Merge branch 'develop' into main

Author: mocsharp

.editorconfig

@@ -1,13 +1,5 @@
-# Copyright 2022 MONAI Consortium
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#     http://www.apache.org/licenses/LICENSE-2.0
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
+# SPDX-FileCopyrightText: © 2021-2022 MONAI Consortium
+# SPDX-License-Identifier: Apache License 2.0
 
 assembly-versioning-scheme: MajorMinorPatchTag
 mode: ContinuousDelivery

.github/.gitversion.yml

@@ -1,3 +1,8 @@
+<!--
+SPDX-FileCopyrightText: © 2021-2022 MONAI Consortium
+SPDX-License-Identifier: Apache License 2.0
+-->
+
 Fixes # .
 
 ### Description

.github/pull_request_template.md

@@ -1,22 +1,14 @@
-# Copyright 2021-2022 MONAI Consortium
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#     http://www.apache.org/licenses/LICENSE-2.0
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
+# SPDX-FileCopyrightText: © 2021-2022 MONAI Consortium
+# SPDX-License-Identifier: Apache License 2.0
+
 
 name: ci
 
 on:
   # Triggers on pushes and on pull requests
   push:
-    branches:
-    - main
-  pull_request:
+    paths-ignore:
+      - 'demos/**'
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
@@ -97,17 +89,12 @@ jobs:
       uses: github/codeql-action/analyze@v1
 
   unit-test:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ubuntu-latest]
-      fail-fast: true
-
+    runs-on: ubuntu-latest
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v2
+      - name: Set up JDK 11
+        uses: actions/setup-java@v1
         with:
-          fetch-depth: 0
+          java-version: 1.11
 
       - uses: actions/setup-dotnet@v1
         with:
@@ -121,18 +108,46 @@ jobs:
           restore-keys: |
             ${{ runner.os }}-nuget
 
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+          
+      - name: Install SonarCloud scanner
+        if: steps.cache-sonar-scanner.outputs.cache-hit != 'true'
+        run: dotnet tool install --global dotnet-sonarscanner
+
       - name: Restore dependencies
         run: dotnet restore
         working-directory: ./src
-
-      - name: Build Solution
-        run: dotnet build -c ${{ env.BUILD_CONFIG }} --nologo ${{ env.SOLUTION }}
+        
+      - name: Begin SonarScanner
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+        run: dotnet sonarscanner begin /k:"Project-MONAI_monai-deploy-informatics-gateway" /o:"project-monai" /d:sonar.login="${{ secrets.SONAR_TOKEN }}" /d:sonar.host.url="https://sonarcloud.io" /d:sonar.cs.opencover.reportsPaths="${{ env.TEST_RESULTS }}/**/*.xml"
         working-directory: ./src
-
-      - name: Run Unit Test
-        run: dotnet test -c ${{ env.BUILD_CONFIG }} -v=minimal --results-directory "${{ env.TEST_RESULTS }}" --collect:"XPlat Code Coverage" --settings coverlet.runsettings ${{ env.SOLUTION }}
+        
+      - name: Build
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+        run: dotnet build -c ${{ env.BUILD_CONFIG }} --nologo "${{ env.SOLUTION }}"
+        working-directory: ./src
+      
+      - name: Test
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+        run: find ~+ -type f -name "*.Test.csproj" | xargs -L1 dotnet test -c ${{ env.BUILD_CONFIG }} -v=minimal -r "${{ env.TEST_RESULTS }}" --collect:"XPlat Code Coverage" --settings coverlet.runsettings 
         working-directory: ./src
 
+      - name: End SonarScanner
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+        run: dotnet sonarscanner end /d:sonar.login="${{ secrets.SONAR_TOKEN }}"
+        working-directory: ./src
+          
       - uses: codecov/codecov-action@v2
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
@@ -261,6 +276,26 @@ jobs:
           sarif_file: ${{ steps.anchore-scan.outputs.sarif }}
           token: ${{ secrets.GITHUB_TOKEN }}
 
+      - name: Integration Test
+        env:
+          TAG: ${{ env.GitVersion_SemVer }}
+        if: ${{ (matrix.os == 'ubuntu-latest') }}
+        run: |
+          pushd tests/Integration.Test
+          ./run.sh
+          popd
+
+      - name: Upload Integration Test Results
+        uses: actions/[email protected]
+        with:
+          name: integration
+          path: |
+            tests/Integration.Test/LivingDoc.html
+            tests/Integration.Test/metrics.log
+            tests/Integration.Test/services.log
+            tests/Integration.Test/run.log
+          retention-days: 30
+
   docs:
     runs-on: ubuntu-latest
     needs: [calc-version]
@@ -377,13 +412,13 @@ jobs:
 
       - name: Unzip docs
         run: |
-          mkdir ~/docs
-          unzip artifacts/mig-docs-${{ env.SEMVER }}.zip -d ~/docs
-          ls -lR ~/docs
+          mkdir userguide
+          unzip artifacts/mig-docs-${{ env.SEMVER }}.zip -d userguide/
+          ls -lR userguide/
 
       - name: Deploy Docs
         uses: peaceiris/actions-gh-pages@v3
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ~/docs
+          publish_dir: userguide/
           publish_branch: docs

.github/workflows/ci.yml

@@ -21,7 +21,7 @@
             "request": "launch",
             "preLaunchTask": "build",
             // If you have changed target frameworks, make sure to update the program path.
-            "program": "${workspaceFolder}/src/InformaticsGateway/bin/Debug/net5.0/Monai.Deploy.InformaticsGateway",
+            "program": "${workspaceFolder}/src/InformaticsGateway/bin/Debug/net6.0/Monai.Deploy.InformaticsGateway",
             "args": [],
             "cwd": "${workspaceFolder}/src/InformaticsGateway",
             // For more information about the 'console' field, see https://aka.ms/VSCode-CS-LaunchJson-Console
@@ -37,4 +37,4 @@
             "request": "attach"
         }
     ]
-}
+}

.vscode/launch.json

@@ -0,0 +1,81 @@
+<!--
+SPDX-FileCopyrightText: © 2021-2022 MONAI Consortium
+SPDX-License-Identifier: Apache License 2.0
+-->
+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+ advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+ address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at [email protected]. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq

CODE_OF_CONDUCT.md

@@ -1,3 +1,7 @@
+<!--
+SPDX-FileCopyrightText: © 2021-2022 MONAI Consortium
+ SPDX-License-Identifier: Apache License 2.0
+-->
 - [Introduction](#introduction)
   - [Communicate with us](#communicate-with-us)
 - [The contribution process](#the-contribution-process)

CONTRIBUTING.md

@@ -1,13 +1,5 @@
-# Copyright 2021 MONAI Consortium
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#     http://www.apache.org/licenses/LICENSE-2.0
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
+# SPDX-FileCopyrightText: © 2021-2022 MONAI Consortium
+# SPDX-License-Identifier: Apache License 2.0
 
 FROM mcr.microsoft.com/dotnet/sdk:6.0-focal as build
 

Dockerfile

@@ -1,13 +1,5 @@
-# Copyright 2022 MONAI Consortium
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#     http://www.apache.org/licenses/LICENSE-2.0
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
+# SPDX-FileCopyrightText: © 2021-2022 MONAI Consortium
+# SPDX-License-Identifier: Apache License 2.0
 
 issue-labels-include:
   - breaking
@@ -54,4 +46,4 @@ close:
     :tada: This issue has been resolved in version {milestone} :tada:
 
     The release is available on:
-    - [GitHub Release](https://github.com/{owner}/{repository}/releases/tag/{milestone})
+    - [GitHub Release](https://github.com/{owner}/{repository}/releases/tag/{milestone})

GitReleaseManager.yaml

@@ -1,3 +1,8 @@
+<!--
+// SPDX-FileCopyrightText: © 2021-2022 MONAI Consortium
+// SPDX-License-Identifier: Apache License 2.0
+ -->
+
 <p align="center">
   <img src="https://raw.githubusercontent.com/Project-MONAI/MONAI/dev/docs/images/MONAI-logo-color.png" width="50%" alt='project-monai'>
 </p>

README.md

@@ -1,3 +1,6 @@
+# SPDX-FileCopyrightText: © 2021-2022 MONAI Consortium
+# SPDX-License-Identifier: Apache License 2.0
+
 codecov:
   require_ci_to_pass: yes