Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-12-15

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All times shown according to UTC.

Time Nick Message
07:29 egonw joined #bioclipse
08:24 olass joined #bioclipse
08:24 olass hi all
08:24 zarah hi olass
08:29 egonw hi olass
08:29 olass hi egonw
08:30 olass egonw: feeling better?
08:30 egonw better than thursday, yes
08:30 egonw but still very tired
08:30 olass but not super?
08:30 olass I see
08:30 egonw no
08:30 egonw you  need super powers today?
08:30 olass nasty bug that
08:31 olass :-)
08:31 olass I'll have a look at the MoleculesTable, trying top display SDF properties
08:31 * egonw is getting his new laptop up and running
08:31 olass cool
08:32 egonw nice machine
08:32 olass did you get the windows laptop?
08:32 olass from my office?
08:32 egonw really small, and light weight
08:32 egonw no, not yet
08:32 egonw my bag was full
08:32 olass ask Magnus if you need a windows cd
08:32 olass and/or antivirus
08:32 egonw yes, no worries
08:32 olass hope you get it up and running
08:32 olass it might or might not need reinstallation of windows
08:33 olass donät remember
08:33 egonw we'll see...
08:33 egonw no worries about that
09:03 Julio joined #bioclipse
09:08 shk3 joined #bioclipse
09:08 Julio joined #bioclipse
09:46 * egonw is booting a second Eclipse
09:46 egonw with 4GB of memory, to instances should be OK
09:47 jonalv joined #bioclipse
09:48 jonalv hi
09:48 zarah hi jonalv
09:50 egonw hi jonalv
09:50 jonalv masak lost his computer. A guy with a knife has it... :(
09:52 egonw Mmmm... here in save old Uppsala?
09:52 egonw save -> safe
09:52 jonalv No I think it was at the central station in Stockholm
09:53 jonalv there had been lots of witnesses...
09:53 egonw but it was not a trade fortunately?
09:53 egonw that is... he the laptop, carl the knife?
09:53 egonw you know, somewhere down his belly
09:54 jonalv hm make that Göteborg
09:56 jonalv egonw: you lost me...
09:56 egonw nevermind
09:56 egonw carl's OK?
09:59 jonalv yea he seem ok
09:59 jonalv as ok as you can be when you lost your computer to a guy with a knife...
09:59 Julio joined #bioclipse
09:59 egonw sure
10:07 egonw olass: you asked me last week to move something around?
10:07 egonw don't think I've done that yet
10:07 egonw what was it again?
10:07 egonw cdk10 to something, right?
10:21 egonw_ joined #bioclipse
10:22 egonw ok, "outdated"
10:27 egonw shk3: do you have all cdk10 deps resolved?
10:27 egonw see -devel ML about moving cdk10 plugins to trunk/outdated
10:28 shk3 yes
10:28 egonw OK, thanx
10:28 egonw OT, I think only Miguel's RDF editor is now depending on it...
10:29 egonw see his blog for what this plugin does...
10:34 jonalv egonw: working from home today?
10:35 egonw yes
10:36 jonalv okey, might you show me some git-svn some other day?
10:42 egonw what d'you wanna know?
10:43 jonalv uhm how I do things
10:43 jonalv I found git svn fetch
10:43 jonalv but then what?
10:43 egonw mom
10:43 egonw http://chem-bla-ics.blogspot.com/search?q=git-svn
10:43 zarah egonw's link is also http://tinyurl.com/6785jz
10:43 egonw in particular:
10:43 egonw http://chem-bla-ics.blogspot.com/2008/09/cd​k-development-with-branches-using-git.html
10:44 zarah egonw's link is also http://tinyurl.com/5t7vd9
10:44 egonw replace svnroot/cdk/cdk with svnroot/bioclipse/bioclipse2
10:44 egonw but maybe you already got that far?
10:45 egonw anyway... that item already has info on the basic update/edit/commit steps
10:45 jonalv I will read it
10:47 egonw CIA-32: another secret mission?
10:47 egonw CIA-32: or just trying to understand the xkdc?
10:51 jonalv egonw: you mean xkcd?
10:51 egonw right
10:58 egonw all: please update you Mylyn configs to set the repos version to 3.0
10:58 egonw for Pele BugZilla
11:30 shk3 what do you think about a wizard in the sdfeditor to create new sdfs by choosing structures/directories from file system?
11:30 egonw sounds good
12:34 egonw olass: ping
12:34 olass egonw: pong
12:34 egonw net.bioclipse.chemoinformatics can contain New Wizards?
12:35 olass which one you mean?
12:35 olass In principle yes
12:35 egonw ok, good
12:35 egonw (it will need change deps)
12:35 olass It should not depend on cdk though
12:35 olass that's why we have it
12:36 olass others can depend on it, not the other way around
12:36 olass agreed?
12:36 egonw right
12:36 olass good
12:36 egonw not sure if you only wanted branding code in it
12:36 egonw for the feature
12:38 gilleain joined #bioclipse
12:38 egonw hi gilleain
12:38 gilleain ¥ø
12:38 gilleain how's it going?
12:38 olass egonw: I thought chemoinfo stuff without dep to anything
12:39 egonw olass: right
12:51 egonw olass: adding a dep on ui.ide is OK?
12:52 olass yup
12:52 egonw it's for using BasicNewFileWizard
12:56 edrin joined #bioclipse
12:56 edrin hi
12:56 zarah hi edrin
12:57 olass hi edrin
12:57 jonalv hi edrin
12:57 zarah hi edrin
13:08 gilleain goodbye cdk10 plugins...
13:10 egonw :)
13:11 gilleain oooh. external jcp selections from the view in bioclipse. great.
13:11 egonw right...
13:11 egonw but only one selection at this moment
13:12 egonw but also atom coloring from outside...
13:12 egonw by using custom IAtomColorer
13:13 gilleain right.
13:18 gilleain ugh. didn't realise that there was an ISelection in JFace. Should have guessed, I suppose.
13:18 egonw :)
13:19 shk3 do we have a policy on what manager methods should do
13:19 shk3 when they try to create a file
13:19 shk3 and the file already exists?
13:20 shk3 overwrite?
13:20 shk3 or should the manager guarantee nothing is overwritten?
13:20 shk3 have a force flag?
13:22 egonw no convention on that, I think
13:22 egonw but sounds like a good proposal
13:22 egonw best way to put this convention into effect is to add a unit test
13:22 egonw for the various situations
13:24 shk3 I tend to the force flag
13:24 shk3 if false,
13:24 shk3 fail on extisting files
13:24 shk3 if true,
13:24 shk3 write anyway
13:24 shk3 then the person using the method has to decide and nothing
13:25 shk3 is done implicitly or assumed
13:26 egonw this is on the manager level, right?
13:27 egonw I'd rather see a exists() method
13:28 egonw and no force flag
13:28 egonw and fail when people are creating a file, when already one exists
13:28 egonw a remove() should then be done before
13:29 egonw cleaner API
13:29 shk3 but shouldn't an overwrite be possible as well?
13:29 egonw the above allows that:
13:30 egonw if (exists(X)) {
13:30 egonw remove(X)
13:30 egonw write(X)
13:30 egonw } else {
13:30 egonw write(X)
13:30 egonw }
13:30 egonw ah, so better:
13:30 egonw if (exists(X)) remove(X);
13:30 egonw write(X);
13:32 egonw if not mistaken, we got all these already...
13:32 egonw let me check
13:32 egonw ah, no ...
13:32 egonw exists seems to be missing
13:33 egonw will add that
13:33 shk3 but that means that a stupid programer can write something which overwrites files without warning
13:33 egonw no
13:34 egonw I said the write() would throw an Exception
13:34 egonw if the file already exists
13:34 egonw where write() == IUIManager.save()
13:36 jonalv AAAAAAAAAHHHHHHH
13:36 shk3 ah ok
13:36 shk3 your exists code would be on the code using the manager
13:36 egonw jonalv: everything OK?
13:37 jonalv egonw: not really no...
13:37 egonw shk3: what do you mean?
13:37 jonalv the console is putting up a big fight...
13:37 gilleain the bioclipse console?
13:37 jonalv gilleain: bingo
13:37 shk3 the code if(exists...
13:37 shk3 would not be in the manager
13:38 shk3 but write() is a manager method?
13:38 egonw there would be such code in write()
13:38 egonw otherwise it cannot throw an exception
13:39 shk3 but if write does the if exists remove then
13:40 shk3 it overwrites?
13:41 egonw no, it will not do the overwrite
13:41 egonw it would throw an Exception
13:42 shk3 but then this if exists is not done in the manager?
13:45 jonalv and the Eclipse debugger sucks
13:46 jonalv AAAAAAHHHHH
13:47 egonw shk3: why do you think that?
13:49 shk3 because if this "if extist remove" is done in the manager
13:49 shk3 in the createblah of the manager
13:50 shk3 it does not need to throw an exception
13:50 shk3 and does the overwrite
13:50 shk3 sorry, I do something
13:50 shk3 please give an explanatin
13:50 shk3 of what you want
13:50 shk3 which also idiots like me can understand
13:50 shk3 thanks
13:50 egonw inside UIManager.save() there would be:
13:51 egonw if (exists(X)) throw new SomeException();
13:51 egonw that's all
13:51 shk3 so the remove is not in the manager?
13:51 egonw no
13:51 shk3 ah
13:52 shk3 so it is in the code using the manager
13:52 egonw right
13:55 jonalv I think that git is making troubles for me
13:58 egonw shk3: almost done adding the exists
14:02 egonw jonalv: ping
14:02 jonalv egonw: pong
14:02 egonw you wrote transform()?
14:02 egonw in ResourcePathTransformater?
14:02 jonalv egonw: probably...
14:02 egonw ok, good enough for me :)
14:02 jonalv or hm I thin I wrote the tests and GPox the code...
14:03 egonw any reason to throw an exception when result == null?
14:03 egonw instead of returning null?
14:03 jonalv uhm hang on
14:03 jonalv you lsot me...
14:03 egonw line 49-50
14:03 jonalv + Eclipse + git +everything is messed up so I can\t look at the code\
14:04 egonw :(
14:04 egonw I'll help tomorrow
14:05 jonalv egonw: could you give me full path to the file?
14:05 egonw /net.bioclipse.core/src/net/bioclips​e/core/ResourcePathTransformer.java
14:06 jonalv vim to the rescue :)
14:06 jonalv I am looking at the code and yea I wrote that...
14:07 jonalv egonw: better to throw exception than to return null and get a strange NPE at some strange location...
14:07 egonw depends on the use case...
14:07 egonw I was using it for an exists() method...
14:07 jonalv egonw: http://c2.com/cgi/wiki?NoNullBeyondMethodScope
14:07 zarah jonalv's link is also http://tinyurl.com/4ndr5p
14:08 egonw ah... interesting...
14:08 egonw did they consider that exceptions make java really show?
14:08 jonalv masak is beside me whishing he was online... :)
14:08 jonalv egonw: Exceptions are for exceptional circumstances...
14:08 egonw yes, I'm only getting started
14:09 egonw I'm also going to convince you of catching Exception's... :)
14:10 egonw OK, fair
14:10 egonw I was hoping to use the method for the exists() code...
14:10 egonw now I just have to duplicate the functionality...
14:10 egonw no problem
14:10 jonalv you lost me...
14:11 jonalv that code creates an IFile. Why do you want to create an IFile when you are checking if something exists?
14:12 egonw well... I get a String (because I need to implement that too, right?)
14:12 egonw and need to see if that exists...
14:12 egonw all other manager calls are using the ResourcePathTransformer for that
14:13 egonw but I understand why that is not possible...
14:13 egonw but still I need that kind of functionality...
14:13 jonalv I don't think I understand your problem. :(
14:15 egonw I need code to check if String filePath exists...
14:15 egonw I'll just do this now:
14:15 egonw masak: note the catch clause ;)
14:15 egonw public boolean exists(String filePath) {
14:15 egonw try {
14:16 egonw return exists(ResourcePathTransformer.getInstance()
14:16 egonw .transform( filePath ));
14:16 egonw } catch (IllegalArgumentException exception) {
14:16 egonw return false;
14:16 egonw }
14:16 egonw }
14:16 egonw that's the use case...
14:16 jonalv masak is not pleased
14:17 egonw masak: that's why I'm asking...
14:17 egonw suggestions please
14:17 jonalv implement that method please...
14:17 egonw as ResourcePathTransformer.exists() ?
14:17 jonalv yea
14:18 egonw ok
14:20 egonw actually... no
14:20 egonw won't do that...
14:20 egonw there is much more going on in there than I like to touch...
14:20 jonalv egonw: what will you do?
14:20 egonw for example
14:20 egonw why is parsePath() trying alternative file names?
14:21 egonw IPath path = new Path(resourceString);
14:21 egonw IFile file = ResourcesPlugin.getWorkspace()
14:21 egonw .getRoot().getFile( path );
14:21 egonw file.exists()
14:21 egonw masak: happy with that?
14:22 jonalv egonw: I wonder if that one does all that we want
14:23 egonw no, it only does parseRelative()
14:23 egonw and not parseURI(), parsePath()
14:24 egonw but the last one is trying alternative file names???
14:24 egonw can someone please explain that?
14:24 egonw that sounds rather unwanted...
14:24 egonw if one then records save(String filePath)
14:25 egonw it will try alternative paths?
14:25 egonw if one then records save(IFile) as save(String filePath)
14:25 jonalv egonw: I don't know
14:26 egonw masak?
14:26 jonalv masak does not know anything about that
14:29 egonw :( that alternatives code is Gpox's....
14:30 egonw @pelezilla 179
14:30 zarah http://tinyurl.com/6nnv93
14:33 gilleain hahahaaa. lolwhat?
14:33 egonw huh?
14:33 gilleain } else if (type.equals("majorPlusOne"))
14:33 gilleain {
14:33 gilleain isotopeNumber++;
14:33 gilleain } else if (type.equals("majorPlusTwo"))
14:33 gilleain {
14:33 gilleain isotopeNumber++;
14:33 gilleain isotopeNumber++;
14:33 gilleain } else if (type.equals("majorPlusThree"))
14:33 gilleain {
14:33 gilleain isotopeNumber++;
14:33 gilleain isotopeNumber++;
14:33 gilleain isotopeNumber++;
14:33 zarah isotopeNumber++;
14:33 gilleain (that)
14:33 gilleain exactly!
14:33 egonw zarah: nah, that's wrong
14:33 zarah egonw: excuse me?
14:34 egonw @karma isotopeNumber
14:34 zarah isotopeNumber has a karma of 6
14:34 gilleain hoho
14:35 jonalv ROFLOL
14:37 egonw shk3: exists() being commited
14:39 gilleain no cia?
14:40 egonw too busy catching illegal import of x-mas presents by some dude in a red dress
14:40 gilleain :)
14:40 jonalv eclipse is totally broken
14:41 jonalv i can't change anything
14:41 egonw I downloaded a fresh Eclipse this weekend
14:41 egonw for my new laptop
14:41 jonalv it just keeps runnign the same old code no mather what changes I make
14:41 egonw works like a charm
14:41 egonw which version did you download?
14:41 jonalv I have spent the day trying to fix bugs but theyt just won't change
14:41 jonalv no matter what I do I get the same behcaoir
14:42 jonalv 3.4.1
14:42 jonalv no sysouts work
14:42 jonalv nothing works
14:42 egonw :(
14:42 egonw not nice
14:42 jonalv AAAAAAGHHHHHHHHH
14:43 gilleain no sysouts? gah
14:43 jonalv my changes does not go trhough
14:43 jonalv it just keeps on running the same binaries
14:45 gilleain the same classfiles?
14:46 jonalv I think so. I don't know what it does..;
14:46 gilleain clean project, I suppose.
14:46 jonalv tried that
14:46 gilleain weird
14:47 gilleain but…how…
14:47 jonalv I don't know
14:48 gilleain cached class files. or perhaps voodoo magic.
14:48 jonalv yea something like that
14:48 jonalv it explains why I can't work anyway...
14:49 gilleain but lets say you delete all traces of eclipse from a machine, re-check out the sources, and build, then there could not be any old classfiles
14:50 gilleain so, delete the .eclipse dir, everything.
14:50 gilleain tiresome, but still, it surely must work.
14:52 * jonalv is downloading a new Eclipse version now..
15:08 jonalv egonw: what is a userscript?
15:15 egonw umm... quite like a bioclipse javascript
15:15 egonw but than in FireFox
15:16 jonalv egonw: you don't think your definition is a bit narrow?
15:17 * jonalv sees the exam question what is a userscript?
15:17 jonalv correct answer:
15:17 jonalv 1. JavaScript
15:17 jonalv 2. in a webbrowser
15:18 jonalv 3. runsd automagicly when the user visits a certain web page
15:18 olass http://userscripts.org/
15:19 jonalv whiskey tango foxtrot
15:19 olass never dance sober?
15:20 jonalv how can they steal that word?
15:20 olass whiskey, vodka, vodka, gin, salsa?
15:22 jonalv it's as if we would steal the word manager and define it as: A Spring empowered object existing in a javascript environment with this and that annotation...
15:22 gilleain anytime, anyplace, anywhere
15:22 gilleain it's a wonderful world you can share
15:25 * jonalv should have stayed in bed today
15:26 gilleain heh. wtf :: whiskey tango foxtrot :: gin sprite walz :: gsw.
15:27 gilleain Anyway; there seems to be a concurrent modification exception in ChemObjects that are notifying listeners of changes.
15:28 gilleain I guess it would be a bad idea to synchronise on the listener list, for speed reasons.
15:40 egonw gilleain: or use the nonotify classes
15:40 gilleain tried that
15:40 gilleain (or shk3 did)
15:41 gilleain I'm thinking that the hub could have a getMolecularFormula method..
15:42 gilleain but, that also there is some inconsistency between hub methods for adding atoms/bonds/rings, to do with handling molecule sets and atomcontainers
15:42 egonw please email
15:42 egonw will check it asap
15:42 gilleain okey
17:21 jonalv I think my branch is working now!
17:21 jonalv finally
17:21 jonalv I am happy again
17:21 jonalv egonw, olass: I am sorry for everything! :)
17:22 olass jonalv: great!
17:22 olass what did you do?
17:22 jonalv reinstalled Eclipse and fixed the errors in the code
17:22 * jonalv has switched to git now...
17:22 jonalv I still have much to learn about git though... :)
17:23 jonalv for example how do I switch branch? :)
17:27 olass cu tomorrow
17:27 * olass will now buy a christmas tree
17:27 olass bye
17:27 jonalv oki
17:43 edrin left #bioclipse
17:43 edrin joined #bioclipse
17:43 edrin hi again
17:44 jonalv hi edrin
17:50 * jonalv is out of here. cya
18:00 edrin egonw: did you take a look in the google docs?
18:01 egonw no :(
19:27 egonw joined #bioclipse
21:42 edrin left #bioclipse
22:37 CIA-32 bioclipse: egonw * r8061 /bioclipse2/trunk/cdk-externals/trunk/ (2 files in 2 dirs): Added three convenience methods
22:37 CIA-32 bioclipse: egonw * r8062 /bioclipse2/trunk/cdk-externals/t​runk/org.openscience.cdk.control/ (2 files in 2 dirs): Use addAtom(C, Point2d(0,0)) first a first atom to an empty canvas... but still does not draw it centered...

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