Camelia, the Perl 6 bug

IRC log for #bioclipse, 2011-11-30

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All times shown according to UTC.

Time Nick Message
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07:45 egonw_ olass: can people save DS results as CSV or Excel?
07:45 olass no
07:45 egonw_ save as anything?
07:45 olass there is a report
07:46 egonw ah, the hamburger...
07:46 olass that can be exported
07:46 olass hamburger?
07:46 egonw data = meat, PDF ... hamburger... no point of return
07:46 olass yes
07:47 olass would be nice to save data as CSV or Excel but currently not possible if not using script
07:47 olass but I made such script to store results as properties
07:48 egonw available from MyExperiment?
07:48 olass don't think so, but that can be arranged
07:48 olass what you need it for?
07:48 egonw please ping me when uploaded...
07:48 olass is this urgent?
07:48 egonw someone asked me about it...
07:49 olass written on my todo then
07:49 egonw thanx
07:49 egonw you can also choose to just send me the script (hoping you have that still around) and then I can upload it
07:49 olass want to test it first, no problem uploading it myself
07:49 egonw btw, just noted that features.bioclipse.net is broken
07:50 egonw ok, excellent
07:50 olass things are in flux, arvid is working on build process
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09:26 egonw Gpox: I released CDK 1.4.6 which should have the methods that were missing in the IMouseEventRelay
10:01 Gpox ok. Is rendererModel fixed too?
10:02 egonw no
10:02 egonw or...
10:02 egonw don't think I have seen a patch...
10:03 egonw olass: replied
10:03 olass thx
10:04 olass egonw: how do I explain this to users of Bioclipse?
10:04 olass what is the feature part?
10:05 egonw yeah, good question
10:05 olass all I see is a bug...
10:05 egonw no, not a bug
10:05 olass should we call it a limitation?
10:05 egonw well, in Bioclipse it may be a bug
10:05 egonw in Bioclipse we fail to communicate this limitation of the algorithm
10:05 olass ok
10:05 olass is this complicated to fix?
10:08 egonw we could in Bioclipse check if the substructure matches isobutane or cyclopentane, and then do a double check after the isomorphism checking
10:08 olass yes, that is a workaround...
10:09 olass but for cdk? any way to fix?
10:09 olass or does that imply changing algorithm?
10:09 egonw yeah, invent a better algorithm
10:09 egonw yes, that's the implication indeed
10:09 egonw it's just that those two substructures have the same bond graph
10:09 egonw and thus cannot be distinguished
10:10 olass how many structures does this apply to?
10:10 egonw just those two
10:11 olass you don't want to add that logic to cdk?
10:11 egonw those are the only two substructures for which the bond graph is identical
10:11 egonw lego building blocks...
10:11 olass ok, but how do we in Bioclipse "do a double check after the isomorphism checking"?
10:12 egonw check for the input substructure and the match of both have an equal amount of atoms
10:12 egonw cyclopentane = 3 atoms, isobutans = 4 atoms
10:12 olass oh, but I just check for isSubgraph
10:12 olass which returns true
10:12 egonw yes
10:13 egonw then check if the query substructure is isobutane or cyclopropane
10:13 egonw and if so, check atom counts
10:13 olass atom counts for what?
10:13 egonw the query and the match
10:13 olass I don't get a match
10:13 olass I get true/false
10:13 olass boolean
10:13 egonw match := atoms in the target structure
10:14 egonw ah... I get your point
10:14 egonw use the method in the same class to get the match instead of a bool
10:14 egonw .getOverlaps()
10:14 olass only in the case of isobutane or cyclopropoane?
10:14 egonw yes
10:15 olass ok, thanks
10:15 olass these limitations are important to have easy access to, IMHO the javadoc is not a supergood place...
10:19 olass but I understand that they do appear there
10:33 egonw yeah, it's the primary location with Java...
10:34 egonw I've added it as TODO to write about this in the book, and will copy it into my blog too...
10:34 egonw to raise a bit more awareness
10:50 olass thanks
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13:11 samuell welcome dl
13:12 egonw hi dl
13:13 samuell What's the problem when "EclipseStarted" class is not found ...
13:13 samuell just the classpath?
13:13 * samuell helps dl get up the bioclipse dev environment
13:14 jonalv samuell++
13:19 dl java.lang.ClassNotFoundException: org.eclipse.core.runtime.adaptor.EclipseStarter
13:19 dl Seems quite basic // samuel
13:21 samuell Is bioclipse yet ready to run on Java 6?
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13:22 samuell There's a lot of validation errors about "requireing java 1.5", when validating plugins in the run configuration ...
13:25 samuell Anyone succeeded to build Bioclipse in Eclipse Galileo?
13:25 samuell Gpox, do you think that should work?
13:26 samuell It seems like we are missing some basic eclipse plugins.
13:26 samuell We don't see any of them in the target platform ...
13:27 jonalv samuell: such as?
13:27 samuell Something containing org.eclipse.core.runtime.adaptor.EclipseStarter
13:27 jonalv I honestly have no idea
13:33 samuell Seems related to valentins bug from October, here: http://pele.farmbio.uu.se/bug​zilla36/show_bug.cgi?id=3086
13:33 samuell ... any status update on that? olass?
13:33 olass no
13:33 olass I have not had time to work on it
13:33 olass patches welcome :)
13:33 samuell (also fails to load org.eclipse.core.runtime.adaptor.EclipseStarter )
13:34 jonalv samuell: may I ask what you are trying to do?
13:34 samuell Daniel Lundins work depending on this :(
13:34 samuell jonalv: Fire up bioclipse, from eclipse
13:34 jonalv samuell: uhm, should be possible one would think...
13:34 dl samuell: See this http://irclog.perlgeek.de/bioclipse/2011-02-03
13:34 samuell hope so :)
13:35 samuell dl: But this time, "adding required plugins in run configurations" didn't help :/
13:37 samuell Still, we get a lot of reported problems when validating plugins in the run config
13:38 samuell But "Add required" does not help.
13:38 jonalv could it be an Eclipse version thing?
13:38 jonalv Gpox: around?
13:39 samuell jonalv: Possibly ... I don't remember that I ever succeeded to run Bioclispe in Eclipse Galileo
13:39 samuell ... have been sticking with Helios
13:39 jonalv are you not using Helios now then?
13:40 samuell Yeah, but Daniel Lundin (dl) is running Galileo
13:40 samuell (the Ubuntu default)
13:40 samuell ... we'll try with Helios now though ...
13:40 jonalv sounds like a plan to me
13:40 samuell jonalv, :)
13:43 olass Gpox: ping
13:43 Gpox olass: pong
13:43 olass Gpox: could you consider merging bioclipse.core master branch into 2.5?
13:44 olass do you see any problems?
13:45 olass I have a problem when nu.xom is not available at runtime
13:45 olass but at compile time
13:52 Gpox it might be missing from a feature then
13:53 Gpox no problem with the merge if you have/will fix the Dataset rename in all other repos
14:19 olass yes, I will do that, it concerns DS
14:19 olass hmm, in fact, let's wait with this
14:19 olass and let me fix that first
14:50 samuell Yep ... eclipse helios worked better ... we got a basic bioclipse up now ...
14:51 samuell Now on to next challenge: RSE and bioclipse.hpc :>
14:51 egonw samuell: can you explain the steps via IRC?
14:51 egonw then I can try it too...
14:51 egonw already have .hpc checked out...
14:51 egonw but now fails still on missing RSE
14:54 samuell Yeah ... has to be installed via update site ...
14:54 samuell ... and then exposed to target platform somehow ...
14:55 samuell We'll try to get that done now ...
14:55 * samuell tries to remember how to expose plugins in the eclipse installation to the target platform ...
14:57 samuell Anyone remembers?
15:04 samuell_ olass, Gpox?
15:05 samuell_ We have installed RSE via the Eclipse update site ... '
15:05 samuell_ ... ant the hpc.product file has the rse features as dependencies ... but they get warning icons for dl
15:06 samuell_ ... so I think we need to add the plugins or features to the target platform somehow, right?
15:06 samuell How to do that?
15:08 egonw can that update site not be made part of the target platform?
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15:11 samuell_ egonw: Yeah, I think we found it ...
15:12 samuell_ the first tab in the target platform file ...
15:39 samuell_ Thanks anyway
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18:23 samuell (guess what ... in ubuntu unity you have no idea how many xchat-windows you have open :((( )
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