fix: sync PPI scheduling and harden preflight

2026-08-22 05:09:52 +08:00
parent 052b0c1d5d
commit 311a49110f
6 changed files with 465 additions and 109 deletions
@@ -34,3 +34,89 @@ def test_multilingual_frontend_keeps_critical_ppi_kaks_state_chain_in_sync() ->

    for start, end in boundaries:
        assert _block(multilingual, start, end) == _block(canonical, start, end)
+
+
+def test_multilingual_frontend_uses_stage_shell_for_ppi_reference_prompts() -> None:
+    multilingual = (ROOT / "apps/web/vue3/index_ml.html").read_text(encoding="utf-8")
+    nearest = _block(
+        multilingual,
+        "const confirmNearestPpiReferenceCandidate = async",
+        "const ppiReferenceDecisionMessage =",
+    )
+    preflight = _block(
+        multilingual,
+        "const runPpiSpeciesResolutionPreflight = async",
+        "const ppiKaksDependencyStages =",
+    )
+
+    assert "showStageConfirmDialog" in nearest
+    assert "ElMessageBox.confirm" not in nearest
+    assert "id: 'ppi_kaks_reference_status'" in preflight
+    assert "ppiNeedsNearReferenceDecision(resolution, requestedStages)" in preflight
+    assert "confirmParams.stage === 'ppi_string_reference_confirmation'" in multilingual
+    assert "confirmParams.stage === 'ppi_kaks_reference_status'" in multilingual
+    assert "Confirm top candidate" in multilingual
+    assert "Reference status acknowledged" in multilingual
+
+
+def test_multilingual_frontend_keeps_ppi_kaks_owner_pauses_isolated() -> None:
+    canonical = (ROOT / "apps/web/vue3/index.html").read_text(encoding="utf-8")
+    multilingual = (ROOT / "apps/web/vue3/index_ml.html").read_text(encoding="utf-8")
+    start = "const ppiKaksOwnedOrthologOwners ="
+    end = "const mergePpiReferenceSpeciesIntoBatch ="
+
+    assert _block(multilingual, start, end) == _block(canonical, start, end)
+    assert "ppiKaksDependencyPauses" in multilingual
+    assert "ppiKaksDependencyPause:" not in _block(multilingual, start, end)
+
+
+def test_multilingual_frontend_uses_hidden_ppi_owned_ortholog_producer() -> None:
+    canonical = (ROOT / "apps/web/vue3/index.html").read_text(encoding="utf-8")
+    multilingual = (ROOT / "apps/web/vue3/index_ml.html").read_text(encoding="utf-8")
+    start = "const ensureOrthologStageForPpiKaks ="
+    end = "const ensurePpiKaksDependencyOwner ="
+    producer = _block(multilingual, start, end)
+
+    assert producer == _block(canonical, start, end)
+    assert "rememberPpiKaksInternalOrthologProducer('ppi'" in producer
+    assert "nextStages.splice" not in producer
+    assert "attachOrthologDependencyToOwners(requestedStages)" not in producer
+
+
+def test_multilingual_frontend_does_not_abort_batch_on_ppi_preflight_pause() -> None:
+    multilingual = (ROOT / "apps/web/vue3/index_ml.html").read_text(encoding="utf-8")
+    start = multilingual.index("const startBatchExecute = async")
+    end = multilingual.index("const ppiSettledForKaks =", start)
+    batch_start = multilingual[start:end]
+
+    assert "await ensureOrthologProducerForPpiKaks();" in batch_start
+    assert "const dependencyPreflightOk = await ensureOrthologProducerForPpiKaks();" not in batch_start
+
+
+def test_multilingual_background_batch_pauses_ppi_kaks_preflight_blocks() -> None:
+    multilingual = (ROOT / "apps/web/vue3/index_ml.html").read_text(encoding="utf-8")
+    helper = _block(
+        multilingual,
+        "const isPpiKaksBackgroundPause =",
+        "const startBackgroundBatchExecution = async",
+    )
+    background = _block(
+        multilingual,
+        "const startBackgroundBatchExecution = async",
+        "const extractDataPathsFromText =",
+    )
+
+    assert "stageId === 'ppi' || stageId === 'kaks'" in helper
+    assert "intentStages.includes('ortholog')" in helper
+    assert "isPpiKaksBackgroundPause(stageId, stageParams, err, intentStages)" in background
+    assert "localStatus[stageId] = 'paused'" in background
+
+
+def test_multilingual_frontend_keeps_transient_fetch_recovery_in_sync() -> None:
+    canonical = (ROOT / "apps/web/vue3/index.html").read_text(encoding="utf-8")
+    multilingual = (ROOT / "apps/web/vue3/index_ml.html").read_text(encoding="utf-8")
+    start = "const fetchWithTransientRetry = async"
+    end = "const ppiKaksOwnedOrthologOwners ="
+
+    assert _block(multilingual, start, end) == _block(canonical, start, end)
+    assert "fetchWithTransientRetry('/api/ppi/species-resolution'" in multilingual
@@ -1291,13 +1291,19 @@ const ppiKaksDependencyPauses = () => ({});

 def test_submit_preflight_maps_kaks_selected_ortholog_owner_to_dependency_owner() -> None:
    html = Path("apps/web/vue3/index.html").read_text(encoding="utf-8")
+    retry_helper = _source_block(
+        html,
+        "const fetchWithTransientRetry = async",
+        "const pollReferenceBundleDownloadTask = async",
+    )
    helper = _source_block(
        html,
        "const runPpiSpeciesResolutionPreflight =",
        "const ppiKaksDependencyStages =",
    )
    result = _run_node(
-        helper
+        retry_helper
+        + helper
        + """
 const jobInfo = {job_id: 'job_1786243816439_04955b'};
 const executionPrefix = () => 'Ft.SPL';
@@ -1784,3 +1790,155 @@ def test_ppi_manifest_and_background_status_queries_use_canonical_owner_identity
    expected = "canonicalizePpiOwnerBiologicalScope({ ...batchPlanParams, ...batchParams, ...stageParams })"
    assert expected in manifest_block
    assert expected in background_block
+
+
+def test_ppi_preflight_retries_one_transient_network_error_before_returning_ready() -> None:
+    html = Path("apps/web/vue3/index.html").read_text(encoding="utf-8")
+    retry_helper = _source_block(
+        html,
+        "const fetchWithTransientRetry = async",
+        "const pollReferenceBundleDownloadTask = async",
+    )
+    preflight = _source_block(
+        html,
+        "const runPpiSpeciesResolutionPreflight = async",
+        "const ppiKaksDependencyStages =",
+    )
+    result = _run_node(
+        retry_helper
+        + preflight
+        + """
+const jobInfo = {job_id: 'job_network_retry'};
+const executionPrefix = () => 'Ft.SPL';
+const canonicalizePpiOwnerBiologicalScope = payload => payload;
+const ppiNeedsNearReferenceDecision = () => false;
+const formatPpiSpeciesResolutionBlockMessage = () => 'not ready';
+const showStageConfirmDialog = async () => true;
+const addAgentMessage = () => {};
+const ElMessageBox = {alert: async () => {}};
+const setTimeout = callback => callback();
+let attempts = 0;
+const fetch = async () => {
+  attempts += 1;
+  if (attempts === 1) {
+    throw new TypeError('NetworkError when attempting to fetch resource.');
+  }
+  return {
+    ok: true,
+    status: 200,
+    statusText: 'OK',
+    json: async () => ({success: true, status: 'ready'})
+  };
+};
+
+(async () => {
+  const outcome = await runPpiSpeciesResolutionPreflight({
+    stage: 'ppi', prefix: 'Ft.SPL', targetSpecies: ['Ft']
+  }, {requestedStages: ['ppi']});
+  console.log(JSON.stringify({attempts, allowed: outcome.allowed}));
+})();
+"""
+    )
+
+    assert result == {"attempts": 2, "allowed": True}
+
+
+def test_ppi_preflight_does_not_retry_a_valid_business_response() -> None:
+    html = Path("apps/web/vue3/index.html").read_text(encoding="utf-8")
+    retry_helper = _source_block(
+        html,
+        "const fetchWithTransientRetry = async",
+        "const pollReferenceBundleDownloadTask = async",
+    )
+    preflight = _source_block(
+        html,
+        "const runPpiSpeciesResolutionPreflight = async",
+        "const ppiKaksDependencyStages =",
+    )
+    result = _run_node(
+        retry_helper
+        + preflight
+        + """
+const jobInfo = {job_id: 'job_business_response'};
+const executionPrefix = () => 'Ft.SPL';
+const canonicalizePpiOwnerBiologicalScope = payload => payload;
+const ppiNeedsNearReferenceDecision = () => false;
+const formatPpiSpeciesResolutionBlockMessage = () => 'reference data missing';
+const showStageConfirmDialog = async () => true;
+const addAgentMessage = () => {};
+const ElMessageBox = {alert: async () => {}};
+const setTimeout = callback => callback();
+let attempts = 0;
+const fetch = async () => {
+  attempts += 1;
+  return {
+    ok: true,
+    status: 200,
+    statusText: 'OK',
+    json: async () => ({success: true, status: 'needs_reference_data'})
+  };
+};
+
+(async () => {
+  const outcome = await runPpiSpeciesResolutionPreflight({
+    stage: 'ppi', prefix: 'Ft.SPL', targetSpecies: ['Ft']
+  }, {requestedStages: ['ppi']});
+  console.log(JSON.stringify({attempts, allowed: outcome.allowed}));
+})();
+"""
+    )
+
+    assert result == {"attempts": 1, "allowed": False}
+
+
+def test_reference_bundle_status_poll_recovers_from_one_transient_network_error() -> None:
+    html = Path("apps/web/vue3/index.html").read_text(encoding="utf-8")
+    helper = _source_block(
+        html,
+        "const fetchWithTransientRetry = async",
+        "const ppiKaksOwnedOrthologOwners =",
+    )
+    result = _run_node(
+        helper
+        + """
+const setTimeout = callback => callback();
+const referenceBundleErrorMessage = (_data, fallback) => fallback;
+const updateReferenceBundleDownloadProgress = () => {};
+let attempts = 0;
+const fetch = async () => {
+  attempts += 1;
+  if (attempts === 1) throw new TypeError('Failed to fetch');
+  return {
+    ok: true,
+    status: 200,
+    json: async () => ({status: 'success', result: {status: 'success', species_code: 'string_taxon_3562'}})
+  };
+};
+
+(async () => {
+  const result = await pollReferenceBundleDownloadTask('task-download');
+  console.log(JSON.stringify({attempts, status: result.status, species: result.species_code}));
+})();
+"""
+    )
+
+    assert result == {"attempts": 2, "status": "success", "species": "string_taxon_3562"}
+
+
+def test_transient_retry_is_not_used_for_download_or_analysis_submission() -> None:
+    html = Path("apps/web/vue3/index.html").read_text(encoding="utf-8")
+    download_submit = _source_block(
+        html,
+        "const downloadRecommendedPpiReferenceBundle = async",
+        "const updateReferenceBundleDownloadProgress =",
+    )
+    execute_submit = _source_block(
+        html,
+        "const submitExecuteRequestWithAutoAnnotation = async",
+        "const waitForDialogTransition = async",
+    )
+
+    assert "fetch('/api/reference-bundle/download'" in download_submit
+    assert "fetchWithTransientRetry('/api/reference-bundle/download'" not in download_submit
+    assert "fetch('/api/execute'" in execute_submit
+    assert "fetchWithTransientRetry('/api/execute'" not in execute_submit
@@ -0,0 +1,33 @@
+from __future__ import annotations
+
+
+def test_startup_hook_warms_the_string_snapshot_cache(monkeypatch) -> None:
+    from apps.web import pipeline_backend
+    from apps.web.vue3 import main
+
+    calls = []
+    monkeypatch.setattr(
+        pipeline_backend,
+        "load_string_snapshot",
+        lambda root: calls.append(root),
+    )
+
+    main.warm_string_species_snapshot_cache()
+
+    assert calls == [pipeline_backend.STRING_SPECIES_SNAPSHOT_ROOT]
+    assert main.warm_string_species_snapshot_cache in main.app.router.on_startup
+
+
+def test_string_snapshot_warm_failure_does_not_abort_web_startup(monkeypatch, capsys) -> None:
+    from apps.web import pipeline_backend
+    from apps.web.vue3 import main
+    from gfa_core.string_species_registry import StringSnapshotError
+
+    def fail_to_warm(_root):
+        raise StringSnapshotError("snapshot unavailable", code="string_registry_unavailable")
+
+    monkeypatch.setattr(pipeline_backend, "load_string_snapshot", fail_to_warm)
+
+    main.warm_string_species_snapshot_cache()
+
+    assert "STRING snapshot cache warm failed" in capsys.readouterr().out