| Time |
Nick |
Message |
| 04:39 |
|
egonw joined #bioclipse |
| 05:24 |
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sneumann_ joined #bioclipse |
| 06:33 |
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olass joined #bioclipse |
| 06:38 |
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rojasm joined #bioclipse |
| 07:10 |
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mgerlich joined #bioclipse |
| 07:23 |
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sneumann_ joined #bioclipse |
| 08:04 |
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jonalv joined #bioclipse |
| 08:04 |
jonalv |
o/ |
| 08:07 |
|
shk3 joined #bioclipse |
| 08:23 |
* jonalv |
is trying to grock the whiteboard pattern |
| 08:23 |
jonalv |
hm or was that "grokk" |
| 08:23 |
jonalv |
I never can remember |
| 08:26 |
olass |
jonalv: I thought you preferred the blackboard pattern? |
| 08:26 |
jonalv |
olass: yea I can see how you would think so... |
| 08:26 |
olass |
well, you always complain about whiteboards... |
| 08:27 |
jonalv |
yup, I might have to rename the poattern but I doubt that is a briliant idea |
| 08:27 |
olass |
:) |
| 08:27 |
jonalv |
I actually ythink I am going to use it for the refresh of the Databaseview |
| 08:27 |
olass |
oh |
| 08:44 |
|
masak joined #bioclipse |
| 08:56 |
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mgerlich joined #bioclipse |
| 08:56 |
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rojasm joined #bioclipse |
| 09:07 |
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edrin joined #bioclipse |
| 09:20 |
edrin |
hi |
| 09:20 |
zarah |
saluton edrin |
| 09:21 |
edrin |
:) http://xkcd.com/612/ |
| 09:24 |
masak |
*lol* |
| 09:26 |
CIA-52 |
bioclipse.core: jonalv master * rcb0a9c4 / (3 files): Added changelistener for updating the Databases view. It's done with my interpretation of the white board pattern. - http://bit.ly/2GWgMw |
| 09:26 |
CIA-52 |
bioclipse.structuredb: jonalv master * racb2633 / (7 files in 2 dirs): Make sure the Databases view get's updated for Structuredb related changes - http://bit.ly/ga5JR |
| 09:53 |
CIA-52 |
bioclipse.ds: Ola Spjuth master * r1dba1f7 / plugins/net.bioclipse.ds/src/net/bioclipse/ds/ui/views/DSView.java : Send cloned molecule to TestRun. Also treat MolTableEditor as special case when clearing test runs since JCP context is lost when another view is clicked upon. - http://bit.ly/5EdYk |
| 09:53 |
CIA-52 |
bioclipse.ds: Ola Spjuth master * rc0cdaef / (6 files in 2 dirs): Rewrote BirtHandlers to extend an abstract base class to handle population of dataset rows. - http://bit.ly/Z4rNj |
| 09:54 |
CIA-52 |
bioclipse.ds: Ola Spjuth master * r5489a9e / (2 files in 2 dirs): Removed unused imports. - http://bit.ly/29MllU |
| 09:54 |
olass |
ok, time for lunch |
| 10:04 |
olass |
ok, now really time for lunch |
| 11:30 |
|
egonw joined #bioclipse |
| 11:30 |
egonw |
moin |
| 11:30 |
zarah |
oh hai egonw |
| 11:33 |
masak |
egonw: \o |
| 11:37 |
egonw |
greetings from Leiden |
| 11:38 |
jonalv |
OH HAI Leiden |
| 11:38 |
masak |
OMG ITS Leiden |
| 11:42 |
jonalv |
olass: you don't happend to know how D&D works on the CNF would you? |
| 11:43 |
CIA-52 |
bioclipse.rdf: Egon Willighagen master * r68a677a / plugins/net.bioclipse.rdf/src/net/bioclipse/rdf/business/RDFManager.java : Fixed a NPE: when no results are found, do not attempt to add it to the result set - http://bit.ly/JWRFT |
| 11:43 |
olass |
Dungeons & Dragons? |
| 11:43 |
CIA-52 |
bioclipse.rdf: Egon Willighagen master * r3caa42a / (2 files in 2 dirs): Version info updated for Bioclipse 2.0.0 - http://bit.ly/12FKG0 |
| 11:43 |
CIA-52 |
bioclipse.rdf: Egon Willighagen master * r593bb46 / .gitignore : Ignore autogenerated bin/ folders - http://bit.ly/ygELG |
| 11:43 |
jonalv |
olass: :) |
| 11:43 |
egonw |
hahaha |
| 11:43 |
olass |
sorry, no |
| 11:43 |
jonalv |
olass: no Drag and Drop |
| 11:43 |
egonw |
was thinking the same thing |
| 11:43 |
egonw |
but working too hard to type it |
| 11:43 |
olass |
DnD is druag and drop |
| 11:43 |
olass |
D&D is... :) |
| 11:44 |
jonalv |
whatever |
| 11:44 |
masak |
Dine 'n' Dance? |
| 11:44 |
jonalv |
olass: can you help? |
| 11:44 |
olass |
Drink and Drive ? |
| 11:44 |
olass |
jonalv: sorry, no |
| 11:44 |
egonw |
Doom and Destruction? |
| 11:44 |
masak |
"don't DnD" |
| 11:44 |
olass |
:) |
| 11:45 |
olass |
jonalv: you can always email eclipe ML |
| 12:22 |
masak |
egonw: how do I do 'git log' from a certain YYYY-MM-DD date? |
| 12:23 |
masak |
egonw: nvm, found --since |
| 12:44 |
egonw |
masak++ |
| 12:45 |
jonalv |
olass: around? |
| 12:51 |
masak |
egonw: what I really need to do is bookmark http://www.kernel.org/pub/software/scm/git/docs/git-rev-parse.html somehow. |
| 12:51 |
zarah |
masak's link is also http://tinyurl.com/5e9cex |
| 13:10 |
olass |
jonalv: pong |
| 13:10 |
* olass |
was an picked up his repaired laptop |
| 13:11 |
jonalv |
olass: when I drag an SDF file. What object am I dragging? |
| 13:11 |
jonalv |
what is it an instance of? |
| 13:11 |
olass |
sorry, don't know |
| 13:12 |
olass |
http://www.eclipse.org/articles/Article-Workbench-DND/drag_drop.html |
| 13:12 |
zarah |
olass's link is also http://tinyurl.com/lhpeft |
| 13:12 |
olass |
that says: java.lang.String[] (list of absolute file paths) |
| 13:12 |
jonalv |
olass: oh I see |
| 13:12 |
olass |
or |
| 13:12 |
olass |
org.eclipse.core.resources.IResource[] |
| 13:12 |
olass |
see #transfer types |
| 13:13 |
olass |
in the doc |
| 13:13 |
jonalv |
but still I don't want IResource to be a possibleChild in my tree |
| 13:13 |
jonalv |
:( |
| 13:27 |
CIA-52 |
bioclipse: shk3 * r11700 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/ (9 files in 6 dirs): added a possibility to enter a csv peak list for new spectrum |
| 13:50 |
egonw |
just for the record... |
| 13:50 |
egonw |
I hate the auto update checking... |
| 13:50 |
shk3 |
rojasm: around? |
| 13:50 |
rojasm |
yes shk3 |
| 13:50 |
shk3 |
did you move medea to git? |
| 13:51 |
egonw |
github.com/miguelrojasch/medea |
| 13:52 |
shk3 |
gives me That page doesn't exist! |
| 13:52 |
shk3 |
in the browser |
| 13:52 |
shk3 |
or is that not a http url? |
| 13:52 |
shk3 |
anyway, how do I check out this? |
| 13:53 |
rojasm |
http://github.com/miguelrojasch/bioclipse.medea/tree/master |
| 13:53 |
zarah |
rojasm's link is also http://tinyurl.com/l2ebjm |
| 13:54 |
shk3 |
thanks |
| 13:54 |
shk3 |
can you give me a hint on how to check out? |
| 13:54 |
shk3 |
using the "clone url" with git should do it? |
| 13:55 |
egonw |
shk3: the clone URL is on that above web page |
| 13:55 |
shk3 |
yes |
| 13:56 |
shk3 |
just trying this |
| 13:56 |
shk3 |
looks good |
| 13:56 |
shk3 |
thanks |
| 13:57 |
shk3 |
is there a reason why the popup prediction is not active? |
| 14:00 |
masak |
"popup prediction"? |
| 14:01 |
shk3 |
well, the prediction via popup menu |
| 14:01 |
shk3 |
rojasm: can you say a word about that? |
| 14:02 |
shk3 |
I would like to use it |
| 14:02 |
shk3 |
if it is just commented out because nobody transferred it to bc2, I would do it |
| 14:02 |
egonw |
we had to disable that |
| 14:02 |
egonw |
because the java source code was not on the build path |
| 14:04 |
shk3 |
shouldn't be a problem to hook the manager method to the menu |
| 14:04 |
shk3 |
shall I do it? |
| 14:06 |
CIA-52 |
bioclipse.structuredb: jonalv master * rb131be0 / plugins/net.bioclipse.structuredb/src/net/bioclipse/structuredb/Label.java : removed old drop method left behind from earlier times - http://bit.ly/fCJGL |
| 14:06 |
CIA-52 |
bioclipse.structuredb: jonalv master * rb4a2759 / (4 files in 4 dirs): |
| 14:06 |
CIA-52 |
bioclipse.structuredb: Implemented some rudimentary drag and drop for Structuredb in the databases |
| 14:06 |
CIA-52 |
bioclipse.structuredb: view. I am not sure this is the way it should be done. I had to define |
| 14:06 |
CIA-52 |
bioclipse.structuredb: org.eclipse.core.resources.IResource as a possible child in the tree. That is |
| 14:06 |
CIA-52 |
bioclipse.structuredb: just wrong nevertheless I have not found any other way to do it. - |
| 14:06 |
CIA-52 |
bioclipse.structuredb: http://bit.ly/hDQPv |
| 14:08 |
egonw |
shk3: yes, please go ahead |
| 14:08 |
egonw |
and consult with Miguel how to get the patch with him |
| 14:09 |
egonw |
shk3: are you planning to move speclipse, specmol and friends to git any time soon? |
| 14:10 |
shk3 |
I don't know |
| 14:10 |
shk3 |
I am a bit scared of git |
| 14:11 |
shk3 |
but I think i will do it |
| 14:11 |
masak |
shk3: the scary part will pass the more you use it. |
| 14:11 |
olass |
shk3: you should |
| 14:11 |
olass |
and let egonw assist |
| 14:11 |
jonalv |
shk3: it's actually nothing to be scared of |
| 14:11 |
* olass |
was scared too, but is getting used to it now |
| 14:12 |
* masak |
was slightly confused by git at first |
| 14:12 |
egonw |
shk3: if you send me a list of plugins and features (including the .tests etc) then I can move it into a git repository |
| 14:13 |
egonw |
shk3: which you could fork and take over then |
| 14:13 |
jonalv |
egonw: how can I from an IFile see if it is an SDF? |
| 14:13 |
egonw |
right click on it |
| 14:13 |
egonw |
and then Properties |
| 14:13 |
jonalv |
egonw: programmatically |
| 14:14 |
egonw |
umm |
| 14:14 |
masak |
jonalv: .rightClick().properties() |
| 14:14 |
masak |
:P |
| 14:14 |
jonalv |
masak: if only... |
| 14:15 |
shk3 |
jonalv: do |
| 14:16 |
shk3 |
IContentTypeManager contentTypeManager = Platform.getContentTypeManager(); |
| 14:16 |
shk3 |
InputStream stream = file.getContents(); |
| 14:16 |
shk3 |
IContentType contentType = contentTypeManager.findContentTypeFor(stream, file.getName()); |
| 14:16 |
shk3 |
and |
| 14:16 |
egonw |
jonalv: check the cdk manager.. there should be something there, IIRC |
| 14:16 |
shk3 |
contentType.getId().equals("whatever") |
| 14:16 |
shk3 |
whatever being id of sdf type |
| 14:16 |
olass |
jonalv: funny, I just made a convenience method for this |
| 14:16 |
shk3 |
and file the IFile |
| 14:17 |
jonalv |
olass: and placed it somewhere in the cdk plugin? :) |
| 14:17 |
olass |
jonalv: in the net.bc.cheminformatics plugin |
| 14:17 |
olass |
well |
| 14:17 |
jonalv |
olass: yes where? We needs it :) |
| 14:17 |
olass |
it is called ChemoinformaticUtils.isMultipleMolecule(IFile file) |
| 14:18 |
olass |
but since we only support SDF for multiple mols.. |
| 14:18 |
jonalv |
olass: commit pls... |
| 14:18 |
olass |
jonalv: hmm, how do I commit to cheminfo repo? |
| 14:18 |
jonalv |
egonw: please help olass get this very important commit into cheminfo repo |
| 14:18 |
* jonalv |
brb |
| 14:19 |
olass |
I have commit rights |
| 14:19 |
CIA-52 |
bioclipse: shk3 * r11701 /bioclipse2/trunk/plugins/net.bioclipse.nmrshiftdb/plugin.xml: added prediction popups to 0D type |
| 14:19 |
egonw |
olass: git remote add origin or so... |
| 14:19 |
olass |
just don't know how to commit to upstream |
| 14:19 |
olass |
egonw: could you tell me full syntax? |
| 14:19 |
egonw |
git remote add origin ssh://myserver.com/var/git/myapp.git |
| 14:20 |
egonw |
replace the last ssh:// with the commit URL provided by GitHub |
| 14:20 |
egonw |
olass: do you know about google? |
| 14:20 |
egonw |
it's a nice website |
| 14:20 |
egonw |
where you can search web pages |
| 14:21 |
olass |
@slap egonw |
| 14:21 |
* zarah |
hits egonw with a hammer, so he breaks into a thousand pieces |
| 14:21 |
olass |
hmm, a bit too harsh, zarah |
| 14:22 |
olass |
egonw: a commit url provided by github? |
| 14:22 |
olass |
strange, never heard about that |
| 14:22 |
olass |
is that the public URL? |
| 14:22 |
olass |
or your private urlk? |
| 14:23 |
egonw |
private one |
| 14:23 |
olass |
ok, will try |
| 14:23 |
egonw |
the public one does not have commit rights |
| 14:23 |
olass |
right |
| 14:23 |
olass |
hmm, will that give me two origin in my repo? |
| 14:23 |
olass |
or should I abandon my fork? |
| 14:24 |
CIA-52 |
bioclipse.cheminformatics: Egon Willighagen master * raae8f74 / plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/business/CDKManager.java : Fixed messages of progress monitor - http://bit.ly/vpz9t |
| 14:24 |
CIA-52 |
bioclipse.cheminformatics: Egon Willighagen master * raf6333a / plugins/net.bioclipse.cdk.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/editor/MultiPageMoleculesEditorPart.java : Merge branch 'master' of git github.com:egonw/bioclipse.cheminformatics - http://bit.ly/IoIuu |
| 14:24 |
egonw |
bugger... |
| 14:24 |
egonw |
olass: you choose |
| 14:25 |
egonw |
I'm fine with merging in a commit from your branch |
| 14:25 |
olass |
well, I want to be able to commit myself |
| 14:25 |
olass |
so will try now |
| 14:26 |
olass |
when you are here to fix any problems |
| 14:28 |
jonalv |
olass: so that convenience method is not commited yet? |
| 14:28 |
olass |
please assist |
| 14:28 |
egonw |
[07/20/09 16:12] <egonw> shk3: if you send me a list of plugins and features (including the .tests etc) then I can move it into a git repository |
| 14:28 |
egonw |
[07/20/09 16:13] <egonw> shk3: which you could fork and take over then |
| 14:28 |
egonw |
olass: if you want to commit directly into my branch, then edit the file .git/config |
| 14:28 |
jonalv |
olass: you want me to assist? |
| 14:29 |
olass |
egonw: how should it look like? |
| 14:29 |
jonalv |
olass: What can I do you for then? |
| 14:29 |
egonw |
olass: right now it should say something with your github account name and bioclipse.cheminformatics |
| 14:29 |
egonw |
change your account name to mine in that line |
| 14:30 |
egonw |
[remote "origin"] |
| 14:30 |
egonw |
url = gitgithub.com:egonw/bioclipse.cheminformatics.git |
| 14:30 |
egonw |
to make it look like the above |
| 14:30 |
shk3 |
egonw: I will come back to that |
| 14:30 |
shk3 |
other stuff to do now |
| 14:31 |
egonw |
sure, fine... |
| 14:32 |
olass |
egonw: argh |
| 14:32 |
olass |
error: Entry 'plugins/net.bioclipse.chemoinformatics/src/net/bioclipse/chemoinformatics/util/ChemoinformaticUtils.java' would be overwritten by merge. Cannot merge. |
| 14:33 |
olass |
I did git pull |
| 14:33 |
egonw |
yeah, you need to do 'git pull' first |
| 14:33 |
olass |
that's what I did |
| 14:33 |
egonw |
then you might have a conflict |
| 14:33 |
egonw |
which you did not commited locally yet? |
| 14:33 |
egonw |
what does 'git status' say |
| 14:33 |
olass |
# Your branch and 'origin/master' have diverged, |
| 14:33 |
olass |
# and have 1 and 3 different commit(s) each, respectively. |
| 14:33 |
olass |
# |
| 14:34 |
olass |
how do I fix this? |
| 14:34 |
egonw |
this is why you can best always develop in branches |
| 14:34 |
egonw |
then you can 'git pull' |
| 14:34 |
egonw |
merge your local changes and commit |
| 14:35 |
egonw |
right now, you can best do is: |
| 14:35 |
egonw |
1. run 'git log' |
| 14:35 |
jonalv |
egonw: can't he just pull and then push? |
| 14:35 |
egonw |
jonalv: no, that's what he has been trying |
| 14:35 |
egonw |
2. write down the hash(es) of your commit(s) |
| 14:35 |
olass |
well, I have not yet committed |
| 14:35 |
egonw |
3. revert your patches |
| 14:36 |
egonw |
4. git pull |
| 14:36 |
olass |
I have changes locally |
| 14:36 |
egonw |
5. git cherry-pick HASH1 |
| 14:36 |
egonw |
5. git cherry-pick HASH2 |
| 14:36 |
egonw |
5. git cherry-pick HASH3 |
| 14:36 |
egonw |
5. git cherry-pick HASH4 |
| 14:36 |
egonw |
etc |
| 14:36 |
egonw |
git stash |
| 14:36 |
olass |
ok, so first commit? |
| 14:36 |
egonw |
or commit |
| 14:36 |
olass |
ok |
| 14:36 |
olass |
will do my two commits then |
| 14:36 |
masak |
egonw: so 'git pull --rebase' isn't enough in this case? |
| 14:37 |
olass |
oh, is rebase the thing maybe? |
| 14:37 |
* masak |
thinks so |
| 14:37 |
masak |
olass: depends on if you want to rebase :) |
| 14:37 |
egonw |
masak: never done --rebase on git pull |
| 14:37 |
olass |
what implications does that have? |
| 14:37 |
masak |
egonw: it's way convenient. :) |
| 14:37 |
egonw |
it so 2009 ? |
| 14:38 |
masak |
olass: http://git.or.cz/gitwiki/GitFaq#Whatisthedifferencebetweenamergeandarebase.3F |
| 14:38 |
zarah |
masak's link is also http://tinyurl.com/3y4bgv |
| 14:38 |
olass |
will I loose any local info? |
| 14:38 |
masak |
olass: well, your working copy should be clean when you do it. |
| 14:38 |
egonw |
just your credit card info |
| 14:38 |
olass |
should I commit first? |
| 14:38 |
masak |
olass: preferably. |
| 14:38 |
masak |
olass: or stash. |
| 14:38 |
egonw |
(which is technically the same) |
| 14:38 |
masak |
depends if you're at a point where you feel you can commit. |
| 14:39 |
olass |
yes |
| 14:40 |
olass |
ok, committed |
| 14:40 |
olass |
here comes the pull --rebase |
| 14:40 |
olass |
hmm, trying git pull first |
| 14:40 |
olass |
seems to work fine |
| 14:40 |
olass |
guess I should have committed first :) |
| 14:40 |
egonw |
yes |
| 14:40 |
masak |
guess an ordinary pull creates one of those merge commits. |
| 14:40 |
egonw |
always do that |
| 14:41 |
olass |
hmm |
| 14:41 |
olass |
yes |
| 14:41 |
* masak |
always always does 'git pull --rebase' nowadays |
| 14:41 |
olass |
I get 4 commits now instead of two |
| 14:41 |
masak |
I have an alias in place for it. |
| 14:41 |
olass |
is that ok? |
| 14:41 |
olass |
2 merge commits too |
| 14:41 |
masak |
olass: is one of them a merge commit? |
| 14:41 |
masak |
olass: aye. |
| 14:41 |
olass |
is that normal? |
| 14:42 |
olass |
and ok? |
| 14:42 |
masak |
olass: sure. |
| 14:42 |
olass |
ok, then here comes the push |
| 14:42 |
masak |
olass: but you won't get them if you do --rebase |
| 14:42 |
egonw |
does anyone know how to (via the github webpage) update my 'fork' with the branch forked from? |
| 14:42 |
CIA-52 |
bioclipse.cheminformatics: Ola Spjuth master * rf241c1e / plugins/net.bioclipse.cdk.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/editor/MultiPageMoleculesEditorPart.java : Created public method to indicate if MolTable is showing JCPEditor or not. - http://bit.ly/KCqtp |
| 14:42 |
CIA-52 |
bioclipse.cheminformatics: Ola Spjuth master * radb7417 / plugins/net.bioclipse.chemoinformatics/src/net/bioclipse/chemoinformatics/util/ChemoinformaticUtils.java : Added convenience method isMultipleMolecule, which currently only detects SDF content types. - http://bit.ly/slRa6 |
| 14:42 |
CIA-52 |
bioclipse.cheminformatics: Ola Spjuth master * rc6f74be / plugins/net.bioclipse.chemoinformatics/src/net/bioclipse/chemoinformatics/util/MoleculeContentTypeViewerFilter.java : Added a ViewerFilter that only shows molecules files and folders to be used in any Viewer - http://bit.ly/a95h6 |
| 14:42 |
CIA-52 |
bioclipse.cheminformatics: Ola Spjuth master * rf3945aa / plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/business/CDKManager.java : Merge branch 'master' of gitgithub.com:egonw/bioclipse.cheminformatics - http://bit.ly/GWLS7 |
| 14:42 |
jonalv |
egonw: can one do that? |
| 14:42 |
olass |
jonalv: does that make you happy? |
| 14:43 |
jonalv |
olass: yep I am gonna pull and try it out now :) |
| 14:46 |
jonalv |
egonw: I think we need to make up our minds. Either we go with cheminformatics or chemoinformatics. Right now we have both around... |
| 14:47 |
shk3 |
sounds like you are having git trouble. I thought that's not existing ;-) |
| 14:48 |
egonw |
no, the thing about git is, you can fix git trouble |
| 14:48 |
egonw |
that's what makes it unique |
| 14:48 |
egonw |
if you have SVN trouble |
| 14:48 |
egonw |
it's early weekend |
| 14:48 |
egonw |
and start from scratch next week |
| 14:48 |
masak |
shk3: it's possible to shoot oneself in the foot with git too. |
| 14:49 |
masak |
but often enough, it's also possible to un-shoot oneself in the foot. |
| 14:49 |
egonw |
but unlike svn, git can do the surgery |
| 14:49 |
egonw |
and even the cosmetic ones |
| 14:49 |
jonalv |
but the foot is always around somewhere so you can get it back... |
| 14:49 |
egonw |
olass: anyway... |
| 14:49 |
egonw |
olass: lesson: |
| 14:49 |
egonw |
always make your local changes in branches |
| 14:49 |
egonw |
and only just before you want to push... |
| 14:49 |
egonw |
you do: |
| 14:49 |
egonw |
1. git checkout master |
| 14:49 |
egonw |
2. git pull |
| 14:50 |
egonw |
3. git merge 6-yourDevelopmentBranch |
| 14:50 |
egonw |
4. git push |
| 14:50 |
olass |
egonw: yes |
| 14:50 |
masak |
(or use 'git pull --rebase') |
| 14:50 |
olass |
I missed this workflow since I switched repo in the middle |
| 14:50 |
masak |
olass: but start by doing it the way egonw says. :) |
| 14:50 |
olass |
will follow it now |
| 14:51 |
olass |
but I learned some more git :) |
| 14:51 |
jonalv |
egonw: oh you do all development in local branches? That is seriously lots of work |
| 14:52 |
egonw |
no, it's not |
| 14:53 |
jonalv |
egonw: if you are working one repo it is not but when doing Bioclispe one is working with many repos... |
| 14:53 |
* jonalv |
might start doing that some day but for now he is not convinced it's worth it... |
| 14:55 |
egonw |
it's worth it for me |
| 14:55 |
egonw |
my work schedule might differ |
| 14:55 |
egonw |
it's saving me time |
| 15:04 |
CIA-52 |
bioclipse.core: jonalv master * r09e9874 / plugins/net.bioclipse.databases/src/net/bioclipse/databases/DatabasesNavigator.java : Always make the refresh in UI thread - http://bit.ly/wVogG |
| 15:04 |
CIA-52 |
bioclipse.structuredb: jonalv master * r1d57c6f / plugins/net.bioclipse.structuredb/src/net/bioclipse/structuredb/viewer/StructureDBDropAdapterAssistant.java : only allow drop of sdf files on StructuredbInstances - http://bit.ly/hm67k |
| 15:05 |
olass |
jonalv: why not allow drop of single mols? |
| 15:05 |
jonalv |
olass: oh, right I am comming to that :) |
| 15:05 |
olass |
:) |
| 15:06 |
jonalv |
will actually do that now |
| 15:06 |
jonalv |
thanks for reminiding me :) |
| 15:08 |
jonalv |
I guess I better join masak.... |
| 15:08 |
jonalv |
I will do that toimorrow instead |
| 15:08 |
jonalv |
cya |
| 15:08 |
olass |
bye |
| 15:09 |
CIA-52 |
bioclipse: shk3 * r11702 /bioclipse2/trunk/plugins/net.bioclipse.nmrshiftdb/plugin.xml: added prediction popups to 0D type |
| 15:26 |
CIA-52 |
bioclipse: shk3 * r11703 /bioclipse2/trunk/plugins/net.bioclipse.nmrshiftdb/ (6 files in 4 dirs): switched prediction to handlers |
| 15:26 |
CIA-52 |
bioclipse: shk3 * r11704 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/plugin.xml: added a prediction top level menu item here |
| 15:49 |
shk3 |
egonw: how do I make modulewise patches for cdk? |
| 16:23 |
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| 19:05 |
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| 19:15 |
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| 19:38 |
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| 19:38 |
egonw |
moin |
| 19:38 |
zarah |
privet egonw |
| 20:29 |
olass |
hio egonw |
| 20:29 |
egonw |
hi olass |
| 20:30 |
egonw |
did you get my last sparql for listing categories |
| 20:30 |
egonw |
and descriptors listed as such? |
| 20:30 |
olass |
oh, is it in the bug? |
| 20:30 |
olass |
did you resolve 2) also? |
| 20:30 |
olass |
great! |
| 20:31 |
olass |
working on importing QSAR responses... |
| 20:31 |
olass |
takes a lot of time... |
| 20:31 |
egonw |
mmm... |
| 20:31 |
egonw |
I think I emailed... |
| 20:31 |
egonw |
mom, let me make the gist |
| 20:32 |
olass |
thanks |
| 20:33 |
CIA-52 |
bioclipse.qsar: Ola Spjuth master * r45ae223 / plugins/net.bioclipse.qsar.ui/src/net/bioclipse/qsar/ui/wizards/ExistingResourcesFilter.java : Added a filter to filter out unwanted resources from a Viewer. - http://bit.ly/wuaFz |
| 20:33 |
CIA-52 |
bioclipse.qsar: Ola Spjuth master * r5b1ba63 / (9 files in 2 dirs): |
| 20:33 |
CIA-52 |
bioclipse.qsar: Added a wizard for adding molecules to QSAR project. |
| 20:33 |
CIA-52 |
bioclipse.qsar: * Page 1: Select molecular files |
| 20:33 |
CIA-52 |
bioclipse.qsar: * Page 2: Optionally select a property that should be imported as response value |
| 20:33 |
CIA-52 |
bioclipse.qsar: + Added PropertyEntry as model object for properties. - http://bit.ly/A5i80 |
| 20:33 |
CIA-52 |
bioclipse.qsar: Ola Spjuth master * r8f86493 / plugins/net.bioclipse.qsar.ui/src/net/bioclipse/qsar/ui/editors/MoleculesPage.java : Rewrote MolEditor to make use of new wizard. Still does not add responses of selectied files, will be up next. - http://bit.ly/Hs8Ej |
| 20:35 |
egonw |
http://gist.github.com/150889 |
| 20:51 |
olass |
egonw: thanks |
| 20:51 |
olass |
will try that asap |
| 20:58 |
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| 21:21 |
olass |
egonw: ping |
| 21:22 |
olass |
would it be possible to define extra descriptors in a second OWL/RDF and load this also before executing your SPARQL queries? |
| 21:23 |
egonw |
yes |
| 21:23 |
egonw |
no problem |
| 21:23 |
olass |
I assumed so |
| 21:23 |
olass |
that way people can add their own descriptors |
| 21:23 |
egonw |
btw, just send a pull request |
| 21:23 |
egonw |
right |
| 21:23 |
olass |
if they don't want to make them public |
| 21:24 |
egonw |
owl++ |
| 21:24 |
olass |
pull request for what? |
| 21:24 |
egonw |
bioclipse.qsar |
| 21:24 |
olass |
? |
| 21:24 |
olass |
why? |
| 21:24 |
egonw |
the new ontology |
| 21:24 |
olass |
oh, just sent not send |
| 21:24 |
egonw |
do I have write access to your version? |
| 21:24 |
egonw |
oops sorry |
| 21:24 |
olass |
:) |
| 21:24 |
egonw |
it's late |
| 21:24 |
olass |
ok, will get it |
| 21:25 |
egonw |
btw, had great dinner with Chris and Miguel |
| 21:25 |
olass |
thanks |
| 21:25 |
olass |
oh, nice |
| 21:25 |
olass |
things are progressin gwell for miguel? |
| 21:25 |
egonw |
met with a couple of people here at a cheminfo workshop |
| 21:25 |
olass |
will he get his thesis? |
| 21:25 |
egonw |
Andreas Bender, Matteo Floris, Thomas Meinl (KNIME) |
| 21:25 |
egonw |
yes, we're working hard on that |
| 21:25 |
olass |
good luck to you all |
| 21:26 |
* olass |
is tired |
| 21:26 |
egonw |
Matteo is now chemoinfo student, former CUBIC |
| 21:26 |
egonw |
yeah, same here |
| 21:26 |
olass |
this week will be work 20h a day |
| 21:26 |
olass |
4 h for sleeping and eating |
| 21:28 |
egonw |
don't do that |
| 21:28 |
egonw |
really |
| 21:28 |
egonw |
it's tempting... |
| 21:28 |
egonw |
but |
| 21:28 |
egonw |
after a few days you are exhausted and get counterproductive |
| 21:29 |
egonw |
http://chem-bla-ics.blogspot.com/2009/07/updating-my-bioclipseqsar-fork-with.html |
| 21:29 |
zarah |
egonw's link is also http://tinyurl.com/kobn92 |
| 21:34 |
olass |
egonw: do you HAVE TO commit before switching branch? |
| 21:34 |
olass |
why? |
| 21:34 |
egonw |
no, you can also stash things |
| 21:35 |
egonw |
but commiting is fine |
| 21:35 |
olass |
oh |
| 21:35 |
egonw |
you can continue a commit later |
| 21:35 |
egonw |
consider this: |
| 21:35 |
egonw |
# do random half finished stuff |
| 21:35 |
egonw |
git commit -m "FIXME: finish this patch" |
| 21:35 |
egonw |
git checkout otherBranch |
| 21:35 |
egonw |
# do other stuff |
| 21:35 |
egonw |
git checkout firstBranch |
| 21:36 |
egonw |
git reset HEAD^1 |
| 21:36 |
egonw |
the last command will undo your last commit (the FIXME one) |
| 21:36 |
egonw |
and you can continue where you were left... |
| 21:36 |
egonw |
alternatively... you can do: |
| 21:36 |
egonw |
# do random half finished stuff |
| 21:36 |
egonw |
git commit -m "FIXME: finish this patch" |
| 21:36 |
egonw |
git checkout otherBranch |
| 21:36 |
egonw |
# do other stuff |
| 21:36 |
egonw |
git checkout firstBranch |
| 21:36 |
egonw |
# finish the commit |
| 21:37 |
egonw |
git commit -m "Now with a proper commit message" |
| 21:37 |
egonw |
# and now the git magic |
| 21:37 |
egonw |
git rebase -i HEAD~2 |
| 21:37 |
egonw |
and replace the 'pick' on the second line with 's', which will cause the last two patches to be merged into one new patch |
| 21:38 |
egonw |
asking you for a new commit message, which will initially consist of the two you gave earlier |
| 21:38 |
egonw |
(Or: yes, you always commit, but that does not mean you cannot finish half done stuff later) |
| 21:40 |
olass |
right |
| 21:40 |
egonw |
:) |
| 21:40 |
egonw |
get sleep now, read it tomorrow again, and then you'll comprehend |
| 21:44 |
olass |
soon, soon |
| 21:46 |
CIA-52 |
bioclipse.qsar: Egon Willighagen master * rc791146 / plugins/net.bioclipse.qsar/ontology/descriptor-algorithms.owl : Synchronizes the QSAR ontology with the QSAR SF project - http://bit.ly/1a8eu5 |
| 21:46 |
olass |
there you go |
| 21:47 |
olass |
ok, now sleep |
| 21:47 |
olass |
good night |
