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  • 02:22
    eliagbayani synchronize #158
  • May 27 23:42
    eliagbayani synchronize #158
  • May 27 20:27
    Travis EOL/eol_website (master) still failing (2460)
  • May 27 20:21

    JRice on master

    Page::Reindexer easier to use (compare)

  • May 27 15:16
    Travis EOL/eol_website (master) still failing (2459)
  • May 27 15:11

    mvitale on master

    MetaMover for migrating metadat… (compare)

  • May 27 14:25
    eliagbayani synchronize #158
  • May 27 12:45
    eliagbayani synchronize #158
  • May 27 09:40
    eliagbayani synchronize #158
  • May 27 09:02
    eliagbayani synchronize #158
  • May 27 06:38
    eliagbayani synchronize #158
  • May 26 15:25
    Travis EOL/eol_website (master) still failing (2458)
  • May 26 15:22
    Travis EOL/eol_website (master) still failing (2457)
  • May 26 15:20

    mvitale on master

    find EditorPageDirectories by f… (compare)

  • May 26 15:17

    mvitale on master

    add units to histogram links Merge branch 'master' of github… (compare)

  • May 26 15:10
    Travis EOL/eol_website (master) still failing (2456)
  • May 26 15:05

    translatewiki on master

    Localisation updates from https… (compare)

  • May 26 10:49
    eliagbayani synchronize #158
  • May 26 07:41
    eliagbayani synchronize #158
  • May 26 06:18
    eliagbayani synchronize #158
Jen Hammock
@jhammock
nope, feel free to sacrifice oauth
Jeremy Rice
@JRice
Low fear. I'm not hitting production at all, yet. Will be repeatedly flogging beta over the next few days, though. :)
Jen Hammock
@jhammock
I meant about the media tab filter “attacks"
feel free to flog beta
Jeremy Rice
@JRice
Yeah, those should still be possible, but lower-risk now. I'll investigate later, it's not at the top of my mental queue. :) But the optimize plus the added index should really quell the flood.
I don't see any of the symptomatic spikes in MySQL query times that we'd been getting, so: so far, so good.
Jeremy Rice
@JRice
Beta's back. Sorry, there was a critical problem with the OAuth-removal process... which ... I do not understand how it "worked" on staging, so ... that's worth figuring out. :\ But... we're back, and OAuthless.
Jeremy Rice
@JRice
(Just FTR: I am stuck in gem-upgrading quagmire again today. ...Very tempting to skip all of the nit-picking and go straight to Rails 5, but trying to avoid that impulse.)
Jeremy Rice
@JRice
....aaaaaand in a moment of deep frustration, I discovered that the gems I was attempting to resolve aren't really affected (in our codebase) by the alert. [sigh]
...I've resolved the other alerts (well, I ignored on low-security threat), so the next step actually is to upgrade Rails...
...but lemme test this one more time (I did update a pair of gems with risks) and merge it to the master branch and test it again.
BTW, I found out why my "staging" test passed when it shouldn't have (I neglected to checkout the BRANCH, duh, when I created the clone of beta), so that won't happen again.
Really itching to get to Rails 5, though. Rails 4 is getting very long in the tooth, and will soon be completely prohibitive in terms of keeping security patches up to date with the number of gems we use. :|
(Getting to Rails 6 should be less painful. Honestly, 4->5 is less painful than 3->4 was... so... they're getting better at these things in the Rails community.)
Jeremy Rice
@JRice
Okay, beta is now running the latest upgrades. Moving on to Rails 5, now. See you in a few weeks. [sob]
(Please don't hesitate to interrupt me.)
Jen Hammock
@jhammock
Good luck!
Jeremy Rice
@JRice
Thanks. I took copious notes from my last attempt, so I'm hoping they help...
Jeremy Rice
@JRice
VERY precarious gem list, going to break soon I fear, because of Refinery (our CMS). I know I periodically complain about this, so ... reiterating my complaint. :)
Jeremy Rice
@JRice
Neat Rails 5 feature is being able to use things like Page.where(BLAH BLAH).not(media_count: 0)
...Was uglier to do those "not" clauses in Rails 4 (ended up looking like raw SQL snippets).
Jorrit Poelen
@jhpoelen
hey y'all - happy 2020! If case you need a break from your daily activities - here's a preprint related to access, stability and reliability of biodiversity datasets in GBIF, iDigBio, DataONE and BHL: Elliott, M. J., Poelen, J. H., & Fortes, J. (2020, January 3). Toward Reliable Biodiversity Dataset References. https://doi.org/10.32942/osf.io/mysfp . Are you surprised by our findings?
Jen Hammock
@jhammock
nice work, @jhpoelen ! I’m not surprised, only because I got a peek at your earlier draft. FTR, I was when I saw them!
Jorrit Poelen
@jhpoelen
thanks @jhammock . Curious to hear your take on the proposed citation format. . . also, am eager to find a way to sit down with the "big" aggregators and have a chat about reliable dataset references. Who do you think would be interested in this work?
Jen Hammock
@jhammock
I don’t reeeeally know, but I think GBIF and BHL both should be...
Jen Hammock
@jhammock
@JRice when you have a moment, could you check on the identifier map? Looks like the current version is not at home
Jeremy Rice
@JRice
Hmmmn.
Drat! They really do seem to be gone. This may have been my fault, I was cleaning up the public directory a few days ago when we had some space-related problem.
....I will regenerate it! :S Apologies!
Jeremy Rice
@JRice
(Takes about 90 minutes.)
Jen Hammock
@jhammock
no worries. It was discovered in passing by me, so the users may not have noticed :)
Jeremy Rice
@JRice
Glad it was you, then!
Jen Hammock
@jhammock
@sckott thanks for the pointer; I hadn’t realized the ropensci traits package was out there already
Yan Wong
@hyanwong
@jhpoelen is that Mick Elliot who wrote a wickedly fast C++ newick parser for large phylogenies? I was wondering what happened to that code (would still like to use it!)
Scott Chamberlain
@sckott
@jhammock yeah, it's sorta like taxize but for traits instead of taxonomic data. traits are much harder to make a consistent interface for. and there's much less open trait data
Jen Hammock
@jhammock
@sckott Indeed, we keep having trait data workshops but getting all the data sources looking even similar is asking a lot. People think about traits in so many different ways
Jeremy Rice
@JRice
Apologies! My wife is stuck at work (well... grand jury duty) and the babysitter has to leave, so I have to cut out early today. I'll keep a half an eye on things, though.
Quick summary: migration is going quite well! ...I'm at a point where the code is actually mmmmmmostly running in Rails 5, with a few major flaws (I18n isn't working, routes aren't all working, etc). ...So I'm entering the "slog" through upgrade bugs much faster than I did last time. So... good?
Jen Hammock
@jhammock
@JRice at your convenience, could we have a beta update, please? There are a bunch of things pending that MV could review
Jeremy Rice
@JRice
Yup.
Jorrit Poelen
@jhpoelen
@hyanwong M Elliott is Michael Elliott, a grad student at the ACIS lab of University of Florida. I doubt he is the same person that helped write the c++ newick parser (is it https://github.com/OpenTreeOfLife/otcetera ? ).
Jeremy Rice
@JRice
Okay, it's up. Cache cleared, assets compiled. No migrations.
Jen Hammock
@jhammock
Thanks!
Michael Vitale
@mvitale
I’m wrapping up for today — more tomorrow
Have a good evening, all
Jen Hammock
@jhammock
Thanks, @mvitale
Yan Wong
@hyanwong
@jhpoelen Sounds different, yes. The newick parser was called Gulo: I don't think it went into otcetera, but was an independent project which sadly seems to have disappeared off the face of the earth, along with its author.
Jorrit Poelen
@jhpoelen
@hyanwong bummer to hear that the newick parser seems to have disappeared.
Jen Hammock
@jhammock
:+1: