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Introduction

This is the Physiome Model Repository (PMR) core package and add-on for Plone to enable the functionality of the entire PMR software suite.

PMR is a software system designed to provide management of models in a user friendly way using a content management system (CMS), which provides the management interface to the underlying model and associated data, which are stored using a distributed version control system (DVCS). This CMS used depended on by PMR is Plone, and currently Mercurial is the only DVCS supported through the extension package pmr2.mercurial.

PMR is constructed in a way where it is extensible, thus additional storage method can be implemented alongside Mercurial along with the presentation views which can be customized for mission specific purposes, such as for the presentation of CellML models (through the package cellml.pmr2) and FieldML (fieldml.pmr2).

The official instance of this software is also called the Physiome Model Repository. It currently hosts over 1000 CellML models and a handful of FieldML models (and its precursor, exnode/exelem models).

Features

Integration of Mercurial with Plone.

  • Can function as a standalone Mercurial repository with the ACL managed by Plone. These are represented as a Workspace in PMR.
  • Push/pull to the Mercurial instance managed by Plone using the same URI as is within the Plone instance.

Extensible presentational layer.

  • Presentation of data within the version control system in PMR are done using Exposures. One may consider them wrappers around specific revisions around a Workspace, which provides a fixed point for users to process the model and/or data there to present them to other users. The default only generators for RST and HTML.
  • Further views will have to be created as extensions to PMR. Please refer to cellml.pmr2 and fieldml.pmr2 for examples on how to extend PMR to suit your presentational needs.

All of PMR is fully extensible.

  • Even the storage layer can be extended. Please refer to internal documentations. At some point a GIT based storage library will be fully supported. Please refer to the pmr2.git package.
  • This extensibility is based on zope.component and related libraries.

Please refer to the changelog for more details.

Installation

Please refer to pmr2.buildout for installation of this package, as the correct installation procedure is tightly tied into buildout.

Known issues and caveats

To report PMR related issues, please use the Physiome Tracker.

Other known minor caveats related to administration of PMR:

  • Some advanced Zope management knowledge may be required.
  • Sometimes pushing doesn't work after installation. This is due to the hgauthpas (The Mercurial credential authentication provider) not placed in the correct order. From the ZMI, go to the acl_users under the Plone instance, plugins, Challenge Plugins, move hgauthpas to the top under Active Plugins.