pbshm-framework 0.7.1

PBSHM Framework

PBSHM Framework

The PBSHM Framework is a preconfigured version of the PBSHM Core and module ecosystem. The goal of the PBSHM Core was to build a base application which facilitated the curation of PBSHM Modules which in turn consume PBSHM Schema data. The purpose of the PBSHM Framework is to provide a single packaged product of the PBSHM Schema, PBSHM Core, and any relevant PBSHM Modules: to showcase the available technology in an easy-to-use manner and enable anyone, regardless of their coding knowledge, to interact with the aforementioned technology.

For more information on the PBSHM Core, please see the GitHub repository. Each module included within the PBSHM Framework is linked below, with details of the module authors and any further information on how to use the module. For more information on how to create a module for PBSHM Core, please see the module template repository.

The minimum version of Python required to run the PBSHM Framework is version 3.11. Click here for details on how to install the PBSHM Framework on your local machine.

Included modules

Below are a list of modules included within the framework and links to the corresponding repositories and guides.

Module	Description	Author	Repo	Documentation
pbshm-channel-toolbox	A collection of tools to help process channel data	dsbrennan	dsbrennan/channel-tools	README
pbshm-ie-toolbox	A collection of tools to help process IE models	dsbrennan	dsbrennan/ie-tools	README
pbshm-network-mcs	An implementation of the Jaccard Index and Maximum Common Subgraph to generate network similarity scores for a a given set of IE models	jgosliga	dynamics-research-group/ag-mcs	README
pbshm-ie-visualiser	A 3D model builder for creating, editing, and viewing IE models	josiemcculloch	dynamics-research-group/pbshm-ie-model-builder	README

Installation

The simplest way to install the PBSHM Framework is via the pbshm-framework python package available through the standard pip commands. It is recommended to install the pbshm-framework package into a dedicated python virtual environment.

Use the following command to install the latest version of the pbshm-framework in your python environment:

pip install pbshm-framework

Once you have installed the PBSHM Framework on your local machine, you must configure your installation to communicate with the PBSHM Database and then you can start the framework.

Upgrade

If you installed the PBSHM Framework via the pbshm-framework python package (as described in the installation instructions): you can upgrade your installation to the latest available version through the following command in your python environment:

pip install --upgrade pbshm-framework

Configure Framework

There are two steps to configuring the PBSHM Framework: entering the details of the database configuration (configure settings), and initialising the database (initialise database).

If this is your first time installing any of the PBSHM Ecosystem, you will need to complete both steps. However, if you already have a working copy of PBSHM Core (or any associated PBSHM Module) on your local machine, you will most likely have already initialised the database with the PBSHM Schema and created a system login. Therefore, you only need to complete the database configuration step (configure settings).

Once these aforementioned steps have been completed, you can now start the framework. Please note that these configuration steps only need to be completed once. When you want to start the framework after installation, you need only use the command highlighted in the starting the framework section.

Configure Settings

To configure the system settings (database credentials, user collection, default collection, etc), simply use the following command and the system will prompt you to enter the required details (please ensure you have configured flask before completing this step):

flask --app rosehips init config

Initialise Database

To initialise the database with the latest version of the PBSHM Schema and create a login for the system, simply use the following command and the system will prompt you for any required login details and install the latest version of the PBSHM Schema into the selected database (please ensure you have configured the system settings before completing this step):

flask --app rosehips init db new-root-user

Starting the Framework

Use the following command to start flask with the rosehips app:

flask --app rosehips run

Bug reporting

If you encounter any issues/bugs with the system or the instructions above, please raise an issue through the issues system on GitHub.