Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-06-30

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All times shown according to UTC.

Time Nick Message
01:15 josephwb joined #opentreeoflife
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12:44 josephwb jimallman: you there?
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13:50 jimallman josephwb: here now, can i help?
13:54 josephwb i sent you an email
13:54 josephwb about Yan not being able to save a study
13:55 josephwb Sorry, there was an error in the study data. Hide details
13:55 josephwb {"description": "Could not write to study #ot_51 ! Details: \n", "error": 1}
13:58 josephwb jimallman ^
13:58 jimallman hrm, thanks. looking into this...
13:59 josephwb ok, thanks
13:59 josephwb sounds like Yan has a whack-ton of trees to contribute
13:59 josephwb 8-|
14:00 josephwb (actually, a metric whack-ton)
14:06 jimallman josephwb: i’m looking at recent errors on the phylesystem-api server (Kayla is also having trouble with uploads)…
14:06 jimallman someone’s getting 'TreeBASE-Access denied’, but i’m not sure why
14:06 josephwb huh
14:07 jimallman wait, that’s from several days ago. false alarm.
14:07 jimallman that was the last logged error in web2py.. still looking.
14:07 josephwb yeah, this was from yesterday
14:10 jimallman OK, assuming he’s not actively working there now, i’m going to try saving a trivial change.
14:13 jimallman i was able to add and remove a tag (trivial change), no problems here.
14:14 josephwb he doesn't need to be added as curator, does he?
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14:17 josephwb jimallman: he doesn't need to be explicitly added as a curator, does he?
14:17 jimallman no, only github account is required. and he’s logged into the editor, so it’s not a missing username problem.
14:18 jimallman i think it’s nexml validation, but there should have been a more useful error message for that.
14:18 josephwb i thought missing usernames were a problem.
14:18 josephwb here he is: https://github.com/hyanwong
14:19 jimallman we have had problems with login w/o usernames in the past, but i believe we fixed that some time ago.
14:20 josephwb ok
14:22 josephwb towodo: you haven't responded to Dail's request for an "ADD to OTT". i think this is something he really wants.
14:26 * jimallman has an unsolicited opinion: i understand where Dail is coming from, but that option could undermine OTT in a major way, if people just default to “add this for me” when a name doesn’t match.
14:26 kcranstn where is that request from dail?
14:27 josephwb opentree issue #343
14:27 josephwb https://github.com/OpenTreeOfLife/opentree/issues/343
14:28 josephwb i agree with you jimallman
14:28 josephwb would be incredibly useful if used correctly
14:28 josephwb but potential for abuse is extremely high
14:28 kcranstn need provenance
14:29 jimallman i suppose if this created a “provisional” taxon, basically add it to a list for consideration and placement..? maybe with suggestions for provenance, hopefully leading to a proper addition of source tree in taxomachine
14:33 josephwb seems like this might be *too easy* to generate an enormous list of new names
14:33 kcranstn if every name in an input tree is new, that doesn’t give us any way to link that tree to the other inputs
14:33 kcranstn new names also need an ancestor
14:34 josephwb good point
14:34 kcranstn mechanism to map internal nodes in the tree to OTT
14:34 josephwb we don't take in internal names
14:34 josephwb the curator, i mean
14:36 josephwb my concern: from the enormous amount of data cleaning from phylografter, I don't entirely trust curators
14:36 josephwb especially for something as important as adding new taxa
14:37 josephwb and it is clear that we are working with different concepts of "taxa"
14:37 towodo josephwb, we've been talking about that feature for over a year.
14:38 josephwb Katz lab *seems* to want to count anything with a sequence in NCBI as a taxon
14:38 towodo without resolution regarding its priority.
14:38 towodo they can use the patch system to add taxa.  They can write scripts and UIs to make it easier to use the patch system.
14:39 josephwb towodo: right
14:39 josephwb but Dail won't do that
14:39 towodo They are asking for developer resources from Jim and me, and there's a ton of things competing
14:39 josephwb or, frankly, many empirical folk
14:39 josephwb hitting a button is very easy
14:40 towodo Priorities are not up to me. there is strong pushback on this particular one from karen and stephen.
14:40 josephwb I would love to use such functionality, but I trust myself ;-)
14:40 towodo Is what I've said above good to relay in email on the main ggroup?
14:40 towodo seems a bit sensitive for that, don't want to open a priority setting free for all there maybe.
14:41 jimallman i think it would be a minor project to add an “inline” taxon-nomination tool in the curator, to automate the patch. but the sequence is awkward: the new taxonomy patch isn’t “realized” in OTT, so we can’t map the OTU to it for a while…
14:41 towodo Personally I think scalability is the top priority, and custom taxon addition doesn't help with that.
14:41 towodo I'm thinking about a service for creating a new OTT id.
14:42 towodo maybe you should have to pay $1 for each one, like a DOI.
14:43 towodo Before that service exists I have to assign permanent meanings to all the existing ones, and a few other tasks
14:43 towodo and I'm going to be busy all summer with non-opentree nescent things...
14:44 towodo so I haven't replied because first I need to manage stress and spin.
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14:58 josephwb jimallman: I've got Yan's tree, trying to get it into the curator.
15:01 jimallman OK, let me know what you find.
15:02 josephwb jimallman: worked fine for me (ot_53)
15:03 jimallman hm. i wonder if Yan could follow up by making a trivial change to this study, just as a test of the plumbing and the missing-username issue. he could add a tag or something, then remove it and save again.
15:03 jimallman josephwb: ^
15:05 josephwb email sent
15:05 josephwb he is trying now
15:09 josephwb jimallman: Yan was successful at adding the focal clade
15:09 josephwb what is going on?
15:16 jimallman josephwb: it’s hard to say without being able to sift through the wreckage of the failed attempt. i’m hoping Mark will have something we can look at.
15:17 josephwb ok
15:17 josephwb shall i get him to try to start a study of his own?
15:28 josephwb jimallman ^
15:31 jimallman sorry josephwb , i was talking to an HVAC repair guy (oh boy)
15:32 jimallman re: starting a new study, i don’t see why not. but do ask him to save frequently so as not to lose (much) work. hopefully that will give us a clue, if he’s doing something… odd in his studies.
15:39 josephwb he has been warned
15:59 josephwb jimallman: Yan was able to upload a study. no idea what went wrong before
16:00 jimallman that’s great / terrible news!
16:01 jimallman meanwhile, i’m chasing some weirdness in our tree-upload tool.. everything’s being treated as NEXUS, even if it’s clearly Newick. conversion errors and mayhem ensue.. i’m narrowing the problem down now.
16:23 jimallman josephwb: what is the name of the file that Yan had trouble with, but you uploaded successfully?
16:24 josephwb i don't know; he sent me the newick, and i just pasted it in.
16:24 jimallman never mind, i’m finding clues in the emails..
16:25 josephwb i emailed him anyways
16:46 josephwb jimallman: Yan says he just pasted the tree in the text box.
16:49 jimallman Hmmm. I can see four attempts on the server to import a tree with ‘Haeckeliidae’ (had to grep for this), and all are marked as successful. Maybe his text got lost the first time..?
16:49 jimallman josephwb: it looks like the Katz lab folks are sending invalid Newick, so that’s a separate issue (unquoted labels with whitespace)...
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17:01 josephwb1 jimallman: Yan is not with the Katzes
17:02 kcranstn has the google event started? does not look like it to me
17:02 josephwb1 is it Dail that is uploading the poorly-formatted trees?
17:02 jimallman josephwb1: understood. i’m chasing multiple bug reports today (joy!)
17:02 josephwb1 kcranstn: yes
17:02 jimallman Dail, Kayla, possibly others.
17:03 josephwb1 i'll let Dail know
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17:49 jimallman josephwb1: i’m already in email contact with Dail and Kayla via Newick errors
17:50 josephwb1 i see that
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17:53 jimallman towodo: let me know if you want help with moving dev => tree.opentreeoflife.org, or other deployments
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17:53 towodo thanks… i have to think it through, the constraints are a bit hairy
17:53 jimallman i’ll be around (currently chasing bugs and working on history / “back button”  support in the curator)
17:54 jimallman … then (hopefully) testing for duplicate studies
17:55 towodo back when i was doing doi lookups i think about 80% of studies had dois recorded.  FYI.  and some number, maybe 5% or less, had no dois.
17:55 jimallman good to know, thanks
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21:21 towodo site is pretty broken. http://devtree.opentreeoflife.org/about/references
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23:16 josephwb jimallman: pushing fixed code now
23:16 jimallman cool, thanks!
23:16 josephwb i don't know if it was me
23:16 josephwb i made a plugin that didn't work
23:16 josephwb assumed it wouldn't hurt anything else
23:17 jimallman bwah-ha-ha…
23:17 jimallman actually, weird that it broke GoLS but nothing else..
23:19 josephwb ok, it works (damn; should have tried b4 making my changes)
23:19 josephwb e.g. curl -X POST http://api.opentreeoflife.org/treemachine/v1/getSyntheticTree -H "content-type:application/json" -d '{"treeID":"otol.draft.22", "format":"arguson", "maxDepth":"3", "subtreeNodeID":"3534540"}'
23:19 josephwb hope i didn't delay you too long
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