Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-01-17

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All times shown according to UTC.

Time Nick Message
23:26 towodo joined #opentreeoflife
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00:13 towodo jimallman, are you there?
00:55 towodo ok, this time I did RTFM, and the M utterly stinks. how in javascript do i tell whether a member is present?
01:01 towodo perusing ECMA-262
01:20 towodo ok, got it
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02:33 jimallman towodo: sorry i missed you, looks like you're back on track.
02:33 towodo i sent you email
02:34 jimallman yeah, if (myObj[ testProp [) is good, or... if (typeof myObj.testProp === undefined) { ...
02:35 towodo my problem now is in python code, default.pt
02:35 jimallman towodo: odd, i'm not seeing an email. when did you send, and to which address?
02:35 towodo s/pt/py/
02:35 jimallman the main webapp, i'm guessing?
02:35 towodo didn't click 'send'. try again now
02:36 towodo yes, where it gets the start node.  Cody changed the contract
02:37 jimallman ok, taking a look now. as you thought, the error message implies a mismatch between expected args and those passed.
02:38 towodo if I read ecma 262 correctly you can say if 'testProp' in myObj … just as in python
02:39 towodo but I haven't tried it
02:40 towodo need to find an interactive javascript interpreter
02:40 towodo although i should probably stay away from it, since i'll just get it confused with python
02:44 jimallman if ... in     does work. if you want to be precise (property exists in this object, and not from its prototype chain), use if ( x.hasOwnProperty('key') ) { //do this }
02:44 jimallman my preferred js interpreter is the console in Firefox or Chrome. very handy, and has some very useful builtin functions (log, trace, time, etc)
02:44 jimallman regarding the unpacking error, is it possibly throwing the exception at the bottom of fetch_current_synthetic_tree_ids? that returns a three-tuple instead of two
02:44 jimallman towodo: ^
02:44 towodo oh that sounds easy. i will try it (js int)
02:44 towodo wha?...
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02:47 Topic for #opentreeoflife is now Open Tree Of Life | opentreeoflife.org | github.com/opentreeoflife | http://irclog.perlgeek.de/opentreeoflife/today
02:47 towodo do I want          return ('ERROR', e.message)   ?
02:47 jimallman yes, try that
02:48 towodo but then the message just gets stored in the treeview_dict ?… how does the error ever get reported?
02:49 jimallman in the master branch, the returned tuple unpacks to three variables in the view context: draftTreeName, lifeNodeID, startingNodeID. practically speaking, we probably never used the second value anyway.
02:50 jimallman re: how does the error ever get reported? i don't have a good answer. in practice, it would fail pretty dramatically in the view. but yes, trapping it here was a bad idea.
02:50 towodo guess I'm going senile, I should have seen that
02:52 jimallman hm, given the changes Cody has made, should we still be passing a desired starting node-name?
02:52 jimallman https://github.com/OpenTreeOfLife/opentree/blob/102861554f7f65646c2d45af4cdf297e37a74e3c/webapp/controllers/default.py#L122
02:52 jimallman i seem to recall he wanted ott id or something else...
02:53 towodo ok, now it's getting further, the next error shows up in the app.
02:53 towodo seems to be a java error.  I can direct to Cody and go to sleep.  thanks
02:53 towodo thanks much that is.
02:53 jimallman sure, or i can pursue from here... are you running this on a public server?
02:54 jimallman if not, happy to help tomorrow.
02:54 jimallman meanwhile, i'm chugging away on the huge-study problem. i have a cunning plan, working out the details tonight...
02:56 towodo actually it's not obviously Cody's problem… the error is downstream of his new method. maybe i'm using the return values incorrectly. well anyhow I'll send him email and continue tomorrow.
02:56 towodo looking forward to hearing the cunning plan. not now though
02:59 jimallman ok, good night!
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11:58 josephwb morning, y'all
11:58 josephwb is there a plan to get phylografter up and running today?
11:59 josephwb again, no rush; i have other things to do. just planning my day.
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13:42 josephwb regarding the phylografter leak: i don't believe any of us here are pulling from phylografter very much, possibly not at all (my main interest is data submission).
13:43 josephwb HOWEVER, i have run the refresh script for both AVATOL_nexsons and phylesystem a few times over the past week. could these be responsible?
13:47 PEM josephwb - yes the refresh script would result in the nexson exporter getting called.  I am somewhat surprised that a couple of exports of only modified studies would cause a serious leak.  When I tested the leak last summer it took a lot of exports to make it show, so I'm surprised the server is crashing so frequently.
13:50 josephwb maybe it is the script which is inefficient.
13:51 josephwb i will look to see exactly what it is doing
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14:19 josephwb okay, phylografter seems to be up again. i won't do any refreshing of studies until i look at the scripts closely.
14:46 blackrim which scripts? just curious if that is relevant to me
14:53 josephwb oh, just the refresh script for AVATOL_nexsons and phylesystem. i believe mark wrote both(?)
14:57 josephwb phylografter was apparently going down because it was being clobbered by something. these are the only things i have been doing.
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15:44 blackrim josephwb: are you doing both scripts? I need to update some ingroup bits for fungi and would be updating the avatol_nexsons one
15:44 blackrim I don't want to bring things down though
15:45 josephwb i'm not doing anything right now; just looking to see if there are inefficiencies in the code.
15:46 josephwb i.e. i'm not refreshing anything.
15:47 blackrim ok
15:47 blackrim it isn't redownloading everything is it? that would definitly bring it down
15:47 josephwb there should be very few updates; i just refreshed it a while ago. should be safe to do(?)
15:48 josephwb that is my worry
15:48 josephwb getting everything
15:48 josephwb the phylesystem refresh is super slow; maybe it is the culprit?
15:48 josephwb avatol refresh is very quick
15:49 blackrim i wonder if the .to_download.json is messed up
15:49 josephwb word
15:49 blackrim ok, yeah, i haven't had any problems with avatol_nexsons so my guess is that isn't a problem unless something has changed recently
15:51 towodo joined #opentreeoflife
15:51 josephwb i agree
15:52 josephwb avatol refresh should be fine
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16:06 travis-ci [travis-ci] OpenTreeOfLife/phylesystem#97 (master - b88c7f9 : josephwb): The build passed.
16:06 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem/compare/4ea4260542cd...b88c7f90d699
16:06 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem/builds/17135764
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17:53 kcranstn thanks for the email, blackrim!
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19:05 blackrim kcranstn: yerp!
19:14 josephwb looks like phylesystem is getting the correct list of studies to download...
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19:17 blackrim like it has always been doing that and there is something wrong somewhere else, or you fixed it and now it is getting the correct list?
19:20 josephwb i haven't fixed anything yet; trying to see where things are going wrong. list of studies is not it.
19:34 josephwb ack. seems to be working correctly. maybe phylografter is crashing for a different reason?!?
19:41 josephwb anyway, i closed the issue.
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19:44 travis-ci [travis-ci] OpenTreeOfLife/phylesystem#98 (master - 77e4463 : josephwb): The build passed.
19:44 travis-ci [travis-ci] Change view : https://github.com/OpenTreeOfLife/phylesystem/compare/b88c7f90d699...77e4463af15d
19:44 travis-ci [travis-ci] Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem/builds/17148802
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20:01 kcranstn towodo - where is this spreadsheet that laura is talking about?
20:01 towodo google docs… i'll find the pointer, hang on
20:03 towodo foo… shared privately. i've invited you
20:03 towodo https://docs.google.com/spreadsheet/ccc?key=0ArU9WnS_OkXMdG40d2NON19mcXFXUF90dmpqUjN6b0E&usp=drive_web#gid=0
20:03 towodo I already wrote a script to process it. with a small mod I can make it just ignore the broken cases (new parent not in OTT)
20:06 towodo I think I'd better stop editing it, some changes I made got undone
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20:31 kcranstn made some more changes to gcmdr that hopefully will make it easier to see what studies are being included
20:31 kcranstn is 425 really the only microbe study??
20:34 kcranstn http://reelab.net/phylografter/study/view/425
20:44 josephwb yup
20:56 kcranstn ok, thanks for confirming
21:07 josephwb i believe there are more, but taxonomic issues prevented them from being added. right, stephen?
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