67554 lines
2.3 MiB
Plaintext
Executable File
67554 lines
2.3 MiB
Plaintext
Executable File
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"id": "wechat_integration_wechatintegration_init",
|
|
"community": 11
|
|
},
|
|
{
|
|
"label": ".login()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
|
|
"source_location": "L75",
|
|
"id": "wechat_integration_wechatintegration_login",
|
|
"community": 11
|
|
},
|
|
{
|
|
"label": "._display_qrcode()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
|
|
"source_location": "L132",
|
|
"id": "wechat_integration_wechatintegration_display_qrcode",
|
|
"community": 11
|
|
},
|
|
{
|
|
"label": ".send_text_message()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
|
|
"source_location": "L149",
|
|
"id": "wechat_integration_wechatintegration_send_text_message",
|
|
"community": 11
|
|
},
|
|
{
|
|
"label": ".send_typing()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
|
|
"source_location": "L171",
|
|
"id": "wechat_integration_wechatintegration_send_typing",
|
|
"community": 11
|
|
},
|
|
{
|
|
"label": ".notify_task_complete()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
|
|
"source_location": "L186",
|
|
"id": "wechat_integration_wechatintegration_notify_task_complete",
|
|
"community": 11
|
|
},
|
|
{
|
|
"label": ".get_messages()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
|
|
"source_location": "L228",
|
|
"id": "wechat_integration_wechatintegration_get_messages",
|
|
"community": 11
|
|
},
|
|
{
|
|
"label": ".start_message_listener()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
|
|
"source_location": "L254",
|
|
"id": "wechat_integration_wechatintegration_start_message_listener",
|
|
"community": 11
|
|
},
|
|
{
|
|
"label": "._call_mcp_tool()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
|
|
"source_location": "L279",
|
|
"id": "wechat_integration_wechatintegration_call_mcp_tool",
|
|
"community": 11
|
|
},
|
|
{
|
|
"label": "._real_mcp_call()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
|
|
"source_location": "L296",
|
|
"id": "wechat_integration_wechatintegration_real_mcp_call",
|
|
"community": 11
|
|
},
|
|
{
|
|
"label": "._mock_call()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
|
|
"source_location": "L363",
|
|
"id": "wechat_integration_wechatintegration_mock_call",
|
|
"community": 11
|
|
},
|
|
{
|
|
"label": "WeChatTaskNotifier",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
|
|
"source_location": "L396",
|
|
"id": "wechat_integration_wechattasknotifier",
|
|
"community": 11
|
|
},
|
|
{
|
|
"label": ".__init__()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
|
|
"source_location": "L407",
|
|
"id": "wechat_integration_wechattasknotifier_init",
|
|
"community": 11
|
|
},
|
|
{
|
|
"label": ".notify_task_started()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
|
|
"source_location": "L412",
|
|
"id": "wechat_integration_wechattasknotifier_notify_task_started",
|
|
"community": 11
|
|
},
|
|
{
|
|
"label": ".notify_task_completed()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
|
|
"source_location": "L426",
|
|
"id": "wechat_integration_wechattasknotifier_notify_task_completed",
|
|
"community": 11
|
|
},
|
|
{
|
|
"label": ".notify_task_failed()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
|
|
"source_location": "L444",
|
|
"id": "wechat_integration_wechattasknotifier_notify_task_failed",
|
|
"community": 11
|
|
},
|
|
{
|
|
"label": "test_wechat_integration()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
|
|
"source_location": "L466",
|
|
"id": "wechat_integration_test_wechat_integration",
|
|
"community": 11
|
|
},
|
|
{
|
|
"label": "test_message_listener()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
|
|
"source_location": "L547",
|
|
"id": "wechat_integration_test_message_listener",
|
|
"community": 11
|
|
},
|
|
{
|
|
"label": "\u5fae\u4fe1\u96c6\u6210\u7c7b \u4f7f\u7528\u65b9\u6cd5: 1. \u521d\u59cb\u5316: wechat = WeChatIntegration() 2. \u767b\u5f55: await w",
|
|
"file_type": "rationale",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
|
|
"source_location": "L59",
|
|
"id": "wechat_integration_rationale_59",
|
|
"community": 11
|
|
},
|
|
{
|
|
"label": "\u767b\u5f55\u5fae\u4fe1 \u6d41\u7a0b: 1. \u8c03\u7528 login_qrcode \u83b7\u53d6\u4e8c\u7ef4\u7801 2. \u663e\u793a\u4e8c\u7ef4\u7801\u4f9b\u7528\u6237\u626b\u63cf",
|
|
"file_type": "rationale",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/wechat_integration.py",
|
|
"source_location": "L76",
|
|
"id": "wechat_integration_rationale_76",
|
|
"community": 11
|
|
},
|
|
{
|
|
"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",
|
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"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",
|
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"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
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/pep/run.py",
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"source_location": "L49",
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"id": "run_pepskill_load_config",
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"community": 1
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},
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{
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"label": "._compute_checksum()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/pep/run.py",
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"source_location": "L58",
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"id": "run_pepskill_compute_checksum",
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"community": 1
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},
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{
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"label": "._record_file()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/pep/run.py",
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"source_location": "L66",
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"id": "run_pepskill_record_file",
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},
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{
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"label": ".parse_fasta()",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/pep/run.py",
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"source_location": "L77",
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"id": "run_pepskill_parse_fasta",
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"community": 1
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},
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{
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"label": ".calculate_properties()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/pep/run.py",
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"source_location": "L98",
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"id": "run_pepskill_calculate_properties",
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"community": 1
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},
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{
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"label": ".plot_properties()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/pep/run.py",
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"source_location": "L146",
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"id": "run_pepskill_plot_properties",
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},
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{
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"label": ".run()",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/pep/run.py",
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"source_location": "L200",
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"id": "run_pepskill_run",
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"community": 1
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},
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{
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"label": "._generate_report()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/pep/run.py",
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"source_location": "L242",
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"id": "run_pepskill_generate_report",
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{
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"label": "._generate_manifest()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/pep/run.py",
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"source_location": "L264",
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"id": "run_pepskill_generate_manifest",
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"community": 1
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},
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{
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"label": "MotifSkill",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/run.py",
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"source_location": "L34",
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"id": "run_motifskill",
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"community": 1
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},
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{
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"label": ".__init__()",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/run.py",
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"source_location": "L37",
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"id": "run_motifskill_init",
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"community": 1
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},
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{
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"label": "._load_config()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/run.py",
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"source_location": "L42",
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"id": "run_motifskill_load_config",
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"community": 1
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},
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{
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"label": "._which()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/run.py",
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"source_location": "L51",
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"id": "run_motifskill_which",
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"community": 1
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},
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{
|
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"label": "._run_command()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/run.py",
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"source_location": "L55",
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"id": "run_motifskill_run_command",
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"community": 1
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},
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{
|
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"label": "._compute_checksum()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/run.py",
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"source_location": "L68",
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"id": "run_motifskill_compute_checksum",
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"community": 1
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},
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{
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"label": "._record_file()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/run.py",
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"source_location": "L76",
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"id": "run_motifskill_record_file",
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"community": 1
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},
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{
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"label": ".run_meme()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/run.py",
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"source_location": "L85",
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"id": "run_motifskill_run_meme",
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},
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{
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"label": ".generate_report()",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/run.py",
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"source_location": "L121",
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"id": "run_motifskill_generate_report",
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},
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{
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"label": ".write_reproducibility_bundle()",
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{
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"label": ".run()",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/motif-analysis/run.py",
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{
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{
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"label": "TestMotifSkill",
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|
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{
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{
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{
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|
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{
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"label": ".test_config_loading()",
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|
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"community": 1
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{
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"label": "# TODO: \u5b9e\u73b0\u5b8c\u6574\u7684 skill \u903b\u8f91",
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|
"file_type": "rationale",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/rnaseq-de/run.py",
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|
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|
"id": "run_rationale_28",
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|
"community": 1
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},
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|
{
|
|
"label": "ExpressionSkill",
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|
"file_type": "code",
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
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|
"source_location": "L48",
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|
"id": "run_expressionskill",
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|
"community": 26
|
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},
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{
|
|
"label": ".__init__()",
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|
"file_type": "code",
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
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|
"source_location": "L51",
|
|
"id": "run_expressionskill_init",
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|
"community": 26
|
|
},
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{
|
|
"label": "._load_config()",
|
|
"file_type": "code",
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
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|
"source_location": "L57",
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|
"id": "run_expressionskill_load_config",
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|
"community": 26
|
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},
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{
|
|
"label": "._compute_checksum()",
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|
"file_type": "code",
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
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|
"source_location": "L66",
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|
"id": "run_expressionskill_compute_checksum",
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"community": 26
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},
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{
|
|
"label": "._record_file()",
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|
"file_type": "code",
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
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|
"source_location": "L74",
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|
"id": "run_expressionskill_record_file",
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"community": 26
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},
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{
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|
"label": ".load_count_matrix()",
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|
"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
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|
"id": "run_expressionskill_load_count_matrix",
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"community": 26
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},
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{
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|
"label": ".load_sample_groups()",
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|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
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},
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{
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"label": ".parse_groups()",
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},
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{
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|
"label": ".run_differential_expression()",
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|
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{
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"label": ".plot_volcano()",
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},
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{
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"label": ".plot_heatmap()",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
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{
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"label": ".plot_pca()",
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{
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"label": ".generate_report()",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
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},
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{
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|
"label": ".write_reproducibility_bundle()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
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"source_location": "L434",
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"id": "run_expressionskill_write_reproducibility_bundle",
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"community": 26
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},
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{
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|
"label": ".run()",
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|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
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|
"source_location": "L489",
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|
"id": "run_expressionskill_run",
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|
"community": 26
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},
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{
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|
"label": ".run_demo()",
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|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
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|
"id": "run_expressionskill_run_demo",
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|
"community": 26
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},
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{
|
|
"label": "._create_mock_output()",
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|
"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
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"source_location": "L583",
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"id": "run_expressionskill_create_mock_output",
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{
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"label": "\u89e3\u6790\u5206\u7ec4\uff0c\u8fd4\u56de {group_name: [sample1, sample2, ...]}",
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"file_type": "rationale",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/run.py",
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|
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"id": "run_rationale_117",
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},
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{
|
|
"label": "test_expression.py",
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|
"file_type": "code",
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/tests/test_expression.py",
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|
"source_location": "L1",
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|
"id": "test_expression",
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|
"community": 47
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},
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{
|
|
"label": "MockModule",
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|
"file_type": "code",
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/tests/test_expression.py",
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|
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|
"id": "test_expression_mockmodule",
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|
"community": 47
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},
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{
|
|
"label": ".__getattr__()",
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|
"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/tests/test_expression.py",
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|
"source_location": "L15",
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|
"id": "test_expression_mockmodule_getattr",
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|
"community": 47
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},
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{
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|
"label": "TestExpressionConfig",
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|
"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/tests/test_expression.py",
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|
"source_location": "L23",
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|
"id": "test_expression_testexpressionconfig",
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},
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{
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"label": ".setUp()",
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|
"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/tests/test_expression.py",
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},
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{
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"label": ".test_config_structure()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/tests/test_expression.py",
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|
"id": "test_expression_testexpressionconfig_test_config_structure",
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},
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{
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|
"label": ".test_config_source()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/tests/test_expression.py",
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"source_location": "L39",
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"id": "test_expression_testexpressionconfig_test_config_source",
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"community": 47
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},
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{
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"label": ".test_parameters()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/tests/test_expression.py",
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"source_location": "L43",
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|
"id": "test_expression_testexpressionconfig_test_parameters",
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"community": 47
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},
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{
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"label": ".test_demo_output_structure()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/tests/test_expression.py",
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"source_location": "L48",
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|
"id": "test_expression_testexpressionconfig_test_demo_output_structure",
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"community": 47
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},
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{
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"label": ".tearDown()",
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|
"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/expression/tests/test_expression.py",
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"source_location": "L66",
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|
"id": "test_expression_testexpressionconfig_teardown",
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{
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"label": "PpiSkill",
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"id": "run_ppiskill_init",
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{
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"label": "._load_config()",
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"id": "run_ppiskill_load_config",
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"community": 1
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{
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"label": "._compute_checksum()",
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"id": "run_ppiskill_compute_checksum",
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{
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"label": "._record_file()",
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"id": "run_ppiskill_record_file",
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"id": "run_ppiskill_load_gene_ids",
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{
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{
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{
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{
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/run.py",
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"community": 1
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{
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/run.py",
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{
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{
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{
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"label": "._record_file()",
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{
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{
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{
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|
|
"source_location": "L161",
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"id": "run_domainskill_write_reproducibility_bundle",
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"community": 1
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},
|
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{
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"label": ".run()",
|
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/run.py",
|
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"source_location": "L188",
|
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"id": "run_domainskill_run",
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"community": 1
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},
|
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{
|
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"label": ".run_demo()",
|
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"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/run.py",
|
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"source_location": "L221",
|
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"id": "run_domainskill_run_demo",
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"community": 1
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},
|
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{
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"label": "test_domain.py",
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"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/tests/test_domain.py",
|
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"source_location": "L1",
|
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"id": "test_domain",
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"community": 1
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},
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{
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"label": "TestDomainSkill",
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"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/tests/test_domain.py",
|
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"source_location": "L14",
|
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"id": "test_domain_testdomainskill",
|
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"community": 1
|
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},
|
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{
|
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"label": ".setUp()",
|
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"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/tests/test_domain.py",
|
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"source_location": "L16",
|
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"id": "test_domain_testdomainskill_setup",
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"community": 1
|
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},
|
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{
|
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"label": ".tearDown()",
|
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"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/tests/test_domain.py",
|
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"source_location": "L20",
|
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"id": "test_domain_testdomainskill_teardown",
|
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"community": 1
|
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},
|
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{
|
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"label": ".test_demo_mode()",
|
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"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/tests/test_domain.py",
|
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"source_location": "L24",
|
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"id": "test_domain_testdomainskill_test_demo_mode",
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"community": 1
|
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},
|
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{
|
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"label": ".test_config_loading()",
|
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"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/domain-analysis/tests/test_domain.py",
|
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"source_location": "L41",
|
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"id": "test_domain_testdomainskill_test_config_loading",
|
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"community": 1
|
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},
|
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{
|
|
"label": "# TODO: \u5b9e\u73b0\u5b8c\u6574\u7684 skill \u903b\u8f91",
|
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"file_type": "rationale",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/rnaseq-enrich/run.py",
|
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"source_location": "L30",
|
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"id": "run_rationale_30",
|
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"community": 1
|
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},
|
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{
|
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"label": "PhylogenySkill",
|
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"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/run.py",
|
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"source_location": "L34",
|
|
"id": "run_phylogenyskill",
|
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"community": 1
|
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},
|
|
{
|
|
"label": ".__init__()",
|
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"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/run.py",
|
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"source_location": "L37",
|
|
"id": "run_phylogenyskill_init",
|
|
"community": 1
|
|
},
|
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{
|
|
"label": "._load_config()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/run.py",
|
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"source_location": "L42",
|
|
"id": "run_phylogenyskill_load_config",
|
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"community": 1
|
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},
|
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{
|
|
"label": "._which()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/skills/phylogeny/run.py",
|
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"source_location": "L52",
|
|
"id": "run_phylogenyskill_which",
|
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"community": 1
|
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},
|
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{
|
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"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",
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"community": 18
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{
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"community": 18
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{
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"file_type": "code",
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"community": 18
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{
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"source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
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"id": "run_domain_run_hmmscan",
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"community": 18
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{
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"community": 18
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{
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"source_location": "L401",
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"id": "run_domain_run_r_plotting",
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"community": 18
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{
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
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"source_location": "L483",
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"id": "run_domain_generate_report",
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"community": 18
|
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},
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{
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"label": "write_manifest()",
|
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"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
|
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"source_location": "L565",
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"id": "run_domain_write_manifest",
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"community": 18
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{
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"label": "write_failure_manifest()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
|
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"source_location": "L572",
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"id": "run_domain_write_failure_manifest",
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"community": 18
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{
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"label": "calculate_domain_metrics()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
|
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"source_location": "L608",
|
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"id": "run_domain_calculate_domain_metrics",
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"community": 18
|
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{
|
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"label": "main()",
|
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"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
|
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"source_location": "L640",
|
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"id": "run_domain_main",
|
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"community": 18
|
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},
|
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{
|
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"label": "\u67e5\u627e\u6307\u5b9a\u9636\u6bb5\u7684\u6700\u65b0 manifest \u6587\u4ef6",
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"file_type": "rationale",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
|
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"source_location": "L106",
|
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"id": "run_domain_rationale_106",
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"community": 18
|
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},
|
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{
|
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"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",
|
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"file_type": "rationale",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
|
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"source_location": "L121",
|
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"id": "run_domain_rationale_121",
|
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"community": 18
|
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},
|
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{
|
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"label": "\u89e3\u6790\u4e9a\u5bb6\u65cf\u6587\u4ef6\u8def\u5f84 \u547d\u540d\u89c4\u5219: {prefix}.geneID.subfamily (\u5982 Ft.SPL.geneID.subfamily) \u4f18\u5148",
|
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"file_type": "rationale",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
|
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"source_location": "L131",
|
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"id": "run_domain_rationale_131",
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"community": 18
|
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},
|
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{
|
|
"label": "\u51c6\u5907 Pfam \u6570\u636e\u5e93\uff08\u8f6f\u8fde\u63a5\u65b9\u5f0f\uff09 Returns: (pfam_hmm_path, success, error_mess",
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|
"file_type": "rationale",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
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"source_location": "L186",
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"id": "run_domain_rationale_186",
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"community": 18
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},
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{
|
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"label": "\u8fd0\u884c hmmscan \u8fdb\u884c\u7ed3\u6784\u57df\u641c\u7d22 Returns: (success, result_dict)",
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"file_type": "rationale",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
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"source_location": "L236",
|
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"id": "run_domain_rationale_236",
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"community": 18
|
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},
|
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{
|
|
"label": "\u89e3\u6790 hmmscan domtblout \u6587\u4ef6 Returns: (domains_list, stats_dict)",
|
|
"file_type": "rationale",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_domain.py",
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"source_location": "L303",
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"id": "run_domain_rationale_303",
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"community": 18
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},
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{
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"source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_identify.py",
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{
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"file_type": "code",
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"source_location": "L48",
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"community": 37
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{
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_karyotype.py",
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"source_location": "L82",
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"community": 37
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{
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/apps/cli/run_karyotype.py",
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"source_location": "L98",
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"community": 37
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"id": "reproducibility_v2_reproducibilitymanager_end_stage",
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"community": 8
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{
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"id": "reproducibility_v2_reproducibilitymanager_save_progress",
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"community": 8
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{
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"id": "reproducibility_v2_reproducibilitymanager_calculate_sha256",
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{
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"label": "._get_tool_versions()",
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"id": "reproducibility_v2_reproducibilitymanager_get_tool_versions",
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{
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"id": "reproducibility_v2_reproducibilitymanager_generate_commands_sh",
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{
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"source_location": "L237",
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"id": "reproducibility_v2_reproducibilitymanager_generate_environment_yml",
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"community": 8
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},
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{
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"source_location": "L58",
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"id": "registry_toolregistry_init",
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{
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"label": ".register()",
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"id": "registry_toolregistry_register",
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{
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"source_location": "L64",
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"id": "registry_toolregistry_get",
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{
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"label": ".list_by_category()",
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"source_location": "L67",
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"id": "registry_toolregistry_list_by_category",
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{
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"label": ".list_all()",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/registry.py",
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"source_location": "L70",
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"id": "registry_toolregistry_list_all",
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"community": 5
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},
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{
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"label": "create_default_registry()",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/registry.py",
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"source_location": "L74",
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"id": "registry_create_default_registry",
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"community": 5
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{
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"label": "stage_registry.py",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_registry.py",
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"source_location": "L1",
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|
"id": "stage_registry",
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"community": 20
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|
},
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{
|
|
"label": "StageTool",
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|
"file_type": "code",
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_registry.py",
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|
"source_location": "L20",
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|
"id": "stage_registry_stagetool",
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|
"community": 20
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|
},
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{
|
|
"label": "StageToolExecutor",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_registry.py",
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"source_location": "L34",
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"id": "stage_registry_stagetoolexecutor",
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"community": 20
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{
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|
"label": ".__init__()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_registry.py",
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"source_location": "L37",
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|
"id": "stage_registry_stagetoolexecutor_init",
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"community": 20
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},
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{
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"label": ".execute()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_registry.py",
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"source_location": "L43",
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"id": "stage_registry_stagetoolexecutor_execute",
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"community": 20
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},
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{
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"label": "StageToolRegistry",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_registry.py",
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"source_location": "L144",
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"id": "stage_registry_stagetoolregistry",
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"label": ".__init__()",
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"source_location": "L147",
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"id": "stage_registry_stagetoolregistry_init",
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"community": 20
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{
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"label": "._register_all_stages()",
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"file_type": "code",
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"source_location": "L152",
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"id": "stage_registry_stagetoolregistry_register_all_stages",
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"label": "Stage-level Tool Registry for Multi-Agent System \u5c06bbav20311\u7684\u5206\u6790\u9636\u6bb5\u811a\u672c\u5c01\u88c5\u4e3aAgent\u53ef\u8c03\u7528\u7684To",
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"file_type": "rationale",
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"id": "stage_registry_rationale_1",
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{
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"label": "\u6267\u884c\u5206\u6790\u9636\u6bb5 Args: stage_tool: \u9636\u6bb5\u5de5\u5177\u5b9a\u4e49 job_id:",
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"file_type": "rationale",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_registry.py",
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{
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"label": "adapter.py",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/adapter.py",
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"source_location": "L1",
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"id": "adapter",
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"community": 5
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},
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{
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"label": "ToolAdapter",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/adapter.py",
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"source_location": "L9",
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"id": "adapter_tooladapter",
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},
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{
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"label": ".__init__()",
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"source_location": "L10",
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"id": "adapter_tooladapter_init",
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{
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"label": ".execute()",
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"source_location": "L15",
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"id": "adapter_tooladapter_execute",
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"community": 5
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},
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{
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"label": ".aexecute()",
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"source_location": "L48",
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"id": "adapter_tooladapter_aexecute",
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},
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{
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"label": "._build_command()",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/adapter.py",
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|
"source_location": "L51",
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|
"id": "adapter_tooladapter_build_command",
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"community": 5
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},
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{
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"label": "._collect_outputs()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/adapter.py",
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"source_location": "L98",
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"id": "adapter_tooladapter_collect_outputs",
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},
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{
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"label": "workflow.py",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/workflow.py",
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|
"source_location": "L1",
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|
"id": "workflow",
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"community": 5
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},
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{
|
|
"label": "WorkflowStatus",
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|
"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/workflow.py",
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|
"source_location": "L10",
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|
"id": "workflow_workflowstatus",
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|
"community": 5
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},
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{
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"label": "Enum",
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"id": "enum",
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},
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{
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|
"label": "WorkflowStep",
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|
"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/workflow.py",
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|
"source_location": "L18",
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|
"id": "workflow_workflowstep",
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|
"community": 5
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},
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|
{
|
|
"label": "WorkflowResult",
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|
"file_type": "code",
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/workflow.py",
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|
"source_location": "L29",
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|
"id": "workflow_workflowresult",
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"community": 5
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},
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|
{
|
|
"label": "GeneFamilyWorkflow",
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|
"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/workflow.py",
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"source_location": "L39",
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"id": "workflow_genefamilyworkflow",
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},
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|
{
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|
"label": ".__init__()",
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|
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|
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|
"source_location": "L40",
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|
"id": "workflow_genefamilyworkflow_init",
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|
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},
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|
{
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|
"label": ".create_identification_workflow()",
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|
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|
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|
"id": "workflow_genefamilyworkflow_create_identification_workflow",
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},
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{
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|
"label": ".create_full_analysis_workflow()",
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|
"id": "workflow_genefamilyworkflow_create_full_analysis_workflow",
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},
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|
{
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|
"label": ".run_workflow()",
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|
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/workflow.py",
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|
"source_location": "L119",
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|
"id": "workflow_genefamilyworkflow_run_workflow",
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|
"community": 5
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|
},
|
|
{
|
|
"label": ".get_available_tools()",
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|
"file_type": "code",
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/workflow.py",
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|
"source_location": "L173",
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|
"id": "workflow_genefamilyworkflow_get_available_tools",
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|
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|
},
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|
{
|
|
"label": "stage_tools.py",
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|
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
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|
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|
"id": "stage_tools",
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|
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|
},
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|
{
|
|
"label": "StageTool",
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|
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
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|
"source_location": "L28",
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|
"id": "stage_tools_stagetool",
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|
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|
},
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|
{
|
|
"label": "StageToolExecutor",
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|
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|
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|
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|
"id": "stage_tools_stagetoolexecutor",
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|
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|
},
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|
{
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|
"label": ".__init__()",
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|
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|
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|
"source_location": "L45",
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|
"id": "stage_tools_stagetoolexecutor_init",
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|
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|
},
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{
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|
"label": ".execute()",
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|
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|
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|
"id": "stage_tools_stagetoolexecutor_execute",
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"community": 7
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|
},
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|
{
|
|
"label": "StageToolRegistry",
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|
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
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|
"source_location": "L152",
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|
"id": "stage_tools_stagetoolregistry",
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|
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|
},
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|
{
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|
"label": ".__init__()",
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|
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|
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|
"source_location": "L403",
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|
"id": "stage_tools_stagetoolregistry_init",
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|
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|
},
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|
{
|
|
"label": "._register_all_stages()",
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|
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|
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|
"source_location": "L408",
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|
"id": "stage_tools_stagetoolregistry_register_all_stages",
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|
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|
},
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|
{
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|
"label": ".register()",
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|
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|
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|
"id": "stage_tools_stagetoolregistry_register",
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|
"community": 7
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|
},
|
|
{
|
|
"label": ".get()",
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|
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|
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|
"source_location": "L417",
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|
"id": "stage_tools_stagetoolregistry_get",
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},
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{
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|
"label": ".list_all()",
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|
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|
"source_location": "L421",
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|
"id": "stage_tools_stagetoolregistry_list_all",
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|
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|
},
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|
{
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|
"label": ".list_by_category()",
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|
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/stage_tools.py",
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|
"source_location": "L425",
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|
"id": "stage_tools_stagetoolregistry_list_by_category",
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},
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{
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|
"label": ".execute()",
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|
"source_location": "L429",
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|
"id": "stage_tools_stagetoolregistry_execute",
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{
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|
"id": "stage_tools_stagetoolregistry_get_execution_order",
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},
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{
|
|
"label": "create_stage_registry()",
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|
"source_location": "L465",
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"id": "stage_tools_create_stage_registry",
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|
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},
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{
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"label": "Stage-level Tool Registry for Multi-Agent System \u5c06bbav20311\u7684\u5206\u6790\u9636\u6bb5\u811a\u672c\u5c01\u88c5\u4e3aAgent\u53ef\u8c03\u7528\u7684To",
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"file_type": "rationale",
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{
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"label": "\u521b\u5efa\u65b0\u7684StageToolRegistry\u5b9e\u4f8b",
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"label": "executor.py",
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{
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"label": "ExecutionStatus",
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{
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"label": "ExecutionResult",
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{
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"source_location": "L34",
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"id": "executor_toolexecutor",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/executor.py",
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"source_location": "L35",
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"id": "executor_toolexecutor_init",
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{
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"label": ".get_tool()",
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"source_location": "L48",
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"id": "executor_toolexecutor_get_tool",
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"community": 5
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},
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{
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"label": ".list_tools()",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/executor.py",
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"source_location": "L51",
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"id": "executor_toolexecutor_list_tools",
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"community": 5
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{
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"label": ".execute()",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/executor.py",
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"source_location": "L56",
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"id": "executor_toolexecutor_execute",
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},
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{
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"label": ".aexecute()",
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"id": "executor_toolexecutor_aexecute",
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{
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"label": "._build_command()",
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{
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"label": "._build_docker_command()",
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"source_location": "L221",
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"id": "executor_toolexecutor_build_docker_command",
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"community": 5
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{
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"label": "._simulate_execution()",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/tools/executor.py",
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"id": "executor_toolexecutor_simulate_execution",
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"community": 5
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},
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{
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"label": "._collect_outputs()",
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"id": "executor_toolexecutor_collect_outputs",
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},
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{
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"label": "intent_parser.py",
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"source_location": "L1",
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"id": "intent_parser",
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"community": 45
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{
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"label": "parse_intent_from_query()",
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"id": "intent_parser_parse_intent_from_query",
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"file_type": "rationale",
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"id": "manager_memorystats",
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},
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{
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{
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"id": "manager_memorymanager_init",
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},
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{
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"label": ".create_session()",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
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"id": "manager_memorymanager_create_session",
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},
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{
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"id": "manager_memorymanager_get_session",
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},
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{
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
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"id": "manager_memorymanager_add_message_to_session",
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},
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{
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"label": ".update_session_state()",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
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|
"source_location": "L44",
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|
"id": "manager_memorymanager_update_session_state",
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|
"community": 4
|
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},
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{
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"label": ".create_case()",
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|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
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"source_location": "L47",
|
|
"id": "manager_memorymanager_create_case",
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"community": 4
|
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},
|
|
{
|
|
"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",
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|
"community": 4
|
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},
|
|
{
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|
"label": ".update_case_results()",
|
|
"file_type": "code",
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
|
|
"source_location": "L68",
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|
"id": "manager_memorymanager_update_case_results",
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},
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{
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"label": ".complete_case()",
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|
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
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|
"source_location": "L74",
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|
"id": "manager_memorymanager_complete_case",
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|
"community": 4
|
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},
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{
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|
"label": ".add_case_feedback()",
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|
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
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|
"source_location": "L77",
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|
"id": "manager_memorymanager_add_case_feedback",
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|
"community": 4
|
|
},
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|
{
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|
"label": ".add_knowledge()",
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|
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
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|
"source_location": "L80",
|
|
"id": "manager_memorymanager_add_knowledge",
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|
"community": 4
|
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},
|
|
{
|
|
"label": ".search_knowledge()",
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|
"file_type": "code",
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
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|
"source_location": "L98",
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|
"id": "manager_memorymanager_search_knowledge",
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|
"community": 4
|
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},
|
|
{
|
|
"label": ".search_knowledge_by_tags()",
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|
"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
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|
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|
"id": "manager_memorymanager_search_knowledge_by_tags",
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|
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},
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{
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"label": ".extract_case_to_knowledge()",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
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"id": "manager_memorymanager_extract_case_to_knowledge",
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},
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{
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"label": "._extract_knowledge_content()",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
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},
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{
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"id": "manager_memorymanager_get_stats",
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},
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{
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/manager.py",
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},
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{
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|
"label": "persistent.py",
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|
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/persistent.py",
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|
"source_location": "L1",
|
|
"id": "persistent",
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|
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|
|
},
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|
{
|
|
"label": "PersistentMemory",
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|
"file_type": "code",
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/persistent.py",
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|
"source_location": "L15",
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|
"id": "persistent_persistentmemory",
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|
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|
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},
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{
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|
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|
"id": "basememory",
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},
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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/memory/persistent.py",
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|
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|
"id": "persistent_persistentmemory_init",
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|
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|
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},
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{
|
|
"label": "._get_file_path()",
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|
"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/persistent.py",
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|
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},
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{
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|
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|
|
"id": "persistent_persistentmemory_serialize",
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},
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{
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{
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{
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{
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},
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{
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"id": "persistent_persistentmemory_exists",
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},
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{
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"source_location": "L136",
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"id": "persistent_persistentmemory_clear",
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},
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{
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"source_location": "L1",
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"id": "base",
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},
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{
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"label": "MemoryEntry",
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|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/base.py",
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|
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|
"id": "base_memoryentry",
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},
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{
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|
"label": "SearchResult",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/memory/base.py",
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"id": "base_searchresult",
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},
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{
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"source_location": "L119",
|
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"id": "message_bus_rationale_119",
|
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"community": 7
|
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},
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{
|
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"label": "\u8ba2\u9605\u6d88\u606f Args: agent_id: Agent ID callback:",
|
|
"file_type": "rationale",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
|
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"source_location": "L168",
|
|
"id": "message_bus_rationale_168",
|
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"community": 7
|
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},
|
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{
|
|
"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",
|
|
"source_location": "L198",
|
|
"id": "message_bus_rationale_198",
|
|
"community": 7
|
|
},
|
|
{
|
|
"label": "\u83b7\u53d6\u6d88\u606f\u5386\u53f2 Args: session_id: \u4f1a\u8bddID\u8fc7\u6ee4 agent_i",
|
|
"file_type": "rationale",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
|
|
"source_location": "L249",
|
|
"id": "message_bus_rationale_249",
|
|
"community": 7
|
|
},
|
|
{
|
|
"label": "\u83b7\u53d6\u4e24\u4e2aAgent\u4e4b\u95f4\u7684\u5bf9\u8bdd Args: agent1: Agent 1 ID",
|
|
"file_type": "rationale",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/message_bus.py",
|
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"source_location": "L275",
|
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"id": "message_bus_rationale_275",
|
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"community": 7
|
|
},
|
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{
|
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"label": "orchestrator.py",
|
|
"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
|
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"source_location": "L1",
|
|
"id": "orchestrator",
|
|
"community": 2
|
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},
|
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{
|
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"label": "Orchestrator",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
|
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"source_location": "L28",
|
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"id": "orchestrator_orchestrator",
|
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"community": 2
|
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},
|
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{
|
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"label": ".__init__()",
|
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"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
|
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"source_location": "L29",
|
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"id": "orchestrator_orchestrator_init",
|
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"community": 2
|
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},
|
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{
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"label": ".ensure_rag_indexed()",
|
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"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
|
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"source_location": "L86",
|
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"id": "orchestrator_orchestrator_ensure_rag_indexed",
|
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"community": 2
|
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},
|
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{
|
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"label": "._get_input_dir()",
|
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"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
|
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"source_location": "L92",
|
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"id": "orchestrator_orchestrator_get_input_dir",
|
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"community": 2
|
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},
|
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{
|
|
"label": "._build_graph()",
|
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"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
|
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"source_location": "L125",
|
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"id": "orchestrator_orchestrator_build_graph",
|
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"community": 2
|
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},
|
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{
|
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"label": "._route_query()",
|
|
"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
|
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"source_location": "L146",
|
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"id": "orchestrator_orchestrator_route_query",
|
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"community": 2
|
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},
|
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{
|
|
"label": "._router_node()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
|
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"source_location": "L294",
|
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"id": "orchestrator_orchestrator_router_node",
|
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"community": 2
|
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},
|
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{
|
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"label": "._knowledge_node()",
|
|
"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
|
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"source_location": "L359",
|
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"id": "orchestrator_orchestrator_knowledge_node",
|
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"community": 2
|
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},
|
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{
|
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"label": "._handle_auto_continue()",
|
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"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
|
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"source_location": "L505",
|
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"id": "orchestrator_orchestrator_handle_auto_continue",
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"community": 2
|
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},
|
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{
|
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"label": "._analysis_node()",
|
|
"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
|
|
"source_location": "L620",
|
|
"id": "orchestrator_orchestrator_analysis_node",
|
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"community": 2
|
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},
|
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{
|
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"label": "._execute_rnaseq_qc()",
|
|
"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
|
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"source_location": "L1182",
|
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"id": "orchestrator_orchestrator_execute_rnaseq_qc",
|
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"community": 2
|
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},
|
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{
|
|
"label": "._execute_rnaseq_align()",
|
|
"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
|
|
"source_location": "L1444",
|
|
"id": "orchestrator_orchestrator_execute_rnaseq_align",
|
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"community": 2
|
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},
|
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{
|
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"label": "._execute_rnaseq_quant()",
|
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"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
|
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"source_location": "L1610",
|
|
"id": "orchestrator_orchestrator_execute_rnaseq_quant",
|
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"community": 2
|
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},
|
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{
|
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"label": "._execute_rnaseq_de()",
|
|
"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
|
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"source_location": "L1778",
|
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"id": "orchestrator_orchestrator_execute_rnaseq_de",
|
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"community": 2
|
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},
|
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{
|
|
"label": "._execute_rnaseq_enrich()",
|
|
"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
|
|
"source_location": "L1932",
|
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"id": "orchestrator_orchestrator_execute_rnaseq_enrich",
|
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"community": 2
|
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},
|
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{
|
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"label": "._execute_kaks()",
|
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"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
|
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"source_location": "L2085",
|
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"id": "orchestrator_orchestrator_execute_kaks",
|
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"community": 2
|
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},
|
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{
|
|
"label": ".run()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
|
|
"source_location": "L2440",
|
|
"id": "orchestrator_orchestrator_run",
|
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"community": 2
|
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},
|
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{
|
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"label": ".run_sync()",
|
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"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
|
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"source_location": "L2443",
|
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"id": "orchestrator_orchestrator_run_sync",
|
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"community": 2
|
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},
|
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{
|
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"label": ".plan()",
|
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"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
|
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"source_location": "L2446",
|
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"id": "orchestrator_orchestrator_plan",
|
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"community": 2
|
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},
|
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{
|
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"label": "._plan_legacy()",
|
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"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
|
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"source_location": "L2548",
|
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"id": "orchestrator_orchestrator_plan_legacy",
|
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"community": 2
|
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},
|
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{
|
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"label": "._parse_intent_from_query()",
|
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"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
|
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"source_location": "L2602",
|
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"id": "orchestrator_orchestrator_parse_intent_from_query",
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"community": 2
|
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},
|
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{
|
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"label": "\u83b7\u53d6\u8f93\u5165\u76ee\u5f55\uff0c\u652f\u6301session_id\u4e0d\u662fjob_id\u7684\u60c5\u51b5 Returns: tuple: (inp",
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"file_type": "rationale",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/orchestrator.py",
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"source_location": "L93",
|
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"id": "orchestrator_rationale_93",
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"community": 7
|
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},
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{
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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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"source_location": "L2447",
|
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"id": "orchestrator_rationale_2447",
|
|
"community": 7
|
|
},
|
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{
|
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"label": "langgraph_orchestrator.py",
|
|
"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
|
|
"source_location": "L1",
|
|
"id": "langgraph_orchestrator",
|
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"community": 9
|
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},
|
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{
|
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"label": "WorkflowMode",
|
|
"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
|
|
"source_location": "L27",
|
|
"id": "langgraph_orchestrator_workflowmode",
|
|
"community": 9
|
|
},
|
|
{
|
|
"label": "GraphState",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
|
|
"source_location": "L35",
|
|
"id": "langgraph_orchestrator_graphstate",
|
|
"community": 2
|
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},
|
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{
|
|
"label": "LangGraphOrchestrator",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
|
|
"source_location": "L76",
|
|
"id": "langgraph_orchestrator_langgraphorchestrator",
|
|
"community": 2
|
|
},
|
|
{
|
|
"label": ".__init__()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
|
|
"source_location": "L91",
|
|
"id": "langgraph_orchestrator_langgraphorchestrator_init",
|
|
"community": 2
|
|
},
|
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{
|
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"label": "._build_graph()",
|
|
"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
|
|
"source_location": "L113",
|
|
"id": "langgraph_orchestrator_langgraphorchestrator_build_graph",
|
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"community": 2
|
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},
|
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{
|
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"label": ".run()",
|
|
"file_type": "code",
|
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
|
|
"source_location": "L184",
|
|
"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",
|
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"id": "langgraph_orchestrator_langgraphorchestrator_router_node",
|
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"community": 9
|
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},
|
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{
|
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"label": "._knowledge_node()",
|
|
"file_type": "code",
|
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"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",
|
|
"source_location": "L285",
|
|
"id": "langgraph_orchestrator_langgraphorchestrator_query_completed_stages_from_manifest",
|
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"community": 9
|
|
},
|
|
{
|
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"label": "._planning_node()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
|
|
"source_location": "L327",
|
|
"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",
|
|
"source_location": "L358",
|
|
"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",
|
|
"source_location": "L377",
|
|
"id": "langgraph_orchestrator_langgraphorchestrator_validator_node",
|
|
"community": 9
|
|
},
|
|
{
|
|
"label": "._diagnosis_node()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
|
|
"source_location": "L441",
|
|
"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",
|
|
"source_location": "L465",
|
|
"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
|
|
},
|
|
{
|
|
"label": "._learning_node()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
|
|
"source_location": "L506",
|
|
"id": "langgraph_orchestrator_langgraphorchestrator_learning_node",
|
|
"community": 9
|
|
},
|
|
{
|
|
"label": "._route_decision()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
|
|
"source_location": "L538",
|
|
"id": "langgraph_orchestrator_langgraphorchestrator_route_decision",
|
|
"community": 2
|
|
},
|
|
{
|
|
"label": "._validate_decision()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
|
|
"source_location": "L557",
|
|
"id": "langgraph_orchestrator_langgraphorchestrator_validate_decision",
|
|
"community": 2
|
|
},
|
|
{
|
|
"label": "._diagnosis_decision()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/core/langgraph_orchestrator.py",
|
|
"source_location": "L566",
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{
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|
"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
|
|
},
|
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{
|
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"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
|
|
},
|
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{
|
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"label": "deepseek.py",
|
|
"file_type": "code",
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"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",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/deepseek.py",
|
|
"source_location": "L10",
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"id": "deepseek_deepseekprovider",
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"community": 6
|
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},
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{
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"label": ".__init__()",
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|
"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/deepseek.py",
|
|
"source_location": "L28",
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"id": "deepseek_deepseekprovider_init",
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"community": 6
|
|
},
|
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{
|
|
"label": ".call()",
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"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/llm/providers/deepseek.py",
|
|
"source_location": "L47",
|
|
"id": "deepseek_deepseekprovider_call",
|
|
"community": 6
|
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},
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{
|
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"label": ".acall()",
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|
"file_type": "code",
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|
"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
|
|
},
|
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{
|
|
"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
|
|
},
|
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{
|
|
"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",
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|
"source_location": "L11",
|
|
"id": "diagnosis_diagnosisagent",
|
|
"community": 0
|
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},
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{
|
|
"label": "BaseAgent",
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|
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|
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|
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"id": "baseagent",
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"community": 2
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},
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{
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|
"label": ".__init__()",
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|
"file_type": "code",
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
|
|
"source_location": "L79",
|
|
"id": "diagnosis_diagnosisagent_init",
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|
"community": 0
|
|
},
|
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{
|
|
"label": ".execute()",
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|
"file_type": "code",
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
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|
"source_location": "L83",
|
|
"id": "diagnosis_diagnosisagent_execute",
|
|
"community": 0
|
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},
|
|
{
|
|
"label": "._diagnose_error()",
|
|
"file_type": "code",
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
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|
"source_location": "L112",
|
|
"id": "diagnosis_diagnosisagent_diagnose_error",
|
|
"community": 0
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|
},
|
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{
|
|
"label": "._match_error_pattern()",
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|
"file_type": "code",
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|
"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
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|
"source_location": "L159",
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|
"id": "diagnosis_diagnosisagent_match_error_pattern",
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"community": 0
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},
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{
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"label": "._attempt_auto_fix()",
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|
"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
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|
"source_location": "L175",
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|
"id": "diagnosis_diagnosisagent_attempt_auto_fix",
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"community": 0
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},
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{
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"label": "._fix_reduce_cpu()",
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|
"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
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|
"source_location": "L185",
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|
"id": "diagnosis_diagnosisagent_fix_reduce_cpu",
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"community": 0
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},
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{
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"label": "._fix_parameter_format()",
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|
"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
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|
"source_location": "L201",
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|
"id": "diagnosis_diagnosisagent_fix_parameter_format",
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|
"community": 0
|
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},
|
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{
|
|
"label": "._llm_diagnose()",
|
|
"file_type": "code",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
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|
"source_location": "L223",
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|
"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",
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|
"source_location": "L265",
|
|
"id": "diagnosis_diagnosisagent_record_error",
|
|
"community": 0
|
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},
|
|
{
|
|
"label": ".get_common_errors()",
|
|
"file_type": "code",
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"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.",
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|
"file_type": "rationale",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/mas/agents/diagnosis.py",
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|
"source_location": "L12",
|
|
"id": "diagnosis_rationale_12",
|
|
"community": 0
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},
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{
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"label": "\u83b7\u53d6\u57fa\u56e0\u8868\u8fbe\u6570\u636e Args: organism: \u751f\u7269\u4f53 gene_id: \u57fa",
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"file_type": "rationale",
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"label": "\u83b7\u53d6\u8f6c\u5f55\u56e0\u5b50\u5bb6\u65cf\u4fe1\u606f Args: species: \u7269\u79cd family: \u5bb6\u65cf",
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"file_type": "rationale",
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"source_file": "/home/xia-lab/wutx/00test/bbav5/gfa_core/api_clients/rnaseq_clients.py",
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|
|
"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
|
|
},
|
|
{
|
|
"label": "simple_query()",
|
|
"file_type": "code",
|
|
"source_file": "/home/xia-lab/wutx/00test/bbav5/scripts/tiqu_miaoshuwenjian.py",
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