Camelia, the Perl 6 bug

IRC log for #bioclipse, 2007-09-28

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All times shown according to UTC.

Time Nick Message
05:50 egonw joined #bioclipse
07:34 CIA-31 bioclipse: jonalv * r3858 /trunk/playground/plugins/net.bioclipse.keyring/ (.classpath META-INF/MANIFEST.MF): Added JUnit to manifest
07:35 jonalv joined #bioclipse
07:36 EskilA joined #bioclipse
07:36 CIA-31 bioclipse: jonalv * r3859 /trunk/playground/plugins/​net.bioclipse.structuredb/ (4 files in 4 dirs): Removed ',' in Structure.sql and changed around with classpath stuff
08:33 CIA-31 bioclipse: jonalv * r3860 /trunk/playground/plugins/n​et.bioclipse.keyring.tests/ (. .project): created net.bioclipse.keyring.tests to house the keyring tests
08:40 olas joined #bioclipse
09:12 CIA-31 joined #bioclipse
09:15 masak joined #bioclipse
09:21 CIA-31 bioclipse: jonalv * r3863 /trunk/playground/plugins/net​.bioclipse.structuredb.tests/ (. .project): copied net.bioclipse.structuredb to net.bioclipse.structuredb.tests
09:36 masak egonw: I'm not sure you saw my question the other day, or maybe I didn't see your reply
09:36 CIA-31 bioclipse: jonalv * r3864 /trunk/playground/plugins/​net.bioclipse.structuredb/ (5 files in 4 dirs): Removed all test related stuff from net.bioclipse.structuredb
09:37 masak egonw: the code that I'm looking at, can I see it running somewhere in Bioclipse? that would make an evaluation easier
09:37 masak or is it undeployed code?
09:38 CIA-31 bioclipse: jonalv * r3865 /trunk/playground/plugins/net​.bioclipse.structuredb.tests/ (8 files in 4 dirs): Removed all non test related stuff from net.bioclipse.structuredb.tests
09:48 thomas_ku joined #bioclipse
09:50 egonw masak: yes, I created a view
09:50 egonw something with "one molecules" in the title
09:51 masak egonw: oki, will look it up
11:12 olas joined #bioclipse
12:45 masak egonw: I tried it now. looks fine. there's a significant lag when resizing, but at least there are no direct artifacts in the picture
12:45 masak everything looks fine
12:45 masak did you hard code the molecule that shows up?
12:46 masak I will now look a bit closer at the source code to see what it is you're doing
12:48 masak anyway, overall I think that your Single Molecule view is neater and has less problems than the multimolecule equivalent
12:48 masak no less because the latter is in mid-development largely due to my tampering with it :/
12:48 masak but still, yours does what it's supposed to and does it well
12:52 steinbeck joined #bioclipse
13:13 jonalv Can I get some help with CDK stuff from someone good with cdk?
13:17 CIA-31 bioclipse: jonalv * r3866 /trunk/playground/plugins/ne​t.bioclipse.structuredb/src/ (3 files in 3 dirs): Attempts to persist the molecule as CML fails strangely. I suspect I am using the CDK-api in the wrong way...
13:30 CIA-31 bioclipse: ospjuth * r3867 /trunk/bioclipse2/:
13:32 CIA-31 bioclipse: ospjuth * r3868 /trunk/bioclipse2/testing/:
13:34 CIA-31 bioclipse: ospjuth * r3869 /trunk/bioclipse2/testing/testCNF/: Initial import of an RCP application for 3.3 with a Common Navigator Framework (CNF) implementation. Utilizes ui.ide, and ui.editors for now.
13:34 CIA-31 bioclipse: ospjuth * r3870 /trunk/bioclipse2/testing/testCNF/ (22 files in 6 dirs): Initial import of an RCP application for 3.3 with a Common Navigator Framework (CNF) implementation. Utilizes ui.ide, and ui.editors for now.
13:35 CIA-31 bioclipse: ospjuth * r3871 /trunk/bioclipse2/testing/testCNF/: Added bin to svn.ignore
13:36 CIA-31 bioclipse: jonalv * r3872 /trunk/playground/plugins/net.biocl​ipse.structuredb/src/net/bioclipse/​structuredb/domain/Structure.java: Should use ChemFile instead of Molecule when reading CML
13:38 jonalv olas++ created /trunk/bioclipse2
13:42 masak olas++ // yay! we have a tangible product!
13:43 olas tada!
13:43 olas I will present on tuesday
13:43 * jonalv is looking forward to tuesday
13:43 masak :)
13:48 egonw olas: why not put bioclipse2/ in branches/ instead of trunk/ ?
13:48 olas well, now its there
13:48 egonw svn move
13:50 olas will not put mych effort in it yet
13:51 egonw do you want me to move it?
13:51 olas if it is very important for you
13:51 * olas is in telephone
13:51 egonw ok, will move it (yes, it's important)
13:52 olas it's not a branch
13:52 olas it's a rewrite
13:53 egonw depends on your perspective
13:53 jonalv put it in rewrites? :)
13:53 egonw but if you insist, I'll create a svn/bioclipse/rewrites dir for you :)
13:53 egonw jonalv: you beat me to it :)
13:53 CIA-31 bioclipse: egonw * r3873 / (branches/bioclipse2/ trunk/bioclipse2/): Moved the new Bioclipse branch (v2) into branches/
13:53 egonw yes, it's a branch
13:54 masak egonw: I agree
13:54 egonw it will reuse a lot of code form the old bioclipse
13:54 CIA-31 bioclipse: biocoder * r3874 /trunk/playground/plugins/net.bioclipse.chart/ (14 files in 7 dirs):
13:54 CIA-31 bioclipse: Functionality for making scatter plots from MatrixGridEditor now working.
13:54 CIA-31 bioclipse: Select two or more columns and choose scatter plot in the context menu.
13:54 masak it's a branch in the sense of "taking the project in a new direction which will eventually merge with the rest"
13:55 jonalv Ohh that will be some merge... *shivers*
13:55 CIA-31 bioclipse: biocoder * r3875 /trunk/plugins/net.bioclipse.statistics/ (2 files in 2 dirs): Made an action for scatter plotting
13:56 masak jonalv: well, the merge will likely be of bc1 parts into bc2, won't it?
13:57 jonalv masak, I have no idea. It feels very far in the future anyway...
13:57 masak it's probably shiver-worthy, but maybe not just from anticipated pain but also hopefully from anticipated joy
13:57 masak hopefully not too many years in the future
13:57 egonw the IBioResource thing is important, but currently tricky, and difficult to use
13:57 egonw practically, that is...
13:58 egonw leading to inconsistent and incorrect use, and bugs...
13:58 jonalv egonw, did you have the time for some cml support?
13:58 egonw jonalv:almost done updating my Eclipse checkout
13:58 jonalv ack
14:09 CIA-31 bioclipse: ospjuth * r3876 /branches/bioclipse2/testing/testCNF/ (4 files in 2 dirs): Fixed product so that plugin runs from generated launch config.
14:13 egonw jonalv: had trouble this morning with java6
14:13 egonw on gutsy...
14:13 jonalv hm
14:13 egonw the repos server did not have all new Java6 deb packages yet
14:13 egonw and jdk, the only one that really matters, was auto removed...
14:13 egonw got installed now again...
14:13 egonw so rebooting eclipse...
14:14 olas left #bioclipse
14:14 jonalv Is gutsy that much better that it is worth running it already?
14:14 egonw no, but I like the cutting edge stuff...
14:14 egonw it *is* amazing how much the manage to improve each half year...
14:14 egonw have to do regular bug reporting
14:14 egonw but it's quite OK...
14:16 jonalv hm I prefer to be 3-4 months after the wave instead and get all the bug fixes.. :)
14:16 jonalv but yes it keeps getting better and better :)
14:19 egonw I get compile errors on net.bioclipse.statistics
14:19 egonw also for net.bioclipse.structuredb
14:20 egonw ah, no the latter is fine...
14:20 jonalv okey what is wrong with structuredb?
14:20 egonw was still out of data with HD
14:20 jonalv que?
14:21 egonw never mind
14:21 egonw who was biocoder again?
14:22 jonalv EskilA
14:22 egonw got some problems for him/her
14:22 egonw EskilA: arond?
14:24 jonalv egonw, but structuredb compiles for you?
14:24 egonw yes
14:24 egonw which test should I run?
14:24 jonalv the dao tests
14:24 jonalv more exactly
14:24 jonalv structuredao
14:25 egonw ack
14:25 jonalv You will get a very long stackstrace but in the end there is a CDKException
14:27 jonalv ...I hope...
14:27 egonw yes
14:28 jonalv Have you got any idea of what's going wrong?
14:28 egonw looking into the problem
14:32 egonw OK, it's really a problem with the CML
14:32 egonw there is a SAX exception thrown
14:32 jonalv okey?
14:32 egonw nothign the CDK can do wrong about that
14:33 jonalv but the cml is generated by cdk aswell...
14:33 egonw but goes via the database?
14:33 jonalv yes
14:34 jonalv something could become broken of course...
14:34 egonw I think it is the character encoding
14:34 jonalv but I can't see anything wrong with String
14:35 jonalv the String
14:36 jonalv The generated String loks like this:
14:36 jonalv <?xml version="1.0" encodin<?xml version="1.0" encoding="ISO-8859-1"?>
14:36 jonalv <molecule id="m1" xmlns="http://www.xml-cml.org/schema"/>g="ISO-8859-1"?>
14:36 jonalv <molecule id="m1" xmlns="http://www.xml-cml.org/schema"/>
14:36 masak egonw: I've now looked again at JChemPaintView
14:36 jonalv and the loaded String like thios:
14:36 masak looks fine
14:36 masak jonalv: nopaste :)
14:36 egonw masak: ok, great. thanx for checking!
14:36 jonalv <?xml version="1.0" encoding="ISO-8859-1"?>
14:36 jonalv <molecule id="m1" xmlns="http://www.xml-cml.org/schema"/>
14:36 masak egonw: I guess the System.out.println lines are just debugging?
14:37 egonw jonalv: make sure the encoding of your database matched ISO-8559-1
14:37 jonalv hm they don't looks the same :)
14:37 egonw I am sure it is not...
14:37 jonalv LOL
14:37 masak jonalv: showing things to other people often does wonders :)
14:37 egonw how did you get the first?
14:38 jonalv that is what Structure.getMoleculeCML returns
14:38 egonw so, it seems a character encoding problem
14:38 masak yes
14:39 jonalv the first is three lines and the second is two line how can that be a character encodning problem?
14:39 egonw not sure where it goes wrong...
14:40 jonalv it seems I have double clicked the paste right+
14:40 masak jonalv: that's why you shouldn't paste at all, you know...
14:40 jonalv friday afternoon...
14:40 masak not into the channel, anyways
14:40 jonalv masak, but it was only two lines...
14:40 masak "but it was only two lines", I know
14:40 masak but look how it went
14:40 masak :)
14:41 masak hm, they look the same
14:41 masak no diff in encoding
14:42 egonw how can you see that??
14:44 jonalv diff says that the strings are equal
14:44 masak egonw: when told that there was a double paste, I saw they were alike
14:45 masak the (declared) encodings are the same
14:45 masak egonw: maybe what you mean is that there's a difference in actual encoding...
14:45 masak but why would that make itself noticed here?
14:45 jonalv But the strings are equal!
14:45 egonw OK, hang on... let me try something
14:45 masak there are no funny non-ASCII characters in there
14:46 egonw if it would be ASCII chars, it would already be wrong ! :)
14:46 egonw (ASCII is an encoding scheme too)
14:46 masak egonw: yes, of course...
14:46 masak egonw: but it's a common denominator of a lot of other encodings
14:47 masak I was talking about the range of characters, not the way they were encoded
14:47 egonw masak: but you got a clue what the DB is using??
14:47 masak egonw: my point is that it shouldn't matter here
14:47 masak but no, no cluse
14:47 masak s/cluse/clue/
14:47 jonalv the DB is hsqldb 100% java so my guess is that it should "just work" on that part
14:47 masak jonalv: there's no "just work" in encoding land
14:48 masak sorry
14:48 masak there's only pain
14:48 jonalv masak, the strings are equal you know...
14:48 masak jonalv: yep. sorry
14:48 * jonalv mumbles: friday afernoon...
14:49 masak egonw: have you tried to expand the view really fast?
14:49 masak turns out the molecule image wraps horizontally
14:49 jonalv egonw, do you think it is a cdk problem?
14:49 masak it's not ideal, and may be fixable
14:50 masak btw, I have a problem with bioclipse starting up twice when I run it from Eclipse
14:50 masak anyone else experienced that?
14:51 egonw jonalv: no, it's not a CDK problem
14:51 masak egonw: ah, rereading your mail from earlier this week, what you want me to do is backport your widget into the multi-molecule view. yes?
14:51 egonw masak: yes, please
14:51 masak that's a good idea, anyway
14:51 masak will try
14:51 egonw masak: about two bioclipse: don't double click :)
14:51 masak also, I will attempt to widgetize the table itself, as per jonalv++'s wishes
14:52 masak egonw: ha ha :)
14:52 masak it starts two slightly different bioclipses
14:52 egonw a pink one too ?
14:52 masak yes, with a pony
14:52 egonw ha, you found the easter egg :)
14:52 masak must be the Friday Afternoon phenomenon
14:53 jonalv egonw, if it is not a CDK-problem then would you happend to be able to tell me what is going on?
14:53 egonw masak: it is triggered by wearing underwear
14:53 masak d'oh!
14:53 egonw jonalv: I got no idea yet
14:54 jonalv oki no more than that it is not cdk...
14:54 egonw it's the XML library that is failing on the CML you pass...
14:55 jonalv can you spot any errors in the xml?
14:55 egonw no, the ASCII version that comes out of my IRC client looks fine...
14:56 jonalv :)
14:56 masak that's the problem with encodings
14:56 jonalv I think I give up for today
14:56 masak jonalv 0 - encodings 1
15:01 egonw it's not encoding
15:01 egonw mmm...
15:01 egonw why are you using org.hsqldb.lib.StringInputStream ??????
15:01 jonalv I am?
15:01 jonalv LOL
15:01 egonw there's likely your encoding problem source
15:02 jonalv maybe that should be a java version?
15:02 jonalv as in sun?
15:02 masak I should certainly think so!
15:02 masak :)
15:02 jonalv I am not very good at all these streams
15:02 masak "everything flows"
15:02 jonalv It's a jungle of streams.... ...or a delta maybee... :)
15:04 masak yikes, I'd forgotten how wrong Structure2DViewer was
15:04 egonw :)
15:04 egonw jonalv: fixing the problem now
15:04 jonalv but ehere is no such thing as another StringInputStream...
15:06 egonw no, you need ByteArrayInputStream
15:07 jonalv right
15:07 jonalv you fix?
15:08 jonalv I will leave now
15:08 jonalv need to be somewhere :)
15:08 jonalv bya
15:08 jonalv bye
15:12 CIA-31 bioclipse: egonw * r3877 /trunk/playground/plugins/net.biocl​ipse.structuredb/src/net/bioclipse/​structuredb/domain/Structure.java: Fixed reading of CML content.
17:06 CIA-31 bioclipse: egonw * r3878 /trunk/playground/plugins/net.bioclipse.cha​rt/src/net/bioclipse/chart/ChartUtils.java: Cleaned up imports, removing one sun.x.y import not found in my classpath.
22:25 CIA-31 joined #bioclipse

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