Specify project GN2

2 files changed, 205 insertions, 0 deletions

diff --git a/issues/gn-uploader/build-uploader-container-20240321.org b/issues/gn-uploader/build-uploader-container-20240321.org
new file mode 100644
index 0000000..d1086df
--- /dev/null
+++ b/issues/gn-uploader/build-uploader-container-20240321.org
@@ -0,0 +1,203 @@
+#+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 <module>
+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
diff --git a/issues/gn-uploader/gn-uploader-container-running-wrong-gn2.gmi b/issues/gn-uploader/gn-uploader-container-running-wrong-gn2.gmi
index c0562ad..fe372c9 100644
--- a/issues/gn-uploader/gn-uploader-container-running-wrong-gn2.gmi
+++ b/issues/gn-uploader/gn-uploader-container-running-wrong-gn2.gmi
@@ -27,3 +27,5 @@ However, when I look at the logs, it seems the container is instead running the
 ```
 
 instead, which seems to be stuck on an older commit without fixes for a circular import bug I'd fixed.
+
+=> ./issues/gn-uploader/build-uploader-container-20240321.org Troubleshooting log: 2024-03-21