Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-10-09

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18:07 jimallman towodo: Are we planning to review pull requests today?
18:07 towodo oh, good question.
18:07 towodo kc’s not here, but there are only a couple
18:08 towodo I’m up for it if you are
18:08 jimallman sure, i racked up a few over the weekend.
18:08 towodo give me 5 minutes then let’s start
18:08 jimallman Actually, i’ve tested them all so i’m going to be an easy yes vote. but maybe that makes me the wrong person..?
18:08 jimallman sure, i’ll be here
18:12 towodo there’s one PR on taxomachine, let’s start there
18:12 towodo https://github.com/OpenTreeOfLife/taxomachine/pull/80
18:14 towodo deploying tests branch to ot17
18:15 jimallman i’m still tracing the logic here.. so Travis will run some of this on each commit to GitHub?
18:15 towodo no, there are 2 things
18:16 towodo Travis runs the tests specificied by .travis.yml
18:16 towodo I run the test script test.sh
18:16 towodo it’s fine if there’s overlap
18:16 jimallman right, test.sh (human) vs run_service_tests.sh (Travis)
18:18 towodo looks like there’s a manual setup step that will be unavoidable… setting the server port
18:19 towodo it looks for nosetests, so fails
18:19 towodo so I’m going to reject this PR for now
18:19 jimallman not sure why there are two default ports cited here, :7474 and :7476
18:20 towodo when cody debugs on his machine he probably uses 7474, which is the neo4j default
18:20 jimallman hm, ok
18:21 towodo I would prefer he use 7476… but the port number shouldn’t be hardwired in any case
18:21 towodo probably there should be config file settings for the ports for the three neo4js
18:21 towodo maybe i’ll make an issue of that
18:22 jimallman makes sense
18:22 jimallman unless we just freeze these with a dedicated port (non-overlapping, obviously) for each service
18:23 jimallman i’m looking to see if ‘nose’ in requirements.txt is enough to support nosetests.. did you pip install requirements.txt?
18:24 towodo https://github.com/OpenTreeOfLife/opentree/issues/480
18:24 towodo why would i have pip installef requirements.txt?… I asked for these to be self contained and people agreed… is that wrong?
18:24 towodo s/installef/installed/
18:25 towodo I want to do this:  for r in repo/*; do $r/test.sh; done
18:25 jimallman no, that makes sense. i suppose tests.sh should then run a virtualenv (if needed) and any needed pip installs…? and then maybe clean up after itself..?
18:25 towodo and not have to worry about random per-repo setup
18:25 towodo yes I think so
18:26 jimallman so maybe a convention for setup and teardown functions in test.sh
18:26 towodo ok, wanna look at https://github.com/OpenTreeOfLife/reference-taxonomy/pull/102 ? you raised the issue
18:26 jimallman or just assume these will happen at start and end of the script
18:27 jimallman sure (though i don’t recall being involved in this one)
18:27 jimallman ah, #96
18:28 towodo the ‘add chromista spreadsheet transducer’ commit was a mistake
18:28 towodo but fairly harmless. it’s a derived file so doesn’t belong under source control
18:29 jimallman these look great (and easy to view nicely in GitHub): https://github.com/OpenTreeOfLife/reference-taxonomy/blob/ott2.8/doc/ott2.4.md
18:30 towodo I’m removing that derived .py file now
18:30 jimallman thanks. so these will be the guts of our web-friendly “release pages”… cool
18:31 jimallman we’ll just have to watch for relative URLs in some places, make sure they still resolve
18:32 jimallman i think this is ready to go. shall i merge?
18:32 towodo just pushed a commit to get rid of the .py
18:32 jimallman right, looks good
18:32 jimallman (i was waiting for that to appear)
18:32 towodo yes, go ahead
18:33 towodo ok, opentree, older to newer
18:33 towodo https://github.com/OpenTreeOfLife/opentree/pull/468
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18:34 towodo reading the conversation
18:34 jimallman sounds good (i don’t see any waiting PRs in other repos)
18:34 towodo (I set up my browser so I can do ‘open all in tabs’ to get all PRs)
18:35 towodo you said this is deployed on devtree?
18:35 jimallman not the latest (just added some accessibility fixes)
18:36 jimallman support for tab and arrow keys… i can deploy to devtree now…
18:36 towodo ok that would be nice (otherwise I can deploy to ot17)
18:36 jimallman it’s on the way...
18:37 jimallman ok, should be working now on devtree.
18:38 jimallman i’ve tested the tree-viewer’s taxon search locally, with wide layout and narrow layout.
18:38 towodo my first test was ‘atta’ … fails
18:38 towodo ‘eciton’ works fine
18:39 towodo arrows work fine
18:39 jimallman drat, i’m looking for a match wtih the search-result text… for Atta, that’s “Atta (genus in tribe Attini)”
18:39 towodo sorry.  maybe it’s a pathological case
18:40 towodo it must have a homonym, but the homonym doesn’t make it into taxomachine
18:40 towodo not sure it’s worth fixing at this point
18:40 jimallman it’s odd, but not exactly rare. maybe an allowable exception?
18:40 jimallman heck, i think i’d prefer that they review anything that’s not obviously a dead-on match
18:41 towodo yes, it’s probably ok. let’s merge
18:41 jimallman there’s a second taxon-search field in the curation app, Metadata tab.
18:41 towodo oh yeah, i’ll look
18:41 jimallman if you wanna look. this has basically the same behavior, except tab order is more “natural” (we tab past the search-context before getting to first search result)
18:41 jimallman arrow keys work the same in both cases
18:43 towodo looks ok
18:43 jimallman agreed
18:43 towodo i’ll merge
18:44 jimallman the next PR *might* conflict, if i don’t merge master into it first…
18:44 towodo if you do a lot of PR merges then they fill up your github activity log
18:45 jimallman hm, i’ve gotta get on board with git-rebase
18:45 towodo sort of annoying if you’re trying to use github as a way to track your work… merges are not “real work”
18:45 towodo https://github.com/OpenTreeOfLife/opentree/pull/469
18:45 jimallman i’ll push this to dev…
18:46 jimallman should be visible at http://devtree.opentreeoflife.org/… ah, here it is
18:47 jimallman just to review: search field was dark, now light. context selection was light, now dark.
18:48 jimallman search icon added to the input field. i think this is more familiar/obvious than before (compare to http://tree.opentreeoflife.org/)
18:51 towodo Not really a bug, but I entered ‘thermo’, very long pause… selected Thermoanaerobacter brockii subsp. brockii , and boy is this thing slow…
18:51 jimallman i’m seeing the same (super-slow results).. is it because there are two (gasp) simultaneous users?
18:52 towodo that would only account for a 50% slowdown :)
18:52 towodo I think the search box could be wider, but I can submit that as a separate issue
18:52 jimallman unless we’re passing some threshold (RAM)?
18:53 jimallman re: wider search, maybe we can ditch the Home link in top nav? it’s really just the same as clicking the OToL logo
18:54 towodo 7 seconds for Pheidole<space>
18:54 jimallman did you mean to merge PR #468? it’s still open...
18:55 towodo I often forget to do ‘confirm merge’
18:55 jimallman fyi - i’m strictly hands-off on taxon search for now
18:55 jimallman ah, i’ve been there too (missed the sneaky confirm button)
18:56 jimallman drat. as i suspected, #469 will require a manual merge. no biggie..
18:56 towodo anyhow all you changed with this PR is the background, and it looks fine. source code changes are obvious. shall I merge?
18:56 jimallman see above
18:56 towodo hmm.
18:56 towodo but there shouldn’t be a problem, just an annoyance, right?
18:57 jimallman right, probably just an overlap on the INPUT tag here: https://github.com/OpenTreeOfLife/opentree/pull/469/files#diff-5c4140cd38a71aec630f2cb93c829379L193
18:57 jimallman wanna come back to this later, or clean up now?
18:57 towodo I’ll run through the ‘use the command line’ business if that’s ok
18:57 jimallman sure! it’s a nice little dance
18:58 towodo hmm… there are a few lines conflicting in layout.html
18:58 towodo left-inner-addon
18:59 jimallman oh yeah, definitely keep that (and the icon element inside)
18:59 towodo so, remove tabindex=“1”, right?
18:59 jimallman the INPUT element was moved into this div (to get the search icon)
19:00 jimallman pls keep tabindex=“1” (used for the previous PR to get modified tab order)
19:00 towodo but it wasn’t just moved, it was modified, tablindex=“1” got removed
19:00 towodo oh i see
19:00 towodo i think
19:00 jimallman “removed” from the diff’s POV, but we want it
19:01 towodo I will move the tabindex= from master to HEAD.
19:01 jimallman sounds right
19:01 towodo that’s the only manual merge required.
19:02 jimallman great! if you push back (git push origin master), that should close the PR as well.
19:03 jimallman i think so, anyway
19:03 towodo yes but I’m going to do it differently. I’ll push out the merge commit and you can check it, then i’ll do the PR merge using the git UI
19:03 jimallman i like it, thanks
19:04 towodo ok take a look
19:04 jimallman mind if i pull it to my local branch and re-deploy to devtree?
19:04 towodo go ahead
19:04 towodo (although re-deploy is always from github… so pulling locally not necessary)
19:05 jimallman true!
19:05 towodo wow I don’t understand why so much changed in that merge commit
19:06 jimallman i think master has come a long way since this PR was created
19:06 jimallman it kinda freaked me out, too.
19:06 towodo it reflects a lot of other work.
19:07 jimallman OK, the combined style + behavior looks good on devtree. let’s merge
19:07 towodo good. https://github.com/OpenTreeOfLife/opentree/pull/474
19:08 towodo oh, i’ve been using this. it’s great
19:08 jimallman do i need to push to devtree?
19:09 towodo I’m a bit buzzled, maybe I misremember
19:09 jimallman the “scold” behavior (3 days old) is interesting: https://github.com/OpenTreeOfLife/opentree/commit/4c517ab89f531e5e0d7f9af5ceee1e71feb54ca7
19:09 towodo s/buzzled/puzzled/
19:09 jimallman i’ll go ahead and push while we discuss
19:11 jimallman ok, working now on devtree
19:11 towodo Hmm, I wonder about the wording.
19:11 towodo do you have an example study handy (that has a treebase deposit)?
19:11 jimallman http://devtree.opentreeoflife.org/curator/study/edit/pg_2584
19:11 jimallman try to upload a file (or import a tree) and you’ll be scolded just once
19:13 jimallman Suggestions on wording are *most* welcome. I’m not at all sure about how I’ve described these constraints.
19:13 towodo Hmm.  I expected to see the scold at “Add a tree to this study”
19:13 jimallman yes, it should appear (just once) when you click “Add new tree”
19:14 jimallman if you’ve already been scolded in the Files tab, it won’t appear again (reload the page to see it here)
19:14 towodo I think they should see it before pasting or uploading, otherwise it’s bait & switch
19:15 jimallman hm, i’ll need to detect paste or keydown in the tree-text field. and so far i’ve had a hard time getting ahead”
19:15 jimallman “getting ahead” of the file widgets
19:15 towodo no need I think, can be static text, conditionally on whether there’s a deposit URL
19:15 jimallman if it’s really annoying, i will try it again
19:17 jimallman i didn’t think about a static warning on both tabs. i could add this pretty easily.
19:17 towodo both tabs?  not just the trees tab?
19:17 jimallman i assume the same logic applies to both Files and Trees
19:17 towodo oh yeah.
19:17 towodo The text can be pretty much the same as what you have now (maybe add the word “any” at the front), just in a different place
19:18 jimallman do you think this should *supplement* the current scold popup, or replace it?
19:18 towodo could just replace it.  no need to harrass them.
19:19 jimallman OK. if it becomes a problem, we can dig this up and pester them some more.
19:20 towodo I know you went to some trouble to get the once-only stuff and so on to work… sorry to be diruptive
19:20 jimallman adding a note to this PR now...
19:20 towodo we can merge now, and do this change as a separate issue
19:20 jimallman ah, sounds good
19:21 towodo looking at the rest of the commits
19:21 * jimallman is adding an issue for the milder scold
19:22 jimallman https://github.com/OpenTreeOfLife/opentree/issues/481
19:22 towodo ‘data in treebase’ link is terrific
19:23 jimallman :)
19:23 jimallman We have the “bones” to support similar friendly messages for other common deposit URLs. not sure if there are any candidates yet...
19:24 towodo clicked ‘download version used in synthesis’ and got {"description": "Study #2634 GET failure", "error": 1}
19:24 jimallman ! will look into this. (that URL should not have changed..)
19:25 towodo that was for Rønsted, N.,
19:25 jimallman same for Whitten, 2007 (first in the list)
19:25 towodo but that’s not part of this PR
19:26 jimallman agreed. pls make a separate issue, i’m guessing i’m using the wrong SHA in this URL:  http://devapi.opentreeoflife.org/phylesystem/v1/study/603?starting_commit_SHA=a2c48df995ddc9fd208986c3d4225112550c8452
19:26 jimallman these URLs, i mean
19:26 towodo I think it’s the same issue as the one i reported on the ggroup (not assigned to a repo because not clear what’s at fault)
19:27 towodo ok, I’ll merge?
19:27 jimallman please do
19:28 towodo https://github.com/OpenTreeOfLife/opentree/pull/479
19:29 jimallman pushing to devtree for review...
19:31 jimallman this is working, but pretty slowly
19:32 jimallman several seconds + to see the Focal Clade search context switch from default ‘All life’ to ‘Mammals’
19:32 towodo I wonder if there’s something wrong with ot10 or ot16… really sluggish on all operations
19:32 towodo looking
19:33 towodo are you doing something with it now?
19:33 jimallman nope, i’m standing by.
19:33 towodo java 122% …
19:34 jimallman it’s very quick to build this request, but the call to http://devapi.opentreeoflife.org/taxomachine/v1/getContextForNames is super-slow to respond
19:34 towodo well, it’s grinding away on something.  i bet taxomachine has gone away with some request
19:35 jimallman as Cody requested, i’m sending lots of names if we have them (in this case, 371 names)
19:35 towodo the machine has 4 CPUs
19:35 jimallman is neo4j smart enough to use them?
19:36 towodo maybe not, I don’t know
19:36 towodo yes, it’s taxomachine eating up that cpu…
19:37 towodo looking at request log
19:37 jimallman quick googling suggests there are some tricks to running neo4j traversals in parallel…
19:38 towodo that’s not the problem here
19:40 towodo I see a bunch of getContextsJson at 20:27 or before
19:40 towodo then at 20:30 there’s a bunch of getContextForNames
19:40 jimallman stuck requests, you mean? or over and done
19:40 towodo no, just requests
19:40 towodo the log doesn’t tell me which ones complete, or what the args are
19:41 towodo last two:127.0.0.1 - - [09/Oct/2014:20:32:03 +0100] "POST /db/data/ext/TNRS/graphdb/getContextForNames HTTP/1.1" 200 260 "http://devtree.opentreeoflife.org/curator/study/edit/pg_2584/?tab=metadata" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/37.0.2062.124 Safari/537.36"
19:41 towodo 127.0.0.1 - - [09/Oct/2014:20:32:27 +0100] "POST /db/data/ext/TNRS/graphdb/getContextForNames HTTP/1.1" 200 207 "http://devtree.opentreeoflife.org/curator/study/edit/2057" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.9; rv:32.0) Gecko/20100101 Firefox/32.0"
19:42 jimallman the requests for getContextJson are probably happening each time a page with taxon search is requested in web2py. i have a standing TODO to cache this, but haven’t gotten around to it.
19:42 towodo we need to start paying attention to performance pretty soon
19:43 towodo why does it say edit/2057 instead of edit/pg_2057 ?
19:44 towodo the firefox is probably me and the chrome is probably you
19:44 jimallman yes, running Chrome here today
19:44 towodo I haven’t upgraded to os x 10.9.5 yet
19:45 towodo are you touching it? lots of requests still coming in.
19:45 towodo hmm, paused
19:46 jimallman yes.  it seems http://devtree.opentreeoflife.org/curator/study/edit/2057 and /pg_2057 have the same behavior.
19:46 jimallman (i was checking those URLs, probably 3-4 page requests)
19:46 towodo ok
19:46 jimallman i’m guessing we treat ‘pg_’ as the default prefix for study IDs?
19:47 towodo that would have been transitional.  probably time to phase it out now and always require explicit prefix.
19:48 towodo i was just wondering where the non-pg_ study id would have come from.  need to fix it at its source
19:48 jimallman yes, i’m not sure. in fact, i don’t think it was from me (it’s not among the test URLs I normally use..)
19:48 towodo taxomachine still humming along, but only 23% CPU now
19:49 towodo I don’t understand how it can take 24% of CPU… thrashing perhaps
19:49 jimallman fyi  - made a proper issue for the need to cache search-context list: https://github.com/OpenTreeOfLife/opentree/issues/482
19:49 towodo I added that swap space, wonder if that could have slowed things down
19:50 towodo wondering if there’s a way from the neo4j console to find out what it’s doing
19:51 jimallman interesting! (and not in a good way)… it seems the curation app’s study list offers URLs without the prefix:  http://devtree.opentreeoflife.org/curator
19:51 jimallman (not always, but for most studies)
19:52 towodo ok, it’s down to 0.3% CPU.  weird.
19:53 jimallman garbage collection? i’ve read some things about neo4j slowdowns for GC, esp. with a too-large heap
19:55 towodo but it’s not allocating any memory… at least it shouldn’t be…
19:55 towodo I have a talk to go to at 4.  I wonder if we can leave this one open, I’m concerned now about server load
19:55 towodo thanks for your help
19:56 jimallman are you looking at ot10:/home/opentree/neo4j-taxomachine/data/graph.db/messages.log  ?
19:57 jimallman tons of seriously blocked threads here
19:59 jimallman some blocked for almost an hour, no idea why though
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20:58 towodo I didn’t even know about that log file
21:33 towodo jimallman, are you there?
21:37 jimallman towodo: here now
21:38 towodo I figured it out
21:38 towodo doing some OTU mapping for ot_209
21:38 jimallman cool! the log file was mentioned here (‘8. The log is your best friend’): http://java.dzone.com/articles/10-caveats-neo4j-users-should
21:39 towodo the bogus homonyms are very annoying
21:39 towodo like C. elegans.  Taxonomy errors
21:39 jimallman hm, are these showing up in fuzzy mapping?
21:39 towodo no
21:39 towodo There are two C. elegans, but one of them is sample contamination in genbank
21:39 jimallman eww
21:40 towodo I had to look at OTT to tell them apart. when I saw one was silva I knew what was going on
21:43 towodo this has to do with https://github.com/OpenTreeOfLife/opentree/issues/460
21:43 towodo if a mouseover on the taxon had showed me the source taxonomies, I would have known
21:44 jimallman ah, good to know.
21:44 jimallman to make #460 a reality, we’ll need its name and ottid, right?
21:44 jimallman with ottid being the more important
21:46 towodo yes, but isn’t that close at hand?
21:48 jimallman should be in most/all cases, yes
21:48 jimallman assuming a name has been mapped.
21:49 towodo oh my gosh I can’t believe the state of scientific publishing.
21:50 jimallman ?
21:50 towodo every taxon in this table (PDF!!!!) has a genbank accession. but the ids aren’t in the table.
21:50 jimallman yep
21:50 towodo not in the article, or in the supplementary material, or in the treebase deposit
21:50 towodo published in 2014.  this is absolutely insane
21:51 towodo ok, well maybe I should back off.  there are ncbi taxon ids, and maybe they used all available accessions for the given taxon id. I’d have to read the m&m
21:52 jimallman it’s not (yet) embarassing enough to omit this stuff, i think. it’s going to take time.
21:55 towodo so why isn’t there a taxon name completion box for OTU mapping? … or is there, let me check
21:55 towodo ooh, it’s tiny and very cramped
21:55 towodo and it doesn’t do completion
21:56 jimallman sorry, where are you looking?
21:56 jimallman is this the “Modified for mapping” box? yes, it does make sense to use TNRS there...
21:57 towodo the column was made very very narrow because the ‘mapped to taxon’ column is very wide
21:57 towodo I don’t get how this works.  I entered a taxon name in the box (copied it from OTT 2.8) and nothing happens.
21:58 towodo you might want to play with the same study in the dev system, it’s very interesting.  treebase 14693
21:58 jimallman the usual… mark this name for mapping (checkbox on left), click Map selected OTUs’
21:58 jimallman thanks, will do.
21:59 jimallman (maybe a really long mapped name is squeezing the middle column?)
21:59 towodo oh… little bit of a learning curve
21:59 towodo yes, the names in ‘mapped to taxon’ are quite long
21:59 towodo it’s a bit of a tease since there’s plenty of whitespace in the window on the left and right
22:00 towodo ok, it said ‘failed mapping’.   And I copied the string from OTT so I know it’s there…  maybe taxomachine threw it away though?…
22:00 towodo nope, no flags.
22:00 jimallman hm, what’s the name?
22:00 towodo Escherichia coli str. K-12 substr. DH10B
22:04 jimallman maybe  strain names are being normalized or something? in the tree-viewer’s taxon search, i get lots of hits on “escherichia coli str” but none is a literal match, they’re all like “Escherichia coli J53”, “Escherichia coli 4_1_47FAA’, “Escherichia coli 541-15”...
22:04 jimallman normalized is not the right word.. munged, i guess, into a common format?
22:05 towodo hmm… that would be unfortunate…
22:05 jimallman i’m mistaken, i think (though TNRS seems to gloss over “str”, which might be sensible)
22:06 towodo yes, there’s no consistency in whether people put in the ‘str.’
22:06 jimallman i find your substrain when searching for “escherichia coli str. K12”. it shows up with two others, as “Escherichia coli str. K-12 substr. DH10B”
22:07 jimallman this exact text is recognized in the main taxon search.. so not sure why it fails in OTU mapping. search context is right?
22:08 towodo ahh… I wonder. no, context is ‘all life’
22:08 jimallman hm, failing for me (in OTU mappnig) too, in ‘All life’
22:09 jimallman trying to map “Escherichia coli “ gives four candidates, but i don’t think our DH10B is among them
22:10 towodo when I enter Escherichia coli K-12 and try fuzzy matching, I get tons of results, only one of which is a K-12
22:10 towodo are the results sorted by match quality score?
22:11 jimallman yes
22:12 towodo funny, I did a search at silva’s site, and it hasn’t come back yet “waiting for seach result, please be patient”. that was at least 5 minutes ago
22:19 towodo jimallman, I also can’t get Escherichia-Shigella to work in ‘modified for mapping’.  works fine in tree browser.
22:20 jimallman i’m afraid i want to punt these questions to Cody
22:20 jimallman …as i’m pretty sure a curl call would get the same results
22:20 towodo I see, you think it could be a difference between the two methods? that makes sense
22:21 jimallman that’s my guess, yes
22:21 towodo I’ll take care of bringing this to him
22:33 jimallman thanks
22:34 towodo how do I get rid of “tree root arbitrary” ? I can’t figure out how to set the root
22:35 towodo it doesn’t offer ‘mark as root’ as an option for the root node
22:35 towodo jimallman ^
22:36 jimallman hm..
22:37 jimallman In the Edit Tree window, Properties tab, there’s a radio button for this
22:37 jimallman Tree root is   (*) confirmed by curator   ( ) arbitrary (for display only)
22:37 towodo ohh… I was looking in all the wrong places…
22:38 jimallman alternately, you could have clicked another root (or edge) and the original root again
22:38 towodo in the tree view you can click on a node and usually it offers ‘set as root’ so I thought that was the way to do it
22:38 jimallman but that’s lame. maybe we need an option (for unconfirmed root node only) like “Confirm this tree root”
22:39 jimallman yes, you can’t currently re-assert the current root from its menu
22:39 towodo my expectations would have been met if ‘set as root’ had been offered for the nominal root as it is for all other nodes
22:40 jimallman i can do this, or (as i mentioned above) “Confirm as tree root”
22:40 jimallman if it’s already the root but not officially confirmed yet
22:40 jimallman (perhaps gray this out if it’s already been confirmed, or explicitly set)
22:40 towodo maybe I’m stupider than the typical curator
22:41 jimallman not likely
22:41 jimallman i’m not against having more than one way to do this, since it won’t clutter the UI
22:49 towodo bizarre… it’s a duplicate… I guess I’ll delete it.  no warning if entered from treebase.

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