Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-08-13

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All times shown according to UTC.

Time Nick Message
04:52 egonw joined #bioclipse
04:59 egonw joined #bioclipse
05:01 sneumann joined #bioclipse
06:37 sneumann joined #bioclipse
06:47 Gpox joined #bioclipse
06:57 egonw hi Gpox
07:07 Gpox hi egonw
07:09 egonw http://github.com/egonw/bioclipse.sdk/tree/master
07:09 zarah egonw's link is also http://tinyurl.com/opseoa
07:20 jonalv joined #bioclipse
07:20 egonw hi jonalv
07:21 CIA-63 bioclipse.sdk: Egon Willighagen master * r3ec7deb / (11 files in 7 dirs): Added template plugin for a New Wizard, which we can now tune for New Project type - http://bit.ly/ivjcE
07:23 jonalv hi egonw
07:25 egonw jonalv: you have commit rights
07:25 jonalv egonw: oki
07:25 jonalv I am just gonna...
07:25 egonw yeah, let's divide tasks a abit
07:26 egonw Gpox: are you joining too in our Bioclipse SDK hackaton?
07:27 CIA-63 bioclipse.structuredb: jonalv master * r87b2c92 / plugins/net.bioclipse.structuredb/src/net/bioclip​se/structuredb/business/SmartsQueryIterator.java : renamed CDKTimedOutException to TimedOutException. - http://bit.ly/15IPOl
07:27 Gpox sure, if you need me
07:31 jonalv egonw: have you manaded to test run the sdk plugin?
07:31 egonw no, just awake too ! :)
07:32 jonalv how would one do that?
07:32 egonw yeah, good point...
07:32 egonw I hope we do not need to set up a full update site for that...
07:33 jonalv egonw: I would think we do. How else would you do it?
07:33 egonw mom
07:33 egonw googling
07:33 jonalv egonw: oh just for testing?
07:33 jonalv no testing should hopefully be possible to do in some other way
07:34 egonw http://www.eclipse.org/articles/Article-Yo​ur%20First%20Plug-in/YourFirstPlugin.html
07:34 zarah egonw's link is also http://tinyurl.com/bkrq3
07:34 egonw see step 7
07:34 egonw yeah, for 'releasing' the thing to others we indeed need an update site...
07:34 egonw but we know how to do that...
07:34 jonalv yup
07:35 egonw BTW, check the link in the README
07:35 jonalv I wonder if maybe I should setup a seperate workspace for this project...
07:36 jonalv I think I will actually
07:37 CIA-63 bioclipse.sdk: Egon Willighagen master * rc01c617 / README : Added a link about how to test the SDK plugin - http://bit.ly/QFbnz
07:41 CIA-63 bioclipse.sdk: Egon Willighagen master * r9a579d4 / (20 files in 12 dirs): Fixed the folder name of the net.bioclipse.sdk plugin to not be 'plugins' - http://bit.ly/2LwYA
07:41 CIA-63 bioclipse.sdk: Egon Willighagen master * r80a69d9 / (20 files in 12 dirs): Moved the net.bioclipse.sdk plugin into the plugins/ folder - http://bit.ly/UDLjU
07:42 CIA-63 bioclipse.cheminformatics: jonalv master * r43314e6 / (3 files in 3 dirs):
07:42 CIA-63 bioclipse.cheminformatics: Created CDKTimedOutException.
07:42 CIA-63 bioclipse.cheminformatics: CDKTimedOutException extends BioclipseException and is used for recognizing when a BioclipseException is because of a timeout inside CDK (e.g. AllringsFinder timeout).
07:42 CIA-63 bioclipse.cheminformatics: Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> - http://bit.ly/2Sk8ta
07:42 CIA-63 bioclipse.cheminformatics: jonalv master * r0efbbd7 / (3 files in 2 dirs):
07:42 CIA-63 bioclipse.cheminformatics: renamed CDKTimedOutException to TimedOutException
07:42 CIA-63 bioclipse.cheminformatics: Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> - http://bit.ly/16dMfb
07:43 egonw jonalv: regarding the last... that should really be in bioclipse.core, not in bioclipse.cheminformatics
07:43 CIA-63 bioclipse.cheminformatics: Arvid Berg master * r6a45928 / (4 files in 2 dirs):
07:43 CIA-63 bioclipse.cheminformatics: Changed save to allow for use of IMoleculesEditorModel.save()
07:43 CIA-63 bioclipse.cheminformatics: Save will use above method while saveAs will open
07:43 CIA-63 bioclipse.cheminformatics: save file dialog.
07:43 CIA-63 bioclipse.cheminformatics: Signed-off-by: Egon Willighagen <egon.willighagen@gmail.com> - http://bit.ly/1G2JIx
07:49 jonalv egonw: I am trying to follow step 7 at that page
07:49 jonalv egonw: have you managed to_
07:50 egonw discovered that I messed up the plugins/ folder
07:50 jonalv egonw: I canät find the button named "Not in workspace"
07:50 egonw so fixed that first
07:50 egonw now setting up a separate workspace too, like you
07:50 egonw I don't see that button either
07:50 egonw so that is of an old eclipse version :(
07:51 jonalv and the problem is that I don't quite understand that step...
07:53 jonalv egonw: it seems that just creatign a "vanilla" run configuration does the trick...
07:53 egonw ack
07:54 egonw was hoping that too
07:54 CIA-63 bioclipse.sdk: Egon Willighagen master * r2574bab / plugins/net.bioclipse.sdk/.sett​ings/org.eclipse.jdt.core.prefs : Removed settings from repository - http://bit.ly/Qjs4f
07:54 jonalv egonw: so where is that wizard? :)
07:54 jonalv is it reachable?
07:54 egonw I hope so...
07:54 egonw mom
07:54 egonw almost there...
07:55 CIA-63 bioclipse.sdk: Egon Willighagen master * rd4dc430 / plugins/net.bioclipse.sdk/.classpath : Removed requirement for Java 6 - http://bit.ly/Bh83S
07:55 egonw ummm
07:55 egonw where do you see that vanilla ?
07:55 egonw Run As .. -> ??
07:55 jonalv egonw: "vanilla flavour" means to not change anything. To go with default
07:56 jonalv egonw: I opened the run configurations and created a new Eclispe Application run configuration
07:56 egonw ack
07:56 egonw can you describe that in the README please?
07:58 jonalv my Eclipse crashed :(
07:59 jonalv egonw: yes will do
08:00 jonalv egonw: you have renamed everyhting so now it does not compile
08:00 jonalv egonw: what are you doing?
08:07 CIA-63 bioclipse.sdk: jonalv master * r3a188d9 / README : Some instructions for how to test run. - http://bit.ly/2XJUYQ
08:08 egonw jonalv: this:
08:08 egonw the plugin file was under plugins/ directly, instead of plugins/net.bioclipse.sdk
08:11 egonw the new wizard does not show up here either...
08:11 egonw but I think that is because it does not know yet where to find the plugin
08:11 egonw which is what the "Not in workspace" procedure is for, I gues...
08:12 egonw mmm...
08:12 egonw no, it actually is listed in the run config
08:13 jonalv egonw: I can't even get the project to comile here... :(
08:13 egonw what error ?
08:13 jonalv egonw: he declared package "net.bioclipse.sdk.wizards" does not match the expected package ""
08:13 jonalv for ManagerPluginNewWizardPage
08:14 jonalv egonw: have you not added the .project file?
08:15 egonw I hav
08:15 egonw e
08:15 egonw you did notice I *moved* the files, not?
08:15 egonw you must remove and reimport
08:16 jonalv I thought I did that..
08:16 jonalv egonw: it seems the bin folder is commited
08:17 jonalv egonw: there is a bin in pluigns
08:17 egonw sure?
08:17 egonw http://github.com/egonw/bioclipse.sdk​/tree/3a188d95fa8c9dbac7ede26d27f1744​429160923/plugins/net.bioclipse.sdk
08:17 zarah egonw's link is also http://tinyurl.com/nnfb3z
08:18 egonw I don't see it there
08:18 jonalv egonw: I removed it now...
08:19 jonalv okey finally things are beginning to look okey
08:19 egonw :)
08:21 egonw ah...
08:21 egonw I see the wizard now!
08:22 jonalv egonw: okey how?
08:22 egonw mom, will write up in README
08:25 CIA-63 bioclipse.sdk: Egon Willighagen master * rfeb93b6 / README : Updated the README on how to test the .sdk plugin - http://bit.ly/19tVpm
08:26 egonw ok, I think the next step is to find the sources for setting up a new project wizard
08:26 egonw @gg OpenNewJavaProjectWizardAction
08:26 zarah egonw: http://dev.eclipse.org/newslists/new​s.eclipse.platform.rcp/msg22189.html
08:27 egonw funny how zarah gets different google results than I do
08:27 egonw ok, seems to be in one of the JDT plugins
08:28 * egonw is importing org.eclipse.jdt.ui as source project
08:28 jonalv egonw: where is that wizard supposed to be?
08:29 egonw which does *not* actually give me source files
08:29 egonw File -> New -> Other
08:29 egonw there is a Bioclipse category
08:29 jonalv egonw: nope not for me :(
08:29 egonw mmm
08:30 CIA-63 bioclipse.sdk: Egon Willighagen master * r1812157 / plugins/net.bioclipse.sdk/META-INF/MANIFEST.MF : As I said, Java5 is enough - http://bit.ly/196Rvu
08:30 CIA-63 bioclipse.sdk: Egon Willighagen master * rd9e6127 / plugins/net.bioclipse.sdk/plugin.xml : Added some whitespace in the human readable text - http://bit.ly/3wtsZS
08:31 egonw did you run from the plugin.xml now?
08:31 jonalv egonw: yes
08:32 egonw mmm... really weird
08:32 egonw just verified... works here
08:32 egonw can you update from git?
08:32 jonalv egonw: I am pulling all the time...
08:33 jonalv LOL now it's suddenly there
08:33 jonalv I don't know what I made different
08:34 jonalv egonw: okey what should I do?
08:34 egonw right
08:34 egonw well...
08:34 egonw we first need to convert our template in git to create a new project...
08:34 egonw so, let's look for the JDT source for the NewProjectWizard first now
08:35 jonalv egonw: which template re you refering to?
08:35 egonw what we have in git now
08:36 jonalv egonw: I am not aware of a template in git
08:36 egonw as in: the current net.bioclipse.sdk code is just a template for what we want to do...
08:36 egonw it does not really do anything useful yet
08:37 jonalv o ah okey now I see how you mean
08:37 egonw ok, the new project wizard does not seem to be in jdt.ui
08:37 egonw ok, pde.ui
08:37 egonw that's the one
08:38 egonw and that one has a pde.ui.source plugin!
08:38 egonw yahoo!
08:38 jonalv egonw: what class shouls I be looking at?
08:38 egonw dunno yet :)
08:38 jonalv o it sounded like you had found something..
08:39 egonw org.eclipse.pde.internal.ui.wizar​ds.plugin.NewPluginProjectWizard
08:39 jonalv BasicNewProjectResourceWizard
08:40 egonw dunno about that one...
08:40 jonalv egonw: I don't have that one...
08:40 egonw that's because it is hidden
08:40 egonw do this:
08:40 egonw open the Plugins view
08:41 egonw look up org.eclipse.pde.ui.source
08:41 egonw and open that as source plugin
08:41 egonw import, not open
08:43 jonalv egonw: that one is Eclipse internal. What are we doing with it? :(
08:44 egonw copy/paste, I'd suggest
08:45 Gpox Do you need to create a plugin, isn't it enough to create a manager class+interface with necessary spring xml?
08:45 masak joined #bioclipse
08:46 egonw Gpox: yes, that's an option...
08:46 egonw Gpox: do you think that is easier?
08:46 egonw masak: hi! joining in on the Bioclipse SDK hackaton?
08:46 egonw Gpox: you suggest starting from a NewFileWizard like thingy?
08:47 egonw we still need to resolve how templating is working...
08:47 Gpox maybe and the wizard pages would be there if deciding to do a plugin wizard instead
08:47 masak egonw: I can at least me something in-between an interested spectator and an active participant. :)
08:47 egonw we need a wizard page for entering info on the managers...
08:47 egonw plenty of things to be done
08:47 masak s/me/be/
08:48 egonw jonalv: what do you think?
08:48 egonw 1. make one integrated wizard for setting up a manager plugin
08:48 egonw 2. a wizard to convert an existing plugin to a manager plugin
08:48 egonw =
08:48 egonw ?
08:48 * egonw is making coffee
08:49 jonalv egonw: what step is it that you want a wizard for?
08:49 jonalv I am guessing that generating the Spring configuration xml file is in there somewhere
08:51 edrin joined #bioclipse
08:51 egonw hi edrin!
08:51 egonw edrin: Last Call! :)
08:52 egonw jonalv: yeah, all the spring.xml,  plugin.xml and other updates needed...
08:52 egonw Gpox: that is why I initially though of a new Project wizar
08:52 egonw +d
08:52 egonw Gpox: because so many files are touched...
08:52 jonalv egonw: but what about adding methods in managers?
08:53 jonalv is that something that might come later?
08:53 egonw and creating new files from a template sounds much easier then editing existing files
08:53 egonw jonalv: ah, very interesting next step...
08:53 egonw jonalv: I'd be happy now to remove all the setting up of spring, plugin, etc hooks...
08:53 egonw jonalv: and have it come up with an empty manager
08:54 jonalv egonw: hooks?
08:54 egonw yeah, the various interfaces...
08:54 egonw the extra activator methods
08:54 jonalv Well then I think I want a "New Biclispe Manager" plugin
08:54 egonw the factory
08:54 egonw really? then we need to edit existing files...
08:54 egonw at least plugin.xml
08:55 jonalv egonw: why?
08:55 egonw the manifest
08:55 egonw the wizard will have to edit those files
08:55 jonalv I thought that would be the "transform into laternative"
08:55 egonw what's that?
08:55 jonalv I want alterative 1
08:56 jonalv The wizard that creates a plugin for managers from scratch
08:56 egonw ah, ok
08:57 egonw yes, I think that is easiest for us too...
08:57 egonw BTW, while making coffee I realized that there is a quicker route to success...
08:57 egonw olas' QSAR plugin has a new project wizard too...!
08:57 egonw let's look at that
08:57 jonalv egonw: oki
08:58 * egonw is booting a second Eclipse instance
08:59 * jonalv can't do that
08:59 egonw NewQSARProjectWizard
09:00 egonw OK, seems easy enough
09:01 egonw jonalv: what about splitting the work up like this:
09:01 jonalv egonw: you think? I have never seen any of these method calls before...
09:01 egonw * I set up this wizard
09:01 egonw * you make a wizard page with the fields people will need to enter ?
09:01 jonalv egonw: sounds good
09:02 * jonalv wonders what fields that might be.. :)
09:02 egonw oh wait...
09:02 egonw better idea...
09:02 egonw masak, Gpox: either of you who wants to make that wizard page?
09:02 egonw jonalv: then you can focus on the template files...
09:03 jonalv masak: maybe you would like to help me with those template files?
09:03 jonalv That is if Gpox feels up to doing the wizard page...
09:04 masak jonalv: sure, ok.
09:04 Gpox sure
09:04 jonalv oki
09:06 CIA-63 bioclipse.sdk: Egon Willighagen master * rb5840fe / (3 files in 2 dirs): Added missing copyright headers - http://bit.ly/Mmm3E
09:07 egonw all: please make sure you update the copyright headers by adding your name, when you contributed to that file
09:07 egonw jonalv: can you put the templates in src/templates
09:07 egonw and have that folder mirror the plugin/ folder structure
09:07 egonw so with META-INF
09:07 egonw so with META-INF/spring
09:07 egonw etc etc
09:08 jonalv yes
09:18 Gpox git://github.com/egonw/bioclipse.sdk.git
09:25 egonw jonalv: ping
09:25 jonalv egonw: pong
09:25 egonw jonalv: it seems that you do not have to add plugin.xml
09:25 jonalv egonw: oki
09:25 egonw olas seems to be using some code for that
09:26 egonw make sure to check the new QSAR project wizard
09:26 egonw I'm about done copy/pasting, and will boot shortly to let you know what files are already created
09:26 jonalv egonw: okey I am writing a template for spring.context.xml right now...
09:26 egonw good!
09:36 CIA-63 bioclipse.sdk: Egon Willighagen master * r6b4ff40 / plugins/net.bioclipse.sdk/src/net/bioclips​e/sdk/wizards/ManagerPluginNewWizard.java : Copied in code from the 'New QSAR Project' wizard, and it now creates a new project! yahoo! - http://bit.ly/gCe9H
09:41 CIA-63 bioclipse.sdk: Egon Willighagen master * r8c951c5 / plugins/net.bioclipse.sdk/src/n​et/bioclipse/sdk/Activator.java :
09:41 CIA-63 bioclipse.sdk: Cleaned up code a bit.
09:41 CIA-63 bioclipse.sdk: * removed nonsense JavaDoc
09:41 CIA-63 bioclipse.sdk: * added missing periods at the end of first JavaDoc sentences
09:41 CIA-63 bioclipse.sdk: * renamed a variable to describe what it 'is' - http://bit.ly/17sCeS
09:53 egonw masak: intermediate question... can one already align two sequences in Bioclipse ?
09:57 masak egonw: yes, I think so.
09:57 masak I'm pretty sure one can.
09:57 masak that's what I took one day from my vacation to fix.
10:05 egonw ic...
10:05 egonw might you blog about that?
10:05 egonw or write a wiki page?
10:05 masak egonw: eventually, yes.
10:05 egonw we might use it in the pharmaceutical bioinformatics course...
10:05 egonw btw, did you see this yet? :
10:05 egonw http://www.pharmbio.org/
10:07 jonalv egonw: nope
10:08 jonalv egonw: looks nice
10:20 CIA-63 bioclipse.sdk: jonalv master * rcfb821f / plugins/net.bioclipse.sdk/src/temp​lates/META-INF/spring/context.xml : Created template for spring/context.xml. - http://bit.ly/jTuf5
10:20 CIA-63 bioclipse.sdk: jonalv master * rb79053b / plugins/net.bioclipse.sdk/src/temp​lates/META-INF/spring/context.xml : fixed some white space - http://bit.ly/3KKR02
10:20 CIA-63 bioclipse.sdk: jonalv master * r0af8e8e / (2 files): Added templates for manager class and interface. - http://bit.ly/6rlJP
10:34 * jonalv @ lunch
10:39 CIA-63 bioclipse.sdk: Carl Masak master * r16613c9 / (2 files in 2 dirs): (log message trimmed)
10:39 CIA-63 bioclipse.sdk: [net.bioclipse.sdk.templating] new Templater.java
10:39 CIA-63 bioclipse.sdk: This class was developed with TDD in less than an hour. It does string
10:39 CIA-63 bioclipse.sdk: templating, using a template string and a set of key/value pairs for
10:39 CIA-63 bioclipse.sdk: replacement. The templater replaces occurrences of the substring
10:39 CIA-63 bioclipse.sdk: '${somekey}' in the template string. There can be several occurrences of
10:39 CIA-63 bioclipse.sdk: the same key in the template string, but passing the same key twice, or
10:39 egonw TDD?
10:39 masak Test-Driven Development.
10:40 masak (1) write failing test, (2) implement the code to pass that test _and_nothing_more_, (3) refactor, (4) goto 1.
10:41 egonw ack
10:43 masak jonalv pointed out that I really should port those six tests from my home-made test framework to JUnit, so maybe I'll do that next. :)
10:43 masak shouldn't be that hard.
10:44 CIA-63 bioclipse.sdk: Egon Willighagen master * rf587901 / plugins/net.bioclipse.sdk/.classpath : Exclude the template to not give false positive upon Java build - http://bit.ly/p57d4
10:44 egonw yes, I'd agree with that...
10:44 egonw moreover, it should be in a separate plugin
10:44 egonw net.bioclipse.sdk.tests
10:44 * masak does that
10:44 masak aye.
10:44 masak I did cut some corners. correcting that now.
10:45 masak "paying my technological debt" :)
10:46 masak egonw: by the way, before I left yesterday, I had gotten the old Groovy console to compile with current Bioclipse.
10:46 masak egonw: I just need to test-drive it, and then I can push.
10:46 egonw oh, cool!
10:47 egonw masak++
10:47 egonw perhaps let me test drive it?
10:47 egonw just put it in your mirror git repository?
10:47 egonw instead of olas .core ?
10:48 masak egonw: I could do that.
10:49 masak egonw: or in a branch, perhaps?
10:49 egonw also possible
10:52 masak egonw: http://github.com/olas/bioclip​se.core/tree/groovy-test-drive
10:52 zarah masak's link is also http://tinyurl.com/oyxtv8
10:52 masak lunch &
10:54 egonw masak: thanx!
10:59 edrin hi egonw,
10:59 edrin yes, thanks for your mail
10:59 edrin egonw: the thing is now *maybe* discussed in the standards mailing list.
10:59 edrin it would be good if it is discussed
11:00 edrin dont know what happens if none discusses it
11:09 egonw I guess it then just defaults to going into the last stage: approval
11:12 egonw I guess no news from bmc bioinfo yet?
11:28 egonw masak: I think you have the extension specs wrong
11:28 egonw I see two entries of JsConsole
11:28 egonw but none for Groovy...
11:29 egonw fixing...
11:33 CIA-63 bioclipse.core: Egon Willighagen groovy-test-drive * r6f48881 / plugins/net.bioclipse.scripting.ui/plugin.xml : Fixed scripting console view entry for the GroovyConsoleView - http://bit.ly/6rFeh
11:36 egonw masak: it does not seem to do much...
11:37 egonw instead I get this exception:
11:37 egonw java.lang.NullPointerException
11:37 egonw at net.bioclipse.scripting.GroovyEnviron​ment.eval(GroovyEnvironment.java:37)
11:39 egonw masak: btw, please add copyright statements to your .java files
11:44 egonw masak: and I see what type of comments you were taking about yesterday... olas--
11:44 egonw //Open project
11:44 egonw project.open(monitor);
11:44 egonw hahahaha
11:46 egonw btw...
11:46 egonw (eclipse refactor out method)++
11:47 masak egonw: yes, olas--
11:47 masak and masak-- for forgetting copyright headers again. :)
11:49 egonw masak++ for fixing it (preemptive)
11:49 egonw but
11:49 egonw masak-- for a not-working-at-all groovy console
11:50 egonw (egonw -- for I-can-use-anything-as-adverb usage? :)
11:50 masak egonw: well, I did say I hadn't tried it.
11:50 egonw :)
11:50 masak egonw: and you simply insisted that you try it first.
11:50 masak so suit yourself. :P
11:50 egonw yes... true
11:51 egonw masak++ for pointing my noise to/on/... the facts
11:57 CIA-63 bioclipse.sdk: Egon Willighagen master * rd3c8c9b / plugins/net.bioclipse.sdk/src/net/bioclips​e/sdk/wizards/ManagerPluginNewWizard.java : Refactored a bit: extraced methods, to make the code overseeable. - http://bit.ly/NY7Ph
12:00 masak another idiotic comment found by jonalv: "/* The constructor */"
12:00 masak NO SHIT, SHERLOCK!?
12:03 egonw :)
12:03 egonw yeah, I typically remove those too...
12:03 masak maybe I should inject some comments like that in code I know others will read.
12:03 masak /* call the method */
12:04 masak /* return from this method */
12:04 masak /* inherit from BaseClass */
12:04 egonw hehehehe
12:10 CIA-63 bioclipse.sdk: Carl Masak master * r04b7af4 / (2 files in 2 dirs): [n.b.sdk.templating] added copyright headers - http://bit.ly/PODIk
12:13 * egonw is integrating the templating in the Wizard's finish() method
12:14 jonalv egonw: nice, I will soon commit more templates
12:14 jonalv |push
12:14 jonalv (when will I learn?)
12:16 egonw hehehehe
12:18 CIA-63 bioclipse.sdk: jonalv master * r7e3aab3 / (2 files): Added IJavaManager and IJavaScriptManager. - http://bit.ly/11fr4W
12:18 CIA-63 bioclipse.sdk: jonalv master * r44be669 / plugins/net.bioclipse.sdk/src/te​mplates/src/ManagerFactory.java : Wrote template for ManagerFactory.java. - http://bit.ly/ixujg
12:18 CIA-63 bioclipse.sdk: jonalv master * r921c109 / plugins/net.bioclipse.sdk/src​/templates/src/Activator.java : Wrote template for Activator.java. - http://bit.ly/MgmCJ
12:21 egonw masak: ping
12:21 egonw masak: the templater has no problem if certain values are passed but not used, correct?
12:27 masak egonw: yes, it does. it explicitly checks for that.
12:27 masak egonw: would you want it not to check for that?
12:27 masak what's your use case?
12:28 egonw I want to pass all variables to all templates
12:28 egonw and it just ignore those unused
12:28 egonw then I don't have to hardcode which template has which parameter
12:28 egonw or dynamically discover that
12:30 masak egonw: I find that throwing an when the substitutions in the template don't match the keys sent in tends to usefully dig up failure modes.
12:30 masak s/an/an exception/
12:30 egonw ok, will proceed with the hard coded way then
12:31 masak I just realized that I only check for unused keys right now, not for unmatched substitutions...
12:31 masak need more tests.
12:50 egonw masak: can I request:
12:50 egonw public Templater(InputStream template) ?
12:50 masak sure. that's a good idea.
12:50 masak I planned to support files somehow, but didn't think through how.
12:50 egonw possibly with priority?
12:50 masak you mean you want it right away?
12:50 egonw yeah, if I would not be asking too much
12:51 masak it wouldn't. I'll get right on it.
12:51 egonw tack
12:56 egonw foobar
13:00 jonalv egonw: how are things comming along?
13:06 egonw slowly, but gradually
13:06 egonw code I have is ugly...
13:07 egonw do you have templates for .classpath and .project too?
13:07 egonw oh wait...
13:07 egonw those might already be created... of course...
13:07 egonw what about the MANIFEST.MF ?
13:08 jonalv egonw: I don't know
13:10 egonw masak: you have seen that jonalv uses ${varName}, right?
13:10 egonw ah, according to your test class you have
13:10 egonw good
13:10 jonalv masak and jonalv has talked to eachother :)
13:11 masak /we can haz talked to each other?
13:11 egonw ah, right
13:11 egonw I get the exception because new Templater(InputStream) is still missing ...
13:11 egonw hahaha
13:11 CIA-63 bioclipse.sdk: Carl Masak master * rb7833d7 / plugins/net.bioclipse.sdk/src/net/bio​clipse/sdk/templating/Templater.java : [Templater] added InputStream constructor - http://bit.ly/8yOUc
13:11 masak egonw: pushed.
13:11 egonw (and hence the params I pass are not found
13:11 egonw tack!
13:12 jonalv so soon we can see this (not) working?
13:12 egonw yes, very soon :)
13:12 * masak gets back to JUnit porting
13:17 egonw jonalv: can you please rename the .java templates to .javat or so?
13:17 jonalv egonw: huh? Why you want that?
13:18 egonw so that the red crosses do not show up...
13:18 egonw because the templates are not valid Java source code
13:18 jonalv okey
13:18 egonw oh wait...
13:18 egonw maybe I have another idea...
13:18 jonalv egonw: oh?
13:18 egonw ok, please disregard my request (at least for now)
13:19 masak .java-template would be nicer, I think.
13:19 jonalv egonw: what did you do?
13:19 egonw let me test...
13:26 egonw OK, made progress now...
13:27 egonw sort of
13:27 egonw at least the template resource is now properly loaded
13:27 egonw but no file is yet created...
13:27 egonw will commit
13:27 jonalv okey
13:28 jonalv I am not sure what I can do...
13:29 CIA-63 bioclipse.sdk: Egon Willighagen master * rbde36ff / plugins/net.bioclipse.sdk/src/net/bioclips​e/sdk/wizards/ManagerPluginNewWizard.java : First files created from templates - http://bit.ly/2e4vxl
13:29 CIA-63 bioclipse.sdk: Egon Willighagen master * r20cb60d / (3 files in 3 dirs): Fixed reading of templates from the classpath: corrected paths and included the templates in the plugin - http://bit.ly/3EsLFz
13:29 egonw template for the MANIFEST.MF
13:31 jonalv hm that soudns trixy
13:31 egonw that's an important missing piece
13:39 CIA-63 bioclipse.sdk: Egon Willighagen master * rccdad20 / plugins/net.bioclipse.sdk/src/net/bioclips​e/sdk/wizards/ManagerPluginNewWizard.java : Fixed writing of the context.xml: proper local, instead of overwriting the plugin.xml - http://bit.ly/DWNbA
13:39 egonw OK, the templating system seems working...
13:39 egonw now, where did the plugin.xml go...
13:39 jonalv egonw: I don't know you said something about not needing that one..
13:40 egonw yes, true
13:40 egonw because initially that was autogenerated...
13:40 egonw so, hence "where did it go"...
13:41 egonw but that was actually the .project
13:41 egonw good...
13:41 egonw so I need a template for that one too...
13:42 egonw with an extension for the JavaScript EP
13:42 CIA-63 bioclipse.sdk: jonalv master * ra236bfe / plugins/net.bioclipse.sdk/src/​templates/META-INF/MANIFEST.MF : template for MANIFEST.MF - http://bit.ly/7WpHq
13:42 jonalv egonw:  oki
13:42 egonw Gpox: how's your progress with a wizard page?
13:53 egonw masak: on second thought...
13:53 egonw I'd really *not* have it about getting passed unused parameters
13:53 egonw if I could, I could handle a set of files as batch
13:54 CIA-63 bioclipse.sdk: jonalv master * r1c6227d / plugins/net.bioclipse.sdk/src/templates/plugin.xml : template for plugin.xml - http://bit.ly/2Q66DX
13:54 egonw without having to care that each of that files does not use *all* variables...
13:54 masak egonw: I'm not sure how you plan to pass in the parameters in a batch in the first place.
13:54 egonw cehck this commit:
13:56 egonw ... pending ...
13:56 CIA-63 bioclipse.sdk: Egon Willighagen master * rc0d2144 / plugins/net.bioclipse.sdk/src/net/bioclips​e/sdk/wizards/ManagerPluginNewWizard.java : Create the Java source files - http://bit.ly/gEXbq
13:57 egonw have a look at that patch
13:57 egonw and how I iterate over all the java source files
13:57 egonw but one will soon have a variable that others don't
13:57 egonw ${managerShortcut}
13:58 masak egonw: fwiw, jonalv agrees with you.
13:58 masak I'll see what I can do to change it.
14:01 masak why is the templates/ directory inside of src/ ?
14:01 masak isn't that what makes Eclipse flag the source as not proper Java?
14:01 jonalv masak: egonw told me to...
14:01 egonw masak: yes
14:02 masak egonw: I think it should be one level up.
14:02 egonw masak: but need to have it show up on the classpath
14:02 masak why?
14:02 egonw masak: dunno... it's Eclipse
14:02 egonw actually... with the 'fix' I made earlier...
14:02 masak icons don't have that problem.
14:02 egonw it may actually work when one level up
14:02 egonw masak: true
14:02 masak this is a similar kind of resource.
14:02 egonw the thing is this, I think
14:03 egonw when the plugin is run from inside Eclipse, it needs to be there...
14:03 egonw but, we are not doing that
14:03 egonw so, yes, I think it can safely go up one level in this case
14:03 egonw in retrospect
14:03 masak I still don't buy that reason. but never mind.
14:04 egonw it's for free...
14:04 egonw not need to buy it...
14:04 jonalv why don't you just try instead of trying to argue until you fifure out how it is?
14:04 egonw sure
14:05 egonw but later, ok?
14:05 masak :)
14:05 CIA-63 bioclipse.sdk: Carl Masak master * rf020390 / (4 files in 3 dirs): [TemplaterTest] converted to JUnit tests - http://bit.ly/42xVhd
14:05 CIA-63 bioclipse.sdk: Carl Masak master * r5d30f60 / plugins/net.bioclipse.sdk/src/net/bio​clipse/sdk/templating/Templater.java : [Templater] removed unused import - http://bit.ly/SxI7L
14:07 CIA-63 bioclipse.sdk: Egon Willighagen master * r193ea3b / (5 files): Placed the manager files in a .business sub package - http://bit.ly/8y0To
14:07 CIA-63 bioclipse.sdk: Egon Willighagen master * r1332e5f / plugins/net.bioclipse.sdk/src/net/bioclips​e/sdk/wizards/ManagerPluginNewWizard.java : Created MANIFEST.MF and plugin.xml too - http://bit.ly/4alDK
14:07 CIA-63 bioclipse.sdk: Egon Willighagen master * r364e484 / (6 files in 2 dirs): Merge branch '3-moreWork' - http://bit.ly/xpaHR
14:07 egonw oh bugger...
14:07 egonw forgot to rebase my branch :(
14:08 egonw in the past one would deliberately 'forget' that...
14:08 egonw just to boost commit statistics...
14:08 egonw but it's so obvious in the git world...
14:08 egonw -- for everyone who makes redundant merge commits
14:08 egonw (one of everyone who makes redundant merge commits)--
14:08 egonw (anyone who makes redundant merge commits)--
14:09 egonw just to be on the safe side :)
14:09 masak egonw: I don't quite get your fascination with reduntant merge commits. for one thing, they're really hard to tell from necessary merge commits.
14:09 egonw they waiste whitespace
14:10 masak ok, well let me stop right here then, and declare that argumentation unwinnable.
14:11 masak some people care if others merge, some don't.
14:12 * egonw is moving the templates/ folder
14:13 masak egonw++
14:15 CIA-63 bioclipse.sdk: Carl Masak master * r1194bae / (2 files in 2 dirs):
14:15 CIA-63 bioclipse.sdk: [Templater] changed semantics of unmatched keys
14:15 CIA-63 bioclipse.sdk: Previously, a provided key needed to have at least one corresponding
14:15 CIA-63 bioclipse.sdk: substitution in the template string. Now, due to popular demand,
14:15 CIA-63 bioclipse.sdk: that restriction is lifted. - http://bit.ly/2evKA
14:15 egonw http://friendfeed.com/egonw/396b785c/writi​ng-am-eclipse-new-project-wizard-to-set-up
14:15 zarah egonw's link is also http://tinyurl.com/pjbhyk
14:16 masak jonalv: `find . -name \*.gif`
14:16 egonw jonalv: if you are free... maybe you can make a catchy icon ?
14:16 jonalv egonw: yup
14:17 jonalv egonw: I was actually going for that...
14:17 jonalv I think we have some we can use...
14:24 * egonw learned to skil of 'git fetch; git rebase origin/master'
14:24 CIA-63 bioclipse.sdk: Egon Willighagen master * r3ee0ff4 / (20 files in 10 dirs): Moved templates folder outside the src/ folder, into the root folder of the project. - http://bit.ly/16Bqce
14:25 egonw Gpox: ping
14:25 egonw jonalv, masak: is Gpox with you at BMC?
14:25 Gpox egonw: pong
14:25 egonw ah :)
14:25 egonw how's wizard page progress?
14:26 Gpox good
14:26 egonw ETA?
14:30 CIA-63 bioclipse.sdk: Carl Masak master * r56780af / (2 files in 2 dirs):
14:30 CIA-63 bioclipse.sdk: [Templater] now catches unmatched substitutions
14:30 CIA-63 bioclipse.sdk: That is, a substring of the form '${key}' inside the template text, without
14:30 CIA-63 bioclipse.sdk: the corresponding key sent in as a parameter to templ.generate(...), now
14:30 CIA-63 bioclipse.sdk: throws an exception. - http://bit.ly/1655YD
14:31 CIA-63 bioclipse.sdk: Carl Masak master * rd84afe7 / plugins/net.bioclipse.sdk.tests/src/​net/bioclipse/sdk/TemplaterTest.java : [TemplaterTest] added copyright header comment - http://bit.ly/m2Uy5
14:31 masak JUnit++
14:34 CIA-63 bioclipse.sdk: Carl Masak master * r02f27a5 / plugins/net.bioclipse.sdk.tests/src/​net/bioclipse/sdk/TemplaterTest.java : [TemplaterTest] inlined a few variables - http://bit.ly/hH0fG
14:35 * egonw is debugging a path creation process
14:41 Gpox egonw: done
14:43 egonw good
14:43 * egonw is fixing some smaller issues
14:44 egonw and ready to hook in the wizard page
14:45 egonw jonalv: we also need a .classpath file
14:45 jonalv egonw: isn't that autogenerated somehow?
14:45 egonw no, does not seem so
14:45 egonw not at this moment, at least
14:46 jonalv egonw: can't you trigger a fix classpatch call somehow?
14:48 egonw perhaps...
14:48 egonw no clue how
14:48 egonw not at this moment
14:48 CIA-63 bioclipse.sdk: Egon Willighagen master * ra03fb26 / plugins/net.bioclipse.sdk/te​mplates/META-INF/MANIFEST.MF : Removed implementation specific plugins - http://bit.ly/210Mgr
14:48 CIA-63 bioclipse.sdk: Egon Willighagen master * rcd2dc44 / plugins/net.bioclipse.sdk/src/net/bioclips​e/sdk/wizards/ManagerPluginNewWizard.java :
14:48 CIA-63 bioclipse.sdk: Some more tweaks in the plugin/ generation.
14:48 CIA-63 bioclipse.sdk: * fixed creation of the src folder
14:48 CIA-63 bioclipse.sdk: * added missing Activator.java
14:48 CIA-63 bioclipse.sdk: * fixed one or two parameters - http://bit.ly/Oq7t1
14:49 egonw jonalv: shall I add it now?
14:49 egonw if you are still working on icons...
14:50 jonalv egonw: yes please
14:50 egonw Gpox: you have write access to the git repos
14:50 egonw ah, you already commited
14:51 egonw CIA--
14:51 Gpox yes
14:51 egonw excelletn :)
14:52 CIA-63 bioclipse.sdk: Egon Willighagen master * r2dbe3f6 / plugins/net.bioclipse.sdk/.classpath : No need to exclude templates/ anymore, as it moved one level up - http://bit.ly/vTY3I
14:54 masak I'm of a mind to add a convenience method to the Templater, which takes an input file, an output file, and the key/value pairs. would anyone benefit from that?
15:04 egonw I think at some point we will
15:04 egonw it just started raining here
15:08 egonw mmm...
15:09 masak http://www.guardian.co.uk/news/blog/20​09/aug/13/squirrel-canada-holiday-snap
15:09 zarah masak's link is also http://tinyurl.com/ksyu2c
15:11 egonw bla
15:12 egonw it does not seem to want to write the .classpath file...
15:13 CIA-63 bioclipse.sdk: jonalv master * r8e0cbf1 / (2 files in 2 dirs):
15:13 CIA-63 bioclipse.sdk: Some form of special icon.
15:13 CIA-63 bioclipse.sdk: It was not so easy. Feel free to try if you dare... - http://bit.ly/2j4TP0
15:13 egonw :)
15:14 egonw grmph...
15:14 egonw apparently, there is something special about creating dot files :(
15:14 jonalv that's unexpected
15:15 egonw for the rest... it seems to work :)
15:16 jonalv that sounds nice at least
15:16 egonw indeed :)
15:16 egonw so, next up...
15:16 egonw * use the values from the new manager page
15:16 egonw * an update site
15:17 egonw * documentation on how to use it
15:17 egonw oh... also...
15:17 egonw maybe we can use code snippets for method patterns?
15:17 egonw like with: sysout Ctrl^Space
15:18 jonalv egonw: I guess.
15:18 jonalv egonw: what code snippets?
15:18 egonw an example method ...
15:19 egonw jonalv: btw, found how to create Manifest the API way...
15:19 jonalv egonw: okey
15:20 egonw but the template is working fine
15:20 egonw we're not doing horribly difficult things here...
15:22 jonalv nope :)
15:28 masak did I hear "template is working fine"? :)
15:33 egonw yeah, seemingly
15:34 masak nice.
15:43 egonw mmm...
15:43 egonw that classpath stuff is not trivial...
15:45 CIA-63 bioclipse.sdk: jonalv master * rd2403ab / plugins/net.bioclipse.sdk/src/net/bioclip​se/sdk/wizards/ManagerDataInputPage.java :
15:45 CIA-63 bioclipse.sdk: fixed automagic packageName and managerName.
15:45 CIA-63 bioclipse.sdk: Now the second page will change if stepping back to first page and changing
15:45 CIA-63 bioclipse.sdk: things there after having already written something in the second page. Not
15:45 CIA-63 bioclipse.sdk: optimal but I don't see a quick and easy fix for it and at least this is better
15:45 CIA-63 bioclipse.sdk: than how it was before... - http://bit.ly/1lJxoJ
15:46 egonw wow...
15:46 egonw progress!
15:46 egonw yeah, a .classpath file !!
15:49 jonalv w00t
15:56 CIA-63 bioclipse.sdk: Egon Willighagen master * re50048c / (2 files in 2 dirs): OK, added the missing .classpath file the API way - http://bit.ly/11Uw3l
15:57 jonalv egonw: so are we sort of done now? :)
15:57 masak :)
15:58 egonw yes, well... getting really close
15:58 egonw todo remains:
15:58 jonalv what's left?
15:58 egonw * update site
16:01 jonalv okey well I guess you are best at that...
16:01 egonw yeah...
16:01 egonw I think the rest is now up to me...
16:01 egonw thanx guys!
16:01 jonalv and then I guess we need a blog post as well
16:01 egonw excellent work!
16:02 egonw yes, I think we do :)
16:02 egonw but first finish and test the update site...
16:02 jonalv yea
16:10 CIA-63 bioclipse.sdk: Egon Willighagen master * r984cb09 / (3 files): Added feature, depending on Eclipse, JDT and PDE - http://bit.ly/19Yn1U
16:10 egonw OK, dinner time now...
16:10 jonalv oki
16:11 egonw tonite I'll do an update site, and test installing it, and running it inside Eclipse
16:13 jonalv egonw++
16:57 egonw joined #bioclipse
17:00 shk3 joined #bioclipse
17:49 egonw joined #bioclipse
19:10 edrin left #bioclipse
19:26 egonw joined #bioclipse
19:38 * egonw is installing the Bioclipse SDK into his Eclipse installation
20:05 shk3 joined #bioclipse

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