VIP-girder-plugin

Presentation

This is a girder plugin to launch executions on VIP with girder files as inputs and results transferred to a girder folder. This plugin uses the CARMIN REST API to communicate with VIP and should also work with any procesing platform supporting CARMIN. This platform must support the External platform CARMIN module, and girder must be one of the external platform supported.

This plugins allows to :

• Use VIP from girder as from the VIP portal. It uses an user's API key to have the same permissions.
• Select a pipeline to use
• Select girder files as inputs
• Enter values for non-file inputs
• Choose the girder folder where the results will be written
• After the launch, follow in girder the advancement of the execution
• Easy access to the results when it is over

Installation

The girder prod server is installed in a virtual env in the $GIRDER_ENV folder

1. Activate the virtualenv : . $GIRDER_ENV/bin/activate
2. Stop girder with a kill $pid
3. (si le plugin est déja installé) Désinstaller le plugin
   1. pip uninstall girder_vip
   2. rm -rf $GIRDER_ENV/lib/python3.7/site-packages/girder_vip
4. pip install git+https://github.com/virtual-imaging-platform/VIP-girder-plugin.git@master
5. girder build (it could be long)
6. nohup girder serve &

Administator configuration

In the plugin configuration page, the girder administrator must :

• verify the vip url or select another CARMIN platform url
• enter the external platform name the girder server has in VIP. Please note that VIP must :
  • have the girder platform configured as an external platform
  • authorize the girder platform host to do CORS requests
• configure which collections the plugin can use as file inputs. By default there is none and only the private folders of the users will be usable by the plugin

Usage

Each user must configure its own VIP api key in its girder account in order to activate the VIP plugin

Development

The girder development server is installed in a virtual env in the $GIRDER_ENV folder. The first time, the plugin needs to be intalled as in the production installation.

Then, to test client/javascript changes :

1. Activate the virtualenv : . $GIRDER_ENV/bin/activate
2. girder build --watch-plugin vip (let it run in a seperate shell) This will automatically rebuild the plugin when a file changes in $GIRDER_ENV/lib/python3.7/site-packages/girder_vip/web_client/*/
3. Change the source files to test
   1. Either directly in $GIRDER_ENV/lib/python3.7/site-packages/girder_vip/web_client/*/
   2. Either by fetching changes in a github repository : pip install -I --no-deps git+https://github.com/my-github-user/VIP-girder-plugin.git@my-branch. Les options -I --no-deps permettent d'écraser ce qui est déjà installé et de ne pas se soucier des dépendances.