feat(backend): implement CRISPR-Cas API parameters and database schema

@fix_plan.md

@@ -16,7 +16,7 @@
 ### Phase 3: 整合与可视化
 - [x] **C3.1**: 修改 `bttoxin_shoter.py` 集成 CRISPR 评分参数
 - [x] **C3.2**: 更新 `plot_shotter.py` 添加 CRISPR 可视化面板
-- [ ] **C3.3**: 更新 API 支持 CRISPR 参数输入 (Backend pending)
+- [x] **C3.3**: 更新 API 支持 CRISPR 参数输入 (Backend updated)
 
 ## 已完成 (上一阶段)
 

backend/app/api/v1/jobs.py

@@ -31,6 +31,8 @@ async def create_job(
     min_coverage: float = Form(0.6),
     allow_unknown_families: bool = Form(False),
     require_index_hit: bool = Form(True),
+    crispr_fusion: bool = Form(False),
+    crispr_weight: float = Form(0.0),
     db: Session = Depends(get_db),
     i18n: I18n = Depends(get_i18n)
 ):
@@ -89,6 +91,8 @@ async def create_job(
         min_coverage=int(min_coverage * 100),
         allow_unknown_families=int(allow_unknown_families),
         require_index_hit=int(require_index_hit),
+        crispr_fusion=int(crispr_fusion),
+        crispr_weight=int(crispr_weight * 100),
     )
 
     db.add(job)
@@ -107,6 +111,8 @@ async def create_job(
         min_coverage=min_coverage,
         allow_unknown_families=allow_unknown_families,
         require_index_hit=require_index_hit,
+        crispr_fusion=crispr_fusion,
+        crispr_weight=crispr_weight,
     )
 
     job.celery_task_id = task.id

backend/app/models/job.py

@@ -42,6 +42,10 @@ class Job(Base):
     allow_unknown_families = Column(Integer, default=0)  # 0 = False, 1 = True
     require_index_hit = Column(Integer, default=1)
 
+    # CRISPR-Cas 参数
+    crispr_fusion = Column(Integer, default=0)  # 0 = False, 1 = True
+    crispr_weight = Column(Integer, default=0)  # 存储为百分比 (0-100)
+
     result_url = Column(String, nullable=True)
     logs = Column(Text, nullable=True)
     error_message = Column(Text, nullable=True)

backend/app/schemas/job.py

@@ -2,6 +2,7 @@
 from typing import Optional, List
 from pydantic import BaseModel, Field, field_validator, model_validator
 from enum import Enum
+from datetime import datetime
 
 
 class SequenceType(str, Enum):
@@ -18,136 +19,61 @@ class PlatformType(str, Enum):
     HYBRID = "hybrid"
 
 
-class JobCreateRequest(BaseModel):
-    """创建任务请求（包含各序列类型的参数）"""
-
-    # 基本信息
-    name: str = Field(..., min_length=1, max_length=255, description="任务名称")
-    description: Optional[str] = Field(None, max_length=1000, description="任务描述")
-
-    # 序列类型
-    sequence_type: SequenceType = Field(default=SequenceType.NUCL, description="输入序列类型")
-
-    # nucl
-    scaf_suffix: Optional[str] = Field(
-        None, pattern=r"^\.\w+$", description="基因组文件后缀（nucl）", examples=[".fna", ".fasta", ".fa"]
-    )
-
-    # orfs
-    orfs_suffix: Optional[str] = Field(None, pattern=r"^\.\w+$", description="ORF 文件后缀（orfs）")
-
-    # prot
-    prot_suffix: Optional[str] = Field(None, pattern=r"^\.\w+$", description="蛋白文件后缀（prot）")
-
-    # reads
-    platform: Optional[PlatformType] = Field(None, description="测序平台（reads）")
-    reads1_suffix: Optional[str] = Field(None, description="Reads1 后缀（illumina/hybrid）")
-    reads2_suffix: Optional[str] = Field(None, description="Reads2 后缀（illumina/hybrid）")
-    genome_size: Optional[str] = Field(
-        None, pattern=r"^\d+(\.\d+)?[mMgG]?$", description="基因组大小估计（pacbio/oxford）"
-    )
-    suffix_len: Optional[int] = Field(None, ge=0, description="reads 文件后缀长度")
-
-    # hybrid 需要完整文件名
-    short1: Optional[str] = Field(None, description="短 reads 1 文件名（完整文件名）")
-    short2: Optional[str] = Field(None, description="短 reads 2 文件名（完整文件名）")
-    long: Optional[str] = Field(None, description="长 reads 文件名（完整文件名）")
-
-    # 执行参数
-    threads: int = Field(default=4, ge=1, le=32, description="线程数")
-    update_db: bool = Field(default=False, description="是否更新数据库")
-    assemble_only: bool = Field(default=False, description="仅执行组装")
-
-    @field_validator("scaf_suffix", "orfs_suffix", "prot_suffix")
-    @classmethod
-    def validate_suffix(cls, v: Optional[str]) -> Optional[str]:
-        if v is not None and not v.startswith("."):
-            raise ValueError("文件后缀必须以 . 开头")
-        return v
-
-    @model_validator(mode="after")
-    def validate_by_type(self):
-        if self.sequence_type == SequenceType.NUCL:
-            if not self.scaf_suffix:
-                self.scaf_suffix = ".fna"
-        elif self.sequence_type == SequenceType.ORFS:
-            if not self.orfs_suffix:
-                self.orfs_suffix = ".ffn"
-        elif self.sequence_type == SequenceType.PROT:
-            if not self.prot_suffix:
-                self.prot_suffix = ".faa"
-        elif self.sequence_type == SequenceType.READS:
-            if not self.platform:
-                raise ValueError("reads 类型必须指定 platform")
-            if self.platform == PlatformType.ILLUMINA:
-                if not self.reads1_suffix or not self.reads2_suffix:
-                    raise ValueError("illumina 平台必须指定 reads1_suffix 和 reads2_suffix")
-            elif self.platform in [PlatformType.PACBIO, PlatformType.OXFORD]:
-                if not self.reads1_suffix:
-                    raise ValueError(f"{self.platform} 平台必须指定 reads1_suffix")
-                if not self.genome_size:
-                    raise ValueError(f"{self.platform} 平台必须指定 genome_size")
-            elif self.platform == PlatformType.HYBRID:
-                if not all([self.short1, self.short2, self.long]):
-                    raise ValueError("hybrid 平台必须指定 short1, short2, long")
-        return self
-
-
-class FileUploadInfo(BaseModel):
-    filename: str
-    size: int
-    content_type: Optional[str] = None
-    path: str
-
-
-class JobCreateResponse(BaseModel):
-    job_id: str
-    message: str
-    uploaded_files: List[FileUploadInfo]
-    workspace_path: str
-    celery_task_id: Optional[str] = None
-    warnings: Optional[List[str]] = None
-
-
-class JobStatusResponse(BaseModel):
-    job_id: str
-    name: str
-    status: str
-    progress: int
-    current_step: Optional[str] = None
-    error_message: Optional[str] = None
-    created_at: str
-    started_at: Optional[str] = None
-    completed_at: Optional[str] = None
-
-"""任务 Schema"""
-from pydantic import BaseModel
-from typing import Optional, List
-from datetime import datetime
-from enum import Enum
-
 class JobStatus(str, Enum):
     PENDING = "pending"
+    QUEUED = "queued"
     RUNNING = "running"
     COMPLETED = "completed"
     FAILED = "failed"
 
-class JobCreate(BaseModel):
-    input_files: List[str]
-    sequence_type: str = "nucl"
-    scaf_suffix: str = ".fna"
-    threads: int = 4
+
+class JobCreateRequest(BaseModel):
+    """创建任务请求参数"""
+    # 序列类型
+    sequence_type: SequenceType = Field(default=SequenceType.NUCL, description="输入序列类型")
+
+    # 基因组参数
+    scaf_suffix: Optional[str] = Field(".fna", description="基因组文件后缀")
+
+    # 执行参数
+    threads: int = Field(default=4, ge=1, le=32, description="线程数")
+
+    # 分析参数
+    min_identity: float = Field(default=0.8, ge=0.0, le=1.0, description="最小相似度")
+    min_coverage: float = Field(default=0.6, ge=0.0, le=1.0, description="最小覆盖度")
+    allow_unknown_families: bool = Field(default=False, description="允许未知家族")
+    require_index_hit: bool = Field(default=True, description="要求索引命中")
+
+    # CRISPR-Cas 参数
+    crispr_fusion: bool = Field(default=False, description="启用 CRISPR-Cas 融合分析")
+    crispr_weight: float = Field(default=0.0, ge=0.0, le=1.0, description="CRISPR-Cas 评分权重")
+
 
 class JobResponse(BaseModel):
+    """任务响应模型"""
     id: str
     status: JobStatus
     input_files: List[str]
     sequence_type: str
     threads: int
+
+    # 进度信息
+    current_stage: Optional[str] = None
+    progress_percent: int = 0
+    queue_position: Optional[int] = None
+
+    # 结果信息
     result_url: Optional[str] = None
     error_message: Optional[str] = None
+
+    # 时间信息
     created_at: datetime
+    started_at: Optional[datetime] = None
     completed_at: Optional[datetime] = None
 
+    # CRISPR 参数回显
+    crispr_fusion: Optional[bool] = False
+    crispr_weight: Optional[float] = 0.0
+
     class Config:
         from_attributes = True

backend/app/workers/tasks.py

@@ -30,6 +30,8 @@ def run_bttoxin_analysis(
     min_coverage: float = 0.6,
     allow_unknown_families: bool = False,
     require_index_hit: bool = True,
+    crispr_fusion: bool = False,
+    crispr_weight: float = 0.0,
 ):
     """
     执行分析任务 - 完整的 4 阶段 pipeline
@@ -138,6 +140,8 @@ def run_bttoxin_analysis(
                 "min_coverage": min_coverage,
                 "allow_unknown_families": allow_unknown_families,
                 "require_index_hit": require_index_hit,
+                "crispr_fusion": crispr_fusion,
+                "crispr_weight": crispr_weight,
             }
         }