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Update licenses & CI (#234)
* Fix build warnings * Update licenses & fix nuget scan * Split CodeQL actions * Make CodeQL-Analyze required for release * Fix minio client setup in integration test Signed-off-by: Victor Chang <[email protected]>
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‎.github/workflows/ci.yml

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@@ -59,16 +59,53 @@ jobs:
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useConfigFile: true
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configFilePath: .github/.gitversion.yml
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CodeQL-Analyze:
63+
runs-on: ubuntu-latest
64+
permissions:
65+
actions: read
66+
contents: read
67+
security-events: write
68+
69+
steps:
70+
- name: Checkout repository
71+
uses: actions/checkout@v3
72+
with:
73+
fetch-depth: 0
74+
75+
- uses: actions/setup-dotnet@v3
76+
with:
77+
dotnet-version: "6.0.x"
78+
79+
- name: Enable NuGet cache
80+
uses: actions/[email protected]
81+
with:
82+
path: ~/.nuget/packages
83+
key: ${{ runner.os }}-nuget-${{ hashFiles('**/packages.lock.json') }}
84+
restore-keys: |
85+
${{ runner.os }}-nuget
86+
87+
- name: Initialize CodeQL
88+
uses: github/codeql-action/init@v2
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with:
90+
languages: csharp
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92+
- name: Restore dependencies
93+
run: dotnet restore
94+
working-directory: ./src
95+
96+
- name: Build Solution
97+
run: dotnet build -c ${{ env.BUILD_CONFIG }} --nologo ${{ env.SOLUTION }}
98+
working-directory: ./src
99+
100+
- name: Perform CodeQL Analysis
101+
uses: github/codeql-action/analyze@v2
102+
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analyze:
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runs-on: ubuntu-latest
64105
permissions:
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actions: read
66107
contents: read
67108
security-events: write
68-
strategy:
69-
fail-fast: false
70-
matrix:
71-
language: [ 'csharp' ]
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steps:
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- name: Checkout repository
@@ -97,13 +134,12 @@ jobs:
97134
restore-keys: |
98135
${{ runner.os }}-nuget
99136
100-
- name: Initialize CodeQL
101-
uses: github/codeql-action/init@v2
102-
with:
103-
languages: ${{ matrix.language }}
104-
105-
- name: Install NuGetDefense
106-
run: dotnet tool install --global NuGetDefense.Tool
137+
- name: Nuget Vulnerabiilty Scan
138+
run: |
139+
dotnet list package --vulnerable 2>&1 | tee vulnerable.txt
140+
echo "Analyzing dotnet list package command log output..."
141+
sh -c "! grep 'has the following vulnerable packages' vulnerable.txt"
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working-directory: ./src
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- name: Restore dependencies
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run: dotnet restore
@@ -120,17 +156,14 @@ jobs:
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sed -i "s/OSSINDEXAPI_USERNAME/$OSSINDEXAPI_USERNAME/g" NuGetDefense.json
121157
nugetdefense -p src/${{ env.SOLUTION }} --settings-file NuGetDefense.json
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- name: Perform CodeQL Analysis
124-
uses: github/codeql-action/analyze@v2
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- name: Secret detection
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uses: gitleaks/[email protected]
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129162
- name: Perform License Scanning
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run: license_finder -r
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- name: Check License Header
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uses: apache/skywalking-eyes@main
166+
uses: apache/skywalking-eyes@v0.4.0
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unit-test:
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runs-on: ubuntu-latest
@@ -448,7 +481,7 @@ jobs:
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release:
449482
if: ${{ contains(github.ref, 'refs/heads/main') || contains(github.ref, 'refs/heads/develop') ||contains(github.head_ref, 'release/') || contains(github.head_ref, 'feature/') || contains(github.head_ref, 'develop') }}
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runs-on: ubuntu-latest
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needs: [calc-version, unit-test, docs, integration-test]
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needs: [calc-version, unit-test, docs, integration-test, analyze]
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env:
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SEMVER: ${{ needs.calc-version.outputs.semVer }}
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PRERELEASELABEL: ${{ needs.calc-version.outputs.preReleaseLabel }}

‎doc/dependency_decisions.yml

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- :who: mocsharp
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:why: MIT (https://github.com/dotnet/dotNext/raw/master/LICENSE)
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:versions:
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- 4.7.3
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- 4.7.4
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:when: 2022-09-01 23:05:32.857032968 Z
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- - :approve
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- DotNext.Threading
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- :who: mocsharp
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:why: MIT (https://github.com/dotnet/dotNext/raw/master/LICENSE)
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:versions:
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- 4.7.3
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- 4.7.4
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:when: 2022-09-01 23:05:33.298402277 Z
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- - :approve
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- FluentAssertions
@@ -778,19 +778,13 @@
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:versions:
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- 4.5.0
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:when: 2022-08-16 23:06:19.647254594 Z
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- - :approve
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- Minio
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- :who: mocsharp
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:why: Apache-2.0 (https://github.com/minio/minio-dotnet/raw/master/LICENSE)
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:versions:
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- 4.0.4
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:when: 2022-08-16 23:06:20.140413803 Z
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- - :approve
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- Minio
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- :who: mocsharp
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:why: Apache-2.0 (https://github.com/minio/minio-dotnet/raw/master/LICENSE)
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:versions:
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- 4.0.5
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- 4.0.6
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:when: 2022-08-16 23:06:20.598551507 Z
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- - :approve
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- Monai.Deploy.Messaging
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- :who: mocsharp
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:why: MIT (https://github.com/coverlet-coverage/coverlet/raw/master/LICENSE)
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:versions:
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- 3.1.2
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- 3.2.0
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:when: 2022-08-16 23:07:29.112978564 Z
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- - :approve
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- fo-dicom
@@ -2363,21 +2357,21 @@
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- :who: mocsharp
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:why: BSD 3-Clause License (https://github.com/NLog/NLog/raw/dev/LICENSE.txt)
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:versions:
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- 5.0.4
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- 5.0.5
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:when: 2022-10-12 03:14:06.538744982 Z
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- - :approve
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- NLog.Extensions.Logging
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- :who: mocsharp
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:why: BSD 2-Clause Simplified License (https://github.com/NLog/NLog.Extensions.Logging/raw/master/LICENSE)
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:versions:
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- 5.0.4
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- 5.1.0
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:when: 2022-10-12 03:14:06.964203977 Z
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- - :approve
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- NLog.Web.AspNetCore
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- :who: mocsharp
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:why: BSD 3-Clause License (https://github.com/NLog/NLog.Web/raw/master/LICENSE)
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:versions:
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- 5.1.4
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- 5.1.5
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:when: 2022-10-12 03:14:07.396706995 Z
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- - :approve
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- fo-dicom.NLog

‎docs/compliance/third-party-licenses.md

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<details>
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<summary>DotNext 4.7.1</summary>
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<summary>DotNext 4.7.4</summary>
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## DotNext
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- Version: 4.7.1
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- Version: 4.7.4
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- Authors: .NET Foundation and Contributors
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- Project URL: https://dotnet.github.io/dotNext/
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- Source: [NuGet](https://www.nuget.org/packages/DotNext/4.7.1)
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- Source: [NuGet](https://www.nuget.org/packages/DotNext/4.7.4)
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- License: [MIT](https://github.com/dotnet/dotNext/raw/master/LICENSE)
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<details>
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<summary>DotNext.Threading 4.7.1</summary>
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<summary>DotNext.Threading 4.7.4</summary>
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## DotNext.Threading
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- Version: 4.7.1
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- Version: 4.7.4
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- Authors: .NET Foundation and Contributors
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- Project URL: https://dotnet.github.io/dotNext/
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- Source: [NuGet](https://www.nuget.org/packages/DotNext.Threading/4.7.1)
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- Source: [NuGet](https://www.nuget.org/packages/DotNext.Threading/4.7.4)
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- License: [MIT](https://github.com/dotnet/dotNext/raw/master/LICENSE)
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@@ -7098,14 +7098,14 @@ Apache License
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<details>
7101-
<summary>Minio 4.0.5</summary>
7101+
<summary>Minio 4.0.6</summary>
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71037103
## Minio
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- Version: 4.0.5
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- Version: 4.0.6
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- Authors: MinIO, Inc.
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- Project URL: https://github.com/minio/minio-dotnet
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- Source: [NuGet](https://www.nuget.org/packages/Minio/4.0.5)
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- Source: [NuGet](https://www.nuget.org/packages/Minio/4.0.6)
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- License: [Apache-2.0](https://github.com/minio/minio-dotnet/raw/master/LICENSE)
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<details>
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<summary>NLog 5.0.4</summary>
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<summary>NLog 5.0.5</summary>
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## NLog
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- Version: 5.0.4
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- Version: 5.0.5
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- Authors: Jarek Kowalski,Kim Christensen,Julian Verdurmen
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- Project URL: https://nlog-project.org/
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- Source: [NuGet](https://www.nuget.org/packages/NLog/5.0.4)
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- Source: [NuGet](https://www.nuget.org/packages/NLog/5.0.5)
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- License: [BSD 3-Clause License](https://github.com/NLog/NLog/raw/dev/LICENSE.txt)
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@@ -8839,14 +8839,14 @@ THE POSSIBILITY OF SUCH DAMAGE.
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<details>
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<summary>NLog.Extensions.Logging 5.0.4</summary>
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<summary>NLog.Extensions.Logging 5.1.0</summary>
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## NLog.Extensions.Logging
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- Version: 5.0.4
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- Version: 5.1.0
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- Authors: Microsoft,Julian Verdurmen
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- Project URL: https://github.com/NLog/NLog.Extensions.Logging
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- Source: [NuGet](https://www.nuget.org/packages/NLog.Extensions.Logging/5.0.4)
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- Source: [NuGet](https://www.nuget.org/packages/NLog.Extensions.Logging/5.1.0)
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- License: [BSD 2-Clause Simplified License](https://github.com/NLog/NLog.Extensions.Logging/raw/master/LICENSE)
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<details>
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<summary>NLog.Web.AspNetCore 5.1.4</summary>
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<summary>NLog.Web.AspNetCore 5.1.5</summary>
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## NLog.Web.AspNetCore
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- Version: 5.1.4
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- Version: 5.1.5
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- Authors: Julian Verdurmen
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- Project URL: https://github.com/NLog/NLog.Web
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- Source: [NuGet](https://www.nuget.org/packages/NLog.Web.AspNetCore/5.1.4)
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- Source: [NuGet](https://www.nuget.org/packages/NLog.Web.AspNetCore/5.1.5)
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- License: [BSD 3-Clause License](https://github.com/NLog/NLog.Web/raw/master/LICENSE)
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@@ -27675,14 +27675,14 @@ accept this license. If you do not accept the license, do not use the software.
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<details>
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<summary>coverlet.collector 3.1.2</summary>
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<summary>coverlet.collector 3.2.0</summary>
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## coverlet.collector
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- Version: 3.1.2
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- Version: 3.2.0
2768327683
- Authors: tonerdo
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- Project URL: https://github.com/coverlet-coverage/coverlet
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- Source: [NuGet](https://www.nuget.org/packages/coverlet.collector/3.1.2)
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- Source: [NuGet](https://www.nuget.org/packages/coverlet.collector/3.2.0)
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- License: [MIT](https://github.com/coverlet-coverage/coverlet/raw/master/LICENSE)
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‎src/CLI/Monai.Deploy.InformaticsGateway.CLI.csproj

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<OutputType>Exe</OutputType>
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<TargetFramework>net6.0</TargetFramework>
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<PublishSingleFile>true</PublishSingleFile>
23-
<SelfContained>true</SelfContained>
2423
<PublishTrimmed>false</PublishTrimmed>
2524
<PublishReadyToRun>true</PublishReadyToRun>
26-
<RuntimeIdentifier>win-x64</RuntimeIdentifier>
27-
<RuntimeIdentifiers>win-x64;linux-x64</RuntimeIdentifiers>
2825
<AssemblyName>mig-cli</AssemblyName>
2926
<PackageLicenseExpression>Apache-2.0</PackageLicenseExpression>
3027
<CodeAnalysisRuleSet>..\.sonarlint\project-monai_monai-deploy-informatics-gatewaycsharp.ruleset</CodeAnalysisRuleSet>

‎src/InformaticsGateway/Services/Storage/ObjectUploadService.cs

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7070
}
7171

72-
private async Task BackgroundProcessing(CancellationToken cancellationToken)
72+
private void BackgroundProcessing(CancellationToken cancellationToken)
7373
{
7474
_logger.ServiceRunning(ServiceName);
7575
var tasks = new List<Task>();
@@ -111,7 +111,7 @@ private async Task StartWorker(int thread, CancellationToken cancellationToken)
111111
}
112112
catch (OperationCanceledException ex)
113113
{
114-
_logger.ServiceCancelled(ServiceName);
114+
_logger.ServiceCancelledWithException(ServiceName, ex);
115115
break;
116116
}
117117
catch (Exception ex)
@@ -123,9 +123,9 @@ private async Task StartWorker(int thread, CancellationToken cancellationToken)
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124124
public Task StartAsync(CancellationToken cancellationToken)
125125
{
126-
var task = Task.Run(async () =>
126+
var task = Task.Run(() =>
127127
{
128-
await BackgroundProcessing(cancellationToken);
128+
BackgroundProcessing(cancellationToken);
129129
}, CancellationToken.None);
130130

131131
Status = ServiceStatus.Running;

‎src/InformaticsGateway/appsettings.Test.json

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1111
},
1212
"messaging": {
1313
"publisherSettings": {
14-
"endpoint": "172.18.0.4",
14+
"endpoint": "172.28.0.1",
1515
"username": "rabbitmq",
1616
"password": "rabbitmq",
1717
"virtualHost": "monaideploy",
1818
"exchange": "monaideploy"
1919
},
2020
"subscriberSettings": {
21-
"endpoint": "172.18.0.4",
21+
"endpoint": "172.28.0.1",
2222
"username": "rabbitmq",
2323
"password": "rabbitmq",
2424
"virtualHost": "monaideploy",
@@ -31,7 +31,7 @@
3131
"bucketName": "monai",
3232
"temporaryBucketName": "monai",
3333
"settings": {
34-
"endpoint": "172.18.0.2:9000",
34+
"endpoint": "172.28.0.1:9000",
3535
"accessKey": "minioadmin",
3636
"accessToken": "minioadmin",
3737
"securedConnection": false,
@@ -59,4 +59,4 @@
5959
}
6060
}
6161
}
62-
}
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}

‎tests/Integration.Test/StepDefinitions/AcrApiStepDefinitions.cs

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193193
{
194194
var minioClient = new MinioClient()
195195
.WithEndpoint(_configuration.StorageServiceOptions.Endpoint)
196-
.WithCredentials(_configuration.StorageServiceOptions.AccessKey, _configuration.StorageServiceOptions.AccessToken);
196+
.WithCredentials(_configuration.StorageServiceOptions.AccessKey, _configuration.StorageServiceOptions.AccessToken)
197+
.Build();
197198

198199
var dicomSizes = _scenarioContext[KeyDicomHashes] as Dictionary<string, string>;
199200
_rabbitMqHooks.MessageWaitHandle.Wait(MessageWaitTimeSpan).Should().BeTrue();

‎tests/Integration.Test/StepDefinitions/ExportServicesStepDefinitions.cs

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var minioClient = new MinioClient()
120120
.WithEndpoint(_configuration.StorageServiceOptions.Endpoint)
121-
.WithCredentials(_configuration.StorageServiceOptions.AccessKey, _configuration.StorageServiceOptions.AccessToken);
121+
.WithCredentials(_configuration.StorageServiceOptions.AccessKey, _configuration.StorageServiceOptions.AccessToken)
122+
.Build();
122123

123124
_outputHelper.WriteLine($"Uploading {fileSpecs.FileCount} files to MinIO...");
124125
foreach (var file in fileSpecs.Files)

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