Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-06-08

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All times shown according to UTC.

Time Nick Message
06:05 Gpox joined #bioclipse
07:04 olass joined #bioclipse
07:11 Gpox joined #bioclipse
07:23 CIA-40 bioclipse: goglepox * r11107 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintWidget.java: Commended out line for atom container bounds generator
07:24 CIA-40 bioclipse: goglepox * r11108 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.ui.sdfeditor/src/net/bioclipse/cdk/ui/sd​feditor/editor/SDFIndexEditorModel.java: Added check for null
07:29 CIA-40 bioclipse: goglepox * r11109 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfedi​tor/CDKFingerPrintPropertyCalculator.java: Use no notification atomcontainer when calculating fingerprints.
07:32 CIA-40 bioclipse: ospjuth * r11110 /bioclipse2/trunk/plugins/net.bi​oclipse.ds/html/maintopic.html: Wrote a simple Help page for DS feature.
07:40 rojasm joined #bioclipse
07:41 CIA-40 bioclipse: ospjuth * r11111 /bioclipse2/trunk/plugins/net.bioclipse.u​i/src/net/bioclipse/ui/Perspective.java: Commented out redundant ShowViewShortcuts since the views are not available.
07:47 CIA-40 bioclipse: ospjuth * r11112 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintView.java: Added public field to access view ID.
07:50 CIA-40 bioclipse: ospjuth * r11113 /bioclipse2/trunk/plugins/net.bioclipse.ds/ (3 files in 3 dirs): Added a perspective for Decision Support.
08:08 shk3 joined #bioclipse
08:20 CIA-40 bioclipse: goglepox * r11114 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfedi​tor/CDKFingerPrintPropertyCalculator.java:
08:20 CIA-40 bioclipse: Fixed serializing of fingerprints
08:20 CIA-40 bioclipse: Fixes bug #1209
08:20 zarah bug #1209 | http://tinyurl.com/n5h582
08:24 jonalv joined #bioclipse
08:25 olass Gpox++
08:31 shk3 hi all
08:31 zarah oh hai shk3
08:31 shk3 hi jonalv
08:31 jonalv hi shk3
08:32 shk3 I have another nwo problem
08:32 shk3 I am trying to catch an exception thrown in a manager method
08:32 shk3 but it seems it's not caught
08:33 shk3 is there anything I need to know about that?
08:34 olass shk3: you can throw a BioclipseException
08:34 olass jonalv: and RuntimeExceptions, right?
08:35 jonalv shk3: yes there are some problems with catching exceptions thrown in managers.
08:35 shk3 ah hm
08:36 jonalv I am not too sure on the spcifics but basically I think BioclipseException can be thrown and caught
08:36 shk3 ok
08:36 shk3 so I need to wrap other exceptions?
08:36 jonalv I seem to remember havign to deal with each exception seperately for ti to work although I can't remember why right now
08:37 jonalv shk3: if you want to be able to catch them yes. They will be wrapped
08:37 shk3 ok
08:37 shk3 I will try that
08:37 jonalv I am not 100% sure that not BioclipseExceptions are wrapped as well
08:37 shk3 thanks so far
08:37 jonalv I guess we need to come up with something here...
08:37 shk3 well, looking at the stack trace
08:37 shk3 it looks like I get a runtimeException
08:38 shk3 wrapping an InvocationTargetException
08:38 jonalv shk3: okey
08:38 shk3 wrapping the "real" exception
08:38 jonalv I am thining maybe one could unwrap it and rethrow the "real" exdfeption there. Given that it is not checked ofcourse
08:38 jonalv in that case w e can do nothing
08:38 * jonalv hates checked exceptions
08:40 shk3 hm ok
08:41 shk3 looks like bioclipseexception has no constructor taking an exception?
08:43 jonalv shk3: it should have
08:47 shk3 doesn't look like this helps
08:47 shk3 the exceptio is totally ignored
08:47 shk3 the catch is not entered
08:47 jonalv shk3: hm, what method is it?
08:48 * jonalv has a small feeling that there might be error management built in to the managers
08:48 jonalv so that the exception either ends up in a dialog or on the JS-console...
08:48 shk3 public void generate3dCoordinates(List<IMolecule> molecule,
08:48 shk3 BioclipseUIJob<List<IMolecule>> uiJob)
08:48 shk3 throws BioclipseException;
08:49 shk3 yes, there is a dialog
08:49 shk3 but I want to have a specific dialog
08:49 shk3 well, olass wants to have it
08:49 jonalv shk3: I seem to remember implementing that...
08:50 jonalv I wonder if we need something like "SpecificBioclipseException" for that :)
08:51 olass ManagerException?
08:51 jonalv ExtendedBioclipseException?
08:57 jonalv shk3: what is the use case?
08:58 shk3 the 3d generation should tell the user in a nice way if there is a NoSuchAtomTypeException
08:59 masak joined #bioclipse
09:01 shk3 can't find the bug
09:01 shk3 but olass requested that
09:01 shk3 and it makes sense
09:02 jonalv masak: please keep arguing against me
09:02 masak jonalv: ok.
09:02 jonalv shk3: I think the best solution right now is to do that inside the manager method in that case
09:02 masak jonalv: I told you, I'm not going to argue unless you pay.
09:02 shk3 hm ok
09:02 jonalv masak: you could be arguing on your spare time...
09:03 masak no I couldn't.
09:03 shk3 but that means I need to pop up a dialog in a manager method?
09:03 jonalv shk3: but the problem with that is that it's hard to know what to do with the exception, we don't want to p[op up a dialog when running JAvaScripts...
09:03 CIA-40 bioclipse: goglepox * r11115 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfedi​tor/handlers/CalculatePropertyHandler.java: Added error handling to avoid classcast exception
09:04 shk3 yes
09:04 shk3 that was my idea as well
09:04 jonalv so I still think it's better to throw a specigic exception for this taht actually survives thorugh the aop layer and then act upon that
09:04 jonalv although masak does not like that...
09:04 shk3 sounds good
09:04 shk3 for me
09:04 shk3 a bit complicated, but it looks like the only way
09:06 masak I dislike it, yes.
09:06 jonalv masak: suggest something better then...
09:06 masak it further mixes in internals of the AOP framework into the rest of the application.
09:08 Gpox maby a handleException on the BioclipseUIJob as you can't catch the exception if you run in a job
09:09 jonalv Gpox: Probably not on the BioclipseUIJob but perhaps on the hook...
09:09 jonalv ...or both
09:10 jonalv I don't know, masak do you have any ideas?
09:10 masak no.
09:14 jonalv olass: did you remove the consolelog when you built RC1?
09:15 olass don't think so
09:15 olass not deliberately
09:15 olass nope, still there in bioclipse.product
09:16 jonalv okey probklem
09:16 jonalv I can not start Bioclispe on this lousy operating system and get logging
09:17 jonalv I don't know how to fing the log file
09:24 jonalv js execution is not working in RC1
09:24 shk3 well, I leave the issue of exception handling to you
09:24 shk3 please tell me if you have come to a decision
09:24 * jonalv is giving it to masak++ :)
09:24 masak hao hao.
09:25 masak olass: there's no download link in the RC1 announcement...
09:25 olass hmm, that is not good
09:26 masak ah, the one on bioclipse.net, I mean.
09:26 jonalv olass: can you hadd RC1 as version on Bugzilla?
09:26 olass ok
09:26 jonalv |add
09:26 olass jonalv: oki
09:27 * jonalv is going to spend some time finding what is not working in Bioclipse RC1 and it's nice to file the bugs to the correct version...
09:29 olass jonalv: added RC1
09:29 jonalv olass++
09:29 masak olass++
09:29 masak (we'll need it)
09:29 masak :P
09:44 masak olass: it says "2.0 beta 4" on the RC1 welcome screen!!!
09:45 masak don't we have a global version setting?
09:48 jonalv masak: if only...
09:48 jonalv :/
09:49 masak olass: might it be a good idea to change versions like this *after* the release, so that there's plenty of time to find and up all of them?
10:01 jonalv shk3: did you manage to come up with a solution?
10:04 shk3 what for? the exception stuff?
10:04 jonalv shk3: yea
10:04 shk3 no
10:04 shk3 I leave it to you
10:05 shk3 you need to decide, I think
10:06 jonalv shk3: please give me some bug ticket if so otherwise I will forget it...
10:08 shk3 #1218
10:14 jonalv olass: ping
10:24 edrin joined #bioclipse
10:25 edrin hi
10:25 zarah privet edrin
10:25 masak ni hao edrin
10:32 * jonalv @ lunch
10:47 olass jonalv: pong
10:53 CIA-40 bioclipse: ospjuth * r11116 /bioclipse2/trunk/plugins/net.bioclipse.ui.busine​ss/src/net/bioclipse/ui/business/UIManager.java: Removed line that outputted "chosen editor + editorID" on ui.open() since this clutters the console. Solves #1219.
10:55 olass edrin: could you please look at bug 1217?
10:58 CIA-40 bioclipse: ospjuth * r11117 /bioclipse2/trunk/plugins/n​et.bioclipse.ui/plugin.xml: Updated intro page to say "Welcome to Bioclipse 2.0". Solves #1220.
11:36 CIA-40 bioclipse: ospjuth * r11118 /bioclipse2/trunk/plugins/ (14 files in 10 dirs): Updated db file to contain FP and Inchi. Also made initialize() method public and available from IDSTest to allow for initialization in background on DSView start.
11:43 jonalv shk3: can you give me the bug about the 3d generations + a file that failes_
12:02 jonalv shk3, olass: ping
12:02 olass pong
12:03 jonalv olass: shk3 told me that you wanted special error messages from cdk.generate3dCoordinates
12:03 jonalv so shk3 asked me for a system to get exceptions in managers to reach the calling code
12:03 * olass cannot remember that at all
12:03 olass ok...
12:03 jonalv for the moment that method is not run as a job
12:04 olass ok, that is not ideal
12:04 shk3 sorry, i was to lunch
12:04 jonalv However when it is run as a job (as it should be) how do you guys expect to act in gui thread  upon an exception in a job thread?
12:04 shk3 there was a bug (I think be olass, but I may be wrong) that a NoSuchAtomTypeException
12:05 shk3 should be displayed like "we cannot do 3d for this due to unusual atom types" or so.
12:05 jonalv olass, shk3: The whole problem is wrongly formulated. What exactly is it you guys want?
12:05 shk3 and not just with default message
12:05 shk3 well, the generate3d methods should throw two exceptions:
12:05 shk3 CDKException and NoSuchAtomTypeException
12:06 shk3 in case of NoSuchAtomType, a message like above shouled come up
12:06 jonalv shk3: the generate3d method should be run as a job, hence no exceptions should be thrown to the calling thread
12:07 * olass agrees with jonalv
12:07 shk3 well, but what to do then?
12:10 jonalv shk3: so the error message we have no is not good enough? How can I see this error message?
12:10 jonalv |now
12:10 jonalv shk3: would you like to have that bug by the way? :)
12:11 jonalv Pz 830
12:11 jonalv @pz 830
12:11 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=830
12:12 shk3 in the sample data,
12:12 shk3 ah, it's not in there
12:12 shk3 I can mail you an example
12:13 shk3 olass: do you remember you filed that bug?
12:13 shk3 I can't find it
12:13 shk3 but it was there
12:13 olass no
12:13 olass don't remember
12:13 * jonalv wait's for a mail then
12:14 jonalv shk3: can I give bug 830 to you?
12:14 shk3 mom
12:14 shk3 well,
12:14 shk3 as long as there is no solution for this error problem,
12:14 shk3 I can't proceed
12:14 shk3 or we give up on it
12:15 shk3 but then, I will be blamed for the bug
12:15 shk3 email sent
12:16 shk3 i search for that bug again
12:16 jonalv shk3: I want to try an see how bad it is.
12:16 jonalv shk3: about 830, can you do that?
12:17 shk3 well, i did it
12:17 shk3 but then I found the exception handling no longer works
12:17 shk3 so...
12:18 jonalv shk3: sry you lost me now...
12:18 jonalv shk3: you rewrote it as a job?
12:18 shk3 yes
12:18 jonalv and what failed?
12:19 CIA-40 bioclipse: carl_masak * r11119 /bioclipse2/trunk/features/se.uu.fa​rmbio.hivpred_feature/feature.xml:
12:19 CIA-40 bioclipse: [hivpred_feature] 'et al.' should have a '.'
12:19 CIA-40 bioclipse: It's Latin for 'et alii' or 'et aliae', hence an abbreviation.
12:19 shk3 that I can no longer catch the NoSuchAtomException
12:19 shk3 and show nice message
12:19 shk3 olass: please search the bugs you filed
12:19 shk3 i can't find this one
12:19 jonalv shk3: well you can't do that now either...
12:19 shk3 but it was there
12:19 shk3 why not?
12:19 jonalv shk3: it's not working now anyway...
12:20 shk3 what is not working?
12:20 shk3 you lost me
12:20 shk3 3d generation is working?
12:20 jonalv shk3: I get the standard error message when trying to generate 3d coords for that file..
12:20 shk3 yes
12:20 shk3 ah sorry
12:21 shk3 this is because right now the modelbuilder3d throws exception only
12:21 shk3 I changed it to throw CDKException or NoSuchAtomException
12:21 shk3 but this change is not accepted for cdk
12:21 shk3 another problem
12:21 jonalv shk3: are you telling me that it has worked?
12:22 shk3 yes
12:22 shk3 but with update of cdk packages in bioclipse,
12:22 jonalv but I thought you said that the aop stuff swallows all exceptions?
12:22 shk3 in non-job mode, it worked
12:22 jonalv ah
12:22 shk3 with update of cdk packages,
12:22 jonalv well there is no way you can get it to work in job-mode
12:22 shk3 model builder got overwritten to throw Exception
12:23 shk3 then I cannot differentiate exceptions
12:23 shk3 but this is another problem
12:23 jonalv shk3: yes
12:23 jonalv shk3: but as I see it there is nothing for me to do
12:23 shk3 olass: can you please check your bugs?
12:23 shk3 sorry, I don't want to discuss this issue for hours without you knowing what I refer to
12:23 olass shk3: for what?
12:24 olass please xplain in more detail
12:24 shk3 for this "give better message when NoSuchAtomException"
12:24 olass @pz NoSuchAtomException
12:24 zarah olass: I couldn't find anything on 'NoSuchAtomException' in the database.
12:24 olass @pz give better message
12:24 zarah olass: I couldn't find anything on 'give better message' in the database.
12:24 olass shk3: are you sure it exists?
12:24 shk3 yes
12:25 olass pelezilla says no
12:25 shk3 i got into lengthy discussions with egon about that stuff
12:25 olass sry, can't find the bug
12:25 shk3 ok, then we leave that
12:25 jonalv shk3: or what do you want me to do in 1218?
12:25 shk3 it's bit unfortunate
12:25 shk3 one of you filed a bug report
12:25 shk3 I tried to fix it
12:26 shk3 got called an idiot and moron
12:26 shk3 now nobody remembers
12:26 shk3 not too great
12:26 jonalv shk3: I think the problem is intresting regardless of the status of the bug ticket...
12:26 shk3 I think so too
12:27 jonalv shk3: so you are saying that 1218 is not an issue when not running as a job?
12:28 masak olass: plugins/net.bioclipse.ui/content/whatcanIdo.xhtml seems out-of-date. it talks about bc2alpha.
12:28 shk3 ha
12:28 shk3 got it:
12:28 shk3 @pz 830
12:28 olass masak: thanks
12:28 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=830
12:29 masak olass: I'm doing some data mining on version strings in the source tree now, to see if there are better solutions.
12:29 shk3 so this is the problem
12:29 shk3 egon reported it
12:29 jonalv shk3: so you are saying that 1218 is not an issue when not running as a job?
12:29 shk3 well, it least it was not
12:29 shk3 sorry, I am a bit lost
12:30 shk3 since I had hours of discussions to get that small change into cdk
12:30 jonalv shk3: if so then there is nothing I can do because there is no way of fixing it for running as jobs
12:30 shk3 that generate3d has throws CDKException, NoSuchAtomTypeException
12:30 shk3 instead of throws Exception
12:30 shk3 it really spoilt me 2 weeks
12:31 shk3 and then it got silently removed again
12:31 shk3 without anybody telling me a work about it
12:31 jonalv shk3: something in cdk?
12:31 shk3 I feel a bit lost with that
12:31 shk3 I wait for egon to comment on the cdk change
12:31 shk3 if I am not allowed to change cdk to throw more specifc exceptions,
12:31 shk3 I cannot do anything about it anyway
12:32 jonalv shk3: yea he has just been moving so it's a bit of a mess I can imagine...
12:32 shk3 Let's wait for egon
12:32 shk3 and then come back to the whole issue
12:34 shk3 sorry, the bug is 860
12:35 shk3 not 830
12:35 edrin @pz 1217
12:35 shk3 @pz 860
12:35 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1217
12:35 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=860
12:35 jonalv I am going to llok at the dialog that shows error messages. It's not doign a great job with wrapped errors...
12:36 shk3 jonalv: just read your comment
12:36 shk3 "
12:36 shk3 A method run
12:36 shk3 as a job can not return nor throw exceptions.
12:36 shk3 "
12:36 shk3 if this is true, then we/egon need to accept this.
12:37 shk3 I will then commit the generate3d as job
12:37 edrin olass: and this is only happening when the hivpred is installed?
12:37 olass ask jonalv
12:37 olass he reported it
12:37 shk3 as comment on bug 860 that it cannot be done in a job
12:38 olass shk3: egonw reported bug 860, not me
12:38 jonalv edrin: yes
12:38 shk3 but I still feel the problem could come up in other situations as well
12:38 shk3 olass: yes, sorry for that
12:38 jonalv edrin: I suggeest you try yourself, that might give some insight...
12:38 olass no worries :)
12:38 shk3 but you understand the problem now?
12:38 jonalv shk3: me?
12:39 shk3 and olass
12:39 olass jonalv: if sonething goes wrong in a job, how do we report that?
12:39 olass Eclipse solves that by returning an IStatus.ERROR
12:39 olass well, a Status with severity=ISTatus.ERROR
12:39 jonalv olass: if called from JavaScript console then on the js console. If called from java then with the Logutils.handleException method wich shows a dialog
12:40 jonalv olass: I am looking into fine tuning that dialogs way of dealing with wrapped exceptions now
12:40 olass oki
12:40 olass soudns good
12:40 olass sounds
12:41 shk3 if that dialog give the message of the exception (the "real one"),
12:42 shk3 it might also fullfill egons bug 860
12:46 jonalv shk3: yea it's hard to know which message that is though, best would be if you could wrap that message in a BioclipseExcpetion. hm or I can probably do that...
12:46 jonalv :)
12:47 edrin jonalv: it could be that this is associated with the code that "collects" the managers in the jsexecution plugin...
12:48 jonalv edrin: yea that is my guess as well, I thought you would be able to pinpoint it further...
12:48 CIA-40 bioclipse: ospjuth * r11120 /bioclipse2/trunk/plugins/​net.bioclipse.ui/content/ (introduction.xhtml root.xhtml whatcanIdo.xhtml): Removed all references to bioclipse2-alpha in help system. We really should update the docs.
12:48 edrin jonalv: i would if there would not be that much to do
12:48 jonalv edrin: okey
12:48 edrin jonalv: i fear i cant do this right now
12:49 jonalv olass: if edrin can't fix this then I think we should remove that feature from the update site...
12:49 olass yes
12:49 edrin jonalv: the code in jsexecution that collects the managers is a copy of the code in the jsenvironment once
12:49 olass a bit sad
12:49 jonalv edrin: code copying is rarely a good way to go...
12:49 edrin jonalv: maybe this is a very simple to solve thing
12:49 edrin i know
12:50 edrin it is a relict
12:50 shk3 olass: documentation is a major issue, i think
12:50 edrin from the time when the jsexecution was running without bc2
12:50 shk3 before the 2.0, release, we could have a few days of documentation writing
12:50 olass jonalv: file me a bug to remove teh se.uu.farmbio.hivpred feature
12:50 shk3 including updating website etc.
12:50 olass and I'll do it for RC2
12:50 jonalv masak: do you think you could have a look at edrins failing code?
12:50 olass shk3: agreed
12:50 olass I am looking into it
12:50 masak jonalv: yes, sure.
12:50 shk3 so that for the release, all is polished
12:51 edrin jonalv: but since jsexecution does not run without bc2 now anyway, you can just remove this code and use the code/plugin api from the jsenvironment to collect teh managers?
12:51 olass shk3: I am not sure we will have time for it
12:51 olass but we'll take it as soon as we can
12:51 olass fixing bioclipse2 is more important than the website
12:51 jonalv edrin: I have no idea, masak is probbaly the one who knows most about that...
12:51 masak edrin: sorry, I missed the earlier part of the discussion. has jsexecution stopped working?
12:51 olass shk3: the help system is what needs the most work
12:51 shk3 yes
12:51 shk3 many plugins still lack help pages
12:51 olass shk3: any help there is welcome
12:52 olass especially on chemoinfo stuff
12:52 edrin masak: well, it works, and also the xmpp featured bc 2 release still works with the hivpred plugin
12:52 shk3 the problem is, i can't really do help for plugins i have not written
12:52 olass shk3: I know
12:52 olass and you shouldn't
12:52 edrin so this is most likely associated with a change related to NWO, specifically one of the newest changes to NWO
12:52 masak edrin: that sounds likely, yes.
12:54 edrin masak: the code in jsexecution that collects the managers uses some "reflection hack", so it did not "depend" on the bc2 plugins, but since jsexecution does depend on bc at other points, too... this code could need cleaning...
12:54 CIA-40 bioclipse: ospjuth * r11121 /bioclipse2/trunk/plugins/net​.bioclipse.ds.dblookup.bursi/ (data/cas_4337_fp_inch.sdf data/cas_4337_props.sdf plugin.xml): A new update to the DB SDF since the last one was missing a linebreak.
12:54 CIA-40 bioclipse: shk3 * r11122 /bioclipse2/trunk/plugins/net.bioclip​se.cdk.jchempaint/doc/jcpEditor.html: upated the icon in the help to the one used in reality
12:54 jonalv edrin: things may have changed name...
12:54 CIA-40 bioclipse: ospjuth * r11123 /bioclipse2/trunk/plugins/net.bioclipse.ds/ (4 files in 3 dirs): Added a job to initialize all Tests in background upon view opening.
12:54 masak edrin: sounds like it could need cleaning up, yes.
12:55 edrin i am very sorry, that this is currently an issue i can't solve...
12:55 edrin i am not home, so cant use my computer
12:55 masak edrin: ok.
12:55 masak edrin: if there's anything I can do, let me know.
12:55 masak I'll have a look at the code right away.
12:57 edrin masak: sorry, gone
12:57 edrin masak: yes, this would be great thanks
12:58 CIA-40 bioclipse: ospjuth * r11124 /bioclipse2/trunk/plugins/net.bioclipse.ds/ (plugin.xml src/net/bioclipse/ds/ui/actions/): Removed ReportHandler since moved to separate plugin.
12:59 CIA-40 bioclipse: shk3 * r11125 /bioclipse2/trunk/plugins/net.bioclip​se.specmol/src/net/bioclipse/specmol/​ui/views/SpecmolLabelProvider.java: changed icon
12:59 masak edrin: it compiles, at least.
12:59 edrin masak:
13:00 edrin masak: yes, the most likely happens when then jsexecution tries to collect the managers... and maybe something was changed either in the platform or in the hivpred plugin, thus it returns not a valid object for hivpred i guess
13:00 masak edrin: best thing I can do right now is to investigate how jsexecution handles its manager bindings. that might prepare me for understanding what hivpred does to disturb it.
13:00 edrin masak: yes, i think thats the right way
13:01 masak glad we agree. :)
13:10 CIA-40 bioclipse: goglepox * r11126 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MultiPageMoleculesEditorPart.java: Added syncing of JCP on save
13:18 CIA-40 bioclipse: jonalv * r11127 /bioclipse2/trunk/plugins/net.bioclipse.core​/src/net/bioclipse/core/util/LogUtils.java: added functionality to LogUtils.handleException for dealing better with wrapped exceptions.
13:19 jonalv shk3: have a look at the genereadte3d coords exception now. If you want to write something else you can wrap it in a BioclispeException and that message will be the first in the dialog.
13:20 shk3 thanks
13:20 shk3 will do that asap
13:20 shk3 just finishing another thing (looks like I can close a bug!!!!)
13:25 jonalv woho :)
13:29 shk3 gives you that feeling of satisfaction
13:47 CIA-40 bioclipse: goglepox * r11128 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui​.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/ (4 files in 2 dirs):
13:47 CIA-40 bioclipse: Changed molTable.parseProperties() to take Collections<String>
13:47 CIA-40 bioclipse: to choose which properties to be stored in the model.
13:47 CIA-40 bioclipse: Fixes bug # 1222
13:47 CIA-40 bioclipse: goglepox * r11129 /bioclipse2/trunk/cdk-externals/trunk/org.o​penscience.cdk.render/src/org/openscience/c​dk/renderer/font/AbstractFontManager.java:
13:47 CIA-40 bioclipse: Changed for < to <= in font mangaer code
13:47 CIA-40 bioclipse: If the sacale is the same or less than the lowest value
13:47 CIA-40 bioclipse: the lowest should be returned
13:47 CIA-40 bioclipse: [jchempaint-primary] r14604
13:47 CIA-40 bioclipse: Fixes bug #1207, #938
13:48 zarah bug #1207 | http://tinyurl.com/mq9xgj
13:50 CIA-40 bioclipse: shk3 * r11130 /bioclipse2/trunk/plugins/net.bioclipse.​nmrshiftdb/src/net/bioclipse/nmrshiftdb/ (9 files in 3 dirs): solves bug #601, also adds an nwo-compliant manager to nmrshiftdb plugin
13:50 zarah bug #601 | http://tinyurl.com/nws2lz
13:51 CIA-40 bioclipse: jonalv * r11131 /bioclipse2/trunk/plugins/net.bi​oclipse.core/src/net/bioclipse/ (4 files in 2 dirs): Made IReturner generic. Fixes bug: #1214
13:51 zarah bug #1214 | http://tinyurl.com/n86ocj
14:04 jonalv shk3: I jsut tried to run hko3.sjs. The progressmonitor is not so nice... I first ticks up to about 99% and then stans at 99% almost forever...
14:04 shk3 yes
14:04 shk3 but I have no idea why
14:04 jonalv shk3: oh and then I get a ConcurrentModification error... :(
14:05 shk3 hm
14:05 shk3 didn't get that
14:05 shk3 i will try
14:11 masak edrin: I notice you used tab characters for indenting the files in n.b.jsexecution. we have a policy not to use tab characters in Bioclipse 2 code.
14:11 masak edrin: would you be OK with me going through all the files, and replacing the tab characters with spaces?
14:12 masak edrin: at the same time, I could shorten some longer-than-80-chars lines, and correct some errors in the comments.
14:13 edrin edrin: no problem, if you have the patience to do this, please do so
14:13 edrin err
14:13 edrin masak:
14:14 edrin no problem, if you have the patience to do this, please do so
14:14 masak :)
14:14 jonalv :)
14:14 masak edrin: I think it'll be easier for me to reason about the code after this.
14:29 CIA-40 bioclipse: jonalv * r11132 /bioclipse2/trunk/plugins/net.bioclipse.script​ing/src/net/bioclipse/scripting/JsThread.java: give a SubProgressMonitor to the managers when running JavaScripts so that extra calls to beginTask does not totally reset the monitor. Fixes bug: #1099
14:29 zarah bug #1099 | http://tinyurl.com/mqkfy8
14:29 CIA-40 bioclipse: shk3 * r11133 /bioclipse2/trunk/plugins/​net.bioclipse.nmrshiftdb/ (META-INF/spring/ META-INF/spring/context.xml plugin.xml): solves bug #601, also adds an nwo-compliant manager to nmrshiftdb plugin
14:29 zarah bug #601 | http://tinyurl.com/nws2lz
14:30 shk3 jonalv: the hko3 example works for me
14:30 jonalv shk3: probably something with threading then... :/
14:30 shk3 but it still has the problem with save-and-open-as-sdf-being paralell.
14:30 shk3 i will use bioclipseuijob for that
14:30 jonalv shk3: oki
14:30 shk3 might be your problem goes away then as well
14:31 jonalv shk3: yea it's possible
14:31 shk3 I have a look at the generate3d stuff first
14:31 jonalv shk3: yea
14:49 CIA-40 bioclipse: ospjuth * r11134 /bioclipse2/trunk/plugins/net.bioclipse.ds.d​blookup/src/net/bioclipse/ds/dblookup/impl/ (DBExactMatchTest.java DBNearestNeighborTest.java): Adapted for new API for properties on MolTableModel.
14:49 shk3 jonalv: which plugins do I need to update to test the new exception handling?
14:50 jonalv shk3: uhm I don't know
14:50 jonalv shk3: do I really have to figure that out?
14:50 jonalv shk3: How about you update everything?
14:50 shk3 well, that takes a while
14:50 shk3 but i will figure out
14:50 masak no, it's one operation.
14:51 jonalv shk3: you should run svn from terminal...
14:51 masak if it isn't your SVN is set up the wrong way.
14:52 masak Subclipse-- # making simple things difficult
14:54 olass subclipse sucks
14:56 masak they should have named it suckclipse.
14:56 CIA-40 bioclipse: goglepox * r11135 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfe​ditor/business/MoleculeTableManager.java: Make use for generics on IReturner
14:57 CIA-40 bioclipse: goglepox * r11136 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfe​ditor/business/MoleculeTableManager.java: Better use of SumMonitor in saveSDF
14:57 CIA-40 bioclipse: goglepox * r11137 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.ui.sdfeditor/src/net/bioclipse/cdk/ui/sd​feditor/editor/SDFIndexEditorModel.java: Allow for more than calculated properties
14:58 olass masak: email them and suggest it!
14:58 olass and please fwd their answer
14:58 masak olass: "dear developers..."
14:58 olass "I have a humble suggestion..."
14:58 masak "have you ever considered..."
15:01 CIA-40 bioclipse: carl_masak * r11138 /bioclipse2/trunk/plugins/net.bioclipse.j​sexecution/src/net/bioclipse/jsexecution/ (8 files in 5 dirs): [n.b.jsexecution] tabs -> spaces
15:03 shk3 jonalv: the error message looks still the same for me
15:03 shk3 sorry
15:04 jonalv as in never mind?
15:04 jonalv shk3: or?
15:06 shk3 well, egon could reopen his bug
15:06 shk3 so i am afraid i have to ming
15:06 jonalv shk3: ming?
15:07 jonalv shk3: you lost me...
15:07 shk3 mind
15:07 shk3 sorry
15:07 jonalv shk3: LOL
15:07 masak MING!
15:07 jonalv so you have updated everything and it still looks the same?
15:08 masak zarah: never mind.
15:08 * zarah never minds
15:08 jonalv shk3: you did look at the extra information int that dialog did you?
15:09 shk3 I don't get that dialog
15:09 shk3 i get one saying:
15:10 shk3 'cdk.generate3dCooardinates' has encountered a problem.
15:10 shk3 An internal error occured during: "cdk.generate3dCoordinates"
15:10 shk3 ah, mom
15:10 shk3 that's because I have the bioclipseuijob stuff used
15:11 shk3 did not yet commit that
15:11 shk3 hm
15:11 shk3 what to do?
15:11 jonalv I don't know what you are doing...
15:11 shk3 do you think I should commit that?
15:14 olass shk3: do not commit things that do not work
15:14 olass that is wrong
15:15 shk3 well, it works
15:15 shk3 it just has that "not too great error message"
15:15 shk3 and it solves a bug
15:15 shk3 I can't see how to discuss this with jonalv with him seeing what's going on
15:16 jonalv shk3: commit it, I will lokk at it
15:16 shk3 ok, thanks
15:16 shk3 I have a look through it and commit
15:17 jonalv shk3: you will probably have to explain again what the problem was though... :)
15:18 CIA-40 bioclipse: ospjuth * r11139 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfe​ditor/business/IMoleculeTableManager.java: Added BioclipseJob<Void> on parseProperties to be able to join a parsing job
15:19 CIA-40 bioclipse: goglepox * r11140 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfe​ditor/business/MoleculeTableManager.java: Added method with IReturner for parseProperties(...)
15:20 jonalv Gpox: Oh nice so I don't have to :)
15:20 jonalv Gpox++
15:21 olass Gpox++
15:21 CIA-40 bioclipse: ospjuth * r11141 /bioclipse2/trunk/plugins/net.bioclip​se.ds.dblookup/src/net/bioclipse/ds/d​blookup/impl/DBExactMatchTest.java: Use new API in parseProperties for joining the job.
15:22 shk3 ok, commited
15:22 CIA-40 bioclipse: shk3 * r11142 /bioclipse2/trunk/plugins/ (4 files in 3 dirs): made the 2d/3d coordinate generation jobs
15:22 shk3 jonalv: retry the C0002 file 3d generation and you will see a rather uninformative message
15:22 shk3 compare this with bug #860
15:22 masak edrin: "Please refer to the eclipse documentation to learn more about asyncExec() and asyncExec()." is that a spelling error?
15:22 * jonalv updates
15:23 edrin yes
15:23 masak edrin: what should it say?
15:23 shk3 Create2dHandlerWithReset l. 100 has the try-catach which should solve this,
15:23 shk3 but which does not work with jobs
15:23 edrin syncExec()
15:23 edrin in one case
15:23 shk3 I hope that made things clear.
15:23 masak ok.
15:23 edrin masak: btw. the load jar code is not properly working, dont use it :)
15:24 masak edrin: ok.
15:24 edrin (just to mention in case you were interested how this works)
15:24 masak not beyond wanting to fix the immediate problem, no.
15:25 edrin okey
15:26 CIA-40 bioclipse: carl_masak * r11143 /bioclipse2/trunk/plugins/net.bioclipse.j​sexecution/src/net/bioclipse/jsexecution/ (5 files in 3 dirs):
15:26 CIA-40 bioclipse: [n.b.jsexecution] shortened long lines
15:26 CIA-40 bioclipse: This was possible for all lines except two long Javadoc lines in
15:26 CIA-40 bioclipse: Activator.java which didn't have any spaces in them.
15:28 * masak digs the comment /* this is a recursive hack */
15:28 shk3 jonalv: did you read my comment?
15:29 jonalv shk3: sry something else turned up first
15:29 shk3 no prob
15:29 shk3 just wanted to make sure you got hold of it
15:29 shk3 I think it's more important to have this in a job than the style of the error message
15:30 shk3 so this was actually a good commit
15:30 * shk3 is down to 3 bugs, btw
15:32 Gpox Then maby you could go through your reported bugs and verify thate the fixed ones are solvved and close them if they are
15:37 masak edrin: can I remove the file ScriptContextFactory? it's empty, save for some commented-out code.
15:43 olass how do I get my bundle classloader?
15:43 olass anyone who knows?
15:50 masak olass: http://dev.eclipse.org/newslists/n​ews.eclipse.platform/msg52143.html
15:50 zarah masak's link is also http://tinyurl.com/l9cko6
15:50 olass jo
15:51 olass that's how I do it
15:51 masak well, good then.
15:54 jonalv shk3: could you write down that thing in a bug for me it seems I don't have tiem to look at it today... :(
15:56 shk3 shall i put it in bug 1218?
15:59 shk3 ok, done so
15:59 shk3 sorry for all the trouble
15:59 jonalv shk3: np
16:00 jonalv shk3: I just can't do all at the same time..
16:00 jonalv shk3: sry
16:00 shk3 np
16:00 shk3 i don't expect that ;-)
16:14 edrin masak: ah, i remember
16:16 edrin masak: i think i added this file once as a "stub/reminder" that should suggest this might be a good location to put "spawn js context" code to, that the javascript console could use to spawn a js context (in case we have various instances of js console one day)
16:17 masak sometimes I sense the cognitive dissonance between our two approaches to scripting is very large.
16:18 * olass nods silently
16:18 edrin masak: this was just a suggestion
16:18 masak yes, of course.
16:19 * olass continues to nod i silence
16:19 masak edrin: can there even be several JS consoles? I mean, is it even possible to open several instances of JsConsoleView?
16:19 edrin i think so
16:19 CIA-40 bioclipse: jonalv * r11144 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfe​ditor/business/MoleculeTableManager.java: one method. Wrapping method that dispatches seems to cause problems. (Too many methods with the same name) Should probably look into that sometime...
16:19 edrin why shouldnt it?
16:19 * olass looks a bit stupid while just nodding but continues to do so anyway
16:20 edrin masak: user could click "New Js Console"... then a new tab is added to the console view.
16:21 edrin the new tab gets to ScriptContextFactory and spawns a new js context.
16:21 edrin this is then the context of the js console instance
16:22 edrin masak: or did you think that the rhino does not support multiple instances, i mean this could be, i am not entirely sure about what's going on within mozilla's code
16:23 masak I think it does, that's probably not a problem.
16:23 CIA-40 bioclipse: ospjuth * r11145 /bioclipse2/trunk/plugins/net.bioclip​se.ds.dblookup/src/net/bioclipse/ds/d​blookup/impl/DBExactMatchTest.java: Removed a debugging line that spawned LOTS of output.
16:24 edrin ok
16:24 edrin masak: you dont like the idea?
16:30 edrin ?
16:30 edrin does this now mean he does not like it?
16:38 olass dunno
16:38 edrin ah ok
16:38 CIA-40 bioclipse: ospjuth * r11146 /bioclipse2/trunk/plugins/net.bioclipse.ds.d​blookup/src/net/bioclipse/ds/dblookup/impl/ (DBExactMatchTest.java DBNearestNeighborTest.java): Added some debugging for tracing initialization error.
16:39 CIA-40 bioclipse: ospjuth * r11147 /bioclipse2/trunk/plugins/net.bioclipse.ds.birt/: Initial import.
16:47 shk3 joined #bioclipse
16:50 CIA-40 bioclipse: ospjuth * r11148 /bioclipse2/trunk/plugins/net.bioclip​se.ds.dblookup/src/net/bioclipse/ds/d​blookup/impl/DBExactMatchTest.java: Handle exception if initialization of tests fails.
17:19 shk3 joined #bioclipse
17:31 edrin left #bioclipse

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