Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-12-01

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All times shown according to UTC.

Time Nick Message
02:48 jimallman joined #opentreeoflife
13:01 jimallman joined #opentreeoflife
13:26 mtholder joined #opentreeoflife
13:26 mtholder jimallman: do you know if there is a softward call today?
13:27 jimallman i’m planning for one, but haven’t seen a confimation
13:40 mtholder thanks
14:44 pmidford2 joined #opentreeoflife
14:45 kcranstn joined #opentreeoflife
15:31 mtholder left #opentreeoflife
16:07 jimallman joined #opentreeoflife
16:39 josephwb joined #opentreeoflife
17:08 josephwb Thought this would be more lively with ms discussion.
17:26 josephwb you there kcranstn?
17:26 kcranstn 2 pm
17:26 kcranstn on another call right now
17:26 josephwb ok
17:34 mtholder joined #opentreeoflife
18:58 blackrim joined #opentreeoflife
19:02 kcranstn hello!
19:03 kcranstn I’ve incorporated Gordon’s suggestions into the doc, and added a bunch of references
19:03 blackrim ok, have you done david and doug's yet? if not, i can do that now
19:03 kcranstn no, I haven’t. If you would, that would be great
19:03 blackrim ok, doing that now
19:03 kcranstn need to work on data packages
19:04 kcranstn where is towodo?
19:04 josephwb he is on the ms page
19:06 towodo joined #opentreeoflife
19:06 kcranstn should we provide the input trees as nexson and newick, or just nexson with a link to documentation about how to convert?
19:06 josephwb i think both
19:06 kcranstn me too
19:07 kcranstn ok, so need to get the nexsons that went into the synthetic tree
19:07 kcranstn do we have an easy way to do that?
19:07 kcranstn and need to get them from a specific commit of phylesystem
19:08 kcranstn I have that commit checked out, but don’t have a script to extract just the ones that went into the tree
19:08 * jimallman is taking notes for the synthesis release page…
19:08 josephwb they don't all have the same commit, do they?
19:08 blackrim i believe that joseph might have them sitting around? the list is easy to get from one of the services
19:09 josephwb i have them, but some may have gotten overwritten by updates since the tree was made
19:09 kcranstn let’s just get them again, then
19:10 josephwb i haven't dwalt with phylesystem directly
19:10 josephwb dealt
19:10 josephwb re: getting a particular commit
19:10 towodo https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-of-Life-APIs#about-tree-of-life
19:10 towodo with study_list=true
19:11 josephwb curl -X POST http://api.opentreeoflife.org/v2/tree_of_life/about -H "content-type:application/json"  -d '{"study_list":false}'
19:11 josephwb beat me
19:12 towodo isn’t there a service to convert a study id to a path within the phylesystem repo? …
19:12 josephwb then this: https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-of-Life-APIs#tree
19:13 josephwb i seem to remember that git SHA was a hidden arg?
19:13 kcranstn yup
19:13 kcranstn https://github.com/OpenTreeOfLife/phylesystem-api/blob/master/docs/README.md#fetch-a-study
19:14 kcranstn towodo - did you look at that readme for ott2.8?
19:14 towodo not yet, will now
19:16 towodo hmm… vertical bars not used for *all* files, only some...
19:16 kcranstn ok
19:19 towodo some of these are very hard to describe precisely… e.g. the otu_* files subset other reports by taxa that occur as OTUs in studies - according to phylografter’s list of studies
19:20 kcranstn we either need to describe them or take them out of the data deposition
19:20 towodo they’re just reports for debugging purposes, really.  maybe should delete them
19:22 towodo did you mean to number all of the sources?
19:22 kcranstn the previous paragraph said it was a priority list, so yes, I did number them
19:23 kcranstn ah, but they don’t render as numbered in plain text
19:23 kcranstn in a markdown viewer they do
19:23 kcranstn or, a non-github viewer
19:23 kcranstn hmmm
19:23 towodo apparently it depends *which* markdown viewer
19:23 kcranstn ok, let’s manually number them
19:24 kcranstn where is that purl documented?
19:24 towodo i think it’s just a matter of changing * to 1. for every one
19:25 towodo if you haven’t started editing I will
19:25 kcranstn I have not
19:27 kcranstn I can’t find that purl with all of the links to the sources
19:28 towodo go to purl.org and seach for jar287 … but since the 2.8 links haven’t escaped I’m thinking of changing the URL structure
19:29 kcranstn I just want to look at the page that it resolves to
19:29 kcranstn but can’t find it
19:29 towodo purl.org/opentree/ott2.8-inputs/
19:29 kcranstn thanks
19:29 towodo I can add those links
19:30 kcranstn what restrictions are there for putting the inputs into Dryad or Dataverse?
19:30 kcranstn NCBI and Hibbett can’t go into Dryad (unless we get David’s permission, because it is currently CC-BY)
19:36 josephwb kcranstn: did you want me to get the nexsons?
19:37 kcranstn sure!
19:37 josephwb ok, still cannot figure out how to pass SHA arg. no examples in doc.,
19:37 kcranstn ^mtholder
19:38 josephwb ok, figured it out. still need doc, tho.
19:38 kcranstn you want to make a PR on the doc, then?
19:39 mtholder starting_commit_SHA as discusse https://github.com/OpenTreeOfLife/phylesystem-api/blob/master/docs/README.md#fetch-a-study
19:39 blackrim joined #opentreeoflife
19:39 josephwb mtholder: this looks right?
19:39 josephwb curl http://api.opentreeoflife.org/v2/study/STUDY_ID/tree/TREE_ID&starting_commit_SHA=GITSHA
19:40 mtholder yeah. I think so
19:40 josephwb ok, thanks
19:47 towodo I’m hesitant to provide a download link to our copy of IRMNG
19:47 kcranstn ok
19:47 towodo it’s legal, but not sure about manners
19:47 kcranstn can we ask Tony?
19:48 towodo I guess so… could take a day due to his being down under, or longer given that he’s retired and isn’t doing irmng any more…
19:48 kcranstn we are providing it on the files.opentreeoflife page
19:48 kcranstn and it is an older version
19:49 towodo we provide the link.  the question is what happens if they change what’s behind the link.
19:49 towodo do we provide a snapshot or no
19:50 kcranstn this URL provides a zip file for download: http://files.opentreeoflife.org/ott/2.8-inputs/
19:54 towodo right, but it’s not a snapshot URL.
19:54 towodo Even if it gives the Jan 31 version today, there’s no assurance that it will tomorrow.
19:54 kcranstn what is that zip file?
19:55 towodo the URL is on the CSIRO site, isn’t it?
19:55 kcranstn I have no idea
19:55 kcranstn I am looking at this IRMNG - http://purl.org/opentree/ott2.8-inputs/IRMNG_DWC-2014-01-30.zip
19:56 towodo oh I see.  yes, that’s a snapshot, and my question is whether to copy that into the data deposit.
19:56 josephwb kcranstn: how would you like the files nexson named?
19:57 towodo in other words whether to retract the purl (which is ok since it hasn’t escaped into the wild)
19:57 kcranstn I am unsure why you are comfortable putting the link on a public URL but not in our data deposit
19:57 kcranstn ok, we are now finally on the same page
19:57 josephwb PREFIX_STUDYID_TREEID.nexson?
19:58 kcranstn ^ josephwb - I think so
19:58 blackrim_ joined #opentreeoflife
19:58 josephwb ok
19:58 blackrim_ ok, i am going to have to run for a bit but the comments from the docs that were sent are in there
19:58 towodo kcranstn, I have a 3:00 meeting… my changes to the README are on github on the readme-2.8 branch
19:58 kcranstn ok, thanks
19:58 towodo I should be back around 4:10
19:59 towodo I have a directory with a modified 2.8 that I will turn into a tarball when the readme is closer to completion (or if you want a draft at any point)
19:59 blackrim_ I will email when I can do more but let me know if something is waiting for me to do. otherwise, seems like things are wrapping up.
19:59 blackrim_ did you want to do the submission karen
19:59 towodo have deleted about.json and the otu_* files
19:59 kcranstn yeah, I can do the submission
19:59 kcranstn still waiting for some stuff from gordon
20:02 blackrim_ ok, do we need to work on a new letter? wondering if there is something that could be going on (maybe doug could draft something if we don't have a start)
20:02 blackrim_ ok, i have to run. more later
20:09 josephwb damn. is mtholder coming back?
20:14 kcranstn he appears to be offline on gchat as well
20:14 kcranstn what’s going on?
20:17 josephwb just weird stuff with curl
20:17 josephwb this works:
20:17 josephwb curl http://api.opentreeoflife.org/v2/study/pg_2827/tree/tree6577
20:18 josephwb but this hangs, like it is waiting for further input:
20:18 josephwb curl http://api.opentreeoflife.org/v2/study/pg_2827/tree/tree6577&starting_commit_SHA=a2c48df995ddc9fd208986c3d4225112550c8452
20:18 josephwb something stupid on my part, fer sure
20:18 jimallman josephwb: looks like your query string is messed up. should start with ? instead of &
20:19 jimallman (then use & for second and subsequent arguments)
20:19 kcranstn curl -X GET http://api.opentreeoflife.org/v2/study/pg_2827/tree/tree6577\?starting_commit_SHA\=a2c48df995ddc9fd208986c3d4225112550c8452
20:19 josephwb thanks jimallman!
20:19 josephwb again, need doc
20:20 kcranstn if you don’t update the doc, then at least make an issue in the api repo
20:21 josephwb is it not automatically generated?
20:21 josephwb like the other api junk
20:22 kcranstn *someone* still needs to make a manual change somewhere in order for the docs to update
20:22 josephwb right. i don't know where that stuff lives for phylesystem, so i will just log an issue
20:32 mtholder joined #opentreeoflife
20:51 josephwb kcranstn: nexsons sent to email
20:51 kcranstn thanks!
21:11 josephwb who is this Nico Franz that is commenting on the ms?
21:12 towodo joined #opentreeoflife
21:12 kcranstn prof at ASU who has been interested in the project for a while
21:12 josephwb suggests we cite his paper ^o)
21:13 kcranstn reminder that this is a public channel that is also logged
21:20 kcranstn towodo - can we chat over G+ about the taxonomy inputs?
21:20 towodo sure
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21:35 towodo left #opentreeoflife
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23:55 josephwb joined #opentreeoflife

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