galaxy Issues with phylogenetic visualisations

reproduced on eu/au, org wasn't processing uploads so I didn't test there. Browser: firefox 123.0 on fedora 39.

Here is a test file, ensure it's uploaded as newick.

((A.olssoni:0.112038213,(A.etheridgei:0.077847429,A.insolitus:0.099160118)1.000:0.024772158)0.822:0.007599289,(A.lucius:0.114136163,Chamaeleolis.barbouri:0.118480033)0.586:0.005775392,(((C.guamuhaya:0.024946956,C.chamaeleonides:0.026488992)1.000:0.091753615,(A.cuvieri:0.087918462,(A.barahonae:0.087645713,A.christophei:0.085645099)0.877:0.009676737)0.888:0.009321961)0.999:0.015032072,(((A.equestris:0.103238807,((A.bartschi:0.087882157,A.vermiculatus:0.081615308)0.998:0.022831987,(A.bahorucoensis:0.114628815,(A.aliniger:0.096918912,A.coelestinus:0.111900872)0.548:0.010531312)0.818:0.006263403)0.748:0.004423624)0.988:0.008963502,(((A.luciae:0.097183457,(A.aeneus:0.057932967,A.richardi:0.058294848)1.000:0.054211298)0.947:0.011584592,(P.nicefori:0.119707992,(A.agassizi:0.079919230,A.microtus:0.086638718)0.998:0.023100142)0.768:0.007101350)1.000:0.020273023,(A.occulatus:0.161429665,(Diplolaemus.darwinii:0.149865535,Phenacosaurus.acutirostrus:0.163660606)1.000:0.036169405)0.574:0.007888565)0.562:0.002582237)0.984:0.007116887,((((A.ophiolepis:0.063383823,A.sagrei:0.061326694)1.000:0.061901936,(A.ahli:0.130768717,((A.equestris2:0.095626231,(A.lineatopus:0.094517009,(A.garmani:0.068897703,A.grahami:0.070781870)1.000:0.027292044)0.497:0.003194941)0.789:0.006371042,(A.lineatus:0.119506403,(A.humilis:0.108520576,A.limifrons:0.112707887)1.000:0.032102291)0.856:0.007943537)0.565:0.010009344)0.601:0.003367963)1.000:0.016218863,((A.bimaculatus:0.104052329,A.wattsi:0.120945126)1.000:0.021146312,((A.brevirostrus:0.096195412,A.distichus:0.086715856)1.000:0.031901490,((Anolis.acutus:0.073619066,A.stratulus:0.064936661)1.000:0.042173701,(A.cristatellus:0.108876325,A.krugi:0.093885183)0.711:0.008361383)0.935:0.009380725)0.887:0.006534556)0.997:0.010828447)0.817:0.003474513,((A.marcanoi:0.122583051,A.strahmi:0.103072538)1.000:0.034296759,((A.alutaceous:0.093801894,A.vanidicus:0.104620885)1.000:0.027894002,(((A.carolinensis:0.052821752,A.maynardi:0.054087446)1.000:0.040905560,(A.loysiana:0.082301718,A.pumilis:0.102100608)0.892:0.010585964)0.867:0.007299079,(A.sheplani:0.134340536,(A.angusticeps:0.050230864,(A.paternus:0.008572260,A.paternus2:0.007116451)1.000:0.046652380)1.000:0.058212520)0.741:0.004669230)0.994:0.011884993)0.904:0.009869425)0.507:0.001600325)0.860:0.003296602)0.608:0.001603994)0.394:0.000846665);

phyloviz

(occurs on eu+au)

[ ] phyloviz opens in the _top, why? I've lost my place now :(
[ ] The layout is hard to read
[ ] hovering over a node shows <br> in the label
[ ] if there's a search button I can't click it

phylogenetic tree visualisation

[ ] Doesn't load at all on AU (ping @cat-bro)
[ ] Switching between each of these visualisation options on EU seems to have no effect. (ping @bgruening @mira-miracoli @sanjaysrikakulam)

Mar 18 '24 10:03 hexylena

@dannon I'm going to look into the "not loading on AU" issue - please let me know if this overlaps with anything you're doing here?

Mar 20 '24 05:03 neoformit

oh cheers @neoformit, i can ping ya in the future. (this was tested due to the aus biocommins phylo tutorial pr that's open so, sure they'd appreciate it working). Let me know if you need any more information

Mar 20 '24 08:03 hexylena

@neoformit Nope, have at it! I'm working on restoring phyloviz as a packaged external viz that should make this all more reliable moving forward, but nothing specific to AU's immediate issue.

Mar 20 '24 12:03 dannon

Sorry I got swamped with other jobs and this keeps getting pushed back on my todo list...

Apr 04 '24 00:04 neoformit

Galaxy Australia has just upgraded to release_24.1 and we can now load the Phylogenetic Tree Visualization. I can't comment on any of the style issues but our issue was that it wouldn't load at all, and now it does which is a plus! https://usegalaxy.org.au/u/cat-bro/h/test-phylo-post-241