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Sync fork 9 - #18

Merged

kkochel merged 224 commits into

mainfrom

sync-fork-9

Dec 5, 2025

Merged

Sync fork 9#18
kkochel merged 224 commits into
mainfrom
sync-fork-9

Commits on Sep 24, 2025
- Create new function for ingest message and correlation id
  kostas-kou
  committed
  1c0ff2b
- Create function for retrieving user and path
  kostas-kou
  committed
  92022fb
- Tests for the db function
  kostas-kou
  committed
  9384310
- Create function in api for accepting file id as parameter
  kostas-kou
  committed
  b37b827
- Unit tests for the msgInfoFileID function
  kostas-kou
  committed
  0bb5ea8
- Modify unit tests for ingestFile function
  kostas-kou
  committed
  57665af
- Add test for ingesting file via file id
  kostas-kou
  committed
  9098641
- Modify swagger
  kostas-kou
  committed
  62c8572
- Update readme for file/ingest
  kostas-kou
  committed
  9aed12d
- Refactor setAccession function to extract JSON parsing and correlation ID retrieval into accessionMsgFilePath function
  kostas-kou
  committed
  425bc45
- Replace db function for finding checksum with a simpler one
  kostas-kou
  committed
  af49e8e
- Add accessionMsgFileID function which creates accession payload from endpoint parameters
  kostas-kou
  committed
  5b763f1
- Enhance setAccession function to handle query parameters and update rbac policy to allow wildcard path for accession
  kostas-kou
  committed
  a886ed5
- Add tests for accession message file path handling and create helper for verified test file
  kostas-kou
  committed
  e1c4cc1
- Add tests for accessionMsgFileID function and handle invalid fileID scenario
  kostas-kou
  committed
  0819583
- Update accession endpoint tests to handle wildcard paths and improve payload handling
  kostas-kou
  committed
  01afc29
- Add test for finalizing file using accession ID via file ID
  kostas-kou
  committed
  e5b292f
- Update file accession endpoint description and parameters for clarity
  kostas-kou
  committed
  f07a437
- Update `/file/accession` endpoint to support query parameters and improve error handling
  kostas-kou
  committed
  b218118
- Close db connections in a couple of tests
  kostas-kou
  committed
  f8adf25
- Apply suggestions from code review
  
  kostas-kou
  and
  jbygdell
  committed
  40f85c4
- Remove wildcard from ingest and accession endpoint
  kostas-kou
  committed
  bc78c32
- Fixes for review commit
  kostas-kou
  committed
  03596fc
- Refactor db function for returning structured FileDetails with correlation ID
  kostas-kou
  committed
  47b5bc9
- Update db function test
  kostas-kou
  committed
  f604d5d
- Refactor ingestFile and setAccession functions
  kostas-kou
  committed
  8482f68
- Update unit tests
  kostas-kou
  committed
  fb3b716
- Update document and swagger
  kostas-kou
  committed
  b6fac68
- Update integration test
  kostas-kou
  committed
  21fdb08
- Add validation for missing accession ID in setAccession function and corresponding test
  kostas-kou
  committed
  73261f3
- Move FileDetails struct definition to database.go
  kostas-kou
  committed
  d099de4
- Apply suggestions from code review
  
  kostas-kou
  and
  jbygdell
  committed
  f85d1a6
- Small fixes
  kostas-kou
  committed
  73c8b40
- Apply suggestions from code review
  
  kostas-kou
  and
  jbygdell
  committed
  64517ef
- Apply suggestions from code review
  
  kostas-kou
  and
  jbygdell
  committed
  a8b0a22
- Fixes mainly for correlation id and checksum
  kostas-kou
  committed
  1310410
- Add return in the default case of ingestFile
  kostas-kou
  committed
  a39cf54
- Rename functions in comments and tests for clarity
  kostas-kou
  committed
  8e4173d
- Apply suggestions from code review
  
  kostas-kou
  and
  nanjiangshu
  committed
  0be5676
Commits on Sep 25, 2025
- Add IngestFileInfo struct and improve PostReq request handling
  kostas-kou
  committed
  3f817d6
- Add test case for nil jsonBody in PostReq function
  kostas-kou
  committed
  9910b99
- Refactor Ingest function
  kostas-kou
  committed
  8b50e72
- Update Ingest unit tests for using struct
  kostas-kou
  committed
  93f11d5
- Rename Ingest test functions for clarity and add new tests for Ingest with file id functionality
  kostas-kou
  committed
  3a61982
Commits on Sep 26, 2025
Commits on Oct 9, 2025
- Update .github/integration/tests/sda/60_api_admin_test.sh
  
  kostas-kou
  and
  nanjiangshu
  authored
  ffb9507
Commits on Oct 10, 2025
- Linter fixes
  kostas-kou
  committed
  d311418
- Bump github.com/quic-go/quic-go
  dependabot[bot]
  authored
  54dc153
- Bump github.com/quic-go/quic-go
  dependabot[bot]
  authored
  d4c0392
Commits on Oct 11, 2025
- Fix finalize with json payload
  kostas-kou
  committed
  ec01065
- Add api integration test for finalize (json payload)
  kostas-kou
  committed
  2e4592b
Commits on Oct 13, 2025
Commits on Oct 14, 2025
Commits on Oct 19, 2025
- Bump the all-modules group across 1 directory with 3 updates
  dependabot[bot]
  authored
  108fc7c
- Merge pull request #2031 from neicnordic/dependabot/go_modules/sda-download/all-modules-e60da6fe41
  jbygdell
  authored
  720b8bb
Commits on Oct 20, 2025
- Update sda/cmd/api/api.go
  
  kostas-kou
  and
  jbygdell
  authored
  eeb6a45
- Bump no.elixir:crypt4gh in /sda-doa in the all-modules group
  dependabot[bot]
  authored
  a1a033c
Commits on Oct 21, 2025
- Merge pull request #2040 from neicnordic/dependabot/maven/sda-doa/all-modules-ebcb5f81e6
  jbygdell
  authored
  eef4d8d
Commits on Oct 22, 2025
- make GetC4GHPublicKey work for different apps
  
  aaperis
  authored and
  jbygdell
  committed
  b034cb3
- get keyhash for a file from db
  
  aaperis
  authored and
  jbygdell
  committed
  e7b3a88
- get stableID by FileID from db
  
  aaperis
  authored and
  jbygdell
  committed
  9d2496e
- close db connection after each test
  
  aaperis
  authored and
  jbygdell
  committed
  344fc06
- add rotatekey stream and queue
  
  aaperis
  authored and
  jbygdell
  committed
  b3e0d1b
- create role rotatekey for sda schema
  
  aaperis
  authored and
  jbygdell
  committed
  906641a
- add rotatekey service
  
  aaperis
  authored and
  jbygdell
  committed
  108c41b
- add setup for rotatekey integration tests
  
  aaperis
  authored and
  jbygdell
  committed
  1ecd711
- cleanup temporary create_role function
  
  aaperis
  authored and
  jbygdell
  committed
  659f12f
- register rotation key in the db during test setup
  
  aaperis
  authored and
  jbygdell
  committed
  5284c27
- send msg to erorr queue of get keyhash fails
  
  aaperis
  authored and
  jbygdell
  committed
  194e450
- fix linting
  
  aaperis
  authored and
  jbygdell
  committed
  2b5cdc9
- checks target key hash both at startup and before processing messages
  
  aaperis
  authored and
  jbygdell
  committed
  d8aa861
- nack after some error messages
  
  aaperis
  authored and
  jbygdell
  committed
  da29787
- add rotatekey integration tests
  
  aaperis
  authored and
  jbygdell
  committed
  c920bd0
- reencrypt headers using the reencrypt service
  
  aaperis
  authored and
  jbygdell
  committed
  227e1f2
- add config unittests for rotatekey
  
  aaperis
  authored and
  jbygdell
  committed
  b3707c6
- throw an error if call to reencrypt returns an empty header
  
  aaperis
  authored and
  jbygdell
  committed
  f12c28c
- enforce processing only one file per message
  
  aaperis
  authored and
  jbygdell
  committed
  1c57182
- rework nacking mechanism
  
  aaperis
  authored and
  jbygdell
  committed
  a4db996
- add error cases in rotatekey integration tests
  
  aaperis
  authored and
  jbygdell
  committed
  556feff
- add rotatekey documentation
  
  aaperis
  authored and
  jbygdell
  committed
  34f12e5
- separate logging from nacking function
  
  aaperis
  authored and
  jbygdell
  committed
  cc4e90d
- handle case with already encrypted with key at info level
  
  aaperis
  authored and
  jbygdell
  committed
  4bd6ab2
- integration test fixes from review suggestions
  
  aaperis
  authored and
  jbygdell
  committed
  3785914
- add CheckKeyHash function
  
  aaperis
  authored and
  jbygdell
  committed
  855f794
- use db.CheckKeyHash instead of getKeyHash
  
  aaperis
  authored and
  jbygdell
  committed
  1321cdf
- get file corrID from delivered message
  
  aaperis
  authored and
  jbygdell
  committed
  64460ea
- add rotatekey-key json schema
  
  aaperis
  authored and
  jbygdell
  committed
  6968dce
- add GetAccessionID db function
  
  aaperis
  authored and
  jbygdell
  committed
  68ed6a7
- rotatekey consumes rotate-key messages
  
  aaperis
  authored and
  jbygdell
  committed
  a96b12e
- remove rotatekey_stream
  
  aaperis
  authored and
  jbygdell
  committed
  26b866e
- add utility function CallReencryptHeader to reencrypt
  
  aaperis
  authored and
  jbygdell
  committed
  3bdd1d8
- replace reencrypt logic with CallReencryptHeader
  
  aaperis
  authored and
  jbygdell
  committed
  a46b25c
- terminate app if target key is deprecated at runtime
  
  aaperis
  authored and
  jbygdell
  committed
  769ab48
- refactoring suggestions frm review
  
  aaperis
  authored and
  jbygdell
  committed
  5d59aa5
- update rotatekey docs with suggestions from review
  
  aaperis
  authored and
  jbygdell
  committed
  0777092
- have the input to GetC4GHPublicKey be the pubkey path
  
  aaperis
  authored and
  jbygdell
  committed
  6e52c6b
- sync: load the pubkey from config
  
  aaperis
  authored and
  jbygdell
  committed
  c110a86
- rework pub key handling logic
  
  aaperis
  authored and
  jbygdell
  committed
  ae85b5f
- remove obsolete c4gh test key
  
  aaperis
  authored and
  jbygdell
  committed
  397e0b8
- add logic to exit gracefully
  
  aaperis
  authored and
  jbygdell
  committed
  c040a11
- more suggestions from review
  
  aaperis
  authored and
  jbygdell
  committed
  d716864
- add test for reencrypt_utils
  
  pahatz
  authored and
  jbygdell
  committed
  ec6cbbd
- check that fileID is uuid conformant
  
  aaperis
  authored and
  jbygdell
  committed
  83ad4d0
- add RotateHeaderKey function
  
  aaperis
  authored and
  jbygdell
  committed
  d1253e5
- update header and keyhash together
  
  aaperis
  authored and
  jbygdell
  committed
  29b271e
- refactor rotatekey to ease unittesting
  
  aaperis
  authored and
  jbygdell
  committed
  86a2978
- refactor message handling
  
  aaperis
  authored and
  jbygdell
  committed
  5b7c625
- requeue message if db error is recoverable and don't otherwise
  
  aaperis
  authored and
  jbygdell
  committed
  dd80f8c
- add func to get reverification data from fileID
  
  aaperis
  authored and
  jbygdell
  committed
  f3b6291
- remove any dependency on accessionID as input
  
  aaperis
  authored and
  jbygdell
  committed
  79ae6f4
- [Test CallReEncryptHeader] ensure correct error response
  jbygdell
  committed
  8b23ac8
- [reencrypt] ensure an error message is always returned on error
  jbygdell
  committed
  a0a5468
- [reencrypt] add test for failed reencryption due to no matching key
  jbygdell
  committed
  ce42231
- [rotateKey] remove check for non exiting nil value
  jbygdell
  committed
  3e9ee50
- [rotateKey] failure to trigger re-validation needs to go to error
  jbygdell
  committed
  93609c3
- [rotateKey] rename rotateHeader to reEncryptHeader
  jbygdell
  committed
  636698c
- [rotate key] add basic test suite.
  jbygdell
  committed
  f93b4aa
- Merge pull request #1918 from neicnordic/rotate-key-service
  aaperis
  authored
  8a092b9
Commits on Oct 27, 2025
- Bump the all-modules group in /sda-sftp-inbox with 2 updates
  dependabot[bot]
  authored
  937ca6e
- Bump the all-modules group in /sda-doa with 2 updates
  dependabot[bot]
  authored
  796d9f3
Commits on Oct 28, 2025
- Merge pull request #2053 from neicnordic/dependabot/maven/sda-doa/all-modules-d8d7275ed9
  kjellp
  authored
  4a94a66
- Merge branch 'main' into feature/admin-api-UUIDs
  kostas-kou
  authored
  ceffb10
- Minor linter fix
  kostas-kou
  committed
  86fcb4a
Commits on Oct 29, 2025
- Merge pull request #2051 from neicnordic/dependabot/maven/sda-sftp-inbox/all-modules-d8d7275ed9
  jbygdell
  authored
  8c59aa2
- Bump chart version
  
  neicnordic
  authored and
  github-actions[bot]
  committed
  1b53e85
- Merge pull request #2013 from neicnordic/bump
  jbygdell
  authored
  c2b9670
Commits on Nov 3, 2025
- Bump the all-modules group in /sda-sftp-inbox with 2 updates
  dependabot[bot]
  authored
  e48edf7
- Bump the all-modules group in /sda-doa with 2 updates
  dependabot[bot]
  authored
  079a1a4
Commits on Nov 4, 2025
- Merge pull request #2061 from neicnordic/dependabot/maven/sda-doa/all-modules-bdd0c9ce94
  jbygdell
  authored
  61511cb
- Merge pull request #2060 from neicnordic/dependabot/maven/sda-sftp-inbox/all-modules-295fbf7d28
  nanjiangshu
  authored
  e326441
- feat: add middleware for checking client version
  nanjiangshu
  committed
  611684d
- feat: update default SelectedMiddleware
  nanjiangshu
  committed
  bf7c84d
- feat: update go mod
  nanjiangshu
  committed
  b6237e3
- feat: add unit tests for ClientVersionMiddleware
  nanjiangshu
  committed
  f75688d
- feat: add unit tests for ChainDefaultMiddleware
  nanjiangshu
  committed
  de1496e
- refactor: parse expectedClientVersion in the config
  nanjiangshu
  committed
  3a5bc7e
- feat: update unit tests
  nanjiangshu
  committed
  f50f887
- feat: fix integration test for sda-download
  nanjiangshu
  committed
  4a9845f
- fix: unit test for config
  nanjiangshu
  committed
  46847f2
- feat: add integration test for client version header
  nanjiangshu
  committed
  679ca1e
- fix: lint, gofmt for sda-download
  nanjiangshu
  committed
  762e5d7
- fix: lint, unhandled-error, for sda-download
  nanjiangshu
  committed
  df527f2
- fix: correctly sanitize userID in removeUserIDPrefix
  nanjiangshu
  committed
  d0a63b3
- refactor: rename expectedcliversion to minimalcliversion
  nanjiangshu
  committed
  b60e9b7
- feat: check token before cli version in the middleware
  nanjiangshu
  committed
  cc8e54b
- fix: integration test after changing the order of check
  nanjiangshu
  committed
  84b7cdc
- refactor: merge unit tests for ChainDefaultMiddleware
  nanjiangshu
  committed
  66f0f06
- feat: remove duplicated logic to return http code
  nanjiangshu
  committed
  cecbe91
- refactor: use a more idiomatic approach for the middleware
  nanjiangshu
  committed
  2e5b967
- feat: apply reviewers comments
  
  nanjiangshu
  and
  jbygdell
  committed
  65e5d73
- feat: improve name and logic for middleware
  nanjiangshu
  committed
  1927dc8
- feat: log error message to debug
  nanjiangshu
  committed
  754a908
- Merge pull request #2047 from neicnordic/feature/download-block-non-supported-version
  nanjiangshu
  authored
  63e7b5d
Commits on Nov 5, 2025
- Merge branch 'main' into feature/admin-api-UUIDs
  kostas-kou
  authored
  bb7b0a8
- Bump github.com/opencontainers/runc
  dependabot[bot]
  authored
  8d45b77
Commits on Nov 6, 2025
- Merge pull request #1934 from neicnordic/feature/admin-api-UUIDs
  kostas-kou
  authored
  e39dbff
Commits on Nov 7, 2025
- Merge pull request #2072 from neicnordic/dependabot/go_modules/sda/go_modules-7d01802d74
  pahatz
  authored
  3377387
- Bump chart version
  
  neicnordic
  authored and
  github-actions[bot]
  committed
  8e64920
- Merge branch 'main' into enhancement/sda-admin-use-ids
  kostas-kou
  authored
  44f0fd6
- Merge pull request #2068 from neicnordic/bump
  jbygdell
  authored
  eb3e69a
Commits on Nov 10, 2025
Commits on Nov 11, 2025
- Update sda-admin/helpers/helpers.go
  
  kostas-kou
  and
  jbygdell
  authored
  56a8d5f
Commits on Nov 12, 2025
- Merge pull request #2073 from neicnordic/dependabot/github_actions/golangci/golangci-lint-action-9.0.0
  jbygdell
  authored
  5ac4af4
- Merge pull request #2074 from neicnordic/dependabot/maven/sda-sftp-inbox/all-modules-c5f4368ff1
  jbygdell
  authored
  3f95ebc
- Merge pull request #2075 from neicnordic/dependabot/maven/sda-doa/all-modules-b6ef16c69a
  nanjiangshu
  authored
  ec1f47e
- Bump chart version
  
  neicnordic
  authored and
  github-actions[bot]
  committed
  a600687
Commits on Nov 14, 2025
- Merge branch 'main' into enhancement/sda-admin-use-ids
  kostas-kou
  authored
  fcda64f
- Merge pull request #2026 from neicnordic/enhancement/sda-admin-use-ids
  kostas-kou
  authored
  2d1d913
Commits on Nov 17, 2025
- Merge pull request #2082 from neicnordic/bump
  jbygdell
  authored
  d350e32
- build(deps): bump golang.org/x/crypto
  dependabot[bot]
  authored
  28d1c61
- build(deps): bump com.squareup.okhttp3:okhttp-jvm
  dependabot[bot]
  authored
  29fb122
Commits on Nov 18, 2025
- Merge pull request #2086 from neicnordic/dependabot/go_modules/sda-download/all-modules-c94709d3c3
  jbygdell
  authored
  ab218d9
- Merge pull request #2087 from neicnordic/dependabot/maven/sda-doa/all-modules-df69034c87
  jbygdell
  authored
  b3c69a8
Commits on Nov 20, 2025
Commits on Nov 24, 2025
- build(deps): bump actions/checkout from 5 to 6
  dependabot[bot]
  authored
  7a75061
Commits on Nov 25, 2025
Commits on Nov 26, 2025
- Merge pull request #2103 from neicnordic/dependabot/github_actions/golangci/golangci-lint-action-9.1.0
  jbygdell
  authored
  6c0142e
Commits on Nov 27, 2025
- build(deps): bump the all-modules group in /sda-doa with 2 updates
  
  dependabot[bot]
  authored and
  Parisa68
  committed
  6734a7c
- replace gson with spring-boot-starter-gson
  Parisa68
  committed
  71f59ce
- Merge pull request #2114 from neicnordic/dependabot/go_modules/sda-download/all-modules-d8d25555fd
  jbygdell
  authored
  ba30378
- Merge pull request #2098 from neicnordic/dependabot/go_modules/sda/golang.org/x/crypto-0.45.0
  jbygdell
  authored
  2e86116
- Merge pull request #2110 from neicnordic/dependabot/maven/sda-doa/all-modules-952e573d1f
  jbygdell
  authored
  f3cc388
- Bump chart version
  
  neicnordic
  authored and
  github-actions[bot]
  committed
  9a78ecd
Commits on Nov 28, 2025
Commits on Nov 29, 2025
- Merge pull request #2094 from neicnordic/bump
  jbygdell
  authored
  12fdac2
Commits on Dec 1, 2025
Commits on Dec 2, 2025
- feat(rotatekey): fix rotatekey test, and update reEncryptHeader func to not take correlation id just file id and publish message with fileid instead
  KarlG-nbis
  committed
  e69e455
- feat(api): revert change to getFileIDByUserPathAndStatus to check for null stable_id, introduce new database func CheckStableIDOwnedByUser to be used when creating dataset to check if a file belong…
  KarlG-nbis
  committed
  7ecbf3f
Commits on Dec 3, 2025
- feat: update some comments, and logs to say fileID instead of correlationID where relevant, and update message handling funcs to use fileID variable instead of delivered.CorrelationId to reduce ris…
  KarlG-nbis
  committed
  b08814c
- feat(postgres): fix typo in changes messages for previous migrations verisons: 15, 16, and 18 priviledge -> privilege
  KarlG-nbis
  committed
  91ff1bd
Commits on Dec 4, 2025

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