From de965846c08ee4fabcba2aade9ab2b15f766c8ee Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 19 Jul 2026 11:59:45 +0200
Subject: [PATCH] Share mulled resolution cache across integration tests

---
 .github/workflows/integration.yaml | 58 ++++++++++++++++++++++++++++++
 test/integration/conftest.py       | 29 +++++++++++++++
 2 files changed, 87 insertions(+)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 410db2fff1e..e3587766997 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -25,8 +25,57 @@ concurrency:
   cancel-in-progress: true
 permissions: {}
 jobs:
+  prepare-mulled-cache:
+    name: Prepare mulled resolution cache
+    runs-on: ubuntu-latest
+    steps:
+      - name: Select weekly cache
+        run: echo "MULLED_CACHE_WEEK=$(date -u +%G-%V)" >> "$GITHUB_ENV"
+      - name: Restore Biocontainers repository index
+        id: restore-mulled-cache
+        uses: actions/cache/restore@v6.1.0
+        with:
+          key: biocontainers-repository-index-${{ env.MULLED_CACHE_WEEK }}
+          path: '${{ runner.temp }}/mulled-resolution-seed'
+      - name: Check out Galaxy for mulled-cache
+        if: steps.restore-mulled-cache.outputs.cache-hit != 'true'
+        uses: actions/checkout@v7.0.0
+        with:
+          path: 'galaxy cache source'
+          persist-credentials: false
+      - name: Fetch Biocontainers repository index
+        id: fetch-mulled-cache
+        if: steps.restore-mulled-cache.outputs.cache-hit != 'true'
+        continue-on-error: true
+        env:
+          SEED_DIRECTORY: '${{ runner.temp }}/mulled-resolution-seed'
+        run: |
+          python3 'galaxy cache source/lib/galaxy/tool_util/deps/mulled/mulled_cache.py' \
+              --namespace biocontainers \
+              --output "$SEED_DIRECTORY/biocontainers.json"
+      - name: Save Biocontainers repository index
+        if: steps.restore-mulled-cache.outputs.cache-hit != 'true' && steps.fetch-mulled-cache.outcome == 'success'
+        uses: actions/cache/save@v6.1.0
+        with:
+          key: biocontainers-repository-index-${{ env.MULLED_CACHE_WEEK }}
+          path: '${{ runner.temp }}/mulled-resolution-seed'
+      - name: Create fallback seed
+        if: steps.fetch-mulled-cache.outcome == 'failure'
+        env:
+          SEED_DIRECTORY: '${{ runner.temp }}/mulled-resolution-seed'
+        run: |
+          mkdir -p "$SEED_DIRECTORY"
+          echo '{"namespace":"biocontainers","repositories":[]}' > "$SEED_DIRECTORY/biocontainers.json"
+      - name: Upload mulled resolution cache seed
+        uses: actions/upload-artifact@v7
+        with:
+          name: mulled-resolution-cache-seed
+          path: '${{ runner.temp }}/mulled-resolution-seed/biocontainers.json'
+          retention-days: 1
+
   test:
     name: Test
+    needs: prepare-mulled-cache
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -63,9 +112,18 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install Python
         run: uv python install
+      - name: Download mulled resolution cache seed
+        uses: actions/download-artifact@v8
+        with:
+          name: mulled-resolution-cache-seed
+          path: '${{ runner.temp }}/mulled-resolution-seed'
       - name: Install Apptainer's singularity
         uses: './galaxy root/.github/actions/install_apptainer'
       - name: Run tests
+        env:
+          GALAXY_TEST_MULLED_RESOLUTION_CACHE_SEED: '${{ runner.temp }}/mulled-resolution-seed/biocontainers.json'
+          GALAXY_CONFIG_OVERRIDE_MULLED_RESOLUTION_CACHE_DATA_DIR: '${{ runner.temp }}/mulled-resolution-cache/data'
+          GALAXY_CONFIG_OVERRIDE_MULLED_RESOLUTION_CACHE_LOCK_DIR: '${{ runner.temp }}/mulled-resolution-cache/locks'
         run: |
           . .ci/minikube-test-setup/start_services.sh
           ./run_tests.sh --coverage -integration test/integration -- --num-shards=4 --shard-id=${{ matrix.chunk }}
diff --git a/test/integration/conftest.py b/test/integration/conftest.py
index afe729466aa..a2d8b6b5a49 100644
--- a/test/integration/conftest.py
+++ b/test/integration/conftest.py
@@ -1,13 +1,42 @@
+import json
+import os
 import tempfile
 
 import pytest
+from beaker.cache import CacheManager
+from beaker.util import parse_cache_config_options
 
+from galaxy.tool_util.deps.mulled.util import NAMESPACE_HAS_REPO_NAME_KEY
 from galaxy_test.conftest import (  # noqa: F401
     pytest_configure,
     pytest_plugins,
 )
 
 
+@pytest.fixture(scope="session", autouse=True)
+def seed_mulled_resolution_cache():
+    """Seed the shared integration-test cache with a Quay namespace index."""
+    seed_path = os.environ.get("GALAXY_TEST_MULLED_RESOLUTION_CACHE_SEED")
+    data_dir = os.environ.get("GALAXY_CONFIG_OVERRIDE_MULLED_RESOLUTION_CACHE_DATA_DIR")
+    lock_dir = os.environ.get("GALAXY_CONFIG_OVERRIDE_MULLED_RESOLUTION_CACHE_LOCK_DIR")
+    if not seed_path or not data_dir or not lock_dir:
+        return
+
+    with open(seed_path) as seed_file:
+        repositories = json.load(seed_file).get("repositories", [])
+    if not repositories:
+        return
+
+    cache_opts = {
+        "cache.type": "file",
+        "cache.data_dir": data_dir,
+        "cache.lock_dir": lock_dir,
+        "cache.expire": os.environ.get("GALAXY_CONFIG_OVERRIDE_MULLED_RESOLUTION_CACHE_EXPIRE", "3600"),
+    }
+    cache = CacheManager(**parse_cache_config_options(cache_opts)).get_cache("mulled_resolution")
+    cache[NAMESPACE_HAS_REPO_NAME_KEY] = repositories
+
+
 @pytest.fixture(scope="session")
 def celery_includes():
     return ["galaxy.celery.tasks"]