"""
GeneIdentify技能单元测试
"""

import pytest
from pathlib import Path
from unittest.mock import Mock, patch

PROJECT_ROOT = Path(__file__).resolve().parents[3]


@pytest.mark.unit
class TestGeneIdentifySkill:
    """测试基因鉴定技能"""
    
    def test_skill_exists(self):
        """测试技能目录存在"""
        skill_dir = PROJECT_ROOT / "skills" / "gene-identify"
        assert skill_dir.exists()
        assert (skill_dir / "SKILL.md").exists()
        assert (skill_dir / "run.py").exists()
    
    def test_skill_documentation(self):
        """测试技能文档完整"""
        skill_doc = PROJECT_ROOT / "skills" / "gene-identify" / "SKILL.md"
        content = skill_doc.read_text()
        
        assert "Gene Identify" in content
        assert "输入" in content
        assert "输出" in content
        assert "使用" in content
    
    def test_skill_config(self):
        """测试技能配置存在"""
        config_file = PROJECT_ROOT / "skills" / "gene-identify" / "config.yaml"
        assert config_file.exists()
    
    def test_required_tools(self):
        """测试必需工具存在"""
        tools_dir = PROJECT_ROOT / "skills" / "gene-identify" / "tools"
        # 工具目录可以不存在，但技能应该能运行
        pass
    
    @pytest.mark.parametrize("input_file,expected", [
        ("protein.fa", True),
        ("genes.fa", True),
        ("", False),
    ])
    def test_input_validation(self, input_file, expected):
        """测试输入验证"""
        # 模拟输入验证
        is_valid = len(input_file) > 0 and input_file.endswith('.fa')
        assert is_valid == expected
    
    def test_output_structure(self):
        """测试输出结构定义"""
        expected_outputs = [
            "report.md",
            "tables/gene_list.csv",
            "tables/statistics.csv",
        ]
        
        for output in expected_outputs:
            assert output  # 确保输出定义存在


@pytest.mark.unit
class TestSkillRegistry:
    """测试技能注册"""
    
    def test_stage_registry_exists(self):
        """测试StageToolRegistry存在"""
        from gfa_core.mas.tools.stage_registry import StageToolRegistry
        assert StageToolRegistry is not None
    
    def test_gene_identify_in_registry(self):
        """测试gene-identify在注册表中"""
        from gfa_core.mas.tools.stage_registry import create_stage_registry
        
        registry = create_stage_registry()
        # 检查是否有gene-identify或类似ID
        stage_ids = list(registry._tools.keys())
        
        # 应该有基因鉴定相关的阶段
        identify_stages = [s for s in stage_ids if 'identif' in s.lower()]
        assert len(identify_stages) > 0