CHANGELOG.md

Changelog

2.35.2 (2025-01-17)

Bug Fixes

• Remove unsupported healthCheckEndpoint config (#362) (9515835)

2.35.1 (2025-01-17)

Bug Fixes

• add initial_delay_seconds in terraform (#360) (6779ffc)

2.35.0 (2025-01-16)

Features

• Dummy PR to trigger release please (#358) (c649ea9)

2.34.4 (2025-01-16)

Bug Fixes

• update happy to latest (#355) (f096ec8)

2.34.3 (2025-01-16)

Bug Fixes

• bump liveness readiness timeouts (#353) (0184ef8)

2.34.2 (2025-01-15)

Bug Fixes

• bump timeout seconds (#351) (652874f)

2.34.1 (2024-12-10)

Bug Fixes

• Adding missing workflow run mappings (#349) (e8b48bb)

2.34.0 (2024-06-10)

Features

• add pinned_alignment_config to SampleForReportResponse (#347) (76d3ca6)

2.33.2 (2024-05-31)

Bug Fixes

• Always stringify object query params (#343) (c28c60f)

2.33.1 (2024-04-30)

Bug Fixes

• Create Bulk Download backward compatibility (#340) (1bd4a71)

2.33.0 (2024-04-29)

Features

• Bump memory and CPU to avoid 500x errors (#337) (3366aaa)

Bug Fixes

• add required types to admin samples response (#336) (9cbf1cb)
• Change validIds field back to number, add new validIdsStrings field (#339) (8a23f0c)

2.32.0 (2024-04-24)

Features

• add nextgen entities and workflows url (#332) (62cf994)
• admin entities + workflows endpoints (#328) (8aae898)

Bug Fixes

• Remove unused resolvers and reorganize (#329) (c119b83)

2.31.0 (2024-04-22)

Features

• Expose errorLabel in fedWorkflowRuns (#330) (662e546)

2.30.2 (2024-04-19)

Bug Fixes

• Update NextGen schema with new errorLabel field and pass it through SampleForReport (#325) (ddfe8d5)
• Update schema (#326) (a510e29)

2.30.1 (2024-04-12)

Bug Fixes

• update schema for artic_v3 wetlab protocol (#322) (e34da61)

2.30.0 (2024-04-11)

Features

• Upgrade Mesh again to enable error logging (#303) (3fb5996)

Bug Fixes

• Make response schema for CreateBulkDownload consistent between flag on/off (#319) (2c7663f)

2.29.6 (2024-04-10)

Bug Fixes

• fix taxon/accession queries (#317) (969c3d7)

2.29.5 (2024-04-10)

Bug Fixes

• fix workflows query syntax and conditionally fire taxon/accession queries in sample report (#314) (e4c0cab)

2.29.4 (2024-04-10)

Bug Fixes

• Bulk Download List fixes (#309) (32b0eff)

2.29.3 (2024-04-09)

Bug Fixes

• query taxa and accessions for info in sample report (#310) (ff2ffde)
• Update collectionId in workflow schema to be nullable (#311) (302c702)

2.29.2 (2024-04-05)

Bug Fixes

• bulk delete id types (#307) (216b2d8)
• make taxon info optional in response (#306) (98bb588)

2.29.1 (2024-04-04)

Bug Fixes

• Handle object type in collection_location_v2 (#304) (4e4a74f)

2.29.0 (2024-04-04)

Features

• Add producingRunId to request schema of sequencingReads (#291) (cad49fd)
• Connect Bulk Downloads to NextGen (both Create Bulk Download and Bulk Download list) (#298) (ea206b7)

Bug Fixes

• Add taxon level to fedSequencingReads (#297) (fd29480)
• increase memory in prod (#277) (76fe22e)
• Update collectionId in entity schema to be nullable (#302) (f7466e3)
• Upgrade @graphql-mesh/cli (#299) (940b02d)

2.28.2 (2024-04-02)

Bug Fixes

• Use new Bulk Downloads Endpoint (#294) (89c5574)

2.28.1 (2024-04-01)

Bug Fixes

• allow for deprecatedById field in aggregate queries (#282) (20ecb02)
• fedBulkDownloads improvements (#249) (2adf599)

2.28.0 (2024-03-29)

Features

• Add new input to fedSequencingReads - workflowRunIds and sampleIds (#283) (3e6ff5e)

Reverts

• Enable more detailed logs in sandbox and staging envs" (#271) (7c12a14)

2.27.0 (2024-03-28)

Features

• federate querying total count of each workflow (#189) (93b8c29)

2.26.1 (2024-03-28)

Bug Fixes

• Add back query log (#272) (49e7f30)

2.26.0 (2024-03-28)

Features

• Add sorting by consensusGenomes field functionality in Fed (#246) (c87eaa2)
• Allow security token to be passed for nextGen calls (#218) (bed5cd2)
• CZID-9499 Add referenceGenome to fedConsensusGenome (#260) (409d793)

2.25.0 (2024-03-28)

Features

• Add includes metadata to BulkDownloadCGOverview (#250) (c2ade09)
• Add sorting by SequencingRead fields (#235) (4bb438d)
• Enable more detailed logs in sandbox and staging envs (#261) (4fda2e1)

2.24.0 (2024-03-26)

Features

• update taxon nullable (#240) (c61d7a9)

Bug Fixes

• change the type of BulkDownloadCGOverview.params (#242) (e71af07)

2.23.5 (2024-03-25)

Bug Fixes

• in Progress CG Overview testing (#238) (1ba36ec)

2.23.4 (2024-03-22)

Bug Fixes

• Bulk download cg overview next gen2 (#236) (2189473)

2.23.3 (2024-03-22)

Bug Fixes

• account for deprecated and bulk-download runs in SampleForReport query (#230) (567a2f2)
• testing cg bulk download overview (#233) (b16f33a)

2.23.2 (2024-03-22)

Bug Fixes

• bulk download overview in progress (#231) (478aeeb)

2.23.1 (2024-03-22)

Bug Fixes

• begin testing BulkDownloadCGOverview to nextGen (#227) (5c2c3a8)

2.23.0 (2024-03-21)

Features

• Also print query inputs in logs. (#212) (c1687a5)

Bug Fixes

• BulkDownloadModal Validation - Reformat query (#219) (c9444f8)
• Edits to fedBulkDownloads (#198) (1cee495)
• Use workflowRunIdsNumbers when available (#225) (cc890fd)

2.22.0 (2024-03-20)

Features

• Add filtering by sampleIds & workflowRunIds on /worklflow_runs for API testing (#223) (167b5a4)
• Add sample name match argument (#221) (6e2607c)
• Parallelize the Rails and NexGen join calls for fedSequencingReads ID query (#216) (6e341d0)

2.21.0 (2024-03-19)

Features

• Add collectionId to where of workflowRunsAggregate so that we can paginate the query (#213) (405f094)

2.20.2 (2024-03-19)

Bug Fixes

• Remove hack for testing (#210) (6cc6315)

2.20.1 (2024-03-18)

Bug Fixes

• Fix issues related to Rails calls made by fedSequencingReads when fetching IDs (#207) (9983ff2)
• Temporarily try seeing if fake paginating the aggregates query would solve the performance problem (#209) (b6b6d4a)

2.20.0 (2024-03-18)

Features

• Connect validation query to nextgen (#204) (481c40e)

2.19.1 (2024-03-18)

Bug Fixes

• fedConsensusGenomes: Make name available in rails (#202) (487ea03)

2.19.0 (2024-03-15)

Features

• Add support for filtering IDs of SequencingReads (#197) (d4eaf77)

2.18.2 (2024-03-15)

Bug Fixes

• Construct nextgen aggregates query appropriately (#199) (949e372)

2.18.1 (2024-03-14)

Bug Fixes

• Fix required fields in sequencingReads not being set when no Rails sample found (#195) (b437d34)

2.18.0 (2024-03-14)

Features

• Add hostOrganism join from Rails (#193) (7446701)

2.17.4 (2024-03-14)

Bug Fixes

• Ziplink querying wrong service (#191) (008ccba)

2.17.3 (2024-03-13)

Bug Fixes

• convert and use workflowRunIdsStrings if passed in (#187) (60c4f16)

2.17.2 (2024-03-13)

Bug Fixes

• make sure query param is a string (#185) (154904f)

2.17.1 (2024-03-13)

Bug Fixes

• Ziplink return from NextGen (#180) (9102025)

2.17.0 (2024-03-13)

Features

• Log NextGen responses when they error (#181) (a7b746e)

2.16.2 (2024-03-12)

Bug Fixes

• Add schema for fedWorkflowRuns for filtering out WorkflowRuns that don't have the correct input entity (#178) (85d3894)

2.16.1 (2024-03-12)

Bug Fixes

• Filter out WorkflowRuns with null sequencing_read inputEntityIds (#176) (deada69)

2.16.0 (2024-03-12)

Features

• query aggregates from NextGen and reformat response (#159) (0f08a5f)

Bug Fixes

• Tsconfig to allow deployment (#175) (305bbbd)
• Use workflowRun IDs in inner consensusGenomes where, not sequencingRead IDs (#171) (f858e3f)

2.15.5 (2024-03-12)

Bug Fixes

• Small Change for new version (#172) (62adf05)

2.15.4 (2024-03-11)

Bug Fixes

• Add sample uploader name to joined data from Rails + Use new array orderBy argument for NextGen (#166) (4914748)
• Update get conditional logic (#169) (2a17d09)

2.15.3 (2024-03-11)

Bug Fixes

• return rails data when no nextgen id available (#167) (b268861)

2.15.2 (2024-03-11)

Bug Fixes

• fix malformed id (#164) (51988c7)

2.15.1 (2024-03-08)

Bug Fixes

• Don't call Rails for the join if there were no sequencing reads returned by NextGen (#162) (5281fca)
• Sample View header & pipeline version (#160) (a23593d)

2.15.0 (2024-03-08)

Features

• Add deprecated filter to federated request (#151) (57057fc)
• federate SampleForReport object (#148) (91f0b1d)
• Join NextGen data with Rails data in resolver (#152) (9aa47f7)
• Update NextGen schema (#158) (bc23402)
• Ziplink NG Connection and Delete to accept strings (#149) (d3afbb8)

Bug Fixes

• Change to underscore entity input format (#157) (8866b51)

2.14.0 (2024-03-07)

Features

• update staging env variables urls (#153) (26afdd7)

2.13.0 (2024-03-06)

Features

• Integrate fedWorkflowRuns and fedSequencingReads with NextGen (#146) (8f51783)

Bug Fixes

• createBulkDownload Change workflowRunIdsStrings type and remove required for workflowRunIds (#145) (256173d)

2.12.0 (2024-03-04)

Features

• Add fed prefix to a few fields (#123) (832210f)
• Create Connection between Fed Server and Next Gen (#137) (b98dd14)
• Re-enable nextgen sources & update schemas (#120) (0304aa4)
• schema edits for workflows, fedWorkflows, BulkDownloadModal and fedConsensusGenomes (#142) (f89e183)
• Update paginated endpoints with limit/offset (#112) (ae755ed)
• Use nodemon to auto restart mesh after files change. (#124) (312dcef)

Bug Fixes

• Revert "fix: return id as a string" (#140) (e8da29b)
• Revert "fix: update mutation to expect a string and tests" (#139) (8c532ee)
• switch "_" objects to prefixed fields (#125) (f7911df)
• update mutation to expect a string and tests (#121) (c72561f)
• update to fedConsensusGenomes (#127) (af20c6c)

2.11.1 (2024-02-23)

Bug Fixes

• return id as a string (#115) (0ffa0b2)

2.11.0 (2024-02-21)

Features

• Add entities to sources (#96) (2fa964c)
• Bulk Download List Endpoints (#107) (1e45857)
• CZID-9342 split workflowRuns endpoint based on ids field (#101) (a2d3a31)
• Feature Flag based routing (#44) (f7c9999)
• Federate sequencingReads and consensusGenomes (#102) (0239be8)
• federate WorkflowsAggregate endpoint (#108) (9001540)

Bug Fixes

• Revert "feat: Feature Flag based routing" (#109) (c9bede2)

2.10.0 (2024-02-12)

Features

• Switch mode to basic to improve performance of unpaginated Rails request (#97) (ed41e0c)

2.9.0 (2024-02-08)

Features

• Federate CreateBulkDownload Endpoint (#91) (6f85f6a)

2.8.0 (2024-02-08)

Features

• Federate the samples NextGen field (#85) (946d7dc)
• Federate workflowRuns endpoint (#89) (3e15fac)

Bug Fixes

• Revert "feat: [CZID-9279] Add entities to graphql sources" (#94) (214d344)
• Update snapshot to fix tests (#95) (db56d3d)

2.7.0 (2024-02-02)

Features

• [CZID-9279] Add entities to graphql sources (#88) (8e38c3a)

2.6.1 (2024-01-30)

Bug Fixes

• ci: Pin happy stack eks to working version (#83) (c172a25)

2.6.0 (2024-01-29)

Features

• allow manual staging deploy, re-enable prod deploy (#82) (c1a07ce)
• ci: Align release process to CZ ID manual release cadence (#72) (83c97c6)
• move get release tag into composite action (#79) (ef26dcf)

Bug Fixes

• Access tag name path correctly (#77) (60ba125)
• Checkout repo with release tag from action (#80) (232a351)
• pass requested release tag to action (#81) (f7c2bb3)
• quote release tag (#78) (929ebf5)

2.5.0 (2024-01-12)

Features

• add MetadataValues query (#54) (721f8b0)
• Add URL's for entities & workflows services in local dev (#63) (26442d4)

Bug Fixes

• add missing property to location file (#64) (c08a63d)
• adding multiple location types and Update metadata values (#60) (9af53fe)
• Change ercc_comparison type from integer to float (#59) (108e0ad)

2.4.0 (2023-12-19)

Features

• add metadata-fields endpoint (#50) (3c16bfc)
• Add two distinct endpoints for notes and name (#47) (353bea2)
• ci: Set ALLOWED_CORS_ORIGINS app config (#52) (bc4e48b)

2.3.0 (2023-12-15)

Features

• added save_metadata_v2 endpoint (#43) (4d692c0)

2.2.0 (2023-12-14)

Features

• restrict CORS origin for graphQL mesh (#38) (2aa22e6)

2.1.1 (2023-12-11)

Bug Fixes

• update KickoffWGSWorkflow response id field (#39) (5f5e096)

2.1.0 (2023-12-07)

Features

• Add CSRF prevention plugin (#13) (64c8215)
• federated /workflow_runs/{args.workflowRunId}/zip_link.json (#25) (e97ab08)

Bug Fixes

• Change schema back to next gen format (#28) (0771869)
• ConsensusGenomeWorkflowResults - add fall back for null values (#34) (17d3193)
• Updated schema for kick off workflow (#27) (9939a7b)
• updates to ConsensusGenomeWorkflowResults type (#33) (b25922a)

2.0.0 (2023-11-28)

⚠ BREAKING CHANGES

• swap sampleId type to ID to support QualityControlQuery (#21)

Features

• swap sampleId type to ID to support QualityControlQuery (#21) (532a648)

1.7.0 (2023-11-21)

Features

• added coverage viz summary (#4) (e20662e)
• added kickoff_workflow (#9) (65ede16)
• ci: promote images from staging when deploying to prod (#5) (3854cbf)
• enable additional variables for PipelineData (#15) (4c23ca7)
• federeated /samples/validate_users_can_delete_objects (#14) (106dc4a)

Bug Fixes

• updated all json schemas (#22) (bb397de)

Reverts

• "chore: swap sampleId type to ID to support QualityControlQuery" (#20) (078b0c2)

1.6.0 (2023-11-02)

Features

• Pass CSRF token when querying CZID Rails graphql (#10) (cf9b8db)

Miscellaneous Chores

• release 1.6.0 (#12) (f805fca)

1.5.0 (2023-10-23)

Release tags and commits not available for version 1.5.0 and below

Features

• api: federate samples/bulk_delete
• api: support snapshot links

1.4.1 (2023-10-20)

Bug Fixes

• cd: revert promote staging images to prod

1.4.0 (2023-10-13)

Features

• cd: promote staging images to prod

1.3.0 (2023-10-10)

Features

• ci: Update stack names and parameterize sensitive infrastructure info

1.2.1 (2023-10-06)

Bug Fixes

• ci: remove staging image promotion in prod deploy

1.2.0 (2023-10-06)

Features

• api: federate GET '/samples/{sampleId}/report_v2' endpt
• ci: improve release flow for graphql federation
• support /samples/[sampleId]/report_v2 url params

Bug Fixes

• api url for local and deployed environments
• ci: use correct env for happy config in deploy staging and prod workflows * release fix taxon schema

1.1.1 (2023-09-29)

Bug Fixes

• ci: deploy-prod action should deploy release tag, not main

1.1.0 (2023-09-28)

Features

• api: federate GET '/samples/index_v2' endpt
• api: federate GET '/samples/index_v2' endpt
• api: federate GET '/samples/{sampleId}.json' endpt
• api: federate GET '/samples/{sampleId}/amr.json' endpt
• api: federate GET '/workflow_runs/{workflowRunId}/results' endpt

1.0.0 (2023-08-11)

Features

• add new sandbox happy env
• add prod release workflow
• happy setup for dev,staging,prod

Bug Fixes

• service needs to be the same name
• service needs to be the same name