Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-05-18

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Time Nick Message
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13:59 kcranstn josephwb?
13:59 josephwb kcranstn
14:00 kcranstn that reference will update
14:00 kcranstn if needed
14:00 josephwb i typed that one in manually a few weeks back
14:00 josephwb will paperpile recognize it?
14:00 kcranstn ah, I didn’t realize you typed it manually
14:00 josephwb sorry that wasn't clear
14:00 kcranstn I’ll update it now
14:01 josephwb ok
14:01 josephwb btw was there a decision made to throw out set notation in favour of plain english?
14:01 kcranstn yes, a few weeks ago
14:01 josephwb emily's stuff is very different
14:02 josephwb really? i cannot imagine jar286 is satified with the inprecision of that new text
14:03 kcranstn plain english != imprecision, necessarily
14:03 josephwb there is a happy medium, for sure, but i think this stuff overshoots it
14:03 kcranstn and emily jane’s changes are very new
14:03 kcranstn have not been reviewed
14:08 jar286 ears burning
14:08 kcranstn EJM has proposed a bunch of changes to the Generating the Synthetic Tree writeup
14:08 jar286 plain english != imprecision, necessarily
14:10 jar286 hmm.  haven’t seen yet
14:14 josephwb i'm not sure that having someone who admits to not fully understanding the method rewrite the text is optimal...
14:14 josephwb i agree with: plain english != imprecision, necessarily
14:14 josephwb of course
14:15 kcranstn Her edits are clearly marked, and help us discuss whether we all understand what’s going on
14:16 jar286 the question is whether someone can read it, and understand (not just pretend to understand).  if you need to be formal to achieve that, you be formal
14:19 josephwb i agree; i often conflict with cody on such things. i prefer plain text when it is appropriate
14:21 jar286 that first paragraph is pretty twisted
14:25 josephwb i feel like we went from text that was near submission quality to something that will take a a lot of work
14:26 jar286 me too, but for you, which text specifically was near submission quality?
14:27 josephwb most of it, i think. but specifically here all of the text that emily is replacing
14:28 kcranstn if you disagree with the edits, reply in the doc
14:29 kcranstn not that helpful to discuss here without EJM
14:29 josephwb i sort of disagree with the general replacement strategy
14:29 josephwb she makes some good points
14:31 jar286 someone is still confused about ‘subtending’ vs. ‘subtended by’ …
14:32 josephwb that is a common problem, i've found, even within a single paper!
14:48 josephwb i think biologists get subtend wrong because we draw our trees with the root on the bottom
14:49 josephwb [i draw mine sideways to make sure i irritate everyone ;) ]
14:49 jar286 could be.
14:50 jar286 It always takes me about five seconds to process the word ‘deeper’ or ‘depth’
14:50 josephwb yes, that too
14:50 jar286 because in CS the trees are upside down and people talk about ‘depth first search’
14:51 josephwb i believe depth is in the supp., with the opposite definition that you would recognize
14:51 jar286 I think the CS inversion goes back to Chomsky and Backus
14:52 josephwb oh, it was "shallow" i was thinking of: shallowest node (the node furthest from the root)
14:53 josephwb i'm surprised you didn't jump on that jar286
14:55 jar286 ‘what I would recognize’ - the problem is I recognize both senses, since I’m living in two worlds - the 5 second delay is to remember which world I’m in and which sense applies
14:58 josephwb hah
15:02 jar286 who wrote this text originally?
15:02 josephwb cody and mark, i believe
15:02 kcranstn cody, with edits from others
15:03 jar286 this looks like a good place to do pair programming
15:03 josephwb *googling pair programming*
15:04 jar286 except, it would be  pair writing, not pair programming
15:04 jar286 this is a situation where not being colocated is a major problem
15:04 kcranstn and being in radically different time zones
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15:13 jar286 as far as I can tell the whole first paragraph is gibberish
15:16 jar286 1. we traverse the TAG bottom up (topological order).
15:18 jar286 2. for each node we pick a set of edges with disjoint subtension, i.e. ones that make a tree.  the set we pick is the ‘best’ set (tbd)
15:19 jar286 3. the synth tree is build top down by choosing the best edge set at each node.
15:31 kcranstn I don’t understand your opposition to rank in this section. We’ve explained the ranks of input trees and labeling of edges previously in the doc
15:38 jar286 rank of an edge is not defined.  the natural definition is that it’s the rank of the tree that the edge is labeled with. but this isn’t said anywhere.
15:38 jar286 kcranstn ^
15:41 kcranstn ok, so add that sentence
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15:43 jar286 right now I’m just trying to understand what the section is saying.  usually I hold off on edits until I understand
15:45 snacktavish I'm just jumping on here to say I'm out for the day! Feel free to revert/resolve as needed. I can read it again tomorrow.
15:46 kcranstn thanks snacktavish!
16:10 mtholder joined #opentreeoflife
16:10 mtholder jimallman, fwiw http://bioinformatics.oxfordjournals.org/content/21/19/3801.full describes a tool calle "treeillustrator", but it does not appear to be maintained.
16:11 jimallman mtholder: good to know, thanks!
16:12 jimallman i’m not a huge fan of the name, so maybe this will nudge us toward something more memorable.
16:13 mtholder da VinTree ?
16:14 josephwb +1
16:15 kcranstn you can always count on mtholder for a name
16:15 kcranstn and the associated groaning
16:41 codiferous joined #opentreeoflife
16:42 codiferous sorry for not being on earlier while editing. i never remember to join irc
16:49 codiferous i have some driving to do today but i will have another look at things tonight before switching priority to ssb meeting for a few days
16:53 josephwb hey jimallman
16:53 jimallman josephwb: yes?
16:53 josephwb the "Loading supporting studies..." on the tree veiwer is taking a long time
16:54 jimallman ok, checking now...
16:54 josephwb https://tree.opentreeoflife.org/opentree/argus/ottol@81461/Aves
16:54 josephwb checking node "Neognathae
16:55 josephwb doesn't matter which node, though
16:55 josephwb doesn't seem to ever complete
16:57 jimallman i see. the call is actually returning promptly, but with an empty list (ie, no supporting studies)
16:57 jimallman something’s definitley goofy.. chasing this now.
16:57 josephwb hmm
16:58 josephwb works on devtree
17:01 josephwb something wrong with treemachine jimallman?
17:02 jimallman or perhaps oti is out of date?
17:02 jar286 oti is missing some studies, but that shouldn’t cause it to hang
17:02 jar286 I reported the bug and said it was high priority
17:02 kcranstn doesn’t sound like it is hanging, just returning an empty list
17:03 josephwb bug for what? oti?
17:03 jimallman i see a good (expected) match for study pg_2542, but no response (empty list of matched results) for all others i’m testing: pg_2715, pg_2731, pg_2822…
17:03 jar286 empty list is due to https://github.com/OpenTreeOfLife/oti/issues/40
17:03 jar286 I thought everyone saw these bug reports
17:04 kcranstn depends on your notification settings
17:23 mtholder joined #opentreeoflife
17:24 jar286 kcranstn, josephwb, here is my version of the synthesis section https://docs.google.com/document/d/1P3B90w28S6IznFVz10oAzQxUSQT4k3m1gBRHY_Z2S0Q/edit
17:31 jimallman thanks jar286, i’m chasing this now (looking for specific validation errors)
17:33 josephwb are high ranks better, or low ranks better?
17:50 kcranstn I’ve been assuming highest rank = 1
17:52 josephwb taxonomy = 0
17:55 josephwb the text suggest that rank 6 is better than rank 5
17:56 josephwb e.g. summing ranks across edges
17:57 josephwb maybe we just need a sentence explaining how ranks are implemented. i'll check the code
17:58 kcranstn a ranked list where the worst item is rank=1 seems non-standard
17:58 josephwb yes, that is what seems confusing
17:58 mtholder josephwb and jimallma, I'm seeing some oddness with "supported by" info on devtree. Is that expected (perhaps because all of the info is not on that server), or should I file an issue?
17:58 mtholder jimallman that is ^
17:58 josephwb mtholder there is an issue
17:58 josephwb or, what do you mean by oddness?
17:59 jimallman mtholder: if you mean the missing (forever loading”) chasing this bug now…
17:59 josephwb see https://github.com/OpenTreeOfLife/oti/issues/40
17:59 mtholder same node has different support
17:59 mtholder depending on which node is the base of view.
17:59 josephwb ack
18:00 josephwb link to a node?
18:00 mtholder I'll start an issue, you can close it if it is a duplicate.
18:00 jimallman ok, thanks.
18:00 mtholder https://devtree.opentreeoflife.org/opentree/opentree3.0@3847594
18:00 mtholder then back up one node and select the Phaseolus+vigna
18:01 mtholder oops sorry. wrong url
18:01 mtholder https://devtree.opentreeoflife.org/opentree/opentree3.0@3846678 and then back up one node.
18:03 josephwb devtree is slooooowwwww
18:04 jar286 indeed
18:04 jar286 nothing going on there
18:05 jar286 0.3% cpu utilization
18:05 jar286 ah, now a few javas, a few apaches
18:05 mtholder https://github.com/OpenTreeOfLife/treemachine/issues/180
18:09 jar286 oops, that was devapi. looking at devtree now
18:09 jar286 no action there either
18:09 josephwb i think mtholder is hogging the bandwidth
18:09 josephwb ;)
18:09 josephwb i still cannot see any tree
18:10 mtholder I am waiting for a page to load - but just one.
18:10 jimallman same here, waiting. load testing!
18:10 jar286 nothing going on on devtree.
18:11 jar286 if something is hanging it’s not because it’s cpu bound
18:12 josephwb Internal Server Error
18:13 jimallman josephwb: how can we get more details (specifically NexsonParseException.errorMessage) here? i don’t understand how OTRepresentationCoverter works here, since we call it with just ‘true’ as the data to convert…https://github.com/OpenTreeOfLife/oti/blob/93f3032acf61716dbec33334cecd2987642c03f5/src/main/java/org/opentree/oti/plugins/studies.java#L211-L222
18:14 josephwb hmm. i don't know the oti code, but will look
18:15 jimallman thanks. currently this returns an exception, but with general properties (exception, fullname, stacktrace) instead of the one we really want (errorMessage)
18:17 josephwb that code looks wrong.
18:18 josephwb was it updated?
18:18 jar286 what do you mean updated?
18:18 jimallman ? i assume i’m on the master branch, since github search defaults there
18:18 jar286 master is deployed on devapi and api
18:19 * jimallman is double-checking for master branch...
18:19 josephwb maybe i am looking at the wrong stuff then
18:19 jimallman this is definitely master on github:  https://github.com/OpenTreeOfLife/oti/blob/master/src/main/java/org/opentree/oti/plugins/studies.java#L211-L222
18:19 jimallman note that this is the newer index_study (versus index_studies)
18:20 josephwb i see index_studies, but not index_study
18:20 jar286 git pull ?
18:20 josephwb isn't "index_studies" the newer one?
18:20 jar286 no, study
18:21 jimallman see deprecation notice here:  https://github.com/OpenTreeOfLife/oti/blob/master/src/main/java/org/opentree/oti/plugins/studies.java#L173
18:21 josephwb ok, i pulled and see that now
18:22 jimallman josephwb: i’m guessing i misunderstood the exception-handling behavior here. i’m guessing an exception is immediately returned (as JSON) before the call to OTRepresentationCoverter.convert
18:23 josephwb should be, but it is not obvious
18:24 josephwb i don't see where it is throwing the exception
18:26 jimallman i assume it’s bubbling up from either readRemoteNexson or addOrReplaceStudy
18:26 jimallman see https://github.com/search?utf8=%E2%9C%93&q=NexsonParseException&type=Code&ref=searchresults
18:27 jimallman (most/all instances of NexsonParseException are in ot-base)
18:27 josephwb are you getting any error message?
18:28 jar286 one thing to do might be to compare the failing version of some study on api with the nonfailing one on devapi
18:30 jimallman josephwb: my simplest curl calls return simplified exception JSON, try this for example
18:30 jimallman curl -vv -H "Content-Type: application/json"     --data '{"url": "http://api.opentreeoflife.org/phylesystem/v1/../default/v1/study/pg_2739"}'     http://api.opentreeoflife.org/v2/studies/inde_study
18:30 jimallman thanks jar286, will try that next…
18:31 josephwb stupid curl paste errors...
18:33 josephwb no error message in there jimallman
18:33 jimallman right, i’m wondering if we can add it somehow..?
18:34 jimallman wow, i see the paste error (sorry about that!)
18:34 josephwb i don't understand why it doesn't come through
18:34 jimallman i can cleanup if you like
18:34 josephwb no, i got it
18:34 josephwb at least, i got it to fail ;)
18:36 josephwb whereever it is throwing is not providing a message
18:36 josephwb seems like "readRemoteNexson" might be the culprit
18:37 jimallman yes, that’s likely
18:37 josephwb no try
18:37 jimallman possible remedy (add errorMessage to JSON exception response):  http://stackoverflow.com/a/4035455
18:37 josephwb i guess it subscribes to the "do or do not. there is no try"
18:37 jimallman i have no idea where this response is defined in our setup...
18:39 jimallman re: “no try”, most of these seem to be explicitly thrown without a try… block, see for example  https://github.com/OpenTreeOfLife/ot-base/blob/5269cb557a0fb7726152f8c431cd5b9832001dfd/src/main/java/org/opentree/nexson/io/NexsonNode.java#L235
18:40 jar286 trys are evil. they typically lose information
18:41 jimallman jar286: do you happen to have a study id that works on dev, fails on production (or vice versa)? if not, i’ll go fish
18:42 jar286 most work on dev, so if you pick one at random from the list I posted, you should get a hit…
18:42 jar286 but I think I have the dev failure list somewhere, hang on
18:42 kcranstn joined #opentreeoflife
18:43 jimallman found one (pg_901)!
18:43 josephwb i think i found the problem
18:43 josephwb maybe
18:43 jar286 only 8 fil on dev.  so chances of a hit are 50:1 are so
18:43 jar286 s/fil/fail/
18:45 josephwb error message was not private. could that be the problem?
18:45 josephwb nevermind
18:46 josephwb ah, but no this.errorMessage
18:48 josephwb not it either
18:59 josephwb try v2 in that curl call
18:59 josephwb i get a message then
18:59 josephwb jimallman ^
19:00 jimallman sorry to be dense.. what’s your revised curl call?
19:00 josephwb change all v1 -> v2
19:00 josephwb curl -v -H "Content-Type: application/json" --data '{"url": "http://api.opentreeoflife.org/phylesystem/v2/../default/v2/study/pg_2739"}' http://api.opentreeoflife.org/v2/studies/index_study
19:01 josephwb that is api
19:01 josephwb curl -v -H "Content-Type: application/json" --data '{"url": "http://devapi.opentreeoflife.org/phylesystem/v2/../default/v2/study/pg_2739"}' http://api.opentreeoflife.org/v2/studies/index_study
19:01 josephwb different exception, tho
19:02 jimallman yes, i tried something like that. i believe the new error means the v2 fetch url (for study nexson) is bad
19:02 mtholder there is a command line invocation of oti
19:02 mtholder that may show the stack trace.
19:02 josephwb it is returned in the curl call
19:03 jimallman good point though, mtholder . i’ve been obsessing about the missing errorMessage, but this is a starting point at least
19:03 jimallman https://github.com/OpenTreeOfLife/ot-base/blob/5269cb557a0fb7726152f8c431cd5b9832001dfd/src/main/java/org/opentree/nexson/io/NexsonTree.java#L249
19:04 jimallman “"The specified root node <BLAH> is different from the observed root of the tree in the NexSON object hierarchy. This is nonsensical.”
19:08 jimallman i’m closely diffing pg_901 (working dev vs. failing production), and two related differences stand out:
19:09 jimallman 1) production tree has a specified root node (“node481006”) in its metadata
19:09 jimallman 2) production tree is marked with ot:unrootedTree, value = false
19:10 jimallman tree1740, i should say
19:11 jimallman perhaps NexsonTree.parseNexson assumes a rooted tree?
19:12 jimallman josephwb: ^
19:12 josephwb i don't know
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19:12 jimallman never mind, unrootedTree = false means this *is* a rooted tree
19:12 josephwb that would be weird
19:14 josephwb yeah, a root is found, because it checks if specifiedRoot != null
19:15 josephwb why does it not return that error message?!?
19:16 jimallman i assume this is a quirk on the JSON representation of java exceptions.. is errorMessage the typical name for this message?
19:16 josephwb i don't think it matters
19:17 josephwb others seem to use just "message"
19:17 jimallman yeah, the full message would be nice. but the traceback gives us the reason, if not the details (would be nice to know hte specified AND “observed” root node ids)
19:18 josephwb i could add it and deploy on dev
19:18 josephwb i do not have thse set up on my local machine
19:18 jimallman same here.
19:19 jimallman josephwb, i leave this one in your hands for now, but ping me here if i can help. i’m going to turn my attention to mtholder’s (even weirder) bug.
19:19 josephwb is deploying on dev ok?
19:19 josephwb don't want to break things
19:19 jimallman i would think so. ok by me, anyway.
19:22 josephwb not sure how to return those things if it refuses to return any message
19:23 * jimallman nods (seems like the first thing to fix, unless you can spit node ids to a log)
19:27 josephwb jimallman do i use devapi or devtree for this?
19:31 jimallman devapi
19:31 jimallman (for all repos but the main opentree)
19:31 josephwb ok
19:31 jimallman some caveats and dependencies, so please ask if not sure
19:32 josephwb why are there so many "v1" in the config files?
19:33 josephwb ack. cannot just update ot-base
19:33 jimallman legacy. all those features have used the v1 api, and i haven’t gotten around to migrating them.
19:33 josephwb as an arg, i mean
19:34 jimallman best to deploy something else that depends on ot-base…
19:34 jimallman treemachine i believe..
19:34 josephwb thanks
19:37 jimallman confirmed: to update ot-base, deploy any of [treemachine, taxomachine, oti]
19:43 kcranstn joined #opentreeoflife
19:50 jar286 why would you want to only update ot-base? it’s only useful as part of something else
19:50 jar286 so if you’re testing oti, deploy oti, etc. and it will pick up new ot-base (I believe…)
20:33 josephwb you there jimallman?
20:33 jimallman yes
20:33 josephwb i tried some things, but am getting back the same error
20:33 josephwb i.e. it references a line that is not there anymore
20:34 josephwb is this a cache thing?
20:34 jimallman hmm.
20:34 josephwb it compiles fine
20:34 jimallman we should not be caching responses from index_study, no
20:34 jimallman example curl call?
20:34 josephwb curl -v -H "Content-Type: application/json" --data '{"url": "http://devapi.opentreeoflife.org/phylesystem/v1/../default/v1/study/pg_2739"}' http://devapi.opentreeoflife.org/v2/studies/index_study
20:35 jimallman thanks. so line 249 no longer exists?
20:35 josephwb it is blank
20:35 jimallman this is like the monolith in 2001…
20:36 jimallman so maybe the running code is still the old stuff?
20:36 josephwb https://github.com/OpenTreeOfLife/ot-base/blob/jwb-test/src/main/java/org/opentree/nexson/io/NexsonTree.java#L240-260
20:36 josephwb yeah
20:36 jimallman interesting!
20:36 jar286 damn deployment system dependencies.
20:37 jar286 when it was first written there were no dependencies…
20:37 jimallman ah, so you’re trying to deploy from branch jwb-test?
20:37 josephwb yes
20:37 jimallman have you tweaked the server-config file?
20:37 josephwb yes
20:37 jar286 and that affected the design.  dependencies on jade and ot-base are a kludge
20:37 josephwb it recognizes changes and compiles accordingly
20:37 jar286 it ought to.
20:37 jar286 it sometimes does.
20:37 josephwb right
20:37 jar286 I’m not completely sure it always does.
20:37 josephwb not sure why it is returning old stuff
20:38 jar286 you can always log in to the server and force whatever builds you want
20:38 josephwb i thought that was a no-no
20:38 jimallman just to confirm: you modified the server-config file like so?    opentree_branch ot-base jwb-test
20:38 josephwb yes
20:39 jar286 not too much of a problem on dev, if you restrict yourself to doing things the deployment system could have done
20:39 jimallman there should be a deployment log that will indicate if it fetched and compiled jwb-test
20:39 jimallman (sorry for the cross-talk)
20:39 josephwb i am on the development branch of opentree
20:39 josephwb should i be on master after the upgrade?
20:40 jimallman no, we generally stay on development for devtree
20:40 josephwb devapi
20:40 josephwb don't confuse me, jimallman!
20:40 jimallman odd, that is probably not actually used in devapi
20:40 josephwb ack!
20:40 jar286 I don’t know if development got all the needed PRs.
20:40 josephwb that's what you confirmed for me, isn't it?
20:41 jar286 someone should checkout development, merge master, push development
20:41 jimallman i can do that..
20:42 josephwb i am going switch ot-base back to master and delete my branch
20:43 jimallman ok, development on github has the latest from master
20:44 jar286 it shouldn’t matter, but josephwb, i suggest you update your development branch
20:44 jar286 for opentree repo
20:44 jimallman agreed, lots of deployment stuff there
20:44 josephwb done
20:44 jimallman including the java 8 check(!)
20:46 josephwb i give up; cody should be able to fix things in a second
20:46 josephwb not a second from now; a second from when he starts
20:46 josephwb he is travelling
20:47 josephwb jimallman do you know what is going on with the bug from mark?
20:47 jar286 can you write down a few notes about what you learned and add them to the issue discussion?
20:47 josephwb me?
20:47 jimallman yes, will do.
20:47 jar286 i was talking to josephwb…
20:48 josephwb did i learn something?
20:48 jar286 it’s unlikely you’d work on something for two hours and not learn something, even if it’s a negative result
20:49 josephwb every change i tried apparently called old code anyway. is that what you want?
20:51 jar286 well hmm… didn’t realize it was that bad.  so maybe you learned that ‘xyzw’ is not the way to deploy (where ‘xyzw’ is whatever you did)
20:51 josephwb ?
20:51 josephwb it updated and compiled correctly, but the results did not reflect the new code
20:52 jar286 did it get deployed to neo4j correctly?  what command did you use to install it?
20:52 jar286 ah… maybe oti doesn’t get recompiled when you only change ot-base and not oti
20:53 josephwb i tried both
20:53 jar286 but oti doesn’t get rebuilt unless there’s a change to the oti repo
20:53 josephwb ./push.sh -c ../../deployed-systems/development/devapi.config oti
20:53 jar286 yes. what you learned was that doing this does not deploy a new version of ot-base.
20:53 jar286 as I said above.
20:54 jar286 ‘I tried various changes, but couldn’t figure out how to update the deployed oti with my new versions of ot-base, so I gave up’
20:54 josephwb ...
20:54 jar286 that is what your comment could say
20:55 jar286 it is almost certainly a bug in the deployment system, which you could report if you like (if you don’t I will)
20:57 jimallman i reviewed the as-admin deployment script earlier, and it sure seems like deploying oti, treemachine, or taxomachine will run install-neo4j-app.sh, which in turn pulls and installs ot-base.
20:58 josephwb seemed like it worked to me
20:58 jimallman via function push_neo4j, called by all three components: https://github.com/OpenTreeOfLife/opentree/blob/9109e2fcdb0d2e679de89ee7f74b1e40212e5ff7/deploy/push.sh#L186-L198
20:59 jimallman the deployment log will clarify which branch was fetched
20:59 jimallman … and whether the build is successful, i’d assume
21:00 jar286 yes, but does rebuilding ot-base force the oti .jar file to be rebuilt?
21:00 josephwb oti does not have restart_apache=yes
21:00 jar286 doesn’t need it.
21:00 josephwb ok
21:00 jar286 and anyhow I think that flag is being ignored now
21:00 jar286 not sure…
21:00 josephwb it is just this:
21:00 josephwb # restart apache to clear the RAM cache (stale results)
21:01 jar286 I thought apache was restarted regardless
21:01 josephwb installing plugin for oti
21:01 josephwb Using branch master of repo oti
21:01 josephwb Branch master set up to track remote branch master from origin.
21:01 josephwb Switched to branch 'master'
21:01 josephwb Your branch is up-to-date with 'origin/master'.
21:01 josephwb Already up-to-date.
21:01 jar286 and anyhow, it doesn’t help to restart apache on devapi, if the cache is on devtree…
21:01 josephwb Repository oti is unchanged since last time
21:01 josephwb Neo4j Server is running at pid 15060
21:01 josephwb Stopping oti neo4j server
21:01 josephwb Stopping Neo4j Server [15060]..... done
21:01 josephwb Starting oti neo4j server
21:02 jar286 see - the oti .jar file didn’t get rebuilt.
21:02 josephwb right
21:03 jar286 I’m sure there’s a way to use maven to do what we need done…
21:04 jar286 I can do it using ‘make’  but it will be grossly nonidiomatic
21:04 jar286 well, maybe not. last I checked maven didn’t understand how to do conditional recompilation like make does.
21:05 jar286 or it didn’t seem to. it’s very hard to tell what it does and doesn’t do, or even what it’s for
21:24 jar286 josephwb, you can always say ./push.sh -f    - a great feature that someone added
21:34 jimallman devtree seems to be dead in the water. josephwb, ok for me to restart apache?
21:37 jimallman josephwb: scratch that, it’s responding now
21:38 jimallman (i had an unrelated problem with my browser, it seems)
21:48 josephwb i am done with trying to fix that oti thing
21:48 jimallman do we think we’re running old ot-base still?
21:48 josephwb might be able to do something with mark's issue, though
21:48 jimallman (on devtree, i mean)
21:48 josephwb i don't know; i reverted to master
21:48 jimallman yes, i’m trying to reproduce mtholder’s bug, but now devtree is not responding
21:49 josephwb ok, please ping me if you see what is what
21:49 josephwb a problem with the arguson?
21:50 jimallman that’s what i was going to check out (it’s almost certainly a discrepancy between target node and the others)… but the server is acting up.
21:50 jar286 devtree is up and running… and listening on ports 80, 443, and 22
21:50 jimallman yes, and it responds to curl requests, but for some reason Chrome sends the initial request and it never returns.
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21:52 jar286 nothing in the apache error log
21:52 jar286 you mean an oti request?
21:53 jimallman nothing in apache logs, or in browser’s tools
21:53 jimallman basic request for http://devtree.opentreeoflife.org/
21:53 jimallman i’ll try another browser…
21:53 josephwb i cannot load anything on devtree
21:55 jar286 nothing in the access log since 21:46
21:55 jimallman restarted apache (sorry, maybe too hasty?)
21:55 jimallman now i’m getting normal load behavior
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21:57 jar286 funny, I don’t see your request in the log
21:57 jar286 access.log
21:57 jimallman ot16:/var/log/apache2/error.log
21:57 jar286 oh… ot16… duh, I was looking at ot14
21:59 jimallman argh. you’re in the right place (ot16 is devtree)
22:00 jar286 if ot16 is devtree, I was in the wrong place
22:01 jimallman right, i’m turned around here
22:01 jimallman time for coffee…
22:15 jar286 I don’t see any josephwb branches on github.  it appears he didn’t push his changes
22:15 jar286 unless he deleted the branch on github
22:16 kcranstn are there commits?
22:16 jar286 you can only see commits that are in branches… I think… so if he deleted the branch you wouldn’t see the commits
22:17 kcranstn oh, I thought you meant deleted-after-merged-PR
22:17 jar286 no, a debugging branch that was never merged to master
22:18 jimallman hm, there was definitely a jwb-test branch in ot-base on GitHub…
22:20 jar286 oh, ok.  too bad he deleted it.
22:21 jimallman i believe i can recover it using my local repo,
22:23 jar286 no, not that important, if you are on a different trail
22:23 jimallman ok, back to the supporting-info bug..
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