Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-08-11

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All times shown according to UTC.

Time Nick Message
05:50 Gpox joined #bioclipse
07:19 malick joined #bioclipse
07:19 olas joined #bioclipse
07:19 olas hi all
07:19 zarah hi olas
07:19 zarah olas: You have new messages. Write '@messages' to read them.
07:19 olas @msg
07:19 zarah olas: masak said I made new icons, but I didn't stop there -- I changed a few things around in StuctureContentProvider.java and StructureLabelProvider.java. thought I'd tell you since the classes has your name on them. so be sure to update before you do any changes of your own.
07:38 olas @tell masak Very nice work with icons. However, bond_aromatic seems to be missing. A missing commit?
07:38 zarah Consider it noted.
07:42 CIA-49 bioclipse: ospjuth * r6551 /bioclipse2/trunk/plugins/net.bioclipse.cdk1​0.jchempaint/src/net/bioclipse/cdk10/jchempa​int/outline/StructureContentProvider.java: Added Si=Silica.
07:42 CIA-49 bioclipse: ospjuth * r6552 /bioclipse2/trunk/plugins/net.bioclipse.cdk​10.jchempaint/src/net/bioclipse/cdk10/jchem​paint/outline/StructureLabelProvider.java: If ImageDesriptor not found, use MissingImageDescriptor.
07:58 jonalv joined #bioclipse
08:08 gilleain joined #bioclipse
08:10 olas hi gilleain
08:10 olas I haven't looked at your updated CMLFileDescriber
08:10 olas will do that today
08:10 gilleain Okay, good.
08:10 olas hmm, will do that now :-)
08:11 gilleain Sadly, it throws errors for some of the test cml files.
08:11 olas why?
08:11 gilleain This is because they are badly formed xml, according to xpp.
08:11 gilleain But the Describer should have better error handling, I think.
08:12 olas have you tested the performance of the describer?
08:12 olas on large files?
08:12 olas or a dir with many files?
08:12 gilleain Not yet. I can do that today.
08:12 olas thanks
08:12 olas would be important to test
08:12 gilleain That reminds me; are Describers called in a particular order?
08:13 egonw joined #bioclipse
08:14 olas well
08:14 gilleain That is, when you click on a file, eclipse (I'm guessing) goes through the Describers in some way, testing each in turn.
08:14 olas not really
08:14 olas you can set priority
08:14 olas low, normal, high
08:14 gilleain hmmm.
08:14 olas but other than that they go in order of first comes first...
08:14 olas why do you ask?
08:15 gilleain Well, if each time you click on a large pdb file, it's trying to scan it as if it were a cml file..
08:15 gilleain Oh well, just a thought, really.
08:16 olas gilleain: that should not happen
08:16 olas it should aonly use the describer if the file extension matches
08:16 olas which is xml and cml
08:16 olas not pdp
08:16 gilleain Oh yes, right. Forgot about that.
08:17 olas but you are right
08:17 olas if you click a large XML file, it will be scanned
08:17 olas that's why describers need to be very fast
08:18 egonw CDK has an file format guesser set up
08:18 egonw which is fast, and which could be used in addition to file extension
08:18 egonw the 2D/3D detection should really only be run on CML files
08:19 olas hmm
08:19 olas could the describer just look at the NS and return invalid else?
08:19 olas that is fast
08:19 olas (maybe it does?)
08:19 olas no
08:19 gilleain no, perhaps it should.
08:20 olas yes
08:20 olas that means it ends quickly if not CML namespace
08:21 olas egonw: we need 2D/3D detection on many formats, such as MDL
08:22 olas hence I wrote a MDLDescriber
08:22 olas if 3D -> open in jmol
08:22 olas if 2D -> JCP
08:22 olas that will be required for (all?) formats IMO
08:22 olas if this is the way we should work
08:22 olas egonw: what's your opinion?
08:24 egonw yes, this sounds good
08:25 * egonw goes into silent mode to process TODO list items
08:31 jonalv Okey I really think something should be done about cdk. Must we remove src/data manually each time?
08:33 olas jonalv: ?
08:33 jonalv olas, ?
08:33 olas I committed a fix
08:33 jonalv you commited a fix?
08:33 olas in build.properties
08:34 jonalv I just removed it manually five minutes ago on Pan...
08:34 jonalv so I am not sure that fix worked
08:34 olas I removed src/data from .
08:34 jonalv intresting
08:34 olas was that an old version that you updated?
08:34 jonalv yea
08:34 olas :-)
08:34 jonalv that's probably it...
08:35 olas if you do "update" and get it back, then we have a problem
08:35 jonalv JChempaint doesn't compile... I am fixing it now...
08:35 olas compiles here
08:35 jonalv uhm or nor, (must install subclipse
08:35 jonalv could you fix it for me olas?
08:36 gilleain is it sensible to run an svn update on the whole tree every morning, or is that quite slow?
08:36 olas it should be fine
08:36 olas I do that
08:36 jonalv it's StructureContentProcider which imports sun.text.CompactShortArray.Iterator. It it doesn't use it though.
08:37 jonalv gilleain, only once a day? :)
08:37 jonalv I do it all the time :)
08:37 gilleain Sorry, I meant once every 5 minutes.
08:37 gilleain :)
08:37 olas that sounds a bit slow
08:37 olas I do it when I hev to
08:37 jonalv it's a bit quicker if done from the console version of subversion though
08:37 olas I monitor this channel
08:38 olas and update plugins I need to update
08:38 olas mornings: full SVN update
08:38 olas sometimes more often if required
08:38 gilleain ok.
08:38 olas gilleain: I can confirm your CMLFiledescirber seems to work fine here
08:38 gilleain Cool.
08:38 olas donät know about performance
08:39 gilleain Will test.
08:39 olas if you add check for namespace it should improve things
08:39 gilleain do all cml files use the cml namespace?
08:40 olas I think so
08:40 olas egonw: please confirm
08:41 gilleain he's in stealth mode.
08:41 egonw gilleain: yes, otherwise it is not CML
08:41 gilleain Ok, thanks.
08:43 EskilA joined #bioclipse
09:03 edrin joined #bioclipse
09:03 edrin hi
09:03 zarah hi edrin
09:19 olas hi edrin
09:20 jonalv hi edrin
09:23 edrin egon, olas, i started a wikipage for Xmpp http://wiki.bioclipse.net/ind​ex.php?title=XmppWebServices
09:23 zarah edrin's link is also http://tinyurl.com/5sjy3e
09:23 edrin not much there yet, though
09:25 olas it's good to start anyway
09:26 olas good
09:26 olas this is what I need
09:26 edrin cool :)
09:26 olas I also need the next step :-)
09:27 olas can I build the jars myself?
09:29 edrin not sure about this...
09:31 edrin the project in trunk is currently a bit complicated... I am trying to merge the client with the component source
09:31 edrin however i can just create a jar for you if you want
09:31 edrin that should work
09:36 olas sure
09:37 olas can you add how to test the coffee-machine-example?
09:37 olas and let me know when you have written more on the next topic :-)
09:37 edrin yes
09:37 edrin will eat now cu later
09:38 olas bye!
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10:10 CIA-49 bioclipse: shk3 * r6553 /bioclipse2/trunk/plugins/n​et.bioclipse.spectrum/src/ (5 files in 3 dirs): some todos in spectrumeditor removed
10:15 thomas_ku joined #bioclipse
10:20 shk3 hi all
10:20 zarah hi shk3
10:20 shk3 is there an official Bioclipse policy about exception handling?
10:20 shk3 especially in cases like
10:20 shk3 building an editor
10:21 shk3 where you can't do anything about it and where errors should no occur anyway.
10:21 shk3 Have a messagebox?
10:21 shk3 StackTrace on console?
10:21 shk3 Logging?
10:21 shk3 perhaps a central method like handleUnhandleableException(ex) somewhere in core would be great.
10:24 egonw olas:
10:24 egonw [12:24] <CIA-34> cdk: egonw * r11988 /cdk/trunk/src/ (4 files in 3 dirs): Added perception + Sybyl mapping of new atom types: O.minus.co2 and O.sp2.co2
10:29 shk3 hi olas
10:32 shk3 hi egonw
10:33 egonw hi shk3
10:35 shk3 sorry for bothering
10:36 shk3 how do you handle exceptions in Bioclipse where you can't do anything?
10:38 egonw dunno...
10:38 egonw it seems uppsala is in a meeting or so
10:40 shk3 I will just do it in my plugin
10:40 shk3 might be worth talking about later
10:40 egonw email the mailing list
10:40 egonw then it will be archived too
10:40 egonw for future reference
11:02 CIA-49 bioclipse: shk3 * r6554 /bioclipse2/trunk/plugins/net.bioclips​e.spectrum/src/net/bioclipse/spectrum/ (5 files in 2 dirs): more todos done
11:02 olas hi
11:02 zarah hi olas
11:02 * olas was on lunch, not a meeting
11:02 olas ask jonalv + masak about error handling
11:02 olas I know they have been thinking about it
11:02 olas but currently there are no defined policy/practice
11:03 olas lggging is always good
11:03 olas and naturally exceptions
11:03 olas but the BioclipseException seems not to be the preferred way
11:03 olas we should have a wiki page
11:04 olas please email devel about this
11:09 shk3 thanks, will do so
11:22 * jonalv is back
11:22 jonalv (don't go and try to fix your broken telephone during lunch hour...)
11:24 jonalv shk3, regardning exceptions. Where is it?
11:32 shk3 everywhere
11:32 shk3 image you want to build the ui of an editor and you read a file for that from your plugin
11:33 shk3 and this is not found, but it is a file in the plugin, a fixed one, so to say.
11:33 * shk3 is to lunch
11:33 edrin http://xkcd.com/461/
11:33 jonalv so in a manager that works with a file.
11:34 jonalv Those methods should be wrapped in a job. There's an aop introduction for that
11:34 jonalv then it's totally okey to just throw a good exception becasue Eclispe will catch it and poop up a dialog with it
11:34 jonalv of course also log it
11:36 egonw edrin: very funny
11:37 egonw this is actual TomTom happenings
11:37 egonw people really stop thinking with such devices
11:38 olas jonalv: eclipse will 'poop' out a dialog! LOL!
11:39 jonalv sry
11:39 jonalv spleing eror
11:44 egonw ha, finally a SF download mirror in NL!
11:44 jonalv nice
11:44 edrin i just bought this last week:http://de.samsungmobile.com/mobile/SGH-i550
11:44 zarah edrin's link is also http://tinyurl.com/5qm6nk
11:45 * egonw just relies on maps.google.com and his memory
11:45 egonw no need for electronic masp
11:46 edrin me usually, too
11:46 edrin but we will go to france soon for holidays... i will need this there maybe ;)
11:48 egonw yes
11:48 egonw print maps are good
11:48 egonw for holidays
12:03 shk3 jonalv: I have a lot of exceptions which end up in the createPartControl method
12:03 shk3 createPartControl can't throw exceptions (the method to overload doesn't do)
12:03 shk3 so you need to do some loggind/message display etc.
12:04 shk3 this should be centralized, i think
12:16 shk3 olas: just looked at the saveas thing
12:16 shk3 shouldn't be a problem using the manager
12:16 shk3 question:
12:16 shk3 what about files types?
12:16 shk3 In jcp, there is a class containing constants for that.
12:17 shk3 but this is not available in net.bc.business
12:17 shk3 what to do?
12:18 olas shk3: think general
12:18 olas there is nothing like that in Bioclipse
12:18 olas but please create some constants in the CDK.business plugin
12:19 olas and write manager methods
12:19 olas and tests that read in a molecule and saves it in another file format
12:19 olas tests go in net.bioclipse.cdk.business.tests
12:19 olas also please test saveas from console
12:19 shk3 ok, will create the constants myself
12:19 shk3 no problem
12:19 olas great
12:20 shk3 btw, console
12:20 shk3 ah, sorry, nothing
12:45 egonw olas: http://sourceforge.net/tracker/inde​x.php?func=detail&amp;aid=2046393&a​mp;group_id=40728&amp;atid=428740
12:45 zarah egonw's link is also http://tinyurl.com/5dv4kt
12:45 egonw olas: sybyl atom typing bug in OB
12:48 olas nice
12:48 egonw found another one
12:49 egonw this is one where both CDK and OB go wrong :)
12:49 olas haha
12:50 olas sounds like you are making good progress
12:54 gilleain Is there a limit in windows to the number of files you can have in one directory?
12:54 gilleain Say, 826?
12:54 gilleain No, that can't be right - never mind.
13:07 shk3 hm, question
13:07 shk3 the method for save I am writing on is
13:07 shk3 public void saveMolecule(ICDKMolecule mol, IFile target, String filetype)
13:07 shk3 saveMolecule was the name which was already there
13:07 shk3 in jcp, it might be a reaction
13:08 shk3 or multiple molecules
13:08 shk3 or whatever
13:08 shk3 should the method be saveChemobject
13:08 shk3 or should we have multiple methods and the save(As) methods should decide which one to use.
13:08 olas the method should be saveMolecule
13:09 olas as that is the one that will be published to console
13:09 olas it might very well use a saveChemObject, but a user should never have to know what a ChemObject is
13:09 olas think how you would like to use it from the console
13:09 olas mol=cdk.fromSmiles("CCCC")
13:10 olas cdk.saveMolecule(mol,"path/to/file", "XYZ")
13:11 shk3 hm, but then if there is a saveChemobject, it could simply call that?
13:11 olas why not?
13:11 olas as long as it is not displayed to the user
13:12 jonalv nah cdk.save(cdk.fromSmiles("CCC"), "path", "Y") is proabbly fine
13:12 olas aha
13:12 olas yea
13:12 olas you could be right
13:12 jonalv shk3, what do you eman by not being able to throw exceptions by the way? You can always throw exceptions can't you?
13:12 * olas think so too
13:15 shk3 not if the method you want to overload does not throw anything
13:15 shk3 I think
13:15 stain runtime exceptions ftw
13:15 shk3 or let's say the method you need to overwrite
13:15 shk3 overwrite would be the right term, I suppose
13:16 jonalv shk3: just throw a runtime exception
13:16 stain you can still add throws BlahException even if it's a runtime - just to be nice
13:16 jonalv it's a message to the user so if the method is run as an eclipse job it should work
13:17 shk3 I have the method
13:17 jonalv but if it's not run as a job then it will crash of course... :)
13:17 shk3 @Override
13:17 shk3 public void createPartControl(Composite parent) {
13:17 shk3 }
13:17 shk3 right now in code
13:17 shk3 if I add a throws IOException (or whichever),
13:17 shk3 eclipse complains about throws clause being incompatible with the method to override
13:18 jonalv no that won't work, but I am not sure yuo should throw exceptions from that method
13:18 shk3 and the java compiler will complain as well
13:18 jonalv isn't that the method buildign up the gui?
13:18 shk3 you said I should
13:18 shk3 ...
13:18 shk3 yes
13:18 jonalv I thought you whre in a mangaer method
13:18 shk3 no
13:18 shk3 there it's easy
13:18 jonalv I ahve no idea hwo swt likes exceptions when it builds up the gui
13:19 jonalv my guess is that it doesn't love it :)
13:19 shk3 well, you can't throw exceptions
13:19 shk3 as i said
13:19 shk3 so you need to catch them
13:20 shk3 but then the gui will be incomplete
13:20 shk3 so you need to tell the user and do logging or whatever
13:20 shk3 and this should be the case in many places
13:20 jonalv yea, is that an editor btw?
13:20 shk3 so a method somewhere you can simply call like announceException(ex) or so
13:21 shk3 would be great
13:21 shk3 editor
13:21 jonalv I just realised what happens with that exception if you throw it. The editor shows the stack trace
13:21 shk3 same problem in views, i suppose
13:21 shk3 but I can't throw it
13:21 jonalv of course you can
13:21 shk3 since I cannot add throws whatever to the method
13:21 shk3 how so?
13:21 jonalv is it a checked exception?
13:21 shk3 yeah
13:21 shk3 unchecked ones are easy
13:22 jonalv just wrap it in a RuntimeException if  you really wanan throw it...
13:22 shk3 hm, that might be a solution
13:22 jonalv throw new RuntimeException( e.getMessage(), e)
13:22 jonalv so you catch it and wrap it...
13:22 jonalv or something like that
13:28 CIA-49 bioclipse: gilleain * r6556 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/net​/bioclipse/ui/contenttypes/CmlFileDescriber.java: Now checks the CML file for the right namespace, and returns invalid if that's not there.
13:28 olas gilleain++
13:28 gilleain Okay, seems that the CmlFileDescriber can handle opening a directory with 800+ small cml files in reasonable time.
13:29 gilleain I might try some converted PDB files next...
13:30 shk3 great
13:30 shk3 we are making progress
13:31 gilleain what do you reckon : ribosome or proteasome? :)
13:38 egonw olas: my OB bug report was actually a duplicate for:
13:38 egonw http://sourceforge.net/tracker/inde​x.php?func=detail&amp;aid=2017902&a​mp;group_id=40728&amp;atid=428740
13:38 zarah egonw's link is also http://tinyurl.com/55gdxv
13:39 egonw and just filed this (new) one: http://sourceforge.net/tracker/inde​x.php?func=detail&amp;aid=2046460&a​mp;group_id=40728&amp;atid=428740
13:39 zarah egonw's link is also http://tinyurl.com/56ykrb
14:14 CIA-49 bioclipse: ospjuth * r6557 /bioclipse2/trunk/plugins/net.bio​clipse.jmol/META-INF/MANIFEST.MF: Removed dep to cdk.ui as not needed.
14:31 CIA-49 bioclipse: shk3 * r6558 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): added save methods
14:57 shk3 for the test, I need an IFile
14:57 shk3 but i have no workspace in the test run
14:57 shk3 what to do?
14:57 gilleain Ack! ls -lSh: 1pma.pdb -- 4.4M, 1pma.cml -- 11M, 1pma.xml -- 55M...
15:03 rguha joined #bioclipse
15:03 rguha helo
15:03 egonw @tell olas Rajarshi is online
15:03 zarah Consider it noted.
15:22 gilleain I guess that bugs in org.openscience.cdk.Polymer go in the cdk bug tracker?
15:23 olas hi rguha
15:23 zarah olas: You have new messages. Write '@messages' to read them.
15:23 rguha olas: yes
15:23 rguha gilleain: yes
15:23 olas @clear-msg
15:23 zarah Messages cleared.
15:23 olas rguha: Unfortunately I have to run off now :-(
15:23 gilleain Ok.
15:23 rguha not a problem
15:23 rguha catch you later
15:23 rguha the QSAR discussion is very interesting
15:23 olas can we talk tomorrow on irc/skype?
15:23 olas yes
15:24 rguha I'll be travelling from tomorrow
15:24 rguha I'll try and be online when I can
15:24 olas oh
15:24 olas then I'll catch you later
15:24 rguha email i probably best till the 20th
15:24 olas gotta run now
15:24 rguha bye
15:24 olas bye all
15:24 olas left #bioclipse
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17:07 egonw moin
17:07 zarah hi egonw
17:09 gilleain hi
17:09 zarah hi gilleain
17:09 egonw hi gilleain
17:09 egonw saw your bug report
17:10 egonw please write a unit test
17:10 egonw that's the best way to ensure it will get fixed
17:10 gilleain Okay, will do.
17:10 gilleain I know it's a bit of corner case, in that not many people convert .pdb to .cml...
17:14 egonw I used to :)
17:15 gilleain They're a lot smaller than the pdb native xml format (about a fifth the size!).
17:17 egonw gilleain: what did you do before joining Chris' group?
17:18 gilleain I worked on a project called TOPS, then did a phd on protein carbonyl-cation backbone motifs.
17:19 egonw what is TOPS?
17:19 gilleain Topologically Oriented Protein Structures. Originally a protein sse cartoon layout project.
17:20 gilleain I was working on topological matching of structures.
17:21 egonw ok
17:24 gilleain One day I will make a tops editor for bioclipse, maybe. Anyway, I should go. bye.
17:24 egonw ok, bye
18:29 egonw joined #bioclipse

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