Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-04-20

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All times shown according to UTC.

Time Nick Message
02:34 jar286 joined #opentreeoflife
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16:47 travis-ci OpenTreeOfLife/phylesystem-api#732 (support-tree-collections - df6bafa : Jim Allman): The build passed.
16:47 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/e253ee1bb4de...df6bafaf7801
16:47 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/59270222
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17:41 travis-ci OpenTreeOfLife/phylesystem-api#733 (support-tree-collections - eb55e30 : Jim Allman): The build passed.
17:41 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/df6bafaf7801...eb55e30eff9c
17:41 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/59277555
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20:04 josephwb you there jimallman?
20:04 jimallman hi josephwb, what’s up?
20:04 josephwb trying to fix the missing metadata problem
20:04 josephwb what are you using in the tree browser
20:04 jimallman not ringing a bell.. is there an issue or email thread for this?
20:05 josephwb nope
20:05 josephwb for supported edges
20:05 josephwb how are you getting that info?
20:05 jimallman ah yes. as far as i know, the current tree browser (devtree) is using the latest ott, which does not have metadata.
20:05 jimallman at least, last i heard
20:05 josephwb yes, that is what i am trying to fix
20:06 jimallman ok. i can backtrack on where the arguson comes from, if you like.
20:06 kcranstn isn’t it treemachine that doesn’t have metadata, not ott?
20:06 josephwb that would be awesome, thanks
20:06 jimallman kcranstn: i believe you’re correct, yes.
20:06 josephwb ott?
20:06 jimallman josephwb: i described it as missing from ott, but it’s actually missing from the latesting synthesis, right?
20:07 josephwb not in the db, yes
20:07 josephwb treemachine db
20:07 josephwb will probably store it in a different way; just wondering how you get it.
20:07 jimallman ok. so to restore metadata, it seems we need another round of synthesis with the metadata included, correct?
20:07 josephwb don't want to break things
20:08 josephwb no
20:08 josephwb we can add it in
20:08 josephwb [theoretically]
20:08 jimallman ok, i’ll walk it backward and try to clarify where the metadata is coming from.
20:08 josephwb sorry, i think we are talking past eachother a bit
20:09 josephwb the new loading procedure ommitted some metadata info
20:09 josephwb i want to put that stuff back in so it will work with services
20:09 kcranstn josephwb - you want to know the method call that gets the support info for the tree browser?
20:09 josephwb yeah
20:11 josephwb is it just stored in the arguson?
20:11 jimallman yes, i believe it’s normally included in the response to treemachine/getSyntheticTree
20:12 josephwb ok, thanks
20:12 kcranstn can you make that happen, josephwb?
20:12 josephwb curl calls are returning incomplete info, the browser has none
20:13 josephwb kcranstn: add metadata? yes, that is what i am trying to do.
20:13 kcranstn cool
20:13 jimallman if found, metadata is added to arguson as property ‘sourceToMetaMap’ (missing of no metadata found)
20:13 jimallman missing IF no data found
20:14 josephwb ok, that sounds like a good place to start, thanks
20:14 josephwb oh wait: what kind of info do you get?
20:14 josephwb studyid
20:14 josephwb treeid
20:14 josephwb gitsha
20:15 josephwb anything else?
20:15 josephwb or just some of those?
20:15 josephwb jimallman ^
20:15 jimallman just a sec, i’ll send a typicl CURL call
20:16 josephwb great
20:16 josephwb seeing an arguson snippet would help
20:17 jimallman curl 'https://api.opentreeoflife.org/cached/treemachine/v1/getSyntheticTree' -H 'Content-Type: application/json' --data-binary '{"treeID":"otol.draft.22","format":"arguson","maxDepth":"3","subtreeNodeID":"134"}'
20:17 jimallman that will give you the arguson for Bacteris on production
20:17 jimallman Bacteria
20:18 josephwb ah, a "v1" call. wouldn't have looked there. thanks.
20:20 jimallman yes, the web apps are using still using mostly v1 APIs
20:20 jimallman (i’m starting to move to v2 for tree collections)
20:20 jimallman compare the previous cURL call to this one, for Bacteria on development (devtree):
20:20 jimallman curl 'https://devapi.opentreeoflife.org/cached/treemachine/v1/getSyntheticTree' -H 'Content-Type: application/json' --data-binary '{"treeID":"otol.draft.22","format":"arguson","maxDepth":"3","subtreeNodeID":"2275490"}'
20:21 jimallman note that in this case, the sourceToMetaMap is there in arguson, but some of its entries are null
20:22 jimallman i believe this is the bit of code that includes the metadata (or not, if not found):
20:22 jimallman https://github.com/OpenTreeOfLife/treemachine/blob/0087bfbdc012aa7982391929fd769f8e6000f72d/src/main/java/org/neo4j/server/rest/repr/ArgusonRepresentationConverter.java#L151-L156
20:23 * jimallman needs to dash, back in 10min
20:30 * jimallman is back now
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