admin/PlantAI-dev
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 1 Wiki Activity

feat: update header and hide extension

Browse Source
This commit is contained in:
sj
2026-08-06 20:12:18 +08:00
parent 35fbee8c85
commit 2623d3114c
2 changed files with 259 additions and 37 deletions
Download Patch File Download Diff File Expand all files Collapse all files
apps/web/vue3/index.html
+259 -37
View File
@@ -136,7 +136,7 @@
.left-panel .el-upload-list { max-height: 120px; overflow-y: auto; }
body { margin: 0; font-family: 'Helvetica Neue', Arial, sans-serif; background: #f5f7fa; }
.header { background: linear-gradient(135deg, #667eea 0%, #764ba2 100%); color: white; padding: 15px 20px; }
.header { background: linear-gradient(135deg, #667eea 0%, #764ba2 100%); color: white; padding: 27px 20px 19px 20px; display: flex; justify-content: space-between; align-items: center; }
.header h1 { margin: 0; font-size: 22px; }
.main-container { display: flex; padding: 10px; gap: 10px; height: calc(100vh - 70px); overflow: hidden; box-sizing: border-box; }
@@ -1237,9 +1237,12 @@
<div id="app" style="display: none;">
<!-- Header -->
<div class="header">
<div style="display: flex; align-items: baseline; gap: 12px; margin-left: 24px;">
<h1 style="margin: 0; font-size: 28px; font-weight: 700;">CropAI</h1>
<span style="font-size: 15px; opacity: 0.85; font-weight: 400;">Evidence-grounded multi-agent artificial intelligence for crop gene-family discovery and transcriptomic decision support</span>
<div style="display: flex; align-items: center; gap: 12px; margin-left: 24px;">
<img src="/static/logo.png" style="height: 60px; margin-right: 8px; margin-top: -10px;">
<div style="margin-top: -5px;">
<h1 style="margin: 0; font-size: 28px; font-weight: 700; display: inline;">CropAI</h1>
<span style="font-size: 15px; opacity: 0.85; font-weight: 400; margin-left: 25px;">Multi-Agent Platform for crop Bioinformatics Analysis</span>
</div>
</div>
</div>
@@ -1360,7 +1363,7 @@
<el-divider style="margin: 12px 0;"></el-divider>
<div style="padding:10px; background:#fff; border:1px solid #dcdfe6; border-radius:0px;">
<div v-if="false" style="padding:10px; background:#fff; border:1px solid #dcdfe6; border-radius:0px;">
<div style="display:flex; align-items:center; justify-content:space-between; gap:8px; margin-bottom:8px;">
<el-tooltip content="上传已跑通过的代码和测试数据；执行通过自然语言触发。" placement="top">
<h4 style="margin:0; color:#303133; cursor:help;">拓展分析阶段</h4>
@@ -13668,17 +13671,18 @@ 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 = '') => {
@@ -13853,11 +13857,32 @@ 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 = '') => {
@@ -13870,21 +13895,37 @@ 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) => {
@@ -14113,6 +14154,60 @@ compare: [[flesh, peel]]`;
};
const ppiKaksDependencyStages = new Set(['ppi', 'kaks']);
const ppiKaksTemporaryCircuitBreakerEnabled = true;
const isPpiKaksTemporarilyUnavailable = stageId => (
ppiKaksTemporaryCircuitBreakerEnabled
&& ppiKaksDependencyStages.has(String(stageId || ''))
);
const ppiKaksTemporaryPauseStageIds = (stages = [], batchParams = {}) => {
const plannedOwnerIds = (stages || [])
.map(stage => getStageId(stage))
.filter(stageId => isPpiKaksTemporarilyUnavailable(stageId));
return (stages || [])
.map(stage => getStageId(stage))
.filter(stageId => {
if (plannedOwnerIds.includes(stageId)) return true;
if (stageId !== 'ortholog') return false;
const orthologStage = (stages || []).find(item => getStageId(item) === 'ortholog');
const owners = ppiKaksOwnedOrthologOwners(orthologStage, batchParams);
return owners.length > 0
&& owners.some(owner => plannedOwnerIds.includes(owner))
&& owners.every(owner => isPpiKaksTemporarilyUnavailable(owner));
});
};
const applyPpiKaksTemporaryCircuitBreaker = () => {
const requestedStages = (batchExecuteStages.value || [])
.map(stage => getStageId(stage))
.filter(stageId => isPpiKaksTemporarilyUnavailable(stageId));
requestedStages.forEach(stageId => {
const message = `${getStageLabel(stageId)} 功能修订中，本次已自动暂停；其它阶段继续执行。`;
storePpiKaksReferencePause([stageId], {
status: 'temporarily_unavailable',
issue_code: 'ppi_kaks_under_revision'
}, message);
});
return ppiKaksTemporaryPauseStageIds(
batchExecuteStages.value || [],
batchExecuteParams.value || {}
);
};
const isPpiKaksTemporarySubmissionBlocked = (stageId, requestBody = {}) => {
if (isPpiKaksTemporarilyUnavailable(stageId)) return true;
if (stageId !== 'ortholog' || !ppiKaksTemporaryCircuitBreakerEnabled) return false;
const batchParams = batchExecuteParams.value || {};
const intentStages = Array.isArray(batchParams.intentStages) ? batchParams.intentStages : [];
if (intentStages.includes('ortholog')) return false;
const dependencyOwner = String(requestBody.dependencyOwner || requestBody.dependency_owner || '').trim();
const autoInsertedFor = firstNonEmptyList(requestBody.autoInsertedFor, requestBody.auto_inserted_for);
if (!['ppi', 'kaks'].includes(dependencyOwner) && !autoInsertedFor.some(owner => ppiKaksDependencyStages.has(owner))) {
return false;
}
const owners = ppiKaksOwnedOrthologOwners(
{ id: 'ortholog', params: { ...requestBody, autoInsertedFor } },
batchParams
);
return owners.length > 0 && owners.every(owner => isPpiKaksTemporarilyUnavailable(owner));
};
const batchIncludesPpiKaks = () => (batchExecuteStages.value || []).some(
stage => ppiKaksDependencyStages.has(getStageId(stage))
);
@@ -14305,6 +14400,12 @@ compare: [[flesh, peel]]`;
attachOrthologDependencyToOwners(requestedStages);
if (stageIds.includes('ortholog')) {
if (requestedStages.includes('ppi')) {
const existingOrtholog = (batchExecuteStages.value || stages).find(stage => getStageId(stage) === 'ortholog');
const existingOwners = ppiKaksOwnedOrthologOwners(existingOrtholog, batchExecuteParams.value || {});
if (!existingOwners.length && (batchExecuteParams.value?.intentStages || []).includes('ortholog')) {
addAgentMessage('assistant', '⏸️ 已保留用户显式请求的独立 Ortholog；PPI 所需的专属参考映射本次单独暂停。');
return false;
}
const ownerState = {
ppiReferenceTaxonId: requestBody.ppiReferenceTaxonId || '',
ppiReferenceStorageKey: requestBody.ppiReferenceStorageKey || '',
@@ -14488,18 +14589,54 @@ compare: [[flesh, peel]]`;
return ensureOrthologStageForPpiKaks(stages, requestedStages, requestBody, preflight.resolution);
};
const preflightPpiKaksDependencyOwners = async (requestedStages = [], ensureOwner) => {
const outcomes = [];
for (const ownerStageId of requestedStages) {
const result = await ensureOwner(ownerStageId);
const status = result && typeof result === 'object'
? (result.status || 'ready')
: (result ? 'ready' : 'paused');
outcomes.push({ ownerStageId, status });
}
return outcomes;
};
const ensureOrthologProducerForPpiKaks = async () => {
const requestedStages = (batchExecuteStages.value || [])
.map(stage => getStageId(stage))
.filter(stageId => ppiKaksDependencyStages.has(stageId));
for (const ownerStageId of requestedStages) {
if (!await ensurePpiKaksDependencyOwner(ownerStageId)) return false;
}
return true;
return preflightPpiKaksDependencyOwners(requestedStages, async ownerStageId => {
try {
const ready = await ensurePpiKaksDependencyOwner(ownerStageId);
if (!ready) {
const pauseMessage = `${getStageLabel(ownerStageId)} 前置数据检查未通过；已只暂停该阶段，其它阶段继续执行。`;
storePpiKaksReferencePause([ownerStageId], { issue_code: 'owner_preflight_blocked' }, pauseMessage);
addAgentMessage('assistant', `⏸️ ${pauseMessage}`);
return { status: 'paused' };
}
return ppiKaksDependencyPauses()[ownerStageId]
? { status: 'paused' }
: { status: 'ready' };
} catch (err) {
const pauseMessage = `${getStageLabel(ownerStageId)} 前置数据检查异常：${err?.message || err}；已只暂停该阶段，其它阶段继续执行。`;
storePpiKaksReferencePause([ownerStageId], { issue_code: 'owner_preflight_error' }, pauseMessage);
addAgentMessage('assistant', `⏸️ ${pauseMessage}`);
return { status: 'paused' };
}
});
};
const submitExecuteRequestWithAutoAnnotation = async (requestBody, stageId) => {
const currentStageId = stageId || requestBody.stage || '';
if (isPpiKaksTemporarySubmissionBlocked(currentStageId, requestBody)) {
return {
success: false,
paused: true,
status: 'temporarily_unavailable',
message: `${getStageLabel(currentStageId)} 功能修订中，当前暂不可用。`
};
}
const submit = async (body) => {
const response = await fetch('/api/execute', { method: 'POST', headers: { 'Content-Type': 'application/json' }, body: JSON.stringify(body) });
const text = await response.text();
@@ -14526,7 +14663,6 @@ compare: [[flesh, peel]]`;
}
return data || {};
};
const currentStageId = stageId || requestBody.stage || '';
const currentBatchIncludesPpiKaks = (batchExecuteStages.value || []).some(stage => ppiKaksDependencyStages.has(getStageId(stage)));
const currentIsDependencyOwner = ppiKaksDependencyStages.has(currentStageId) || ppiKaksDependencyStages.has(requestBody.stage);
const shouldRunPpiKaksPreflight = currentIsDependencyOwner || (currentStageId === 'ortholog' && currentBatchIncludesPpiKaks);
@@ -14977,10 +15113,10 @@ compare: [[flesh, peel]]`;
await loadInterspeciesSpeciesOptions();
}
normalizeBatchExecutionSpeciesForStages();
const dependencyPreflightOk = await ensureOrthologProducerForPpiKaks();
if (!dependencyPreflightOk) {
addAgentMessage('assistant', '⏸️ 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;
if (ppiKaksTemporaryCircuitBreakerEnabled) {
applyPpiKaksTemporaryCircuitBreaker();
} else {
await ensureOrthologProducerForPpiKaks();
}
isBatchExecuting.value = true;
shouldStopBatchExecute.value = false;
@@ -15360,6 +15496,21 @@ compare: [[flesh, peel]]`;
const stageId = getStageId(stage);
const stageAction = getStageAction(stage);
const stageName = typeof stage === 'object' ? (stage.name || getStageLabel(stageAction)) : getStageLabel(stageAction);
const temporarilyPausedStages = ppiKaksTemporaryPauseStageIds(
batchExecuteStages.value || [],
batchExecuteParams.value || {}
);
if (temporarilyPausedStages.includes(stageId)) {
const pause = ppiKaksDependencyPauses()[stageAction] || {
type: 'temporarily_unavailable',
reason: 'ppi_kaks_under_revision',
message: `${stageName} 功能修订中，本次已自动暂停；其它阶段继续执行。`
};
stageExecutionStatus.value[stageId] = 'paused';
recordStagePause(stageId, pause);
addAgentMessage('assistant', `⏸️ ${pause.message}`);
return;
}
console.log(`[DEBUG-STAGE] executeStageWithConfirmation START: ${stageId}`);
@@ -15493,6 +15644,19 @@ compare: [[flesh, peel]]`;
)) {
return;
}
if (
err.status === 'temporarily_unavailable' &&
(ppiKaksDependencyStages.has(stageAction) || stageAction === 'ortholog')
) {
stageExecutionStatus.value[stageId] = 'paused';
recordStagePause(stageId, {
type: 'temporarily_unavailable',
reason: 'ppi_kaks_under_revision',
message: err.message || `${stageName} 功能修订中`
});
addAgentMessage('assistant', `⏸️ ${err.message || `${stageName} 功能修订中`}`);
return;
}
if (
err.status === 'needs_reference_data' &&
(ppiKaksDependencyStages.has(stageAction) || stageAction === 'ortholog')
@@ -18926,6 +19090,12 @@ compare: [[flesh, peel]]`;
const doExecute = async () => {
console.log('[DEBUG] doExecute called, closing dialog');
if (isPpiKaksTemporarilyUnavailable(confirmParams.stage)) {
clearAutoExecuteTimer();
confirmDialogVisible.value = false;
ElMessage.warning(`${getStageLabel(confirmParams.stage)} 功能修订中，当前暂不可用`);
return;
}
if (gwasPrefixMissingFor(confirmParams)) {
clearAutoExecuteTimer();
ElMessage.warning('请填写 GWAS 物种简称（用于结果前缀）');
@@ -21786,9 +21956,27 @@ compare: [[flesh, peel]]`;
throw createStructuredExecuteError(data);
};
const isPpiKaksBackgroundPause = (stageId, stageParams = {}, err = {}, intentStages = []) => {
const resolution = err.ppiSpeciesResolution || err.responseData?.ppi_species_resolution || null;
const status = String(err.status || resolution?.status || '').trim();
const isPreflightBlock = Boolean(resolution) || [
'needs_reference_data', 'confirmation_required', 'needs_ortholog',
'unresolved', 'ppi_kaks_dependency_resolution_blocked', 'temporarily_unavailable'
].includes(status);
if (!isPreflightBlock) return false;
if (stageId === 'ppi' || stageId === 'kaks') return true;
if (stageId !== 'ortholog' || intentStages.includes('ortholog')) return false;
const dependencyOwner = String(stageParams.dependencyOwner || '').trim();
const autoInsertedFor = Array.isArray(stageParams.autoInsertedFor) ? stageParams.autoInsertedFor : [];
return dependencyOwner === 'ppi'
|| dependencyOwner === 'kaks'
|| autoInsertedFor.some(owner => owner === 'ppi' || owner === 'kaks');
};
const startBackgroundBatchExecution = async (stages, plan, planData = {}) => {
const batchId = `bg_${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;
@@ -21819,6 +22007,18 @@ compare: [[flesh, peel]]`;
let completed = 0;
let failed = 0;
let paused = 0;
const temporarilyPausedStages = ppiKaksTemporaryPauseStageIds(stages, {
...(plan.params || {}),
intentStages
});
temporarilyPausedStages.forEach(stageId => {
if (localStatus[stageId] !== 'paused') {
localStatus[stageId] = 'paused';
paused++;
}
});
while (true) {
const pending = stageIds.filter(stageId => localStatus[stageId] === 'pending');
@@ -21834,6 +22034,21 @@ 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', `⏸️ 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')) {
@@ -21862,15 +22077,21 @@ 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', `⚙️ 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', `✅ 后台阶段 ${stageName} 完成`);
} catch (err) {
if (isPpiKaksBackgroundPause(stageId, stageParams, err, intentStages)) {
localStatus[stageId] = 'paused';
paused++;
addAgentMessage('assistant', `⏸️ 后台阶段 ${stageName} 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 }));
@@ -21878,7 +22099,7 @@ compare: [[flesh, peel]]`;
}));
}
addAgentMessage('assistant', `📦 后台批次完成：成功 ${completed}/${stageIds.length}，失败 ${failed}/${stageIds.length}`);
addAgentMessage('assistant', `📦 后台批次完成：成功 ${completed}/${stageIds.length}，暂停 ${paused}/${stageIds.length}，失败 ${failed}/${stageIds.length}`);
await refreshResults();
};
@@ -22620,6 +22841,7 @@ compare: [[flesh, peel]]`;
...plan.params,
stages: activeExecutionStages,
plan: { ...plan, stages: activeExecutionStages.map(stage => getStageId(stage)).filter(Boolean) },
intentStages: Array.isArray(planData.intent?.stages) ? planData.intent.stages : [],
source: isMethodologySubfamilyPlan ? 'methodology' : (plan.params || {}).source,
methodologyPhase: isMethodologySubfamilyPlan ? 'methodology_dag' : (plan.methodology_phase || planData.methodology_phase || (plan.params || {}).methodologyPhase),
completed_stages: planData.completed_stages || []
apps/web/vue3/static/logo.png
BIN
View File
Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 75 KiB