Hi All,
What's the state of the Example XML files? I also had someone else asking
for BioAssay/BioAssayData examples.
Cheers,
Michael
-----Original Message-----
From: Rengakrishnan Subramanian [mailto:subbu@...]
Sent: Thursday, October 24, 2002 3:05 PM
To: Miller, Michael (Rosetta)
Subject: RE: [Mged-mage] Bug Report in MAEstk
Thats great to hear. I will try my hand on it too. In the meantime, are
there
any other sample test programs that I can use to test MAGE-Java?
--subbu
On Thu, 24 Oct 2002, Miller, Michael (Rosetta) wrote:
>Date: Thu, 24 Oct 2002 14:49:34 -0700
>From: "Miller, Michael (Rosetta)" <Michael_Miller@...>
>To: 'Rengakrishnan Subramanian' <subbu@...>
>Cc: 'mged mage' <mged-mage@...>
>Subject: RE: [Mged-mage] Bug Report in MAEstk
>
>Hi Subbu,
>
>The Java parsing code is still a work in progress. I've not been able to
>work on it since the beginning of this year, but it's good that Kjell is
>taking a crack at it. And anything you can add would be appreciated.
>
>Michael
>
>Michael Miller
>Senior Application Developer
>Rosetta Biosoftware
>michael_miller@...
>www.rosettabio.com
>
>
>> -----Original Message-----
>> From: Rengakrishnan Subramanian [mailto:subbu@...]
>> Sent: Thursday, October 24, 2002 2:16 PM
>> To: Kjell Petersen
>> Cc: Mged-Mage; Roby Joehanes
>> Subject: Re: [Mged-mage] Bug Report in MAEstk
>>
>>
>>
>> Thanks for the quick response.
>>
>> I downloaded the latest mage-src from
>> http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/mged/MAGE-Java/
>> mage-src.jar (says
>> 3 weeks old). It had compile errors, when I improted it into
>> eclipse. (If I
>> remember right, 34 compile errors).
>>
>> I also tried getting MAGE-Java/ as a module with all the java
>> and class files. I
>> tried running org/biomage/tools/xmlutils/ImportExport.java
>> file. It would crash
>> with the error:
>>
>> Exception in thread "main" java.lang.NoClassDefFoundError:
>> org/biomage/tools/xmlutils/MAGEContentHandler$Association
>>
>> On exploring this, I saw that the directory
>> org/biomage/tools/xmlutils/ had
>> MAGEContentHandler$Assn.class and not
>> MAGEContentHandler$Association.class.
>>
>> I was wondering if you could suggest me a stable version of
>> MAGE-Java. I would
>> greatly appreciate if you could help me out with this.
>>
>> thanks again,
>> --subbu
>>
>> On Thu, 24 Oct 2002, Kjell Petersen wrote:
>>
>> >Date: Thu, 24 Oct 2002 13:08:14 +0200 (CEST)
>> >From: Kjell Petersen <kjellp@...>
>> >To: Rengakrishnan Subramanian <subbu@...>
>> >Cc: Mged-Mage <Mged-mage@...>,
>> > Roby Joehanes <robbyjo@...>
>> >Subject: Re: [Mged-mage] Bug Report in MAEstk
>> >
>> >
>> >Hi!
>> >
>> >The tar.gz/jar versions are quite old, I started with these
>> but quickly
>> >started using the CVS version instead. The current one is still not
>> >complete, but changes are just around the corner.
>> >
>> >Cheers,
>> >Kjell
>> >
>> >On Wed, 23 Oct 2002, Rengakrishnan Subramanian wrote:
>> >
>> >>
>> >> Hi all,
>> >>
>> >> We downloaded MAGEstk java source code from
>> >>
>> http://prdownloads.sourceforge.net/mged/MAGE-Java-2002-02-22-s
>> rc.tar.gz and
>> >> tried to use it. We encountered the following:
>> >>
>> >> 1. We compiled using JDK 1.4 and encountered atleast 10
>> compilation errors, which
>> >> included errors like
>> >> return = true;
>> >> xyz.lenght();
>> >>
>> >> We rectified these compilation errors. Also, We tried
>> compiling this using
>> >> Eclipse (an IDE, http://www.eclipse.org) and we
>> encountered the same
>> >> compilation errors.
>> >>
>> >> 2. After successful compilation, we compiled and ran :
>> >>
>> >> org/biomage/tools/xmlutils/Importer.java Emblyeast.xml
>> >>
>> >> and encountered the following error:
>> >> Illegal parameter exception: wrong number of arguments at
>> >> parser.parse(asArg[0]);
>> >>
>> >> in the Importer.java file.
>> >>
>> >> 3. We investigated the reason behind this error and it turns out:
>> >>
>> >> a. MAGEContentHandler.java has a problem with its
>> makeAssociation method.
>> >>
>> >> b. This method relies on Java Reflection API to resolve
>> the XML tags.
>> >>
>> >> c. We saw that there is a method overloading in
>> addToContact_list() in
>> >> AuditAndSecurity_package.java file in AuditAndSecurity/
>> directory. The
>> >> reflection API resolves method name using only the
>> 'name' of the method and
>> >> not according to the parameters and their types, which
>> leads to an error
>> >> invoking setMethod.invoke() in MAGEContentHandler.java file.
>> >>
>> >> d. We fixed this by checking the parameters and their types.
>> >>
>> >> e. However, we encountered many more such errors.
>> >>
>> >> 4. a. We are wondering if we are making any mistakes.
>> >>
>> >> b. Has anyone else encountered these and tried to resolve them?
>> >>
>> >> c. It would be of great help if anybody can provide us
>> with feedback/input
>> >> to resolve these.
>> >>
>> >>
>> >> thanks and best regards,
>> >> --subbu
>> >>
>> >>
>> >>
>> >>
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>> >
>>
>>
>>
>>
>>
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