| Time |
S |
Nick |
Message |
| 05:15 |
|
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sneumann joined #bioclipse |
| 05:56 |
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egonw joined #bioclipse |
| 06:24 |
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jonalv joined #bioclipse |
| 06:49 |
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sneumann joined #bioclipse |
| 07:01 |
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Gpox joined #bioclipse |
| 07:25 |
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annzi joined #bioclipse |
| 07:40 |
|
jonalv |
Gpox: |
| 07:40 |
|
jonalv |
Gpox: ping |
| 07:40 |
|
Gpox |
pong |
| 07:41 |
|
jonalv |
Gpox: I am trying the jchempaint editor in 2.4.0.RC1 |
| 07:41 |
|
jonalv |
I don't seem to be able to save |
| 07:41 |
|
|
olass joined #bioclipse |
| 07:41 |
|
jonalv |
on Ubuntu I got an error message on mac nothing happends |
| 07:41 |
|
olass |
moin |
| 07:41 |
|
zarah |
saluton olass |
| 07:45 |
|
Gpox |
jonalv: bug report? is in only when you save as? |
| 07:46 |
|
jonalv |
@pz 1975 |
| 07:46 |
|
zarah |
http://pele.farmbio.uu.se/cgi-[…]w_bug.cgi?id=1975 |
| 07:46 |
|
jonalv |
Gpox: den |
| 07:55 |
|
olass |
jonalv++ //I never thanked you for the release! |
| 07:56 |
|
jonalv |
:) |
| 07:56 |
|
olass |
good job! |
| 07:56 |
|
* jonalv |
is oin bug hunt now. olass will you join me? |
| 07:56 |
|
olass |
did you tag also? |
| 07:56 |
|
* olass |
is already hunting |
| 07:56 |
|
jonalv |
olass: yes I created tags |
| 07:56 |
|
* olass |
will also be in tel conf for most of the day |
| 07:56 |
|
jonalv |
they are in my forks |
| 07:57 |
|
olass |
as it should be |
| 07:57 |
|
olass |
pull reqs? |
| 07:57 |
|
jonalv |
olass: right yea I should maybe send such |
| 07:57 |
|
olass |
please push for core (if you have not done that) |
| 07:57 |
|
olass |
or send patches |
| 07:57 |
|
olass |
either or |
| 07:58 |
|
jonalv |
but to be honest I think it's too much work sending pull requests to everyone |
| 07:58 |
|
* jonalv |
is looking forwards to the bioclipse account on github |
| 07:58 |
|
olass |
I agree |
| 07:59 |
|
olass |
we'll set that up when I get back |
| 07:59 |
|
olass |
jonalv: since I will leave for holiday, is it OK if I assign some new bugs to you (instead of myself as before) so they don't get lost? |
| 07:59 |
|
olass |
previously I kept many bugs for later |
| 07:59 |
|
jonalv |
olass: hm hopw much work is it, do you think we could do it? |
| 07:59 |
|
olass |
let's do it when I get back please |
| 07:59 |
|
olass |
I want to be in on this |
| 08:00 |
|
jonalv |
:) |
| 08:00 |
|
jonalv |
olass: yea I guess I can take the bugs |
| 08:00 |
|
olass |
for distribution I mean |
| 08:00 |
|
jonalv |
I will try to get rid of them... :) |
| 08:00 |
|
olass |
not that you should solve them all :) |
| 08:00 |
|
olass |
hehe |
| 08:22 |
|
Gpox |
grr |
| 08:25 |
|
jonalv |
Gpox: huh? |
| 08:25 |
|
olass |
lejon? |
| 08:25 |
|
Gpox |
logger.setLevel(Level.INFO); |
| 08:25 |
|
Gpox |
logger.setLevel(Level.INFO); |
| 08:25 |
|
Gpox |
@pz 1975 |
| 08:25 |
|
zarah |
http://pele.farmbio.uu.se/cgi-[…]w_bug.cgi?id=1975 |
| 08:26 |
|
Gpox |
it uses setLevel which caues the error but the logger isn't even used in anywhere in that class |
| 08:59 |
|
Gpox |
jonalv: I can take bug 1977 if you are not working on it |
| 08:59 |
|
jonalv |
@pz 1977 |
| 08:59 |
|
zarah |
http://pele.farmbio.uu.se/cgi-[…]w_bug.cgi?id=1977 |
| 08:59 |
|
jonalv |
Gpox: please go ahead :) |
| 09:00 |
|
Gpox |
allready see the error, new Shell() |
| 09:00 |
|
jonalv |
okcool, Gpox++ |
| 09:29 |
|
CIA-69 |
bioclipse.ds: Ola Spjuth jcp-moltable-events * r35309a1 / plugins/net.bioclipse.ds.ui/src/net/bioclipse/ds/ui/views/Eventview.java : Fixed events. - http://bit.ly/9imk0h |
| 09:31 |
|
|
annzi joined #bioclipse |
| 09:34 |
|
|
masak joined #bioclipse |
| 09:39 |
|
|
egonw joined #bioclipse |
| 09:39 |
|
egonw |
annzi: http://github.com/egonw/chembl.rdf |
| 09:39 |
|
zarah |
egonw's link is also http://tinyurl.com/ygu5bqw |
| 09:39 |
|
egonw |
moin all |
| 09:39 |
|
zarah |
saluton egonw |
| 09:45 |
|
masak |
public static void moin(String[] _) {} |
| 09:56 |
|
CIA-69 |
bioclipse.moss: Egon Willighagen 1-mossProps * rcbceb48 / plugins/net.bioclipse.moss.business/src/net/bioclipse/moss/business/props/MossProperties.java : Added template properties class. (+48 more commits...) - http://bit.ly/93pxPT |
| 09:57 |
|
egonw |
jonalv: RC1 is not based on CDK 1.3.5 |
| 09:57 |
|
egonw |
or is it? |
| 09:57 |
|
* egonw |
is confused... |
| 09:57 |
|
jonalv |
egonw: beats me I just copied olass text... :) |
| 09:58 |
|
jonalv |
egonw: will you test the Ubuntu version? |
| 09:58 |
|
egonw |
jonalv-- (for not thinking for himself) |
| 09:58 |
|
egonw |
jonalv: yes, I guess so |
| 09:58 |
|
jonalv |
cool |
| 09:59 |
|
* jonalv |
@ lunch |
| 10:28 |
|
CIA-69 |
bioclipse.moss: annzi master * re3a7fe7 / plugins/net.bioclipse.moss.business/plugin.xml : removed duplicated line (+16 more commits...) - http://bit.ly/cHu6Tb |
| 10:56 |
|
egonw |
all: do we have plugins, bundles, or whatever, for JFreeChart? |
| 11:04 |
|
olass |
egonw: we have that in net.b.chart plugin I think |
| 11:05 |
|
olass |
maybe we should refactor this out to a net.b.jfreechart plugin, with unpacked jars |
| 11:05 |
|
olass |
Gpox: what do you suggest? |
| 11:05 |
|
egonw |
yeah, annzi is using it too |
| 11:05 |
|
olass |
and I am using it in HIVDRC plugins |
| 11:05 |
|
egonw |
:) |
| 11:06 |
|
olass |
on the other hand, the net.bc.chart can reexport the packages |
| 11:06 |
|
olass |
but I guess it is nic eto have a proper plugin for jfreechart |
| 11:06 |
|
egonw |
I rather see separate bundels, personally... |
| 11:06 |
|
egonw |
indeed |
| 11:08 |
|
Gpox |
http://www.springsource.com/re[…]hQuery=jfreechart |
| 11:08 |
|
zarah |
Gpox's link is also http://tinyurl.com/2dtvlae |
| 11:08 |
|
egonw |
no newer version? |
| 11:08 |
|
egonw |
.chart uses .10 |
| 11:09 |
|
olass |
add to TP? |
| 11:09 |
|
egonw |
anzzi has .13 |
| 11:09 |
|
Gpox |
probably |
| 11:10 |
|
Gpox |
1.0.13 latest version |
| 11:10 |
|
egonw |
right |
| 11:15 |
|
CIA-69 |
bioclipse.moss: Egon Willighagen master * r6ca7ac4 / plugins/net.bioclipse.moss.business/src/net/bioclipse/moss/business/chemblMoss/ui/Activator.java : Removed redundant file - http://bit.ly/9PkewG |
| 11:15 |
|
CIA-69 |
bioclipse.moss: Egon Willighagen master * r3a1a4f2 / plugins/net.bioclipse.moss.business/src/net/bioclipse/moss/business/MossManager.java : Fixed layout of copyright header - http://bit.ly/atsuOV |
| 11:48 |
|
CIA-69 |
bioclipse.cheminformatics: Arvid Berg 2.4.x * r4c6cbd4 / (4 files): |
| 11:48 |
|
CIA-69 |
bioclipse.cheminformatics: Changed handler to use shell from event. |
| 11:48 |
|
CIA-69 |
bioclipse.cheminformatics: Also did some cleanup of the code to simplify the introduction of the shell parameter. |
| 11:48 |
|
CIA-69 |
bioclipse.cheminformatics: Solves bug 1977 - http://bit.ly/9YmLFq |
| 11:48 |
|
zarah |
bug #1977 | http://tinyurl.com/3anjq6y |
| 11:50 |
|
|
jonalv joined #bioclipse |
| 12:15 |
|
CIA-69 |
bioclipse.moss: Egon Willighagen master * rd951313 / plugins/net.bioclipse.moss.business/src/net/bioclipse/moss/business/MossManager.java : Removed unused import - http://bit.ly/aD6J0G |
| 12:15 |
|
CIA-69 |
bioclipse.moss: Egon Willighagen master * r9ca920c / plugins/net.bioclipse.moss.business/META-INF/MANIFEST.MF : Dependencies on Bioclipse functionality should use Bundle-Depends, not Import-Pacakge - http://bit.ly/dcQUmD |
| 12:15 |
|
CIA-69 |
bioclipse.moss: Egon Willighagen master * r08249a4 / features/net.bioclipse.moss_feature/feature.xml : Added current ChEMBL dependency - http://bit.ly/cSnsPM |
| 12:15 |
|
CIA-69 |
bioclipse.moss: Egon Willighagen master * r5e17e13 / features/net.bioclipse.moss_feature/moss.product : Updated the MoSS product definition - http://bit.ly/8XgJDu |
| 12:31 |
|
egonw |
jonalv: bug report |
| 12:31 |
|
egonw |
BioclipseExceptions do not get nicely displayed in the console |
| 12:31 |
|
egonw |
but it dumps a javax.script.ScriptException instead |
| 12:32 |
|
egonw |
javax.script.ScriptException: sun.org.mozilla.javascript.WrappedException: |
| 12:32 |
|
egonw |
Wrapped java.lang.reflect.UndeclaredThrowableException (<Unknown source>#1) in |
| 12:32 |
|
egonw |
<Unknown source> at line number 1 |
| 12:33 |
|
jonalv |
egonw: is that what's going on? |
| 12:33 |
|
jonalv |
egonw: how can I reproduce easily? |
| 12:42 |
|
jonalv |
egonw: do you have a minute? |
| 12:42 |
|
jonalv |
I can't reproduce |
| 12:43 |
|
egonw |
yes, in 5 minutes or so... |
| 12:57 |
|
jonalv |
olass: regarding 1210 |
| 12:57 |
|
jonalv |
@pz 1210 |
| 12:57 |
|
zarah |
http://pele.farmbio.uu.se/cgi-[…]w_bug.cgi?id=1210 |
| 12:57 |
|
jonalv |
olass: what is the problem? |
| 12:58 |
|
egonw |
annzi: moss.createMoSSProperties(moss.createMoSSProperties().toString()) |
| 12:58 |
|
egonw |
roundtripping moss properties in JSON :) |
| 13:06 |
|
CIA-69 |
bioclipse.moss: Egon Willighagen master * rba13b12 / (3 files in 2 dirs): Implemented roundtripping of moss properties in JSON (+6 more commits...) - http://bit.ly/bD2YvE |
| 13:17 |
|
egonw |
jonalv: no, adding throws BioclipseException to the IMossManager interface does not help |
| 13:17 |
|
jonalv |
as expected |
| 13:18 |
|
egonw |
there *is* another diff |
| 13:18 |
|
egonw |
fromSMILES has an alternative in the interface with a hook |
| 13:18 |
|
jonalv |
mhm? |
| 13:18 |
|
jonalv |
whic one is being run? |
| 13:19 |
|
egonw |
no idea |
| 13:19 |
|
CIA-69 |
bioclipse.moss: Egon Willighagen master * rd012a82 / plugins/net.bioclipse.moss.business/src/net/bioclipse/moss/business/IMossManager.java : Methods throws an BioclipseException: added this info to the interface too now - http://bit.ly/a25yne |
| 13:19 |
|
egonw |
how can I tell? |
| 13:19 |
|
egonw |
olass: ping |
| 13:19 |
|
jonalv |
egonw: debug? System.out.println, logger.Debug... |
| 13:20 |
|
jonalv |
egonw: maybe it's time to add debug flag to the dispatcher? |
| 13:20 |
|
egonw |
yes, interesting idea! |
| 13:20 |
|
egonw |
jonalv++ |
| 13:20 |
|
jonalv |
olass: ping |
| 13:21 |
|
egonw |
I was first |
| 13:21 |
|
egonw |
olass: implemented bioclipse.isOnline() |
| 13:21 |
|
jonalv |
egonw: actually no I don't thin so |
| 13:21 |
|
egonw |
patch or direct commit? |
| 13:21 |
|
egonw |
true, if you count that questions half an hour ago |
| 13:21 |
|
egonw |
-s |
| 13:21 |
|
egonw |
singluar |
| 13:22 |
|
egonw |
> bioclipse.isOnline() |
| 13:22 |
|
jonalv |
egonw: it's the same question I am waiting for an answer on... |
| 13:22 |
|
egonw |
true |
| 13:22 |
|
egonw |
@pz online |
| 13:22 |
|
zarah |
[1398] Generate HTML from update sites http://tinyurl.com/32vb3kz |
| 13:22 |
|
zarah |
[1411] XML-feature is not operational http://tinyurl.com/nlswk5 |
| 13:22 |
|
zarah |
[343] Task list in Bioclipse for sett... http://tinyurl.com/3ydypjq |
| 13:22 |
|
zarah |
[319] Server for automatic builds wit... http://tinyurl.com/37r8ho2 |
| 13:22 |
|
zarah |
Entire list at http://tinyurl.com/3x3k7cb |
| 13:22 |
|
egonw |
@pz isOnline |
| 13:22 |
|
zarah |
egonw: I couldn't find anything on 'isOnline' in the database. |
| 13:25 |
|
egonw |
olass: please let me know if I can commit the bioclipse.isOnline() functionality |
| 13:33 |
|
|
samuell joined #bioclipse |
| 13:36 |
|
jonalv |
egonw, Gpox: Who wrote "snapshoot" for Jchempaint? |
| 13:36 |
|
olass |
egonw: please do |
| 13:36 |
|
olass |
jonalv: pong |
| 13:37 |
|
jonalv |
olass: please explain what your oroblem is with the updates site dialog |
| 13:37 |
|
olass |
I don't see the apply /restore to default buttons until I resize the dialog |
| 13:38 |
|
olass |
jonalv: ping me if you'd like a screenshot |
| 13:38 |
|
jonalv |
olass: hm that is strange |
| 13:38 |
|
Gpox |
jonalv: I did |
| 13:38 |
|
jonalv |
olass: I can confirm that behavior |
| 13:39 |
|
jonalv |
Gpox: was it not possible to use png? jpg is very ugly... |
| 13:42 |
|
jonalv |
olass: why is it? It is only on mac, on Windows it looks good and also on Ubuntu |
| 13:43 |
|
CIA-69 |
bioclipse.core: Egon Willighagen 2.4.x * ra1eb48b / (2 files): Implemented bioclipse.isOnline() - http://bit.ly/9nSQI1 |
| 13:49 |
|
|
samuell left #bioclipse |
| 13:50 |
|
Gpox |
jonalv: fixed |
| 13:50 |
|
jonalv |
Gpox: fixed what? |
| 13:51 |
|
Gpox |
png |
| 13:51 |
|
jonalv |
ah sweet |
| 13:53 |
|
egonw |
olass: and did you see I rebased that qsar patch? |
| 13:54 |
|
olass |
no, but thanks |
| 13:54 |
|
olass |
in the bug? |
| 13:54 |
|
egonw |
Gpox: why not use the IFile file for defining a better image.png file name? |
| 13:55 |
|
egonw |
olass: yeah, in the same report |
| 13:55 |
|
egonw |
Gpox: oh... you are |
| 13:55 |
|
egonw |
Gpox: nvm :) |
| 13:55 |
|
egonw |
stupid diffs only showing a small snippet |
| 13:56 |
|
CIA-69 |
bioclipse.cheminformatics: Arvid Berg 2.4.x * r5f965e5 / plugins/net.bioclipse.cdk.jchempaint/src/net/bioclipse/cdk/jchempaint/handlers/SnapshotHandler.java : Change snapshot to use png and method from widget to retrive the image - http://bit.ly/bnSCyx |
| 13:57 |
|
olass |
egonw++ |
| 14:11 |
|
CIA-69 |
bioclipse.core: jonalv 2.4.x * ra88e371 / plugins/net.bioclipse.ui/src/net/bioclipse/ui/prefs/UpdateSitesPreferencePage.java : call pack() on parent too, fixes bug: #1210 - http://bit.ly/9O3kZN |
| 14:11 |
|
zarah |
bug #1210 | http://tinyurl.com/yg2supz |
| 14:13 |
|
olass |
egonw: what was the bug number again for teh rebased qsar commit? |
| 14:13 |
|
egonw |
@pz isValid |
| 14:13 |
|
zarah |
[1537] Implement isValidDescriptorDef... http://tinyurl.com/2ufvn9a |
| 14:13 |
|
zarah |
Entire list at http://tinyurl.com/3abc7hs |
| 14:13 |
|
egonw |
zarah++ |
| 14:15 |
|
egonw |
Gpox: ping |
| 14:15 |
|
Gpox |
pong |
| 14:16 |
|
egonw |
Gpox: can everyone now move to the new-target-platform ? |
| 14:16 |
|
Gpox |
I don't see why not |
| 14:17 |
|
egonw |
olass: can I propse to replace target.platform with the new one then? |
| 14:17 |
|
olass |
+1 |
| 14:17 |
|
egonw |
Gpox: can you make it so? |
| 14:17 |
|
egonw |
slyrus: please take note of this |
| 14:17 |
|
egonw |
and everyone else who has a bioclipse2.4 workspace |
| 14:18 |
|
CIA-69 |
bioclipse.cheminformatics: Arvid Berg 2.4.x * rd86e9bd / plugins/net.bioclipse.cdk.jchempaint/src/net/bioclipse/cdk/jchempaint/widgets/JChemPaintEditorWidget.java : |
| 14:18 |
|
CIA-69 |
bioclipse.cheminformatics: Only update dirty flag on undo/redo |
| 14:18 |
|
CIA-69 |
bioclipse.cheminformatics: Not when adding or removing actions from the undo stack. |
| 14:18 |
|
CIA-69 |
bioclipse.cheminformatics: solves bug 1979 - http://bit.ly/aknW8J |
| 14:18 |
|
zarah |
bug #1979 | http://tinyurl.com/385u8r7 |
| 14:22 |
|
CIA-69 |
bioclipse.core: Arvid Berg 2.4.x * r2e87679 / (2 files): Replaced target-platform.target with new-target-platform.target - http://bit.ly/cNJTxh |
| 14:22 |
|
|
samuell joined #bioclipse |
| 14:23 |
|
jonalv |
google make it so |
| 14:23 |
|
zarah |
jonalv: http://en.wikiquote.org/wiki/Jean-Luc_Picard |
| 14:23 |
|
jonalv |
sweet zarah++ |
| 14:23 |
|
jonalv |
google++ |
| 14:24 |
|
egonw |
(J-L)++ |
| 14:24 |
|
|
samuell left #bioclipse |
| 14:28 |
|
CIA-69 |
bioclipse.chembl: Egon Willighagen master * r7b55e93 / (5 files): Added a ChEMBL feature - http://bit.ly/9ALcAs |
| 14:28 |
|
CIA-69 |
bioclipse.chembl: Egon Willighagen master * r0bbb4c4 / (2 files in 2 dirs): Updated the version numbers to something relating to the 2.4.0 series - http://bit.ly/bLja2N |
| 14:30 |
|
CIA-69 |
bioclipse.chembl: Egon Willighagen master * r5f1916e / (5 files): Added a feature for Annzi's ChEMBL-MoSS mashup - http://bit.ly/d7qMa9 |
| 14:36 |
|
olass |
egonw: qsar patch does not apply to 2.4.x branch |
| 14:36 |
|
egonw |
que? |
| 14:36 |
|
egonw |
mmm |
| 14:36 |
|
egonw |
it did here... |
| 14:36 |
|
egonw |
mom |
| 14:41 |
|
egonw |
mmm... seems I rebased on the wrong branch |
| 14:42 |
|
egonw |
sorry about that |
| 14:43 |
|
jonalv |
egonw: did you figure anyhting out about that exception handling? |
| 14:43 |
|
egonw |
jonalv: nope |
| 14:44 |
|
jonalv |
egonw: can I reproduce the problem? |
| 14:44 |
|
egonw |
yes, with the updated bioclipse.moss repos |
| 14:48 |
|
egonw |
olass: please try the new patch |
| 14:48 |
|
olass |
will do |
| 14:50 |
|
jonalv |
egonw: which branch in moss? |
| 14:50 |
|
egonw |
master, /me thinks |
| 14:51 |
|
CIA-69 |
bioclipse.qsar: Egon Willighagen 2.4.x * r1424697 / (3 files in 2 dirs): Added implementation of isValidDescriptor(); assumes RDF/XML. Implements #1537. - http://bit.ly/calTTV |
| 14:52 |
|
egonw |
good :) |
| 14:53 |
|
olass |
thanks |
| 14:56 |
|
jonalv |
egonw: right, and then what do I do? |
| 15:01 |
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egonw |
moss.createMoTAB("{'foo':1}") |
| 15:01 |
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egonw |
note the TAB |
| 15:19 |
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edrin |
hello |
| 15:21 |
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zarah |
hi edrin |
| 15:21 |
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zarah |
edrin: You have new messages. Write '/msg zarah @messages' to read them. |
| 15:21 |
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egonw |
hi edrin |
| 15:21 |
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edrin |
hi egon |
| 15:38 |
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CIA-69 |
bioclipse.chembl: Egon Willighagen master * r5fafa12 / (22 files in 9 dirs): Moved the chEMBL-MoSS mashup code into a separate plugin - http://bit.ly/b9BlmI |
| 15:41 |
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CIA-69 |
bioclipse.moss: Egon Willighagen master * rfe902cd / (14 files in 5 dirs): Removed ChEMBL depending code, which is now available as separate plugin in the bioclipse.chembl repository - http://bit.ly/b4YHad |
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