We are pleased to announce new version 1.2.0. This is probably one of the biggest and most significant OpenCGA release in terms of new features and improvements, during this release a total of 23,528 additions and 16,107 deletions were applied. To highlight some of the most significant improvements: now you can define internal releases, more secure session tokens with JWT, huge performance improvement in ACl queries, many new acceptance tests, ... Here you can find an overview of the most notable improvements.

General

More coming soon.

• QA and testing: We have now more than 400 acceptance tests with Fitnesse! This release has added about 50 new tests. The test coverage is now about 60%.
• Command line: some bugs as count functionality are fixed. Some cleanups, new parameters added and an improved help are other improvements.

Catalog

• Allow to create Project releases: A new release field has been added to data models. This allows users to define and create internal releases automatically for any project without having to replicate the data. Therefore, Catalog and Variants data are now be associated with a particular release, you can query Catalog data in any previous release.
• JSON Web Tokens (JWT): Session tokens have been migrated to JWT (https://jwt.io/) standard. JWT allows to implement federated systems by authenticating users across different applications. JWT session tokens are not stored in Catalog any more, this has reduced the number queries needed during login. Tokens are now sent in the HTTP header instead of old sid query parameter, note that sid query parameter will still work during next releases.
• Rewrite ACLs implementation: ACL permissions have been re-implemented to improve performance, robustness and reduce code. Thanks to this most of the permissions are now part of the queries reducing the number of queries needed.
• Multi-group support: Users can now belong to more than one group. Permissions defined in different groups of one user are resolved as the union of them.
• Improve synchronisation from LDAP: Users will be registered and imported automatically the first time they login. Also, the groups they belong to will be synced in each login, this will provide and automatic validation and synchronisation with LDAP groups.
• Private Variable Sets and Annotations: Variable Sets can now be defined as private. In such a case, only users with the a new permission will be able to see or edit private annotations from those variable sets..
• Propagate permission between Samples and Individuals: A new propagate parameter has been added to both Sample and Individual ACL web service to also propagate permissions to the other related entries.
• Improve data model consistency: Some data models such as File contained an array of sampleIds instead of an array of Sample objects, this is inconsistent with other data models. This type of change has been applied to File, Job and Cohort data models.
• New members group: A new default special group members has been added. This group will keep track of all the users from the groups or with any permission in the study. This members group allows to keep track of all users in one study making easier to remove users. Also, permissions can be set to members groups.
• New REST web services: New search web service in project has been added.

As a result of some of these changes Catalog performance has been improved significantly and the number of queries executed have dropped to 50%.

Storage

Coming soon.

Breaking changes

In order to implement some of the improvements and new features in Catalog such as release we had to do some changes in the database. We have implemented several migration scripts that can be run to upgrade to new schema. You can find the scripts at https://gist.github.com/pfurio/2ca0cb2da46eac9e309101066f8758f5.

Another migration script has been developed to fix a small bug in Variant Storage database, you can find it at https://gist.github.com/j-coll/3dec01abc70644943d33de78105c633e.

Sorry for any inconvenience caused. We do not expect many more changes in coming releases, as always we will try to minimise them.

Issues

You can find more detailed information about all issues at https://github.com/opencb/opencga/issues?q=is%3Aissue+milestone%3Av1.2.0+is%3Aclosed