tooluniverse 0.1.4__tar.gz → 0.2.0__tar.gz

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Files changed (29) hide show
  1. {tooluniverse-0.1.4/src/tooluniverse.egg-info → tooluniverse-0.2.0}/PKG-INFO +21 -23
  2. {tooluniverse-0.1.4 → tooluniverse-0.2.0}/README.md +11 -17
  3. tooluniverse-0.2.0/pyproject.toml +37 -0
  4. tooluniverse-0.2.0/setup.cfg +4 -0
  5. {tooluniverse-0.1.4 → tooluniverse-0.2.0}/src/tooluniverse/data/fda_drug_labeling_tools.json +543 -167
  6. {tooluniverse-0.1.4 → tooluniverse-0.2.0}/src/tooluniverse/data/opentarget_tools.json +81 -57
  7. tooluniverse-0.2.0/src/tooluniverse/generate_mcp_tools.py +113 -0
  8. tooluniverse-0.2.0/src/tooluniverse/mcp_server.py +3340 -0
  9. {tooluniverse-0.1.4 → tooluniverse-0.2.0/src/tooluniverse.egg-info}/PKG-INFO +21 -23
  10. {tooluniverse-0.1.4 → tooluniverse-0.2.0}/src/tooluniverse.egg-info/SOURCES.txt +3 -1
  11. tooluniverse-0.2.0/src/tooluniverse.egg-info/entry_points.txt +4 -0
  12. tooluniverse-0.2.0/src/tooluniverse.egg-info/requires.txt +8 -0
  13. tooluniverse-0.1.4/pyproject.toml +0 -3
  14. tooluniverse-0.1.4/setup.cfg +0 -31
  15. tooluniverse-0.1.4/src/tooluniverse.egg-info/requires.txt +0 -3
  16. {tooluniverse-0.1.4 → tooluniverse-0.2.0}/LICENSE +0 -0
  17. {tooluniverse-0.1.4 → tooluniverse-0.2.0}/src/tooluniverse/__init__.py +0 -0
  18. {tooluniverse-0.1.4 → tooluniverse-0.2.0}/src/tooluniverse/base_tool.py +0 -0
  19. {tooluniverse-0.1.4 → tooluniverse-0.2.0}/src/tooluniverse/data/__init__.py +0 -0
  20. {tooluniverse-0.1.4 → tooluniverse-0.2.0}/src/tooluniverse/data/fda_drugs_with_brand_generic_names_for_tool.py +0 -0
  21. {tooluniverse-0.1.4 → tooluniverse-0.2.0}/src/tooluniverse/data/monarch_tools.json +0 -0
  22. {tooluniverse-0.1.4 → tooluniverse-0.2.0}/src/tooluniverse/data/special_tools.json +0 -0
  23. {tooluniverse-0.1.4 → tooluniverse-0.2.0}/src/tooluniverse/execute_function.py +0 -0
  24. {tooluniverse-0.1.4 → tooluniverse-0.2.0}/src/tooluniverse/graphql_tool.py +0 -0
  25. {tooluniverse-0.1.4 → tooluniverse-0.2.0}/src/tooluniverse/openfda_tool.py +0 -0
  26. {tooluniverse-0.1.4 → tooluniverse-0.2.0}/src/tooluniverse/restful_tool.py +0 -0
  27. {tooluniverse-0.1.4 → tooluniverse-0.2.0}/src/tooluniverse/utils.py +0 -0
  28. {tooluniverse-0.1.4 → tooluniverse-0.2.0}/src/tooluniverse.egg-info/dependency_links.txt +0 -0
  29. {tooluniverse-0.1.4 → tooluniverse-0.2.0}/src/tooluniverse.egg-info/top_level.txt +0 -0
{tooluniverse-0.1.4/src/tooluniverse.egg-info → tooluniverse-0.2.0}/PKG-INFO RENAMED
@@ -1,16 +1,20 @@
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  Metadata-Version: 2.4
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  Name: tooluniverse
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- Version: 0.1.4
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- Summary: A collection of biomedical tools designed for use by Agentic AI.
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- Home-page: https://github.com/mims-harvard/TxAgent
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- Author: Shanghua Gao
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- Author-email: shanghuagao@gmail.com
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- Requires-Python: >=3.6
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+ Version: 0.2.0
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+ Summary: A comprehensive collection of biomedical tools for Agentic AI, offering integration with the ToolUniverse SDK and MCP Server to support advanced biomedical workflows.
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+ Author-email: Shanghua Gao <shanghuagao@gmail.com>
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+ Project-URL: Homepage, https://github.com/mims-harvard/TxAgent
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+ Requires-Python: >=3.10
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  Description-Content-Type: text/markdown
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  License-File: LICENSE
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  Requires-Dist: requests
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  Requires-Dist: numpy
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  Requires-Dist: graphql-core
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+ Requires-Dist: fastapi
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+ Requires-Dist: uvicorn
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+ Requires-Dist: fastmcp
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+ Requires-Dist: pydantic
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+ Requires-Dist: pyyaml
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  Dynamic: license-file
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  # ToolUniverse
@@ -22,6 +26,7 @@ Dynamic: license-file
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  [![TxAgent](https://img.shields.io/badge/Code-TxAgent-purple)](https://github.com/mims-harvard/TxAgent)
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  [![ToolUniverse](https://img.shields.io/badge/Code-ToolUniverse-purple)](https://github.com/mims-harvard/ToolUniverse)
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  [![HuggingFace](https://img.shields.io/badge/HuggingFace-TxAgentT1-yellow)](https://huggingface.co/collections/mims-harvard/txagent-67c8e54a9d03a429bb0c622c)
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+ [![Model context protocol (MCP)](https://img.shields.io/badge/Model_Context_Protocol_(MCP)_Supported-green)](README_USAGE.md#running-the-mcp-server)
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  <body>
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  <section class="hero">
@@ -102,26 +107,13 @@ pip install tooluniverse
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  # Usage
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- **Get all tools**
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+ ToolUniverse supports both a Python SDK and an MCP server interface.
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+ - You can use the Python SDK to interact with ToolUniverse programmatically in your Python projects.
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+ - You can connect to the ToolUniverse MCP server for remote tool execution and integration with other agentic systems.
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- ```
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- from tooluniverse import ToolUniverse
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- tooluni = ToolUniverse()
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- tooluni.load_tools()
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- tool_name_list, tool_desc_list = tooluni.refresh_tool_name_desc()
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- print(tool_name_list)
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- print(tool_desc_list)
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- ```
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+ For more detailed usage examples, see the [README_USAGE](README_USAGE.md) page.
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- **Function call to a tool**
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- ```
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- from tooluniverse import ToolUniverse
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- tooluni = ToolUniverse()
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- tooluni.load_tools()
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- query = {"name": "get_indications_by_drug_name", "arguments": {"drug_name": "KISUNLA"}}
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- tooluni.run(query)
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- ```
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  ## Citation
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  ```
@@ -139,3 +131,9 @@ tooluni.run(query)
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  ## Contact
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  If you have any questions or suggestions, please email [Shanghua Gao](mailto:shanghuagao@gmail.com) and [Marinka Zitnik](mailto:marinka@hms.harvard.edu).
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+ ## Core contributors
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+
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+ [Shanghua Gao](https://shgao.site);
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+ [Richard Zhu](https://www.linkedin.com/in/richard-zhu-4236901a7/);
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+ [Zhenglun Kong](https://zlkong.github.io/homepage/);
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+ [Sufian Aldogom](saldogom@mit.edu)
{tooluniverse-0.1.4 → tooluniverse-0.2.0}/README.md RENAMED
@@ -7,6 +7,7 @@
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  [![TxAgent](https://img.shields.io/badge/Code-TxAgent-purple)](https://github.com/mims-harvard/TxAgent)
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  [![ToolUniverse](https://img.shields.io/badge/Code-ToolUniverse-purple)](https://github.com/mims-harvard/ToolUniverse)
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  [![HuggingFace](https://img.shields.io/badge/HuggingFace-TxAgentT1-yellow)](https://huggingface.co/collections/mims-harvard/txagent-67c8e54a9d03a429bb0c622c)
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+ [![Model context protocol (MCP)](https://img.shields.io/badge/Model_Context_Protocol_(MCP)_Supported-green)](README_USAGE.md#running-the-mcp-server)
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  <body>
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  <section class="hero">
@@ -87,26 +88,13 @@ pip install tooluniverse
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  # Usage
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- **Get all tools**
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+ ToolUniverse supports both a Python SDK and an MCP server interface.
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+ - You can use the Python SDK to interact with ToolUniverse programmatically in your Python projects.
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+ - You can connect to the ToolUniverse MCP server for remote tool execution and integration with other agentic systems.
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- ```
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- from tooluniverse import ToolUniverse
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- tooluni = ToolUniverse()
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- tooluni.load_tools()
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- tool_name_list, tool_desc_list = tooluni.refresh_tool_name_desc()
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- print(tool_name_list)
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- print(tool_desc_list)
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- ```
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+ For more detailed usage examples, see the [README_USAGE](README_USAGE.md) page.
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- **Function call to a tool**
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- ```
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- from tooluniverse import ToolUniverse
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- tooluni = ToolUniverse()
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- tooluni.load_tools()
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- query = {"name": "get_indications_by_drug_name", "arguments": {"drug_name": "KISUNLA"}}
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- tooluni.run(query)
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- ```
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  ## Citation
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  ```
@@ -124,3 +112,9 @@ tooluni.run(query)
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  ## Contact
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  If you have any questions or suggestions, please email [Shanghua Gao](mailto:shanghuagao@gmail.com) and [Marinka Zitnik](mailto:marinka@hms.harvard.edu).
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+ ## Core contributors
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+
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+ [Shanghua Gao](https://shgao.site);
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+ [Richard Zhu](https://www.linkedin.com/in/richard-zhu-4236901a7/);
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+ [Zhenglun Kong](https://zlkong.github.io/homepage/);
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+ [Sufian Aldogom](saldogom@mit.edu)
tooluniverse-0.2.0/pyproject.toml ADDED
@@ -0,0 +1,37 @@
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+ [build-system]
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+ requires = ["setuptools", "wheel"]
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+ build-backend = "setuptools.build_meta"
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+
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+ [project]
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+ name = "tooluniverse"
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+ version = "0.2.0"
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+ description = "A comprehensive collection of biomedical tools for Agentic AI, offering integration with the ToolUniverse SDK and MCP Server to support advanced biomedical workflows."
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+ authors = [
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+ { name = "Shanghua Gao", email = "shanghuagao@gmail.com" }
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+ ]
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+ dependencies = [
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+ "requests",
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+ "numpy",
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+ "graphql-core",
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+ "fastapi",
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+ "uvicorn",
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+ "fastmcp",
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+ "pydantic",
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+ "pyyaml"
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+ ]
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+ requires-python = ">=3.10"
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+ readme = "README.md"
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+
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+ [project.urls]
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+ Homepage = "https://github.com/mims-harvard/TxAgent"
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+
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+ [project.scripts]
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+ tooluniverse-mcp = "tooluniverse.mcp_server:run_server"
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+ tooluniverse-mcp-claude = "tooluniverse.mcp_server:run_claude_desktop"
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+ generate-mcp-tools = "tooluniverse.generate_mcp_tools:run_generate"
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+
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+ [tool.setuptools.packages.find]
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+ where = ["src"]
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+
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+ [tool.setuptools.package-data]
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+ tooluniverse = ["data/*"]
tooluniverse-0.2.0/setup.cfg ADDED
@@ -0,0 +1,4 @@
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+ [egg_info]
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+ tag_build =
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+ tag_date = 0
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+