Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-03-21

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All times shown according to UTC.

Time Nick Message
07:27 egonw joined #bioclipse
09:41 edrin1 joined #bioclipse
11:06 edrin1 egonw: when trying to create a binding with cml.xml as file it works fine.
11:07 edrin1 when saving the returned schema of service as file and trying with this file it causes an exception but not a infinite loop/CPU exhaust...
11:07 edrin1 service used is xmpp.getFunction("descriptor.ws1.bmc.uu.se", "BCUT");
11:14 edrin joined #bioclipse
12:34 CIA-58 bioclipse: edrin_t * r9438 /bioclipse2/trunk/plugins/ (4 files in 4 dirs): now printing large Strings to the console does not freeze bc anymore. Instead Strings are cut.
12:55 edrin egonw available?
12:55 egonw yes
12:55 egonw saw your commit
12:56 egonw just got online
12:56 edrin hi :)
12:56 edrin i updated jsexecution jseditor and xws4j plugins for bc2
12:56 edrin if you update, eclipse will not freeze anymore when working with "large" xmpp stanzas
12:57 egonw problem fixed?
12:57 edrin as they are not written to console anymore
12:57 edrin not the cml binding problem
12:57 edrin but the problem that large strings freeze the app
12:57 edrin i truncate the string
12:57 edrin when they are larger than 25000
12:58 edrin the eclipse console does not like printing "large" messages. and even trying this in small chunks does not work thus i just trunk the large strings
12:59 edrin this means you do not have to turn off debug mode of xws4j anymore
12:59 egonw ok
13:00 edrin egonw: with the following line you can save the input schema of a IoSchemata to a file from a js script you run in jseditor
13:00 edrin jst.saveToFile(JavaDOMTools.w3cElem​entToString(ios.getInputSchema()), "c:/input-test123.xsd");
13:00 egonw can you send me the xsd you had xws4j download from the BCUT service which you saved to file?
13:00 edrin example:
13:00 egonw ah, ok good
13:00 edrin JavaDOMTools = Packages.net.bioclipse.xws.JavaDOMTools;
13:00 edrin f = xmpp.getFunction("descriptor.ws1.bmc.uu.se", "BCUT");
13:00 edrin ios = f.getIoSchemataSync(30000);
13:00 edrin jst.saveToFile(JavaDOMTools.w3cElem​entToString(ios.getInputSchema()), "c:/input-test123.xsd");
13:01 edrin this saves the input schema of BCUT to the indicated file name
13:02 edrin i have updated xws4j-binding, it is now possible to create binding by providing the schema xsd files (independent of xws4j and xmpp stream)
13:03 edrin it works when providing cml.xml but it fails when providing "input-test123.xsd"
13:03 edrin it fails then with an exception
13:04 edrin in contrast to when doing it from within bc2, there is still the endless loop...
13:04 egonw ack
13:04 egonw will try the above JS
13:04 edrin ok :)
13:05 edrin as the failing of the using .xsd and directly over xmpp is very different there must be another error, too
13:06 edrin within xws4j, when it comes to converting DOM elements to XMLObjects
13:14 egonw how do I get access to jst. ?
13:15 edrin egonw: only available if you run a script in the editor
13:15 egonw :(
13:15 egonw ok
13:15 edrin no official API yet
13:15 edrin it's doing many hax0r stuff
13:16 edrin and i think masak must agree to provide them in jsconsole
13:17 edrin must shop some food, will write the "test service" console app afterwards
13:17 egonw ok
13:18 edrin if you want to debug xws4j-binding: there is only one location where it always fails:
13:19 edrin net.bioclipse.xws.binding.t​ools.Xsd2Class.compileXsd() <- there the endless loop and exception would occurre
13:19 edrin cu in 30 min
13:41 egonw edrin: I might have a possible cause for the problem
13:41 egonw all line breaks are removed in the tranmission
13:42 egonw I cannot even open the save file in a plain RCP text editor, without having it hang
13:42 egonw adding the line breaks solves that
13:42 egonw I xmldiff-ed the schemas, and the looke pretty much identical
13:43 egonw Eclipse really seem to have a problem with String without any \n's...
13:45 egonw since the original XSD does have those new lines...
13:46 egonw they seem to get lost somewhere in the transmission...
13:51 edrin egonw: i understand, but the problem is not eclipse as it does not process the dom/string, the Element I pass to XMLBeans seems to kill XMLBeans.
13:51 egonw well, things can be confounded...
13:51 egonw anyway... I think we need to solve this missing newline issue too
13:52 edrin interestingly when creating the w3c Java DOM Element from the saved file it makes XMLBeans to throw an exception, while the Java DOM W3C Element I extract from the XMPP stanza directly makes it to freeze/loop infinite
13:53 edrin egonw: yes, but i fear that we cannot guarantee that stuff passed through various xml parsers (like in ejabberd) will always look the same afterwards...
13:53 edrin for example ejabberd removes all comments, too
13:55 egonw yes, that's another I notes... comments being lost :) but I won't worry about that
13:55 egonw edrin: but newlines actually are content...
13:55 egonw newlines inside elements (except fronting and tailing one) are not ignorable whitespace...
13:55 egonw so, ejabberd loosing those is a really bad idea, and a serious bug in my opinion
13:56 egonw anyway...
13:56 edrin i see
13:56 egonw the XML does not have to look the same way
13:56 edrin in fact it should not lose them
13:56 egonw all non-relevant whitespace can differ
13:56 edrin for example in chat messages there are newlines, too
13:56 egonw as well use use of prefixes and NS declarations...
13:57 edrin hm... i think there was something regarding newline in xml... as newline are different on different OS, maybe there is a rule for newline in xml?
13:58 edrin egonw: http://rifers.org/paste/show/8939 this exception i get when using the saved file to create binding
13:58 zarah edrin's link is also http://tinyurl.com/dfdcls
13:58 shk3 joined #bioclipse
13:59 egonw edrin: OK, that indicates that NS have been messed up...
14:00 edrin hm
14:00 egonw a shame that it does not give a line number...
14:00 edrin this should not happen
14:00 egonw not sure which tool did that...
14:00 egonw this is serious indeed
14:01 edrin it's talking about 1999 and 2001
14:01 egonw yes, but I only have line 1
14:04 edrin interesting in xml.cml it finds 1999 only once while it finds it several times in the saved string
14:04 edrin notepad.exe can open the file ;)
14:04 egonw oh, not line 1999, but the year 1999 ?
14:04 edrin eclipse can not
14:04 edrin yes
14:04 egonw http://www.w3.org/1999/xhtml
14:05 egonw http://www.w3.org/2001/XMLSchema
14:05 zarah egonw's link is also http://tinyurl.com/erkmb
14:05 egonw note: XML Schema versus XHTML
14:05 egonw that's what I said:
14:05 egonw it has the wrong namespace for the simpleType element
14:05 edrin yes
14:05 edrin ok
14:05 edrin maybe it does not like xhtml
14:06 egonw OK, I now see where it goes wrong
14:06 edrin egonw: one must consider that all messages in xmpp are wraped from the main xml stream...
14:06 egonw line 2910
14:06 egonw in my case
14:06 egonw the first definition of a CML element
14:06 egonw abundance
14:06 edrin maybe they overwrite or define the namespace in the main xmpp stream
14:06 egonw directly after the xFractArray attribGroup
14:07 egonw ah, no ...
14:07 egonw earlier too
14:07 egonw OK, check
14:07 egonw positiveNumberType
14:08 egonw that seems to be the first XSD element to be assigned the XHTML NS
14:08 egonw very inconsistent
14:08 egonw OK, at least we found the problem
14:09 edrin ok?
14:09 egonw the XML Scheme received by Bioclipse is broken
14:09 egonw question is:
14:09 egonw what piece of code broke it
14:09 edrin ejabberd
14:09 edrin no?
14:09 edrin hm
14:09 egonw dunno
14:09 edrin JSO could be, too
14:09 egonw the xws4j outputs the messages it send, right?
14:10 edrin output where and what message?
14:10 egonw so, I can check in the log if it happens before the message hits ejabberd
14:10 egonw the <iq> message send to ejabberd
14:10 edrin yes
14:10 edrin you mean the component, yes
14:10 edrin it prints the stuff
14:10 edrin to console
14:10 edrin good idea
14:12 egonw OK, will be offline for a while
14:12 edrin to check it?
14:12 edrin ok weekend :)
14:14 edrin egonw: i could request the schema within PSI XML Konsole
14:16 egonw yes, sounds good
14:16 egonw that way you can test if the IQ it receives is already messed up
14:16 egonw bbl
14:58 egonw edrin: ping
14:58 egonw I just checked the log of the component
14:58 egonw <xsd:simpleType xmlns="http://www.w3.org/1999/xhtml" id="st.positiveNumberType" name="positiveNumberType">
14:58 egonw or...
14:58 egonw the component sends correct XML
14:59 egonw but without space!
14:59 egonw sorry
14:59 edrin ok
14:59 egonw but without new lines!
14:59 egonw so, the problem is after the component
14:59 edrin ic
15:00 edrin egonw: if you have psi available in the XML console: activate it and send the following stanza
15:00 edrin <iq id='JSO-0.12.5-3' to='descriptor.ws1.bmc.uu.se' type='set'><command xmlns='http://jabber.org/protocol/commands' action='execute' node='BCUT'><iodata xmlns='urn:xmpp:tmp:io-data' type='io-schemata-get'/></command></iq>
15:00 zarah edrin's link is also http://tinyurl.com/6bmxzt
15:01 edrin this requests the schemata from the service and
15:01 edrin the result should be display in the PSI XML Console
15:01 egonw will try
15:02 egonw mmm...
15:02 egonw how does that work?
15:02 egonw when I give it XML Input... and hit transmit
15:02 egonw nothing much happend
15:02 egonw nothing much happens
15:03 edrin did you activate the xml console (small hook left bottom)?
15:03 egonw 'Enable' ? yes
15:03 edrin ok, and you are logged in?
15:04 egonw yes, think so
15:04 egonw you can check
15:04 egonw I see you online
15:04 egonw you should see me online too
15:04 edrin ok
15:04 edrin and did you see the message stanza i just sent in the xml console?
15:04 egonw no
15:05 edrin is it the right console ? maybe you opened it for the wrong xmpp account`?
15:05 egonw ok, got something now
15:06 egonw thr returned <iq> does *not* seem to have the NS problem
15:06 edrin where can i see this?
15:07 egonw in that xml console
15:07 edrin ok
15:07 egonw the returned message should look like:
15:07 egonw </xsd:schema>
15:07 egonw </out>
15:07 egonw </iodata>
15:07 egonw </command>
15:07 egonw </iq>
15:07 egonw </xsd:element>
15:07 egonw with that last line as first...
15:07 egonw that is, just before </xsd:schema>
15:09 egonw oh...
15:09 egonw no, that's actually the case to in the crap content
15:09 egonw mom
15:09 egonw ah, no, it is not...
15:09 egonw the XML schema saved with bioclipse ends with:
15:09 egonw </element>
15:09 egonw </xsd:schema>
15:10 egonw where the NS of  </element> is the XHTML namespace...
15:10 egonw so, ejabberd is not the problem
15:10 edrin yes, i copy/pasted it to a text file and tried to create binding with it: same Exception as before
15:11 egonw what did you copy/paste?
15:11 edrin all content within <in> </in>
15:11 egonw from PSI XML Console?
15:11 edrin yes
15:12 edrin oh
15:12 egonw sure?
15:12 edrin the exception is different this time
15:12 egonw because that looks fine here...
15:12 egonw ah...
15:12 egonw ok please put on that pastebin
15:12 edrin http://rifers.org/paste/show/8940
15:13 zarah edrin's link is also http://tinyurl.com/dlbcrz
15:13 egonw mmm... my PSI seems to hang when I typed 'hi' in reply :)
15:14 edrin oh
15:14 egonw mmm... the simpleType for that on is in the XSD
15:14 egonw did you copy the full content?
15:14 edrin yes
15:19 edrin and did copy paste again, same outcome
15:20 egonw edrin: i'm going to have a fairly long conference call now...
15:20 egonw will have to get back on this later...
15:20 edrin ok
15:20 edrin sure
15:20 edrin cu later
15:32 shk3 hi egonw
15:40 shk3 egonw listening?
15:40 egonw sorry
15:40 egonw in a teleconference
15:42 shk3 no problem
15:42 shk3 any date for bc release fixed?
15:42 egonw no, no fixed date
15:43 shk3 ok
15:43 shk3 i won't be here next week
15:43 shk3 once back, I can join in again
15:43 egonw yes, seen that
15:43 egonw i don't think it will be released next week
15:49 shk3 ok
15:49 shk3 we will see
17:07 mib_7hbrsiji joined #bioclipse
17:07 mib_7hbrsiji cool
17:32 CIA-58 bioclipse: edrin_t * r9439 /xws/trunk/xws4j-binding/src/net/bio​clipse/xws/binding/BatchBinder.java: spelling error
17:48 CIA-58 bioclipse: edrin_t * r9440 /xws/trunk/xws4j-is-service-on/: Initial import.
17:50 CIA-58 bioclipse: edrin_t * r9441 /xws/trunk/xws4j-is-service-on/ (7 files in 5 dirs):
17:50 CIA-58 bioclipse: a simple test app to check for the availability of a XMPP service.
17:50 CIA-58 bioclipse: Initial import.
18:00 edrin egonw: interesting: when creating a binding for BCUT with the batch binder (console app to create binding via xmpp) it does fail with an exception instead of an endless loop...
18:00 edrin egonw: a tool to test availability of a service is available now in svn
18:21 egonw edrin: that was a very lengthy conf call I had
18:21 egonw exhausted now... will go offline now, eat and relax a bit
18:21 egonw will be back online tomorrow
18:21 egonw thanx for the is-service-on!

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