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@imedina imedina released this 20 Sep 16:53
· 10691 commits to develop since this release
v1.2.0
118b3d0

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

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