conflict in dependency

[Francois Le Fevre]

Dear all,
I am trying to import a basic biopax file :
ftp://ftp.ebi.ac.uk/pub/databases/rhea/biopax/
I ahev set up a minimal maven project but I have encountered a
conflict between jars.
could you help me?

If you try the small project attached: it is working.
If you add the following dependencies , it does not work

Exception in thread "main" org.biopax.paxtools.util.BioPaxIOException:
Unexpected element at start: 6
at org.biopax.paxtools.io.SimpleIOHandler.readNameSpaces(SimpleIOHandler.java:131)
at org.biopax.paxtools.io.BioPAXIOHandlerAdapter.convertFromOWL(BioPAXIOHandlerAdapter.java:212)
at fr.cea.ig.biopax.biopax.App.main(App.java:31)


Thank for your help!
Francois

<!-- flf1 -->
<!-- dependency>
<groupId>org.apache.ws.commons.axiom</groupId>
<artifactId>axiom-api</artifactId>
<version>1.2.10</version>
<exclusions>
<exclusion>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
</exclusion>
<exclusion>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.ws.commons.axiom</groupId>
<artifactId>axiom-impl</artifactId>
<version>1.2.10</version>
<exclusions>
<exclusion>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
</exclusion>
<exclusion>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
</exclusion>
</exclusions>
</dependency-->
<!-- dependency>
<groupId>org.apache.ws.commons.axiom</groupId>
<artifactId>axiom-dom</artifactId>
<version>1.2.10</version>
<exclusions>
<exclusion>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
</exclusion>
</exclusions>
</dependency-->
<!-- flf2 -->


--


Francois Le Fevre
Management Informatique Innovation Biotechnologies
Paris, France
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[IgorRodchenkov]

Dear Francois,

Sorry for that.

Unfortunately, it's a known but tricky issue (paxtools-core, SimpleIOHandler uses javax.xml.stream api and Java StAX factory auto-discovery, which mostly works...), which we'll try to fix in the next paxtools release. In meantime, could you try using JenaIOHandler instead, or experiment with other external dependencies (do you really need axis, xml-apis, etc?..)

Best,

IR.

[Francois Le Fevre]

Ok i have witch to jena implentation. It works.
Thaqnks for this advice.
Francois