Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-06-04

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All times shown according to UTC.

Time Nick Message
00:06 kcranstn joined #opentreeoflife
00:07 kcranstn @towodo: do we always need the version number, or can we assume current if none?
00:07 towodo https://github.com/OpenTreeOfLife/treemachine/issues/93
00:08 towodo I think the tree name will always be delivered by that method, probably always versioned although maybe two names should be delivered in the return object
00:08 kcranstn hmmm… extra confusion. does version = API or draft tree?
00:08 kcranstn I was thinking former, but this issue is latter
00:08 towodo API version goes in the request URL.
00:08 towodo tree version is returned by getDraftTreeID
00:09 kcranstn yes
00:09 towodo they are independent.
00:09 kcranstn I was referring to this (from your email): I think I will shorten the URLs, replacing /ext/GoLS/graphdb/ with /v0/“
00:09 kcranstn re: question about always needing version
00:10 towodo oh.
00:11 towodo i think putting the api version number in the url is a 'best practice'
00:11 towodo it lets you version the api incompatibly, and code will either work (because old version was kept) or fail noticeably (due to 404). the failure mode is undetected incompatible change
00:14 towodo not my idea, I've seen it around a lot, and I think more than one person on this project wanted it
00:14 kcranstn ok
00:17 towodo i need to get something to eat…  taxomachine should be working soon. URL change is relatively easy. other apps are more involved.
00:17 kcranstn cool
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17:52 travis-ci [travis-ci] OpenTreeOfLife/phylesystem-api#539 (master - c3cfcb4 : Mark T. Holder): The build passed.
17:52 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/c70e6bd81cc5...c3cfcb47b1d2
17:52 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/26781386
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18:32 josephwb @blackrim: ncbi looks to be back up
18:35 towodo kcranstn, I did some work on the api documentation and am trying to get the oti and phylesystem methods to work
18:35 kcranstn how’s that going?
18:37 towodo stuck on two fronts.  the asterales system has run out of memory (ridiculous), so will need to get a new server.  the new big server is failing due to some api web2py problem
18:38 towodo I'm hoping for jim's help on the web2py problem.  it needs to be fixed before the oti index can be set up
18:38 towodo I guess I could redirect the methods to the dev system… that would solve the immediate problem...
18:38 mtholder I think jim is traveling. What is the problem?
18:39 blackrim josephwb: yeah, noticed (i sent them a message a while ago)
18:39 towodo I split the web2py setup script so that the api can be installed without installing the webapp/curator.  Maybe I made a mistake
18:39 mtholder that should be OK
18:39 towodo here's the symptom: http://api.opentreeoflife.org/api/v1/study/pg_1630
18:40 towodo or http://api.opentreeoflife.org/api/study_list
18:40 towodo (those URIs will be changed to phylesystem/ )
18:40 mtholder http://api.opentreeoflife.org/api/default/study_list works
18:40 mtholder so it looks like a routing issue.
18:41 towodo I looked at SITES.routes.py and didn't understand it
18:41 mtholder (adding default to the other gives an internal server error - not sure what is up with that).
18:42 towodo I guess I can try installing SITES.route.py on the problematic machine, although this jumps a module boundary. think that might work?
18:44 towodo but duke wouldn't have had that file around.
18:44 mtholder ot10 just has a routes.py file in its web2py. I'm looking at that for inspiration.
18:45 mtholder I think that you may need the opentree/SITES.routes.py installed in web2py... that is not great...
18:47 towodo well, maybe.  I can try it but I don't like voodoo
18:49 mtholder looking at opentree/webapp/routes.py jim has some notes on routing there.
18:49 mtholder basically: a minimal opentree/SITES.routes.py should go in the web2py dir, and then each app should have its own routes.py if it needs to tweak things.
18:55 towodo ok, SITES.routes.py gets rid of the need for /default/ , study_list call now works.  I don't get it.
18:55 towodo it looks like each app *does* have its own routes.py (opentree does at least)
18:56 mtholder I don't fully grok it either. Jim's notes allude to a parametric vs nonparametric router choice.
18:56 mtholder looks like that routes.py, puts web2py into a parametric routing mode, whatever that means.
18:57 mtholder phylesystem-api does not have a routes.py, perhaps it should.
19:04 towodo well in any case installing SITES.routes.py works.  magic.  and I kludged it to not require doing git_refresh of the opentree repo on the api server (copies the file from the deploying machine using scp)
19:04 towodo thanks
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19:17 travis-ci [travis-ci] OpenTreeOfLife/phylesystem-api#540 (master - 9623efd : Mark T. Holder): The build passed.
19:17 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/c3cfcb47b1d2...9623efd700a1
19:17 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/26787938
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19:22 travis-ci [travis-ci] OpenTreeOfLife/phylesystem-api#541 (master - 8d7fd57 : Mark T. Holder): The build has errored.
19:22 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/9623efd700a1...8d7fd577e404
19:22 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/26788660
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19:35 towodo kcranstn, we need Cody's help for 'return the studies that include specific OTT IDs'
19:35 kcranstn @blackrim - is Cody around?
19:37 towodo kcranstn, I think I'm done fixing the urls in the apis doc.
19:38 kcranstn yay, thanks!
19:39 towodo and I've inserted links (for your use) to other documentation, and source code in some cases
19:39 towodo I think the new api server fully works, except that the oti indexing hasn't run yet.
19:40 towodo I'll start that running tonight
19:42 kcranstn is there any way for the study calls to be consistent across phylesystem / oti?
19:42 kcranstn i.e. hide from users that there are two different services providing study info
19:50 towodo This hangs: http://dev.opentreeoflife.org/opentree/argus/otol.draft.22@1425509/Noctuidae
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20:13 towodo https://my.mayday.us/t/6ab4-Jonathan-Rees
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20:20 travis-ci [travis-ci] OpenTreeOfLife/phylesystem-api#542 (treesource - aff7b39 : Mark T. Holder): The build passed.
20:20 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/15e185418dae...aff7b39277b8
20:20 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/26793431
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21:06 travis-ci [travis-ci] OpenTreeOfLife/phylesystem-api#543 (treesource - 6cf5a66 : Mark T. Holder): The build passed.
21:06 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/aff7b39277b8...6cf5a668d2ba
21:06 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/26797598
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