Refactor: Unified pipeline execution, simplified UI, and fixed Docker config

- Backend: Refactored tasks.py to directly invoke run_single_fna_pipeline.py for consistency.
- Backend: Changed output format to ZIP and added auto-cleanup of intermediate files.
- Backend: Fixed language parameter passing in API and tasks.
- Frontend: Removed CRISPR Fusion UI elements from Submit and Monitor views.
- Frontend: Implemented simulated progress bar for better UX.
- Frontend: Restored One-click load button and added result file structure documentation.
- Docker: Fixed critical Restarting loop by removing incorrect image directive in docker-compose.yml.
- Docker: Optimized Dockerfile to correct .pixi environment path issues and prevent accidental deletion of frontend assets.

scripts/plot_shotter.py

@@ -18,8 +18,9 @@ Dependencies:
 from __future__ import annotations
 
 import argparse
+import json
 from pathlib import Path
-from typing import List, Optional
+from typing import List, Optional, Dict, Any
 
 import pandas as pd
 
@@ -29,6 +30,8 @@ try:
 except Exception:
     _HAS_SNS = False
 
+import matplotlib
+matplotlib.use("Agg")
 import matplotlib.pyplot as plt
 
 
@@ -265,6 +268,65 @@ def _labels(lang: str):
     return zh if lang == "zh" else en
 
 
+def _format_crispr_section(crispr_data: Dict[str, Any], lang: str) -> List[str]:
+    """Format CRISPR analysis results as a Markdown section."""
+    L = {
+        "zh": {
+            "title": "## CRISPR-Cas 融合分析",
+            "summary": "CRISPR-Cas 系统检测摘要",
+            "associations": "CRISPR-毒素关联",
+            "arrays": "检测到的 CRISPR Arrays",
+            "proximal": "邻近关联 (Proximity)",
+            "spacer": "Spacer 匹配",
+            "none": "未检测到显著关联。",
+            "table_header": "类型 | 毒素 | 距离 (bp) | Array ID",
+            "table_sep": "--- | --- | --- | ---"
+        },
+        "en": {
+            "title": "## CRISPR-Cas Fusion Analysis",
+            "summary": "CRISPR-Cas System Detection Summary",
+            "associations": "CRISPR-Toxin Associations",
+            "arrays": "Detected CRISPR Arrays",
+            "proximal": "Proximity",
+            "spacer": "Spacer Match",
+            "none": "No significant associations detected.",
+            "table_header": "Type | Toxin | Distance (bp) | Array ID",
+            "table_sep": "--- | --- | --- | ---"
+        }
+    }
+    txt = L.get(lang, L["en"])
+    lines = []
+    lines.append(txt["title"])
+    lines.append("")
+
+    # Summary
+    if "summary" in crispr_data:
+        s = crispr_data["summary"]
+        lines.append(f"- **{txt['proximal']}**: {s.get('proximal_pairs', 0)}")
+        lines.append(f"- **{txt['spacer']}**: {s.get('spacer_matches', 0)}")
+        lines.append("")
+
+    # Associations Table
+    assocs = crispr_data.get("associations", [])
+    if assocs:
+        lines.append(f"### {txt['associations']}")
+        lines.append("")
+        lines.append(txt["table_header"])
+        lines.append(txt["table_sep"])
+        for a in assocs:
+            atype = a.get("type", "unknown")
+            toxin = a.get("toxin", "")
+            dist = a.get("distance", "-")
+            aid = a.get("array_id", "")
+            lines.append(f"{atype} | {toxin} | {dist} | {aid}")
+        lines.append("")
+    else:
+        lines.append(txt["none"])
+        lines.append("")
+
+    return lines
+
+
 def write_summary_md(
     out_path: Path,
     strain_scores_path: Path,
@@ -275,11 +337,18 @@ def write_summary_md(
     species_heatmap_path: Optional[Path],
     merge_unresolved: bool,
     args_namespace,
+    crispr_data: Optional[Dict] = None,
 ):
     labels = _labels(getattr(args_namespace, "lang", "zh"))
     lines: List[str] = []
-    lines.append(labels["summary"]) 
+    lines.append(labels["summary"])
     lines.append("")
+
+    # CRISPR Section (Top)
+    if crispr_data:
+        lines.extend(_format_crispr_section(crispr_data, getattr(args_namespace, "lang", "zh")))
+        lines.append("")
+
     # Parameters
     lines.append(labels["params"])
     lines.append(f"- allow_unknown_families: {getattr(args_namespace, 'allow_unknown_families', 'NA')}")
@@ -359,6 +428,7 @@ def write_report_md(
     species_heatmap_path: Optional[Path],
     merge_unresolved: bool,
     args_namespace,
+    crispr_data: Optional[Dict] = None,
 ):
     if mode == "summary":
         return write_summary_md(
@@ -371,6 +441,7 @@ def write_report_md(
             species_heatmap_path,
             merge_unresolved,
             args_namespace,
+            crispr_data,
         )
 
     L = _labels(lang)
@@ -551,6 +622,7 @@ def main():
         species_heatmap_path=species_png,
         merge_unresolved=args.merge_unresolved,
         args_namespace=args,
+        crispr_data=crispr_data,
     )
     print(f"Saved: {summary_md}")