Camelia, the Perl 6 bug

IRC log for #bioclipse, 2007-10-11

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All times shown according to UTC.

Time Nick Message
00:32 bjarni joined #bioclipse
01:04 EskilA joined #bioclipse
01:04 EskilA left #bioclipse
06:35 viklund Oops, forgot to logout y-day...
07:16 thomas_ku joined #bioclipse
07:39 egonw joined #bioclipse
08:21 jonalv joined #bioclipse
08:21 masak joined #bioclipse
08:32 EskilA joined #bioclipse
08:39 viklund Going down, to upgrade my computer with a new harddrive. 750Gb YAY!!
08:39 olas joined #bioclipse
08:39 olas hi
08:39 egonw hi olas
08:39 olas hi egonw
08:40 egonw we need a Commit Digest service...
08:40 olas was it fun at Nature HQ?
08:40 EskilA helo
08:40 egonw olas: yes, Nature HQ was great
08:40 olas did you meet with PMR?
08:41 egonw no, why?
08:41 CIA-31 bioclipse: ospjuth * r3958 /trunk/playground/plugins/net.bioclipse.ta​verna.ui/src/net/bioclipse/taverna/model/ (5 files in 2 dirs): Added a TavernaModel with PropertySource
08:41 egonw I did not visit Cambridge at all
08:41 olas oh, just thought you would
08:41 olas oh, ok
08:43 CIA-31 bioclipse: ospjuth * r3959 /trunk/playground/plugins/net.bioclipse.taverna.​ui/src/net/bioclipse/taverna/ui/Activator.java: Added logging to Activator
08:43 CIA-31 bioclipse: ospjuth * r3960 /trunk/playground/plugins/net.bioclipse.tave​rna.ui/src/net/bioclipse/taverna/ui/editors/ (. TavernaEditor.java TavernaEditorContributor.java): Started working on an MPE for Taverna WF.
08:44 CIA-31 bioclipse: ospjuth * r3961 /trunk/playground/plugins/​net.bioclipse.taverna.ui/ (META-INF/MANIFEST.MF plugin.xml): Updated manifest for editor + resource
09:10 viklund joined #bioclipse
09:11 viklund Back
09:12 thomas_ku olas: do make progress with the taverna plugin?
09:16 egonw scripting laguage request: JRuby (see depth-first.com)
09:26 masak egonw: looks interesting
09:26 masak color-coded Ruby always looks so nice
09:31 masak egonw: JRuby is on its way into Bioclipse
09:31 masak I'm working on that
09:32 egonw happy to hear that
09:32 masak along with BeanShell, Groovy and better Rhino integration
09:33 egonw what is the ETA?
09:34 masak egonw: for full support, same as Bioclipse2
09:34 egonw ack
09:34 masak right now I'm trying to get as much into the current Bioclipse as possible
09:35 masak toying with command shells, mostly, which is fairly unsupported on the Eclipse platform
09:37 masak lunch &
09:41 olas thomas_ku: Making progress with tavenra in Bioclipse
09:41 olas got execution working
09:41 olas rendering still not fully working, but should be able to sort that out
09:41 olas will need to work on an MPE for taverna and actions to execute it
09:42 olas problems are mostly how to get input into the WF
09:42 olas Will need to write support for DataThing...
09:42 olas just needs some work
09:42 olas (and time is something I don't have too much of)
09:43 olas but will work on this
09:43 thomas_ku that sounds good
09:44 * olas is on lunch
10:38 egonw olas: around?
10:41 EskilA joined #bioclipse
11:01 viklund Ok
11:01 viklund Now I got a test-service running
11:01 masak great
11:01 masak that was quick
11:02 viklund I thought maybe you can try and call it from JAVA just to see if it works
11:02 jonalv what does it do?
11:02 masak viklund: (it's Java)
11:02 viklund It returns the string "Hello world" when you call Hi
11:02 viklund masak: sry
11:02 masak np. I don't go around shouting PERL
11:02 egonw viklund: service -> what library?
11:02 egonw and what standard?
11:02 viklund it's @ SOAP::Lite
11:03 egonw ah, OK
11:03 viklund s/@//g
11:03 masak :)
11:03 viklund I want to see if Just Works...
11:03 masak viklund: where's it at?
11:03 viklund url is: http://artedi.ebc.uu.se/cgi-bin/soap_server.pl
11:03 masak ah
11:03 * masak tries
11:03 viklund and module (or whatever)
11:03 viklund http://artedi.ebc.uu.se/Demo
11:04 viklund the first one is called proxy in SOAP::Lite and the second one uri
11:04 jonalv masak, do you know how to try it from Java?
11:04 viklund if that makes sense?
11:04 viklund call the method hi()
11:04 masak jonalv: don't know
11:04 masak guess we'll have to find a SOAP module in Java
11:05 masak viklund: the first one asks me if I want to download an empty Perl file, the second one gives a 404 in the browser
11:05 viklund Sounds ok...
11:05 jonalv or wait until olas is back...
11:06 viklund I'll mail you my test-script
11:06 masak jonalv: yes, of course
11:06 masak I'm just curious
11:06 jonalv curiosity is always  good :)
11:07 masak IBM has a Java SOAP implementation: http://www.alphaworks.ibm.com/tech/soap4j
11:07 viklund masak: strange, I sent it to your ibg mailadress
11:07 masak viklund: please don't
11:08 viklund masak: I thought I did, noticed afterwords when it said "Invite Masak to gmail?"...
11:08 masak ah
11:08 viklund s/afterwords/afterwards/
11:08 masak tell-tale sign
11:08 masak no, you noticed afterwords :)
11:08 viklund ok
11:08 masak they were "Invite masak to gmail?" :)
11:08 viklund now you got it at gmail?
11:08 * masak checks
11:08 viklund s/\?/!/
11:09 masak oh, ok
11:09 masak yes
11:09 viklund requires SOAP::Lite of course...
11:09 masak of course
11:09 viklund but there you see how it works in perl, I guess it's similar in Java.
11:09 masak no idea
11:09 masak but prolly, yea
11:10 viklund masak: have you tried it?
11:10 masak works fine
11:10 viklund ah, now
11:11 * viklund watching logfiles
11:12 viklund maybe I should use this: http://www.fudgie.org/ ?
11:13 masak viklund: wow
11:13 viklund now all we need to verify is that it's possible to call from Java
11:14 viklund masak: Yes, I know, that guy is crazy...
11:14 masak viklund: olas++ can probably verify that quite easily
11:14 viklund I think so too
11:14 * olas is back from lunch
11:15 viklund great!
11:15 masak olas: ok, plz backlog and try it out :)
11:15 olas not really good on this
11:15 olas mom
11:15 olas brb
11:16 viklund huh
11:16 masak viklund: it's german
11:16 viklund masak: ??
11:16 masak it has nothing to do with mothers
11:16 masak it's an abbreviation for "moment"
11:16 viklund I interpered it as moment, yes
11:16 masak oki
11:16 viklund I just liked the stacked three letter words...
11:16 masak hah
11:17 viklund yep
11:17 jonalv pah
11:17 masak tss
11:17 jonalv hmm
11:17 masak ehm?
11:17 viklund ...
11:17 masak that's not a word!
11:17 masak grr
11:18 jonalv lol
11:19 viklund It takes time to migrate 500Gb data to a 750 Gb disk...
11:20 viklund or, rather, 340Gb data...
11:20 masak how thick is the hose between?
11:21 masak (in bytes/s)
11:21 viklund they're on the same controller...
11:22 masak ok
11:22 viklund I don't know how fast it is, rsync dosn't tell me. But I would say, very fast
11:23 viklund masak: Do you have two ips?
11:23 viklund ahh, one linux and one mac...
11:24 viklund I find that kind of multitasking disturbing...
11:24 * olas is back (again)
11:24 olas wher were we
11:24 olas you have a standard service up and ruinning
11:24 olas and want to call it from Java
11:24 olas do you have a WSDL?
11:25 viklund hmm, not yet, maybe I can get SOAP::Lite to emit it
11:25 olas well, I will need a WSDL to get my axis to generate a client
11:25 olas please check it up
11:26 viklund One step ahead of you ;)
11:28 masak viklund: I don't know nothing about two IPs
11:28 viklund ;)
11:28 olas viklund: give me the URI to the WSDL or send it to me
11:28 viklund well, maybe it was jonathan...
11:28 masak prolly
11:28 viklund olas: as soon as I have one...
11:35 viklund hmm, SOAP::Lite dosn't emit a WSDL and WSDL::Generator requires perl 5.6...
11:35 CIA-31 bioclipse: ospjuth * r3962 /trunk/playground/plugins/net.biocl​ipse.taverna.ui/logger.properties: Added logger props
11:35 CIA-31 bioclipse: ospjuth * r3963 /trunk/playground/plugins/net.bio​clipse.taverna.ui/wf_static.png: Added static image for demo purposes
11:36 viklund ahh, http://www.wsdlgenerator.com/
11:38 olas viklund: http://search.cpan.org/dist/Pod-WSDL/
11:38 viklund hmm
11:38 viklund olas++ really nice
11:38 viklund I'll try that later!
11:38 masak viklund: you don't have 5.6?
11:39 viklund no, 5.8
11:39 masak ah, so it doesn't require 5.6 or later, only 5.6?
11:39 masak that's unusual
11:40 viklund masak: yes
11:40 viklund olas: ok, here it is: http://search.cpan.org/dist/Pod-WSDL/
11:40 viklund oops
11:40 viklund http://artedi.ebc.uu.se/cgi-bin/HelloWorld.wsdl
11:40 viklund was what I meant..
11:40 viklund I'm mixing up my clipboards...
11:41 olas ok
11:41 masak viklund: that gives a 500 in the browser
11:41 masak premature end of script headers
11:41 viklund If that dosn't work I'll try the Pod::WSDL
11:41 viklund it should work, it worked for me...
11:41 olas will try to generate a client in Java right away
11:42 viklund masak: I copied that string from my browser window, ff asked wheter I wanted to download it.
11:42 masak same here
11:43 masak and the contents are a 500 error
11:43 viklund hmm, you are right
11:44 olas yes, 500
11:44 viklund olas, masak: try http://artedi.ebc.uu.se/course/HelloWorld.wsdl
11:45 viklund that at least gets me something (I got the 500 too and I saw it in the logs)
11:45 masak now works
11:45 olas but I get validation errors for the wsdl
11:46 viklund ok, I suspected that that might happen...
11:46 viklund It starts with a definitions element...
11:47 viklund ahh
11:47 olas cvc-attribute.3: The value '' of attribute 'name' on element 'part' is not valid with respect to its type, 'NCName'.dndsClientHelloWorld.wsdlline 1411921032158882408
11:47 olas does that say you anything?
11:47 masak name attributes cannot be empty, apparently
11:47 masak it's for hiRequest
11:48 olas cvc-complex-type.2.3: Element 'portType' cannot have character [children], because the type's content type is element-only
11:50 olas viklund: can you correct for this?
11:51 viklund olas: I'm testing Pos::WSDL rfirst...
11:51 olas ok
11:51 viklund Pod
12:01 viklund olas, masak: new try: http://artedi.ebc.uu.se/course/Demo.wsdl
12:03 masak looks good to me
12:03 masak but I don't have a validator
12:03 viklund it will fail though
12:04 masak viklund: looks like portType still has children
12:04 viklund I just realised
12:04 masak yes
12:04 masak can you do something about it?
12:05 viklund masak: the portType I don't know about, but there are other missing stuff...
12:05 olas WSDL seems ok...
12:05 viklund it should have children too
12:05 viklund I think
12:06 olas oh no
12:07 olas cvc-attribute.3: The value '' of attribute 'parameterOrder' on element 'wsdl:operation' is not valid with respect to its type, 'NMTOKENS'
12:07 olas cvc-minLength-valid: Value '' with length = '0' is not facet-valid with respect to minLength '1' for type 'NMTOKENS'.
12:07 olas no idea what this means
12:07 masak the second one seems fairly obvious
12:07 viklund olas: any lines?
12:08 olas Severity and DescriptionPathResourceLocationCreation TimeId cvc-attribute.3: The value '' of attribute 'parameterOrder' on element 'wsdl:operation' is not valid with respect to its type, 'NMTOKENS'.testDemo.wsdlline 24119210445718862395
12:08 olas Severity and DescriptionPathResourceLocationCreation TimeId cvc-minLength-valid: Value '' with length = '0' is not facet-valid with respect to minLength '1' for type 'NMTOKENS'.testDemo.wsdlline 24119210445718862394
12:08 olas Severity and DescriptionPathResourceLocationCreation TimeId cvc-minLength-valid: Value '' with length = '0' is not facet-valid with respect to minLength '1' for type 'NMTOKENS'.testDemo.wsdlline 29119210445718862396
12:08 olas Severity and DescriptionPathResourceLocationCreation TimeId cvc-attribute.3: The value '' of attribute 'parameterOrder' on element 'wsdl:operation' is not valid with respect to its type, 'NMTOKENS'.testDemo.wsdlline 29119210445718862397
12:08 olas that's all 4
12:08 olas so 24 and 29
12:09 viklund try again. I just removed the paramterOrder attributes...
12:10 olas ok
12:10 viklund (I'm comparing my wsdl with an example on w3.org, they don't have it so it should be ok without)
12:11 olas I get a warning, but no errors:
12:11 olas the warning is:
12:11 olas Severity and DescriptionPathResourceLocationCreation TimeId WS-I: (BP2406) The use attribute of a soapbind:body, soapbind:fault, soapbind:header and soapbind:headerfault does not have value of "literal".testDemo.wsdlline 36119210473547462398
12:12 olas but as said, no error
12:12 olas I will generate and test a client
12:12 viklund ok, whatever...
12:12 * olas has no idea if this is gonna work
12:12 viklund I might look at those later...
12:15 * viklund is waiting with anticipation...
12:19 viklund The wsdl works from SOAP::Lite at least, that's something
12:21 * olas is trying to remember the syntax in java for calling axis
12:22 viklund perl oneliner:
12:22 viklund perl "-MSOAP::Lite service=>'http://artedi.ebc.uu.se/course/Demo.wsdl'" -le 'print hi()'
12:22 viklund that was fun!
12:23 olas works!
12:23 masak yes
12:23 olas hello, world
12:23 viklund gr8t
12:23 viklund tested bye()?
12:23 olas will do
12:23 viklund ok, that's some part of the way at least...
12:24 olas goodbye, cruel world
12:24 masak bye works too
12:24 viklund now me and björn need to specify the input/output from the service
12:24 olas yup
12:24 masak hello, RESTful world!
12:25 viklund and then we can let you know, but at least we now know that we can implement the beast in perl at our end
12:25 viklund ;)
12:25 olas sure thing
12:25 olas The beauty of SOA
12:25 viklund yep
12:25 viklund masak: updated!
12:25 olas but rely on simple data types for I/O
12:25 masak viklund: testing
12:26 viklund yes, but that's the first step
12:26 masak viklund: works fine
12:27 masak why don't you update the 'goodbye' message to 'goodbye, non-reusable-script-solutions world' too? :)
12:31 viklund hehe
12:34 viklund can you test this wsdl too?
12:34 viklund http://artedi.ebc.uu.se/course/Temperatures.wsdl
12:35 viklund It converts between farenheit and celsius...
12:35 viklund It's a parameter test...
12:36 viklund unedited I might add, with paramters the parameterOrder is non-empty
12:41 olas ok
12:43 viklund Pod::WSDL was really nice though...
12:44 viklund I see you calling...
12:45 olas nope
12:46 olas dunno why¨
12:46 olas org.xml.sax.SAXException: Bad types (float -> double)
12:47 viklund hmm
12:47 olas this is what I run:
12:47 viklund I can try with float instead of double...
12:47 olas double hi=-1; double bye=-1;  double cin=20.56; double fin=30.56;  hi = locator.getTemperatures().c2F(cin); bye = locator.getTemperatures().f2C(fin);  System.out.println(String.valueOf(hi)); System.out.println(String.valueOf(bye));
12:48 olas so don't think the fault is on my side
12:48 viklund try again with the new wsdl
12:50 olas works!
12:51 viklund ok, I should avoid specing doubles then..
12:51 olas :-)
12:52 olas viklund: Do you think you can write up a wiki page with some tips for developing Web services for Bioclipse in Perl?
12:52 olas on bioclipse wiki, please
12:52 viklund sure
12:52 olas masak: around?
12:52 masak olas: sure
12:52 viklund once we got this running all the way I think is a good time to write it
12:53 olas you seem experienced with resizing of images and so on
12:53 * masak runs
12:53 masak :)
12:53 olas could you look at my lupcomming commit
12:53 masak oki
12:54 olas how to get an Image that is resized when the view is resized?
12:54 olas (editor in thiis case)
12:54 masak hm
12:54 CIA-31 bioclipse: ospjuth * r3964 /trunk/playground/plugins/net.biocli​pse.taverna.ui/src/net/bioclipse/tav​erna/ui/editors/TavernaEditor.java: Added a canvas for displaying a WF image in MPE. Does not resize when editor is resized.
12:54 masak have a look in JChemPaintView that egonw wrote recently
12:55 masak he supposedly does image resizing
12:55 olas yea, could do that
12:55 olas if he handles images
12:55 masak though if it's of the type you want, I cannot tell
12:55 masak it's CDK molecule structures
12:55 olas but think he has a custom widget, right?
12:56 masak olas: yes, he does
12:57 olas and I have an image
12:57 olas anyway, will add a scrollbar first
12:57 olas that's probably best
12:57 olas so no need for you to assist (yet)
12:58 masak olas: hm, I'll read up on what Structure2DView does
12:58 masak it does Images at least
13:02 masak in an SWT table, is there a known way to make the rightmost column fill up the remaining horizontal space?
13:09 olas good question
13:09 olas should be
13:10 olas but don't know
13:10 masak olas: how to write to the status bar in Bioclipse?
13:10 masak ...or do you prefer writing messages to the Bioclipse console?
13:14 olas to console preferably
13:15 olas don't remember status bar...
13:15 masak olas: oki, will do
13:15 olas we'll need some sort of guide for that in bc2
13:19 masak olas: good idea
13:24 CIA-31 bioclipse: ospjuth * r3965 /trunk/playground/plugins/net.biocli​pse.taverna.ui/src/net/bioclipse/tav​erna/ui/editors/TavernaEditor.java: Added scrollbars to TavernaEditor canvas in MPE
13:26 CIA-31 bioclipse: ospjuth * r3966 /trunk/playground/plugins/net.bioclipse.​taverna.ui/ConditionalBranchChoice.xml: Added a sample Taverna workflow for testing purposes
13:28 CIA-31 bioclipse: ospjuth * r3967 /trunk/playground/plugins/net.bioclipse.tave​rna.ui/src/net/bioclipse/taverna/ui/views/: Removed unused view
13:29 CIA-31 bioclipse: ospjuth * r3968 /trunk/playground/plugins/net.b​ioclipse.taverna.ui/plugin.xml: Forgot to remove entry in plugin.xml
13:29 CIA-31 bioclipse: ospjuth * r3969 /trunk/playground/plugins/net.biocli​pse.taverna.ui/src/net/bioclipse/tav​erna/ui/editors/TavernaEditor.java: Use XMLEditor instead of TextEditor
13:47 CIA-31 bioclipse: carl_masak * r3970 /trunk/plugins/net.bioclipse.cdk.ui/src/net/b​ioclipse/plugins/views/Structure2DView.java:
13:47 CIA-31 bioclipse: [Structure2DView.java]
13:47 CIA-31 bioclipse: * renamed static final ints xsize and ysize to MOLECULE_XSIZE and MOLECULE_YSIZE, respectively
13:47 CIA-31 bioclipse: * there's no such thing as a 'standard constructor' in Java
13:47 CIA-31 bioclipse: * various whitespace improvements
13:47 CIA-31 bioclipse: * broke some lines before binop instead of after
13:47 CIA-31 bioclipse: * replaced okMessage calls with BioclipseConsole.writeToConsole calls
13:49 masak egonw: Structure2DView now uses your molecule structure widget
13:49 masak it's an improvement
13:54 masak egonw: would it be possible to make the molecules clickable in your widget?
13:54 masak that would reduce the code in Structure2DView immensely
14:24 egonw olas: is quite easy...
14:25 egonw just look at my code
14:25 egonw masak: what kind of clicking?
14:25 egonw olas: check that SWT widget tutorial...
14:25 egonw section: Compound Widget Example
14:26 masak egonw: the kind where an editor opens for the molecule
14:26 egonw where it explains how to add a ControlAdapter() to act on SWT parent widget resizes
14:26 egonw masak: just add a mouse listener?
14:26 masak egonw: I was hoping for that answer :)
14:26 masak will do
14:26 egonw the JCP widget is just a SWT widget, so can can manually add a listener...
14:27 egonw masak: check the same SWT widget tutorial as Ola is now looking at :)
14:27 egonw a but later in that tutorial is the 'Events and listeners' section...
14:27 egonw with a ImageClickedEvent example...
14:27 * olas is not lookingh at that doc but is happy enough with a scrollbar
14:28 * olas is investigating what a DataThing is...
14:28 egonw masak: in the SWT widget you need addMouseListener(new MouseAdapter)
14:28 masak egonw: ok, goodie
14:29 masak the reason I'm asking is that if I remove all button code from Structure2DView, the code gets so much slimmer
14:30 olas why is ther ebutton code?
14:38 egonw masak: yes, that sounds a very good thing to do
14:46 masak olas: well,
14:46 masak there are SDF files containing several molecules
14:47 masak the buttons are for showing temp cml files back-generated from the structures
14:48 olas why on a button?
14:48 masak something pressable, I think the idea was
14:49 olas you can listen for mouse-clicks on almost everything
14:49 olas or?
14:49 masak yes
14:49 olas so, why a button?
14:49 masak olas: maybe the idea was also to enhance that these molecules are clickable
14:49 masak actually I don't know, I didn't write it
14:49 masak anyway, it complicates the code
14:50 olas I see no reason to have buttons
14:50 masak would be better to make everything clickable
14:50 olas actually, I really dislike it
14:50 masak olas: I know, me and shk3_ discussed it yesterday
14:50 jonalv Yes it seems a bit wrong
14:50 masak olas: ok, so I scrap the buttons now :)
14:50 masak stand by
14:50 olas fine with me
14:51 olas but I didn't write it
14:51 CIA-31 bioclipse: carl_masak * r3971 /trunk/plugins/net.bioclipse.cdk.ui/src/net/b​ioclipse/plugins/views/Structure2DView.java:
14:51 CIA-31 bioclipse: [Structure2DView.java]
14:51 CIA-31 bioclipse: * buttons gone
14:51 olas so I don't know what the button is for
14:51 olas :-)
14:51 olas Let's see if someone complains
14:51 masak olas: don't think so
14:51 masak olas: the buttons had a "View Source" function
14:51 masak not sure it would have been very useful
14:52 olas good
14:53 masak hooray for code simplification!
14:53 * masak feels productive scrapping 200 LOC
14:53 * egonw is going home
14:53 egonw olas: no one will complain..
14:54 egonw the buttons are, IMHO, an ugly hack only
14:54 egonw cu tomorrow
14:54 jonalv 200LOC ?!
14:54 masak though clickability would perhaps be nice
14:54 masak jonalv: well,
14:54 masak it was no easy feat getting that molecule on that button :P
14:55 olas toffifee for that?
14:55 masak olas: oh, right
14:55 CIA-31 bioclipse: jonalv * r3972 /trunk/playground/plugins/net.bioclipse.keyring/ (3 files in 3 dirs): Moved delete button to the right vertical position
14:55 * masak eats toffifee
14:55 olas well, it was not a bug...
14:55 masak olas: doesn't matter
14:55 masak 1 commit = 1 toffifee
14:55 * olas is making many small commits
14:56 masak good for code, bad for teeth
14:56 jonalv masak, is making as many commits as possible... :)
14:56 masak mm, commits
14:56 masak pavlov was right :)
14:57 * viklund sighs
15:00 jonalv :)
15:33 CIA-31 bioclipse: ospjuth * r3973 /trunk/playground/plugins/net.bioclipse.taverna/ (. build.properties): Updated build with deps
15:51 CIA-31 bioclipse: ospjuth * r3974 /trunk/playground/plugins/net.bioclipse.taverna/ (88 files in 3 dirs): Added libs but now it's not working...
16:36 CIA-31 bioclipse: ospjuth * r3975 /trunk/playground/plugins/net.b​ioclipse.taverna/src/main/java/ (2 files in 2 dirs): Added and uses resource from classpath
16:43 CIA-31 bioclipse: ospjuth * r3976 /trunk/playground/plugins/net.bioclips​e.taverna/src/main/java/net/sf/taverna​/example/WorkflowLauncherWrapper.java: Removed verbose output
16:45 olas left #bioclipse
18:00 EskilA left #bioclipse

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