Releases: umccr/data-portal-apis
Releases · umccr/data-portal-apis
Release 2.2.5
Milestone
Release Validation Documentation
What's Changed
- Added Lambda entrypoint for Google LIMS update by provided ID by @victorskl in #727
- Fixed syntax warning by prepending raw string to regex query by @victorskl in #728
- Added Subject endpoint WGTS results from BYOB by OrcaBus by @victorskl in #729
- Fixed load data script by @victorskl in #730
- Bumped dependencies by @victorskl in #731
- Added Subject analysis results sash output from BYOB by @victorskl in #732
- Release 2.2.5 by @victorskl in #733
Full Changelog: 2.2.4...2.2.5
Contributors
victorskl
Assets 2
Release 2.2.4
Milestone
Release Validation Documentation
What's Changed
- Added note about Alignment QC batch mode vs skip step trigger by @victorskl in #714
- Bumped toolchain versions and yarn-v4.4.0 by @victorskl in #715
- Bumped dependencies by @victorskl in #716
- Pinned numpy 1.x by @victorskl in #717
- Upgraded to JavaScript aws-sdk-v3 by @victorskl in #719
- Upgraded to Python3.12 by @victorskl in #720
- Bumped dependencies by @victorskl in #721
- Pinned transitive dependency axios 1.7.4 by @victorskl in #722
- Bumped dependencies by @victorskl in #724
- Added viewing ctTSO sample analysis results from v2.6.0 pipeline by @victorskl in #723
- Release 2.2.4rc1 by @victorskl in #725
Full Changelog: 2.2.3...2.2.4
Contributors
victorskl
Assets 2
Release 2.2.3
Release 2.2.2
Milestone
Release Validation Documentation
What's Changed
- Added the plan about automated pipeline extension by @victorskl in #665
- Deprecated data domain name pattern by @victorskl in #666
- Added Portal database backup documentation by @victorskl in #667
- Add script to generate bssh sqs event payload by @reisingerf in #668
- Fix: Running local docker-compose.yml by @williamputraintan in #670
- Fixed docker compose mysql-8.4 for CodeBuild CI by @victorskl in #675
- PRID typos by @pdiakumis in #677
- Fixed and pinned docker compose mysql-8.0 for CodeBuild CI and local dev by @victorskl in #676
- Added Portal Run ID documentation by @victorskl in #669
- Added test case to debug & verify wgs rerun lib skip auto-pairing by @victorskl in #679
- Improved RNAsum v1 input keys test cases by @victorskl in #680
- Update RNAsum orchestration by @skanwal in #674
- Added ggshield config by @victorskl in #681
- Fixed BSSH mock event generator script by @victorskl in #682
- Upgraded to yarn-4.2.2 by @victorskl in #683
- Fix/security issue fix from dependabot alerts by @raylrui in #687
- Release 2.2.2rc1 by @victorskl in #688
- replace status page domain name by @raylrui in #689
- Added Portal LabMetadata LibraryID suffix annotation treatment by @victorskl in #690
- Added documentation on how to trigger DRAGEN Alignment QC by @victorskl in #692
- Added Tumor Normal engineParameter override for tesUseInputManifest never by @victorskl in #693
- Updated LabMetadata model enum for assay, type, source by @victorskl in #695
- Added support for EventBridge S3 event processing by @victorskl in #696
- Updated doc for WTS sample with multiple lane FASTQs by @victorskl in #697
- Updated LabMetadata model enum for assay, type, source - migration script by @victorskl in #698
- Bumped dependencies by @victorskl in #699
- Fixed pandas dataframe applymap future warning by @victorskl in #700
- Updated doc library_suffix.md by @victorskl in #701
- Implemented Subject endpoint to include ctTSOv2 results from ICAv2 BYOB by @victorskl in #702
- Fixed Subject having no ctTSOv2 assay library by @victorskl in #703
- Release 2.2.2rc2 by @victorskl in #704
- Feat: Additional Filter for S3 Objects by @williamputraintan in #706
- add content disposition header for s3 presign api by @raylrui in #705
- add filename in disposition header by @raylrui in #708
- Bumped dependencies by @victorskl in #709
- Release 2.2.2rc3 by @victorskl in #710
- Release 2.2.2 by @victorskl in #711
New Contributors
- @pdiakumis made their first contribution in #677
- @raylrui made their first contribution in #687
Full Changelog: 2.2.1...2.2.2
Contributors
victorskl, skanwal, and 4 other contributors
Assets 2
Release 2.2.1
Milestone
What's Changed
- Updated documentation by @victorskl in #648
- Updated PORTAL_RELEASE.md documentation by @victorskl in #649
- Improved TSO ctDNA Lambda handler by @victorskl in #650
- Improved WorkflowRunStateChange schema for usabiliy by @reisingerf in #651
- Updated documentation by @victorskl in #654
- Add support for lab metadata tracking sheet 2024 by @reisingerf in #653
- Add
results_sashin subject API by @williamputraintan in #659 - Fixed transcriptome orchestration step skip if FastqListRow empty by @victorskl in #656
- Improved Pipeline Automation documentation by @victorskl in #657
- Bumped dependencies by @victorskl in #658
- Refine filter on get
sash_resultsby @williamputraintan in #660 - Release 2.2.1-rc1 by @reisingerf in #661
- Release 2.2.1 by @reisingerf in #662
Full Changelog: 2.2...2.2.1
Contributors
victorskl, reisingerf, and williamputraintan
Assets 2
Release 2.2
Milestone
What's Changed
- Removed GDS MIME type guess at server side by @victorskl in #585
- [STG] Removed GDS MIME type guess at server side by @victorskl in #586
- [PROD] Removed GDS MIME type guess at server side by @victorskl in #587
- Upgraded to yarn v3 berry by @victorskl in #591
- Improved ICA endpoint mocking by @victorskl in #592
- Reinforced DevSecOps by @victorskl in #593
- Bumped dependencies by @victorskl in #594
- Added parameter to wts launch that uses high mem instance for arriba fusion step by @alexiswl in #588
- Update pairing logic to allow clinical normal and tumor research samples by @alexiswl in #596
- Bumped dependencies by @victorskl in #598
- Added LabMetadata processing for 2018 and 2017 sheets by @victorskl in #599
- [STG] Added LabMetadata processing for 2018 and 2017 sheets by @victorskl in #600
- [PROD] Added LabMetadata processing for 2018 and 2017 sheets by @victorskl in #601
- Bumped dependencies by @victorskl in #603
- Added filter WTS arriba fusions report by Subject by @victorskl in #604
- Added filter for DRAGEN germline VCFs by Subject by @victorskl in #605
- Fixed models import from Python package by @victorskl in #608
- Fixed unittest for orchestration WTS step changes by @victorskl in #607
- Run QC for WTS alongside WGS by @alexiswl in #597
- Improved FastqListRow lookup filter by specific SequenceRun instance by @victorskl in #609
- Handle differing workflow parameters between wts qc and wgs qc by @alexiswl in #611
- Updated Portal metadata documentation by @victorskl in #612
- Started fixing discovery of holmes endpoints by @andrewpatto in #595
- Improved DRAGEN Alignment QC impl by @victorskl in #613
- Added drawio doc around Portal Automation architecture by @victorskl in #614
- Refactored Workflow model unique key to portal_run_id by @victorskl in #615
- Star Alignment Automation by @reisingerf in #616
- Refactored WorkflowHelper portal_run_id generator to use IdHelper by @victorskl in #617
- Implemented orchestrator NG handler by @victorskl in #618
- Implemented oncoanalyser wts automation by @victorskl in #619
- Implemented oncoanalyser wgs automation by @victorskl in #621
- Fastq list rows are now inside the tso500_sample configuration for cttso by @alexiswl in #620
- Added code coverage to toolchain by @victorskl in #622
- Implemented automation for oncoanalyser wgts existing both by @victorskl in #623
- Upgraded Portal backend to Python3.11 and Node18 by @victorskl in #624
- Fixed CodeBuild to use localised yarn with npx by @victorskl in #625
- Bumped toolchain versions: localstack:2.3, haproxy:2.8, prism:5 by @victorskl in #626
- Bumped dependencies by @victorskl in #627
- Fixed serverless long Lambda name by @victorskl in #628
- Removed serverless domain manager stage variable by @victorskl in #629
- Implemented SASH automation by @victorskl in #630
- Removed transcriptome BAM fingerprinting from orchestrator by @victorskl in #631
- Improved QC implementation and reinforced unit testing by @victorskl in #633
- Improved SQS Lambda handler partial batch responses - ReportBatchItemFailures by @victorskl in #632
- Improved ICA ENS and AWS Batch SQS Lambda handlers response in dict by @victorskl in #634
- Fixed QC workflow trigger wrong workflow typing by @victorskl in #635
- Improved star alignment step implementation by @victorskl in #636
- Disabled ReportBatchItemFailures response for SQS Standard queue by @victorskl in #637
- Improved workflow service layer running workflow lookup by @victorskl in #638
- Bumped dependencies by @victorskl in #640
- Release 2.2rc1 by @victorskl in #639
- Rollback SQS Standard queue event router handler behaviour by @victorskl in #641
- Release 2.2rc2 by @victorskl in #642
- Bumped dependencies by @victorskl in #643
- Release 2.2rc3 by @victorskl in #644
- Bumped dependencies by @victorskl in #645
- Release 2.2rc4 by @victorskl in #646
- Release 2.2 by @victorskl in #647
Full Changelog: 2.1...2.2
Contributors
andrewpatto, victorskl, and 2 other contributors
Assets 2
Release 2.1
Milestone
What's Changed
- Bumped dependencies by @victorskl in #543
- Bumped dependencies by @victorskl in #546
- Updated swagger and endpoints doc by @victorskl in #549
- Updated doc new base domain endpoint by @victorskl in #550
- Bump django from 4.1.6 to 4.1.7 by @dependabot in #552
- Bump werkzeug from 2.2.2 to 2.2.3 by @dependabot in #553
/fastqAPI Additional filters by @williamputraintan in #554- Accept
Content-Dispositionas header in GDS presign by @williamputraintan in #556 - Allow
Content-Dispositionin CORS by @williamputraintan in #557 - Deprecated manops domain and endpoint by @victorskl in #560
- Update API-gateway Serverless CORS by @williamputraintan in #570
- Added workDirectory to primary data helper by @alexiswl in #565
- Cleaned up loaddata script by @alexiswl in #569
- Fix: 561 - ctTSO NTC should be run by @reisingerf in #567
- Added support for TSO BAM fingerprinting through Holmes by @victorskl in #566
- DRAFT: Add support for filtering out metadata for libraries not sequenced yet by @reisingerf in #571
- Solved multiple WTS libraries by using latest to their sequencing time by @victorskl in #573
- Updated umccrise step to take germline as input rather than its own step by @alexiswl in #572
- Fixed tumor normal and RNAsum to use sequenced only library by @victorskl in #574
- Fixed pairing endpoint to use sequenced only library by @victorskl in #575
- Added example for GDS folders bundler and downloader scripts by @victorskl in #576
- Improved gds bundler README and fixed minor typo by @victorskl in #577
- Update umccrise output directory key by @alexiswl in #578
- Added TSO tsv output in Subject analysis summary by @victorskl in #579
- Implemented LIMS and Metadata aggregation endpoints by @victorskl in #580
- Fixed GDS PreSigned URL Override to allow opening report in inline browser tab by @victorskl in #581
- Bumped dependencies by @victorskl in #582
- Release 2.1rc1 by @victorskl in #583
- Release 2.1 by @victorskl in #584
Full Changelog: 2.0...2.1
Contributors
victorskl, alexiswl, and 3 other contributors
Assets 2
Release 2.0
Milestone
What's Changed
- Updated additional Athena RStudio ODBC steps by @victorskl in #510
- Added doc for Portal Athena with athenacli REPL shell by @victorskl in #511
- Fixed global skip list by @victorskl in #512
- Fixed LabMetadata SampleName column nullable by @victorskl in #513
- Fixed unittest LabMeta SampleName column nullable by @victorskl in #516
- Deprecate Portal Report processing by @victorskl in #515
- Fixed unittest for deprecated Portal Report processing by @victorskl in #517
- Fixed Supported ctTSO LabMetadata sample Type Assay combo by @victorskl in #514
- Added somalier extract for TSO ctDNA BAM by @victorskl in #518
- Disabled TSO500 ctDNA BAM somalier extract step by @victorskl in #519
- Added Portal GDS downloader through PreSigned URLs by @victorskl in #520
- Fixed unit test on Holmes Somalier service discovery by @victorskl in #522
- Bumped dependencies by @victorskl in #523
- Refactored drf_yasg OpenAPI Swagger generator to local only by @victorskl in #524
- Release 2.0rc1 by @victorskl in #525
- Added ENS event subscription for Staging by @victorskl in #526
- Added support for portal.umccr.org domain by @victorskl in #527
- Release 2.0rc2 by @victorskl in #528
- Release 2.0 by @victorskl in #529
- Added Cognito Portal data2 client ID to API Gateway JWT Authorizer audience by @victorskl in #530
- Added Cognito Portal data2 client ID to API Gateway JWT Authorizer audience by @victorskl in #531
- Added Cognito Portal data2 client ID to API Gateway JWT Authorizer audience by @victorskl in #532
- Bumped dev dependencies by @victorskl in #534
- Added support for lab metadata sheet 2023 by @victorskl in #535
- [STG] Added support for lab metadata sheet 2023 by @victorskl in #536
- [PROD] Added support for lab metadata sheet 2023 by @victorskl in #537
- Updated callers to Holmes by @andrewpatto in #538
- [STG] Updated callers to Holmes by @victorskl in #539
- [PROD] Updated callers to Holmes by @victorskl in #540
Full Changelog: 1.1.1...2.0
Contributors
andrewpatto and victorskl
Assets 2
Release 1.1.1
a25cc94
This commit was signed with the committer’s verified signature.
victorskl
Victor San Kho Lin
Milestone
What's Changed
- Improved LabMetadata stats handling by @victorskl in #502
- Release 1.1.1 by @victorskl in #503
Full Changelog: 1.1.0...1.1.1
Contributors
victorskl
Assets 2
Release 1.1.0
44a6c5c
This commit was signed with the committer’s verified signature.
victorskl
Victor San Kho Lin
Milestone
What's Changed
- Bumped dev dependencies by @victorskl in #474
- Bump django from 4.0.5 to 4.0.6 by @dependabot in #476
- Updated doc on IAM endpoint role permission requirement by @victorskl in #477
- Updated doc on Tumor Normal Lambda entrypoint by @victorskl in #478
- Updated doc Pipeline Lambda entry and Portal Athena by @victorskl in #479
- Bumped dependencies by @victorskl in #483
- Fixed CodeBuild Python environment by @victorskl in #486
- Bash please!! by @victorskl in #487
- add manops viewset by @williamputraintan in #488
- update manops domain by @williamputraintan in #489
- Remove 'wgs' regex for GPL reports on GDS by @scwatts in #490
- Added Portal Athena CLI use case by @victorskl in #491
- Bump django from 4.0.6 to 4.0.7 by @dependabot in #492
- Added Portal ICA Pipeline ENS subscription doc by @victorskl in #493
- Fixed duplicate tumor normal trigger in concurrent Sequencing by @victorskl in #494
- Added transcriptome
dragen_wtsLambda entrypoint by @victorskl in #495 - Refactored liborca
get_files_from_gds_by_suffixto libica.app.gds by @victorskl in #496 - Refactored with tooling from libumccr 0.3.0 by @victorskl in #497
- Bumped dependencies by @victorskl in #498
- Release 1.1.0 by @victorskl in #499
New Contributors
Full Changelog: 1.0.0...1.1.0
Contributors
scwatts, victorskl, and 2 other contributors