| Time |
S |
Nick |
Message |
| 07:07 |
|
|
egonw joined #bioclipse |
| 07:27 |
|
CIA-55 |
bioclipse: egonw * r8786 /bioclipse2/trunk/plugins/net.bioclipse.jmol/jars/Jmol.jar: Uploaded Jmol bug fix release 11.6.16 |
| 07:49 |
|
CIA-55 |
bioclipse: egonw * r8787 /bioclipse2/trunk/cdk-externals/trunk/ (30 files in 10 dirs): Updated from jchempaint-primary (commit 14177) |
| 08:15 |
|
|
Gpox joined #bioclipse |
| 08:15 |
|
egonw |
hi Gpox |
| 08:15 |
|
egonw |
Gpox: I have updated JCP from jchempaint-primary |
| 08:15 |
|
egonw |
with the help of gilleain |
| 08:18 |
|
CIA-55 |
bioclipse: egonw * r8788 /bioclipse2/trunk/cdk-externals/trunk/org.openscience.cdk.control/src/org/openscience/cdk/controller/ControllerHub.java: Fixed two NPE sources |
| 08:27 |
|
|
olass joined #bioclipse |
| 08:27 |
|
olass |
moin |
| 08:27 |
|
olass |
hi |
| 08:27 |
|
olass |
@ping |
| 08:27 |
|
zarah |
olass: pong |
| 08:28 |
|
egonw |
olass: does any data_install extension get it's own project? |
| 08:28 |
|
egonw |
or do all end up in a single project? |
| 08:28 |
|
olass |
drugbank creates its own project, if that's what you mean |
| 08:29 |
|
egonw |
ok, that's indeed what I wanted to know |
| 08:29 |
|
egonw |
because it still also has a DrugBank folder... |
| 08:29 |
|
olass |
there are menas for this in the recent changes of the EP |
| 08:29 |
|
egonw |
which is kind of redundant then |
| 08:29 |
|
olass |
yes |
| 08:29 |
|
olass |
please remove that one |
| 08:29 |
|
egonw |
will fix that |
| 08:29 |
|
olass |
it SHOULD work |
| 08:29 |
|
olass |
please file bug if it doesn't and I'll fix it |
| 08:30 |
|
egonw |
btw: http://pele.farmbio.uu.se/bioclipse/docs/eps/ |
| 08:30 |
|
zarah |
egonw's link is also http://tinyurl.com/czt988 |
| 08:30 |
|
olass |
the key thing here is that you can reuse the net.bc.data wizard |
| 08:30 |
|
egonw |
it does, irght? |
| 08:30 |
|
olass |
I saw that |
| 08:30 |
|
egonw |
you did that, not? |
| 08:30 |
|
olass |
nice |
| 08:30 |
|
olass |
yes |
| 08:31 |
|
olass |
Egon: this is nice |
| 08:31 |
|
olass |
but it is not really what bug 318 was about |
| 08:31 |
|
olass |
maybe I made myself unclear |
| 08:31 |
|
olass |
will comment in bug |
| 08:32 |
|
egonw |
oh... yes, please do :) |
| 08:32 |
|
olass |
I mean, the docs are REALLY great |
| 08:32 |
|
egonw |
good we now verify things actually being fixed :) |
| 08:32 |
|
olass |
indeed |
| 08:34 |
|
egonw |
Gpox, olass: I tried the CDKMolecule property source last night |
| 08:34 |
|
egonw |
but did not get it to work |
| 08:34 |
|
egonw |
CDKMOlecule getAdapter() is not called |
| 08:34 |
|
egonw |
not even the BioResource.getAdapter |
| 08:34 |
|
olass |
BioResource is BC1 |
| 08:34 |
|
olass |
BioObject |
| 08:34 |
|
egonw |
BioObjet ? |
| 08:34 |
|
egonw |
the super class of CDKMolecule |
| 08:34 |
|
olass |
hmm |
| 08:34 |
|
olass |
hmm |
| 08:34 |
|
olass |
that used t owork... |
| 08:34 |
|
olass |
Gpox: do you know anything about this? |
| 08:35 |
|
egonw |
it works for selections in the Outline |
| 08:35 |
|
egonw |
but I don't get it working for things in the MDLmolfile editor |
| 08:35 |
|
egonw |
Gpox: and I did not see properties either when I selected an entry in the SDFEditor |
| 08:35 |
|
egonw |
so, this morning I'll focus on Pref pages... |
| 08:36 |
|
CIA-55 |
bioclipse: goglepox * r8789 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchempaint.view/src/net/bioclipse/cdk/jchempaint/view/JChemPaintView.java: Changed how JChemPaintView reacts on selections resolves bug #15 |
| 08:36 |
|
zarah |
bug #015 | http://tinyurl.com/5nrsdv |
| 08:36 |
|
CIA-55 |
bioclipse: goglepox * r8790 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/editor/MoleculeTable.java: Removed deprecated class |
| 08:36 |
|
Gpox |
Is there a CDKMoleculePropertySource? |
| 08:36 |
|
zarah |
Gpox: You have new messages. Write '/msg zarah @messages' to read them. |
| 08:36 |
|
egonw |
ah, maybe this fix also does help my bug... |
| 08:37 |
|
egonw |
Gpox: no, I made CDKMolecule implement IPropertySource |
| 08:37 |
|
egonw |
at least as a start |
| 08:37 |
|
egonw |
Gpox: but since getAdapter() was not being called... I could not get it to pass an new class anyway |
| 08:41 |
|
Gpox |
how do you check that? |
| 08:41 |
|
Gpox |
is the PropertySource changes commited? |
| 08:42 |
|
Gpox |
because getAdapter in CDKMolecule is called for IPropertySource |
| 08:42 |
|
egonw |
no, did not commit, because it did not work |
| 08:43 |
|
egonw |
break point |
| 08:43 |
|
egonw |
in CDKMolecule.getAdapter() |
| 08:43 |
|
egonw |
Gpox: yes, that's what I guessed... but it did not happen :( |
| 08:43 |
|
egonw |
OK, I'll try again... in particular, commit 8789 looks relevant... |
| 08:44 |
|
egonw |
Gpox: something else... |
| 08:44 |
|
egonw |
we really need drawing on an empty canvas working, not necessarily today, but at least for 2.0 |
| 08:44 |
|
Gpox |
no i only changed things in JChemPaintView |
| 08:44 |
|
egonw |
Gpox: oh :( |
| 08:44 |
|
egonw |
ok |
| 08:49 |
|
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steinbeck joined #bioclipse |
| 08:49 |
|
steinbeck |
moin |
| 08:50 |
|
egonw |
hi steinbeck! |
| 08:50 |
|
steinbeck |
Hi egonw |
| 09:14 |
|
olass |
egonw, Gpox: I need to build beta2 today |
| 09:15 |
|
olass |
Could you settle with finishing up at 13? |
| 09:15 |
|
egonw |
olass: yes, sounds good |
| 09:15 |
|
olass |
Gpox? |
| 09:17 |
|
olass |
I just want to make sure you have no open refactorings at that time that would compromize the beta2 release |
| 09:17 |
|
olass |
but I know, you work in patches so that should not be a problem |
| 09:18 |
|
Gpox |
ok |
| 09:26 |
|
olass |
egonw: How about that BO data repository? |
| 09:26 |
|
olass |
we had that in bc1 |
| 09:27 |
|
olass |
since it is SO easy to add more data, compiling a feature/plugin with data takes 3 minutes |
| 09:27 |
|
egonw |
will ask jerome on #cdk |
| 09:27 |
|
olass |
please do |
| 09:27 |
|
egonw |
but, yes, we can still distrib the data from bc1 |
| 09:27 |
|
olass |
sure, just check it is not in sample-data |
| 09:28 |
|
olass |
I have a feeling that there is some overlap |
| 09:28 |
|
egonw |
yes, very likely |
| 09:29 |
|
olass |
AFAIK, sample data took some sample data from BO |
| 09:29 |
|
olass |
well, I did I guess :-) |
| 09:30 |
|
olass |
egonw: should I set it up for BC2? |
| 09:30 |
|
olass |
I think I will do it faster than you... |
| 09:32 |
|
egonw |
yes,please do |
| 09:32 |
|
egonw |
olass: use version 2.1 |
| 09:32 |
|
egonw |
see this blog item: |
| 09:32 |
|
egonw |
http://pansanel.blogspot.com/2[…]s-release-21.html |
| 09:32 |
|
zarah |
egonw's link is also http://tinyurl.com/agzjve |
| 09:33 |
|
egonw |
no, there should be a newer one... |
| 09:33 |
|
olass |
egonw: can you look into how to generate Javadoc API for Bioclipse in Eclipse? It should be straightforward... |
| 09:33 |
|
olass |
and should be part of the Help |
| 09:33 |
|
olass |
ok, will file a bug :-) |
| 09:34 |
|
egonw |
of a developers feature? |
| 09:34 |
|
egonw |
sounds good |
| 09:34 |
|
olass |
hmm |
| 09:34 |
|
egonw |
was thinking the same thing |
| 09:34 |
|
olass |
API for all plugins |
| 09:34 |
|
olass |
like Eclipse does |
| 09:34 |
|
egonw |
yes, but should not end up in bioclipse by default |
| 09:34 |
|
olass |
indeed |
| 09:34 |
|
olass |
right |
| 09:34 |
|
olass |
I see your point |
| 09:35 |
|
olass |
Eclipse is for development, Bioclipse is for working :-) |
| 09:35 |
|
egonw |
right |
| 09:35 |
|
olass |
a devel feature would be nice |
| 09:35 |
|
olass |
will file a bug |
| 09:35 |
|
olass |
cdk-debug could go in there |
| 09:35 |
|
olass |
right? |
| 09:36 |
|
olass |
hmm, maybe not |
| 09:36 |
|
olass |
that would require dep to cdk |
| 09:36 |
|
egonw |
right, no need for that |
| 09:36 |
|
olass |
on the other hand, a devel feature might be OK to require some libs |
| 09:36 |
|
olass |
right |
| 09:36 |
|
olass |
a chemoinfo-devel feature in the future |
| 09:36 |
|
olass |
:-) |
| 09:36 |
|
egonw |
2.1 does seem to be the latest version: |
| 09:36 |
|
egonw |
http://pansanel.blogspot.com/2[…]s-release-21.html |
| 09:37 |
|
zarah |
egonw's link is also http://tinyurl.com/agzjve |
| 09:37 |
|
egonw |
https://sourceforge.net/projec[…]p?group_id=169897 |
| 09:37 |
|
olass |
is this the latest? |
| 09:37 |
|
egonw |
yes, it seems so |
| 09:37 |
|
egonw |
but I know he was talking to carsten about an update |
| 09:37 |
|
olass |
I hate SF links with https... |
| 09:43 |
|
olass |
egonw: a question |
| 09:43 |
|
olass |
jpansanel calls it "chemical structures" |
| 09:43 |
|
olass |
can we really call it BO data repository then? |
| 09:44 |
|
egonw |
yes |
| 09:44 |
|
egonw |
see the blue obelisk web site |
| 09:44 |
|
egonw |
it's listed there |
| 09:44 |
|
egonw |
btw, I like the idea of a Blue Obelisk dinner in Stockholm |
| 09:45 |
|
olass |
yes |
| 09:55 |
|
olass |
egonw: so id=net.bioclipse.data.blueobelisk and name "Blue Obelisk Data Repository" is good? |
| 09:56 |
|
olass |
or "Blue Obelisk Chemical Structures Repository"? |
| 10:01 |
|
egonw |
second, please |
| 10:02 |
|
olass |
ok |
| 10:13 |
|
olass |
egonw: I might need your help with this after all |
| 10:14 |
|
egonw |
just put a pref page in the wrong plugin :( |
| 10:14 |
|
olass |
I need to remove all non-mol/cml files from the BO data |
| 10:14 |
|
olass |
I am not so fluent with bash/unix commands |
| 10:14 |
|
egonw |
I am... |
| 10:14 |
|
olass |
could you help me? |
| 10:14 |
|
egonw |
please commit |
| 10:14 |
|
egonw |
file a bug report |
| 10:14 |
|
olass |
will do |
| 10:14 |
|
egonw |
will finish the current bug fix I am working on... |
| 10:15 |
|
olass |
ok |
| 10:15 |
|
egonw |
first |
| 10:16 |
|
CIA-55 |
bioclipse: ospjuth * r8791 /bioclipse2/trunk/plugins/net.bioclipse.data.blueobelisk/: Initial import. |
| 10:25 |
|
|
edrin joined #bioclipse |
| 10:29 |
|
egonw |
oi oi oi... |
| 10:30 |
|
egonw |
another new bug :( |
| 10:30 |
|
egonw |
guys, we *really* need unit testing... |
| 10:31 |
|
olass |
yes |
| 10:33 |
|
olass |
we have unit testing |
| 10:33 |
|
olass |
it's just not extensive |
| 10:34 |
|
olass |
and I donät understand why people don't run it |
| 10:34 |
|
olass |
just because it is not run automatically doesn't mean you can't run it manually! |
| 10:34 |
|
egonw |
well... and the plain lack of unit tests... |
| 10:35 |
|
egonw |
in the CDK, each new bug first results in a new unit test |
| 10:35 |
|
egonw |
in bioclipse we just 'fix' it... |
| 10:35 |
|
egonw |
so it can easily get broken later again, without anyone noticing |
| 10:35 |
|
olass |
I know |
| 10:35 |
|
olass |
this is something we really should improve in the future |
| 10:52 |
|
olass |
egonw: this commit will take a while |
| 10:53 |
|
olass |
getting really slow UL speed |
| 10:53 |
|
egonw |
ok |
| 10:53 |
|
olass |
at 10 % now... |
| 10:54 |
|
olass |
grrr SF is so damn SLOW sometimes! |
| 11:21 |
|
CIA-55 |
bioclipse: ospjuth * r8792 /bioclipse2/trunk/plugins/net.bioclipse.data.blueobelisk/data/ (3434 files in 33 dirs): Updated BO data repo 2.1. Contains non-molecule files that needs removal. |
| 11:29 |
|
egonw |
OK, done with the first CDK pref page |
| 11:29 |
|
egonw |
fixing bug 300 along the line |
| 11:30 |
|
CIA-55 |
bioclipse: egonw * r8793 /bioclipse2/trunk/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/business/CDKManager.java: Fixed a NPE: just assume zero implicit hydrogens if atom type is not recognized |
| 11:32 |
|
egonw |
quote "People fear computers becoming smarter and taking over the world, but currently computers are not very smart and they already have taken over the world! " |
| 11:33 |
|
egonw |
from: http://friendfeed.com/e/0d59cf[…]r-Pedro-Domingos/ |
| 11:33 |
|
zarah |
egonw's link is also http://tinyurl.com/bkzqs5 |
| 11:33 |
|
CIA-55 |
bioclipse: egonw * r8794 /bioclipse2/trunk/cdk-externals/trunk/org.openscience.cdk.libiocml/src/ (4 files in 3 dirs): Patched the CMLWriter to have the option to not output the XML declaration |
| 11:34 |
|
CIA-55 |
bioclipse: egonw * r8795 /bioclipse2/trunk/plugins/net.bioclipse.cdk.business/ (5 files in 2 dirs): Added a preference page for how to output CML with CDKMolecule.getCML() |
| 11:35 |
|
CIA-55 |
bioclipse: egonw * r8796 /bioclipse2/trunk/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/domain/CDKMolecule.java: Rewrote code to do nice indentation again, but without the XML declaration which broken embedding of the CML in other snippets earlier (fixes #300) |
| 11:35 |
|
zarah |
bug #300 | http://tinyurl.com/cgqh23 |
| 11:44 |
|
egonw |
http://www.steinbeck-molecular[…]h-nation-meeting/ |
| 11:44 |
|
zarah |
egonw's link is also http://tinyurl.com/ae6zee |
| 11:44 |
|
egonw |
check out the speaker list ;) |
| 11:47 |
|
olass |
looks great |
| 11:47 |
|
olass |
congrats |
| 11:54 |
|
|
jonalv joined #bioclipse |
| 11:54 |
|
jonalv |
oh hai |
| 11:54 |
|
zarah |
jonalv: You have new messages. Write '/msg zarah @messages' to read them. |
| 11:55 |
|
egonw |
hej jonalv |
| 11:56 |
|
egonw |
olass: do you want *all* HTML removed? |
| 11:56 |
|
egonw |
or shall we keep in the _en.html ? |
| 11:57 |
|
egonw |
nevermind |
| 11:57 |
|
egonw |
all the data in the HTML should be part of the CML anyway |
| 11:57 |
|
egonw |
if not, we'll file bug reports |
| 11:57 |
|
egonw |
the HTML should really just be a derive from the CML |
| 12:09 |
|
egonw |
olass: removing the HTML is slow too :) |
| 12:10 |
|
egonw |
Gpox: is there a reason why there are not icons for: |
| 12:10 |
|
egonw |
1. deleting atoms and bonds |
| 12:10 |
|
egonw |
2. drawing other rings in addition to benzene? |
| 12:15 |
|
egonw |
olass: ping |
| 12:15 |
|
egonw |
how are we doing in terms of the time? |
| 12:15 |
|
egonw |
we're past the commit deadline now... |
| 12:15 |
|
egonw |
the HTML removal commit is still in progress... |
| 12:17 |
|
jonalv |
edrin: Could you write a doctors certificate for me describing that it is not good for my health to be forced into writing my lab repports using MS Word? ;) |
| 12:18 |
|
egonw |
hahaha... |
| 12:18 |
|
edrin |
oh is it not? |
| 12:18 |
|
jonalv |
I am pretty sure itäs doing bad thing to my blood pressure |
| 12:19 |
|
jonalv |
:) |
| 12:19 |
|
edrin |
jonalv: here we even have to do it with a MS Word running on a remote desktop windows machine we have to connect to... sometimes in 16 colors only. |
| 12:19 |
|
edrin |
this is doing bad things on our blood pressure |
| 12:20 |
|
jonalv |
but... why? |
| 12:20 |
|
olass |
egonw: pong |
| 12:20 |
|
olass |
I still need one hour probably |
| 12:20 |
|
egonw |
ok |
| 12:20 |
|
olass |
and then some testing |
| 12:20 |
|
edrin |
and it gets even worse when we have to use the Adobe Photoshop on the remote machine in 16 colors, and dragging&dropping stuff on a remote screen is very evil, too |
| 12:21 |
|
olass |
jonalv: is it possible for you to test on windows? |
| 12:21 |
|
olass |
in 1-2 hours? |
| 12:21 |
|
jonalv |
olass: technically yes, schematically no not really |
| 12:21 |
|
edrin |
jonalv: this is because of our system admin................. |
| 12:21 |
|
olass |
jonalv: practivally is sufficient answer |
| 12:21 |
|
jonalv |
olass: I might be able to take a quick test run |
| 12:21 |
|
olass |
ok |
| 12:22 |
|
olass |
soudns good |
| 12:22 |
|
olass |
just see if it boots in enough |
| 12:22 |
|
olass |
it's just a beta2 |
| 12:23 |
|
edrin |
this means, everyone here has a core 2 duo machine, with Windows 2000 running, we are not allowed to install *any* software, only a MS Word 6.0 (from 1995?) is preinstalled. everything else must be done on the remote desktop... |
| 12:23 |
|
olass |
egonw: my subclipse seriously broke things with bo data repo |
| 12:23 |
|
olass |
were you able to cehck it out? |
| 12:24 |
|
edrin |
they are doing this to save time... this way they have to install stuff only on one server |
| 12:24 |
|
egonw |
yes, no problem |
| 12:24 |
|
olass |
all data? |
| 12:24 |
|
olass |
how big was it? |
| 12:25 |
|
egonw |
dunno |
| 12:25 |
|
olass |
ok |
| 12:25 |
|
CIA-55 |
bioclipse: ospjuth * r8797 /bioclipse2/trunk/plugins/net.bioclipse.data.blueobelisk/ (13 files in 8 dirs): Updated for src files in bo data. |
| 12:25 |
|
egonw |
~5MB |
| 12:25 |
|
egonw |
5.4 |
| 12:25 |
|
olass |
damn |
| 12:26 |
|
egonw |
jonalv: ping |
| 12:26 |
|
olass |
hmmm |
| 12:26 |
|
jonalv |
egonw: yes? |
| 12:26 |
|
egonw |
olass: too, actually |
| 12:26 |
|
egonw |
trying to run the CDKManagerTest |
| 12:26 |
|
egonw |
and it fails on CDKMOlecule.toString |
| 12:26 |
|
egonw |
because that is using the Activitor |
| 12:26 |
|
olass |
sry, no time |
| 12:27 |
|
egonw |
which is actually null |
| 12:27 |
|
egonw |
which means that when we do things properly, unit testing only from a PluginTest makes sense |
| 12:27 |
|
jonalv |
egonw: yes it would mean that, or you could mock |
| 12:28 |
|
olass |
egonw: that is what I have been telling you all the time :-) |
| 12:28 |
|
olass |
but unit tests are important too |
| 12:28 |
|
olass |
as they run fast |
| 12:29 |
|
egonw |
yeah, but not if they fail if run incorrectly |
| 12:29 |
|
CIA-55 |
bioclipse: egonw * r8798 /bioclipse2/trunk/plugins/net.bioclipse.data.blueobelisk/data/ (2182 files in 32 dirs): Removed HTML (fixes #485) |
| 12:29 |
|
zarah |
bug #485 | http://tinyurl.com/csxx3y |
| 12:29 |
|
egonw |
hahahaha... |
| 12:29 |
|
egonw |
2128 files :) |
| 12:30 |
|
olass |
was that the nasty hack? |
| 12:32 |
|
egonw |
no, that's behind us already |
| 12:36 |
|
egonw |
olass: sorry... |
| 12:37 |
|
egonw |
but there are a few bugs in the CDKManager/CDKMolecule which really needs fixing... |
| 12:37 |
|
olass |
ok |
| 12:37 |
|
egonw |
so, I hope I indeed still have 23 minutes |
| 12:37 |
|
olass |
no worries |
| 12:37 |
|
olass |
it must be today |
| 12:37 |
|
olass |
and I have to leave at like 17 |
| 12:37 |
|
egonw |
and I won't bother sending bug reports to the authors this time |
| 12:37 |
|
olass |
just do it :-) |
| 12:38 |
|
olass |
I am struggling here too |
| 12:45 |
|
CIA-55 |
bioclipse: egonw * r8799 /bioclipse2/trunk/plugins/net.bioclipse.cdk.business.test/src/net/bioclipse/cdk/business/test/CDKManagerTest.java: Fixed unit test: actually test something; removed use of toString() which always fails with a NPE when not run as plugin test |
| 12:46 |
|
CIA-55 |
bioclipse: egonw * r8800 /bioclipse2/trunk/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/domain/CDKMolecule.java: Don't set the Prefs ahead of initialization, but in the constructor. Fixes a NPE |
| 12:47 |
|
CIA-55 |
bioclipse: egonw * r8801 /bioclipse2/trunk/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/domain/CDKMolecule.java: Reuse local constructors to increase consistency |
| 12:47 |
|
CIA-55 |
bioclipse: egonw * r8802 /bioclipse2/trunk/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/domain/CDKMolecule.java: Take into account the use case where the manager is used, but not in a plugin setting (as with CDKManagerTest) |
| 12:48 |
|
CIA-55 |
bioclipse: egonw * r8803 /bioclipse2/trunk/plugins/net.bioclipse.cdk.business.test/src/net/bioclipse/cdk/business/test/CDKManagerTest.java: Fixed a unit test: -> UNIT TESTS ARE SUPPOSED TO TEST SOMETHING <- (come on, that's basic, not??) |
| 12:48 |
|
egonw |
olass: yes, getting foul again |
| 12:49 |
|
olass |
:-) |
| 12:49 |
|
olass |
you have my support |
| 12:52 |
|
egonw |
and right now... all tests of the CDKManagerPluginTest fail |
| 12:52 |
|
egonw |
because I cannot instantiate a CDKManager |
| 12:53 |
|
egonw |
jonalv: ping |
| 12:53 |
|
jonalv |
egonw: yes |
| 12:53 |
|
egonw |
jonalv: where did we put that call again, to force loading of a manager earlier this week? |
| 12:53 |
|
jonalv |
egonw: I can't remember |
| 12:54 |
|
egonw |
ok |
| 12:54 |
|
egonw |
neither do I |
| 12:54 |
|
jonalv |
in the beforeclass? |
| 12:54 |
|
egonw |
I'll search |
| 12:54 |
|
egonw |
yes, that sounds like it |
| 12:54 |
|
egonw |
tack! |
| 12:55 |
|
egonw |
jonalv: it actually fails just after our net.bioclipse.ui.Activator.getDefault() |
| 12:55 |
|
egonw |
so that was not a fix, but a mere conincidence that it worked after adding that line :( |
| 12:55 |
|
jonalv |
egonw: is this a pluign test_ |
| 12:56 |
|
egonw |
yes |
| 12:56 |
|
jonalv |
k |
| 12:57 |
|
olass |
egonw: what version is the drugbank plugin? |
| 12:57 |
|
egonw |
dunno... copied something from another plugin |
| 12:57 |
|
olass |
oh |
| 12:57 |
|
egonw |
Bsomething, I guess |
| 12:57 |
|
olass |
ok, will use bioclipse versioning then |
| 12:57 |
|
olass |
no, I mean the actual data |
| 12:58 |
|
egonw |
oh |
| 12:58 |
|
olass |
does it have a version? |
| 12:58 |
|
egonw |
umm... no idea when we copied it |
| 12:59 |
|
olass |
ok |
| 12:59 |
|
olass |
will be bc versioning for now then |
| 13:00 |
|
egonw |
yes |
| 13:05 |
|
CIA-55 |
bioclipse: ospjuth * r8804 /bioclipse2/trunk/plugins/net.bioclipse.data.blueobelisk/ (6 files in 3 dirs): Added extension of EP to install BO data repo. Solves bug #486. |
| 13:05 |
|
zarah |
bug #486 | http://tinyurl.com/celc3e |
| 13:06 |
|
CIA-55 |
bioclipse: ospjuth * r8805 /bioclipse2/trunk/plugins/ (14 files in 13 dirs): Set version to 2.0.0.B20090213. This is Beta2 release, taking versioning in parts. |
| 13:07 |
|
egonw |
f**k |
| 13:07 |
|
CIA-55 |
bioclipse: ospjuth * r8806 /bioclipse2/trunk/plugins/net.bioclipse.data.blueobelisk/ (build.properties plugin.xml): Updated name and build.props to include data on export. |
| 13:10 |
|
olass |
EGONW: ABOUT THE INCHI PLUGIN |
| 13:10 |
|
olass |
oops |
| 13:10 |
|
olass |
did not mean to shout |
| 13:10 |
|
olass |
caps lock horror |
| 13:10 |
|
olass |
anyways |
| 13:10 |
|
egonw |
right... |
| 13:10 |
|
olass |
egonw: how about the inchi plugin? |
| 13:10 |
|
egonw |
mom |
| 13:10 |
|
olass |
you were talking about an easy fix |
| 13:11 |
|
egonw |
yes |
| 13:11 |
|
egonw |
jonalv: ping |
| 13:11 |
|
olass |
30 mins? |
| 13:11 |
|
olass |
more? |
| 13:11 |
|
egonw |
jonalv: what was that osgi> command line again to list plugin states? |
| 13:11 |
|
egonw |
olass: yes, should work... |
| 13:11 |
|
jonalv |
egonw: ss |
| 13:13 |
|
egonw |
jonalv: ACTIVE is good, right? |
| 13:13 |
|
jonalv |
egonw: uhm depends on whether you want it to be running... |
| 13:13 |
|
olass |
masak: around? |
| 13:14 |
|
egonw |
oh... OK, right |
| 13:14 |
|
egonw |
so, not good :( |
| 13:14 |
|
egonw |
RUNNING should be the state... ok |
| 13:14 |
|
egonw |
ok, that's the problem then |
| 13:14 |
|
egonw |
sort of fits the picture... |
| 13:14 |
|
jonalv |
olass: I think I see masak in #farmbio |
| 13:14 |
|
egonw |
cdkbla.Activator.getDefault() returns null... |
| 13:14 |
|
olass |
right |
| 13:14 |
|
egonw |
for I don't know what reason :( |
| 13:18 |
|
CIA-55 |
bioclipse: egonw * r8807 /bioclipse2/trunk/plugins/net.bioclipse.gist/src/net/bioclipse/gist/Activator.java: Fixed the error message: correct manager name |
| 13:18 |
|
jonalv |
Is olas building next Bioclipse relase today? |
| 13:18 |
|
olass |
yes |
| 13:18 |
|
olass |
in 30 mins |
| 13:19 |
|
egonw |
can anyone else try to run CDKManagerPluginTest, please? |
| 13:19 |
|
CIA-55 |
bioclipse: egonw * r8808 /bioclipse2/trunk/plugins/net.bioclipse.inchi.business.test/src/net/bioclipse/inchi/business/test/InChIManagerTest.java: Added unit test for situations where not stereochemistry is given: creating InChI should not fail on that |
| 13:19 |
|
jonalv |
and the webservices? WSDb+fetch. Are they going in? |
| 13:19 |
|
olass |
jonalv: why do you ask? |
| 13:19 |
|
jonalv |
"pz 464 |
| 13:20 |
|
jonalv |
@pz 464 |
| 13:20 |
|
zarah |
http://tinyurl.com/afd97m |
| 13:20 |
|
jonalv |
@pz 463 |
| 13:20 |
|
zarah |
http://tinyurl.com/djs457 |
| 13:20 |
|
egonw |
how do I get a manager to send a message to the console? |
| 13:21 |
|
jonalv |
egonw: use js.print |
| 13:21 |
|
egonw |
js is which manager? |
| 13:21 |
|
jonalv |
the javascript manager |
| 13:21 |
|
olass |
jonalv: it is a beta2 |
| 13:21 |
|
jonalv |
okey |
| 13:21 |
|
olass |
RC it would not |
| 13:22 |
|
olass |
ok with you? |
| 13:22 |
|
olass |
we have many otehr bugs open... |
| 13:22 |
|
* jonalv |
dives back into receptor lab now |
| 13:22 |
|
olass |
I agree it is not good |
| 13:22 |
|
egonw |
olass: inchi is in |
| 13:22 |
|
egonw |
fixed the problem |
| 13:23 |
|
olass |
great |
| 13:23 |
|
olass |
egonw++ |
| 13:24 |
|
egonw |
can anyone else try to run CDKManagerPluginTest, please? |
| 13:24 |
|
egonw |
can anyone else try to run CDKManagerPluginTest, please? |
| 13:24 |
|
egonw |
can anyone else try to run CDKManagerPluginTest, please? |
| 13:24 |
|
zarah |
can anyone else try to run CDKManagerPluginTest, please? |
| 13:25 |
|
olass |
egonw: ok |
| 13:25 |
|
CIA-55 |
bioclipse: egonw * r8809 /bioclipse2/trunk/plugins/net.bioclipse.inchi.business.test/src/net/bioclipse/inchi/business/test/InChIManagerTest.java: Fixed the unit test: the correct InChI |
| 13:25 |
|
CIA-55 |
bioclipse: ospjuth * r8810 /bioclipse2/trunk/ (18 files in 18 dirs): Set version to 2.0.0.B20090213. This is Beta2 release, second half of plugins. |
| 13:26 |
|
CIA-55 |
bioclipse: egonw * r8811 /bioclipse2/trunk/plugins/net.bioclipse.inchi.business/src/net/bioclipse/inchi/business/InChIManager.java: Don't fail if we get a warning: that just typically indicates missing info on the input, such as undefined stereo centeres (see InChIManagerTest.testGenerateStereo()) |
| 13:26 |
|
egonw |
on one hand it is nice, two days of just hacking after a while of just meeting and writing... |
| 13:26 |
|
egonw |
but then again... |
| 13:27 |
|
egonw |
you find so many stupid bugs all over the place |
| 13:29 |
|
olass |
ok egonw, did run it |
| 13:29 |
|
olass |
I see failures |
| 13:29 |
|
egonw |
but it runs? |
| 13:30 |
|
olass |
sure |
| 13:30 |
|
egonw |
well.. not here... |
| 13:30 |
|
olass |
it can be a mess |
| 13:30 |
|
egonw |
ok, what is the fail rate? |
| 13:30 |
|
olass |
this is how I solve it |
| 13:30 |
|
olass |
hmm |
| 13:30 |
|
olass |
11 Errors 1 fails total is 49 |
| 13:30 |
|
olass |
set target platform |
| 13:31 |
|
egonw |
ack will try |
| 13:31 |
|
olass |
in run config, remove all, add required plugins 2 times, run |
| 13:31 |
|
olass |
perhaps create a new run config |
| 13:31 |
|
olass |
but yes, it runs here |
| 13:33 |
|
edrin |
jonalv: is your web service bug still active? |
| 13:33 |
|
jonalv |
edrin: I guess so |
| 13:34 |
|
edrin |
jonalv: so downloading file fails? |
| 13:34 |
|
edrin |
or opening the file? |
| 13:34 |
|
jonalv |
edrin: I can try again... |
| 13:34 |
|
edrin |
or only if the file was only downloaded 2x ? |
| 13:34 |
|
jonalv |
gah now it deletes all html files I just saw it downlaod last time I rebased |
| 13:34 |
|
jonalv |
what are you people doing_ |
| 13:34 |
|
edrin |
or the file was "incomplete" deleted in the meantime? |
| 13:35 |
|
edrin |
jonalv: ? |
| 13:35 |
|
edrin |
why html files? |
| 13:35 |
|
olass |
jonalv: read commit messages and you will understand |
| 13:35 |
|
edrin |
is this plugin related? |
| 13:36 |
|
|
maclean joined #bioclipse |
| 13:36 |
|
jonalv |
edrin: I was talking about rebasing Bioclipse |
| 13:37 |
|
edrin |
rebasing? what does this mean? |
| 13:37 |
|
jonalv |
zarah: google git rebase |
| 13:37 |
|
zarah |
jonalv: http://www.kernel.org/pub/soft[…]s/git-rebase.html |
| 13:38 |
|
CIA-55 |
bioclipse: ospjuth * r8812 /bioclipse2/trunk/features/ (5 files in 5 dirs): Set version to 2.0.0.B20090213. This is Beta2 release, features. |
| 13:39 |
|
olass |
edrin: why have you set LGPL on net.bc.jseditor? |
| 13:39 |
|
olass |
we only have EPL on our plugins here |
| 13:40 |
|
olass |
Can I change it? |
| 13:40 |
|
olass |
if not we cannot have the plugin in Bioclipse |
| 13:40 |
|
edrin |
oh it should be EPL? |
| 13:41 |
|
olass |
edrin: yes, that is an official demand on all our core bioclipse plugins |
| 13:41 |
|
edrin |
sure, i will change it at weekend then |
| 13:41 |
|
olass |
I am building now |
| 13:41 |
|
edrin |
ok |
| 13:41 |
|
olass |
please change now |
| 13:41 |
|
olass |
else it will miss beta2 release |
| 13:41 |
|
edrin |
i cant, i am not home |
| 13:41 |
|
olass |
:-( |
| 13:41 |
|
olass |
sry |
| 13:41 |
|
edrin |
you can change it if you want |
| 13:41 |
|
olass |
ok, will do |
| 13:42 |
|
edrin |
how does the license look? |
| 13:42 |
|
olass |
EPL? |
| 13:42 |
|
edrin |
olass: in webservice plugin, there are some files with lgpl, too |
| 13:42 |
|
egonw |
edrin: that is no problem |
| 13:42 |
|
edrin |
why not? |
| 13:42 |
|
jonalv |
edrin: it seems to be working now |
| 13:42 |
|
egonw |
as long as the BC related code it EPL |
| 13:42 |
|
olass |
edrin: I have told you many times we use EPL in Bioclipse |
| 13:42 |
|
olass |
we link in LGPL |
| 13:43 |
|
edrin |
ah |
| 13:43 |
|
edrin |
ok |
| 13:43 |
|
olass |
ok? |
| 13:43 |
|
olass |
good |
| 13:43 |
|
edrin |
yes sure |
| 13:43 |
|
egonw |
edrin: that is no problem <- if is is third party stuff |
| 13:43 |
|
olass |
all our code is EPL |
| 13:43 |
|
edrin |
ok, dont mind |
| 13:43 |
|
edrin |
dont even know epl |
| 13:43 |
|
olass |
linked in libs (like cdk or xws4j) can be LGPL as far as I'm concerned |
| 13:43 |
|
olass |
@gg eclipse public license |
| 13:43 |
|
zarah |
olass: http://www.eclipse.org/legal/epl-v10.html |
| 13:44 |
|
edrin |
olass: yes, i was talking about some source .java files in the webservice plugin... there are very few of them that have the same header... |
| 13:45 |
|
olass |
please change them as soon as you can |
| 13:45 |
|
edrin |
i think for example the ResourceCreator file |
| 13:45 |
|
olass |
will file yopu a bug |
| 13:45 |
|
edrin |
jonalv: ok, if it is working, can you disable the bug? |
| 13:45 |
|
olass |
edrin: are you really reading your bug list on a regular basis? |
| 13:45 |
|
olass |
need to know if I can rely on that |
| 13:46 |
|
olass |
when it comes to releases |
| 13:46 |
|
edrin |
i think so |
| 13:47 |
|
edrin |
i get emails |
| 13:47 |
|
olass |
you need to review it constantly |
| 13:47 |
|
edrin |
how can i see bugs assigned to me? |
| 13:47 |
|
olass |
you donät get emails for everything |
| 13:47 |
|
olass |
:-( |
| 13:47 |
|
olass |
I guess that answers my question.... |
| 13:48 |
|
olass |
@pz |
| 13:48 |
|
zarah |
olass: Pelezilla is at http://bugs.bioclipse.net |
| 13:48 |
|
egonw |
grmp... |
| 13:48 |
|
egonw |
my patch won't commit... |
| 13:48 |
|
olass |
click Search existing bug reports |
| 13:48 |
|
olass |
edrin: this is for you |
| 13:48 |
|
edrin |
yes |
| 13:48 |
|
edrin |
and then? |
| 13:48 |
|
olass |
in box Email adresses,. Bug .... |
| 13:49 |
|
edrin |
Zarro Boogs found. |
| 13:49 |
|
olass |
in left textarea, write "aliban" |
| 13:49 |
|
edrin |
i am logged in |
| 13:49 |
|
olass |
[14:51] < olass> in left textarea, write "aliban" |
| 13:49 |
|
edrin |
Zarro Boogs found. |
| 13:49 |
|
olass |
in Status, I usually select NEW, ASSIGNED, and REOPENED |
| 13:50 |
|
olass |
and in Target I click "2.0" to only see bugs for the 2.0 release |
| 13:50 |
|
edrin |
olass: yes, this i somehow got |
| 13:50 |
|
olass |
I see your bugs |
| 13:51 |
|
edrin |
and what did you enter? |
| 13:51 |
|
olass |
aliban |
| 13:51 |
|
olass |
[14:52] < olass> in Status, I usually select NEW, ASSIGNED, and REOPENED |
| 13:52 |
|
olass |
http://pele.farmbio.uu.se/cgi-[…]es=&chfieldfrom=& |
| 13:52 |
|
edrin |
ah advanced search |
| 13:52 |
|
zarah |
olass's link is also http://tinyurl.com/cha64r |
| 13:52 |
|
olass |
sure |
| 13:54 |
|
edrin |
ok, they are all resolved I think, except the writing sample scripts |
| 13:54 |
|
CIA-55 |
bioclipse: ospjuth * r8813 /bioclipse2/trunk/plugins/net.bioclipse.jseditor/META-INF/MANIFEST.MF: Set version to 2.0.0.B20090213 and updated props for JSeditor plugin. |
| 13:54 |
|
edrin |
back in 10 min |
| 13:54 |
|
olass |
edrin: please mark as resolved |
| 13:55 |
|
CIA-55 |
bioclipse: ospjuth * r8814 /bioclipse2/trunk/features/net.bioclipse_feature/feature.xml: Replaced net.sf.jseditor with net.bioclipse.jseditor. |
| 13:56 |
|
maclean |
olass: can I close #430 |
| 13:56 |
|
maclean |
+ ? |
| 13:56 |
|
olass |
why do you ask me? |
| 13:56 |
|
maclean |
@bug 430 |
| 13:56 |
|
olass |
mom |
| 13:56 |
|
zarah |
http://tinyurl.com/dbhapw |
| 13:56 |
|
maclean |
I ask you on the grounds that you opened (and re-opened :) it... |
| 13:56 |
|
olass |
maclean, no , please mark as fixed |
| 13:57 |
|
maclean |
oky |
| 13:57 |
|
olass |
then I see it, and then I will try it |
| 13:57 |
|
olass |
then close it |
| 13:57 |
|
olass |
:-) |
| 13:57 |
|
maclean |
or reopen it... |
| 13:58 |
|
olass |
@tell masak: js.jar exists in net.bioclipse.jseditor but also in net.bioclipse.scripting. |
| 13:58 |
|
zarah |
Consider it noted. |
| 13:58 |
|
olass |
@tell edrin: js.jar exists in net.bioclipse.jseditor but also in net.bioclipse.scripting. |
| 13:58 |
|
zarah |
Consider it noted. |
| 13:58 |
|
olass |
grr |
| 13:59 |
|
olass |
lets hope it is the same version at least |
| 13:59 |
|
maclean |
egonw : so can I set bug #482 to FIXED? I saw you updated cdk-external. |
| 13:59 |
|
CIA-55 |
bioclipse: ospjuth * r8815 /bioclipse2/trunk/plugins/net.bioclipse.jseditor/build.properties: Updated build to include icons. |
| 14:00 |
|
egonw |
@pz #482 |
| 14:00 |
|
zarah |
http://tinyurl.com/b36k93 |
| 14:00 |
|
egonw |
yes, maclean fixed that |
| 14:00 |
|
maclean |
ok |
| 14:01 |
|
egonw |
hahahaha |
| 14:01 |
|
egonw |
though ola asked about that one being FIXED |
| 14:01 |
|
egonw |
which I addressed you in third person when replying :) |
| 14:01 |
|
maclean |
yeah thought so |
| 14:01 |
|
maclean |
:) |
| 14:01 |
|
egonw |
olass: plugin unit test failed, because the workspace was messed up... deleting it solved it... |
| 14:02 |
|
egonw |
olass: I get 12 failures too... |
| 14:02 |
|
CIA-55 |
bioclipse: ospjuth * r8816 /bioclipse2/trunk/plugins/net.bioclipse.jseditor/ (5 files in 4 dirs): Removed js.jar from jseditor as it should depend on net.bc.scripting which provides this jar. |
| 14:02 |
|
egonw |
checking them now |
| 14:02 |
|
olass |
ok |
| 14:02 |
|
olass |
good |
| 14:02 |
|
maclean |
by the way, about the oval highlight, Gpox - is the intention to have an circle for each bond (so 2 for a double bond, 3 for a triple..)? |
| 14:03 |
|
egonw |
oh.. btw, can you check rendering of triple bonds? |
| 14:03 |
|
egonw |
it fails for me |
| 14:03 |
|
egonw |
jonalv: I got for UnsupportedOperation fails in CDKManagerPluginTest |
| 14:03 |
|
jonalv |
egonw: four? |
| 14:04 |
|
maclean |
in bioclipse-jcp? |
| 14:05 |
|
* maclean |
assumes so, and will test there |
| 14:05 |
|
maclean |
I know it works in swing-jcp, so it's probably the renderer options |
| 14:06 |
|
egonw |
maclean: yes, rendering opts in bc-jcp is up next for me |
| 14:07 |
|
maclean |
I can do that - do you want the facade approach of a published method for each option? |
| 14:07 |
|
maclean |
(only the sensible ones - the user should not be setting the scale, or the color map, I think) |
| 14:08 |
|
egonw |
I think everything should be available from the command line... |
| 14:08 |
|
egonw |
even scale... |
| 14:08 |
|
maclean |
hmmm, I don't |
| 14:08 |
|
egonw |
GUI will only contain save stuff... |
| 14:08 |
|
egonw |
zoom: yes, scale: no |
| 14:09 |
|
egonw |
color map -> what's that then? |
| 14:09 |
|
egonw |
not how atoms are colored, |
| 14:09 |
|
maclean |
zoom - for sure |
| 14:09 |
|
* olass |
is building now |
| 14:09 |
|
egonw |
but an internal map of allocated colors? |
| 14:09 |
|
CIA-55 |
bioclipse: ospjuth * r8817 /bioclipse2/trunk/plugins/net.bioclipse.ui/toc.xml: Fixed incorrect Help paths. |
| 14:09 |
|
egonw |
that should indeed not be visible |
| 14:09 |
|
maclean |
egonw : exactly |
| 14:09 |
|
egonw |
OK, that calls for a split up of rendering options... |
| 14:10 |
|
egonw |
of implementation specific stuff |
| 14:10 |
|
egonw |
and user settable stuff |
| 14:10 |
|
egonw |
-t |
| 14:10 |
|
maclean |
egonw : well, that's what the internal RenderingParameters was for :) |
| 14:11 |
|
olass |
@tell masak: output from running JSEditor is not in Javascript Console |
| 14:11 |
|
zarah |
Consider it noted. |
| 14:13 |
|
egonw |
maclean: btw, sure, you're welcome to implement your suggestion |
| 14:13 |
|
maclean |
hmmm, forgot about that - invalid thread access. |
| 14:13 |
|
egonw |
maclean: but I don't want to keep you too much from CASE stuff |
| 14:13 |
|
maclean |
egonw : okay, will do |
| 14:13 |
|
egonw |
but it's your call |
| 14:14 |
|
edrin |
olass: it is the same version |
| 14:14 |
|
zarah |
edrin: You have new messages. Write '/msg zarah @messages' to read them. |
| 14:15 |
|
olass |
edrin: I have replaced it |
| 14:15 |
|
edrin |
olass: will the xws4j plugin be in the release? |
| 14:15 |
|
olass |
see r8816 |
| 14:15 |
|
olass |
release is SF release |
| 14:15 |
|
olass |
xws4j will be on update site, yes |
| 14:15 |
|
edrin |
ah |
| 14:15 |
|
edrin |
then |
| 14:15 |
|
edrin |
there is still one problem |
| 14:16 |
|
edrin |
we must find a way to "import" the exports of xws4j in the jseditor and scripting console plugin |
| 14:16 |
|
edrin |
at runtime |
| 14:17 |
|
edrin |
as we do not want everything to depend on xws4j |
| 14:17 |
|
olass |
edrin: this is too late for anything |
| 14:17 |
|
olass |
no time |
| 14:17 |
|
edrin |
otherwise we can not use the Async API of xws4j in bioclipse scripting |
| 14:17 |
|
olass |
if things don't work, it will not go on update site |
| 14:17 |
|
olass |
deadline was yesterday, as you know |
| 14:17 |
|
edrin |
olass: the thing works |
| 14:18 |
|
olass |
ok |
| 14:18 |
|
edrin |
olass: i am talking about a general issue |
| 14:18 |
|
olass |
please, not now |
| 14:18 |
|
olass |
too busy with release |
| 14:18 |
|
edrin |
ok |
| 14:18 |
|
olass |
file a bug or write email |
| 14:18 |
|
edrin |
is it a release candidate or a beta? |
| 14:18 |
|
olass |
beta2 |
| 14:18 |
|
edrin |
ah ok |
| 14:18 |
|
olass |
that's why webservices can go |
| 14:18 |
|
edrin |
i will write an email |
| 14:18 |
|
olass |
and jseditor |
| 14:19 |
|
olass |
since they really do not live up to demands of an RC |
| 14:19 |
|
olass |
with open bugs |
| 14:19 |
|
olass |
in pelezilla |
| 14:19 |
|
olass |
and untested |
| 14:22 |
|
CIA-55 |
bioclipse: gilleain * r8818 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchempaint.view/src/net/bioclipse/cdk/jchempaint/view/JChemPaintWidget.java: |
| 14:22 |
|
CIA-55 |
bioclipse: - 'Highlight radius model' is no longer used. |
| 14:22 |
|
CIA-55 |
bioclipse: - 'Bond distance' is now specified in screen space, not model space. |
| 14:23 |
|
maclean |
egonw : that fixes the double/triple bonds. |
| 14:23 |
|
egonw |
ok, thanx... great |
| 14:23 |
|
egonw |
olass: it's too late for the release, I guess? |
| 14:24 |
|
maclean |
:( sorry olass, I read the thing earlier about only sending patches... |
| 14:24 |
|
olass |
not yet |
| 14:24 |
|
olass |
have not built final |
| 14:24 |
|
edrin |
olass: did the test of webservice work for you? |
| 14:24 |
|
olass |
taking things step by step |
| 14:24 |
|
olass |
edrin: no time now |
| 14:24 |
|
edrin |
ok |
| 14:24 |
|
* olass |
is building |
| 14:25 |
|
olass |
and testing |
| 14:25 |
|
olass |
edrin: I got a pdb |
| 14:25 |
|
olass |
so that sort of worked |
| 14:25 |
|
edrin |
yes |
| 14:25 |
|
olass |
but managers still have failing tests |
| 14:25 |
|
edrin |
good |
| 14:25 |
|
edrin |
do they? |
| 14:25 |
|
olass |
last I ran them |
| 14:25 |
|
olass |
maclean: we are not using patches yet |
| 14:26 |
|
maclean |
ok |
| 14:26 |
|
edrin |
i could not figure out why the tests did not work |
| 14:26 |
|
olass |
edrin: part is that cdk cannot parse pdb |
| 14:26 |
|
edrin |
i dont even know what they test ;) |
| 14:26 |
|
edrin |
ah |
| 14:26 |
|
edrin |
ok, this i cannot change |
| 14:27 |
|
olass |
it's a cdk thing |
| 14:27 |
|
olass |
filed for 2.1 |
| 14:28 |
|
olass |
but please make the tests test that the manager actually works for a number of test cases |
| 14:28 |
|
olass |
without using cdk |
| 14:28 |
|
olass |
theu MUST pass in order to make 2.0.0 |
| 14:28 |
|
olass |
but you can test them in other ways |
| 14:28 |
|
edrin |
ok |
| 14:28 |
|
olass |
like e.g. compare to an already downloaded pdb |
| 14:29 |
|
olass |
ok, final call |
| 14:29 |
|
olass |
I am syncing for binary build |
| 14:30 |
|
olass |
all is well so far |
| 14:30 |
|
olass |
have tested a binary on mac |
| 14:30 |
|
olass |
egonw: can you test on linux? |
| 14:30 |
|
egonw |
yes |
| 14:30 |
|
olass |
in 10 mins or so I guess |
| 14:33 |
|
CIA-55 |
bioclipse: ospjuth * r8819 /bioclipse2/trunk/plugins/net.bioclipse.ui/bioclipse.product: Final bioclipse.product for beta2. |
| 14:34 |
|
egonw |
A20090123 -> A20090213 ... subtle... took me some seconds to spot it :) |
| 14:35 |
|
olass |
B |
| 14:35 |
|
CIA-55 |
bioclipse: ospjuth * r8820 /bioclipse2/trunk/plugins/net.bioclipse.ui/bioclipse.product: bioclipse.product now has correct version as well: 2.0.0.B20090213 |
| 14:36 |
|
olass |
egonw: I never learn: are you on 32 bit or 64? |
| 14:36 |
|
egonw |
32 |
| 14:36 |
|
olass |
good |
| 14:40 |
|
olass |
Bioclipse2beta2 is ~63 Mb |
| 14:40 |
|
olass |
for download |
| 14:41 |
|
egonw |
link? |
| 14:42 |
|
egonw |
5 bioclipse paper cites now |
| 14:43 |
|
egonw |
3 self-cites, 1 broad revies, 1 real |
| 14:43 |
|
olass |
on pele |
| 14:43 |
|
egonw |
it's a start |
| 14:43 |
|
olass |
/home/ola/bioclipse/. |
| 14:43 |
|
egonw |
ack |
| 14:43 |
|
olass |
linux version is there in 30 secs |
| 14:43 |
|
olass |
oh no |
| 14:43 |
|
olass |
:-( |
| 14:43 |
|
olass |
6 mins... |
| 14:44 |
|
egonw |
ah, I can see it grow |
| 14:44 |
|
olass |
ok |
| 14:44 |
|
egonw |
50MB to go |
| 14:46 |
|
edrin |
egonw: do you have PMIDs of the articles citing bc ? |
| 14:47 |
|
egonw |
DOIs |
| 14:47 |
|
edrin |
whatever |
| 14:47 |
|
edrin |
links |
| 14:47 |
|
edrin |
url pls |
| 14:47 |
|
egonw |
10.1021/ac070741j |
| 14:47 |
|
edrin |
:) |
| 14:47 |
|
egonw |
no, not even DOIs for all |
| 14:47 |
|
egonw |
WoS is not everything... |
| 14:48 |
|
edrin |
hm |
| 14:48 |
|
edrin |
google fails |
| 14:48 |
|
zarah |
edrin: http://failblog.org/ |
| 14:48 |
|
egonw |
edrin: will email |
| 14:48 |
|
edrin |
:) |
| 14:48 |
|
egonw |
google fails? |
| 14:48 |
|
zarah |
egonw: http://failblog.org/ |
| 14:48 |
|
egonw |
on what? |
| 14:48 |
|
edrin |
with the 10.1021/ac070741j |
| 14:49 |
|
egonw |
why not resolve the normal way: |
| 14:49 |
|
egonw |
dx.doi.org/DOI |
| 14:49 |
|
egonw |
thus: dx.doi.org/10.1021/ac070741j |
| 14:50 |
|
edrin |
ok, got it |
| 14:50 |
|
olass |
egonw: UL finished, please test |
| 14:51 |
|
egonw |
olass: downloading |
| 14:51 |
|
egonw |
ETA: 4m |
| 14:52 |
|
edrin |
egonw, olass: plz read&comment&add to the manuscript outline today/weekend saturday morning, |
| 14:52 |
|
edrin |
i want to compile stuff together |
| 14:52 |
|
egonw |
yes |
| 14:52 |
|
egonw |
edrin: BC2 beta is almost done... |
| 14:52 |
|
edrin |
next week two medics are coming back and need help from me |
| 14:52 |
|
olass |
what do you mean with compile stuff together? |
| 14:52 |
|
egonw |
after that it's a week of a lot of writing.. |
| 14:52 |
|
egonw |
including yours |
| 14:52 |
|
edrin |
ok |
| 14:53 |
|
edrin |
olass: i will add citations, reformat stuff |
| 14:53 |
|
edrin |
update wiki |
| 14:53 |
|
edrin |
prepare wiki rather |
| 14:54 |
|
edrin |
next week an other project will start, and this will consume my time |
| 14:56 |
|
egonw |
olass: ping |
| 14:57 |
|
egonw |
olass: in the welcome screen... the text is in between the background and the icons -> unreadable |
| 14:57 |
|
egonw |
btw, intro++ |
| 14:57 |
|
egonw |
really nice work! |
| 14:58 |
|
edrin |
oh |
| 14:59 |
|
egonw |
installing new features -> points to a general welcome cheat sheet... intentional, or just missing proper cheat sheet? |
| 14:59 |
|
edrin |
thx, got your mail |
| 14:59 |
|
edrin |
egonw: <- |
| 15:00 |
|
egonw |
ack |
| 15:01 |
|
olass |
egonw: that is an eclipse error, nothing we can do about it |
| 15:01 |
|
egonw |
ah, OK |
| 15:01 |
|
egonw |
was just wondering... |
| 15:02 |
|
olass |
egonw: it runs? |
| 15:02 |
|
olass |
in 40 secs you can test the update site |
| 15:03 |
|
egonw |
yes, it runs... |
| 15:03 |
|
egonw |
and I did not spot regressions |
| 15:03 |
|
olass |
any errors? |
| 15:03 |
|
egonw |
extractsmiles.js does not work |
| 15:04 |
|
olass |
file bugs |
| 15:04 |
|
olass |
ut's a beta2 |
| 15:04 |
|
olass |
now I will upload to SF |
| 15:04 |
|
egonw |
yes, sounds like a good plan |
| 15:04 |
|
olass |
have to assume win version works |
| 15:04 |
|
jonalv |
oh hai |
| 15:04 |
|
egonw |
will take forever too :) |
| 15:04 |
|
olass |
yes |
| 15:04 |
|
jonalv |
was there a windows verison? |
| 15:04 |
|
jonalv |
did someone test that one? |
| 15:04 |
|
olass |
no |
| 15:04 |
|
olass |
can you? |
| 15:04 |
|
egonw |
olass: please put them on pele |
| 15:05 |
|
olass |
ok |
| 15:05 |
|
egonw |
all, then I can continue upload |
| 15:05 |
|
jonalv |
yea I can. can I have a link? |
| 15:05 |
|
egonw |
olass: better... |
| 15:05 |
|
egonw |
I'll upload them all... |
| 15:05 |
|
edrin |
extractsmiles.js <- is this run in the jseditor? |
| 15:05 |
|
egonw |
so that you can spend the last 40 minutes on writing a blog item |
| 15:05 |
|
olass |
egonw: yes, that is better |
| 15:05 |
|
egonw |
edrin: yes |
| 15:05 |
|
olass |
great |
| 15:05 |
|
* olass |
is uploading to pele |
| 15:05 |
|
olass |
need to build 3 more versions as well :-) |
| 15:06 |
|
egonw |
right |
| 15:06 |
|
edrin |
egonw: are other .js working in jseditor? |
| 15:06 |
|
olass |
edrin: it is probably an error of the script |
| 15:06 |
|
edrin |
egonw: did it not work because of jseditor? |
| 15:06 |
|
egonw |
edrin: dunno... did not test that |
| 15:06 |
|
edrin |
ok, so other .js are working |
| 15:06 |
|
egonw |
will explore later |
| 15:06 |
|
olass |
jonalv: ETA 6 mins for win version on pele |
| 15:06 |
|
jonalv |
oki |
| 15:07 |
|
olass |
egonw: please test update site |
| 15:07 |
|
olass |
I cannot do it here |
| 15:07 |
|
olass |
seems to work |
| 15:07 |
|
olass |
but no time to DL all |
| 15:07 |
|
egonw |
olass: tested drugbank feature |
| 15:08 |
|
egonw |
that worked fine |
| 15:08 |
|
olass |
please test all |
| 15:08 |
|
edrin |
egonw: did you test it from .js script? |
| 15:08 |
|
egonw |
olass: doing so... |
| 15:09 |
|
egonw |
I do miss a few things |
| 15:09 |
|
egonw |
I think |
| 15:09 |
|
olass |
:-) |
| 15:09 |
|
egonw |
CDK Feature |
| 15:09 |
|
olass |
? |
| 15:09 |
|
olass |
that is not in release |
| 15:09 |
|
egonw |
why not? |
| 15:09 |
|
olass |
mom |
| 15:09 |
|
olass |
but easy to add if you like |
| 15:10 |
|
olass |
does inchi work? |
| 15:10 |
|
olass |
any other feature you are missing? |
| 15:10 |
|
olass |
well, too late ti remove inchi now anyways |
| 15:10 |
|
egonw |
inchi should work fine now |
| 15:11 |
|
olass |
"should" :-) |
| 15:11 |
|
olass |
please test xmpp |
| 15:11 |
|
egonw |
tested it on a few entries in the DrugBank SDF |
| 15:11 |
|
egonw |
the thing why it was failing so much... |
| 15:11 |
|
egonw |
it has a feature to fail on warnings... |
| 15:11 |
|
olass |
test on a file in sampledata with only 2D coordinates |
| 15:11 |
|
egonw |
for example when the input is not clear on stereochemistry |
| 15:12 |
|
egonw |
which it often is not |
| 15:12 |
|
olass |
ok |
| 15:12 |
|
egonw |
and I had it fail on that |
| 15:12 |
|
egonw |
but fixed that |
| 15:12 |
|
egonw |
seems to work fine |
| 15:12 |
|
olass |
good |
| 15:12 |
|
olass |
how is 2D editing? |
| 15:12 |
|
egonw |
good |
| 15:12 |
|
egonw |
I like the moving of selections |
| 15:12 |
|
olass |
I don't |
| 15:12 |
|
egonw |
there are a few remaining issues... |
| 15:12 |
|
olass |
indeed |
| 15:12 |
|
egonw |
like drawing on an empty canvas |
| 15:12 |
|
edrin |
egonw: is the jseditor working "in general" ? |
| 15:13 |
|
olass |
edrin: it send s output to some rhino console instead of JSConsole |
| 15:13 |
|
olass |
bad |
| 15:13 |
|
egonw |
no, JSeditor is not working |
| 15:13 |
|
edrin |
olass: no, not bad, we were discussing this |
| 15:13 |
|
egonw |
Wrapped org.eclipse.core.runtime.AssertionFailedException: null argument: (line: #1) |
| 15:13 |
|
olass |
edrin: did you not test the jseditor? |
| 15:14 |
|
edrin |
i did, it worked for me |
| 15:14 |
|
olass |
exporting to binary? |
| 15:14 |
|
edrin |
egonw> Wrapped org.eclipse.core.runtime.AssertionFailedException: null argument: (line: #1) <- that's an error in the script |
| 15:14 |
|
olass |
egonw: add a new js line |
| 15:14 |
|
olass |
js file |
| 15:14 |
|
olass |
cdk.fromSMILES("CC").getCML() |
| 15:14 |
|
olass |
that worked for me |
| 15:14 |
|
maclean |
olass : you don't like the moving of selections? |
| 15:14 |
|
edrin |
egonw: create a .js file and add xmpp.connect(); |
| 15:15 |
|
maclean |
whyfor not? |
| 15:15 |
|
jonalv |
@pz |
| 15:15 |
|
zarah |
jonalv: Pelezilla is at http://bugs.bioclipse.net |
| 15:15 |
|
egonw |
confirmed |
| 15:15 |
|
olass |
maclean: it should not highlight in outline when a user hovers over an atom |
| 15:15 |
|
egonw |
the scripts are bad |
| 15:15 |
|
egonw |
not the editor |
| 15:15 |
|
olass |
AND |
| 15:15 |
|
edrin |
phuuu |
| 15:15 |
|
egonw |
can't see the difference yet, though |
| 15:15 |
|
maclean |
olass : that's not moving of selections. |
| 15:15 |
|
olass |
ah |
| 15:15 |
|
olass |
ok |
| 15:16 |
|
olass |
hovering over a symbol is not indicated currently |
| 15:16 |
|
olass |
that is a major thing for me |
| 15:16 |
|
maclean |
indicated how? |
| 15:16 |
|
maclean |
it's indicated with a highlight element |
| 15:16 |
|
olass |
hover over a bond -> indicated |
| 15:17 |
|
olass |
hover over an atom not rendered as a symbol -> indicated |
| 15:17 |
|
olass |
hover over an atom rendered as a symbol -> not indicated |
| 15:17 |
|
egonw |
olass: I think that's because the highlite is smaller than the symbol |
| 15:17 |
|
egonw |
I see that now and then too |
| 15:17 |
|
maclean |
yes |
| 15:18 |
|
maclean |
this is why |
| 15:18 |
|
olass |
well, it's bad now |
| 15:18 |
|
maclean |
also, it's underneath |
| 15:19 |
|
edrin |
olass: regarding the "printing to another console issue" we were discussing this, and i think we agreed that it is totally confusing if a scipt prints to the jsconsole |
| 15:19 |
|
olass |
ok, if you and masak agrees on it then I'm fine with it |
| 15:19 |
|
edrin |
i think so |
| 15:19 |
|
edrin |
masak: aruond? |
| 15:19 |
|
edrin |
no |
| 15:19 |
|
olass |
no |
| 15:19 |
|
edrin |
jonalv: do you remember? |
| 15:19 |
|
jonalv |
edrin: no not really |
| 15:20 |
|
olass |
edrin: I'd really like you to make things certain in the future |
| 15:20 |
|
jonalv |
edrin: where shoudl output go then? |
| 15:20 |
|
edrin |
jonalv: on a console for scripts run from editor |
| 15:20 |
|
olass |
edrin: please send email to bioclipse-devel discussing things |
| 15:20 |
|
egonw |
olass: the whitespace of the symbol needs to be transparent... |
| 15:20 |
|
edrin |
i am currently writing one |
| 15:20 |
|
olass |
egonw: I just want it to work |
| 15:20 |
|
olass |
spare me the details :-) |
| 15:21 |
|
* olass |
donät know a thing about 2D drawing |
| 15:21 |
|
jonalv |
edrin: I think I remember saying that you and masak should come up with a solution. Anyway that's what I think now. |
| 15:22 |
|
CIA-55 |
bioclipse: gilleain * r8821 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchempaint.view/src/net/bioclipse/cdk/jchempaint/view/JChemPaintWidget.java: Bumped up the highlight distance to make it visible under atom symbols. |
| 15:22 |
|
olass |
juuuust a bit too late |
| 15:22 |
|
maclean |
egonw: no the symbol has to have an opaque background in order to write over the bonds |
| 15:22 |
|
maclean |
oops |
| 15:23 |
|
maclean |
sorry |
| 15:23 |
|
olass |
egonw: could you please tag? |
| 15:23 |
|
edrin |
i think we said that it makes sense to not queue all scripts in one loop to have the possibility of parallel scripts, and that it makes sense to not print stuff from the editor to the console, because this does not make sense as these are two independent contexts |
| 15:23 |
|
olass |
that last commit will sort of be in the wrong place... |
| 15:24 |
|
olass |
edrin: masak is not here |
| 15:24 |
|
olass |
please use email |
| 15:26 |
|
edrin |
olass: one thing we should change is the two options: run in main thread and run in its own thread, I agree |
| 15:31 |
|
* egonw |
making the tag |
| 15:31 |
|
egonw |
not entirely correct |
| 15:31 |
|
egonw |
as it will contain the two patches from gilleain |
| 15:32 |
|
CIA-55 |
bioclipse: egonw * r8822 /bioclipse2/tags/2.0.0.B20090213/: Tagged the second beta release |
| 15:32 |
|
maclean |
oh well, there's always the rc. :) |
| 15:32 |
|
egonw |
indeed |
| 15:33 |
|
maclean |
and anyway, my last commit brought out a bug in the highlight generator... |
| 15:34 |
|
egonw |
:) |
| 15:35 |
|
maclean |
Gpox didn't say, but do we really want a circle per bond for the highlight? |
| 15:35 |
|
maclean |
it kind of makes a lozenge shape for double bonds |
| 15:35 |
|
egonw |
one single oval, I'd say |
| 15:35 |
|
maclean |
ah good - that's what I've just changed it to :) |
| 15:36 |
|
maclean |
(sorry Gpox...) |
| 15:36 |
|
Gpox |
no it was just to visulaize the highlight radius trying to fix the context menu |
| 15:37 |
|
Gpox |
It used to use the bond generator and change the width |
| 15:37 |
|
Gpox |
dunno where that whent |
| 15:38 |
|
maclean |
it was making an anonymous visitor, and visiting all the generated line elements, then making an oval element for each |
| 15:38 |
|
egonw |
olass: don't forget the solaris version |
| 15:38 |
|
jonalv |
olass: ETA Windows version? |
| 15:38 |
|
egonw |
jonalv: -10m |
| 15:39 |
|
egonw |
jonalv: on pele |
| 15:39 |
|
maclean |
but, the main thing was that most parameters are now specified in screen space, and then scaled down to model space when needed |
| 15:39 |
|
egonw |
home/ola/bioclipse/bioclipse-2.0.0.B20090213.win32.win32.x86.zip |
| 15:39 |
|
maclean |
like double highlightRadiusModel = model.getHighlightDistance() / model.getScale() |
| 15:39 |
|
jonalv |
in ten minutes? |
| 15:39 |
|
egonw |
no, 10minutes ago |
| 15:39 |
|
jonalv |
oh |
| 15:40 |
|
* jonalv |
stops waiting then :) |
| 15:40 |
|
egonw |
:) |
| 15:44 |
|
egonw |
beta2 uploaded to SF |
| 15:45 |
|
egonw |
win32, os/x, linux, 32bit only at this moment |
| 15:45 |
|
egonw |
olass: can we still expect 64bit and solaris flavors? |
| 15:48 |
|
maclean |
oh! |
| 15:48 |
|
maclean |
it's Friday 13th |
| 15:49 |
|
maclean |
no wonder I forgot my passcard... |
| 15:49 |
|
jonalv |
hm the jchempaint teditor is named cml file editor. Is that really correct? Can it handle a cml file with multiple molecules? Can it handle a cml file with a spectrum? egonw ? |
| 15:49 |
|
egonw |
see wiki.bioclipse.net |
| 15:49 |
|
egonw |
no, it cannot |
| 15:49 |
|
maclean |
cml file with mol+spectrum = specmol? |
| 15:49 |
|
edrin |
jonalv: is the jseditor working for you? |
| 15:49 |
|
egonw |
it's still CML |
| 15:50 |
|
egonw |
it's *a* CMLEditor |
| 15:50 |
|
egonw |
not *the* CMLEditor |
| 15:50 |
|
jonalv |
edrin: I only tried the js scripts in the example. They seems outdated.. :( |
| 15:50 |
|
edrin |
jonalv: what means outdated? maybe i did something wrong? |
| 15:50 |
|
edrin |
jonalv: i wrote a mail to the dev listregarding scripting and the dynamic import? |
| 15:51 |
|
jonalv |
edrin: yes? |
| 15:51 |
|
edrin |
jonalv: does this explain why we need this dynamic addition of libs |
| 15:51 |
|
edrin |
? |
| 15:51 |
|
* jonalv |
reads edrins mail.... |
| 15:52 |
|
jonalv |
edrin: "Julian Kölle"? (How many names do you have?) |
| 15:52 |
|
edrin |
this is my mailing list mail |
| 15:54 |
|
maclean |
huh. 'switch workspace' now works...sortof...except that it doesn't seem to actually switch |
| 15:54 |
|
olass |
cool |
| 15:54 |
|
olass |
maclean: file a bug for shk3 |
| 15:54 |
|
maclean |
ok |
| 15:54 |
|
CIA-55 |
bioclipse: ospjuth * r8823 /bioclipse2/trunk/features/net.bioclipse.cdk_feature/feature.xml: Updated version for release. |
| 15:55 |
|
jonalv |
edrin: yea, but I am afraid I personally don't know what to do... |
| 15:56 |
|
edrin |
it is a really complicated thing |
| 16:02 |
|
egonw |
olass: can we commit to trunk again? |
| 16:02 |
|
olass |
have you tagged? |
| 16:02 |
|
* jonalv |
feels that he already has his hands in enough complicated stuff with AOP and managers in Bioclipse... |
| 16:03 |
|
egonw |
maclean, Gpox: I hacked up a pref page for JCP with the default bond color, but it is not hooked up to the JCP manager yet |
| 16:03 |
|
egonw |
olass: yes |
| 16:03 |
|
olass |
please go ahead |
| 16:03 |
|
maclean |
ok |
| 16:03 |
|
* olass |
is uploading files to pele |
| 16:03 |
|
* olass |
is also writing a blog post to announce bioclipse2-beta2 |
| 16:03 |
|
egonw |
olass: good |
| 16:04 |
|
egonw |
I'll post them to SF then... |
| 16:04 |
|
olass |
will be very similar to beta1 :-) |
| 16:04 |
|
olass |
yup |
| 16:04 |
|
egonw |
good :) |
| 16:04 |
|
olass |
great |
| 16:04 |
|
egonw |
olass: make sure to mention: |
| 16:04 |
|
egonw |
the new welcome page |
| 16:04 |
|
olass |
indeed |
| 16:04 |
|
CIA-55 |
bioclipse: egonw * r8824 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchempaint/ (5 files in 2 dirs): Added template for JCP preferences |
| 16:04 |
|
egonw |
the new demo data |
| 16:04 |
|
egonw |
and the lots of bugs fixed since beta |
| 16:04 |
|
egonw |
1 |
| 16:05 |
|
CIA-55 |
bioclipse: egonw * r8825 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchempaint/src/net/bioclipse/cdk/jchempaint/preferences/ (JChemPaintPreferencePage.java PreferenceConstants.java): Preference bond color (not linked to the JCPManager yet...) |
| 16:05 |
|
egonw |
olass: you did the solaris one too? |
| 16:05 |
|
egonw |
sparc or i386 (or even both)? |
| 16:06 |
|
* egonw |
will soon install OpenSolaris on a virtual machine |
| 16:07 |
|
olass |
sparc |
| 16:07 |
|
olass |
yes, I did |
| 16:07 |
|
olass |
eclipse only supports sparc/gtk2 it seems |
| 16:07 |
|
maclean |
hmmm egonw: PreferenceConstants.P_BOOLEAN not found |
| 16:08 |
|
olass |
egonw: please test update site again, added cdk feature |
| 16:09 |
|
egonw |
maclean: ack, comtting fix now |
| 16:09 |
|
egonw |
olass: ack |
| 16:09 |
|
maclean |
oki |
| 16:09 |
|
CIA-55 |
bioclipse: egonw * r8826 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchempaint/src/net/bioclipse/cdk/jchempaint/preferences/PreferenceInitializer.java: Compile fix... refactor/rename of field clearly had not worked :( |
| 16:10 |
|
egonw |
URL of the second update site? |
| 16:10 |
|
egonw |
is that update2? |
| 16:10 |
|
egonw |
that's the bioclipse2 update site, right? |
| 16:10 |
|
egonw |
should I use that one? |
| 16:11 |
|
egonw |
ah, indeed |
| 16:11 |
|
egonw |
I see the CDK Feature now |
| 16:15 |
|
jonalv |
hm there is a Services menu un the top menu now. It has a Biocinformatics service called clustalwLocal. This seems a bit strange... |
| 16:18 |
|
* egonw |
is going to make a walk |
| 16:19 |
|
egonw |
olass: please email any left over jobs regarding the release... |
| 16:19 |
|
egonw |
I'll do the remaining upload to SF anyway... |
| 16:19 |
|
egonw |
but if there is other stuff... just email me |
| 16:19 |
|
jonalv |
egonw: are there new tags in pelezilla for bugs in the new release? |
| 16:19 |
|
egonw |
jonalv: good one... |
| 16:19 |
|
egonw |
please file a bug report... |
| 16:19 |
|
egonw |
will add those later tonite too |
| 16:19 |
|
jonalv |
lol |
| 16:19 |
|
jonalv |
oki |
| 16:22 |
|
olass |
egonw++ |
| 16:30 |
|
CIA-55 |
bioclipse: gilleain * r8827 /bioclipse2/trunk/cdk-externals/trunk/org.openscience.cdk.render/src/org/openscience/cdk/renderer/generators/HighlightGenerator.java: Single oval per bond, scaled to suit the screen. |
| 16:40 |
|
CIA-55 |
bioclipse: gilleain * r8828 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchempaint.view/src/net/bioclipse/cdk/jchempaint/view/JChemPaintWidget.java: Use the default parameters as much as possible. |
| 16:48 |
|
edrin |
jonalv: egonw managed to get a Wrapped exception in the current beta, [16:13:18] <egonw> Wrapped org.eclipse.core.runtime.AssertionFailedException: null argument: (line: #1) |
| 16:49 |
|
edrin |
jonalv: you can ask him how he did it |
| 16:49 |
|
edrin |
jonalv: you could also try a script with the following content: |
| 16:49 |
|
edrin |
xmpp.connect(); |
| 16:50 |
|
edrin |
(in a .js file run with the jseditor) |
| 16:50 |
|
edrin |
as you probably do not have account data set, it will throw an exception ... |
| 16:50 |
|
jonalv |
edrin: but what does the editor do to create those exceptions and do we want that in the console somehow? |
| 16:51 |
|
edrin |
the exceptions are not from the editor, they are from the script |
| 16:51 |
|
edrin |
meaning, a manager call throws an exception because the there was an error |
| 16:52 |
|
jonalv |
yea but what wraps it_ |
| 16:52 |
|
edrin |
it is wraped with an excpetion thrown by the rhino context i think |
| 16:53 |
|
edrin |
you push in a script in rhino, rhino compiles and runs it, rhino detects exceptions in the script, aborts, and throws its own exception that wraps the exception in the scripts |
| 16:53 |
|
edrin |
did i get it? |
| 16:53 |
|
jonalv |
okey so perhaps we are unwrapping them? |
| 16:54 |
|
edrin |
you mean remove the "wrap" in the text line? |
| 16:54 |
|
edrin |
in sense of 'cosmetics' ;) ? |
| 16:55 |
|
jonalv |
what? No I don't know... |
| 16:55 |
|
edrin |
"perhaps we are unwrapping them" this is what i did not get |
| 16:56 |
|
jonalv |
I mean perhaps masak unwrapped them in his console... |
| 16:57 |
|
edrin |
and what comes out then? |
| 16:57 |
|
edrin |
jonalv: what happens if you type xmpp.connect() in the console ? |
| 16:57 |
|
jonalv |
you get: Could not create default client: the plug-in has set invalide account data in |
| 16:57 |
|
jonalv |
preferences. |
| 16:57 |
|
jonalv |
that is the message |
| 16:57 |
|
jonalv |
which is sort of what we thought was the best idea... |
| 16:57 |
|
jonalv |
perhaps it is not... |
| 17:00 |
|
edrin |
well |
| 17:00 |
|
edrin |
i think for a console it is good |
| 17:00 |
|
edrin |
because a console is more interactive than a script |
| 17:01 |
|
jonalv |
yes |
| 17:02 |
|
edrin |
if one is writing a more complex script the user most likely knows some background of the API he/she is using, more detailed info is helpful here |
| 17:03 |
|
jonalv |
yup |
| 17:03 |
|
jonalv |
I am giving up now. cya. |
| 17:03 |
|
edrin |
CU |
| 17:03 |
|
edrin |
cu |
| 17:03 |
|
edrin |
caps |
| 17:35 |
|
CIA-55 |
bioclipse: gilleain * r8829 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchempaint/src/net/bioclipse/cdk/jchempaint/business/ (IJChemPaintManager.java JChemPaintManager.java): Rendering options methods. |
| 17:51 |
|
maclean |
feck |
| 18:05 |
|
egonw |
maclean: I'll check that 8829 patch tonite and hack it up with the prefs page in bc2 |
| 19:26 |
|
edrin |
egonw: what are you currently doing? |
| 19:26 |
|
edrin |
isn't the release already released? |
| 19:26 |
|
edrin |
/the beta |
| 19:27 |
|
egonw |
doing some last BC2 uploads... |
| 19:27 |
|
egonw |
no, there are many tastes now... |
| 19:27 |
|
egonw |
e.g. OS/X for PPC, Solaris for Sparc |
| 19:27 |
|
edrin |
tastes? |
| 19:27 |
|
edrin |
tasks? |
| 19:27 |
|
edrin |
ah ok |
| 19:27 |
|
edrin |
fucking experiment failed! |
| 19:29 |
|
egonw |
https://sourceforge.net/projec[…]release_id=660851 |
| 19:29 |
|
egonw |
7 different downloads |
| 19:43 |
|
|
maclean joined #bioclipse |
| 19:44 |
|
edrin |
cu later guy |
| 19:44 |
|
edrin |
guys |
| 19:44 |
|
|
edrin left #bioclipse |
| 19:58 |
|
CIA-55 |
bioclipse: gilleain * r8830 /bioclipse2/trunk/ (21 files in 5 dirs): Minor changes to accommodate cleanup of RendererModel use by generators. |
| 20:10 |
|
maclean |
hmmm. no margin. |
| 20:28 |
|
CIA-55 |
bioclipse: gilleain * r8831 /bioclipse2/trunk/cdk-externals/trunk/org.openscience.cdk.render/src/org/openscience/cdk/renderer/ (RendererModel.java RenderingParameters.java): Make the atom radius (used for compact atom elements) a double rather than an int. |
| 20:29 |
|
CIA-55 |
bioclipse: gilleain * r8832 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchempaint/src/net/bioclipse/cdk/jchempaint/business/ (IJChemPaintManager.java JChemPaintManager.java): Atom radius should be a double, not an int. |
| 20:31 |
|
CIA-55 |
bioclipse: gilleain * r8833 /bioclipse2/trunk/cdk-externals/trunk/org.openscience.cdk.render/src/org/openscience/cdk/renderer/Renderer.java: Respect the model margin parameter. |
| 20:36 |
|
egonw |
hi maclean |
| 20:36 |
|
maclean |
hi |
| 20:36 |
|
maclean |
been adding stuff |
| 20:36 |
|
egonw |
yes, noticed |
| 20:36 |
|
egonw |
was doing some pelezilla admin stuff... |
| 20:36 |
|
egonw |
fixing the Version field |
| 20:36 |
|
maclean |
oh right |
| 20:37 |
|
egonw |
you did not like reflection right... then don't read Jim's blog: |
| 20:37 |
|
egonw |
http://wwmm.ch.cam.ac.uk/blogs/downing/?p=289 |
| 20:37 |
|
zarah |
egonw's link is also http://tinyurl.com/dbxtf8 |
| 20:38 |
|
maclean |
ooh argh! my precious eyes! |
| 20:38 |
|
maclean |
reflection = good |
| 20:38 |
|
maclean |
reflection in java = aargh! |
| 20:39 |
|
maclean |
it's just so hard to read, and that makes it dangerous |
| 20:39 |
|
egonw |
true |
| 20:40 |
|
* egonw |
is trying to figure out how to hook up the pref page with the new JCPmanager commands |
| 20:40 |
|
maclean |
ah, right yes I forgot to d othat |
| 20:40 |
|
maclean |
btw, if you see any missing preferences, say now |
| 20:40 |
|
egonw |
now? |
| 20:40 |
|
egonw |
next week fine too? |
| 20:41 |
|
maclean |
well, sure :) |
| 20:41 |
|
egonw |
I think I found something... |
| 20:41 |
|
maclean |
I just meant that now's a good opportunity |
| 20:41 |
|
egonw |
btw, these pref pages are brilliant... |
| 20:41 |
|
egonw |
so looking forward to just making a JChemPaint branding of bioclipse |
| 20:43 |
|
maclean |
Rajarshi is driving forward usability of the code :) |
| 20:43 |
|
egonw |
yes, he had quite some experience with the old renderer |
| 20:43 |
|
egonw |
good to have them do test driving... |
| 20:43 |
|
egonw |
btw, I (electronically) met today a PhD in Stockholm (BO ML) |
| 20:43 |
|
egonw |
who did a basic chemical editor: |
| 20:43 |
|
maclean |
oh? |
| 20:44 |
|
egonw |
really basic |
| 20:45 |
|
maclean |
I think every chemist who programs makes a chemical editor at some point |
| 20:45 |
|
egonw |
yes, guess so :) |
| 20:45 |
|
maclean |
now, with the cdk, they can all do it more easily! |
| 20:45 |
|
maclean |
:) |
| 20:47 |
|
egonw |
indeed |
| 20:47 |
|
egonw |
we'll need to start writing some tutorials... |
| 20:48 |
|
egonw |
maybe something for a tutorial at the CDK workshop... |
| 20:48 |
|
egonw |
btw, I'll start a "Bioclipse for CDK Developers" series in my blog... |
| 20:48 |
|
maclean |
well, I will try and re-write these essay emails I've been sending to the list. |
| 20:48 |
|
egonw |
:) |
| 20:48 |
|
egonw |
or convert them to CDK News papers |
| 20:48 |
|
maclean |
I think a nice test case would be an editor for peptides. |
| 20:49 |
|
egonw |
that reminds me... |
| 20:49 |
|
egonw |
we need a template mode... |
| 20:49 |
|
egonw |
with a nice Bioclipse View with a list of templates... |
| 20:50 |
|
egonw |
just a MOleculesTable |
| 20:50 |
|
maclean |
oh definitely |
| 20:50 |
|
egonw |
or maybe buttons... |
| 20:50 |
|
egonw |
depending on the size... |
| 20:50 |
|
egonw |
mmm... |
| 20:50 |
|
maclean |
hmm. auto-generated buttons? |
| 20:50 |
|
egonw |
possibly |
| 20:51 |
|
egonw |
ah, missing prop: default bond color |
| 20:51 |
|
egonw |
or am I overlooking that one? |
| 20:51 |
|
maclean |
ah, yes, I've missed out colors |
| 20:51 |
|
egonw |
it's the one field I actually now have in the pref page :) |
| 20:51 |
|
maclean |
I didn't know how those would work on the command line |
| 20:51 |
|
egonw |
indeed |
| 20:51 |
|
maclean |
maybe they shouldn't be published? |
| 20:51 |
|
egonw |
I have jcp.newPoint2d(x,y) |
| 20:52 |
|
egonw |
I can imagine a jcp.newColor(R,G,B) |
| 20:52 |
|
maclean |
true |
| 20:53 |
|
egonw |
and font? |
| 20:53 |
|
egonw |
is that available? |
| 20:53 |
|
maclean |
ah no |
| 20:53 |
|
maclean |
only double and bool ones |
| 20:53 |
|
maclean |
jcp.makeFont? |
| 20:53 |
|
egonw |
will get back on that... |
| 20:53 |
|
egonw |
not sure what FontFieldEditor has :) |
| 20:54 |
|
maclean |
ooh h-bonds |
| 20:54 |
|
egonw |
yes, that would be nice too... |
| 20:54 |
|
egonw |
HBondGenerator |
| 20:54 |
|
egonw |
but no support for that in the CDK just yet |
| 20:54 |
|
egonw |
post 1.2 |
| 20:54 |
|
maclean |
sure |
| 20:54 |
|
egonw |
grmp... |
| 20:54 |
|
egonw |
I really need to get that release out... |
| 20:57 |
|
maclean |
oops message to cdk-jcp list bounced :) |
| 20:57 |
|
egonw |
I can approve |
| 20:57 |
|
egonw |
shall I? |
| 20:58 |
|
egonw |
or not? |
| 20:58 |
|
egonw |
it's the size... |
| 20:58 |
|
egonw |
it did not bounce... it's merely on hold for manual approval... |
| 20:58 |
|
maclean |
nah, don't bother - I forwared it to rajarshi |
| 20:58 |
|
egonw |
OK, I just have to hit the button |
| 20:58 |
|
maclean |
oh right, thatnks |
| 20:58 |
|
egonw |
well, it has nice screenies... |
| 20:59 |
|
egonw |
accepted |
| 20:59 |
|
maclean |
\o/ |
| 21:00 |
|
maclean |
right, I'm off to watch NCIS, have a good evening egonw |
| 23:58 |
|
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edrin joined #bioclipse |
