Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
  • Oct 16 17:01
    bredelings commented #54
  • Oct 16 06:30
    gaurav commented #54
  • Oct 15 16:57
    bredelings commented #54
  • Oct 15 16:56
    bredelings commented #54
  • Oct 15 16:56
    bredelings commented #54
  • Oct 15 16:44
    bredelings closed #101
  • Oct 15 15:12
    bredelings commented #54
  • Oct 15 15:12
    bredelings commented #54
  • Oct 14 23:49
    hlapp commented #54
  • Oct 14 20:45
    bredelings commented #54
  • Oct 14 20:23

    bredelings on treap-solver

    Add function same_component2( ). Add edge::reverse() member func… Store struct edge instead of pa… and 12 more (compare)

  • Oct 13 22:19
    hlapp commented #54
  • Oct 13 19:28

    mtholder on allow-subtree-of-taxonomy

    Merge remote-tracking branch 'o… (compare)

  • Oct 13 18:50

    mtholder on allow-subtree-of-taxonomy

    tolerate parsing subtree of OTT (compare)

  • Oct 13 18:49

    mtholder on allow-subtree-of-taxonomy

    (compare)

  • Oct 13 18:17

    bredelings on treap-solver

    Factor out code to place the no… Implement remove( ). Fix split( ). and 3 more (compare)

  • Oct 13 09:36
    dependabot[bot] labeled #158
  • Oct 13 09:36
    dependabot[bot] opened #158
  • Oct 13 09:36

    dependabot[bot] on maven

    Bump junit from 4.8.1 to 4.13.1… (compare)

  • Oct 09 00:41

    mtholder on bump_fossil_higher

    revised py versions for travis (compare)

Eschenholz
@eschenholz_twitter
hi, i found a misplaced group on the tree. is here the right place to talk about that?
Emily Jane McTavish
@snacktavish
Hi @eschenholz_twitter! You can comment on the node, to flag that information, or even better, upload a published tree to the study curator https://tree.opentreeoflife.org/curator that places the taxon in the right place!
Eschenholz
@eschenholz_twitter
thank you, i'll comment
Benjamin Redelings
@bredelings
I have a fix for the otcetera crash on the development branch of otcetera.
Luna Luisa Sanchez Reyes
@LunaSare
Awesome @bredelings
I’m pretty sure I just broke it again 😬
Luna Luisa Sanchez Reyes
@LunaSare
thought I was running my tests on dev but I was sending them to production again...
Mark T. Holder
@mtholder
I"ll redeploy
Mark T. Holder
@mtholder
I think that it is all back now
Benjamin Redelings
@bredelings
@LunaSare When Mark redeployed, he installed the fix on api. (Previously, I had tested it on devapi, but not api). Can you try again now?
I'm still a but confused about exactly what was crashing.
It does seem to be something associated with study ot_1876, but I'm not completely sure if it was the conflict call or not.
I'm now seeing:
$ curl 'https://api.opentreeoflife.org/v3/conflict/conflict-status?tree1=ot_1876%23tree1&tree2=synth&use_cache=false'
{
    "message": "[/v3/conflict/conflict-status] Error: Query tree has only 0 leaves with an OTT id!"
}
Previously, the "message" was from an assert( ) line, but it was not actually crashing the server. So there could be another issue.
Benjamin Redelings
@bredelings
@LunaSare Drat, the problem is not fixed.
It just does not always occur. More debugging...
I'll try and reproduce it locally.
Luna Luisa Sanchez Reyes
@LunaSare
Thanks @bredelings! I was definitely trying conflict again with study ot_1876 when I crashed it yesterday, let me know if any more specifics would be helpful!
Benjamin Redelings
@bredelings
@LunaSare Cool, that is helpful. I think I just need to debug this locally, as it appears to be a "heisenbug" -- i.e. a bug that appears only when you are not looking at it.
Well, maybe not quite that bad.
Mark T. Holder
@mtholder
I'm going to deploy a branch of peyotl-for-phylesystem-api onto devtree (hopefully, this won't step on @jimallman 's toes. (or anyone elses'))
Mark T. Holder
@mtholder
sort-of got phylesystem-api working with the script-managed trees option using: https://github.com/OpenTreeOfLife/phylesystem-0
nm.
still rejecting that study.
I had to edit the opentree-shared.conf on devapi to replace ot56 with devphylesystemapi in order to get the forwarding to work.
that may mean that I should have been updating the server name on devphylesystemapi rather the confs ondevapi
Benjamin Redelings
@bredelings
@LunaSare OK, I think you can try conflict on ot_1876 against api again.
The first fix wasn't.
After checking with valgrind, it looks like this one is better.
Luna Luisa Sanchez Reyes
@LunaSare

@LunaSare Cool, that is helpful. I think I just need to debug this locally, as it appears to be a "heisenbug" -- i.e. a bug that appears only when you are not looking at it.

Agh, that’s annoying… I’m glad it is not a “schroedinbug”, that one sounds way scarier tbh

After checking with valgrind, it looks like this one is better.

That’s great @bredelings. I’ll try conflict again then 🙊

Benjamin Redelings
@bredelings
Great, please do.
Luna Luisa Sanchez Reyes
@LunaSare
Yay, it’s working!
Mark T. Holder
@mtholder
OK. @jimallman I finally have the phylesystem-api on dev returning a nexson blob for https://devtree.opentreeoflife.org/curator/study/view/tt_217 , but I think that it is not the nexson blob the JS was expecting.
I can try to diagnose, but you might find it faster than I do
Jim Allman
@jimallman
no worries, i'm sure it's failing some kind of client-side validation (or code that presumes too much).
Matt
@mjy

Greetings tree-folk. Just popping in to note that we've started work on this repo, that was discussed a long time ago: https://github.com/SpeciesFileGroup/otu_mapping_widget. In essence we're stealing your OTU->Name widget and trying to make it generic, because we need a nearly identical interface.

I'd love to have your feedback on what worked and didn't, what you didn't have time to work on but would have like to have, etc. In theory the interface we build will be software agnostic, hopefully utlimately pluggable into your tools if it becomes useful.

Jim Allman
@jimallman
Hi @mjy ! Have you tried our bulk-TNRS tool? This uses the same UI as we do for per-study OTU mapping, but it loads and saves all work in ZIP archives. Most useful for mapping entire sets of OTU labels that follow a particular lab's or project's nomenclature.
As with most of our webapps, it was built using the web2py framework, but almost all of the logic here is client-side JS, plus calls to existing OpenTree APIs. You can follow that traffic and see how we bundle arguments using in-browser dev tools, e.g. the Network tab in Google Chrome.
Jim Allman
@jimallman
oh, here's a well-hidden README to help with testing and re-use of the TNRS code.
Matt
@mjy
Thanks @jimallman. Have not tried. We're really trying to just focus on the resolution bit, not how or what is being resolved. For example we could configure the same widget to map People to People. It's really the UI/UX of matching two columns (that have hooks for external things), and a hook to say "I'm done" (then externally trigger the Zip creation, or the batch upload, or the batch update etc... all that external bit is seperate).
I'll definitely checkout the bulk tool- definitely sounds like similar concepts.
Yan Wong
@hyanwong
I guess you must have noticed that Homo sapiens is marked as extinct on the current OpenTree?
There is presumably an issue for that somewhere.
Jim Allman
@jimallman
yes, this is definitely a Known Issue:
OpenTreeOfLife/feedback#480
Yan Wong
@hyanwong
:thumbsup: :skull:
Yan Wong
@hyanwong
If anyone is interested, we have just preprinted a paper on how OneZoom works, and interacts with the OpenTree. It's at https://www.biorxiv.org/content/10.1101/2020.10.14.323055v1 - do let me know if you think anything needs changing, and whether we have done justice to the OpenTree efforts! It was quite hard to squeeze it all in to the required length, so there's a fair bit of the description in the supporting material PDF.