Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-09-03

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All times shown according to UTC.

Time Nick Message
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01:01 towodo joined #opentreeoflife
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01:46 towodo jimallman, the new server ot20 is in place, but MIT CSAIL seems to be off the internet - can’t get to ot10. so no tgz copying tonight
01:54 towodo transient…
01:55 towodo ARGH! The treemachine .tgz disappeared!
01:58 towodo I guess I can rebuild it from the graph.db directory on ot10.  too tired now, will copy taxomachine tarball now
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11:55 josephwb morning, ilbot3.
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12:46 josephwb joined #opentreeoflife
12:48 towodo morning josephwb, do you still have a tarball of the latest treemachine db?
12:49 josephwb it should be on dev
12:49 josephwb i haven't made anything newer
12:49 towodo it got deleted.  i think dev ran out of space and someone scrambled to find room
12:50 josephwb ok, i can copy it back there if you like
12:50 josephwb or somewhere else?
12:50 towodo well i wonder if you could copy it to ot20 instead
12:50 josephwb i can do that
12:50 josephwb running for the bus in a second, tho
12:51 josephwb but i can do it as soon as i get in
12:51 towodo oh ok… later then
12:51 josephwb unless there is a script ready to go?
12:51 josephwb is there a config for ot20?
12:52 towodo yes but i need about 3 minutes to set the ssh config so you can get in
12:52 josephwb ok, i need to leave before that, so i will do it when i get in
12:52 josephwb sorry
12:52 towodo that’s fine
13:23 towodo kcranstn, do you think we can put a tree that lacks eukaryota on the production site?…
13:23 kcranstn danger!
13:23 towodo i would think not
13:24 kcranstn I am more comfortable with errors like that if we had results of the regression tests (and linked to the souce tree that contradicts monophyly)
13:24 towodo agreed
13:25 towodo interesting that nobody noticed. I guess we never asked for review
13:26 towodo it’s been up only since aug 14
13:39 josephwb joined #opentreeoflife
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14:12 towodo kcranstn, i’m asking romina to take a look at the fungi in the aug 14 tree.
14:13 kcranstn ok
14:51 codiferous joined #opentreeoflife
14:57 josephwb i think fungi should be fine
14:57 josephwb i think it is one of the microbe studies
14:58 towodo fungi is of independent interest - this is the first the romina & david will have a chance to review the April version of Index Fungorum
15:00 towodo jimallman, starting hangout now
15:01 jimallman yes, on my way
16:03 josephwb so, no more direct commits to master?
16:03 josephwb what if i am fixing a simple error (say, to an iterator). do i need to create a new branch?
16:03 josephwb jimallman kcrastn towodo ^
16:04 josephwb kcranstn ^
16:17 josephwb no one?
16:54 jimallman hi josephwb. i’m not sure we got an answer for simple fixes.
16:55 kcranstn let’s start with the simple rule of no direct commits to master (or merging your own PRs)
17:05 towodo joined #opentreeoflife
18:20 josephwb jimallman: is the curator going to be down?
18:21 jimallman production curation app will certainly need to shut down during the changeover, and we’ll probably block it for awhile beforehand. i’m waiting on a sign from towodo that he’s close to ready for the changeover.
18:22 josephwb ok, thanks. chasing down the errant study.
18:22 josephwb looks like we got an unrooted / improperly-rooted tree
18:23 josephwb can you give me some warning when it is about to go down (or, beforehand)?
18:23 towodo joined #opentreeoflife
18:24 josephwb i should be able to just reroot it, download it, and we will be good to go
18:24 josephwb not trvial though. 1000+ tips. want to be sure it is rooted correctly.
18:32 towodo josephwb, I’m probably still an hour or two away from doing the oti index build, which is when the curator app needs to go down.  Not sure if it’s today or tomorrow. I’ll send a message out to the opentreeoflife google group
18:42 josephwb ok, thanks.
18:42 josephwb i've got the study, and the original tree, so shouldn't be long now
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19:05 josephwb ok, i got that one fixed (study of cyanobacteria with chloroplast outgroups, except it was rooted with chloroplasts internal)
19:05 josephwb i will run some tests, and if they pass go ahead with the big kahuna
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21:01 towodo jimallman, you there?
21:02 jimallman yes, hi
21:02 towodo I was trying to set up Danio, which I thought was going to be populated from the master branches of the repos, but I just noticed you’re putting things in Cavia
21:02 towodo I don’t understand this
21:03 jimallman oh drat. i forgot you were moving on to Danio
21:03 jimallman so now Cavia branch does not reflect the deployed Cavia  :-/
21:04 towodo right.  is the problem that there are unreviewed commits in the master branch, so we don’t want to populate production from master?
21:05 jimallman yes, this is just following the new (more cautious) policy. if all PRs for Cavia have been accepted, i could just create a new PR for Danio, or create the Danio branch directly from master.
21:05 jimallman nope, there are three outstanding PRs for Cavia: https://github.com/OpenTreeOfLife/opentree/pulls
21:06 towodo ‘nope’ what?
21:09 jimallman nope = we can’t just create Danio from opentree/master
21:10 jimallman until we have a decision (review) of these PRs
21:10 jimallman at least in principle, i would treat all PRs merged as a decision that all this (ie, current master) is good enough for Danio
21:11 towodo ok let’s see if we can get the reviews done
21:11 jimallman thanks
21:12 josephwb i added to the "flow" thread by bringing up what to do with straight-up DB updates
21:12 josephwb mostly treemachine, i imagine
21:13 towodo I answered
21:13 josephwb sometimes taxomachine (though less frequently)
21:13 josephwb oh, just came in
21:13 josephwb right, so sort of what we do now, but we make sure people look at it!
21:14 josephwb checking for "known" clades is a good idea
21:14 josephwb should be able to automate that...
21:15 josephwb with the new plugin (now called "node_info", i believe), this will be easy-peasy
21:15 josephwb and we can of course script that
21:15 josephwb so, yeah, i think that will be good for the review process
21:16 josephwb further, we can have scripts that take a taxon as an argument, so people can check on their group of interest
21:16 josephwb *should have had this long ago*
21:18 josephwb but pushing a DB to dev is still straightforward, yes?
21:19 towodo basically, yes (although there are things that can go wrong, like putting the wrong root dir for the tar file, or running out of space)
21:22 josephwb right, okay, thanks
21:26 towodo ok… I’m at the point where I need the Danio branches. reviewing some PRs.
21:26 towodo setp 9 in https://docs.google.com/document/d/1JU3kXu7zQHG0ZriwkUIbZuR9QhTitykRKeV8L1491IU/edit
21:27 towodo s/setp/step/
21:29 towodo once again I need one or two studies loaded to dev but not yet OTU-mapped, for review
21:32 towodo I guess I can ‘clear all mappings’
21:34 jimallman yes, that should do the trick
21:35 towodo wow there’s some weird stuff in the taxonomy
21:37 towodo the checkbox / X are appearing on top of the orange and blue text boxes on the right
21:42 towodo it would be nice if the taxa suggestions were clickable to get more information (lineage, source taxonomies, etc) …
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23:03 jimallman kcranstn: i screwed up by targeting Cavia with these pull requests, by the way. Now that towodo is moving on to Danio, we’ll just merge all the recent stuff to that branch (from Cavia, or just be creating Danio from master). I’ll take one last look to make sure nothing sneaks into the Danio branch that hasn’t been reviewed.
23:04 kcranstn ok, sounds good
23:04 kcranstn thanks for splitting up that giant PR
23:05 kcranstn just merged that fuzzy matching PR to Cavia
23:05 jimallman no prob. i can share the steps for this, if we think it’s a situation people will encounter again. (or we can just expect more “hygienic” branching.)
23:06 jimallman ok, as soon as we get the green light (merge) for PR #412, i’ll coordinate with towodo and figure out how we move all this to Danio
23:08 kcranstn I’d like towodo to look at 412
23:16 * jimallman nodes
23:16 jimallman nods

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