#!/usr/bin/env python3
"""
Annotation Skill Tests - 功能注释技能测试
"""

import json
import os
import sys
import tempfile
import unittest
from pathlib import Path

sys.path.insert(0, str(Path(__file__).parent.parent))

from run import AnnotationSkill


class TestAnnotationSkill(unittest.TestCase):
    """测试功能注释技能"""
    
    def setUp(self):
        self.skill = AnnotationSkill()
        self.temp_dir = Path(tempfile.mkdtemp())
    
    def tearDown(self):
        import shutil
        if self.temp_dir.exists():
            shutil.rmtree(self.temp_dir)
    
    def test_find_emapper(self):
        """测试查找emapper.py"""
        try:
            python_path, emapper_path = self.skill._find_emapper()
            self.assertTrue(Path(python_path).exists())
            self.assertTrue(Path(emapper_path).exists())
        except RuntimeError:
            self.skipTest("emapper.py not installed")
    
    def test_parse_annotations(self):
        """测试解析annotations文件"""
        annot_file = self.temp_dir / "test.emapper.annotations"
        annot_file.write_text("""## emapper-version: 2.1.12
#query\tseed_ortholog\tevalue\tscore\teggnog_OGs\tmax_annot_lvl\tCOG_category\tDescription\tPreferred_name\tGOs\tEC\tKEGG_ko\tKEGG_Pathway\tKEGG_Module\tKEGG_Reaction\tKEGG_rclass\tBRITE\tKEGG_TC\tCAZy\tBiGG_Reaction\tPFAMs
Gene001\t10090.1\t1e-50\t200.0\tCOG0001@1|root\tEukaryota\tJ\tDesc\tGENE1\tGO:0005524\t-\tko:K00001\t-\t-\t-\t-\t-\t-\t-\t-\tPF00001
Gene002\t10090.2\t2e-45\t180.0\tCOG0002@1|root\tEukaryota\tK\tDesc\tGENE2\tGO:0003677\t-\tko:K00002\t-\t-\t-\t-\t-\t-\t-\t-\tPF00002
Gene003\t10090.3\t5e-40\t160.0\tCOG0003@1|root\tEukaryota\tL\tDesc\tGENE3\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\tPF00003
""")
        
        stats = self.skill._parse_annotations(annot_file)
        
        self.assertEqual(stats["total_genes"], 3)
        self.assertEqual(stats["with_go"], 2)
        self.assertEqual(stats["with_kegg"], 2)
        self.assertEqual(stats["with_cog"], 3)
        self.assertEqual(stats["with_pfam"], 3)
        self.assertEqual(stats["go_count"], 2)
        self.assertEqual(stats["kegg_count"], 2)
    
    def test_demo_mode(self):
        """测试Demo模式"""
        result = self.skill.run_demo(self.temp_dir)
        
        self.assertEqual(result["status"], "success")
        self.assertTrue(Path(result["annotations"]).exists())
        self.assertTrue(Path(result["report"]).exists())
        
        # 检查输出文件
        annot_file = Path(result["annotations"])
        self.assertTrue(annot_file.exists())
        
        # 检查统计
        self.assertEqual(result["stats"]["total_genes"], 3)
    
    def test_config_loading(self):
        """测试配置加载"""
        config = self.skill.config
        
        self.assertIn("skill", config)
        self.assertIn("parameters", config)
        self.assertIn("emapper", config["parameters"])
        
        emapper_params = config["parameters"]["emapper"]
        self.assertIn("mode", emapper_params)
        self.assertIn("evalue", emapper_params)
        self.assertIn("cpu", emapper_params)


if __name__ == "__main__":
    unittest.main()