Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-05-16

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Time Nick Message
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05:02 CIA-45 bioclipse: egonw * r5632 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.jche​mpaint/src/net/bioclipse/cdk10/jchempaint/action/ (16 files): Replaced MDLMolfileEditor cast with a cast to the respective interface, to allow future other file format editors
05:02 CIA-45 bioclipse: egonw * r5633 /bioclipse2/trunk/plugins/net.bioclipse.cd​k10.jchempaint/src/net/bioclipse/cdk10/jch​empaint/ui/editor/MDLMolfileEditor.java: Disabled text tab, because synching resource models is not implemented (yet)
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07:09 olas joined #bioclipse
07:09 olas hi all
07:16 EskilA joined #bioclipse
08:12 egonw joined #bioclipse
08:14 egonw olas: the JCP editor is now operational
08:14 egonw I need to fix two toolbar icons missing
08:14 egonw and implement the doSave()
08:24 jonalv joined #bioclipse
08:41 olas great egonw!
08:41 egonw looking at the save as now
08:42 olas super
08:43 jonalv save what as?
08:44 olas save molecules in different file formats
08:44 olas saveAs
08:44 olas from JCP
08:44 jonalv aha nice
08:48 steinbeck joined #bioclipse
08:49 olas I will plan the first alpha-release of Bioclipse branch 1.3.x, towards 2.0
08:49 olas will email about that to the ML
08:49 olas will be a wiki page
08:49 olas with things that need fixing for that
08:50 olas with JCP working, it's not too distant
08:52 jonalv are we continuing Bioclipse 1 development?
08:55 olas no
08:55 olas well
08:56 jonalv what news can be in 1.3.x then?
08:56 olas 1.3.1 is the devel branchtowards 2.0
08:56 jonalv huh?
08:56 olas currently head in bioclipse2
08:56 olas all plugins in bioclipse2 is vrsioned 1.3.1
08:56 jonalv you saying that 1.2 and 1.3 is not even a little bit the same?
08:56 olas exactly
08:56 jonalv that sounds unintuitive
08:56 rojasm joined #bioclipse
08:56 olas 1.2 = bioclipse1
08:57 olas 1.3=bioclipse2
08:57 olas it's just that we are not at the step of a 2.0 RC yet
08:57 jonalv why bot make 2=2?
08:57 jonalv 1.2=2 is kjust strange
08:57 olas olas (11:00:27 AM): it's just that we are not at the step of a 2.0 RC yet
08:57 jonalv call it 2.0 alpha then?
08:57 olas this was decided a long time ago on this list
08:58 olas soon, soon
08:58 * jonalv still thinkgs it's unintuitive
08:58 olas ok
08:58 steinbeck :-)
08:58 olas I'm fine with that
08:58 steinbeck 2.0 pre-pre-alpha
08:58 jonalv It totally fooled me anyway
08:59 olas ok
08:59 olas glad you now are enlightened
08:59 olas I will write this in the release notes so you need not worry
08:59 jonalv oki
09:00 olas It's just that it will be quite some time until 2.0 final release, and we want to release several version prior to that
09:00 jonalv actually I was telling masak yesterday that I thought it was time for a testbuild of what we are going to soon call bioclipse 2
09:00 olas :-)
09:00 olas The first part will be more or less chemoinformatics
09:00 olas the next part will be bioinformatics
09:00 olas makes sense to split it up that way
09:00 jonalv yea so it seems
09:01 olas but bioinformatics is important too
09:01 jonalv but right now we really should fix the borken console
09:01 olas damn borked console!
09:02 jonalv It really must run things in threads. Right now it steals the main gui thread and that's bad when it heads of into really-long-time-sdf-parsing actions
09:02 olas I agree with you
09:02 olas and I also like your thought of splitting managers in 2 parts, one for GUI and one for console
09:04 jonalv well it was just a solution I made that I thought more plugins might have use of. It can be done totally without any major changes and only where it's needed
09:04 jonalv Only downside is that you will have to write a new class that implements all the methods of the manager interace
09:04 jonalv but it's worth it
09:05 * jonalv likes the decorator pattern
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09:27 egonw olas: quick editor question...
09:27 egonw for the MDLEditor
09:28 egonw if the TextEditor bit has no EditorInput...
09:28 egonw it means I have to set that somewhere?
09:28 egonw might that be because the tab is currently no instantiated and shown?
09:28 egonw mmm...
09:28 egonw that's easily tested...
09:35 egonw ok, doSave() seems to work too now
09:36 egonw the editor stays 'dirty'...
09:36 egonw and now looking into fixign that...
09:38 EskilA_ joined #bioclipse
09:39 olas egonw: did you solve the problem?
09:39 * olas is off for lunch
09:40 egonw the save as is working now, yes
09:40 olas cool
09:40 olas is it using the CDKManager?
09:40 egonw I only need to figure out where to best reset the isDirty state
09:40 egonw huh?
09:40 olas should we not have a method in the Manager that does the actual saving in format?
09:40 * egonw does not know about the link between edtiors and managers
09:40 olas that's the Bioclipse2 way
09:41 olas there's no link
09:41 egonw that sounds good
09:41 olas but in order to be able to script
09:41 jonalv that would be great because than it can be used from the JSconsole as well
09:41 egonw but let's move that until after then end of May deadline
09:41 olas you need to place the functionality in the manager
09:41 olas and then call it from the editor
09:41 olas ok
09:41 olas no prob
09:41 egonw ack, yes sounds that the way forward
09:41 egonw for now, I'm just happy that we have JCP editor functionality again...
09:41 olas and it will also keep jonalv from screaming :-)
09:41 olas me too
09:41 olas it's a key piece
09:42 olas now: lunch!
09:42 * jonalv has started reading the book about threads now :)
09:46 CIA-45 bioclipse: egonw * r5634 /bioclipse2/trunk/plugins/net.bioclipse.cd​k10.jchempaint/src/net/bioclipse/cdk10/jch​empaint/ui/editor/MDLMolfileEditor.java: Implemented save
10:00 rojasm hi everyone
10:01 rojasm is there some explanation how to set the local database with bioclipse2?
10:03 jonalv rojasm, what do you mean?
10:03 rojasm I have some directory with several molecules
10:04 jonalv you want to reset the workspace?
10:04 rojasm And I want to visualize in the Bioclipse explorer
10:04 jonalv hang on I am checking
10:05 jonalv I think I would recommend importing them
10:05 jonalv but I am not sure that works
10:05 rojasm ok I check
10:07 rojasm It works fine
10:07 rojasm if I import the file
10:07 rojasm which I want e.g. a paar structures
10:07 jonalv okey, good
10:07 rojasm but my directory contains 40.000 molecules
10:07 jonalv oh aha
10:08 rojasm and I don't think it is a good idea to important then
10:08 jonalv just copy paste perhaps?
10:08 rojasm can I not use the localdatabase functionality
10:08 jonalv but that would mean making a copy of all them
10:08 jonalv structuredb?
10:08 rojasm yes
10:09 rojasm I check if I have this plugin
10:09 rojasm no I had closed
10:09 jonalv there is no gui for it yet :(
10:10 rojasm Project 'net.bioclipse.structuredb' is missing required source folder: 'tests/'net.bioclipse.structuredbBuild path121093256180157875
10:10 rojasm I have this problem
10:11 jonalv huh strange
10:11 rojasm maybe I have old version
10:12 jonalv but It's not ready for what you want to do with it yet
10:12 jonalv It can only be used from the javascript console for the moment
10:13 jonalv Try creating a new project and pointing the project to a test folder containing a few of your molecules. That might work
10:13 rojasm ok
10:15 * jonalv is heading to lunch now. Good luck! and cya later
10:22 steinbeck__ joined #bioclipse
10:44 edrin egonw: did you have time to look at the xep? i want to finish this now/today or tomorrow
10:50 egonw edrin: it's on my desk
10:50 egonw will email this afternoon/tonite
10:56 olas joined #bioclipse
11:06 edrin cool
11:12 olas egonw: is the http://cheminfo.informatics.indiana.e​du/~rguha/code/java/pharmacophore.rng an XML Schema?
11:12 olas can I rename it to .xsd and use it?
11:13 olas is it a DS schema?
11:13 olas like http://bp1.blogger.com/_JV9_q-dLKr0/R5CHobtuXRI/​AAAAAAAAAEk/ZEflI7PYy6k/s1600-h/00_ds_schema.PNG ?
11:13 olas egonw: let me know when you get back
11:19 egonw it's a relax NG schema
11:19 olas what's that?
11:19 egonw something similar to XML Schema
11:19 olas can I convert it to an XML Schema?
11:19 egonw but simplier
11:19 egonw not sure...
11:19 egonw let me check google
11:19 olas please do
11:20 egonw http://www.thaiopensource.com/relaxng/trang.html
11:21 egonw http://packages.ubuntu.com/hardy/trang
11:21 egonw cool
11:21 egonw did not know that tool
11:21 egonw was actually something I have been looking for :)
11:21 olas I'll try that
11:22 olas can you convert that schema for me?
11:22 * olas is not on ubuntu
11:22 egonw the first link has a general download
11:22 olas ok, will look
11:22 egonw seems java
11:23 olas hmm, it's from 2003
11:23 egonw http://www.thaiopensource.com​/download/trang-20030619.zip
11:23 egonw yes
11:23 egonw relax ng and xml schema go back a long time already :)
11:23 olas true
11:23 egonw unlike BC, some software can get finished
11:23 olas haha :-)
11:28 olas worked like a charm!
11:30 egonw great
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11:41 CIA-45 bioclipse: carl_masak * r5635 /bioclipse2/trunk/plugins/net.bioclipse.ui/sr​c/net/bioclipse/ui/views/JsConsoleView.java: [JsConsoleView} removed unused imports
12:36 steinbeck__ joined #bioclipse
12:45 masak olas: what's an InfiniteProgress?
12:47 egonw for processes with undefined end?
12:47 egonw sounds interesting...
12:47 egonw maybe it's for cases when you do not know on beforehand when the process is finished...
12:47 egonw or maybe it's just for infinate loops :)
12:54 olas InfiniteProgress? Where did you come upon that?
13:20 masak in a class I wrote
13:21 masak suddenly one day, it imported an org.eclipse.core.internal.file​system.local.InfiniteProgress
13:21 masak and I thought that was strange
13:23 masak turns out it was collateral damage from a commit jonalv made, though
13:26 masak jonalv: please refrain from importing internal classes
13:26 jonalv masak: Keep up the good work cleaning up the code!
13:26 masak bastard.
13:27 jonalv masak, let's dive back into fixing this JS console threading!
13:27 * masak mumbles
13:29 * olas VERY much would like to see the console fixed
13:30 * olas is building his first EMF-based editor :-)
13:30 olas with good progress
13:30 olas just that SF slows me down so much...
13:31 egonw yes!
13:31 egonw got that dirty thing fixed
13:32 masak olas: we're looking at it now
13:32 egonw just to stuble onto the next 'feature'
13:32 masak the problem is tricky
13:32 masak it's looking back at us
13:32 jonalv it's complicated...
13:34 CIA-45 bioclipse: egonw * r5636 /bioclipse2/trunk/plugins/net.bioclipse.cd​k10.jchempaint/src/net/bioclipse/cdk10/jch​empaint/ui/editor/MDLMolfileEditor.java: Removed duplicate code; add busy indication upon saving
13:34 CIA-45 bioclipse: egonw * r5637 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk10.jchempaint/src/net/bio​clipse/cdk10/jchempaint/ui/editor/ (JCPPage.java MDLMolfileEditor.java): Fixed reseting of dirty-ness upon saving
13:47 olas egonw: would be great if you could also set up the CMLEditor
13:47 olas should be very similar
13:47 egonw did you figure out how to make the editor validating?
13:47 egonw using that general WTP XML editor?
13:47 olas no :-(
13:47 olas hmm
13:47 olas never used that
13:48 olas there's a basic XMl editor in net.bioclipse.ui
13:48 egonw ic
13:48 olas with the drawback that it needs to be opened using a IFile
13:48 olas so need some tweaking to be general
13:48 egonw ok
13:48 olas the WTP XML editor does not have that drawback
13:48 egonw we should email the WTP project guys
13:48 olas and is validating
13:49 egonw and ask them how we can reuse their editor...
13:49 olas so maybe we should use it?
13:49 olas yes
13:49 olas please do
13:49 egonw added to the list in my TODO booklet
13:49 olas ack
13:49 egonw ummm... if I can find it
13:50 malick left #bioclipse
13:51 egonw added
13:55 CIA-45 bioclipse: egonw * r5638 /bioclipse2/trunk/plugins/net.bioclipse​.cdk10.jchempaint/src/net/bioclipse/cdk​10/jchempaint/ui/editor/JCPPage.java: Also reset JCPModel isModified upon save
13:56 CIA-45 bioclipse: egonw * r5639 /bioclipse2/trunk/plugins/net.bioclipse​.cdk10.jchempaint/src/net/bioclipse/cdk​10/jchempaint/ui/editor/JCPPage.java: Only fire a change event, if the bool actually changed
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14:29 CIA-45 bioclipse: carl_masak * r5640 /bioclipse2/trunk/plugins/net.bioclipse​.structuredb/src/net/bioclipse/structur​edb/business/IStructuredbManager.java: [IStructuredbManager] JavaDoc punctuation
14:30 CIA-45 bioclipse: carl_masak * r5641 /bioclipse2/trunk/plugins/ (5 files in 2 dirs):
14:30 CIA-45 bioclipse: [net.bioclipse.scripting]
14:30 CIA-45 bioclipse: [JsConsoleView]
14:30 CIA-45 bioclipse: * command evaluation is now executed in a separate thread
14:30 CIA-45 bioclipse: * collateral: extra newline on some results
14:31 jonalv we did it! :)
14:31 jonalv finally
14:34 egonw cheers
14:38 CIA-45 bioclipse: egonw * r5642 /bioclipse2/trunk/plugins/net.bioclipse.cd​k10.jchempaint/src/net/bioclipse/cdk10/jch​empaint/ui/editor/MDLMolfileEditor.java: Removed obsolete comment
14:39 * jonalv is trying to import a 6MB sdf file into structuredb, it takes a long time...
14:40 egonw that should not take so long
14:40 egonw seconds, I'd say...
14:40 jonalv I haven't even done 5%
14:40 jonalv I wonder what going on...
14:41 egonw weird
14:41 egonw any code I can try here?
14:41 jonalv of course it calculates fingerprints and stuff
14:42 jonalv Yea just update everything and run structuredb then write something like this in the console
14:43 jonalv structuredb.createLocalInstance("db");
14:43 jonalv structuredb.addStructuresFromSDF("db", "path to sdf file)
14:43 jonalv you can get a path to an sdf file by simple dragging it to the console
14:44 egonw ok, mom
14:44 egonw 5642?
14:44 egonw that's the right revision?
14:45 jonalv I am running 5641 but yea
14:45 egonw yeah, don't think that comment removal will make much of a difference :)
14:45 CIA-45 bioclipse: carl_masak * r5643 /bioclipse2/trunk/plugins/net.bioclipse.ui/sr​c/net/bioclipse/ui/views/JsConsoleView.java: [JsConsoleView] tab completion gives up after .5 seconds if js busy
14:46 * egonw is about to copy/paste commands into the console
14:46 jonalv you might wanna have that last one from masak though.
14:46 egonw nah...
14:46 jonalv or just don't touch tab :)
14:46 * egonw notes no visual creation of the local db
14:46 egonw which tabs should I not touch?
14:46 jonalv there is none
14:46 egonw of views?
14:47 jonalv structuredb has no gui yet
14:47 jonalv and it's very much a work in progress. It lacks a bunch of delete methods and some other stuff too
14:48 masak egonw: jonalv is referring to the tab completion feature
14:48 egonw why use the console for showing the progress??
14:48 egonw masak: ah, ack
14:48 masak before r5643, it locks up
14:48 egonw won't use that...
14:49 masak egonw: as to why use the console, it's based on the old idea of a text-only bc2
14:49 masak ...I think
14:49 egonw hahahah
14:49 jonalv among other things, yea
14:49 egonw a text-only BC2
14:49 masak anyway, it's pretty cool
14:49 egonw yeah, let's drop RCP
14:50 masak I don't mind if it's removed
14:50 egonw seriously... I'm impressed with the console
14:50 masak but I like looking at it now
14:50 egonw and really like that resource path file stuff drag/drop
14:50 masak egonw: just don't read source :)
14:50 egonw hehehehe
14:50 jonalv it got a lot worse today :)
14:50 masak I used to be proud, until about two hours ago
14:50 masak then we raped my code...
14:51 * egonw is looking for a large SDF on his disc
14:51 jonalv have you tried a small one?
14:51 egonw yeah, with two molecules...
14:51 jonalv oh
14:51 egonw took quite long really...
14:51 egonw at least two seconds...
14:51 jonalv mhm...
14:51 masak yes
14:52 masak it's so you notice the progress
14:52 masak (not really)
14:52 jonalv I never said databases where fast.
14:52 jonalv I wonder what takes up most time...
14:52 masak I bet it's all the classes and abstractions
14:52 masak we should get rid of those :)
14:53 egonw it's progressing...
14:53 egonw but for a 330kB file, it's taking too long
14:53 jonalv egonw, I create smiles, and fingerprints and stuff for each molecule
14:53 egonw we wonders where it's spending so much time
14:54 egonw the current performance is not acceptable...
14:54 masak glad we agree on that
14:54 jonalv where can I get a 300kb sdf file?
14:55 masak jonalv: duplicate the molecules in one that you have
14:55 egonw you can do a search in PubChem and then download the result set as SDF
14:55 egonw that's easiest
14:55 masak jonalv: yes, what he said
14:56 egonw ok, got to go now
14:56 jonalv cya
14:56 egonw I'll get that profiler online we use for the CDK
14:57 egonw and do some testing...
14:57 jonalv feel free to do that!
14:57 jonalv THat would be great
14:57 egonw it's proprietary code, but free for open source projects
14:57 jonalv okey
14:57 egonw and integrates very well with Eclipse
14:57 egonw will email
14:57 egonw later
14:57 jonalv nice
14:57 jonalv cya
14:57 egonw got to buy, make and eat dinner first now
14:57 egonw bbl
15:06 * jonalv is off
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20:12 rojasm joined #bioclipse
21:13 rojasm good afternoon!
21:14 rojasm how I can visualize the Editor for SDFiles in Bioclipse like the framework http://bioclipse.blogspot.com/2008/04/sdfe.html

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