diff --git a/AGENTS.md b/AGENTS.md
index 65a35a5..9c9391f 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -499,3 +499,29 @@ docker exec bttoxin-pipeline curl http://127.0.0.1:8000/api/health
4. **Health Check Path**:
- **Cause**: Nginx routed `/health` to `/api/health` but backend expected `/health`.
- **Fix**: Update Nginx config to proxy pass to correct endpoint.
+
+### Post-Mortem: Consistency Refactoring & Fixes (2026-01-20 Update)
+
+**Summary:**
+Major refactoring to ensure consistency between script execution and web pipeline, fix severe container startup failures, and simplify user experience.
+
+**1. Unified Pipeline Execution**
+- **Problem**: Web backend manually orchestrated pipeline steps, leading to discrepancies with the standalone script (e.g., missing plots, different file formats).
+- **Fix**: Refactored `backend/app/workers/tasks.py` to directly subprocess `scripts/run_single_fna_pipeline.py`.
+- **Result**: Web output is now guaranteed identical to manual script execution.
+
+**2. Result Format & Cleanup**
+- **Change**: Switched output format from `.tar.gz` to `.zip`.
+- **Feature**: Added automatic cleanup of intermediate directories (`digger/`, `shoter/`) to save disk space; only the final ZIP and logs are retained.
+- **Frontend**: Updated download logic to handle `.zip` files.
+
+**3. Frontend Simplification**
+- **Change**: Removed CRISPR Fusion UI elements (beta feature) to reduce complexity.
+- **Change**: Replaced complex multi-stage status indicators with a "Simulated Progress Bar" for better UX during black-box script execution.
+- **Fix**: Restored "One-click load" button and fixed TypeScript build errors caused by removed variables.
+
+**4. Critical Docker Fixes**
+- **Fix (Restart Loop)**: Removed incorrect `image: postgres` directive in `docker-compose.yml` that caused the web service to run database software instead of the app.
+- **Fix (Env Path)**: Updated `.dockerignore` to exclude host `.pixi` directory, preventing "bad interpreter" errors caused by hardcoded host paths in the container.
+- **Fix (404 Error)**: Removed erroneous `rm -rf /app/frontend` in Dockerfile that was accidentally deleting built frontend assets.
+- **Optimization**: Configured `npmmirror` registry to resolve build timeouts in CN network environments.
diff --git a/README.md b/README.md
index 9d76fe6..de7cdc3 100644
--- a/README.md
+++ b/README.md
@@ -407,6 +407,27 @@ The setup uses Traefik for SSL termination and routing. The backend API and fron
For detailed Docker deployment information, see [DOCKER_DEPLOYMENT.md](DOCKER_DEPLOYMENT.md)
+### Building the Image Manually
+
+To build the image manually, ensure you set the correct build context so that `pixi.toml` can be found.
+
+```bash
+# Option 1: From project root (specifying context)
+docker build \
+ --network=host \
+ -f web/zly/docker/dockerfiles/Dockerfile.traefik \
+ -t hotwa/bttoxin-app:latest \
+ web/zly
+
+# Option 2: Enter directory first
+cd web/zly
+docker build \
+ --network=host \
+ -f docker/dockerfiles/Dockerfile.traefik \
+ -t hotwa/bttoxin-app:latest \
+ .
+```
+
## Troubleshooting
### pixi not found
diff --git a/README_CN.md b/README_CN.md
index 58a5cfe..b08ff3c 100644
--- a/README_CN.md
+++ b/README_CN.md
@@ -404,6 +404,27 @@ Docker 部署采用单容器模式，使用 Nginx 同时托管前端静态资源
详细的 Docker 部署信息请参阅 [DOCKER_DEPLOYMENT.md](DOCKER_DEPLOYMENT.md)
+### 手动构建镜像
+
+若要手动构建镜像，请确保设置正确的构建上下文（build context），以便 Docker 能找到 `pixi.toml`。
+
+```bash
+# 选项 1：从项目根目录（指定上下文）
+docker build \
+ --network=host \
+ -f web/zly/docker/dockerfiles/Dockerfile.traefik \
+ -t hotwa/bttoxin-app:latest \
+ web/zly
+
+# 选项 2：先进入目录
+cd web/zly
+docker build \
+ --network=host \
+ -f docker/dockerfiles/Dockerfile.traefik \
+ -t hotwa/bttoxin-app:latest \
+ .
+```
+
## 故障排除
### 找不到 pixi
diff --git a/backend/app/workers/tasks.py b/backend/app/workers/tasks.py
index 86605ea..a5b818f 100644
--- a/backend/app/workers/tasks.py
+++ b/backend/app/workers/tasks.py
@@ -126,42 +126,60 @@ def run_bttoxin_analysis(
logger.info(f"Job {job_id}: Creating zip bundle")
zip_path = output_path / f"pipeline_results_{job_id}.zip"
- # 需要打包的子目录
- subdirs_to_zip = ["digger", "shoter", "logs"]
+ # 在创建新 ZIP 前，删除目录下任何现有的 zip/tar.gz 文件，防止递归打包
+ for existing_archive in output_path.glob("*.zip"):
+ try:
+ existing_archive.unlink()
+ except Exception:
+ pass
+ for existing_archive in output_path.glob("*.tar.gz"):
+ try:
+ existing_archive.unlink()
+ except Exception:
+ pass
+
+ # 定义映射关系：原始目录 -> 压缩包内展示名称
+ dir_mapping = {
+ "digger": "1_Toxin_Mining",
+ "shotter": "2_Toxicity_Scoring",
+ "logs": "Logs"
+ }
with zipfile.ZipFile(zip_path, 'w', zipfile.ZIP_DEFLATED) as zipf:
- # 添加输入文件
- zipf.write(input_file, arcname=input_file.name)
+ # 1. 添加输入文件 (放入 Input 目录)
+ zipf.write(input_file, arcname=f"Input/{input_file.name}")
- # 添加结果目录
- for subdir_name in subdirs_to_zip:
- subdir_path = output_path / subdir_name
- if subdir_path.exists():
- for root, dirs, files in os.walk(subdir_path):
+ # 2. 添加结果目录 (重命名)
+ for src_name, dest_name in dir_mapping.items():
+ src_path = output_path / src_name
+ if src_path.exists():
+ for root, dirs, files in os.walk(src_path):
for file in files:
file_path = Path(root) / file
- # 保持相对路径结构
- arcname = file_path.relative_to(output_path)
+ # 排除压缩包自己（如果有意外情况）
+ if file_path == zip_path:
+ continue
+
+ # 计算相对路径，例如 digger/Results/foo.txt -> Results/foo.txt
+ rel_path = file_path.relative_to(src_path)
+ # 构造新的归档路径 -> 1_Toxin_Mining/Results/foo.txt
+ arcname = Path(dest_name) / rel_path
zipf.write(file_path, arcname=str(arcname))
- # 删除原始结果目录 (保留 logs 以便调试? 或者也删除)
- # 根据需求：只保留压缩包
+ # 删除原始结果目录
logger.info(f"Job {job_id}: Cleaning up intermediate files")
- for subdir_name in subdirs_to_zip:
- subdir_path = output_path / subdir_name
- if subdir_path.exists():
- shutil.rmtree(subdir_path)
+ # 需要清理的原始目录名
+ dirs_to_clean = ["digger", "shotter", "context", "logs", "stage"]
+ for d in dirs_to_clean:
+ d_path = output_path / d
+ if d_path.exists():
+ shutil.rmtree(d_path)
# 删除 tar.gz (如果脚本生成了)
tar_gz = output_path / "pipeline_results.tar.gz"
if tar_gz.exists():
tar_gz.unlink()
- # 移除 stage 目录 (run_single_fna_pipeline 生成的)
- stage_dir = output_path / "stage"
- if stage_dir.exists():
- shutil.rmtree(stage_dir)
-
# 验证 Zip 是否生成
if not zip_path.exists():
raise Exception("Failed to create result zip file")
diff --git a/docker/dockerfiles/Dockerfile.traefik b/docker/dockerfiles/Dockerfile.traefik
index a6e2125..9f7ae19 100644
--- a/docker/dockerfiles/Dockerfile.traefik
+++ b/docker/dockerfiles/Dockerfile.traefik
@@ -11,7 +11,7 @@ WORKDIR /app
COPY . .
# Install dependencies
-RUN pixi install
+RUN pixi install -e digger -e pipeline -e webbackend
# Setup external database for BtToxin_Digger
# Using the copy from tools directory included in COPY . .
diff --git a/frontend/src/locales/en.json b/frontend/src/locales/en.json
index 828f6d4..5827127 100644
--- a/frontend/src/locales/en.json
+++ b/frontend/src/locales/en.json
@@ -1,6 +1,4 @@
-{
- "nav": {
- "home": "Home",
+{ "nav": { "home": "Home",
"contact": "Contact",
"tool": "Prediction Tool",
"docs": "Documentation"
@@ -111,7 +109,23 @@
},
"output": {
"title": "Output Description",
- "desc": "After analysis, you will receive a compressed package containing heatmaps and detailed data, including toxin hit lists, target score matrices, and visualization reports."
+ "desc": "After analysis, you will receive a compressed package containing heatmaps and detailed data, including toxin hit lists, target score matrices, and visualization reports.",
+ "structure": {
+ "title": "Result File Structure",
+ "desc": "The downloaded zip package contains the following directories:"
+ },
+ "files": {
+ "input_dir": "Original Input Files",
+ "mining_dir": "BtToxin_Digger Mining Results",
+ "all_toxins": "Core Result: Predicted Toxin Gene List",
+ "scoring_dir": "Shoter Toxicity Scoring Results",
+ "report": "Comprehensive Analysis Report (Markdown)",
+ "strain_heatmap": "Strain Target Activity Heatmap",
+ "hit_heatmap": "Single Sequence Activity Heatmap",
+ "strain_tsv": "Strain Target Score Raw Data",
+ "toxin_tsv": "Toxin Support Data",
+ "logs": "Execution Logs"
+ }
},
"note": {
"title": "About BtToxin_Shoter",
diff --git a/frontend/src/locales/zh.json b/frontend/src/locales/zh.json
index 89f40c8..7114354 100644
--- a/frontend/src/locales/zh.json
+++ b/frontend/src/locales/zh.json
@@ -101,7 +101,23 @@
},
"output": {
"title": "输出说明",
- "desc": "分析完成后，您将获得一个包含热图和详细数据的压缩包，包括毒素命中列表、靶标评分矩阵和可视化报告。"
+ "desc": "分析完成后，您将获得一个包含热图和详细数据的压缩包，包括毒素命中列表、靶标评分矩阵和可视化报告。",
+ "structure": {
+ "title": "结果文件结构",
+ "desc": "下载的压缩包解压后包含以下目录："
+ },
+ "files": {
+ "input_dir": "原始输入文件目录",
+ "mining_dir": "BtToxin_Digger 毒素挖掘结果",
+ "all_toxins": "核心结果：预测到的毒素基因列表",
+ "scoring_dir": "Shoter 毒性评分结果",
+ "report": "综合分析报告 (Markdown)",
+ "strain_heatmap": "菌株靶标活性评分热图",
+ "hit_heatmap": "单序列活性评分热图",
+ "strain_tsv": "菌株靶标评分原始数据",
+ "toxin_tsv": "毒素支持度数据",
+ "logs": "运行日志目录"
+ }
},
"note": {
"title": "关于 BtToxin_Shoter",
diff --git a/frontend/src/views/TaskMonitorView.vue b/frontend/src/views/TaskMonitorView.vue
index 22b3653..9a83a43 100644
--- a/frontend/src/views/TaskMonitorView.vue
+++ b/frontend/src/views/TaskMonitorView.vue
@@ -62,12 +62,12 @@
- {{ $t('status.running.progress', { percent: simulatedProgress }) }}
+ {{ $t('status.running.progress', { percent: simulatedProgress.toFixed(1) }) }}
diff --git a/frontend/src/views/TutorialView.vue b/frontend/src/views/TutorialView.vue
index d8d7b00..2934639 100644
--- a/frontend/src/views/TutorialView.vue
+++ b/frontend/src/views/TutorialView.vue
@@ -145,18 +145,19 @@ const { t } = useI18n()
-pipeline_results.zip
-├── digger/
+pipeline_results_{id}.zip
+├── Input/ # {{ t('tutorial.output.files.input_dir') }}
+│ └── filename.fna
+├── 1_Toxin_Mining/ # {{ t('tutorial.output.files.mining_dir') }}
│ ├── Results/Toxins/
│ │ └── All_Toxins.txt # {{ t('tutorial.output.files.all_toxins') }}
│ └── ...
-├── shotter/
+├── 2_Toxicity_Scoring/ # {{ t('tutorial.output.files.scoring_dir') }}
+│ ├── shotter_report.md # {{ t('tutorial.output.files.report') }}
│ ├── strain_target_scores.png # {{ t('tutorial.output.files.strain_heatmap') }}
│ ├── per_hit_{id}.png # {{ t('tutorial.output.files.hit_heatmap') }}
-│ ├── shotter_report.md # {{ t('tutorial.output.files.report') }}
-│ ├── strain_target_scores.tsv # {{ t('tutorial.output.files.strain_tsv') }}
-│ └── toxin_support.tsv # {{ t('tutorial.output.files.toxin_tsv') }}
-└── logs/ # {{ t('tutorial.output.files.logs') }}
+│ └── ...
+└── Logs/ # {{ t('tutorial.output.files.logs') }}
diff --git a/pixi.toml b/pixi.toml
index e3d9330..b982f3b 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -1,6 +1,6 @@
[workspace]
name = "bttoxin-pipeline"
-channels = ["conda-forge", "bioconda", "bioconda/label/cf201901"]
+channels = ["conda-forge", "bioconda"]
platforms = ["linux-64"]
version = "0.1.0"
channel-priority = "disabled"
@@ -8,6 +8,9 @@ channel-priority = "disabled"
# =========================
# digger 环境：bioconda 依赖
# =========================
+[feature.digger]
+channels = ["bioconda", "conda-forge", "bioconda/label/cf201901"]
+
[feature.digger.dependencies]
bttoxin_digger = "==1.0.10"
perl = "==5.26.2"