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fix: sync PPI scheduling and harden preflight

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This commit is contained in:
wtx
2026-08-22 05:09:52 +08:00
parent 052b0c1d5d
commit 311a49110f
6 changed files with 465 additions and 109 deletions
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apps/web/vue3/index.html
+17 -2
View File
@@ -14188,10 +14188,25 @@ compare: [[flesh, peel]]`;
};
};
const fetchWithTransientRetry = async (input, init = {}) => {
const retryDelays = [500, 1500];
for (let attempt = 0; ; attempt += 1) {
try {
return await fetch(input, init);
} catch (err) {
const message = String(err?.message || err || '');
const transient = err instanceof TypeError
|| /NetworkError|Failed to fetch|Load failed/i.test(message);
if (!transient || attempt >= retryDelays.length) throw err;
await new Promise(resolve => setTimeout(resolve, retryDelays[attempt]));
}
}
};
const pollReferenceBundleDownloadTask = async (taskId, options = {}) => {
const intervalMs = Number(options.intervalMs || 3000);
while (true) {
const response = await fetch(`/api/task/${encodeURIComponent(taskId)}`);
const response = await fetchWithTransientRetry(`/api/task/${encodeURIComponent(taskId)}`);
const data = await response.json().catch(() => ({}));
if (!response.ok) {
throw new Error(referenceBundleErrorMessage(data, `Reference species data status request failed (HTTP ${response.status})`));
@@ -14533,7 +14548,7 @@ compare: [[flesh, peel]]`;
if (requestedStages.length === 1 && requestedStages[0] === 'ppi') {
canonicalizePpiOwnerBiologicalScope(payload);
}
const response = await fetch('/api/ppi/species-resolution', {
const response = await fetchWithTransientRetry('/api/ppi/species-resolution', {
method: 'POST',
headers: { 'Content-Type': 'application/json' },
body: JSON.stringify(payload)
apps/web/vue3/index_ml.html
+151 -106
View File
@@ -5033,7 +5033,7 @@
</div>
<!-- 阶段特定参数 -->
<div v-if="!['ppi_kaks_reference_data', 'ppi_kaks_download_fallback'].includes(confirmParams.stage)" class="param-group">
<div v-if="!['ppi_kaks_reference_data', 'ppi_kaks_download_fallback', 'ppi_string_reference_confirmation', 'ppi_kaks_reference_status'].includes(confirmParams.stage)" class="param-group">
<h5>{{ t('基本参数') }}</h5>
<div class="param-row">
<div class="param-field param-field--wide">
@@ -6575,12 +6575,21 @@ RNA-seq KEGG/fgsea 会优先使用物种级 KEGG gene set；没有物种级缓
</div>
<div v-else-if="gwasConfirmationBlockedFor(confirmParams)" class="param-dialog-footer__status" style="font-size: 14px;">⏸ 等待选择有效 VCF</div>
<div v-else-if="confirmParams.stage === 'ppi_kaks_download_fallback'" class="param-dialog-footer__status" style="font-size: 14px;">⏸ 下载失败兜底需要手动确认</div>
<div v-else-if="confirmParams.stage === 'ppi_string_reference_confirmation'" class="param-dialog-footer__status" style="font-size: 14px;">⏸ Manual reference confirmation required</div>
<div v-else-if="confirmParams.stage === 'ppi_kaks_reference_status'" class="param-dialog-footer__status" style="font-size: 14px;">Reference status acknowledged</div>
<div v-else class="param-dialog-footer__status" style="font-size: 14px;">⏸ 倒计时已暂停，请确认参数后手动执行</div>
<div class="param-dialog-footer__actions">
<template v-if="isDirectReplotDialog">
<el-button @click="cancelStageConfirmDialog">{{ t('取消') }}</el-button>
<el-button type="primary" :loading="isExecuting" @click="confirmStageExecute">{{ t('确认重绘') }}</el-button>
</template>
<template v-else-if="confirmParams.stage === 'ppi_string_reference_confirmation'">
<el-button @click="skipStageExecute">Cancel PPI</el-button>
<el-button type="primary" @click="confirmStageExecute">Confirm top candidate</el-button>
</template>
<template v-else-if="confirmParams.stage === 'ppi_kaks_reference_status'">
<el-button type="primary" @click="confirmStageExecute">OK</el-button>
</template>
<template v-else>
<el-button type="danger" @click="stopBatchExecute">⏹️ 停止全部</el-button>
<el-button v-if="stageConfirmCountdown > 0" @click="clearStageConfirmTimer">{{ t('暂停倒计时') }}</el-button>
@@ -13907,32 +13916,16 @@ compare: [[flesh, peel]]`;
? resolution.candidates
: (Array.isArray(resolution.species_resolution?.candidates) ? resolution.species_resolution.candidates : []);
if (!candidates.length) return null;
const candidateLines = candidates.map((candidate, index) => {
const name = candidate.selected_string_name || candidate.species_name || '-';
const taxon = candidate.selected_string_taxon_id || candidate.taxon_id || '-';
const lca = candidate.lca_name || candidate.lca_taxon_name || candidate.lca_taxon_id || '-';
const distance = candidate.topology_distance ?? candidate.distance_edges ?? candidate.distance ?? '-';
const version = candidate.string_version || resolution.string_version || resolution.species_resolution?.string_version || '-';
return `${index + 1}. ${name} / STRING TaxID ${taxon} / LCA ${lca} / 拓扑边数 ${distance} / STRING ${version}`;
});
const selected = candidates[0];
const selectedTaxon = String(selected.selected_string_taxon_id || selected.taxon_id || '').trim();
if (!selectedTaxon) return null;
try {
await ElMessageBox.confirm(
[
t('string-close-species-line1'),
'',
...candidateLines,
'',
t('string-close-species-line2')
].join('\n'),
t('string-close-species-title'),
{ type: 'warning', confirmButtonText: t('string-confirm-first-candidate'), cancelButtonText: t('string-cancel-ppi') }
);
} catch (_err) {
return null;
}
const accepted = await showStageConfirmDialog({
id: 'ppi_string_reference_confirmation',
name: 'Confirm the STRING reference species for PPI',
dependencies: [],
params: { resolution, candidates }
}, 1, 1);
if (!accepted) return null;
return {
taxonId: selectedTaxon,
storageKey: `string_taxon_${selectedTaxon}`,
@@ -14051,17 +14044,18 @@ compare: [[flesh, peel]]`;
const clearPpiKaksReferencePause = (requestedStages = []) => {
const pauseStageIds = ppiKaksPauseStageIds(requestedStages);
const current = batchExecuteParams.value || {};
if (current.ppiKaksDependencyPause) {
const next = { ...current };
delete next.ppiKaksDependencyPause;
batchExecuteParams.value = next;
}
pauseStageIds.forEach(stageId => {
const nextPauses = { ...(current.ppiKaksDependencyPauses || {}) };
requestedStages.forEach(ownerStageId => delete nextPauses[ownerStageId]);
const next = { ...current, ppiKaksDependencyPauses: nextPauses };
delete next.ppiKaksDependencyPause;
batchExecuteParams.value = next;
[...pauseStageIds, 'ortholog'].forEach(stageId => {
clearStagePause(stageId);
if (stageExecutionStatus.value[stageId] === 'paused') {
stageExecutionStatus.value[stageId] = 'pending';
}
});
applyStoredPpiKaksPauseStatuses();
};
const applyArabidopsisFallbackForPpiKaks = (requestedStages = [], reason = '') => {
@@ -14280,10 +14274,25 @@ compare: [[flesh, peel]]`;
};
};
const fetchWithTransientRetry = async (input, init = {}) => {
const retryDelays = [500, 1500];
for (let attempt = 0; ; attempt += 1) {
try {
return await fetch(input, init);
} catch (err) {
const message = String(err?.message || err || '');
const transient = err instanceof TypeError
|| /NetworkError|Failed to fetch|Load failed/i.test(message);
if (!transient || attempt >= retryDelays.length) throw err;
await new Promise(resolve => setTimeout(resolve, retryDelays[attempt]));
}
}
};
const pollReferenceBundleDownloadTask = async (taskId, options = {}) => {
const intervalMs = Number(options.intervalMs || 3000);
while (true) {
const response = await fetch(`/api/task/${encodeURIComponent(taskId)}`);
const response = await fetchWithTransientRetry(`/api/task/${encodeURIComponent(taskId)}`);
const data = await response.json().catch(() => ({}));
if (!response.ok) {
throw new Error(referenceBundleErrorMessage(data, `Reference species data status request failed (HTTP ${response.status})`));
@@ -14303,11 +14312,32 @@ compare: [[flesh, peel]]`;
}
};
const ppiKaksPauseStageIds = (requestedStages = []) => {
const ids = new Set((requestedStages || []).filter(Boolean));
const plannedIds = new Set((batchExecuteStages.value || []).map(stage => getStageId(stage)).filter(Boolean));
if (plannedIds.has('ortholog')) ids.add('ortholog');
return Array.from(ids);
const ppiKaksOwnedOrthologOwners = (orthologStage = {}, batchParams = {}) => {
const stageParams = orthologStage && typeof orthologStage === 'object' ? (orthologStage.params || {}) : {};
const intentStages = Array.isArray(batchParams.intentStages) ? batchParams.intentStages : [];
if (intentStages.includes('ortholog')) return [];
const dependencyOwner = String(stageParams.dependencyOwner || '').trim();
if (dependencyOwner === 'ppi' || dependencyOwner === 'kaks') return [dependencyOwner];
const autoInsertedFor = Array.isArray(stageParams.autoInsertedFor)
? stageParams.autoInsertedFor.filter(owner => owner === 'ppi' || owner === 'kaks')
: [];
if (autoInsertedFor.length) return Array.from(new Set(autoInsertedFor));
if (intentStages.includes('kaks')) return ['kaks'];
return [];
};
const ppiKaksPauseStageIds = (requestedStages = []) => (
Array.from(new Set((requestedStages || []).filter(Boolean)))
);
const ppiKaksDependencyPauses = () => {
const current = batchExecuteParams.value || {};
if (current.ppiKaksDependencyPauses && typeof current.ppiKaksDependencyPauses === 'object') {
return current.ppiKaksDependencyPauses;
}
const legacyPause = current.ppiKaksDependencyPause;
const legacyOwner = Array.isArray(legacyPause?.requestedStages) ? legacyPause.requestedStages[0] : '';
return legacyOwner ? { [legacyOwner]: legacyPause } : {};
};
const storePpiKaksReferencePause = (requestedStages = [], resolution = {}, message = '') => {
@@ -14320,21 +14350,37 @@ compare: [[flesh, peel]]`;
requestedStages,
pauseStageIds
};
batchExecuteParams.value = {
...(batchExecuteParams.value || {}),
ppiKaksDependencyPause: pauseInfo
};
const nextPauses = { ...ppiKaksDependencyPauses() };
requestedStages.forEach(ownerStageId => {
if (ownerStageId) nextPauses[ownerStageId] = pauseInfo;
});
const next = { ...(batchExecuteParams.value || {}), ppiKaksDependencyPauses: nextPauses };
delete next.ppiKaksDependencyPause;
batchExecuteParams.value = next;
return pauseInfo;
};
const applyStoredPpiKaksPauseStatuses = () => {
const pause = batchExecuteParams.value?.ppiKaksDependencyPause;
const pauseStageIds = Array.isArray(pause?.pauseStageIds) ? pause.pauseStageIds : [];
pauseStageIds.forEach(stageId => {
if (!stageId) return;
stageExecutionStatus.value[stageId] = 'paused';
recordStagePause(stageId, pause);
const pauses = ppiKaksDependencyPauses();
Object.values(pauses).forEach(pause => {
const pauseStageIds = Array.isArray(pause?.pauseStageIds) ? pause.pauseStageIds : [];
pauseStageIds.forEach(stageId => {
if (!stageId) return;
stageExecutionStatus.value[stageId] = 'paused';
recordStagePause(stageId, pause);
});
});
const orthologStage = (batchExecuteStages.value || []).find(stage => getStageId(stage) === 'ortholog');
const orthologOwners = ppiKaksOwnedOrthologOwners(orthologStage, batchExecuteParams.value || {});
const plannedOwners = new Set((batchExecuteStages.value || [])
.map(stage => getStageId(stage))
.filter(stageId => stageId === 'ppi' || stageId === 'kaks'));
const activeOrthologOwners = orthologOwners.filter(owner => plannedOwners.has(owner));
if (activeOrthologOwners.length && activeOrthologOwners.every(owner => Boolean(pauses[owner]))) {
const pause = pauses[activeOrthologOwners[0]];
stageExecutionStatus.value.ortholog = 'paused';
recordStagePause('ortholog', pause);
}
};
const mergePpiReferenceSpeciesIntoBatch = (speciesCode, requestedStages = [], policySource = 'ppi_kaks_reference_bundle_download', replaceExisting = false) => {
@@ -14588,7 +14634,7 @@ compare: [[flesh, peel]]`;
if (requestedStages.length === 1 && requestedStages[0] === 'ppi') {
canonicalizePpiOwnerBiologicalScope(payload);
}
const response = await fetch('/api/ppi/species-resolution', {
const response = await fetchWithTransientRetry('/api/ppi/species-resolution', {
method: 'POST',
headers: { 'Content-Type': 'application/json' },
body: JSON.stringify(payload)
@@ -14603,21 +14649,23 @@ compare: [[flesh, peel]]`;
return { allowed: true, resolution, message: '' };
}
if (options.allowNeedsOrtholog === true && resolution.status === 'needs_ortholog') {
if (!ppiNeedsNearReferenceDecision(resolution)) {
if (!ppiNeedsNearReferenceDecision(resolution, requestedStages)) {
return { allowed: true, resolution, message: '' };
}
}
const message = formatPpiSpeciesResolutionBlockMessage(resolution);
if (
options.suppressNeedsReferenceDataAlert === true
&& (resolution.status === 'needs_reference_data' || ppiNeedsNearReferenceDecision(resolution))
&& (resolution.status === 'needs_reference_data' || ppiNeedsNearReferenceDecision(resolution, requestedStages))
) {
return { allowed: false, resolution, message };
}
await ElMessageBox.alert(message, 'PPI/KaKs 需要先处理参考物种/Ortholog', {
type: resolution.status === 'invalid_mapping' ? 'error' : 'warning',
confirmButtonText: '知道了'
});
await showStageConfirmDialog({
id: 'ppi_kaks_reference_status',
name: 'PPI/KaKs Reference Status',
dependencies: [],
params: { resolution, requestedStages }
}, 1, 1);
addAgentMessage('assistant', message);
return { allowed: false, resolution, message };
};
@@ -14851,62 +14899,23 @@ compare: [[flesh, peel]]`;
};
const ensureOrthologStageForPpiKaks = (stages, requestedStages, requestBody, resolution = {}) => {
const stageIds = stages.map(stage => getStageId(stage)).filter(Boolean);
const recoveredReferenceApplied = applyResolvedPpiReferenceToBatch(resolution, requestedStages, requestBody);
if (recoveredReferenceApplied) {
addAgentMessage('assistant', t('✅ PPI/KaKs 前置数据检查通过：检测到已下载近源参考 ') + resolution.reference_species + t('，将用该参考先生成 Ortholog mapping。'));
addAgentMessage('assistant', `✅ PPI/KaKs 前置数据检查通过：检测到已下载近源参考 ${resolution.reference_species}，将用该参考先生成 Ortholog mapping。`);
}
const mappingLabel = ppiOrthologMappingLabel(resolution);
if (mappingLabel && resolution?.status !== 'needs_ortholog') {
addAgentMessage('assistant', t('✅ PPI/KaKs 前置数据检查通过：检测到已有 Ortholog 映射（') + mappingLabel + t('），将复用该映射执行 ') + requestedStages.join('、') + '。');
requestedStages.forEach(owner => rememberPpiKaksInternalOrthologProducer(owner, null));
addAgentMessage('assistant', `✅ PPI/KaKs 前置数据检查通过：检测到已有 Ortholog 映射（${mappingLabel}），将复用该映射执行 ${requestedStages.join('、')}。`);
return true;
}
attachOrthologDependencyToOwners(requestedStages);
if (stageIds.includes('ortholog')) {
if (requestedStages.includes('ppi')) {
const ownerState = {
ppiReferenceTaxonId: requestBody.ppiReferenceTaxonId || '',
ppiReferenceStorageKey: requestBody.ppiReferenceStorageKey || '',
ppiReferenceSelectionMode: requestBody.ppiReferenceSelectionMode || '',
ppiReferenceUserConfirmed: requestBody.ppiReferenceUserConfirmed === true
};
batchExecuteStages.value = (batchExecuteStages.value || stages).map(stage => (
getStageId(stage) === 'ortholog'
? buildPpiOwnedOrthologStage(requestBody, ownerState, requestedStages)
: stage
));
}
addAgentMessage('assistant', t('✅ PPI/KaKs 前置数据检查通过：当前批次已有 Ortholog，将先生成同源映射再继续下游分析。'));
return true;
}
const insertAt = Math.max(0, stages.findIndex(stage => ppiKaksDependencyStages.has(getStageId(stage))));
const orthologStage = requestedStages.includes('ppi')
? buildPpiOwnedOrthologStage(requestBody, requestBody, requestedStages)
: {
id: 'ortholog',
name: 'Ortholog',
dependencies: ['identify'],
params: {
...requestBody,
autoInsertedFor: requestedStages,
requestedStages,
referencePolicySource: 'ppi_kaks_dependency_preflight'
}
};
const nextStages = [...(batchExecuteStages.value || stages)];
nextStages.splice(insertAt < 0 ? 0 : insertAt, 0, orthologStage);
batchExecuteStages.value = nextStages;
stageExecutionStatus.value.ortholog = 'pending';
if (Array.isArray(batchExecuteParams.value?.completed_stages)) {
batchExecuteParams.value = {
...(batchExecuteParams.value || {}),
completed_stages: batchExecuteParams.value.completed_stages.filter(stageId => stageId !== 'ortholog')
};
}
if (!requestedStages.includes('ppi')) return true;
const orthologStage = buildPpiOwnedOrthologStage(requestBody, requestBody, ['ppi']);
rememberPpiKaksInternalOrthologProducer('ppi', orthologStage);
const reason = resolution?.issue_code === 'stale_ortholog_reference_conflict'
? '已有 Ortholog 映射与当前 PPI/KaKs 参考物种不一致'
: '缺少可用同源映射';
addAgentMessage('assistant', t('✅ PPI/KaKs 前置数据检查通过：') + reason + t('，已自动插入 Ortholog，将先生成 mapping 再执行 ') + requestedStages.join('、') + '。');
addAgentMessage('assistant', `✅ PPI 前置数据检查通过：${reason}；执行 PPI 时将先在内部生成专属同源映射。`);
return true;
};
@@ -15679,11 +15688,7 @@ compare: [[flesh, peel]]`;
await loadInterspeciesSpeciesOptions();
}
normalizeBatchExecutionSpeciesForStages();
const dependencyPreflightOk = await ensureOrthologProducerForPpiKaks();
if (!dependencyPreflightOk) {
addAgentMessage('assistant', t('⏸️ PPI/KaKs 前置数据检查未通过，已暂停批量执行；请补齐参考注释包或确认参考物种后重新执行。'));
return;
}
await ensureOrthologProducerForPpiKaks();
isBatchExecuting.value = true;
shouldStopBatchExecute.value = false;
@@ -22701,9 +22706,27 @@ compare: [[flesh, peel]]`;
throw createStructuredExecuteError(data);
};
const isPpiKaksBackgroundPause = (stageId, stageParams = {}, err = {}, intentStages = []) => {
const resolution = err.ppiSpeciesResolution || err.responseData?.ppi_species_resolution || null;
const status = String(err.status || resolution?.status || '').trim();
const isPreflightBlock = Boolean(resolution) || [
'needs_reference_data', 'confirmation_required', 'needs_ortholog',
'unresolved', 'ppi_kaks_dependency_resolution_blocked'
].includes(status);
if (!isPreflightBlock) return false;
if (stageId === 'ppi' || stageId === 'kaks') return true;
if (stageId !== 'ortholog' || intentStages.includes('ortholog')) return false;
const dependencyOwner = String(stageParams.dependencyOwner || '').trim();
const autoInsertedFor = Array.isArray(stageParams.autoInsertedFor) ? stageParams.autoInsertedFor : [];
return dependencyOwner === 'ppi'
|| dependencyOwner === 'kaks'
|| autoInsertedFor.some(owner => owner === 'ppi' || owner === 'kaks');
};
const startBackgroundBatchExecution = async (stages, plan, planData = {}) => {
const batchId = `bg_${Date.now()}`;
const stageIds = stages.map(getStageId).filter(Boolean);
const intentStages = Array.isArray(planData.intent?.stages) ? planData.intent.stages : [];
const stageMap = {};
stages.forEach(stage => {
stageMap[getStageId(stage)] = stage;
@@ -22734,6 +22757,7 @@ compare: [[flesh, peel]]`;
let completed = 0;
let failed = 0;
let paused = 0;
while (true) {
const pending = stageIds.filter(stageId => localStatus[stageId] === 'pending');
@@ -22749,6 +22773,21 @@ compare: [[flesh, peel]]`;
const executable = limitGwasModelHeavyWave(executableCandidates, localStatus);
if (executable.length === 0) {
const pausedDeps = pending.filter(stageId => {
let deps = stageDependencies[stageId] || [];
if (stageId === 'rnaseq_fgsea' && !stageIds.includes('rnaseq_kegg_enrich')) {
deps = deps.filter(dep => dep !== 'rnaseq_kegg_enrich');
}
return deps.some(dep => localStatus[dep] === 'paused');
});
if (pausedDeps.length > 0) {
pausedDeps.forEach(stageId => {
localStatus[stageId] = 'paused';
paused++;
});
addAgentMessage('assistant', t('⏸️ 后台批次中以下阶段等待上游暂停项处理: ') + pausedDeps.map(getStageLabel).join(', '));
continue;
}
const blocked = pending.filter(stageId => {
let deps = stageDependencies[stageId] || [];
if (stageId === 'rnaseq_fgsea' && !stageIds.includes('rnaseq_kegg_enrich')) {
@@ -22777,15 +22816,21 @@ compare: [[flesh, peel]]`;
localStatus[stageId] = 'running';
const stage = stageMap[stageId] || stageId;
const stageName = getStageName(stage);
const stageParams = (plan.stages_detail || []).find(s => s.id === stageId)?.params || plan.params || {};
addAgentMessage('assistant', t('⚙️ 后台执行阶段: ') + stageName + '...');
try {
const stageParams = (plan.stages_detail || []).find(s => s.id === stageId)?.params || plan.params || {};
await executeStageDirect(stageId, stageParams);
localStatus[stageId] = 'completed';
completed++;
addAgentMessage('assistant', t('✅ 后台阶段 ') + stageName + t(' 完成'));
} catch (err) {
if (isPpiKaksBackgroundPause(stageId, stageParams, err, intentStages)) {
localStatus[stageId] = 'paused';
paused++;
addAgentMessage('assistant', t('⏸️ 后台阶段 ') + stageName + t(' 前置数据未就绪，已暂停；其它阶段继续执行。'));
return;
}
localStatus[stageId] = 'failed';
failed++;
addAgentMessage('assistant', await showFailureDiagnosis(stageId, err, { fallbackMessage: err.message }));
@@ -22793,7 +22838,7 @@ compare: [[flesh, peel]]`;
}));
}
addAgentMessage('assistant', t('📦 后台批次完成：成功 ') + completed + '/' + stageIds.length + t('，失败 ') + failed + '/' + stageIds.length);
addAgentMessage('assistant', t('📦 后台批次完成：成功 ') + completed + '/' + stageIds.length + t('，暂停 ') + paused + '/' + stageIds.length + t('，失败 ') + failed + '/' + stageIds.length);
await refreshResults();
};
apps/web/vue3/main.py
+19
View File
@@ -4312,6 +4312,25 @@ def initialize_agent_conversation_store() -> None:
agent_conversation_store = PersistentConversationStore(repository)
@app.on_event("startup")
def warm_string_species_snapshot_cache() -> None:
"""Warm the fixed STRING snapshot before the first PPI preflight request."""
started_at = time.perf_counter()
try:
from apps.web import pipeline_backend
snapshot = pipeline_backend.load_string_snapshot(
pipeline_backend.STRING_SPECIES_SNAPSHOT_ROOT
)
elapsed = time.perf_counter() - started_at
print(
"[PPI] STRING snapshot cache warmed "
f"in {elapsed:.3f}s: {snapshot.snapshot_id}"
)
except Exception as exc:
print(f"[WARN] STRING snapshot cache warm failed: {exc}")
class AgentConversationCreateRequest(BaseModel):
user_id: str = "default"
title: str = ""
tests/unit/test_multilingual_ppi_scheduler_parity.py
+86
View File
@@ -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
tests/unit/test_ppi_owner_scheduling_task5.py
+159 -1
View File
@@ -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
tests/unit/test_string_snapshot_startup_warm.py
+33
View File
@@ -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