Migrate composite GitHub Actions from java-common-libs to ci-core

.github/actions/setup-java-maven/action.yml

@@ -1,26 +1,112 @@
-name: 'Setup Java and Maven'
-description: 'Composite action to set up Java and Maven environment for OpenCB/Xetabase projects'
-
-# TODO: Define inputs for Java version, Maven version, cache configuration, etc.
-# inputs:
-#   java-version:
-#     description: 'Java version to set up'
-#     required: false
-#     default: '11'
-
-# TODO: Define outputs if needed
-# outputs:
-#   java-version:
-#     description: 'Installed Java version'
-#     value: ${{ steps.setup.outputs.java-version }}
+name: "Setup Java, dependencies and Maven cache"
+description: "Set up JDK, clone and optionally compile dependencies, and configure Maven cache using a key that includes dependencies_sha"
+
+inputs:
+  java_version:
+    description: "Java version to use"
+    required: false
+    default: "11"
+  storage_hadoop:
+    description: "Hadoop flavour, used as part of the Maven cache key"
+    required: false
+    default: "hdi5.1"
+  dependency_repos:
+    description: "Comma-separated list of dependency repositories (e.g. 'java-common-libs,biodata,cellbase')"
+    required: false
+    default: ""
+  require_cache_hit:
+    description: "If true, fail the job when the Maven cache is not found for the current dependencies_sha"
+    required: false
+    default: "false"
+outputs:
+  dependencies_sha:
+    description: "Hash that represents dependency commits (OpenCGA/java-common-libs/biodata/cellbase, etc.)"
+    value: ${{ steps.clone_dependencies.outputs.dependencies_sha }}
+  cache-hit:
+    description: "True if the Maven cache key with this dependencies_sha was already present"
+    value: ${{ steps.maven_cache.outputs.cache-hit }}
 
 runs:
-  using: 'composite'
+  using: "composite"
   steps:
-    # TODO: Add steps to set up Java
-    # TODO: Add steps to set up Maven
-    # TODO: Add caching for Maven dependencies
-    # TODO: Configure Maven settings if needed
-    - name: Placeholder
+    - name: Set up JDK
+      # This step installs the requested JDK version for the job
+      uses: actions/setup-java@v4
+      with:
+        distribution: "temurin"
+        java-version: ${{ inputs.java_version }}
+
+    - name: Clone dependencies and compute dependencies_sha
+      id: clone_dependencies
+      if: ${{ inputs.dependency_repos != '' }}
+      shell: bash
+      run: |
+        # This step clones the dependency repositories using the helper script
+        # and computes a stable dependencies_sha based on all dependency commits.
+        #
+        # It expects get_same_branch.sh to:
+        #   - clone or checkout each repo on the same branch as the caller
+        #   - update DEPENDENCIES_SHA in-place
+        #   - finally write `dependencies_sha=<hash>` into $GITHUB_OUTPUT
+
+        if [ -f "java-common-libs/.github/workflows/scripts/get_same_branch.sh" ]; then
+          chmod +x java-common-libs/.github/workflows/scripts/get_same_branch.sh
+
+          # Initialize DEPENDENCIES_SHA with the current repo SHA so that
+          # main project changes also affect the final cache key.
+          export DEPENDENCIES_SHA="${{ github.sha }}"
+
+          java-common-libs/.github/workflows/scripts/get_same_branch.sh \
+            "${{ github.ref_name }}" \
+            "${{ inputs.dependency_repos }}"
+        else
+          echo "get_same_branch.sh script not found. Skipping dependency checkout."
+          # Fallback: use only the current repo SHA as dependencies_sha
+          DEPENDENCIES_SHA="${{ github.sha }}"
+          echo "dependencies_sha=${DEPENDENCIES_SHA}" >> "$GITHUB_OUTPUT"
+        fi
+
+    - name: Cache local Maven repository
+      id: maven_cache
+      # This step restores and saves the Maven local repository cache, using
+      # storage_hadoop and dependencies_sha as part of the cache key.
+      uses: actions/cache@v4
+      with:
+        path: ~/.m2/repository
+        key: ${{ runner.os }}-maven-${{ inputs.storage_hadoop }}-${{ steps.clone_dependencies.outputs.dependencies_sha || github.sha }}
+        restore-keys: |
+          ${{ runner.os }}-maven-${{ inputs.storage_hadoop }}-
+        ## Force cache hit to avoid analyzing with incomplete dependencies
+        fail-on-cache-miss: ${{ inputs.require_cache_hit }}
+    - name: Compile dependencies (only if cache did not hit)
+      if: ${{ inputs.dependency_repos != '' && steps.maven_cache.outputs.cache-hit != 'true' }}
+      shell: bash
+      run: |
+        # This step compiles dependency repositories only when the Maven cache
+        # for the current dependencies_sha was not found.
+        #
+        # It expects compile_same_branch.sh to:
+        #   - iterate over the comma-separated dependency_repos list
+        #   - run `mvn clean install -DskipTests` on each dependency
+        #   - populate ~/.m2/repository with the latest built artifacts
+
+        if [ -f "java-common-libs/.github/workflows/scripts/compile_same_branch.sh" ]; then
+          chmod +x java-common-libs/.github/workflows/scripts/compile_same_branch.sh
+          java-common-libs/.github/workflows/scripts/compile_same_branch.sh "${{ inputs.dependency_repos }}"
+        else
+          echo "compile_same_branch.sh script not found. Skipping dependency compilation."
+        fi
+
+    - name: Cache summary
+      # This step writes a small summary into the GitHub job summary, so it is
+      # easy to inspect which dependencies_sha and cache key were used.
       shell: bash
-      run: echo "Setup Java and Maven action - to be implemented"
+      run: |
+        {
+          echo "## Java / Maven cache summary"
+          echo ""
+          echo "- Java version: \`${{ inputs.java_version }}\`"
+          echo "- Dependencies sha: \`${{ steps.clone_dependencies.outputs.dependencies_sha || 'No dependencies' }}\`"
+          echo "- Maven cache key: \`${{ runner.os }}-maven-${{ inputs.storage_hadoop }}-${{ steps.clone_dependencies.outputs.dependencies_sha }}\`"
+          echo "- Maven cache hit: \`${{ steps.maven_cache.outputs.cache-hit || 'false' }}\`"
+        } >> "$GITHUB_STEP_SUMMARY"

.github/actions/test-summary/action.yml

@@ -1,26 +1,187 @@
-name: 'Test Summary'
-description: 'Composite action to generate and publish test summaries for OpenCB/Xetabase projects'
-
-# TODO: Define inputs for test results paths, formats, etc.
-# inputs:
-#   test-results-path:
-#     description: 'Path to test results'
-#     required: false
-#     default: '**/target/surefire-reports/*.xml'
-
-# TODO: Define outputs if needed
-# outputs:
-#   summary:
-#     description: 'Test summary'
-#     value: ${{ steps.summary.outputs.summary }}
+name: "Test summary"
+description: "Generate a Markdown summary of Surefire test results and write it to GITHUB_STEP_SUMMARY"
+
+inputs:
+  report_paths:
+    description: "Glob pattern for Surefire XML reports"
+    required: false
+    default: "./**/surefire-reports/TEST-*.xml"
+  title:
+    description: "Title for the test summary section"
+    required: false
+    default: "Test summary"
+  include_module_table:
+    description: "Whether to include the per-module breakdown table"
+    required: false
+    default: "true"
+
+outputs:
+  total_success:
+    description: "Total number of successful tests"
+    value: ${{ steps.generate_summary.outputs.total_success }}
+  total_failed:
+    description: "Total number of failed tests"
+    value: ${{ steps.generate_summary.outputs.total_failed }}
+  total_errors:
+    description: "Total number of tests with errors"
+    value: ${{ steps.generate_summary.outputs.total_errors }}
+  total_skipped:
+    description: "Total number of skipped tests"
+    value: ${{ steps.generate_summary.outputs.total_skipped }}
+  total_tests:
+    description: "Total number of tests"
+    value: ${{ steps.generate_summary.outputs.total_tests }}
 
 runs:
-  using: 'composite'
+  using: "composite"
   steps:
-    # TODO: Add steps to collect test results
-    # TODO: Add steps to parse test results
-    # TODO: Add steps to generate summary
-    # TODO: Add steps to publish summary to GitHub Actions UI
-    - name: Placeholder
+    - name: Generate test summary
+      id: generate_summary
       shell: bash
-      run: echo "Test summary action - to be implemented"
+      env:
+        REPORT_GLOB: ${{ inputs.report_paths }}
+        SUMMARY_TITLE: ${{ inputs.title }}
+        INCLUDE_MODULE_TABLE: ${{ inputs.include_module_table }}
+      run: |
+        # Use Python to parse Surefire XML reports and generate a Markdown summary
+        python - << 'PY'
+        import glob
+        import os
+        import xml.etree.ElementTree as ET
+        import sys
+
+        report_glob = os.environ.get("REPORT_GLOB", "./**/surefire-reports/TEST-*.xml")
+        title = os.environ.get("SUMMARY_TITLE", "Test summary")
+        include_module_table = os.environ.get("INCLUDE_MODULE_TABLE", "true").lower() == "true"
+        github_step_summary = os.environ.get("GITHUB_STEP_SUMMARY")
+        github_output = os.environ.get("GITHUB_OUTPUT")
+
+        # Collect all report files
+        report_files = glob.glob(report_glob, recursive=True)
+
+        # Data structures for totals and per-module aggregation
+        total = {
+            "tests": 0,
+            "failures": 0,
+            "errors": 0,
+            "skipped": 0,
+        }
+        modules = {}
+
+        def update_counts(target, tests, failures, errors, skipped):
+          target["tests"] += tests
+          target["failures"] += failures
+          target["errors"] += errors
+          target["skipped"] += skipped
+
+        for path in report_files:
+          try:
+            tree = ET.parse(path)
+            root = tree.getroot()
+          except Exception as e:
+            # Skip malformed XML files
+            continue
+
+          # Surefire can be <testsuite> or <testsuites> root
+          suites = []
+          if root.tag == "testsuite":
+            suites = [root]
+          elif root.tag == "testsuites":
+            suites = list(root.findall("testsuite"))
+
+          if not suites:
+            continue
+
+          # Deduce module name from path (dir before 'target')
+          # Example: some-module/target/surefire-reports/TEST-*.xml -> module = 'some-module'
+          parts = path.split(os.sep)
+          module_name = "root"
+          if "target" in parts:
+            idx = parts.index("target")
+            if idx > 0:
+              module_name = parts[idx - 1]
+
+          if module_name not in modules:
+            modules[module_name] = {
+              "tests": 0,
+              "failures": 0,
+              "errors": 0,
+              "skipped": 0,
+            }
+
+          for suite in suites:
+            def get_int(attr_name):
+              value = suite.attrib.get(attr_name, "0")
+              try:
+                return int(value)
+              except ValueError:
+                return 0
+
+            tests = get_int("tests")
+            failures = get_int("failures")
+            errors = get_int("errors")
+            skipped = get_int("skipped")
+
+            update_counts(total, tests, failures, errors, skipped)
+            update_counts(modules[module_name], tests, failures, errors, skipped)
+
+        # Compute derived values
+        def compute_success(data):
+          return max(0, data["tests"] - data["failures"] - data["errors"] - data["skipped"])
+
+        total_success = compute_success(total)
+
+        # Build Markdown summary
+        lines = []
+
+        lines.append(f"## {title}")
+        lines.append("")
+        if not report_files:
+          lines.append("_No test reports were found with pattern:_")
+          lines.append(f"`{report_glob}`")
+        else:
+          # Overall table
+          lines.append("### Overall")
+          lines.append("")
+          lines.append("| Success | Failed | Errors | Skipped | Total |")
+          lines.append("| --- | --- | --- | --- | --- |")
+          lines.append(
+            f"| {total_success} | {total['failures']} | {total['errors']} | {total['skipped']} | {total['tests']} |"
+          )
+          lines.append("")
+
+          if include_module_table and modules:
+            lines.append("### By module")
+            lines.append("")
+            lines.append("| Module | Success | Failed | Errors | Skipped | Total |")
+            lines.append("| --- | --- | --- | --- | --- | --- |")
+            for module_name in sorted(modules.keys()):
+              data = modules[module_name]
+              success = compute_success(data)
+              lines.append(
+                f"| {module_name} | {success} | {data['failures']} | {data['errors']} | {data['skipped']} | {data['tests']} |"
+              )
+            lines.append("")
+
+          # Optional detail: number of XML report files found
+          lines.append(f"_Processed {len(report_files)} Surefire report file(s)._")
+
+        markdown = "\n".join(lines)
+
+        # Write to step summary if available
+        if github_step_summary:
+          with open(github_step_summary, "a", encoding="utf-8") as f:
+            f.write(markdown + "\n")
+
+        # Write outputs for reuse
+        if github_output:
+          def write_output(name, value):
+            with open(github_output, "a", encoding="utf-8") as f:
+              f.write(f"{name}={value}\n")
+
+          write_output("total_success", total_success)
+          write_output("total_failed", total["failures"])
+          write_output("total_errors", total["errors"])
+          write_output("total_skipped", total["skipped"])
+          write_output("total_tests", total["tests"])
+        PY