Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-03-21

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Time Nick Message
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16:53 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#406 (nudge-oti-index - 5a2a9e0 : Jim Allman): The build passed.
16:53 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/db5961c33282...5a2a9e04887f
16:53 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org/builds/21267540
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16:54 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#408 (master - d987fea : Jim Allman): The build passed.
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17:30 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#409 (nudge-oti-index - 51ebf1f : Jim Allman): The build passed.
17:30 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/5a2a9e04887f...51ebf1f7b35f
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17:34 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/d987fea6501c...1e637aefc6a6
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17:42 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#413 (master - 6a00bc7 : Jim Allman): The build passed.
17:42 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/1e637aefc6a6...6a00bc7c772c
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18:45 jimallman towodo: do you have time today for a quick java testing tutorial?
18:45 towodo sure.
18:45 towodo you can use eclipse, or not.  I don't.
18:46 jimallman neat! like you, i'd prefer to work from the command line vs Eclipse.
18:46 towodo what I do is pretty much the same as what the deploy script does.  I like to set up my directories the same way...
18:46 jimallman ok, i'll take a closer look there.
18:46 towodo but that isn't necessary.  That would be neo4j-treemachine as a sibling to repo
18:47 towodo the deploy script will tell you how to download neo4j and create an instance of it
18:47 jimallman (i also find that matching the deployed layout helps me keep things straight.)
18:47 towodo setup/install-neo4j-apps.sh
18:48 towodo are you doing taxomachine, treemachine, or oti?
18:48 jimallman for now, just oti
18:48 towodo btw I have considered generalizing the install script so that it will work on a local machine.  wouldn't be hard.
18:49 jimallman yeah, i was just wondering if that would work on my machine
18:49 jimallman running just install-neo4j-apps.sh, i mean
18:49 towodo probably not.  needs a few tweaks.  mostly in functions.sh
18:50 towodo e.g. if JAVA_HOME is already set then it shouldn't clobber it.  need to accommodate variant local java installations
18:51 jimallman i see. fwiw, i'm on OS X Mavericks, and this is my (underutilized) Java:
18:51 jimallman $ java -version
18:51 jimallman java version "1.6.0_65"
18:51 jimallman Java(TM) SE Runtime Environment (build 1.6.0_65-b14-462-11M4609)
18:51 jimallman Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-462, mixed mode)
18:52 jimallman i can try working from the install script for awhile, and holler if i hit an obstacle...
18:52 towodo that should work, but can't be sure.  neo4j claims that 1.6 is unsupported and it wants 1.7
18:52 jimallman ah, good to know
18:53 towodo but, I've been running 1.6.0_65 with neo4j on my mac, and it works just fine.
18:53 towodo you get a warning but nothing bad seems to happen.
18:53 jimallman i like it. i'm expecting to use/test just a tiny slice of it here
18:53 towodo so I wouldn't bother trying to install 1.7 (although it's a Good Idea on general principle and for security reasons)
19:03 towodo git_refresh doesn't work locally yet but it's pretty easy to convert that into a git clone command
19:04 towodo you will need to do mvn_install.sh in your clones of the jade and ot-base repos
19:04 towodo (just going through the install script)
19:04 towodo you don't need taxomachine
19:05 jimallman right, i was planning to walk through the script as if called just for 'oti'
19:05 towodo at least I don't think you do. not sure now that I think about it
19:05 towodo right.
19:05 jimallman i figured this would flush out dependencies. since i believe we have machines that have only oti installed
19:08 jimallman this script is actually pretty short and sweet. i'd like to just give it a try and bug you again if i hit a wall...
19:09 towodo one change I would make is to use a symbolic link instead of making a copy. (where it says cp -p -f repo/$APP/target/$jar neo4j-$APP/plugins/ )
19:10 towodo that way you can recompile the oti plugin and don't have to remember to copy the new version over each time
19:10 towodo the script probably ought to do that too...
19:10 jimallman ah, thanks
19:13 towodo I'm trying to decide what URLs to give to the new GET methods for treemachine et al.
19:15 jimallman are you planning to proxy these to handle the GET<=>POST switcheroo?
19:15 towodo http://treemachine.opentreeoflife.org:7474/xxx/yyy/getSyntheticTree?
19:15 towodo the switcheroo happens inside the Java code.  I finally figured out how to do that
19:15 jimallman great!
19:16 jimallman do you have a caching solution in mind, or in place?
19:16 towodo we use an apache proxy probably on the webapp host to do caching
19:16 jimallman ok
19:16 towodo I'm trying to avoid bespoke caching.  too many ways it can go wrong
19:17 jimallman i'm looking at existing URLs. this definitely seems like too much:
19:18 jimallman http://ec2-54-203-212-107.us-west-2.compute.amazonaws.com/treemachine/ext/GoLS/graphdb/getSyntheticTree
19:18 towodo the question is whether we need to design an http API for other people to use… if so then hostnames and the spelling of the URLs matters
19:18 jimallman i like http://treemachine.opentreeoflife.org/getSyntheticTree
19:19 jimallman but i need to see what's alongside GoLS/ ... maybe something we need
19:21 towodo the way things are set up internally in neo4j there has to be xxx/yyy before the method name
19:21 jimallman i'm seeing: GoLS, PhylografterUpdater, GetSASJsons, GremlinPlugin, GetJsons, CypherPlugin
19:21 towodo we could put a version number in there, as the api does
19:22 jimallman hm, then maybe v1/GoLS  (or other plugin identifier)?
19:22 jimallman http://treemachine.opentreeoflife.org/v1/GoLS/getSyntheticTree
19:22 towodo the only one we need GETs for right now is GoLS, as far as I know… but I guess it should be open ended
19:23 towodo yes I guess that makes sense.
19:23 jimallman yeah, i'm not sure what the Get*Jsons plugins do, but they sound like good candidates for caching
19:24 towodo "I have commented out the entire class since it was causing compilation errors."
19:27 jimallman i see, dead code. looks like GetSASJsons is mostly for D3 visualization, so it should be accessible by URL
19:27 jimallman https://github.com/OpenTreeOfLife/treemachine/blob/master/src/main/java/opentree/plugins/GetSASJsons.java
19:29 jimallman (i mean it's probably used for Rick's visualizations, nothing in the current synth-tree viewer)
19:30 towodo no, it's used for Stephen's D3 tree browser.  I don't think Rick uses any of this code
20:05 jimallman so far, so good here. i've installed maven 3 and am into a sensible build+test cycle. FYI - i had to bump up a version dependency (Maven Shade plugin) for compatibility with newish version of Maven 3.1.1, but that might just be a quirk on Mac so i'm not committing the version tweak.
20:36 towodo ok.  yes I forgot about maven.  I think I did a source install under /usr/local.
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23:30 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#414 (local-dep - de0b01a : Mark T. Holder): The build passed.
23:30 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/504979aa5b18...de0b01a190d9
23:30 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org/builds/21291808
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