This is probably one of the most significant OpenCGA release in terms of new features and improvements.
General
Catalog
New release feature: A new release field has been added to all data models. This change enables researchers to tag or identify the data introduced in Catalog as part of different releases. Can be useful if data is ingested in batches.
JSON Web Tokens (JWT): Session tokens generated by OpenCGA have been moved to the standard JWT. This allows identifying one same user across different applications using federation among other things. Tokens are sent in the header instead of as a query parameter.
Overhaul of ACLs physical implementation: ACLs are now checked as part of the query to the database, improving the performance and reducing the number of calls made.
Multi-group support: Users can now belong to more than one group. Permissions defined to different groups of a user are resolved as the union of them.
Improve synchronisation from LDAP: If an LDAP user logs in and it was not registered in Catalog, it will be automatically imported. Besides, synchronised groups with LDAP where the user belongs or belonged to will be resynced.
Private Variable Sets and Annotations: Variable sets can now be defined as private. In such a case, only users with the new proper permission will be able to see or edit those private annotations.
Propagate permission between Samples and Individuals: A new propagate parameter has been added to both sample and individual acl webservices to also propagate permissions to the other related entries if set.
Data model fixes: Some data models such as file contained an array of sample ids instead of an array of samples. This kind of change has been applied to all missing data models to satisfy that all contain a list of other data models instead of ids.
New members group: A new internal members group has been added. This group will keep track of all the users with some kind of permission in the study. Plus, actions such as completely remove access to one user to anywhere in the study is now as easy as removing that user from the members group.
New REST web services
QA and testing: more than 1,000 acceptance tests in Fitnesse! we have added about 200 new tests
