Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-10-13

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All times shown according to UTC.

Time Nick Message
06:38 Gpox joined #bioclipse
07:30 olass joined #bioclipse
07:33 miguelrojasch joined #bioclipse
07:43 jonalv joined #bioclipse
07:49 sneumann joined #bioclipse
07:53 egonw joined #bioclipse
07:53 egonw moin
07:53 zarah hi egonw
07:56 egonw jonalv: can you join #cdk ?
07:57 jonalv egonw: oki
07:57 egonw jonalv: as you might have noted, I am *not* at BMC
08:01 stain olass: how did it go with your JAXB issues..?
08:01 stain should we try a skype-screensharing-thing?
08:02 olass stain: sure
08:02 olass 5 mins?
08:02 * olass is in tel
08:02 stain aoh, perhaps later today.. I have a meeting in an hour.. s
08:02 olass stain: ok
08:03 olass ping me when you can
08:03 stain ok ;)
08:06 samuell joined #bioclipse
08:08 samuell morning
08:10 egonw hi samuell
08:10 jonalv hi samuell
08:10 samuell hi guys
08:11 egonw samuell, jonalv: thanx for your comments
08:11 samuell egonw: You're welcome
08:13 samuell btw, I'm thinking for today to learn what all the different files in plugin's tree structure means. Any hints and links are most welcome.
08:14 egonw created with the SDK?
08:14 egonw there is that wiki page by jonalv
08:14 egonw how to write a manager 2
08:14 egonw which is recommended
08:14 samuell Yep, I'm going to read that yes
08:15 samuell (Just started a little bit yesterday)
08:15 samuell Ok, guess I better read that first, then maybe things will be more clear.
08:18 * samuell is grabbing a coffe. brb.
09:14 samuell Ok, have read "how to make a manager" now. I was a good article (I'll have to come back to some details later though).
09:15 samuell I will still need to learn a bit on the files that are general eclipse stuff, like product/feature/target files etc.
09:16 egonw just ping if you have questions
09:26 samuell Ok
09:46 samuell egonw: Last time we got the basic plugin working, you had created a "features" folder for the dr-prolog plugin.
09:46 egonw yes
09:46 samuell Where should that be put?
09:47 samuell inside the bioclipse.core folder or?
09:47 egonw repository/plugins -> is where the plugins go
09:47 egonw repository/features -> is where the features go
09:47 egonw repository/externals -> is where the plugins go which just wrap third party libs
09:47 samuell Ok... inside the plugin-repository then?
09:48 egonw what do you mean with plugin repository ?
09:48 egonw the git repos, rigth?
09:48 samuell Because in my workspace I have checked out bioclipse core and the plugins in separate folders
09:48 samuell workspace/bioclipse.core
09:48 samuell workspace/bioclipse.blipkit
09:48 egonw ok, that sounds good
09:49 egonw each git repos in a separate sub folder
09:49 egonw right?
09:49 samuell Yep
09:49 samuell So, should it be
09:49 samuell workspace/bioclipse.blipkit/features .... ?
09:50 samuell I was looking at a backup of the old files (with the drprolog-plugin) and could not find such a folder under the drprolog repo folder.
09:50 samuell That's why I'm wondering.
09:50 egonw yes:
09:50 egonw workspace/bioclipse.blipkit/features
09:50 egonw workspace/bioclipse.blipkit/plugins
09:50 egonw workspace/bioclipse.blipkit/externals
09:50 samuell Ok.
09:51 samuell And the feature files, will they automatically be recognized by Eclipse, or
09:51 samuell does one need to do anything special to get them included?
09:51 samuell (Thinking I'll try to copy the feature files you created for drprolog, and modify them for blipkit)
09:51 egonw features/net.bioclipse.blipkit_feature/
09:51 egonw is a normal eclipse 'project'
09:52 egonw with a .project
09:52 egonw but also a feature.xml
09:52 egonw see other feature plugins as example
09:52 samuell Ok.
09:52 egonw so, you should in the end have:
09:52 egonw workspace/bioclipse.blipkit/features/feature​s/net.bioclipse.blipkit_feature/feature.xml
09:52 egonw and a bit more in that folder
09:52 egonw you can put the blipkit.product in that folder too
09:53 samuell Ok
09:53 egonw the blipkit.product will consist of the features:
09:53 egonw bioclipse.platform
09:53 egonw bioclipse.rdf
09:53 egonw bioclipse.blipkit
09:53 egonw (and perhaps more when we get to applications)
09:53 samuell Ok
09:56 samuell Thanks
10:30 samuell I can't seem to get the product file to work.
10:31 samuell If I copy the bioclipse.product file, what are the information that needs to be identical, what needs to be changed, and what doesn't matter?
10:35 samuell Well, it seems my blipkit.product contained a list of lots of plugins, which was not really needed.
10:39 egonw samuell: copy the .product
10:39 egonw and *only* change
10:39 egonw the list of features
10:40 samuell Ok, yep (And maybe adding -noUpdate flag ? )
10:40 egonw yes, useful
10:40 egonw samuell++
10:40 samuell :) (Saw it in your commit to drprolog plugin)
10:40 egonw samuell++ (for reading commit messages)
10:59 samuell Got blipkit answering to the JS console now. :)
10:59 samuell egonw++ for helping.
11:01 egonw really?
11:01 samuell The main problem was that I had some very strange issue with the "@PublishedMethod" annotation. It would not get recognized correctly.
11:01 egonw you can run a prolog statement inside Bioclipse already?
11:01 samuell No, sorry, no
11:01 egonw ah, just the manager :)
11:01 samuell I mean, I get the plugin to answer
11:01 egonw ok, good :)
11:01 egonw you got me shocked for a second ...
11:01 egonw :)
11:02 samuell Yeah, I should think about what I'm saying
11:02 samuell :)
11:16 samuell How do I import existing Java source code, so that I can import it with an import statement
11:17 samuell import jpl.*;
11:17 samuell I need to create a project in Eclipse for the code, right?
11:17 samuell How can I make it be recognized as "jpl"?
11:36 masak joined #bioclipse
11:38 egonw yes, you need to make a plugin in externals/
11:39 mgerlich joined #bioclipse
11:48 samuell egonw: Yeah, thanks. jonalv stopped by, so I got help from him
11:48 egonw jonalv++
12:04 samuell Yep
12:10 samuell By some strange reason the manager won't show up in the JS Console again.
12:10 samuell Are there any general hints here?
12:32 masak samuell: depends on whether you can dig up any error messages that indicate something went wrong, I guess.
12:32 samuell masak: Yeah, well.
12:32 samuell true
12:43 egonw samuell: for me it often is a dependency gone bad
12:44 samuell egonw: Ok... Well for now I did just restore from the working version. Will compare working and not working version to see if I can get a clue
12:45 samuell *doh* the problem was very stupid
12:45 egonw good analytical mind
12:45 egonw it always is
12:45 egonw computers just do what you tell them to
12:45 samuell yep :)
12:46 samuell Seems like I had by accident renamed the .java files, but that was not seen inside Eclipse.
12:56 samuell jonalv: JFYI, I'm getting "java.lang.NoClassDefFoundError: jpl/Query" when trying to instantiate a class in the library that we made into a plugin.
12:56 jonalv hm
12:56 jonalv don't really know
12:57 samuell It does not complain with any red marks before. Hmm.
12:57 samuell (That is, the import seems to work)
12:59 samuell Ok, well no worries. Will have to study the error log to get clues.
13:00 samuell The three (or so) last lines in this error log: http://wiki.bioclipse.net/index.php?ti​tle=User:Samuell/ErrorLog20091013_1459
13:00 zarah samuell's link is also http://tinyurl.com/ykwobfy
13:01 jonalv samuell: do you have that plguin in the run configuration when you are running?
13:01 samuell Where do I set the run configuration?
13:02 samuell In the blipkit.product file?
13:02 jonalv hm maybe, I am not 100% sure about what you are doing
13:04 samuell The blipkit.product file refers to blipkit_feature, which has the jpl plugin as a required one.
13:10 jonalv http://github.com/egonw/cdk/blob/mast​er/src/main/org/openscience/cdk/finge​rprint/PubchemFingerprinter.java#L602
13:10 zarah jonalv's link is also http://tinyurl.com/yzowuq5
20:30 egonw_ joined #bioclipse

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