Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-04-10

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Time Nick Message
02:52 travis-ci joined #opentreeoflife
02:52 travis-ci OpenTreeOfLife/phylesystem-api#716 (support-tree-collections - a681fe3 : Jim Allman): The build passed.
02:52 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/8c0420a222c3...a681fe3ddac9
02:52 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/57896784
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03:59 travis-ci OpenTreeOfLife/phylesystem-api#717 (support-tree-collections - 8368f3d : Jim Allman): The build passed.
03:59 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/a681fe3ddac9...8368f3d8b628
03:59 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/57900457
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04:03 travis-ci OpenTreeOfLife/phylesystem-api#718 (support-tree-collections - e77cb9a : Jim Allman): The build passed.
04:03 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/8368f3d8b628...e77cb9a80182
04:03 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/57900627
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04:09 travis-ci OpenTreeOfLife/phylesystem-api#719 (support-tree-collections - 815dca5 : Jim Allman): The build passed.
04:09 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/e77cb9a80182...815dca549506
04:09 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/57901076
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04:19 travis-ci OpenTreeOfLife/phylesystem-api#720 (support-tree-collections - 7f463b8 : Jim Allman): The build passed.
04:19 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/815dca549506...7f463b8e9d79
04:19 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/57901648
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12:39 mtholder joined #opentreeoflife
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13:11 mtholder hi, jimallman_ did you deploy the curator to devtree (to trigger the NCL update)? I hadn't done that, so I'm perplexed why it is working there.
13:12 mtholder that was re: https://github.com/OpenTreeOfLife/opentree/issues/624#issuecomment-91551055
13:13 jimallman_ i’ve been testing the collections API on devapi since last night, so i’ve deployed a few times.
13:13 mtholder Ah. cool
13:13 jimallman_ but nevery specifying a non-standard branch/SHA for ncl.
13:13 jimallman_ never specifying, i mean.
13:14 mtholder I just pushed the fix to NCL's master
13:14 mtholder I can't remember if the deploy pulls, but I guess it must or this would not be working.
13:15 jimallman_ hmm. ok, that doesn’t entirely make sense to me (why it started working before push to master), but i can live with a small mystery.
13:15 mtholder oh. wait, you just pushed last night (your time)?
13:15 mtholder that would be weird
13:17 jimallman_ here’s where ncl install is triggered, in install-web2py-apps.sh:  https://github.com/OpenTreeOfLife/opentree/blob/25b9c7f2314dd30552e5c83fee3074a4adaada42/deploy/setup/install-web2py-apps.sh#L126-L130
13:18 mtholder install-ncl.sh does a pull if the directory is there (and a clone if it isn't). So it should pull if there is new content in the NCL at https://github.com/mtholder/ncl.git
13:19 jimallman_ yes, and it seems to always use master (so what’s up there?):  https://github.com/OpenTreeOfLife/opentree/blob/master/curator/install-ncl.sh
13:20 mtholder odd. on devtree  tail log/messages shows:
13:20 mtholder Tue Apr 7 06:19:13 UTC 2015 jima ot16  Installing NCL at commit c44e9b69f247cbfe27631305449c6f4b8d6284ff
13:21 mtholder which should be too old.
13:21 jimallman_ d’oh! i forgot, it’s still using my workaround!
13:22 jimallman_ i’m emulating the curation app, by passing firstAvailable*ID arguments to to_nexml
13:22 mtholder OK. make sense
13:22 jimallman_ that avoids the auto-generated ids, so no problem
13:22 mtholder the bug definitely was only in the other branch of logic.
13:22 jimallman_ right, the workaround slipped my mind. sorry for confusion.
13:22 mtholder it is always nice when the world is orderly and passing all sanity checks.
13:22 * jimallman_ nods
13:22 mtholder well maybe the whole world doesn't pass such checks...
13:23 jimallman_ our little world, at least.
13:23 jimallman_ speaking of which, i’m enjoying the kudos on the improved synth-tree.
13:23 * jimallman_ is stepping away to answer the door..
13:59 jimallman_ mtholder: do you know off-hand where peyotl (in typical deployment) should find its config file?
13:59 jimallman_ i don’t see an environment value PEYOTL_CONFIG_FILE;  /home/opentree/.peyotl/config doesn’t exist; and peyotl/default.conf doesn’t have a [phylesystem] section.
13:59 mtholder on which server does the config not exist?
14:00 jimallman_ i’m checking api and devapi.
14:00 mtholder ok. I see that. one sec...
14:01 mtholder I think that in phylesystem-api we pass in the locations of the phylesystem repos from the phylesystem-api config.
14:01 jimallman_ (that’s ot20 and ot10, respectively)
14:01 jimallman_ using the env variables?
14:02 mtholder back in a minute...
14:18 jimallman_ mtholder: no worries. i think i see the problem in my refactored code, will chase it from here.
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16:12 jimallman_ REMINDER: i’m running refactored peyotl on devapi, and it has some rough edges. holler if this is creating problems and i’ll revert to the master branch of peyotl.
16:49 josephwb joined #opentreeoflife
16:49 josephwb hey jimallman
17:01 josephwb are you there jimallman_
17:40 jimallman_ josephwb: hi! sorry, broke for lunch
17:40 josephwb hey
17:40 josephwb sent email; didjya see?
17:41 josephwb don't see what i did wrong…
17:41 jimallman_ just found your email… sniffing around the server (devtree) now...
17:41 josephwb great
17:42 josephwb thanks
17:43 jimallman_ i see the new (pending) graph.db, but not the old
17:43 jimallman_ admin@ip-10-254-159-74:/home/opentree/neo4j-treemachine/data$ ls
17:43 jimallman_ graph.db.new
17:43 jimallman_ (that’s garbled.. it was a call to ls in /home/opentree/neo4j-treemachine/data
17:44 josephwb did i do it wrong?
17:44 jimallman_ not that i can see. it looks like the deployment script is trying to move the old graph.db out of the way, but it balks when it can’t find it… checking the script now...
17:46 josephwb why wouldn't the old one be there?
17:46 jimallman_ not sure yet.. here’s the script: https://github.com/OpenTreeOfLife/opentree/blob/master/deploy/setup/install-db.sh#L22-L39
17:46 josephwb i was suppoed to use devtree, not devapi, right?
17:48 jimallman_ good question.. actually, i think it belongs on devapi.
17:48 jimallman_ maybe it assumes a prior graph.db because we haven’t installed treemachine here before
17:48 josephwb ah.
17:49 josephwb it was confusing. no doc.
17:49 jimallman_ yep. the closest is to look at the OPENTREE_COMPONENTS in each config file.
17:49 jimallman_ this shows the default (expected) components for each server
17:50 jimallman_ so yes, i suspect the same push command would work, just use devapi.config instead of devtree.config
17:52 josephwb will do
17:53 josephwb doing
17:54 josephwb i was confused, because devapi states: "# No opentree webapp on this server"
17:55 josephwb so, what is devtree for, then?
17:55 jimallman_ devtree holds the (user-facing) webapps, ie the synth-tree viewer and curation tool
17:55 jimallman_ devapi has some web2py stuff, mainly phylesystem-api
17:57 josephwb ok
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17:57 josephwb [still confused, but ok]
17:57 jimallman_ that comment (above) refers to the default web2py app. there’s got to be one, but in this case it can’t be ‘opentree’, so we specify the default ‘welcome’ app (sort of a hello-world app for web2py)
17:57 josephwb did i break devtree?
17:57 jimallman_ hm, let’s see. i already have it in a goofy state due to my testing peyotl changes
17:59 jimallman_ synth-tree is getting a 404 from the call to http://devapi.opentreeoflife.org/treemachine/v1/getSyntheticTree, but it responds in the browser… checking this now
18:02 jimallman_ hm, the ‘cached’ controller on devapi is broken (returns 404). i’ll chase this, pretty sure it’s not your problem.
18:03 josephwb i am pushing right now
18:05 jimallman_ ah, i’ll wait then.
18:06 josephwb copied over, now extracting
18:08 josephwb taking longer, so must be working!
18:11 josephwb do you know how long this takes?
18:15 josephwb erg. i didn't "screen" this.
18:19 josephwb jimallman_: if i kill this, it will be bad, right?
18:19 jimallman_ possibly, but we can clobber it (it should be safely in graph.db.new)
18:19 josephwb need to go to the airport at some point; can't wait forever
18:19 josephwb "Extracting database from downloads/treemachine.db.tgz"
18:19 jimallman_ lemme check the files, see if anything’s growing…
18:20 josephwb ok
18:21 jimallman_ there’s a ton of stuff in graph.db.new, dated Apr 7..?
18:21 jimallman_ be right back...
18:21 josephwb yes
18:24 josephwb ok, i've got to leave. what should i do?
18:24 josephwb kill, screen, redo?
18:24 josephwb jimallman_?
18:25 jimallman_ kill and redo, if you have time
18:26 jimallman_ hm, there are new files since last time i checked. so i think it’s working, slowly!
18:26 jimallman_ josephwb: ^
18:26 pmidford2 joined #opentreeoflife
18:28 josephwb ok, bye
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19:00 travis-ci OpenTreeOfLife/phylesystem-api#721 (support-tree-collections - 3403d19 : Jim Allman): The build passed.
19:00 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/7f463b8e9d79...3403d19c2567
19:00 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/57992553
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19:05 travis-ci OpenTreeOfLife/phylesystem-api#722 (support-tree-collections - 798e5b8 : Jim Allman): The build passed.
19:05 travis-ci Change view : https://github.com/OpenTreeOfLife/phylesystem-api/compare/3403d19c2567...798e5b809850
19:05 travis-ci Build details : http://travis-ci.org/OpenTreeOfLife/phylesystem-api/builds/57994310
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19:11 josephwb joined #opentreeoflife
19:11 josephwb ack jimallman_
19:11 josephwb "rm: cannot remove `neo4j-treemachine/data/graph.db.new': Directory not empty"
19:11 kcranstn rm -r ?
19:11 josephwb [made it to the airport ;) ]
19:12 jimallman_ josephwb: do you need to remove this? the earlier process comlpeted
19:12 josephwb i am using the deploy script
19:12 jimallman_ completed
19:12 josephwb did it? i killed it.
19:13 jimallman_ hm. odd. it seemed done to me:  https://devtree.opentreeoflife.org/
19:13 jimallman_ and it moved graph.db.new to graph.db, as expected.
19:14 jimallman_ (meanwhile, my branch of phylesystem-api was lagging badly behind master. i’ve merged in those changes, which fixed the missing-tree bug)
19:16 jimallman_ josephwb: thoughts?
19:16 josephwb idunno
19:16 josephwb i killed it mid-extraction
19:17 jimallman_ and yet here it is.. and again, the script definitely kept going, copied it to the final destination etc.
19:17 josephwb that's good.
19:17 jimallman_ can you see new stuff in the tree?
19:17 josephwb i'm not sure what is different
19:18 jimallman_ ah, ok
19:18 jimallman_ fee free to push it again, if you have time.
19:18 josephwb see, this is confusing: it is hosted on devtree, but i push to devapi
19:18 josephwb https://devtree.opentreeoflife.org/opentree/argus/otol.draft.22@132
19:19 jimallman_ yes, devtree provides the web app, and uses the APIs on devapi to fetch data.
19:19 josephwb yeesh
19:19 jimallman_ same with the curation app, of course
19:19 jimallman_ SOA (service-oriented architecture)! very trendy..
19:19 josephwb that is fine; it is just the names that are confusing
19:20 jimallman_ yeah, i definitely get turned around too
19:20 josephwb i only do this 1.5 times a year
19:20 jimallman_ yeah, that’s not helping
19:21 josephwb ack! there is a tip called "Rhea fossils"
19:21 kcranstn is that in OTT?
19:21 josephwb checking
19:21 josephwb not in the taxonomy we are using
19:22 josephwb something is messed up
19:22 jimallman_ it shows up in the taxon search (tree viewer)
19:22 josephwb we use a filtered taxonomy (throw out "dubious")
19:22 kcranstn 2562003 3600818 |   857863  |   Rhea fossilis   |   species |   gbif:4966398    |
19:22 kcranstn no flags
19:22 kcranstn in ott2.8
19:22 josephwb "fossilis"
19:22 josephwb crap
19:22 josephwb not "fossils"
19:23 josephwb i am an idiot
19:23 kcranstn oops
19:23 jimallman_ hey, i missed it too!
19:23 josephwb too much time staring at documents i'm not allowed to talk about
19:23 kcranstn ?
19:23 jimallman_ i think if he told us, he’d have to kill us.
19:24 josephwb some seedy government thing
19:24 kcranstn I didn’t think they gave canadians that kind of clearance?
19:24 josephwb shh...
19:25 josephwb jimallman_ can you confirm this db is dated 7 April?
19:25 josephwb i have no idea how many nodes are "new" (same input as before)
19:26 josephwb fyi, this seedy governmental organization has a spellchecker that does not recognize the word "transformative". heh.
19:28 jimallman_ ok, checking file dates now… but Apr 7 sounds like what i saw before
19:29 jimallman_ josephwb: yes, most files in graph.db are dated April 7 (a few after midnight on the 8th)
19:33 josephwb ok, good
19:38 josephwb thanks for your help once again, jimallman_
19:39 jimallman_ no problem! i needed a refresher on this, and it revealed my lagging code (which surely saved some headaches)
19:40 josephwb probably have to delete db on devtree/downloads
19:41 josephwb i imagine that is easy for you
19:41 josephwb i am going to shut down my computer for a bit
19:44 josephwb yeah, i cannot log into ot16
19:44 josephwb ttyl
19:46 josephwb joined #opentreeoflife
19:46 josephwb back. stephen thinks it is the same (old) tree
19:46 josephwb jimallman_ ^
19:56 josephwb i checked, and it does seem to be 7 April. maybe stephen is looking in the wrong place
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20:03 josephwb hey jimallman_
20:03 josephwb it looks to be the old one (somehow)
20:04 josephwb the new db does not have metadata in it
20:04 josephwb but citations are displayed
20:06 josephwb hullo jimallman_?
20:11 * jimallman_ is back now, catching up..
20:12 jimallman_ josephwb: citations are displayed, like this you mean?   https://devtree.opentreeoflife.org/opentree/argus/otol.draft.22@132
20:12 josephwb the "supported by" bits; that is not in the db
20:13 josephwb we have a different loading procedure, and have to add metadata nodes back in
20:13 josephwb sources are just represented by integers
20:14 jimallman_ hrm. ok. and you’re sure that treemachine data was the latest (again, dates are ~Apr 7)?
20:14 * jimallman_ is looking to make sure we’re not fetching that data in some other way...
20:14 josephwb yes, but again i killed it, so i am confused...
20:15 jimallman_ do you have time to try it again? if not, i can do it if i have access to the zipped archive
20:15 josephwb i don't think there is a link to such info at all
20:15 josephwb yes, i am preparing again
20:15 josephwb retarring
20:16 josephwb (deleted my copy)
20:16 jimallman_ kewl
20:16 jimallman_ and yes, you’re quite right. the arguson sourceToMetaMap has all the citation info
20:17 josephwb ah.
20:17 josephwb weird
20:17 josephwb how is that possible
20:17 josephwb ?
20:18 jimallman_ under the circumstances, i suspect you’re right. somehow we’re still showing the old data.
20:18 jimallman_ maybe we need to restart neo4j? (the treemachine instance, i mean)
20:19 josephwb ah
20:19 josephwb duh, yeah.
20:19 josephwb the script would do that, right? but i killed it.
20:19 jimallman_ i’m not 100% on that (would have thought it was done), but it’s worth a try. looking for the incantation now..
20:21 josephwb i am going to try to push again, tho
20:21 josephwb worried that things did not complete correctly
20:23 jimallman_ ok, sounds good
20:27 josephwb pushing now

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