Issues:
Every class that has an association or composition eventually will need its own custom view page template, e.g. sed_view. For the moment I have set the default view for these classes to dev_view ( a copy of base_view ).
An association in UML is cast as a ReferenceField in the resulting class schema. Open the association and add the widget:label tag to the class that is being associated.
The default description text for a class should be a informative description of the class, not the instance, derived from the SED-ML manual.
Apply 'searchable' tags to the appropriate class attributes.
I choose 'isTidyHtmlWithCleanup' as the MathML validator. Will this work?
What should be added to our implementation of SED-ML to make it more than merely a mirror image of the SED-ML XML format?
- The ability to attach files at various points, e.g. parameter files.
- Additional output types, e.g. animations.
- Custom page templates
- Custom search form
- Custom catalog indexes
- Custom portlet(s)
- Custom viewlet(s)
Found an article on SBRML - a markup language for associating systems biology data with models. At a glance the schema seems bigger than SED-ML's, but SBRML appears to be SBML specific.
Spoke with Chris about publishing the Mercurial repositories and deploying Plone. Both can be accomplished in their own project space on a server in the DMZ. Chris said he would supply me with login credentials for both accounts. I will install Plone and Chris (or Maarten) will help me configure Apache/nginx and Varnish. Chris will install the required Mercurial packages; after which I can clone the repositories to their new home.
Added simplugin.h to list of header files. NB: this is the only tutorial in which simplugin.h appears.
Declared, and defined, a virtual function named DefaultLeafML() which merely returns a QString naming a LeafML filename sans path.
Moved Cell::SetMagnification() and Cell::SetOffset() from main() to MainBase::Init().
Declare exportCellData().
Add an 'Export cell areas' to the file dropdown menu which invokes - surprise - Main::exportCellData():
void Main::exportCellData(void) {
QFile file("areas.csv");
if ( file.open( IO_WriteOnly ) ) {
QTextStream stream( &file );
mesh.CSVExportCellData(stream);
mesh.CSVExportMeshData(stream);
file.close();
}
}
Include <QTextStream>
Set the boundary_poloygon pointer to zero in the class constructor, and delete it, if it exists, in the class destructor.
Declare Compactness(), CSVExportCellData() and CSVExportMeshData():
double Compactness(double *res_compactness=0, double *res_area=0, double *res_cell_area=0); void CSVExportCellData(QTextStream &csv_stream) const; void CSVExportMeshData(QTextStream &csv_stream);
In mesh::clear(), delete the boundary_polygon only if the pointer hasn't been assigned:
if (boundary_polygon) {
delete boundary_polygon;
boundary_polygon=0;
}
Ditto for mesh::clean().
Define the code for Compactness(), CSVExportCellData() and CSVExportMeshData().
In InstallModel(), find and load the default LeafML file.
Declare DefaultLeafML():
// Default LeafML-file to be read after model startup virtual QString DefaultLeafML(void);
Define DefaultLeafML(). Returns an empty QString:
QString SimPluginInterface::DefaultLeafML(void) { return QString(); }
In Mesh::XMLReadCells() - Delete the boundary_ploygon only if its pointer has been assigned.
Wrote Simon van Mourik about his missing libiconv-2.dll.
Added a Q3FileDialog in canvas.cpp:Main::exportCellData(void) to choose where to write the exported cell data.
Added new parameters to control perodic cell exprt data.
Added code to relize perodic cell export.
Tried several alternatives for Mercurial's pretxnchangegroup.forbid_2heads hook.
Tried to install Rhode Code from: http://packages.python.org/RhodeCode.
All goes tolerably until you tick in the url; at which point RhodeCode complains that:
Exception happened during processing of request from ('127.0.0.1', 35803)
Traceback (most recent call last):
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File "/ufs/guravage/opt/Python-2.6.2/lib/python2.6/SocketServer.py", line 320, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/ufs/guravage/opt/Python-2.6.2/lib/python2.6/SocketServer.py", line 615, in __init__
self.handle()
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 442, in handle
BaseHTTPRequestHandler.handle(self)
File "/ufs/guravage/opt/Python-2.6.2/lib/python2.6/BaseHTTPServer.py", line 329, in handle
self.handle_one_request()
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 437, in handle_one_request
self.wsgi_execute()
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 287, in wsgi_execute
self.wsgi_start_response)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/cascade.py", line 130, in __call__
return self.apps[-1](environ, start_response)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Paste-1.7.5.1-py2.6.egg/paste/registry.py", line 379, in __call__
app_iter = self.application(environ, start_response)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/RhodeCode-1.0.0rc1-py2.6.egg/rhodecode/lib/middleware/https_fixup.py", line 33, in __call__
return self.application(environ, start_response)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/middleware.py", line 163, in __call__
self.app, new_environ, catch_exc_info=True)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/util.py", line 48, in call_wsgi_application
app_iter = application(environ, start_response)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/WebError-0.10.2-py2.6.egg/weberror/errormiddleware.py", line 156, in __call__
return self.application(environ, start_response)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/RhodeCode-1.0.0rc1-py2.6.egg/rhodecode/lib/middleware/simplehg.py", line 55, in __call__
return self.application(environ, start_response)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Beaker-1.5.4-py2.6.egg/beaker/middleware.py", line 152, in __call__
return self.wrap_app(environ, session_start_response)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Routes-1.12.3-py2.6.egg/routes/middleware.py", line 131, in __call__
response = self.app(environ, start_response)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/wsgiapp.py", line 98, in __call__
self.setup_app_env(environ, start_response)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/wsgiapp.py", line 203, in setup_app_env
pylons_obj.translator = _get_translator(lang, pylons_config=self.config)
File "/ufs/guravage/.archive/mas/mr/rhodecode/lib/python2.6/site-packages/Pylons-1.0-py2.6.egg/pylons/i18n/translation.py", line 165, in _get_translator
raise LanguageError('IOError: %s' % ioe)
LanguageError: IOError: [Errno 2] No translation file found for domain: 'rhodecode'
This procedure fails as before.
However, upon inspection I saw that the i18n directory was missing from my build but present in the rhodecode clone from bitbucket. While I think that the easy_install rhodecode invocation is necessary to install the various subsidiary packages, moving the cloned rhodecode into the site-packages directory seems to have made most functionality work. e.g. graphical logs and diff highlighting.
I think that if Chris can install RhodeCode, I can serve individual instance from my home directory.
Walking through the new SED-ML schema I see that they've dropped the generic simulation class and added AddXML and RemoveXML model change classes. Adding several more SED-ML examples for the symposium might still be justified - though they become obsolete the moment I introduce the new schema changes.
Tweaked .bashrc and virtualenvwrapper.sh to facilitate virtualenv and virtualenvwrapper - many unbound variables!
Pushed recent changes to repository from where Roeland can retrieve and test them.
OK. RhodeCode RC4 works out of the box, excepting cutehg and PyQt4.
Installing RhodeCode locally on the nhypnos is a real pain. In addition to the previous list of dependencies, for the caterpie, add these for the nhypnos:
OK. Forget sip bison, flex, m4, Qt and the rest. Let's install just the minimum.
First, install sqlite; we'll see in a minute that Python requires it. The sources are available at: http://www.sqlite.org/download.html.
Second, install Python. My initial attempt complained it was missing the following bits and pieces:
Python build finished, but the necessary bits to build these modules were not found: _bsddb _sqlite3 _ssl _tkinter bsddb185 dl imageop readline sunaudiodev To find the necessary bits, look in setup.py in detect_modules() for the module's name.
So install sqlite first. And, since Python's configure script doesn't have an option for it, I had to tweak setup.py to enumerate the path where it would find sqlite;
Third, install RhodeCode. I first installed it using easy_install, but while the result worked, the changelog view did not display the branch/merge graphics. I then cloned the code from its bitbucket repository:
clone https://litsol@bitbucket.org/marcinkuzminski/rhodecode
Replacing the egg installed by easy_install by this code does display the branch/merge graphics.
Fourth, setup and serve rhodecode. Following the instructions posted online at: http://packages.python.org/RhodeCode/setup.html#setup works as advertised:
paster make-config RhodeCode production.ini paster setup-app production.ini paster serve production.ini
All that's left is an apache rewrite rule directing virtualleaf.project.cwi.nl/repository to port 5000, or whaterver we change it to, on the nhypnos.
Added incrementIterations(), getIterations() and int iterations to mesh.h. incrementIterations() is called in TIMESTEP in VirtualLeaf.cpp. The actual counter, iterations is initalized to zero in the Mesh class constructor.
The iterations are inquired in two places: for the frame count in MainBase::Plot in VirtualLeaf.cpp` and for the export cell data interval in ``Main::TimeStepWrap in canvas.cpp.
The questions remain: Should we use this count, and if yes, where should it be incremented? The previous count was incremented in Main::TimeStepWrap. Or should we simply use (int)mesh.getTime()? Since this is not an ordinal count, the results look strange.