Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-10-17

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All times shown according to UTC.

Time Nick Message
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07:16 olas joined #bioclipse
07:16 olas moin
07:16 zarah hi olas
07:17 rojasm joined #bioclipse
07:56 olas @tell jonalv he'd like to talk about batch processing of molecules in a large SDF
07:56 zarah Consider it noted.
08:00 olas @tell jonalv: he emailed you
08:00 zarah Consider it noted.
08:01 olas time for coffee
08:23 gilleain joined #bioclipse
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09:18 shk3 hi olas
09:19 olas hi
09:19 zarah hi olas
09:19 shk3 we couldn't reproduce your problem with jcp
09:28 Gpox there are two jcp-editors in bioclipse at the moment, the one with yellow triangle as icon don't work
09:28 edrin hi
09:28 zarah hi edrin
09:31 jonalv olas: Did someone update the wiki for running bc2 after egons 150 CDK-plugins commit
09:31 zarah jonalv: You have new messages. Write '@messages' to read them.
09:32 jonalv zarah: just tell me..
09:32 zarah jonalv: 1 h 35 m 20 s ago, olas said he'd like to talk about batch processing of molecules in a large SDF
09:32 zarah jonalv: 1 h 31 m 5 s ago, olas said he emailed you
09:32 olas shk3: I see
09:32 olas will look into it more
09:37 shk3 gpox: the yellow triangle editor is the cdk trunk based one, as far as i can see
09:37 Gpox yes
09:38 shk3 if you choose JChemPaintEditor in context menu, you get the 1.0 based one
09:41 Gpox no, you should choose MDL/CML-fileEditor to get 1.0, JChemPaintEditor is the one based on cdk trunk
09:51 shk3 oh, ok, wrong way round
10:10 gilleain Huh. You can't have anonymous Visitors, it seems.
10:10 gilleain because:
10:10 gilleain elementList.accept(new Visitor() {
10:11 gilleain public void visitList(ElementList e) {
10:11 gilleain for (Element ee : e.elements) { ee.accept(this); }
10:11 gilleain }
10:11 gilleain won't work.
10:14 gilleain Oh no, wait. Never mind I am an idiot.
10:37 thomasku joined #bioclipse
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10:47 egonw moin
10:47 zarah hi egonw
10:47 egonw online from home :)
10:47 egonw we picked up the ADSL modem this morning
10:49 Gpox joined #bioclipse
10:54 charlgren joined #bioclipse
11:06 egonw will be back later
11:40 CIA-30 bioclipse: shk3 * r7322 /bioclipse2/trunk/plugins/net.bioclipse.nmrs​hiftdb/src/net/bioclipse/nmrshiftdb/wizards/ (3 files): the server now always comes from preferences
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12:29 edrin what's going on?
12:32 maclean All sorts.
12:32 jonalv is something going on?
12:33 maclean Probably.
12:33 maclean Things often go on.
12:34 * jonalv is working on Brunn
12:35 edrin ok :)
12:40 olas edrin: could we, instead of passing round an Element pass around a Document?
12:40 olas that way I could serialize and deserialize it simpler I guess...
12:40 * olas is talking xws4j now
12:40 edrin olas: i know
12:41 olas what do you think?
12:41 edrin olas: i was trying to use XMLBeans, it was really happy with Elements...
12:41 olas that way we can validate the document against a schema as well...
12:41 edrin what is the difference between elemtent and document? is there one?
12:41 olas Document is the root type
12:41 olas if you do document.getDocumentElement() you get the root element
12:42 edrin does it implement Element interface?
12:42 olas no
12:42 olas it contains Elements
12:42 olas changing to Document would just add benefits
12:42 edrin btw. what lib are u using for serializing ?
12:42 olas trying Xerces and EMF now
12:43 olas I think it makes sense to pass around a complete XML document
12:43 olas that can be validated
12:43 olas don�t you think so?
12:43 edrin i am playing around with XmlBeans... i am now trying to write code that does a XML Schema to Java Class compliation and then i will try to autoserialize input/ output stuff with it
12:43 olas egonw: you know a lot of xml
12:43 olas can you comment?
12:44 olas edrin: I want to use EMF
12:44 olas hence I need a Document
12:44 egonw Document is the root element plus the preamble...
12:45 egonw <?xml ?>
12:45 egonw stuff
12:45 egonw like that
12:45 olas any drawbacks passing round a Document or just it's elements?
12:45 egonw so, a Document contains the root element
12:45 olas yes
12:45 egonw olas: depends on the needs
12:45 edrin olas: i will read my code again on weekend and then see how i could change it. i just passed around Elements because they are eaten by many libs and JSO library just converts to Element and not do doc
12:45 egonw with SOAPEnvelop, I'd pass around Element, not Document
12:45 egonw because SOAPEnvelop contect cannot be a Document
12:46 olas but if I have a schema, can I validate an Element then?
12:46 edrin yes, in my opinion element is more plain...
12:46 egonw so you'd have to extra wrap it
12:46 edrin olas: yes you can
12:46 egonw you could wrap it just for validation
12:46 olas how?
12:46 olas in EMF?
12:46 edrin olas: in xws4j lib the component is already validating!
12:46 egonw in XOM: new Document().setRootElement() I think
12:46 edrin pls wait
12:47 olas egonw: I am not using XOM
12:47 edrin i will give you the class with validation code. although i am not sure if validating works... never testet it ;)
12:47 egonw I'm sure any DOM will have an equivalent
12:48 edrin i think so, too
12:48 olas I don�t think you see my problem here...
12:48 * olas will soon give up
12:48 edrin olas: just a second...
12:49 olas edrin: I don't think there's anything you can do to help me
12:50 olas EMF must read a complete serialization
12:50 olas if I don't have a Document I can't serialize that
12:50 olas and hence cannot use EMF
12:50 edrin olas: regarding EMF... i was trying to use it. this lib is very bad documented in my opinion...
12:50 olas maybe you could do it in another much harder way
12:51 olas but I don�t know EMF that well
12:51 edrin olas: there is an irc channel: #eclipse-modeling
12:51 olas oh
12:51 olas will ask there
12:51 edrin olas: from what i have seen I do not like EMF...
12:51 edrin olas: they idle a lot...
12:51 olas I do
12:51 olas EMF is realle REALLY great
12:51 edrin olas: last time it took them 6 hours to answer
12:52 olas but complex
12:53 egonw olas: with serialization, you mean String?
12:53 olas yes
12:53 egonw how would EMF use an XML document String to create a data model?
12:54 edrin olas: http://bioclipse.svn.sourceforge.net/view​vc/bioclipse/xws/trunk/xws4j/src/net/bioc​lipse/xws/component/xmpp/process/ProcessF​actory.java?revision=6617&amp;view=markup
12:54 edrin see function boolean validateRunInput(String functionname, IoDataElement iodata)
12:54 zarah edrin's link is also http://tinyurl.com/5pf4qa
12:54 olas yes?
12:54 olas and?
12:55 olas oh, you mean that you already validate?
12:55 olas fine
12:55 edrin in theory the component should already validate input according to functions Input XML Schema
12:55 olas it still doesn't solve my problem
12:55 edrin in theory... yes.
12:55 olas but good to know
12:55 edrin i never tried though...
12:56 edrin i had the feeling it always said "valid" ...
12:57 egonw olas: so, what exactly is the problem?
12:58 egonw converting an Element to String can't be the problem
12:58 olas no
12:58 olas reading it back in EMF is the problem
12:58 olas since it is not a complete Document
12:59 olas methods seem not to like a String without DocumentRoot
13:01 edrin olas: i had the feeling EMF does not generate Java Class from a xsd that will have functions or variables matching the element names like xml_object.getUserName() or int xml_object.userphonenumber = 1234;
13:01 egonw olas: can you please post your String on a pastebin?
13:01 olas what string?
13:02 egonw that you like to insert into EMF
13:02 olas serialized by EMF?
13:02 olas ok
13:03 egonw sorry, I don't understand your work/dataflow
13:03 olas http://paste2.org/p/88050
13:03 olas I first serialized with EMF, and this one I can read back
13:03 olas then I serialized the element with Xereces, and obviously I loose the DocumentRoot
13:06 edrin olas: i dont see a problem...
13:06 egonw I see a problem
13:07 egonw it lost the root element!
13:07 egonw not good!
13:07 olas yes
13:07 egonw very bad
13:07 edrin ah now i see
13:07 olas since we pass around the element, we loose the DocumentRoot
13:07 edrin and that is because of xws4j?
13:07 olas no
13:07 egonw olas: please use these, IMHO useful, conventions...
13:07 egonw this is an <element>
13:07 egonw this is an @attribute
13:08 olas DocumentRoot implements Node not Element
13:08 egonw a bit longer, but more semantic
13:08 egonw olas: right, that's where you have me confused
13:08 olas sry
13:08 olas but you see my point
13:08 egonw because <hivpref:DocumentRoot> must be an Element
13:08 egonw period
13:08 olas Node
13:08 egonw otherwise the XML lib is really broken
13:08 olas mom
13:09 egonw please test with 'instanceof Element'
13:09 egonw because any DOM should see the root element as an Element
13:09 egonw btw, Element == instanceof Node
13:09 edrin yep
13:09 olas hmmm maybe I'm doing something wrong here..
13:10 olas I have a Document
13:10 olas and then send the document.getDocumentElement() to XWS
13:10 olas maybe I can send something else from the document?
13:11 edrin i think getDocumentElement() should be ok, no?
13:11 olas that does not send DocumentRoot
13:11 olas but the element it contains
13:11 olas hence my pastebin result
13:12 edrin you mean the xerces part?
13:12 egonw getDocumentElement comes from which Class?
13:13 egonw then I can check its JavaDoc
13:13 edrin Document
13:13 edrin i think http://java.sun.com/j2se/1.4.2/docs/api/or​g/w3c/dom/Document.html#getDocumentElement() no?
13:13 zarah edrin's link is also http://tinyurl.com/5hf754
13:13 egonw yes, with package please :)
13:14 egonw there are *many* DOMs around...
13:14 edrin ok, then i do not know
13:14 egonw just Document is too vague :)
13:15 egonw the JavaDoc edrin just gave would indicate that this method is fine...
13:15 egonw but it clearly is not
13:15 olas hmm
13:15 egonw olas: please pastebin your code full code snippet
13:15 olas maybe I can read it in without the DocumentRoot
13:15 olas will ask on EMF mailinglist
13:15 edrin in any case please consider, you cannot pass around "full" documents with xmpp... but you should be able to pass around elements with its namespace. <!--comments --> get removed
13:15 olas thx for your help
13:17 edrin therefore you must pass around the document's root element ...
13:17 edrin without this <?xml version="1.0" encoding="ASCII"?> things...
13:18 edrin egonw: do you know XMLBeans?
13:18 egonw no, not yet
13:18 egonw URL?
13:19 edrin http://xmlbeans.apache.org/
13:20 edrin it's looking rather robust... i am currently trying to built a xws-binding generator on top of it... will be very hax0r though
13:21 edrin for fast serializing XStream (http://xstream.codehaus.org/) is very cool. See the "two minutes tutorial". However it does not support XML Schema stuff... cant generate java class from xsd.
13:27 edrin btw. is bioclipse2 depending on JDK ?
13:27 edrin because the xws4j-bining tools will need the java compiler
13:30 egonw ha, an extra 40MB? of download
13:30 egonw brb
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13:42 jonalv The Bioclipse download just keeps growing... :)
13:45 egonw grpmh...
13:45 egonw my stupid home desktop is not getting an IP :(
13:46 rojasm joined #bioclipse
13:46 olas egonw: that complicates things...
13:51 egonw bloody ADSL modems :(\
13:53 olas at least you're online
13:54 * olas is still working on EMF -> DOM -> EMF
14:12 shk3 bioclipse wiki is down
14:15 egonw bbl
14:15 egonw going to reset that ADSL
14:15 egonw and see if I can reach its web interface...
14:23 edrin1 joined #bioclipse
14:24 edrin1 hi
14:24 zarah hi edrin1
14:27 egonw joined #bioclipse
14:42 egonw olas: ping
14:42 olas egonw: pong
14:42 egonw olas: might you reset my pele password?
14:42 olas ok
14:42 olas mom
14:42 egonw seem to have lost it :(
14:43 olas done
14:43 olas same as I gave you last time
14:43 olas works?
14:43 egonw yes
14:43 egonw thanx
14:43 olas no pr
14:48 egonw so far, I hate telia ADSL :(
14:48 egonw seems it tied IP to a MAC or so...
14:48 egonw because I can't even plugin my desktop, as only my laptop can get an IP :(
14:49 olas use a switch
14:49 olas and copy MAC to the switch
14:49 egonw yeah. buy a switch
14:49 egonw which gets me to...
14:50 egonw olas: what are (good) computer equipement shops in sweden?
14:50 egonw I know the dutch shop chains...
14:50 egonw but not here...
14:50 olas you really should ask jonalv
14:50 olas or Gpox
14:50 egonw jonalv, Gpox: what are (good) computer equipement shops in sweden?
14:50 olas I sometimes order from web stores
14:50 jonalv I just order my stuff from the web..
14:51 olas or go to a supermarket-like
14:51 olas Elgiganten
14:51 egonw jonalv: web store like?
14:51 olas MediaMarkt
14:51 olas order online I mean
14:51 jonalv datorbutiken.se
14:51 jonalv at least I think I bought my computer from them... :)
14:56 shk3 joined #bioclipse
14:57 egonw OK, going to give up for now... :(
14:58 egonw so, only internet on my laptop for now...
15:01 egonw cu next week
15:40 edrin joined #bioclipse
15:40 edrin hi
15:40 zarah hi edrin
15:40 edrin1 hi
15:40 zarah hi edrin1
15:40 edrin how are you, edrin1?
15:41 edrin1 thanks, good, and you ?
15:41 edrin me, too
15:41 maclean Attack of the clones!
15:41 edrin edrin1: you'll take his head
15:41 edrin1 yes, and you the legs
15:41 maclean Run away!
15:42 edrin1 hehe
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