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  • Jun 16 21:37

    bredelings on refactor-component-merging

    Add an apt-update. (compare)

  • Jun 16 21:27

    bredelings on refactor-component-merging

    Add --standardize option for tr… Don't define `splits`, just use… Don't define aliases, reference… and 1 more (compare)

  • Jun 16 19:40

    jimallman on development

    typo (compare)

  • Jun 16 19:38

    jimallman on development

    Fix initial toggle text for all… Merge branch 'synthesis_queue' … (compare)

  • Jun 16 19:38

    jimallman on synthesis_queue

    Fix initial toggle text for all… (compare)

  • Jun 16 18:30

    jimallman on development

    Keep second (full details) row … Merge branch 'synthesis_queue' … (compare)

  • Jun 16 18:29

    jimallman on synthesis_queue

    Keep second (full details) row … (compare)

  • Jun 16 18:04

    jimallman on development

    add toggle for each synthesis r… Merge branch 'synthesis_queue' … (compare)

  • Jun 16 18:04

    jimallman on synthesis_queue

    add toggle for each synthesis r… (compare)

  • Jun 16 17:59

    jimallman on development

    move support scripts for synth-… Merge branch 'synthesis_queue' … (compare)

  • Jun 16 17:59

    jimallman on synthesis_queue

    move support scripts for synth-… (compare)

  • Jun 16 17:56

    jimallman on development

    KO wrap new details view Merge branch 'synthesis_queue' … (compare)

  • Jun 16 17:56

    jimallman on synthesis_queue

    KO wrap new details view (compare)

  • Jun 16 17:54

    jimallman on development

    Allow easy cloning of an existi… Show synth-run details in main … Merge branch 'synthesis_queue' … (compare)

  • Jun 16 17:54

    jimallman on synthesis_queue

    Allow easy cloning of an existi… Show synth-run details in main … (compare)

  • Jun 16 17:08

    jimallman on development

    Show any collection ids provided Merge branch 'synthesis_queue' … (compare)

  • Jun 16 17:07

    jimallman on synthesis_queue

    Show any collection ids provided (compare)

  • Jun 16 15:24

    jimallman on development

    Rough layout for new-synth-run … Merge branch 'synthesis_queue' … (compare)

  • Jun 16 15:23

    jimallman on synthesis_queue

    Rough layout for new-synth-run … (compare)

  • Jun 08 19:04
    jimallman synchronize #1265
Benjamin Redelings
@bredelings
I don't suppose we can delete these?
Jim Allman
@jimallman
yes, you can clobber the issue on Github and they will disappear (click the little octo-cat icon to see the thread as an issue on GH)
Benjamin Redelings
@bredelings
Cool, I closed the 2 issues. That seems like a good system.
Mark T. Holder
@mtholder
I'm putting the site into maintenance mode to redeploy changes to the web-app
OK. redeployed. Seems to be working as far as I can tell
Jim Allman
@jimallman
now showing live synth-queue data in the curation app (in the history of a collection): https://devtree.opentreeoflife.org/curator/collection/edit/josephwb/aves?tab=history
Jim Allman
@jimallman
this raises some interesting questions about the data provided:
  • Can we capture the date_completed field, as used in the archive's config.json file? That would help to place these synth runs correctly in the collection's history.
  • Alternately, should we sort these by SHA instead of date? I see that lots of SHAs are missing from the current synth-run data, but this might be more accurate unless we can guarantee that a synth run will always use the latest/current version of a collection!
  • As a convenience feature, it would be great to include the root_taxon_name property as well, so we can show it in the curation app (with a taxo-browser link based on its root_ott_id).
  • Would curators be interested in seeing the num_source_studies, num_source_trees for each, as well?
  • Is there an owner/runner for each synth run? I don't see it captured anywhere, but it might be nice to know who pushed the button.
  • Finally, I'm always a fan of capturing some kind of description/comment, e.g. "Trying again with Aves sorted earlier". I don't see anything like this, but maybe it's something to consider as we accumulate lots of lookalike synth runs.
Jim Allman
@jimallman
fyi, i just checked /v3/tree_of_life/about and it offers information about source trees, but not about the collections used in synthesis.
@mtholder ^
Mark T. Holder
@mtholder
sorry for the delay on deploying the ws_wrapper PR, @jimallman . I'm having some VPN issues that I'm trying to correct.
Jim Allman
@jimallman
no worries! i'll keep working elsewhere
Mark T. Holder
@mtholder
given that I'm still having VPN issues, I may put the next draft version of the tree onto devapi
that could cause an interruption of API calls while the otcetera-based tools reboot
@jimallman ^
Jim Allman
@jimallman
ok, i'll check periodically (or just let me know when it's up and running)
Mark T. Holder
@mtholder
still copying the new version of ott and the synth tree over
Mark T. Holder
@mtholder
OK. going to redeploy now
Mark T. Holder
@mtholder
some problem with the OTC launch and apache config. I think I've got it...
otc relaunching...
Mark T. Holder
@mtholder
sorry. I tried to back out of the changes, but I'm seeing some weirdness on devtree now.
I have a couple of appointments this afternoon. I'll try to clear up my mess tomorrow
for some reason it seems to be reporting all of the taxa as not existing in the tree
this is after trying to redeploy tree 12.3
@jimallman ^
Jim Allman
@jimallman
funky! no worries, i can keep building UI assuming that the method will soon be available. (i have some captured JSON already.)
Mark T. Holder
@mtholder
I have figured out the VPN issue, so I should be able to debug and diagnose this soon (hopefully this weekend).
Mark T. Holder
@mtholder
I think the otc server is working on devapi now, but there are some issues with CORS and the caching that are causing the browser to not work
@jimallman ^
Jim Allman
@jimallman
thanks! i'll investigate
Jim Allman
@jimallman
@mtholder Is this the CORS problem that would be fixed my OpenTreeOfLife/ws_wrapper#6? Or something else related to caching?
Jim Allman
@jimallman
ah, i see that it's also affecting /v3/collections/find_collections. (fwiw, this is not being called through the web2py RAM cache.)
jimallman @jimallman is double-checking current phylesystem-api branch on devapi...
Mark T. Holder
@mtholder
I think I have it fixed
at least for the tree viewing
@jimallman ^
I still have not fixed the CORS thing on ot38 with ws_wrapper
Jim Allman
@jimallman
yes, i see that `find_collections' is responding now.. i was just adding some test code to devphylesystemapi, so i was a bit surprised :-)
Mark T. Holder
@mtholder
It was apache conf
from the redeployment on devapi, if you compare ~admin/fixed/opentree-shared.conf to ~admin/broken/opentree-shared.conf
you'll see the differences. I think it was disagreement between calling the devphylesystemapi machine by that subdomain name vs the ot## number for it.
so the CORS was not happy about the redirect.
Jim Allman
@jimallman
ah, cool. yes, ot## should never be used if we can use canonical domain names
good catch!
i'll revert my test junk
Mark T. Holder
@mtholder
I (finally) got your ws_wrappers PR merged and deployed on ot38
@jimallman
Jim Allman
@jimallman
sweet! thanks
Mark T. Holder
@mtholder
I had omitted several needed flags in tree build 13.0. So, I'm about to deploy the next draft on devapi
Mark T. Holder
@mtholder
This is not exactly a thorough analysis, but... 13.1 looks less terrible than 13.0
Karen Cranston
@kcranston
good to set the bar low