implement update test data

.github/workflows/tools_update_test_data.yaml

@@ -0,0 +1,141 @@
+on: [push, pull_request]
+
+name: 'Test action for tools with update test data'
+
+env:
+  GALAXY_FORK: galaxyproject
+  GALAXY_BRANCH: master
+  MAX_CHUNKS: 4
+
+jobs:
+  setup-pr-tools:
+    name: Setup as in PR for tools
+    runs-on: ubuntu-latest
+    outputs:
+      galaxy-head-sha: ${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
+      repository-list: ${{ steps.discover.outputs.repository-list }}
+      tool-list: ${{ steps.discover.outputs.tool-list }}
+      chunk-count: ${{ steps.discover.outputs.chunk-count }}
+      chunk-list: ${{ steps.discover.outputs.chunk-list }}
+    strategy:
+      matrix:
+        python-version: [3.7]
+    steps:
+    - name: Print github context properties
+      run: |
+        echo 'event: ${{ github.event_name }}'
+        echo 'sha: ${{ github.sha }}'
+        echo 'ref: ${{ github.ref }}'
+        echo 'head_ref: ${{ github.head_ref }}'
+        echo 'base_ref: ${{ github.base_ref }}'
+        echo 'event.before: ${{ github.event.before }}'
+        echo 'event.after: ${{ github.event.after }}'
+    - name: Determine latest commit in the Galaxy repo
+      id: get-galaxy-sha
+      run: echo "::set-output name=galaxy-head-sha::$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)"
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip and .planemo
+      uses: actions/cache@v2
+      id: cache-pip-planemo
+      with:
+        path: |
+          ~/.cache/pip
+          ~/.planemo
+        key: cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
+    # Install the `wheel` package so that when installing other packages which
+    # are not available as wheels, pip will build a wheel for them, which can be cached.
+    - name: Install wheel
+      run: pip install wheel
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+    - name: Introduce a change on test tool1 and 2
+      run: |
+        git config --global user.name "Arthur Dent"
+        git config --global user.email "[email protected]"
+        sed -i -e 's/echo test/echo updated/' test/tools/tool1/tool1.xml
+        sed -i -e 's/echo test/echo updated/' test/tools/tool2/tool2.xml
+        git commit -m bump test/tools/
+    - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
+      uses: ./
+      id: discover
+      with:
+        create-cache: ${{ steps.cache-pip.outputs.cache-hit != 'true' || steps.cache-planemo.outputs.cache-hit != 'true' }}
+        galaxy-fork: ${{ env.GALAXY_FORK }}
+        galaxy-branch: ${{ env.GALAXY_BRANCH }}
+        max-chunks: ${{ env.MAX_CHUNKS }}
+        python-version: ${{ matrix.python-version }}
+        update-test-data: true
+    - name: Check commit range
+      run: if ! grep "\.\." <<<$(echo ${{ steps.discover.outputs.commit-range }}); then echo "wrong commit range"; exit 1; fi
+    - name: Check content of repository list
+      run: |
+        if ! grep -q "tool1" <<<$(echo "${{ steps.discover.outputs.repository-list }}"); then echo "tool1 must be in repo list"; exit 1; fi
+        if ! grep -q "tool2" <<<$(echo "${{ steps.discover.outputs.repository-list }}"); then echo "tool2 must be in repo list"; exit 1; fi
+    - name: Check content of tool list
+      run: |
+        if ! grep -q "tool1.xml" <<<$(echo "${{ steps.discover.outputs.tool-list }}"); then echo "tool1.xml must be in tool list"; exit 1; fi
+        if ! grep -q "tool2.xml" <<<$(echo "${{ steps.discover.outputs.tool-list }}"); then echo "tool2.xml must be in tool list"; exit 1; fi
+    - name: Check number of chunks
+      run: if [ "${{ steps.discover.outputs.chunk-count }}" != "1" ]; then echo "wrong chunk-count"; exit 1; fi
+
+
+  test-tools:
+    name: Test testing of tools
+    needs: [setup-pr-tools]
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        chunk: ${{ fromJson(needs.setup-pr-tools.outputs.chunk-list) }}
+        python-version: [3.7]
+    services:
+      postgres:
+        image: postgres:11
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+    # checkout the repository
+    # and use it as the current working directory
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 1
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache .cache/pip and .planemo
+      uses: actions/cache@v2
+      id: cache-pip-planemo
+      with:
+        path: |
+          ~/.cache/pip
+          ~/.planemo
+        key: cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup-pr-tools.outputs.galaxy-head-sha }}
+    - name: Introduce a change on test tool1 and 2
+      run: |
+        sed -i -e 's/echo test/echo updated/' test/tools/tool1/tool1.xml
+        sed -i -e 's/echo test/echo updated/' test/tools/tool2/tool2.xml
+    - name: Planemo test tools
+      uses: ./
+      id: test-tools
+      with:
+        mode: test
+        repository-list: ${{ needs.setup-pr-tools.outputs.repository-list }}
+        galaxy-fork: ${{ env.GALAXY_FORK }}
+        galaxy-branch: ${{ env.GALAXY_BRANCH }}
+        chunk: ${{ matrix.chunk }}
+        chunk-count: ${{ needs.setup-pr-tools.outputs.chunk-count }}
+        update-test-data: true
+    - name: Check if test updated the test data
+      run: |
+        if ! grep -q "updated" test/tools/tool1/test-data/test.txt; then echo "test data for tool1 has not been updated"; exit 1; fi
+    - uses: actions/upload-artifact@v2
+      with:
+        name: 'Tool test output ${{ matrix.chunk }}'
+        path: upload

README.md

@@ -63,6 +63,7 @@ Optional inputs:
 - `galaxy-source` (default `galaxyproject`)
 - `max-chunks` (default `20`)
 - `python-version` (default `"3.7"`)
+- `update-test-data` Boolean that sets the number of chunks to one. See documentation in test mode.
 
 Outputs:
 
@@ -107,6 +108,7 @@ Optional inputs:
 - `galaxy-branch`
 - `galaxy-source`
 - `python-version`
+- `update-test-data` Boolean that triggers the update of test data for failed tests. If you intend to commit the changes during IUC style CI the also set this in setup mode (which will set the number of chunks to 1).
 
 Output:
 

action.yml

@@ -59,6 +59,9 @@ inputs:
   workflow-namespace:
     description: 'Github namespace under which to create workfow repositories'
     default: 'iwc-workflows'
+  update-test-data:
+    description: 'Flag to trigger update of test data for test mode'
+    default: false
   github-token:
     description: '(Secret!) Github PAT token. Needed for creating workflow repositories with workflow-upload'
     default: ''
@@ -126,6 +129,7 @@ runs:
         WORKFLOW_NAMESPACE: ${{ inputs.workflow-namespace }}
         GITHUB_TOKEN: ${{ inputs.github-token }}
         WORKFLOWS: ${{ inputs.workflows }}
+        UPDATE_TEST_DATA: ${{ inputs.update-test-data }}
         GITHUB_EVENT_NAME_OVERRIDE: ${{ inputs.github-event-name-override }}
         GITHUB_REF_OVERRIDE: ${{ inputs.github-ref-override }}
 

planemo_ci_actions.sh

@@ -50,7 +50,7 @@ if [ "$REPOSITORIES" == "" ] && [ "$MODE" == "setup" ]; then
       fi
       ;;
     esac
-  elif [ "$GITHUB_EVENT_NAME" = "pull_request" ]; then
+  elif [ "$GITHUB_EVENT_NAME" = "pull_request" ] || [ "$GITHUB_EVENT_NAME" = "repository_dispatch" ]; then
     COMMIT_RANGE="HEAD~.."
   fi
   echo "$COMMIT_RANGE" > commit_range.txt
@@ -85,11 +85,15 @@ if [ "$REPOSITORIES" == "" ] && [ "$MODE" == "setup" ]; then
     ln -s repository_list.txt count_list.txt
   fi
 
-  CHUNK_COUNT=$(wc -l < count_list.txt)
-  if [ "$CHUNK_COUNT" -gt "$MAX_CHUNKS" ]; then
-    CHUNK_COUNT=$MAX_CHUNKS
-  elif [ "$CHUNK_COUNT" -eq 0 ]; then
+  if [ "$UPDATE_TEST_DATA" == "true" ]; then
     CHUNK_COUNT=1
+  else
+    CHUNK_COUNT=$(wc -l < count_list.txt)
+    if [ "$CHUNK_COUNT" -gt "$MAX_CHUNKS" ]; then
+      CHUNK_COUNT=$MAX_CHUNKS
+    elif [ "$CHUNK_COUNT" -eq 0 ]; then
+      CHUNK_COUNT=1
+    fi
   fi
   echo $CHUNK_COUNT > chunk_count.txt
 else
@@ -158,7 +162,10 @@ if [ "$MODE" == "test" ]; then
     fi
     if [ "$WORKFLOWS" == "true" ]; then
       PLANEMO_OPTIONS+=("${PLANEMO_WORKFLOW_OPTIONS[@]}")
-    fi  
+    fi
+    if [ "$UPDATE_TEST_DATA" == "true" ]; then
+      PLANEMO_OPTIONS+=("--update_test_data")
+    fi
     json=$(mktemp -u -p json_output --suff .json)
     PIP_QUIET=1 planemo test "${PLANEMO_OPTIONS[@]}" "${PLANEMO_TEST_OPTIONS[@]}" --test_output_json "$json" "${TOOL_GROUP[@]}" || true
     docker system prune --all --force --volumes || true

test/tools/tool1/test-data/test.txt

@@ -0,0 +1 @@
+test

test/tools/tool1/tool1.xml

@@ -16,11 +16,7 @@
     <tests>
         <test>
             <param name="bool" value="true"/>
-            <output name="out">
-                <assert_contents>
-                    <has_text text="test"/>
-                </assert_contents>
-            </output>
+            <output name="out" value="test.txt"/>
         </test>
     </tests>
     <help><![CDATA[

test/tools/tool2/test-data/test.txt

@@ -0,0 +1 @@
+test

test/tools/tool2/tool2.xml

@@ -16,11 +16,7 @@
     <tests>
         <test>
             <param name="bool" value="true"/>
-            <output name="out">
-                <assert_contents>
-                    <has_text text="test"/>
-                </assert_contents>
-            </output>
+            <output name="out" value="test.txt"/>
         </test>
     </tests>
     <help><![CDATA[