Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-03-18

| Channels | #opentreeoflife index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
00:11 kcranstn joined #opentreeoflife
01:04 travis-ci joined #opentreeoflife
01:04 travis-ci OpenTreeOfLife/phylesystem-api#695 (support-tree-collections - e5e56b1 : Jim Allman): The build passed.
01:04 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/commit/e5e56b16d591
01:04 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/54807595
01:04 travis-ci left #opentreeoflife
01:31 kcranstn joined #opentreeoflife
01:53 travis-ci joined #opentreeoflife
01:53 travis-ci OpenTreeOfLife/phylesystem-api#696 (support-tree-collections - c66b1df : Jim Allman): The build passed.
01:53 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/e5e56b16d591...c66b1df9f5ad
01:53 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/54811163
01:53 travis-ci left #opentreeoflife
01:55 travis-ci joined #opentreeoflife
01:55 travis-ci OpenTreeOfLife/phylesystem-api#697 (support-tree-collections - 81da2ff : Jim Allman): The build passed.
01:55 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/c66b1df9f5ad...81da2fffad99
01:55 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/54811322
01:55 travis-ci left #opentreeoflife
02:18 josephwb joined #opentreeoflife
02:19 josephwb hey jimallman
02:19 jimallman howdy
02:20 josephwb noob question: how does one map taxa in the curator now? i can't figure it out. there used to be a button.
02:20 josephwb do i have to manually select each one?
02:20 jimallman hrm.. this has not changed.
02:20 josephwb [it's been a couple of months]
02:20 jimallman oh, mapping now requires a checkbox (in the leftmost column)
02:21 josephwb yeah, just saw that (new to me)
02:21 jimallman it was our attempt to balance user choice with sweet, sweet automation
02:21 josephwb and now it is going
02:21 jimallman kewl
02:21 josephwb thanks
02:21 jimallman no prob! i’m off to make a snack, but will be around for awhile tonight
02:22 josephwb is it using a newer taxonomy than 2.8?
02:22 josephwb seems to be finding more stuff
14:33 kcranstn joined #opentreeoflife
14:36 josephwb joined #opentreeoflife
16:03 jar286 joined #opentreeoflife
16:12 kcranstn joined #opentreeoflife
16:59 josephwb joined #opentreeoflife
16:59 josephwb hey jimallman
16:59 jimallman howdy
16:59 josephwb i uploaded a tree which had bad labels. deleted tree, replaced with good version, but bad labels still shown in OTU mapping
17:00 josephwb how to purge?
17:00 josephwb other than deleting study and starting over
17:00 jimallman !
17:01 jimallman this implies that the bad labels are either present in another tree, or we’re holding to them (as stale otus)
17:01 josephwb no other tree
17:01 jimallman try this: use OTU Mapping tab, and click on the magnifying glass next to a bad label. does it pop up a tree?
17:02 josephwb "This OTU doesn't appear in any tree. (This is not expected.)"
17:02 josephwb so, encountered before, it seems
17:02 jimallman ok, it sounds like i’m not being careful to remove stale otus when deleting a tree.
17:02 jimallman good catch
17:03 jimallman for now, i guess starting over with the study is probably best :-/    but i’ll definitely make an issue for this on GitHub
17:03 josephwb ok, thanks
17:07 jimallman wait! there’s another option
17:07 jimallman if re-creating the study is painful, you could instead use the list filters in OTU Mapping
17:08 josephwb already deleted/restarted
17:08 jimallman OK. for future reference, then… change “In all trees” to “In preferred trees” (and mark your new tree, of course)
17:08 kcranstn joined #opentreeoflife
17:08 jimallman this should hide the old/unused OTUs for now.
17:09 josephwb i am getting different shades of orange for homonymns. a little confusing
17:09 josephwb one is a brown (matches key); other is bright orange
17:10 josephwb bright one is on its own; brown one has alt possibilities
17:10 josephwb i.e. "possible mappings"
17:10 josephwb not clear what the bright one is until i hogver over it
17:11 josephwb hogver -> hover
17:12 josephwb does that make sense?
17:13 jimallman hm, that sounds like the old coloring for root (and other special) nodes..
17:13 jimallman can you send a URL?
17:13 jimallman meanwhile, here’s a new issue, please edit as needed: https://github.com/OpenTreeOfLife/opentree/issues/618
17:17 josephwb https://tree.opentreeoflife.org/curator/study/edit/ot_243/?tab=otu-mapping
17:18 josephwb Centruroides sculpturatus = brown
17:18 josephwb Eremobates sp. = orange
17:18 josephwb [i am logged in at the moment; don't know if that is a problem]
17:19 josephwb logged out
17:22 josephwb is it ok if i log back in and edit?
17:43 josephwb did it anyway. mwahaha
17:43 josephwb done now
17:49 * jimallman was on the phone, catching up now...
17:50 jimallman hm, these look the same to me (gray text, orange tint)
17:50 jimallman josephwb: but maybe you’ve made edits that change what i’m looking at
17:50 josephwb nope
17:51 josephwb i will send a screenshot in a second
17:51 jimallman thanks!
17:51 josephwb BTW, you are not a "white & gold" person, are you?
17:51 jimallman perish the thought
17:51 josephwb those people are cray-zee
17:51 jimallman i was a bit literal about it, so robin’s egg blue and olive green
17:52 jimallman cuz obviously color is contextual, so without better lighting cues i didn’t fall into either camp
17:52 josephwb i would have expected html code from you
17:52 jimallman don’t tempt me (hex colors are a nice party trick)
17:52 jimallman doing them off the top of your head, i mean
17:53 jimallman someday anthropologists will note the 2015 dress-color mania, and probably attribute to hormones in the water supply.
17:54 jimallman like the ergot-fungus dancing in medieval Europe
17:54 jimallman those wacky ancient people!
17:55 josephwb email sent; couldn't figure out if i could do it here
17:55 josephwb btw: using Iceweasel
18:14 josephwb different, right?
18:18 jimallman i would hope Iceweasel is identical to Firefox for our purpose..
18:18 josephwb you got my email?
18:18 jimallman anyway, the screenshot shows that i was looking in the wrong place entirely. so thanks for that.
18:18 jimallman checking now...
18:22 jimallman ah, i see the problem. it’s subtle… CSS overrides color based on whether the link (colored lozenge) has the ‘href’ attribute or not.
18:22 jimallman these should be the same color (taxon homonym), but Eremobates is missing its HREF. my bad, will make an issue for this.
18:26 josephwb i am so good
18:26 josephwb (at finding work for you)
18:28 josephwb sent you another email: i had initialized a study. author wants to change licence, but it is linked to me
18:28 kcranstn can you put these in issues, instead of emails to Jim?
18:29 josephwb of course; just determining if they are indeed issues first
18:32 jimallman hi kcranstn, i’m making issues as needed: https://github.com/OpenTreeOfLife/opentree/issues/619
18:32 kcranstn thanks!
18:33 jimallman josephwb: i’m still trying to get my head around that latest email. is the problem that you initially created the study, implying that the license is “in your name"?
18:33 jimallman (because you’re listed as its submitter)
18:38 jimallman oh, i see. she’s editing an existing study (submitted by josephwb) and trying to apply CC-0 “retroactively”.
18:39 jimallman the good news is, she’ll be added to the “Submitted by” line after saving any changes, including this one. but her name may not appear until opening the study fresh.
18:40 jimallman more importantly(?) the assignment of the license isn’t clearly tied to any single curator. kcranstn, do you think this is a problem? obviously we can clear things up by checking the git history, but …
18:42 kcranstn license should be tied to study, not curator
18:43 kcranstn from commits, we can tell who assigned the license
18:52 jimallman i’m inclined to agree. and the clicked option actually says, “I am an author, or can act on behalf of the authors, to apply a CC0 waiver to these data.”
18:53 jimallman once a license or waiver has been applied, i believe we lock this down.
19:14 jimallman here’s an issue to address the user’s confusion on this point (comments welcome, of course):
19:14 jimallman https://github.com/OpenTreeOfLife/opentree/issues/620
19:14 jimallman kcranstn, josephwb ^
19:17 kcranstn commented on issue
19:18 jar286 maybe we need a ‘how to cite’ page
19:18 jar286 I’m not a fan of over-attribution
19:19 kcranstn are you arguing against a curator list for each study?
19:19 jar286 no, history should be complete
19:20 jar286 it sounded like the question was how to cite/refer/attribute off the site
19:20 jar286 but details would be nice
19:20 kcranstn I think much of the conversation was over private email, so hard to keep track
19:21 kcranstn I am confused about what the problem is
19:29 kcranstn thanks for the update on the issue, that helped
19:34 jimallman maybe josephwb can provide more context
19:46 josephwb hmm. that's all i know
19:47 josephwb i started a study. author came along, wanted to contribute. couldn't change licence
19:55 jar286 contribute what - other trees to the same study?
19:56 jar286 CC0 is independent of the curator, it’s about the original data
19:56 jar286 I still don’t understand what happened
20:11 josephwb well, contribute the same tree i already uiploaded (albeit an incorrectly-rooted tree)
20:13 josephwb i guess the issue is that i might choose "These data have no applied waiver or license, and I have no authority to apply a waiver"
20:13 josephwb author wants to do something else
20:13 kcranstn so we want to allow an author to apply a CC0 waiver
20:13 josephwb e.g. CC0
20:13 josephwb i guess
20:14 jar286 I thought that was doable… I remember asking for it
20:15 jar286 nope.
20:18 josephwb i wonder: for a curator entering their first ever study, would it be possible to have a splash screen saying what is expected from a curator (i.e. all the metadata we want)?
20:18 josephwb this particular author was not aware of this, i think
20:19 kcranstn good point about better documentation re:curation
20:19 kcranstn the status feature was supposed to help communicate that, but it never really got designed well / finished
20:20 josephwb docs are a pain to find and read. i am thinking of something like a splash screen on the first curation event.
20:20 josephwb pain for noobs, that is
20:21 kcranstn the workflow should just be better designed so that people don’t have to guess what is needed
20:21 josephwb yeah
20:21 kcranstn +1 to that
20:29 jimallman hi all, sorry i was away in GitHub and missed the conversation here.
20:29 jimallman it should be possible to assign a waiver for an existing study, provided none has previously been assigned. i did it myself in a test earlier today.
20:30 jimallman my guess is either (a) she balked at the prompting text for this, which is implied since she could see it, or
20:30 jimallman (b) something was already assigned (license or waiver) so this option was blocked.
20:31 josephwb https://tree.opentreeoflife.org/curator/study/view/pg_2647/?tab=metadata'
20:31 josephwb so, (a)
20:32 josephwb not all that prompting, tho
20:32 jimallman ? i see the “view” page, so no prompting text and “Waiver or license: None”
20:33 jimallman choosing Edit shows the prompt (and checkbox) for CC-0, but no other license options. maybe this is the weirdness, that we should assume the initial submission resolved any questions about license + waiver, so this checkbox should be gone.
20:33 * jimallman is now looking for old threads on this topic…
20:34 jimallman btw, nice use of curator notes here!
20:36 kcranstn it would be great to have a big “are you an author? add a CC-0 license to this study!” button
20:37 jimallman we can certainly do that, but we’ve discussed how a submitter will often be acting “on behalf” of an author. would they balk at assigning CC-0 if we phrase it this way?
20:37 jimallman i suppose we could add it in addition to the existing prompts for cc0
20:38 kcranstn we are clear in the wording now, but it would be nice to encourage an author to add a waiver to an existing study that doens’t have one
20:38 * jimallman nods
20:39 josephwb i don't think most users are going to know what the various flavours of waivers are, and which is appropriate
20:39 josephwb i certainly don't
20:39 josephwb other than CC) == bueno
20:39 josephwb CC0
20:40 josephwb maybe an information button?
20:40 jimallman we do offer a key to those options, in the Create Study workflow
20:40 jimallman shows available licenses and waivers, with a link to each
20:41 josephwb i am there now, and don't see that
20:41 kcranstn I don’t see that either
20:41 josephwb https://tree.opentreeoflife.org/curator/study/create
20:41 jimallman hm, i coulda sworn (i remember building a popup for this)
20:42 josephwb i remember that too
20:42 josephwb many moons ago
20:43 jimallman i do not see it in the current code. swept away in a redesign, perhaps? there was a lot of churn in this workflow, iirc
20:44 jimallman i can make a note to revive it and restore it here (and presumably in the Edit page as well, to help explain existing studies)
20:52 jimallman https://github.com/OpenTreeOfLife/opentree/issues/621
21:03 jimallman all: I’ve just confirmed that the “Apply CC-0” checkbox and prompt will only appear for an existing study that has no license applied. I’m pretty sure this was just intended as a cleanup tool for older studies that had no license/waiver set when they were created.
21:04 jimallman see commit message here: https://github.com/OpenTreeOfLife/opentree/commit/18ea34dc9cc6c9f6d4aa1da2e8bc5e55a472007a
21:06 jimallman …and this related issue “Retrospective CC0”:  https://github.com/OpenTreeOfLife/opentree/issues/369
21:26 * jimallman is signing off for a bit, but will check back here
23:49 jar286 joined #opentreeoflife

| Channels | #opentreeoflife index | Today | | Search | Google Search | Plain-Text | summary