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OpenCGA is still under a very active development, we are heading to the first stable release in 2017 Q2, you can find more detailed information in GitHub Releases at https://github.com/opencb/opencga/releases.

1.1.0 (Not released yet)

Catalog

  • [ENHANCEMENT] Support integers and floats separately in variables and annotations. (#545)
  • [BUG] Fix link race condition. (#551)
  • [FEATURE] New parameter "propagate" added to individual entry point when setting permissions to also propagate permissions to the related samples. (#558)
  • [FEATURE] Added support to give permissions using queries in sample, individual and file entry points. (#560)
  • [CHANGE] Acl entry points improved. (#561)
  • [FIX] Queries to webservices are no longer returning parameters that are not of interest. (#569)
  • [FEATURE] Added new admin command line to synchronise and add users from LDAP groups. (#573)
  • [FEATURE] Added new family data model. (#582)
  • [FEATURE] Added list<Sample> to individual/create entrypoint. (#583)
  • [FEATURE] Added new /status, /ping and /about entrypoints. (#572)
  • [ENHANCEMENT] Support creating an individual when calling to the sample create entrypoint. (#586)
  • [DEPRECATE] Deprecated species from individual data model. (#588)
  • [ENHANCEMENT] Support passing a name or id in parameter variableSetId in the corresponding endpoints. (#589)
  • [ENHANCEMENT] Support passing an array of annotationSets when creating an annotable entry (sample, cohort, individual and family). (#590)
  • [ENHANCEMENT] Added new type parameter to sample data model. (#591)
  • [FEATURE] Added father and mother information in attributes parameter of individual. (#592)
  • [ENHANCEMENT] Added support to change public/private user registration  (#594)

Variant Storage

  • [FEATURE] Make optional to merge non same overlappings variants in MongoDB (#574)
  • [ENHANCEMENT] Filter VcfRecord before converting into Variant object when possible (#577)
  • [ENHANCEMENT] Not loading new overlapping variants in HBase (#581)
  • [FEATURE] Implement a benchmark framework for OpenCGA Storage (#248)

Relevant changes - migration

  • Add new permissions to admin user in the general configuration file. To add: VIEW_STUDY, UPDATE_STUDY and SHARE_STUDY
  • Added sampleIds parameter in each individual entry. 
  • For #545 we will need a migration script that will convert all the NUMERIC variables into DOUBLE.
  • Changes of #574 require to execute a migration script on all Variants databases in MongoDB: opencga_574_add_studies_field_to_stage.js


1.0.0

Catalog

  • [FIX] Authenticated users can now see public data (#501)
  • Permissions assigned to individuals are directly propagated to samples (#509)
  • [CHANGED] CREATE and UPDATE permissions have been merged into WRITE (#506)
  • [CHANGED] Permissions given to folders are now propagated in the database (#505), this increase significantly the performance of the ACL resolution 
  • [CHANGED] Changes in session data model (#479)

Storage

  • Complete the implementation of exclude and include of fields for Variant queries (#515)

Clients

  • [Python] new Python client implemented following the same architecture than Java and Javascript clients (https://github.com/opencb/opencga/pull/516). This improves the quality significantly and add many new features, thanks Antonio Rueda!
  • Java and Javascript client libs use always POST when available

Server

  • [REST] Add new files/create using POST to create new folders and files with some content (#514)
  • [REST] Rename parameters from acl/update (2617993)
  • [REST] Hide from Swagger all create and update ACL web services using GET (cbea817), these should always use POST, this affects to studies, samples, files, ... (these will be removed in version 1.1) 
  • [REST] Complete the implementation of exclude and include of fields for Variant queries
  • [REST] Remove from users the GET methods to create and update filters (5125a22)
  • [REST] Add a warning to Swagger to all create and update methods using GET (ee6d66). It is encourage that all create and update actions use always POST
  • [GRPC] Complete the implementation of exclude and include of fields for Variant queries

1.0.0-rc3 (January 2017)

General

  • Major changes in maven properties and configuration files. (#480)
  • catalog-configuration.yml and configuration.yml have been merged. (#476)

Catalog

  • Added support to fetch shared projects and studies.
  • Added organism information to the project data model. (#455)
  • Renamed diskUsage and diskQuota for size and quota respectively in all data models were present.
  • Closed sessions are now removed from the array of sessions (but they can still be found in the audit collection). (#475)

Storage

  • Improve error handling for storage operations (#447#463#465)
  • Add param --resume to opencga-analysis.sh and opencga-storage.sh command line (#465)
  • Import and export variants datasets (#459#460)
  • Enable gRPC as top level feature (#492)
  • New top layer StorageManager connecting catalog with storage (#486)
  • Shade proto and guava dependencies for Hadoop (#440)

Server

  • Create and update webservices have been all implemented via POST.

Known issues

  • OpenCGA storage hadoop is not available in this version. To compile use this line:

    mvn clean install -DskipTests -pl '!:opencga-storage-hadoop-core'

1.0.0-rc2 (November 2016)


1.0.0-rc1 (September 2016)

This release constitutes the first release candidate (RC1). This is the biggest release ever with more than 1,400 commits, special mention to j-coll and pfurio for their contribution in Catalog, Storage and Server components.

General

  • New command line interfaces (CLI) for users (opencga.sh), admins (opencga-admin.sh) and analysis (opencga-analysis.sh)

Catalog

  • New catalog configuration file using YAML.
  • New authorisation method. A big list of permission have been defined.
  • New smart id resolver. Numerical ids are no longer mandatory and ids are now resolved internally given the alias.
  • New and improved java and python command lines.
  • New javascript, java and R client implementations.
  • Support for annotations in cohorts.

Storage

  • Many performance improvements and fixes in MongoBD storage engine, the most notable include a new load strategy to improve file merging scalability
  • New storage engine based on Apache HBase, this is completely functional but is tagged as beta until more tests are done.
  • New custom variant annotation implemented

Server

  • An experimental gRPC server implemented


v0.7.0

Third Beta

v0.6.0

Second Beta

v0.5.0

First Beta

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