls /export2/guix-containers/genenetwork/uploader/var/log/ debug gunicorn-genenetwork2.log mcron.log messages mysqld.log nscd.log secure.1.gz wtmp guix-daemon.log maillog mcron.log.1.gz messages.1.gz nginx secure virtuoso.log #+END_SRC The file =/export2/guix-containers/genenetwork/uploader/var/log/gunicorn-genenetwork2.log= is still showing up. Stop all containers for good measure: #+BEGIN_SRC shell $ sudo systemctl stop genenetwork-uploader-container.service $ sudo systemctl stop genenetwork-container.service $ sudo systemctl stop genenetwork-development-container.service $ sudo rm -fv /export2/guix-containers/genenetwork/uploader/var/log/gunicorn-g* removed '/export2/guix-containers/genenetwork/uploader/var/log/gunicorn-genenetwork2.log' $ ls /export2/guix-containers/genenetwork/uploader/var/log/ debug gunicorn-genenetwork2.log mcron.log messages mysqld.log nscd.log secure.1.gz wtmp guix-daemon.log maillog mcron.log.1.gz messages.1.gz nginx secure virtuoso.log #+END_SRC The file =/export2/guix-containers/genenetwork/uploader/var/log/gunicorn-genenetwork2.log= is still showing up. Something else is running and recreating the file and I have no idea what it is. Restart all containers: #+BEGIN_SRC shell $ sudo systemctl start genenetwork-uploader-container.service $ sudo systemctl start genenetwork-container.service $ sudo systemctl start genenetwork-development-container.service #+END_SRC