Merge pull request #1 from qbicsoftware/feature/allow-query-of-hierarchy

Allow query of sample hierarchy

.github.settings.xml

@@ -0,0 +1,14 @@
+<settings>
+    <servers>
+        <server>
+            <id>nexus-snapshots</id>
+            <username>${env.MAVEN_REPO_USERNAME}</username>
+            <password>${env.MAVEN_REPO_PASSWORD}</password>
+        </server>
+        <server>
+            <id>nexus-releases</id>
+            <username>${env.MAVEN_REPO_USERNAME}</username>
+            <password>${env.MAVEN_REPO_PASSWORD}</password>
+        </server>
+    </servers>
+</settings>

.github/CODEOWNERS

@@ -0,0 +1 @@
+* @qbicsoftware/itss

.github/pr-labels.yml

@@ -0,0 +1,3 @@
+feature: ['feature/*', 'feat/*']
+fix: ['fix/*', 'hotfix']
+chore: ['chore/*', 'documentation/*', 'docs/*', 'ci/*', 'refactor/*']

.github/release.yml

@@ -0,0 +1,20 @@
+changelog:
+  exclude:
+    labels:
+      - ignore-for-release
+    authors:
+      - JohnnyQ5
+      - github-actions
+  categories:
+    - title: New Features 🚀
+      labels:
+        - feature
+    - title: Bugfixes 🪲
+      labels:
+        - fix
+    - title: Documentation & CI 🪂
+      labels:
+        - chore
+    - title: Others 🧃
+      labels:
+        - "*"

.github/workflows/build-package.yml

@@ -0,0 +1,29 @@
+name: Build Maven Package
+
+on:
+  push:
+    branches:
+      - '**'
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ main, master ]
+
+jobs:
+  package:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up JDK 11
+        uses: actions/setup-java@v1
+        with:
+          java-version: 11
+      - name: Load local Maven repository cache
+        uses: actions/cache@v2
+        with:
+          path: ~/.m2/repository
+          key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
+          restore-keys: |
+            ${{ runner.os }}-maven-
+      - name: Run mvn package
+        run: mvn -B package --file pom.xml

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,83 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ main, master, development, release/*, hotfix/* ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ main, master ]
+  schedule:
+    - cron: '21 1 * * 4'
+
+jobs:
+  analyze:
+    name: analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'java' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Learn more about CodeQL language support at https://git.io/codeql-language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+    - name: Set up JDK 11
+      uses: actions/setup-java@v1
+      with:
+        java-version: 11
+        settings-path: ${{ github.workspace }}
+
+    - name: Load local Maven repository cache
+      uses: actions/cache@v2
+      with:
+        path: ~/.m2/repository
+        key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
+        restore-keys: |
+           ${{ runner.os }}-maven-
+           
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v1
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

.github/workflows/create-release.yml

@@ -0,0 +1,96 @@
+name: Create Release
+
+on:
+  workflow_dispatch:
+    inputs:
+      versionTag:
+        description: 'Version Tag (semantic version)'
+        required: true
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up JDK 11
+        uses: actions/setup-java@v1
+        with:
+          java-version: 11
+          settings-path: ${{ github.workspace }}
+
+      - name: Load local Maven repository cache
+        uses: actions/cache@v2
+        with:
+          path: ~/.m2/repository
+          key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
+          restore-keys: |
+            ${{ runner.os }}-maven-
+
+      - name: Set up git
+        run: |
+          git config --global user.email "[email protected]"
+          git config --global user.name "JohnnyQ5"
+
+      - name: Set version in Maven project
+        run:  mvn versions:set -DnewVersion=${{ github.event.inputs.versionTag }}
+
+      - name: Build with Maven
+        run: mvn -B package --file pom.xml
+
+      - name: Create Release Notes
+        if: ${{ !startsWith(github.ref, 'refs/tags/')
+          && !( contains(github.event.inputs.versionTag, 'alpha')
+          || contains(github.event.inputs.versionTag, 'beta')
+          || contains(github.event.inputs.versionTag, 'rc')) }}
+        uses: actions/[email protected]
+        with:
+          github-token: ${{secrets.JOHNNY_Q5_REPORTS_TOKEN}}
+          script: |
+            await github.request(`POST /repos/${{ github.repository }}/releases`, {
+              tag_name: "${{ github.event.inputs.versionTag }}",
+              generate_release_notes: true
+            });
+
+      - name: Create Pre-Release Notes
+        if: ${{ !startsWith(github.ref, 'refs/tags/')
+          && ( contains(github.event.inputs.versionTag, 'alpha')
+          || contains(github.event.inputs.versionTag, 'beta')
+          || contains(github.event.inputs.versionTag, 'rc')) }}
+        uses: actions/[email protected]
+        with:
+          github-token: ${{secrets.JOHNNY_Q5_REPORTS_TOKEN}}
+          script: |
+            await github.request(`POST /repos/${{ github.repository }}/releases`, {
+              tag_name: "${{ github.event.inputs.versionTag }}",
+              generate_release_notes: true,
+              prerelease: true
+            });
+
+      - name: Publish artefact to QBiC Nexus Repository
+        run: mvn --quiet --settings $GITHUB_WORKSPACE/.github.settings.xml deploy
+        env:
+          MAVEN_REPO_USERNAME: ${{ secrets.NEXUS_USERNAME }}
+          MAVEN_REPO_PASSWORD: ${{ secrets.NEXUS_PASSWORD }}
+
+      - name: Switch to new branch
+        run: git checkout -b release/set-version-to-${{ github.event.inputs.versionTag }}
+
+      - name: Set remote branch
+        run: git push --set-upstream origin release/set-version-to-${{ github.event.inputs.versionTag }}
+
+      - name: Checkin commit
+        run: git commit . -m 'Set version to ${{ github.event.inputs.versionTag }}'
+
+      - name: Push to Github
+        run: git push
+
+      - name: Open PR with version bump
+        uses: actions/[email protected]
+        with:
+          github-token: ${{secrets.JOHNNY_Q5_REPORTS_TOKEN}}
+          script: |
+            await github.request(`POST /repos/${{ github.repository }}/pulls`, {
+              title: 'Update version to ${{ github.event.inputs.versionTag }}',
+              head: 'release/set-version-to-${{ github.event.inputs.versionTag }}',
+              base: 'master'
+            });

.github/workflows/label-pull-requests.yml

@@ -0,0 +1,15 @@
+name: Label Pull Requests
+
+on:
+  pull_request:
+    types: [ opened, edited ]
+
+jobs:
+  label:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: TimonVS/pr-labeler-action@v3
+        with:
+          configuration-path: .github/pr-labels.yml # optional, .github/pr-labeler.yml is the default value
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/nexus-publish-snapshots.yml

@@ -0,0 +1,46 @@
+# This workflow will build a package using Maven and then publish it to
+# qbic-repo.qbic.uni-tuebingen.de packages when a release is created
+# For more information see: https://github.com/actions/setup-java#apache-maven-with-a-settings-path
+
+name: Deploy Snapshot
+
+on:
+  push:
+    branches:
+      - development
+
+jobs:
+  publish_snapshots:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up JDK 11
+        uses: actions/setup-java@v1
+        with:
+          java-version: 11
+          settings-path: ${{ github.workspace }}
+
+      - name: Load local Maven repository cache
+        uses: actions/cache@v2
+        with:
+          path: ~/.m2/repository
+          key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
+          restore-keys: |
+            ${{ runner.os }}-maven-
+      # Remove existing snapshot tags which are not supposed to be present
+      - name: Remove snapshot tags
+        run: mvn versions:set -DremoveSnapshot
+      # Set the SNAPSHOT for this build and deployment
+      - name: Set version in Maven project
+        run:  mvn versions:set -DnewVersion='${project.version}-SNAPSHOT'
+
+      - name: Build with Maven
+        run: mvn -B package --file pom.xml
+
+      - name: Publish artefact to QBiC Nexus Repository
+        run: mvn --settings $GITHUB_WORKSPACE/.github.settings.xml deploy
+        env:
+          MAVEN_REPO_USERNAME: ${{ secrets.NEXUS_USERNAME }}
+          MAVEN_REPO_PASSWORD: ${{ secrets.NEXUS_PASSWORD }}

.github/workflows/run-tests.yml

@@ -0,0 +1,31 @@
+name: Run Maven Tests
+
+on:
+  push:
+    branches:
+      - '**'
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ main, master ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up JDK 11
+        uses: actions/setup-java@v1
+        with:
+          java-version: 11
+
+      - name: Load local Maven repository cache
+        uses: actions/cache@v2
+        with:
+          path: ~/.m2/repository
+          key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
+          restore-keys: |
+            ${{ runner.os }}-maven-
+
+      - name: Run tests
+        run: mvn clean verify

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2024 QBiC
+Copyright (c) 2018-2024 University of Tübingen
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal