#3 Java toolkit (2004-11-29) does not merge files

closed-fixed
None
5
2005-01-10
2004-11-30
Ian Fore
No

The MAGEReader constructor has the capability to take a
directory name as its argument and parse all the XML files
contained therein to produce a single MAGEJava object.

With the 2003-10-24 distribution (MAGEstk-2003-10-24-v1.1-
compatible.jar) this worked fine.

With the new distribution (MAGEstk-2004-11-29-v1.1-
compatible.jar) the following error occurs.

java.lang.NullPointerException
at
org.biomage.tools.xmlutils.MAGEContentHandler.mergePckgs(MAGE
ContentHandler.java:314)
at
org.biomage.tools.xmlutils.MAGEContentHandler.endDocument(MA
GEContentHandler.java:251)
at
org.apache.xerces.parsers.AbstractSAXParser.endDocument(Abstra
ctSAXParser.java:741)
...

This appears to be an error when the toolkit attempts to merge
several files into one MAGEJava object.

I used as an example the data for the E-MEXP-1 experiment from
the ArrayExpress database. This contains several xml files which
make the experiment and its associated objects. This files are by
downloading the zipped package available at http://
www.ebi.ac.uk/arrayexpress/query/result?
queryFor=Experiment&eAccession=E-MEXP-1

Discussion

  • Kjell Petersen

    Kjell Petersen - 2004-12-09
    • status: open --> closed
     
  • Kjell Petersen

    Kjell Petersen - 2004-12-09
    • assigned_to: nobody --> kjellpetersen
    • status: closed --> closed-accepted
     
  • Kjell Petersen

    Kjell Petersen - 2005-01-10

    Logged In: YES
    user_id=860965

    Errors experienced when loading the E-MEXP-1 directory using
    MAGEReader has two origins:

    1. Identical identifiers for different objects. Typically
    the MAGE top object shares the identifier of a contained
    object important for that file, like a protocol or an
    ArrayDesign. This is in contradiction to MGED best
    practices, and probably the standard.

    2. When MAGEJava was made Identifiable, it was also treated
    more like a normal object in the MAGEContentHandler in
    several ways, resulting in that it was pushed to the
    objectStack as the rest of the objects. Thus it ends up as a
    unreferenced object at the end of the parsing, and is
    treated as if it's a package object... : Solution, in
    MAGEContentHandler.createMAGEobject(), at the end push every
    created object but MAGEJava objects.

     
  • Kjell Petersen

    Kjell Petersen - 2005-01-10
    • status: closed-accepted --> closed-fixed
     
  • Kjell Petersen

    Kjell Petersen - 2005-01-10

    Logged In: YES
    user_id=860965

    The changes to MAGEContentHandler have been checked in to
    the CVS source. I propose to wait with generating a new
    release to after the Stanford jamboree, to include a larger
    number of features/bugfixes in the release.

    I have a set of jar files that I can distribute upon
    request, and I will monitor the mailing list.

     

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