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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.

1.2.0

Catalog

  • [ENHANCEMENT] Hide deprecated webservices. (#599)
  • [ENHANCEMENT] Set ontologyTerms array during Sample/Individual /create and /update webservices. (#613)
  • [FIX] Fix behaviour where individual ids are not recognized when creating new family. (#617)

1.1.0 (June 2017)

Catalog

  • [ENHANCEMENT] Support integers and floats type for variables. (#545)
  • [BUG] Fix link race condition. (#551)
  • [FEATURE] Add new parameter propagate to Individual web service when setting permissions to propagate permissions to the related samples. (#558)
  • [FEATURE] Add support to give permissions using queries in sample, individual and file web services. (#560)
  • [CHANGE] Change Acl REST web services. (#561)
  • [FIX] Not return fields that are of no interest (using include/exclude). (#569)
  • [FEATURE] Add new admin command line to synchronise and add users from LDAP groups. (#573)
  • [FEATURE] Added new Family data model. (#582)
  • [FEATURE] Add list<Sample> to individual/create web service. (#583)
  • [FEATURE] Add new /meta/status, /meta/ping and /meta/about web services. (#572)
  • [ENHANCEMENT] Support creating an Individual when calling to the Sample create web service. (#586)
  • [DEPRECATE] Deprecate species field of Individual data model. (#588)
  • [ENHANCEMENT] Deprecate usage of variableSetId. Add field variableSet to corresponding web services that accepts an id or a name. (#589)
  • [ENHANCEMENT] Support passing an array of annotationSets when creating an Annotable entry (Sample, Cohort, Individual and Family). (#590)
  • [ENHANCEMENT] Add new type field to Sample model. (#591)
  • [FEATURE] Add father and mother information in attributes field of Individual. (#592)
  • [ENHANCEMENT] Add support to change public/private User registration  (#594)
  • [DEPRECATE] Deprecate all xx/create and xx/update GET webservices. (#598)

Variant Storage

  • [FEATURE] Make optional to merge non same overlapping variants in MongoDB (#574)
  • [FEATURE] Implement a benchmark framework for OpenCGA Storage (#248)
  • [ENHANCEMENT] Filter VcfRecord before converting into Variant object when possible (#577)
  • [BUGFIX] Not loading new overlapping variants in HBase (#581)
  • [ENHANCEMENT] Increment variant size threshold for CellBase annotation (#596)
  • [BUGFIX] Fix ArrayIndexOutOfBounds when loading variants data (#597)
  • [FEATURE] Add VCF export to gRPC command line (#606)

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. 
  • Catalog changes require this migration script: opencga-1.1.0-migration.js
  • Changes of #574 require to execute a migration script on all Variants databases in MongoDB: opencga_574_add_studies_field_to_stage.js


1.0.2

General

  • [BUGFIX] Fix VCF output format (#584)

Catalog

  • [ENHANCEMENT] New dateOfBirth field added to Individual (#580) and somatic field to Sample (#576)
  • [ENHANCEMENT] Performance improvement when annotating new variants (#575)


1.0.0 (February 2017)

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

ArrayIndexOutOfBounds when loading data #597

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