Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-07-09

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All times shown according to UTC.

Time Nick Message
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03:09 travis-ci [travis-ci] OpenTreeOfLife/phylesystem-api#569 (Bos - 778a9db : Jim Allman): The build passed.
03:09 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/Bos
03:09 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/29470829
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14:12 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
14:19 jimallman towodo: when you have a minute, i’d like a second pair of eyes. i’m having trouble starting apache2 on ot14, apparently “missing private key” (though everything seems to me to be in place, and matching the setup on ot11)
14:20 towodo ouch.
14:21 towodo it’s important, how about now.  â€¦ I’m in an audio averse environment unfortunately
14:24 jimallman no problem, chat is fine for me.
14:25 jimallman it seems we have ssl support (checked via ‘apache2ctl -M’ and dpkg)…
14:26 jimallman i have the same private key (non-passphrase) as on ot11, and the complete certificate chain installed.
14:26 towodo we’re at slightly different versions of debian on the two machines, FWIW… shouldn’t make a difference
14:26 jimallman i’ve set reasonable-seeming permissions for all certs and keys (checking against ot11), but apache still fails to start.
14:27 jimallman configtest says the syntax is OK, but the ssl error log says “private key not found”
14:28 towodo hmm. very odd.
14:28 jimallman i see we have a second version of the private key (“.with-passphrase”). I don’t need this, correct?
14:28 jimallman on ot11, that is
14:28 towodo correct
14:29 towodo one debugging route: scp -r  the /etc/apache2 directory  to your local machine, for both ot11 and ot14, and do diff -r
14:29 towodo brute force
14:29 jimallman i like it! will try this
14:34 jimallman diffed /etc/apache2 for ot11 vs ot14. absolutely no difference (i added a file and tweaked another, just to be sure it’s working as expected)
14:34 jimallman i’ll keep staring at ownership and permissions, i guess..
14:34 jimallman towodo: ^
14:35 towodo oh no
14:35 towodo i hate this kind of thing…
14:35 jimallman yeah, the error message is soo cryptic. i’m trying to flush out more detail..
14:36 jimallman another possible issue is compatibility of cert and private key, but i’ve checked them against the ones on ot11 and they seem identical. should confirm with diff..
14:37 towodo sometimes at this point i download the sources (apache) and start reading them.
14:37 jimallman do you know a foolproof way to scp something that’s owned remotely by root? i can scp admin@ot14:blah, but for private keys i’ve resorted to cat and the clipboard, which seems dicey.
14:37 jimallman i can momentarily relax permissions, i guess, or make a copy for admin…
14:38 towodo copy it to a temporary location, then sudo mv and sudo chown ?
14:39 jimallman yep, just thought there might be a remote-sudo trick in scp :)
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15:38 jimallman towodo: just FYI - i found the problem! a glitch in my clumsy clipboard method had changed the private key file.
15:38 jimallman an educational detour...
15:39 jimallman back to testing here
15:39 towodo don’t understand why you were using clipboard.
15:39 towodo you can use ssh with a shell command, you know.. maybe a command involving ‘cat’ and ‘sudo’
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15:49 josephwb u there jimallman?
15:49 jimallman towodo: yes, it was a shortcut that had worked for me in the past. i spot checked the result, but there was a subtle error in the middle.
15:49 jimallman dumb
15:49 jimallman josephwb: hi!
15:49 josephwb when i try to download the tree from this study: http://devtree.opentreeoflife.org/curator/study/view/pg_412/?tab=metadata
15:49 josephwb i get this error:
15:49 josephwb "{"description": "Expecting version of NexSON to be specified using \"output_nexml2json\" argument (or via some other mechanism)", "error": 1}"
15:49 josephwb i tried newick and nexus
15:50 jimallman josephwb: are you using the buttons in “Working wiht study data in other tools”?
15:50 josephwb yes
15:50 josephwb nexson works
15:50 josephwb nexml does not
15:50 josephwb nor nexus
15:50 josephwb nor newick
15:51 josephwb all with the same error
15:51 josephwb seems to be trying to do a nexson, even when i ask for something else
15:51 jimallman some of this was spit-balling in the UI. i need to re-test each against the latest APIs about drop any formats we can’t support. sorry about that.
15:51 josephwb ok
15:52 jimallman adding it to my list (there might be an open ticket for it already). i’ll dim or remove the buttons that don’t work… t
15:52 josephwb i think the "Trees as Newick" can be shortened to just "Newick". As it stands, the text runs off the button (Mac, Safari)
15:53 jimallman is there such a thing as a multi-tree Newick file? if not, i should probably remove that one.
15:53 josephwb yes, that exists
15:53 jimallman (or we’d need to build a zip or other archive w/ all trees)
15:54 josephwb newick is likely to be the most used
15:54 josephwb we need it
15:55 jimallman ok, will pursue this with mtholder
15:55 josephwb thanks
15:57 josephwb is there no way to access the tree string from the editor (the one that was originally pasted in)?
15:57 josephwb i can get the nexson and convert it, just wondering if there is a more direct route
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20:53 josephwb hi, jimallman?
20:53 jimallman josephwb: howdy
20:53 josephwb i got yer email
20:53 jimallman helpful?
20:53 josephwb when i go to the Files tab, it is empty
20:53 josephwb http://devtree.opentreeoflife.org/curator/study/view/pg_412/?tab=files
20:54 jimallman hmm. was tree2166 imported in the Trees tab?
20:54 josephwb oh, it is a PG study
20:54 jimallman if so, we should have captured the text (or file) in the supporting Files
20:55 jimallman not sure whether we can do something analogous during import-from-pg.. a question for Mark, i think
20:55 josephwb i thought it was a new OT study for some reason
20:56 josephwb i guess PG studies do not have associate "Files"
20:56 josephwb do they?
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20:57 josephwb got kicked ogg
20:57 josephwb off
20:58 josephwb jimallman: i guess PG studies do not have tree strings as associated "Files"
20:59 jimallman see above, we don’t capture the source data when importing from pg (it’s probably just the relational data in pg, so not sure how we’re represent that)
20:59 josephwb right, thought so
20:59 josephwb i will just convert nexson files until the newick export is fixed
21:00 jimallman thanks. i’ll take that up with mtholder, hopefully it’s low-hanging fruit
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