Re: [cellml-discussion] CellML DOM API 1.4, CORBA and Java help
Thanks for the reply. There is a CellML-API that was developed in Java some years ago. For our project, we particularly want to use the modularity available in CellML 1.1. in particular the ability to integrate more than one CellML file in together. This is actually the reason why we want to use CellML in our projects. I'm not sure if an old API would have this capability? 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. Thanks. I've added myself to the tracking for this bug. Regards, Morgan ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] CellML DOM API 1.4, CORBA and Java help
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: [EMAIL PROTECTED] [mailto:cellml-discussion- [EMAIL PROTECTED] 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Best Regards, Justin Marsh. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] CellML DOM API 1.4, CORBA and Java help
Randall Britten wrote: 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. Hi, Please note that I have created a tracker item for the question at https://tracker.physiomeproject.org/show_bug.cgi?id=1119 and answered some of the questions there. If you are interested in following this issue, you will be able to create an account on the tracker and add yourself to the CC list, so you will receive mail every time a comment is added to the tracker item. Best regards, Andrew 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: [EMAIL PROTECTED] [mailto:cellml-discussion- [EMAIL PROTECTED] 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Best Regards, Justin Marsh. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list
