Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-09-09

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All times shown according to UTC.

Time Nick Message
06:38 Gpox joined #bioclipse
07:02 CIA-61 bioclipse.sdk: Egon Willighagen master * rd499bf5 / plugins/net.bioclipse.sdk/build.properties : Added the missing templates from the exported jar - http://bit.ly/aVBZX
07:02 CIA-61 bioclipse.sdk: Egon Willighagen master * rf1255c9 / (2 files): Overwritten the getImportPackages(), but it does not seem to get run :( So, still no proper MANIFEST.MF with Import-Package: org.apache.log4j - http://bit.ly/bkokU
07:02 CIA-61 bioclipse.sdk: Egon Willighagen master * rf2f09f7 / (3 files in 3 dirs): Put 1.1.8 on the update site, fixing the missing templates - http://bit.ly/1amljU
07:27 Gpox joined #bioclipse
07:30 egonw joined #bioclipse
07:34 jonalv joined #bioclipse
07:40 Gpox http://pele.farmbio.uu.se/cgi-bin/bugzilla/bugl​ist.cgi?query_format=advanced&short_desc_ty​pe=allwordssubstr&short_desc=&product=B​ioclipse+2&component=JChemPaint+Feature&amp​;target_milestone=---&target_milestone=2.4+​release&target_milestone=2.6+release&ta​rget_milestone=2.1+release&target_milestone​=2.2+release&target_milestone=2.0+release&a​mp;long_desc_type=substring&long_desc=&​bug_file_loc_type=allwordssubstr&bug_file_l​oc=&deadlinefrom=&deadlineto=&bug_
07:40 zarah Gpox's link is also http://tinyurl.com/mubdj8
07:40 egonw Gpox: tack
07:43 Rijnbeek joined #bioclipse
07:48 egonw the wiki: https://sourceforge.net/apps/mediaw​iki/cdk/index.php?title=JChemPaintW​orkshop2009#Wed_Morning_Programme
08:02 olass joined #bioclipse
08:10 samuell joined #bioclipse
08:12 jonalv egonw: intresting link, however I need a password to look at that... :/
08:13 egonw the wiki: http://sourceforge.net/apps/mediaw​iki/cdk/index.php?title=JChemPaint​Workshop2009#Wed_Morning_Programme
08:13 zarah egonw's link is also http://tinyurl.com/n83qsf
08:13 egonw try that link
08:14 jonalv egonw: that worked
08:15 jonalv hm are you guys doing gui testing? sounds intresting :)
08:16 egonw yeah...
08:16 egonw we're going to get some coffee now...
08:16 egonw meet upstairs?
08:17 jonalv egonw: ah oki
08:19 shk3 joined #bioclipse
08:36 masak joined #bioclipse
08:50 jonalv Gpox: what was the name of the new fancy progressmontior class?
09:03 * olass suggests to leave for Sven Dufva at 11.40
09:03 olass else it can be crowded
09:06 egonw olass: yes, that's what jonalv and I talked about too...
09:06 egonw to be at 11:45 at Sven's
09:07 olass perfect
09:07 egonw we'll go outside here at the reception...
09:07 egonw so, we meet at D7
09:08 egonw or C6 actually
09:09 egonw the nearest exist on that side for the 7 wing
10:44 egonw samuell: ping
10:44 samuell egonw:pong
10:44 egonw have you seen I uploaded Bioclipse SDK 1.1.8?
10:44 egonw it should fix the lack of source file.s..
10:45 egonw the templates were not exported into the jar :(
10:45 egonw they now are
10:45 samuell Ah, no... have been reading the (interesting) book
10:45 egonw ok, good
10:45 samuell Ok, thanks!
10:45 egonw so, you can delete the plugin folder you created yesterday, and create a new one...
10:45 egonw that should have some 6 or more .java files then
10:45 samuell Ok
10:46 samuell Will try it out in a minute.
10:48 Gpox joined #bioclipse
11:01 samuell egonw: Done. I now have 6 instead of 1 java file :)
11:04 egonw excellent
11:04 egonw make sure to do that Step 7
11:06 samuell Yep, done. That removed a few red marks.
11:34 samuell egonw: I got a lot of other errors though, when trying to start Bioclipse.
11:34 samuell One of them being: No property tester contributes a property projectPersistentProperty org.eclipse.team.core.repository to type class org.eclipse.core.internal.resources.Project
11:34 samuell Sorry...
11:35 samuell I meant: Unable to find feature.xml in directory: /home/samuel/projects/bioclipse/bioclipse​.core/features/net.bioclipse.sdk_feature
11:39 egonw please remove that feature from your workspace
11:39 egonw should no longer be there
11:39 egonw file a bug report on pele for me to check that folder is really removed
11:40 samuell Ok
11:41 edrin hi
11:41 zarah saluton edrin
11:44 masak saluton edrin
11:51 jonalv saluton edrin
11:51 zarah saluton edrin
12:01 * masak hugs zarah
12:17 masak olass: http://wiki.bioclipse.net/index.p​hp?title=Bioclipse2_release_plan
12:17 zarah masak's link is also http://tinyurl.com/5guree
12:17 masak is linked from the main page on the wiki.
12:17 masak it says "Bioclipse 2.0 is scheduled for July 8th"
12:18 olass masak: thx
12:18 olass wiki needs update
12:18 olass there is a bug
12:18 olass but I will fix this immediately
12:18 masak olass++
12:18 masak also, there's a big onion in the background on the wiki...
12:19 * olass likes the onion
12:19 * masak doesn't, really
12:20 * jonalv would like the bioclipse logo in the bacvkground instead
12:20 masak the onion is the null design of the 00's
12:21 olass did anyone make a copy of the planned release dates from the whiteboard?
12:21 * olass has forgotten
12:21 jonalv olass: I sent you a google calendar with thsoe ates
12:22 olass you did?
12:22 olass please resend
12:22 olass my email seems to block you
12:22 olass (maybe for a good reason?)
12:23 jonalv olass: The calendar is shared with ola.spjuth@gmail.com
12:23 olass I seldom check that email
12:23 olass please avoid it
12:24 jonalv olass: Google calendar is a google thing so I think I mst use that one...
12:24 jonalv olass: I might be wrong thoguh...
12:24 jonalv masak: do you know?
12:24 masak jonalv: from http://wiki.bioclipse.net/index.php?title=H​ow_to_make_a_manager_2#Testing_the_manager "To help you write your managers in a way that Bioclipse understand what you mean, there is a test framework to test against expected pattern (those listed above)." -- it's not at all clear which patterns you're referring to.
12:24 zarah masak's link is also http://tinyurl.com/ouun2r
12:26 masak jonalv: know what? how to make olass check his Gmail account?
12:26 jonalv masak: sry, what?
12:26 olass what?
12:28 olass masak: http://wiki.bioclipse.net/index.p​hp?title=Bioclipse2_release_plan
12:28 zarah olass's link is also http://tinyurl.com/5guree
12:28 olass updated
12:28 olass also updated front page on wiki
12:28 masak goodie.
12:32 * jonalv restarts his computer
12:37 * samuell is going for a (late, i know) lunch, brb.
12:39 jonalv joined #bioclipse
13:05 samuell joined #bioclipse
13:10 * samuell is wondering why he can build Bioclipse with Java 6 (sun) but not java 1.5.0 (sun) ... (Maybe messed up sth.)
14:12 masak egonw++ # nice blog post
14:12 egonw tack
14:12 masak though 'Math.abs(bond).getStereo()' looks like a typo to me.
14:12 egonw oh, yes
14:12 egonw tack
14:13 egonw yeah, had to shorten the code a bit for readability...
14:13 egonw thanx for the catch
14:13 masak np
14:13 egonw fixed
14:13 egonw if you don't mind, please close the report :)
14:13 masak it looks better now. closing.
14:22 masak olass: does the Sequence Editor work for you with Eclipse 3.5?
14:22 olass masak: sry, have not tested it
14:22 olass writing boring grant application :(
14:22 masak I see. no worries.
14:22 masak jonalv: does the Sequence Editor work for you with Eclipse 3.5?
14:23 jonalv masak: no idea
14:23 masak jonalv: after you try it out, could you let me know?
14:24 olass masak: you have problems?
14:24 masak aye.
14:26 CIA-61 bioclipse.structuredb: jonalv master * raa478d2 / (5 files in 2 dirs): delete annotation together with molecules test - http://bit.ly/JjhXO
14:26 CIA-61 bioclipse.structuredb: jonalv master * r939f067 / (14 files in 6 dirs):
14:26 CIA-61 bioclipse.structuredb: Added delete molecules when deleting label.
14:26 CIA-61 bioclipse.structuredb: When deleting a label it is now possible to also delete the molecuels with that label. - http://bit.ly/t0cVF
14:32 jonalv masak: I can haz sequence editor!
14:36 masak blrk.
14:37 egonw_ joined #bioclipse
14:48 grandm44 joined #bioclipse
15:06 edrin olass: what are you going to apply for?
15:12 olass some stupid small swedish grant
15:12 olass not my idea i have to admit :L
15:39 CIA-61 bioclipse.core: jonalv master * r2cd8111 / plugins/net.bioclipse.core/src/net/bi​oclipse/core/util/TimeCalculater.java : avoid division by 0 - http://bit.ly/3UC2MP
15:39 CIA-61 bioclipse.core: jonalv master * rf3c30f6 / plugins/net.bioclipse.usermanager/src/net/bioclips​e/usermanager/dialogs/UserManagerLoginDialog.java :
15:39 CIA-61 bioclipse.core: reopen the login dialog if given wrong name/pass
15:39 CIA-61 bioclipse.core: Fixes bug: #1588 - http://bit.ly/sYzm2
15:39 zarah bug #1588 | http://tinyurl.com/nchmrz
16:18 edrin left #bioclipse
16:23 samuell Any special steps needed in order to start a newly created Biomanager, together with Bioclipse?
16:24 samuell Have created a Biomanager using the Bioclipse SDK Wizard (http://chem-bla-ics.blogspot.com/2009/09​/updated-bioclipse-sdk-eclipse-35.html), but don't get the manager to respond to the javascript console after starting Bioclipse.
16:24 zarah samuell's link is also http://tinyurl.com/ms8sfz
16:25 samuell Or, the manager does not seem to get loaded at all.
16:30 samuell Oh, sorry, I see there seems to be information on that when reading on in the wiki (http://wiki.bioclipse.net/index.ph​p?title=How_to_make_a_manager_2#Ho​oking_in_all_the_Spring_AOP_stuff).
16:30 samuell Never mind.
16:30 zarah samuell's link is also http://tinyurl.com/ouun2r
17:00 samuell Hmm, I see now that the methods in the green area of http://tinyurl.com/l4pp84 is "getJS[Plugin name]Manager" while the Bioclipse SDK Wizard has created the method "getJavaScript[Plugin name]Manager". Which one is correct, and/or does it matter?
17:23 egonw_ joined #bioclipse
17:36 egonw_ moin
17:36 zarah privet egonw_
17:36 egonw_ hi samuell
17:36 egonw_ samuell: still around?
17:36 samuell yep
17:36 egonw just replied
17:37 samuell On mail?
17:37 samuell Ok, I got the mail now. Thx... will read.
17:39 samuell Ok, will try putting a repo at github. (Only thing I've done so far, though, is following the wizard).
17:53 egonw yeah, no worries...
17:53 egonw but that makes talking about your code easier
18:13 samuell Yeah, that's true.
18:13 samuell Now it's available at: http://github.com/samuell/bi​oclipse.drprolog/tree/master
18:13 zarah samuell's link is also http://tinyurl.com/nznb84
18:15 egonw samuell: please email olas for an wiki account
18:15 egonw oh... something else...
18:48 egonw samuell: ping
18:49 egonw just in case you are around...
18:49 egonw save me emailing you :)
18:49 samuell yep, I'm here
18:50 egonw I'll fork, and make some patches...
18:50 egonw should be done in about 10 minutes...
18:50 egonw then
18:50 egonw I'll send you a merge request...
18:50 egonw where you can use github to take over my patches...
18:50 egonw I'll explain them when done...
18:51 samuell Ok
18:51 egonw pull request
18:51 egonw that's the proper name :)
18:52 samuell Yep. Looking forward :)
18:57 egonw oh, btw...
18:58 egonw please go to github .drprolog admin page
18:58 egonw and then the Service Hooks tab
18:58 egonw and enable CIA
18:58 samuell Ok...
18:59 egonw and Email, pointing to bioclipse-commit@lists.sf.net
19:00 samuell Email? Should I enter that e-mail address somewhere at githup?
19:00 samuell (github)
19:00 samuell Ah... now I see it... The Email link
19:01 samuell Sorry.
19:01 samuell Done.
19:01 samuell What is that?
19:01 samuell CIA et.c.?
19:01 egonw you'll see in a moment :)
19:01 egonw ok...
19:01 egonw hit the Fork Queue menu
19:02 egonw and I gope this is showing up my two patches
19:02 egonw may require a refresh
19:02 samuell Yep!
19:02 egonw ok, you should be able to select them with the toggle button
19:02 egonw and then to Apply or so...
19:03 egonw after that worked, it will ask for final confirmation for back integrating into your master branch
19:03 samuell Ah...
19:03 samuell One of them is red... does that matter?
19:03 egonw about commit messages...
19:03 egonw please have them describe what the patch actually changes...
19:03 egonw yes that matters
19:03 egonw apply the first...
19:03 egonw and then go back
19:03 egonw it will likely work better then
19:04 samuell So, a summary of the patch message will do...?
19:05 samuell (as commit message)
19:05 samuell First patch applied
19:05 CIA-61 bioclipse.drprolog: Egon Willighagen master * r3235c43 / (20 files in 10 dirs):
19:05 CIA-61 bioclipse.drprolog: Setting up the proper hierarchy for Bioclipse git repositories: plugins/ for the
19:05 CIA-61 bioclipse.drprolog: plugins, features/ for the features, and externals/ for plugins for third party
19:05 CIA-61 bioclipse.drprolog: libraries (well, the last few are not really added, as there is nothing in them)
19:05 CIA-61 bioclipse.drprolog: Signed-off-by: Samuel Lampa <samuel.lampa@rilnet.com> - http://bit.ly/pw0df
19:06 egonw samuell: that's the CIA in action :)
19:06 egonw samuell: yes, a summary is fine
19:07 samuell Ah, IC. So, any understandable meaning of the abbreviation, "CIA" ? :)
19:12 CIA-61 bioclipse.drprolog: Egon Willighagen master * r7c9b4f2 / (6 files in 2 dirs):
19:12 CIA-61 bioclipse.drprolog: Removed autogenerated files from the repository
19:12 CIA-61 bioclipse.drprolog: Signed-off-by: Samuel Lampa <samuel.lampa@rilnet.com> - http://bit.ly/m5bIU
19:18 samuell Still got errors though. "Project 'net.bilclipse.drprolog' is missing required source folder: 'src'" (though I can see it in the navigator)
19:18 samuell Well, it's missing on disk.
19:20 samuell Or, the paths seem to be messed up.
19:20 samuell I have a folder: ".../net.bioclipse.drprolog/plug​ins/net.bioclipse.drprolog/src"
19:20 samuell But it is getting late... ^^
19:23 samuell If you look at http://github.com/samuell/bi​oclipse.drprolog/tree/master , you'll see that the folder structure is quite different from before. But is that intentional or not?
19:23 zarah samuell's link is also http://tinyurl.com/nznb84
19:26 samuell Ah, now I understand your patch summary... (uh... seems I'm getting tired... thinking too slow...) So course the changes were intentional.
19:32 egonw ah... right
19:32 egonw sorry...
19:32 egonw was away from keyboard
19:32 egonw yes, since the plugin folder moved...
19:32 egonw you need to remove .drprolog from your workspace
19:32 egonw and readd it
19:33 samuell Ok... will try
19:44 samuell Trying to reimport it as a project in Eclipse without success. Eclipse won't recognize the "pulled out" folder as a project.
19:44 egonw well, I noted that .project was missing...
19:44 egonw that might be the problem...
19:44 egonw let me add one...
19:44 egonw hang on
19:45 samuell Ok :)
19:56 egonw still working...
19:58 egonw had to set up your branch as remote too
19:59 egonw so that I could easily rebase...
19:59 egonw now donw
19:59 egonw now done
19:59 samuell Ok
20:01 egonw mmm...
20:01 samuell Well, I hope you don't feel urged to sit up in the eveningh either!
20:01 egonw I should really try to get used to pushing patches to branching on github
20:01 egonw not at all :)
20:01 samuell good :)
20:03 egonw ok, you can pull
20:03 samuell Ok
20:04 samuell Hmm... says "already up to date..." hmm...
20:05 samuell So, should I go:
20:05 samuell git pull origin master
20:05 samuell ?
20:05 egonw no, using the fork queue again
20:05 egonw and when that is done, you can pull them with the above command to your local clone
20:06 samuell My fork queue is empty...
20:06 egonw ok, hang on
20:06 samuell Ah... github showing a cached version of the page
20:07 samuell Cite (github): "This data is out of date. We are showing you a cached version. Please refresh in a minute for more up to date data."
20:08 samuell How annoying...
20:09 egonw hang on
20:13 egonw ok, check your email
20:13 samuell Ok
20:13 egonw you should have email from github
20:14 * samuell is waiting for email to arrive...
20:14 egonw or perhaps try the fork queue again
20:16 samuell Yep, trying both... continuously
20:16 egonw OK
20:16 egonw I'm going offline now...
20:16 samuell Seems like github is a little bit overloaded
20:16 egonw watch a tiny of TV
20:16 egonw and then sleep
20:16 egonw yeah, too popular
20:16 samuell Yup, it's time to ...
20:16 samuell Going home too.
20:17 samuell Better luck tomorrow.
20:18 egonw right
20:18 egonw bye
20:18 samuell Thanks for help today!
20:18 samuell Bye

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