Run Explorer compatibility checks in CI

.github/workflows/search-backend-conformance.yml

@@ -0,0 +1,218 @@
+name: Search backend conformance
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '17 3 * * 0'
+
+permissions:
+  contents: read
+
+concurrency:
+  group: search-backend-conformance
+  cancel-in-progress: false
+
+env:
+  SYNBIOHUB_DOCKER_REF: marpaia/sbol-db-and-explorer
+  SBOL_TEST_SUITE_REVISION: 0044284331b2f915a6e4b9d50e1cbf3ea2f62dcd
+  SYNBIOHUB_CONFORMANCE_IMAGE: synbiohub/synbiohub:search-conformance
+
+jobs:
+  build:
+    name: Build SynBioHub image
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    steps:
+      - uses: actions/checkout@v5
+        name: Checkout SynBioHub
+      - name: Build Docker image
+        run: |
+          docker build . \
+            --file docker/Dockerfile \
+            --tag "$SYNBIOHUB_CONFORMANCE_IMAGE"
+      - name: Package Docker image
+        run: |
+          docker save "$SYNBIOHUB_CONFORMANCE_IMAGE" | gzip > sbh.tar.gz
+      - uses: actions/upload-artifact@v4
+        name: Upload Docker image
+        with:
+          name: search-conformance-sbh-image
+          path: sbh.tar.gz
+          retention-days: 1
+
+  sbolexplorer:
+    name: Full corpus (SBOLExplorer)
+    needs: build
+    runs-on: ubuntu-latest
+    timeout-minutes: 360
+    env:
+      COMPOSE_PROJECT_NAME: search-conformance-explorer
+      SYNBIOHUB_IMAGE: synbiohub/synbiohub:search-conformance
+      SYNBIOHUB_PORT: '37777'
+      TRIPLESTORE_PORT: '38890'
+      EXPLORER_PORT: '33162'
+      ELASTICSEARCH_PORT: '39200'
+    steps:
+      - uses: actions/checkout@v5
+        name: Checkout SynBioHub
+      - uses: actions/checkout@v5
+        name: Checkout SynBioHub Docker topologies
+        with:
+          repository: SynBioHub/synbiohub-docker
+          ref: ${{ env.SYNBIOHUB_DOCKER_REF }}
+          path: synbiohub-docker
+      - uses: actions/checkout@v5
+        name: Checkout pinned SBOLTestSuite corpus
+        with:
+          repository: SynBioDex/SBOLTestSuite
+          ref: ${{ env.SBOL_TEST_SUITE_REVISION }}
+          path: SBOLTestSuite
+      - uses: actions/download-artifact@v4
+        name: Download SynBioHub image
+        with:
+          name: search-conformance-sbh-image
+      - name: Import SynBioHub image
+        run: |
+          gzip --decompress --stdout sbh.tar.gz | docker load
+      - name: Create artifact directory
+        run: mkdir -p artifacts/search-backends
+      - name: Start sbol-db with SBOLExplorer
+        run: |
+          docker compose \
+            -f synbiohub-docker/docker-compose.sboldb.yml \
+            -f synbiohub-docker/docker-compose.sboldb-store-only.yml \
+            -f synbiohub-docker/docker-compose.explorer.yml \
+            up -d --wait --wait-timeout 600
+      - name: Run full-corpus SBOLExplorer baseline
+        run: |
+          python3 tests/search-backends/run-conformance.py \
+            --topology sboldb-explorer-fixed \
+            --base-url http://127.0.0.1:37777/ \
+            --corpus-root SBOLTestSuite \
+            --report artifacts/search-backends/sboldb-explorer-fixed.json
+      - name: Capture SBOLExplorer topology logs
+        if: always()
+        run: |
+          docker compose \
+            -f synbiohub-docker/docker-compose.sboldb.yml \
+            -f synbiohub-docker/docker-compose.sboldb-store-only.yml \
+            -f synbiohub-docker/docker-compose.explorer.yml \
+            logs --no-color > artifacts/search-backends/sboldb-explorer-fixed.compose.log 2>&1 || true
+      - name: Stop SBOLExplorer topology
+        if: always()
+        run: |
+          docker compose \
+            -f synbiohub-docker/docker-compose.sboldb.yml \
+            -f synbiohub-docker/docker-compose.sboldb-store-only.yml \
+            -f synbiohub-docker/docker-compose.explorer.yml \
+            down --volumes --remove-orphans
+      - uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: search-conformance-sbolexplorer
+          path: artifacts/search-backends/
+          if-no-files-found: error
+          retention-days: 30
+
+  sboldb:
+    name: Full corpus (sbol-db)
+    needs: build
+    runs-on: ubuntu-latest
+    timeout-minutes: 360
+    env:
+      COMPOSE_PROJECT_NAME: search-conformance-sboldb
+      SYNBIOHUB_IMAGE: synbiohub/synbiohub:search-conformance
+      SYNBIOHUB_PORT: '27777'
+      TRIPLESTORE_PORT: '28890'
+    steps:
+      - uses: actions/checkout@v5
+        name: Checkout SynBioHub
+      - uses: actions/checkout@v5
+        name: Checkout SynBioHub Docker topologies
+        with:
+          repository: SynBioHub/synbiohub-docker
+          ref: ${{ env.SYNBIOHUB_DOCKER_REF }}
+          path: synbiohub-docker
+      - uses: actions/checkout@v5
+        name: Checkout pinned SBOLTestSuite corpus
+        with:
+          repository: SynBioDex/SBOLTestSuite
+          ref: ${{ env.SBOL_TEST_SUITE_REVISION }}
+          path: SBOLTestSuite
+      - uses: actions/download-artifact@v4
+        name: Download SynBioHub image
+        with:
+          name: search-conformance-sbh-image
+      - name: Import SynBioHub image
+        run: |
+          gzip --decompress --stdout sbh.tar.gz | docker load
+      - name: Create artifact directory
+        run: mkdir -p artifacts/search-backends
+      - name: Start sbol-db native search topology
+        run: |
+          docker compose \
+            -f synbiohub-docker/docker-compose.sboldb.yml \
+            -f synbiohub-docker/docker-compose.sboldb-search.yml \
+            up -d --wait --wait-timeout 600
+      - name: Run full-corpus sbol-db candidate
+        run: |
+          python3 tests/search-backends/run-conformance.py \
+            --topology sboldb-native \
+            --base-url http://127.0.0.1:27777/ \
+            --metrics-url http://127.0.0.1:28890/metrics \
+            --corpus-root SBOLTestSuite \
+            --report artifacts/search-backends/sboldb-native.json
+      - name: Capture sbol-db topology logs
+        if: always()
+        run: |
+          docker compose \
+            -f synbiohub-docker/docker-compose.sboldb.yml \
+            -f synbiohub-docker/docker-compose.sboldb-search.yml \
+            logs --no-color > artifacts/search-backends/sboldb-native.compose.log 2>&1 || true
+      - name: Stop sbol-db topology
+        if: always()
+        run: |
+          docker compose \
+            -f synbiohub-docker/docker-compose.sboldb.yml \
+            -f synbiohub-docker/docker-compose.sboldb-search.yml \
+            down --volumes --remove-orphans
+      - uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: search-conformance-sboldb
+          path: artifacts/search-backends/
+          if-no-files-found: error
+          retention-days: 30
+
+  compare:
+    name: Compare full-corpus reports
+    needs: [sbolexplorer, sboldb]
+    if: always()
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@v5
+        name: Checkout SynBioHub
+      - uses: actions/download-artifact@v4
+        name: Download SBOLExplorer report
+        with:
+          name: search-conformance-sbolexplorer
+          path: artifacts/search-backends/baseline
+      - uses: actions/download-artifact@v4
+        name: Download sbol-db report
+        with:
+          name: search-conformance-sboldb
+          path: artifacts/search-backends/candidate
+      - name: Compare backend reports
+        run: |
+          python3 tests/search-backends/compare-reports.py \
+            --baseline artifacts/search-backends/baseline/sboldb-explorer-fixed.json \
+            --candidate artifacts/search-backends/candidate/sboldb-native.json \
+            --output artifacts/search-backends/comparison.json
+      - uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: search-conformance-comparison
+          path: artifacts/search-backends/comparison.json
+          if-no-files-found: error
+          retention-days: 30

.github/workflows/test.yml

@@ -2,6 +2,9 @@ name: Integration testing
 
 on: push
 
+env:
+  SYNBIOHUB_DOCKER_REF: marpaia/sbol-db-and-explorer
+
 jobs:
   build:
     name: Build Docker image
@@ -144,9 +147,58 @@ jobs:
       - name: Run tests
         run: |
           tests/test.sh --stopaftertestsuite
+  explorer-compatibility:
+    name: Explorer compatibility (${{ matrix.label }})
+    needs: build
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - label: Virtuoso + SBOLExplorer
+            store: virtuoso
+            search: sbol-explorer
+          - label: sbol-db + SBOLExplorer
+            store: sboldb
+            search: sbol-explorer
+          - label: sbol-db + sbol-db
+            store: sboldb
+            search: sbol-db
+    env:
+      SBH_TRIPLESTORE: ${{ matrix.store }}
+      SBH_SEARCH_BACKEND: ${{ matrix.search }}
+      SBH_DOCKER_DIR: ${{ github.workspace }}/synbiohub-docker
+      SBH_EXPLORER_INDEX_TIMEOUT: "600"
+    steps:
+      - uses: actions/checkout@v5
+        name: Checkout SynBioHub
+      - uses: actions/checkout@v5
+        name: Checkout SynBioHub Docker topologies
+        with:
+          repository: SynBioHub/synbiohub-docker
+          ref: ${{ env.SYNBIOHUB_DOCKER_REF }}
+          path: synbiohub-docker
+      - uses: actions/download-artifact@v4
+        name: Download Docker image
+        with:
+          name: sbh-image
+      - name: Import saved Docker image
+        run: |
+          gzip --decompress --stdout sbh.tar.gz | docker load
+      - uses: actions/setup-python@v6
+        name: Install Python
+        with:
+          python-version: '3.9'
+      - name: Install test dependencies
+        run: |
+          pip install -r tests/test_requirements.txt
+      - name: Run indexed Explorer HTML contract
+        run: |
+          tests/test.sh --stopaftertestsuite
   publish:
     name: Publish snapshot image
-    needs: [search-backend-harness, sboltests, sbhtests, sboltests-sboldb, sbhtests-sboldb]
+    needs: [search-backend-harness, sboltests, sbhtests, sboltests-sboldb, sbhtests-sboldb, explorer-compatibility]
     runs-on: ubuntu-latest
     if: endsWith(github.ref, 'master')
     steps:

tests/search-backends/README.md

@@ -20,6 +20,19 @@ Accepted empty documents remain recorded but are correctly non-probeable. The
 run also verifies private search visibility, anonymous isolation,
 private-to-public publication, removal, and an observable index completion.
 
+## Automation
+
+The `Integration testing` workflow runs the focused indexed-HTML contract on
+every push for Virtuoso with SBOLExplorer, sbol-db with SBOLExplorer, and
+sbol-db with its compatibility listener. Each row explicitly rebuilds the
+configured index and compares the complete `/search/I0462` HTML snapshot.
+
+The `Search backend conformance` workflow runs the full pinned corpus every
+Sunday and on manual dispatch. It runs the SBOLExplorer baseline and sbol-db
+candidate on separate runners, uploads both JSON reports and their Compose
+logs, and then uploads the comparison report. Each workflow's
+`SYNBIOHUB_DOCKER_REF` selects its companion topology revision.
+
 ## Run one topology
 
 For the native sbol-db row, pass the main listener's metrics endpoint so job