From 4f3da9cddc6064d6fd4e60612ae7dd0d1f552602 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 5 Apr 2024 12:41:19 +0200
Subject: Fallback and debugging

---
 issues/systems/fallback-errors.gmi                 | 17 ++++++++--
 ...ping-code-with-genenetwork-system-container.gmi | 38 +++++++++++++++++++++-
 2 files changed, 52 insertions(+), 3 deletions(-)

diff --git a/issues/systems/fallback-errors.gmi b/issues/systems/fallback-errors.gmi
index 3c44e50..ed80c8e 100644
--- a/issues/systems/fallback-errors.gmi
+++ b/issues/systems/fallback-errors.gmi
@@ -18,7 +18,8 @@ Note that some issues may be related to production (i.e. the same). Note also I
 
 * [X] 502 timeout errors
 * [X] Rqtl2 not working
-* [ ] 413 error
+* [X] 413 error
+* [ ] BNW error
 * [ ] Monitor service - both systemd and sheepdog
 * [ ] Files in /tmp
 
@@ -174,12 +175,14 @@ has links to
 
 We can't use those because the SHA may change. So we have to host a local copy. That is fine.
 
-## 413 Request Entity Too Large
+## 413 Request Entity Too Large (fixed)
 
 On mapping from
 
 => https://fallback.genenetwork.org/show_trait?trait_id=10002&dataset=HET3-ITPPublish
 
+This resolved itself - probably a permission issue.
+
 ## Files generated in /tmp (later)
 
 Not unique file names appearing in TMPDIR:
@@ -211,3 +214,13 @@ The following button does not display:
 ```
 
 it is part of font-awesome and apparently not loaded properly. Actually the stylesheet is loaded twice(!) in mapping_results.html AND we use two different class names (fas and fa). Changing the class name fixed it.
+
+# BNW gives a jquery error
+
+This is probably a jquery update is causing
+
+```
+Uncaught TypeError: data1.join is not a function
+    <anonymous> https://bnw.genenetwork.org/sourcecodes/layout_cyto.php?My_key=jFv:102
+    jQuery 4
+```
diff --git a/topics/systems/debug-and-developing-code-with-genenetwork-system-container.gmi b/topics/systems/debug-and-developing-code-with-genenetwork-system-container.gmi
index 2e3a83c..131474c 100644
--- a/topics/systems/debug-and-developing-code-with-genenetwork-system-container.gmi
+++ b/topics/systems/debug-and-developing-code-with-genenetwork-system-container.gmi
@@ -226,4 +226,40 @@ Now we can use guix bioinformatics with
 
 and it should show the genenetwork stack. Now you can build a machine using -L. See for example:
 
-=> gndev-deploy
+=> https://git.genenetwork.org/gn-machines/tree/specials/gndev-deploy.sh
+
+# Scripts
+
+## Get a login on the VM
+
+e.g. guix-vm-login $pid
+
+```
+guix-vm-login:
+  #! /bin/bash
+  echo "Login to guix container"
+  pid=$1
+  shift
+  cmd="nsenter -at $pid /run/current-system/profile/bin/bash --login $*"
+  echo $cmd
+  $cmd
+```
+
+e.g. guix-vm-run $pid tail -f /var/log/gunicorn-genenetwork3.log
+
+```
+guix-vm-run:
+  #! /bin/bash
+  echo "Login to guix container"
+  pid=$1
+  shift
+  cmd="nsenter -at $pid /run/current-system/profile/bin/$*"
+  echo $cmd
+  $cmd
+```
+
+# Troubleshooting
+
+## Updating the VM does not show latest fixes
+
+It may be another service is using the port(s) of your VM. Check /var/log/gunicorn-$name.log. Another possibility is that you are checking the wrong URL - both things happened to me ;)
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