diff options
| -rw-r--r-- | issues/systems/fallback-errors.gmi | 17 | ||||
| -rw-r--r-- | topics/systems/debug-and-developing-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 ;) |