Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-02-24

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
00:28 ChanServ joined #bioclipse
05:02 masak joined #bioclipse
07:36 Gpox joined #bioclipse
08:09 rojasm joined #bioclipse
08:11 masak Pelezilla is a bit sad today...
08:11 masak @pz rhino
08:12 masak dang, now I probably tied up Smart Girl as well...
08:12 masak zarah: ping
08:13 masak yup.
08:13 egonw joined #bioclipse
08:13 masak egonw: greetings.
08:13 masak egonw: Pelezilla is a bit sad today.
08:13 egonw moin
08:13 egonw how so?
08:13 masak it times out on searches.
08:15 egonw seems to work here...
08:15 zarah read timeout
08:15 zarah masak: pong, dear
08:15 zarah oh hai egonw
08:15 egonw how can I reproduce?
08:15 egonw hi zarah
08:15 masak egonw: zarah just did it for you.
08:15 masak that was the reply to a search I made.
08:15 egonw ah... ic
08:15 egonw @pz flickers
08:15 masak you can try again through zarah, but it'll tie her up... oh well.
08:16 egonw ok, same here
08:16 masak I'd submit a bug ticket, but... :)
08:17 zarah Internal Server Error
08:17 egonw reboot mysql
08:17 masak zarah: you're a smart girl, you know that.
08:17 zarah masak: I bet you tell that to all the girls. Over.
08:17 egonw @pz flickers
08:17 zarah [451] JCP flickers on windows            http://tinyurl.com/b4c8sl
08:17 zarah [433] Jmol flickers when Bioclipse wi... http://tinyurl.com/actmul
08:17 zarah Entire list at http://tinyurl.com/aryzx4
08:17 masak egonw++
08:23 masak @tell olass http://java.sun.com/docs/books/jls/​third_edition/html/packages.html#7.7
08:23 zarah masak's link is also http://tinyurl.com/3lpsu9
08:23 zarah Consider it noted.
08:26 olass joined #bioclipse
08:26 CIA-55 bioclipse: ospjuth * r9009 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/ne​t/bioclipse/ui/ApplicationWorkbenchAdvisor.java: Caught NPE in auto updates. Fixes #532.
08:26 zarah bug #532 | http://tinyurl.com/d34kco
08:45 grandm44 joined #bioclipse
08:48 edrin joined #bioclipse
08:48 olass @pz
08:48 zarah olass: Pelezilla is at http://bugs.bioclipse.net
08:48 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
08:48 edrin hello
08:48 egonw hi olass
08:48 olass hi
08:48 zarah privet edrin
08:48 egonw hi edrin
08:48 olass @msg
08:48 zarah saluton olass
08:48 zarah olass: 25 m 41 s ago, masak said http://java.sun.com/docs/books/jls/​third_edition/html/packages.html#7.7
08:49 olass right
08:51 olass I am having problems submitting bugs to pelezilla from mylyn
08:51 olass anyone else experiencing the same?
08:51 masak yes.
08:51 masak egonw: pz acting up again.
08:51 olass ok
08:51 olass why is this?
08:51 masak olass: this happened half an hour ago.
08:51 masak it was something with mysql, IIUC.
08:52 olass and how is it resolved?
08:52 masak applying egonw to the problem.
08:52 olass sounds like a good solution
08:52 egonw mom, on the phone with Jarl
08:52 masak oki
08:53 masak Pelezilla++ # only truly appreciated when missed
08:53 edrin when checking out jsexecution, change the folder path
09:03 masak I have build failures in net.bioclipse.biojava.ui, net.bioclipse.biomoby, net.bioclipse.biomoby.tests, net.bioclipse.cdk10, net.bioclipse.qsar.ui, and net.bioclipse.rdf.ui
09:04 masak the persons responsible are encouraged to investigate.
09:04 stain joined #bioclipse
09:05 egonw back
09:05 egonw I installed mtop
09:05 egonw there is a single query that blocks the rest...
09:06 egonw SELECT ... FROM bugs INNER JOIN profiles AS map_assigned_to ON (bugs.assigned_to = map_assigned_to.userid) LEFT JOIN longdescs AS longdescs_ ON (bugs.bug_id = longdescs_.bug_id ) LEFT JOIN longdes
09:06 egonw cut off...
09:06 egonw OK, who has installed the new Mylyn plugin already?
09:06 egonw (I have)
09:06 egonw yesterday or so...
09:07 masak egonw: olass is afk, talking to Gpox.
09:07 masak I don't even have the old Mylyn.
09:09 egonw OK, tried making a change, and update via Mylyn
09:09 egonw seems to be OK
09:09 masak thanks.
09:10 masak @pz 567
09:10 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=567
09:10 egonw ok...
09:11 egonw @pz 567
09:11 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=567
09:11 egonw OK, zarah did not trigger that query...
09:11 egonw did anyone do something special?
09:11 masak egonw: well, the above command doesn't even need the web.
09:12 masak egonw: I was doing searches through the web interface...
09:12 egonw OK, good point
09:12 egonw what kind of search?
09:12 egonw there is one thing that causes the above bad SQL
09:12 masak looking for bugs without a milestone.
09:12 egonw ok, please do it again
09:12 egonw let's see...
09:12 masak ok, hold on.
09:13 masak now it worked.
09:13 egonw mmm...
09:13 masak and it was instantaneous.
09:13 edrin masak: if you checkout jsexecution, update the pathname of svn folder/project at your location
09:13 egonw ok, so that's not it either
09:14 masak edrin: I have checked it out.
09:14 shk3 joined #bioclipse
09:14 masak edrin: and imported it.
09:15 edrin ok
09:15 edrin no rhino left
09:16 masak well, two instances.
09:21 edrin where?
09:21 masak I added that as a comment to the ticket.
09:22 masak when I reopened it just now.
09:22 edrin what is the bug number?
09:25 masak http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=567
09:25 zarah masak's link is also http://tinyurl.com/b542as
09:26 maclean joined #bioclipse
09:26 masak maclean: OH HAI
09:26 maclean hai
09:27 egonw this is why I like SF...
09:27 egonw no crap with failing services... just complain
09:27 egonw OK, who is using PZ at this moment
09:27 egonw in the last 2 minutes
09:27 egonw and what did you do?
09:27 maclean not I
09:27 masak I've been using it.
09:27 masak not doing any searches though.
09:28 masak just showing pages.
09:28 egonw what was the last three things you did?
09:28 masak access a ticket, access a ticket, and access a ticket.
09:28 egonw a single one, lik 567?
09:28 masak yup.
09:28 egonw ok
09:28 masak I claim innocence. :)
09:28 masak Gpox is innocent too.
09:29 masak he has been talking to me, explaining design decisions.
09:29 maclean it seems like a reasonable use of a bug-tracking system :)
09:29 masak one would think so.
09:29 maclean oh, unintentional documentation comedy :
09:29 maclean "Simply override the getResourceUndoContextPolicy() method of your WorkspaceEditingDomainFactory to return an IResourceUndoContextPolicy, usually a subclass of AbstractResourceUndoContextPolicy, which has convenient override hooks"
09:30 maclean "Simply!"
09:30 masak :D
09:30 edrin masak: i don't know these plugins, no clue who added these lines to it
09:30 masak edrin: might be very old references, then.
09:30 masak edrin: we should reassign to the guilty parties.
09:31 edrin i think they are not related to my plugin
09:31 edrin they most likely exist much longer
09:31 masak @ask olass did you write the biomoby.ui plugin?
09:31 zarah Consider it noted.
09:31 egonw OK, who has IP 66.249.71.111 ?
09:32 masak egonw: no-one here at UU.
09:33 maclean 66 Is the US, no?
09:33 grandm44 yes, says geoip
09:33 grandm44 hello
09:33 zarah hello grandm44, you fantastic person you
09:33 edrin http://whois.domaintools.com/66.249.71.111
09:33 zarah edrin's link is also http://tinyurl.com/cxzgzs
09:33 maclean google
09:33 zarah maclean: No hits.
09:33 edrin OrgName:    Google Inc.
09:33 egonw indeed
09:33 maclean hah. thanks zarah.
09:34 egonw just discovered that too
09:34 edrin crawl-66-249-71-111.googlebot.com
09:36 CIA-55 bioclipse: carl_masak * r9010 /bot/trunk/zarah.pl: [zarah] no longer says anything if people say just 'google'
09:36 grandm44 i was on vacation, but I still have the the same problem with "instanceof JChemPaintEditor" which throws an execption at runtime. Someone can help me ?
09:37 egonw sure...
09:37 egonw go ahead...
09:37 egonw where is it a problem? .java file and line
09:37 grandm44 http://bioclipse.pastebin.com/m74c61a24
09:37 zarah grandm44's link is also http://tinyurl.com/ctts4m
09:37 grandm44 no compilation problem
09:43 grandm44 I call the following from a custom plugin, launched from a custom feature in bioclipse.product. http://bioclipse.pastebin.com/m2919ca30
09:43 zarah grandm44's link is also http://tinyurl.com/dbogfd
09:44 maclean Are you running using features, or using plugins?
09:44 maclean And, if the second, are all the plugins selected in the run configuration?
09:45 grandm44 I use both a feature which contains a plugin, and the feature is included in the run configuration
09:46 egonw OK, I have updated the robots.txt...
09:46 egonw not sure when Google will read it again...
09:46 CIA-55 bioclipse: carl_masak * r9011 /bot/trunk/zarah.pl: [zarah] now only allows 'tell me' with nothing after
09:46 egonw so might have to keep rebooting PZ every now and then
09:46 egonw grandm44: did you add the cheminfo feature?
09:47 masak zarah: reboot, dear.
09:47 grandm44 yes
09:47 zarah joined #bioclipse
09:47 masak zarah: tell me...
09:47 zarah masak: Unknown syntax, I... I just don't get it.
09:47 masak zarah: tell me
09:47 zarah masak: Unknown syntax, I... I just don't get it.
09:47 masak zarah: tell me gossip
09:47 zarah masak: Unknown syntax, I... I just don't get it.
09:48 masak hm. too little understanding.
09:48 masak fixing.
09:48 grandm44 i have net.bioclipse_feature, net.bioclipse.chemoinformatics_feature, and my "stuff_feature".
09:48 egonw ok
09:49 egonw and I see the jcp added to the JS env
09:49 egonw so, it has booted fine too...
09:49 grandm44 yes...
09:49 egonw does your plugin depend on the cdk.jchempaint plugin?
09:50 egonw Gpox: ping
09:50 Gpox egonw: pong
09:50 maclean personally, I found that things didn't work unless I had all 4 features specified
09:51 egonw maclean: all 4? I typically run 2 features
09:51 CIA-55 bioclipse: carl_masak * r9012 /bot/trunk/zarah.pl: [zarah] added understanding
09:51 egonw Gpox: can you explain the Exprt-package of cdk.jchempaint?
09:51 maclean yes, but that doesn't seem to work
09:51 zarah joined #bioclipse
09:51 egonw what's that uses clause?
09:52 egonw at line 34 of the MANIFEST.MF
09:52 egonw I was checking of the JCPEditor is visible from other plugins...
09:52 egonw Gpox: any clue why grandm44 gets a ClassNotFOund exception on the JCPEditor at runtime?
09:53 maclean afk
09:53 grandm44 egonw: if I had cdk.jchempaint to the dependencies tab, in required Plug-ins, I get a compil error "Build path contains duplicate entry: 'net.bioclipse.cdk.jchempaint' for project 'stuff'"
09:54 egonw for which plugin?
09:54 Gpox egonw: no. No idea whay there is a uses:= in the manifest wither
09:54 egonw Gpox: can you remove it please, and export those packages that should be exported?
09:55 grandm44 egonw: for my plugin "stuff"
09:55 egonw well, it should depend on it...
09:56 egonw grandm44: can you please copy/paste the plugins MANIFEST.MF?
09:58 grandm44 http://bioclipse.pastebin.com/mf05d8bf
09:58 zarah grandm44's link is also http://tinyurl.com/bmzr95
09:58 egonw ok, remove those 2 Import-Package: lines
09:59 egonw then add net.bioclipse.cdk.jchempaint as required plugin
10:00 CIA-55 bioclipse: goglepox * r9013 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.jchempaint/META-INF/MANIFEST.MF: Removed uses:=... from MANIFEST.MF
10:00 grandm44 i get a compil error
10:00 jonalv joined #bioclipse
10:00 grandm44 No available bundle exports package 'net.bioclipse.cdk.jchempaint'
10:02 egonw are you using Import-Package for that?
10:02 egonw please use: Require-Bundle
10:02 grandm44 ah! ok
10:03 egonw grandm44: the latter defines a plugin dependency...
10:03 egonw the Import-Pacakge: is a specialty you should try to never use
10:03 grandm44 ok. noted.
10:04 grandm44 it compils, but i get a warning now: Header  already defined
10:04 grandm44 i try to boot
10:07 grandm44 Same thing :-( http://bioclipse.pastebin.com/m19b0f4d9
10:07 zarah grandm44's link is also http://tinyurl.com/bysdrc
10:09 jonalv Am I the only one having problems with pelezilla?
10:09 egonw jonalv: everyone is...
10:09 jonalv zarah: @pz trouble...
10:09 zarah jonalv: are you making fun of me?
10:09 egonw PZ is being indexed by google
10:10 jonalv egonw: and that totally crashes it?
10:10 egonw and they found a nasty query in Bugzilla which makes MySQL break
10:10 masak egonw: we need a robots file.
10:10 egonw no, it's more like an infinite loop
10:10 egonw masak: yes, installed one
10:10 masak egonw++
10:10 egonw see my IRC message earlier
10:10 masak ok.
10:10 egonw not sure when it will be picked up by Google
10:10 masak egonw: lunch in 5.
10:10 masak fairly quickly, I guess.
10:10 egonw masak: also, I have not experience with robots.txt
10:11 egonw if you do, please check my attempt
10:11 masak I don't, but I can check anyway.
10:11 * egonw is eating sandwhiches (do I have it right this time?)
10:11 masak oh, so you're not coming?
10:11 masak then I booked for one too many.
10:12 egonw cool
10:12 egonw mtop can kill individual SQL queries
10:12 egonw so, I don't have to reboot mysql all the time :)
10:13 egonw grandm44: if you send me your full 'stuff' plugin... then I could try here...
10:13 grandm44 egonw: if I remove the Require-Bundle line, it compiles ok but I get the runtime error. If I add "Require-Bundle: net.bioclipse.cdk.jchempai​nt;bundle-version="2.0.0"" to the MANIFEST.MF, I get the error "Build path contains duplicate entry: 'net.bioclipse.cdk.jchempaint' for project 'stuff'"
10:14 grandm44 ok i send
10:14 egonw grandm44: try to clean classpath and project...
10:14 egonw ok, thanx
10:14 egonw grandm44: much easier for me to find the problem then
10:17 egonw grandm44: it seems DCC is blocked
10:17 grandm44 ok, where do i send it to you ?
10:24 edrin where is ola gone?
10:24 egonw course
10:25 edrin ok
10:44 egonw grandm44: here's the deal
10:44 egonw right click on your project
10:44 egonw pick Properties
10:44 egonw the go to the Java Build Path section
10:44 egonw Projects TAB
10:45 egonw remove cdk.jchempaint as 'Required projects on the build path'
10:45 grandm44 done
10:45 egonw and make the Manifest.mf look like:
10:45 egonw http://bioclipse.pastebin.com/m546ac449
10:45 zarah egonw's link is also http://tinyurl.com/df42o2
10:46 egonw that solves that duplicate entry error
10:46 grandm44 done and tested, no runtime error anymore :) thanx
10:46 egonw Bioclipse boots fine for me then
10:47 egonw good :)
10:51 edrin left #bioclipse
10:54 ChanServ joined #bioclipse
11:05 ChanServ joined #bioclipse
11:07 maclean joined #bioclipse
11:46 CIA-55 bioclipse: carl_masak * r9015 /bot/trunk/zarah.pl: [zarah] now understands 'ping me' et al
11:48 egonw ping me?
11:48 maclean egonw: ping
11:48 maclean lolol
11:48 egonw :)
11:50 maclean hmmm. it is alright to be using pele, right?
11:54 egonw yes
11:54 egonw it's google
11:54 egonw I'm keeping an eye on the MySQL load...
11:54 egonw and kill bad SQLs
11:55 masak egonw: she still needs to be addressed directly.
11:55 masak or with '@'.
11:55 egonw so, I'm fighting google bots for a job
11:55 masak zarah: reboot.
11:55 egonw beats quake :)
11:55 zarah joined #bioclipse
11:55 masak egonw: don't worry, their motto is "don't be evil" :P
11:55 masak zarah: ping me
11:56 zarah masak: ping
11:56 masak zarah: pong
11:56 zarah masak: excuse me?
11:56 masak oops :)
11:56 egonw zarah: ping masak
11:56 zarah Consider it noted.
11:56 egonw mmm...
11:56 maclean google doom admin
11:56 zarah maclean: http://www.cs.unm.edu/~dlchao/flake/doom/
11:56 masak egonw: that's as specced.
11:56 zarah masak: You have new messages. Write '/msg zarah @messages' to read them.
11:56 masak @clear
11:56 zarah masak: Messages cleared.
11:57 egonw maclean: yeah, I only need a mashup with mtop
11:57 egonw @google mtop mysql
11:57 zarah egonw: http://mtop.sourceforge.net/
11:58 maclean oops I managed to submit the same comment twice.
11:58 maclean sorry.
11:58 CIA-55 bioclipse: carl_masak * r9016 /bot/trunk/zarah.pl: [zarah] now ignores pongs
11:58 masak zarah: reboot again.
11:58 zarah joined #bioclipse
11:58 masak zarah: pong FTW!
11:59 masak zarah++
11:59 maclean hmmm. gmail isn't working either. is there a google-storm on?
12:00 masak Gmail not working!?
12:00 masak :(
12:00 egonw no, it's being slow
12:00 masak what is the world coming to?
12:00 egonw with time outs
12:01 masak this sucks.
12:01 masak now how are people going to contact me?
12:01 egonw your mobile
12:01 egonw hahahahaha
12:01 maclean Carrier pidgeon.
12:01 masak egonw: didn't see that coming. :P
12:01 masak maclean: unladen?
12:01 masak or with a coconut?
12:02 maclean :)
12:02 maclean Two of them could carry it in a line held between them!
12:02 masak oh right, that was an african swallow.
12:02 masak one minute later, and GMail is _still_ down! what is this?
12:03 maclean hmmm. I am playing that fun game : update bioclipse, and guess which plugins you are missing...
12:03 masak been playing that a lot lately.
12:04 maclean someone mentioned Buckminster (project management/dependency tool)
12:04 egonw http://www.sciencetext.com/google-mail-outage.html
12:04 zarah egonw's link is also http://tinyurl.com/btzpw9
12:04 maclean I took a quick look at it, and it might be a good idea
12:05 masak waaah! Gmail outage.
12:05 maclean do not want.
12:06 masak http://www.textually.org/textually/a​rchives/images/set3/do-not-want.jpg
12:06 zarah masak's link is also http://tinyurl.com/cnepxz
12:06 maclean hee hee
12:07 maclean hmmm. now I am updating my eclipse so that I can update biolclipse. oh fun.
12:08 masak maclean: we should make a package manager which handles all updates automatically for us, painlessly.
12:09 maclean no, no - no programming of programming environments!
12:09 maclean "IDE fever", as I call it.
12:10 edrin joined #bioclipse
12:10 edrin left #bioclipse
12:12 masak maclean: don't worry, it'll be fully customizable (via XML), and you'll finally have a use for that second core!
12:13 maclean hah.
12:13 maclean accursed XML.
12:13 masak it has its uses.
12:13 maclean used sparingly
12:13 masak just not configuration files, please :/
12:14 maclean indeed
12:14 olass joined #bioclipse
12:15 egonw fortunately Eclipse is not using XML for config files
12:15 * masak likes JSON and YAML
12:15 CIA-55 bioclipse: egonw * r9017 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: Fixed expected SMILESes; renamed files here and there to make them unique to tests
12:15 CIA-55 bioclipse: egonw * r9018 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: Added unit test for bug #583
12:16 zarah bug #583 | http://tinyurl.com/d78jpk
12:16 CIA-55 bioclipse: egonw * r9019 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java:
12:16 CIA-55 bioclipse: Don't complain about overwrite being true (people are using it as a default, it
12:16 CIA-55 bioclipse: seems... what are they thinking?? Just confused about the crappy API I guess...
12:16 CIA-55 bioclipse: PS. this is just talking to myself... not to other developers...), just guess
12:16 CIA-55 bioclipse: the format based on the extension... blah, juck... (fixes #583)
12:16 zarah bug #583 | http://tinyurl.com/d78jpk
12:21 CIA-55 bioclipse: egonw * r9020 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/business/ICDKManager.java: Fixed help summary: filetype is not a param for this method; added note on the output format type (fixes #586)
12:21 zarah bug #586 | http://tinyurl.com/cj7n9m
12:22 olass masak: regarding json and yaml; Do you see any use of it in Bioclipse?
12:22 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
12:22 olass @msg
12:22 zarah olass: 2 h 50 m 54 s ago, masak said did you write the biomoby.ui plugin?
12:22 olass masak: yes
12:22 masak olass: ok, you just bought yourself a bug ticket :)
12:22 olass it is unstable and unmaintained currently
12:23 olass please feel free
12:23 masak olass: re JSON/YAML, I don't know.
12:23 maclean aren't plugin.xml files config files?
12:23 masak they're neat, well-supported formats for hierarchical config-like data.
12:23 olass maclean: in what respect?
12:23 maclean they configure stuff
12:24 masak :P
12:24 maclean they're also files
12:24 olass maclean: the plugin.xml, build.properties, and MANIFEST.MF are all manifest files
12:24 maclean ohhhh
12:24 olass :-)
12:24 maclean they manifest stuff, then
12:24 olass lol
12:24 masak wait a minute. manifest files?
12:25 olass I have read it
12:25 masak ok
12:25 masak that settles it, then. :)
12:26 maclean so it is written, so shall it be.
12:26 olass hmm, maybe build.props is not part of the manifest...
12:28 olass manifest.mf is low-level OSGI stuff, plugin.xml is on a higher eclipse-level
12:28 olass so I have understood things
12:33 olass to all: would it be possible for me to release beta3 today?
12:34 olass or are there many things in progress that will finish during the day/tomorrow?
12:34 olass egonw, gilleain, Gpox ?
12:34 egonw "I see Bioclipse as a tool for chemists."
12:35 * egonw is just bug fixing
12:35 olass "I see Bioclispe as a tool in life science"
12:35 egonw that was a quote from the wild
12:35 egonw not from me
12:35 egonw we desperately need to get some sequence stuff online after 2.0
12:35 olass yes
12:35 maclean "I see Bioclipse as something that's taking a loong time to update today"
12:36 egonw olass: regarding the update...
12:36 egonw see the 'stable managers' wiki
12:36 olass it's not an RC
12:36 olass but a beta
12:36 maclean olass: I'm working on undo/redo for bioclipse-jcp, but it's hard.
12:36 olass maclean: great!
12:36 maclean I don't think it will be done today, but.
12:39 CIA-55 bioclipse: egonw * r9021 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: No need to catch exceptions... JUnit already does that for you
12:40 CIA-55 bioclipse: egonw * r9022 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: Fixed unit test: use symmertrical SMILES, so that the test does not fail on canonicalness issues
12:40 CIA-55 bioclipse: egonw * r9023 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: Properly fixed the unit test: using the right save method, and ChemFile's are not supported yet
13:09 CIA-55 bioclipse: egonw * r9024 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: Fixed unit test: unique file name; use ResourcePathTransformer to get the IFile, instead of using a IMockFile which did not give the proper contents
13:10 CIA-55 bioclipse: egonw * r9025 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: Fixed unit test: the file has 30 items, not 1
13:11 CIA-55 bioclipse: egonw * r9026 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Moved setReader until after testing the reader == null
13:12 CIA-55 bioclipse: egonw * r9027 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Complain if the input file == null
13:12 CIA-55 bioclipse: egonw * r9028 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Reuse the just created monitoy
13:28 CIA-55 bioclipse: egonw * r9029 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: Better testing: added testing of the counting too
13:29 egonw everyone: CDKManager is now unit test fail free...
13:29 egonw please keep it that way
13:29 CIA-55 bioclipse: egonw * r9030 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.debug.test/src/net/bioclipse/cdk/deb​ug/test/CDKDebugManagerPluginTest.java: Use the proper way for setting up managers in PluginTests
13:29 egonw so, if you make only the slightest change to CDKManager or ICDKManager, you better make sure to run the unit tests
13:32 egonw same for CDKDebugManager
13:35 rojasm1 joined #bioclipse
13:35 CIA-55 bioclipse: egonw * r9031 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.debug.test/src/net/bioclipse/cdk/deb​ug/test/CDKDebugManagerPluginTest.java: Added trick to ensure the managers are properly loaded
13:58 masak (Add CVS Repository dialog)++
13:58 masak I pasted :pserver:anonymous@jmathtools.cvs.sourceforge.net:/cvsroot/jmathtools
13:59 masak and it threw everything in the proper input box!
13:59 masak amazing.
14:00 maclean that is nice, isn't it
14:02 masak aye, very much so.
14:04 CIA-55 bioclipse: egonw * r9032 /bioclipse2/trunk/plugins/net.​bioclipse.inchi.business.test/ (2 files in 2 dirs): Use the proper way for setting up managers in PluginTests
14:05 masak egonw: what does "juck" mean?
14:06 egonw dunno
14:06 masak ok.
14:06 masak nvm.
14:08 maclean "yuck"
14:08 maclean (from the context)
14:08 masak makes sense.
14:09 grandm44_ joined #bioclipse
14:29 CIA-55 bioclipse: egonw * r9033 /bioclipse2/trunk/plugins/net.bioclipse.cml.tests/ (3 files in 3 dirs): Added missing plugin test
14:30 egonw olass: ping
14:30 olass pong
14:30 egonw please see the wiki...
14:30 egonw regarding the manager unit testing...
14:30 egonw good to go
14:31 egonw I'm now onto running the gists
14:31 olass nice work
14:31 olass will check
14:31 olass @wiki
14:31 olass zarah: you don't know the bioclipse wiki?
14:31 zarah olass: excuse me?
14:31 egonw http://wiki.bioclipse.net/index.php?title​=List_of_stable_managers_in_bioclipse_2.0​#ValidateCMLManager__-_Responsible:_Egon
14:31 zarah egonw's link is also http://tinyurl.com/68dyxn
14:31 egonw http://wiki.bioclipse.net/index.php?title​=List_of_stable_managers_in_bioclipse_2.0
14:31 zarah egonw's link is also http://tinyurl.com/68dyxn
14:31 olass aah, egonw - my personal bot :-)
14:32 * egonw just likes beta3 to be release today
14:32 olass egonw++
14:32 egonw olass: please with RDF Feature on the main update site
14:32 olass but I have one thing
14:32 olass that Gpox is working on
14:32 olass that I REALLY want in beta3
14:32 egonw ah, that's why he is so silent
14:33 olass he's rewriting the moltable
14:33 olass looks really promising
14:33 egonw excellent...
14:33 egonw new features in 2.0
14:33 olass so might wait one more day
14:33 olass sorry?
14:34 egonw nvm
14:34 olass egonw: about the JCPManager unit tests...
14:34 egonw yes?
14:34 egonw it is possible...
14:34 olass should we have these in 2.0?
14:34 egonw no
14:34 olass ok
14:34 olass will move it down then
14:34 egonw because that's so much GUI, we know when it works or not
14:35 olass yes
14:35 egonw it's sooooo visible
14:35 olass will move to unstable managers
14:35 egonw no, please don't
14:35 olass oh?
14:35 egonw it's just junit untested
14:35 egonw but it is used
14:35 egonw the manager is used
14:35 olass hmm, ok
14:36 olass just because it is used does not mean it's stable :-)
14:36 olass page should say "tested managers"
14:37 egonw or you could leave it as is
14:37 olass yup
14:37 olass will do
14:37 egonw because not tested does not mean unstable either
14:37 olass right
14:39 edrin joined #bioclipse
14:42 maclean egonw : is there a reason that I should not use DefaultChemObjectBuilder in the net.bioclipse.cdk.jchempaint plugin?
14:42 egonw yes
14:42 egonw because we need that code to be implementation free...
14:42 egonw and only depending on cdk.interfaces
14:42 olass egonw: I get PZ error
14:42 egonw that's really, really important
14:43 olass I can't set component
14:43 egonw yeah, google is at is again...
14:43 olass the combo is blank
14:43 maclean sigh
14:43 egonw refresh bug
14:43 olass egonw: how to resolve that?
14:43 egonw maclean: what's the problem?
14:46 maclean egonw: I want to make a new chem model (or an IChemModel)
14:53 maclean but I guess I just can't do that.
15:07 shk3 seems pelezilla is down
15:07 shk3 and the svn server
15:09 maclean yup, pelezilla has been having problems - backlog
15:11 masak Google is attacking us today.
15:15 egonw shk3: try again
15:15 egonw maclean: where?
15:15 stain but gmail is back!
15:15 egonw maclean: in general... someChemObject.getBuilder().newChemObject()
15:16 maclean egonw: I'm working round it
15:16 maclean yes, that's fine if you have someChemObject...
15:16 egonw if you do not... then the API is broken
15:16 egonw (wrt to that design goal)
15:16 egonw maclean: where is it?
15:17 maclean in the editor.
15:17 maclean jcp editor
15:17 egonw in bioclipse?
15:17 egonw or in the JCP app?
15:17 maclean yes, in bioclipse
15:17 egonw JCPEditor?
15:17 egonw which line?
15:18 maclean lines on my computer, not in svn
15:18 maclean you can't set up a hub with a blank chem model
15:19 egonw OK...
15:19 egonw in the JCP code you must not use DefaultCOB
15:19 egonw but, and code outside the CDK code base, using a builder is fine
15:19 egonw such as the JCPEditor...
15:19 egonw but please use the NoNotificationChemObjectBuilder instead
15:21 maclean what do you think about altering the hub very slightly to handle adding null ChemModels?
15:21 maclean hmmm. it's a little unappealing actually
15:21 egonw please explain
15:22 maclean well, if you can't create an IChemModel, you can't create a hub
15:23 maclean but you could still create a hub with a null model, and then lazily generate it if you tried to add to a null model
15:23 egonw it's OK for the JCPEditor to use NoNotificationChemObjectBuilde​r.getInstance().newChemModel()
15:24 maclean oh
15:24 maclean ok, well I'll do that then.
15:24 maclean but the hub does need to be able to handle more than chemModels, at some point, so the idea is not wasted
15:25 egonw the hub can use .getBuilder().netBla()
15:25 egonw should, must
15:25 * maclean reverts local hub changes
15:25 maclean egonw : indeed.
15:27 maclean hub.addAtom(IAtom atom) {  getContainerForAtom(atom).addAtom(atom); }
15:27 CIA-55 bioclipse: egonw * r9034 /bioclipse2/trunk/plugins/net.bioclipse.jmol/src​/net/bioclipse/jmol/business/IJmolManager.java: Clarified that these methods require an active editor
15:27 maclean Hub::getContainerForAtom(IAtom atom) { if (chemModel == null) return atom.getBuilder().newAtom(); }
15:28 CIA-55 bioclipse: egonw * r9035 /bioclipse2/trunk/plugins/net.bioclipse.jmol/sr​c/net/bioclipse/jmol/business/JmolManager.java: Throw a meaningfull error when there is no (required) active Jmol editor (addresses #563)
15:28 zarah bug #563 | http://tinyurl.com/byv2he
15:29 egonw maclean: I think you'll also have to bootstrap a new IAtomContainer...
15:29 maclean oh, indeed, yes
15:30 maclean it would be easier to extend that pattern for hubs that contain reactions, reactionsets, crystals...
15:30 maclean (easier than the current, that is)
15:32 egonw what pattern?
15:33 maclean getContainerForAtom(IAtom), getContainerForBond(IBond)...
15:33 maclean although....
15:34 maclean anyway - I'm not doing any of that yet, so don't worry about it now :)
15:34 maclean and I say "yet" - I don't intend to make such changes  - just a suggestion.
15:49 egonw OK :)
15:52 egonw got to run to catch the bus
16:07 CIA-55 bioclipse: gilleain * r9036 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Changed the access level of variables from package protected (default), to private.
16:12 olass maclean: around?
16:13 olass I want to report a bug but have difficulties writing it down
16:13 olass could you work together with me?
16:14 olass hmm, I guess I can write it down...
16:14 olass ok, will try
16:16 shk3 maclean is talking to christoph
16:16 shk3 live
16:16 olass ok
16:21 olass maclean: filed bug #590 for you
16:21 olass let me know if the description is unclear
16:25 maclean ok
16:26 maclean "(makes him aggressive")? - is this personal experience?
16:27 olass :-)
16:29 maclean f) Click cleanup...
16:30 maclean Arvid's addAtom module did allow you to choose the direction, it's just that people didn't like that either...
16:31 * maclean is starting to notice a trend here...
16:31 maclean the compromise position is to use "sprout-hold".
16:31 maclean where if you just click on an atom, you get a sprouted bond
16:32 maclean if you click and hold, you get a bond that can be manipulated
16:32 maclean maybe I should write this down in the bug report.
16:54 egonw joined #bioclipse
16:54 egonw hej
16:58 maclean hej
17:02 egonw and bye again
17:02 egonw dinner
17:05 steinbeck joined #bioclipse
17:10 ChanServ joined #bioclipse
17:15 CIA-55 bioclipse: carl_masak * r9037 /bioclipse2/trunk/plugins/ (2 files in 2 dirs):
17:15 CIA-55 bioclipse: removed last traces of 'net.bioclipse.rhino'
17:15 CIA-55 bioclipse: The plugin.xml consisted of a commented out mention, it turned out. Removed
17:15 CIA-55 bioclipse: all commented-out things from that file. The exsd file seems to simply be
17:15 CIA-55 bioclipse: a fossil; scripting things run fine in bc2 without it.
17:29 CIA-55 bioclipse: egonw * r9038 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business/src/net/bioclipse/cdk/d​omain/CDKMoleculePropertySource.java: Added IChemObject.properties to the Properties view (fixes #519)
17:29 zarah bug #519 | http://tinyurl.com/cbtmyh
17:45 CIA-55 bioclipse: shk3 * r9039 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/ne​t/bioclipse/ui/ApplicationActionBarAdvisor.java: removed the switch workspace. see bug #476 for discussion
17:45 zarah bug #476 | http://tinyurl.com/b3pgu7
17:47 CIA-55 bioclipse: shk3 * r9040 /bioclipse2/trunk/plugins/net.bioclips​e.cml/src/net/bioclipse/cml/managers/ (IValidateCMLManager.java ValidateCMLManager.java): made the manager stateless
17:47 CIA-55 bioclipse: shk3 * r9041 /bioclipse2/trunk/plugins/net.bioclips​e.cml/src/net/bioclipse/cml/managers/ (IValidateCMLManager.java ValidateCMLManager.java): formatting
17:53 CIA-55 bioclipse: shk3 * r9042 /bioclipse2/trunk/plugins/net.bioclipse.cml/src/ne​t/bioclipse/cml/managers/ValidateCMLManager.java: removed unused code
18:02 CIA-55 bioclipse: shk3 * r9043 /bioclipse2/trunk/plugins/n​et.bioclipse.spectrum/src/ (2 files in 2 dirs): moved method
18:03 CIA-55 bioclipse: shk3 * r9044 /bioclipse2/trunk/plugins/net.biocl​ipse.specmol/src/net/bioclipse/spec​mol/business/SpecmolManager.java: moved method
18:04 CIA-55 bioclipse: shk3 * r9045 /bioclipse2/trunk/plugins/net.biocli​pse.nmrshiftdb/src/net/bioclipse/nmr​shiftdb/wizards/PredictWizard.java: moved method
18:25 CIA-55 bioclipse: shk3 * r9046 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.ui/src/net/bioclipse/cdk/ui/handlers/ (Create2dHandler.java Create3dHandler.java): solves bug #571 (double warning if overwrite)
18:25 zarah bug #571 | http://tinyurl.com/dl6sdb
19:50 edrin left #bioclipse

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary