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Sync fork 6 - #14

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kkochel wants to merge 375 commits into

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sync_fork_6

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Sync fork 6#14
kkochel wants to merge 375 commits into
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Commits on Feb 25, 2025
Commits on Feb 26, 2025
- Merge pull request #1362 from neicnordic/feature/auth-tokens
  pahatz
  authored
  3bf4493
- Merge pull request #1394 from neicnordic/feature/download_svc
  jbygdell
  authored
  c07bede
- Bump chart version
  
  neicnordic
  authored and
  github-actions[bot]
  committed
  b5fb522
- Merge pull request #1443 from neicnordic/bump
  aaperis
  authored
  7f64fe8
- Bump github.com/go-jose/go-jose/v3 in /sda in the go_modules group
  dependabot[bot]
  authored
  f3ce6b7
Commits on Feb 28, 2025
- Merge pull request #1446 from neicnordic/dependabot/go_modules/sda/go_modules-e2b1dc0a79
  jbygdell
  authored
  d389071
Commits on Mar 3, 2025
Commits on Mar 4, 2025
Commits on Mar 5, 2025
- Remove junit dependency to avoid conflict
  Parisa68
  committed
  5cb63ec
- Merge pull request #1442 from neicnordic/fix/junit-conflict
  Parisa68
  authored
  182e6b2
- Read issuer URL from environment variable
  Parisa68
  committed
  95bf0ce
- Replace deprecated jwk.dumps with JsonWebKey.import_key per AuthlibDeprecationWarning
  Parisa68
  committed
  290db2b
- Merge pull request #1448 from neicnordic/refactor/doa-mockauth
  Parisa68
  authored
  2516bbc
- Bump the all-modules group across 1 directory with 5 updates
  
  dependabot[bot]
  authored and
  Parisa68
  committed
  1d18ae0
- Merge pull request #1461 from neicnordic/dependabot/maven/sda-doa/all-modules-f75d9e76c1
  Parisa68
  authored
  017240a
- Bump chart version
  
  neicnordic
  authored and
  github-actions[bot]
  committed
  362802f
- Remove obsolete info and add overview and installation sections
  Parisa68
  committed
  966f3d5
- add info related to sda-doa targets
  Parisa68
  committed
  c7281ae
- add permission info
  Parisa68
  committed
  4eec403
- correct default values
  Parisa68
  committed
  5133d4f
Commits on Mar 6, 2025
- Merge pull request #1449 from neicnordic/bump
  aaperis
  authored
  89938a3
- Merge pull request #1462 from neicnordic/readme-updates-for-sad-doa
  Parisa68
  authored
  9c12349
Commits on Mar 10, 2025
- Bump the all-modules group in /sda-doa with 2 updates
  dependabot[bot]
  authored
  0025e09
Commits on Mar 11, 2025
- Merge pull request #1468 from neicnordic/dependabot/maven/sda-doa/all-modules-1f2ac5652a
  kjellp
  authored
  84455ed
- remove unnecessary lines from log
  Parisa68
  committed
  eef9e3a
- Bump the all-modules group in /sda-download with 2 updates
  
  dependabot[bot]
  authored and
  aaperis
  committed
  cf4b0e6
- Merge pull request #1469 from neicnordic/dependabot/go_modules/sda-download/all-modules-572cabda0a
  aaperis
  authored
  1826794
- Merge pull request #1464 from neicnordic/fix/doa-log
  Parisa68
  authored
  14ad323
- Bump the all-modules group in /sda with 7 updates
  
  dependabot[bot]
  authored and
  aaperis
  committed
  b55176f
- Merge pull request #1470 from neicnordic/dependabot/go_modules/sda/all-modules-8efb596a9b
  aaperis
  authored
  6c41008
- Bump chart version
  
  neicnordic
  authored and
  github-actions[bot]
  committed
  b14afd9
Commits on Mar 12, 2025
- Merge pull request #1475 from neicnordic/bump
  jbygdell
  authored
  87cc036
Commits on Mar 13, 2025
- Bump golang.org/x/net in /sda in the go_modules group
  dependabot[bot]
  authored
  09c4035
- Merge pull request #1476 from neicnordic/dependabot/go_modules/sda/go_modules-c153b83258
  jbygdell
  authored
  c390d84
- Bump golang.org/x/net in /sda-download in the go_modules group
  
  dependabot[bot]
  authored and
  aaperis
  committed
  e6eaf20
Commits on Mar 14, 2025
- Merge pull request #1477 from neicnordic/dependabot/go_modules/sda-download/go_modules-c153b83258
  aaperis
  authored
  bc9e549
- Bump chart version
  
  neicnordic
  authored and
  github-actions[bot]
  committed
  9370a30
- doc: fix typos in README
  MalinAhlberg
  committed
  dde2179
- fix: show error msg and standard page when ega login fails
  MalinAhlberg
  committed
  ab126a2
- [auth] fix: handle cega-nss being down
  MalinAhlberg
  committed
  84c323c
- [auth] add case for bad service credentials to ega server
  MalinAhlberg
  committed
  4c37612
- [auth] refactor error handeling
  MalinAhlberg
  committed
  a7999d3
- [auth] handle more errors
  MalinAhlberg
  committed
  b456ef0
- auth: refactor
  MalinAhlberg
  committed
  7c7e03a
Commits on Mar 17, 2025
Commits on Mar 18, 2025
Commits on Mar 20, 2025
- Apply suggestions from code review
  
  jbygdell
  and
  MalinAhlberg
  authored
  21541fa
- Apply suggestions from code review
  jbygdell
  authored
  4899656
- Update sda/cmd/api/swagger_v1.yml
  
  jbygdell
  and
  dbampalikis
  authored
  7dcc051
- Expand the SubmissionFileInfo struct to also contain the file stable ID
  jbygdell
  committed
  8c5d328
- [internal/database] Add bool to selectively return the accession ID
  jbygdell
  committed
  074542d
- [API] don't return the accession ID of files to a submitter
  jbygdell
  committed
  31d721e
Commits on Mar 21, 2025
- Apply suggestions from code review
  jbygdell
  authored
  4b224c5
- Bump github.com/golang-jwt/jwt/v5 in /sda in the go_modules group
  dependabot[bot]
  authored
  a002f9c
Commits on Mar 24, 2025
Commits on Mar 25, 2025
Commits on Mar 26, 2025
- Allow delay in GetFileSize from storage
  MalinAhlberg
  committed
  66c896f
- [storage] tests: add expectedDelay in storage tests
  MalinAhlberg
  committed
  2c0b57f
- [storage] tests: getfilesize waits for s3 to write
  MalinAhlberg
  committed
  bf5f2b9
- Merge pull request #1483 from neicnordic/fix/ingest-waits-for-s3
  MalinAhlberg
  authored
  ddbc4d6
- Bump chart version
  
  neicnordic
  authored and
  github-actions[bot]
  committed
  587f443
Commits on Mar 27, 2025
Commits on Mar 28, 2025
Commits on Mar 31, 2025
Commits on Apr 1, 2025
- make check robust to library changes
  aaperis
  committed
  fe167c7
- Merge pull request #1527 from neicnordic/dependabot/go_modules/sda-download/all-modules-b032d566c7
  aaperis
  authored
  72bf251
Commits on Apr 2, 2025
Commits on Apr 3, 2025
Commits on Apr 4, 2025
- [s3inbox] send overwrite message when file is reuploaded
  MalinAhlberg
  committed
  8ae9be3
- [tests] check that an extra message is sent
  MalinAhlberg
  committed
  a28e20e
- [s3inbox]tests: add minio container
  MalinAhlberg
  committed
  259bd7d
- [s3inbox] tests: real S3 for proxy tests
  
  jbygdell
  authored and
  MalinAhlberg
  committed
  8b3b6f1
- [s3inbox] tests: Fix healthcheck tests
  
  jbygdell
  authored and
  MalinAhlberg
  committed
  1039af2
- [s3inbox] tests: improve tests
  MalinAhlberg
  committed
  000c8ad
Commits on Apr 7, 2025
- [s3inbox] remove newlines etc
  MalinAhlberg
  committed
  b3b7ec9
- Apply suggestions from code review
  
  MalinAhlberg
  and
  jbygdell
  authored
  4c4f273
- Bump golang.org/x/crypto in /sda-download in the all-modules group
  dependabot[bot]
  authored
  f916fda
- Bump the all-modules group in /sda with 7 updates
  dependabot[bot]
  authored
  b43c330
- Bump net.logstash.logback:logstash-logback-encoder
  dependabot[bot]
  authored
  57c04be
Commits on Apr 8, 2025
- Merge pull request #1543 from neicnordic/feat/send-remove-message-on-overwrite
  MalinAhlberg
  authored
  ae33000
- Bump net.logstash.logback:logstash-logback-encoder
  
  dependabot[bot]
  authored and
  Parisa68
  committed
  a17fb2d
- Merge pull request #1576 from neicnordic/dependabot/maven/sda-doa/all-modules-4aa4aef47f
  Parisa68
  authored
  7b9317b
- Merge pull request #1580 from neicnordic/dependabot/maven/sda-sftp-inbox/all-modules-4aa4aef47f
  aaperis
  authored
  3edb5e5
- Merge pull request #1579 from neicnordic/dependabot/go_modules/sda/all-modules-bde378e3f7
  aaperis
  authored
  57d0144
- Merge pull request #1575 from neicnordic/dependabot/go_modules/sda-download/all-modules-b8ea8a95a2
  jbygdell
  authored
  2a81441
- [Ingest] break apart the main work loop to make it more testable #minor
  jbygdell
  committed
  4ece2da
- [ingest_test] Set up suite for live testing
  jbygdell
  committed
  797eaf0
- [ingest_test] add cases for `cancel` messages
  jbygdell
  committed
  31cda54
- [ingest_test] add file ingest scenarios
  jbygdell
  committed
  168b235
- [internal/database] move `SetArchvied` from SQL to GO
  jbygdell
  committed
  3a40f00
- [internal/database] GetFileInfo needs to be able to handle null values
  jbygdell
  committed
  6e60415
- [ingest_test] ingest verified file
  jbygdell
  committed
  4951e97
- [intetrnal/database] expand file info struct with all checksums
  jbygdell
  committed
  945e3b7
- [ingest] use proper checksum names
  jbygdell
  committed
  ff364a2
- [ingest] calculate checksum if file is cancelled.
  jbygdell
  committed
  c457cb2
- [api_test] update to use new checksum names
  jbygdell
  committed
  7de98c8
- [verify] use full checksum names
  jbygdell
  committed
  17fd690
- [sync_test] use full checksum names
  jbygdell
  committed
  476ee16
- [ingest] app struct needs to be declared inside of the main function
  jbygdell
  committed
  04899d7
- [ingest] improve error messges
  jbygdell
  committed
  efb7d1f
- [ingest_test] add test for missing file in the inbox
  jbygdell
  committed
  51926cf
- [verify] move SetVerified from SQL to GO
  jbygdell
  committed
  0156cf3
- [tests] fix SetVerified
  jbygdell
  committed
  ed88d21
- [integration_tests] Ensure messages correlation ids are unique
  jbygdell
  committed
  cb574c4
- Apply suggestions from code review
  
  jbygdell
  and
  nanjiangshu
  committed
  9a97917
- Apply suggestions from code review
  
  jbygdell
  and
  MalinAhlberg
  committed
  4f1afb0
- update compose volume mounts for sda-doa src and pom.xml
  Parisa68
  committed
  3758fe9
Commits on Apr 9, 2025
Commits on Apr 10, 2025
- Add test to ensure 2 submitter's can upload to the same relative path
  jbygdell
  committed
  d053cf5
- [postgres] update `unique_ingested`constraint
  jbygdell
  committed
  98350ad
Commits on Apr 11, 2025
- [s3inbox] Use Predefined S3 client
  jbygdell
  committed
  1248101
- [s3inbox test] Add comments to S3 backend test
  jbygdell
  committed
  153fa67
Commits on Apr 14, 2025
Commits on Apr 15, 2025
Commits on Apr 16, 2025
- Merge pull request #1571 from neicnordic/feature/s3inbox-stores-size-in-db
  jbygdell
  authored
  ce06f55
- [actions] make linter action work with v2 of golangci-lint
  jbygdell
  committed
  1d6d752
- [gosec] fix false positives
  jbygdell
  committed
  28ba3b0
- [revive] use any instead of interface{}
  jbygdell
  committed
  2804c8b
- [deep-exit] ignore for now, refactoring required
  jbygdell
  committed
  05f2d97
- [revive] fix blank lines at block boundaries
  jbygdell
  committed
  5e39998
- [revive] don't use variable names that match library names
  jbygdell
  committed
  e5a86d4
- [revive] Don't capitalize local variables
  jbygdell
  committed
  176e529
- [revive] variable naming
  jbygdell
  committed
  62660e4
- [revive] Use errors.New where applicable
  jbygdell
  committed
  644259e
- [revive] remove redundant aliases
  jbygdell
  committed
  7537ebd
- [revive] return early
  jbygdell
  committed
  4b74de4
- [revive] don't use defer inside of loops
  jbygdell
  committed
  2410fa8
- [sda-download] ignore unnecessary-stmt error
  jbygdell
  committed
  36cee5b
- [static check] sda
  jbygdell
  committed
  d2768c7
- [static check] sda-admin
  jbygdell
  committed
  477d6f2
- [static-check] sda-download
  jbygdell
  committed
  56990b8
- Final linter config file
  jbygdell
  committed
  7e61315
- Merge pull request #1606 from neicnordic/dependabot/github_actions/codecov/codecov-action-5.4.2
  pahatz
  authored
  8831fcb
- Bump golang.org/x/net in /sda-download in the go_modules group
  dependabot[bot]
  authored
  4bb9620
- Bump golang.org/x/net in /sda in the go_modules group
  dependabot[bot]
  authored
  d34d57f
Commits on Apr 21, 2025
- Bump the all-modules group in /sda-download with 2 updates
  dependabot[bot]
  authored
  1fab6fe
Commits on Apr 22, 2025
Commits on Apr 23, 2025
- fix: update rbac for testing purposes
  
  MalinAhlberg
  authored and
  aaperis
  committed
  99f8fa5
- fix typos and improve documentation
  
  MalinAhlberg
  authored and
  aaperis
  committed
  70d9265
- [tests] failing(!!) test for double verifying of a file
  
  MalinAhlberg
  authored and
  aaperis
  committed
  f9dcaa9
- handle already verified file better
  aaperis
  committed
  7b9fa07
- set verified status for file already verified
  aaperis
  committed
  e97d5a4
- simplify logic for already verified files
  aaperis
  committed
  8ffbbef
- remove explicit test for already verified file
  aaperis
  committed
  c49a323
- further simplify logic for already verified files
  aaperis
  committed
  1545a71
- remove non-essential test permissions
  aaperis
  committed
  498b20f
- Merge pull request #1618 from neicnordic/bugfix/syncapi-log-error
  jbygdell
  authored
  8e5c8dc
- add suggestion from review
  aaperis
  committed
  8b5ea7c
Commits on Apr 24, 2025
- Merge pull request #1600 from neicnordic/tests/make-verify-fail
  aaperis
  authored
  4012b19
- Bump chart version
  
  neicnordic
  authored and
  github-actions[bot]
  committed
  46b5f82
- Merge pull request #1524 from neicnordic/bump
  jbygdell
  authored
  bb2b1ad
Commits on Apr 28, 2025
Commits on Apr 29, 2025
- Merge pull request #1633 from neicnordic/dependabot/maven/sda-doa/all-modules-b08d437810
  aaperis
  authored
  02757e8
- Merge pull request #1631 from neicnordic/dependabot/maven/sda-sftp-inbox/all-modules-3873938a75
  aaperis
  authored
  6bdbbde
- Merge pull request #1632 from neicnordic/dependabot/go_modules/sda-download/all-modules-4e023c56e3
  aaperis
  authored
  a1d7ac5
- Bump chart version
  
  neicnordic
  authored and
  github-actions[bot]
  committed
  ebe2754
Commits on Apr 30, 2025
- Merge pull request #1637 from neicnordic/bump
  aaperis
  authored
  895cb45
Commits on May 5, 2025
Commits on May 6, 2025
- Merge pull request #1644 from neicnordic/dependabot/go_modules/sda-download/all-modules-aed88fd9d2
  aaperis
  authored
  20aa321
- Merge pull request #1645 from neicnordic/dependabot/maven/sda-sftp-inbox/all-modules-d3c53caf09
  aaperis
  authored
  ad7e1e3
- Merge pull request #1649 from neicnordic/dependabot/go_modules/sda/all-modules-4914e57640
  aaperis
  authored
  b39dc2e
- Merge pull request #1642 from neicnordic/dependabot/github_actions/golangci/golangci-lint-action-8.0.0
  aaperis
  authored
  6cd7248
- Bump chart version
  
  neicnordic
  authored and
  github-actions[bot]
  committed
  dd570ff
- Merge pull request #1641 from neicnordic/bump
  jbygdell
  authored
  9c34965
Commits on May 9, 2025
- require a pubkey for s3inbox when resigning jwt
  aaperis
  committed
  1cc947e
- bump chart version
  aaperis
  committed
  f41a6f9
Commits on May 12, 2025
Commits on May 13, 2025

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