From 1ef47f9a42a00a6edb038c9595902a7c091796a9 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 5 Apr 2024 10:13:40 +0200
Subject: Fallback and debugging
---
issues/systems/fallback-errors.gmi | 57 +++++++++++++++++++++++++++++++-------
1 file changed, 47 insertions(+), 10 deletions(-)
(limited to 'issues/systems')
diff --git a/issues/systems/fallback-errors.gmi b/issues/systems/fallback-errors.gmi
index e0111de..3c44e50 100644
--- a/issues/systems/fallback-errors.gmi
+++ b/issues/systems/fallback-errors.gmi
@@ -4,7 +4,7 @@ This page tracks outstanding problems with
=> https://fallback.genenetwork.org/
-Note that some issues may be related to produciton (i.e. the same).
+Note that some issues may be related to production (i.e. the same). Note also I created my own development VM in just an hour, so I don't have to mess with the fallback while others are using it.
# Tags
@@ -17,15 +17,16 @@ Note that some issues may be related to produciton (i.e. the same).
# Tasks
* [X] 502 timeout errors
-* [ ] Rqtl2 not working
+* [X] Rqtl2 not working
* [ ] 413 error
* [ ] Monitor service - both systemd and sheepdog
+* [ ] Files in /tmp
-## 502 timeout errors
+## 502 timeout errors (fixed)
These should no longer happen. It required relaxing timeouts on nginx and gunicorn.
-## Rqtl2/HK/Pairscan not working
+## Rqtl2/HK/Pairscan not working (fixed)
URL error on result of
@@ -61,7 +62,7 @@ and in the code we mostly see another addition of the slash - except for this pa
=> https://en.wikipedia.org/wiki/URL
-# R/qtl JSONDecodeError
+# R/qtl JSONDecodeError (fixed)
After adding the slash to GN3 URLs (see above) led to the next error:
@@ -119,7 +120,9 @@ So, for some reason Rscript is not in the path for GN3. So I added that to the p
=> /topics/systems/debug-and-developing-code-with-genenetwork-system-container.gmi
-## QTLReaper showing font problem
+That way I was able to troubleshoot the paths and added them to the containers.
+
+## QTLReaper showing font problem (fixed)
Try HK on
@@ -144,19 +147,40 @@ COUR_FILE = "./gn2/wqflask/static/fonts/courbd.ttf"
so most likely GN2 is not running from that actually source dir.
-## Pair scan runs, but does not show image
+## Pair scan runs, but does not show image (fixed)
Pair scan shows a table on the fallback, but not the image. On CD and production no pair scan results!
+=> https://gndev.genenetwork.org/show_trait?trait_id=10150&dataset=BXDPublish
+
+Takes about a minute for 26 mice. The csv files are generated in /tmp/gn3, but no image. The relevant code is
+
+```
+
+
+
+```
+
+The problem is with Karl's D3 panels, we get an error 'TypeError: d3.scaleLinear is not a function'. That 1.7.1 release is a bit old, so let's try updating that first. After updating to 1.8.4 we have the same error. D3 is at 3.5.17 - that is 2016(!).
+
+Now the latest versions of D3 do *not* provide the actual JS through github. The page
+
+=> https://d3js.org/getting-started
+
+has links to
+
+=> https://d3js.org/d3.v7.js
+=> https://d3js.org/d3.v7.min.js
+
+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
On mapping from
=> https://fallback.genenetwork.org/show_trait?trait_id=10002&dataset=HET3-ITPPublish
-## Purescript genome browser icons not showing
-
-## Files generated in /tmp
+## Files generated in /tmp (later)
Not unique file names appearing in TMPDIR:
@@ -168,9 +192,22 @@ Not unique file names appearing in TMPDIR:
-rw-r--r-- 1 gunicorn-genenetwork2 gunicorn-genenetwork2 835 Apr 2 07:03 -logP.png
```
+These are created by the HK run. Harmless for now, but if two people run HK at the same time we'll get a conflict.
+
Unique file names, but lingering on file system - note they are root because I created them outside a container
```
-rw-r--r-- 1 root root 10M Apr 2 07:03 4OJCzmGV.cross
-rw-r--r-- 1 root root 10M Apr 2 07:03 6cExgwkd.cross
```
+
+# Purescript browser buttons not showing (fixed)
+
+The following button does not display:
+
+```
+