diff --git a/.gitignore b/.gitignore index 78279f7..9bab96c 100644 --- a/.gitignore +++ b/.gitignore @@ -46,4 +46,4 @@ paper_writer_service/paper.log # 部署方案文档（含主机凭据，不入库） docs/DEPLOY_PAPER_176.md # Python 覆盖率运行时产物(coverage.py --cov 生成) -.coverage \ No newline at end of file +.coveragevstore/vstore.log diff --git a/agent/qa/src/rag/qa_v1_1_73/bioflow_agent.py b/agent/qa/src/rag/qa_v1_1_73/bioflow_agent.py index 68ec3ec..b98786d 100644 --- a/agent/qa/src/rag/qa_v1_1_73/bioflow_agent.py +++ b/agent/qa/src/rag/qa_v1_1_73/bioflow_agent.py @@ -48,6 +48,9 @@ _CHAIN_TO_CAPABILITY = { "rnaseq": "bioflow-rnaseq", } +# 能力名 → chain 名（反向映射，供规划阶段从命中能力回填 chain，续接多轮对话） +_CAPABILITY_TO_CHAIN = {v: k for k, v in _CHAIN_TO_CAPABILITY.items()} + def _chain_to_capability(chain: str) -> Optional[str]: """把 chain 名（gene_family/rnaseq）映射为能力名；未知返回 None。""" @@ -323,6 +326,7 @@ def _make_payload( chain: Optional[str] = None, readiness: Optional[Dict[str, Any]] = None, versioning: Optional[Dict[str, Any]] = None, + plan: Optional[Dict[str, Any]] = None, ) -> Dict[str, Any]: payload: Dict[str, Any] = { "success": True, @@ -346,6 +350,8 @@ def _make_payload( payload["bioflow"]["readiness"] = readiness if versioning: payload["bioflow"]["versioning"] = versioning + if plan: + payload["bioflow"]["plan"] = plan return payload @@ -637,16 +643,24 @@ def _try_bioflow_agent_impl( if isinstance(card_result, dict) and str(card_result.get("card") or "").strip() in CARD_TYPES: return _route_card_result(card_result, llm_client, capabilities, bioflow, progress_callback) - # NL 路径：活跃任务续接优先（有活跃任务时跳过意图预筛，直接按任务 chain 续接） + # NL 路径：活跃任务/生信链续接优先，其次意图预筛 active_job_id = (bioflow or {}).get("active_job_id") + chain = str((bioflow or {}).get("chain") or "").strip() if active_job_id: + # 有活跃任务：跳过意图预筛，按任务 chain 续接（任务链不可变） manifests = _registered_capabilities(capabilities) - cap_name = _chain_to_capability((bioflow or {}).get("chain") or "") + cap_name = _chain_to_capability(chain) if cap_name: manifests = [m for m in manifests if m.name == cap_name] else: - # 无活跃任务：门 2 + 门 3 意图预筛（新任务入口） + # 无活跃任务：先门 2 + 门 3 意图预筛（新任务入口） manifests = _candidate_capabilities(question, capabilities) + # 意图未命中但 session 留有生信链（上轮规划）→ 续接该链（如路径选择「1」） + if not manifests and chain: + cap_name = _chain_to_capability(chain) + if cap_name: + registered = _registered_capabilities(capabilities) + manifests = [m for m in registered if m.name == cap_name] if not manifests: return None @@ -678,24 +692,40 @@ def _try_bioflow_agent_impl( tool_results = (audit or {}).get("tool_results") or {} readiness = None versioning = None + new_job_id = None + plan = None for name, result_text in tool_results.items(): + if name in ("create_gene_family_job", "create_rnaseq_job"): + jid = _extract_job_id(result_text) + if jid: + new_job_id = jid data = _try_parse_json(result_text) if not isinstance(data, dict): continue + if name.startswith("plan_") and data.get("ok"): + plan = { + "candidates": data.get("candidates") or [], + "auto_filled": data.get("auto_filled") or [], + "reuse_archive": data.get("reuse_archive"), + "reuse_name": data.get("reuse_name"), + "fallback": data.get("fallback"), + } if name == "check_readiness": readiness = _map_readiness(data) elif name == "propose_change": versioning = _map_versioning(data) + effective_chain = chain or (_CAPABILITY_TO_CHAIN.get(manifests[0].name) if manifests else "") return _make_payload( question, answer, audit=audit, capabilities=[m.name for m in manifests], - active_job_id=(bioflow or {}).get("active_job_id"), - chain=(bioflow or {}).get("chain"), + active_job_id=(bioflow or {}).get("active_job_id") or new_job_id, + chain=effective_chain or None, readiness=readiness, versioning=versioning, + plan=plan, ) diff --git a/agent/qa/src/rag/qa_v1_1_73/tool_runner.py b/agent/qa/src/rag/qa_v1_1_73/tool_runner.py index 260d448..49b1520 100644 --- a/agent/qa/src/rag/qa_v1_1_73/tool_runner.py +++ b/agent/qa/src/rag/qa_v1_1_73/tool_runner.py @@ -96,6 +96,7 @@ class ToolRunner: break assistant_message: Dict[str, Any] = {"role": "assistant", "content": content or ""} tool_call_blocks: List[Dict[str, Any]] = [] + messages.append(assistant_message) for call in tool_calls: name = str(call.get("name") or call.get("function", {}).get("name") or "") raw_args = call.get("arguments") or call.get("function", {}).get("arguments") or {} @@ -129,7 +130,6 @@ class ToolRunner: audit["tool_results"][name] = result_text messages.append({"role": "tool", "tool_call_id": call_id, "content": result_text}) assistant_message["tool_calls"] = tool_call_blocks - messages.append(assistant_message) continue # 最后一轮：拿最终文本（无工具或轮次用尽后由调用方用 messages 再 complete 一次） return self._final_text(system_text, messages, tools), audit diff --git a/sdk/app/services/history.py b/sdk/app/services/history.py index 9c07b58..376b9d2 100644 --- a/sdk/app/services/history.py +++ b/sdk/app/services/history.py @@ -7,9 +7,26 @@ assemble_history(db, session_id, rounds=3, budget): """ from __future__ import annotations +import html as html_mod +import re from typing import Any, List from ..config import get_settings +from ..db import loads_json + + +def _blocks_text(blocks_json) -> str: + """从落库 blocks 提取 assistant 答案纯文本（text 块 html 去标签）。""" + blocks = loads_json(blocks_json, default=[]) + parts = [] + for b in blocks: + if not isinstance(b, dict) or b.get("type") != "text": + continue + h = b.get("html") or b.get("text") or "" + t = html_mod.unescape(re.sub(r"<[^>]+>", "", str(h))).strip() + if t: + parts.append(t) + return "\n".join(parts) async def assemble_history( @@ -40,7 +57,7 @@ async def assemble_history( return [] try: rows = await db.fetchall( - "SELECT role, status, text FROM messages " + "SELECT role, status, text, blocks FROM messages " "WHERE session_id = ? AND role IN ('user','assistant') " "AND status != 'streaming' " "ORDER BY created_at ASC, rowid ASC", @@ -55,6 +72,8 @@ async def assemble_history( for row in reversed(rows): role = row["role"] text = (row["text"] or "").strip() + if not text and role == "assistant": + text = _blocks_text(row["blocks"]) if not text: continue if role == "assistant": diff --git a/ui/src/components/chat/FlowFileCard.vue b/ui/src/components/chat/FlowFileCard.vue index 0064625..1e8ba9a 100644 --- a/ui/src/components/chat/FlowFileCard.vue +++ b/ui/src/components/chat/FlowFileCard.vue @@ -66,6 +66,7 @@ function handleFiles(fileList) { chat.uploadBioflowFileToJob(jobId.value, file, { onProgress: (pct) => { const rec = props.block.files.find((x) => x.name === file.name && x.status === 'uploading'); + console.log('[bioflow-upload] onProgress pct=', pct, 'recFound=', !!rec, 'files=', (props.block.files || []).length); if (rec) rec.progress = pct; }, }) diff --git a/ui/src/components/chat/FlowPathCard.vue b/ui/src/components/chat/FlowPathCard.vue index 1f1ed49..45cc41e 100644 --- a/ui/src/components/chat/FlowPathCard.vue +++ b/ui/src/components/chat/FlowPathCard.vue @@ -61,6 +61,7 @@ function backToSelect() { /** 复用名 → 表单默认值来源标注（与后端 params 预填配合；来源标注在表单卡展示） */ async function confirmCreate() { const cand = selectedCandidate.value; + console.log('[bioflow-card] confirmCreate selected=', selected.value, 'cand=', !!cand, 'jobId=', props.block.jobId); if (!cand || confirming.value) return; if (props.block.jobId) return; // 已创建过（防重复创建；FR-BIO 任务幂等语义） confirming.value = true; diff --git a/ui/src/stores/chat.js b/ui/src/stores/chat.js index c261dc5..ca0bdcf 100644 --- a/ui/src/stores/chat.js +++ b/ui/src/stores/chat.js @@ -19,6 +19,7 @@ import { useSessionsStore } from './sessions.js'; import { PHASE_LABEL, PHASE_DESC, T } from '../i18n/labels.js'; import { MODES } from '../config/modes.js'; import { renderMarkdown } from '../components/chat/markdown.js'; +console.log('[bioflow-version] chat.js raw.bioflow-fix v2 loaded'); // ---- P3 文档生成：独立分支（send/_runStream 零改动） ---- import { DOCGEN_STEPS, CAP_BADGES, DG as DG_LABELS } from '../i18n/docgen.js'; @@ -2316,18 +2317,41 @@ export const useChatStore = defineStore('chat', { try { const data = await uploadBioflowFile(jobId, form, { onUploadProgress: (e) => { - item.progress = e.pct; + console.log('[bioflow-upload] onUploadProgress pct=', e.pct, 'loaded=', e.loaded, 'total=', e.total); + // item 是原始对象，直接改会绕过 Vue 响应式——经响应式数组找代理更新 + const rec = found && Array.isArray(found.blk.files) + ? found.blk.files.find((x) => x.name === item.name && x.status === 'uploading') + : null; + if (rec) rec.progress = e.pct; + else item.progress = e.pct; if (typeof onProgress === 'function') onProgress(e.pct, item); }, }); - item.status = 'done'; - item.progress = 1; - item.fileId = (data && data.data && data.data.file_id) || null; + const doneRec = found && Array.isArray(found.blk.files) + ? found.blk.files.find((x) => x.name === item.name) + : null; + if (doneRec) { + doneRec.status = 'done'; + doneRec.progress = 1; + doneRec.fileId = (data && data.data && data.data.file_id) || null; + } else { + item.status = 'done'; + item.progress = 1; + item.fileId = (data && data.data && data.data.file_id) || null; + } if (found) this.scrollSeq++; return (data && data.data) || data || {}; } catch (err) { - item.status = 'error'; - item.error = err?.message || BF.fileUploadError; + const errRec = found && Array.isArray(found.blk.files) + ? found.blk.files.find((x) => x.name === item.name) + : null; + if (errRec) { + errRec.status = 'error'; + errRec.error = err?.message || BF.fileUploadError; + } else { + item.status = 'error'; + item.error = err?.message || BF.fileUploadError; + } if (found) this.scrollSeq++; throw err; } @@ -2458,6 +2482,7 @@ export const useChatStore = defineStore('chat', { * 经 BioflowAgent 工具执行 + 自然语言复述；卡片与自然语言两条通道语义一致。 * card ∈ path_selection|form_confirm|file_upload|archive_choice|extension_action。 */ async sendCardResult(card, payload, { text = '', userMsg = null } = {}) { + console.log('[bioflow-card] sendCardResult', card, 'busy=', this.busy); if (this.busy) return; const sessions = useSessionsStore(); if (!this.sessionId) { @@ -2550,10 +2575,12 @@ export const useChatStore = defineStore('chat', { const p = ev.payload || {}; const answer = p.answer || ''; updateLocal(() => { - const blocks = [ - { type: 'bioflow_path', status: 'done', candidates: [] }, - { type: 'text', html: answer }, - ]; + const blocks = []; + // 仅路径选择卡回填 path 块（候选由上一轮路径卡承载）；其余卡操作只出自然语言复述 + if (card === 'path_selection') { + blocks.push({ type: 'bioflow_path', status: 'done', candidates: [] }); + } + blocks.push({ type: 'text', html: answer }); const bfPayload = p.bioflow || {}; if (bfPayload.readiness) { blocks.push({ type: 'bioflow_readiness', ...bfPayload.readiness, error: null }); @@ -2689,7 +2716,12 @@ export const useChatStore = defineStore('chat', { // S2：bioflow 帧（生信对话编排）不推 pipeline 相位——生信消息走 // bioflow 块，由 sendCardResult / bioflow 分支消费，此处仅记录。 const isBioflow = typeof p.stage === 'string' && p.stage.startsWith('bioflow_'); - if (isBioflow) return; + if (isBioflow) { + // 生信消息：一旦收到 bioflow 帧，立即移除检索 pipeline 骨架（避免闪烁残留） + const pi = (aMsg.blocks || []).findIndex((b) => b && b.type === 'pipeline'); + if (pi >= 0) aMsg.blocks.splice(pi, 1); + return; + } if (!ctx.completedOnce && phase !== 'done') this._advancePipeline(aMsg, phase, label); if (phase === 'done') { // 上游 completed 事件：当前相位定格 done（此时 complete 尚未到达） @@ -2728,18 +2760,68 @@ export const useChatStore = defineStore('chat', { // complete 帧之后流即关闭：同步收口，避免「流自然结束」误判为连接中断 endTask(); const payload = ev.payload || {}; + // S2 多轮续接：生信规划返回的 chain/active_job_id 写回 session， + // 下轮（如路径选择「1」）据此跳过意图预筛续接生信 agent。 + const bf = payload.bioflow || (payload.raw && payload.raw.bioflow) || {}; + if (bf.chain || bf.active_job_id) { + updateSessionQuiet(sessionId, { + meta: { bioflow: { active_job_id: bf.active_job_id || "", chain: bf.chain || "" } }, + }).catch(() => {}); + // 任务事件订阅：自然语言路径建任务后补 connectJobEvents， + // 把 stage_await_files / stage_await_confirm / stage_failed / job_done + // 桥接进消息块（文件卡/表单卡/诊断卡/交付卡），与卡片路径一致。 + if (bf.active_job_id) { + try { + const bioflow = useBioflowStore(); + const jobId = bf.active_job_id; + bioflow.connectJobEvents(jobId, sessionId, { + onEvent: (type, data, seq) => { + const frame = patchBioflowEvent(aMsg, { type, data }); + if (frame) this.scrollSeq++; + if (type === 'stage_await_confirm' && data) { + patchBioflowGuidance(aMsg, data.guidance); + patchBioflowForm(aMsg, data); + this.scrollSeq++; + } else if (type === 'stage_await_files' && data) { + patchBioflowGuidance(aMsg, data.guidance || data.message); + patchBioflowFile(aMsg, data); + this.scrollSeq++; + } else if (type === 'stage_failed' && data) { + patchBioflowGuidance(aMsg, data.guidance); + patchBioflowDiagnosis(aMsg, data); + this.scrollSeq++; + } else if (type === 'job_done' && data) { + patchBioflowGuidance(aMsg, data.guidance); + if (data.delivery) patchBioflowDelivery(aMsg, data.delivery); + const blk = patchBioflowArchiveSuggest(aMsg, data.job_id || jobId); + if (blk) blk.jobId = data.job_id || jobId; + this.scrollSeq++; + } + }, + }); + } catch { /* EventSource 不可用：任务事件仍由快照兜底 */ } + } + } const blocks = qaToBlocks(payload); + const isBioflow = !!(bf && bf.handled); updateLocal(() => { // text 块先不放：由揭示动画以 stream 块渐进显示，终了替换为最终 text - aMsg.blocks = [ - aMsg.blocks[0], - ...blocks.filter((b) => b.type !== 'text'), - ]; + // 生信消息不显示检索 pipeline 骨架——直接挂生信卡片 + 自然语言。 + aMsg.blocks = isBioflow + ? [...blocks.filter((b) => b.type !== 'text')] + : [aMsg.blocks[0], ...blocks.filter((b) => b.type !== 'text')]; + // 生信卡片：路径卡/就绪卡/版本卡（与自然语言 answer 同时出现） + if (bf.plan) patchBioflowPlan(aMsg, bf.plan); + if (bf.readiness) patchBioflowReadiness(aMsg, bf.readiness); + if (bf.versioning) patchBioflowVersioning(aMsg, bf.versioning); aMsg.raw = payload.raw ?? payload; - const pipe = aMsg.blocks[0]; - pipe.status = 'done'; - pipe.steps.forEach((s) => { s.state = 'done'; }); + if (!isBioflow) { + const pipe = aMsg.blocks[0]; + pipe.status = 'done'; + pipe.steps.forEach((s) => { s.state = 'done'; }); + } }); + console.log('[bioflow-debug] onComplete blocks=', (aMsg.blocks || []).map((b) => b && b.type), 'bf.handled=', !!(bf && bf.handled), 'bf.plan=', !!(bf && bf.plan)); ctx.completedOnce = true; // 揭示动画（FR-CHAT-010）：stream 块瞬态、不落库 if (payload.answer) { @@ -2747,6 +2829,7 @@ export const useChatStore = defineStore('chat', { } else { updateLocal(() => { aMsg.status = 'done'; }); } + console.log('[bioflow-debug] after reveal blocks=', (aMsg.blocks || []).map((b) => b && b.type)); const dur = ((Date.now() - startAt) / 1000).toFixed(1) + 's'; // FR-PRIV-005：onComplete 整体替换 blocks 后 flush 私有 pending（防丢块） this._flushPrivate(aMsg);