Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-04-30

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All times shown according to UTC.

Time Nick Message
00:29 jar286 joined #opentreeoflife
02:23 jimallman joined #opentreeoflife
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10:01 mtholder joined #opentreeoflife
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12:50 kcranstn joined #opentreeoflife
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14:01 josephwb jar286 just replied to your email re: java 8
14:03 jar286 thanks
14:04 josephwb sounds like it works on wheezy
14:05 jar286 “Tested on Debian Wheezy but it should work with any Debian version”
14:05 josephwb what is the emoticon for "thumbs-up"?
14:05 jar286 👍
14:06 jar286 that was uncidode https://www.google.com/webhp?sourceid=chrome-instant&ion=1&espv=2&ie=UTF-8#q=unicode%20thumbs%20up
14:21 josephwb joined #opentreeoflife
14:25 kcranstn joined #opentreeoflife
14:49 jar286 let’s see… oracle wants me to agree to what they call a ‘license’ but is actually a contract…
14:50 josephwb hey jimallman
14:50 josephwb sent you a preview of the arguson update, since we cannot test it on dev at the moment
14:50 jar286 kcranstn, this license is no good. it’s non-transferable.
14:51 jar286 http://www.oracle.com/technetwork/java/javase/terms/license/index.html
14:53 jar286 thinking about what this means for us
14:53 kcranstn why does it need to be transferable?
14:54 jar286 it means I cannot let you use java. you have to independently agree to the license (click-through)
14:54 jar286 not clear what “use” means
14:55 jar286 does it mean use the web site?  probably not, but it could be read that way
14:55 jar286 in any case, I cannot agree to the click-through, and then give you a way to copy the software without you also doing the click-through
14:56 jar286 i.e. every open tree developer has to agree to the terms of the so-called ‘license’
14:56 kcranstn sigh
14:57 kcranstn aren’t we using java is a fairly standard way? how do other users deal with this issue?
14:57 jar286 the install page joseph gave gives a way to script the click-through. I’d have to read the license carefully to see whether we’re allowed to do that
14:58 jar286 I don’t know.  I suspect people either use openjdk (no click-through, no dubious terms), or they just do the click-throughs.  or they ignore the ‘license’
14:58 kcranstn and can’t use openjdk on our version of debian
14:58 kcranstn ?
14:58 jar286 risky.
14:59 jar286 jim says that debian’s database does not say it’s compatible
14:59 jar286 I haven’t yet figured out how to install it withough doing a wholesale upgrade to unstable
14:59 jar286 it can probably be done, but it’s going to be work
14:59 jar286 could be 5 minutes, could be 5 hours, I don’t know
15:00 jar286 could be 5 days, if recompiling and bug fixing needed
15:00 kcranstn unstable sounds scary
15:00 jar286 it is.
15:00 josephwb sounds exciting!
15:00 josephwb i don't know if i am using that now. i think i am.
15:00 jar286 I mean Debian has very good process and QC, so unstable is not nearly as scary as it would be anywhere else
15:01 kcranstn that = openjdk or oracle?
15:01 josephwb that == unstable
15:03 jar286 we can just do the click through in our install sequence I guess… I find it repugnant but we may have no choice
15:03 jar286 here’s what it looks like
15:03 jar286 You MUST agree to the license available in http://java.com/license if you want
15:03 jar286 to use Oracle JDK.
15:03 jar286 In order to install this package, you must accept the license terms, the "Oracle
15:03 jar286 Binary Code License Agreement for the Java SE Platform Products and JavaFX ".
15:03 jar286 Not accepting will cancel the installation.
15:03 jar286 Do you accept the Oracle Binary Code license terms?
15:03 jar286 this is a legally binding contract
15:04 kcranstn and how would we be acting contrary to the contract?
15:04 josephwb i use "testing", but not "unstable", it seems
15:05 jar286 I would have to read it more carefully than I have so far… there’s lots of stuff about kiosks and mobile apps
15:06 jar286 can’t run the licensed software on a smartphone…
15:10 jar286 it’s worth putting some time into getting openjdk-8 running in wheezy
15:10 jar286 a good feature of the agreement is that you can get out of it simply by deleting all copies
15:11 jar286 one thing that’s not clear is whether, if the agreement is in effect, it applies to openjdk
15:12 jar286 i.e. does it make you relinquish rights that would have been granted to you by another license
15:13 jar286 I also wonder if Duke policy prevents me from signing a contract, I would have to check that
15:18 jar286 nothing in the staff handbook…
15:23 jar286 when I worked in pharma, it was strictly verboten for an employee to accept even a license (much less a contract) without legal review
15:23 kcranstn I doubt that level of strictness in this context
15:25 jar286 “Oracle grants you a non-exclusive, non-transferable, limited license without license fees to reproduce and use internally …”
15:25 jar286 the *and use* part is egregious
15:25 jar286 it means I can’t load java onto a server, and then let you log in to the server and use java
15:25 jar286 goes way beyond copyright
15:25 jar286 you have to agree independently with oracle to be able to use it
15:30 jar286 will look into openjdk again after lunch.
18:13 kcranstn joined #opentreeoflife
18:20 jar286 No PR review today
18:23 josephwb kcranstn have you given thought to a new synth tree name?
18:23 josephwb or even if you want to do that?
18:23 kcranstn tree name, or version number?
18:23 jar286 anything as long as it’s different
18:24 jar286 sorry to jump in...
18:24 kcranstn that’s ok
18:24 josephwb give me a string
18:24 kcranstn this feels like major version 3.0, but awkward to go to 3 from 22
18:25 jar286 synthetic tree id = open_tree_v3.0 ? or opentree3.0 ?
18:25 kcranstn opentree3.0
18:25 jar286 version 22 was version 22 of something else
18:25 josephwb "otol.draft.2"
18:25 josephwb 22
18:25 josephwb "otol.draft.22"
18:25 jar286 ‘otol’ is deprecated
18:25 josephwb yes!
18:26 josephwb we should get rid of it
18:26 jar286 opentreedraft3.0
18:26 kcranstn do we need the draft?
18:26 jar286 seems funny to call something draft when there will never be a non-draft
18:26 kcranstn will it ever be non-draft?
18:26 josephwb need to make sure jimallman keeps in step; name is hardcoded in places
18:26 jar286 the CRC handbook doesn’t call itself ‘draft’
18:27 kcranstn opentree3.0
18:27 kcranstn I’ll make an issue for opentree repo
18:27 jar286 yet it its versions are successive approximations to an unreachable truth
18:27 josephwb "synthesis" somewhere, maybe?
18:27 josephwb maybe not
18:27 jar286 it *is* the open tree, isn’t it?
18:28 jar286 jim will make the name be a parameter, wouldn’t worry too much about that.  could even come from the deployment system config
18:28 josephwb yup
18:28 josephwb shouldn't be too hard
18:29 josephwb for him
18:29 josephwb i can change the name in the complete db at anytime
18:29 kcranstn https://github.com/OpenTreeOfLife/opentree/issues/629
18:29 josephwb so, yeah, whatever you guys want
18:30 josephwb weird that you can edit other peoples comments on github
18:30 josephwb [just fixed a typo in that issue]
18:30 kcranstn cool, thanks
18:33 mtholder joined #opentreeoflife
18:33 josephwb hey mtholder. finished db is up on dev. 12 unsupported (the ones i already sent you)
18:34 mtholder great. thanks.
18:34 mtholder that is an improvement.
18:34 kcranstn yay!
18:34 josephwb i haven't looked into what is going on
18:34 mtholder i'll try to look into whether they are otcetera or treemachine issues.
18:34 josephwb thanks!
18:34 mtholder (over the weekend that is).
18:35 josephwb you are way more efficient at that, and i am bleary-eyed staring at trees
18:35 mtholder can you post the newick somewhere?
18:35 josephwb no problem
18:35 mtholder the api on dev helps, but the full tree is nice too.
18:35 josephwb i will send the link out to the list so ruchi can do her voodoo too
18:36 kcranstn I’ve already warned her and gordon this is coming
18:46 mtholder k
18:47 mtholder not sure where that k came from.
18:47 kcranstn l
18:47 kcranstn m
18:49 josephwb email sent
19:00 mtholder left #opentreeoflife
19:03 jar286 josephwb, why not put tree loading into a separate maven project?
19:03 jar286 this kind of thing is what maven is designed for
19:04 josephwb i don't know how easy that would be
19:04 josephwb how about upgrading debian?
19:05 kcranstn see jar286 email about needing to go to unstable
19:05 jar286 I’m looking into it but there is a huge number of questions
19:05 josephwb but that is with an earlier debian
19:05 jar286 e.g. can we upgrade from wheezy to testing without making new AWS instances
19:06 jar286 so I’d like to pursue the two tracks in parallel.
19:06 jar286 dspace is an example of a multi-maven-project system, you could look there to see how its directory structure is, but the idea is fairly simple
19:07 jar286 the treemachine repo has two subdirs, one for each project
19:07 josephwb loading is so integrated into treemachine that i don't want to be the person to splice it out
19:07 jar286 each project has a pom.xml and src/
19:07 jar286 it’’s not just a set of separate classes?
19:08 josephwb maybe the problem is overlapping dependencies?
19:08 josephwb i don't know
19:08 josephwb overlapping imports, that is
19:08 josephwb even if they are not used
19:09 jar286 doesn’t sound *that* bad… you make an initial cut at separation, and then let the compiler tell you what to do
19:11 josephwb i have no idea where i would even start with that.
19:12 josephwb probably easy for someone else
19:13 jar286 part of your training as a software whiz
19:14 jar286 rite of passage is to refactor someone else’s code that you don’t understand
19:14 josephwb beyond messing with the pom, i don't know
19:14 josephwb anyway, this seems awfully heavyhanded just to get a plugin to work, doesn't it?
19:15 josephwb i can compile the plugin on my machine and copy it over to dev
19:15 josephwb (if that would work)
19:16 jar286 I don’t think you can run a java-8-compiled library in a java-7 vm.
19:16 josephwb oh, right
19:16 jar286 and that doesn’t solve the deployment problem - it takes us back to doing everything manually, and that’s not an option
19:17 jar286 like I say I’ll look into the OS upgrade, but I’d appreciate some effort on the UM end.  you didn’t answer my question of why 8 is needed in the first place
19:19 josephwb loading
19:19 josephwb i sent it in the email
19:19 jar286 “testing” does not get security updates in a timely manner
19:20 josephwb it isn't used in the plugins (well, maybe once or twice, but they could be replaced)
19:20 josephwb it seems the pom has "excludes"; maybe that is the way to go? i have no idea.
19:20 jar286 I don’t see anything in email about what 8 features are needed
19:21 josephwb i can dig it out if you like. it is in BipartOracle
19:21 jar286 if you can do exclude, you can do multiple projects.
19:22 jar286 wait I don’t get it.  you are somehow able to generate a .jar file that can run on devapi?
19:23 josephwb i haven't tried
19:23 josephwb but like you said, probably wouldn't work
19:23 josephwb i will let you in on a secret: i don't know anything about anything
19:24 josephwb i will see if i can eke out something
19:25 jar286 I don’t get it. you’ve been installing treemachine plugins on devapi
19:25 jar286 Wed Apr 29 20:06:45 BST 2015 josephwb ot10  Finished installing treemachine plugin
19:26 jar286 that’s constructed using java 7, right?
19:26 jar286 has to be, since java 8 isn’t on devapi ?
19:27 josephwb i swicthed back to master to get curl calls to work
19:27 josephwb master = java 7
19:31 josephwb i.e. tried to compile plugins on new branch, failed, so switched back
19:31 jar286 oh.
19:32 jar286 can a new tree database be loaded into an old treemachine?… I guess not.
19:32 josephwb i am going to take a short break and then see what i might be able to do so that java 8 is not required on the server machines
19:33 jar286 thanks
19:36 josephwb things are similar enough between dbs that most curl calls work (get source tree does not)
19:36 josephwb indeed, on dev now there is a new db but old code
19:37 josephwb what i could do is make the relevant changes in master (java 7) and then everything would work
19:37 josephwb ok, really going now
19:38 jar286 right
19:55 jar286 kcranstn, looking hopeful… if we upgrade to jessie, we should be able to run openjdk 8.  reading now about how to do each of these.
19:55 kcranstn whew
19:56 kcranstn thanks for researching this
19:56 jar286 jessie is brand-new, just released last weekend; testing is a clone of jessie as of that time, and contains the versions of openjddk dependencies that we need
19:56 jar286 and there’s a way to mix and match unstable/stable
20:05 josephwb excludes might be easy on our side
20:06 josephwb playing with it now
20:06 jar286 doing the os upgrade seems tractable, if a bit of work
20:07 josephwb i should know in a few minutes if i can pull this off, i think
20:45 josephwb holy crap. i think i might be able to do this...
20:46 kcranstn :)
20:57 josephwb nah, spoke too soon. why did i think i could wrangle maven?
21:03 kcranstn motivational speech by jar286?
21:04 josephwb far smarter people than i (and there are a lot of those) have thrown up their hands with maven
21:10 kcranstn I start throwing my hands up at java
21:36 jar286 upgrading ot17 from wheezy to jessie… this takes a long time
22:15 kcranstn joined #opentreeoflife
22:44 jar286 success!
22:44 jar286 java -version
22:44 jar286 java version "1.8.0_05"
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23:35 josephwb sweet, because i failed completely
23:39 josephwb ot17 isn't dev, is it?
23:39 josephwb jar286 ^
23:43 josephwb i don't really know what ot17 is. ot10 is what i'd like to push things to for testing. is that on the docket?
23:45 josephwb ok, i got to go. please let me know if/when dev is updated to debian jessie / java 8
23:45 josephwb kcranstn and jar 286 ^

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