Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-05-21

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All times shown according to UTC.

Time Nick Message
02:26 josephwb joined #opentreeoflife
12:10 jar286 joined #opentreeoflife
14:33 scrollback joined #opentreeoflife
17:25 josephwb joined #opentreeoflife
17:25 josephwb hey jimallman
17:25 josephwb "Approve all and continue" isn't doing anything in the curator for me
17:25 jimallman josephwb: howedy
17:26 jimallman odd. i’ll take a look
17:26 josephwb https://tree.opentreeoflife.org/curator/study/edit/ot_289/?tab=otu-mapping
17:26 josephwb set conetxt to birds, all mapping are corrcet
17:26 josephwb let me log out of it
17:27 jimallman no need, i should be able to test in the client
17:27 jimallman (w/o saving changes)
17:27 josephwb oh
17:27 jimallman but i don’t see any otus listed.
17:27 josephwb same for you?
17:27 jimallman two trees, but no otus in OTO Mapping tab
17:27 josephwb oh, i didn't save the tree. just a sec
17:27 jimallman my bad, no trees listed
17:27 jimallman yes, thanks
17:28 josephwb try now
17:28 jimallman now there’s a tree, thanks
17:29 josephwb i can approve individuals, just not all at once
17:29 jimallman tesitng “clear” and “reject all” functions, so far so good
17:30 jimallman the “approve all” logic takes a little time, so it’s doing something (wrong)
17:30 jimallman this might need a tweak to accommodate the recent display changes, where we always see mapping option(s) as if there were more than one result.
17:31 josephwb should i leave this study unmapped for testing?
17:31 josephwb [reject all works]
17:31 jimallman i suspect i can reproduce on dev, actually. lemme see…
17:31 josephwb i can give you the newick if you'd like
17:32 jimallman hold on. i doubt it has to do with any particular tree.
17:32 josephwb i know, but it is an easy mapping exercize for testing
17:34 josephwb i approved things; easy enough to unmap for testing
17:34 jimallman agreed, send the newick
17:34 jimallman i’ll re-import (into a random study) on devtree
17:36 josephwb will do
17:36 josephwb should i make an issue?
17:37 jimallman sure, thanks.
17:37 josephwb in the top opentree repo?
17:38 jimallman yes, please (almost certainly a bug in client-side code)
17:38 josephwb ok
17:41 josephwb https://github.com/OpenTreeOfLife/opentree/issues/643
17:55 josephwb erg. my next tree has 1061 tips; not going to individually approve those
17:56 josephwb getting error: "Something went wrong in taxomachine:"
17:56 josephwb wit hno further error
17:56 josephwb with no further error message
17:56 jimallman where is this error?
17:56 josephwb jimallman ^
17:56 josephwb in a red band along the bottom of the window
17:56 josephwb popped up a couple of times
17:57 jimallman hm, what was your action immediately before?
17:57 josephwb map all taxa
17:57 josephwb https://tree.opentreeoflife.org/curator/study/edit/ot_290/?tab=otu-mapping
17:58 josephwb context = birds
17:58 jimallman hm, ok
18:00 josephwb is it from "Failed mapping"?
18:02 josephwb keeps popping up, even though mapping is ostensibly done
18:02 jimallman trying a quick test with initial settings (no search context, fuzzy matching off). no errors so far.
18:04 jimallman restarted mapping with ‘birds’ context, nothing so far… i don’t think this is from mapping :-/
18:04 josephwb took a while until the first one
18:05 jimallman almost done mapping the first “page” of otus… no error message yet.
18:05 josephwb hmm
18:05 jimallman hm, finished the page w/ no errors.
18:05 josephwb "Sorry, there was an error in the study data."
18:06 jimallman each mapping attempt is a call to taxomachine, so maybe it’s just overloaded?d
18:06 josephwb why does the curator hate me today?
18:06 jimallman when did THAT message appear (“error in study data”)?
18:06 josephwb tried to save after approving some mapping
18:06 josephwb ok, saved when i re-tried
18:06 jimallman hm, well that sucks
18:07 jimallman i have no idea what to make of these.
18:07 jimallman glad it saved on second attempt
18:07 jimallman i’m going to return to the first issue (failure of ‘Approva All’) and try to get a fix in for this.
18:08 josephwb ok
18:10 josephwb re-tried mapping; getting same error
18:11 josephwb the 2nd issue
18:11 josephwb [not officially an issue]
18:17 jimallman 2nd issue is “Something went wrong in taxomachine” messages? or failure to save?
18:18 josephwb “Something went wrong in taxomachine”
18:18 jimallman ok
18:19 jimallman odd that it’s not happening for me. it might be worth a look in the browser’s dev tools, in the Network tab (to see if there are more details)
18:20 josephwb i am using Safari
18:21 jimallman ok, retracing your steps now...
18:23 josephwb only thing we did differently is the context
18:23 jimallman josephwb: do you see a Develop menu in Safari?
18:23 jimallman (main menubar?)
18:24 josephwb yes
18:24 jimallman in that menu, choose Develop > Show Page Resources, then click the XHR folder on the left
18:25 jimallman XHRs, that is. this is a log of all the contextQuery operations that fired when mapping the otus.
18:26 jimallman i’m hoping there might be a visible difference in some of these, to indicate 500 or other error responses.
18:26 josephwb ok
18:28 jimallman can you see the contextQuery entries in XHRs?
18:28 josephwb um
18:29 josephwb ah, things are popping up
18:29 josephwb it contains ot_290
18:29 josephwb getContextForNames
18:29 josephwb what am i suppoed to look at?
18:30 jimallman look for contextQuery entries (instead of getContextForNames). if you don’t see them, restart your auto-mapping operation. this list should continue to grow as your auto-mapping is going on.
18:30 josephwb i clicked on a red 999+
18:30 josephwb [Error] Failed to load resource: the server responded with a status of 404 (Not Found) (bootstrap-tagsinput.min.js.map, line 0)
18:31 jimallman ok to ignore that.. i’m sending a screenshot of expected output
18:31 kcranstn joined #opentreeoflife
18:31 josephwb ok, lots of contextQuery
18:32 jimallman screenshot coming to you in an email
18:32 jimallman josephwb: ^
18:35 josephwb jimallman but what am i looking for within that?
18:36 josephwb [not getting the error now...]
18:36 jimallman look for visible errors in the contextQuery entries. i’m hoping there might be some kind of difference (red text?), so you don’t need to click each one and check the info on the right (Request & Response > Code)
18:37 josephwb ok
18:37 jimallman if you’re not getting the error, we’re stuck. i don’t get these errors on my machine.
18:37 josephwb unampping and trying again
18:37 jimallman me too! maybe we can cause an overload and get the error :)
18:39 jimallman annoying smooth operation here.. no errors so far
18:40 josephwb me too...
18:40 jimallman yep, finished the page here w/ no errors.
18:41 josephwb no ah there we go
18:41 josephwb was about to say no failed mappings
18:41 jimallman ok. check the contextQuery entries near the bottom of the list (you might want to pause mapping)
18:43 josephwb so many files...
18:43 jimallman better yet, try clicking the Errors token (little red stopsign) above the dev console, and see if the errors is there
18:44 josephwb in a log it says this: "!!! something went terribly wrong"
18:44 josephwb yes
18:44 josephwb that is where i am
18:44 josephwb MISSING ID for this message:
18:44 josephwb findHighestElementOrdinalNumberstudy-editor.js:5707
18:44 josephwb getNextElementOrdinalNumberstudy-editor.js:5683
18:44 josephwb getNextAvailableElementIDstudy-editor.js:5671
18:44 josephwb successstudy-editor.js:862
18:44 josephwb ljquery.js:2:17016
18:44 josephwb fireWithjquery.js:2:34627
18:44 josephwb Tjquery.js:2:81019
18:44 josephwb rjquery.js:2:86579
18:44 josephwb study-editor.js:5708
18:44 jimallman ok, i think i get you.
18:45 josephwb i will send you a screenshot
18:45 jimallman ignore the MISSING ID messages (old stuff from incomplete annotations), look AFTER (below) that
18:45 jimallman (MISSING ID is all from the initial page load)
18:47 jimallman if the errors don’t show up below MISSING IDs, etc, then we’ll need to click Resources (the little blue file drawer at left) and re-open the XHRs folder on the left.
18:47 josephwb pic sent
18:48 jimallman ah yes, the mapping errors are the ones with contextQuery on the right side
18:48 jimallman “The network connection was lost.”
18:48 jimallman are you in fact on a dodgy network connection today?
18:48 josephwb maybe
18:49 josephwb i'll try again in my office later
18:50 jimallman we do try to report the actual error from the server, in the console below “!!! something went terribly wrong”. it looks like there WAS no response text in this case.
18:51 jimallman it looks like my code Does The Right Thing in these cases and marks this OTU as a failed mapping, but your report suggests that we’re leaving the study data in a funky state (since it fails to save). i’ll take a closer look.
18:52 josephwb gotta go; battery almost dead
18:52 josephwb l8r
19:19 jar286 joined #opentreeoflife
19:40 jar286 joined #opentreeoflife
19:54 josephwb joined #opentreeoflife
19:55 josephwb jimallman: on a different network, no error
19:55 josephwb still cannot approve all
19:55 jimallman right, i’m testing the fix now and will make a PR for it…
19:55 josephwb ok, thanks
19:55 josephwb gotta go
23:00 jimallman joined #opentreeoflife

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