Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-01-12

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All times shown according to UTC.

Time Nick Message
00:44 towodo joined #opentreeoflife
01:02 towodo joined #opentreeoflife
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12:27 towodo joined #opentreeoflife
14:58 josephwb you there jimallman?
14:58 jimallman yes, hi
14:58 josephwb hi
14:58 josephwb curator still cannot find a real study for me. ot_214
14:59 josephwb i search for Jarvis, hits nothing
14:59 jimallman did you just add this one?  (like, in the last few days?)
14:59 josephwb nope. before the break.
14:59 jimallman ok. i think we need to force a full re-indexing of oti.
15:00 josephwb ok, just checking
15:00 josephwb thanks
15:00 jimallman thanks for the nudge, i meant to do it after we fixed the oti bug that causes this.
15:00 josephwb this was ~12 December
15:00 jimallman right. we had a fix (you merged) in code, but it wasn’t pushed out to production
15:01 josephwb yeah, that sounds right
15:04 * jimallman is re-indexing oti now, will report when it’s done (but first, coffee!)
15:34 mtholder joined #opentreeoflife
16:11 towodo damnit. I need to put ‘push to production’ on my calendar for every weekend.  will do so now
16:28 jimallman josephwb: this has been done for awhile now. please re-check for your study
16:28 jimallman towodo: no prob, i meant to follow up on this
16:29 josephwb jimallman: a while now? like today?
16:29 jimallman josephwb: yes, i mean in the last hour (forgot to ping you here)
16:29 josephwb yup, there it is. thanks.
16:29 jimallman 3 studies failed to index, investigating these now…
16:32 towodo it’s on my calendar but I haven’t pushed yet
16:33 towodo looking at logs to see if anyone’s working, but that’s hard since most GETs are from the botnet
16:34 towodo looks like maybe someone is using the site. something about Facilispora
16:35 josephwb i am logged in to edit a study; will log out now.
16:35 josephwb done
16:35 josephwb mine was birds, tho
16:36 towodo right, it’s hard to tell whether someone’s at work.
16:36 towodo maybe looking at timestamps in the sessions directory will help
16:38 towodo nope, includes bots
16:43 jimallman towodo: i re-indexed oti, haven’t pushed anything else to production.
16:43 jimallman meanwhile, i entered a ticket for the failed studies: https://github.com/OpenTreeOfLife/oti/issues/34
16:44 towodo does production need to be updated for the purpose of what Joseph is going?
16:45 josephwb i'm not doing anything important. i think romina is doing active work, tho.
16:45 towodo i’ll send her email
16:49 towodo can I do the deploy at 5pm? giving everyone who might care some warning?
16:49 josephwb i'm fine with anything
16:49 towodo I think I’ll say 5pm, it’s more orderly. thanks
16:57 towodo ok, 5pm
17:03 kcranstn joined #opentreeoflife
17:04 kcranstn what is it about the study list that takes it so long to load?
17:05 kcranstn and can we do something about that?
17:07 kcranstn supposed to be giving a project presentation for nescent informatics group, and I can’t get the curator page to launch
17:08 kcranstn devtree load quick
17:10 kcranstn and I am getting a login error on the dev site… :(
17:10 kcranstn “admin disabled because unable to access password file"
17:10 kcranstn jimallman? towodo?
17:21 kcranstn and the main tree.opentreeoflife.org page is giving that whoops error
17:21 kcranstn so, fail all around
17:22 kcranstn Cross-Origin Request Blocked: The Same Origin Policy disallows reading the remote resource at https://api.opentreeoflife.org/treemachine/v1/getSyntheticTree. This can be fixed by moving the resource to the same domain or enabling CORS.
17:22 kcranstn Cross-Origin Request Blocked: The Same Origin Policy disallows reading the remote resource at https://api.opentreeoflife.org/taxomachine/v1/autocompleteQuery. This can be fixed by moving the resource to the same domain or enabling CORS.
17:22 kcranstn firefox. tree works on chrome
17:23 towodo ‘the main tree.opentreeoflife.org page’ works for me, what URL is broken?
17:24 kcranstn works for me on chrome
17:24 towodo study list load took 1-2 secs
17:24 towodo I’m using ff
17:24 kcranstn mine never loaded
17:24 kcranstn I may get you to do the demo, then ;)
17:24 towodo that’s fine… I’ll run through everything now
17:38 * jimallman just got back here.. catching up now
17:39 kcranstn I think maybe private browsing modes in firefox and chrome are causing problems
17:39 kcranstn because things are working for towodo
17:40 jimallman thanks for the heads-up, chasing this now…
17:40 kcranstn I can send the chrome errors too (different than the ff errors)
17:40 jimallman yes, please! i’m surprised by the cross-domain errors, thought we had this completely covered.
17:43 kcranstn curator in ff: Blocked loading mixed active content "http://api.opentreeoflife.org/oti/v1/findAllStudies"[Learn More]
17:46 jimallman odd, i’m having no problems with the main tree-view page (https://tree.opentreeoflife.org/ OR http://tree.opentreeoflife.org/) in Chrome and FF (Mac v34.0). initial load is good, and jumping to nodes too.
17:46 * jimallman is moving to the curator to reproduce problems there
17:47 jimallman agreed that the study list is slow (4 sec for me)
17:47 jimallman … then 2 sec (maybe it’s being cached now?)
17:55 jimallman towodo, kcranstn: the mixed-content warning (study list won’t load in HTTPS) is due to stale config on production. this was recently changed to a scheme-relative URL (starting with “//“). i can do a hot-fix on current production for this, but i’ll need to restart apache. OK to do this now, or should this wait?
17:57 kcranstn wait
17:57 kcranstn until after 2 pm
17:57 jimallman ok, standing by. meanwhile, you can load the study list by switching to HTTP for that page (sorry)
18:00 jimallman left #opentreeoflife
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18:59 towodo jimallman, I may not be at a computer at 5… any chance you could do the push.sh?
19:00 towodo have to pick up daughter from basketball
19:00 jimallman sure! both production pushes (tree and api), yes?
19:00 towodo I guess, but I think there are only changes for tree (not sure)
19:01 jimallman ‘production’ branch for opentree repo, and ‘master’ for all others?
19:01 towodo no, ‘master’ for all
19:01 jimallman (i’m pretty sure there are pending changes to api.opentreeofilfe.org, like the HTTPS glitch in oti study-list)
19:01 towodo there is no ‘production’ or shouldn’t be
19:01 towodo ok
19:01 jimallman doh, right
19:01 towodo during PR review we pushed to master
19:02 * jimallman nodes
19:02 jimallman nods
19:02 * jimallman is setting a reminder now
19:03 towodo thanks much
19:03 towodo I’ll ask olivia if I can get wifi at the high school
19:04 jimallman sure thing. i’ll check in here (IRC) at 5pm before pushing anything.
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21:41 towodo josephwb, I get that the worst case running time for brute-force synthesis is O(a^2 * b^3), where a = number of trees, b = # vertexes per tree
21:41 towodo sound right?
21:41 towodo obviously much less on normal inputs
21:59 towodo jimallman, i’m here
21:59 jimallman gotcha.
21:59 towodo I can just go ahead and do it.
21:59 jimallman i’ll just stand by, in case you hit a snag (blocked port or similar)
22:00 jimallman thanks
22:02 towodo no session activity in the last 7 minutes…
22:06 towodo doing ./push.sh -c ../../deployed-systems/production/tree.config  , right?
22:06 towodo having just done git pull in the opentree repo
22:07 jimallman looks right to me
22:07 jimallman (assuming no weird local modifications to tree.config)
22:09 jimallman towodo: when you can break concentration, i have a couple of questions about release pages
22:09 towodo right. there were none, I checked
22:09 towodo interesting, it’s pulling/updating all branches.  maybe this should be suppressed.
22:09 towodo recompling ncl …
22:10 jimallman hmm. i think there’s a subtle ncl dependency in opentree, actually
22:10 towodo well, certainly from peyotl
22:10 jimallman yep
22:10 kcranstn I am here too (for the release pages questions)
22:10 jimallman great, thanks!
22:13 jimallman OK, questions: as i understand it, we want release pages for synthesis and taxonomy, correct? and detailed phylesystem stats are not “page-worthy, except as the source for our area chart (showing growing OTUs in synthesis)…
22:13 kcranstn I can see having a taxonomy page, a synthetic tree page and a general statistics / progress page
22:14 jimallman agreed, i’m working on a top-level “release history” page that includes the area chart with markers on the dates where we had a (synthesis or taxo) release…
22:14 kcranstn the latter includes the area chart
22:15 kcranstn I like that plan about linking the area chart to release pages
22:15 towodo hanging in ‘loading study list’
22:15 jimallman towodo mentioned “synthesis and analysis” the other day, which makes me think i missed something else.. not sure what he meant by analysis
22:15 jimallman towodo: OK, checking the config file on production...
22:15 kcranstn I think it was that the pulldown menu said synthesis but dates didn’t match
22:16 kcranstn points in the area chart might be more frequent that dates for synthetic tree / taxonomy versions
22:17 jimallman kcranstn: this is a quirk of how we’re massaging the data, we basically merged the dated records for synth and phylesystem records, so that any date in either list would be in the page’s dataset. i can change this.
22:17 towodo jimallman, how do I debug this?
22:17 jimallman towodo: the oti base URL in webapp/private/config still has the “http:” prefix, but it shouldn’t.
22:18 jimallman tracing this backward now… to where we build this config file.
22:18 towodo why didn’t this show up in production?
22:18 towodo i mean dev?
22:18 towodo I should have deployed to dev first.
22:18 towodo dev to dev, that is.
22:19 towodo or even master to dev.
22:19 kcranstn towodo is confusing me
22:19 jimallman i thought it was tested on dev.. but it only shows up if a curator is already logged in (thus in HTTPS), so it might have slipped by
22:19 towodo let me start over. i should have deployed the master branch to devtree first, as a final test before deploying master to tree.
22:20 jimallman i see. this var (OTI_BASE_URL) looks right in deployed-systems/production/tree.config, starts with “//…”
22:20 jimallman this should give us a similar (scheme-relative) URL in the final webapp/private/config
22:21 towodo maybe I screwed up push.sh
22:21 towodo but I don’t think my changes to it were merged.
22:21 towodo double checking that
22:22 towodo no, my recent changes are still out on a branch
22:23 jimallman i see a likely bug in push.sh… line 106
22:23 jimallman https://github.com/OpenTreeOfLife/opentree/blob/master/deploy/push.sh#L105-L106
22:24 towodo right, I remember talking about this but don’t remember the resolution
22:24 jimallman i believe we’re good now to remove this scheme.. i’m patching it in the server-side code (as we’ve done elsewhere)
22:24 towodo but why should that matter?  OTI doesn’t need https
22:26 towodo really we’re looking at tree.config, not the line in push.sh
22:26 towodo tree.config overrides push.sh
22:26 towodo but it’s the same problem
22:26 jimallman it shouldn’t handle either HTTP or HTTPS (so we can handle both).. we need it for the findAllStudies method, used in the study list (curation homepage) else we get the mixed-content warning
22:26 jimallman but you’re right, we should be using the OTI_BASE_URL from tree.config…
22:26 towodo ahh. right. mixed content.
22:27 towodo tree.config also has the http:
22:27 towodo I could just patch it to say https:
22:28 towodo installing emacs
22:28 jimallman tree.config should have no scheme (start with “//…”), like so: OTI_BASE_URL=//${OPENTREE_API_HOST}/oti/v1
22:28 jimallman that’s what i’m showing here..
22:29 towodo looks like it’s been tested on devtree. so good to go.
22:30 towodo so I’ll edit it on my laptop, push to master, and redeploy. sound right?
22:31 jimallman editing push.sh? tree.config? i’m lost
22:31 towodo tree.config
22:32 jimallman ok, is it current scheme-less, or http:// ?
22:32 towodo oh right, i don’t need to push to github.
22:32 towodo sufficient to edit locally. i’ll try it
22:32 towodo here goes
22:33 towodo interesting. this is a bug that wouldn’t have been caught by deploying to devtree.
22:34 jimallman why is that? we support HTTPS, login, etc the same on both..
22:34 towodo the bug is in deployed-systems, which is specific to production / development
22:34 jimallman ah, i see.
22:34 towodo if devtree.config works, we don’t know that tree.config works
22:35 jimallman right. did you opt for scheme-relative OTI_BASE_URL, or https://… ?
22:35 towodo javascript console is interesting, but obviously not a problem
22:35 jimallman i’d prefer the former, which is what i’m seeing in the latest production/tree.config… so i’m not sure why it was failing.
22:36 towodo maybe I didn’t pull? but I thought I did. let me check
22:36 jimallman remember, it’s the other deployed-systems repo
22:37 towodo looks like i didn’t pull.  i started to but got confused by trying to stash some local changes
22:38 jimallman been there!
22:38 towodo let me straighten that out
22:43 towodo jimallman, there’s a new PR assigned to you.
22:43 * jimallman is heading there now...
22:46 jimallman ok, so net change is entirely to comments (looks like http: was removed in both)
22:46 towodo jimallman, I wonder if synthetic tree updates could be detected just by looking at the git commit log…
22:46 * jimallman merged the PR
22:47 * towodo tnx
22:47 jimallman does synthesis make a characteristic commit? i don’t recall
22:47 towodo it could.
22:47 towodo in future.
22:47 jimallman true
22:47 towodo ok, gotta work on dinner
22:47 jimallman we’ve talked about creating artifacts as the basis for a synthesis-release page.. maybe that
22:47 jimallman that’s automated, at least created a dated folder..
22:48 jimallman food for thought!
22:48 towodo thanks for the help
22:48 jimallman sure thing! hey, one quick question if you have a sec..
22:48 jimallman the other day you mentioned “analysis and synthesis” when we were talking about stats and releases
22:48 jimallman what did you mean by “analysis”?
22:49 jimallman (if you’re away from keyboard… i’ll check in later)
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