Camelia, the Perl 6 bug

IRC log for #bioclipse, 2007-12-13

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
08:19 olas joined #bioclipse
08:22 steinbeck joined #bioclipse
08:22 jonalv joined #bioclipse
09:21 masak joined #bioclipse
10:12 masak philosophical quandry:
10:47 masak I solved the threading problem in the logger
10:48 masak by inserting the Display.getDefault( new Runnable() { ... } ) thing that jonalv++ wrote about
10:52 masak problem is, Display is part of an swt package
10:52 masak so now Logger depends on something graphical
10:52 masak does that mean I should move Logger to net.bioclipse.ui?
10:53 masak :/
10:57 CIA-31 bioclipse: carl_masak * r4468 /branches/bioclipse2/core/plugins/n​et.bioclipse.ui/src/net/bioclipse/u​i/views/ScriptingConsoleView.java:
10:57 CIA-31 bioclipse: [ScriptingConsoleView.java]
10:57 CIA-31 bioclipse: *attempt to fix a bug that kaskelot++ discovered
11:02 masak well, that didn't work... :(
12:17 masak joined #bioclipse
12:24 CIA-31 bioclipse: carl_masak * r4469 /branches/bioclipse2/core/plugins/net.biocli​pse.core/src/net/bioclipse/core/Logger.java:
12:24 CIA-31 bioclipse: [Logger.java]
12:24 CIA-31 bioclipse: * modified to not cause illegal thread access in SWT
12:24 CIA-31 bioclipse: * this causes the logger to import an SWT widget
12:24 CIA-31 bioclipse: ** should Logger be moved to net.bioclipse.ui because of this?
12:42 EskilA joined #bioclipse
12:45 edrin joined #bioclipse
12:48 edrin hi
12:48 steinbeck Cheers
12:50 masak hi
12:57 CIA-31 bioclipse: ospjuth * r4470 /trunk/plugins/net.bioclipse.statistics/ (4 files in 3 dirs): Replaced jar with nebula plugin
12:58 CIA-31 bioclipse: ospjuth * r4471 /trunk/features/net.bioclipse.s​tatistics-feature/feature.xml: Added nebula plugin to feature
12:58 CIA-31 bioclipse: ospjuth * r4472 /trunk/plugins/org.eclipse.nebula.widgets.grid/ (META-INF/MANIFEST.MF build.properties): Fixed build props
12:59 CIA-31 bioclipse: ospjuth * r4473 /trunk/plugins/net.bioclipse​.chart/META-INF/MANIFEST.MF: Exported packages
13:08 egonw joined #bioclipse
13:09 egonw moin
13:17 thomas_ku joined #bioclipse
13:18 CIA-31 bioclipse: ospjuth * r4474 /trunk/ (6 files in 5 dirs): Added jar, deps, and FIXME: for array size
13:23 edrin hi egonw
13:49 EskilA joined #bioclipse
13:54 CIA-32 joined #bioclipse
14:10 CIA-32 bioclipse: ospjuth * r4475 /trunk/plugins/net.bioclipse.chart/ (8 files in 4 dirs): Deleted ktable and fixed export to actually include built classes. Did that by creating custom jar.
14:10 CIA-32 bioclipse: ospjuth * r4476 /trunk/plugins/net.bioclipse.statistics/ (6 files in 4 dirs): Removed Ktable jar and ktable model/editor.
14:14 masak joined #bioclipse
14:17 CIA-32 bioclipse: carl_masak * r4477 /branches/bioclipse2/core/plugins/n​et.bioclipse.ui/src/net/bioclipse/u​i/views/ScriptingConsoleView.java:
14:17 CIA-32 bioclipse: [ScriptingConsoleView.java]
14:17 CIA-32 bioclipse: * factored out common functionality into method
14:17 CIA-32 bioclipse: * fixed the combined BS/onPrompt bug that conspired
14:17 CIA-32 bioclipse:  to make things work but for the wrong reasons
14:17 CIA-32 bioclipse: * printMessage now only moves cursor if it is
14:17 CIA-32 bioclipse:  situated on the command line
14:17 kaskelot joined #bioclipse
14:51 masak http://bioclipse.blogspot.com/20​07/12/first-stab-at-logging.html
15:01 DrGTO joined #bioclipse
15:02 DrGTO goodday
15:02 egonw hi DrGTO
15:02 masak hello DrGTO
15:03 DrGTO back with another question :)
15:03 DrGTO as I know some of you are involved with cml, right?
15:03 egonw yes
15:03 edrin who is DrGTO?
15:04 DrGTO :)
15:04 thomas_ku joined #bioclipse
15:04 DrGTO chemist from TIB
15:05 edrin hello, nice to meet you
15:05 DrGTO I was playing around with webservices from WWMM server, testing services to get molweight from cml. And .... hell where are the protons gone?
15:06 DrGTO marvin doesnt write protons to cml?
15:06 egonw no idea...
15:06 egonw got a URL?
15:06 egonw masak: read your blog...
15:06 masak egonw: cool
15:07 masak ok
15:07 egonw masak: but I don't get it... why does that code need to go into the Activator?
15:07 masak egonw: it doesn't
15:07 masak (hm, maybe I should add that)
15:07 masak it's just a convenient place to start an extra thread that does a bit of test logging
15:08 DrGTO http://wwmm-svc.ch.cam.ac.uk/wwmm/html/index.html <--- Webservice  server. Outdated, maybe?
15:08 masak let me just add that right away
15:09 egonw ha :)
15:09 masak thx for the feedback :)
15:09 DrGTO i converted to cml with openbabel and then try to get molweight based on cml. benzene has 72 instead of 78 ..
15:10 egonw mmmm... don't get any CML output at all...
15:11 egonw DrGTO: you see that -x2 option...
15:11 egonw ?
15:11 DrGTO yeah, wondered what that was ...
15:11 egonw extra OB option...
15:11 egonw add this one:
15:17 CIA-32 bioclipse: egonw * r4478 /trunk/makeHelpWebsite.pl: Be a bit more specific, so that Ola can remove the 'plugin/' bit
15:20 egonw DrGTO: add '-h' as option
15:20 egonw that will add hydrogens upon conversion to CML
15:20 egonw or should...
15:20 DrGTO ah, thanks
15:20 egonw can't test, because I don't get any CML at all
15:20 DrGTO still wonder, why it doesnt work via the webpage ...
15:21 egonw something broken I guess...
15:21 DrGTO are there any other webservices available? I found some on chemspider
15:21 egonw at IU
15:21 egonw google for "web services Rajarshi"
15:22 DrGTO ah, chemspider doesnt support the options flag
15:23 DrGTO in case someone doesnt know soapUI tool. Great stuff!
15:43 CIA-32 bioclipse: carl_masak * r4479 /branches/bioclipse2/core/plugins/net.bioclips​e.core/src/net/bioclipse/core/Activator.java:
15:43 CIA-32 bioclipse: [Activator.java]
15:43 CIA-32 bioclipse: * minor touch-up
15:43 CIA-32 bioclipse: ** removed whitespace
15:43 CIA-32 bioclipse: ** removed comment
15:52 edrin good night
15:55 edrin left #bioclipse
16:04 CIA-32 bioclipse: updatebjarni * r4480 /branches/bioclipse2/core/plugins/net.bioclipse.u​i/src/net/bioclipse/ui/views/JsConsoleView.java: R experiments.
16:06 CIA-32 bioclipse: updatebjarni * r4481 /branches/bioclipse2/core/plugins/net.bioclipse.r/ (META-INF/MANIFEST.MF src/net/bioclipse/r/R.java): R experiments.
16:32 egonw for those interested... over at #kubuntu-devel. there will be a 30 minute bzr tutorial, right now
16:51 jonalv joined #bioclipse
19:16 shk3 joined #bioclipse
19:16 shk3 hi masak
19:16 masak hi!
19:16 masak long time no see
19:16 shk3 yes
19:17 shk3 busy with work and other stuff
19:17 masak yep, me too
19:17 shk3 spent this week and last week in ludwighafen
19:17 shk3 is the new bioclipse already out?
19:17 masak which one, 1.2.0 or 2.0?
19:17 shk3 the rc
19:17 masak I think rc2 is the latest 1.2.0
19:18 shk3 the one ola announced for today?
19:18 masak oh, maybe I missed that announcement
19:18 shk3 anyway, I found something which, if true, is a real problem.
19:18 shk3 could you test?
19:18 shk3 just filed a bug.
19:18 masak sure
19:18 shk3 great
19:18 shk3 the last bug, high priority
19:19 masak um, do you have an URL? :)
19:19 shk3 https://sourceforge.net/tracker/ind​ex.php?func=detail&amp;aid=1850268&​amp;group_id=150681&amp;atid=778609
19:19 masak thx
19:20 masak sounds serious indeed
19:20 masak let me just test it, and I'll be right back
19:21 shk3 thanks
19:21 shk3 perhaps my setup here is wrong or so...
19:21 masak it should still work, if you ask me
19:23 shk3 works for you?
19:23 masak I'm not quite there yet
19:24 shk3 ok
19:24 masak updating right now
19:24 masak usually, I do bc2 work nowadays
19:24 masak so I suspect I don't have a recent checkout of bc1
19:25 shk3 ok
19:25 shk3 i am still trying to get bc1 right...
19:26 masak how do I go about creating a molecule as you describe in the bug report?
19:27 masak this is my chance to learn a bit of bc1 :)
19:27 shk3 do new->molecule
19:27 masak yes
19:27 masak ah
19:27 shk3 I am just updating to make sure i have the latest stuff
19:28 masak which one do I choose under supported formats?
19:28 shk3 mdl mol format
19:29 shk3 or whatever it is called
19:29 masak ok
19:29 masak found it
19:29 shk3 jcp should open
19:29 masak ah, is that something I should have checked out? :/
19:30 masak I only get the text file right now
19:30 shk3 what does it look like?
19:30 shk3 does it have $$$$ in it?
19:30 masak nope
19:30 masak just
19:30 masak CDK 12/13/07,20:28
19:30 masak a bunch of zeros
19:30 shk3 that looks good
19:30 masak 0999 V20000
19:30 masak M END
19:30 shk3 could be jcp doing wrong
19:30 masak what's jcp? I don't think I have it
19:31 shk3 jchempaint
19:31 masak ah
19:31 masak I'll check it out
19:31 shk3 net.bc.cdk.jchhempaint
19:31 masak thx
19:33 masak ok, downloaded
19:33 masak here we go again
19:33 shk3 doing it myself
19:34 masak ok, so now I get what appears to be a blank jcp editor
19:34 masak with two tabs, one called JChemPaint and one Source
19:35 shk3 yes
19:35 shk3 so do i
19:35 masak is this desired behaviour?
19:35 shk3 paint somethin
19:35 shk3 g
19:35 shk3 a ring or so
19:35 shk3 save
19:35 masak ok
19:35 shk3 and close
19:35 shk3 unload best
19:36 shk3 (there is a "unsaved" message which is wrong)
19:36 shk3 and open in external text editor best
19:36 masak eh
19:36 masak how do I draw things?
19:36 masak I have found the toolbar
19:36 masak up above
19:36 shk3 right
19:36 shk3 click ring
19:36 shk3 and click in pane
19:37 masak and when I click tools, all I get is debug messages on stdout
19:37 masak nothing else
19:37 shk3 you need to click on the drawing panel after selection of tool
19:37 masak does this have anything to do with the rumors I keep hearing about jcp not working on Macs?
19:37 masak :(
19:38 shk3 not sure
19:38 shk3 could be
19:38 masak if so, this seriously needs fixing...
19:38 shk3 if you choose a ring, it is framed?
19:38 masak I get nothing
19:38 masak no matter what I click
19:38 shk3 hm, bad
19:38 shk3 I will paste this dialog into the bug report
19:38 masak :)
19:39 shk3 somebody could check
19:39 shk3 because doing a molecule is a central task
19:39 masak I will lead a mob up to the castle, demanding jcp on Mac
19:39 masak carrying pitchforks and torches
19:39 shk3 I thought it works
19:40 shk3 I remember there were mac problems, but not sure what exactly
19:40 masak from what I've heard, it's got something to do with SWT and possibly AWT
19:40 shk3 yes
19:40 shk3 that's a problem on mac
19:40 masak there are also very loose rumors about a fix, but my memory fails me here
19:41 shk3 so does mine
19:41 masak I'll talk to olas about it
19:41 shk3 please
19:41 shk3 just to tell the problem:
19:41 shk3 I can paint in jcp and it looks good
19:41 masak mm
19:41 shk3 but:
19:42 shk3 after closing, the file contains two molecules
19:42 shk3 as confirmed by viewing in text editor
19:42 masak hm, strange
19:42 shk3 (when opening it in jcp, I get two children, but they have the same name, which
19:42 shk3 seems to be a problem with child nodes, so not directly related)
19:43 masak ok
19:44 shk3 thanks for trying
19:44 shk3 I will do further testing
19:44 shk3 how is bc2 going?
19:45 masak very well, at least what we have so far
19:45 shk3 good a stable core would be great
19:45 masak kaskelot and I coded in early R support today
19:48 masak I finally learned how to synchronize threads over an object
19:48 masak all in all, a good day
19:49 shk3 great
19:49 shk3 sorry I can't really contribute to bc2
19:50 shk3 do you have the new resource model working?
19:50 masak not yet
19:51 masak though I think there are not many obstacles left now
19:52 shk3 good
19:53 shk3 ok, I will have a walk and do some bc1 testing later.
19:53 masak ok
19:53 shk3 please talk with ola about that problem, because it could be a major one.
19:53 masak I'll let olas know about the two jcp bugs
19:53 * shk3 is away
20:05 egonw_ joined #bioclipse
20:07 CIA-32 bioclipse: shk3 * r4492 /trunk/plugins/net.bioclipse.nmrshiftdb/src/net​/bioclipse/wizards/DownloadSpectraWizard.java: if no spectra found, a message is shown
22:24 CIA-32 joined #bioclipse
22:34 CIA-32 bioclipse: shk3 * r4493 /trunk/plugins/net.bioclipse.nmrshiftdb/ (2 files in 2 dirs): better wording
23:22 CIA-25 joined #bioclipse

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary