Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-01-14

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All times shown according to UTC.

Time Nick Message
23:05 fooasdfasdfa joined #opentreeoflife
23:05 fooasdfasdfa testing now from WikiIRC
23:05 fooasdfasdfa https://kiwiirc.com/client/irc.freenode.net
23:06 fooasdfasdfa left #opentreeoflife
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23:07 fooasdfasdfa it's me (Jim) again, still in KiwiIRC
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23:11 directuser Jim again, testing this direct link: https://kiwiirc.com/client/irc.freenode.net/opentreeoflife
23:12 directuser left #opentreeoflife
00:45 jimallman joined #opentreeoflife
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01:03 guest|9200 this is Jim one more time, testing the link from a GitHub README file...
01:03 guest|9200 so far, so good
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01:45 guest|13244 OK, this is pretty handy
01:45 guest|13244 let's see what happens if I close the window without leaving the channel + network properly (like a noob)...
02:06 marktholder joined #opentreeoflife
02:07 mtholder marktholder: testing notification through the kiwiirc page that jimallman configured
02:07 jimallman marktholder: hi!
02:08 marktholder jimallman: hi. This is pretty nice.
02:08 marktholder this being kiwi
02:08 jimallman yes, it's a pretty smooth onramp.
02:08 jimallman and no obstacles to a serious IRC user
02:09 jimallman marktholder, mtholder: does it highlight messages that include your WikiIRC name?
02:09 jimallman s/WikiIRC/KiwiIRC
02:10 marktholder I don't think so.
02:10 marktholder It does beep when my nick is mentioned...
02:10 jimtest joined #opentreeoflife
02:10 jimallman jimtest: hi, testing a new name
02:10 jimallman no names in this line
02:10 jimallman jimtest: trying again
02:10 jimallman and here's jimtest in the middle of a message
02:11 jimallman marktholder: yes, it beeps audibly and (in the default skin, at least) highlights the line
02:11 marktholder I take that back. it does highlight them. I just was using a skin that was bad for my poor color vision.
02:12 PEM joined #opentreeoflife
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02:15 jimallman PEM: hi!
02:15 PEM Hi
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13:41 topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
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14:43 blackrim presumably this is the new channel?
14:44 mtholder yup
14:46 mtholder duke was able to get the name changes, so that what used to be logged under otol now shows up in http://irclog.perlgeek.de/opentreeoflife/2014-01-14
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15:09 towodo checking out the new irc channel… looking at log
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15:15 kcranstn what's the timezone on the log?
15:16 kcranstn seems to be GMT
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15:46 jimtest i'm not having any luck with the search feature (in channel log): http://irclog.perlgeek.de/opentreeoflife/search/
15:46 jimtest maybe it only searches prior transcripts?
15:46 jimtest i'll check again tomorrow
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16:30 towodo dev.opentreeoflife.org is on the blink
16:34 mtholder joined #opentreeoflife
16:46 jimallman towodo: looks like it's failing to find the starting-node ID for the synthetic tree. is this the asterales subset?
16:47 towodo I haven't touched ot3 or ot2. So I don't know. Not sure how it could have been reconfigured if you didn't do it.
16:47 towodo let me look at the log files
16:51 towodo no logs on ot2
16:51 towodo logs on ot3 say 'jima' updated opentree repo at 2:27 UTC on Jan 14
16:53 towodo the error could result either from a new db version (no "life") or from a plugin update
16:53 towodo or i guess from a configuration change (pointing to a different neo4j host)
16:53 towodo this is weird
16:54 towodo i'd say switch to ot4 for neo4j service but we really need to get some timings before abandoning ot2
16:55 towodo ah, taxomachine db was updated on ot2 1/12.  that's Cody
16:55 towodo although i don't know how that could create this problem
16:56 towodo will send email to the software list proposing to update ot2 to latest deploy system, and urge people (i.e. Cody) to use it
16:57 towodo also will make sure that install-db puts a message in the log (will look now)
16:57 towodo it dows
16:57 towodo it does
17:16 jimallman towodo: i'll check my config file.. maybe i screwed things up when i did my push.
17:18 jimallman yes, looks like my config file specified ot3 as both OPENTREE_HOST and OPENTREE_NEO4J_HOST
17:18 jimallman towodo: should i push opentree again, with ot2 as the OPENTREE_NEO4J_HOST?
17:19 towodo that would do it.
17:19 towodo yes
17:19 jimallman coming right up...
17:20 towodo i'm preparing a config file for ot2 so i can patch it
17:20 towodo although maybe no need since now I see it's not Cody's fault… i saw a modified file and couldn't think of any other reason for it. sorry Cody
17:21 jimallman done and working now.
17:22 towodo jimallman: How did this come about? curious. you must have had a working config file earlier.
17:23 jimallman yes, i keep a few around...  'ot3.config' is the current version (OPENTREE_HOST=ot3, OPENTREE_NEO4J_HOST=ot2)... i have an alternate version 'ot3a.config' that specifies ot3 for both
17:24 jimallman this was created last week while troubleshooting another problem. sounds like i should get rid of it.
17:24 towodo or modify it.
17:25 jimallman the only difference (confirmed via diff) is the OPENTREE_NEO4J_HOST setting, so i'll just go back to my previous 'ot3.config'
17:25 towodo the OPENTREE_COMPONENTS will help this problem a bit because if neo4j isn't installed at all then the error will be more dramatic thus easier to diagnose
17:26 jimallman right.. i wonder if we can/should store the config file (or settings) used in previous pushes. i'm concerned about these kinds of mysteries, particularly
17:26 jimallman in the case of alternate branches
17:26 towodo not a bad idea.
17:26 towodo actually i think that's done now
17:27 jimallman ah, i should look deeper for this history/transcript...
17:27 towodo but i just added the feature.  it's in setup/CONFIG
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17:27 towodo just the latest one though
17:27 jimallman thanks, i'll take a look
17:28 jimallman ah, i see. neat!
17:29 towodo I guess we could copy it to the log file on each push, but that would clutter the log file
17:29 towodo or there could be a second log file
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17:34 guest|1736 testing
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17:36 towodo ok, updated deployment system on ot2, so if anyone does any further operations they will be logged
17:42 jimallman towodo: cool, thanks
17:43 towodo well… assuming they go through the deployment system… I guess that was a no-op, never mind
17:43 towodo but at least i have a working config file for ot2.
17:47 towodo jimallman: this problem with 'important' taxa getting buried is annoying. wondering if there's some really low-tech fix, like sorting on the size as found in javascript, as opposed to size as found in treemachine (true size)
17:48 towodo I'm looking at cyanobacteria on ot4
17:48 jimallman hm, i can take a look in the argus code.. i believe we're sorting client-side before burying stuff under "more", so it might just be a tweak there
17:48 towodo oh, no, looking at it on dev / ot2. sorry. but the problem remainds
17:49 towodo yes i imagine just a tweak to the sort order (number of children, then alphabetic)
17:49 jimallman is number of children a good enough reckoning of size? or recursive (number of descendants)?
17:49 towodo I don't know… was trying to keep it cheap… recursive is better though
17:49 jimallman ...bearing in mind that argus only "sees" a few levels into the clade
17:50 jimallman i'll try it based on the descendants we have in view
17:50 towodo yes, I acknowledge this is a shortcut.  maybe it's a broader group discussion
17:51 towodo could be phased. (1) without treemachine cooperation, sort using current info in javascript (2) with true size from treemachine
17:53 towodo 'developer resources' page is not up to date i think… i added a link but don't see it
17:57 jimallman towodo: is that in branch 'master'? latest change there is mine, 7 days back:
17:57 jimallman https://github.com/OpenTreeOfLife/opentree/blob/master/webapp/views/about/developer_resources.html
17:58 dukeleto jimallman: the IRC link in the readme is really nice!
17:58 jimallman yeah, KiwiIRC is good stuff, very friendly
18:00 jimallman i do wish there was a more central place to put it on GitHub... we might need to sprinkle this button in all repos, home pages, etc.
18:00 kcranstn joined #opentreeoflife
18:00 kcranstn anyone else having problems with kiwiirc not reconnecting after sleep?
18:01 jimallman hm, for me it occasionally loses the connection, but always reconnects.. haven't tried a proper OS sleep, though.
18:01 towodo jimallman: Foo. My pull request mixes good commits with bad ones.
18:02 towodo the recent three are good. the earlier two commits are for smasher.
18:02 kcranstn who is towodo?
18:02 jimallman towodo=jar
18:02 kcranstn of course
18:02 towodo sorry, towodo is jar
18:03 jimallman TOtal WOrld DOmination, apparently his rapper name
18:03 towodo I thought it was original. oh well
18:03 jimallman no, it's good! mine could use a bit more attitude
18:05 jimallman towodo: i assume you meant this pull request? https://github.com/OpenTreeOfLife/opentree/pull/181
18:05 jimallman hm, but that only has four commits..
18:05 towodo sorry, i didn't do the pull request for the latest one. see under branches
18:06 towodo the 5th is sort of trivial, from today
18:06 jimallman i see, jar-misc
18:06 towodo so how do we do surgery on a branch, or pull request? cherry-pick commits from a set?
18:07 towodo i think we just want to flush the oldest two so we don't resurrect smasher
18:07 jimallman i think you can diff the branch (as if to make a pull request, then edit the range), like so:
18:07 jimallman https://github.com/OpenTreeOfLife/opentree/compare/master...3c41e4f
18:08 jimallman ah, killing the older ones can be done with 'git revert {SHA}'
18:08 towodo do I do that locally, then push again? i can try
18:09 jimallman yes. note that it requires a clean working tree, so you'll need to stash any loose ends
18:09 towodo what about untracked files?
18:12 jimallman those should present no problem
18:13 jimallman and of course, updating this branch-diff will tell you whether the result is what you expected: https://github.com/OpenTreeOfLife/opentree/compare/master...jar-misc
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18:32 guest|47012 this is jim, testing kcranstn's reported sleep bug...
18:35 guest|47012 joined #opentreeoflife
18:35 guest|47012 ...and i'm back
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18:36 guest|47012 krancstn: so far i've been able to reconnect (automatically) after sleep. but i did have trouble connecting from kiwiirc login page a while ago.
18:36 * guest|47012 is jimallman
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18:41 jimallman towodo: it looks like we're already doing the sort-by-descendants count (or sorting by children, at least) in argus:
18:41 jimallman https://github.com/OpenTreeOfLife/opentree/blob/master/webapp/static/js/argus/drawtree.js#L300
18:41 blackrim joined #opentreeoflife
18:42 blackrim is it possible that my university is blocking the port that would allow for standalone clients to connect to IRC? I can't seem to connect except in a web app (of course, I can connect from home)
18:42 jimallman i think it's even a proper, deep count of descendants (will need to confirm):
18:42 jimallman https://github.com/OpenTreeOfLife/opentree/blob/master/webapp/static/js/argus/drawtree.js#L1715
18:45 jimallman blackrim: yes, i believe freenode traffic is always on port 6667.
18:46 jimallman ssh tunnel with port forwarding might be a fix
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18:50 jimallman blackrim: from http://freenode.net/irc_servers.shtml  : "All freenode servers listen on ports 6665, 6666, 6667, 6697 (SSL only), 7000 (SSL only), 7070 (SSL only), 8000, 8001 and 8002."
19:05 blackrim thanks jim, yeah, I will port forward
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19:56 * guest|88234 is jima, testing page reload...
19:57 guest|88234 la la la
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19:57 guest|38369 now i'm back, but with a different userid
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20:08 towodo well foo. i'll have to look more closely at what people have been complaining about
20:25 mtholder phylografter is down. Is that old news?
20:25 kcranstn not to me
20:26 mtholder I'll send an email to rick, peter, and lyndon...
20:26 kcranstn thanks
20:26 kcranstn we should be monitoring that
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20:29 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#267 (master - 3be22c1 : Jonathan "Duke" Leto): The build passed.
20:29 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/5386bb134aa8...3be22c1b766b
20:29 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org/builds/16955083
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20:35 blackrim joined #opentreeoflife
20:35 blackrim ok, I finally got through the university network with ssl and a crazy port number. that will show those admins
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20:39 jimallman blackrim: yarrrr
20:40 guest|38369 left #opentreeoflife
20:40 blackrim is the joining and leaving attempts to refresh?
20:41 jimallman not sure. i've been testing a few different ways of connecting, so guest### is probably just me.
20:41 blackrim gotcha
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20:54 josephwb first!
20:57 blackrim welcome joseph from the room nextdoor
20:58 blackrim I feel like we should really move this to AIM. that is where the real chat begins
20:59 josephwb we should put the general instructions you gave me up somewhere so that people like Ruchi can quickly join in.
21:00 blackrim does someone (maybe jim or mark or duke) have some general instructions for how others should come over here that they could send on the open tree mailing? Maybe just using http://webchat.freenode.net/ or https://kiwiirc.com/client (I feel like there may be a bar for some others to join)
21:01 blackrim If not, I will just send something that does the connecting to webchat.freenode.net because that is probably the least intense
21:03 josephwb What's the mac equivalent of pidgin again?
21:03 mtholder I have not had a problem with using https://kiwiirc.com/client/irc.freenode.net/opentreeoflife but I think that kcranstn did have some issues with it.
21:03 blackrim adium is the mac version of pidgin
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21:06 blackrim sent an email to opentree (directed to Ruchi). so we will see if that works
21:06 josephwb I had to change the port (7070) and add ssl to get it to work, but that may be a Michigan issue.
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21:07 travis-ci [travis-ci] OpenTreeOfLife/phylesystem#95 (master - deb7a0e : josephwb): The build passed.
21:07 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem/compare/468f4931bf00...deb7a0ee7937
21:07 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem/builds/16956978
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21:08 towodo blackrim, i'm assuming you will answer the 'where is the tree of life' question
21:08 towodo hyman hartman told me: 'There is no tree of life'
21:10 blackrim that is an odd question because I am stuck on what the word 'where' means. for the second bit, it seems like a lot of folks get stuck on the semantics of tree.
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21:18 josephwb1 test connecting via mac
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21:25 * asgjsd slaps josephwb1 around a bit with a large trout
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21:29 jimallman re; IRC clients for OS X, Colloquy is also pretty good.
21:30 ruchi joined #opentreeoflife
21:30 blackrim aha! so the webchat.freenode.net seems to be a good alt to kiwiirc (i see ruchi made it)
21:31 ruchi yeah I did :)
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21:43 ruchi So I guess this the place to raise questions. I am looking for the latest "newick format" tree of life.
21:44 blackrim I think that there are only old ones and really bad ones right now because we have been changing the taxonomy so much
21:44 blackrim however, the last one that was in newick is here http://files.opentreeoflife.org/other/curnewicks/index.html
21:45 blackrim I am working on making a new one now, but the recent taxonomy changes have moved some things around (and aren't likely to be settled because things are being edited now by the empirical folks)
21:45 mtholder note that that one may not correspond to the list of inputs that you have, ruchi.
21:46 blackrim aha, that is right mark. it will be close but not exact because at that point we hadnt been recording that information (that won't be the case on the next full build). if there is something else that is better for you to work with I can also try and build that (something simpler or more compact)
21:46 ruchi That will be a problem.
21:47 mtholder ruchi, the synthetic tree of life from blackrim's treemachine also uses the structure of the OTT taxonomy. I'm not sure if we have that in newick for you to use as an input.
21:48 ruchi ANother question: in general how much time it takes to build a ToL from say 50 something input trees? (a rough guess will work)
21:48 blackrim I do have a newick of the taxonomy I am currently using (but again, these have been updated 5 times by Jonathan over the last 3 days so rapid changes are afoot)
21:49 blackrim I would say a few hours from loading everything to synthesizing to export to newick for 50 trees and the whole tree of life
21:50 ruchi Will a ToL be a part of the first paper that Karen mentioned?
21:50 blackrim yes
21:50 mtholder Karen mentioned a data sharing paper in email today that would be ready in a couple of weeks. that paper won't have the ToL.
21:51 blackrim oh, woops, sorry
21:51 ruchi oh ok
21:51 mtholder I think that paper is just by her, Luke Harmon, and Maureen O'Leary.
21:51 blackrim oh the 10 simple rules paper
21:51 mtholder yup
21:52 mtholder maybe there are other authors. I'm not sure.
21:52 blackrim nope, that sounds right
21:54 ruchi I had to run my method on a ToL with some input trees. It doesn't matter if this ToL is final or not.
21:55 blackrim do you want me to make just a test set of inputs? or is that not helpful
21:57 ruchi That will be great.
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21:58 blackrim ok, I will get those together for you and send you a list and a newick for the tree of life generated as well as the input taxonomy. will that be sufficient?
21:59 ruchi Yup for now.
22:03 blackrim ok, I will do that. Might take a day but soon
22:06 ruchi Not a problem. Thank you!
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