Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-07-28

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All times shown according to UTC.

Time Nick Message
07:01 Gpox joined #bioclipse
07:36 jonalv joined #bioclipse
07:37 jonalv moin
07:37 zarah hi jonalv
07:40 jonalv dz
08:09 olas joined #bioclipse
08:34 masak joined #bioclipse
08:38 egonw joined #bioclipse
08:38 malic1 joined #bioclipse
08:39 malic1 left #bioclipse
09:01 CIA-49 bioclipse: carl_masak * r6273 /bioclipse2/trunk/externals/:
09:01 CIA-49 bioclipse: * added directory externals/ as a container for third-party components
09:01 CIA-49 bioclipse: * added cdk to externals
09:01 egonw olas: pinged Dan Z. about the jumbo jar
09:02 masak general question: what's nu.psnet.quickimage?
09:03 masak should it go the way of CDK?
09:04 olas masak: yes
09:04 olas it shows immages in Bioclipse
09:04 olas egonw: did see that
09:04 olas great
09:05 olas hope he can replace it soon
09:07 edrin joined #bioclipse
09:07 edrin hi
09:07 zarah hi edrin
09:13 masak olas: strange thing is, nu.psnet.quickimage doesn't seem to be an external
09:14 masak I'll just svn mv it
09:15 CIA-49 bioclipse: carl_masak * r6274 /bioclipse2/trunk/ (externals/nu.psnet.quickimage/ plugins/nu.psnet.quickimage/): [nu.psnet.quickimage] moved into externals/
09:16 olas masak: it's not strange
09:16 olas I put it there
09:16 olas sinc ethere is no SVN for it
09:16 olas hence we can't use externals
09:16 masak ah
09:16 masak no svn?
09:16 masak so, they're using CVS?
09:16 masak :)
09:23 masak olas: re JSDT: I did some spelunking into it on Friday. got completely lost, didn't even find an editor. will try more today.
09:23 masak it's a big project
09:27 olas I suggest we use th SF JSEditor
09:28 olas and not waste time there
09:28 masak oki
09:28 olas for now at least
09:28 olas sounds ok?
09:28 masak definitely
09:28 * masak downloads jseditor
09:35 CIA-49 bioclipse: jonalv * r6275 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java:
09:35 CIA-49 bioclipse: Now sorts methods when doing for example "help svn"
09:35 CIA-49 bioclipse: fixes #2027851
09:42 EskilA joined #bioclipse
10:16 egonw funny read: http://gaussling.wordpress.com/2008/07​/26/mathematicians-discover-new-digit/
10:16 zarah egonw's link is also http://tinyurl.com/6fqyqw
11:00 malic1 joined #bioclipse
11:08 malic1 left #bioclipse
11:16 masak I like the list of 12 points in this article: http://www.codinghorror.com​/blog/archives/000568.html
11:16 zarah masak's link is also http://tinyurl.com/5hhg5e
11:19 olas Could we implement the Hot dog stand skin for Bioclipse? - http://www.codinghorror.com​/blog/archives/000341.html
11:19 zarah olas's link is also http://tinyurl.com/38u25p
11:25 masak olas: low prio, low prio
11:26 olas ack
11:29 egonw does OS/X have a hot dog stand mode?
11:29 egonw ubuntu doesn't
11:29 egonw I think
11:38 malic1 joined #bioclipse
11:53 masak egonw: I can assure you Mac OS X doesn't have one
12:40 shk3 joined #bioclipse
12:40 shk3 hi all
12:40 zarah hi shk3
12:40 zarah shk3: You have new messages. Write '@messages' to read them.
12:41 shk3 @messages
12:41 zarah shk3: olas said http://help.eclipse.org/stable/index.js​p?topic=/org.eclipse.platform.doc.isv/g​uide/runtime_content_contributing.htm and http://blog.cypal-solutions.com/2008/04​/content-type-specific-file-icons.html
12:41 zarah shk3: olas said would be great if you could write a wiki page about content types and describers
12:41 zarah shk3: olas said http://www.developer.com/ja​va/data/article.php/3648736
12:41 zarah shk3: egonw said that nmrshiftdb.ice.mpg.de is down in some kind: header, footer but no front page content
12:51 CIA-49 bioclipse: shk3 * r6276 /bioclipse2/trunk/plugins/net.bioclipse.cml/ (3 files in 2 dirs): working on spectrum editor
12:52 CIA-49 bioclipse: shk3 * r6277 /bioclipse2/trunk/plugins/net.bioclipse.sp​ectrum/src/net/bioclipse/spectrum/editor/ (11 files): working on spectrum editor
12:55 olas shk3: could you have a look at Bioclispe 2 bugs
12:55 olas group: 2.0-alpha
12:55 olas there is one assigned to you
12:56 olas please either comment on it or implement it
12:56 olas (if you have time)
12:58 shk3 olas: will do so
12:58 shk3 I just had a look at the links you gave me for content types
12:59 shk3 I did it like desribed there - the problem is, it doesn't work (as explained in my email, if you read this).
12:59 shk3 no idea what to do right now.
13:05 olas read it
13:06 olas got no solution now
13:06 olas will look at this later
13:06 CIA-49 bioclipse: carl_masak * r6278 /bioclipse2/trunk/plugins/n​et.bioclipse.scripting.ui/ (3 files in 3 dirs):
13:06 CIA-49 bioclipse: [plugin.xml] better descriptiong of JsConsoleView
13:06 CIA-49 bioclipse: [JsConsoleManager.java] implemented clear()
13:06 CIA-49 bioclipse: [ScriptingConsoleView.java] made clear() reinsert the prompt,
13:06 CIA-49 bioclipse:  since it is now (through thread magic) called _after_ normal
13:06 CIA-49 bioclipse:  prompt insertion
13:12 shk3 olas: find my xml for the content type at http://pastebin.com/d1069666c
13:12 zarah shk3's link is also http://tinyurl.com/6g2cpd
13:36 jonalv zarah: tell shk3 Please don't commit java 6 code. For example @overides when implementing methods from interfaces. That is not correct java 5 and Bioclipse is _not_ java 6 yet
13:36 zarah Consider it noted.
13:41 CIA-49 bioclipse: jonalv * r6279 /bioclipse2/trunk/plugins/net.bioclipse.cml/src/ne​t/bioclipse/cml/managers/ValidateCMLManager.java: removed non-java5 @overides
13:43 jonalv zarah: tell shk3 I would like to talk to you about the ValidateCMLManager...
13:43 zarah Consider it noted.
13:43 CIA-49 bioclipse: carl_masak * r6280 /bioclipse2/trunk/plugins/net.bioclipse.sc​ripting.ui/src/net/bioclipse/scripting/ui/ (3 files in 2 dirs):
13:43 CIA-49 bioclipse: [JsConsoleView] rewired clear(), created print()
13:43 CIA-49 bioclipse: [JsConsoleManager] implemented print(), factored out common code
13:43 CIA-49 bioclipse: [IJsConsoleManager] declared print()
13:45 CIA-49 bioclipse: carl_masak * r6281 /bioclipse2/trunk/plugins/: removed external org.openscience.cdk in plugins/
13:51 olas shk3: around?
13:58 CIA-49 bioclipse: ospjuth * r6282 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (4 files in 2 dirs):
13:58 CIA-49 bioclipse: Check for online updates on startup. If update site contains features versioned
13:58 CIA-49 bioclipse: greater than the same installed feature, it is downloaded and installed
13:58 CIA-49 bioclipse: automatically using a Job. Also installs any feature patches on update site.
13:58 CIA-49 bioclipse: Defaults to run, but adding program argument '-noUpdate' overrides this. Added
13:58 CIA-49 bioclipse: '-noUpdate' to bioclipse.product, as no updates should be installed when run in
13:58 CIA-49 bioclipse: development mode from Eclipse.
14:00 shk3 olas: ye
14:00 zarah shk3: You have new messages. Write '@messages' to read them.
14:00 shk3 s
14:00 shk3 @messages
14:00 zarah shk3: jonalv said Please don't commit java 6 code. For example @overides when implementing methods from interfaces. That is not correct java 5 and Bioclipse is _not_ java 6 yet
14:00 zarah shk3: jonalv said I would like to talk to you about the ValidateCMLManager...
14:01 shk3 jonals: sorry for java 6 code
14:01 shk3 will change code level to java 5
14:01 jonalv shk3: hi :)
14:01 jonalv yea
14:01 jonalv I was in the same situation a while a go :)
14:01 jonalv everyone complaining on me...
14:01 jonalv :)
14:01 shk3 i didn't notice
14:02 jonalv I know better to change compliance lvl than trying to remove all auto generated stuff
14:02 jonalv regarding the manager
14:03 jonalv I am not sure you want to introduce states in it. I am not saying it is wrong just that maybe it would be better to have an object?
14:03 jonalv perhaps...
14:03 shk3 what do you mean with states?
14:04 edrin is the rhino script plugin already ported from bc1 to bc2?
14:05 jonalv edrin: no not really :)
14:05 edrin :/
14:05 edrin that's a pitty
14:05 edrin pity
14:05 masak edrin: anything in particular you'd like?
14:05 olas edrin: can you test a URL for me?
14:05 olas http://pele.farmbio.uu.se/pmd/
14:05 zarah olas's link is also http://tinyurl.com/5943h4
14:05 olas can you see the report there?
14:06 olas just testing if the port opening is working
14:06 edrin yes
14:06 olas thx
14:06 jonalv shk3: the info ablut the evalutation will be stored in the instance variables of the manager. So the managaer will have different states after you run a validation and before...
14:06 edrin PMD report
14:06 edrin Problems found
14:06 edrin #FileLineProblem
14:06 edrin 1 /opt/bioclipse2/plugins/net.bioclipse.analys​is/src/net/bioclipse/analysis/Activator.java 1 All methods are static. Consider using Singleton instead. Alternatively, you could add a private constructor or make the class abstract to silence this warning.
14:06 jonalv I am just saying that maybe a validation should return a validation object instead containing all the inof...
14:06 edrin masak: i would like to run my old scripts in bc2
14:07 masak edrin: I'm looking at importing a js editor as we speak
14:07 edrin masak: i need to test my libs,
14:07 edrin ah good
14:07 masak it won't be the old one, though
14:07 shk3 ah, don't think this has a purpose
14:07 shk3 I just copied the code from bc1 and adopted it
14:07 olas ok, port 80 is open on pele
14:07 masak edrin: I'm seeing if I can import this one: http://sourceforge.net/projects/jseditor
14:07 zarah masak's link is also http://tinyurl.com/5gd3u7
14:08 olas we got an online server for bioclipse :-)
14:08 edrin masak:  the old one? i think bc1 did not have an explicit js editor
14:08 masak edrin: well, it did have an editor
14:08 olas it had a text-editor
14:08 masak yes.
14:08 olas and a run JS action
14:08 masak with a "run" button
14:08 masak yes.
14:08 edrin masak: yes, but not specific for js
14:08 masak ok, I see.
14:09 masak didn't know that.
14:09 edrin yes, maybe we should have the js run button
14:09 olas or something similar
14:09 olas it was sort of hard to find IMO
14:09 * masak suggests "or something similar"
14:09 masak or maybe both
14:09 edrin it was able to run script in gui thread an separate thread...
14:10 masak edrin: we do that in the console, too
14:10 edrin masak: how do you switch between gui thread and separate thread?
14:10 masak we don't.
14:11 masak or rather, the GUI thread has to be treated separately with asyncExec
14:11 jonalv js is never run in the gui thread I think
14:11 edrin olas: yes, it was hard to find... a "run" on right click of the file would be better i guess
14:12 masak edrin++ # I agree
14:12 edrin in what plugin is the rhino .jar located?
14:13 edrin olas: the link you showed me, what is it?
14:13 masak edrin: net.bioclipse.scripting
14:14 masak along with the ruby and groovy jars
14:14 edrin ah ok
14:14 olas edrin: nightly reports on bioclipse codebase using PMD set up by jonalv++ and masak++
14:14 olas well, not exactly nightly yet but soon
14:14 masak olas: I got JSEditor to run, but it doesn't do anything cool
14:15 masak no color coding, no special menus, no nothing
14:15 edrin masak: the jseditor project is active?
14:15 masak edrin: actively developed, you mena?
14:15 masak dunno
14:15 edrin yes...
14:15 edrin last update of homepage is of 2004
14:15 masak indeed.
14:16 edrin :/
14:16 masak olas: :/
14:16 olas it's just an editor
14:16 olas with syntax highlighting
14:16 olas we will extend it for bioclipse
14:16 masak not even that, over here
14:16 olas oh
14:16 olas not?
14:16 masak no syntax highlighting...
14:16 olas what is it for then?
14:16 masak exactly my question
14:17 olas maybe a dead project?
14:17 edrin i remember the was no highlighting when i tried it
14:17 jonalv sounds like taht
14:17 masak could be
14:17 edrin i think i tried it in eclipse wdt...
14:17 masak ok... I retract my claim
14:17 masak it does have syntax highlighting
14:18 masak and now the outline reacts, too
14:18 masak it looks decent
14:18 edrin does it?
14:18 masak yes.
14:18 edrin do you have a screenshot?
14:18 masak hold on
14:19 edrin :)
14:25 masak my usual facilities for making a screenshot on Mac OS X don't seem to work today
14:25 masak and I tried pretty hard
14:25 masak sorry :/
14:28 masak anyway,
14:28 * masak checks whether JsEditor integrates into bc2
14:29 shk3 question: looks like dirty files in jcp editor do not have the * in the title.
14:29 shk3 is this missing or intended?
14:29 jonalv missing
14:29 masak ...and in the JsEditor, undoing does not make files clean again :)
14:29 jonalv I though Gpox had a look on that the other day
14:31 shk3 ah
14:32 shk3 because i am just working on the spectrum editor
14:32 shk3 and if an editor page is dirty,
14:32 shk3 the * is not there,
14:32 shk3 but when closing, I get the
14:32 shk3 "do you want to save".
14:32 shk3 Looks like these are somehow differently handeled.
14:32 shk3 Any idea?
14:33 jonalv you should call some fire method that checks for dirty and updates the gui
14:33 jonalv I can\t remmebr the name of it though...
14:33 jonalv maybe olas know...
14:35 shk3 firePropertyChange(PROP_DIRTY)
14:35 shk3 that's what I am doing
14:37 jonalv then you of course must have a correctly implemented isDirty otr what\s it called but I am guessing you have that too...
14:37 jonalv Then I don\t know...
14:38 shk3 yes, i have that
14:38 shk3 it seems to work since the "do you want to save" works
14:38 shk3 will find that out
14:38 shk3 enough to do before it's ready anyway
14:38 jonalv mhm
14:45 shk3 looks like you have to do a firePropertyChange(PROP_DIRTY); on the multipageeditorpart as well
14:45 shk3 then the * shows up
14:47 jonalv oh okey, good to know :)
14:49 CIA-49 bioclipse: ospjuth * r6283 /bioclipse2/trunk/plugins/net.bioclipse.ui/s​rc/net/bioclipse/ui/DefaultPerspective.java: Removed hardcoded ref to JSConsoleView.
14:57 CIA-49 bioclipse: carl_masak * r6284 /bioclipse2/trunk/externals​/net.sourceforge.jseditor/ (97 files in 20 dirs): [net.sourceforge.jseditor] added to externals/
14:59 CIA-49 bioclipse: ospjuth * r6285 /bioclipse2/trunk/plugins/net.bioc​lipse.ui/plugin_customization.ini: On help, start with our default Help page.
15:05 masak ...and JsEditor works out-of-the-box in bc2!
15:05 masak JsEditor++
15:06 olas did you add a contributor with RUN tasks?
15:07 masak olas: no, getting to that
15:31 masak olas: tomorrow I'm going to look at that HTML Help conversion
15:32 masak any pointers on where to start?
15:40 olas no
15:40 olas I have no idea what you want to do
15:42 masak olas: well, I do. but I'm interested in the format to convert to
15:43 * masak gets all the answers in olas++'s office
15:45 CIA-49 bioclipse: ospjuth * r6286 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (52 files in 12 dirs): Added a lot of help from bioclipse1. Still long way to go and much to update, but at least a start.
15:47 olas left #bioclipse
15:48 CIA-49 bioclipse: carl_masak * r6287 /bioclipse2/trunk/plugins/net.bioclipse.scrip​ting.ui/src/net/bioclipse/scripting/ui/views/ (ActionHistoryView.java JsConsoleView.java VirtualView.java):
15:48 CIA-49 bioclipse: [ActionHistoryView] removed unused imports
15:48 CIA-49 bioclipse: [JsConsoleView] here too
15:48 CIA-49 bioclipse: [VirtualView] imports, javadoc, generics
16:22 CIA-49 bioclipse: jonalv * r6288 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): added bin to svn:ignore
16:35 CIA-49 bioclipse: jonalv * r6289 /bioclipse2/trunk/plugins/ (net.bioclipse.pcore.edit/ net.bioclipse.spectrum/): added bin to svn:ignore
16:39 CIA-49 bioclipse: jonalv * r6290 /bioclipse2/trunk/plugins/ (4 files in 3 dirs): Refactored methods dealing with files into comming in three flavours.
16:58 edrin left #bioclipse
16:59 CIA-49 bioclipse: carl_masak * r6291 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java:
16:59 CIA-49 bioclipse: [JsConsoleView] now no things are added to a tab-completed name
16:59 CIA-49 bioclipse: if the command starts with "help " or "man "
17:24 CIA-49 bioclipse: shk3 * r6292 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/ (5 files in 2 dirs): working on spectrum editor
17:57 CIA-49 bioclipse: ospjuth * r6293 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (31 files in 8 dirs): Updated help pages.

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