diff options
Diffstat (limited to 'issues')
| -rw-r--r-- | issues/systems/fallback-errors.gmi | 57 |
1 files changed, 47 insertions, 10 deletions
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 + +``` + <div class="qtlcharts" id="chart_container"> + <div id="pairscan_chart"></div> + </div> +``` + +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: + +``` + <button id="scrollLeft" type="button" > + <i class="fas fa-arrow-left"></i> +``` + +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. |