fix: integrate deployed reports with PPI KaKs handoff

apps/web/pipeline_backend.py

@@ -3412,6 +3412,7 @@ RNA_SEQ_STAGES = {
     "rnaseq_wgcna",
     "rnaseq_candidate_family",
     "rnaseq_family_score",
+    "rnaseq_report",
 }
 
 
@@ -8441,7 +8442,32 @@ def run_stage(
             expected_stages = [str(value).strip() for value in expected_stages if str(value).strip()]
         report_action = str(kwargs.get("report_action") or kwargs.get("reportAction") or "generate").strip()
         if report_action == "generate" and not expected_stages:
-            return "❌ 基因家族结果报告生成需要非空 expected_stages", manifest
+            report_stage_order = (
+                "identify", "phylogeny", "reference_classification", "motif",
+                "domain", "structure", "combo", "promoter", "tfbs",
+                "synteny", "karyotype", "interspecies_synteny", "pep",
+            )
+            recovered_stages = set()
+            for candidate in final_dir.glob("*.manifest.json"):
+                try:
+                    payload = json.loads(candidate.read_text(encoding="utf-8"))
+                except (OSError, json.JSONDecodeError):
+                    continue
+                candidate_stage = str(payload.get("stage") or "").strip()
+                candidate_prefix = str(
+                    payload.get("prefix")
+                    or (payload.get("parameters") or {}).get("prefix")
+                    or ""
+                ).strip()
+                if (
+                    candidate_stage in report_stage_order
+                    and str(payload.get("status") or "") == "success"
+                    and candidate_prefix == prefix
+                ):
+                    recovered_stages.add(candidate_stage)
+            expected_stages = [stage_id for stage_id in report_stage_order if stage_id in recovered_stages]
+        if report_action == "generate" and not expected_stages:
+            return "❌ 基因家族结果报告生成需要非空 expected_stages，且当前前缀没有可恢复的成功 manifest", manifest
         stage_statuses = kwargs.get("stage_statuses") or kwargs.get("stageStatuses") or {}
         if isinstance(stage_statuses, str):
             try:
@@ -8450,6 +8476,8 @@ def run_stage(
                 return "❌ 基因家族结果报告的 stage_statuses 不是合法 JSON", manifest
         if not isinstance(stage_statuses, dict):
             return "❌ 基因家族结果报告的 stage_statuses 必须是对象", manifest
+        if not stage_statuses:
+            stage_statuses = {stage_id: "success" for stage_id in expected_stages}
         report_use_model_raw = kwargs.get("report_use_model", kwargs.get("reportUseModel", True))
         rnaseq_scope_id = str(kwargs.get("rnaseq_scope_id") or kwargs.get("rnaseqScopeId") or "").strip()
         cmd = [
@@ -11465,6 +11493,42 @@ def run_stage(
             return "✅ RNA-seq WGCNA completed.", wgcna_manifest
         return f"❌ RNA-seq WGCNA failed (exit code: {code}). Log: {log_file}", wgcna_manifest if wgcna_manifest.exists() else manifest
 
+    if stage == "rnaseq_report":
+        report_action = str(kwargs.get("rnaseq_report_action") or kwargs.get("report_action") or "generate").strip().lower()
+        if report_action not in {"generate", "open"}:
+            report_action = "generate"
+        expected_raw = kwargs.get("rnaseq_expected_stages") or kwargs.get("expected_stages") or ""
+        if isinstance(expected_raw, (list, tuple, set)):
+            expected_arg = ",".join(str(item).strip() for item in expected_raw if str(item).strip())
+        else:
+            expected_arg = str(expected_raw or "").strip()
+        report_scope_id = str(kwargs.get("rnaseq_scope_id") or kwargs.get("rnaseqScopeId") or "").strip()
+        report_use_model = kwargs.get("rnaseq_report_use_model", kwargs.get("report_use_model", True))
+        report_cmd = [
+            sys.executable,
+            "apps/cli/run_rnaseq_report.py",
+            "--workspace", str(ws),
+            "--prefix", prefix,
+            "--job-id", job.job_id,
+            "--action", report_action,
+            "--log-file", str(log_file),
+        ]
+        if report_scope_id:
+            report_cmd.extend(["--rnaseq-scope-id", report_scope_id])
+        if expected_arg:
+            report_cmd.extend(["--expected-stages", expected_arg])
+        if not _truthy(report_use_model):
+            report_cmd.append("--no-model")
+        print(f"[CMD] {' '.join(report_cmd)}")
+        code = run_cmd_logged(report_cmd, log_file, cwd=Path("."))
+        report_manifest = final_dir / f"{prefix}.rnaseq_report.manifest.json"
+        if code == 0 and report_manifest.exists():
+            action_label = "打开" if report_action == "open" else "生成"
+            return f"✅ RNA-seq 结果报告已{action_label}。日志：{log_file}", report_manifest
+        if code == 2:
+            return "⚠️ 暂无可生成的 RNA-seq 结果：当前 prefix/scope 下没有成功阶段。", None
+        return f"❌ RNA-seq 结果报告生成失败（exit code: {code}）。日志：{log_file}", report_manifest if report_manifest.exists() else None
+
     if stage == "rnaseq_candidate_family":
         _SPECIES_RESOURCE_ALIASES = {
             "os": ["Os", "Oryza", "Oryza_sativa", "rice"],

apps/web/vue3/main.py

@@ -4746,7 +4746,7 @@ def _celery_start_script_for_current_profile() -> Path:
     port = os.environ.get("PLANTAI_WEB_PORT", "").strip()
     if prefix.endswith("_9000") or redis_url.endswith("/10") or port == "9000":
         return PROJECT_ROOT / "start_celery_9000.sh"
-    return PROJECT_ROOT / "start_celery_7880.sh"
+    return PROJECT_ROOT / "scripts" / "legacy_startup" / "start_celery_7880.sh"
 
 
 def _current_celery_profile() -> Dict[str, Any]:
@@ -4756,7 +4756,11 @@ def _current_celery_profile() -> Dict[str, Any]:
         prefix = get_queue_prefix()
     except Exception:
         prefix = os.environ.get("BBAV5_QUEUE_PREFIX", "plantai_dev_7880").strip() or "plantai_dev_7880"
-    redis_default = "redis://localhost:6379/10" if prefix.endswith("_9000") or os.environ.get("PLANTAI_WEB_PORT", "").strip() == "9000" else "redis://localhost:6379/9"
+    current_port = os.environ.get("PLANTAI_WEB_PORT", "").strip()
+    if prefix.endswith("_9000") or current_port == "9000":
+        redis_default = "redis://localhost:6379/10"
+    else:
+        redis_default = "redis://localhost:6379/9"
     redis_url = os.environ.get("BBAV5_REDIS_URL", redis_default).strip() or redis_default
     script = _celery_start_script_for_current_profile()
     log_dir = Path(os.environ.get("BBAV5_CELERY_LOG_DIR", "") or f"logs/celery_{prefix}")
@@ -8647,7 +8651,7 @@ def run_stage_sync(task_id: str, stage: str, job_id: str, params: dict):
 async def root():
     """返回Vue3前端页面"""
     return FileResponse(
-        Path(__file__).parent / "index.html",
+        Path(__file__).parent / "index_ml.html",
         headers={
             "Cache-Control": "no-cache, no-store, must-revalidate",
             "Pragma": "no-cache",
@@ -17217,7 +17221,78 @@ def _gene_family_report_plan_context(job_id: str, prefix: str = "") -> Optional[
             "rnaseqScopeId": "",
         }
         reports.append((path.stat().st_mtime, context))
-    return max(reports, key=lambda item: item[0])[1] if reports else None
+    if reports:
+        return max(reports, key=lambda item: item[0])[1]
+
+    # Older jobs may have complete, successful stage manifests but no saved
+    # confirmation-plan snapshot. Reconstruct a deterministic report plan from
+    # one manifest prefix rather than rejecting those verifiable results.
+    report_stage_order = (
+        "identify",
+        "phylogeny",
+        "reference_classification",
+        "motif",
+        "domain",
+        "structure",
+        "combo",
+        "promoter",
+        "tfbs",
+        "synteny",
+        "karyotype",
+        "interspecies_synteny",
+        "pep",
+    )
+    report_stage_set = set(report_stage_order)
+    recovered_by_prefix: Dict[str, Dict[str, tuple[float, Dict[str, Any]]]] = {}
+    for path in final_dir.glob("*.manifest.json") if final_dir.is_dir() else ():
+        try:
+            manifest = json.loads(path.read_text(encoding="utf-8"))
+        except (OSError, json.JSONDecodeError):
+            continue
+        stage = str(manifest.get("stage") or "").strip()
+        manifest_prefix = str(
+            manifest.get("prefix")
+            or (manifest.get("parameters") or {}).get("prefix")
+            or ""
+        ).strip()
+        if (
+            stage not in report_stage_set
+            or str(manifest.get("status") or "") != "success"
+            or not manifest_prefix
+            or (requested_prefix and manifest_prefix != requested_prefix)
+        ):
+            continue
+        stage_map = recovered_by_prefix.setdefault(manifest_prefix, {})
+        candidate = (path.stat().st_mtime, manifest)
+        if stage not in stage_map or candidate[0] > stage_map[stage][0]:
+            stage_map[stage] = candidate
+
+    if not recovered_by_prefix:
+        return None
+
+    def recovered_rank(item: tuple[str, Dict[str, tuple[float, Dict[str, Any]]]]) -> tuple[int, int, float, str]:
+        manifest_prefix, stage_map = item
+        latest_mtime = max((entry[0] for entry in stage_map.values()), default=0.0)
+        return (
+            1 if "identify" in stage_map else 0,
+            len(stage_map),
+            latest_mtime,
+            manifest_prefix,
+        )
+
+    recovered_prefix, recovered_stages = max(recovered_by_prefix.items(), key=recovered_rank)
+    planned = [stage for stage in report_stage_order if stage in recovered_stages]
+    if not planned:
+        return None
+    return {
+        "prefix": recovered_prefix,
+        "expectedStages": planned,
+        "stageStatuses": {stage: "success" for stage in planned},
+        "scopeId": "",
+        "analysisRoute": "",
+        "memberSetId": "",
+        "rnaseqScopeId": "",
+    }
 
 
 async def _run_agent_chat(
@@ -25417,7 +25492,7 @@ async def root():
     """
     返回前端首页
     """
-    index_file = WEB_DIR / "index.html"
+    index_file = WEB_DIR / "index_ml.html"
     if index_file.exists():
         return FileResponse(
             str(index_file),