v1.2.0

Catalog

• [FIX] Fix job search by input and output files. (#533)
• [ENHANCEMENT] Hide deprecated webservices. (#599)
• [ENHANCEMENT] Set ontologyTerms array during Sample/Individual /create and /update webservices. (#613)
• [FEATURE] Add the concept of release in OpenCGA. (#616)
• [FIX] Fix behaviour where individual ids are not recognized when creating new family. (#617)
• [FEATURE] Implement JWT based session management (#618)
• [ENHANCEMENT] Change List<Long> for List<Object> in corresponding data models (#621)
• [ENHANCEMENT] Make ACL permissions part of the query (#628)
• [FIX] Fix count parameter not working in search webservices and command line (#629)
• [CHANGE] Change annotationsets REST webservices. (#631)
• [FEATURE] Support multigroups (#633)
• [ENHANCEMENT] Return HTTP 403 error code when user tries to access not granted data (#636)
• [FEATURE] Add a new members group for every study (#642)
• [FEATURE] Automatically sync OpenCGA groups with external LDAP groups during login (#647)
• [FEATURE] Add new projects/search webservice (#651)
• [FEATURE] Add new confidential parameter to VariableSet data model. It allows defining confidential variable sets and corresponding annotation sets, so a new special permission will be needed to access them. (#653)
• [FEATURE] Propagate permissions from samples to individuals. (#657)
• [ENHANCEMENT] Return HTTP 401 error code when user is not successfully logged in or the token is invalid. (#658)

Variant Storage

• [FEATURE] Improve Solr integration with VariantStorage when querying (#638)
• [ENHANCEMENT] Improve Solr variant iterator by using Solr cursors (#640)
• [ENHANCEMENT] Variant Solr Search manager improvements (#639)
• [ENHANCEMENT] Configure VariantMerger and VariantNormalizer with VCFHeader (#630)
• [ENHANCEMENT] Store DisplayConsequenceType from VariantAnnotation at MongoDB (#659)
• [ENHANCEMENT] Return VariantTraitAssociation as TraitAssociation (EvidenceEntry) (#692)
• [FEATURE] Remove files from variants storage (#192)
• [FEATURE] Command line and rest endpoints for remove operations on variant storage (#623)
• [FEATURE] Simple merge mode for loading variants in opencga-storage-hadoop (#609)
• [FEATURE] VariantQueryParam INCLUDE_FORMATS. Select format fields to return (#608)
• [FEATURE] Store other genotype fields on storage-hadoop (#602)
• [FEATURE] Export variant statistics (#309)
• [FIX] Sample filter not working when the sample is in multiple files (#641)
• [FIX] Possible error loading overlaping multiallelic variants (#626)
• [FIX] Do not delete files (or related entries) from catalog if still loaded in variants storage (#625)
• [FIX] Avoid OutOfMemoryError updating storage metadata from catalog (#645)
• [FIX] Error indexing vcf files containing "variants" in the file name(#691)

Relevant changes

• CLI install changed and need two additional parameters 1: secretKey, algorithm
• Configuration file has changed and need to be adopted on all opencga installation
• No logout
• Changes on #616, #618, #621, #628 and #633 require several migration scripts to be run over the Catalog database: https://gist.github.com/pfurio/2ca0cb2da46eac9e309101066f8758f5
• Changes on #192 and #626 require to execute a migration script on all Variants databases in MongoDB: https://gist.github.com/j-coll/3dec01abc70644943d33de78105c633e
• Changes in VariantAnnotation model. See variantAnnotation.avdl
• Field "exonNumber" replaced with "exonOverlap".
• Added field "traitAssociation" that will replace "variantTraitAssociation" in next releases.

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