Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-09-23

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Time Nick Message
01:52 towodo joined #opentreeoflife
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17:28 codiferous hellowdo towodo
17:36 codiferous i suppose i should have said hellowodo or hellwodo
17:39 codiferous thinking about mtholder's proposal for mapping newick nodes to json
17:41 josephwb joined #opentreeoflife
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17:45 josephwb hey jimallman
17:46 jimallman hi josephwb
17:47 josephwb is there a way to: 1) stop neo4j , 2) recompile (say, treemachine), 3) restart neo4j? All this, without a new code commit.
17:47 josephwb with commits, works fine
17:47 josephwb had a maven screw up, just needed to recompile
17:47 josephwb pushed a trivial commit to get it recognized as "new", forcing recompile
17:48 josephwb this is on dev
17:50 josephwb i.e. if I do the push.sh -c … dealy, it doesn't do anything if there is no change to the code
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17:52 josephwb towodo might know this?
17:53 towodo back from errands
17:53 towodo might know what?
17:53 towodo i’ll look at the log
17:54 towodo right, push.sh tries to act like ‘make’ in avoiding unnecessary work.  if the git repo is unchanged it doesn’t recompile
17:55 towodo but you can always log in and do things like neo4j stop or compile
17:55 codiferous can there be a flag to the push script to force a recompile?
17:55 codiferous i regularly need to do this
17:55 josephwb this is the first time i've had maven screw up on the server
17:56 codiferous sometimes just because of the maven bug that produces NoClassDefFound errors
17:56 josephwb YES!
17:56 towodo ouch.
17:56 josephwb that is what i got. thought I broke things. (i didn't)
17:56 josephwb i pushed a comment commit, it recompiled, everything is fine
17:57 codiferous yeah. i've encountered that bug at least 10 times on the dev server
17:57 josephwb towodo: when I log in, and type "neo4j status", it says command not found
17:57 towodo I’ve never seen a problem like this.  â€˜make’ has a -f (force) flag…
17:57 josephwb i guess not in the path
17:57 towodo ~/neo4j-taxomachine/bin/neo4j status
17:58 towodo there are 3 neo4j instances so it doesn’t make sense to put one of them in the path
17:58 josephwb of course
17:58 codiferous here are five git commits to trigger recompiles on taxomachine:
17:58 codiferous Meconopsis:taxomachine cody$ git log --all --grep="trivial"
17:58 codiferous commit 72651394d0a73affd01f5c30d286ea016e73eddd
17:58 codiferous Author: Cody Hinchliff <cody.hinchliff@gmail.com>
17:58 codiferous Date:   Thu Sep 18 13:36:00 2014 -0400
17:58 codiferous trivial
17:59 codiferous commit 0dd76678e56731d2573cc49ade91a5962bdbfe32
17:59 codiferous Author: cody hinchliff <cody.hinchliff@gmail.com>
17:59 codiferous Date:   Fri Sep 5 17:19:25 2014 -0400
17:59 codiferous trivial commit to trigger recompile
17:59 codiferous commit 8dd2ab8be26df89110b23531d36f27662f14dd36
17:59 codiferous Author: Cody Hinchliff <cody.hinchliff@gmail.com>
17:59 codiferous Date:   Fri Aug 22 09:21:04 2014 -0400
17:59 codiferous trivial commit to triggger recompile
17:59 codiferous commit 5f21b7b96054a8d57641be36025257405513ff5c
17:59 codiferous Author: Cody Hinchliff <cody.hinchliff@gmail.com>
18:00 josephwb ok, i see how to do this on ot10
18:03 josephwb ssh ot10
18:03 josephwb neo4j-treemachine/bin/neo4j stop
18:03 josephwb cd repo/treemachine/
18:03 josephwb ./mvn_serverplugins.sh
18:03 josephwb [wait]
18:03 josephwb ~/neo4j-treemachine/bin/neo4j
18:03 josephwb logout
18:04 josephwb but a "-f" in push.sh would be easier
18:15 codiferous towodo
18:15 towodo I’m on a call, sorry. done at 3 or 3:30
18:16 josephwb i have a shell script that i can put on ot10. similar to above, but works for any of treemachine, taxomachine, oti
18:16 mtholder still a pain, but does ssh-ing in, and backing the checked out HEAD up one commit (then running push.sh as normal) work?
18:18 towodo just add the -f flag to push.sh.  shouldn’t be too hard
18:19 codiferous towodo, i was actually just going to bug you about your thoughts on mark's newick-with-metadata proposal: https://docs.google.com/document/d/1QqmjiEXlFwLExfhk7PFdZhOjY9NMhkdXrZ7QSw28gSA/edit#heading=h.9qc87z8qvbyv
18:19 codiferous joseph already has a use-case that would be vastly simpler with something like this
18:20 codiferous it is not urgent
18:21 codiferous i like the -f flag solution, i humbly and respectfully request that you be the one to add it to the push.sh script (unless there is a volunteer)
18:23 josephwb doesn't look quite as simple as towodo implied...
18:57 mtholder joined #opentreeoflife
18:57 josephwb btw i am looking at the "-f" for push.sh
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20:15 josephwb towodo: think I got "-f" working. PR here: https://github.com/OpenTreeOfLife/opentree/pull/448
20:20 towodo looks good so far as it goes.  as a second pass I’d add recompilation of ot-base, peyotl, ncl, but that can wait
20:21 josephwb good point; i wasn't thinking of those
20:22 josephwb ack. i think some tabs slipped in. let me fix that.
20:23 josephwb oh, wait, is it my spaces that are offensive here?
20:23 josephwb (lots of tabs)
20:24 towodo M-x untabify
20:25 josephwb ok, so doesn't look like just my edits
20:27 towodo I’m not consistent about tabs.  I haven’t bothered to figure out how to configure emacs properly
20:31 josephwb ok, got rid of tabs
20:42 codiferous towodo, can you merge https://github.com/OpenTreeOfLife/taxomachine/pull/72
20:45 towodo looking at travis log
20:46 codiferous there are no automated regression tests yet
20:46 towodo I can see that…
20:47 codiferous you can run the tests.sh script to do a very basic test of the services, but you have to run it on a machine running a taxomachine server
20:47 towodo right.  that would be devapi?
20:47 codiferous suppose i should modify the script so that it accepts the server as an argument, right now it looks at locahost:7474
20:47 codiferous and yes, devapi unless you have a local taxomachine db
20:48 towodo I think that would be a good idea
20:48 codiferous ah, but that is tricky because it uses nosetests
20:48 codiferous hm
20:48 josephwb towodo: i cleaned up some formatting (spacing) things. done with that push.sh PR now (for real)
20:48 towodo nose tests?
20:49 codiferous a python test package
20:49 codiferous simplifies test writing/running
20:50 towodo ok… I’ve got a backlog
20:50 codiferous i will think about how to deal with the server specification step
20:51 codiferous for now, i have tested that locally using the same db that is on dev
20:51 codiferous would be nice to get it pushed so that ongoing changes don't pile up further
20:54 towodo does it depend on https://github.com/OpenTreeOfLife/ot-base/pull/11 ?
20:57 codiferous no
21:03 codiferous oh...
21:03 codiferous maybe
21:03 codiferous there was another pull request for ot-base but i closed it
21:03 codiferous because all its commits were included in #11
21:04 codiferous so, yes, currently i does depend on that, but i can reopen the older one...
21:06 codiferous https://github.com/OpenTreeOfLife/ot-base/pull/9
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22:40 josephwb towodo: do you want me to add recompilation of ot-base, peyotl, ncl to the push.sh PR before you review it?
22:41 towodo no don’t bother.  I really want to rewrite it
22:41 josephwb got it.
22:42 towodo btw I’m setting up the asterales system so I can use it for testing all these PRs
22:42 josephwb ok.
22:42 josephwb cody and i were able to run it very easily ourselves today (testing other stuff)
22:43 towodo I created the mini-phylesystem for it a few weeks ago
22:43 towodo now I just need the taxomachine and treemachine databases
22:43 josephwb i have to go pick up my son at soccer now, but let me know if you need anything from me.
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22:59 towodo love the new gmail client ‘view issue’ and ‘view pull request’ buttons
23:00 kcranstn those just showed up today! nice
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