Release 0.3.0

What's Changed

• add workflow run status count api by @raylrui in #558
• Update Python service skel by @reisingerf in #557
• Feat (metadata-manager): Update model by @williamputraintan in #535
• fix(filemanager): swap docker hub images for AWS public ECR by @mmalenic in #565
• Feat (MM): Custom CSV Importer for MM by @williamputraintan in #566
• refactor(filemanager): match AWS behaviour for delete markers by @mmalenic in #568
• Bug fixes for 0.2.1 by @alexiswl in #573
• Feat (MM): State Change Event by @williamputraintan in #569
• Fix orcabus_id filter (w/ prefixes) by @williamputraintan in #582
• Feat(MM): API Serializer Expansion by @williamputraintan in #583
• Fix error when checking source uris have been transferred by @alexiswl in #588
• Add OrcaBus ID by @reisingerf in #579
• feat(filemanager): ingest_id tagging and object move tracking by @mmalenic in #585
• fix(filemanager): version_id for S3 API calls by @mmalenic in #587
• Add RESOLVED state as supported WorkflowRun state by @reisingerf in #594
• feat(filemanager): accept multiple keys in API by @mmalenic in #596
• Friday changes: by @alexiswl in #589
• Fix: Drop incomplete record before metadata processing by @williamputraintan in #598
• feat(filemanager): docker caching and current state default by @mmalenic in #601
• Feature/analysis journey by @reisingerf in #599
• Feat (MM): History API for Models by @williamputraintan in #606
• wfm update for ui fix by @raylrui in #608
• cttsov2 job checker requires permissions to list executions by @alexiswl in #603
• Add fastqc / sequali stats to fastq list row events for first 1 million reads by @alexiswl in #602
• Pieriandx needs 'SUCCEEDED' status as positive terminal status not 'COMPLETE' by @alexiswl in #604
• Handle orcabus_id with prefix when saving model objects by @reisingerf in #612
• feat: filemanager partitions by @mmalenic in #615
• fix(filemanager): resetting current state should include old verisons by @mmalenic in #616
• wfr/ feat-comments-resolved-status-mutation-module by @raylrui in #613
• Oncoanalyser / Sash stack and glue services by @alexiswl in #610
• Feat: Add Authoriser Based on User Pool Group by @williamputraintan in #617
• Bumped dependencies by @victorskl in #620
• Remove unused stacky tables by @alexiswl in #619
• feat(event-source): ignore cache directories by @mmalenic in #621
• Updated json paths for portal run id and workflow run name by @alexiswl in #623
• feat(event-source): add archive bucket as event source by @mmalenic in #625
• Fix library lookup with prefixed orcabusId by @reisingerf in #626
• Fixed roket get-individual-id step by @alexiswl in #630
• Retry lambdas with delay of 60 seconds by @alexiswl in #631
• Allow samplesheet overwrite by @alexiswl in #632
• Need to collect camelCase orcabus Id when retrieving object from metadata manager by @alexiswl in #635
• Feat(MM): Add Sync Metadata Endpoint by @williamputraintan in #627
• Feat/analysis run api update by @raylrui in #628
• Delete partial files before retrying copy job by @alexiswl in #636
• Added ora file decompression fastq pair component by @alexiswl in #624
• Upgrade memory for pieriandx glue lambdas by @alexiswl in #634
• CodeBuild doesn't support git-lfs by @alexiswl in #642
• [skip ci]: Added ora pipeline and reference path to staging and production envs by @alexiswl in #639
• Only save payload if present by @reisingerf in #646
• Add analysis size option per microservice by @alexiswl in #638
• Manually transfer files that are smaller than 8 MiB or dont have an etag by @alexiswl in #643
• Need to set 'keep_flowcell_layout' to true for wrapica collection of runinfo xml by @alexiswl in #648
• Fix (MM): Allow nullable description for sync by @williamputraintan in #649
• Fix WRSC not having a payload by @reisingerf in #650
• Set cttsov2 icav2 storage configuration to LARGE by @alexiswl in #652
• Pull the snomed databases from github if they're not on the local system by @alexiswl in #654
• fix-ora-compression-manager by @alexiswl in #656
• Prevent the ntc samples running through cttsov2 by @alexiswl in #658
• PierianDx Production Fixes by @alexiswl in #659
• HotFix(authorization-manager): Sanitize Authorization Header by @williamputraintan in #661
• Update dragen somatic pipeline id by @alexiswl in #665
• feat(fmannotator): add DLQ for fmannotator function by @mmalenic in #664
• Fixed oncoanalyser Batch trigger initial status SUBMITTED by @victorskl in #667
• Wrong typescript boolean logic which meant there was no event rule by @alexiswl in #671
• Fix literal placeholders in nf step functions by @alexiswl in #674
• hotfix(filemanager): add permissions that allow API/inventory functions to access pipeline-*-cache buckets by @mmalenic in #670
• Sanitise subject id for oncoanalyser / sash / nf workflows by @alexiswl in #680
• Update v2 samplesheet maker version by @alexiswl in #678
• Fix status for non-terminal by @alexiswl in #682
• Fix Rnasum dataset input parameter by @alexiswl in #684
• Setup to rearrange the outputs for the ora compression manager by @alexiswl in #666
• Chore(mm): Miscellaneous Update by @williamputraintan in #686
• Update rnasum pipeline version to 1.1.5 by @alexiswl in #685
• fix(filemanager): longer presigned URLs by @mmalenic in #688
• Fix(mm): Broken Comparison on Update by @williamputraintan in #691
• Added lambda layer for workflows API endpoint + RNASum Lambda by @alexiswl in #692
• Fix rnasum rerun lambda by @alexiswl in #702
• feat(filemanager): add fastq bucket to ingester event source by @mmalenic in #700
• add distinct to remove duplicate results by @raylrui in #706
• Add holmes glue by @alexiswl in #708
• Allow validation only for ora decompression by @alexiswl in #703
• Retry 5 mins when capacity is limited by @alexiswl in #712
• Feat(wfm): rnasum rerun api by @williamputraintan in #713
• Few lambda fixes by @alexiswl in #715
• Feat(pipeline): Disable Dev Automatic Deployment by @williamputraintan in #714
• Fix(MM): Add reason on history for add in m2m relationship by @williamputraintan in #716
• Rate limit ora compression workflow by @alexiswl in #720
• feat: dump postgres records by @mmalenic in #709
• Feat(mm): Allow Library Filtered by Project by @williamputraintan in #723
• feat(data-migrate): data mover task by @mmalenic in #726
• Don't extend portal run id to sequencer run, by @alexiswl in #731
• Set sample type to ctDNA for cttsov2 triggers by @alexiswl in #730
• Sleep command should then loop to list-executions by @alexi...

Release 0.2.3

What's Changed

• Merge pull request #588 from umccr/hotfix/bssh-fastq-copy-quick-fix by @victorskl in #590

Full Changelog: 0.2.2...0.2.3

Release 0.2.2

What's Changed

• Merge pull request #573 from umccr/prod-patch/0-2-1 by @victorskl in #574

Full Changelog: 0.2.1...0.2.2

Release 0.2.1

What's Changed

• Payloads use Rgid not RgId by @alexiswl in #551
• TSO500L Data shouldn't have lane data by @alexiswl in #550
• [skip ci]: Add prod example to cache bucket by @alexiswl in #549
• Add lane to bclconvert samplesheet if it doesn't exist by @alexiswl in #552
• Change(WorkflowRunManager): add more query and search terms by @raylrui in #540
• Set cttso v2 nf outputs by @alexiswl in #553
• Initialise library set to prevent sfn failing by @alexiswl in #555
• Fix cttso outputs sfn by @alexiswl in #556

Full Changelog: 0.2.0...0.2.1

Release 0.2.0

What's Changed

• build(deps): bump django from 5.0.3 to 5.0.7 in /lib/workload/stateless/stacks/metadata-manager/deps by @dependabot in #404
• build(deps): bump certifi from 2024.2.2 to 2024.7.4 in /lib/workload/stateless/stacks/bs-runs-upload-manager/layers by @dependabot in #394
• Bump djangorestframework from 3.15.0 to 3.15.2 in /lib/workload/stateless/stacks/metadata-manager/deps by @dependabot in #380
• feat: filemanager filter query parameters by @mmalenic in #409
• build(deps): bump django from 5.0.6 to 5.0.7 in /lib/workload/stateless/stacks/workflow-manager/deps by @dependabot in #410
• build(deps): bump certifi from 2024.2.2 to 2024.7.4 in /lib/workload/stateless/stacks/cttso-v2-pipeline-manager/layers by @dependabot in #412
• Feat(metadata-manager): Schema Change by @williamputraintan in #411
• Added AWSLambdaSQSQueueExecutionRole policy to SRM Lambda role by @victorskl in #413
• feat: filemanager current state by @mmalenic in #415
• Feature(metadata-manager): Additional API by @williamputraintan in #416
• Fix (MM): Dependency Issue by @williamputraintan in #419
• build(deps): bump django from 5.0.5 to 5.0.7 in /lib/workload/stateless/stacks/sequence-run-manager/deps by @dependabot in #420
• feat(filemanager): add database mocking to local API server by @mmalenic in #418
• Feat(MM): Upgrade OpenAPI Version 3 by @williamputraintan in #421
• build(deps): bump object_store from 0.10.1 to 0.10.2 in /lib/workload/stateless/stacks/filemanager by @dependabot in #422
• feat(filemanager): attribute updating API by @mmalenic in #424
• Feat: Running Microservice API Locally by @williamputraintan in #425
• Chore: Upgrade OpenAPI3 for DRF Microservice by @williamputraintan in #426
• build(deps): bump djangorestframework from 3.15.1 to 3.15.2 in /lib/workload/stateless/stacks/sequence-run-manager/deps by @dependabot in #428
• fix: add filemanager to local API setup by @mmalenic in #429
• Refactor glue constructs by @alexiswl in #393
• build(deps): bump djangorestframework from 3.15.1 to 3.15.2 in /lib/workload/stateless/stacks/workflow-manager/deps by @dependabot in #430
• Wrap launch analysis step function segment into a parallel chunk to reduce step output sizes by @alexiswl in #432
• Fixed cttsov2 post-processing docker architecture ARM_64 by @victorskl in #433
• fix(filemanager): Dockerfile caching layer and debug build by @mmalenic in #442
• Convert Oversized python lambdas to DockerImage Functions by @alexiswl in #434
• Update ssm parameter pipeline constants for new icav2 pipelines by @alexiswl in #445
• Updated SRM processing to Singleton Lambda pattern by @victorskl in #448
• Improved Django skel template by @victorskl in #447
• build(deps-dev): bump certifi from 2024.2.2 to 2024.7.4 in /lib/workload/stateless/stacks/bssh-icav2-fastq-copy-manager/layers by @dependabot in #449
• Fixed minor stacky glues issues by @victorskl in #450
• Fix(SRM && WFM): Update OpenAPI Docs by @williamputraintan in #452
• Add tags to event data for workflowrunstatechange events by @alexiswl in #451
• feat: filemanager API wildcards by @mmalenic in #457
• Upgraded Django5.1 and bumped dependencies for MM, SRM, WFM services by @victorskl in #466
• refactor(filemanager): remove object table by @mmalenic in #465
• fix(filemanager): local s3-load should not use object by @mmalenic in #467
• Fixed Workflow Manager API filter by attributes by @victorskl in #469
• Harmonised API v1 versioning namespace base URL by @victorskl in #468
• Bumped dependencies by @victorskl in #471
• refactor(filemanager): API style by @mmalenic in #472
• build(deps): bump axios from 1.7.3 to 1.7.4 by @dependabot in #473
• feat: filemanager presigned route by @mmalenic in #475
• [skip ci]: Updated GH prbuild.yml by @victorskl in #480
• [skip ci]: Fixed GH prbuild.yml by @victorskl in #484
• [draft]: Added dependabot.yml config file by @victorskl in #485
• Bumped PGM dependencies by @victorskl in #474
• Updated dependabot.yml config applies-to security-updates only by @victorskl in #493
• refactor(filemanager): misc simpler and clearer API by @mmalenic in #492
• fix(filemanager): presigned URL access by @mmalenic in #499
• Removed dependabot.yml config and revert to its default setting by @victorskl in #501
• Django pagination fix by @reisingerf in #502
• Add support for linked libraries to WRSC event schema by @reisingerf in #503
• Stacky updates for generating umccrise events by @alexiswl in #505
• Use the new metadata library endpoint for queries by @alexiswl in #504
• initialised umccrise pipeline manager by @alexiswl in #506
• Fix/filemanager api tidy by @mmalenic in #507
• metadata-manager: model refactoring by @williamputraintan in #508
• Fixed metadata endpoint allow dot sep in PK by @victorskl in #510
• Feature/workflow library link by @reisingerf in #513
• refactor: filemanager indexes by @mmalenic in #514
• build(deps): bump micromatch from 4.0.7 to 4.0.8 by @dependabot in #517
• fix: filemanager migration by @mmalenic in #519
• Fixed WorkflowRun State creation business logic by @victorskl in #516
• Fix Django OpenAPI Schema by @williamputraintan in #520
• filemanager: attributes route and misc CORS changes by @mmalenic in #515
• Fix/workflowrun state handling by @reisingerf in #521
• Fix issue with WRSC generation when a libary record exists by @reisingerf in #522
• Fix: Metadata Filter && Sortable Endpoint by @williamputraintan in #523
• WFM - Extend API capabilities - ongoing workflowrun filter by @reisingerf in #524
• Feature/add umccrise rnasum and glues by @alexiswl in #525
• Updated stacky with new metadata manager by @alexiswl in #509
• build(deps): bump micromatch from 4.0.5 to 4.0.8 in /lib/workload/stateful/stacks/postgres-manager by @dependabot in #526
• Bumped dependencies by @victorskl in #527
• filemanager: annotate portal run id by @mmalenic in #529
• Feat: Update API Gateway Configuration by @williamputraintan in #531
• refactor(filemanager): compile database and migrations by @mmalenic in #534
• Change(WorkflowRunManager): update the workflowrun model by @raylrui in #536
• Enabled dynamodb PITR by @victorskl in #537
• Bumped dependencies by @victorskl in #538
• Trimmed basespace upload manager dependencies by @victorskl in #539
• Fix (MM): Library synchronisation issue by @williamputraintan in #542
• Fixed metadata sheet processing year input data type by @victorskl in #543

Full Changelog: 0.1.0...0.2.0

Release 0.1.0

What's Changed

• Update build script by @williamputraintan in #1
• Pre commit hook Added by @williamputraintan in #3
• Improve project setup by @victorskl in #10
• Refactor setup schemaregistry by @reisingerf in #18
• Implemented externalise config constants pass-down as props pattern by @victorskl in #19
• Bumped dependencies and fixed lints by @victorskl in #20
• Refactored project setup on initial structure by @victorskl in #13
• Reinforced DevSecOps setup with scanners TruffleHog & GGShield by @victorskl in #21
• Serverless MySQL by @williamputraintan in #22
• Refactored OrcaBus Stateless component with MicroService by @victorskl in #23
• Init CDK-Pipeline by @williamputraintan in #24
• Updated pipeline to use UMCCR AWS accounts by @victorskl in #25
• Improved Django template skel profile by @victorskl in #26
• Updated SequenceRunStateChange Event schema with proper envelope by @victorskl in #29
• Implemented Sequence Run Manager microservice app by @victorskl in #28
• FileManager microservice Rust skel by @brainstorm in #27
• Improved SequenceRunStateChange Event schema by @victorskl in #30
• Improved Django Skel by removing base setting as default by @victorskl in #31
• Rust skel fixups by @brainstorm in #33
• Improved GHA CI build and local dev DX by @victorskl in #32
• Implemented Sequence Run Manager BSSH event processing by @victorskl in #36
• Bumped baseline toolchain Python and Node dependencies by @victorskl in #41
• Init Metadata Manager by @williamputraintan in #35
• Initial dev for the Metadata Manager by @williamputraintan in #42
• Bump webpki from 0.22.0 to 0.22.1 in /skel/rust-api by @dependabot in #43
• Bump webpki from 0.22.1 to 0.22.2 in /skel/rust-api by @dependabot in #44
• Filemanager: S3 events persistence by @brainstorm in #37
• Bump django from 4.2.3 to 4.2.7 in /skel/django-api/src by @dependabot in #51
• Bump werkzeug from 2.3.6 to 3.0.1 in /skel/django-api/src by @dependabot in #48
• Bump axios from 1.4.0 to 1.6.1 in /lib/workload/stateless/metadata_manager/src by @dependabot in #52
• Bump django from 4.2.3 to 4.2.7 in /lib/workload/stateless/sequence_run_manager/src by @dependabot in #50
• Bump @babel/traverse from 7.21.4 to 7.23.2 by @dependabot in #46
• Bump django from 4.2.3 to 4.2.7 in /skel/django-proc/src by @dependabot in #49
• Bump @babel/traverse from 7.22.8 to 7.23.2 in /lib/workload/stateless/metadata_manager/src by @dependabot in #45
• Bump werkzeug from 2.3.6 to 2.3.8 in /lib/workload/stateless/sequence_run_manager/src by @dependabot in #55
• Rust skel bump by @brainstorm in #56
• Refresh and fix some AWS Rust SDK API changes by @brainstorm in #58
• Remove _deprecated by @brainstorm in #59
• Fix SQS events, update localstack, speed up compilte/test cycle w/ sc… by @brainstorm in #61
• Fix sqs events upgrade localstack by @brainstorm in #62
• Bump rustix from 0.38.13 to 0.38.21 in /lib/workload/stateful/filemanager by @dependabot in #60
• [doc] Add Rust SCCACHE to speed up local builds by @brainstorm in #63
• Simplify local development and debugging setup by @brainstorm in #65
• More idempotent scripts by @brainstorm in #66
• Bump openssl from 0.10.59 to 0.10.60 in /skel/rust-api by @dependabot in #64
• Init for MetadataManager by @williamputraintan in #67
• Filemanager: fix ingestion/deployment by @brainstorm in #74
• filemanager: setup testing by @mmalenic in #75
• Remove the lock and bump up the toml by @brainstorm in #78
• filemanager: deploy changes and fixes by @mmalenic in #79
• Added Swagger UI and Dependencies Bumped by @williamputraintan in #83
• Gitpod by @andrewpatto in #80
• Project setup refactor by @victorskl in #87
• Metadata Manager Restructuring by @williamputraintan in #89
• feat: de-duplicate events at the database level by @mmalenic in #88
• Update RDS Construct by @williamputraintan in #91
• build(deps): bump h2 from 0.3.21 to 0.3.24 in /lib/workload/stateful/filemanager by @dependabot in #84
• Initiate CDK Pipeline by @williamputraintan in #92
• feat(filemanager): move SQS and DLQ to stateful stack by @mmalenic in #101
• feat(filemanager): ensure events are ingested in the correct order by @mmalenic in #93
• refactor: filemanager deployment code and Makefile by @mmalenic in #98
• build(deps): bump django from 4.2.7 to 4.2.10 in /skel/django-proc/src by @dependabot in #95
• build(deps): bump django from 4.2.7 to 4.2.10 in /lib/workload/stateless/sequence_run_manager by @dependabot in #96
• build(deps): bump django from 4.2.7 to 4.2.10 in /skel/django-api/src by @dependabot in #97
• build(deps): bump undici from 5.25.2 to 5.28.3 in /lib/workload/stateless/metadata_manager by @dependabot in #105
• build(deps): bump ip from 2.0.0 to 2.0.1 by @dependabot in #107
• build(deps): bump ip from 2.0.0 to 2.0.1 in /lib/workload/stateless/metadata_manager by @dependabot in #108
• fix: event source name rule should be an array by @mmalenic in #112
• fix: queue service name and secret name by @mmalenic in #118
• fix(filemanager): deserialize event bridge messages by @mmalenic in #121
• fix(filemanager): correctly deal with null version_id by @mmalenic in #125
• postgres-manager: Initiate postgres-manager by @williamputraintan in #126
• fix(postgres-manager): failing unit test from cdk-nag by @williamputraintan in #128
• fix(filemanager): re-run sqlx prepare with all targets by @mmalenic in #124
• fix(filemanager): sqlx queries by @mmalenic in #134
• Fix: Codebuild UnitTest by @williamputraintan in #132
• codepipeline notication by @williamputraintan in #130
• fix(filemanager): ingest constraints by @mmalenic in #136
• fix(filemanager): query files by @mmalenic in #142
• Postgres Manager Enhancement by @williamputraintan in #149
• Added sequence_run_manager database config by @victorskl in #151
• refactor: swap rust function by @mmalenic in #152
• fix(pipeline): install Rust for unit tests by @mmalenic in #154
• fix: pipeline error caused by filemanager containerized build by @mmalenic in #156
• Implemented SequenceRunManager app deployment by @victorskl in #155
• Fixed SequenceRunManager architecture to ARM64 by @victorskl in #163
• Update Readme and Refactor Pipeline Code by @williamputraintan in #157
• Trimmed down the sequence_run_manager by @victorskl in #171
• Fixed deployment by removing sequence_run_manager HttpStage by @victorskl in #172
• build(deps): bump postgres versions to match RDS instance by @mmalenic in #173
• fix: filemanager uuids by @mmalenic in #161
• Improved sequence_run_manager API Gateway setup by @victorskl in https://github.com/umcc...