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Hi

While I think that the approach you are taking to use the CellML api via
CORBA is probably your best option at the moment, there is one other option
to consider. There is a CellML-API that was developed in Java some years
ago. Sarala uses this for her work. While it is not actively maintained,
it may be worth looking at, and so should be mentioned. I don't know of any
locations on the web where it is available, but one or two people have
copies of it on their systems.

Does anyone else have some info on the old Java-CellML api?

Also note that we do recognise the importance of making the CellML api
accessible from Java, please see
https://tracker.physiomeproject.org/show_bug.cgi?id=306, and we will try and
help you with this.

Regards,
Randall

> -----Original Message-----
> From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion-
> bounces at cellml.org] On Behalf Of Morgan Taschuk
> Sent: Thursday, 19 June 2008 3:47 a.m.
> To: CellML Discussion List
> Subject: [cellml-discussion] CellML DOM API 1.4, CORBA and Java help
>
> Hello!
>
> Having failed using the CellML 1.1 spec to generate Java bindings, I'm
> trying to install the CellML DOM API 1.4 on Kubuntu Gutsty 7.10 and
> bind it to Java with CORBA. I'm having (several) problems.
>
> 1) I can't start the CORBA server. I've found the appropriate files, I
> think, under CellML_DOM_API_1_4/sources/cellml_corba_server, but I
> can't actually get the server to start. There appears to be a fragment
> of a make file in that dir, but I don't know where the super make file
> is located. A general make on the project doesn't touch that
> directory.
>
> A side thought: there are scripts to start the server in
> CellML_DOM_API_1_4/scripts/, but they're hard-coded to
> CELLML_BIN_DIR=/people/amil082/code/CellML_DOM_API. The commented out
> section #CELLML_BIN_DIR=/usr/sbin points to an empty directory for me.
>
> 2) Related to 1), I found the Physiome tracker item #254
> (https://tracker.physiomeproject.org/show_bug.cgi?id=254) and saw that
> the configure script is fairly new, so I did a 'make clean' and 'make
> distclean' on the project and tried running 'aclocal && autoconf &&
> automake'. That didn't work, so I tried cleaning again, and re-running
> configure. Now make doesn't work! Output:
>
> CellML_DOM_API_1_4$ make
>
> make all-recursive
> make[1]: Entering directory `/home/mtaschuk/Desktop/CellML_DOM_API_1_4'
> Making all in gsl
> make[2]: Entering directory
> `/home/mtaschuk/Desktop/CellML_DOM_API_1_4/gsl'
> Makefile:314: warning: overriding commands for target `distclean'
> Makefile:250: warning: ignoring old commands for target `distclean'
> rm -f gsl*.h
> HEADERLIST="../gsl*.h ../*/gsl*.h"; \
> for h in $HEADERLIST; do \
> BASENAME=`basename $h`; \
> test -r $BASENAME || ln -s $h $BASENAME; \
> done
> make[2]: Leaving directory
> `/home/mtaschuk/Desktop/CellML_DOM_API_1_4/gsl'
> Making all in utils
> make[2]: Entering directory
> `/home/mtaschuk/Desktop/CellML_DOM_API_1_4/utils'
> /bin/bash ../libtool --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I..
> -g -O2 -c -o placeholder.lo `test -f 'placeholder.c' || echo
> './'`placeholder.c
> ../libtool: line 1314: func_opt_split: command not found
> libtool: Version mismatch error. This is libtool 2.2, but the
> libtool: definition of this LT_INIT comes from libtool 2.1a.
> libtool: You should recreate aclocal.m4 with macros from libtool 2.2
> libtool: and run autoconf again.
> make[2]: *** [placeholder.lo] Error 63
> make[2]: Leaving directory
> `/home/mtaschuk/Desktop/CellML_DOM_API_1_4/utils'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/home/mtaschuk/Desktop/CellML_DOM_API_1_4'
> make: *** [all] Error 2
>
> 3) I used idlj to generate the Java binding. That worked, but now I
> have about 400 interfaces in CellML_DOM_API_1_4/interfaces/cellml-api
> and NO idea where to start.
>
> Help?
>
> Regards,
> Morgan
>
>
> On Wed, Jun 18, 2008 at 6:03 AM, Justin Marsh <j.marsh at auckland.ac.nz>
> wrote:
> > Hi all,
> >
> > The CellML DOM API 1.4 has now been released at
> > http://www.cellml.org/downloads/cellml_api/releases/1.4
> >
> > Should you find any bugs in this release, or have feature
> > requests, please report it to our bugtracker at
> > https://tracker.physiomeproject.org, or alternatively email
> > me at j.marsh at auckland.ac.nz
> >
> > Best Regards,
> > Justin Marsh.
> > _______________________________________________
> > cellml-discussion mailing list
> > cellml-discussion at cellml.org
> > http://www.cellml.org/mailman/listinfo/cellml-discussion
> >
> _______________________________________________
> cellml-discussion mailing list
> cellml-discussion at cellml.org
> http://www.cellml.org/mailman/listinfo/cellml-discussion

---

• [cellml-discussion] CellML DOM API 1.4, CORBA and Java help, Morgan Taschuk, 06/19/2008
  • [cellml-discussion] CellML DOM API 1.4, CORBA and Java help, Randall Britten, 06/19/2008
    • [cellml-discussion] CellML DOM API 1.4, CORBA and Java help, Andrew Miller, 06/19/2008
    • [cellml-discussion] CellML DOM API 1.4, CORBA and Java help, Andrew Miller, 06/19/2008
  • Message not available
    • [cellml-discussion] CellML DOM API 1.4, CORBA and Java help, Morgan Taschuk, 06/19/2008
      • [cellml-discussion] CellML DOM API 1.4, CORBA and Java help, Sarala Dissanayake, 06/20/2008

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