v1.3.2

Catalog

• [FIX] Add missing individual-sample indexes (#790)
• [FIX] Fix smart name resolution (#791)

v1.3.1

Catalog

• [FIX] Propagation of permissions sample-individual not working (#780)
• [ENHANCEMENT] Ask for admin password automatically when using admin command line (#785)
• [FIX] Filtering by file size not working (#786)

Storage

• [FIX] Read and load full VCF header in catalog (#783)
• [FIX] Fix some studies cohort stats not returned from Solr (#787)

v1.3.0

General

• [FEATURE] Admin migration command line (#690)
• [FEATURE] Implement AutoComplete for CLI (#714)

Catalog

• [REMOVE] Remove ACL from data models. (#666)
• [ENHANCEMENT] Clean old code and refactoring. (#667, #668, #669, #670)
• [ENHANCEMENT] Remove some hidden and deprecated methods from webservices and command line (#672)
• [CHANGE] Changes to family data model (#677)
• [FEATURE] Add new analysis tool webservices (#679)
• [FEATURE] Add version support for Sample, Individual and Family (#684)
• [ENHANCEMENT] Clean and remove unnecessary dependencies for the client module (#687)
• [ENHANCEMENT] Change some fields from Clinical Analysis (BETA) data model (#688, #702)
• [ENHANCEMENT] Remove unnecessary Relatives data model (#693)
• [ENHANCEMENT] Improve some individual webservices to better support the Individual-Sample relation (#701)
• [CHANGE] Change individual parameter in the sample/create webservice (#703)
• [CHANGE] Internal modification regarding the way the Sample-Individual relation was stored (#706)
• [ENHANCEMENT] Add new admins group in studies (#711)
• [ENHANCEMENT] Add new stats field to Sample data model (#717)
• [CHANGE] Rename ontologyTerms field in Sample, Individual and diseases field in Family for phenotypes (#718)
• [FEATURE] Add new option to export and import data from/to catalog (#720)
• [ENHANCEMENT] Improve groupby webservices (#721)
• [ENHANCEMENT] Support a list of ids in all GET webservices (#727)
• [CHANGE] Internal modification: Change ACL delimiter used (#740)

Variant Storage

• [FEATURE] Make use of the new VariantMetadata model from Biodata (#673)
• [FEATURE] Major support of Symbolic variants in Variants Storage (#695)
• [FEATURE] Create profiles to select hadoop flavour (#707)
• [FEATURE] Store info fields on storage-hadoop improvement storage (#704)
• [FEATURE] Allow loading multiple variant files from the same sample with non overlapping variants (#696)
• [FEATURE] New optional pipeline step "fill-gaps" (#713)
• [CHANGE] Rename some Variant REST query parameters (#751)
• [CHANGE] GO and EXPRESSION filter must be combined as an AND with other region (#694)
• [CHANGE] Update CellBase to v4.5.3 improvement (#770)
• [ENHANCEMENT] Speed up GENOTYPE filter with FILES filter, when possible (#675)
• [ENHANCEMENT] Add field "source" to VariantQueryResult (#758)
• [ENHANCEMENT] Indicate if "numTotalResults" is an approximated count in VariantQueryResult (#749)
• [ENHANCEMENT] Improve FILTER query param (#723)
• [FIX] Inconsistent configuration param to select variant annotator (#747)
• [FIX] Duplicate Key Warn/Error in Stage Collection (#766)
• [FIX] IllegalArgumentException when CellBaseRestVariantAnnotator skips a variant (#746)
• [FIX] Concurrent table modification error when loading in Hadoop with merge=basic (#709)

v1.2.2

Second patch version on top of OpenCGA v1.2.0

Catalog

• [FIX] Fix LDAP connection lost after server restart.

Storage

• [FIX] Fix error indexing a vcf file, existing file with the same name in different folder. #768

v1.3.0-rc

Release candidate 1.3.0

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 #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