Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2013-12-09

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All times shown according to UTC.

Time Nick Message
01:41 dukeleto joined #otol
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19:14 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#212 (local - 63b45c5 : Jonathan "Duke" Leto): The build passed.
19:14 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/44a061e6b43d...63b45c5033f7
19:14 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org/builds/15185578
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19:26 dukeleto jimallman: howdy
19:26 jimallman dukeleto: hey there!
19:26 jimallman thanks for the heads-up on the port change. it seems the service is already running there on dev
19:26 jimallman $ wget -v http://localhost:7478/db/data/
19:27 jimallman this returns a list that includes the expected QueryServices and IndexServices...
19:28 jimallman so I''d like to go ahead and tweak api's private/config file and see what happens...
19:31 jimallman no dice, still getting weird errors on the search API. does this look like what you're expecting?
19:31 jimallman http://dev.opentreeoflife.org/api/v1/search/study?ot:studyPublicationReference=Tank
19:32 dukeleto jimallman: try using a hyphen instead of a :
19:33 jimallman will do
19:33 jimallman tried this via HTTP (in browser): http://dev.opentreeoflife.org/api/v1/search/study?ot-studyPublicationReference=Tank
19:33 dukeleto jimallman: web2py doesn't recognize URLs with colons as valid
19:33 dukeleto jimallman: and I just added the port change in my deployment branch here: https://github.com/OpenTreeOfLife/opentree/commit/abc6ab4f9d9e143a06298240b9608e7235a14456
19:34 jimallman got a 200 response: "No file found at this path (this is somewhat unexpected)"
19:34 dukeleto jimallman: yes, seeing that too
19:34 dukeleto jimallman: looking into it now
19:34 jimallman yes, the colon-in-URL thing rings a bell. FWIW, i might have overcome this in the main open tree web app, would need to refer to my notes to remember the trick.
19:35 jimallman dukeleto: thanks! sorry for the distraction.
19:35 dukeleto jimallman: http://dev.opentreeoflife.org/api/search/v1/study/ot-studyPublicationReference/Tank
19:35 dukeleto jimallman: that is the URL structure, but it is showing errors from OTI
19:36 jimallman cool, I thought maybe the URL parts were switched around...
19:37 jimallman is this the JAVA_HOME problem you and jar discovered a few days ago?
19:38 jimallman if so, maybe i should push the latest master to dev and try again...
19:39 dukeleto jimallman: no, that prevented anything from even starting
19:39 jimallman ah, ok
19:39 jimallman i saw it in this thread with the same symptom: NoClassDefFound error
19:42 dukeleto jimallman: i am not totally sure
19:44 dukeleto jimallman: i am going to push to dev again and see what messages pop up
19:45 jimallman sounds good...
19:46 dukeleto jimallman: no dice. I will try master to see if that changes anything
19:51 dukeleto jimallman: is dev.opentreeoflife.org an ec2 machine?
19:51 jimallman definitely AWS, yes..
19:52 jimallman ec2-54-202-237-199.us-west-2.compute.amazonaws.com
19:52 jimallman (confirmed, both ping at the same IP)
19:53 dukeleto jimallman: and it is debian, correct?
19:53 * jimallman is checking now...
19:54 jimallman $ uname -a
19:54 jimallman Linux ip-10-248-9-37 3.2.0-4-amd64 #1 SMP Debian 3.2.46-1 x86_64 GNU/Linux
19:54 jimallman so yes, Debian
19:54 dukeleto jimallman: i think it is. debian uses username of "admin" but ubuntu uses "ubuntu"
19:54 dukeleto jimallman: trying to get the hang of deploying to different machines
19:55 jimallman yes, i've followed the conversation but not closely.
19:55 jimallman a little more info, from $ cat /etc/debian_version
19:55 jimallman 7.1
19:55 dukeleto jimallman: a deploy to dev from the master branch is happening now
19:57 * jimallman is going to grab some coffee, back in a minute
19:57 dukeleto jimallman: but my change to the oti_port is not on the master branch of opentree.git ...
19:57 dukeleto coffee is a good idea
19:59 dukeleto jimallman: seems like there are still bugs in install-neo4j-apps.sh: https://gist.github.com/leto/7879749
20:05 jimallman ok, i made a pull request to address this the other day... might be time to merge it and test
20:05 jimallman https://github.com/OpenTreeOfLife/opentree/pull/144
20:05 * jimallman is merging now...
20:06 jimallman please try again. this should fix the neo4j status check and restart it if needed
20:06 jimallman dukeleto: ^
20:07 dukeleto jimallman: ok, trying now
20:15 dukeleto jimallman: it gets past that, but still gets 500s when trying to index due to NoClassDefFoundError
20:15 jimallman yes, i'm seeing the same 'NoClassDefFoundError'...
20:16 jimallman looking at deployment scripts, to see if we're not putting org/opentree/oti on the java path..?
20:16 jimallman (this is not my strong suit, but sometimes i can figure it out)
20:22 jimallman dukeleto: some useful curl queries... (i'm working my way up from here)
20:22 jimallman https://gist.github.com/jimallman/f4efe7eee881df073ac8
20:26 jimallman i see that once we start to explore the details of a service, we can't find the needed classes (org.opentree.graphdb.NodeIndexDescription, I think):
20:26 jimallman curl -X POST http://dev.opentreeoflife.org/oti/ext/QueryServices/graphdb/getSearchablePropertiesForStudies
20:27 jimallman dukeleto: more methods added here (but they fail due to missing classes):
20:27 jimallman https://gist.github.com/jimallman/f4efe7eee881df073ac8
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20:28 travis-ci [travis-ci] OpenTreeOfLife/treenexus#66 (leto_study_1003 - 9a981e8 : Duke Leto): The build passed.
20:28 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/treenexus/commit/9a981e86b8a2
20:28 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/treenexus/builds/15188679
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20:29 travis-ci [travis-ci] OpenTreeOfLife/treenexus#68 (leto_study_1003 - ab4f266 : Duke Leto): The build passed.
20:29 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/treenexus/compare/9a981e86b8a2...ab4f2664f266
20:29 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/treenexus/builds/15188683
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20:29 travis-ci [travis-ci] OpenTreeOfLife/treenexus#67 (leto_study_1003 - 9a981e8 : Duke Leto): The build passed.
20:29 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/treenexus/compare/9a981e86b8a2...9a981e86b8a2
20:29 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/treenexus/builds/15188681
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20:41 dukeleto jimallman: perhaps it is a difference between debian and ubuntu?
20:41 jimallman dukeleto: i've searched the deployment scripts, and i can't find any place that specifies a class path for Java
20:42 jimallman hm, so the very same deployment tool works on ubuntu?
20:43 jimallman i looked in src/main/java/org/opentree and target/classes/org/opentree, no sign of graphdb classes there either
20:44 dukeleto jimallman: that seems to be jonathan's intention, but little differences in ubuntu vs. debian keep cropping up
20:45 dukeleto jimallman: perhaps mvn_install.sh is not being called?
20:46 dukeleto jimallman: it doesn't seem to be, from what I can see
20:46 * jimallman is looking at that script now, it's new to me
20:47 jimallman dukeleto: where is that file? i don't see it in the /deploy area... oh, in oti perhaps?
20:48 jimallman ah yes, there it is
20:49 jimallman dukeleto: yes, this looks like the stuff. i'm guessing ot-base might have the graphdb classes
20:49 dukeleto jimallman: it seems that only the oti dependencies of that script. It is mentioned in the OTI readme
20:50 dukeleto jimallman: it is being run here: https://github.com/OpenTreeOfLife/opentree/blob/master/deploy/setup/install-neo4j-apps.sh#L32
20:52 jimallman hm, it does seem to have run at least once on dev:
20:52 jimallman https://gist.github.com/jimallman/ec6e07ee7e94dc7ba6f9
20:52 jimallman so it looks like the classes are here and compiled. again, i'm guessing it's a CLASSPATH problem, but i don't know how to fix it.
21:01 dukeleto jimallman: sounds like an issue on OTI with details so we can get feedback from Cody is the way forward
21:02 jimallman agreed. maybe pointing to the (apparently) missing classes will help
21:11 jimallman dukeleto: yeah, i can only track this as far as /home/opentree/neo4j-oti/plugins/oti-neo4j-plugins-0.0.1-SNAPSHOT.jar ... apparently this should contain all the needed classes. i'm guessing it's incomplete
21:14 jimallman i'll put together a follow-up email for Cody...
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21:19 travis-ci [travis-ci] OpenTreeOfLife/treenexus#69 (testing_deploy - ea087f8 : Duke Leto): The build passed.
21:19 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/treenexus/compare/5762c8194c71...ea087f8031f0
21:19 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/treenexus/builds/15190998
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22:25 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#213 (local - 450fcfc : Jonathan "Duke" Leto): The build passed.
22:25 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/api.opentreeoflife.org/compare/63b45c5033f7...450fcfcef2aa
22:25 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/api.opentreeoflife.org/builds/15194374
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