Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-06-19

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Time Nick Message
00:01 towodo joined #opentreeoflife
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12:04 towodo joined #opentreeoflife
12:45 kcranstn http://files.opentreeoflife.org/other/curnewicks/life_synth.tre
12:45 kcranstn not found
12:48 kcranstn https://github.com/OpenTreeOfLife/feedback/issues/40
13:02 mtholder joined #opentreeoflife
13:10 towodo it's compressed.  index page is wrong
13:15 mtholder I guess that index is not versioned, right?
13:27 josephwb joined #opentreeoflife
13:28 towodo mtholder, it's in opentree/deploy/files.opentreeoflife.org/other/curnewicks/index.html
13:30 kcranstn joined #opentreeoflife
13:36 kcranstn https://github.com/OpenTreeOfLife/treemachine/issues/101
13:37 kcranstn new rule: we should never rely on manually posted versions of artifacts?
13:49 jimallman joined #opentreeoflife
13:51 josephwb as Towodo states in his email, curnewicks was set up for debugging only
13:52 josephwb we will be doing a whack of debugging over the next week or so.
13:52 josephwb don't think we need/want to post each iteration of those
13:52 towodo I am recovering the recent whole tree file… missed it when making the new files.opentreeoflife.org
13:53 josephwb i say we chuck it (curnewicks), and just link to the tree as towodo suggests
13:53 kcranstn sounds good to me
13:57 kcranstn this all came about because james rosindell (onezoom) was asking for a download link
13:57 towodo ok now there's something to link to again … http://files.opentreeoflife.org/trees/
13:57 kcranstn yay!
14:07 kcranstn I will tackle cleaning up the developer resources page later today
14:08 mtholder joined #opentreeoflife
14:08 towodo excellent
14:26 mtholder joined #opentreeoflife
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14:59 towodo josephwb, are you there?
15:01 towodo mtholder, what about you?
15:06 mtholder yes
15:06 mtholder I'm here-ish
15:06 mtholder towodo^
15:08 towodo well that will do.  i picked names in random draw for award of the first irc prize
15:08 mtholder woohoo!
15:09 towodo so you win.
15:11 towodo to be fair, if jimallman pipes up within 2 minutes, he gets one too
15:11 mtholder I'm adding this to my CV right now...
15:11 jimallman yip
15:13 jimallman It’s an honor just to be nominated.
15:13 josephwb i'm here
15:13 towodo yes but you didn't reply in two minutes.
15:13 mtholder in your face josephtb
15:14 towodo sorry, that should be 5 minutes, but still
15:23 josephwb what is up?
15:35 mtholder joined #opentreeoflife
15:35 towodo josephwb, it came time for me to award the irc prizes, as i had threatened to do earlier.
15:35 josephwb ack
15:35 towodo people on irc at the randomly selected time are ordered randomly.  first to answer in 5 minutes gets the prize.
15:36 josephwb prize?
15:36 josephwb doesn't ilbot3 win all of the time?
15:36 * towodo Maybe you had to be there.  It was in jest.  And now I'm following up
15:37 towodo are you there?
15:37 towodo never answers me when I address him/her
15:38 i1bot3 yes. I'm here.
15:38 josephwb shenanigans
15:56 josephwb hmm. getSyntheticTree returns nothing if no subtreeNodeID is provided
15:56 josephwb should we default this to the root of the synthetic tree?
15:56 josephwb what do you think mtholder?
15:57 mtholder I think that would be nice if it is easy to do.
15:57 i1bot3 I agree
15:57 josephwb well, looks like it is unanimous
15:57 josephwb i am doing this from within R
15:57 josephwb very easy for me to set the default there
15:58 josephwb but maybe should instead do this in treemachine
15:58 mtholder it would certainly be nice to have some API calls in cURL that will continue to work as we change the tree.
15:58 mtholder so a treemachine default would be ideal.
15:58 josephwb right
15:58 josephwb i'll look into it
16:06 mtholder gotta head to NC... bye
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17:01 josephwb jimallman: is it cool if I update treemachine now?
17:02 jimallman josephwb: sure, OK by me (i just updated the webapp)…
17:02 josephwb what do i need to make sure is recently pulled when i do this?
17:02 josephwb opentree
17:02 josephwb anything else
17:02 josephwb ?
17:04 josephwb want to avoid sync issues you and mark brought up the other day
17:05 josephwb ok, just pulled everything to be safe and am updating now
17:07 jimallman josephwb: sounds like a reasonable approach :)
17:07 jimallman s/reasonable/safe
17:07 josephwb hmm, my changes are not there
17:08 josephwb should i use api or devapi?
17:08 josephwb well, neither reflect changes
17:09 josephwb that should have updated "devapi", right jimallman
17:10 josephwb here is what i get:
17:10 josephwb curl -X POST http://devapi.opentreeoflife.org/treemachine/v1/getSyntheticTree -H "content-type:application/json" -d '{"format":"newick", "maxDepth":"3", "subtreeNodeID":"3534540"}'
17:10 josephwb {
17:10 josephwb "message" : "Node 3534540 not found",
17:10 josephwb "exception" : "NotFoundException",
17:10 josephwb "fullname" : "org.neo4j.graphdb.NotFoundException",
17:10 josephwb "stacktrace" : [ "org.neo4j.kernel.impl.core.NodeManager.getNodeById(NodeManager.java:339)", "org.neo4j.kernel.InternalAbstractGraphDatabase.getNodeById(InternalAbstractGraphDatabase.java:959)", "opentree.GraphDatabaseAgent.getNodeById(GraphDatabaseAgent.java:89)", "opentree.GraphExplorer.reconstructSyntheticTree(GraphExplorer.java:2463)", "opentree.plugins.GoLS.getSyntheticTree(GoLS.java:375)", "java.lang.reflect.Method.invoke(
17:11 josephwb same call to "api" get:
17:11 josephwb curl -X POST http://api.opentreeoflife.org/treemachine/v1/getSyntheticTree -H "content-type:application/json" -d '{"format":"newick", "maxDepth":"3", "subtreeNodeID":"3534540"}'
17:11 josephwb {
17:11 josephwb "newick" : "(JG37-AG-4,SHA-26,P2-11E,((Caldilineaceae)Caldilineales)Caldilineae,((Oscillochloridaceae,Roseiflexaceae,FFCH7168,Chloroflexaceae)Chloroflexales,(Herpetosiphonaceae)Herpetosiphonales,AKIW781)Chloroflexia,Elev-1554,((Ardenticatenaceae)Ardenticatenales)Ardenticatenia,SL56_marine_group,MSB-5B2,KZNMV-5-B42,(AKYG1722,(bacterium_Ellin6537)JG30-KF-CM45,(Sphaerobacterales)Sphaerobacteridae,(Thermomicrobiaceae)Thermomicrobial
17:11 josephwb "treeID" : "otol.draft.22"
17:12 josephwb is the graph DB different on "api" and "devapi"?
17:17 kcranstn_ joined #opentreeoflife
17:22 jimallman josephwb: apologies, i stepped away to make lunch. catching up now...
17:24 towodo josephwb, the push.sh script only moves the contents of the local setup/ directory.  everything else is obtained from github, from the branches specified in the config files.
17:25 towodo yes, the graph db is different on api and devapi.
17:25 jimallman josephwb: fwiw, i think that’s a dead node id. i get the same result in the tree-viewer app: http://devtree.opentreeoflife.org/opentree/argus/otol.draft.22@3534540
17:26 towodo api is the synthetic tree from april.  devapi is the one stephen just pushed (I think).  (can check by doing ls -l downloads on ot10)
17:26 jimallman … but other node ids work fine, including the default ‘cellular organisms’: http://devtree.opentreeoflife.org/opentree/argus/otol.draft.22@127
17:26 josephwb ok, thanks
17:28 josephwb so, deployed changes will be reflected on just devapi?
17:28 towodo let me change the question.  when you do push.sh -c otxx.config … , only otxx will be altered.
17:29 josephwb ok, it is the otX -> api/devapi mapping that eludes me
17:29 towodo see my previous email about which servers are part of prod/dev and how.
17:29 josephwb oti10 = which one?
17:30 josephwb must have missed that one
17:30 towodo hang on, getting link
17:31 towodo https://groups.google.com/forum/#!topic/opentreeoflife-software/JLwviBidLuQ
17:31 josephwb now starred. thanks.
17:32 towodo ot10 = devapi
17:32 josephwb email says "devtree"
17:32 josephwb is that deprecated?
17:33 towodo email says *references* ot10
17:33 josephwb yes, it does
17:33 towodo I think the email is correct, except that it doesn't say that ot10 = devapi.
17:34 towodo but you can always look at the deployed-servers repo for this information too
17:34 towodo it's just a bit harder to read there.
17:41 josephwb towodo and jimallman: just performed "push" again
17:41 josephwb lots of warnings
17:41 josephwb [WARNING] We have a duplicate javax/*
17:42 towodo you pushed to ot10 using the ot10 config in deployed-systems ?
17:42 josephwb yes
17:42 towodo is the warning while building treemachine?
17:43 jimallman josephwb: i think that’s just noise (pre-existing artifacts from prior compilation)…
17:43 josephwb when building the plugins for treemachine
17:43 towodo if it's one of the neo4j app builds then yes, there's always tons of junk.  don't you get that when you build locally?
17:44 towodo maybe it's only when building the plugin .jar, as jim says, and when you build locally you only make the command line .jar ?
17:46 towodo this because nobody wants to invest in learning how to use maven properly
17:46 josephwb yes, i see it locally too
17:49 josephwb jimallman: how do you get the nodeId from the webapp? i think i am missing something
17:49 josephwb i want a valid one to test with
17:50 jimallman it’s in the URL…. look for {synth-tree-id}@{neo4j-node-id}
17:50 jimallman josephwb: ^
17:50 josephwb that's what i thought
17:51 josephwb so, Aves is 466700
17:51 jimallman URL changes as you move through the tree, so use Search to get the current neo4j node id for any taxon
17:52 jimallman i’m getting 81461 for Aves.. which site are you looking at?
17:52 jimallman http://dev.opentreeoflife.org/opentree/argus/ottol@81461/Aves
17:52 jimallman http://devtree.opentreeoflife.org/opentree/argus/ottol@81461/Aves
17:52 josephwb when i clicked on the Aves node, the URL changed to 466700
17:53 * jimallman might have steered you wrong.. URL probably shows ott id… checking now.
17:53 josephwb yes, it dfoes
17:53 josephwb does
17:54 josephwb so, searching for Aves got me: opentree/argus/ottol@81461/Aves
17:55 josephwb clicking on Aves gets me: opentree/otol.draft.22@466700/Aves
17:55 josephwb first one it ottid
17:55 josephwb second is node?!?
17:56 mtholder joined #opentreeoflife
17:57 jimallman oh, i remember now! two different forms of URL, for different ways of finding a node.
17:57 jimallman if first part is “ottol”, second part is ott id
17:58 jimallman otherwise first part is interpreted as a draft of the synthetic tree (basically, this is always current) and the second as a neo4j id in that tree
17:58 jimallman this scheme was intended to let us reconstruct views from prior synthetic trees, but we currently don’t keep them around.
17:59 jimallman so you can get to Aves (on current devtree) from either of these URLs:
17:59 jimallman http://devtree.opentreeoflife.org/opentree/otol.draft.22@340780/Aves
18:00 jimallman http://devtree.opentreeoflife.org/opentree/argus/ottol@81461/Aves
18:01 jimallman in both cases, the actual call to getSyntheticTree will use the assigned neo4j node for the specified (default=current) synthetic tree: subtreeNodeID: "340780"
18:01 jimallman josephwb: hope that’s semi-clear ^
18:04 jimallman ProTip: In Chrome, you can use the Network tab of its developer tools to see all the AJAX calls like getSyntheticTree, and even right-click to ‘Copy as cURL’ and re-run them in a terminal. sweet!
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18:18 josephwb towodo: I am doing ls -l downloads on ot10
18:18 josephwb there is a treemachine.db.tgz from 18 June
18:19 josephwb you said stephen pushed a new synthesis there?
18:20 josephwb i don't think he has done a full one recently (i.e. with the new taxonomy)
18:37 josephwb ok, my brain doesn't understand what is going on here.
18:37 josephwb i want a valid nodeId for testing so, of course, i go with Aves
18:37 josephwb curl -X POST http:/devapi.opentreeoflife.org/taxomachine/v1/autocompleteBoxQuery -H "content-type:application/json" -d '{"queryString":"Aves","contextName":"All life"}'
18:37 josephwb [ {
18:37 josephwb "ottId" : 81461,
18:37 josephwb "nodeId" : 678634,
18:37 josephwb "exact" : true,
18:37 josephwb "name" : "Aves",
18:37 josephwb "higher" : true
18:37 josephwb } ]
18:38 josephwb "nodeId" = 678634, right?
18:38 josephwb now, lets gran the subtree starting at that node
18:38 codiferous ah! whoops, forgot about that
18:38 codiferous taxomachine node ids are different from treemachine's
18:38 josephwb curl -X POST http://devapi.opentreeoflife.org/treemachine/v1/getSyntheticTree -H "content-type:application/json" -d '{"treeID":"otol.draft.22", "format":"newick", "maxDepth":"3", "subtreeNodeID":"678634"}'
18:38 josephwb {
18:38 josephwb "newick" : "Xiphidiopsis_altiterga;",
18:38 josephwb "treeID" : "otol.draft.22"
18:38 josephwb }
18:38 josephwb ah!
18:38 josephwb thank you
18:38 josephwb my brain was going to implode
18:39 josephwb so, is a taxomachine nodeId useful in any way?
18:39 codiferous not for treemachine
18:39 codiferous possibly not for anything
18:40 codiferous since every taxonomy node should have a unique ottid
18:41 josephwb ok, how about this: curl -X POST http://api.opentreeoflife.org/treemachine/v1/getDraftTreeID
18:41 josephwb {
18:41 josephwb "startNodeOTTId" : 93302,
18:41 josephwb "draftTreeName" : "otol.draft.22",
18:41 josephwb "startNodeTaxName" : "cellular organisms",
18:41 josephwb "startNodeID" : 215
18:41 josephwb }
18:41 josephwb 215 is the start node
18:42 codiferous yep
18:42 josephwb curl -X POST http://devapi.opentreeoflife.org/treemachine/v1/getSyntheticTree -H "content-type:application/json" -d '{"format":"newick", "subtreeNodeID":"215"}'
18:42 josephwb {
18:42 josephwb "newick" : "Protomyces_gravidus;",
18:42 josephwb "treeID" : "otol.draft.22"
18:42 josephwb }
18:42 josephwb huh?
18:42 josephwb wait
18:42 josephwb those are 2 different machines
18:42 josephwb curl -X POST http:/devapi.opentreeoflife.org/treemachine/v1/getDraftTreeID
18:42 josephwb {
18:42 josephwb "startNodeOTTId" : 93302,
18:42 josephwb "draftTreeName" : "otol.draft.22",
18:42 josephwb "startNodeTaxName" : "cellular organisms",
18:42 josephwb "startNodeID" : 127
18:42 josephwb }
18:42 josephwb 127 is root
18:43 josephwb ok, it works
18:43 josephwb *phew*
18:43 josephwb but not when leaving the subtreeNodeID blank
18:43 codiferous still gets life?
18:43 codiferous or blank, as it appears
18:43 josephwb curl -X POST http://devapi.opentreeoflife.org/treemachine/v1/getSynthetiTree -H "content-type:application/json" -d '{"format":"newick"}'
18:43 josephwb {
18:43 josephwb "newick" : "life;",
18:43 josephwb "treeID" : "otol.draft.22"
18:43 josephwb }
18:44 codiferous yeah. which ot is devapi?
18:44 josephwb BUT, if I do curl -X POST http://devapi.opentreeoflife.org/treemachine/v1/getSynthetiTree -H "content-type:application/json" -d '{"format":"newick", "subtreeNodeID":""}'
18:44 josephwb it works
18:44 josephwb well, cody, devapi is ot10
18:44 josephwb (i just asked jonathan that)
18:45 josephwb subtreeNodeID is supposed to be an optional arg
18:45 codiferous looks like it is getting set to the life node id in the plugin
18:46 josephwb when i do "subtreeNodeID":"" it is correct (cellular_organisms)
18:46 josephwb only when it is absent does it do the  weird life thing
18:46 codiferous line 352 in https://github.com/OpenTreeOfLife/treemachine/blob/master/src/main/java/opentree/plugins/GoLS.java
18:46 codiferous that's where it should be set to the synthesisRootNodeId
18:46 josephwb my conditions are: 1) is it null, 2) is the length zero
18:47 codiferous probably should also add that length zero check to that conditional
18:47 codiferous (in the plugin)
18:47 codiferous oh, it's already there... odd. anyway
18:48 josephwb the issue seems to be if the arg is not present, it is neither null nor length zero
18:48 josephwb wha?
18:48 codiferous if it isn't present, then it will be null
18:48 josephwb right, right?
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19:47 * towodo off to my daughter's 8th grade graduation
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