Merge branch 'develop' into adjust_repr_use

.github/workflows/basic_sdk_functionality_tests.yml

@@ -0,0 +1,174 @@
+name: Basic kb-sdk functionality tests
+
+on:
+  pull_request:
+    branches:
+      - develop
+      - main
+      - master
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - closed
+
+jobs:
+  test_kb-sdk_builds:
+    if: "!contains(github.event.head_commit.message, 'skip ci')"
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-20.04, ubuntu-latest]
+        language: [perl, python, java]
+        test_type: [base] #, example]
+        auth: [token, env_var]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      # build kb-sdk from source and test basic functions
+      - name: Set up JDK 1.8
+        uses: actions/setup-java@v3
+        with:
+          distribution: temurin
+          java-version: 8.0.362+9
+
+      - name: Build with Ant
+        run: |
+          make
+
+      - name: Add bin to $PATH
+        run: |
+          echo "$GITHUB_WORKSPACE/bin" >> $GITHUB_PATH
+
+      - name: checking kb-sdk functions
+        env:
+          KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }}
+          LANGUAGE_TOKEN: ${{ matrix.language }}
+        run: |
+          env
+          kb-sdk help
+          kb-sdk version
+
+      # the following steps create a KBase app using the SDK
+      # and runs some checks to ensure the app generated
+      # is functional and that the SDK can test it.
+      - name: init base repo
+        if: matrix.test_type == 'base'
+        env:
+          LANGUAGE_TOKEN: ${{ matrix.language }}
+        run: |
+          kb-sdk init -l $LANGUAGE_TOKEN -u user SampleApp
+
+      - name: init example repo
+        if: matrix.test_type == 'example'
+        env:
+          LANGUAGE_TOKEN: ${{ matrix.language }}
+        run: |
+          kb-sdk init -l $LANGUAGE_TOKEN -u user --example SampleApp
+
+      - name: test ${{ matrix.test_type }} repo, using test.cfg for auth
+        if: matrix.auth == 'token'
+        run: |
+          cd SampleApp
+          kb-sdk test || true
+
+      - name: test ${{ matrix.test_type }} repo, using test.cfg for auth, add env var to test.cfg
+        if: matrix.auth == 'token'
+        env:
+          KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }}
+        run: |
+          cd SampleApp
+          sed -i "s/test_token=/test_token=$KBASE_TEST_TOKEN/" test_local/test.cfg
+          kb-sdk test
+
+      - name: test ${{ matrix.test_type }} repo, using env var for auth
+        if: matrix.auth == 'env_var'
+        env:
+          KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }}
+        run: |
+          cd SampleApp
+          kb-sdk test
+
+      - name: make resulting app available as artefact in case of failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v3
+        with:
+          name: kbaseapp-${{ matrix.language }}-${{ matrix.test_type }}-${{ matrix.os }}
+          path: SampleApp
+
+
+  test_existing_repos:
+    if: "!contains(github.event.head_commit.message, 'skip ci')"
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-20.04, ubuntu-latest]
+        # TODO: add a Java app. WsLargeDataIO does not currently build as it relies on a Java
+        # repo that no longer exists.
+        app: [KBaseReport]  # , WsLargeDataIO]
+        auth: [token, env_var]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Set up JDK 1.8
+        uses: actions/setup-java@v3
+        with:
+          distribution: temurin
+          java-version: 8.0.362+9
+
+      - name: Build with Ant
+        run: |
+          make
+
+      - name: Add bin to $PATH
+        run: |
+          echo "$GITHUB_WORKSPACE/bin" >> $GITHUB_PATH
+
+      - name: checking basic kb-sdk functions
+        run: |
+          env
+          kb-sdk help
+          kb-sdk version
+
+      # the following steps check out and run the tests of an existing KBase app
+      - name: Checkout existing kbase module ${{ matrix.app }}
+        uses: actions/checkout@v3
+        with:
+          repository: kbaseapps/${{ matrix.app }}
+          path: kbase_app
+
+      - name: run repo tests, using test.cfg for auth
+        if: matrix.auth == 'token'
+        run: |
+          cd kbase_app
+          kb-sdk test || true
+
+      - name: run repo tests, using test.cfg for auth
+        if: matrix.auth == 'token'
+        env:
+          KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }}
+        run: |
+          cd kbase_app
+          sed -i "s/test_token=/test_token=$KBASE_TEST_TOKEN/" test_local/test.cfg
+          kb-sdk test
+
+      - name: run repo tests, using env var for auth
+        if: matrix.auth == 'env_var'
+        env:
+          KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }}
+        run: |
+          cd kbase_app
+          kb-sdk test
+
+      - name: make resulting app available as artefact in case of failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v3
+        with:
+          name: kbaseapp-${{ matrix.app }}-${{ matrix.os }}
+          path: kbase_app