Home

Welcome to the Wiki of Shanoir‐NG !

• The Shanoir-NG Wiki is the first source of information.
• From this Wiki all additional informations will be linked.
• Some additional documentations (mostly old) can be found in /shanoir-ng/docs folder.

Find general information and news on our website:

• Project Shanoir
• News

Users

User tutorial

• User tutorial (linked on home page of Shanoir-NG Web-GUI)

Roles and rights

• Specification on roles and rights
• Specification on data user agreement (DUA)
• Specification on access by center limitation

Solr search/downloads

• Search specification
• Download options

Study storage volume

• Specifications

Subject tags

• Specification
• Tutorial

ShanoirUploader (includes ShanoirToolKit/ShanoirTK since Shanoir-NG introduction)

• ShanoirUploader Wiki

Virtual Imaging Platform (VIP)

• VIP processing through Shanoir

Operations (OPS): installation, updates and maintenance (administration)

What do I have to do to install Shanoir-NG on a new server?

• Deployment, see readme.md
• Deployment of shanoir-ng-dev, see installation notes

Maintenance

• Scheduled tasks
• Storage
• Import from PACS configuration

Virtual Imaging Platform (VIP)

• Configuring connection with a VIP instance

Developers (DEV)

Roadmap

• Roadmap process
• Roadmap
• Release notes

Shanoir-NG-REST-API

• REST-Tutorial
• MS Studies
• MS Import
• MS Datasets
• MS Datasets Details
• MS Preclinical

DICOMWeb-REST-API

• DICOMWeb

Viewers

• OHIF-Viewer

Architecture (Macro + Micro)

• Integration of new MS Boutiques

Setup your development environment

• Installations: Git Java Maven Eclipse
• Installation: Docker

Docker + Docker Compose

• Remote debugging with docker-compose
• Docker compose with Shanoir front on host-machine
• Build and run Shanoir front with docker-compose via volume sharing
• Installation of Bruker2Dicom, Dicom2Nifti docker image
• How redeploy a single container using docker-compose

Contributions

• Contributing to Shanoir
• Shanoir-NG Workflow based on forking workflow: The steps to follow is described by command lines and schemas in the google doc

Imports and exports

• Imports overview
• Imports architecture
• Import DICOM Process Steps
• Import DICOM ShanoirUploader
• Mass Import ShanoirUploader
• BIDS Specification
• MR Spectroscopy
• PT Specification
• Shanoir Exchange Format (SEF)
• Study Cards Specification
• Re-apply Study Cards Specification
• Develop a new import type

Security/Keycloak

• Securing Keycloak

DCM4CHEE (internal PACS of Shanoir-NG)

• DCM4CHEE GitHub page
• DICOM files storage
• Connect to web interface of dcm4chee archive 5

Angular frontend

• Web components

Microservices

• Keycloak
• Challenge scores
• How to add a new micro-service

Testing

• Automated testing: Selenium tests
• Tests configuration
• Security Integration Tests

Qualif

We can redeploy on qualif:

• « build-shanoir-ng-new » pour reconstruire les images,
• et « reset-qualif-shanoir » pour relancer le déploiement (50 min)
• /var/log/dk/deploy-nightly-qualif.log
• /var/log/dk/qualif/dbdump-pre-migration.sql all databases before migration (as created by the ms)
• /var/log/dk/qualif/dbdump-post-migration.sql all databases after migration
• /var/log/dk/qualif/dbdump-prod-studies.sql production users db
• /var/log/dk/qualif/dbdump-prod-users.sql production studies db
• dk exec -t -i qualif-database mysql -uxxxx -pxxxx
• Logs: /var/log/dk/qualif/shanoir-ng
• https://shanoir-qualif.irisa.fr/auth/admin

ShanoirToolKit (ShanoirTK)

• not maintained anymore as separate tool, now part of ShanoirUploader to provide the same functionality