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    {
      "label": "\u53d1\u9001\u6587\u672c\u6d88\u606f                  Args:             user_id: \u7528\u6237\u5fae\u4fe1ID             message: \u6d88",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
      "source_location": "L150",
      "id": "wechat_integration_rationale_150",
      "community": 11
    },
    {
      "label": "\u53d1\u9001\"\u6b63\u5728\u8f93\u5165...\"\u72b6\u6001                  Args:             user_id: \u7528\u6237\u5fae\u4fe1ID",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
      "source_location": "L172",
      "id": "wechat_integration_rationale_172",
      "community": 11
    },
    {
      "label": "\u53d1\u9001\u4efb\u52a1\u5b8c\u6210\u901a\u77e5                  Args:             user_id: \u7528\u6237\u5fae\u4fe1ID             task_inf",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
      "source_location": "L187",
      "id": "wechat_integration_rationale_187",
      "community": 11
    },
    {
      "label": "\u83b7\u53d6\u65b0\u6d88\u606f\uff08\u957f\u8f6e\u8be2\uff09                  Args:             timeout: \u8f6e\u8be2\u8d85\u65f6\u65f6\u95f4\uff08\u79d2\uff09",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
      "source_location": "L229",
      "id": "wechat_integration_rationale_229",
      "community": 11
    },
    {
      "label": "\u542f\u52a8\u6d88\u606f\u76d1\u542c\u5faa\u73af                  Args:             callback: \u6d88\u606f\u5904\u7406\u56de\u8c03\u51fd\u6570             poll_",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
      "source_location": "L255",
      "id": "wechat_integration_rationale_255",
      "community": 11
    },
    {
      "label": "\u8c03\u7528 MCP \u5de5\u5177                  \u9996\u5148\u5c1d\u8bd5\u4f7f\u7528\u771f\u5b9e\u7684 mcp-wechat-server\uff0c\u5982\u679c\u5931\u8d25\u5219\u56de\u9000\u5230\u6a21\u62df\u6a21\u5f0f",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
      "source_location": "L280",
      "id": "wechat_integration_rationale_280",
      "community": 11
    },
    {
      "label": "\u4efb\u52a1\u901a\u77e5\u5668 - \u4e0e bbav20311 \u4efb\u52a1\u7cfb\u7edf\u96c6\u6210          \u4f7f\u7528\u793a\u4f8b:         notifier = WeChatTaskNotifier(",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
      "source_location": "L397",
      "id": "wechat_integration_rationale_397",
      "community": 11
    },
    {
      "label": "pipeline_backend_patch.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/pipeline_backend_patch.py",
      "source_location": "L1",
      "id": "pipeline_backend_patch",
      "community": 80
    },
    {
      "label": "apply_patch_to_pipeline_backend()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/pipeline_backend_patch.py",
      "source_location": "L64",
      "id": "pipeline_backend_patch_apply_patch_to_pipeline_backend",
      "community": 80
    },
    {
      "label": "\u81ea\u52a8\u5e94\u7528\u8865\u4e01\u5230 pipeline_backend.py",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/pipeline_backend_patch.py",
      "source_location": "L65",
      "id": "pipeline_backend_patch_rationale_65",
      "community": 80
    },
    {
      "label": "test_router.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/tests/unit/agents/test_router.py",
      "source_location": "L1",
      "id": "test_router",
      "community": 58
    },
    {
      "label": "classify()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/test_router.py",
      "source_location": "L9",
      "id": "test_router_classify",
      "community": 58
    },
    {
      "label": "example_task_with_wechat.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/example_task_with_wechat.py",
      "source_location": "L1",
      "id": "example_task_with_wechat",
      "community": 31
    },
    {
      "label": "run_identify_with_notification()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/example_task_with_wechat.py",
      "source_location": "L22",
      "id": "example_task_with_wechat_run_identify_with_notification",
      "community": 31
    },
    {
      "label": "run_pipeline_with_notifications()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/example_task_with_wechat.py",
      "source_location": "L77",
      "id": "example_task_with_wechat_run_pipeline_with_notifications",
      "community": 31
    },
    {
      "label": "main()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/example_task_with_wechat.py",
      "source_location": "L152",
      "id": "example_task_with_wechat_main",
      "community": 31
    },
    {
      "label": "\u8fd0\u884c\u57fa\u56e0\u5bb6\u65cf\u9274\u5b9a\u4efb\u52a1\uff0c\u5e76\u53d1\u9001\u5fae\u4fe1\u901a\u77e5          \u4f7f\u7528\u793a\u4f8b:         await run_identify_with_notification(\"",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/example_task_with_wechat.py",
      "source_location": "L23",
      "id": "example_task_with_wechat_rationale_23",
      "community": 31
    },
    {
      "label": "\u8fd0\u884c\u591a\u9636\u6bb5 pipeline\uff0c\u6bcf\u4e2a\u9636\u6bb5\u90fd\u53d1\u9001\u901a\u77e5          \u4f7f\u7528\u793a\u4f8b:         await run_pipeline_with_notifica",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/example_task_with_wechat.py",
      "source_location": "L82",
      "id": "example_task_with_wechat_rationale_82",
      "community": 31
    },
    {
      "label": "enable_persistent_memory.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/enable_persistent_memory.py",
      "source_location": "L1",
      "id": "enable_persistent_memory",
      "community": 81
    },
    {
      "label": "create_persistent_memory_manager()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/enable_persistent_memory.py",
      "source_location": "L15",
      "id": "enable_persistent_memory_create_persistent_memory_manager",
      "community": 81
    },
    {
      "label": "test_persistent_memory()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/enable_persistent_memory.py",
      "source_location": "L47",
      "id": "enable_persistent_memory_test_persistent_memory",
      "community": 81
    },
    {
      "label": "check_cost.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/check_cost.py",
      "source_location": "L1",
      "id": "check_cost",
      "community": 55
    },
    {
      "label": "get_cost_summary()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/check_cost.py",
      "source_location": "L13",
      "id": "check_cost_get_cost_summary",
      "community": 55
    },
    {
      "label": "get_cost_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/check_cost.py",
      "source_location": "L27",
      "id": "check_cost_get_cost_report",
      "community": 55
    },
    {
      "label": "get_agent_cost()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/check_cost.py",
      "source_location": "L41",
      "id": "check_cost_get_agent_cost",
      "community": 55
    },
    {
      "label": "get_suggestions()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/check_cost.py",
      "source_location": "L55",
      "id": "check_cost_get_suggestions",
      "community": 55
    },
    {
      "label": "print_summary()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/check_cost.py",
      "source_location": "L69",
      "id": "check_cost_print_summary",
      "community": 55
    },
    {
      "label": "print_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/check_cost.py",
      "source_location": "L111",
      "id": "check_cost_print_report",
      "community": 55
    },
    {
      "label": "main()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/check_cost.py",
      "source_location": "L120",
      "id": "check_cost_main",
      "community": 55
    },
    {
      "label": "notify_integration.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/notify_integration.py",
      "source_location": "L1",
      "id": "notify_integration",
      "community": 31
    },
    {
      "label": "call_mcp_tool()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/notify_integration.py",
      "source_location": "L28",
      "id": "notify_integration_call_mcp_tool",
      "community": 31
    },
    {
      "label": "check_login_status()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/notify_integration.py",
      "source_location": "L78",
      "id": "notify_integration_check_login_status",
      "community": 31
    },
    {
      "label": "send_text_message()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/notify_integration.py",
      "source_location": "L87",
      "id": "notify_integration_send_text_message",
      "community": 31
    },
    {
      "label": "notify_task_start()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/notify_integration.py",
      "source_location": "L96",
      "id": "notify_integration_notify_task_start",
      "community": 31
    },
    {
      "label": "notify_task_complete()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/notify_integration.py",
      "source_location": "L118",
      "id": "notify_integration_notify_task_complete",
      "community": 31
    },
    {
      "label": "test_notification()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/notify_integration.py",
      "source_location": "L175",
      "id": "notify_integration_test_notification",
      "community": 31
    },
    {
      "label": "\u901a\u77e5\u4efb\u52a1\u5f00\u59cb          \u4f7f\u7528\u793a\u4f8b:         notify_task_start(\"wxid_xxx\", \"task_001\", \"identif",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/notify_integration.py",
      "source_location": "L97",
      "id": "notify_integration_rationale_97",
      "community": 31
    },
    {
      "label": "\u901a\u77e5\u4efb\u52a1\u5b8c\u6210          \u4f7f\u7528\u793a\u4f8b:         notify_task_complete(             \"wxid_xxx\",",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/notify_integration.py",
      "source_location": "L126",
      "id": "notify_integration_rationale_126",
      "community": 31
    },
    {
      "label": "wechat_bot.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_bot.py",
      "source_location": "L1",
      "id": "wechat_bot",
      "community": 59
    },
    {
      "label": "call_mcp_tool()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_bot.py",
      "source_location": "L20",
      "id": "wechat_bot_call_mcp_tool",
      "community": 59
    },
    {
      "label": "send_message()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_bot.py",
      "source_location": "L63",
      "id": "wechat_bot_send_message",
      "community": 59
    },
    {
      "label": "get_messages()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_bot.py",
      "source_location": "L71",
      "id": "wechat_bot_get_messages",
      "community": 59
    },
    {
      "label": "handle_message()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_bot.py",
      "source_location": "L76",
      "id": "wechat_bot_handle_message",
      "community": 59
    },
    {
      "label": "main()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_bot.py",
      "source_location": "L137",
      "id": "wechat_bot_main",
      "community": 59
    },
    {
      "label": "# TODO: \u5b9e\u9645\u8c03\u7528 bbav20311 \u5206\u6790\u4efb\u52a1",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_bot.py",
      "source_location": "L128",
      "id": "wechat_bot_rationale_128",
      "community": 59
    },
    {
      "label": "tasks.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/tasks.py",
      "source_location": "L1",
      "id": "tasks",
      "community": 74
    },
    {
      "label": "get_orchestrator()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/tasks.py",
      "source_location": "L18",
      "id": "tasks_get_orchestrator",
      "community": 74
    },
    {
      "label": "execute_agent_task()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/tasks.py",
      "source_location": "L35",
      "id": "tasks_execute_agent_task",
      "community": 74
    },
    {
      "label": "celery_app.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/celery_app.py",
      "source_location": "L1",
      "id": "celery_app",
      "community": 74
    },
    {
      "label": "wechat_task_bridge.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_task_bridge.py",
      "source_location": "L1",
      "id": "wechat_task_bridge",
      "community": 11
    },
    {
      "label": "WeChatTaskBridge",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_task_bridge.py",
      "source_location": "L42",
      "id": "wechat_task_bridge_wechattaskbridge",
      "community": 11
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_task_bridge.py",
      "source_location": "L49",
      "id": "wechat_task_bridge_wechattaskbridge_init",
      "community": 11
    },
    {
      "label": ".start()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_task_bridge.py",
      "source_location": "L54",
      "id": "wechat_task_bridge_wechattaskbridge_start",
      "community": 11
    },
    {
      "label": "._handle_message()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_task_bridge.py",
      "source_location": "L78",
      "id": "wechat_task_bridge_wechattaskbridge_handle_message",
      "community": 11
    },
    {
      "label": "._parse_command()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_task_bridge.py",
      "source_location": "L95",
      "id": "wechat_task_bridge_wechattaskbridge_parse_command",
      "community": 11
    },
    {
      "label": "._get_help_message()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_task_bridge.py",
      "source_location": "L141",
      "id": "wechat_task_bridge_wechattaskbridge_get_help_message",
      "community": 11
    },
    {
      "label": "._get_system_status()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_task_bridge.py",
      "source_location": "L175",
      "id": "wechat_task_bridge_wechattaskbridge_get_system_status",
      "community": 11
    },
    {
      "label": "._get_task_list()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_task_bridge.py",
      "source_location": "L191",
      "id": "wechat_task_bridge_wechattaskbridge_get_task_list",
      "community": 11
    },
    {
      "label": "._get_task_detail()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_task_bridge.py",
      "source_location": "L216",
      "id": "wechat_task_bridge_wechattaskbridge_get_task_detail",
      "community": 11
    },
    {
      "label": "._cancel_task()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_task_bridge.py",
      "source_location": "L252",
      "id": "wechat_task_bridge_wechattaskbridge_cancel_task",
      "community": 11
    },
    {
      "label": "._handle_analysis_request()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_task_bridge.py",
      "source_location": "L268",
      "id": "wechat_task_bridge_wechattaskbridge_handle_analysis_request",
      "community": 11
    },
    {
      "label": "._execute_task()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_task_bridge.py",
      "source_location": "L320",
      "id": "wechat_task_bridge_wechattaskbridge_execute_task",
      "community": 11
    },
    {
      "label": "test_bridge()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_task_bridge.py",
      "source_location": "L394",
      "id": "wechat_task_bridge_test_bridge",
      "community": 11
    },
    {
      "label": "\u5fae\u4fe1\u4efb\u52a1\u6865\u63a5\u5668          \u5c06\u5fae\u4fe1\u6d88\u606f\u8f6c\u6362\u4e3a bbav20311 \u5206\u6790\u4efb\u52a1",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_task_bridge.py",
      "source_location": "L43",
      "id": "wechat_task_bridge_rationale_43",
      "community": 11
    },
    {
      "label": "\u5904\u7406\u5206\u6790\u8bf7\u6c42                  \u4f7f\u7528 bbav20311 \u7684\u610f\u56fe\u8bc6\u522b\u548c\u4efb\u52a1\u7cfb\u7edf",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_task_bridge.py",
      "source_location": "L269",
      "id": "wechat_task_bridge_rationale_269",
      "community": 11
    },
    {
      "label": "run.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/karyotype/run.py",
      "source_location": "L1",
      "id": "run",
      "community": 1
    },
    {
      "label": "load_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/rnaseq-align/run.py",
      "source_location": "L16",
      "id": "run_load_config",
      "community": 1
    },
    {
      "label": "run_skill()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/rnaseq-quant/run.py",
      "source_location": "L16",
      "id": "run_run_skill",
      "community": 1
    },
    {
      "label": "main()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/karyotype/run.py",
      "source_location": "L65",
      "id": "run_main",
      "community": 1
    },
    {
      "label": "Load skill configuration",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/rnaseq-align/run.py",
      "source_location": "L17",
      "id": "run_rationale_17",
      "community": 1
    },
    {
      "label": "Run the RNA-seq alignment skill",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/rnaseq-align/run.py",
      "source_location": "L32",
      "id": "run_rationale_32",
      "community": 1
    },
    {
      "label": "parse_yn00_output()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/kaks/run.py",
      "source_location": "L25",
      "id": "run_parse_yn00_output",
      "community": 1
    },
    {
      "label": "\u89e3\u6790yn00\u8f93\u51fa\u6587\u4ef6\uff0c\u63d0\u53d6Ka, Ks, Ka/Ks",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/kaks/run.py",
      "source_location": "L26",
      "id": "run_rationale_26",
      "community": 1
    },
    {
      "label": "# TODO: Implement full analysis pipeline",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/kaks/run.py",
      "source_location": "L83",
      "id": "run_rationale_83",
      "community": 1
    },
    {
      "label": "utils.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/kaks/utils.py",
      "source_location": "L1",
      "id": "utils",
      "community": 29
    },
    {
      "label": "compute_checksum()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/kaks/utils.py",
      "source_location": "L20",
      "id": "utils_compute_checksum",
      "community": 29
    },
    {
      "label": "check_tool()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/kaks/utils.py",
      "source_location": "L29",
      "id": "utils_check_tool",
      "community": 29
    },
    {
      "label": "get_tool_version()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/kaks/utils.py",
      "source_location": "L37",
      "id": "utils_get_tool_version",
      "community": 29
    },
    {
      "label": "parse_cds_fasta()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/kaks/utils.py",
      "source_location": "L64",
      "id": "utils_parse_cds_fasta",
      "community": 29
    },
    {
      "label": "parse_ortholog_pairs()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/kaks/utils.py",
      "source_location": "L73",
      "id": "utils_parse_ortholog_pairs",
      "community": 29
    },
    {
      "label": "extract_sequences()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/kaks/utils.py",
      "source_location": "L89",
      "id": "utils_extract_sequences",
      "community": 29
    },
    {
      "label": "run_muscle_alignment()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/kaks/utils.py",
      "source_location": "L105",
      "id": "utils_run_muscle_alignment",
      "community": 29
    },
    {
      "label": "run_pal2nal()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/kaks/utils.py",
      "source_location": "L125",
      "id": "utils_run_pal2nal",
      "community": 29
    },
    {
      "label": "create_yn00_ctl()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/kaks/utils.py",
      "source_location": "L146",
      "id": "utils_create_yn00_ctl",
      "community": 29
    },
    {
      "label": "run_yn00()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/kaks/utils.py",
      "source_location": "L162",
      "id": "utils_run_yn00",
      "community": 29
    },
    {
      "label": "parse_yn00_output()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/kaks/utils.py",
      "source_location": "L181",
      "id": "utils_parse_yn00_output",
      "community": 29
    },
    {
      "label": "calculate_divergence_time()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/kaks/utils.py",
      "source_location": "L223",
      "id": "utils_calculate_divergence_time",
      "community": 29
    },
    {
      "label": "\u89e3\u6790CDS FASTA\u6587\u4ef6\uff0c\u8fd4\u56de\u57fa\u56e0ID\u5230\u5e8f\u5217\u7684\u5b57\u5178",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/kaks/utils.py",
      "source_location": "L65",
      "id": "utils_rationale_65",
      "community": 29
    },
    {
      "label": "\u89e3\u6790\u540c\u6e90\u57fa\u56e0\u5bf9\u6587\u4ef6\uff0c\u683c\u5f0f: gene1\\tgene2",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/kaks/utils.py",
      "source_location": "L74",
      "id": "utils_rationale_74",
      "community": 29
    },
    {
      "label": "\u4eceCDS\u5b57\u5178\u4e2d\u63d0\u53d6\u6307\u5b9a\u57fa\u56e0\u7684\u5e8f\u5217\u5e76\u5199\u5165\u6587\u4ef6",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/kaks/utils.py",
      "source_location": "L90",
      "id": "utils_rationale_90",
      "community": 29
    },
    {
      "label": "\u8fd0\u884cpal2nal\u5c06\u86cb\u767d\u6bd4\u5bf9\u8f6c\u6362\u4e3a\u5bc6\u7801\u5b50\u6bd4\u5bf9",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/kaks/utils.py",
      "source_location": "L126",
      "id": "utils_rationale_126",
      "community": 29
    },
    {
      "label": "example_usage.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/example_usage.py",
      "source_location": "L1",
      "id": "example_usage",
      "community": 66
    },
    {
      "label": "run_annotation_skill()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/example_usage.py",
      "source_location": "L11",
      "id": "example_usage_run_annotation_skill",
      "community": 66
    },
    {
      "label": "integrate_with_pipeline()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/example_usage.py",
      "source_location": "L50",
      "id": "example_usage_integrate_with_pipeline",
      "community": 66
    },
    {
      "label": "\u8c03\u7528 annotation skill \u8fdb\u884c\u529f\u80fd\u6ce8\u91ca          Args:         protein_fasta: \u86cb\u767d\u5e8f\u5217FASTA\u6587\u4ef6\u8def\u5f84",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/example_usage.py",
      "source_location": "L12",
      "id": "example_usage_rationale_12",
      "community": 66
    },
    {
      "label": "\u96c6\u6210\u5230\u57fa\u56e0\u5bb6\u65cf\u5206\u6790 pipeline \u7684\u793a\u4f8b          \u5728\u57fa\u56e0\u9274\u5b9a\u540e\uff0c\u5bf9\u9274\u5b9a\u51fa\u7684\u57fa\u56e0\u5bb6\u65cf\u6210\u5458\u8fdb\u884c\u529f\u80fd\u6ce8\u91ca",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/example_usage.py",
      "source_location": "L51",
      "id": "example_usage_rationale_51",
      "community": 66
    },
    {
      "label": "run_api.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run_api.py",
      "source_location": "L1",
      "id": "run_api",
      "community": 32
    },
    {
      "label": "AnnotationAPISkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run_api.py",
      "source_location": "L44",
      "id": "run_api_annotationapiskill",
      "community": 32
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run_api.py",
      "source_location": "L47",
      "id": "run_api_annotationapiskill_init",
      "community": 32
    },
    {
      "label": "._load_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run_api.py",
      "source_location": "L53",
      "id": "run_api_annotationapiskill_load_config",
      "community": 32
    },
    {
      "label": "._compute_checksum()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run_api.py",
      "source_location": "L67",
      "id": "run_api_annotationapiskill_compute_checksum",
      "community": 32
    },
    {
      "label": "._record_file()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run_api.py",
      "source_location": "L74",
      "id": "run_api_annotationapiskill_record_file",
      "community": 32
    },
    {
      "label": ".read_fasta()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run_api.py",
      "source_location": "L82",
      "id": "run_api_annotationapiskill_read_fasta",
      "community": 32
    },
    {
      "label": ".submit_to_eggnog()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run_api.py",
      "source_location": "L100",
      "id": "run_api_annotationapiskill_submit_to_eggnog",
      "community": 32
    },
    {
      "label": ".get_go_terms()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run_api.py",
      "source_location": "L115",
      "id": "run_api_annotationapiskill_get_go_terms",
      "community": 32
    },
    {
      "label": ".run_api_annotation()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run_api.py",
      "source_location": "L135",
      "id": "run_api_annotationapiskill_run_api_annotation",
      "community": 32
    },
    {
      "label": ".generate_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run_api.py",
      "source_location": "L204",
      "id": "run_api_annotationapiskill_generate_report",
      "community": 32
    },
    {
      "label": ".run()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run_api.py",
      "source_location": "L242",
      "id": "run_api_annotationapiskill_run",
      "community": 32
    },
    {
      "label": ".run_demo()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run_api.py",
      "source_location": "L264",
      "id": "run_api_annotationapiskill_run_demo",
      "community": 32
    },
    {
      "label": "main()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run_api.py",
      "source_location": "L300",
      "id": "run_api_main",
      "community": 32
    },
    {
      "label": "\u63d0\u4ea4\u5e8f\u5217\u5230eggNOG\uff0c\u8fd4\u56denogname",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run_api.py",
      "source_location": "L101",
      "id": "run_api_rationale_101",
      "community": 32
    },
    {
      "label": "AnnotationSkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run.py",
      "source_location": "L30",
      "id": "run_annotationskill",
      "community": 1
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run.py",
      "source_location": "L33",
      "id": "run_annotationskill_init",
      "community": 1
    },
    {
      "label": "._load_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run.py",
      "source_location": "L39",
      "id": "run_annotationskill_load_config",
      "community": 1
    },
    {
      "label": "._which()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run.py",
      "source_location": "L47",
      "id": "run_annotationskill_which",
      "community": 1
    },
    {
      "label": "._find_emapper()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run.py",
      "source_location": "L50",
      "id": "run_annotationskill_find_emapper",
      "community": 1
    },
    {
      "label": "._run_command()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run.py",
      "source_location": "L74",
      "id": "run_annotationskill_run_command",
      "community": 1
    },
    {
      "label": "._compute_checksum()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run.py",
      "source_location": "L92",
      "id": "run_annotationskill_compute_checksum",
      "community": 1
    },
    {
      "label": "._record_file()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run.py",
      "source_location": "L99",
      "id": "run_annotationskill_record_file",
      "community": 1
    },
    {
      "label": "._parse_annotations()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run.py",
      "source_location": "L107",
      "id": "run_annotationskill_parse_annotations",
      "community": 1
    },
    {
      "label": ".run_emapper()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run.py",
      "source_location": "L162",
      "id": "run_annotationskill_run_emapper",
      "community": 1
    },
    {
      "label": ".generate_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run.py",
      "source_location": "L211",
      "id": "run_annotationskill_generate_report",
      "community": 1
    },
    {
      "label": ".write_reproducibility_bundle()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run.py",
      "source_location": "L262",
      "id": "run_annotationskill_write_reproducibility_bundle",
      "community": 1
    },
    {
      "label": ".run()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run.py",
      "source_location": "L285",
      "id": "run_annotationskill_run",
      "community": 1
    },
    {
      "label": ".run_demo()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run.py",
      "source_location": "L308",
      "id": "run_annotationskill_run_demo",
      "community": 1
    },
    {
      "label": "\u67e5\u627e emapper.py \u8def\u5f84\u548c\u5bf9\u5e94\u7684 python \u89e3\u91ca\u5668         \u8fd4\u56de: (python_path, emapper_path)",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/run.py",
      "source_location": "L51",
      "id": "run_rationale_51",
      "community": 1
    },
    {
      "label": "test_annotation.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/tests/test_annotation.py",
      "source_location": "L1",
      "id": "test_annotation",
      "community": 1
    },
    {
      "label": "TestAnnotationSkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/tests/test_annotation.py",
      "source_location": "L18",
      "id": "test_annotation_testannotationskill",
      "community": 1
    },
    {
      "label": ".setUp()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/tests/test_annotation.py",
      "source_location": "L21",
      "id": "test_annotation_testannotationskill_setup",
      "community": 1
    },
    {
      "label": ".tearDown()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/tests/test_annotation.py",
      "source_location": "L25",
      "id": "test_annotation_testannotationskill_teardown",
      "community": 1
    },
    {
      "label": ".test_find_emapper()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/tests/test_annotation.py",
      "source_location": "L30",
      "id": "test_annotation_testannotationskill_test_find_emapper",
      "community": 1
    },
    {
      "label": ".test_parse_annotations()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/tests/test_annotation.py",
      "source_location": "L39",
      "id": "test_annotation_testannotationskill_test_parse_annotations",
      "community": 1
    },
    {
      "label": ".test_demo_mode()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/tests/test_annotation.py",
      "source_location": "L59",
      "id": "test_annotation_testannotationskill_test_demo_mode",
      "community": 1
    },
    {
      "label": ".test_config_loading()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/annotation/tests/test_annotation.py",
      "source_location": "L74",
      "id": "test_annotation_testannotationskill_test_config_loading",
      "community": 1
    },
    {
      "label": "Run the RNA-seq quantification skill",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/rnaseq-quant/run.py",
      "source_location": "L25",
      "id": "run_rationale_25",
      "community": 1
    },
    {
      "label": "PepSkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/pep/run.py",
      "source_location": "L40",
      "id": "run_pepskill",
      "community": 1
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/pep/run.py",
      "source_location": "L43",
      "id": "run_pepskill_init",
      "community": 1
    },
    {
      "label": "._load_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/pep/run.py",
      "source_location": "L49",
      "id": "run_pepskill_load_config",
      "community": 1
    },
    {
      "label": "._compute_checksum()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/pep/run.py",
      "source_location": "L58",
      "id": "run_pepskill_compute_checksum",
      "community": 1
    },
    {
      "label": "._record_file()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/pep/run.py",
      "source_location": "L66",
      "id": "run_pepskill_record_file",
      "community": 1
    },
    {
      "label": ".parse_fasta()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/pep/run.py",
      "source_location": "L77",
      "id": "run_pepskill_parse_fasta",
      "community": 1
    },
    {
      "label": ".calculate_properties()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/pep/run.py",
      "source_location": "L98",
      "id": "run_pepskill_calculate_properties",
      "community": 1
    },
    {
      "label": ".plot_properties()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/pep/run.py",
      "source_location": "L146",
      "id": "run_pepskill_plot_properties",
      "community": 1
    },
    {
      "label": ".run()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/pep/run.py",
      "source_location": "L200",
      "id": "run_pepskill_run",
      "community": 1
    },
    {
      "label": "._generate_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/pep/run.py",
      "source_location": "L242",
      "id": "run_pepskill_generate_report",
      "community": 1
    },
    {
      "label": "._generate_manifest()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/pep/run.py",
      "source_location": "L264",
      "id": "run_pepskill_generate_manifest",
      "community": 1
    },
    {
      "label": "MotifSkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/run.py",
      "source_location": "L34",
      "id": "run_motifskill",
      "community": 1
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/run.py",
      "source_location": "L37",
      "id": "run_motifskill_init",
      "community": 1
    },
    {
      "label": "._load_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/run.py",
      "source_location": "L42",
      "id": "run_motifskill_load_config",
      "community": 1
    },
    {
      "label": "._which()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/run.py",
      "source_location": "L51",
      "id": "run_motifskill_which",
      "community": 1
    },
    {
      "label": "._run_command()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/run.py",
      "source_location": "L55",
      "id": "run_motifskill_run_command",
      "community": 1
    },
    {
      "label": "._compute_checksum()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/run.py",
      "source_location": "L68",
      "id": "run_motifskill_compute_checksum",
      "community": 1
    },
    {
      "label": "._record_file()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/run.py",
      "source_location": "L76",
      "id": "run_motifskill_record_file",
      "community": 1
    },
    {
      "label": ".run_meme()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/run.py",
      "source_location": "L85",
      "id": "run_motifskill_run_meme",
      "community": 1
    },
    {
      "label": ".generate_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/run.py",
      "source_location": "L121",
      "id": "run_motifskill_generate_report",
      "community": 1
    },
    {
      "label": ".write_reproducibility_bundle()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/run.py",
      "source_location": "L160",
      "id": "run_motifskill_write_reproducibility_bundle",
      "community": 1
    },
    {
      "label": ".run()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/run.py",
      "source_location": "L187",
      "id": "run_motifskill_run",
      "community": 1
    },
    {
      "label": ".run_demo()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/run.py",
      "source_location": "L221",
      "id": "run_motifskill_run_demo",
      "community": 1
    },
    {
      "label": "test_motif.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/tests/test_motif.py",
      "source_location": "L1",
      "id": "test_motif",
      "community": 1
    },
    {
      "label": "TestMotifSkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/tests/test_motif.py",
      "source_location": "L14",
      "id": "test_motif_testmotifskill",
      "community": 1
    },
    {
      "label": ".setUp()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/tests/test_motif.py",
      "source_location": "L16",
      "id": "test_motif_testmotifskill_setup",
      "community": 1
    },
    {
      "label": ".tearDown()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/tests/test_motif.py",
      "source_location": "L20",
      "id": "test_motif_testmotifskill_teardown",
      "community": 1
    },
    {
      "label": ".test_demo_mode()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/tests/test_motif.py",
      "source_location": "L24",
      "id": "test_motif_testmotifskill_test_demo_mode",
      "community": 1
    },
    {
      "label": ".test_config_loading()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/tests/test_motif.py",
      "source_location": "L41",
      "id": "test_motif_testmotifskill_test_config_loading",
      "community": 1
    },
    {
      "label": "# TODO: \u5b9e\u73b0\u5b8c\u6574\u7684 skill \u903b\u8f91",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/rnaseq-de/run.py",
      "source_location": "L28",
      "id": "run_rationale_28",
      "community": 1
    },
    {
      "label": "ExpressionSkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
      "source_location": "L48",
      "id": "run_expressionskill",
      "community": 26
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
      "source_location": "L51",
      "id": "run_expressionskill_init",
      "community": 26
    },
    {
      "label": "._load_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
      "source_location": "L57",
      "id": "run_expressionskill_load_config",
      "community": 26
    },
    {
      "label": "._compute_checksum()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
      "source_location": "L66",
      "id": "run_expressionskill_compute_checksum",
      "community": 26
    },
    {
      "label": "._record_file()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
      "source_location": "L74",
      "id": "run_expressionskill_record_file",
      "community": 26
    },
    {
      "label": ".load_count_matrix()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
      "source_location": "L83",
      "id": "run_expressionskill_load_count_matrix",
      "community": 26
    },
    {
      "label": ".load_sample_groups()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
      "source_location": "L102",
      "id": "run_expressionskill_load_sample_groups",
      "community": 26
    },
    {
      "label": ".parse_groups()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
      "source_location": "L116",
      "id": "run_expressionskill_parse_groups",
      "community": 26
    },
    {
      "label": ".run_differential_expression()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
      "source_location": "L128",
      "id": "run_expressionskill_run_differential_expression",
      "community": 26
    },
    {
      "label": ".plot_volcano()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
      "source_location": "L211",
      "id": "run_expressionskill_plot_volcano",
      "community": 26
    },
    {
      "label": ".plot_heatmap()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
      "source_location": "L255",
      "id": "run_expressionskill_plot_heatmap",
      "community": 26
    },
    {
      "label": ".plot_pca()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
      "source_location": "L305",
      "id": "run_expressionskill_plot_pca",
      "community": 26
    },
    {
      "label": ".generate_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
      "source_location": "L360",
      "id": "run_expressionskill_generate_report",
      "community": 26
    },
    {
      "label": ".write_reproducibility_bundle()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
      "source_location": "L434",
      "id": "run_expressionskill_write_reproducibility_bundle",
      "community": 26
    },
    {
      "label": ".run()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
      "source_location": "L489",
      "id": "run_expressionskill_run",
      "community": 26
    },
    {
      "label": ".run_demo()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
      "source_location": "L532",
      "id": "run_expressionskill_run_demo",
      "community": 26
    },
    {
      "label": "._create_mock_output()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
      "source_location": "L583",
      "id": "run_expressionskill_create_mock_output",
      "community": 26
    },
    {
      "label": "\u89e3\u6790\u5206\u7ec4\uff0c\u8fd4\u56de {group_name: [sample1, sample2, ...]}",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
      "source_location": "L117",
      "id": "run_rationale_117",
      "community": 26
    },
    {
      "label": "test_expression.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/tests/test_expression.py",
      "source_location": "L1",
      "id": "test_expression",
      "community": 47
    },
    {
      "label": "MockModule",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/tests/test_expression.py",
      "source_location": "L14",
      "id": "test_expression_mockmodule",
      "community": 47
    },
    {
      "label": ".__getattr__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/tests/test_expression.py",
      "source_location": "L15",
      "id": "test_expression_mockmodule_getattr",
      "community": 47
    },
    {
      "label": "TestExpressionConfig",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/tests/test_expression.py",
      "source_location": "L23",
      "id": "test_expression_testexpressionconfig",
      "community": 47
    },
    {
      "label": ".setUp()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/tests/test_expression.py",
      "source_location": "L25",
      "id": "test_expression_testexpressionconfig_setup",
      "community": 47
    },
    {
      "label": ".test_config_structure()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/tests/test_expression.py",
      "source_location": "L33",
      "id": "test_expression_testexpressionconfig_test_config_structure",
      "community": 47
    },
    {
      "label": ".test_config_source()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/tests/test_expression.py",
      "source_location": "L39",
      "id": "test_expression_testexpressionconfig_test_config_source",
      "community": 47
    },
    {
      "label": ".test_parameters()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/tests/test_expression.py",
      "source_location": "L43",
      "id": "test_expression_testexpressionconfig_test_parameters",
      "community": 47
    },
    {
      "label": ".test_demo_output_structure()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/tests/test_expression.py",
      "source_location": "L48",
      "id": "test_expression_testexpressionconfig_test_demo_output_structure",
      "community": 47
    },
    {
      "label": ".tearDown()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/tests/test_expression.py",
      "source_location": "L66",
      "id": "test_expression_testexpressionconfig_teardown",
      "community": 47
    },
    {
      "label": "PromoterSkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/promoter-analysis/run.py",
      "source_location": "L31",
      "id": "run_promoterskill",
      "community": 1
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/promoter-analysis/run.py",
      "source_location": "L34",
      "id": "run_promoterskill_init",
      "community": 1
    },
    {
      "label": "._load_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/promoter-analysis/run.py",
      "source_location": "L39",
      "id": "run_promoterskill_load_config",
      "community": 1
    },
    {
      "label": "._compute_checksum()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/promoter-analysis/run.py",
      "source_location": "L47",
      "id": "run_promoterskill_compute_checksum",
      "community": 1
    },
    {
      "label": "._record_file()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/promoter-analysis/run.py",
      "source_location": "L54",
      "id": "run_promoterskill_record_file",
      "community": 1
    },
    {
      "label": ".run()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/promoter-analysis/run.py",
      "source_location": "L62",
      "id": "run_promoterskill_run",
      "community": 1
    },
    {
      "label": ".generate_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/promoter-analysis/run.py",
      "source_location": "L92",
      "id": "run_promoterskill_generate_report",
      "community": 1
    },
    {
      "label": ".write_reproducibility_bundle()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/promoter-analysis/run.py",
      "source_location": "L127",
      "id": "run_promoterskill_write_reproducibility_bundle",
      "community": 1
    },
    {
      "label": ".run_demo()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/promoter-analysis/run.py",
      "source_location": "L150",
      "id": "run_promoterskill_run_demo",
      "community": 1
    },
    {
      "label": "test_promoter.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/promoter-analysis/tests/test_promoter.py",
      "source_location": "L1",
      "id": "test_promoter",
      "community": 1
    },
    {
      "label": "TestPromoterSkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/promoter-analysis/tests/test_promoter.py",
      "source_location": "L14",
      "id": "test_promoter_testpromoterskill",
      "community": 1
    },
    {
      "label": ".setUp()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/promoter-analysis/tests/test_promoter.py",
      "source_location": "L16",
      "id": "test_promoter_testpromoterskill_setup",
      "community": 1
    },
    {
      "label": ".tearDown()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/promoter-analysis/tests/test_promoter.py",
      "source_location": "L20",
      "id": "test_promoter_testpromoterskill_teardown",
      "community": 1
    },
    {
      "label": ".test_demo_mode()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/promoter-analysis/tests/test_promoter.py",
      "source_location": "L24",
      "id": "test_promoter_testpromoterskill_test_demo_mode",
      "community": 1
    },
    {
      "label": ".test_config_loading()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/promoter-analysis/tests/test_promoter.py",
      "source_location": "L36",
      "id": "test_promoter_testpromoterskill_test_config_loading",
      "community": 1
    },
    {
      "label": "StructureSkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/structure/run.py",
      "source_location": "L31",
      "id": "run_structureskill",
      "community": 1
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/structure/run.py",
      "source_location": "L34",
      "id": "run_structureskill_init",
      "community": 1
    },
    {
      "label": "._load_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/structure/run.py",
      "source_location": "L39",
      "id": "run_structureskill_load_config",
      "community": 1
    },
    {
      "label": "._compute_checksum()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/structure/run.py",
      "source_location": "L48",
      "id": "run_structureskill_compute_checksum",
      "community": 1
    },
    {
      "label": "._record_file()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/structure/run.py",
      "source_location": "L56",
      "id": "run_structureskill_record_file",
      "community": 1
    },
    {
      "label": ".run()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/structure/run.py",
      "source_location": "L65",
      "id": "run_structureskill_run",
      "community": 1
    },
    {
      "label": ".generate_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/structure/run.py",
      "source_location": "L104",
      "id": "run_structureskill_generate_report",
      "community": 1
    },
    {
      "label": ".write_reproducibility_bundle()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/structure/run.py",
      "source_location": "L138",
      "id": "run_structureskill_write_reproducibility_bundle",
      "community": 1
    },
    {
      "label": ".run_demo()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/structure/run.py",
      "source_location": "L165",
      "id": "run_structureskill_run_demo",
      "community": 1
    },
    {
      "label": "test_structure.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/structure/tests/test_structure.py",
      "source_location": "L1",
      "id": "test_structure",
      "community": 1
    },
    {
      "label": "TestStructureSkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/structure/tests/test_structure.py",
      "source_location": "L14",
      "id": "test_structure_teststructureskill",
      "community": 1
    },
    {
      "label": ".setUp()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/structure/tests/test_structure.py",
      "source_location": "L16",
      "id": "test_structure_teststructureskill_setup",
      "community": 1
    },
    {
      "label": ".tearDown()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/structure/tests/test_structure.py",
      "source_location": "L20",
      "id": "test_structure_teststructureskill_teardown",
      "community": 1
    },
    {
      "label": ".test_demo_mode()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/structure/tests/test_structure.py",
      "source_location": "L24",
      "id": "test_structure_teststructureskill_test_demo_mode",
      "community": 1
    },
    {
      "label": ".test_config_loading()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/structure/tests/test_structure.py",
      "source_location": "L39",
      "id": "test_structure_teststructureskill_test_config_loading",
      "community": 1
    },
    {
      "label": "GeneIdentifySkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/gene-identify/run.py",
      "source_location": "L33",
      "id": "run_geneidentifyskill",
      "community": 1
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/gene-identify/run.py",
      "source_location": "L36",
      "id": "run_geneidentifyskill_init",
      "community": 1
    },
    {
      "label": "._load_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/gene-identify/run.py",
      "source_location": "L41",
      "id": "run_geneidentifyskill_load_config",
      "community": 1
    },
    {
      "label": "._run_command()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/gene-identify/run.py",
      "source_location": "L51",
      "id": "run_geneidentifyskill_run_command",
      "community": 1
    },
    {
      "label": "._compute_checksum()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/gene-identify/run.py",
      "source_location": "L75",
      "id": "run_geneidentifyskill_compute_checksum",
      "community": 1
    },
    {
      "label": "._record_file()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/gene-identify/run.py",
      "source_location": "L83",
      "id": "run_geneidentifyskill_record_file",
      "community": 1
    },
    {
      "label": ".run_hmmer_search()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/gene-identify/run.py",
      "source_location": "L92",
      "id": "run_geneidentifyskill_run_hmmer_search",
      "community": 1
    },
    {
      "label": ".parse_hmmer_results()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/gene-identify/run.py",
      "source_location": "L122",
      "id": "run_geneidentifyskill_parse_hmmer_results",
      "community": 1
    },
    {
      "label": ".generate_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/gene-identify/run.py",
      "source_location": "L139",
      "id": "run_geneidentifyskill_generate_report",
      "community": 1
    },
    {
      "label": ".write_reproducibility_bundle()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/gene-identify/run.py",
      "source_location": "L179",
      "id": "run_geneidentifyskill_write_reproducibility_bundle",
      "community": 1
    },
    {
      "label": ".run()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/gene-identify/run.py",
      "source_location": "L206",
      "id": "run_geneidentifyskill_run",
      "community": 1
    },
    {
      "label": ".run_demo()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/gene-identify/run.py",
      "source_location": "L243",
      "id": "run_geneidentifyskill_run_demo",
      "community": 1
    },
    {
      "label": "test_identify.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/gene-identify/tests/test_identify.py",
      "source_location": "L1",
      "id": "test_identify",
      "community": 1
    },
    {
      "label": "TestGeneIdentifySkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/gene-identify/tests/test_identify.py",
      "source_location": "L14",
      "id": "test_identify_testgeneidentifyskill",
      "community": 1
    },
    {
      "label": ".setUp()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/gene-identify/tests/test_identify.py",
      "source_location": "L16",
      "id": "test_identify_testgeneidentifyskill_setup",
      "community": 1
    },
    {
      "label": ".tearDown()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/gene-identify/tests/test_identify.py",
      "source_location": "L20",
      "id": "test_identify_testgeneidentifyskill_teardown",
      "community": 1
    },
    {
      "label": ".test_demo_mode()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/gene-identify/tests/test_identify.py",
      "source_location": "L24",
      "id": "test_identify_testgeneidentifyskill_test_demo_mode",
      "community": 1
    },
    {
      "label": ".test_config_loading()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/gene-identify/tests/test_identify.py",
      "source_location": "L39",
      "id": "test_identify_testgeneidentifyskill_test_config_loading",
      "community": 1
    },
    {
      "label": "SummarySkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/summary/run.py",
      "source_location": "L13",
      "id": "run_summaryskill",
      "community": 35
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/summary/run.py",
      "source_location": "L14",
      "id": "run_summaryskill_init",
      "community": 35
    },
    {
      "label": "._load_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/summary/run.py",
      "source_location": "L18",
      "id": "run_summaryskill_load_config",
      "community": 35
    },
    {
      "label": "._compute_checksum()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/summary/run.py",
      "source_location": "L23",
      "id": "run_summaryskill_compute_checksum",
      "community": 35
    },
    {
      "label": "._record_file()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/summary/run.py",
      "source_location": "L29",
      "id": "run_summaryskill_record_file",
      "community": 35
    },
    {
      "label": ".generate_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/summary/run.py",
      "source_location": "L33",
      "id": "run_summaryskill_generate_report",
      "community": 35
    },
    {
      "label": ".write_reproducibility_bundle()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/summary/run.py",
      "source_location": "L67",
      "id": "run_summaryskill_write_reproducibility_bundle",
      "community": 35
    },
    {
      "label": ".run_demo()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/summary/run.py",
      "source_location": "L73",
      "id": "run_summaryskill_run_demo",
      "community": 35
    },
    {
      "label": "test_summary.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/summary/tests/test_summary.py",
      "source_location": "L1",
      "id": "test_summary",
      "community": 35
    },
    {
      "label": "TestKaryotype",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/summary/tests/test_summary.py",
      "source_location": "L7",
      "id": "test_summary_testkaryotype",
      "community": 35
    },
    {
      "label": ".setUp()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/summary/tests/test_summary.py",
      "source_location": "L8",
      "id": "test_summary_testkaryotype_setup",
      "community": 35
    },
    {
      "label": ".tearDown()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/summary/tests/test_summary.py",
      "source_location": "L12",
      "id": "test_summary_testkaryotype_teardown",
      "community": 35
    },
    {
      "label": ".test_demo()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/summary/tests/test_summary.py",
      "source_location": "L15",
      "id": "test_summary_testkaryotype_test_demo",
      "community": 35
    },
    {
      "label": ".test_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/summary/tests/test_summary.py",
      "source_location": "L18",
      "id": "test_summary_testkaryotype_test_config",
      "community": 35
    },
    {
      "label": "StringAPI",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L36",
      "id": "run_stringapi",
      "community": 1
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L52",
      "id": "run_stringapi_init",
      "community": 1
    },
    {
      "label": ".get_network()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L56",
      "id": "run_stringapi_get_network",
      "community": 1
    },
    {
      "label": "generate_string_url()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L84",
      "id": "run_generate_string_url",
      "community": 1
    },
    {
      "label": "parse_ortholog_mapping()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L106",
      "id": "run_parse_ortholog_mapping",
      "community": 1
    },
    {
      "label": "PpiSkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L132",
      "id": "run_ppiskill",
      "community": 1
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L135",
      "id": "run_ppiskill_init",
      "community": 1
    },
    {
      "label": "._load_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L142",
      "id": "run_ppiskill_load_config",
      "community": 1
    },
    {
      "label": "._compute_checksum()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L151",
      "id": "run_ppiskill_compute_checksum",
      "community": 1
    },
    {
      "label": "._record_file()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L159",
      "id": "run_ppiskill_record_file",
      "community": 1
    },
    {
      "label": ".load_gene_ids()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L170",
      "id": "run_ppiskill_load_gene_ids",
      "community": 1
    },
    {
      "label": ".load_ortholog_mapping()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L180",
      "id": "run_ppiskill_load_ortholog_mapping",
      "community": 1
    },
    {
      "label": ".map_gene_ids()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L186",
      "id": "run_ppiskill_map_gene_ids",
      "community": 1
    },
    {
      "label": ".analyze_network()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L210",
      "id": "run_ppiskill_analyze_network",
      "community": 1
    },
    {
      "label": ".save_network()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L265",
      "id": "run_ppiskill_save_network",
      "community": 1
    },
    {
      "label": ".run()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L272",
      "id": "run_ppiskill_run",
      "community": 1
    },
    {
      "label": "._generate_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L348",
      "id": "run_ppiskill_generate_report",
      "community": 1
    },
    {
      "label": "._generate_manifest()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L378",
      "id": "run_ppiskill_generate_manifest",
      "community": 1
    },
    {
      "label": "\u751f\u6210STRING\u7f51\u9875\u94fe\u63a5          Args:         proteins: \u86cb\u767dID\u5217\u8868         species: STRING\u7269\u79cdID",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L85",
      "id": "run_rationale_85",
      "community": 1
    },
    {
      "label": "\u89e3\u6790\u540c\u6e90\u57fa\u56e0\u6620\u5c04\u6587\u4ef6          \u683c\u5f0f: source_id\\ttarget_id (\u6bcf\u884c\u4e00\u4e2a\u6620\u5c04\u5bf9)     \u793a\u4f8b: FtPinG0000212200.",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L107",
      "id": "run_rationale_107",
      "community": 1
    },
    {
      "label": "\u6620\u5c04\u57fa\u56e0ID\u5230\u76ee\u6807\u7269\u79cd                  \u5982\u679c\u6709\u540c\u6e90\u6620\u5c04\uff0c\u8f6c\u6362\u4e3a\u6620\u5c04\u540e\u7684ID         \u5982\u679c\u6ca1\u6709\u6620\u5c04\uff0c\u8fd4\u56de\u539f\u59cbID (\u5047\u8bbe\u5df2\u7ecf\u662f\u76ee\u6807\u7269\u79cd\u7684",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L187",
      "id": "run_rationale_187",
      "community": 1
    },
    {
      "label": "\u5206\u6790\u4e92\u4f5c\u7f51\u7edc                  Returns:             Dict with keys: interactions, stats",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L212",
      "id": "run_rationale_212",
      "community": 1
    },
    {
      "label": "\u8fd0\u884cPPI\u5206\u6790                  Args:             gene_ids_file: \u57fa\u56e0ID\u5217\u8868\u6587\u4ef6             s",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/ppi/run.py",
      "source_location": "L275",
      "id": "run_rationale_275",
      "community": 1
    },
    {
      "label": "InterspeciesSkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/interspecies/run.py",
      "source_location": "L13",
      "id": "run_interspeciesskill",
      "community": 36
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/interspecies/run.py",
      "source_location": "L14",
      "id": "run_interspeciesskill_init",
      "community": 36
    },
    {
      "label": "._load_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/interspecies/run.py",
      "source_location": "L18",
      "id": "run_interspeciesskill_load_config",
      "community": 36
    },
    {
      "label": "._compute_checksum()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/interspecies/run.py",
      "source_location": "L23",
      "id": "run_interspeciesskill_compute_checksum",
      "community": 36
    },
    {
      "label": "._record_file()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/interspecies/run.py",
      "source_location": "L29",
      "id": "run_interspeciesskill_record_file",
      "community": 36
    },
    {
      "label": ".generate_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/interspecies/run.py",
      "source_location": "L33",
      "id": "run_interspeciesskill_generate_report",
      "community": 36
    },
    {
      "label": ".write_reproducibility_bundle()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/interspecies/run.py",
      "source_location": "L52",
      "id": "run_interspeciesskill_write_reproducibility_bundle",
      "community": 36
    },
    {
      "label": ".run_demo()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/interspecies/run.py",
      "source_location": "L58",
      "id": "run_interspeciesskill_run_demo",
      "community": 36
    },
    {
      "label": "test_interspecies.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/interspecies/tests/test_interspecies.py",
      "source_location": "L1",
      "id": "test_interspecies",
      "community": 36
    },
    {
      "label": "TestKaryotype",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/interspecies/tests/test_interspecies.py",
      "source_location": "L7",
      "id": "test_interspecies_testkaryotype",
      "community": 36
    },
    {
      "label": ".setUp()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/interspecies/tests/test_interspecies.py",
      "source_location": "L8",
      "id": "test_interspecies_testkaryotype_setup",
      "community": 36
    },
    {
      "label": ".tearDown()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/interspecies/tests/test_interspecies.py",
      "source_location": "L12",
      "id": "test_interspecies_testkaryotype_teardown",
      "community": 36
    },
    {
      "label": ".test_demo()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/interspecies/tests/test_interspecies.py",
      "source_location": "L15",
      "id": "test_interspecies_testkaryotype_test_demo",
      "community": 36
    },
    {
      "label": ".test_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/interspecies/tests/test_interspecies.py",
      "source_location": "L18",
      "id": "test_interspecies_testkaryotype_test_config",
      "community": 36
    },
    {
      "label": "DomainSkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/run.py",
      "source_location": "L34",
      "id": "run_domainskill",
      "community": 1
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/run.py",
      "source_location": "L37",
      "id": "run_domainskill_init",
      "community": 1
    },
    {
      "label": "._load_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/run.py",
      "source_location": "L42",
      "id": "run_domainskill_load_config",
      "community": 1
    },
    {
      "label": "._which()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/run.py",
      "source_location": "L51",
      "id": "run_domainskill_which",
      "community": 1
    },
    {
      "label": "._run_command()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/run.py",
      "source_location": "L55",
      "id": "run_domainskill_run_command",
      "community": 1
    },
    {
      "label": "._compute_checksum()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/run.py",
      "source_location": "L68",
      "id": "run_domainskill_compute_checksum",
      "community": 1
    },
    {
      "label": "._record_file()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/run.py",
      "source_location": "L76",
      "id": "run_domainskill_record_file",
      "community": 1
    },
    {
      "label": ".run_hmmscan()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/run.py",
      "source_location": "L85",
      "id": "run_domainskill_run_hmmscan",
      "community": 1
    },
    {
      "label": ".generate_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/run.py",
      "source_location": "L124",
      "id": "run_domainskill_generate_report",
      "community": 1
    },
    {
      "label": ".write_reproducibility_bundle()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/run.py",
      "source_location": "L161",
      "id": "run_domainskill_write_reproducibility_bundle",
      "community": 1
    },
    {
      "label": ".run()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/run.py",
      "source_location": "L188",
      "id": "run_domainskill_run",
      "community": 1
    },
    {
      "label": ".run_demo()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/run.py",
      "source_location": "L221",
      "id": "run_domainskill_run_demo",
      "community": 1
    },
    {
      "label": "test_domain.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/tests/test_domain.py",
      "source_location": "L1",
      "id": "test_domain",
      "community": 1
    },
    {
      "label": "TestDomainSkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/tests/test_domain.py",
      "source_location": "L14",
      "id": "test_domain_testdomainskill",
      "community": 1
    },
    {
      "label": ".setUp()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/tests/test_domain.py",
      "source_location": "L16",
      "id": "test_domain_testdomainskill_setup",
      "community": 1
    },
    {
      "label": ".tearDown()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/tests/test_domain.py",
      "source_location": "L20",
      "id": "test_domain_testdomainskill_teardown",
      "community": 1
    },
    {
      "label": ".test_demo_mode()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/tests/test_domain.py",
      "source_location": "L24",
      "id": "test_domain_testdomainskill_test_demo_mode",
      "community": 1
    },
    {
      "label": ".test_config_loading()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/tests/test_domain.py",
      "source_location": "L41",
      "id": "test_domain_testdomainskill_test_config_loading",
      "community": 1
    },
    {
      "label": "# TODO: \u5b9e\u73b0\u5b8c\u6574\u7684 skill \u903b\u8f91",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/rnaseq-enrich/run.py",
      "source_location": "L30",
      "id": "run_rationale_30",
      "community": 1
    },
    {
      "label": "PhylogenySkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/run.py",
      "source_location": "L34",
      "id": "run_phylogenyskill",
      "community": 1
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/run.py",
      "source_location": "L37",
      "id": "run_phylogenyskill_init",
      "community": 1
    },
    {
      "label": "._load_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/run.py",
      "source_location": "L42",
      "id": "run_phylogenyskill_load_config",
      "community": 1
    },
    {
      "label": "._which()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/run.py",
      "source_location": "L52",
      "id": "run_phylogenyskill_which",
      "community": 1
    },
    {
      "label": "._run_command()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/run.py",
      "source_location": "L56",
      "id": "run_phylogenyskill_run_command",
      "community": 1
    },
    {
      "label": "._compute_checksum()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/run.py",
      "source_location": "L84",
      "id": "run_phylogenyskill_compute_checksum",
      "community": 1
    },
    {
      "label": "._record_file()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/run.py",
      "source_location": "L92",
      "id": "run_phylogenyskill_record_file",
      "community": 1
    },
    {
      "label": ".run_alignment()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/run.py",
      "source_location": "L101",
      "id": "run_phylogenyskill_run_alignment",
      "community": 1
    },
    {
      "label": ".run_tree()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/run.py",
      "source_location": "L141",
      "id": "run_phylogenyskill_run_tree",
      "community": 1
    },
    {
      "label": ".generate_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/run.py",
      "source_location": "L189",
      "id": "run_phylogenyskill_generate_report",
      "community": 1
    },
    {
      "label": ".write_reproducibility_bundle()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/run.py",
      "source_location": "L226",
      "id": "run_phylogenyskill_write_reproducibility_bundle",
      "community": 1
    },
    {
      "label": ".run()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/run.py",
      "source_location": "L253",
      "id": "run_phylogenyskill_run",
      "community": 1
    },
    {
      "label": ".run_demo()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/run.py",
      "source_location": "L290",
      "id": "run_phylogenyskill_run_demo",
      "community": 1
    },
    {
      "label": "test_phylogeny.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/tests/test_phylogeny.py",
      "source_location": "L1",
      "id": "test_phylogeny",
      "community": 1
    },
    {
      "label": "TestPhylogenySkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/tests/test_phylogeny.py",
      "source_location": "L14",
      "id": "test_phylogeny_testphylogenyskill",
      "community": 1
    },
    {
      "label": ".setUp()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/tests/test_phylogeny.py",
      "source_location": "L16",
      "id": "test_phylogeny_testphylogenyskill_setup",
      "community": 1
    },
    {
      "label": ".tearDown()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/tests/test_phylogeny.py",
      "source_location": "L20",
      "id": "test_phylogeny_testphylogenyskill_teardown",
      "community": 1
    },
    {
      "label": ".test_demo_mode()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/tests/test_phylogeny.py",
      "source_location": "L24",
      "id": "test_phylogeny_testphylogenyskill_test_demo_mode",
      "community": 1
    },
    {
      "label": ".test_config_loading()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/tests/test_phylogeny.py",
      "source_location": "L41",
      "id": "test_phylogeny_testphylogenyskill_test_config_loading",
      "community": 1
    },
    {
      "label": "compute_file_hash()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/rnaseq-qc/run.py",
      "source_location": "L20",
      "id": "run_compute_file_hash",
      "community": 1
    },
    {
      "label": "get_tool_versions()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/rnaseq-qc/run.py",
      "source_location": "L32",
      "id": "run_get_tool_versions",
      "community": 1
    },
    {
      "label": "# TODO: \u5b9e\u73b0\u5b8c\u6574\u7684 skill \u903b\u8f91",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/rnaseq-qc/run.py",
      "source_location": "L82",
      "id": "run_rationale_82",
      "community": 1
    },
    {
      "label": "SyntenySkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/synteny/run.py",
      "source_location": "L30",
      "id": "run_syntenyskill",
      "community": 1
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/synteny/run.py",
      "source_location": "L33",
      "id": "run_syntenyskill_init",
      "community": 1
    },
    {
      "label": "._load_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/synteny/run.py",
      "source_location": "L38",
      "id": "run_syntenyskill_load_config",
      "community": 1
    },
    {
      "label": "._compute_checksum()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/synteny/run.py",
      "source_location": "L46",
      "id": "run_syntenyskill_compute_checksum",
      "community": 1
    },
    {
      "label": "._record_file()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/synteny/run.py",
      "source_location": "L53",
      "id": "run_syntenyskill_record_file",
      "community": 1
    },
    {
      "label": ".run()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/synteny/run.py",
      "source_location": "L61",
      "id": "run_syntenyskill_run",
      "community": 1
    },
    {
      "label": ".generate_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/synteny/run.py",
      "source_location": "L94",
      "id": "run_syntenyskill_generate_report",
      "community": 1
    },
    {
      "label": ".write_reproducibility_bundle()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/synteny/run.py",
      "source_location": "L131",
      "id": "run_syntenyskill_write_reproducibility_bundle",
      "community": 1
    },
    {
      "label": ".run_demo()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/synteny/run.py",
      "source_location": "L154",
      "id": "run_syntenyskill_run_demo",
      "community": 1
    },
    {
      "label": "test_synteny.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/synteny/tests/test_synteny.py",
      "source_location": "L1",
      "id": "test_synteny",
      "community": 1
    },
    {
      "label": "TestSyntenySkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/synteny/tests/test_synteny.py",
      "source_location": "L14",
      "id": "test_synteny_testsyntenyskill",
      "community": 1
    },
    {
      "label": ".setUp()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/synteny/tests/test_synteny.py",
      "source_location": "L16",
      "id": "test_synteny_testsyntenyskill_setup",
      "community": 1
    },
    {
      "label": ".tearDown()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/synteny/tests/test_synteny.py",
      "source_location": "L20",
      "id": "test_synteny_testsyntenyskill_teardown",
      "community": 1
    },
    {
      "label": ".test_demo_mode()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/synteny/tests/test_synteny.py",
      "source_location": "L24",
      "id": "test_synteny_testsyntenyskill_test_demo_mode",
      "community": 1
    },
    {
      "label": ".test_config_loading()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/synteny/tests/test_synteny.py",
      "source_location": "L33",
      "id": "test_synteny_testsyntenyskill_test_config_loading",
      "community": 1
    },
    {
      "label": "KaryotypeSkill",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/karyotype/run.py",
      "source_location": "L13",
      "id": "run_karyotypeskill",
      "community": 1
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/karyotype/run.py",
      "source_location": "L14",
      "id": "run_karyotypeskill_init",
      "community": 1
    },
    {
      "label": "._load_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/karyotype/run.py",
      "source_location": "L18",
      "id": "run_karyotypeskill_load_config",
      "community": 1
    },
    {
      "label": "._compute_checksum()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/karyotype/run.py",
      "source_location": "L23",
      "id": "run_karyotypeskill_compute_checksum",
      "community": 1
    },
    {
      "label": "._record_file()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/karyotype/run.py",
      "source_location": "L29",
      "id": "run_karyotypeskill_record_file",
      "community": 1
    },
    {
      "label": ".generate_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/karyotype/run.py",
      "source_location": "L33",
      "id": "run_karyotypeskill_generate_report",
      "community": 1
    },
    {
      "label": ".write_reproducibility_bundle()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/karyotype/run.py",
      "source_location": "L52",
      "id": "run_karyotypeskill_write_reproducibility_bundle",
      "community": 1
    },
    {
      "label": ".run_demo()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/karyotype/run.py",
      "source_location": "L58",
      "id": "run_karyotypeskill_run_demo",
      "community": 1
    },
    {
      "label": "test_karyotype.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/karyotype/tests/test_karyotype.py",
      "source_location": "L1",
      "id": "test_karyotype",
      "community": 1
    },
    {
      "label": "TestKaryotype",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/karyotype/tests/test_karyotype.py",
      "source_location": "L7",
      "id": "test_karyotype_testkaryotype",
      "community": 1
    },
    {
      "label": ".setUp()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/karyotype/tests/test_karyotype.py",
      "source_location": "L8",
      "id": "test_karyotype_testkaryotype_setup",
      "community": 1
    },
    {
      "label": ".tearDown()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/karyotype/tests/test_karyotype.py",
      "source_location": "L12",
      "id": "test_karyotype_testkaryotype_teardown",
      "community": 1
    },
    {
      "label": ".test_demo()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/karyotype/tests/test_karyotype.py",
      "source_location": "L15",
      "id": "test_karyotype_testkaryotype_test_demo",
      "community": 1
    },
    {
      "label": ".test_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/skills/karyotype/tests/test_karyotype.py",
      "source_location": "L18",
      "id": "test_karyotype_testkaryotype_test_config",
      "community": 1
    },
    {
      "label": "conftest.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/tests/conftest.py",
      "source_location": "L1",
      "id": "conftest",
      "community": 50
    },
    {
      "label": "project_root()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/tests/conftest.py",
      "source_location": "L15",
      "id": "conftest_project_root",
      "community": 50
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      "id": "string_api_stringapi",
      "community": 14
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/string_api.py",
      "source_location": "L34",
      "id": "string_api_stringapi_init",
      "community": 14
    },
    {
      "label": ".get_network()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/string_api.py",
      "source_location": "L47",
      "id": "string_api_stringapi_get_network",
      "community": 14
    },
    {
      "label": ".get_interaction_partners()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/string_api.py",
      "source_location": "L89",
      "id": "string_api_stringapi_get_interaction_partners",
      "community": 14
    },
    {
      "label": ".get_protein_info()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/string_api.py",
      "source_location": "L123",
      "id": "string_api_stringapi_get_protein_info",
      "community": 14
    },
    {
      "label": ".save_network_to_file()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/string_api.py",
      "source_location": "L153",
      "id": "string_api_stringapi_save_network_to_file",
      "community": 14
    },
    {
      "label": "test_string_api()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/string_api.py",
      "source_location": "L190",
      "id": "string_api_test_string_api",
      "community": 14
    },
    {
      "label": "\u521d\u59cb\u5316STRING API\u5ba2\u6237\u7aef                  Args:             species: \u7269\u79cd\u4ee3\u7801\uff08ath, osa, zma\u7b49",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/string_api.py",
      "source_location": "L35",
      "id": "string_api_rationale_35",
      "community": 14
    },
    {
      "label": "\u83b7\u53d6\u86cb\u767d\u4e92\u4f5c\u7f51\u7edc                  Args:             proteins: \u86cb\u767dID\u5217\u8868             require",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/string_api.py",
      "source_location": "L51",
      "id": "string_api_rationale_51",
      "community": 14
    },
    {
      "label": "\u83b7\u53d6\u6307\u5b9a\u86cb\u767d\u7684\u4e92\u4f5c\u4f19\u4f34                  Args:             protein: \u86cb\u767dID             require",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/string_api.py",
      "source_location": "L93",
      "id": "string_api_rationale_93",
      "community": 14
    },
    {
      "label": "\u83b7\u53d6\u86cb\u767d\u8be6\u7ec6\u4fe1\u606f                  Args:             proteins: \u86cb\u767dID\u5217\u8868                  Re",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/string_api.py",
      "source_location": "L124",
      "id": "string_api_rationale_124",
      "community": 14
    },
    {
      "label": "\u4fdd\u5b58\u7f51\u7edc\u6570\u636e\u5230\u6587\u4ef6                  Args:             network_data: \u7f51\u7edc\u6570\u636e             outp",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/string_api.py",
      "source_location": "L157",
      "id": "string_api_rationale_157",
      "community": 14
    },
    {
      "label": "run_rnaseq_qc.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_rnaseq_qc.py",
      "source_location": "L1",
      "id": "run_rnaseq_qc",
      "community": 42
    },
    {
      "label": "compute_file_hash()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_rnaseq_qc.py",
      "source_location": "L29",
      "id": "run_rnaseq_qc_compute_file_hash",
      "community": 42
    },
    {
      "label": "get_tool_versions()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_rnaseq_qc.py",
      "source_location": "L41",
      "id": "run_rnaseq_qc_get_tool_versions",
      "community": 42
    },
    {
      "label": "load_samples_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_rnaseq_qc.py",
      "source_location": "L76",
      "id": "run_rnaseq_qc_load_samples_config",
      "community": 42
    },
    {
      "label": "run_fastqc()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_rnaseq_qc.py",
      "source_location": "L90",
      "id": "run_rnaseq_qc_run_fastqc",
      "community": 42
    },
    {
      "label": "run_cutadapt()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_rnaseq_qc.py",
      "source_location": "L105",
      "id": "run_rnaseq_qc_run_cutadapt",
      "community": 42
    },
    {
      "label": "get_sample_stats()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_rnaseq_qc.py",
      "source_location": "L139",
      "id": "run_rnaseq_qc_get_sample_stats",
      "community": 42
    },
    {
      "label": "generate_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_rnaseq_qc.py",
      "source_location": "L193",
      "id": "run_rnaseq_qc_generate_report",
      "community": 42
    },
    {
      "label": "generate_manifest()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_rnaseq_qc.py",
      "source_location": "L233",
      "id": "run_rnaseq_qc_generate_manifest",
      "community": 42
    },
    {
      "label": "main()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_rnaseq_qc.py",
      "source_location": "L366",
      "id": "run_rnaseq_qc_main",
      "community": 42
    },
    {
      "label": "\u52a0\u8f7d\u6837\u672c\u914d\u7f6e\u6587\u4ef6\uff08\u652f\u6301\u5408\u5e76\u683c\u5f0f\uff1asamples + groups + compare\uff09",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_rnaseq_qc.py",
      "source_location": "L77",
      "id": "run_rnaseq_qc_rationale_77",
      "community": 42
    },
    {
      "label": "run_kaks_v2.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_kaks_v2.py",
      "source_location": "L1",
      "id": "run_kaks_v2",
      "community": 38
    },
    {
      "label": "compute_file_hash()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_kaks_v2.py",
      "source_location": "L20",
      "id": "run_kaks_v2_compute_file_hash",
      "community": 38
    },
    {
      "label": "get_tool_versions()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_kaks_v2.py",
      "source_location": "L32",
      "id": "run_kaks_v2_get_tool_versions",
      "community": 38
    },
    {
      "label": "parse_fasta()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_kaks_v2.py",
      "source_location": "L68",
      "id": "run_kaks_v2_parse_fasta",
      "community": 38
    },
    {
      "label": "find_matching_id()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_kaks_v2.py",
      "source_location": "L87",
      "id": "run_kaks_v2_find_matching_id",
      "community": 38
    },
    {
      "label": "parse_pairs()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_kaks_v2.py",
      "source_location": "L105",
      "id": "run_kaks_v2_parse_pairs",
      "community": 38
    },
    {
      "label": "run_kaks_pair()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_kaks_v2.py",
      "source_location": "L118",
      "id": "run_kaks_v2_run_kaks_pair",
      "community": 38
    },
    {
      "label": "load_gene_list()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_kaks_v2.py",
      "source_location": "L230",
      "id": "run_kaks_v2_load_gene_list",
      "community": 38
    },
    {
      "label": "filter_pairs_by_gene_list()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_kaks_v2.py",
      "source_location": "L246",
      "id": "run_kaks_v2_filter_pairs_by_gene_list",
      "community": 38
    },
    {
      "label": "main()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_kaks_v2.py",
      "source_location": "L265",
      "id": "run_kaks_v2_main",
      "community": 38
    },
    {
      "label": "\u8fd0\u884c\u5355\u4e2a\u57fa\u56e0\u5bf9\u7684Ka/Ks\u5206\u6790          \u53c2\u6570:     - gene1: Ft\u57fa\u56e0 (\u7528cds1/pep1)     - gene2: Ath\u57fa\u56e0 (",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_kaks_v2.py",
      "source_location": "L119",
      "id": "run_kaks_v2_rationale_119",
      "community": 38
    },
    {
      "label": "\u52a0\u8f7d\u57fa\u56e0\u5217\u8868\uff0c\u8fd4\u56de\u57fa\u56e0ID\u96c6\u5408\uff08\u53bb\u9664\u7248\u672c\u53f7\uff09",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_kaks_v2.py",
      "source_location": "L231",
      "id": "run_kaks_v2_rationale_231",
      "community": 38
    },
    {
      "label": "\u8fc7\u6ee4\u57fa\u56e0\u5bf9\uff0c\u53ea\u4fdd\u7559\u4e24\u4e2a\u57fa\u56e0\u90fd\u5728\u5bf9\u5e94\u5217\u8868\u4e2d\u7684\u5bf9          pairs\u6587\u4ef6\u683c\u5f0f: Ft\u57fa\u56e0 <tab> Ath\u57fa\u56e0 <tab> score (\u5982 .anch",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_kaks_v2.py",
      "source_location": "L247",
      "id": "run_kaks_v2_rationale_247",
      "community": 38
    },
    {
      "label": "run_domain.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L1",
      "id": "run_domain",
      "community": 18
    },
    {
      "label": "get_tool_versions()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L46",
      "id": "run_domain_get_tool_versions",
      "community": 18
    },
    {
      "label": "prepare_directories()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L77",
      "id": "run_domain_prepare_directories",
      "community": 18
    },
    {
      "label": "compute_file_hash()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L93",
      "id": "run_domain_compute_file_hash",
      "community": 18
    },
    {
      "label": "find_latest_manifest()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L105",
      "id": "run_domain_find_latest_manifest",
      "community": 18
    },
    {
      "label": "read_manifest()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L114",
      "id": "run_domain_read_manifest",
      "community": 18
    },
    {
      "label": "resolve_project_root()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L120",
      "id": "run_domain_resolve_project_root",
      "community": 18
    },
    {
      "label": "resolve_subfamily_file()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L130",
      "id": "run_domain_resolve_subfamily_file",
      "community": 18
    },
    {
      "label": "prepare_pfam_database()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L185",
      "id": "run_domain_prepare_pfam_database",
      "community": 18
    },
    {
      "label": "run_hmmscan()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L234",
      "id": "run_domain_run_hmmscan",
      "community": 18
    },
    {
      "label": "parse_domtblout()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L302",
      "id": "run_domain_parse_domtblout",
      "community": 18
    },
    {
      "label": "run_r_plotting()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L401",
      "id": "run_domain_run_r_plotting",
      "community": 18
    },
    {
      "label": "generate_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L483",
      "id": "run_domain_generate_report",
      "community": 18
    },
    {
      "label": "write_manifest()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L565",
      "id": "run_domain_write_manifest",
      "community": 18
    },
    {
      "label": "write_failure_manifest()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L572",
      "id": "run_domain_write_failure_manifest",
      "community": 18
    },
    {
      "label": "calculate_domain_metrics()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L608",
      "id": "run_domain_calculate_domain_metrics",
      "community": 18
    },
    {
      "label": "main()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L640",
      "id": "run_domain_main",
      "community": 18
    },
    {
      "label": "\u67e5\u627e\u6307\u5b9a\u9636\u6bb5\u7684\u6700\u65b0 manifest \u6587\u4ef6",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L106",
      "id": "run_domain_rationale_106",
      "community": 18
    },
    {
      "label": "\u89e3\u6790\u9879\u76ee\u6839\u76ee\u5f55     \u4ece workspace/{job_id}/ \u5411\u4e0a\u56de\u6eaf\u5230\u9879\u76ee\u6839\u76ee\u5f55     \u5047\u8bbe\u7ed3\u6784: .../bba/workspace/{job_id",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L121",
      "id": "run_domain_rationale_121",
      "community": 18
    },
    {
      "label": "\u89e3\u6790\u4e9a\u5bb6\u65cf\u6587\u4ef6\u8def\u5f84     \u547d\u540d\u89c4\u5219: {prefix}.geneID.subfamily (\u5982 Ft.SPL.geneID.subfamily)     \u4f18\u5148",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L131",
      "id": "run_domain_rationale_131",
      "community": 18
    },
    {
      "label": "\u51c6\u5907 Pfam \u6570\u636e\u5e93\uff08\u8f6f\u8fde\u63a5\u65b9\u5f0f\uff09          Returns:         (pfam_hmm_path, success, error_mess",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L186",
      "id": "run_domain_rationale_186",
      "community": 18
    },
    {
      "label": "\u8fd0\u884c hmmscan \u8fdb\u884c\u7ed3\u6784\u57df\u641c\u7d22          Returns:         (success, result_dict)",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L236",
      "id": "run_domain_rationale_236",
      "community": 18
    },
    {
      "label": "\u89e3\u6790 hmmscan domtblout \u6587\u4ef6          Returns:         (domains_list, stats_dict)",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L303",
      "id": "run_domain_rationale_303",
      "community": 18
    },
    {
      "label": "\u8fd0\u884c R \u7ed8\u56fe\u811a\u672c tree_domain.R          Args:         tree_file: \u7cfb\u7edf\u53d1\u80b2\u6811\u6587\u4ef6 (Newick)",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L406",
      "id": "run_domain_rationale_406",
      "community": 18
    },
    {
      "label": "\u751f\u6210 domain_report.md \u62a5\u544a",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
      "source_location": "L485",
      "id": "run_domain_rationale_485",
      "community": 18
    },
    {
      "label": "run_rnaseq_enrich_v2.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_rnaseq_enrich_v2.py",
      "source_location": "L1",
      "id": "run_rnaseq_enrich_v2",
      "community": 56
    },
    {
      "label": "compute_file_hash()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_rnaseq_enrich_v2.py",
      "source_location": "L69",
      "id": "run_rnaseq_enrich_v2_compute_file_hash",
      "community": 56
    },
    {
      "label": "get_tool_versions()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_rnaseq_enrich_v2.py",
      "source_location": "L81",
      "id": "run_rnaseq_enrich_v2_get_tool_versions",
      "community": 56
    },
    {
      "label": "check_gene_id_format()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_rnaseq_enrich_v2.py",
      "source_location": "L104",
      "id": "run_rnaseq_enrich_v2_check_gene_id_format",
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    },
    {
      "label": "\u83b7\u53d6\u7279\u5b9aAgent\u7684\u6210\u672c\u7edf\u8ba1          Args:         agent_name: Agent\u540d\u79f0",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/web/vue3/main.py",
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    },
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    },
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      "label": "conversation-sidebar.js",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/apps/web/vue3/conversation-sidebar.js",
      "source_location": "L1",
      "id": "conversation_sidebar",
      "community": 90
    },
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      "label": "api_config.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_config.py",
      "source_location": "L1",
      "id": "api_config",
      "community": 34
    },
    {
      "label": "APIConfig",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_config.py",
      "source_location": "L16",
      "id": "api_config_apiconfig",
      "community": 34
    },
    {
      "label": "ConfigManager",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_config.py",
      "source_location": "L24",
      "id": "api_config_configmanager",
      "community": 34
    },
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_config.py",
      "source_location": "L36",
      "id": "api_config_configmanager_init",
      "community": 34
    },
    {
      "label": "._load_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_config.py",
      "source_location": "L40",
      "id": "api_config_configmanager_load_config",
      "community": 34
    },
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_config.py",
      "source_location": "L50",
      "id": "api_config_configmanager_load_from_env",
      "community": 34
    },
    {
      "label": ".get_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_config.py",
      "source_location": "L73",
      "id": "api_config_configmanager_get_config",
      "community": 34
    },
    {
      "label": ".get_endpoint()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_config.py",
      "source_location": "L93",
      "id": "api_config_configmanager_get_endpoint",
      "community": 34
    },
    {
      "label": ".get_setting()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_config.py",
      "source_location": "L98",
      "id": "api_config_configmanager_get_setting",
      "community": 34
    },
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_config.py",
      "source_location": "L103",
      "id": "api_config_configmanager_has_api_key",
      "community": 34
    },
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      "label": "get_config_manager()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_config.py",
      "source_location": "L113",
      "id": "api_config_get_config_manager",
      "community": 34
    },
    {
      "label": "get_api_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_config.py",
      "source_location": "L121",
      "id": "api_config_get_api_config",
      "community": 34
    },
    {
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      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_config.py",
      "source_location": "L1",
      "id": "api_config_rationale_1",
      "community": 34
    },
    {
      "label": "API \u914d\u7f6e\u7ba1\u7406\u5668          \u7ba1\u7406\u6240\u6709 API \u7684\u914d\u7f6e\uff0c\u652f\u6301\uff1a     1. YAML \u914d\u7f6e\u6587\u4ef6     2. \u73af\u5883\u53d8\u91cf     3. \u9ed8\u8ba4\u503c",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_config.py",
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      "community": 34
    },
    {
      "label": "\u83b7\u53d6\u6307\u5b9a\u670d\u52a1\u7684\u914d\u7f6e                  Args:             service: \u670d\u52a1\u540d\u79f0\uff08ncbi, pfam, phytozome",
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      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_config.py",
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      "community": 34
    },
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility.py",
      "source_location": "L1",
      "id": "reproducibility",
      "community": 30
    },
    {
      "label": "ReproducibilityBundle",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility.py",
      "source_location": "L14",
      "id": "reproducibility_reproducibilitybundle",
      "community": 30
    },
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility.py",
      "source_location": "L17",
      "id": "reproducibility_reproducibilitybundle_init",
      "community": 30
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility.py",
      "source_location": "L25",
      "id": "reproducibility_reproducibilitybundle_add_command",
      "community": 30
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility.py",
      "source_location": "L34",
      "id": "reproducibility_reproducibilitybundle_generate_commands_sh",
      "community": 30
    },
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility.py",
      "source_location": "L89",
      "id": "reproducibility_reproducibilitybundle_generate_environment_yml",
      "community": 30
    },
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility.py",
      "source_location": "L139",
      "id": "reproducibility_reproducibilitybundle_generate_checksums",
      "community": 30
    },
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility.py",
      "source_location": "L162",
      "id": "reproducibility_reproducibilitybundle_calculate_sha256",
      "community": 30
    },
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility.py",
      "source_location": "L170",
      "id": "reproducibility_reproducibilitybundle_copy_to_project_reproducibility",
      "community": 30
    },
    {
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility.py",
      "source_location": "L183",
      "id": "reproducibility_create_reproducibility_bundle",
      "community": 30
    },
    {
      "label": "\u53ef\u590d\u73b0\u6027\u652f\u6301\u6a21\u5757 \u81ea\u52a8\u751f\u6210 commands.sh, environment.yml, checksums.sha256",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility.py",
      "source_location": "L1",
      "id": "reproducibility_rationale_1",
      "community": 30
    },
    {
      "label": "\u590d\u5236\u5230\u9879\u76ee\u7ea7 reproducibility \u76ee\u5f55",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility.py",
      "source_location": "L171",
      "id": "reproducibility_rationale_171",
      "community": 30
    },
    {
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      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility.py",
      "source_location": "L189",
      "id": "reproducibility_rationale_189",
      "community": 30
    },
    {
      "label": "reproducibility_v2.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility_v2.py",
      "source_location": "L1",
      "id": "reproducibility_v2",
      "community": 8
    },
    {
      "label": "StageRecorder",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility_v2.py",
      "source_location": "L26",
      "id": "reproducibility_v2_stagerecorder",
      "community": 8
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      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility_v2.py",
      "source_location": "L29",
      "id": "reproducibility_v2_stagerecorder_init",
      "community": 8
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    {
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility_v2.py",
      "source_location": "L38",
      "id": "reproducibility_v2_stagerecorder_complete",
      "community": 8
    },
    {
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility_v2.py",
      "source_location": "L44",
      "id": "reproducibility_v2_stagerecorder_to_dict",
      "community": 8
    },
    {
      "label": "ReproducibilityManager",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility_v2.py",
      "source_location": "L57",
      "id": "reproducibility_v2_reproducibilitymanager",
      "community": 8
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility_v2.py",
      "source_location": "L64",
      "id": "reproducibility_v2_reproducibilitymanager_init",
      "community": 8
    },
    {
      "label": "._collect_system_info()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility_v2.py",
      "source_location": "L82",
      "id": "reproducibility_v2_reproducibilitymanager_collect_system_info",
      "community": 8
    },
    {
      "label": ".start_stage()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility_v2.py",
      "source_location": "L108",
      "id": "reproducibility_v2_reproducibilitymanager_start_stage",
      "community": 8
    },
    {
      "label": ".end_stage()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility_v2.py",
      "source_location": "L120",
      "id": "reproducibility_v2_reproducibilitymanager_end_stage",
      "community": 8
    },
    {
      "label": "._save_progress()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility_v2.py",
      "source_location": "L127",
      "id": "reproducibility_v2_reproducibilitymanager_save_progress",
      "community": 8
    },
    {
      "label": "._calculate_sha256()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility_v2.py",
      "source_location": "L141",
      "id": "reproducibility_v2_reproducibilitymanager_calculate_sha256",
      "community": 8
    },
    {
      "label": "._get_tool_versions()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility_v2.py",
      "source_location": "L149",
      "id": "reproducibility_v2_reproducibilitymanager_get_tool_versions",
      "community": 8
    },
    {
      "label": ".generate_commands_sh()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility_v2.py",
      "source_location": "L179",
      "id": "reproducibility_v2_reproducibilitymanager_generate_commands_sh",
      "community": 8
    },
    {
      "label": ".generate_environment_yml()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility_v2.py",
      "source_location": "L237",
      "id": "reproducibility_v2_reproducibilitymanager_generate_environment_yml",
      "community": 8
    },
    {
      "label": ".generate_checksums()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility_v2.py",
      "source_location": "L287",
      "id": "reproducibility_v2_reproducibilitymanager_generate_checksums",
      "community": 8
    },
    {
      "label": ".generate_provenance()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility_v2.py",
      "source_location": "L308",
      "id": "reproducibility_v2_reproducibilitymanager_generate_provenance",
      "community": 8
    },
    {
      "label": ".copy_to_project()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility_v2.py",
      "source_location": "L331",
      "id": "reproducibility_v2_reproducibilitymanager_copy_to_project",
      "community": 8
    },
    {
      "label": ".finalize()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/reproducibility_v2.py",
      "source_location": "L342",
      "id": "reproducibility_v2_reproducibilitymanager_finalize",
      "community": 8
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    {
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      "file_type": "rationale",
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      "community": 44
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    {
      "label": "\u6267\u884c\u81ea\u7136\u8bed\u8a00\u67e5\u8be2                  \u8fd4\u56de: {\"type\": \"result\"|\"confirmation\"|\"error\", \"message",
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      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/pipeline_api_integration.py",
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      "id": "expression_pipeline_expressionconfig",
      "community": 57
    },
    {
      "label": "ExpressionResult",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/pipelines/expression_pipeline.py",
      "source_location": "L36",
      "id": "expression_pipeline_expressionresult",
      "community": 57
    },
    {
      "label": "run_r_expression()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/pipelines/expression_pipeline.py",
      "source_location": "L51",
      "id": "expression_pipeline_run_r_expression",
      "community": 57
    },
    {
      "label": "find_differential_genes()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/pipelines/expression_pipeline.py",
      "source_location": "L90",
      "id": "expression_pipeline_find_differential_genes",
      "community": 57
    },
    {
      "label": "add_functional_annotation()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/pipelines/expression_pipeline.py",
      "source_location": "L159",
      "id": "expression_pipeline_add_functional_annotation",
      "community": 57
    },
    {
      "label": "generate_summary_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/pipelines/expression_pipeline.py",
      "source_location": "L177",
      "id": "expression_pipeline_generate_summary_report",
      "community": 57
    },
    {
      "label": "run_expression_pipeline()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/pipelines/expression_pipeline.py",
      "source_location": "L214",
      "id": "expression_pipeline_run_expression_pipeline",
      "community": 57
    },
    {
      "label": "cost_tracker.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/cost_tracker.py",
      "source_location": "L1",
      "id": "cost_tracker",
      "community": 28
    },
    {
      "label": "CostEntry",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/cost_tracker.py",
      "source_location": "L16",
      "id": "cost_tracker_costentry",
      "community": 28
    },
    {
      "label": "AgentCostStats",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/cost_tracker.py",
      "source_location": "L31",
      "id": "cost_tracker_agentcoststats",
      "community": 28
    },
    {
      "label": "CostTracker",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/cost_tracker.py",
      "source_location": "L43",
      "id": "cost_tracker_costtracker",
      "community": 28
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/cost_tracker.py",
      "source_location": "L64",
      "id": "cost_tracker_costtracker_init",
      "community": 28
    },
    {
      "label": "._load_today_entries()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/cost_tracker.py",
      "source_location": "L75",
      "id": "cost_tracker_costtracker_load_today_entries",
      "community": 28
    },
    {
      "label": "._estimate_cost()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/cost_tracker.py",
      "source_location": "L88",
      "id": "cost_tracker_costtracker_estimate_cost",
      "community": 28
    },
    {
      "label": ".track()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/cost_tracker.py",
      "source_location": "L97",
      "id": "cost_tracker_costtracker_track",
      "community": 28
    },
    {
      "label": ".get_agent_stats()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/cost_tracker.py",
      "source_location": "L152",
      "id": "cost_tracker_costtracker_get_agent_stats",
      "community": 28
    },
    {
      "label": ".get_summary()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/cost_tracker.py",
      "source_location": "L178",
      "id": "cost_tracker_costtracker_get_summary",
      "community": 28
    },
    {
      "label": ".generate_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/cost_tracker.py",
      "source_location": "L211",
      "id": "cost_tracker_costtracker_generate_report",
      "community": 28
    },
    {
      "label": ".get_optimization_suggestions()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/cost_tracker.py",
      "source_location": "L248",
      "id": "cost_tracker_costtracker_get_optimization_suggestions",
      "community": 28
    },
    {
      "label": "get_cost_tracker()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/cost_tracker.py",
      "source_location": "L278",
      "id": "cost_tracker_get_cost_tracker",
      "community": 28
    },
    {
      "label": "track_cost()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/cost_tracker.py",
      "source_location": "L286",
      "id": "cost_tracker_track_cost",
      "community": 28
    },
    {
      "label": "print_cost_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/cost_tracker.py",
      "source_location": "L300",
      "id": "cost_tracker_print_cost_report",
      "community": 28
    },
    {
      "label": "\u6210\u672c\u8ffd\u8e2a\u7cfb\u7edf - \u76d1\u63a7Token\u6d88\u8017\u548cAPI\u8c03\u7528\u6210\u672c \u53c2\u8003Claude Code\u7684cost-tracker.ts\u5b9e\u73b0",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/cost_tracker.py",
      "source_location": "L1",
      "id": "cost_tracker_rationale_1",
      "community": 28
    },
    {
      "label": "Token\u6210\u672c\u8ffd\u8e2a\u5668          \u529f\u80fd:     1. \u8bb0\u5f55\u6bcf\u6b21LLM\u8c03\u7528\u7684token\u6d88\u8017     2. \u6309Agent\u7edf\u8ba1\u6210\u672c     3. \u6309\u65f6\u95f4\u6bb5\u7edf\u8ba1",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/cost_tracker.py",
      "source_location": "L44",
      "id": "cost_tracker_rationale_44",
      "community": 28
    },
    {
      "label": "\u8bb0\u5f55\u4e00\u6b21LLM\u8c03\u7528\u6210\u672c                  Args:             agent_name: Agent\u540d\u79f0             p",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/cost_tracker.py",
      "source_location": "L107",
      "id": "cost_tracker_rationale_107",
      "community": 28
    },
    {
      "label": "config.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/config.py",
      "source_location": "L1",
      "id": "config",
      "community": 24
    },
    {
      "label": "ModelConfig",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/config.py",
      "source_location": "L9",
      "id": "config_modelconfig",
      "community": 24
    },
    {
      "label": "ProviderConfig",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/config.py",
      "source_location": "L14",
      "id": "config_providerconfig",
      "community": 24
    },
    {
      "label": "LLMConfig",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/config.py",
      "source_location": "L22",
      "id": "config_llmconfig",
      "community": 24
    },
    {
      "label": "ToolInputConfig",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/config.py",
      "source_location": "L27",
      "id": "config_toolinputconfig",
      "community": 24
    },
    {
      "label": "ToolOutputConfig",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/config.py",
      "source_location": "L33",
      "id": "config_tooloutputconfig",
      "community": 24
    },
    {
      "label": "ToolParameterConfig",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/config.py",
      "source_location": "L38",
      "id": "config_toolparameterconfig",
      "community": 24
    },
    {
      "label": "ToolConfig",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/config.py",
      "source_location": "L46",
      "id": "config_toolconfig",
      "community": 24
    },
    {
      "label": "Settings",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/config.py",
      "source_location": "L58",
      "id": "config_settings",
      "community": 24
    },
    {
      "label": "BaseSettings",
      "file_type": "code",
      "source_file": "",
      "source_location": "",
      "id": "basesettings",
      "community": 24
    },
    {
      "label": "llm_config_path()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/config.py",
      "source_location": "L84",
      "id": "config_llm_config_path",
      "community": 24
    },
    {
      "label": "tools_config_path()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/config.py",
      "source_location": "L88",
      "id": "config_tools_config_path",
      "community": 24
    },
    {
      "label": "ConfigLoader",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/config.py",
      "source_location": "L92",
      "id": "config_configloader",
      "community": 24
    },
    {
      "label": ".__new__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/config.py",
      "source_location": "L98",
      "id": "config_configloader_new",
      "community": 24
    },
    {
      "label": ".load_llm_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/config.py",
      "source_location": "L109",
      "id": "config_configloader_load_llm_config",
      "community": 24
    },
    {
      "label": ".load_tools_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/config.py",
      "source_location": "L138",
      "id": "config_configloader_load_tools_config",
      "community": 24
    },
    {
      "label": ".get_provider_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/config.py",
      "source_location": "L150",
      "id": "config_configloader_get_provider_config",
      "community": 24
    },
    {
      "label": ".get_tool_config()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/config.py",
      "source_location": "L154",
      "id": "config_configloader_get_tool_config",
      "community": 24
    },
    {
      "label": ".get_default_provider()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/config.py",
      "source_location": "L158",
      "id": "config_configloader_get_default_provider",
      "community": 24
    },
    {
      "label": ".get_default_model()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/config.py",
      "source_location": "L162",
      "id": "config_configloader_get_default_model",
      "community": 24
    },
    {
      "label": "rag.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/rag.py",
      "source_location": "L1",
      "id": "rag",
      "community": 2
    },
    {
      "label": "RAGSearchResult",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/rag.py",
      "source_location": "L20",
      "id": "rag_ragsearchresult",
      "community": 2
    },
    {
      "label": "RAGRetriever",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/rag.py",
      "source_location": "L28",
      "id": "rag_ragretriever",
      "community": 2
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/rag.py",
      "source_location": "L31",
      "id": "rag_ragretriever_init",
      "community": 2
    },
    {
      "label": "._check_health()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/rag.py",
      "source_location": "L37",
      "id": "rag_ragretriever_check_health",
      "community": 2
    },
    {
      "label": ".is_available()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/rag.py",
      "source_location": "L56",
      "id": "rag_ragretriever_is_available",
      "community": 2
    },
    {
      "label": ".count_chunks()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/rag.py",
      "source_location": "L60",
      "id": "rag_ragretriever_count_chunks",
      "community": 2
    },
    {
      "label": ".search()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/rag.py",
      "source_location": "L71",
      "id": "rag_ragretriever_search",
      "community": 2
    },
    {
      "label": ".chat()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/rag.py",
      "source_location": "L121",
      "id": "rag_ragretriever_chat",
      "community": 2
    },
    {
      "label": ".get_context()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/rag.py",
      "source_location": "L175",
      "id": "rag_ragretriever_get_context",
      "community": 2
    },
    {
      "label": ".aindex_pdf_directory()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/rag.py",
      "source_location": "L202",
      "id": "rag_ragretriever_aindex_pdf_directory",
      "community": 2
    },
    {
      "label": "get_rag_retriever()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/rag.py",
      "source_location": "L217",
      "id": "rag_get_rag_retriever",
      "community": 2
    },
    {
      "label": "RAG API\u5ba2\u6237\u7aef\u6a21\u5757  \u5bf9\u63a5 gene-family-mas \u9879\u76ee\u7684RAG\u670d\u52a1",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/rag.py",
      "source_location": "L1",
      "id": "rag_rationale_1",
      "community": 2
    },
    {
      "label": "\u641c\u7d22\u76f8\u5173\u6587\u6863                  Args:             query: \u67e5\u8be2\u6587\u672c             top_k: \u8fd4\u56de\u7ed3\u679c\u6570\u91cf",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/rag.py",
      "source_location": "L77",
      "id": "rag_rationale_77",
      "community": 2
    },
    {
      "label": "\u5bf9\u8bdd\u5f0f\u68c0\u7d22                  Args:             query: \u7528\u6237\u95ee\u9898                      Return",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/rag.py",
      "source_location": "L122",
      "id": "rag_rationale_122",
      "community": 2
    },
    {
      "label": "\u5c06\u641c\u7d22\u7ed3\u679c\u8f6c\u6362\u4e3a\u4e0a\u4e0b\u6587\u6587\u672c                  Args:             results: \u641c\u7d22\u7ed3\u679c\u5217\u8868             max",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/rag.py",
      "source_location": "L180",
      "id": "rag_rationale_180",
      "community": 2
    },
    {
      "label": "\u6ce8\u610f: \u672c\u5730\u7d22\u5f15\u529f\u80fd\u5df2\u5f03\u7528\uff0c\u4f7f\u7528\u8fdc\u7a0bRAG API                  Args:             directory: PDF\u76ee\u5f55",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/rag.py",
      "source_location": "L203",
      "id": "rag_rationale_203",
      "community": 2
    },
    {
      "label": "registry.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/registry.py",
      "source_location": "L1",
      "id": "registry",
      "community": 5
    },
    {
      "label": "ToolParameter",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/registry.py",
      "source_location": "L21",
      "id": "registry_toolparameter",
      "community": 5
    },
    {
      "label": "ToolInput",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/registry.py",
      "source_location": "L32",
      "id": "registry_toolinput",
      "community": 5
    },
    {
      "label": "ToolOutput",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/registry.py",
      "source_location": "L39",
      "id": "registry_tooloutput",
      "community": 5
    },
    {
      "label": "ToolMetadata",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/registry.py",
      "source_location": "L45",
      "id": "registry_toolmetadata",
      "community": 5
    },
    {
      "label": "ToolRegistry",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/registry.py",
      "source_location": "L57",
      "id": "registry_toolregistry",
      "community": 5
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/registry.py",
      "source_location": "L58",
      "id": "registry_toolregistry_init",
      "community": 5
    },
    {
      "label": ".register()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/registry.py",
      "source_location": "L61",
      "id": "registry_toolregistry_register",
      "community": 5
    },
    {
      "label": ".get()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/registry.py",
      "source_location": "L64",
      "id": "registry_toolregistry_get",
      "community": 5
    },
    {
      "label": ".list_by_category()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/registry.py",
      "source_location": "L67",
      "id": "registry_toolregistry_list_by_category",
      "community": 5
    },
    {
      "label": ".list_all()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/registry.py",
      "source_location": "L70",
      "id": "registry_toolregistry_list_all",
      "community": 5
    },
    {
      "label": "create_default_registry()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/registry.py",
      "source_location": "L74",
      "id": "registry_create_default_registry",
      "community": 5
    },
    {
      "label": "stage_registry.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_registry.py",
      "source_location": "L1",
      "id": "stage_registry",
      "community": 20
    },
    {
      "label": "StageTool",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_registry.py",
      "source_location": "L20",
      "id": "stage_registry_stagetool",
      "community": 20
    },
    {
      "label": "StageToolExecutor",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_registry.py",
      "source_location": "L34",
      "id": "stage_registry_stagetoolexecutor",
      "community": 20
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_registry.py",
      "source_location": "L37",
      "id": "stage_registry_stagetoolexecutor_init",
      "community": 20
    },
    {
      "label": ".execute()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_registry.py",
      "source_location": "L43",
      "id": "stage_registry_stagetoolexecutor_execute",
      "community": 20
    },
    {
      "label": "StageToolRegistry",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_registry.py",
      "source_location": "L144",
      "id": "stage_registry_stagetoolregistry",
      "community": 20
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_registry.py",
      "source_location": "L147",
      "id": "stage_registry_stagetoolregistry_init",
      "community": 20
    },
    {
      "label": "._register_all_stages()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_registry.py",
      "source_location": "L152",
      "id": "stage_registry_stagetoolregistry_register_all_stages",
      "community": 20
    },
    {
      "label": "Stage-level Tool Registry for Multi-Agent System \u5c06bbav20311\u7684\u5206\u6790\u9636\u6bb5\u811a\u672c\u5c01\u88c5\u4e3aAgent\u53ef\u8c03\u7528\u7684To",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_registry.py",
      "source_location": "L1",
      "id": "stage_registry_rationale_1",
      "community": 20
    },
    {
      "label": "\u6267\u884c\u5206\u6790\u9636\u6bb5                  Args:             stage_tool: \u9636\u6bb5\u5de5\u5177\u5b9a\u4e49             job_id:",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_registry.py",
      "source_location": "L45",
      "id": "stage_registry_rationale_45",
      "community": 20
    },
    {
      "label": "adapter.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/adapter.py",
      "source_location": "L1",
      "id": "adapter",
      "community": 5
    },
    {
      "label": "ToolAdapter",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/adapter.py",
      "source_location": "L9",
      "id": "adapter_tooladapter",
      "community": 5
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/adapter.py",
      "source_location": "L10",
      "id": "adapter_tooladapter_init",
      "community": 5
    },
    {
      "label": ".execute()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/adapter.py",
      "source_location": "L15",
      "id": "adapter_tooladapter_execute",
      "community": 5
    },
    {
      "label": ".aexecute()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/adapter.py",
      "source_location": "L48",
      "id": "adapter_tooladapter_aexecute",
      "community": 5
    },
    {
      "label": "._build_command()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/adapter.py",
      "source_location": "L51",
      "id": "adapter_tooladapter_build_command",
      "community": 5
    },
    {
      "label": "._collect_outputs()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/adapter.py",
      "source_location": "L98",
      "id": "adapter_tooladapter_collect_outputs",
      "community": 5
    },
    {
      "label": "workflow.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/workflow.py",
      "source_location": "L1",
      "id": "workflow",
      "community": 5
    },
    {
      "label": "WorkflowStatus",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/workflow.py",
      "source_location": "L10",
      "id": "workflow_workflowstatus",
      "community": 5
    },
    {
      "label": "Enum",
      "file_type": "code",
      "source_file": "",
      "source_location": "",
      "id": "enum",
      "community": 5
    },
    {
      "label": "WorkflowStep",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/workflow.py",
      "source_location": "L18",
      "id": "workflow_workflowstep",
      "community": 5
    },
    {
      "label": "WorkflowResult",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/workflow.py",
      "source_location": "L29",
      "id": "workflow_workflowresult",
      "community": 5
    },
    {
      "label": "GeneFamilyWorkflow",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/workflow.py",
      "source_location": "L39",
      "id": "workflow_genefamilyworkflow",
      "community": 5
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/workflow.py",
      "source_location": "L40",
      "id": "workflow_genefamilyworkflow_init",
      "community": 5
    },
    {
      "label": ".create_identification_workflow()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/workflow.py",
      "source_location": "L43",
      "id": "workflow_genefamilyworkflow_create_identification_workflow",
      "community": 5
    },
    {
      "label": ".create_full_analysis_workflow()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/workflow.py",
      "source_location": "L67",
      "id": "workflow_genefamilyworkflow_create_full_analysis_workflow",
      "community": 5
    },
    {
      "label": ".run_workflow()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/workflow.py",
      "source_location": "L119",
      "id": "workflow_genefamilyworkflow_run_workflow",
      "community": 5
    },
    {
      "label": ".get_available_tools()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/workflow.py",
      "source_location": "L173",
      "id": "workflow_genefamilyworkflow_get_available_tools",
      "community": 5
    },
    {
      "label": "stage_tools.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
      "source_location": "L1",
      "id": "stage_tools",
      "community": 7
    },
    {
      "label": "StageTool",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
      "source_location": "L28",
      "id": "stage_tools_stagetool",
      "community": 7
    },
    {
      "label": "StageToolExecutor",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
      "source_location": "L42",
      "id": "stage_tools_stagetoolexecutor",
      "community": 7
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
      "source_location": "L45",
      "id": "stage_tools_stagetoolexecutor_init",
      "community": 7
    },
    {
      "label": ".execute()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
      "source_location": "L51",
      "id": "stage_tools_stagetoolexecutor_execute",
      "community": 7
    },
    {
      "label": "StageToolRegistry",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
      "source_location": "L152",
      "id": "stage_tools_stagetoolregistry",
      "community": 7
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
      "source_location": "L403",
      "id": "stage_tools_stagetoolregistry_init",
      "community": 7
    },
    {
      "label": "._register_all_stages()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
      "source_location": "L408",
      "id": "stage_tools_stagetoolregistry_register_all_stages",
      "community": 7
    },
    {
      "label": ".register()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
      "source_location": "L413",
      "id": "stage_tools_stagetoolregistry_register",
      "community": 7
    },
    {
      "label": ".get()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
      "source_location": "L417",
      "id": "stage_tools_stagetoolregistry_get",
      "community": 7
    },
    {
      "label": ".list_all()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
      "source_location": "L421",
      "id": "stage_tools_stagetoolregistry_list_all",
      "community": 7
    },
    {
      "label": ".list_by_category()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
      "source_location": "L425",
      "id": "stage_tools_stagetoolregistry_list_by_category",
      "community": 7
    },
    {
      "label": ".execute()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
      "source_location": "L429",
      "id": "stage_tools_stagetoolregistry_execute",
      "community": 7
    },
    {
      "label": ".get_execution_order()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
      "source_location": "L441",
      "id": "stage_tools_stagetoolregistry_get_execution_order",
      "community": 7
    },
    {
      "label": "create_stage_registry()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
      "source_location": "L465",
      "id": "stage_tools_create_stage_registry",
      "community": 7
    },
    {
      "label": "Stage-level Tool Registry for Multi-Agent System \u5c06bbav20311\u7684\u5206\u6790\u9636\u6bb5\u811a\u672c\u5c01\u88c5\u4e3aAgent\u53ef\u8c03\u7528\u7684To",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
      "source_location": "L1",
      "id": "stage_tools_rationale_1",
      "community": 7
    },
    {
      "label": "\u5206\u6790\u9636\u6bb5\u5de5\u5177\u6267\u884c\u5668 - \u590d\u7528 pipeline_backend.run_stage()",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
      "source_location": "L43",
      "id": "stage_tools_rationale_43",
      "community": 7
    },
    {
      "label": "\u6267\u884c\u5206\u6790\u9636\u6bb5 - \u4f7f\u7528 pipeline_backend.run_stage()",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
      "source_location": "L53",
      "id": "stage_tools_rationale_53",
      "community": 7
    },
    {
      "label": "\u521b\u5efa\u65b0\u7684StageToolRegistry\u5b9e\u4f8b",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
      "source_location": "L466",
      "id": "stage_tools_rationale_466",
      "community": 7
    },
    {
      "label": "executor.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/executor.py",
      "source_location": "L1",
      "id": "executor",
      "community": 5
    },
    {
      "label": "ExecutionStatus",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/executor.py",
      "source_location": "L13",
      "id": "executor_executionstatus",
      "community": 5
    },
    {
      "label": "ExecutionResult",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/executor.py",
      "source_location": "L22",
      "id": "executor_executionresult",
      "community": 5
    },
    {
      "label": "ToolExecutor",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/executor.py",
      "source_location": "L34",
      "id": "executor_toolexecutor",
      "community": 5
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/executor.py",
      "source_location": "L35",
      "id": "executor_toolexecutor_init",
      "community": 5
    },
    {
      "label": ".get_tool()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/executor.py",
      "source_location": "L48",
      "id": "executor_toolexecutor_get_tool",
      "community": 5
    },
    {
      "label": ".list_tools()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/executor.py",
      "source_location": "L51",
      "id": "executor_toolexecutor_list_tools",
      "community": 5
    },
    {
      "label": ".execute()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/executor.py",
      "source_location": "L56",
      "id": "executor_toolexecutor_execute",
      "community": 5
    },
    {
      "label": ".aexecute()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/executor.py",
      "source_location": "L139",
      "id": "executor_toolexecutor_aexecute",
      "community": 5
    },
    {
      "label": "._build_command()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/executor.py",
      "source_location": "L150",
      "id": "executor_toolexecutor_build_command",
      "community": 5
    },
    {
      "label": "._build_docker_command()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/executor.py",
      "source_location": "L221",
      "id": "executor_toolexecutor_build_docker_command",
      "community": 5
    },
    {
      "label": "._simulate_execution()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/executor.py",
      "source_location": "L241",
      "id": "executor_toolexecutor_simulate_execution",
      "community": 5
    },
    {
      "label": "._collect_outputs()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/executor.py",
      "source_location": "L363",
      "id": "executor_toolexecutor_collect_outputs",
      "community": 5
    },
    {
      "label": "intent_parser.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/utils/intent_parser.py",
      "source_location": "L1",
      "id": "intent_parser",
      "community": 45
    },
    {
      "label": "parse_intent_from_query()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/utils/intent_parser.py",
      "source_location": "L42",
      "id": "intent_parser_parse_intent_from_query",
      "community": 45
    },
    {
      "label": "_extract_gene_family()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/utils/intent_parser.py",
      "source_location": "L83",
      "id": "intent_parser_extract_gene_family",
      "community": 45
    },
    {
      "label": "_extract_species()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/utils/intent_parser.py",
      "source_location": "L103",
      "id": "intent_parser_extract_species",
      "community": 45
    },
    {
      "label": "_extract_stages()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/utils/intent_parser.py",
      "source_location": "L112",
      "id": "intent_parser_extract_stages",
      "community": 45
    },
    {
      "label": "_determine_task_type()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/utils/intent_parser.py",
      "source_location": "L125",
      "id": "intent_parser_determine_task_type",
      "community": 45
    },
    {
      "label": "parse_gene_family()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/utils/intent_parser.py",
      "source_location": "L136",
      "id": "intent_parser_parse_gene_family",
      "community": 45
    },
    {
      "label": "parse_species()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/utils/intent_parser.py",
      "source_location": "L141",
      "id": "intent_parser_parse_species",
      "community": 45
    },
    {
      "label": "parse_stages()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/utils/intent_parser.py",
      "source_location": "L146",
      "id": "intent_parser_parse_stages",
      "community": 45
    },
    {
      "label": "Intent Parser - \u786c\u7f16\u7801\u89c4\u5219\u89e3\u6790\u7528\u6237\u610f\u56fe \u4ece orchestrator.py \u63d0\u53d6\u5e76\u6269\u5c55",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/utils/intent_parser.py",
      "source_location": "L1",
      "id": "intent_parser_rationale_1",
      "community": 45
    },
    {
      "label": "\u4ece\u67e5\u8be2\u4e2d\u89e3\u6790\u610f\u56fe - \u786c\u7f16\u7801\u89c4\u5219          Args:         query: \u7528\u6237\u81ea\u7136\u8bed\u8a00\u67e5\u8be2              Returns:",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/utils/intent_parser.py",
      "source_location": "L43",
      "id": "intent_parser_rationale_43",
      "community": 45
    },
    {
      "label": "manager.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/manager.py",
      "source_location": "L1",
      "id": "manager",
      "community": 6
    },
    {
      "label": "MemoryStats",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
      "source_location": "L12",
      "id": "manager_memorystats",
      "community": 4
    },
    {
      "label": "MemoryManager",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
      "source_location": "L19",
      "id": "manager_memorymanager",
      "community": 4
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
      "source_location": "L20",
      "id": "manager_memorymanager_init",
      "community": 4
    },
    {
      "label": ".create_session()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
      "source_location": "L30",
      "id": "manager_memorymanager_create_session",
      "community": 4
    },
    {
      "label": ".get_session()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
      "source_location": "L38",
      "id": "manager_memorymanager_get_session",
      "community": 4
    },
    {
      "label": ".add_message_to_session()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
      "source_location": "L41",
      "id": "manager_memorymanager_add_message_to_session",
      "community": 4
    },
    {
      "label": ".update_session_state()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
      "source_location": "L44",
      "id": "manager_memorymanager_update_session_state",
      "community": 4
    },
    {
      "label": ".create_case()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
      "source_location": "L47",
      "id": "manager_memorymanager_create_case",
      "community": 4
    },
    {
      "label": ".get_case()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
      "source_location": "L65",
      "id": "manager_memorymanager_get_case",
      "community": 4
    },
    {
      "label": ".update_case_results()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
      "source_location": "L68",
      "id": "manager_memorymanager_update_case_results",
      "community": 4
    },
    {
      "label": ".complete_case()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
      "source_location": "L74",
      "id": "manager_memorymanager_complete_case",
      "community": 4
    },
    {
      "label": ".add_case_feedback()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
      "source_location": "L77",
      "id": "manager_memorymanager_add_case_feedback",
      "community": 4
    },
    {
      "label": ".add_knowledge()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
      "source_location": "L80",
      "id": "manager_memorymanager_add_knowledge",
      "community": 4
    },
    {
      "label": ".search_knowledge()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
      "source_location": "L98",
      "id": "manager_memorymanager_search_knowledge",
      "community": 4
    },
    {
      "label": ".search_knowledge_by_tags()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
      "source_location": "L105",
      "id": "manager_memorymanager_search_knowledge_by_tags",
      "community": 4
    },
    {
      "label": ".extract_case_to_knowledge()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
      "source_location": "L108",
      "id": "manager_memorymanager_extract_case_to_knowledge",
      "community": 4
    },
    {
      "label": "._extract_knowledge_content()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
      "source_location": "L132",
      "id": "manager_memorymanager_extract_knowledge_content",
      "community": 4
    },
    {
      "label": ".get_stats()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
      "source_location": "L144",
      "id": "manager_memorymanager_get_stats",
      "community": 4
    },
    {
      "label": ".clear_all()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
      "source_location": "L151",
      "id": "manager_memorymanager_clear_all",
      "community": 4
    },
    {
      "label": "persistent.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/persistent.py",
      "source_location": "L1",
      "id": "persistent",
      "community": 4
    },
    {
      "label": "PersistentMemory",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/persistent.py",
      "source_location": "L15",
      "id": "persistent_persistentmemory",
      "community": 4
    },
    {
      "label": "BaseMemory",
      "file_type": "code",
      "source_file": "",
      "source_location": "",
      "id": "basememory",
      "community": 4
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/persistent.py",
      "source_location": "L18",
      "id": "persistent_persistentmemory_init",
      "community": 4
    },
    {
      "label": "._get_file_path()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/persistent.py",
      "source_location": "L24",
      "id": "persistent_persistentmemory_get_file_path",
      "community": 4
    },
    {
      "label": "._serialize()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/persistent.py",
      "source_location": "L32",
      "id": "persistent_persistentmemory_serialize",
      "community": 4
    },
    {
      "label": "._deserialize()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/persistent.py",
      "source_location": "L42",
      "id": "persistent_persistentmemory_deserialize",
      "community": 4
    },
    {
      "label": ".store()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/persistent.py",
      "source_location": "L60",
      "id": "persistent_persistentmemory_store",
      "community": 4
    },
    {
      "label": ".retrieve()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/persistent.py",
      "source_location": "L80",
      "id": "persistent_persistentmemory_retrieve",
      "community": 4
    },
    {
      "label": ".delete()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/persistent.py",
      "source_location": "L105",
      "id": "persistent_persistentmemory_delete",
      "community": 4
    },
    {
      "label": ".exists()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/persistent.py",
      "source_location": "L114",
      "id": "persistent_persistentmemory_exists",
      "community": 4
    },
    {
      "label": ".clear()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/persistent.py",
      "source_location": "L136",
      "id": "persistent_persistentmemory_clear",
      "community": 4
    },
    {
      "label": "base.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/base.py",
      "source_location": "L1",
      "id": "base",
      "community": 0
    },
    {
      "label": "MemoryEntry",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/base.py",
      "source_location": "L10",
      "id": "base_memoryentry",
      "community": 4
    },
    {
      "label": "SearchResult",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/base.py",
      "source_location": "L20",
      "id": "base_searchresult",
      "community": 4
    },
    {
      "label": "BaseMemory",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/base.py",
      "source_location": "L27",
      "id": "base_basememory",
      "community": 4
    },
    {
      "label": "ABC",
      "file_type": "code",
      "source_file": "",
      "source_location": "",
      "id": "abc",
      "community": 6
    },
    {
      "label": "store()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/base.py",
      "source_location": "L29",
      "id": "base_store",
      "community": 0
    },
    {
      "label": "retrieve()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/base.py",
      "source_location": "L33",
      "id": "base_retrieve",
      "community": 0
    },
    {
      "label": "delete()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/base.py",
      "source_location": "L37",
      "id": "base_delete",
      "community": 0
    },
    {
      "label": "exists()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/base.py",
      "source_location": "L41",
      "id": "base_exists",
      "community": 0
    },
    {
      "label": "clear()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/base.py",
      "source_location": "L45",
      "id": "base_clear",
      "community": 0
    },
    {
      "label": "conversation.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L1",
      "id": "conversation",
      "community": 10
    },
    {
      "label": "ConversationStatus",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L14",
      "id": "conversation_conversationstatus",
      "community": 5
    },
    {
      "label": "str",
      "file_type": "code",
      "source_file": "",
      "source_location": "",
      "id": "str",
      "community": 5
    },
    {
      "label": "Conversation",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L22",
      "id": "conversation_conversation",
      "community": 10
    },
    {
      "label": "ConversationSummary",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L48",
      "id": "conversation_conversationsummary",
      "community": 10
    },
    {
      "label": "ConversationManager",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L58",
      "id": "conversation_conversationmanager",
      "community": 10
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L69",
      "id": "conversation_conversationmanager_init",
      "community": 10
    },
    {
      "label": "._load_user_index()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L83",
      "id": "conversation_conversationmanager_load_user_index",
      "community": 10
    },
    {
      "label": "._save_user_index()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L93",
      "id": "conversation_conversationmanager_save_user_index",
      "community": 10
    },
    {
      "label": "._get_conv_file()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L99",
      "id": "conversation_conversationmanager_get_conv_file",
      "community": 10
    },
    {
      "label": ".create_conversation()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L107",
      "id": "conversation_conversationmanager_create_conversation",
      "community": 10
    },
    {
      "label": "._save_conversation()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L142",
      "id": "conversation_conversationmanager_save_conversation",
      "community": 10
    },
    {
      "label": ".get_conversation()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L149",
      "id": "conversation_conversationmanager_get_conversation",
      "community": 10
    },
    {
      "label": ".list_user_conversations()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L165",
      "id": "conversation_conversationmanager_list_user_conversations",
      "community": 10
    },
    {
      "label": ".add_message()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L204",
      "id": "conversation_conversationmanager_add_message",
      "community": 10
    },
    {
      "label": ".get_messages()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L236",
      "id": "conversation_conversationmanager_get_messages",
      "community": 10
    },
    {
      "label": ".update_title()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L249",
      "id": "conversation_conversationmanager_update_title",
      "community": 10
    },
    {
      "label": ".delete_conversation()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L259",
      "id": "conversation_conversationmanager_delete_conversation",
      "community": 10
    },
    {
      "label": ".archive_conversation()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L276",
      "id": "conversation_conversationmanager_archive_conversation",
      "community": 10
    },
    {
      "label": ".link_to_job()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L286",
      "id": "conversation_conversationmanager_link_to_job",
      "community": 10
    },
    {
      "label": "Conversation Manager - \u7c7b\u4f3cChatGPT\u7684\u591a\u4f1a\u8bdd\u7ba1\u7406 \u652f\u6301\u7528\u6237\u7ef4\u5ea6\u3001\u4f1a\u8bdd\u5217\u8868\u3001\u5386\u53f2\u6d88\u606f",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L1",
      "id": "conversation_rationale_1",
      "community": 10
    },
    {
      "label": "\u4f1a\u8bdd\u72b6\u6001 - \u4f7f\u7528str\u7ee7\u627f\u4ee5\u4fbfJSON\u5e8f\u5217\u5316",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L15",
      "id": "conversation_rationale_15",
      "community": 5
    },
    {
      "label": "\u4f1a\u8bdd\u7ba1\u7406\u5668          \u529f\u80fd\uff1a     1. \u521b\u5efa/\u5220\u9664/\u5f52\u6863\u4f1a\u8bdd     2. \u6309\u7528\u6237\u5217\u51fa\u6240\u6709\u4f1a\u8bdd     3. \u83b7\u53d6\u4f1a\u8bdd\u6d88\u606f\u5386\u53f2     4. \u81ea\u52a8\u66f4",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L59",
      "id": "conversation_rationale_59",
      "community": 10
    },
    {
      "label": "\u5217\u51fa\u7528\u6237\u7684\u6240\u6709\u4f1a\u8bdd\uff08\u7c7b\u4f3cChatGPT\u5de6\u4fa7\u8fb9\u680f\uff09                  Returns:             List[Conversation",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/conversation.py",
      "source_location": "L172",
      "id": "conversation_rationale_172",
      "community": 10
    },
    {
      "label": "case.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/case.py",
      "source_location": "L1",
      "id": "case",
      "community": 4
    },
    {
      "label": "AnalysisCase",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/case.py",
      "source_location": "L12",
      "id": "case_analysiscase",
      "community": 4
    },
    {
      "label": "CaseMemory",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/case.py",
      "source_location": "L27",
      "id": "case_casememory",
      "community": 4
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/case.py",
      "source_location": "L28",
      "id": "case_casememory_init",
      "community": 4
    },
    {
      "label": "._init_db()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/case.py",
      "source_location": "L36",
      "id": "case_casememory_init_db",
      "community": 4
    },
    {
      "label": ".store()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/case.py",
      "source_location": "L64",
      "id": "case_casememory_store",
      "community": 4
    },
    {
      "label": ".retrieve()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/case.py",
      "source_location": "L93",
      "id": "case_casememory_retrieve",
      "community": 4
    },
    {
      "label": ".delete()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/case.py",
      "source_location": "L106",
      "id": "case_casememory_delete",
      "community": 4
    },
    {
      "label": ".exists()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/case.py",
      "source_location": "L113",
      "id": "case_casememory_exists",
      "community": 4
    },
    {
      "label": ".clear()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/case.py",
      "source_location": "L120",
      "id": "case_casememory_clear",
      "community": 4
    },
    {
      "label": "._row_to_case()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/case.py",
      "source_location": "L124",
      "id": "case_casememory_row_to_case",
      "community": 4
    },
    {
      "label": ".list_by_user()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/case.py",
      "source_location": "L140",
      "id": "case_casememory_list_by_user",
      "community": 4
    },
    {
      "label": ".list_by_gene_family()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/case.py",
      "source_location": "L149",
      "id": "case_casememory_list_by_gene_family",
      "community": 4
    },
    {
      "label": ".list_by_status()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/case.py",
      "source_location": "L158",
      "id": "case_casememory_list_by_status",
      "community": 4
    },
    {
      "label": ".update_status()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/case.py",
      "source_location": "L167",
      "id": "case_casememory_update_status",
      "community": 4
    },
    {
      "label": ".add_feedback()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/case.py",
      "source_location": "L175",
      "id": "case_casememory_add_feedback",
      "community": 4
    },
    {
      "label": "knowledge.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/knowledge.py",
      "source_location": "L1",
      "id": "knowledge",
      "community": 4
    },
    {
      "label": "KnowledgeEntry",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/knowledge.py",
      "source_location": "L10",
      "id": "knowledge_knowledgeentry",
      "community": 4
    },
    {
      "label": "KnowledgeMemory",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/knowledge.py",
      "source_location": "L22",
      "id": "knowledge_knowledgememory",
      "community": 4
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/knowledge.py",
      "source_location": "L23",
      "id": "knowledge_knowledgememory_init",
      "community": 4
    },
    {
      "label": ".store()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/knowledge.py",
      "source_location": "L28",
      "id": "knowledge_knowledgememory_store",
      "community": 4
    },
    {
      "label": ".retrieve()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/knowledge.py",
      "source_location": "L40",
      "id": "knowledge_knowledgememory_retrieve",
      "community": 4
    },
    {
      "label": ".delete()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/knowledge.py",
      "source_location": "L44",
      "id": "knowledge_knowledgememory_delete",
      "community": 4
    },
    {
      "label": ".exists()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/knowledge.py",
      "source_location": "L51",
      "id": "knowledge_knowledgememory_exists",
      "community": 4
    },
    {
      "label": ".clear()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/knowledge.py",
      "source_location": "L54",
      "id": "knowledge_knowledgememory_clear",
      "community": 4
    },
    {
      "label": ".search()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/knowledge.py",
      "source_location": "L58",
      "id": "knowledge_knowledgememory_search",
      "community": 4
    },
    {
      "label": "._cosine_similarity()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/knowledge.py",
      "source_location": "L89",
      "id": "knowledge_knowledgememory_cosine_similarity",
      "community": 4
    },
    {
      "label": ".search_by_tags()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/knowledge.py",
      "source_location": "L102",
      "id": "knowledge_knowledgememory_search_by_tags",
      "community": 4
    },
    {
      "label": ".search_by_category()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/knowledge.py",
      "source_location": "L117",
      "id": "knowledge_knowledgememory_search_by_category",
      "community": 4
    },
    {
      "label": ".add_entry()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/knowledge.py",
      "source_location": "L132",
      "id": "knowledge_knowledgememory_add_entry",
      "community": 4
    },
    {
      "label": "session.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/session.py",
      "source_location": "L1",
      "id": "session",
      "community": 4
    },
    {
      "label": "SessionData",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/session.py",
      "source_location": "L13",
      "id": "session_sessiondata",
      "community": 4
    },
    {
      "label": "SessionMemory",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/session.py",
      "source_location": "L21",
      "id": "session_sessionmemory",
      "community": 4
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/session.py",
      "source_location": "L24",
      "id": "session_sessionmemory_init",
      "community": 4
    },
    {
      "label": ".store()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/session.py",
      "source_location": "L40",
      "id": "session_sessionmemory_store",
      "community": 4
    },
    {
      "label": ".retrieve()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/session.py",
      "source_location": "L62",
      "id": "session_sessionmemory_retrieve",
      "community": 4
    },
    {
      "label": ".delete()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/session.py",
      "source_location": "L90",
      "id": "session_sessionmemory_delete",
      "community": 4
    },
    {
      "label": ".exists()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/session.py",
      "source_location": "L101",
      "id": "session_sessionmemory_exists",
      "community": 4
    },
    {
      "label": ".clear()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/session.py",
      "source_location": "L118",
      "id": "session_sessionmemory_clear",
      "community": 4
    },
    {
      "label": ".add_message()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/session.py",
      "source_location": "L124",
      "id": "session_sessionmemory_add_message",
      "community": 4
    },
    {
      "label": ".get_messages()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/session.py",
      "source_location": "L133",
      "id": "session_sessionmemory_get_messages",
      "community": 4
    },
    {
      "label": ".update_state()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/session.py",
      "source_location": "L137",
      "id": "session_sessionmemory_update_state",
      "community": 4
    },
    {
      "label": "SessionMemory with persistent backend",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/session.py",
      "source_location": "L22",
      "id": "session_rationale_22",
      "community": 4
    },
    {
      "label": "fast_intent.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/fast_intent.py",
      "source_location": "L1",
      "id": "fast_intent",
      "community": 64
    },
    {
      "label": "_complete_dependencies()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/fast_intent.py",
      "source_location": "L61",
      "id": "fast_intent_complete_dependencies",
      "community": 64
    },
    {
      "label": "fast_intent_recognition()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/fast_intent.py",
      "source_location": "L103",
      "id": "fast_intent_fast_intent_recognition",
      "community": 64
    },
    {
      "label": "should_use_fast_intent()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/fast_intent.py",
      "source_location": "L162",
      "id": "fast_intent_should_use_fast_intent",
      "community": 64
    },
    {
      "label": "\u5feb\u901f\u610f\u56fe\u8bc6\u522b - \u57fa\u4e8e\u5173\u952e\u8bcd\u5339\u914d\uff0c\u65e0\u9700LLM\u8c03\u7528",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/fast_intent.py",
      "source_location": "L1",
      "id": "fast_intent_rationale_1",
      "community": 64
    },
    {
      "label": "\u5feb\u901f\u610f\u56fe\u8bc6\u522b - \u57fa\u4e8e\u5173\u952e\u8bcd\u5339\u914d          Returns:         dict: {\"stage\": str, \"stages\": List[s",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/fast_intent.py",
      "source_location": "L104",
      "id": "fast_intent_rationale_104",
      "community": 64
    },
    {
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      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/state.py",
      "source_location": "L1",
      "id": "state",
      "community": 5
    },
    {
      "label": "WorkflowStatus",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/state.py",
      "source_location": "L5",
      "id": "state_workflowstatus",
      "community": 5
    },
    {
      "label": "GraphState",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/state.py",
      "source_location": "L13",
      "id": "state_graphstate",
      "community": 2
    },
    {
      "label": "TypedDict",
      "file_type": "code",
      "source_file": "",
      "source_location": "",
      "id": "typeddict",
      "community": 2
    },
    {
      "label": "create_initial_state()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/state.py",
      "source_location": "L38",
      "id": "state_create_initial_state",
      "community": 5
    },
    {
      "label": "message_bus.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L1",
      "id": "message_bus",
      "community": 7
    },
    {
      "label": "MessageType",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L13",
      "id": "message_bus_messagetype",
      "community": 7
    },
    {
      "label": "MessagePriority",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L22",
      "id": "message_bus_messagepriority",
      "community": 7
    },
    {
      "label": "AgentMessage",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L30",
      "id": "message_bus_agentmessage",
      "community": 7
    },
    {
      "label": ".to_dict()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L43",
      "id": "message_bus_agentmessage_to_dict",
      "community": 7
    },
    {
      "label": "from_dict()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L59",
      "id": "message_bus_from_dict",
      "community": 7
    },
    {
      "label": "MessageBus",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L75",
      "id": "message_bus_messagebus",
      "community": 7
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L87",
      "id": "message_bus_messagebus_init",
      "community": 7
    },
    {
      "label": ".start()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L95",
      "id": "message_bus_messagebus_start",
      "community": 7
    },
    {
      "label": ".stop()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L100",
      "id": "message_bus_messagebus_stop",
      "community": 7
    },
    {
      "label": "._process_messages()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L104",
      "id": "message_bus_messagebus_process_messages",
      "community": 7
    },
    {
      "label": ".send()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L118",
      "id": "message_bus_messagebus_send",
      "community": 7
    },
    {
      "label": "._deliver_message()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L142",
      "id": "message_bus_messagebus_deliver_message",
      "community": 7
    },
    {
      "label": ".subscribe()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L167",
      "id": "message_bus_messagebus_subscribe",
      "community": 7
    },
    {
      "label": ".unsubscribe()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L179",
      "id": "message_bus_messagebus_unsubscribe",
      "community": 7
    },
    {
      "label": ".request()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L196",
      "id": "message_bus_messagebus_request",
      "community": 7
    },
    {
      "label": ".get_message_history()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L246",
      "id": "message_bus_messagebus_get_message_history",
      "community": 7
    },
    {
      "label": ".get_conversation()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L273",
      "id": "message_bus_messagebus_get_conversation",
      "community": 7
    },
    {
      "label": "get_message_bus()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L302",
      "id": "message_bus_get_message_bus",
      "community": 7
    },
    {
      "label": "init_message_bus()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L310",
      "id": "message_bus_init_message_bus",
      "community": 7
    },
    {
      "label": "Agent\u6d88\u606f\u603b\u7ebf\u7cfb\u7edf \u652f\u6301Agent\u95f4\u5f02\u6b65\u6d88\u606f\u4f20\u9012\u548c\u534f\u4f5c",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L1",
      "id": "message_bus_rationale_1",
      "community": 7
    },
    {
      "label": "Agent\u6d88\u606f\u603b\u7ebf          \u652f\u6301\uff1a     - \u70b9\u5bf9\u70b9\u6d88\u606f\u4f20\u9012     - \u5e7f\u64ad\u6d88\u606f     - \u6d88\u606f\u8ba2\u9605/\u53d1\u5e03     - \u6d88\u606f\u5386\u53f2\u8bb0\u5f55     -",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L76",
      "id": "message_bus_rationale_76",
      "community": 7
    },
    {
      "label": "\u53d1\u9001\u6d88\u606f                  Args:             message: \u8981\u53d1\u9001\u7684\u6d88\u606f                  Returns",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L119",
      "id": "message_bus_rationale_119",
      "community": 7
    },
    {
      "label": "\u8ba2\u9605\u6d88\u606f                  Args:             agent_id: Agent ID             callback:",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L168",
      "id": "message_bus_rationale_168",
      "community": 7
    },
    {
      "label": "\u53d6\u6d88\u8ba2\u9605                  Args:             agent_id: Agent ID             callback:",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
      "source_location": "L180",
      "id": "message_bus_rationale_180",
      "community": 7
    },
    {
      "label": "\u53d1\u9001\u8bf7\u6c42\u5e76\u7b49\u5f85\u54cd\u5e94                  Args:             sender: \u53d1\u9001\u8005Agent ID             rec",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
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      "id": "message_bus_rationale_198",
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    {
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      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
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      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
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      "id": "message_bus_rationale_275",
      "community": 7
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      "label": "orchestrator.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
      "source_location": "L1",
      "id": "orchestrator",
      "community": 2
    },
    {
      "label": "Orchestrator",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
      "source_location": "L28",
      "id": "orchestrator_orchestrator",
      "community": 2
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    {
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
      "source_location": "L29",
      "id": "orchestrator_orchestrator_init",
      "community": 2
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    {
      "label": ".ensure_rag_indexed()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
      "source_location": "L86",
      "id": "orchestrator_orchestrator_ensure_rag_indexed",
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
      "source_location": "L92",
      "id": "orchestrator_orchestrator_get_input_dir",
      "community": 2
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    {
      "label": "._build_graph()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
      "source_location": "L125",
      "id": "orchestrator_orchestrator_build_graph",
      "community": 2
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    {
      "label": "._route_query()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
      "source_location": "L146",
      "id": "orchestrator_orchestrator_route_query",
      "community": 2
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    {
      "label": "._router_node()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
      "source_location": "L294",
      "id": "orchestrator_orchestrator_router_node",
      "community": 2
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    {
      "label": "._knowledge_node()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
      "source_location": "L359",
      "id": "orchestrator_orchestrator_knowledge_node",
      "community": 2
    },
    {
      "label": "._handle_auto_continue()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
      "source_location": "L505",
      "id": "orchestrator_orchestrator_handle_auto_continue",
      "community": 2
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    {
      "label": "._analysis_node()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
      "source_location": "L620",
      "id": "orchestrator_orchestrator_analysis_node",
      "community": 2
    },
    {
      "label": "._execute_rnaseq_qc()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
      "source_location": "L1182",
      "id": "orchestrator_orchestrator_execute_rnaseq_qc",
      "community": 2
    },
    {
      "label": "._execute_rnaseq_align()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
      "source_location": "L1444",
      "id": "orchestrator_orchestrator_execute_rnaseq_align",
      "community": 2
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    {
      "label": "._execute_rnaseq_quant()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
      "source_location": "L1610",
      "id": "orchestrator_orchestrator_execute_rnaseq_quant",
      "community": 2
    },
    {
      "label": "._execute_rnaseq_de()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
      "source_location": "L1778",
      "id": "orchestrator_orchestrator_execute_rnaseq_de",
      "community": 2
    },
    {
      "label": "._execute_rnaseq_enrich()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
      "source_location": "L1932",
      "id": "orchestrator_orchestrator_execute_rnaseq_enrich",
      "community": 2
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    {
      "label": "._execute_kaks()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
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      "id": "orchestrator_orchestrator_execute_kaks",
      "community": 2
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
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    {
      "label": ".run_sync()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
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      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
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      "community": 7
    },
    {
      "label": "\u751f\u6210\u5206\u6790\u8ba1\u5212\uff0c\u4e0d\u5b9e\u9645\u6267\u884c\uff08V2\u7248\u672c - \u4f7f\u7528LLM\u9a71\u52a8\uff09                  \u7528\u4e8e\u524d\u7aef\u5c55\u793a\u89c4\u5212\u7ed3\u679c\uff0c\u8ba9\u7528\u6237\u786e\u8ba4\u540e\u518d\u6267\u884c",
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      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
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      "community": 9
    },
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      "community": 2
    },
    {
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      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
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      "id": "langgraph_orchestrator_langgraphorchestrator",
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      "file_type": "code",
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      "id": "langgraph_orchestrator_langgraphorchestrator_init",
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
      "source_location": "L113",
      "id": "langgraph_orchestrator_langgraphorchestrator_build_graph",
      "community": 2
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      "label": ".run()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
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      "id": "langgraph_orchestrator_langgraphorchestrator_run",
      "community": 2
    },
    {
      "label": "._router_node()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
      "source_location": "L190",
      "id": "langgraph_orchestrator_langgraphorchestrator_router_node",
      "community": 9
    },
    {
      "label": "._knowledge_node()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
      "source_location": "L258",
      "id": "langgraph_orchestrator_langgraphorchestrator_knowledge_node",
      "community": 9
    },
    {
      "label": "._query_completed_stages_from_manifest()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
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      "id": "langgraph_orchestrator_langgraphorchestrator_query_completed_stages_from_manifest",
      "community": 9
    },
    {
      "label": "._planning_node()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
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      "id": "langgraph_orchestrator_langgraphorchestrator_planning_node",
      "community": 9
    },
    {
      "label": "._execution_node()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
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      "id": "langgraph_orchestrator_langgraphorchestrator_execution_node",
      "community": 9
    },
    {
      "label": "._validator_node()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
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      "community": 9
    },
    {
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
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      "id": "langgraph_orchestrator_langgraphorchestrator_diagnosis_node",
      "community": 9
    },
    {
      "label": "._result_parser_node()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
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      "id": "langgraph_orchestrator_langgraphorchestrator_result_parser_node",
      "community": 9
    },
    {
      "label": "._discovery_node()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
      "source_location": "L484",
      "id": "langgraph_orchestrator_langgraphorchestrator_discovery_node",
      "community": 9
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    {
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
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      "id": "langgraph_orchestrator_langgraphorchestrator_learning_node",
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    },
    {
      "label": "._route_decision()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
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      "id": "langgraph_orchestrator_langgraphorchestrator_route_decision",
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    },
    {
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
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      "file_type": "code",
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      "file_type": "code",
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    },
    {
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
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    },
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      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
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      "community": 9
    },
    {
      "label": "LangGraph \u7f16\u6392\u5668          \u5de5\u4f5c\u6d41\u56fe\uff1a          Router -> [\u6761\u4ef6\u5206\u652f]         \u251c\u2500\u2500 FAQ -> Knowle",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
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    },
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      "file_type": "rationale",
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      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
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    {
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    },
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    },
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      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/model_selector.py",
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    {
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      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/model_selector.py",
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    },
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    },
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    },
    {
      "label": "call()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/base.py",
      "source_location": "L39",
      "id": "base_call",
      "community": 0
    },
    {
      "label": "acall()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/base.py",
      "source_location": "L43",
      "id": "base_acall",
      "community": 0
    },
    {
      "label": "stream()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/base.py",
      "source_location": "L47",
      "id": "base_stream",
      "community": 0
    },
    {
      "label": "astream()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/base.py",
      "source_location": "L51",
      "id": "base_astream",
      "community": 0
    },
    {
      "label": "._build_messages()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/base.py",
      "source_location": "L54",
      "id": "base_basellmprovider_build_messages",
      "community": 6
    },
    {
      "label": "glm.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/glm.py",
      "source_location": "L1",
      "id": "glm",
      "community": 6
    },
    {
      "label": "GLMProvider",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/glm.py",
      "source_location": "L10",
      "id": "glm_glmprovider",
      "community": 6
    },
    {
      "label": "BaseLLMProvider",
      "file_type": "code",
      "source_file": "",
      "source_location": "",
      "id": "basellmprovider",
      "community": 6
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/glm.py",
      "source_location": "L29",
      "id": "glm_glmprovider_init",
      "community": 6
    },
    {
      "label": ".call()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/glm.py",
      "source_location": "L48",
      "id": "glm_glmprovider_call",
      "community": 6
    },
    {
      "label": ".acall()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/glm.py",
      "source_location": "L67",
      "id": "glm_glmprovider_acall",
      "community": 6
    },
    {
      "label": ".stream()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/glm.py",
      "source_location": "L70",
      "id": "glm_glmprovider_stream",
      "community": 6
    },
    {
      "label": ".astream()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/glm.py",
      "source_location": "L82",
      "id": "glm_glmprovider_astream",
      "community": 6
    },
    {
      "label": "GLM Provider - \u4f7f\u7528\u963f\u91cc\u4e91\u767e\u70bc\u5e73\u53f0",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/glm.py",
      "source_location": "L1",
      "id": "glm_rationale_1",
      "community": 6
    },
    {
      "label": "\u667a\u8c31GLM\u6a21\u578bProvider - \u901a\u8fc7\u963f\u91cc\u4e91\u767e\u70bc\u5e73\u53f0\u8c03\u7528          \u652f\u6301\u7684\u6a21\u578b:     - glm-4: \u6700\u5f3a\u6a21\u578b\uff0c\u9002\u5408\u590d\u6742\u5206\u6790\u63a8\u7406     - g",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/glm.py",
      "source_location": "L11",
      "id": "glm_rationale_11",
      "community": 6
    },
    {
      "label": "kimi.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/kimi.py",
      "source_location": "L1",
      "id": "kimi",
      "community": 6
    },
    {
      "label": "KimiProvider",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/kimi.py",
      "source_location": "L10",
      "id": "kimi_kimiprovider",
      "community": 6
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/kimi.py",
      "source_location": "L31",
      "id": "kimi_kimiprovider_init",
      "community": 6
    },
    {
      "label": ".call()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/kimi.py",
      "source_location": "L55",
      "id": "kimi_kimiprovider_call",
      "community": 6
    },
    {
      "label": ".acall()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/kimi.py",
      "source_location": "L74",
      "id": "kimi_kimiprovider_acall",
      "community": 6
    },
    {
      "label": ".stream()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/kimi.py",
      "source_location": "L77",
      "id": "kimi_kimiprovider_stream",
      "community": 6
    },
    {
      "label": ".astream()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/kimi.py",
      "source_location": "L89",
      "id": "kimi_kimiprovider_astream",
      "community": 6
    },
    {
      "label": "Kimi Provider - \u4f7f\u7528\u963f\u91cc\u4e91\u767e\u70bc\u5e73\u53f0",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/kimi.py",
      "source_location": "L1",
      "id": "kimi_rationale_1",
      "community": 6
    },
    {
      "label": "Kimi\u6a21\u578bProvider - \u901a\u8fc7\u963f\u91cc\u4e91\u767e\u70bcCoding Plan\u5e73\u53f0\u8c03\u7528          \u652f\u6301\u7684\u6a21\u578b:     - kimi-k2.5: \u6700\u5f3a\u6a21\u578b\uff0c\u9002\u5408",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/kimi.py",
      "source_location": "L11",
      "id": "kimi_rationale_11",
      "community": 6
    },
    {
      "label": "deepseek.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/deepseek.py",
      "source_location": "L1",
      "id": "deepseek",
      "community": 6
    },
    {
      "label": "DeepSeekProvider",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/deepseek.py",
      "source_location": "L10",
      "id": "deepseek_deepseekprovider",
      "community": 6
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/deepseek.py",
      "source_location": "L28",
      "id": "deepseek_deepseekprovider_init",
      "community": 6
    },
    {
      "label": ".call()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/deepseek.py",
      "source_location": "L47",
      "id": "deepseek_deepseekprovider_call",
      "community": 6
    },
    {
      "label": ".acall()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/deepseek.py",
      "source_location": "L66",
      "id": "deepseek_deepseekprovider_acall",
      "community": 6
    },
    {
      "label": ".stream()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/deepseek.py",
      "source_location": "L69",
      "id": "deepseek_deepseekprovider_stream",
      "community": 6
    },
    {
      "label": ".astream()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/deepseek.py",
      "source_location": "L81",
      "id": "deepseek_deepseekprovider_astream",
      "community": 6
    },
    {
      "label": "DeepSeek Provider - \u4f7f\u7528\u963f\u91cc\u4e91\u767e\u70bc\u5e73\u53f0",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/deepseek.py",
      "source_location": "L1",
      "id": "deepseek_rationale_1",
      "community": 6
    },
    {
      "label": "DeepSeek\u6a21\u578bProvider - \u901a\u8fc7\u963f\u91cc\u4e91\u767e\u70bc\u5e73\u53f0\u8c03\u7528          \u652f\u6301\u7684\u6a21\u578b:     - deepseek-chat: \u901a\u7528\u5bf9\u8bdd\u6a21\u578b",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/deepseek.py",
      "source_location": "L11",
      "id": "deepseek_rationale_11",
      "community": 6
    },
    {
      "label": "minimax.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/minimax.py",
      "source_location": "L1",
      "id": "minimax",
      "community": 6
    },
    {
      "label": "MiniMaxProvider",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/minimax.py",
      "source_location": "L10",
      "id": "minimax_minimaxprovider",
      "community": 6
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/minimax.py",
      "source_location": "L27",
      "id": "minimax_minimaxprovider_init",
      "community": 6
    },
    {
      "label": ".call()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/minimax.py",
      "source_location": "L46",
      "id": "minimax_minimaxprovider_call",
      "community": 6
    },
    {
      "label": ".acall()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/minimax.py",
      "source_location": "L65",
      "id": "minimax_minimaxprovider_acall",
      "community": 6
    },
    {
      "label": ".stream()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/minimax.py",
      "source_location": "L68",
      "id": "minimax_minimaxprovider_stream",
      "community": 6
    },
    {
      "label": ".astream()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/minimax.py",
      "source_location": "L80",
      "id": "minimax_minimaxprovider_astream",
      "community": 6
    },
    {
      "label": "MiniMax Provider - \u4f7f\u7528\u963f\u91cc\u4e91\u767e\u70bc\u5e73\u53f0",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/minimax.py",
      "source_location": "L1",
      "id": "minimax_rationale_1",
      "community": 6
    },
    {
      "label": "MiniMax\u6a21\u578bProvider - \u901a\u8fc7\u963f\u91cc\u4e91\u767e\u70bc\u5e73\u53f0\u8c03\u7528          \u652f\u6301\u7684\u6a21\u578b:     - minimax-text-01: \u6587\u672c\u6a21\u578b\uff0c\u9002\u5408\u77e5\u8bc6",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/minimax.py",
      "source_location": "L11",
      "id": "minimax_rationale_11",
      "community": 6
    },
    {
      "label": "ollama.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/ollama.py",
      "source_location": "L1",
      "id": "ollama",
      "community": 6
    },
    {
      "label": "OllamaProvider",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/ollama.py",
      "source_location": "L9",
      "id": "ollama_ollamaprovider",
      "community": 6
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/ollama.py",
      "source_location": "L12",
      "id": "ollama_ollamaprovider_init",
      "community": 6
    },
    {
      "label": "._get_client()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/ollama.py",
      "source_location": "L26",
      "id": "ollama_ollamaprovider_get_client",
      "community": 6
    },
    {
      "label": "._convert_messages()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/ollama.py",
      "source_location": "L30",
      "id": "ollama_ollamaprovider_convert_messages",
      "community": 6
    },
    {
      "label": ".call()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/ollama.py",
      "source_location": "L46",
      "id": "ollama_ollamaprovider_call",
      "community": 6
    },
    {
      "label": ".acall()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/ollama.py",
      "source_location": "L87",
      "id": "ollama_ollamaprovider_acall",
      "community": 6
    },
    {
      "label": ".stream()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/ollama.py",
      "source_location": "L126",
      "id": "ollama_ollamaprovider_stream",
      "community": 6
    },
    {
      "label": ".astream()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/ollama.py",
      "source_location": "L130",
      "id": "ollama_ollamaprovider_astream",
      "community": 6
    },
    {
      "label": "diagnosis.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
      "source_location": "L1",
      "id": "diagnosis",
      "community": 0
    },
    {
      "label": "DiagnosisAgent",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
      "source_location": "L11",
      "id": "diagnosis_diagnosisagent",
      "community": 0
    },
    {
      "label": "BaseAgent",
      "file_type": "code",
      "source_file": "",
      "source_location": "",
      "id": "baseagent",
      "community": 2
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
      "source_location": "L79",
      "id": "diagnosis_diagnosisagent_init",
      "community": 0
    },
    {
      "label": ".execute()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
      "source_location": "L83",
      "id": "diagnosis_diagnosisagent_execute",
      "community": 0
    },
    {
      "label": "._diagnose_error()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
      "source_location": "L112",
      "id": "diagnosis_diagnosisagent_diagnose_error",
      "community": 0
    },
    {
      "label": "._match_error_pattern()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
      "source_location": "L159",
      "id": "diagnosis_diagnosisagent_match_error_pattern",
      "community": 0
    },
    {
      "label": "._attempt_auto_fix()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
      "source_location": "L175",
      "id": "diagnosis_diagnosisagent_attempt_auto_fix",
      "community": 0
    },
    {
      "label": "._fix_reduce_cpu()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
      "source_location": "L185",
      "id": "diagnosis_diagnosisagent_fix_reduce_cpu",
      "community": 0
    },
    {
      "label": "._fix_parameter_format()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
      "source_location": "L201",
      "id": "diagnosis_diagnosisagent_fix_parameter_format",
      "community": 0
    },
    {
      "label": "._llm_diagnose()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
      "source_location": "L223",
      "id": "diagnosis_diagnosisagent_llm_diagnose",
      "community": 0
    },
    {
      "label": ".record_error()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
      "source_location": "L265",
      "id": "diagnosis_diagnosisagent_record_error",
      "community": 0
    },
    {
      "label": ".get_common_errors()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
      "source_location": "L277",
      "id": "diagnosis_diagnosisagent_get_common_errors",
      "community": 0
    },
    {
      "label": "create_diagnosis_agent()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
      "source_location": "L292",
      "id": "diagnosis_create_diagnosis_agent",
      "community": 0
    },
    {
      "label": "DiagnosisAgent V2 - \u9519\u8bef\u8bca\u65ad\u4e0e\u4fee\u590d \u81ea\u52a8\u8bca\u65ad\u5206\u6790\u5931\u8d25\u539f\u56e0\u5e76\u63d0\u4f9b\u4fee\u590d\u5efa\u8bae",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
      "source_location": "L1",
      "id": "diagnosis_rationale_1",
      "community": 0
    },
    {
      "label": "\u8bca\u65adAgent V2          \u529f\u80fd\uff1a     1. \u5206\u6790\u9519\u8bef\u65e5\u5fd7\uff0c\u5b9a\u4f4d\u95ee\u9898     2. \u63d0\u4f9b\u4fee\u590d\u5efa\u8bae     3. \u81ea\u52a8\u4fee\u590d\u5e38\u89c1\u95ee\u9898     4.",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
      "source_location": "L12",
      "id": "diagnosis_rationale_12",
      "community": 0
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    {
      "label": "\u6267\u884c\u4efb\u52a1\u89c4\u5212                  \u6839\u636e\u7528\u6237\u610f\u56fe\u751f\u6210\u5206\u6790\u6267\u884c\u8ba1\u5212",
      "file_type": "rationale",
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    {
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      "community": 0
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      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/knowledge.py",
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      "id": "knowledge_knowledgeagent_execute",
      "community": 0
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      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/knowledge.py",
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      "id": "knowledge_knowledgeagent_rag_qa",
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      "id": "knowledge_knowledgeagent_get_timestamp",
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    {
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      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/knowledge.py",
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      "id": "knowledge_knowledgeagent_get_conversation_history",
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      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/knowledge.py",
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      "label": "KnowledgeAgent V2 - \u589e\u5f3a\u7248\u77e5\u8bc6\u68c0\u7d22 \u96c6\u6210RAG\uff0c\u652f\u6301\u6587\u732e\u95ee\u7b54\u548c\u5f15\u7528",
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      "id": "knowledge_rationale_1",
      "community": 0
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    {
      "label": "\u77e5\u8bc6Agent V2          \u529f\u80fd\uff1a     1. RAG\u68c0\u7d22\u589e\u5f3a\u95ee\u7b54     2. \u6587\u732e\u5f15\u7528\u548c\u6765\u6e90\u6807\u6ce8     3. \u591a\u8f6e\u5bf9\u8bdd\u4e0a\u4e0b\u6587\u4fdd\u6301     4",
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      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/knowledge.py",
      "source_location": "L40",
      "id": "knowledge_rationale_40",
      "community": 0
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    {
      "label": "RAG\u95ee\u7b54 - Agentic RAG with LLM\u751f\u6210                  1. \u68c0\u7d22\u76f8\u5173\u6587\u732e         2. \u7ec4\u88c5\u4e0a\u4e0b\u6587",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/knowledge.py",
      "source_location": "L81",
      "id": "knowledge_rationale_81",
      "community": 0
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    {
      "label": "\u6df7\u5408\u6a21\u5f0f\u95ee\u7b54                  \u5148\u5c1d\u8bd5RAG\uff0c\u5982\u679c\u68c0\u7d22\u4e0d\u5230\u518d\u4f7f\u7528\u76f4\u63a5\u95ee\u7b54",
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      "id": "knowledge_rationale_250",
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    {
      "label": "\u7d22\u5f15\u6587\u6863\u5230RAG                  Args:             documents: \u6587\u6863\u5217\u8868\uff0c\u6bcf\u9879\u5305\u542bcontent\u548cmetadata",
      "file_type": "rationale",
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    {
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      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L199",
      "id": "rnaseq_clients_phytozomeclient_get_gene_expression",
      "community": 3
    },
    {
      "label": "TAIRClient",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L222",
      "id": "rnaseq_clients_tairclient",
      "community": 3
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L232",
      "id": "rnaseq_clients_tairclient_init",
      "community": 3
    },
    {
      "label": "._rate_limited_request()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L240",
      "id": "rnaseq_clients_tairclient_rate_limited_request",
      "community": 3
    },
    {
      "label": ".search_locus()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L251",
      "id": "rnaseq_clients_tairclient_search_locus",
      "community": 3
    },
    {
      "label": "PlantTFDBClient",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L273",
      "id": "rnaseq_clients_planttfdbclient",
      "community": 3
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L283",
      "id": "rnaseq_clients_planttfdbclient_init",
      "community": 3
    },
    {
      "label": "._rate_limited_request()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L291",
      "id": "rnaseq_clients_planttfdbclient_rate_limited_request",
      "community": 3
    },
    {
      "label": ".search_tf()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L302",
      "id": "rnaseq_clients_planttfdbclient_search_tf",
      "community": 3
    },
    {
      "label": ".get_family_info()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L324",
      "id": "rnaseq_clients_planttfdbclient_get_family_info",
      "community": 3
    },
    {
      "label": "\u8f6c\u5f55\u7ec4\u6570\u636e\u5e73\u53f0 API \u5ba2\u6237\u7aef  \u96c6\u6210\u591a\u4e2a\u8f6c\u5f55\u7ec4\u6570\u636e\u5e93\u548c\u5de5\u5177\u5e73\u53f0",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L1",
      "id": "rnaseq_clients_rationale_1",
      "community": 3
    },
    {
      "label": "Ensembl Plants API \u5ba2\u6237\u7aef          \u690d\u7269\u57fa\u56e0\u7ec4\u6570\u636e\u5e93     URL: https://plants.ensembl.org/",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L26",
      "id": "rnaseq_clients_rationale_26",
      "community": 3
    },
    {
      "label": "\u83b7\u53d6\u57fa\u56e0\u4fe1\u606f                  Args:             species: \u7269\u79cd\u540d\u79f0\uff08\u5982 arabidopsis_thaliana\uff09",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L57",
      "id": "rnaseq_clients_rationale_57",
      "community": 3
    },
    {
      "label": "\u83b7\u53d6\u57fa\u56e0\u8868\u8fbe\u6570\u636e                  Args:             species: \u7269\u79cd\u540d\u79f0             gene_id: \u57fa",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L79",
      "id": "rnaseq_clients_rationale_79",
      "community": 3
    },
    {
      "label": "\u83b7\u53d6\u540c\u6e90\u57fa\u56e0                  Args:             species: \u6e90\u7269\u79cd             gene_id: \u57fa\u56e0 I",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L114",
      "id": "rnaseq_clients_rationale_114",
      "community": 3
    },
    {
      "label": "Phytozome API \u5ba2\u6237\u7aef          \u690d\u7269\u6bd4\u8f83\u57fa\u56e0\u7ec4\u5b66\u5e73\u53f0     URL: https://phytozome-next.jgi.doe.go",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L139",
      "id": "rnaseq_clients_rationale_139",
      "community": 3
    },
    {
      "label": "\u641c\u7d22\u57fa\u56e0                  Args:             organism: \u751f\u7269\u4f53\uff08\u5982 Athaliana_447_TAIR10\uff09",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L174",
      "id": "rnaseq_clients_rationale_174",
      "community": 3
    },
    {
      "label": "\u83b7\u53d6\u57fa\u56e0\u8868\u8fbe\u6570\u636e                  Args:             organism: \u751f\u7269\u4f53             gene_id: \u57fa",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L200",
      "id": "rnaseq_clients_rationale_200",
      "community": 3
    },
    {
      "label": "TAIR (The Arabidopsis Information Resource) API \u5ba2\u6237\u7aef          \u62df\u5357\u82a5\u6570\u636e\u5e93     URL: htt",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L223",
      "id": "rnaseq_clients_rationale_223",
      "community": 3
    },
    {
      "label": "\u641c\u7d22\u57fa\u56e0\u4f4d\u70b9                  Args:             locus_name: \u4f4d\u70b9\u540d\u79f0\uff08\u5982 AT1G01010\uff09",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L252",
      "id": "rnaseq_clients_rationale_252",
      "community": 3
    },
    {
      "label": "PlantTFDB (Plant Transcription Factor Database) API \u5ba2\u6237\u7aef          \u690d\u7269\u8f6c\u5f55\u56e0\u5b50\u6570\u636e\u5e93     U",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L274",
      "id": "rnaseq_clients_rationale_274",
      "community": 3
    },
    {
      "label": "\u641c\u7d22\u8f6c\u5f55\u56e0\u5b50                  Args:             species: \u7269\u79cd\uff08\u5982 ath, osa, zma\uff09",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L303",
      "id": "rnaseq_clients_rationale_303",
      "community": 3
    },
    {
      "label": "\u83b7\u53d6\u8f6c\u5f55\u56e0\u5b50\u5bb6\u65cf\u4fe1\u606f                  Args:             species: \u7269\u79cd             family: \u5bb6\u65cf",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
      "source_location": "L325",
      "id": "rnaseq_clients_rationale_325",
      "community": 3
    },
    {
      "label": "ncbi_client.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/ncbi_client.py",
      "source_location": "L1",
      "id": "ncbi_client",
      "community": 3
    },
    {
      "label": "NCBIGene",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/ncbi_client.py",
      "source_location": "L17",
      "id": "ncbi_client_ncbigene",
      "community": 3
    },
    {
      "label": "NCBIClient",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/ncbi_client.py",
      "source_location": "L27",
      "id": "ncbi_client_ncbiclient",
      "community": 3
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/ncbi_client.py",
      "source_location": "L36",
      "id": "ncbi_client_ncbiclient_init",
      "community": 3
    },
    {
      "label": "._rate_limited_request()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/ncbi_client.py",
      "source_location": "L52",
      "id": "ncbi_client_ncbiclient_rate_limited_request",
      "community": 3
    },
    {
      "label": ".search()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/ncbi_client.py",
      "source_location": "L69",
      "id": "ncbi_client_ncbiclient_search",
      "community": 3
    },
    {
      "label": ".fetch()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/ncbi_client.py",
      "source_location": "L100",
      "id": "ncbi_client_ncbiclient_fetch",
      "community": 3
    },
    {
      "label": ".summary()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/ncbi_client.py",
      "source_location": "L132",
      "id": "ncbi_client_ncbiclient_summary",
      "community": 3
    },
    {
      "label": ".search_gene()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/ncbi_client.py",
      "source_location": "L168",
      "id": "ncbi_client_ncbiclient_search_gene",
      "community": 3
    },
    {
      "label": ".get_sequence()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/ncbi_client.py",
      "source_location": "L201",
      "id": "ncbi_client_ncbiclient_get_sequence",
      "community": 3
    },
    {
      "label": ".link()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/ncbi_client.py",
      "source_location": "L236",
      "id": "ncbi_client_ncbiclient_link",
      "community": 3
    },
    {
      "label": "NCBI API \u5ba2\u6237\u7aef  NCBI E-utilities API URL: https://www.ncbi.nlm.nih.gov/ API Docs:",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/ncbi_client.py",
      "source_location": "L1",
      "id": "ncbi_client_rationale_1",
      "community": 3
    },
    {
      "label": "NCBI E-utilities API \u5ba2\u6237\u7aef          \u7528\u4e8e\u67e5\u8be2\u57fa\u56e0\u3001\u86cb\u767d\u8d28\u3001\u5e8f\u5217\u7b49\u4fe1\u606f",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/ncbi_client.py",
      "source_location": "L28",
      "id": "ncbi_client_rationale_28",
      "community": 3
    },
    {
      "label": "\u521d\u59cb\u5316\u5ba2\u6237\u7aef                  Args:             api_key: NCBI API \u5bc6\u94a5\uff08\u53ef\u63d0\u9ad8\u901f\u7387\u9650\u5236\u5230 10 reque",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/ncbi_client.py",
      "source_location": "L37",
      "id": "ncbi_client_rationale_37",
      "community": 3
    },
    {
      "label": "\u641c\u7d22 NCBI \u6570\u636e\u5e93                  Args:             db: \u6570\u636e\u5e93\u540d\u79f0\uff08gene, protein, nucleoti",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/ncbi_client.py",
      "source_location": "L70",
      "id": "ncbi_client_rationale_70",
      "community": 3
    },
    {
      "label": "\u83b7\u53d6\u8bb0\u5f55\u8be6\u60c5                  Args:             db: \u6570\u636e\u5e93\u540d\u79f0             ids: ID \u5217\u8868",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/ncbi_client.py",
      "source_location": "L101",
      "id": "ncbi_client_rationale_101",
      "community": 3
    },
    {
      "label": "\u83b7\u53d6\u8bb0\u5f55\u6458\u8981                  Args:             db: \u6570\u636e\u5e93\u540d\u79f0             ids: ID \u5217\u8868",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/ncbi_client.py",
      "source_location": "L133",
      "id": "ncbi_client_rationale_133",
      "community": 3
    },
    {
      "label": "\u641c\u7d22\u57fa\u56e0                  Args:             symbol: \u57fa\u56e0\u7b26\u53f7             organism: \u7269\u79cd",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/ncbi_client.py",
      "source_location": "L169",
      "id": "ncbi_client_rationale_169",
      "community": 3
    },
    {
      "label": "\u83b7\u53d6\u5e8f\u5217                  Args:             db: \u6570\u636e\u5e93\uff08nuccore, protein\uff09             id",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/ncbi_client.py",
      "source_location": "L203",
      "id": "ncbi_client_rationale_203",
      "community": 3
    },
    {
      "label": "\u83b7\u53d6\u6570\u636e\u5e93\u95f4\u94fe\u63a5                  Args:             dbfrom: \u6e90\u6570\u636e\u5e93             dbto: \u76ee\u6807\u6570\u636e\u5e93",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/ncbi_client.py",
      "source_location": "L237",
      "id": "ncbi_client_rationale_237",
      "community": 3
    },
    {
      "label": "multi_api_query.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/multi_api_query.py",
      "source_location": "L1",
      "id": "multi_api_query",
      "community": 3
    },
    {
      "label": "APIResult",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/multi_api_query.py",
      "source_location": "L20",
      "id": "multi_api_query_apiresult",
      "community": 3
    },
    {
      "label": "MultiAPIQuery",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/multi_api_query.py",
      "source_location": "L30",
      "id": "multi_api_query_multiapiquery",
      "community": 3
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/multi_api_query.py",
      "source_location": "L38",
      "id": "multi_api_query_multiapiquery_init",
      "community": 3
    },
    {
      "label": ".query_all()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/multi_api_query.py",
      "source_location": "L56",
      "id": "multi_api_query_multiapiquery_query_all",
      "community": 3
    },
    {
      "label": "._get_api_calls()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/multi_api_query.py",
      "source_location": "L102",
      "id": "multi_api_query_multiapiquery_get_api_calls",
      "community": 3
    },
    {
      "label": "._execute_with_timeout()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/multi_api_query.py",
      "source_location": "L161",
      "id": "multi_api_query_multiapiquery_execute_with_timeout",
      "community": 3
    },
    {
      "label": ".generate_unified_report()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/multi_api_query.py",
      "source_location": "L197",
      "id": "multi_api_query_multiapiquery_generate_unified_report",
      "community": 3
    },
    {
      "label": "._merge_promoter_results()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/multi_api_query.py",
      "source_location": "L243",
      "id": "multi_api_query_multiapiquery_merge_promoter_results",
      "community": 3
    },
    {
      "label": "._merge_protein_results()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/multi_api_query.py",
      "source_location": "L261",
      "id": "multi_api_query_multiapiquery_merge_protein_results",
      "community": 3
    },
    {
      "label": "._merge_gene_results()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/multi_api_query.py",
      "source_location": "L286",
      "id": "multi_api_query_multiapiquery_merge_gene_results",
      "community": 3
    },
    {
      "label": "\u591a API \u5e76\u884c\u67e5\u8be2\u6a21\u5757  \u53c2\u8003 ClawBio \u7684 gwas-lookup \u6a21\u5f0f \u540c\u65f6\u67e5\u8be2\u591a\u4e2a\u6570\u636e\u5e93\uff0c\u5408\u5e76\u7ed3\u679c",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/multi_api_query.py",
      "source_location": "L1",
      "id": "multi_api_query_rationale_1",
      "community": 3
    },
    {
      "label": "\u591a API \u5e76\u884c\u67e5\u8be2\u7ba1\u7406\u5668          \u53c2\u8003 ClawBio gwas-lookup \u7684\u5e76\u884c\u67e5\u8be2\u6a21\u5f0f     \u540c\u65f6\u67e5\u8be2\u591a\u4e2a\u6570\u636e\u5e93\uff0c\u7edf\u4e00\u8fd4\u56de\u7ed3\u679c",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/multi_api_query.py",
      "source_location": "L31",
      "id": "multi_api_query_rationale_31",
      "community": 3
    },
    {
      "label": "\u521d\u59cb\u5316                  Args:             max_workers: \u6700\u5927\u5e76\u884c\u7ebf\u7a0b\u6570             timeout:",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/multi_api_query.py",
      "source_location": "L39",
      "id": "multi_api_query_rationale_39",
      "community": 3
    },
    {
      "label": "\u5e76\u884c\u67e5\u8be2\u6240\u6709\u76f8\u5173 API                  Args:             query_type: \u67e5\u8be2\u7c7b\u578b\uff08'gene', 'protei",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/multi_api_query.py",
      "source_location": "L57",
      "id": "multi_api_query_rationale_57",
      "community": 3
    },
    {
      "label": "\u83b7\u53d6 API \u8c03\u7528\u914d\u7f6e                  Args:             query_type: \u67e5\u8be2\u7c7b\u578b             para",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/multi_api_query.py",
      "source_location": "L103",
      "id": "multi_api_query_rationale_103",
      "community": 3
    },
    {
      "label": "\u6267\u884c\u5355\u4e2a API \u67e5\u8be2\uff08\u5e26\u8ba1\u65f6\uff09                  Args:             api_name: API \u540d\u79f0",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/multi_api_query.py",
      "source_location": "L162",
      "id": "multi_api_query_rationale_162",
      "community": 3
    },
    {
      "label": "\u751f\u6210\u7edf\u4e00\u62a5\u544a                  Args:             results: \u5404 API \u7684\u67e5\u8be2\u7ed3\u679c             query",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/multi_api_query.py",
      "source_location": "L199",
      "id": "multi_api_query_rationale_199",
      "community": 3
    },
    {
      "label": "plantcare_client.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/plantcare_client.py",
      "source_location": "L1",
      "id": "plantcare_client",
      "community": 3
    },
    {
      "label": "CisElement",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/plantcare_client.py",
      "source_location": "L16",
      "id": "plantcare_client_ciselement",
      "community": 3
    },
    {
      "label": "PlantCAREClient",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/plantcare_client.py",
      "source_location": "L25",
      "id": "plantcare_client_plantcareclient",
      "community": 3
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/plantcare_client.py",
      "source_location": "L34",
      "id": "plantcare_client_plantcareclient_init",
      "community": 3
    },
    {
      "label": "._rate_limited_request()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/plantcare_client.py",
      "source_location": "L48",
      "id": "plantcare_client_plantcareclient_rate_limited_request",
      "community": 3
    },
    {
      "label": ".search_elements()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/plantcare_client.py",
      "source_location": "L59",
      "id": "plantcare_client_plantcareclient_search_elements",
      "community": 3
    },
    {
      "label": "._parse_sequence_for_elements()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/plantcare_client.py",
      "source_location": "L82",
      "id": "plantcare_client_plantcareclient_parse_sequence_for_elements",
      "community": 3
    },
    {
      "label": ".get_element_details()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/plantcare_client.py",
      "source_location": "L122",
      "id": "plantcare_client_plantcareclient_get_element_details",
      "community": 3
    },
    {
      "label": ".analyze_promoter()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/plantcare_client.py",
      "source_location": "L173",
      "id": "plantcare_client_plantcareclient_analyze_promoter",
      "community": 3
    },
    {
      "label": "._categorize_element()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/plantcare_client.py",
      "source_location": "L203",
      "id": "plantcare_client_plantcareclient_categorize_element",
      "community": 3
    },
    {
      "label": "PlantCARE API \u5ba2\u6237\u7aef  PlantCARE \u662f\u4e00\u4e2a\u690d\u7269\u987a\u5f0f\u4f5c\u7528\u8c03\u63a7\u5143\u4ef6\u6570\u636e\u5e93 URL: http://bioinformatics.psb.uge",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/plantcare_client.py",
      "source_location": "L1",
      "id": "plantcare_client_rationale_1",
      "community": 3
    },
    {
      "label": "PlantCARE \u6570\u636e\u5e93\u5ba2\u6237\u7aef          \u7528\u4e8e\u67e5\u8be2\u542f\u52a8\u5b50\u533a\u57df\u7684\u987a\u5f0f\u4f5c\u7528\u8c03\u63a7\u5143\u4ef6",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/plantcare_client.py",
      "source_location": "L26",
      "id": "plantcare_client_rationale_26",
      "community": 3
    },
    {
      "label": "\u521d\u59cb\u5316\u5ba2\u6237\u7aef                  Args:             rate_limit: \u8bf7\u6c42\u95f4\u9694\uff08\u79d2\uff09\uff0c\u907f\u514d\u8fc7\u8f7d\u670d\u52a1\u5668",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/plantcare_client.py",
      "source_location": "L35",
      "id": "plantcare_client_rationale_35",
      "community": 3
    },
    {
      "label": "\u641c\u7d22\u987a\u5f0f\u4f5c\u7528\u5143\u4ef6                  Args:             sequence: DNA \u5e8f\u5217\uff08\u542f\u52a8\u5b50\u533a\u57df\uff09",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/plantcare_client.py",
      "source_location": "L60",
      "id": "plantcare_client_rationale_60",
      "community": 3
    },
    {
      "label": "\u89e3\u6790\u5e8f\u5217\u4e2d\u7684\u987a\u5f0f\u4f5c\u7528\u5143\u4ef6                  \u57fa\u4e8e PlantCARE \u5df2\u77e5\u5143\u4ef6\u6a21\u5f0f\u8fdb\u884c\u5339\u914d",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/plantcare_client.py",
      "source_location": "L83",
      "id": "plantcare_client_rationale_83",
      "community": 3
    },
    {
      "label": "\u83b7\u53d6\u5143\u4ef6\u8be6\u7ec6\u4fe1\u606f                  Args:             element_name: \u5143\u4ef6\u540d\u79f0\uff08\u5982 \"G-box\"\uff09",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/plantcare_client.py",
      "source_location": "L123",
      "id": "plantcare_client_rationale_123",
      "community": 3
    },
    {
      "label": "\u5168\u9762\u5206\u6790\u542f\u52a8\u5b50\u533a\u57df                  Args:             promoter_sequence: \u542f\u52a8\u5b50\u5e8f\u5217",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/plantcare_client.py",
      "source_location": "L174",
      "id": "plantcare_client_rationale_174",
      "community": 3
    },
    {
      "label": "pfam_client.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/pfam_client.py",
      "source_location": "L1",
      "id": "pfam_client",
      "community": 3
    },
    {
      "label": "PfamEntry",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/pfam_client.py",
      "source_location": "L16",
      "id": "pfam_client_pfamentry",
      "community": 3
    },
    {
      "label": "PfamClient",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/pfam_client.py",
      "source_location": "L25",
      "id": "pfam_client_pfamclient",
      "community": 3
    },
    {
      "label": ".__init__()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/pfam_client.py",
      "source_location": "L36",
      "id": "pfam_client_pfamclient_init",
      "community": 3
    },
    {
      "label": "._rate_limited_request()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/pfam_client.py",
      "source_location": "L51",
      "id": "pfam_client_pfamclient_rate_limited_request",
      "community": 3
    },
    {
      "label": ".search_protein()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/pfam_client.py",
      "source_location": "L62",
      "id": "pfam_client_pfamclient_search_protein",
      "community": 3
    },
    {
      "label": ".get_family_info()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/pfam_client.py",
      "source_location": "L95",
      "id": "pfam_client_pfamclient_get_family_info",
      "community": 3
    },
    {
      "label": ".search_by_keyword()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/pfam_client.py",
      "source_location": "L129",
      "id": "pfam_client_pfamclient_search_by_keyword",
      "community": 3
    },
    {
      "label": ".get_hmm_model()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/pfam_client.py",
      "source_location": "L167",
      "id": "pfam_client_pfamclient_get_hmm_model",
      "community": 3
    },
    {
      "label": ".get_clan_info()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/pfam_client.py",
      "source_location": "L181",
      "id": "pfam_client_pfamclient_get_clan_info",
      "community": 3
    },
    {
      "label": ".analyze_protein_domains()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/pfam_client.py",
      "source_location": "L209",
      "id": "pfam_client_pfamclient_analyze_protein_domains",
      "community": 3
    },
    {
      "label": "Pfam API \u5ba2\u6237\u7aef  Pfam \u662f\u4e00\u4e2a\u86cb\u767d\u8d28\u5bb6\u65cf\u6570\u636e\u5e93\uff0c\u57fa\u4e8e\u9690\u9a6c\u5c14\u53ef\u592b\u6a21\u578b (HMM) URL: https://pfam.xfam.org/ API:",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/pfam_client.py",
      "source_location": "L1",
      "id": "pfam_client_rationale_1",
      "community": 3
    },
    {
      "label": "Pfam \u6570\u636e\u5e93\u5ba2\u6237\u7aef          \u7528\u4e8e\u67e5\u8be2\u86cb\u767d\u8d28\u5bb6\u65cf\u4fe1\u606f\u3001HMM \u6a21\u578b\u3001\u7ed3\u6784\u57df\u67b6\u6784",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/pfam_client.py",
      "source_location": "L26",
      "id": "pfam_client_rationale_26",
      "community": 3
    },
    {
      "label": "\u521d\u59cb\u5316\u5ba2\u6237\u7aef                  Args:             rate_limit: \u8bf7\u6c42\u95f4\u9694\uff08\u79d2\uff09",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/pfam_client.py",
      "source_location": "L37",
      "id": "pfam_client_rationale_37",
      "community": 3
    },
    {
      "label": "\u641c\u7d22\u86cb\u767d\u8d28\u7684\u7ed3\u6784\u57df                  Args:             protein_id: \u86cb\u767d\u8d28 ID\uff08UniProt ID\uff09",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/pfam_client.py",
      "source_location": "L63",
      "id": "pfam_client_rationale_63",
      "community": 3
    },
    {
      "label": "\u83b7\u53d6 Pfam \u5bb6\u65cf\u8be6\u7ec6\u4fe1\u606f                  Args:             pfam_acc: Pfam \u767b\u5f55\u53f7\uff08\u5982 PF03110\uff09",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/pfam_client.py",
      "source_location": "L96",
      "id": "pfam_client_rationale_96",
      "community": 3
    },
    {
      "label": "\u6309\u5173\u952e\u8bcd\u641c\u7d22 Pfam \u5bb6\u65cf                  Args:             keyword: \u641c\u7d22\u5173\u952e\u8bcd             pag",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/pfam_client.py",
      "source_location": "L130",
      "id": "pfam_client_rationale_130",
      "community": 3
    },
    {
      "label": "\u83b7\u53d6 HMM \u6a21\u578b\uff08\u5982\u679c\u53ef\u7528\uff09                  Args:             pfam_acc: Pfam \u767b\u5f55\u53f7",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/pfam_client.py",
      "source_location": "L168",
      "id": "pfam_client_rationale_168",
      "community": 3
    },
    {
      "label": "\u83b7\u53d6 Clan\uff08\u8d85\u5bb6\u65cf\uff09\u4fe1\u606f                  Args:             clan_acc: Clan \u767b\u5f55\u53f7\uff08\u5982 CL0016\uff09",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/pfam_client.py",
      "source_location": "L182",
      "id": "pfam_client_rationale_182",
      "community": 3
    },
    {
      "label": "\u5206\u6790\u86cb\u767d\u8d28\u5e8f\u5217\u7684\u7ed3\u6784\u57df                  \u6ce8\u610f\uff1a\u8fd9\u9700\u8981\u63d0\u4ea4\u5230 Pfam \u641c\u7d22\uff08\u53ef\u80fd\u9700\u8981\u7f51\u9875\u754c\u9762\uff09                  Args:",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/pfam_client.py",
      "source_location": "L210",
      "id": "pfam_client_rationale_210",
      "community": 3
    },
    {
      "label": "eggnog_crawler.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/scripts/eggnog_crawler.py",
      "source_location": "L1",
      "id": "eggnog_crawler",
      "community": 48
    },
    {
      "label": "read_fasta()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/scripts/eggnog_crawler.py",
      "source_location": "L24",
      "id": "eggnog_crawler_read_fasta",
      "community": 48
    },
    {
      "label": "submit_to_eggnog()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/scripts/eggnog_crawler.py",
      "source_location": "L42",
      "id": "eggnog_crawler_submit_to_eggnog",
      "community": 48
    },
    {
      "label": "get_go_terms()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/scripts/eggnog_crawler.py",
      "source_location": "L60",
      "id": "eggnog_crawler_get_go_terms",
      "community": 48
    },
    {
      "label": "get_kegg_terms()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/scripts/eggnog_crawler.py",
      "source_location": "L79",
      "id": "eggnog_crawler_get_kegg_terms",
      "community": 48
    },
    {
      "label": "get_cog_category()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/scripts/eggnog_crawler.py",
      "source_location": "L98",
      "id": "eggnog_crawler_get_cog_category",
      "community": 48
    },
    {
      "label": "save_emapper_annotations()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/scripts/eggnog_crawler.py",
      "source_location": "L115",
      "id": "eggnog_crawler_save_emapper_annotations",
      "community": 48
    },
    {
      "label": "main()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/scripts/eggnog_crawler.py",
      "source_location": "L128",
      "id": "eggnog_crawler_main",
      "community": 48
    },
    {
      "label": "\u63d0\u4ea4\u5e8f\u5217\u5230eggNOG\uff0c\u8fd4\u56denogname (ENOG ID)",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/scripts/eggnog_crawler.py",
      "source_location": "L43",
      "id": "eggnog_crawler_rationale_43",
      "community": 48
    },
    {
      "label": "\u4fdd\u5b58.emapper.annotations\u683c\u5f0f\u6587\u4ef6",
      "file_type": "rationale",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/scripts/eggnog_crawler.py",
      "source_location": "L116",
      "id": "eggnog_crawler_rationale_116",
      "community": 48
    },
    {
      "label": "which()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/scripts/run_motif.py",
      "source_location": "L10",
      "id": "run_motif_which",
      "community": 17
    },
    {
      "label": "run_cmd()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/scripts/run_motif.py",
      "source_location": "L14",
      "id": "run_motif_run_cmd",
      "community": 17
    },
    {
      "label": "default_label()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/scripts/run_motif.py",
      "source_location": "L20",
      "id": "run_motif_default_label",
      "community": 17
    },
    {
      "label": "tiqu_miaoshuwenjian.py",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/scripts/tiqu_miaoshuwenjian.py",
      "source_location": "L1",
      "id": "tiqu_miaoshuwenjian",
      "community": 73
    },
    {
      "label": "parse_description_from_html()",
      "file_type": "code",
      "source_file": "/home/xia-lab/wutx/00test/bbav5/scripts/tiqu_miaoshuwenjian.py",
      "source_location": "L17",
      "id": "tiqu_miaoshuwenjian_parse_description_from_html",
      "community": 73
    },
    {
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