v1.1.2

Second maintenance release. The main issue fixed is to read number of connections from the configuration file: 8d2971b

v1.1.1

Maintenance release, the only fix is in the VCF exporter https://github.com/opencb/opencga/issues/610

v1.1.0

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 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

v1.0.2

Maintenance version 1.0.2

v1.0.1

Storage:

• Fix a bug when querying using the new Solr index: some variants were not returned under some filter combinations. (#568)
• Add assembly parameter to CellBase REST annotator (#571)

Catalog:

• Project owner is now returned when querying for shared projects (#564)
• Minor bug fix in command line. (#563 )
• Individual can be associated to a sample when creating a new sample (previously this was made in two steps). (#566)
• Opencga swagger documentation now works in HTTPS (#565)
• Added missing parameters to individual/update endpoint. (#562)

First stable version v1.0.0

Frist production ready version 1.0.0

New development version v1.0.0-rc3

The most important changes are:

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

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'

Development version v1.0.0-rc2.1

New pre-release version 1.0.0-rc2.1

OpenCGA v0.7.0

Most important changes include:

• OpenCGA-Storage
  • Optimized variant model
  • Better support for multi-allelic variants
  • VCF transform step generates an avro file, much smaller.
  • Extended and improved Variant filters
  • Ga4gh models and WS
• Catalog
  • Catalog audit system
  • Catalog authorization with ACLs and roles
  • Annotations for individuals
• General
  • Python client

OpenCGA v0.6.0

Most important changes include:

• Upgrade java version from 1.7 to 1.8
• Change license to Apache License 2.0
• Variant Storage study-oriented, instead of file-oriented
• MongoDB variants data model optimizations
• Sample annotations with complex structures
• Implemented missing catalog methods
• Added RestWS tests
• Many small bugfixes and improvements