| 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/calvinandhobbes/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/DilbertDailyStrip/~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.bioclipse.cdk.business/src/net/bioclipse/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.core/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/tests/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.bioclipse.cdk.business.test/src/net/bioclipse/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.bioclipse.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.bioclipse.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.bioclipse.cdk.business/src/net/bioclipse/cdk/business/ICDKManager.java: Added annotation for existing tests in CDKManagerPluginTest |
| 19:38 |
CIA-53 |
bioclipse: egonw * r7602 /bioclipse2/trunk/plugins/net.bioclipse.cdk.business.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 |
NDQwNGRlNDRjM2I2ZTMyNDAwMzg3Y2U1MTI1OTI5ODYmMTMmVm0wd2QyUXlVWGxWV0d4WFlUSm9WMVl3Wkc5V1ZsbDNXa2M1YWxKc1dqQlVWbHBQVjBaYWMySkVUbGhoTVVwVVZtcEdZV015U2tWVWJHaG9UV3N3ZUZacVFtRlRNazE1VTJ0V1ZXSkhhRzlVVm1oRFZWWmFkR1ZHV214U2JHdzFWa2QwYzJGc1NuUmhSemxWVmpOT00xcFZXbUZrUjA1R1pFWlNUbFpVVmtwV2JURXdZVEZrU0ZOclpHcFRSVXBZVkZWYWQxTkdVbFZTYlVacVZtdGFNRlZ0ZUZOVWJVWTJVbFJHVjFaRmIzZFdha1poVjBaT2NtSkdTbWxTTW1oWlYxZDRiMkl3TUhoWGJHUllZbFZhY2xWc1VrZFhiR3QzV2tSU1Zr |
| 19:59 |
egonw |
MXJjRWxhU0hCSFZqSkZlVlZZWkZwV1JWcHlWVEJhVDJOc2NFaGpSbEpUVmxoQ1dsWnJXbGRoTVZWNVZXNU9hbEp0VWxsWmJGWmhZMVpzY2xkdFJteFdiVko1VmpJMWExWXdNVVZTYTFwV1lrWktSRlpxUVhoa1ZsWjFWMnhhYUdFeGNGbFhhMVpoVkRKT2RGTnJaRlJpVjNoWVZXcE9iMWRHV25STlNHUnNVakJzTkZVeWRHdGhWazVHVjJ4U1dtSkhhRlJXTVZwWFkxWktjbVJHVWxkaVJtOTNWMnhXYjJFeFdYZE5WVlpUWVRGd1dGbHJaRzlqYkZweFUydGFiRlpzV2xwWGExcHJZVWRGZUdOR2JGaGhNVnBvVmtSS1QyUkdUbkphUmxKcFZqTm9WVlpHWTNoaU1XUnpWMWhvWVZKR1NuQlVWbHBY |
| 19:59 |
egonw |
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| 19:59 |
egonw |
aGliVkp5V1d0YWQyVkdWblJrUkVKV1RXdHdTVlpYY0VOWGJGcFhZMFJPV21FeVVrZGFWV1JQVTBVNVYyRkhhRTVXYmtKMlZteG9kMUl5UlhoYVJXUldZbXR3YUZWdE1XOWpSbHB4VkcwNVYxWnNjRWhYVkU1dllWVXhXRlZzYUZkTlYyaDJWMVphUzFKc1RuUlBWbFpYVFRGS05sWkhkR0ZXYlZaWVZXdG9hMUp0VWs5V2FrWkxVMnhrVjFadFJsWk5WbXcxVld4b2MxWnNXa1pUYkdoWFlXczFkbGxWV21GalZrcHpXa1pvVjJKclNrbFdWbVEwV1ZaWmVGTnJXbE5XUlZVNQ== |
| 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 |
