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  • Aug 06 19:56

    jimallman on development

    Smarter form behavior Merge branch 'import-tnrs-names… (compare)

  • Aug 06 19:56

    jimallman on import-tnrs-nameset-in-curation

    Smarter form behavior (compare)

  • Aug 06 17:23

    jimallman on development

    Rough client-side logic for tes… Merge branch 'import-tnrs-names… (compare)

  • Aug 06 17:22

    jimallman on import-tnrs-nameset-in-curation

    Rough client-side logic for tes… (compare)

  • Aug 06 16:32

    jimallman on development

    Merge pull request #1241 from O… Merge pull request #1244 from O… Rough markup for nameset-import… and 3 more (compare)

  • Aug 06 16:32

    jimallman on import-tnrs-nameset-in-curation

    Stub support functions (JS) to … (compare)

  • Aug 06 16:13

    jimallman on import-tnrs-nameset-in-curation

    Cleanup of nameset-submission UI (compare)

  • Aug 06 15:12

    jimallman on import-tnrs-nameset-in-curation

    Rough markup for nameset-import… (compare)

  • Aug 05 18:12

    jimallman on development

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  • Aug 05 18:11
    jimallman synchronize #1251
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    jimallman on smarter-cookie-management

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  • Aug 05 18:09
    jimallman opened #1251
  • Aug 05 18:04

    jimallman on development

    Removed duplicate (no-op) event… Merge branch 'smarter-cookie-ma… (compare)

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    jimallman on development

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Mark T. Holder
@mtholder
awesome. Thanks, @bredelings
Benjamin Redelings
@bredelings
I ended up merging the fixes to the development branch, and then rebasing the new-conflict on top of that in order to keep the new-conflict changes on devapi.
:-)
That way, we could deploy the development branch on production and call it master if everything works.
We could also merge the whole thing (including conflict protocol changes) to development and deploy on production, provided we also update the opentree app on production.
Benjamin Redelings
@bredelings
BTW I did all this with building + restarting otc by hand. I don't know if the germinator scripts are supposed to work...
Emily Jane McTavish
@snacktavish
very snazzy!
Benjamin Redelings
@bredelings
Oops... found another bug...
Benjamin Redelings
@bredelings
OK, bug fixed and deployed on devapi.
I've now added a new fuzzy-matching test, as well as a ctrie test to the otcetera test cases. But if people want to give the autocomplete bar on devtree some testing, that might be helpful.
BTW, I was thinking about adding a fuzzy prefix match. Right now we have fuzzy complete matches and exact prefix matches, but no fuzzy prefix match.
Benjamin Redelings
@bredelings
I'm also thinking about adding the ability to read in amendment files on startup.
It might be good to write the code to read them, since it could be used in multiple ways.
Jim Allman
@jimallman
@snacktavish You asked about the ability to print (and presumably download) conflict views from the input-tree viewer:
Screen Shot 2020-07-16 at 3.46.36 PM.png
This is working as expected for me. Clicking either button from a conflict view sends a matching PDF (or SVG) file. This is testing on Chrome/Mac, but I would expect the same results elsewhere, since (iirc) both features use the "live" view. Are you seeing something different? If so, what browser+platform?
Emily Jane McTavish
@snacktavish
@jimallman Ah, yes, the print function does work as expected (I hadn't tried that), it is the save as SVG that I was trying and not getting the expected results when I open in inkscape.
Screenshot from 2020-07-20 10-36-20.png
Screenshot from 2020-07-20 10-35-50.png
Jim Allman
@jimallman
ah, i see what you mean. these SVG images look fine in the browser, but not in Inkscape. hmmm.
Jim Allman
@jimallman
we generate an internal stylesheet to manage path colors+style, but Inkscape apparently doesn't handle this well. researching now...
Jim Allman
@jimallman
@snacktavish, i found the issue. you need to rename the stylesheet element from style to svg:style, then it seems to be recognized in Inkscape. i'll try this change in the curation tool and see if it behaves in other views.
(but the workaround above can be used with any images you need in the short term)
Emily Jane McTavish
@snacktavish
Ah cool! Thank you.
may be an inkspace-problem rather than an us-problem :P
Jim Allman
@jimallman
yes, it's Inkscape's fussiness (why not recognize any CSS sheet!?), but ultimately it comes down to browser behavior, which is technically correct but annoying. i'm working out the details of how to create elements in the non-standard svg namespace... should have something working by tonight.
Emily Jane McTavish
@snacktavish
thanks!
Jim Allman
@jimallman
@snacktavish I have a working fix for Inkscape on devtree (and a matching PR). please give it another try when you have a chance.
Emily Jane McTavish
@snacktavish
whoah, cool!
Karen Cranston
@kcranston
that is amazing
Jim Allman
@jimallman
pretty cool
Emily Jane McTavish
@snacktavish
I want to get a list of all of the tip ottids in the synthetic tree. I was going to pull them out of the synth tree file, but realized I'll get internal nodes as well. is the full list available anywhere handy?
Emily Jane McTavish
@snacktavish
@mtholder @bredelings
Mark T. Holder
@mtholder
I think the files in https://files.opentreeoflife.org/synthesis/opentree12.3/output/cleaned_ott/ have the complement - the OTT IDs pruned
you can get them from an otcetera tool:
otc-count-leaves -l PARENT_OF_SYNTH_OUT/opentree12.3/labelled_supertree/labelled_supertree.tre
which takes about 4 seconds on my machine.
It's possible that the leaf list is somewhere else in the synth archive, but I can't remember it being anywhere.
Benjamin Redelings
@bredelings
That sounds like the best way to get the leaves.
You can also use time otc-tree-tool --show-leaves ~/Devel/OpenTree/synth-trees/opentree12.3/labelled_supertree/labelled_supertree.tre > leaves. The only difference is that the leaves look like "ott47378" versus "47378".
Emily Jane McTavish
@snacktavish
Ah nice! I ended up reading it into dendropy, which took a few min, but wasn't terrible. That seems much quicker for future though. (although I'd have to compile otcetera on my machine, so maybe not :P)
Benjamin Redelings
@bredelings
@snacktavish Compiling otcetera without the http stuff (restbed lib) should be pretty easy.
Benjamin Redelings
@bredelings
sudo apt install libboost-all-dev 
sudo apt install meson ninja-build # or `pip install meson ninja`
git clone git@github.com:OpenTreeOfLife/otcetera.git
cd otcetera
meson build -Dwebservices=false -Dprefix=<directory>
cd build
ninja install
Benjamin Redelings
@bredelings
I suppose we should add that to the README.md
Emily Jane McTavish
@snacktavish
ooh ya! That does sound handy.
Ive been playing with vis!
Here is a tree of all families in OpenTree (around 9,000), with overlays that show the number of studies supporting and conflicting with each branch.
the color max is for 5 studies (in support or conflict), although the numbers actually go up to 15-17