Introduction

This is the buildout for PMR2. This set of configuration is used to build the complete PMR2 project for development and the staging and production sites for the Physiome Model Repository.

Usage

To ease maintenance, the buildout configuration is split up into separate files for specific tasks, such as development, staging or deployment. Please refer to the specific configuration file for further configuration options.

Prerequisite

Before this buildout will build correctly, a number of packages and dependencies must be provided. If this is to be done on a Debian/Ubuntu based system, these packages must be installed:

• build-essential
• libxml2-dev
• libxslt1-dev
• python2.6-dev or python2.7-dev (depending on version of system python)

Debian 8 specific

• zlib1g-dev (for lxml)
• libjpeg-dev (for Pillow)

Optional Dependencies

Some of these can be made optional - just remove the unneeded packages from the eggs and the zcml sections in the buildout.cfg file.

If CellML API support is included

• gcc-4, as gcc-5+ results in compilation error.
• cmake-2.8 and above, but 3.7.2 and above may fail to generate the header files and results in compilation error
• libgsl0-dev
• omniidl4 (or packages that offer that; omniidl on Debian 7.5; some distributions may require the whole omniORB package).

If the enable-telicems flag is to be enabled, the following will also need to be present:

• bison-2.5, <3.0; >=bison-3.0 was reported to NOT work.
• flex

If virtuoso integration (for the semantic reasoning, i.e. support for the RICORDO related packages) is to be included:

• unixodbc-dev
• may need to compile virtuoso for the odbc bridge shipped with Ubuntu has reportedly cause segfaults.

Develop

To get the standard development site set up, just clone this repoistory, call bootstrap, with the specific version 1.5.2 as buildout 2 no longer isolate the system python in the way that it used to work.

After that, run the buildout as normal; this will just use the default buildout.cfg and the development site will be built.

Example:

$ git clone ${REPO_URI}/pmr2.buildout.git
Initialized empty Git repository in /.../pmr2.buildout/.git/
...
Resolving deltas: 100% (...), done.
$ cd pmr2.buildout
$ python bootstrap.py
Downloading http://pypi.python.org/.../setuptools-0.6c11-py2.6.egg
Creating directory '/.../pmr2.buildout/bin'.
Creating directory '/.../pmr2.buildout/parts'.
Creating directory '/.../pmr2.buildout/eggs'.
Creating directory '/.../pmr2.buildout/develop-eggs'.
Getting distribution for 'zc.buildout==1.4.4'.
Got zc.buildout 1.4.4.
Generated script '/.../pmr2.buildout/bin/buildout'.
$ bin/buildout

The development buildout uses mr.developer, which will then clone the repositories with the packages that make up PMR2 into the src directory. Other dependencies will then be fetched, this will take some time.

After buildout completes, the development site may be started like so:

$ bin/zeoserver-testing start  # start the zeoserver in background
$ bin/instance-testing fg      # run test server in the foreground

Or run tests associated with PMR2:

$ bin/test -s pmr2 -s cellml -s fieldml

Staging or Deployment

This is achieved using the staging or development buildout configuration. A specific a configuration file may be specified for bin/buildout. For example, if this is a deployment instance, this may be issued:

$ bin/buildout -c deploy-instance.cfg

This will not use mr.developer to clone the repository, instead the packaged versions of PMR2 related eggs will be fetched instead. The version fetched is specified in version.cfg.

Quick start on using the testing instance

Assuming the Develop section was followed, the test server should have successfully been installed and running in the foreground. Point a browser to the location (should be http://localhost:8280/). Follow the instructions on that page to create the default Plone site (if default credentials are used, it should be admin/admin for login/password).

Once the default Plone site is added, select Site Setup using the user drop-down menu on the upper-right corner of the site, then Add-ons.

On that page a list of products available for installation will be presented. Select Physiome Model Repository 2, then select Install. Any other relevant add-ons to install from that screen may be selected.

Once Physiome Model Repository 2 is installed, under the Site Setup menu there should be a new menu item called PMR2 Core Configuration, under the Add-on Product Configuration. This should also be shown under the Site Setup sidebar.

The settings present should be reviewed; while the default directories are usable, production users should change it to an alternative location outside of Zope to avoid potential issues where the Zope/Plone installer and/or buildout prune or overwrite the contents within the parts directory. When the options are configured select Apply and Create Objects to create the Workspace and Exposure containers along with the relevant filesystem locations.

Retruning back the the home page, two new tabs should become visible, which are 'workspace' and 'exposure' respectively. Select 'workspace' from the main content tabs, then using the 'Add new...' menu, select 'PMR2 Workspace' to create a new workspace.

User specific permissions to the newly created workspace can be granted with the sharing tab. If other users requires push permission that can be granted. As the owner has push permissions by default, the contents can be accessed using the respective DVCS that is backed by the current workspace.