Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-09-18

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All times shown according to UTC.

Time Nick Message
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01:03 mjwhy Jon H. you lurking?
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11:11 josephwb morning phylo pholks
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11:37 josephwb you there jimallman?
11:48 josephwb you there now jimallman?
11:49 josephwb hey ilbot3
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12:32 josephwb hey mtholder
12:32 josephwb i think i fixed the tree_id bug you reported
12:32 josephwb but I cannot deploy it on dev, and do not have a local instance to test
12:34 josephwb instructions on how to deploy are on the issue page: https://github.com/OpenTreeOfLife/treemachine/issues/128
12:34 josephwb maybe jimallman can do it?
12:34 josephwb *walking kids to school now*
12:49 mtholder jospehwb thanks. it is not a blocker for me. I can drop the arg as you suggested. just wanted to report it.
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13:05 mtholder kcranstn, I left some notes on the bottom of the annotations google doc
13:06 mjwhy joined #opentreeoflife
13:07 kcranstn thanks, checking now
13:07 kcranstn I like that suggestion
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13:09 mtholder cool. i'll generate some examples and work on the implementation
13:10 jimallman josephwb: here now. do we need to push to dev?
13:10 mtholder not on my account...
13:10 josephwb yes please
13:10 josephwb jimallman: you got the branch info, yes?
13:11 * jimallman is catching up on email + notifications...
13:11 josephwb the treemachine branch is "pluginsv2"
13:11 josephwb ok, gotta run to family appointments. be back later.
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13:17 * jimallman has pushed treemachine@apiv2 to dev, appears to be working
13:17 jimallman somewhere josephwb is smiling
13:18 jimallman oops, i meant treemachine@pluginsv2 (that’s what i pushed)
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13:40 jimallman is there a special gathering this morning? i don’t see my peeps…
13:46 jimallman codiferous: ^
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14:03 jhill1 what licence to OT generally use for code?
14:03 kcranstn bsd
14:03 jhill1 ta
14:04 kcranstn some gpl, though, because of neo4j
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14:31 jhill1 Is there coffee downstairs yet?
14:31 kcranstn yes, and I don’t think we have consumed it all yet
14:32 jhill1 Good and good!
14:46 josephwb joined #opentreeoflife
14:47 josephwb thanks for deploying that jimallman
14:47 josephwb if only all bugs were so simple to fix...
14:51 mjwhy we need a place (wiki likely) to document the shared bindings/method names being used by the API wrappers... can an OT dev suggest/stub something?
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14:53 towodo files.opentreeoflife.org/ott/aster.tgz
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15:29 kcranstn mtholder: “Note that it is generally better to avoid the create() method and instead generate document IDs on the client side. This is due to the fact that the underlying HTTP POST method is not idempotent, and an automatic retry due to a problem somewhere on the networking stack may cause multiple documents being created in the database."
15:33 towodo having trouble understanding match_names … how do I map my query names to the returned results?  are the “id” fields of the results the names that I fed in, or some other name (e.g. the primary name associated with the returned OTT id)?
15:34 codiferous joined #opentreeoflife
15:35 towodo I’ll assume “id” is the query string for now
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16:39 josephwb hey jimallman
16:40 jimallman hi josephwb
16:40 josephwb how does one specify which version of nexson in a call to the api?
16:41 josephwb i am talking about a study query, not a tree from the curator
16:43 jimallman just a sec…
16:45 jimallman https://github.com/OpenTreeOfLife/phylesystem-api/tree/master/docs#get-arguments
16:47 josephwb karolisr ^
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16:47 jimallman the key is this query-string variable (which may not be sufficientlly documented)
16:47 jimallman ?output_nexml2json=1.0.0
16:49 jeetononymous Question for anyone who is familiar with it: find_studies returns a dictionary with a single element, "matched_studies". Always, it seems. Any reason to work with this outer dictionary, i.e. if wrappers simply return the dereferenced "matched_studies" value?
16:49 josephwb thanks jimallman
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17:25 BarbBanbury Is there a webex link for this afternoon?
17:25 kcranstn posting now
17:25 BarbBanbury thank you!
17:25 kcranstn posted
17:25 kcranstn (might need to refresh the page) https://github.com/OpenTreeOfLife/hackathon/wiki/Schedule
17:28 kcranstn mtholder?
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17:35 mtholder krcanstn
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18:07 mtholder josephwb, codiferous, jimallman, towodo: the taxonomy example curls aren't working with me:
18:08 mtholder curl -X POST http://devapi.opentreeoflife.org/v2/taxonomy/subtree -H 'Content-type:application/json' -d '{"ott_id":515698}'
18:08 mtholder "message" : "org/opentree/exceptions/MultipleHitsException",
18:08 mtholder "exception" : "NoClassDefFoundError",
18:08 mtholder ...
18:09 jimallman hmm
18:10 josephwb cody fixed it.
18:11 towodo cody said try again now
18:11 josephwb maven! :-@
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20:25 blackrim jeetononymous:  you there
20:27 jeetononymous yessir
20:30 blackrim does dendropy do well with the BEAST consensus files (with that dictionary of things at each internal node)? just going to experiment but figured I would ask first
20:32 jeetononymous Yes. All comments are stored as a list associated with each node. By default, these are the raw values of the stuff inside the comment. However, if you pass in "extract_comment_metadata=True", then the BEAST-style comments get parsed out to key/value pairs and promoted to full Annotation objects associated with the node.
20:32 blackrim ok, you pass that on Tree.get_from_path
20:33 jeetononymous yep. ``tree = Tree.get_from_path("a.nex", "nexus", extract_comment_metadata=True)
20:33 blackrim word
20:34 jeetononymous E.g. of this can be found here: https://github.com/OpenTreeOfLife/phylostylotastic/blob/master/converters/annotate-with-support-values.py
20:34 blackrim thx <- with an x
20:43 josephwb hey codiferous
20:44 josephwb getting unexpected behaviour from infer_context in R
20:44 josephwb with underscores in names:
20:44 josephwb > tnrs_infer_context("taxon_names"=c("Stellula_calliope", "Struthio_camelus"))
20:44 josephwb $context_name
20:44 josephwb [1] "All life"
20:44 josephwb $context_ott_id
20:44 josephwb [1] 805080
20:44 josephwb $ambiguous_names
20:44 josephwb $ambiguous_names[[1]]
20:44 josephwb [1] "stellula_calliope"
20:44 josephwb $ambiguous_names[[2]]
20:44 josephwb [1] "struthio_camelus"
20:44 josephwb Without underscores:
20:44 josephwb > tnrs_infer_context("taxon_names"=c("Stellula calliope", "Struthio camelus"))
20:44 josephwb $context_name
20:44 josephwb [1] "Birds"
20:44 josephwb $context_ott_id
20:44 josephwb [1] 81461
20:44 josephwb $ambiguous_names
20:44 josephwb list()
20:45 josephwb We can address this on the R side, but maybe taxomachine should do this?
20:53 codiferous josephwb, we are leaving underscore-whitespace parsing up to clients
20:54 josephwb ok
20:54 josephwb easy enough, just curious
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