Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-12-17

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Time Nick Message
00:32 kcranstn just saw that message from towodo. I think he was bragging… ;)
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16:43 josephwb hey jimallman
16:44 josephwb is there a way to search for a taxon using the curator?
16:47 josephwb hmm. curator is not finding a study that is def there...
16:47 kcranstn new study?
16:47 kcranstn (i.e. potential delay in oti indexing?)
16:48 josephwb idunno.
16:48 josephwb Jarvis study; ot_214
16:48 josephwb i can get to the study by entering address, but cannot find it by searching
16:48 josephwb http://tree.opentreeoflife.org/curator/study/view/ot_214
16:48 jimallman josephwb: no taxon search feature, no.
16:51 josephwb hmm. doesn't find ot_210 either
16:52 josephwb http://tree.opentreeoflife.org/curator/study/view/ot_210
16:52 josephwb when searching for Fischer
16:52 josephwb does find ot_211
16:52 jimallman agreed, it seems there are gaps in oti.
16:53 josephwb not just latest
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17:05 josephwb hey jimallman
17:05 josephwb trying to check the newick thingy
17:05 josephwb don't know what the original problematic study was (hence me asking for taxon search)
17:06 josephwb tried other study
17:06 josephwb names are original name, not mapped names
17:06 josephwb won't people want the mapped names?
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17:19 jimallman josephwb: that does seem reasonable, yes. but let’s ask mtholder. (i just provide the button. :)
17:20 jimallman perhaps a new GH issue, or piggy-back this question on the existing issue
17:21 kcranstn what’s the trigger for oti indexing?
17:23 kcranstn https://github.com/OpenTreeOfLife/phylesystem-1/settings/hooks
17:23 kcranstn failures on webhooks for phylesystem
17:24 jimallman i see failures from some of the defunct test servers (ot10, etc) but api.opentreeoflife.org hooks look happy.
17:24 kcranstn looks like the ones failing are duplicates of the non-failing (ot## vs api)
17:24 * jimallman is looking more closely
17:27 jimallman kcranstn: i see what’s happening. these are outbound calls from GitHub to the various sites that added this hook.
17:28 jimallman some are no longer responding, so we see errors here.
17:28 jimallman each time *anyone* pushes to phylesystem-1, they all get this nudge
17:28 jimallman OK if I clean up the unused hooks (with errors)?
17:28 kcranstn fine with me
17:28 kcranstn make an issue, though and tag mtholder
17:29 kcranstn just for tracking
17:30 jimallman agreed. meanwhile, there are two triggers on api.opentreeoflife.org, and neither show any recent failures.
17:30 jimallman one of these triggers is for the v1 method, the other is for API v2. a race condition, perhaps?
17:45 jimallman josephwb: kcranstn: it seems there’s an open issue on this (chasing a fix now): https://github.com/OpenTreeOfLife/phylesystem-api/issues/130
17:53 josephwb thanks jimallman
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18:06 josephwb ack. cannot figure out how to search for taxa. documentation not helping.
18:09 josephwb i can search according to year:
18:09 josephwb curl -X POST http://api.opentreeoflife.org/v2/studies/find_studies -H "content-type:application/json" -d '{"property":"ot:studyYear","value":"2014","verbose":true}'
18:10 josephwb but not by taxon:
18:10 josephwb curl -X POST http://api.opentreeoflife.org/v2/studies/find_studies -H "content-type:application/json" -d '{"property":"ot:ottTaxonName","value":"Apodidae","verbose":true}'
18:10 josephwb I get this in response:
18:10 josephwb "error" : "unrecognized property: ot:ottTaxonName"
18:10 josephwb but it is a property:
18:10 josephwb curl -X POST http://api.opentreeoflife.org/v2/studies/properties
18:11 josephwb searching by curator works too
18:14 josephwb "focalCladeOTTTaxonName" works, but "focalCladeTaxonName" does not.
18:15 josephwb actually, "focalCladeTaxonName" works (good property), just doesn't match anything.
18:16 josephwb jimallman: do you know why this doesn't work:
18:16 josephwb curl -X POST http://api.opentreeoflife.org/v2/studies/find_studies -H "content-type:application/json" -d '{"property":"ot:ottTaxonName","value":"Apodidae","verbose":true}'
18:17 jimallman looking now...
18:17 josephwb thanks
18:20 jimallman josephwb: the “filtered” study list in the curation app is JS-powered, not using the API.
18:21 jimallman it seems to find Apodidae in the study’s title. no results for “Geomydidae”, even though it’s the’ot:focalCladeOTTTaxonName’ for study 1500 (but not in its title).
18:21 jimallman Oops. i stand corrected, i just misspelled “Geoemydidae”. (guessing i’m not the first)
18:22 jimallman but back to the API...
18:24 jimallman regarding ‘ot:ottTaxonName’, i see this listed as a tree property, but not a study property. can we search on either?
18:24 josephwb yes
18:24 jimallman (i’m not even sure what that property would *be* for a tree… its root node? or are there many values?)
18:24 josephwb (i think)
18:25 josephwb i just want all studies that include that taxon
18:26 jimallman i get better results using ‘find_trees’, like so:
18:26 jimallman curl -X POST http://api.opentreeoflife.org/v2/studies/find_trees -H "content-type:application/json" -d '{"property":"ot:ottTaxonName""value":"Apodidae","verbose":true}'
18:27 jimallman these results include (possibly redundant?) properties for ‘ot:studyId’
18:28 josephwb yes, that works better
18:29 josephwb ok, i see now.
18:29 josephwb the properties associate with different searches
18:30 josephwb not clear
18:30 josephwb https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-of-Life-APIs#properties
18:30 josephwb maybe just me
18:31 kcranstn is cody around? he wrote these services?
18:31 jimallman i was just guessing..
18:31 josephwb no, he is travelling
18:32 josephwb ok, so jimallman fixed my specific tip taxon search
18:32 jimallman i studies/properties is doing “double duty” since it includes services for both studies and trees. tricky.
18:33 josephwb what about "get me all studies that contain any bird"?
18:33 josephwb yes!
18:33 josephwb that is what confused me.
18:33 jimallman i would be surprised and delighted if we could do that.
18:33 josephwb phylografter can do it. we cannot?
18:34 jimallman “get me all studies that contain any bird”? not that i know of, but i am surprised every day.
18:40 josephwb jimallman: http://www.reelab.net/phylografter/stree/otus_within
18:40 jimallman cool.
18:41 jimallman definitely worth a feature request (i can’t recall if we’ve discussed this before.)
18:42 josephwb i imagine it would be popular.
18:42 josephwb for me right now, i just want to know how many bird studies we have.
18:44 josephwb where does the properties thing come from? phylesystem? oti?
18:46 jimallman pretty sure that’s all handled in oti
18:46 jimallman https://github.com/OpenTreeOfLife/oti/blob/b40405f7f45e1a776cc0500b01776b598d15799d/src/main/java/org/opentree/oti/plugins/studies.java#L151
18:46 josephwb thanks
18:47 josephwb should they be separated?
18:49 josephwb or is it a doc problem?
18:49 josephwb (or am i just an idiot?)
18:54 kcranstn should what be separated?
18:59 josephwb the tree vs. study search properties
19:01 josephwb https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-of-Life-APIs#properties
19:22 jimallman tough call. i think this is part of the simplified API organization, which has studies/ but not trees/
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19:32 travis-ci OpenTreeOfLife/phylesystem-api#656 (master - 6c289fd : Jim Allman): The build passed.
19:32 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/3faed293133c...6c289fd1ba1f
19:32 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/44367861
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19:54 josephwb jomallman: the taxon search is indeed possible. have to know ottid, though.
19:54 josephwb curl -X POST http://api.opentreeoflife.org/v2/studies/find_trees -H "content-type:application/json" -d '{"property":"ot:ottId","value":"81461","verbose":true}'
19:56 josephwb or, by name:
19:56 josephwb curl -X POST http://api.opentreeoflife.org/v2/studies/find_trees -H "content-type:application/json" -d '{"property":"ot:ottTaxonName","value":"Aves","verbose":true}'
19:56 josephwb these need to be explictly pointed out in the documentation.
19:57 josephwb oops. misspelled jimallman above.
19:58 jimallman great! happy to be wrong about that one.
19:58 jimallman so this matches if ANY element of a tree has this ot:ottId or ot:ottTaxonName? or just its ingroup?
19:59 jimallman and does this match on descendants, like all descendants of Aves? (i’m guessing yes, since that was your original question)
19:59 jimallman josephwb: ^
20:01 josephwb any descendant
20:02 josephwb very useful.
20:04 josephwb i will try to cleanup the doc a bit.
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20:48 travis-ci OpenTreeOfLife/phylesystem-api#657 (indexing-url-fixes - e9aa3ce : Jim Allman): The build passed.
20:48 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/commit/e9aa3ce4b81a
20:48 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/44376961
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21:16 travis-ci OpenTreeOfLife/phylesystem-api#659 (master - 36dff75 : Joseph W. Brown): The build passed.
21:16 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/6c289fd1ba1f...36dff75d548e
21:16 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/44380485
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21:16 travis-ci OpenTreeOfLife/phylesystem-api#660 (indexing-url-fixes - 8f70e58 : Jim Allman): The build passed.
21:16 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/e9aa3ce4b81a...8f70e586c5f2
21:16 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/44380511
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21:25 jimallman josephwb: kcranstn: I found the problem with oti indexing. We needed to tweak some method calls, since the IndexServices are “unversioned” in the API. We’ll need to deploy the new code and trigger a full re-indexing of oti as well.
21:29 josephwb good work
21:29 jimallman kcranstn: towodo: should we plan on a PR review Thurs?  https://github.com/pulls?user=OpenTreeOfLife
21:29 kcranstn yes!
21:31 jimallman josephwb: thanks! once again, i’m surprised we didn’t realize how broken this has been.. mtholder has suggested that the nudge tool submits a GH issue when it fails. not a bad idea, but i’ll need to get a refresher on the GH issues API: https://github.com/OpenTreeOfLife/phylesystem-api/issues/131
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21:37 towodo yes
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