feat:sync-report-workflows-and-migration-runtime

2026-08-10 11:40:20 +08:00
parent 1c2cfc5b6e
commit b725a9c125
27 changed files with 882 additions and 344 deletions
@@ -0,0 +1,66 @@
+#!/usr/bin/env python3
+"""Generate or open a formal RNA-seq evidence report."""
+from __future__ import annotations
+
+import argparse
+import sys
+from pathlib import Path
+
+
+PROJECT_ROOT = Path(__file__).absolute().parents[2]
+if str(PROJECT_ROOT) not in sys.path:
+    sys.path.insert(0, str(PROJECT_ROOT))
+
+from gfa_core.rnaseq_report import NoSuccessfulRNASeqEvidence, generate_rnaseq_report
+
+
+def _csv(value: str) -> list[str] | None:
+    values = [item.strip() for item in str(value or "").split(",") if item.strip()]
+    return values or None
+
+
+def main() -> int:
+    parser = argparse.ArgumentParser(
+        description="Generate a deterministic formal RNA-seq result report from successful manifests."
+    )
+    parser.add_argument("--workspace", required=True, help="RNA-seq job workspace containing final/")
+    parser.add_argument("--prefix", required=True, help="RNA-seq output prefix")
+    parser.add_argument("--job-id", default="")
+    parser.add_argument("--rnaseq-scope-id", default="")
+    parser.add_argument(
+        "--expected-stages",
+        default="",
+        help="Comma-separated stages selected for the current RNA-seq batch",
+    )
+    parser.add_argument("--action", choices=("generate", "open"), default="generate")
+    parser.add_argument("--no-model", action="store_true", help="Disable optional LLM language enhancement")
+    parser.add_argument("--log-file", default="", help="Accepted for pipeline runner compatibility")
+    args = parser.parse_args()
+
+    try:
+        result = generate_rnaseq_report(
+            Path(args.workspace),
+            args.prefix,
+            rnaseq_scope_id=args.rnaseq_scope_id,
+            expected_stages=_csv(args.expected_stages),
+            use_model=not args.no_model,
+            action=args.action,
+            job_id=args.job_id,
+        )
+    except NoSuccessfulRNASeqEvidence as exc:
+        print(str(exc), file=sys.stderr)
+        return 2
+    except Exception as exc:
+        print(f"RNA-seq 结果报告生成失败：{type(exc).__name__}: {exc}", file=sys.stderr)
+        return 1
+
+    reuse = "（复用最新报告）" if result.reused else ""
+    print(
+        f"RNA-seq 结果报告已就绪{reuse}: {result.report_path} "
+        f"[coverage={result.coverage_status}, stages={','.join(result.included_stages)}]"
+    )
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())
@@ -3355,6 +3355,7 @@ RNA_SEQ_STAGES = {
    "rnaseq_wgcna",
    "rnaseq_candidate_family",
    "rnaseq_family_score",
+    "rnaseq_report",
 }


@@ -8383,7 +8384,32 @@ 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:
@@ -8392,6 +8418,8 @@ 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 = [
@@ -11407,6 +11435,42 @@ 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"],
@@ -1243,9 +1243,12 @@
        <el-config-provider :locale="elLocale">
        <!-- Header -->
        <div class="header" style="display:flex; align-items:center; justify-content:space-between;">
-            <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?v=20260809" alt="OMaaX" 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>
            <el-select v-model="currentLang" @change="switchLang" size="small" style="width:110px;margin-right:20px;">
                <el-option :label="t('中文')" value="zh"></el-option>
@@ -1282,6 +1285,7 @@
                        <el-option label="KaKs - KaKs Analysis" value="kaks"></el-option>
                        <el-option label="Expression (使用FPKM) - Differential Expression" value="expression"></el-option>
                        <el-option label="Combo - Combined Plot(Tree+Motif+Structure+Domain)" value="combo"></el-option>
+                        <el-option label="Gene Family Result Report - 基因家族结果报告" value="gene_family_report"></el-option>
                        <el-option label="Run All - Complete Pipeline" value="all"></el-option>
                        <el-option label="GWAS Format - TASSEL VCF → HapMap" value="gwas_fmt"></el-option>
                        <!-- RNA-seq拆分选项 -->
@@ -1297,6 +1301,7 @@
                        <el-option label="RNA-Seq fgsea - 排序富集分析" value="rnaseq_fgsea"></el-option>
                        <el-option label="RNA-Seq WGCNA - 加权共表达分析" value="rnaseq_wgcna"></el-option>
                        <el-option label="RNA-Seq Candidate Family - 候选家族筛选" value="rnaseq_candidate_family"></el-option>
+                        <el-option label="RNA-Seq Result Report - 结果报告" value="rnaseq_report"></el-option>
                    </el-select>

                    <el-button
@@ -1787,7 +1792,7 @@
                    </div>
                    <!-- lightWeightExtensionTest:start -->
                    <div id="lightweight-extension-test-drop-zone"
-                        style="display:none;margin-top:8px;border:1px dashed #409EFF;padding:10px;font-size:12px;color:#606266;background:#f8fbff;"
+                        style="display:block;margin-top:8px;border:1px dashed #409EFF;padding:10px;font-size:12px;color:#606266;background:#f8fbff;"
                         @dragover.prevent
                         @drop.prevent="handleLightweightExtensionFolderDrop($event)">
                        <div style="font-weight:600;color:#303133;">拖入固定结构拓展包</div>
@@ -8778,6 +8783,7 @@ RNA-seq KEGG/fgsea 会优先使用物种级 KEGG gene set；没有物种级缓
                    { stage: 'tfbs', label: 'tfbs', group: 'gene_family', default_cpu: 4, max_cpu: 4 },
                    { stage: 'ortholog', label: 'ortholog', group: 'gene_family', default_cpu: 4, max_cpu: 4 },
                    { stage: 'kaks', label: 'kaks', group: 'gene_family', default_cpu: 4, max_cpu: 4 },
+                    { stage: 'gene_family_report', label: 'report', group: 'gene_family', default_cpu: 4, max_cpu: 4 },
                    { stage: 'rnaseq_qc', label: 'qc', group: 'rnaseq', default_cpu: 8, max_cpu: 20 },
                    { stage: 'rnaseq_align', label: 'align', group: 'rnaseq', default_cpu: 8, max_cpu: 20 },
                    { stage: 'rnaseq_quant', label: 'quant', group: 'rnaseq', default_cpu: 6, max_cpu: 8 },
@@ -8785,7 +8791,8 @@ RNA-seq KEGG/fgsea 会优先使用物种级 KEGG gene set；没有物种级缓
                    { stage: 'rnaseq_enrich', label: 'enrich', group: 'rnaseq', default_cpu: 4, max_cpu: 4 },
                    { stage: 'rnaseq_go_enrich', label: 'go enrich', group: 'rnaseq', default_cpu: 4, max_cpu: 4 },
                    { stage: 'rnaseq_kegg_enrich', label: 'kegg enrich', group: 'rnaseq', default_cpu: 4, max_cpu: 4 },
-                    { stage: 'rnaseq_candidate_family', label: 'candidate', group: 'rnaseq', default_cpu: 4, max_cpu: 4 }
+                    { stage: 'rnaseq_candidate_family', label: 'candidate', group: 'rnaseq', default_cpu: 4, max_cpu: 4 },
+                    { stage: 'rnaseq_report', label: 'report', group: 'rnaseq', default_cpu: 4, max_cpu: 4 }
                ]);
                let runtimeMonitorTimer = null;
                let resourceMonitorTimer = null;
@@ -9076,6 +9083,22 @@ RNA-seq KEGG/fgsea 会优先使用物种级 KEGG gene set；没有物种级缓
 	                        requestBody.candidateMaxDegProteins = numberParam(firstDefinedParam(src.candidateMaxDegProteins, src.max_deg_proteins, src.maxDegProteins, confirmParams.candidateMaxDegProteins), 500);
 	                        requestBody.candidateRunInterproscan = firstDefinedParam(src.candidateRunInterproscan, src.run_interproscan, src.runInterproscan, confirmParams.candidateRunInterproscan) || 'auto';
 	                    }
+	                    if (stageName === 'gene_family_report') {
+	                        requestBody.expectedStages = src.expectedStages || [];
+	                        requestBody.stageStatuses = src.stageStatuses || {};
+	                        requestBody.reportAction = src.reportAction || 'generate';
+	                        requestBody.reportUseModel = src.reportUseModel !== false;
+	                        requestBody.scopeId = src.scopeId || '';
+	                        requestBody.analysisRoute = src.analysisRoute || '';
+	                        requestBody.memberSetId = src.memberSetId || '';
+	                        requestBody.rnaseqScopeId = src.rnaseqScopeId || '';
+	                    }
+	                    if (stageName === 'rnaseq_report') {
+	                        requestBody.rnaseqScopeId = firstDefinedParam(src.rnaseqScopeId, src.rnaseq_scope_id, activeRnaseqScopeId.value) || '';
+	                        requestBody.rnaseqExpectedStages = rnaseqListParam(firstDefinedParam(src.rnaseqExpectedStages, src.expected_stages), []);
+	                        requestBody.rnaseqReportAction = firstDefinedParam(src.rnaseqReportAction, src.report_action) || 'generate';
+	                        requestBody.rnaseqReportUseModel = booleanParam(firstDefinedParam(src.rnaseqReportUseModel, src.report_use_model), true);
+	                    }
 	                    return requestBody;
 	                };
                const isRnaseqQueue = (name) => {
@@ -9832,7 +9855,9 @@ compare: [[flesh, peel]]`;
                    // batch it may be the stage that generates gene2ko, so wait
                    // for it to avoid submitting fgsea before the background exists.
                    'rnaseq_fgsea': ['rnaseq_de', 'rnaseq_kegg_enrich'],
-                    'rnaseq_candidate_family': ['rnaseq_de', 'rnaseq_go_enrich', 'rnaseq_kegg_enrich', 'rnaseq_fgsea']
+                    'rnaseq_candidate_family': ['rnaseq_de', 'rnaseq_go_enrich', 'rnaseq_kegg_enrich', 'rnaseq_fgsea'],
+                    'gene_family_report': [],
+                    'rnaseq_report': []
                };

                // 阶段执行状态跟踪
@@ -10185,6 +10210,7 @@ compare: [[flesh, peel]]`;
                    { name: 'pep', label: '1️⃣2️⃣ PEP', status: 'pending', images: [], files: [], elapsed_time: 0 },
                    { name: 'expression', label: '1️⃣3️⃣ Expression (FPKM)', status: 'pending', images: [], files: [], elapsed_time: 0 },
                    { name: 'combo', label: '6️⃣ Combo', status: 'pending', images: [], files: [], elapsed_time: 0 },
+                    { name: 'gene_family_report', label: '📄 Gene Family Result Report', status: 'pending', images: [], files: [], elapsed_time: 0 },
                    // RNA-seq stages
                    { name: 'rnaseq_qc', label: '1️⃣5️⃣ RNA-seq QC', status: 'pending', images: [], files: [], elapsed_time: 0 },
                    { name: 'rnaseq_align', label: '1️⃣6️⃣ RNA-seq Align', status: 'pending', images: [], files: [], elapsed_time: 0 },
@@ -10196,7 +10222,8 @@ compare: [[flesh, peel]]`;
                    { name: 'rnaseq_kegg_enrich', label: '2️⃣2️⃣ RNA-seq KEGG Enrich', status: 'pending', images: [], files: [], elapsed_time: 0 },
                    { name: 'rnaseq_fgsea', label: '2️⃣3️⃣ RNA-seq fgsea', status: 'pending', images: [], files: [], elapsed_time: 0 },
                    { name: 'rnaseq_wgcna', label: '2️⃣4️⃣ RNA-seq WGCNA', status: 'pending', images: [], files: [], elapsed_time: 0 },
-                    { name: 'rnaseq_candidate_family', label: '2️⃣5️⃣ RNA-seq Candidate Family', status: 'pending', images: [], files: [], elapsed_time: 0 }
+                    { name: 'rnaseq_candidate_family', label: '2️⃣5️⃣ RNA-seq Candidate Family', status: 'pending', images: [], files: [], elapsed_time: 0 },
+                    { name: 'rnaseq_report', label: '2️⃣6️⃣ RNA-seq Result Report', status: 'pending', images: [], files: [], elapsed_time: 0 }
                ]);
                // 新版结果区域 - 展开的阶段
                const activeStages = ref('phylogeny');
@@ -10205,7 +10232,7 @@ compare: [[flesh, peel]]`;
                const rnaseqResultStageNames = new Set([
                    'rnaseq_qc', 'rnaseq_align', 'rnaseq_quant', 'rnaseq_sample_qc',
                    'rnaseq_de', 'annotation', 'rnaseq_go_enrich', 'rnaseq_kegg_enrich',
-                    'rnaseq_fgsea', 'rnaseq_wgcna', 'rnaseq_candidate_family'
+                    'rnaseq_fgsea', 'rnaseq_wgcna', 'rnaseq_candidate_family', 'rnaseq_report'
                ]);
                const wgsPopulationGwasStageNames = new Set([
                    'wgs_qc', 'wgs_index', 'wgs_align', 'wgs_markdup', 'wgs_bam_qc',
@@ -10653,12 +10680,15 @@ compare: [[flesh, peel]]`;
                const isJumpFile = (filename, stageName = '') => {
                    const lower = String(filename || '').toLowerCase();
                    if (lower.endsWith('.ppi_url.txt')) return true;
+                    if (stageName === 'rnaseq_report' && lower.endsWith('.rnaseq_report.html')) return true;
+                    if (stageName === 'gene_family_report' && lower.endsWith('.gene_family_report.html')) return true;
                    return stageName === 'rnaseq_qc' && lower.endsWith('_multiqc_report.html');
                };

                const isReportOrManifestFile = (filename) => {
                    const lower = String(filename || '').toLowerCase();
-                    return lower.endsWith('.manifest.json') || lower.endsWith('_report.md') || lower.endsWith('.report.md') || lower.endsWith('report.md');
+                    return lower.endsWith('.manifest.json') || lower.endsWith('_report.md') || lower.endsWith('.report.md') || lower.endsWith('report.md')
+                        || (lower.endsWith('.html') && (lower.includes('rnaseq_report') || lower.includes('gene_family_report')));
                };

                const resultDisplayFiles = (stage) => {
@@ -10904,6 +10934,12 @@ compare: [[flesh, peel]]`;
                    selectedResultStage.value = stageName;
                    selectedFile.value = file.name;

+                    const selectedLowerName = String(file.name || '').toLowerCase();
+                    if (['rnaseq_report', 'gene_family_report'].includes(stageName) && selectedLowerName.endsWith('.html')) {
+                        window.open(file.path, '_blank');
+                        return;
+                    }
+
                    if (stageName === 'gwas_fmt' && ['sorted_vcf', 'tassel_hapmap'].includes(String(file.role || ''))) {
                        window.open(file.path, '_blank');
                        return;
@@ -15027,6 +15063,87 @@ compare: [[flesh, peel]]`;
                    await startBatchExecute();
                };

+
+                const autoGenerateGeneFamilyReportAfterBatch = async (batchStages = []) => {
+                    const stageIds = batchStages.map(stage => getStageId(stage)).filter(Boolean);
+                    if (stageIds.includes('gene_family_report')) return;
+                    const geneFamilyStages = new Set([
+                        'identify', 'phylogeny', 'reference_classification', 'motif', 'domain', 'structure',
+                        'promoter', 'tfbs', 'synteny', 'karyotype', 'interspecies_synteny', 'ppi', 'kaks',
+                        'pep', 'expression', 'combo'
+                    ]);
+                    const expectedStages = [...new Set(stageIds.filter(stageId => geneFamilyStages.has(stageId)))];
+                    if (expectedStages.length === 0) return;
+                    const hasSuccessfulEvidence = expectedStages.some(
+                        stageId => stageExecutionStatus.value[stageId] === 'completed'
+                    );
+                    if (!hasSuccessfulEvidence) {
+                        addAgentMessage('assistant', t('暂无可生成的基因家族结果：本批次没有成功阶段。'));
+                        return;
+                    }
+                    const stageStatuses = Object.fromEntries(expectedStages.map(stageId => {
+                        const status = stageExecutionStatus.value[stageId];
+                        return [stageId, status === 'completed' ? 'success' : status === 'failed' ? 'failed' : 'missing'];
+                    }));
+                    const batchParams = batchExecuteParams.value || {};
+                    const planParams = batchParams.plan?.params || {};
+                    try {
+                        stageExecutionStatus.value.gene_family_report = 'running';
+                        await executeSingleStageWithParams('gene_family_report', {
+                            expectedStages,
+                            stageStatuses,
+                            reportAction: 'generate',
+                            reportUseModel: true,
+                            scopeId: batchParams.scopeId || planParams.scopeId || '',
+                            analysisRoute: batchParams.analysisRoute || planParams.analysisRoute || '',
+                            memberSetId: batchParams.memberSetId || planParams.memberSetId || '',
+                            rnaseqScopeId: batchParams.rnaseqScopeId || planParams.rnaseqScopeId || ''
+                        });
+                        stageExecutionStatus.value.gene_family_report = 'completed';
+                        setResultStageFilter('gene_family_report');
+                        await refreshResults(jobInfo.job_id, 'gene_family_report');
+                        addAgentMessage('assistant', t('已根据本批次成功的基因家族阶段自动生成结果报告。'));
+                    } catch (error) {
+                        stageExecutionStatus.value.gene_family_report = 'failed';
+                        addAgentMessage('assistant', `${t('基因家族批次已结束，但结果报告生成失败：')}${error?.message || error}`);
+                    }
+                };
+
+
+                const autoGenerateRnaseqReportAfterBatch = async (batchStages = []) => {
+                    const stageIds = batchStages.map(stage => getStageId(stage)).filter(Boolean);
+                    if (stageIds.includes('rnaseq_report')) return;
+                    const expectedStages = [...new Set(stageIds.filter(stageId =>
+                        (String(stageId).startsWith('rnaseq_') || ['annotation', 'annotation_go', 'annotation_kegg'].includes(stageId))
+                        && stageId !== 'rnaseq_report'
+                    ))];
+                    if (expectedStages.length === 0) return;
+                    const hasSuccessfulEvidence = expectedStages.some(
+                        stageId => stageExecutionStatus.value[stageId] === 'completed'
+                    );
+                    if (!hasSuccessfulEvidence) {
+                        addAgentMessage('assistant', t('暂无可生成的 RNA-seq 结果：本批次没有成功阶段。'));
+                        return;
+                    }
+                    try {
+                        stageExecutionStatus.value.rnaseq_report = 'running';
+                        await executeSingleStageWithParams('rnaseq_report', {
+                            prefix: executionPrefix(expectedStages[0]),
+                            rnaseqScopeId: activeRnaseqScopeId.value || '',
+                            rnaseqExpectedStages: expectedStages,
+                            rnaseqReportAction: 'generate',
+                            rnaseqReportUseModel: true
+                        });
+                        stageExecutionStatus.value.rnaseq_report = 'completed';
+                        setResultStageFilter('rnaseq_report');
+                        await refreshResults(jobInfo.job_id, 'rnaseq_report');
+                        addAgentMessage('assistant', t('已根据本批次成功的 RNA-seq 阶段自动生成结果报告。'));
+                    } catch (error) {
+                        stageExecutionStatus.value.rnaseq_report = 'failed';
+                        addAgentMessage('assistant', `${t('RNA-seq 批次已结束，但结果报告生成失败：')}${error?.message || error}`);
+                    }
+                };
+
                const startBatchExecute = async () => {
                    if (isBatchExecuting.value) return;
                    if (!batchExecutionUserConfirmed.value) return;
@@ -15076,10 +15193,10 @@ compare: [[flesh, peel]]`;
                        const allStages = ['genome_prepare',
                                          'identify', 'identify_refine', 'subfamily_confirm', 'phylogeny', 'reference_classification', 'motif', 'domain', 'structure', 'promoter', 'tfbs',
                                          'synteny', 'karyotype', 'interspecies_synteny', 'ppi', 'kaks', 'pep',
-                                          'expression', 'rnaseq_qc', 'rnaseq_align', 'rnaseq_quant', 'rnaseq_sample_qc',
+                                          'expression', 'gene_family_report', 'rnaseq_qc', 'rnaseq_align', 'rnaseq_quant', 'rnaseq_sample_qc',
                                          'rnaseq_de', 'annotation',
                                          'rnaseq_go_enrich', 'rnaseq_kegg_enrich', 'rnaseq_fgsea', 'rnaseq_wgcna',
-                                          'rnaseq_candidate_family'];
+                                          'rnaseq_candidate_family', 'rnaseq_report'];
                        const jobId = jobInfo.job_id;

                        for (const stage of allStages) {
@@ -15136,6 +15253,11 @@ compare: [[flesh, peel]]`;
                        }).length;
                        const totalCount = stages.length;

+                        if (pausedCount === 0) {
+                            await autoGenerateGeneFamilyReportAfterBatch(stages);
+                            await autoGenerateRnaseqReportAfterBatch(stages);
+                        }
+
                        if (failedCount > 0) {
                            addAgentMessage('assistant', t('⚠️ 批量执行完成：成功 ') + completedCount + '/' + totalCount + t('，失败 ') + failedCount + '/' + totalCount);
                        } else if (pausedCount > 0) {
@@ -4676,7 +4676,7 @@ 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]:
@@ -4686,7 +4686,11 @@ 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}")
@@ -8568,7 +8572,7 @@ 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",
@@ -17132,7 +17136,78 @@ 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(
@@ -25246,7 +25321,7 @@ 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),
@@ -714,4 +714,3 @@ window.__I18N_EN__ = {
  " 个分析阶段": " analysis stages",
  " 个阶段": " stages"
 };
-
@@ -63,7 +63,7 @@ env BBAV5_QUEUE_PREFIX=plantai_dev_7908 \
  BBAV5_REDIS_URL=redis://localhost:6379/9 \
  BBAV5_CELERY_LOG_DIR=logs/celery_plantai_dev_7908 \
  BBAV5_WORKER_NAME_PREFIX=plantai_dev_7908 \
-  ./start_celery_7880.sh
+  ./start_celery_9000.sh

 env BBAV5_QUEUE_PREFIX=plantai_dev_7908 \
  BBAV5_REDIS_URL=redis://localhost:6379/9 \
@@ -700,11 +700,14 @@ def build_report_data(
        ),
    ]
    sections.extend(stage_sections)
+    # The integrated conclusion has a fixed evidence contract. Do not take the
+    # first arbitrary observations because plan ordering can displace one of
+    # the three core facts requested for delivery.
    integrated_observations = [
-        section.observations[0]
-        for section in stage_sections
-        if section.observations
-    ][:3]
+        stage_sections_by_name[stage].observations[0]
+        for stage in ("identify", "phylogeny", "reference_classification")
+        if stage in stage_sections_by_name and stage_sections_by_name[stage].observations
+    ]
    sections.extend(
        [
            ReportSection(
@@ -52,6 +52,7 @@ STAGE_SCRIPT_MAP = {
    "annotation_kegg": "run_annotation.py",
    "rnaseq_wgcna": "run_rnaseq_wgcna.py",
    "rnaseq_candidate_family": "run_rnaseq_candidate_family.py",
+    "rnaseq_report": "run_rnaseq_report.py",
    "rnaseq_sample_qc": "run_rnaseq_sample_qc.py",
    "genome_prepare": "run_genome_prepare.py",
    "genome_prepare_v2": "run_genome_prepare.py",
@@ -341,6 +342,11 @@ DIAGNOSIS_STAGE_COVERAGE = {
        "postflight": ["candidate_family_ranking", "evidence_matrix", "recommendation", "rag_queries", "rag_references"],
        "failure": ["annotation_missing", "id_mapping"],
    },
+    "rnaseq_report": {
+        "preflight": ["successful_rnaseq_manifest", "prefix_scope_identity"],
+        "postflight": ["report_markdown", "evidence_snapshot", "coverage_status"],
+        "failure": ["no_successful_rnaseq_evidence", "scope_mismatch", "artifact_missing"],
+    },
    "annotation": {
        "preflight": ["protein_background", "tool_availability"],
        "postflight": ["gene2go", "gene2ko", "annotation_coverage"],
@@ -74,6 +74,7 @@ class IntentAgentV2(BaseAgent):
        "rnaseq_de": "RNA-seq差异表达分析 - 从原始FASTQ数据开始，进行质控→比对→定量→差异表达分析（DESeq2）",
        "rnaseq_enrich": "RNA-seq富集分析 - GO/KEGG通路富集分析（RNA-seq流程最后一步）",
        "rnaseq_candidate_family": "RNA-seq候选家族筛选 - 整合DEG、InterPro/Pfam和GO/KEGG富集，输出候选基因家族排名",
+        "rnaseq_report": "RNA-seq结果报告 - 从当前成功阶段生成可追溯的正式Markdown报告",
        "enrichment": "富集分析 - 基于基因家族鉴定结果进行GO/KEGG通路富集分析",
        "ncbi_fetch_sequences": "NCBI序列下载 - 根据GeneID、基因名或基因list下载protein/CDS序列"
    }
@@ -440,6 +441,22 @@ class IntentAgentV2(BaseAgent):
        has_rnaseq_marker = any(kw in query_lower for kw in ["rnaseq", "rna-seq", "rna seq", "转录组"])
        explicit_gene_family_context = any(kw in query_lower for kw in ["基因家族", "家族表达", "表达量", "热图", "heatmap"])

+        if has_rnaseq_marker and any(
+            keyword in query_lower
+            for keyword in ["生成结果报告", "打开结果报告", "结果报告", "生成报告", "打开报告"]
+        ):
+            action = "open" if "打开" in query_lower else "generate"
+            return {
+                "gene_family": "",
+                "species": "",
+                "stages": ["rnaseq_report"],
+                "primary_stage": "rnaseq_report",
+                "description": "打开或生成当前RNA-seq正式结果报告",
+                "requirements": ["至少一个成功的RNA-seq阶段manifest"],
+                "params": {"rnaseqReportAction": action},
+                "confidence": 0.99,
+            }
+
        stage_force_rules = [
            ("rnaseq_candidate_family", ["候选家族", "候选基因家族", "家族排名", "tf注释", "tf family", "tffamily", "pfam注释", "deg注释", "差异基因注释"], "执行RNA-seq候选家族筛选"),
            ("rnaseq_fgsea", ["fgsea", "gsea", "排序富集", "基因集富集"], "执行RNA-seq fgsea排序富集分析"),
@@ -377,6 +377,7 @@ class PlanningAgentV2(BaseAgent):
        "rnaseq_fgsea": [],
        "rnaseq_wgcna": [],
        "rnaseq_candidate_family": [],
+        "rnaseq_report": [],
    }
    
    # 各阶段依赖 (来自PreFlight)
@@ -20,6 +20,7 @@ ANALYSIS_KEYWORDS = {
    "rnaseq_kegg_enrich": ["kegg富集", "kegg分析", "kegg", "pathway"],
    "rnaseq_fgsea": ["fgsea", "gsea", "排序富集", "基因集富集"],
    "rnaseq_candidate_family": ["候选家族", "候选基因家族", "家族排名", "tf注释", "tf family", "tffamily", "pfam注释", "deg注释", "差异基因注释"],
+    "rnaseq_report": ["rnaseq结果报告", "rna-seq结果报告", "转录组结果报告", "rnaseq报告", "rna-seq报告"],
    "rnaseq_enrich": ["富集分析", "功能富集"],
    "identify": ["鉴定", "identify", "识别", "找出", "鉴定基因家族"],
    "identify_refine": ["修订成员", "修订鉴定成员", "修改成员", "删除基因", "删除", "去除基因", "去掉基因", "移除基因", "补充基因", "遗漏基因", "重建蛋白", "人工修订id", "curated members", "refine identify"],
@@ -61,6 +62,7 @@ RNASEQ_STAGES = {
    "rnaseq_kegg_enrich",
    "rnaseq_fgsea",
    "rnaseq_candidate_family",
+    "rnaseq_report",
    "rnaseq_enrich",
 }

@@ -179,6 +181,21 @@ def fast_intent_recognition(query: str) -> Optional[Dict[str, Any]]:
    except Exception:
        pass
    has_rnaseq_marker = any(marker in query_lower for marker in RNASEQ_MARKERS)
+    if has_rnaseq_marker and any(
+        keyword in query_lower
+        for keyword in ["生成结果报告", "打开结果报告", "结果报告", "生成报告", "打开报告"]
+    ):
+        action = "open" if "打开" in query_lower else "generate"
+        return {
+            "stage": "rnaseq_report",
+            "stages": ["rnaseq_report"],
+            "gene_family": "",
+            "species": "",
+            "prefix": "",
+            "params": {"rnaseqReportAction": action},
+            "confidence": 0.99,
+            "method": "rnaseq_report_deterministic",
+        }
    header_clean_context = any(kw in query_lower for kw in [
        "id处理", "处理id", "修订id", "简化id", "清理id", "id简化",
        "去掉注释", "去除注释", "注释信息", "长注释",
@@ -793,6 +793,26 @@ CAPABILITIES: Dict[str, StageCapability] = {
        repair_candidates=["gff_id_overlap_report", "motif_database_fallback_to_jaspar", "artifact_reresolve"],
        rerun_policy="manual",
    ),
+    "rnaseq_report": StageCapability(
+        stage="rnaseq_report",
+        cli="apps/cli/run_rnaseq_report.py",
+        env="test4py311",
+        category="rnaseq",
+        consumes=[
+            ArtifactNeed("successful_rnaseq_manifests", "manifest", alternatives=["final_manifest_scan"]),
+        ],
+        provides=[
+            ArtifactProduct("rnaseq_report", "markdown", "{prefix}.rnaseq_report.md"),
+            ArtifactProduct("rnaseq_report_evidence", "json", "{prefix}.rnaseq_report.evidence.json"),
+            ArtifactProduct("rnaseq_report_model", "json", "{prefix}.rnaseq_report.model.json"),
+            ArtifactProduct("rnaseq_report_manifest", "manifest", "{prefix}.rnaseq_report.manifest.json"),
+        ],
+        scope_modes=["rnaseq_scope_id"],
+        preflight_checks=["at_least_one_successful_rnaseq_manifest", "prefix_scope_identity_consistent"],
+        postflight_checks=["deterministic_markdown_exists", "evidence_snapshot_exists", "coverage_recorded"],
+        repair_candidates=["manifest_recovery", "regenerate_from_current_snapshot"],
+        rerun_policy="manual_or_after_selected_batch_terminal",
+    ),
    "summary": StageCapability(
        stage="summary",
        cli="apps/cli/run_summary.py",
@@ -90,6 +90,7 @@ PIPELINE_STAGES = {
    "rnaseq_go_enrich",
    "rnaseq_kegg_enrich",
    "rnaseq_candidate_family",
+    "rnaseq_report",
 }

 STAGE_DEPENDENCIES = {
@@ -173,6 +174,9 @@ STAGE_DEPENDENCIES = {
    "rnaseq_go_enrich": ["rnaseq_de"],
    "rnaseq_kegg_enrich": ["rnaseq_de"],
    "rnaseq_candidate_family": ["rnaseq_de", "rnaseq_go_enrich", "rnaseq_kegg_enrich", "rnaseq_fgsea"],
+    # A report is a snapshot of whatever RNA-seq evidence is already successful.
+    # Static dependencies would incorrectly prevent intentional mid-pipeline reports.
+    "rnaseq_report": [],
 }

 PARALLEL_GROUPS = [
@@ -271,6 +275,7 @@ STAGE_RESOURCE_PROFILES = {
    "rnaseq_kegg_enrich": {"queue": "rnaseq", "resource_class": "rnaseq", "default_cpu": 4, "max_cpu": 4},
    "rnaseq_fgsea": {"queue": "rnaseq", "resource_class": "rnaseq", "default_cpu": 4, "max_cpu": 4},
    "rnaseq_candidate_family": {"queue": "rnaseq", "resource_class": "rnaseq", "default_cpu": 4, "max_cpu": 4},
+    "rnaseq_report": {"queue": "light", "resource_class": "light", "default_cpu": 4, "max_cpu": 4},
 }

 DEFAULT_STAGE_RESOURCE_PROFILE = {
@@ -391,6 +396,7 @@ STAGE_ORDER = [
    "rnaseq_kegg_enrich",
    "rnaseq_fgsea",
    "rnaseq_candidate_family",
+    "rnaseq_report",
    "rnaseq_enrich",
    "gene_family_report",
 ]
@@ -469,6 +475,7 @@ STAGE_INFO = {
    "rnaseq_enrich": {"name": "RNA-seq富集分析", "estimated_time": 15, "cpu": 4},
    "rnaseq_fgsea": {"name": "RNA-seq fgsea分析", "estimated_time": 15, "cpu": 4},
    "rnaseq_candidate_family": {"name": "RNA-seq候选家族筛选", "estimated_time": 20, "cpu": 4},
+    "rnaseq_report": {"name": "RNA-seq结果报告", "estimated_time": 2, "cpu": 4},
 }

 EXECUTABLE_STAGES = {
@@ -544,6 +551,7 @@ EXECUTABLE_STAGES = {
    "rnaseq_enrich",
    "rnaseq_fgsea",
    "rnaseq_candidate_family",
+    "rnaseq_report",
 }


@@ -33,6 +33,7 @@ RNASEQ_STATUS_STAGES = {
    "rnaseq_fgsea",
    "rnaseq_wgcna",
    "rnaseq_candidate_family",
+    "rnaseq_report",
    "annotation",
    "annotation_go",
    "annotation_kegg",
@@ -1516,6 +1516,19 @@ class StageToolRegistry:
            "timeout": 7200,
            "conda_env": "rnaseq"
        },
+        # 24. Formal RNA-seq Result Report
+        {
+            "id": "rnaseq_report",
+            "name": "RNA-seq Result Report",
+            "script": "run_rnaseq_report.py",
+            "category": "rnaseq",
+            "description": "Generate a scoped formal Markdown report from successful RNA-seq manifests",
+            "required_inputs": [],
+            "outputs": ["rnaseq_report", "rnaseq_report_evidence", "rnaseq_report_model"],
+            "parameters": {"cpu": 4},
+            "timeout": 1800,
+            "conda_env": "test4py311"
+        },
        # Combo Plot - 组合图
        {
            "id": "combo",
@@ -0,0 +1,313 @@
+"""Lightweight, provider-free RNA-seq manifest evidence snapshot.
+
+The live interpretation view and the formal report share this module so scope
+selection and manifest provenance have one implementation.  It intentionally
+does not import the MAS agent package.
+"""
+from __future__ import annotations
+
+import json
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Any, Iterable
+
+
+REPORT_STAGE = "rnaseq_report"
+SUCCESS_STATUSES = {"success", "partial_success"}
+GLOBAL_LEGACY_STAGES = {
+    "rnaseq_qc",
+    "rnaseq_align",
+    "rnaseq_quant",
+    "annotation",
+    "annotation_go",
+    "annotation_kegg",
+}
+RNASEQ_STAGE_NAMES = {
+    "rnaseq_qc": "RNA-seq质控",
+    "rnaseq_align": "RNA-seq比对",
+    "rnaseq_quant": "RNA-seq定量",
+    "rnaseq_sample_qc": "RNA-seq样本质量评估",
+    "rnaseq_de": "RNA-seq差异表达",
+    "annotation": "背景功能注释",
+    "annotation_go": "GO背景自动注释",
+    "annotation_kegg": "KEGG/KO背景自动注释",
+    "rnaseq_go_enrich": "RNA-seq GO富集分析",
+    "rnaseq_kegg_enrich": "RNA-seq KEGG富集分析",
+    "rnaseq_enrich": "RNA-seq富集分析（兼容入口）",
+    "rnaseq_fgsea": "RNA-seq fgsea排序富集",
+    "rnaseq_wgcna": "RNA-seq WGCNA共表达分析",
+    "rnaseq_candidate_family": "RNA-seq候选家族筛选",
+    "rnaseq_family_score": "RNA-seq候选家族评分",
+}
+RNASEQ_STAGE_ORDER = list(RNASEQ_STAGE_NAMES)
+
+
+@dataclass(frozen=True)
+class RNASeqManifestSelection:
+    rnaseq_scope_id: str
+    discovered_scope_ids: tuple[str, ...]
+    manifests: dict[str, dict[str, Any]]
+
+
+def read_json(path: Path) -> dict[str, Any]:
+    try:
+        data = json.loads(path.read_text(encoding="utf-8"))
+        return data if isinstance(data, dict) else {}
+    except (OSError, json.JSONDecodeError):
+        return {}
+
+
+def manifest_identity_value(manifest: dict[str, Any], key: str) -> str:
+    context = manifest.get("stage_context") or manifest.get("stageContext") or {}
+    params = manifest.get("parameters") or {}
+    return str(manifest.get(key) or params.get(key) or context.get(key) or "").strip()
+
+
+def is_rnaseq_evidence_stage(stage: str) -> bool:
+    stage = str(stage or "").strip()
+    return stage != REPORT_STAGE and (
+        stage.startswith("rnaseq_") or stage in {"annotation", "annotation_go", "annotation_kegg"}
+    )
+
+
+def stage_sort_key(stage: str) -> tuple[int, str]:
+    try:
+        return RNASEQ_STAGE_ORDER.index(stage), stage
+    except ValueError:
+        return len(RNASEQ_STAGE_ORDER), stage
+
+
+def _manifest_score(path: Path, manifest: dict[str, Any]) -> tuple[int, int, int, float]:
+    status = str(manifest.get("status") or "")
+    status_rank = 2 if status == "success" else 1 if status == "partial_success" else 0
+    metrics = manifest.get("metrics") if isinstance(manifest.get("metrics"), dict) else {}
+    artifacts = manifest.get("artifacts") if isinstance(manifest.get("artifacts"), dict) else {}
+    try:
+        mtime = path.stat().st_mtime
+    except OSError:
+        mtime = 0.0
+    return status_rank, len(metrics), len(artifacts), mtime
+
+
+def select_rnaseq_manifests(
+    final_dir: Path,
+    prefix: str,
+    *,
+    rnaseq_scope_id: str = "",
+) -> RNASeqManifestSelection:
+    """Select one non-mixing manifest per RNA-seq stage for a prefix/scope."""
+    final_dir = Path(final_dir)
+    pattern = f"{prefix}.*.manifest.json" if prefix else "*.manifest.json"
+    candidates: list[tuple[Path, dict[str, Any]]] = []
+    latest_by_scope: dict[str, float] = {}
+    for path in sorted(final_dir.glob(pattern)) if final_dir.exists() else []:
+        manifest = read_json(path)
+        stage = str(manifest.get("stage") or "")
+        if not is_rnaseq_evidence_stage(stage):
+            continue
+        manifest_prefix = str(manifest.get("prefix") or "").strip()
+        if prefix and manifest_prefix and manifest_prefix != prefix:
+            continue
+        candidates.append((path, manifest))
+        scope = manifest_identity_value(manifest, "rnaseq_scope_id")
+        if scope:
+            try:
+                latest_by_scope[scope] = max(latest_by_scope.get(scope, 0.0), path.stat().st_mtime)
+            except OSError:
+                latest_by_scope.setdefault(scope, 0.0)
+
+    discovered = sorted(latest_by_scope, key=lambda item: (-latest_by_scope[item], item))
+    resolved_scope = str(rnaseq_scope_id or "").strip() or (discovered[0] if discovered else "")
+    selected_paths: dict[str, Path] = {}
+    selected: dict[str, dict[str, Any]] = {}
+    for path, manifest in candidates:
+        stage = str(manifest.get("stage") or "")
+        scope = manifest_identity_value(manifest, "rnaseq_scope_id")
+        if resolved_scope and scope and scope != resolved_scope:
+            continue
+        if resolved_scope and not scope and stage not in GLOBAL_LEGACY_STAGES:
+            continue
+        existing = selected.get(stage)
+        if existing is not None and _manifest_score(selected_paths[stage], existing) >= _manifest_score(path, manifest):
+            continue
+        manifest = dict(manifest)
+        manifest["_manifest_path"] = str(path)
+        selected[stage] = manifest
+        selected_paths[stage] = path
+    return RNASeqManifestSelection(resolved_scope, tuple(discovered), selected)
+
+
+def _compact_value(value: Any, limit: int = 240) -> str:
+    if isinstance(value, (dict, list)):
+        text = json.dumps(value, ensure_ascii=False, sort_keys=True)
+    else:
+        text = str(value)
+    return text if len(text) <= limit else text[: limit - 1] + "…"
+
+
+def resolve_artifact_path(
+    final_dir: Path,
+    item: dict[str, Any],
+    *,
+    require_exists: bool = False,
+) -> Path | None:
+    """Resolve artifacts after a workspace has been moved or mounted elsewhere."""
+    final_dir = Path(final_dir)
+    workspace = final_dir.parent
+    candidates: list[Path] = []
+    for raw in (item.get("full_path"), item.get("path")):
+        if not raw:
+            continue
+        path = Path(str(raw))
+        candidates.append(path if path.is_absolute() else workspace / path)
+        if path.is_absolute():
+            candidates.append(final_dir / path.name)
+
+    unique: list[Path] = []
+    seen: set[str] = set()
+    for path in candidates:
+        identity = str(path)
+        if identity not in seen:
+            seen.add(identity)
+            unique.append(path)
+    for path in unique:
+        if path.exists():
+            return path
+    if require_exists:
+        return None
+    return unique[0] if unique else None
+
+
+def build_rnaseq_evidence_snapshot(
+    final_dir: Path,
+    prefix: str,
+    *,
+    rnaseq_scope_id: str = "",
+    include_stages: Iterable[str] | None = None,
+    selection: RNASeqManifestSelection | None = None,
+) -> dict[str, Any]:
+    """Build a compact evidence object without invoking an LLM or agent cache."""
+    selection = selection or select_rnaseq_manifests(
+        final_dir, prefix, rnaseq_scope_id=rnaseq_scope_id
+    )
+    allowed = {str(stage) for stage in include_stages or [] if str(stage).strip()}
+    manifests = {
+        stage: manifest
+        for stage, manifest in selection.manifests.items()
+        if not allowed or stage in allowed
+    }
+    stages = sorted(manifests, key=stage_sort_key)
+    stage_flow: list[dict[str, Any]] = []
+    findings: list[dict[str, Any]] = []
+    reviews: list[dict[str, Any]] = []
+    cards: list[dict[str, Any]] = []
+    risks: list[dict[str, Any]] = []
+    card_index = 0
+    for stage in stages:
+        manifest = manifests[stage]
+        status = str(manifest.get("status") or "unknown")
+        metrics = manifest.get("metrics") if isinstance(manifest.get("metrics"), dict) else {}
+        parameters = manifest.get("parameters") if isinstance(manifest.get("parameters"), dict) else {}
+        artifacts = manifest.get("artifacts") if isinstance(manifest.get("artifacts"), dict) else {}
+        metric_items = list(sorted(metrics.items()))[:12]
+        metric_summary = ", ".join(f"{key}={_compact_value(value, 80)}" for key, value in metric_items[:5])
+        key_result = metric_summary or f"登记产物 {len(artifacts)} 个"
+        stage_flow.append(
+            {
+                "id": stage,
+                "name": RNASEQ_STAGE_NAMES.get(stage, stage),
+                "status": status,
+                "key_result": key_result,
+            }
+        )
+        findings.append(
+            {
+                "stage": stage,
+                "title": RNASEQ_STAGE_NAMES.get(stage, stage),
+                "description": f"manifest 状态为 {status}；{key_result}。",
+            }
+        )
+        limitations: list[str] = []
+        if status == "partial_success":
+            limitations.append("该阶段为 partial_success，结果可用但不完整。")
+        elif status != "success":
+            limitations.append("该阶段未成功，不纳入正式结论。")
+        missing_artifacts: list[str] = []
+        for name, item in sorted(artifacts.items()):
+            if not isinstance(item, dict):
+                continue
+            path = resolve_artifact_path(final_dir, item)
+            exists = bool(path and path.exists())
+            card_index += 1
+            cards.append(
+                {
+                    "id": f"RNA-E{card_index:04d}",
+                    "stage": stage,
+                    "claim": f"产物 {name}",
+                    "evidence": f"path={path or ''}, exists={exists}",
+                    "source_type": "raw_file" if exists else "manifest",
+                }
+            )
+            if not exists:
+                missing_artifacts.append(str(name))
+        for key, value in metric_items:
+            card_index += 1
+            cards.append(
+                {
+                    "id": f"RNA-E{card_index:04d}",
+                    "stage": stage,
+                    "claim": f"指标 {key}",
+                    "evidence": _compact_value(value),
+                    "source_type": "manifest",
+                }
+            )
+        safe_parameter_items = [
+            (key, value)
+            for key, value in sorted(parameters.items())
+            if not any(secret in str(key).lower() for secret in ("api_key", "token", "secret", "password"))
+        ][:10]
+        for key, value in safe_parameter_items:
+            card_index += 1
+            cards.append(
+                {
+                    "id": f"RNA-E{card_index:04d}",
+                    "stage": stage,
+                    "claim": f"参数 {key}",
+                    "evidence": _compact_value(value),
+                    "source_type": "manifest",
+                }
+            )
+        if missing_artifacts:
+            shown = missing_artifacts[:12]
+            remainder = len(missing_artifacts) - len(shown)
+            suffix = f"（另有 {remainder} 个，详见 evidence JSON）" if remainder else ""
+            message = f"manifest 登记但文件不存在的产物：{', '.join(shown)}{suffix}"
+            limitations.append(message)
+            risks.append({"stage": stage, "severity": "high", "message": message})
+        if status not in SUCCESS_STATUSES:
+            risks.append({"stage": stage, "severity": "high", "message": f"阶段状态为 {status}，不得作为成功证据。"})
+        reviews.append({"stage": stage, "stage_name": RNASEQ_STAGE_NAMES.get(stage, stage), "limitations": limitations})
+
+    successful = [stage for stage in stages if str(manifests[stage].get("status") or "") in SUCCESS_STATUSES]
+    return {
+        "schema": "rnaseq_manifest_evidence_v1",
+        "metadata": {
+            "prefix": prefix,
+            "rnaseq_scope_id": selection.rnaseq_scope_id,
+            "discovered_scope_ids": list(selection.discovered_scope_ids),
+            "included_stages": stages,
+            "successful_stages": successful,
+            "interpretation_boundary": "仅陈述当前 prefix 与 RNA-seq scope 下 manifest/产物支持的事实；富集、相关性和候选排序不得写成调控因果。",
+        },
+        "stage_flow": {"visualization": " -> ".join(stages), "stages": stage_flow},
+        "key_findings": findings,
+        "stage_reviews": reviews,
+        "evidence_cards": cards,
+        "risk_flags": risks,
+        "major_claims": [],
+        "biological_story": (
+            f"当前报告汇总了 {len(successful)} 个成功或部分成功的 RNA-seq 阶段。"
+            "跨阶段生物学解释必须以各阶段数值、图表和风险标记为边界。"
+        ),
+        "next_steps": ["补齐缺失或失败阶段后重新生成报告，以刷新证据快照。"],
+    }
@@ -18,7 +18,7 @@ import mimetypes
 import os
 import re
 from dataclasses import dataclass
-from datetime import datetime
+from datetime import datetime, timedelta, timezone
 from pathlib import Path
 from typing import Any, Iterable
 from urllib.parse import unquote
@@ -79,8 +79,21 @@ class RNASeqReportResult:
    reused: bool = False


+BEIJING_TIMEZONE = timezone(timedelta(hours=8))
+
+
 def _now() -> str:
-    return datetime.now().astimezone().isoformat(timespec="seconds")
+    return datetime.now(BEIJING_TIMEZONE).isoformat(timespec="seconds")
+
+
+def _display_generated_at(value: str) -> str:
+    try:
+        parsed = datetime.fromisoformat(value)
+        if parsed.tzinfo is None:
+            parsed = parsed.replace(tzinfo=BEIJING_TIMEZONE)
+        return parsed.astimezone(BEIJING_TIMEZONE).strftime("%Y-%m-%d %H:%M:%S")
+    except (TypeError, ValueError):
+        return str(value or "").replace("T", " ")


 def _read_json(path: Path) -> dict[str, Any]:
@@ -1224,7 +1237,7 @@ def _render_deterministic_markdown(
    lines = [
        f"# {prefix} RNA-seq 结果解读报告",
        "",
-        f"生成时间：{generated_at}  ",
+        f"生成时间（北京时间）：{_display_generated_at(generated_at)}  ",
        f"任务编号：`{workspace.name}`",
        "",
        "**任务结果路径：**  ",
@@ -0,0 +1,45 @@
+# RNA-seq Result Report Contract v1
+
+## Stage
+
+- Stage id: `rnaseq_report`
+- Script: `apps/cli/run_rnaseq_report.py`
+- Scope: one exact `prefix + rnaseq_scope_id` evidence snapshot
+- Purpose: materialize a formal, reproducible RNA-seq Markdown result report without depending on frontend session state.
+
+## Inputs
+
+- At least one RNA-seq/annotation manifest with status `success` or `partial_success` under `final/`.
+- All selected evidence must match the requested prefix and RNA-seq scope. Legacy unscoped QC/alignment/quantification/annotation manifests may be treated as experiment-global evidence.
+- `expected_stages` is optional and records the stages selected for the current batch. It controls coverage only; it must not become a static execution dependency.
+- An existing configured `LLMManager` provider is optional. No provider or model name is required by this stage.
+
+If no successful RNA-seq evidence exists, the stage must return `暂无可生成的 RNA-seq 结果` and must not create an empty report.
+
+## Required Outputs
+
+- `final/{prefix}.rnaseq_report.md`
+- `final/{prefix}.rnaseq_report.evidence.json`
+- `final/{prefix}.rnaseq_report.model.json`
+- `final/{prefix}.rnaseq_report.manifest.json`
+
+The manifest stage status is `success` whenever these outputs are generated. Content completeness is recorded separately as `metrics.coverage_status = complete|partial`.
+
+## Generation Semantics
+
+- `generate`: always rebuild from the current manifest snapshot.
+- `open`: reuse a fresh report; regenerate first when the source/request fingerprint changed.
+- The deterministic Markdown body is always complete enough to read without an API.
+- Optional model output is a labeled language-enhancement section only. Model failure must retain the deterministic report and be recorded in `.model.json`.
+- `rnaseq_report` manifests are excluded from their own evidence scan.
+
+## Boundary With Deep Interpretation
+
+Both features may call the pure `gfa_core.rnaseq_evidence` snapshot builder. The formal report must not call `/api/agent/interpret`, read its session cache, or replace the frontend deep-interpretation view.
+
+## Validation
+
+- Every manifest artifact path exists and its digest is recorded.
+- Evidence contains only the selected prefix/scope.
+- `coverage_status=complete` only when every expected stage has status `success`.
+- Missing, failed, or `partial_success` expected stages yield `coverage_status=partial` while the report manifest remains `success`.
@@ -33,10 +33,6 @@

 各阶段依次写明分析对象、源结果中的直接观察、谨慎解释、限制，并仅在有助复核时列出少量相对路径。

-### 2.2 语言边界
-
-预测关系统一表述为线索；没有逐成员表或独立证据时，不指定候选基因，不声称功能改变或调控关系已经证实。
-
 <!-- GFA_SECTION common.completeness -->
 ## 三、结果总览与完整性检查

@@ -2,15 +2,19 @@
 # PlantAI-dev 9000 服务管理脚本
 # 用法: bash manage_plantai.sh {start|stop|restart|status} [--port PORT]
 # 默认端口: 9000
-#
-# 项目: /home/xzq/5090/teamWorkspace/zh/PlantAI-dev
-# 端口: 9000 (web), Redis DB 14 (queue prefix: plantai_dev_9002)

 set -euo pipefail

+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+if [ -f "$SCRIPT_DIR/.env" ]; then
+    set -a
+    . "$SCRIPT_DIR/.env"
+    set +a
+fi
+
 # 解析命令行参数：第一个参数是命令，后面可选 --port / -p
 CMD=""
-WEB_PORT="9000"
+WEB_PORT="${PLANTAI_WEB_PORT:-9000}"
 for arg in "$@"; do
    case "$arg" in
        start|stop|restart|status)
@@ -33,12 +37,15 @@ done
 CMD="${CMD:-status}"

 # Conda 环境：启动脚本内部也依赖这个环境
-CONDA_ENV="${CONDA_ENV:-/home/xzq/miniconda3/envs/test4py311}"
+CONDA_BASE="${BBAV5_CONDA_BASE:-/home/xia-lab/miniconda3}"
+DEFAULT_ENV="${BBAV5_DEFAULT_ENV:-test4py311}"
+CONDA_ENV="${CONDA_ENV:-$CONDA_BASE/envs/$DEFAULT_ENV}"
 export PATH="$CONDA_ENV/bin:$PATH"

 # 项目配置（与 .env 和启动脚本保持一致）
-PROJECT_DIR="/home/xzq/5090/teamWorkspace/zh/PlantAI-dev"
-QUEUE_PREFIX="plantai_dev_9002"
+PROJECT_DIR="$SCRIPT_DIR"
+QUEUE_PREFIX="${BBAV5_QUEUE_PREFIX:-plantai_4090_9000}"
+REDIS_URL="${BBAV5_REDIS_URL:-redis://localhost:6379/10}"
 WEB_LOG="/tmp/plantai_${WEB_PORT}.log"
 CELERY_LOG="/tmp/celery_${WEB_PORT}.log"

@@ -46,28 +53,49 @@ red()  { echo -e "\033[31m$*\033[0m"; }
 green(){ echo -e "\033[32m$*\033[0m"; }
 cyan() { echo -e "\033[36m$*\033[0m"; }

+web_pid_for_port() {
+    ss -tlnp 2>/dev/null \
+        | grep ":$WEB_PORT " \
+        | grep -oP 'pid=\K\d+' \
+        | head -n 1 \
+        || true
+}
+
+web_process_cwd() {
+    readlink -f "/proc/$1/cwd" 2>/dev/null || true
+}
+
+web_pid_belongs_to_project() {
+    [ "$(web_process_cwd "$1")" = "$PROJECT_DIR" ]
+}
+
 status() {
    echo ""
    cyan "=== PlantAI-dev ${WEB_PORT} 服务状态 ==="
    echo ""

    # Web 服务
-    WEB_PID=$(ss -tlnp 2>/dev/null | grep ":$WEB_PORT " | grep -oP 'pid=\K\d+' || true)
+    WEB_PID="$(web_pid_for_port)"
    if [ -n "${WEB_PID:-}" ]; then
-        green "[✓] Web  服务运行中  (端口 $WEB_PORT, PID $WEB_PID)"
+        WEB_CWD="$(web_process_cwd "$WEB_PID")"
+        if web_pid_belongs_to_project "$WEB_PID"; then
+            green "[✓] Web  服务运行中  (端口 $WEB_PORT, PID $WEB_PID)"
+        else
+            red "[!] 端口 $WEB_PORT 被其他项目占用  (PID $WEB_PID, cwd ${WEB_CWD:-未知})"
+        fi
    else
        red "[✗] Web  服务未启动  (端口 $WEB_PORT)"
    fi

    # Redis
-    if redis-cli ping > /dev/null 2>&1; then
-        green "[✓] Redis 运行中  (localhost:6379)"
+    if redis-cli -u "$REDIS_URL" ping > /dev/null 2>&1; then
+        green "[✓] Redis 运行中  ($REDIS_URL)"
    else
        red "[✗] Redis 未启动"
    fi

    # Celery workers
-    CELERY_COUNT=$(pgrep -fc "$QUEUE_PREFIX" || echo 0)
+    CELERY_COUNT="$(pgrep -fc "$QUEUE_PREFIX" || true)"
    if [ "$CELERY_COUNT" -gt 0 ]; then
        green "[✓] Celery workers 运行中  (${CELERY_COUNT} 进程, 队列前缀: $QUEUE_PREFIX)"
        echo "    Worker 列表:"
@@ -86,13 +114,18 @@ stop() {
    echo ""

    # 停止 Web 服务
-    WEB_PID=$(ss -tlnp 2>/dev/null | grep ":$WEB_PORT " | grep -oP 'pid=\K\d+' || true)
+    WEB_PID="$(web_pid_for_port)"
    if [ -n "${WEB_PID:-}" ]; then
+        WEB_CWD="$(web_process_cwd "$WEB_PID")"
+        if ! web_pid_belongs_to_project "$WEB_PID"; then
+            red "[!] 拒绝停止：端口 $WEB_PORT 属于其他项目  (PID $WEB_PID, cwd ${WEB_CWD:-未知})"
+            return 1
+        fi
        echo "正在停止 Web 服务 (PID $WEB_PID)..."
        kill "$WEB_PID" 2>/dev/null || true
        sleep 1
-        # 如果还没死，强制 kill
-        if ss -tlnp 2>/dev/null | grep -q ":$WEB_PORT"; then
+        # 仅强制停止仍属于本项目的原进程，避免 PID 复用造成误杀。
+        if kill -0 "$WEB_PID" 2>/dev/null && web_pid_belongs_to_project "$WEB_PID"; then
            kill -9 "$WEB_PID" 2>/dev/null || true
        fi
        green "[✓] Web 服务已停止"
@@ -125,12 +158,18 @@ start() {
    echo ""

    # 检查是否已在运行
-    if ss -tlnp 2>/dev/null | grep -q ":$WEB_PORT"; then
-        red "[!] 端口 $WEB_PORT 已被占用，请先停止服务"
+    WEB_PID="$(web_pid_for_port)"
+    if [ -n "${WEB_PID:-}" ]; then
+        WEB_CWD="$(web_process_cwd "$WEB_PID")"
+        if web_pid_belongs_to_project "$WEB_PID"; then
+            red "[!] 本项目 Web 已在端口 $WEB_PORT 运行  (PID $WEB_PID)"
+        else
+            red "[!] 端口 $WEB_PORT 被其他项目占用  (PID $WEB_PID, cwd ${WEB_CWD:-未知})"
+        fi
        exit 1
    fi

-    if ! redis-cli ping > /dev/null 2>&1; then
+    if ! redis-cli -u "$REDIS_URL" ping > /dev/null 2>&1; then
        red "[!] Redis 未运行，请先启动 Redis"
        exit 1
    fi
@@ -141,7 +180,7 @@ start() {
    echo "正在启动 Celery workers..."
    nohup bash start_celery_9000.sh > "$CELERY_LOG" 2>&1 &
    sleep 3
-    CELERY_COUNT=$(pgrep -fc "$QUEUE_PREFIX" || echo 0)
+    CELERY_COUNT="$(pgrep -fc "$QUEUE_PREFIX" || true)"
    if [ "$CELERY_COUNT" -gt 0 ]; then
        green "  [✓] Celery workers 已启动 (${CELERY_COUNT} 进程)"
    else
@@ -1,79 +0,0 @@
-#!/bin/bash
-# 重启bbav20311服务并加载新提示词
-
-echo "=============================================="
-echo "重启BBAV20311服务 - 加载新提示词"
-echo "=============================================="
-echo ""
-
-# 1. 查找并停止现有服务
-echo "1. 停止现有服务..."
-MAIN_PID=$(ps aux | grep "python3 main.py" | grep -v grep | grep -v restart | awk '{print $2}' | head -1)
-
-if [ -n "$MAIN_PID" ]; then
-    echo "   找到主服务PID: $MAIN_PID"
-    kill -15 $MAIN_PID 2>/dev/null
-    sleep 2
-    echo "   已发送停止信号"
-else
-    echo "   未找到运行中的主服务"
-fi
-
-# 2. 激活conda环境
-echo ""
-echo "2. 激活conda环境..."
-source ~/anaconda3/etc/profile.d/conda.sh
-conda activate test4py311
-echo "   环境: $(conda info --envs | grep '*')"
-
-# 3. 验证提示词文件
-echo ""
-echo "3. 验证提示词文件..."
-PROMPT_COUNT=$(ls /home/xia-lab/wutx/00test/bbav20311/prompts/*_agent.md 2>/dev/null | wc -l)
-echo "   提示词文件数量: $PROMPT_COUNT"
-
-if [ "$PROMPT_COUNT" -eq 8 ]; then
-    echo "   ✅ 所有提示词文件存在"
-else
-    echo "   ⚠️ 提示词文件数量不匹配"
-fi
-
-# 4. 启动服务
-echo ""
-echo "4. 启动服务..."
-cd /home/xia-lab/wutx/00test/bbav20311
-nohup python3 main.py > /tmp/bbav20311_restart.log 2>&1 &
-NEW_PID=$!
-echo "   新PID: $NEW_PID"
-
-# 5. 等待服务启动
-echo ""
-echo "5. 等待服务启动..."
-sleep 5
-
-# 6. 验证服务
-echo ""
-echo "6. 验证服务..."
-if ps -p $NEW_PID > /dev/null; then
-    echo "   ✅ 服务进程运行中"
-    
-    # 测试API
-    HTTP_STATUS=$(curl -s -o /dev/null -w "%{http_code}" http://localhost:7865/api/info 2>/dev/null)
-    if [ "$HTTP_STATUS" = "200" ]; then
-        echo "   ✅ API响应正常 (HTTP 200)"
-    else
-        echo "   ⚠️ API响应异常 (HTTP $HTTP_STATUS)"
-    fi
-else
-    echo "   ❌ 服务启动失败"
-    exit 1
-fi
-
-echo ""
-echo "=============================================="
-echo "重启完成"
-echo "=============================================="
-echo "PID: $NEW_PID"
-echo "日志: /tmp/bbav20311_restart.log"
-echo "提示词: /home/xia-lab/wutx/00test/bbav20311/prompts/"
-echo "=============================================="
@@ -1,22 +0,0 @@
-#!/bin/bash
-# WebUI for bbav5 project
-# Port: 8788, State: ~/.hermes/webui-bbav5
-
-export HERMES_WEBUI_PORT=8788
-export HERMES_WEBUI_STATE_DIR="$HOME/.hermes/webui-bbav5"
-export HERMES_WEBUI_DEFAULT_WORKSPACE="/home/xia-lab/wutx/00test/bbav5"
-export HERMES_WEBUI_AGENT_DIR="/home/xia-lab/wutx/01model/hermes-agent"
-
-# Create state dir if not exists
-mkdir -p "$HERMES_WEBUI_STATE_DIR"
-
-cd /home/xia-lab/wutx/01model/hermes-webui
-
-echo "Starting WebUI for bbav5..."
-echo "  Port: $HERMES_WEBUI_PORT"
-echo "  Workspace: $HERMES_WEBUI_DEFAULT_WORKSPACE"
-echo "  State: $HERMES_WEBUI_STATE_DIR"
-echo "  URL: http://127.0.0.1:8788"
-
-source /home/xia-lab/wutx/01model/hermes-agent/venv/bin/activate
-python server.py
@@ -1,14 +0,0 @@
-#!/bin/bash
-# 启动Celery Worker
-
-cd /home/xia-lab/wutx/00test/bbav5
-
-# 使用conda环境的Python和Celery
-CONDA_ENV="/home/xia-lab/miniconda3/envs/test4py311"
-export PATH="$CONDA_ENV/bin:$PATH"
-
-echo "Starting Celery Worker with conda environment: test4py311"
-"$CONDA_ENV/bin/celery" -A celery_app worker --loglevel=info --concurrency=2 &
-
-echo "Celery Worker started!"
-echo "To monitor tasks, run: $CONDA_ENV/bin/celery -A celery_app flower --port=5555"
@@ -1,93 +0,0 @@
-#!/bin/bash
-# Start resource-specific Celery workers for the PlantAI-dev project.
-
-set -euo pipefail
-
-SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-EXTERNAL_BBAV5_QUEUE_PREFIX="${BBAV5_QUEUE_PREFIX-}"
-EXTERNAL_BBAV5_REDIS_URL="${BBAV5_REDIS_URL-}"
-EXTERNAL_BBAV5_CELERY_LOG_DIR="${BBAV5_CELERY_LOG_DIR-}"
-EXTERNAL_BBAV5_WORKER_NAME_PREFIX="${BBAV5_WORKER_NAME_PREFIX-}"
-if [ -f "$SCRIPT_DIR/.env" ]; then
-    set -a
-    . "$SCRIPT_DIR/.env"
-    set +a
-fi
-if [ -n "$EXTERNAL_BBAV5_QUEUE_PREFIX" ]; then
-    BBAV5_QUEUE_PREFIX="$EXTERNAL_BBAV5_QUEUE_PREFIX"
-fi
-if [ -n "$EXTERNAL_BBAV5_REDIS_URL" ]; then
-    BBAV5_REDIS_URL="$EXTERNAL_BBAV5_REDIS_URL"
-fi
-if [ -n "$EXTERNAL_BBAV5_CELERY_LOG_DIR" ]; then
-    BBAV5_CELERY_LOG_DIR="$EXTERNAL_BBAV5_CELERY_LOG_DIR"
-fi
-if [ -n "$EXTERNAL_BBAV5_WORKER_NAME_PREFIX" ]; then
-    BBAV5_WORKER_NAME_PREFIX="$EXTERNAL_BBAV5_WORKER_NAME_PREFIX"
-fi
-
-PROJECT_ROOT="${BBAV5_PROJECT_ROOT:-$SCRIPT_DIR}"
-cd "$PROJECT_ROOT"
-
-CONDA_BASE="${BBAV5_CONDA_BASE:-/home/xia-lab/miniconda3}"
-DEFAULT_ENV="${BBAV5_DEFAULT_ENV:-test4py311}"
-CONDA_ENV="$CONDA_BASE/envs/$DEFAULT_ENV"
-export PATH="$CONDA_ENV/bin:$PATH"
-export BBAV5_QUEUE_PREFIX="${BBAV5_QUEUE_PREFIX:-plantai_dev_7880}"
-export BBAV5_REDIS_URL="${BBAV5_REDIS_URL:-redis://localhost:6379/9}"
-WORKER_NAME_PREFIX="${BBAV5_WORKER_NAME_PREFIX:-${BBAV5_QUEUE_PREFIX//[^A-Za-z0-9_]/_}}"
-
-LOG_DIR="${BBAV5_CELERY_LOG_DIR:-logs/celery_plantai_dev_7880}"
-mkdir -p "$LOG_DIR"
-
-CELERY="$CONDA_ENV/bin/celery"
-APP="celery_app"
-LOGLEVEL="${BBAV5_CELERY_LOGLEVEL:-info}"
-HOSTNAME_VALUE="$(hostname)"
-
-DEFAULT_CONCURRENCY="${BBAV5_DEFAULT_CONCURRENCY:-1}"
-HEAVY_CONCURRENCY="${BBAV5_HEAVY_CONCURRENCY:-2}"
-MEDIUM_CONCURRENCY="${BBAV5_MEDIUM_CONCURRENCY:-2}"
-LIGHT_CONCURRENCY="${BBAV5_LIGHT_CONCURRENCY:-4}"
-RNASEQ_CONCURRENCY="${BBAV5_RNASEQ_CONCURRENCY:-2}"
-
-worker_online() {
-    local name="$1"
-    if [ "${BBAV5_CELERY_FORCE_START:-0}" = "1" ]; then
-        return 1
-    fi
-    pgrep -f -- "--hostname=${name}@%h" >/dev/null 2>&1
-}
-
-start_worker() {
-    local name="$1"
-    local queue="$2"
-    local concurrency="$3"
-    if [ "$concurrency" -le 0 ]; then
-        echo "Skipping ${name}: concurrency=${concurrency}"
-        return
-    fi
-    if worker_online "$name"; then
-        echo "Skipping ${name}: worker process already exists (${name}@%h)"
-        return
-    fi
-    echo "Starting ${name}: queue=${queue}, concurrency=${concurrency}"
-    "$CELERY" -A "$APP" worker \
-        --detach \
-        --loglevel="$LOGLEVEL" \
-        --hostname="${name}@%h" \
-        --queues="$queue" \
-        --concurrency="$concurrency" \
-        --prefetch-multiplier=1 \
-        --logfile="$LOG_DIR/${name}.log" \
-        --pidfile="$LOG_DIR/${name}.pid"
-}
-
-start_worker "${WORKER_NAME_PREFIX}_default" "${BBAV5_QUEUE_PREFIX}.default" "$DEFAULT_CONCURRENCY"
-start_worker "${WORKER_NAME_PREFIX}_heavy" "${BBAV5_QUEUE_PREFIX}.heavy" "$HEAVY_CONCURRENCY"
-start_worker "${WORKER_NAME_PREFIX}_medium" "${BBAV5_QUEUE_PREFIX}.medium" "$MEDIUM_CONCURRENCY"
-start_worker "${WORKER_NAME_PREFIX}_light" "${BBAV5_QUEUE_PREFIX}.light" "$LIGHT_CONCURRENCY"
-start_worker "${WORKER_NAME_PREFIX}_rnaseq" "${BBAV5_QUEUE_PREFIX}.rnaseq" "$RNASEQ_CONCURRENCY"
-
-echo "Celery workers started with queue prefix: ${BBAV5_QUEUE_PREFIX}"
-echo "Logs: ${LOG_DIR}"
@@ -26,13 +26,13 @@ if [ -n "$EXTERNAL_BBAV5_WORKER_NAME_PREFIX" ]; then
    BBAV5_WORKER_NAME_PREFIX="$EXTERNAL_BBAV5_WORKER_NAME_PREFIX"
 fi
 if [ -z "${BBAV5_QUEUE_PREFIX-}" ]; then
-    BBAV5_QUEUE_PREFIX="plantai_dev_9000"
+    BBAV5_QUEUE_PREFIX="plantai_4090_9000"
 fi
 if [ -z "${BBAV5_REDIS_URL-}" ]; then
    BBAV5_REDIS_URL="redis://localhost:6379/10"
 fi
 if [ -z "${BBAV5_CELERY_LOG_DIR-}" ]; then
-    BBAV5_CELERY_LOG_DIR="logs/celery_plantai_dev_9000"
+    BBAV5_CELERY_LOG_DIR="logs/celery_plantai_4090_9000"
 fi
 if [ -z "$EXTERNAL_BBAV5_WORKER_NAME_PREFIX" ]; then
    unset BBAV5_WORKER_NAME_PREFIX
@@ -51,11 +51,11 @@ export BBAV5_PROJECT_ENV_FILE="${BBAV5_PROJECT_ENV_FILE:-$PROJECT_ROOT/.env}"
 export BBAV5_LIGHTWEIGHT_EXTENSION_STORE="${BBAV5_LIGHTWEIGHT_EXTENSION_STORE:-$PROJECT_ROOT/.runtime/lightweight-extension/store}"
 export BBAV5_LIGHTWEIGHT_INPUT="${BBAV5_LIGHTWEIGHT_INPUT:-$PROJECT_ROOT/input}"
 export BBAV5_LIGHTWEIGHT_WORKSPACE="${BBAV5_LIGHTWEIGHT_WORKSPACE:-$PROJECT_ROOT/workspace}"
-export BBAV5_QUEUE_PREFIX="${BBAV5_QUEUE_PREFIX:-plantai_dev_9000}"
+export BBAV5_QUEUE_PREFIX="${BBAV5_QUEUE_PREFIX:-plantai_4090_9000}"
 export BBAV5_REDIS_URL="${BBAV5_REDIS_URL:-redis://localhost:6379/10}"
 WORKER_NAME_PREFIX="${BBAV5_WORKER_NAME_PREFIX:-${BBAV5_QUEUE_PREFIX//[^A-Za-z0-9_]/_}}"

-LOG_DIR="${BBAV5_CELERY_LOG_DIR:-logs/celery_plantai_dev_9000}"
+LOG_DIR="${BBAV5_CELERY_LOG_DIR:-logs/celery_plantai_4090_9000}"
 mkdir -p "$LOG_DIR"

 CELERY="$CONDA_ENV/bin/celery"
@@ -1,73 +0,0 @@
-#!/bin/bash
-# Start PlantAI-dev Celery workers for the port-9000 runtime profile.
-
-set -euo pipefail
-
-SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-cd "${BBAV5_PROJECT_ROOT:-$SCRIPT_DIR}"
-
-CONDA_BASE="${BBAV5_CONDA_BASE:-/home/xia-lab/miniconda3}"
-DEFAULT_ENV="${BBAV5_DEFAULT_ENV:-test4py311}"
-CONDA_ENV="$CONDA_BASE/envs/$DEFAULT_ENV"
-export PATH="$CONDA_ENV/bin:$PATH"
-
-export BBAV5_PROJECT_ROOT="${BBAV5_PROJECT_ROOT:-$SCRIPT_DIR}"
-export PLANTAI_PROJECT_ROOT="${PLANTAI_PROJECT_ROOT:-$SCRIPT_DIR}"
-export BBAV5_QUEUE_PREFIX="${BBAV5_QUEUE_PREFIX:-plantai_dev_9000}"
-export BBAV5_REDIS_URL="${BBAV5_REDIS_URL:-redis://localhost:6379/10}"
-
-WORKER_NAME_PREFIX="${BBAV5_WORKER_NAME_PREFIX:-${BBAV5_QUEUE_PREFIX//[^A-Za-z0-9_]/_}}"
-LOG_DIR="${BBAV5_CELERY_LOG_DIR:-logs/celery_plantai_dev_9000}"
-mkdir -p "$LOG_DIR"
-
-CELERY="$CONDA_ENV/bin/celery"
-APP="celery_app"
-LOGLEVEL="${BBAV5_CELERY_LOGLEVEL:-info}"
-
-DEFAULT_CONCURRENCY="${BBAV5_DEFAULT_CONCURRENCY:-1}"
-HEAVY_CONCURRENCY="${BBAV5_HEAVY_CONCURRENCY:-2}"
-MEDIUM_CONCURRENCY="${BBAV5_MEDIUM_CONCURRENCY:-2}"
-LIGHT_CONCURRENCY="${BBAV5_LIGHT_CONCURRENCY:-4}"
-RNASEQ_CONCURRENCY="${BBAV5_RNASEQ_CONCURRENCY:-2}"
-
-worker_online() {
-    local name="$1"
-    if [ "${BBAV5_CELERY_FORCE_START:-0}" = "1" ]; then
-        return 1
-    fi
-    pgrep -f -- "--hostname=${name}@%h" >/dev/null 2>&1
-}
-
-start_worker() {
-    local name="$1"
-    local queue="$2"
-    local concurrency="$3"
-    if [ "$concurrency" -le 0 ]; then
-        echo "Skipping ${name}: concurrency=${concurrency}"
-        return
-    fi
-    if worker_online "$name"; then
-        echo "Skipping ${name}: worker process already exists (${name}@%h)"
-        return
-    fi
-    echo "Starting ${name}: queue=${queue}, concurrency=${concurrency}"
-    "$CELERY" -A "$APP" worker \
-        --detach \
-        --loglevel="$LOGLEVEL" \
-        --hostname="${name}@%h" \
-        --queues="$queue" \
-        --concurrency="$concurrency" \
-        --prefetch-multiplier=1 \
-        --logfile="$LOG_DIR/${name}.log" \
-        --pidfile="$LOG_DIR/${name}.pid"
-}
-
-start_worker "${WORKER_NAME_PREFIX}_default" "${BBAV5_QUEUE_PREFIX}.default" "$DEFAULT_CONCURRENCY"
-start_worker "${WORKER_NAME_PREFIX}_heavy" "${BBAV5_QUEUE_PREFIX}.heavy" "$HEAVY_CONCURRENCY"
-start_worker "${WORKER_NAME_PREFIX}_medium" "${BBAV5_QUEUE_PREFIX}.medium" "$MEDIUM_CONCURRENCY"
-start_worker "${WORKER_NAME_PREFIX}_light" "${BBAV5_QUEUE_PREFIX}.light" "$LIGHT_CONCURRENCY"
-start_worker "${WORKER_NAME_PREFIX}_rnaseq" "${BBAV5_QUEUE_PREFIX}.rnaseq" "$RNASEQ_CONCURRENCY"
-
-echo "Celery workers started with queue prefix: ${BBAV5_QUEUE_PREFIX}"
-echo "Redis: ${BBAV5_REDIS_URL}"
-echo "Logs: ${LOG_DIR}"
@@ -24,6 +24,12 @@ done
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 cd "$SCRIPT_DIR"

+if [ -f "$SCRIPT_DIR/.env" ]; then
+    set -a
+    . "$SCRIPT_DIR/.env"
+    set +a
+fi
+
 CONDA_BASE="${BBAV5_CONDA_BASE:-/home/xia-lab/miniconda3}"
 DEFAULT_ENV="${BBAV5_DEFAULT_ENV:-test4py311}"
 CONDA_ENV="$CONDA_BASE/envs/$DEFAULT_ENV"
@@ -33,23 +39,18 @@ export PATH="$CONDA_ENV/bin:$PATH"
 # the caller's shell; GWAS/other sandboxes have dedicated restart scripts.
 export BBAV5_PROJECT_ROOT="$SCRIPT_DIR"
 export PLANTAI_PROJECT_ROOT="$SCRIPT_DIR"
-if [ -f "$SCRIPT_DIR/.env" ]; then
-    set -a
-    . "$SCRIPT_DIR/.env"
-    set +a
-fi
 export BBAV5_PROJECT_ENV_FILE="${BBAV5_PROJECT_ENV_FILE:-$SCRIPT_DIR/.env}"
 export BBAV5_LIGHTWEIGHT_EXTENSION_STORE="${BBAV5_LIGHTWEIGHT_EXTENSION_STORE:-$SCRIPT_DIR/.runtime/lightweight-extension/store}"
 export BBAV5_LIGHTWEIGHT_INPUT="${BBAV5_LIGHTWEIGHT_INPUT:-$SCRIPT_DIR/input}"
 export BBAV5_LIGHTWEIGHT_WORKSPACE="${BBAV5_LIGHTWEIGHT_WORKSPACE:-$SCRIPT_DIR/workspace}"
-export BBAV5_QUEUE_PREFIX="${BBAV5_QUEUE_PREFIX:-plantai_dev_9000}"
+export BBAV5_QUEUE_PREFIX="${BBAV5_QUEUE_PREFIX:-plantai_4090_9000}"
 export BBAV5_REDIS_URL="${BBAV5_REDIS_URL:-redis://localhost:6379/10}"
 export PLANTAI_WEB_PORT="$PORT"
 export PLANTAI_RESTART_SCRIPT="$SCRIPT_DIR/restart_plantai_9000.sh"
-export GENE_FAMILY_MAS_API="http://127.0.0.1:7926"
-export DUAL_KB_QA_BASE_URL="http://127.0.0.1:7926"
-export RAG_API_URL="http://127.0.0.1:7926/api/v1/qa-v1-1-73/chat"
-export DUAL_KB_QA_ROUTE="qa-v1-1-73"
+export GENE_FAMILY_MAS_API="${GENE_FAMILY_MAS_API:-${DUAL_KB_QA_BASE_URL:-http://127.0.0.1:7920}}"
+export DUAL_KB_QA_BASE_URL="${DUAL_KB_QA_BASE_URL:-$GENE_FAMILY_MAS_API}"
+export RAG_API_URL="${RAG_API_URL:-$GENE_FAMILY_MAS_API}"
+export DUAL_KB_QA_ROUTE="${DUAL_KB_QA_ROUTE:-qa-v1-1-73}"
 export PLANTAI_AGENT_STATE_DB="$SCRIPT_DIR/.runtime/agent-state/agent-state.sqlite3"

 PORT="$PLANTAI_WEB_PORT"