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Recent Releases of org.opencb.cellbase:cellbase

org.opencb.cellbase:cellbase - v6.6.0

What's Changed

  • TASK-7772 - Upgrade java-driver and MongoDB versions by @jtarraga in https://github.com/opencb/cellbase/pull/732

Full Changelog: https://github.com/opencb/cellbase/compare/v6.5.0...v6.6.0

- Java
Published by github-actions[bot] 11 months ago

org.opencb.cellbase:cellbase - v6.5.0

What's Changed

  • TASK-6880 - CI/CD workflow to delete task docker images on merge fails by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/719
  • TASK-7463 Modify CellBase clinical variant builders by @jtarraga in https://github.com/opencb/cellbase/pull/721
  • TASK-7531 - Port Patch 5.8.5 -> 6.5.0 XB 1.10.9 - 2.5.0 by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/724

Full Changelog: https://github.com/opencb/cellbase/compare/v6.4.0...v6.5.0

- Java
Published by github-actions[bot] about 1 year ago

org.opencb.cellbase:cellbase - v6.2.3

What's Changed

  • TASK-7463 Modify CellBase clinical variant builders by @jtarraga in https://github.com/opencb/cellbase/pull/721
  • TASK-7589 - Port Patch 5.8.5 -> 6.2.3 Xetabase 1.10.9 -> 2.2.3 by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/722

Full Changelog: https://github.com/opencb/cellbase/compare/v6.2.2...v6.2.3

- Java
Published by github-actions[bot] about 1 year ago

org.opencb.cellbase:cellbase - v7.0.0

What's Changed

  • TASK-6647 - Fix Port Patch 1.10.4 -> 2.2.1 develop by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/706
  • TASK-6879 - Adapt GitHub Actions, CICD workflows and release scripts to new SDLC by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/709
  • TASK-6780 - Port Patch 6.2.1 -> 7.0.0 - Xetabase 2.2.1 -> 3.0.0 by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/711
  • TASK-7097 - Port Patch 6.3.0 -> 7.0.0 Xetabase 2.3.0 -> 3.0.0 by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/713
  • TASK-7155: Upgrade MongoDB to v7.0 by @jtarraga in https://github.com/opencb/cellbase/pull/714
  • TASK-7371 - Cellbase does not compile by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/717
  • Port patch 6.4.0 -> 7.0.0 by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/718
  • TASK-7417 - New github workflow to manually delete dockers from DockerHub by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/720

Full Changelog: https://github.com/opencb/cellbase/compare/v6.4.0...v7.0.0

- Java
Published by github-actions[bot] about 1 year ago

org.opencb.cellbase:cellbase - v5.8.5

What's Changed

  • TASK-7463 Modify CellBase clinical variant builders by @jtarraga in https://github.com/opencb/cellbase/pull/721

Full Changelog: https://github.com/opencb/cellbase/compare/v5.8.4...v5.8.5

- Java
Published by github-actions[bot] about 1 year ago

org.opencb.cellbase:cellbase - v6.4.0

What's Changed

  • TASK-7301 - PR approve workflow also runs on PR comment by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/715
  • TASK-7362 - Cellbase does not compile on GitHub Actions by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/716

Full Changelog: https://github.com/opencb/cellbase/compare/v6.3.0...v6.4.0

- Java
Published by github-actions[bot] over 1 year ago

org.opencb.cellbase:cellbase - v6.3.0

What's Changed

  • TASK-6879 - Adapt GitHub Actions, CICD workflows and release scripts to new SDLC by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/708
  • TASK-5318 - Implement custom annotator to allow clients private files by @jtarraga in https://github.com/opencb/cellbase/pull/695
  • TASK-7038 - Port Patch 6.2.2 -> 6.3.0 - Xetabase 2.2.2 -> 2.3.0 by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/712

Full Changelog: https://github.com/opencb/cellbase/compare/v6.2.2...v6.3.0

- Java
Published by github-actions[bot] over 1 year ago

org.opencb.cellbase:cellbase - v6.2.2

What's Changed

  • TASK-7030 - Fix CellBase configuration file by @jtarraga in https://github.com/opencb/cellbase/pull/710

Full Changelog: https://github.com/opencb/cellbase/compare/v6.2.1...v6.2.2

- Java
Published by github-actions[bot] over 1 year ago

org.opencb.cellbase:cellbase - v6.2.1

What's Changed

  • Fix CellBase endpoint: meta/{species}/versions by @jtarraga in https://github.com/opencb/cellbase/pull/688
  • TASK-5789 - Add dbSNP to CellBase by @jtarraga in https://github.com/opencb/cellbase/pull/689
  • TASK-6347 Fix normalization issue in ClinVar by @jtarraga in https://github.com/opencb/cellbase/pull/693
  • TASK-6647 - Fix Port Patch 1.10.4 -> 2.2.1 - release by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/705
  • TASK-6399 - CI/CD: Include save reports option for tasks workflows by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/694
  • TASK-6515 - Port Patch 1.10.6(.1) -> 2.2.1 by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/702
  • TASK-6807 - Pull request approve workflow Fail by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/707

Full Changelog: https://github.com/opencb/cellbase/compare/v6.2.0...v6.2.1

- Java
Published by github-actions[bot] almost 2 years ago

org.opencb.cellbase:cellbase - v6.2.0

What's Changed

  • TASK-4970 - New CI/CD should be triggered when a PR is approved for OpenCGA repository by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/691
  • TASK-6026 - Refactor the build.sh, test.sh, and run.sh scripts to remove commands and unify the scripts by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/692

Full Changelog: https://github.com/opencb/cellbase/compare/v6.1.0...v6.2.0

- Java
Published by github-actions[bot] almost 2 years ago

org.opencb.cellbase:cellbase - v5.8.4

What's Changed

  • TASK-6347 Fix normalization issue in ClinVar by @jtarraga in https://github.com/opencb/cellbase/pull/693

Full Changelog: https://github.com/opencb/cellbase/compare/v5.8.3...v5.8.4

- Java
Published by github-actions[bot] almost 2 years ago

org.opencb.cellbase:cellbase - v6.1.0

Full Changelog: https://github.com/opencb/cellbase/compare/v6.0.0...v6.1.0

- Java
Published by github-actions[bot] about 2 years ago

org.opencb.cellbase:cellbase - v5.8.3

What's Changed

  • Fix CellBase endpoint: meta/{species}/versions by @jtarraga in https://github.com/opencb/cellbase/pull/688
  • TASK-5789 - Add dbSNP to CellBase by @jtarraga in https://github.com/opencb/cellbase/pull/689

Full Changelog: https://github.com/opencb/cellbase/compare/v5.8.2...v5.8.3

- Java
Published by github-actions[bot] about 2 years ago

org.opencb.cellbase:cellbase - v6.0.0

What's Changed

  • TASK-5425 - PortPatch 1.10.1 -> 2.0.0 by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/680
  • TASK-4437 - Update general dependencies from dependabot (security alerts) by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/681
  • TASK-5444 - Fix OpenCB repository versions to conform to XetaBase 2.0.0 version by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/685
  • TASK-5385 Add mitochondrial data from Gnomad v3.1.2 by @jtarraga in https://github.com/opencb/cellbase/pull/687
  • TASK-5392 by @imedina in https://github.com/opencb/cellbase/pull/684

Full Changelog: https://github.com/opencb/cellbase/compare/v5.8.2...v6.0.0

- Java
Published by juanfeSanahuja over 2 years ago

org.opencb.cellbase:cellbase - v5.8.2

What's Changed

  • TASK-5457 Fix CellBase annotation queries for SV variants by @jtarraga in https://github.com/opencb/cellbase/pull/683
  • TASK-5447 Fix CellBase variant annotation queries failing if data source does not exist by @jtarraga in https://github.com/opencb/cellbase/pull/682
  • TASK-5571 Autocomplete with ontologies not working for CMH by @jtarraga in https://github.com/opencb/cellbase/pull/686

Full Changelog: https://github.com/opencb/cellbase/compare/v5.8.1...v5.8.2

- Java
Published by juanfeSanahuja over 2 years ago

org.opencb.cellbase:cellbase - v5.8.1

What's Changed

  • TASK-5212 Fix 'cellbase-admin.sh build' for clinical variants by @jtarraga in https://github.com/opencb/cellbase/pull/678
  • TASK-5340 Fix CellBase web services initialization by @jtarraga in https://github.com/opencb/cellbase/pull/679

Full Changelog: https://github.com/opencb/cellbase/compare/v5.8.0...v5.8.1

- Java
Published by github-actions[bot] over 2 years ago

org.opencb.cellbase:cellbase - v5.8.0

What's Changed

  • TASK-5025 CellBase CI/CD fails due to a JUnit test error by @jtarraga in https://github.com/opencb/cellbase/pull/667
  • TASK-4976 Fix error handling when an exception raises in the CellBase Rest server constructors by @jtarraga in https://github.com/opencb/cellbase/pull/668
  • TASK-4976 Fix error handling when an exception raises in the CellBase Rest server constructors by @jtarraga in https://github.com/opencb/cellbase/pull/669
  • TASK-5120 - Port Patch 1.6.5 -> 1.10.0 by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/674
  • TASK-4988 Fix CellBase CLI to create API keys that only include a quota by @jtarraga in https://github.com/opencb/cellbase/pull/676
  • TASK-5061 - Replace the mongoDB step in the Cellbase build with a kubectl that tunnels to a machine where the test data already exists by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/675
  • TASK-2095 - Duplicated libraries at opencga/build/libs by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/671

Full Changelog: https://github.com/opencb/cellbase/compare/v5.7.0...v5.8.0

- Java
Published by github-actions[bot] over 2 years ago

org.opencb.cellbase:cellbase - v5.4.1

What's Changed

  • TASK-4032 - CI/CD new Workflow to publish CELLBASE docker on TASK branch by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/649
  • TASK-3809 Fix variant annotation for consequence types by @jtarraga in https://github.com/opencb/cellbase/pull/645
  • TASK-3808 CellBase token management to allow users to access to restricted/licensed data sources by @jtarraga in https://github.com/opencb/cellbase/pull/642
  • TASK-5025 CellBase CI/CD fails due to a JUnit test error by @jtarraga in https://github.com/opencb/cellbase/pull/667
  • TASK-4976 Fix error handling when an exception raises in the CellBase Rest server constructors by @jtarraga in https://github.com/opencb/cellbase/pull/668

Full Changelog: https://github.com/opencb/cellbase/compare/v5.3.0...v5.4.1

- Java
Published by github-actions[bot] over 2 years ago

org.opencb.cellbase:cellbase - v5.7.0

What's Changed

  • TASK-4761 by @jtarraga in https://github.com/opencb/cellbase/pull/662
  • TASK-4641- Implement an API key to control the number of queries by @jtarraga in https://github.com/opencb/cellbase/pull/660
  • TASK-4967 - ArrayOutOfBounds using cellbase client by @j-coll in https://github.com/opencb/cellbase/pull/664

Full Changelog: https://github.com/opencb/cellbase/compare/v5.6.0...v5.7.0

- Java
Published by github-actions[bot] almost 3 years ago

org.opencb.cellbase:cellbase - v5.6.0

What's Changed

  • TASK-4530 Fix CellBase normalization configuration by @jtarraga in https://github.com/opencb/cellbase/pull/655
  • TASK-4289 - Upgrade JVM to 8u372 in opencga Docker by @juanrizetta in https://github.com/opencb/cellbase/pull/656
  • TASK-4464 by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/658
  • TASK-1111 Add Pharmagenomics data to CellBase by @jtarraga in https://github.com/opencb/cellbase/pull/653
  • TASK-4225 by @jtarraga in https://github.com/opencb/cellbase/pull/659

Full Changelog: https://github.com/opencb/cellbase/compare/v5.5.0...v5.6.0

- Java
Published by imedina almost 3 years ago

org.opencb.cellbase:cellbase - v5.2.10

What's Changed

  • TASK-4530 Fix CellBase normalization configuration by @jtarraga in https://github.com/opencb/cellbase/pull/655

Full Changelog: https://github.com/opencb/cellbase/compare/v5.2.9...v5.2.10

- Java
Published by github-actions[bot] about 3 years ago

org.opencb.cellbase:cellbase - v5.5.0

What's Changed

  • TASK-4163 by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/650
  • TASK-4157 Implement support for setting a default data release for each CellBase version by @jtarraga in https://github.com/opencb/cellbase/pull/654

Full Changelog: https://github.com/opencb/cellbase/compare/v5.4.0...v5.5.0

- Java
Published by github-actions[bot] about 3 years ago

org.opencb.cellbase:cellbase - Release v5.1.8

See http://docs.opencb.org/display/cellbase/Release+Notes for the full list of features and fixes in this release.

- Java
Published by github-actions[bot] about 3 years ago

org.opencb.cellbase:cellbase - v5.4.0

What's Changed

  • TASK-4032 - CI/CD new Workflow to publish CELLBASE docker on TASK branch by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/649
  • TASK-3809 Fix variant annotation for consequence types by @jtarraga in https://github.com/opencb/cellbase/pull/645
  • TASK-3808 CellBase token management to allow users to access to restricted/licensed data sources by @jtarraga in https://github.com/opencb/cellbase/pull/642

Full Changelog: https://github.com/opencb/cellbase/compare/v5.3.0...v5.4.0

- Java
Published by github-actions[bot] about 3 years ago

org.opencb.cellbase:cellbase - v5.3.0

What's Changed

  • TASK-2270 by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/641
  • TASK-3953 - CI/CD in task.yml to deploy project dependencies by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/643

Full Changelog: https://github.com/opencb/cellbase/compare/v5.2.9...v5.3.0

- Java
Published by github-actions[bot] over 3 years ago

org.opencb.cellbase:cellbase - v5.2.9

What's Changed

  • TASK-2579 Fix PubMed data loading by @jtarraga in https://github.com/opencb/cellbase/pull/638

Full Changelog: https://github.com/opencb/cellbase/compare/v5.2.8...v5.2.9

- Java
Published by github-actions[bot] over 3 years ago

org.opencb.cellbase:cellbase - v5.2.8

What's Changed

  • remove static to fix concurrency issues by @julie-sullivan in https://github.com/opencb/cellbase/pull/619
  • TASK-1201 - Use dataRelease from Cellbase in OpenCGA by @j-coll in https://github.com/opencb/cellbase/pull/636

Full Changelog: https://github.com/opencb/cellbase/compare/v5.2.7...v5.2.8

- Java
Published by github-actions[bot] over 3 years ago

org.opencb.cellbase:cellbase - v5.2.7

- Java
Published by imedina over 3 years ago

org.opencb.cellbase:cellbase - v5.1.7

- Java
Published by imedina over 3 years ago

org.opencb.cellbase:cellbase - v5.0.4

- Java
Published by imedina over 3 years ago

org.opencb.cellbase:cellbase - v4.12.2

Fix consequence types for CNVs with two copies.

- Java
Published by julie-sullivan over 3 years ago

org.opencb.cellbase:cellbase - v4.12.1

Fix CNVExtraPadding param for overlap queries too.

- Java
Published by julie-sullivan over 3 years ago

org.opencb.cellbase:cellbase - v4.12.0

Fix CNVpadding bug

- Java
Published by julie-sullivan over 3 years ago

org.opencb.cellbase:cellbase - v5.1.6

See http://docs.opencb.org/display/cellbase/Release+Notes for the full list of features and fixes in this release.

What's Changed

  • TASK-2273 by @imedina in https://github.com/opencb/cellbase/pull/622

Full Changelog: https://github.com/opencb/cellbase/compare/v5.1.5...v5.1.6

- Java
Published by github-actions[bot] over 3 years ago

org.opencb.cellbase:cellbase - v5.2.6

What's Changed

  • TASK-1718 by @juanfeSanahuja in https://github.com/opencb/cellbase/pull/608
  • TASK-2154 - Pycellbase error when handling query results by @dapregi in https://github.com/opencb/cellbase/pull/618

New Contributors

  • @juanfeSanahuja made their first contribution in https://github.com/opencb/cellbase/pull/608

Full Changelog: https://github.com/opencb/cellbase/compare/v5.2.5...v5.2.6

- Java
Published by imedina over 3 years ago

org.opencb.cellbase:cellbase - v4.9.9

Made HGVS calculations threadsafe.

- Java
Published by julie-sullivan over 3 years ago

org.opencb.cellbase:cellbase - Release v5.1.5

See http://docs.opencb.org/display/cellbase/Release+Notes for the full list of features and fixes in this release.

What's Changed

  • TASK-2041 by @jtarraga in https://github.com/opencb/cellbase/pull/615
  • TASK-2041 by @jtarraga in https://github.com/opencb/cellbase/pull/616
  • TASK-2109 by @jtarraga in https://github.com/opencb/cellbase/pull/617

Full Changelog: https://github.com/opencb/cellbase/compare/v5.1.4...v5.1.5

- Java
Published by github-actions[bot] almost 4 years ago

org.opencb.cellbase:cellbase - v4.10.3

Security patches

- Java
Published by julie-sullivan almost 4 years ago

org.opencb.cellbase:cellbase - v4.10.2

Full Changelog: https://github.com/opencb/cellbase/compare/v4.9.10...v4.10.2

- Java
Published by imedina almost 4 years ago

org.opencb.cellbase:cellbase - v5.2.5

What's Changed

  • TASK-1776 by @jtarraga in https://github.com/opencb/cellbase/pull/606

Full Changelog: https://github.com/opencb/cellbase/compare/v5.2.4...v5.2.5

- Java
Published by imedina almost 4 years ago

org.opencb.cellbase:cellbase - v5.2.4

What's Changed

  • Add backwards compatibility for response and result by @dapregi in https://github.com/opencb/cellbase/pull/605

Full Changelog: https://github.com/opencb/cellbase/compare/v5.2.3...v5.2.4

- Java
Published by imedina almost 4 years ago

org.opencb.cellbase:cellbase - v5.2.3

What's Changed

  • Task 1623 by @phamidko in https://github.com/opencb/cellbase/pull/603

Full Changelog: https://github.com/opencb/cellbase/compare/v5.2.2...v5.2.3

- Java
Published by imedina almost 4 years ago

org.opencb.cellbase:cellbase - v5.2.2

What's Changed

  • TASK-1401 by @jtarraga in https://github.com/opencb/cellbase/pull/599
  • TASK-1547 by @jtarraga in https://github.com/opencb/cellbase/pull/601

Full Changelog: https://github.com/opencb/cellbase/compare/v5.2.1...v5.2.2

- Java
Published by imedina almost 4 years ago

org.opencb.cellbase:cellbase - Release v5.1.4

See http://docs.opencb.org/display/cellbase/Release+Notes for the full list of features and fixes in this release.

- Java
Published by github-actions[bot] almost 4 years ago

org.opencb.cellbase:cellbase - v5.0.3

What's Changed

  • TASK-960 by @j-coll in https://github.com/opencb/cellbase/pull/591
  • TASK-1547 by @jtarraga in https://github.com/opencb/cellbase/pull/601

Full Changelog: https://github.com/opencb/cellbase/compare/v5.0.2...v5.0.3

- Java
Published by imedina almost 4 years ago

org.opencb.cellbase:cellbase - Release v5.1.3

See http://docs.opencb.org/display/cellbase/Release+Notes for the full list of features and fixes in this release.

- Java
Published by github-actions[bot] almost 4 years ago

org.opencb.cellbase:cellbase - Release v5.1.2

See http://docs.opencb.org/display/cellbase/Release+Notes for the full list of features and fixes in this release.

- Java
Published by github-actions[bot] almost 4 years ago

org.opencb.cellbase:cellbase - v4.10.1

Remove obsolete log4j JAR

- Java
Published by julie-sullivan almost 4 years ago

org.opencb.cellbase:cellbase - v5.2.0

What's Changed

  • TASK-937 by @imedina in https://github.com/opencb/cellbase/pull/589
  • TASK-558 by @jtarraga in https://github.com/opencb/cellbase/pull/592
  • TASK-839 by @jtarraga in https://github.com/opencb/cellbase/pull/593
  • TASK-558 by @jtarraga in https://github.com/opencb/cellbase/pull/594

Full Changelog: https://github.com/opencb/cellbase/compare/v5.1.1...v5.2.0

- Java
Published by imedina about 4 years ago

org.opencb.cellbase:cellbase - Release v5.1.1

See http://docs.opencb.org/display/cellbase/Release+Notes for the full list of features and fixes in this release.

- Java
Published by github-actions[bot] about 4 years ago

org.opencb.cellbase:cellbase - Release v5.1.0

See http://docs.opencb.org/display/cellbase/Release+Notes for the full list of features and fixes in this release.

- Java
Published by github-actions[bot] about 4 years ago

org.opencb.cellbase:cellbase - Release v4.10.0

  • Associate ClinVar SCVs with VCVs when returning clinical information
  • Return other variants considered as part of phased MNV annotation
  • Phased MNV variants not returning transcript in additionalProperties

- Java
Published by julie-sullivan about 4 years ago

org.opencb.cellbase:cellbase - v4.9.8

Add optional filter to variant annotation

- Java
Published by julie-sullivan about 4 years ago

org.opencb.cellbase:cellbase - v5.0.1

- Java
Published by imedina over 4 years ago

org.opencb.cellbase:cellbase - v4.9.7

Upgrade log4j to 2.17.1

https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2021-44832

- Java
Published by julie-sullivan over 4 years ago

org.opencb.cellbase:cellbase - v5.0.0

- Java
Published by imedina almost 5 years ago

org.opencb.cellbase:cellbase - v5.0.0-rc

- Java
Published by imedina about 5 years ago

org.opencb.cellbase:cellbase - Release v4.9.2

Another HGVSp fix See #548

- Java
Published by julie-sullivan about 5 years ago

org.opencb.cellbase:cellbase - Release v4.9.3

Demoted log message to DEBUG from INFO

- Java
Published by julie-sullivan about 5 years ago

org.opencb.cellbase:cellbase - Release v4.9.4

  • no HGVS is calculated for symbolic variants.
  • Transcript HGVS no longer fails for long insertions.
  • No HGVSp is calculated for insertions falling on an incomplete first codon.

See #550

- Java
Published by julie-sullivan about 5 years ago

org.opencb.cellbase:cellbase - Release v4.9.5

Fixed bug which caused some ClinVar accessions not to be returned in certain queries.

- Java
Published by julie-sullivan about 5 years ago

org.opencb.cellbase:cellbase - Release v4.9.6

  • Fixed small edge case in which the wrong ClinVar accession was returned when two variants were annotated at the same time and had the same coordinates.
  • Fixed HGVSp bug where certain variants threw an exception

- Java
Published by julie-sullivan about 5 years ago

org.opencb.cellbase:cellbase - v4.9.0

  • Increase Cellbase threshold for indels annotation from 50bp
  • updated the parser to parse the latest Clinvar file format (2021-01).
  • HGVSp - update to handle more cases
  • MNVs - fixed off-by-one error

- Java
Published by imedina over 5 years ago

org.opencb.cellbase:cellbase -

- Java
Published by imedina over 5 years ago

org.opencb.cellbase:cellbase -

  • Protein HGVS is now returned as part of the CellBase VariantAnnotation payload
  • Protein-level variation is now checked when annotating clinical variant data, i.e. when annotating variants with ClinVar, COSMIC, DOCM & IARCTP53 data. (simply activate checkAminoAcidChange on variants/{variant}/annotation requests)
  • ClinVar SCVs are now also provided as part of ClinVar data
  • Both ClinVar and COSMIC parsers updated to ClinVar Feb 2020 and COSMIC v90 versions

- Java
Published by javild over 6 years ago

org.opencb.cellbase:cellbase -

  • Bugfix on samples data order not matching input VCF order after annotation

- Java
Published by javild almost 7 years ago

org.opencb.cellbase:cellbase -

  • Variant annotator now fully supports phased annotation

- Java
Published by javild almost 7 years ago

org.opencb.cellbase:cellbase - v4.6.2

  • Bugfix: sort query param restored

- Java
Published by imedina over 7 years ago

org.opencb.cellbase:cellbase -

  • Bug fixed could potentially lead Command Line to raise Null Pointer Exception

- Java
Published by javild almost 8 years ago

org.opencb.cellbase:cellbase -

  • Variant Annotator compatible with VEP e90
  • Variant Annotator performance improved up to 3x
  • Clinical variants are now normalised
  • New clinical data source: Database Of Curated Mutations (DOCM)
  • New status WS provides details about the status of the installation: tomcats, DB machines, etc.
  • New ping WS
  • Unit tests improved

- Java
Published by javild almost 8 years ago

org.opencb.cellbase:cellbase -

  • Parser updated to deal with ClinVar May 2018 release
  • Variant annotator now understands "MT", "chrMT", "M" and "chrM" as the mitochondrial chromosome

- Java
Published by imedina almost 8 years ago

org.opencb.cellbase:cellbase -

  • Decomposition of block substitutions/MNVs was causing some problems when combined with custom annotation. A new CLI flag --skip-decompose has been enabled to prevent the normalization process from decomposing while indexing custom annotation files into RocksDB and annotating with the CellBase annotator.

- Java
Published by javild about 8 years ago

org.opencb.cellbase:cellbase -

  • variant-annotation command no longer fails once the annotation process has finished
  • Java REST Client
    • Bugfix. When multiple ids were used as an input each of them returning more than 1000 results, could potentially happen that these result lists were not appropriately processed.
    • Thread safe issue fixed at CellBaseClient.
  • Gene model: transcripts.xrefs field will now always include geneName, geneId, transcriptName and transcriptId, even if the Ensembl API returns no xrefs at all
  • Improved initialisation of heritableTraitList and genomicFeatureList during ClinVar parsing to avoid Avro serialization issues
  • If no path at all was provided for the variant-annotation output, i.e. -o test.json.gz rather than -o ./test.json.gz, an error was raised. This is now checked and error avoided.

- Java
Published by javild over 8 years ago

org.opencb.cellbase:cellbase -

  • Bug fix: HGVS variant annotation fixed

- Java
Published by javild over 8 years ago

org.opencb.cellbase:cellbase -

  • Important bugfix: variant-annotation CLI now correctly passes the assembly argument when annotating through WS
  • REST client is now able to handle variant id parsing problems, e.g. 1:645710:A:INS:ME:ALU
  • New variant-annotation parameter added to the CLI: --max-open-files can limit the number of file kept open by RocksDB
  • All writes/reads are now in UTF-8
  • HGVS normalization errors do no longer interrupt the whole annotation process and raise a warning instead
  • Perl scripts querying ENSEMBL APIs improved to properly change ENSEMBL version as appropriate
  • Annotator execution is no longer interrupted if an error raises while trying to normalize a variant. Likewise, will not get interrupted if errors raise during HTSJDK parsing of VCF lines. Warnings will be shown and corresponding variants skipped

- Java
Published by javild over 8 years ago

org.opencb.cellbase:cellbase -

  • Adaptors no longer modify the QueryOptions object they receive: avoids a potential out of memory exception
  • Variant annotation processes properly terminate in case an exception is run during the execution
  • HGVS bugfix: a bug was found when variant was located within a coding exon, between coding start and coding end, if the coding start did not coincide with the exon start position
  • Swagger works now with https
  • Data types within swagger documentation fixed: used to generate massive useless error logs
  • Deprecated clinical WS fixed
  • Imprecise queries require now all Variant.sv.getCi* != null
  • dgiDB URL was outdated and has been fixed

- Java
Published by javild over 8 years ago

org.opencb.cellbase:cellbase -

Variant annotation

  • Copy Number Variants and Structural Variants are now annotated: CNVs, INS, DEL, INV, DUP, TANDEM-DUP, BND
  • Variant Annotator handles imprecise definition of variant limits
  • Variant annotator can also provide consequence type prediction for not decomposed MNVs
  • Exon overlap added to returned variant annotation
  • Cytobands added to returned variant annotation
  • New annotation sources:
    • The Database of Genomics Variants
    • TRF simple repeats
    • WindowMasker
    • Genomic super duplications
  • Population frequencies from reference projects, PASS and non-PASS variants are now provided
  • Returned list of SO terms refined to improve VEP comparison result; 99.999% coincidence against VEP e83
  • Data model changes to the VariantAnnotation object
    • Deprecated field union { null, VariantTraitAssociation } variantTraitAssociation New traitAssociation field must be used instead: union { null, array<EvidenceEntry> } traitAssociation
    • Field union { null, int } exonNumber; present in previos 4.5.0-rc* releases is no longer available. This field was not present in stable 4.0.* releases. New Field: union { null, array<ExonOverlap> } exonOverlap is used instead.
    • Other additional fields: union { null, array<Cytoband> } cytoband; union { null, array<Repeat> } repeat; # Clinical functionality
  • WARNING: previous feature/clinical/* REST endpoints have been deprecated and will no longer supported
  • New "clinical" category
  • Re-implementation of all clinical variants functionality
    • Homogenization of data models: all clinical variant sources are integrated into Variant objects
    • New web services added
  • New IARCTP53 data source integrated # New CellBase client libraries
  • PyCellBase: http://docs.opencb.org/display/cellbase/REST+Clients http://docs.opencb.org/display/cellbase/Python+client+library
  • CellBaseR https://bioconductor.org/packages/release/bioc/html/cellbaseR.html
  • Reimplemented Java client; provided within the CellBase code, cellbase-client module
  • New JavaScript client # ENSEMBL e89 GRCh38 data ready
  • Code adapted to be compatible with e89 GRCh38 data. # Additional Web Service improvements
  • Transcripts within genes can now be filtered by annotation flag, e.g. "basic"
  • "search" method added to transcript category
  • New meta/about web service returns server code version and commit
  • New genomic/region//repeat web service to search for repeated regions
  • Gene expression searches improved # Created new documentation site http://docs.opencb.org/display/cellbase/CellBase+Home # Improved logs
  • WS now log every query; facilitates diagnosis of server side problems
  • sl4j is now used for logging; date, time and thread are recorded for each log entry Configuration
  • Support for several Neo4j databases
  • Number of mongo connections per host can now be customized at the configuration file

- Java
Published by javild almost 9 years ago

org.opencb.cellbase:cellbase - CellBase v4.5.0-rc development release

- Java
Published by imedina over 9 years ago

org.opencb.cellbase:cellbase -

- Java
Published by imedina almost 10 years ago

org.opencb.cellbase:cellbase - CellBase v4.0.0 Stable Release

  • Data:
    • upgraded to ENSEMBL 82
    • new sources: HPO, GERP++, Gene Expression Atlas, GoNL, EXaC, UK10K, 1kG phase 3, ESP
  • Completely new Java DB Adaptor API
  • REST API:
    • Improvements over available methods and new end points
    • Comprehensively documented. API specification available through the Swagger interface
  • Much more (and better) documentation at the GitHub wiki
  • Major tests improvements
  • New Variant data model used to store and handle ENSEMBL variation data - standardizes variant handling within OpenCB
  • Major improvements on variant annotation:
    • Complete refactoring of the variant annotation code
    • New Variant Annotation data model
    • New annotation data: GERP++, CADD, UniProt, InterPro, population frequencies from GoNL, EXaC, UK10K, 1kG phase 3, ESP
  • Many performance improvements, bug fixes and code clean ups

- Java
Published by javild almost 10 years ago

org.opencb.cellbase:cellbase -

- Java
Published by imedina almost 10 years ago

org.opencb.cellbase:cellbase - CellBase v3.2.0 Stable Release

New stable CellBase v3.2.0. Many changes have been made and many tests and bugs need to be fixed. Major changes include: - Many new queries and web services implemented - New data sources and functionality added such as Gene Expression Atlas (EBI), InterPro or DGIdb among others - Variant Annotation: - data model improvements - variants are now annotated with Uniprot, InterPro, gene expression and gene drug interactions - New CellBase server installed at University of Cambridge at bioinfo.hpc.cam.ac.uk/cellbase, beta available at bioinfodev.hpc.cam.ac.uk/cellbase - Swagger, README and documentation have been significantly improved - Performance improvements all across CellBase, many bugs fixed and code clean ups

Some issues solved:

https://github.com/opencb/cellbase/issues?q=milestone%3Av3.2.0

- Java
Published by imedina almost 11 years ago

org.opencb.cellbase:cellbase - CellBase v3.1.0 Stable Release

New stable CellBase v3.1.0. Many changes have been made and many tests and bugs need to be fixed. Major changes include: - New cellbase-app CLI using JCommander, this allows to download, build and load automatically CellBase - New Variant Annotator developed, it has been tested and benchmarked against Ensembl VEP - Swagger, README and documentation has been improved - New data sources and functionality added. Human GRCh38 supported - New data installation at University of Cambridge at bioinfo.hpc.cam.ac.uk/cellbase - License changed to Apache License 2.0 - Performance improvements all across CellBase, many bugs fixed and code clean ups

Some issues developed:

https://github.com/opencb/cellbase/issues?q=milestone%3Av3.1.0

- Java
Published by imedina about 11 years ago

org.opencb.cellbase:cellbase - CellBase v3.1.0-RC.1

Second release candidate of CellBase v3.1.0. Many changes have been made and many tests and bugs need to be fixed. Major changes include: - New cellbase-app CLI has been finished and tested - New Variant Annotator has been tested and benchmarked against Ensembl VEP - Some new web services developed - Swagger, README and documentation has been improved - Some new data sources and functionality added - performance improvements, many bugs fixed and code clean ups

- Java
Published by imedina about 11 years ago

org.opencb.cellbase:cellbase - CellBase v3.1.0-RC

This is the first release candidate of CellBase v3.1.0. Many changes have been made and many tests and bugs need to be fixed. Major changes include: - New cellbase-app replace old cellbase-build and there is a new data downloader and build - A new Variant Annotator has been developed - New CLI using JCommander has been developed - Swagger, README and documentation has been improved - Some new data sources and functionality

- Java
Published by imedina over 11 years ago

org.opencb.cellbase:cellbase - v3.0.0

The main features of this release are: - migrate the storage engine from MySQL to MongoDB database to provide a higher performance and scalability - cellbase-build has been improved, now the building is faster and more automatic - CellBase now uses maven modules organization - data models have been migrated to biodata repository - new database such as UniProt and IntAct have been added - swagger has been integrated

- Java
Published by imedina over 11 years ago