Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-07-03

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All times shown according to UTC.

Time Nick Message
04:26 masak joined #bioclipse
07:16 shk3 joined #bioclipse
07:19 rojasm joined #bioclipse
07:28 Gpox joined #bioclipse
07:32 egonw joined #bioclipse
07:36 edrin joined #bioclipse
07:36 edrin hi again
07:47 shk3 hi
07:52 egonw hi shk3
07:52 egonw shk3: please check the bug report I filed yesterday with Bioclipse
07:52 egonw your AtomEditor API changes broke the BC2 JCP editor
07:52 egonw and I do not know how to fix it, so need your feedback
07:52 egonw (or fix)
07:56 olas joined #bioclipse
07:56 olas hi all
07:57 jonalv joined #bioclipse
07:57 egonw hi olas
07:58 shk3 hi alas
07:58 shk3 olas
07:58 egonw shk3: how did you fix the problem?
07:58 shk3 egonw: bug solved
07:59 shk3 by properly adjusting the constructor
07:59 egonw excellent, thanx
07:59 jonalv hi all
07:59 egonw hi jonalv
08:00 shk3 just updated bc2 and get a lot of errors
08:00 shk3 core problem seems to be that in net.bc.core
08:01 shk3 everything with org.springframework isn't found
08:01 shk3 how do I add this?
08:01 jonalv set target platfrom
08:02 shk3 that's in?
08:03 jonalv in net.bioclipse.target.platform open the target-platfrom.target
08:03 jonalv click Set as Target Platform in the upper right corner of the editor that opens
08:03 olas shk3: my room telephone at BMC is +46-18-4714281, or from a local BM;C phone just 4281. My cellphone: +46-70-4250628
08:03 olas since you asked earlier :-)
08:04 shk3 yeah, thanks
08:04 shk3 remember the building was pretty large...
08:04 shk3 so might help in finding you
08:06 shk3 wow, errors gone
08:06 shk3 that's what I call "properly working setup"
08:09 jonalv shk3: Can you run bioclipse 2 now without errors on the console and with managers in the javascript console?
08:11 shk3 no
08:11 shk3 sorry
08:11 shk3 i can't run it at all
08:11 shk3 "no application id found"
08:11 jonalv olas: can we clean away the testCNF project?
08:12 jonalv shk3: Are you running the setup from the product in net.bioclipse.ui?
08:13 shk3 zes
08:14 shk3 just updating the classpath, perhaps that helps
08:14 shk3 no
08:15 shk3 apart from the app id not found
08:15 shk3 i get lots of
08:15 shk3 bundle X has already been installed
08:18 jonalv shk3: please paste complete log and I will have a look. Might find something :)
08:19 shk3 where to paste?
08:21 olas pastebin?
08:21 olas paste2
08:22 shk3 http://pastebin.com/d1a64e095
08:22 shk3 but be warned: it's a lot
08:23 olas shk3: are you using ganymede?
08:23 olas 3.4?
08:23 shk3 no
08:23 shk3 shall I update?
08:23 olas then there's your problem
08:24 olas go get it from eclipse.org
08:24 shk3 ah, missed that
08:24 olas not update
08:24 olas dl
08:24 olas that is the poit of all this :-)
08:24 shk3 yeah, well, update
08:24 olas no
08:24 olas download
08:24 olas update is not an option
08:24 shk3 but I can reuse my workspace, can't I?
08:24 olas probably :-)
08:24 shk3 ok, getting the new version is still an update
08:24 olas nothing is certain in the Eclipse world
08:24 shk3 isn't it?
08:25 olas just wanted to be clear: do not use the update in Eclipse
08:25 shk3 thanks, got that
08:25 olas so if you say update, I'd say you would use the update function
08:25 olas :-)
08:26 egonw olas: huh? so, we now actually need 3.4?
08:27 egonw for bc2?
08:27 shk3 ah, you missed it as well
08:27 egonw yes
08:32 olas hmm
08:32 olas maybe I wasn't as expressive in my mail to bc-devel
08:32 jonalv shk3: I am helping olas with some problems now. gonna check your trace later...
08:32 olas but the thought is, yes, we will require development with Eclipse 3.4 as soon as the new target platform is there
08:33 olas it might work with 3.2
08:33 olas oh 3.3
08:33 olas but no guarantee
08:34 jonalv olas: lol now I get anotehr strange error at my machine...
08:34 olas hmmmmm
08:35 olas I get the feeling that the new TP is not 100% ready yet...
08:35 shk3 jonalv: thanks anyway
08:35 shk3 don't worry, we can sort things out on monday anyway
08:39 egonw TP?
08:39 jonalv target platfrom I am guessing... :)
08:39 egonw ah, ic
08:40 egonw anyway, so I should use 3.4 for further testing, not 3.3, right?
08:40 egonw my stacktraces yesterday were based on 3.3
08:41 jonalv egonw: I am running 3.4. I don't see any reason why it shouldn't work on 3.3 but there might be some differences that I can't think of now...
08:41 jonalv I think we have enough troubles as it is and that we should run the same version of eclispe at least :)
08:42 jonalv And after all it's time to take the step isn't it? :)
08:42 egonw right
08:43 jonalv okey now it works for me again. I didn't do anything different at all...
08:48 shk3 hm, new errors in eclipse 3.4
08:48 shk3 The System Bundle's start level can not be modified.
08:49 shk3 Platform not running
08:49 shk3 http://pastebin.com/d57e3a97e
08:49 shk3 in case somebody wants to have a look
08:51 egonw jonalv: on 3.4, I get upon structuredb + require -> validate, the 'problems' .usermanager -> package uses conflict: Require-Bundle: org.springframework.bundle.sptring.aop; bundle-version="0.0.0"
08:52 egonw jonalv: but it boots fine
08:52 egonw without any stack traces
08:52 egonw jonalv++
08:53 egonw structuredb. TAB works too
08:53 egonw olas: would be good to send a message around to -user too, about 3.4 required for BC2 branch
08:53 olas yup
08:53 olas when it works, yes
08:54 egonw structuredb + required works fine so far
08:54 olas egonw: please read
08:54 olas http://pastebin.com/m5e08c14
08:54 egonw INFO - A new local instance of Structuredb namedbla has been created
08:54 egonw (missing space)
08:55 egonw olas: ack
08:55 olas so i DID write it
08:55 olas but maybe I wasn't explicit enough
08:55 egonw "
08:55 egonw #
08:55 egonw I will email here after the
08:55 egonw #
08:55 egonw update is complete.
08:55 egonw "
08:55 olas jonal did email
08:55 egonw from that email
08:55 olas jonalv
08:55 egonw so, I was awaiting a confirm :)
08:56 olas from me?
08:56 olas jonalv is the TP master here
08:56 egonw from the email you put on pastebin
08:56 olas sure
08:56 jonalv egonw: glad to hear that something finally works :)
08:56 * olas prefers to drop this conv
08:57 jonalv shk3: that's the same error I had a few minutes ago. When I retried from the product it wasn't there any longer and all just worked...
08:57 jonalv I wonder if there might be some therad raceing during boot...
08:57 jonalv ANd some thread get's done to quick when that error arises...
08:58 jonalv but that's just a guess...
08:58 shk3 sorry, retrying doesn't help
08:58 olas delet run config?
08:58 olas or add req plugins in run config?
08:59 shk3 hm, what i did was renunning this set as targer platform
08:59 shk3 now i get
08:59 shk3 ClassDefNotFound org/eclipse/swt/SWTError
08:59 shk3 and
08:59 shk3 The activator net.bioclipse.ui.Activator for bundle net.bioclipse.ui is invalid
09:00 egonw mmm...
09:00 egonw try PDE -> udpate classfix, and Menu -> Project -> Clean
09:02 shk3 doesn't help
09:02 shk3 still the same
09:03 masak shk3: I have your error, too
09:05 jonalv okey so this is the status now:
09:05 jonalv shk3, masak: have the error about run level. I had that but it dissapered when I tryed to track it down
09:06 jonalv Gpox: has no error at all
09:06 * jonalv has no error at all
09:06 shk3 sorrry, no.
09:06 jonalv olas: has some strange problem with cdk not starting correctly
09:06 shk3 I proceeded to other errrors
09:06 jonalv shk3: okey?
09:06 * jonalv is not keeping up :)
09:06 shk3 org.osgi.framework.BundleException: The activator org.eclipse.ui.internal.WorkbenchPlugin for bundle org.eclipse.ui.workbench is invalid
09:06 shk3 and classdefnot found
09:07 egonw shk3: can you try just:
09:07 shk3 no idea why
09:07 egonw deselect all plugins + structuredb + required
09:07 shk3 sure i can try
09:07 egonw does that work?
09:07 shk3 in the run config_
09:07 shk3 ?
09:07 egonw yes, run config dialog, 'plugins' tab
09:08 shk3 which should be left?
09:08 egonw just structuredb
09:08 egonw only structuredb
09:08 shk3 that's enough?
09:08 egonw then hit the 'add required' buttong
09:08 shk3 ok
09:08 shk3 ah, ok
09:09 shk3 net.bioclipse.usermanager has a package conflict
09:09 egonw yes, had that too...
09:09 shk3 i try running nevertheless
09:09 egonw ignore it for now
09:09 egonw yes, please do
09:10 egonw and check the Eclipse console for stacktraces
09:10 shk3 jupp
09:10 egonw I got none
09:10 shk3 so do i
09:10 shk3 i even have modules on the console
09:10 shk3 cdk  clear  molecule  services  structuredb  userManager
09:10 shk3 great
09:10 shk3 thanks for your help
09:11 shk3 not sure what exactly did it
09:11 shk3 but it works
09:12 jonalv could I get some feedback on the command: "help structuredb" or in genereal help <any manager>
09:12 egonw a bit short, I'd say :)
09:12 shk3 help structuredb gives me a fairly long explanation
09:12 egonw long?
09:13 egonw maybe I should update...
09:13 shk3 well, lots of methods
09:13 egonw anyway...
09:13 egonw back into work mode
09:13 shk3 long is relative
09:15 jonalv yea, I was working on this yesterday but I am not quite sure about what we want...
09:16 egonw integration with the Help view
09:16 egonw umm... that thing we used for tutorials
09:16 egonw in BC1
09:16 shk3 is it supposed to replace html help?
09:17 * egonw thinks the 'help' command should trigger opening that view
09:17 egonw what was the name again... ?
09:17 shk3 would be an option
09:17 egonw CheatSheets
09:18 EskilA joined #bioclipse
09:19 shk3 but there is the "normal" help as well
09:19 shk3 isn't it?
09:19 shk3 that's different from cheat sheets
09:19 egonw yes, different
09:24 shk3 ok, thanks. I will got to the mensa and probably be in the chat in the afternoon.
09:24 shk3 in any case tomorrow
09:24 egonw bye
09:24 shk3 will work on the cdk plugin, so I know features of bc2 till monday
09:24 olas shk3: sounds great
09:24 olas we'll be here in the afternoon as well
09:26 jonalv ah I ahve totally forgotten about the Eclipse help system. Maybe we want that too. The thing with this help system is that it is all written directly in the interface for the managaer
09:26 jonalv so it's easy to remember to update it when changes are made
09:27 egonw don't undertsand what you mean
09:28 jonalv since these help texts are in the managers interface file they are easier to keep up to date
09:30 egonw yeah, that would have to be split out...
09:30 egonw the nice things of CheatSheets is, that they can do 'actions' too...
09:30 egonw such as run tihngs on the console
09:31 jonalv the interface looks like this: http://tinyurl.com/5n9tlb
09:32 egonw ah, using annotation...
09:32 jonalv yea
09:33 egonw well, that should be easy to convert to HTML
09:33 jonalv yea, we can have both :)
09:33 egonw rigth
09:33 egonw and have a build script make the HTML
09:34 egonw btw, the dbs will show up in a virtual folder, not?
09:34 egonw if only to see them show up upon creating
09:34 jonalv egonw: it's in  the service view at the moment
09:34 egonw ah, ok
09:35 jonalv please have a look :)
09:35 egonw will do next week, ok?
09:35 jonalv sure :)
09:35 egonw need to finish a report before 12:30
09:56 olas egonw: virtualView is only for virtual resources that are serializable to byte[]
09:56 olas instead of files
09:56 olas so virtualView will not have resources such as Web services or db's
09:57 egonw ok
09:57 olas at least that is how we envisioned it
09:57 egonw intuitively, I'd see a db show up as resource
09:57 egonw but I understand
10:04 olas we could see it that way in future versions
10:04 olas but there's a big difference with a db like StructureDB and a public repo, like ArrayExpress or Genebank
10:05 olas but you could be right that we could have DB's in different places
10:06 egonw yeah, true
10:06 egonw there is so much new in BC2, that I keep loosing the oversight
10:06 egonw sorry about that
10:09 olas no, it's a good question and a good proposal
10:09 olas that design is probably the hardest in bc2
10:09 olas how do people want to work?
10:09 olas it's something that time will tell I assume
10:09 egonw right
10:56 jonalv joined #bioclipse
10:56 * jonalv back from lunch :)
10:56 jonalv my computer had run out of battery... :(
11:09 jonalv http://markmail.org/message/4xaihd5sbryxrh6l
11:13 * jonalv also has the System Bundle's start level error now... :/
11:47 edrin left #bioclipse
12:10 EskilA joined #bioclipse
12:11 edrin joined #bioclipse
13:05 shk3 joined #bioclipse
13:05 shk3 f***, errors again in Bioclipse
13:06 olas monday, monday
13:06 olas the solution seems to be: set target platform
13:06 olas every time you boot eclipse :-(
13:06 olas jonalv promised to email eclipse ML about it and ask
13:06 shk3 will try
13:09 shk3 hm, increases errors from 49 to 853
13:09 shk3 rebuild doesnÄ
13:09 shk3 't help
13:10 egonw joined #bioclipse
13:10 jonalv olas: right, I might have done that. Please keep remining me :)
13:10 zarah joined #bioclipse
13:11 jonalv hi zarah
13:11 zarah jonalv: You have new messages. Write '@messages' to read them.
13:11 jonalv zarah: messages
13:11 zarah jonalv: masak said border det här funka först?
13:11 masak oops
13:11 masak jonalv: write something again
13:11 jonalv soething again
13:12 masak I should probably do an extra save of the messages file once messages are reported
13:12 jonalv zarah: tell masak it seems to work :)
13:12 masak hold on
13:12 zarah Consider it noted.
13:12 zarah masak: You have new messages. Write '@messages' to read them.
13:12 masak @massages
13:12 zarah masak: jonalv said it seems to work :)
13:12 masak @tell jonalv except if you do a restart between a @messages and a @tell. subtle bug :)
13:13 zarah Consider it noted.
13:13 jonalv zarah: tell me...
13:13 zarah Consider it noted.
13:13 zarah jonalv: You have new messages. Write '@messages' to read them.
13:13 jonalv zarah: messages
13:13 zarah jonalv: masak said except if you do a restart between a @messages and a @tell. subtle bug :)
13:14 jonalv zarah: seen shk3
13:14 zarah I have not seen shk3
13:14 jonalv zarah: seen shk3?
13:14 zarah I have not seen shk3
13:14 olas @tell egonw: he has a question for you on #cdk
13:14 zarah Consider it noted.
13:15 jonalv olas: that was evil... How is egonw to know who he is?
13:17 shk3 I am here
13:17 masak @seen shk3
13:17 egonw jonalv: no worries... I know who I am :)
13:17 zarah shk3 was last seen 2008-07-03T13:17:06 in #bioclipse saying 'I am here'
13:17 zarah masak: You have new messages. Write '@messages' to read them.
13:18 egonw @messages
13:18 zarah egonw: You have no new messages.
13:18 egonw mmm...
13:18 masak hm?
13:18 egonw yeah, ola asked zarah to relay a message
13:18 shk3 @messages
13:18 zarah shk3: You have no new messages.
13:18 egonw but zarah did not do it
13:18 masak ah, olas wrote 'egonw:'!
13:18 masak gotta fix that
13:18 egonw ah, ic
13:18 shk3 hä?
13:18 shk3 what's all this?
13:19 masak shk3: we have a bot
13:19 masak zarah: hi
13:19 zarah hello masak :)
13:19 egonw zarah: how old are you?
13:19 olas masak++ for bringing zarah here
13:19 olas karma masak
13:19 zarah masak has a karma of 3
13:19 olas olas++
13:19 zarah shame on you, olas, giving yourself karma like that
13:19 egonw karma egonw
13:19 zarah egonw has a karma of 0
13:19 masak actually it was jonalv++ who brought zarah here
13:19 egonw oi...
13:19 masak egonw: everyone starts at 0
13:19 egonw how does one get karma?
13:19 masak egonw++
13:20 egonw commits ?
13:20 olas no
13:20 masak karma egonw
13:20 zarah egonw has a karma of 1
13:20 egonw ah...
13:20 egonw egonw++
13:20 zarah shame on you, egonw, giving yourself karma like that
13:20 egonw egonw++
13:20 zarah shame on you, egonw, giving yourself karma like that
13:20 egonw egonw++
13:20 zarah shame on you, egonw, giving yourself karma like that
13:20 masak egonw: I've thought of connecting it to commits
13:20 egonw hahahah
13:20 olas how much karma does one need to get a toffifee?
13:20 olas 10?
13:20 masak olas: 0
13:20 egonw good question!
13:20 jonalv masak: We really should parse commits and give a karma per commit
13:21 olas only good commits
13:21 jonalv masak: you should, that... :)
13:21 masak jonalv: yes
13:23 masak zarah: restart
13:23 zarah joined #bioclipse
13:23 egonw zarah: restart
13:23 zarah egonw: You have new messages. Write '@messages' to read them.
13:23 egonw @messages
13:23 zarah egonw: olas said he has a question for you on #cdk
13:23 masak egonw: I fixed that
13:23 egonw nice
13:23 masak egonw: oh, and you can't restart
13:23 masak :)
13:23 olas who can?
13:23 egonw yeah, just testing DOS attacks :)
13:23 masak only jonalv and I
13:24 masak of course, if you want to be able to restart zarah, just change the source and restart zarah >:-)
13:25 jonalv the restart commando performs svn up :)
13:25 masak yes, we're very proud
13:25 masak jonalv++
13:27 jonalv masak++
13:27 egonw blah
13:28 jonalv lol
13:28 masak :)
13:30 olas masak--
13:30 olas jonalv--
13:31 masak hey! :)
13:31 olas you canät give yourself too much karma!
13:31 masak hahah
13:31 olas please update zarah to not accept karma from people in same room
13:31 masak olas: wut?
13:31 jonalv olas: huh??
13:31 olas mek is not on IRC!
13:31 olas that way I loose karma...
13:32 jonalv LOL
13:32 masak olas: gissa vem som sitter karma-datafilen, förresten :)
13:32 masak oops.
13:32 masak wrong lang
13:35 olas and wrong subject too
13:35 olas :O
13:36 egonw public Iterator<ICDKMolecule> creatConformerIterator( InputStream instream );
13:36 egonw typo
13:38 masak egonw: looks good to me
13:38 egonw creatEConformerIterator
13:38 masak ah
13:39 masak yes
13:46 jonalv karma zarah
13:46 zarah zarah has a karma of 5
13:47 masak not bad
13:48 masak zarah: dz you're a very popular bot, you :)
13:48 zarah no, YOU'RE the cute one! :)
13:48 masak :)
13:51 olas zarah: dz
13:51 zarah you're welcome, olas :)
13:51 egonw dz?
13:52 olas danke zshön?
13:52 olas @tell masak please explain dz for egonw
13:52 masak egonw, olas: dziekuje
13:52 zarah Consider it noted.
13:52 zarah masak: You have new messages. Write '@messages' to read them.
13:52 masak @msg
13:52 zarah masak: olas said please explain dz for egonw
13:52 masak I did.
13:53 olas zarah: please don't tell masak things he alredy said
13:53 olas zarah: is that ok?
13:53 masak actually it's dziękuje
13:53 masak but who's counting?
13:54 egonw btw, did you see: http://cdk.sourceforge.net/maps/people/
13:54 zarah egonw's link is also http://tinyurl.com/459djg
13:54 egonw (plug, plug)
13:54 egonw oh, zarah, thanx
13:54 masak @thanks
13:54 zarah you're welcome, masak :)
13:54 * egonw wonders what the tinyurl.com business model is
13:55 masak 1. short urls
13:55 masak 2. ???
13:55 masak 3. profit!
13:55 egonw 1. spend money
13:55 egonw 2. no return
13:55 egonw 3. no profit!
13:55 egonw maybe user profiles?
13:55 masak :)
13:56 masak they do carry some ads
13:56 masak and they do accept donations
13:57 olas and no work involved
13:57 masak pretty neat, actually
13:58 egonw ads?
13:58 egonw it does just refer, not?
13:59 egonw oh, upon making the url
14:00 masak unless you're a bot, I guess
14:00 egonw rigth :)
14:00 egonw or using a helper script of any other kind
14:05 egonw zarah: will you support bioclipse.core annotation? for on-IRC user help?
14:05 masak egonw: interesting idea_
14:06 egonw not really bc2 core business, though
14:06 egonw that is, not really important at this stage, I'd say
14:06 masak egonw: we discussed a mini-database of terms the other day
14:06 masak like this:
14:06 egonw not so many users hang out here anyway
14:06 masak @desc bioclipse
14:06 egonw yeah. that would be fairly cheap
14:06 masak also:
14:06 masak @google eclipse target platform
14:06 zarah I can't do that; complain with masak and jonalv
14:06 masak yeah :/
14:26 * egonw is going to make a commit, and hopes it shows up on his FF account: http://friendfeed.com/egonw
14:34 olas got bc2 3.4 to work
14:34 olas somehow it didn't like me stripping plugin.xml, even though it's empty!
14:34 jonalv olas: w00t
14:34 olas after monday will be release
14:34 olas alpha
14:34 masak olas: "stripping" plugin.xml?
14:34 olas where's our commit bot?
14:34 masak you emptied it completely?
14:35 olas @explain strip
14:35 masak "to remove one's clothes, slowly"
14:35 olas should give wikipedias definition of a word
14:35 masak :)
14:35 olas the strip
14:35 olas that's in vegas
14:35 olas what a coincidence!
14:36 masak indeed
15:20 egonw olas: I am moving all non test files from cdk/src/data into cdk/src/main
15:20 egonw olas: something else...
15:20 edrin left #bioclipse
15:21 egonw is it really the only option to not export src/test by removing it from the build path?
15:53 egonw @tell olas you can remove src/data from the export
15:53 zarah Consider it noted.
15:53 egonw @tell olas it should now only contain test files, no runtime data anymore
15:53 zarah Consider it noted.
15:53 * egonw is leaving
15:53 egonw bye all
16:15 masak egonw++
16:33 olas @msg
16:33 zarah olas: egonw said you can remove src/data from the export
16:33 zarah olas: egonw said it should now only contain test files, no runtime data anymore
16:33 olas @tell olas++
16:33 zarah shame on you, olas, giving yourself karma like that
16:33 zarah Consider it noted.
16:33 olas @msg
16:33 zarah olas: You have no new messages.
16:33 olas damn
16:34 olas @tell egonw egonw++
16:34 zarah Consider it noted.
16:34 olas @tell olas olas++
16:34 zarah shame on you, olas, giving yourself karma like that
16:34 zarah olas: You can tell yourself!
16:34 olas @msg
16:34 zarah olas: You have no new messages.
16:34 olas :-(
16:34 olas left #bioclipse
16:34 masak hahahah
16:35 jonalv zarah: tell masak jonalv++
16:35 zarah shame on you, jonalv, giving yourself karma like that
16:35 zarah Consider it noted.
16:35 jonalv karma
16:35 zarah has a karma of 0
16:35 jonalv karma jonalv
16:35 zarah jonalv has a karma of 2
16:36 masak zarah: restart
16:36 zarah joined #bioclipse
16:36 masak @messages
16:36 zarah masak: You have no new messages.
16:36 masak :D
16:36 jonalv zarah: tell masak jonalv++
16:36 zarah shame on you, jonalv, giving yourself karma like that
16:36 zarah Consider it noted.
16:37 masak karma jonalv
16:37 zarah jonalv has a karma of 2
16:37 zarah masak: You have new messages. Write '@messages' to read them.
16:37 masak @msg
16:37 zarah masak: jonalv said jonalv++
16:37 masak karma jonalv
16:37 zarah jonalv has a karma of 2
16:37 masak haha!
16:46 jonalv it was worth a try... :)
19:29 egonw joined #bioclipse
19:30 egonw moin
19:30 zarah egonw: You have new messages. Write '@messages' to read them.
19:30 egonw @messages
19:30 zarah egonw: olas said egonw++
19:30 egonw karme
19:31 egonw karma egonw
19:31 zarah egonw has a karma of 3

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