| Time |
Nick |
Message |
| 06:09 |
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egonw_ joined #bioclipse |
| 07:48 |
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Gpox joined #bioclipse |
| 07:51 |
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olass joined #bioclipse |
| 07:51 |
olass |
moin |
| 07:51 |
zarah |
privet olass |
| 08:29 |
egonw_ |
moin |
| 08:29 |
zarah |
oh hai egonw_ |
| 08:45 |
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sneumann joined #bioclipse |
| 09:24 |
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| 09:41 |
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| 10:07 |
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miguelrojasch joined #bioclipse |
| 10:51 |
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jonalv joined #bioclipse |
| 10:51 |
jonalv |
oh hai |
| 10:51 |
zarah |
ni hao jonalv |
| 10:51 |
jonalv |
I forgot to sign in. ooops... :) |
| 11:08 |
* samuell |
goes for lunch |
| 12:27 |
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jonalv joined #bioclipse |
| 12:27 |
jonalv |
o/ |
| 12:31 |
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edrin joined #bioclipse |
| 12:32 |
edrin |
hi |
| 12:32 |
zarah |
hello edrin, you fantastic person you |
| 12:44 |
egonw |
jonalv++ (for joining http://blueobelisk.stackexchange.com) |
| 12:44 |
zarah |
egonw's link is also http://tinyurl.com/ygkhvp6 |
| 12:45 |
jonalv |
egonw: yea, only problem is that I can't even vote for answers... Appharently I need something called 'reputation'. Too much bootstrapping for my taste I think... :( |
| 12:48 |
egonw |
just leave two comments somewhere, and I'll get you reputation |
| 12:50 |
egonw |
oh, and read this page: http://blueobelisk.stackexchange.com/questions/10/how-can-we-bootstrap-critical-mass-for-this-forum |
| 12:50 |
zarah |
egonw's link is also http://tinyurl.com/yep8z5d |
| 12:55 |
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masak joined #bioclipse |
| 13:18 |
CIA-51 |
bioclipse.structuredb: jonalv master * r2d9039c / plugins/net.bioclipse.structuredb/src/net/bioclipse/structuredb/DBMoleculesEditorModel.java : |
| 13:18 |
CIA-51 |
bioclipse.structuredb: Made StructureDB compile. |
| 13:18 |
CIA-51 |
bioclipse.structuredb: Fixes bug: #1692 - http://bit.ly/2HQAgw |
| 13:18 |
zarah |
bug #1692 | http://tinyurl.com/ydkdjd5 |
| 13:30 |
samuell |
How to print out to the console from a JS script? |
| 13:33 |
masak |
samuell: by using the js manager. |
| 13:33 |
masak |
js.print() and js.say() |
| 13:33 |
samuell |
Ah... |
| 13:33 |
samuell |
Thanks! |
| 13:33 |
masak |
np. |
| 13:51 |
egonw |
say() does the newline, right? |
| 13:54 |
masak |
yes. |
| 13:54 |
* egonw |
needs to make more use of that |
| 13:54 |
masak |
it's a more pronouncible spelling of 'println' :) |
| 13:54 |
egonw |
js.print() feels so natural |
| 13:54 |
egonw |
like println() |
| 13:55 |
masak |
trust me, js.say() feels natural after a while, too. |
| 13:55 |
masak |
also, use Perl 5.10. it has &say :) |
| 14:03 |
jonalv |
samuell: How do I change an image in this new mediawiki version? |
| 14:04 |
samuell |
jonalv: Hmm... should be as normal... experienced problems? |
| 14:04 |
samuell |
Link? |
| 14:04 |
jonalv |
it looks different... |
| 14:04 |
jonalv |
ah the upload option was only there if I was loged in. |
| 14:05 |
jonalv |
I guess I was expecting to be asked to log in when trying to do it... |
| 14:05 |
samuell |
Ok |
| 14:08 |
jonalv |
samuell: it's not wroking |
| 14:09 |
jonalv |
samuell: I uploaded a new verison of the image at: http://wiki.bioclipse.net/index.php?title=Structure_DB |
| 14:09 |
zarah |
jonalv's link is also http://tinyurl.com/y8qk9o8 |
| 14:09 |
jonalv |
but it is still the same |
| 14:09 |
samuell |
Oh, ok |
| 14:10 |
samuell |
Could be something with file permissions, that has changed after our upgrade |
| 14:10 |
jonalv |
I have tried a couple of times and the history looks right but the current refuses to hagne |
| 14:11 |
samuell |
Ok, even after Ctrl + Shift + R? |
| 14:11 |
samuell |
Then it is surely file permissions... |
| 14:11 |
samuell |
I'll see if I can fix it |
| 14:12 |
jonalv |
samuell: Ctrl + Shift + R> |
| 14:12 |
jonalv |
samuell: what do you mean with Ctrl + Shift + R? |
| 14:14 |
samuell |
(Deep refresh in firefox) |
| 14:14 |
samuell |
(Might not be the same in your browser) |
| 14:15 |
jonalv |
samuell: Ctrl + Shift + R does nothing for me... |
| 14:16 |
samuell |
It is probably a different command... what it does is to empty the browser cache, but that can be done in the menus also I guess |
| 14:17 |
samuell |
Otherwise trying to look at the picture itself only, and refreshing, would do the same trick: http://wiki.bioclipse.net/images/StructuredbClassDiagram.png |
| 14:17 |
zarah |
samuell's link is also http://tinyurl.com/5z5cvk |
| 14:17 |
samuell |
Does that still show the old image? |
| 14:19 |
jonalv |
samuell: no when I refresh it chanes to the new one |
| 14:20 |
samuell |
Ok... then it was indeed a problem with the browser cache |
| 14:20 |
samuell |
I use to have the same problem |
| 14:20 |
samuell |
...until I realize that I have to "deep-refresh" again |
| 14:21 |
jonalv |
samuell: okey, thanks |
| 14:21 |
jonalv |
firefox-- |
| 14:21 |
samuell |
jonalv: np! |
| 14:23 |
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Gpox joined #bioclipse |
| 14:35 |
CIA-51 |
bioclipse.structuredb: jonalv master * r33cca81 / (classDiagram.class.violet classDiagram.png): Class diagram for new slim StructureDB - http://bit.ly/3TlkG6 |
| 14:35 |
egonw |
jonalv: is the wiki updated? |
| 14:35 |
egonw |
or do I need to look up the png in git ? |
| 14:35 |
jonalv |
egonw: I have struggled a while and placed the new png on the wiki |
| 14:35 |
egonw |
:) |
| 14:35 |
egonw |
jonalv++ |
| 14:35 |
egonw |
(for struggling but persisting) |
| 14:49 |
jonalv |
egonw: do you know anythign about this stack trace: http://pastebin.com/mc119858 |
| 14:50 |
egonw |
can you verify the input? |
| 14:50 |
egonw |
I think the molecule passed to the InChI library is not correct |
| 14:51 |
jonalv |
it's cycloPropane created from the cyclopropane testdata used by StructurDB |
| 14:51 |
jonalv |
is that file broken? |
| 14:51 |
jonalv |
egonw: I think it has worked before... |
| 14:52 |
jonalv |
egonw: http://github.com/jonalv/bioclipse.structuredb/blob/master/plugins/net.bioclipse.structuredb.tests/tests/testData/cyclopropane.mol |
| 14:52 |
zarah |
jonalv's link is also http://tinyurl.com/yhtdzmg |
| 14:56 |
egonw |
looks OK |
| 15:00 |
jonalv |
egonw: so what can the problem be then? |
| 15:02 |
egonw |
no idea |
| 15:02 |
egonw |
did you try a system out of the input as it goes to the inchi lib? |
| 15:02 |
egonw |
the actual data model? |
| 15:06 |
jonalv |
egonw: nope, I don't een know what I would expect at that stage... |
| 15:07 |
egonw |
try to debug CDKMolecule at line 437 |
| 15:07 |
egonw |
and dump what ever is passed to the calculateInchi() method ... |
| 15:07 |
egonw |
oh, wait... |
| 15:07 |
egonw |
at org.openscience.cdk.inchi.InChIGeneratorFactory.getInstance(InChIGeneratorFactory.java:96) |
| 15:08 |
egonw |
it fails when the factory is instantiated... |
| 15:08 |
egonw |
mmm... perhaps a platform thingy... |
| 15:08 |
egonw |
did you move to 64 bit OS/X or so? |
| 15:08 |
jonalv |
egonw: I am commiting and then you can test run as well. Since you seem to be on the problem anyways... :) |
| 15:08 |
egonw |
perhaps ask on blueobelisk.stackexchange.com ? ;) |
| 15:08 |
egonw |
my bet is a platform issue |
| 15:09 |
jonalv |
egonw: I ahve already asked there... :) |
| 15:09 |
CIA-51 |
bioclipse.structuredb: jonalv master * rb485cc1 / (11 files in 2 dirs): |
| 15:09 |
CIA-51 |
bioclipse.structuredb: removed domain objects. |
| 15:09 |
CIA-51 |
bioclipse.structuredb: Domain tests except InChI related once pass - http://bit.ly/3oxFc2 |
| 15:09 |
egonw |
ah, indeed :) |
| 15:09 |
egonw |
jonalv++ |
| 15:09 |
egonw |
@karma jonalv |
| 15:09 |
zarah |
jonalv has a karma of 175 |
| 15:11 |
jonalv |
egonw: if so then Inchi generation shouldn\t work at ll in Bioclipse. gonna try that.. |
| 15:12 |
egonw |
true |
| 15:12 |
jonalv |
egonw: nope I get them inside Bioclispe |
| 15:12 |
jonalv |
|Bioclipse |
| 15:13 |
egonw |
exceptions or inchis? |
| 15:14 |
jonalv |
egonw: inchis |
| 15:14 |
jonalv |
sry I was trying to aviod having to spell that strane word |
| 15:14 |
jonalv |
but I guess all lower case is a good solution... |
| 15:22 |
egonw |
then I guess it is a classpath issue? |
| 15:22 |
jonalv |
egonw: possible |
| 15:23 |
jonalv |
egonw: I have no idea |
| 15:23 |
jonalv |
egonw: but how could it be a classpath issue? When running JUnit tests everything is on the class path in Eclipse, right? |
| 15:24 |
jonalv |
egonw: + a NullPointerException is a strange exception to get... |
| 15:24 |
egonw |
not running as plugin unit test? |
| 15:24 |
jonalv |
egonw: nope |
| 15:24 |
jonalv |
egonw: not these |
| 15:24 |
jonalv |
egonw: could that be the reason? |
| 15:24 |
egonw |
dunno |
| 15:25 |
jonalv |
hm... But when you run CDK tests you don't run em as plugin tests do you? |
| 15:26 |
egonw |
I do |
| 15:26 |
egonw |
I now always run as plugin tests |
| 15:26 |
jonalv |
egonw: I don't mean Bioclispe ones but CDK ones |
| 15:27 |
egonw |
ah, no, those are indeed not run as plugin tests :) |
| 15:34 |
jonalv |
egonw: so it should be possible to get it working... |
| 15:34 |
jonalv |
I am moving on with the rest right now |
| 15:34 |
jonalv |
going to have to come back to that one later... |
| 16:15 |
CIA-51 |
bioclipse.core: jonalv 2.2.x * rb72fe70 / plugins/net.bioclipse.ui/src/net/bioclipse/ui/prefs/UpdateSitesEditDialog.java : fixed layot - http://bit.ly/3y8PBR |
| 16:15 |
CIA-51 |
bioclipse.core: jonalv 2.2.x * rdc80843 / plugins/net.bioclipse.ui/src/net/bioclipse/ui/prefs/UpdateSitesEditDialog.java : new attempt at layout - http://bit.ly/2XQ0Eo |
| 16:15 |
CIA-51 |
bioclipse.core: Ola Spjuth 2.2.x * rb38102d / plugins/net.bioclipse.ui/src/net/bioclipse/ui/prefs/UpdateSitesEditDialog.java : Move Textbox down in dialog. - http://bit.ly/370YXW |
| 16:15 |
CIA-51 |
bioclipse.core: Carl Masak 2.2.x * raa23262 / plugins/net.bioclipse.scripting.ui/src/net/bioclipse/scripting/ui/views/JsConsoleView.java : |
| 16:15 |
CIA-51 |
bioclipse.core: [JsConsoleView] now summarizes long lists on output |
| 16:15 |
CIA-51 |
bioclipse.core: A 'long list' is any list of more than two elements. The summary looks like |
| 16:15 |
CIA-51 |
bioclipse.core: "List<$T> of size $size". - http://bit.ly/qwcHx |
| 16:54 |
CIA-51 |
bioclipse.structuredb: jonalv master * r1439d1c / (37 files in 9 dirs): |
| 16:54 |
CIA-51 |
bioclipse.structuredb: Removed stuff until StructureDB compiles again. |
| 16:54 |
CIA-51 |
bioclipse.structuredb: Next step will be to remove stuff until it runs again. (And probably add some stuff as well) - http://bit.ly/1wVcfB |
| 18:00 |
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| 19:23 |
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| 19:23 |
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| 19:47 |
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| 19:54 |
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| 20:40 |
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