Release 0.6.0

Milestone

• https://github.com/umccr/data-portal-apis/milestone/2?closed=1

What's Changed

• Added tumor normal pairing R example by @victorskl in #293
• Add POST to presign endpoint by @reisingerf in #294
• Enable negative-control processing by @reisingerf in #296
• Dragen WTS automation by @skanwal in #277
• Refactored GDS event processing (#298) by @victorskl in #300
• Add CTTSO500 report ingestion by @brainstorm in #203
• Filter pairing of run tumors that are an intersection of subject tumors by @alexiswl in #302
• Fastq API endpoint can be queried by project owner by @andrei-seleznev in #305
• Added project_owner input filter in fastq lambda by @victorskl in #306
• Pinned container names for local dev compose stack by @victorskl in #307
• Bumped Python 3.9 and Node 14 (#308) by @victorskl in #309
• Fixed CodeBuild docker-compose by @victorskl in #310
• Allowed CORS Origins from status and sscheck domains by @victorskl in #311
• Fixed dependabot ansi-regex alert by @victorskl in #312
• ICA Pipeline enhanced models (#239) by @victorskl in #254
• Implemented LibraryRun (#299) by @victorskl in #313
• library run api implementation by @williamputraintan in #315
• Implement sequence api by @williamputraintan in #320
• Revert Search Field from 'all' literal by @williamputraintan in #323
• Improved to use automated ICA service token rotation (#258) by @victorskl in #324
• Updated DRAGEN WGS QC workflow lane aware and no merge (#276) by @victorskl in #326
• Implemented linking between Workflow and LibraryRun (#325) by @victorskl in #327
• Fixed with WTS Lambda to consume from queue by @victorskl in #328
• Harmonised LibraryRun library_id to FastqListRow rglb by @victorskl in #329
• Release 0.6.0 by @victorskl in #330

Full Changelog: 0.5.0...0.6.0

Release 0.5.0

Milestone

• https://github.com/umccr/data-portal-apis/milestone/3?closed=1

What's Changed

• Added T/N pairing empty metadata handling by @victorskl in #279
• Handled LIMS update for same Library ID across different lanes by @victorskl in #280
• Added project_owner and project_name filter to metadata endpoint by @victorskl in #283
• Added sscheck app client id to allow api gateway authorizer audience by @victorskl in #284
• Improved LabMetadata importing by @victorskl in #286
• Implemented pairing domain model by @victorskl in #288
• Improved workflow update step by @victorskl in #289
• Bumped dependencies and fixed test case by @victorskl in #290
• Bump axios from 0.21.1 to 0.21.4 by @dependabot in #291
• Release 0.5.0 by @victorskl in #292

Full Changelog: 0.4.0...0.5.0

Release 0.4.0

Milestone

• https://github.com/umccr/data-portal-apis/milestone/1?closed=1

What's Changed

• Added R examples on accessing FASTQs through Portal API by @victorskl in #249
• Updated to native docker compose by @victorskl in #250
• Moved CI images to quay by @victorskl in #251
• Bump tar from 6.1.0 to 6.1.5 by @dependabot in #252
• First look at updating engine parameters by @alexiswl in #248
• Updated t/n pairs logic and created strip_topup_rerun from library func by @alexiswl in #262
• Bumped dependencies and fixed yarn audit by @victorskl in #264
• Fixed DRAGEN_TSO_CTDNA workflow maxScatter engine parameter by @victorskl in #267
• Fixed and improved T/N pairing impl by @victorskl in #269
• Fixed engine parameter mid path issue by @victorskl in #270
• Release 0.4.0 by @victorskl in #271

Full Changelog: 0.3.0...0.4.0

Release 0.3.0

What's Changed

• Retire demux_metadata lambda by @reisingerf in #220
• Google lims export by @reisingerf in #225
• Updated bclconvert settings for 10x samples by @alexiswl in #228
• Pipeline refactor: Introducing Pipeline werkzeug by @victorskl in #227
• Renamed GERMLINE to DRAGEN_WGS_QC by @victorskl in #230
• Ct tso automation by @alexiswl in #232
• Updated WGS QC workflow input to library_id by @victorskl in #233
• Fixed TSO ctDNA and WGS QC FastqListRow to dict by @victorskl in #234
• Added simple skip step in orchestrator lambda event interface by @victorskl in #236
• Improved BCL Convert output split_sheets parsing by @victorskl in #237
• 10X adapters aren't all nextera adapters by @alexiswl in #235
• read 1 and read 2 need to be cwl file objects for dragen_tso_ctdna workflow by @alexiswl in #238
• Implemented workaround non-ideal metadata lookup by @victorskl in #241
• Fixed DRAGEN_WGS_QC workflow input CWL File object by @victorskl in #242
• Harmonised Library ID use across metadata lookup by @victorskl in #245
• Implemented WorkflowRule model by @victorskl in #246
• Fixed unittest to ignore libgdrive append_records by @victorskl in #247

Full Changelog: 0.2.0...0.3.0

Release 0.2.0

What's Changed

• Add GDS file search lambda by @reisingerf in #152
• Bumped MySQL version 5.7 by @victorskl in #156
• Bump django from 3.1.1 to 3.1.6 by @dependabot in #158
• Genomics report model and endpoints by @brainstorm in #136
• Bump djangorestframework from 3.11.1 to 3.11.2 by @dependabot in #159
• Added X-Ray support by @victorskl in #160
• Deployed Python dependencies as Lambda layer by @victorskl in #161
• Added serverless-prune-plugin by @victorskl in #162
• Bump y18n from 4.0.0 to 4.0.1 by @dependabot in #163
• Bump django from 3.1.6 to 3.1.8 by @dependabot in #164
• Bcl convert output handler by @alexiswl in #157
• Fixed db migration merged by @victorskl in #165
• Fixed build issue with serverless by @victorskl in #166
• Fixed buildspec exclude serverless cli check by @victorskl in #167
• Improved CI build setup by @victorskl in #168
• Refactored gspread sheet download to libgdrive by @victorskl in #171
• Refactored LIMS processing package by @victorskl in #172
• Fixed orchestrator bcl convert output parsing by @victorskl in #173
• Implemented report persisting by @victorskl in #174
• Refactored S3 package by @victorskl in #175
• Implemented report processing through sqs queue by @victorskl in #176
• Fixed s3 testcase mock by @victorskl in #177
• Allowed report s3 object link none by @victorskl in #178
• Refactored gds module by @victorskl in #179
• Fixed germline jobs fastq preparation by @victorskl in #180
• ICA pipeline slack notification title and color format by @victorskl in #182
• Improved report type parsing from key by @victorskl in #184
• Added ops limit for Report data ingestion by @victorskl in #185
• Upgraded to Django 3.2 by @victorskl in #186
• Migrated to libica by @victorskl in #187
• Compact dependencies by @victorskl in #188
• Bump migration timeout by @victorskl in #189
• Removed report s3object fk constraint by @victorskl in #190
• Lab metadata ingestion by @andrei-seleznev in #181
• Improved labmetadata by @victorskl in #191
• Fixed yarn audit serverless dependency xmlhttprequest-ssl by @victorskl in #195
• Reports API by @brainstorm in #200
• implemented labmeta api endpoint by @andrei-seleznev in #194
• Subject view labmetadata endpoints by @andrei-seleznev in #199
• Add MultiQC report type by @brainstorm in #201
• Quick patch to prevent manual workflows from running by @alexiswl in #202
• Updated germline workflow to split top ups / reruns on the same run a… by @alexiswl in #206
• Addition of T/N workflow by @reisingerf in #204
• Deprecated nested routing by @victorskl in #207
• Added s3crawler offline tool to index S3 objects by @victorskl in #209
• Allow multiple tumor samples per subject by @reisingerf in #210
• Updated serverless v2 by @victorskl in #211
• Migrated to APIGateway v2 HttpApi by @victorskl in #212
• Added OpenAPI Swagger generator by @victorskl in #213
• Rolled back Werkzeug to v1 by @victorskl in #214
• Fixed CORS OPTIONS Preflight request by @victorskl in #215
• Added ICA pipeline related endpoints by @victorskl in #216
• Added keyword filter on reports and metadata endpoint by @victorskl in #217
• Bumped serverless version by @victorskl in #219
• override-cycles batchname fix by @alexiswl in #221
• Bump django from 3.2.3 to 3.2.4 by @dependabot in #222
• Improved Report format and reporting source check by @victorskl in #224

Full Changelog: 0.1.0...0.2.0

Release 0.1.0

What's Changed

• Bump handlebars from 4.0.11 to 4.1.2 by @dependabot in #1
• Bump diff from 3.4.0 to 3.5.0 by @dependabot in #2
• Bump nwmatcher from 1.4.3 to 1.4.4 by @dependabot in #3
• Bump js-yaml from 3.12.0 to 3.13.1 by @dependabot in #4
• Bump lodash from 4.17.5 to 4.17.15 by @dependabot in #5
• Bump extend from 3.0.1 to 3.0.2 by @dependabot in #6
• Bump merge from 1.2.0 to 1.2.1 by @dependabot in #7
• Bump mem from 1.1.0 to 4.3.0 by @dependabot in #8
• Bump cryptiles from 3.1.2 to 4.1.3 by @dependabot in #10
• merge by @jayai2014 in #11
• manual fix on package vuln by @jayai2014 in #12
• moved iam role out to terraform by @jayai2014 in #13
• Merge in new backend by @jayai2014 in #14
• Merge to master by @jayai2014 in #15
• Bump django from 2.1.4 to 2.1.11 by @dependabot in #16
• New lims processor by @jayai2014 in #17
• Bump ecdsa from 0.13.2 to 0.13.3 by @dependabot in #18
• Dev by @jayai2014 in #19
• Dev by @jayai2014 in #20
• Add empty result handling for random sampling by @jayai2014 in #21
• Api change and documentation by @jayai2014 in #22
• added linked keyword for search query and storage stats api by @jayai2014 in #23
• Added missing test and fixed issue for incorrect s3 lims results by @jayai2014 in #24
• Code refactoring & improvement. Enabled testing in pipeline by @jayai2014 in #25
• Code refactoring and improvement by @jayai2014 in #26
• Added parameter to skip create association when updating LIMS rows by @victorskl in #28
• Added lims endpoint by @victorskl in #30
• Added get lims by id endpoint by @victorskl in #31
• Added ordering filter for lims endpoint by @victorskl in #32
• Added search filter to lims endpoint by @victorskl in #33
• Removed rn field by @victorskl in #34
• Implemented Subject and S3 endpoints by @victorskl in #35
• Bump django from 2.1.11 to 2.1.15 by @dependabot in #36
• Added Subject and S3 endpoints by @victorskl in #37
• Fixed CloudFormation API path by @victorskl in #38
• Fixed serverless requirements zip by @victorskl in #39
• Added optional slash router by @victorskl in #40
• Added allow regex in Subject S3 key search filter by @victorskl in #41
• Upgrade backend to django 3 by @victorskl in #42
• Added fix for data type size by @victorskl in #43
• Added exceptions handling by @victorskl in #44
• Added illumina_id to ordering fields by @victorskl in #45
• Bump django from 3.0.2 to 3.0.3 by @dependabot in #46
• Implemented run specific endpoint by @victorskl in #47
• Added run endpoints to serverless config by @victorskl in #48
• Added serverless specific certificate arn by @victorskl in #49
• Added buildspec and serverless to use WAF_NAME env variable by @victorskl in #50
• Added Serverless remove documentation by @victorskl in #51
• Implemented S3 Object tagging by @victorskl in #52
• Added S3 objects backlog tagger by @victorskl in #53
• Added support for S3 operations by @victorskl in #54
• Improved Glacier Restore API by @victorskl in #55
• Bumped Python3.8 by @victorskl in #56
• Fixed S3 restore request by @victorskl in #57
• Implemented LIMS data update automation by @victorskl in #58
• Changed to Yarn for package dependency management by @victorskl in #59
• Fixed serverless lambda timeout warning by @victorskl in #61
• Refactored to use setuptools by @victorskl in #62
• Reverted back Moto version by @victorskl in #63
• Added analysis results for subject landing view by @victorskl in #64
• Fixed serverless-wsgi plugin depends on werkzeug by @victorskl in #65
• Fixed serverless-python-requirements plugin slim package default pattern by @victorskl in #66
• Added support for IAP ENS GDS Files events by @victorskl in #67
• Fixed IAP ENS SQS message attribute value key by @victorskl in #68
• Fixed test stub for IAP ENS SQS message attributes by @victorskl in #69
• Added timezone support for GDS File timeCreated by @victorskl in #70
• Improved service layer by @victorskl in #71
• Fixed environ warning log by @victorskl in #72
• Implemented libgds and gdscrawler by @victorskl in #73
• Implemented gds endpoints by @victorskl in #74
• Reverted back to Requirements Files by @victorskl in #75
• Improved project setup by @victorskl in #76
• Made LIMS bucket processing obsolete by @victorskl in #77
• Fixed mkvar script STAGE use pass in args by @victorskl in #78
• Added support for IAP ENS bssh.runs event by @victorskl in #79
• Added support for slack notification by @victorskl in #80
• Bump django from 3.0.4 to 3.0.7 by @dependabot in #81
• Added libiap for integrating with IAP services by @victorskl in #82
• Implemented IAP pipeline workflows launch orchestration by @victorskl in #83
• Improved IAP pipeline workflows by @victorskl in #84
• Added workflow run name by @victorskl in #85
• Changed to workflow wes.runs event by @victorskl in #86
• Skip workflow run if not in Portal workflow runs automation by @victorskl in #87
• Updated workflow run name convention by @victorskl in #88
• Added workflow slack notification by @victorskl in #89
• Fixed workflow run output json by @victorskl in #90
• Added automated workflow notification send only once by @victorskl in #91
• Added support for workflow update fallback scenarios by @victorskl in #92
• Fixed workflow Running status and RunStarted event type pair by @victorskl in #93
• Refactored pipeline workflow code base by @victorskl in #94
• Improved lambdas handler return by @victorskl in #95
• Updated query for new umccrise analysis output by @victorskl in #96
• Improved ENV vars to sync from SSM Parameter Store by @victorskl in #97
• Fixed launching duplicate BCL Convert workflow by @victorskl in https://github.com/umccr/dat...