.. header:: 
   ###Title###

.. footer:: 
   ###Page###


================
The Virtual Leaf
================


Friday 11 June 2010
-------------------

Issues:

 1. 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 ).

 2. 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.

 3. The default description text for a class should be a informative
    description of the class, not the instance, derived from the
    SED-ML manual.

 4. Apply 'searchable' tags to the appropriate class attributes.

 5. I choose 'isTidyHtmlWithCleanup' as the MathML validator. Will
    this work?

 6. 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? 

     a. The ability to attach files at various points, e.g. parameter files.

     b. Additional output types, e.g. animations.

     c. Custom page templates

     d. Custom search form

     e. Custom catalog indexes

     f. Custom portlet(s)

     g. Custom viewlet(s)


Friday 24 September 2010
------------------------

To Do:
 1. Publish our mercurial repositories (Chris/Martin). This may mesh with deploying Plone.

 2. Create a vleaf mailing list (Henk).

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.



Monday 27 September 2010
------------------------

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.



Tuesday 5 October 20010
-----------------------


tutorial0.pro
+++++++++++++

Added simplugin.h to list of header files. NB: this is the only
tutorial in which simplugin.h appears.


auxingrowthplugin.h
+++++++++++++++++++

Declared, and defined, a virtual function named ``DefaultLeafML()``
which merely returns a QString naming a LeafML filename sans path.



VirtualLeaf.cpp
+++++++++++++++

Moved ``Cell::SetMagnification()`` and ``Cell::SetOffset()`` from
``main()`` to ``MainBase::Init()``.


canvas.h
++++++++

Declare ``exportCellData()``.


canvas.cpp
++++++++++

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();
    }
  }


mesh.h
++++++

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);


mesh.cpp
++++++++

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()``.



modelcatalogue.cpp
++++++++++++++++++

In ``InstallModel()``, find and load the default LeafML file.

simplugin.h
+++++++++++

Declare ``DefaultLeafML()``::

  // Default LeafML-file to be read after model startup
  virtual QString DefaultLeafML(void);


simplugin.cpp
+++++++++++++

Define ``DefaultLeafML()``. Returns an empty ``QString``::

 QString SimPluginInterface::DefaultLeafML(void) { return QString(); }


xmlwrite.cpp
++++++++++++

In ``Mesh::XMLReadCells()`` - Delete the boundary_ploygon only if its
pointer has been assigned.



Wednesday 6 October 2010
------------------------

Wrote Simon van Mourik about his missing libiconv-2.dll.


Thursday 7 October 2010
-----------------------

Added a Q3FileDialog in ``canvas.cpp:Main::exportCellData(void)`` to
choose where to write the exported cell data.


Friday 8 October 2010
---------------------

Added new parameters to control perodic cell exprt data.

Added code to relize perodic cell export.



Monday 11 October 2010
----------------------

Mercurial hooks
+++++++++++++++

Tried several alternatives for Mercurial's ``pretxnchangegroup.forbid_2heads`` hook. 

1. http://bitbucket.org/dgc/headcount: **Headcount** ``ui`` complains of a missing data member
2. http://stackoverflow.com/questions/1705921/useful-mercurial-hooks: **forbid2_heads.py** doesn't load
3. http://davidherron.com/node/961: **forbid2_heads.sh** works as advertised


Mercurial Repositories
++++++++++++++++++++++

Tried to install Rhode Code from: http://packages.python.org/RhodeCode. 

1. http://bitbucket.org/marcinkuzminski/rhodecode
2. http://packages.python.org/RhodeCode, http://pypi.python.org/pypi/RhodeCode/1.0.0rc3
3. http://hg.python-works.com (demo,demo)
4. http://bitbucket.org/bfrog/cutehg
5. http://pypi.python.org/pypi/SIP, http://www.riverbankcomputing.com/hg/sip
6. http://pypi.python.org/pypi/PyQt
7. http://ask.github.com/celery

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'


RE-INSTALL
++++++++++

1. easy_install mercurial
2. mkdir src
3. cd src
4. hg clone http://www.riverbankcomputing.com/hg/sip
5. cd sip
6. python build.py prepare
7. python configure.py
8. make
9. make install
10. cd \.\.
11. wget http://www.riverbankcomputing.com/static/Downloads/PyQt4/PyQt-x11-gpl-4.7.7.tar.gz
12. tar xzf PyQt-x11-gpl-4.7.7.tar.gz
13. cd PyQt-x11-gpl-4.7.7
14. python configure.py
15. make
16. make install
17. cd \.\.
18. hg clone https://litsol@bitbucket.org/bfrog/cutehg
19. cd cutehg
20. python setup.py build
21. python setup.py install
22. cd \.\.
23. easy_install rhodecode, http://pypi.python.org/pypi/RhodeCode/1.0.0rc2


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.



Tuesday 12 October 2010
-----------------------

RhodeCode
+++++++++

I think that if Chris can install RhodeCode, I can serve individual
instance from my home directory.


SED-ML L1V1RC1
++++++++++++++

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.


Wednesday 13 October 2010
-------------------------

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.



Friday 15 October 2010
----------------------

Rhodecode
+++++++++

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:

1. Python
2. Bison (for sip)
3. Flex (for sip)
4. m4 (for Bison)
5. Qt (for PyQt)
6. GLIBCXX_3.4.9 (for Qt) - I draw the line at (re)installing GCC!

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.


The Virtual Leaf
++++++++++++++++

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.