I am sorry: something is again very massy at my side:
>>> I did a clean and a fresh build. The error was reproducible.
>>> Now I could not reproduce it.
>>> I packed out everything (classes, biding file) from the email I
posted; I can not reproduce. But I have an other error message
indicating, I am doing something wrong; but what?
I am sorry again. And thanks again.
Tamas
===========================
[java] org.jibx.runtime.JiBXException: Expected "organism" end tag,
found "name" start tag (line 30, col 26)
[java] at
org.jibx.runtime.impl.UnmarshallingContext.parsePastCurrentEndTag(UnmarshallingContext.java:837)
===========================
xml-file:
[...]
<gene>
<name type="primary" evidence="bizi">CFTR</name>
<name type="synonym" evidence="bizi">ABCC7</name>
</gene>
<organism key="1">
<name type="scientific">E. Coli</name>
<name type="abbrev">EC</name>
</organism>
[...]
================================
Binding file
<binding>
<mapping...>
[...]
<collection name="gene" field="gene"/>
<structure name="organism" field="organism">
<value style="attribute" name="key" field="key"/>
<collection name="name" field="name"/>
</structure>
</mapping>
<mapping name="name" class="org.biohegedus.obiodb.bindings.SwissProtGN">
<value style="text" field="name"/>
<value style="attribute" name="evidence" field="evidence"/>
<value style="attribute" name="type" field="type"/>
</mapping>
<mapping name="name" class="org.biohegedus.obiodb.bindings.SwissProtOrgN">
<value style="text" field="sname"/>
<value style="attribute" name="type" field="type"/>
</mapping>
</binding>
Mocky Habeeb wrote:
I don't know for sure, but it sounds like it might be a problem with an
out of date class file. Have you tried deleting all your class files and
doing a fresh build?
Mocky
-----Original Message-----
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Tamas
Hegedus
Sent: Monday, August 29, 2005 8:35 AM
To: [email protected]
Subject: [jibx-users] java.lang.VerifyError (bug?)
Hi,
When I introduced the last strucure
<structure name="organism" field="organism">
and the last mapping
<mapping name="name"
class="org.biohegedus.obiodb.bindings.SwissProtOrgN">
into my binding file, the binding was OK, but I got the VerifyError
message indicatind some bug(?).
I tried to check the bug-tracking system, but as I am not familiar with
anything similar to that, so I found the best way to email.
=============================
run:
[java] Exception in thread "main" java.lang.VerifyError: (class:
org/biohegedus/obiodb/bindings/JiBX_MungeAdapter, method:
JiBX_SwissProt_bndg_newinstance_1_4 signature:
(Lorg/jibx/runtime/impl/UnmarshallingContext;)[[Ljava/lang/String;)
Wrong return type in function
[java] at
org.biohegedus.obiodb.bindings.SwissProt.JiBX_SwissProt_bndg_unmarshal_1
_0(Unknown
Source)
[java] at
org.biohegedus.obiodb.bindings.JiBX_SwissProt_bndgSwissProt_access.unmar
shal()
[java] at
org.jibx.runtime.impl.UnmarshallingContext.unmarshalElement(Unmarshallin
gContext.java:2569)
[java] at org.biohegedus.obiodb.MyMain.main(Unknown Source)
[java] Java Result: 1
==============================
I also attached the output of the org.jibx.binding.Compile -v -l
==============================
Thanks,
Tamas
!!!!!!!!!!!!!!!!!!!!!!!!!
The attachments are too big for the mail-list (>20K). You can download
it from http://www.biohegedus.org/SwissProtClasses.tar
http://www.biohegedus.org/sp_bind_outp.tar
--
Tamas Hegedus, PhD | phone: (1) 919-966 0329
UNC - Biochem & Biophys | fax: (1) 919-966 5178
5007A Thurston-Bowles Bldg | mailto:[EMAIL PROTECTED]
Chapel Hill, NC, 27599-7248 | http://biohegedus.org
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