Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-11-10

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All times shown according to UTC.

Time Nick Message
06:39 egonw joined #bioclipse
08:32 egonw joined #bioclipse
08:34 Gpox joined #bioclipse
08:38 jonalv joined #bioclipse
08:38 egonw moin
08:38 zarah hi egonw
08:38 jonalv hi
08:38 zarah hi jonalv
08:38 zarah jonalv: You have new messages. Write '@messages' to read them.
08:38 jonalv zarah: tell me
08:38 zarah jonalv: 8 m 46 s ago, masak said simma idag?
08:48 malick joined #bioclipse
08:50 egonw jonalv: please add CoverageTest's for your managers
08:50 egonw Gpox: do you have set up Manager's too?
08:51 jonalv egonw: do I have a bug report about it_
08:51 jonalv egonw: how do I do that_ >(
08:51 jonalv sdfljk
08:51 egonw no
08:51 jonalv sry...
08:51 jonalv I am not awake yet...
08:51 egonw no worries
08:51 egonw it's easy...
08:52 jonalv been a busy weekend... :)
08:52 egonw just copy cdk.business.test/blabla/CoverageTest.java
08:52 jonalv okey sounds good
08:52 jonalv is there a wiki page perhaps?
08:52 egonw and check the changes I made to: http://wiki.bioclipse.net/index.php?title​=List_of_stable_managers_in_bioclipse_2.0
08:52 zarah egonw's link is also http://tinyurl.com/68dyxn
08:56 egonw ok, added details in links to that wiki page
08:56 egonw on what and where
08:56 jonalv okey
08:56 jonalv egonw: which days are you at bmc?
08:56 egonw Gpox: did you set up managers too?
08:56 egonw Tue-Thu, I think
08:56 egonw not today
08:56 Gpox no i haven't
08:57 egonw unles there is something really urgent
08:57 egonw Gpox: btw, I've merged my JChemPaintManager code...
08:58 egonw nothing much there yet, though :(
08:59 edrin joined #bioclipse
09:02 egonw hi edrin
09:02 egonw I'm now copy/pasting content
09:23 jonalv http://www.gocomics.com/ca​lvinandhobbes/2008/11/10/
09:23 zarah jonalv's link is also http://tinyurl.com/6xxzl6
09:30 egonw jonalv: this one is funnier :)
09:30 egonw http://feedproxy.google.com/~r/D​ilbertDailyStrip/~3/iO-SAYRClvs/
09:30 zarah egonw's link is also http://tinyurl.com/6esyq8
09:30 egonw (IMHO)
09:31 jonalv yea that one was good too. And it was a new one for me :)
09:36 edrin hi egonw
09:36 edrin good to know :)
09:37 edrin i just realized that one disadvantage of svn is that i can never access it in my lab...
09:39 egonw huh? ssh port 22 is blocked??
09:40 egonw that sucks
09:43 edrin all i can do here is: web browser + email... (and some jabber) because we are not allowed to install programs. thus i cant install a svn client; they do this for security reasons that ppl do not install viruses; but it is worth to not that they neither user http proxy nor firewalls in general...)
09:43 egonw hehehehe
09:43 egonw that's even funnier than that Dilbert strip
09:44 jonalv it sort of sums up all the Dilbert strips I think... :(
09:44 egonw indeed :)
09:44 jonalv I wouldn't want to work at such a place
09:44 edrin and indeed 1 year ago 100% of all computers were found to be infected with p2p servers and trojans for "already" several months/years
09:45 jonalv I would actively seek to change my situation either by 1. find a new place to work at. 2. try to change the setup at the loication
09:45 edrin jonalv: I tried 2)
09:45 edrin they hate me
09:45 edrin :]
09:46 jonalv haha
09:47 jonalv egonw: all the bugs about missing unit tests, are those autogenerated?
09:47 egonw nope :(
09:48 egonw combo of 'git annotate' + filing bug reports in mylyn
09:48 egonw mylyn has a nice + function for bugs...
09:48 jonalv aha
09:48 egonw which create sub tasks
09:48 egonw so not too much work...
09:48 egonw just a lot of copy/pasting
09:48 egonw the subtask autoadds the block/depends for the bugs
09:48 egonw which is nice
09:49 jonalv Because I am not sure I understand what I am supposed to do...
09:50 egonw add unit tests
09:50 egonw each @Published manager method should/must have a unit test
09:50 * jonalv hates windows
09:51 jonalv It restarts without asking
09:51 jonalv when it comes back online it sais
09:51 jonalv I have installed nww updates and neeeded to restart...
09:51 egonw hehehehe
09:51 jonalv and oh btw there are new updates available
09:51 egonw yeah, that sounds like microsoft
09:51 jonalv gah
09:51 jonalv couldn't it have installed those too?
09:52 jonalv the biggest problem is that it steals mouse + keyboard when it restarts... :(
09:55 rojasm joined #bioclipse
09:56 egonw hi rojasm
09:56 jonalv egonw: Uhm this CovrageTest class. Is it copied into each new test plugin?
09:56 egonw yes
09:56 egonw soon...
09:57 egonw I'll refactor it, to share code
09:57 jonalv code copying feels ugly...
09:57 egonw yes, I know
09:57 egonw but had not found a nice place to put the common code yet...
09:57 egonw because:
09:57 egonw 1.net.bioclipse.tests depends on all test plugins (so, not suitable)
09:57 egonw 2.net.bioclipse.core is not about testing (so, don't like it there either)
09:58 egonw (2. is where the Annotation stuff resides)
09:58 jonalv It sounds to me as we need a net.bioclipse.core.tests
09:59 egonw edrin: just FYI, I finished copy-pasting content from Google Docs into SVN
10:04 edrin :)
10:04 edrin egonw: and also from the office .doc?
10:05 egonw huh?
10:06 egonw did you email me something?
10:06 edrin yes
10:06 egonw oh... no
10:06 egonw overlooked that
10:06 egonw sorry
10:06 edrin :)
10:06 edrin well,
10:06 edrin maybe we should rather paste it into google docs for now
10:07 edrin so i could work on it in my institute, too
10:07 egonw rather not...
10:07 edrin hehe
10:07 egonw I was thinking about setting up a tunnel
10:07 egonw but 80 is already used on pele
10:07 egonw and so is SMTP
10:08 egonw edrin: happy with git?
10:08 egonw then you can email me your patches
10:09 egonw and I can put up the repository on Pele's web pages
10:10 edrin what is git?
10:10 edrin found page
10:10 edrin looking
10:11 jonalv zarah: google git
10:11 zarah jonalv: http://git.or.cz/
10:11 edrin how can i use it in windows`?
10:12 egonw ok, never mind :)
10:12 jonalv zarah: google git on windows
10:12 zarah jonalv: http://kylecordes.com/2008​/03/22/git-windows-works/
10:13 egonw edrin: ok, going to try to route SVN via apache+SSL
10:13 malick joined #bioclipse
10:14 edrin :)
10:15 jonalv @pelezilla logging data
10:15 zarah [Bug 77] paths in windows slash problems http://tinyurl.com/578aen
10:15 zarah [Bug 24] Install sampledata action di... http://tinyurl.com/5z6fej
10:15 zarah [Bug 41] Do something about the huge ... http://tinyurl.com/67mutl
10:15 zarah [Bug 27] Reading of OWL files for ato... http://tinyurl.com/6lrpw4
10:15 zarah Entire list at http://tinyurl.com/6za2fx
10:15 egonw he, that's closed bugs too
10:15 egonw or not?
10:16 egonw ah, 27 is fixed, but not closed
10:16 jonalv I think it's all
10:16 jonalv closed too
10:17 egonw ok, that's will be interesting ...
10:18 egonw @pelezilla manager
10:18 zarah [Bug 106] missing manager unit test f... http://tinyurl.com/5s4wyd
10:18 zarah [Bug 107] missing manager unit test f... http://tinyurl.com/65p3jp
10:18 zarah [Bug 108] missing manager unit test f... http://tinyurl.com/5ok8h9
10:18 zarah [Bug 109] missing manager unit test f... http://tinyurl.com/6crhlx
10:18 zarah [Bug 19] Concurrency: Wrap manager ca... http://tinyurl.com/68xjfj
10:18 zarah Entire list at http://tinyurl.com/5nbxsw
10:18 egonw ha, at least it only picks 5 of them :)
10:18 egonw zarah: smart girl :)
10:18 zarah egonw: please rephrase or stop trying to be witty :)
10:18 jonalv zarah: you are the smart girl
10:18 zarah jonalv: that was not so easy for a little bot to understand
10:18 jonalv zarah: you are the smart one
10:18 zarah jonalv: no, YOU are the smart one!
10:19 jonalv :)
10:20 egonw edrin: ok, svn via webdav is too difficult for me right now
10:20 egonw would need more time to work that out...
10:21 edrin egonw: maybe we should concentrate on the article
10:21 jonalv there is a cloud doing svn?
10:21 jonalv cool
10:22 edrin if you have open office, juts edit the file, ad text in your color of choice, send back, and i will work on
10:23 egonw it's your pick... you'll have to do the laying out
10:23 edrin ok
10:24 edrin then use openoffice
10:24 egonw 2 or 3?
10:24 edrin because that's the only thing valuable here at work
10:24 edrin i dont mind...
10:24 egonw 3 then, please
10:24 edrin ok
10:24 egonw which has better change tracking
10:24 edrin that's good :)
10:28 * jonalv -> lunch
11:27 malick joined #bioclipse
11:38 malick joined #bioclipse
11:49 * jonalv is back...
11:58 egonw mmm
11:58 egonw CIA-53: are you awake?
12:00 egonw CIA-53: or watching Quantum of Solace?
12:00 egonw to learn from the master?
12:13 jonalv egonw: can you explain this test coverage framework a little? :)
12:14 egonw yes, ask away
12:15 jonalv what's the genreal idea?
12:15 jonalv :)
12:15 egonw it checks if all published manager methods are tested
12:15 jonalv I see a @TestClass annotation
12:16 egonw yes, and the methods have @TestMethods
12:16 jonalv and I see a @TestMethods annotation
12:16 egonw containing a comma-separated list of test methods
12:16 egonw right :)
12:16 jonalv and I see a row way longer than 80 cols...
12:17 egonw hahahaha
12:17 egonw umm... I guess it does support +'s
12:17 jonalv so each method on each manager interface should have an annotation for each method saying which tests that run that method?
12:17 jonalv (yea it does)
12:18 egonw yes
12:18 jonalv and the test case tells us whether there are any unannotated methods in the interface?
12:19 egonw yes, and checks if that method really exists
12:20 egonw it's a cheap way of having the system complain about missing unit tests
12:20 jonalv ah
12:20 jonalv yea I think I like it
12:20 egonw I just ran into a problem :(
12:20 egonw well, a limitation more
12:20 jonalv is this direct from cdk?
12:20 egonw yes, we use this setup in the CDK too
12:21 jonalv okey what's the problem? :)
12:21 egonw some things cannot be tested as unit test, but
12:21 egonw only as plugin unit test
12:21 egonw because some methods require an open workspace
12:22 jonalv okey, in what way is that a problem?
12:22 egonw ok, lunch first
12:22 egonw that there basically are two test classes
12:22 egonw two options:
12:22 jonalv yea...
12:22 egonw 1. make TestClass accepted a comma-separated list
12:22 egonw or
12:22 egonw 2. PluginTestClass and PluginTestMethods
12:22 jonalv or possibly more than two test classes I suppose...
12:22 egonw and have the CoverageTest look at that too
12:23 egonw yes, sure
12:23 egonw ok, lunch now
12:23 egonw bbl
12:23 jonalv cya
12:27 egonw ok, as usual...
12:28 egonw lunch before keyboard :)
12:28 egonw I'm in favor of option 2
12:28 jonalv aha
12:28 jonalv I am in favor of option 1
12:29 jonalv also I would like to get a list of all missing test methods
12:29 jonalv or rather a list of all methods that is missing the test annotation...
12:29 egonw that goes to STDOUT
12:30 jonalv oh I see
12:30 jonalv that's not optimal I think
12:30 jonalv It can get kind of swallowed up in logging output...
12:31 jonalv + I want our our test server to rpoert the stack trace soehow
12:31 jonalv but I am not sure that the entire standard out is a great idea...
12:32 jonalv or can you convince of something else?
12:32 egonw no
12:33 egonw only thing is that JUnit has not so good reporting mechanism for feedback
12:33 jonalv There is the message part of the assertion statmenets...
12:33 jonalv or what do you mean?
12:34 egonw true, but that's not suited for multiline messages
12:34 jonalv why not?
12:34 jonalv (I have seen that done a lot...)
12:35 egonw really?
12:35 egonw ok, file a bug report
12:35 egonw ok, back to 1 or 2
12:36 egonw Gpox: please join in if you have thoughts on this (or anyone else)
12:36 jonalv I prefer 1 because otherwise you will neeed two versions of the method annotation too
12:37 jonalv it means _many_ annotations...
12:37 egonw true, and we can still count how many methods are in plugin tests and in the normal unit tests...
12:37 jonalv and honestly writing managers is something that is quickly becomming very complicated. (We should create that Eclipse plugin that generates all this stuff automagicly soon)
12:39 egonw how difficult can that be?
12:39 egonw ola has already done 'New Project' like things, not?
12:39 jonalv yea in Bioclipse and that should be the same :)
12:39 egonw yes, I'd say so :)
12:39 jonalv good thing :)
12:40 egonw ok, you add missing coverage testing and unit tests...
12:40 egonw I'll have a go at Create New -> Bioclipse Manager Test Plugin
12:41 jonalv hm it would have to create two plugins actually
12:41 egonw 2?
12:41 jonalv both the plugin with all Spring stuff + a test plugin with all the testing stuff
12:41 jonalv so Create New Bioclipse Plugin with Manager...
12:42 egonw ah, ok
12:43 jonalv The main reason for this was to autogenerate the spring configuration cml-file right?
12:43 jonalv *xml
12:43 jonalv :)
12:43 egonw and others
12:48 jonalv egonw: is there a good test cml containing a molecule with different conformers? (no, I am not sure how to use that word :)
12:48 egonw that sounds like a a good question...
12:49 egonw no, don't think so
12:49 jonalv could you make on for me?
12:49 jonalv *one
12:50 egonw <moleculeList convention="bioclipse:conformerList"><molecule id="conformer1"/>...</moleculeList>
12:50 charlgren joined #bioclipse
12:50 jonalv huh what's that?
12:50 egonw CML
12:50 jonalv charlgren: hi
12:50 egonw well... not really, because I forgot to add:
12:50 jonalv but it contains Bioclipse in it
12:50 egonw xmlns="http://www.cml-xml.org/schema"
12:51 jonalv is that convention defined now?
12:51 egonw nope
12:51 egonw good to remind me about that, btw
12:51 jonalv Okey I am lost now...
12:51 egonw there currently is not controlled vocabulary of used CML conventions
12:51 jonalv that sounds dangerous...
12:52 charlgren jonalv: hi, nice to see you're back
12:52 egonw jonalv: umm.. yes
12:52 jonalv charlgren: yea, uhm let's talk in #farmbio instead...
12:52 egonw I have on my wish list for a long time a web page listing conventions
12:54 jonalv egonw: but isn't conformers something that is defined for cml in some other way? Do we have to use our own?
12:54 jonalv egonw: it feels like there is not much point in that...
12:54 jonalv I think I will toss this bug to someone else. Actually I don't know why I got it...
12:56 jonalv egonw: Do you want it or should I just give it to olas?
12:58 jonalv egonw: congratulations you will get it... :)
12:59 egonw ok, yes, assign it to me
13:00 jonalv oh I can add a context too :)
13:01 egonw please do
13:04 jonalv mylyn + bugzilla is so cool :)
13:05 egonw yes, I think so too :)
13:12 jonalv egonw: when it checks which methods are tested does it only go by names of the method or by signature?
13:14 egonw name
13:14 egonw becuase unit tests do not have parameters
13:14 jonalv uhm but methods do
13:14 egonw general methods yes
13:15 jonalv yea and that was what the question was about
13:15 egonw oh...
13:15 egonw that way around...
13:15 jonalv yea :)
13:15 egonw it uses introspection to see what the manager has to offer
13:15 egonw so, each method will be checked
13:15 egonw but only those marked with @Published
13:15 jonalv right so our methods that come in three flavours all need the annotation
13:16 jonalv oh okey
13:16 egonw yes
13:16 jonalv only the publisehd ones
13:16 jonalv then we are safe
13:16 jonalv then we only need to annotate the publisehd flavour
13:16 jonalv perfect
13:17 jonalv This _really_ needs to be documented soon... :)
13:21 jonalv and with "this" I mean the whole process of manager creation and with "_really_" I mean that we probably should have done it already... :)
13:21 egonw yeah, looking into a plugin for creating manager plugins now
13:22 jonalv awesome
13:24 * jonalv did update from within Eclipse. It takes ages... :(
13:34 jonalv okey I can't reasign the bug after I have fixed it. What is our policy on this?
13:34 jonalv egonw, Gpox, masak: ?
13:34 egonw open it again
13:34 jonalv and?
13:34 egonw and then reassign
13:34 jonalv reasign and then mark as fixed?
13:34 egonw ummm... actually weird...
13:35 egonw mom
13:35 jonalv but then |I will mark it as fixed after I have reassigned it to someone lese... That seems weird...
13:35 egonw http://en.wikipedia.org/wiki/Image​:Bugzilla_Lifecycle_color-aqua.svg
13:35 zarah egonw's link is also http://tinyurl.com/5d7jkd
13:36 egonw so, you're not supposed to reassign it
13:36 egonw after having fixed it...
13:36 egonw the owner can close it
13:36 egonw or the QA guys
13:36 egonw (which we don't have)
13:36 egonw or the owner
13:36 jonalv but who is the owner?
13:36 egonw I *did* get an email that you fixed it...
13:36 jonalv isn't that the one current having it assigned?
13:37 egonw I meant the submitter
13:37 jonalv aha
13:37 jonalv I guess we don't have QA people yet...
13:37 egonw but your patch is not good
13:37 jonalv perhaps we should?
13:37 egonw you're not testing the right method
13:37 egonw you *should* test numberOfEntriesInSDF(String)
13:37 egonw not
13:37 jonalv egonw: I am not?
13:37 egonw numberOfEntriesInSDF(IFile)
13:37 egonw subtile difference, but important
13:38 jonalv egonw: uhm actually no I can't do that
13:38 egonw well... in the pluginTests you can
13:38 egonw which is why I said earlier that I encountered a problem :)
13:38 egonw I ran into the same issue :)
13:38 jonalv the functionality between the String and the IFile variant is covered by another test
13:39 jonalv these test only tests the actual functionality of the manager, not the functionality of the magic...
13:39 jonalv "magic"
13:39 jonalv :)
13:40 egonw ah, but do they test that this magic is used properly too?
13:41 jonalv hm I guess not...
13:41 jonalv But...
13:41 jonalv hm...
13:41 egonw from CDK experience, I found this subtile difference important to be tested...
13:41 egonw really... people mess up
13:42 jonalv but do we really want to run all of this as plugin tests? They take forever to run and we don't even know if they can be run automagicly on pele. Or do we?
13:42 egonw yes
13:43 egonw but that does not mean the IFile version can still be tested too in the 'normal' test
13:43 egonw really, both should be tested...
13:43 egonw ok, going to fetch some coffee
13:43 egonw be back in 15 minutes or so
13:45 jonalv but one is a subset of the other pretty much. Besides the CoverageTest doesn't cover both... :/
13:45 jonalv this is important stuff and not trivial it seems... :)
13:50 malick joined #bioclipse
13:51 jonalv egonw: please ping me when you get back, I am not convinced we are done with this structure...
14:01 jonalv @pelezilla
14:01 zarah [Bug 77] paths in windows slash problems http://tinyurl.com/578aen
14:01 zarah [Bug 78] CR/LF problems on windows       http://tinyurl.com/6eznsa
14:01 zarah [Bug 70] Faulty instanceof as IMolecu... http://tinyurl.com/5u7vag
14:01 zarah [Bug 73] Bioclipse 2.0.0 final is not... http://tinyurl.com/6phlff
14:01 zarah [Bug 71] Bioclipse2 lacks a QualityAs... http://tinyurl.com/6gmsm5
14:01 zarah Entire list at http://tinyurl.com/59wwod
14:10 * egonw is back
14:10 jonalv egonw: yey :)
14:11 jonalv egonw: How do we write coverage tests that catches this?
14:11 egonw I'll update it to check the one or more classes mentioned in TestClass
14:12 egonw and, yes I think I'd like to run all tests as plugin tests too...
14:12 egonw so, the latter should possible extend the former
14:12 egonw discussed that with Ola
14:12 egonw but he rather saw different tests
14:12 jonalv you want to extend? How do we do that?
14:13 * jonalv hasn't thought about these tests at all :)
14:13 egonw public class Foo extends Bar {} ?
14:13 jonalv well yea but perhaps I didn't understand you correctly
14:14 jonalv do you want to have the plugin tests extending the normal tests?
14:14 jonalv How do we benefit from that?
14:14 jonalv it feels like everything more or less must be rewritten anyway. or?
14:16 egonw nevermind that for now
14:16 egonw yes, that's what Ola thought too...
14:16 egonw have not looked much at the plugin tests yet
14:17 jonalv egonw: but this is sort of what I need for now. If not this then I still think that my test is testing the right thing
14:17 egonw what do you need exactly
14:17 egonw ?
14:18 jonalv Something that specifies that my test is not testing what it should test
14:18 egonw ah, right
14:19 egonw well, for that we need actual code coverage testing...
14:19 egonw like with Emma...
14:19 jonalv Emma?
14:19 egonw but I had trouble with it in combination with JUnit4
14:20 jonalv You think that I should just move the test over to the plugin test and test the method taking a string instead?
14:20 egonw the test method should not have any parameters at all, I think
14:20 jonalv I don't think they can have paramaters...
14:22 jonalv egonw: are you working on alternative 1 or 2 btw?
14:22 egonw 1
14:22 jonalv ETA?
14:23 egonw well, I start now..
14:23 egonw so let's make ETA: 17:00
14:23 jonalv oh :(
14:23 egonw was looking to the NewBioclipseProject wizard
14:23 egonw hang on...
14:23 jonalv aha
14:24 jonalv Then I will wait with my missing-tests-bugs until that's up and running :)
14:24 egonw ack
14:28 egonw ok, so a new plugin .core.test ?
14:28 egonw or .core.testS?
14:29 jonalv I think core.tests is the way we usually nae them...
14:29 jonalv *name
14:31 egonw ack
14:31 * egonw thinks ola will be so pleased to see so many new plugins
14:31 egonw hahahaha
14:31 egonw when the cat is from home ....
14:32 jonalv yea
14:32 jonalv :)
14:32 jonalv it's only because he checks them out and updates them  manually using subclipse
14:32 egonw current count BC2 alone: 76
14:32 egonw but that's including .tests
14:32 jonalv updating takes longer when you have many pluigns... :)
14:33 egonw yeah, I update from the command line
14:33 jonalv if you are using subclipse
14:33 jonalv yea I do that too
14:33 jonalv (mostly at least)
14:33 egonw umm...
14:33 egonw problem
14:33 egonw core.tests already exists
14:33 jonalv okey?
14:34 jonalv oh is that a problem?
14:34 egonw yes, because we need something to put the AbstractCoverageTest in
14:34 jonalv and what's wrong with putting it there?
14:34 egonw circular depedencies
14:34 jonalv oh hopw?
14:35 jonalv *how?
14:35 egonw because core.tests depends on bla.busines.test(s)
14:35 jonalv no
14:35 jonalv not mine anyyway..
14:36 jonalv or am I looking at the wrong place?
14:36 egonw oh...
14:36 egonw that's bioclipse.tests
14:36 egonw ok, mixing up things now
14:36 egonw sorry about that
14:37 jonalv bioclipse.tests contains the test suite that runs _all_ tests so yes it depends on _everything_
14:38 * jonalv <- afk for a little while...
14:47 * jonalv is back
14:48 egonw ok, I got a patch
14:49 jonalv okey?
14:49 egonw being commited as we speak
14:51 egonw ok, apparently need to update first
14:51 jonalv aha
14:51 egonw it's good that it checks
14:51 egonw SVN just fails horribly
14:51 jonalv uhm okey you lost me
14:52 jonalv SVN checks
14:52 CIA-53 bioclipse: egonw * r7595 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Added missing unit test for determineFormat
14:52 * jonalv is still using svn btw... :)
14:53 CIA-53 bioclipse: egonw * r7596 /bioclipse2/trunk/plugins/ (7 files in 6 dirs): Extracted common coverage testing code
14:56 egonw jonalv: I did not update your manager coverage test class
14:56 egonw ok, next stop: TestClass -> TestClasses
14:56 CIA-53 bioclipse: egonw * r7590 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/business/ICDKManager.java: Forgot to add the annotation
14:56 jonalv egonw: _my_ manager coverage test class. Uhm which one would that be?
14:56 egonw oh... thought you uploaded one ... hahaha
14:57 * jonalv is lost now...
14:57 CIA-53 bioclipse: egonw * r7591 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): Added unit test for generate3DCoordinates (closes #92)
15:00 CIA-53 bioclipse: egonw * r7589 /bioclipse2/trunk/plugins/net.bioclipse.cor​e/src/net/bioclipse/core/TestMethods.java: Added some notes on the comma-separated bits
15:00 egonw ha.. CIA is waking up..
15:00 egonw morning in the USA
15:00 CIA-53 bioclipse: egonw * r7592 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Added missing unit test for generate2DCoordinates (closes #93)
15:01 jonalv egonw: are you commited?
15:02 jonalv :)
15:02 egonw that's old stuff...
15:02 egonw commited earlier today...
15:02 egonw [16:00] <egonw> ha.. CIA is waking up..
15:02 egonw [16:00] <egonw> morning in the USA
15:02 jonalv yea it's funny :)
15:02 jonalv so I should try you new comma seperated coverage test now?
15:03 egonw no, not yet
15:04 CIA-53 bioclipse: egonw * r7597 /bioclipse2/trunk/plugins/ (7 files in 4 dirs): Renamed and added JavaDoc: TestClassES, so more than one now
15:16 egonw ok, done impl phase...
15:17 egonw now into testing phase
15:17 CIA-53 bioclipse: jonalv * r7598 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): whitespace
15:17 jonalv egonw: tell me when I can start using it :)
15:18 egonw in a few minutes, I think
15:18 egonw output looks good
15:18 * jonalv is starting to get in to the structuredb model again...
15:18 jonalv ir might take a few days...
15:19 egonw committing
15:21 CIA-53 bioclipse: egonw * r7599 /bioclipse2/trunk/plugins/net.bioclipse​.core.tests/src/net/bioclipse/core/test​s/coverage/AbstractCoverageTest.java: Refactored to take into account multiple test classes, as well as fixed output to not use STDOUT but report as assert message
15:22 CIA-53 bioclipse: jonalv * r7594 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): added test for cdk.numberOfEntriesInSDF. fixes #96
15:22 CIA-53 bioclipse: jonalv * r7593 /bioclipse2/trunk/plugins/net.bioclip​se.cdk.business.test/src/net/bioclips​e/cdk/AllCDKBusinessTestsSuite.java: added CoverageTest to AllCDKBusinessTestsSuite
15:33 egonw got to do something with the kids now...
15:33 egonw will be back tonite
15:33 egonw jonalv: happy with the new AbstractCoverageTest?
15:33 jonalv egonw: oh I haven't checked
15:34 jonalv will do. Got stuck with some reflection stugg in a structredb test :)
15:34 egonw ok
15:34 jonalv *stuff
15:34 jonalv egonw: but it's there now?
15:57 CIA-53 bioclipse: egonw * r7587 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/business/test/CDKManagerTest.java: Added missing unit test for cdk.addExplicitHydrogens (closes #85)
15:58 CIA-53 bioclipse: egonw * r7588 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/business/test/CDKManagerTest.java: Added missing unit test for cdk.addExplicitHydrogens (closes #84)
16:10 CIA-53 bioclipse: jonalv * r7600 /bioclipse2/trunk/plugins/ (6 files in 3 dirs): [Structuredb] Made Property.name unique
16:34 edrin egonw: what about plugging in taverna?
16:34 jonalv is egonw still around_
16:35 egonw no, have to make dinner
16:35 egonw edrin: yes, that has to go in...
16:35 egonw edrin: will look at that this week
16:35 jonalv egonw: I am in trouble...
16:35 egonw but I think that's an important aspect
16:35 egonw should not be too difficult
16:36 egonw jonalv: oh? you are locked out of your room?
16:36 jonalv egonw: I am looking at CDKManagerPlugintest and I am sort of worried by what I see...
16:36 jonalv or rather, I don't understand what I am loking at and that worries me
16:37 egonw oh... that's not good
16:37 egonw I've not looked at it yet...
16:37 egonw that's olas' code
16:37 jonalv Nothing looks like what I want to write...
16:37 egonw :(
16:37 egonw ok, then write what you do like
16:37 egonw and we'll compare things tomorrow
16:37 egonw maybe I can make sense of what olas did
16:38 jonalv I don't know how to create a file
16:38 egonw otherwise, file a bug report
16:38 edrin ok
16:38 egonw so that we can consult Ola when he gets back
16:38 egonw ah...
16:38 egonw ok, check CDKManagerTest.testDetermineFormat
16:38 egonw maybe that's an option
16:38 egonw have not tried the MockFIle route, which olas is using, not?
16:39 egonw btw, to figure out who is author of code in a file, use 'svn annotate'
16:39 egonw svn annotate <SOME_FILE>
16:39 egonw ok, got to go make dinner now
16:39 egonw bbl
16:39 jonalv egonw: testDetermineFormat is not following the workspace relative way of doing things that I thought we had agread upon...
16:46 jonalv zarah: tell egonw testDetermineFormat does not work because it uses absolute path for a method that expects a workspace realtive path. That test also needs to be run as a pluign-test, and it need to create a file some other way just as I do...
16:46 zarah Consider it noted.
17:27 edrin left #bioclipse
19:29 edrin joined #bioclipse
19:29 edrin hi egonw
19:31 egonw hi edrin
19:32 zarah egonw: You have new messages. Write '@messages' to read them.
19:32 egonw @msg
19:32 zarah egonw: 2 h 46 m 6 s ago, jonalv said testDetermineFormat does not work because it uses absolute path for a method that expects a workspace realtive path. That test also needs to be run as a pluign-test, and it need to create a file some other way just as I do...
19:36 egonw @tell jonalv indeed. Fixed in SVN now.
19:36 zarah Consider it noted.
19:37 CIA-53 bioclipse: egonw * r7601 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/business/ICDKManager.java: Added annotation for existing tests in CDKManagerPluginTest
19:38 CIA-53 bioclipse: egonw * r7602 /bioclipse2/trunk/plugins/net.bioclipse.cdk.bus​iness.test/src/net/bioclipse/cdk/business/test/ (CDKManagerPluginTest.java CDKManagerTest.java): Moved testDetermineFormat to the plugin tests, fixing the TMP file issue
19:58 egonw http://hugeurl.com/ :)
19:59 egonw or, if you like:
19:59 egonw http://www.hugeurl.com/?
19:59 egonw NDQwNGRlNDRjM2I2ZTMyNDAwMzg3Y2U1MTI1OTI5ODYmMTMmV​m0wd2QyUXlVWGxWV0d4WFlUSm9WMVl3Wkc5V1ZsbDNXa2M1YW​xKc1dqQlVWbHBQVjBaYWMySkVUbGhoTVVwVVZtcEdZV015U2t​WVWJHaG9UV3N3ZUZacVFtRlRNazE1VTJ0V1ZXSkhhRzlVVm1o​RFZWWmFkR1ZHV214U2JHdzFWa2QwYzJGc1NuUmhSemxWVmpOT​00xcFZXbUZrUjA1R1pFWlNUbFpVVmtwV2JURXdZVEZrU0ZOcl​pHcFRSVXBZVkZWYWQxTkdVbFZTYlVacVZtdGFNRlZ0ZUZOVWJ​VWTJVbFJHVjFaRmIzZFdha1poVjBaT2NtSkdTbWxTTW1oWlYx​ZDRiMkl3TUhoWGJHUllZbFZhY2xWc1VrZFhiR3QzV2tSU1Zr
19:59 egonw MXJjRWxhU0hCSFZqSkZlVlZZWkZwV1JWcHlWVEJhVDJOc2NFa​GpSbEpUVmxoQ1dsWnJXbGRoTVZWNVZXNU9hbEp0VWxsWmJGWm​hZMVpzY2xkdFJteFdiVko1VmpJMWExWXdNVVZTYTFwV1lrWkt​SRlpxUVhoa1ZsWjFWMnhhYUdFeGNGbFhhMVpoVkRKT2RGTnJa​RlJpVjNoWVZXcE9iMWRHV25STlNHUnNVakJzTkZVeWRHdGhWa​zVHVjJ4U1dtSkhhRlJXTVZwWFkxWktjbVJHVWxkaVJtOTNWMn​hXYjJFeFdYZE5WVlpUWVRGd1dGbHJaRzlqYkZweFUydGFiRlp​zV2xwWGExcHJZVWRGZUdOR2JGaGhNVnBvVmtSS1QyUkdUbkph​UmxKcFZqTm9WVlpHWTNoaU1XUnpWMWhvWVZKR1NuQlVWbHBY
19:59 egonw VFRGU1ZtRkhPVmROVjFKSldWVmFjMWR0UlhsaFJWSmFaV3RhV​0ZwRlZYaFdNVkowWlVkc1UySllZM2hXYTFwaFZURlZlRmR1U2​s1V1ZscFVXVlJHZDFZeGJISlhhM1JUVW14d2VGVldhRzloTVZ​welYycENXbFpXY0ROWmEyUkdaV3hHY21KR1pGZE5NRXBKVm10​U1MxVXhXWGhhU0ZaVllrWktjRlpxU205bGJHUllaVWM1YVUxc​mJEUldNalZUVkd4a1NGVnNXbFZXYkhCWVZHdGFhMk5zV25Sa1​JtUnBWbGhDTmxaVVNURlVNVnAwVW01S1QxWnNTbUZVVmxwM1p​XeHJlV1ZJWkZOTlZrcDVWR3hhVDJGV1NuUlBWRTVYWVRGd2FG​bHFTa1psVmtweVdrWm9hV0Y2Vm5oV1ZFSnZVVEZzVjFWc1ds
19:59 egonw aGliVkp5V1d0YWQyVkdWblJrUkVKV1RXdHdTVlpYY0VO​WGJGcFhZMFJPV21FeVVrZGFWV1JQVTBVNVYyRkhhRTVX​YmtKMlZteG9kMUl5UlhoYVJXUldZbXR3YUZWdE1XOWpS​bHB4VkcwNVYxWnNjRWhYVkU1dllWVXhXRlZzYUZkTlYy​aDJWMVphUzFKc1RuUlBWbFpYVFRGS05sWkhkR0ZXYlZa​WVZXdG9hMUp0VWs5V2FrWkxVMnhrVjFadFJsWk5WbXcx​Vld4b2MxWnNXa1pUYkdoWFlXczFkbGxWV21GalZrcHpX​a1pvVjJKclNrbFdWbVEwV1ZaWmVGTnJXbE5XUlZVNQ==
20:05 edrin uhm
20:11 egonw nevermind
20:19 egonw did you receive my email?
20:20 edrin yes
20:20 edrin it seems to work fine
20:20 edrin i can see the changes
20:20 egonw ok, good
20:20 edrin and can even edit it with MS word
20:21 edrin back in one minute
20:25 edrin joined #bioclipse
20:25 edrin back
21:50 edrin egonw
22:41 CIA-53 bioclipse: egonw * r7603 /bioclipse2/trunk/plugins/ (19 files in 12 dirs): Added test set up for cdk.debug

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