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Sync fork 5 #10

Merged
merged 373 commits into from
Jan 19, 2025
Merged

Sync fork 5 #10

merged 373 commits into from
Jan 19, 2025

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kkochel
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@kkochel kkochel commented Nov 28, 2024

Related issue(s) and PR(s)
This PR closes [issue number].

Description

How to test

jbygdell and others added 30 commits November 20, 2024 15:02
…actions/codecov/codecov-action-5.0.2

Bump codecov/codecov-action from 4.6.0 to 5.0.2
This allows the use of an annotated JSON file instead of the default compact CSV format used by the casbin library.
Bumps the all-modules group in /sda-download with 2 updates: [github.com/lestrrat-go/jwx/v2](https://github.com/lestrrat-go/jwx) and [github.com/stretchr/testify](https://github.com/stretchr/testify).


Updates `github.com/lestrrat-go/jwx/v2` from 2.1.2 to 2.1.3
- [Release notes](https://github.com/lestrrat-go/jwx/releases)
- [Changelog](https://github.com/lestrrat-go/jwx/blob/v2.1.3/Changes)
- [Commits](lestrrat-go/jwx@v2.1.2...v2.1.3)

Updates `github.com/stretchr/testify` from 1.9.0 to 1.10.0
- [Release notes](https://github.com/stretchr/testify/releases)
- [Commits](stretchr/testify@v1.9.0...v1.10.0)

---
updated-dependencies:
- dependency-name: github.com/lestrrat-go/jwx/v2
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: all-modules
- dependency-name: github.com/stretchr/testify
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-modules
...

Signed-off-by: dependabot[bot] <support@github.com>
Bumps the all-modules group in /sda with 5 updates:

| Package | From | To |
| --- | --- | --- |
| [github.com/aws/aws-sdk-go-v2/feature/s3/manager](https://github.com/aws/aws-sdk-go-v2) | `1.17.38` | `1.17.40` |
| [github.com/aws/aws-sdk-go-v2/service/s3](https://github.com/aws/aws-sdk-go-v2) | `1.67.0` | `1.68.0` |
| [github.com/casbin/casbin/v2](https://github.com/casbin/casbin) | `2.100.0` | `2.101.0` |
| [github.com/lestrrat-go/jwx/v2](https://github.com/lestrrat-go/jwx) | `2.1.2` | `2.1.3` |
| [github.com/stretchr/testify](https://github.com/stretchr/testify) | `1.9.0` | `1.10.0` |


Updates `github.com/aws/aws-sdk-go-v2/feature/s3/manager` from 1.17.38 to 1.17.40
- [Release notes](https://github.com/aws/aws-sdk-go-v2/releases)
- [Commits](aws/aws-sdk-go-v2@credentials/v1.17.38...credentials/v1.17.40)

Updates `github.com/aws/aws-sdk-go-v2/service/s3` from 1.67.0 to 1.68.0
- [Release notes](https://github.com/aws/aws-sdk-go-v2/releases)
- [Commits](aws/aws-sdk-go-v2@service/s3/v1.67.0...service/s3/v1.68.0)

Updates `github.com/casbin/casbin/v2` from 2.100.0 to 2.101.0
- [Release notes](https://github.com/casbin/casbin/releases)
- [Changelog](https://github.com/casbin/casbin/blob/master/.releaserc.json)
- [Commits](casbin/casbin@v2.100.0...v2.101.0)

Updates `github.com/lestrrat-go/jwx/v2` from 2.1.2 to 2.1.3
- [Release notes](https://github.com/lestrrat-go/jwx/releases)
- [Changelog](https://github.com/lestrrat-go/jwx/blob/v2.1.3/Changes)
- [Commits](lestrrat-go/jwx@v2.1.2...v2.1.3)

Updates `github.com/stretchr/testify` from 1.9.0 to 1.10.0
- [Release notes](https://github.com/stretchr/testify/releases)
- [Commits](stretchr/testify@v1.9.0...v1.10.0)

---
updated-dependencies:
- dependency-name: github.com/aws/aws-sdk-go-v2/feature/s3/manager
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: all-modules
- dependency-name: github.com/aws/aws-sdk-go-v2/service/s3
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-modules
- dependency-name: github.com/casbin/casbin/v2
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-modules
- dependency-name: github.com/lestrrat-go/jwx/v2
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: all-modules
- dependency-name: github.com/stretchr/testify
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-modules
...

Signed-off-by: dependabot[bot] <support@github.com>
Bumps the all-modules group in /sda-sftp-inbox with 2 updates: [org.springframework.boot:spring-boot-starter-parent](https://github.com/spring-projects/spring-boot) and commons-io:commons-io.


Updates `org.springframework.boot:spring-boot-starter-parent` from 3.3.5 to 3.4.0
- [Release notes](https://github.com/spring-projects/spring-boot/releases)
- [Commits](spring-projects/spring-boot@v3.3.5...v3.4.0)

Updates `commons-io:commons-io` from 2.17.0 to 2.18.0

---
updated-dependencies:
- dependency-name: org.springframework.boot:spring-boot-starter-parent
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-modules
- dependency-name: commons-io:commons-io
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-modules
...

Signed-off-by: dependabot[bot] <support@github.com>
Bumps [aquasecurity/trivy-action](https://github.com/aquasecurity/trivy-action) from 0.28.0 to 0.29.0.
- [Release notes](https://github.com/aquasecurity/trivy-action/releases)
- [Commits](aquasecurity/trivy-action@0.28.0...0.29.0)

---
updated-dependencies:
- dependency-name: aquasecurity/trivy-action
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 5.0.2 to 5.0.7.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](codecov/codecov-action@v5.0.2...v5.0.7)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Bumps the all-modules group in /sda-doa with 1 update: [org.springframework.boot:spring-boot-starter-parent](https://github.com/spring-projects/spring-boot).


Updates `org.springframework.boot:spring-boot-starter-parent` from 3.3.5 to 3.4.0
- [Release notes](https://github.com/spring-projects/spring-boot/releases)
- [Commits](spring-projects/spring-boot@v3.3.5...v3.4.0)

---
updated-dependencies:
- dependency-name: org.springframework.boot:spring-boot-starter-parent
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-modules
...

Signed-off-by: dependabot[bot] <support@github.com>
…da-doa/all-modules-a85b14af58

Bump org.springframework.boot:spring-boot-starter-parent from 3.3.5 to 3.4.0 in /sda-doa in the all-modules group
…les/sda/all-modules-fbf7d6953a

Bump the all-modules group in /sda with 5 updates
…les/sda-download/all-modules-6f611a882c

Bump the all-modules group in /sda-download with 2 updates
…actions/aquasecurity/trivy-action-0.29.0

Bump aquasecurity/trivy-action from 0.28.0 to 0.29.0
…actions/codecov/codecov-action-5.0.7

Bump codecov/codecov-action from 5.0.2 to 5.0.7
…da-sftp-inbox/all-modules-81c95be742

Bump the all-modules group in /sda-sftp-inbox with 2 updates
aaperis and others added 29 commits January 9, 2025 11:40
and do a small refactoring
- add serveDecrypted object variable
- repurpose obsolete c4gh secret logic
- update README
if they are run more than once
to increase success rate of date comparison
Co-authored-by: Nanjiang Shu <nanjiang.shu@gmail.com>
Bumps the all-modules group with 3 updates in the /sda-doa directory: [org.springframework.boot:spring-boot-starter-parent](https://github.com/spring-projects/spring-boot), [io.minio:minio](https://github.com/minio/minio-java) and [org.junit.jupiter:junit-jupiter-api](https://github.com/junit-team/junit5).


Updates `org.springframework.boot:spring-boot-starter-parent` from 3.4.0 to 3.4.1
- [Release notes](https://github.com/spring-projects/spring-boot/releases)
- [Commits](spring-projects/spring-boot@v3.4.0...v3.4.1)

Updates `io.minio:minio` from 8.5.14 to 8.5.15
- [Release notes](https://github.com/minio/minio-java/releases)
- [Commits](minio/minio-java@8.5.14...8.5.15)

Updates `org.junit.jupiter:junit-jupiter-api` from 5.11.3 to 5.11.4
- [Release notes](https://github.com/junit-team/junit5/releases)
- [Commits](junit-team/junit5@r5.11.3...r5.11.4)

---
updated-dependencies:
- dependency-name: org.springframework.boot:spring-boot-starter-parent
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: all-modules
- dependency-name: io.minio:minio
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: all-modules
- dependency-name: org.junit.jupiter:junit-jupiter-api
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: all-modules
...

Signed-off-by: dependabot[bot] <support@github.com>
…da-doa/all-modules-902c0b9248

Bump the all-modules group across 1 directory with 3 updates
…nfigurable-s3-endpoint-for-download

Configurable s3 endpoint for download
Bumps the all-modules group in /sda-download with 3 updates: [github.com/neicnordic/crypt4gh](https://github.com/neicnordic/crypt4gh), [google.golang.org/grpc](https://github.com/grpc/grpc-go) and google.golang.org/protobuf.


Updates `github.com/neicnordic/crypt4gh` from 1.12.0 to 1.13.0
- [Release notes](https://github.com/neicnordic/crypt4gh/releases)
- [Changelog](https://github.com/neicnordic/crypt4gh/blob/master/.goreleaser.yml)
- [Commits](neicnordic/crypt4gh@v1.12.0...v1.13.0)

Updates `google.golang.org/grpc` from 1.69.2 to 1.69.4
- [Release notes](https://github.com/grpc/grpc-go/releases)
- [Commits](grpc/grpc-go@v1.69.2...v1.69.4)

Updates `google.golang.org/protobuf` from 1.36.1 to 1.36.2

---
updated-dependencies:
- dependency-name: github.com/neicnordic/crypt4gh
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-modules
- dependency-name: google.golang.org/grpc
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: all-modules
- dependency-name: google.golang.org/protobuf
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: all-modules
...

Signed-off-by: dependabot[bot] <support@github.com>
Bumps the all-modules group in /sda with 8 updates:

| Package | From | To |
| --- | --- | --- |
| [github.com/aws/aws-sdk-go-v2](https://github.com/aws/aws-sdk-go-v2) | `1.32.7` | `1.32.8` |
| [github.com/aws/aws-sdk-go-v2/config](https://github.com/aws/aws-sdk-go-v2) | `1.28.7` | `1.28.10` |
| [github.com/aws/aws-sdk-go-v2/credentials](https://github.com/aws/aws-sdk-go-v2) | `1.17.48` | `1.17.51` |
| [github.com/aws/aws-sdk-go-v2/feature/s3/manager](https://github.com/aws/aws-sdk-go-v2) | `1.17.45` | `1.17.48` |
| [github.com/aws/aws-sdk-go-v2/service/s3](https://github.com/aws/aws-sdk-go-v2) | `1.72.0` | `1.72.2` |
| [github.com/neicnordic/crypt4gh](https://github.com/neicnordic/crypt4gh) | `1.12.0` | `1.13.0` |
| [google.golang.org/grpc](https://github.com/grpc/grpc-go) | `1.69.2` | `1.69.4` |
| google.golang.org/protobuf | `1.36.1` | `1.36.2` |


Updates `github.com/aws/aws-sdk-go-v2` from 1.32.7 to 1.32.8
- [Release notes](https://github.com/aws/aws-sdk-go-v2/releases)
- [Changelog](https://github.com/aws/aws-sdk-go-v2/blob/main/changelog-template.json)
- [Commits](aws/aws-sdk-go-v2@v1.32.7...v1.32.8)

Updates `github.com/aws/aws-sdk-go-v2/config` from 1.28.7 to 1.28.10
- [Release notes](https://github.com/aws/aws-sdk-go-v2/releases)
- [Changelog](https://github.com/aws/aws-sdk-go-v2/blob/main/changelog-template.json)
- [Commits](aws/aws-sdk-go-v2@config/v1.28.7...config/v1.28.10)

Updates `github.com/aws/aws-sdk-go-v2/credentials` from 1.17.48 to 1.17.51
- [Release notes](https://github.com/aws/aws-sdk-go-v2/releases)
- [Changelog](https://github.com/aws/aws-sdk-go-v2/blob/main/changelog-template.json)
- [Commits](aws/aws-sdk-go-v2@credentials/v1.17.48...credentials/v1.17.51)

Updates `github.com/aws/aws-sdk-go-v2/feature/s3/manager` from 1.17.45 to 1.17.48
- [Release notes](https://github.com/aws/aws-sdk-go-v2/releases)
- [Changelog](https://github.com/aws/aws-sdk-go-v2/blob/main/changelog-template.json)
- [Commits](aws/aws-sdk-go-v2@credentials/v1.17.45...credentials/v1.17.48)

Updates `github.com/aws/aws-sdk-go-v2/service/s3` from 1.72.0 to 1.72.2
- [Release notes](https://github.com/aws/aws-sdk-go-v2/releases)
- [Changelog](https://github.com/aws/aws-sdk-go-v2/blob/main/changelog-template.json)
- [Commits](aws/aws-sdk-go-v2@service/s3/v1.72.0...service/s3/v1.72.2)

Updates `github.com/neicnordic/crypt4gh` from 1.12.0 to 1.13.0
- [Release notes](https://github.com/neicnordic/crypt4gh/releases)
- [Changelog](https://github.com/neicnordic/crypt4gh/blob/master/.goreleaser.yml)
- [Commits](neicnordic/crypt4gh@v1.12.0...v1.13.0)

Updates `google.golang.org/grpc` from 1.69.2 to 1.69.4
- [Release notes](https://github.com/grpc/grpc-go/releases)
- [Commits](grpc/grpc-go@v1.69.2...v1.69.4)

Updates `google.golang.org/protobuf` from 1.36.1 to 1.36.2

---
updated-dependencies:
- dependency-name: github.com/aws/aws-sdk-go-v2
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: all-modules
- dependency-name: github.com/aws/aws-sdk-go-v2/config
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: all-modules
- dependency-name: github.com/aws/aws-sdk-go-v2/credentials
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: all-modules
- dependency-name: github.com/aws/aws-sdk-go-v2/feature/s3/manager
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: all-modules
- dependency-name: github.com/aws/aws-sdk-go-v2/service/s3
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: all-modules
- dependency-name: github.com/neicnordic/crypt4gh
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-modules
- dependency-name: google.golang.org/grpc
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: all-modules
- dependency-name: google.golang.org/protobuf
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: all-modules
...

Signed-off-by: dependabot[bot] <support@github.com>
…les/sda/all-modules-a18c2d850e

Bump the all-modules group in /sda with 8 updates
…les/sda-download/all-modules-797b85aa4a

Bump the all-modules group in /sda-download with 3 updates
@kkochel kkochel merged commit 4501faa into main Jan 19, 2025
28 checks passed
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10 participants