tooluniverse 0.1.3__py3-none-any.whl → 0.2.0__py3-none-any.whl

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Files changed (13) hide show
  1. tooluniverse/data/fda_drug_labeling_tools.json +543 -167
  2. tooluniverse/data/opentarget_tools.json +81 -57
  3. tooluniverse/generate_mcp_tools.py +113 -0
  4. tooluniverse/graphql_tool.py +1 -1
  5. tooluniverse/mcp_server.py +3340 -0
  6. tooluniverse/openfda_tool.py +2 -1
  7. {tooluniverse-0.1.3.dist-info → tooluniverse-0.2.0.dist-info}/METADATA +23 -24
  8. tooluniverse-0.2.0.dist-info/RECORD +21 -0
  9. {tooluniverse-0.1.3.dist-info → tooluniverse-0.2.0.dist-info}/WHEEL +1 -1
  10. tooluniverse-0.2.0.dist-info/entry_points.txt +4 -0
  11. tooluniverse-0.1.3.dist-info/RECORD +0 -18
  12. {tooluniverse-0.1.3.dist-info → tooluniverse-0.2.0.dist-info/licenses}/LICENSE +0 -0
  13. {tooluniverse-0.1.3.dist-info → tooluniverse-0.2.0.dist-info}/top_level.txt +0 -0
tooluniverse/openfda_tool.py CHANGED
@@ -3,6 +3,7 @@ from .base_tool import BaseTool
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  import copy
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  import re
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  import json
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+ import os
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  def check_keys_present(api_capabilities_dict, keys):
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  for key in keys:
@@ -219,7 +220,7 @@ class FDATool(BaseTool):
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  if self.exists is None:
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  self.exists = self.return_fields
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  self.endpoint_url = endpoint_url
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- self.api_key = api_key
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+ self.api_key = api_key or os.getenv('FDA_API_KEY')
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  def run(self, arguments):
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  arguments = copy.deepcopy(arguments)
{tooluniverse-0.1.3.dist-info → tooluniverse-0.2.0.dist-info}/METADATA RENAMED
@@ -1,16 +1,21 @@
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- Metadata-Version: 2.2
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+ Metadata-Version: 2.4
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  Name: tooluniverse
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- Version: 0.1.3
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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
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@@ -21,6 +26,7 @@ Requires-Dist: graphql-core
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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">
@@ -101,26 +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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  ```
@@ -138,3 +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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133
 
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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.dist-info/RECORD ADDED
@@ -0,0 +1,21 @@
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+ tooluniverse/__init__.py,sha256=j44hf13WM50HQJRi7aloeTG6y6872wJtfX8ydsaiJFI,652
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+ tooluniverse/base_tool.py,sha256=WMGgr02lhEsVzHgt7NIeynXQ2wZtu97yZI-lQWOSoSs,1145
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+ tooluniverse/execute_function.py,sha256=CmA8AIfyolkcooASD2_3pXgF1BqESU5_VUqdHSYiM_M,10139
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+ tooluniverse/generate_mcp_tools.py,sha256=LXE6cZzkbuMZbqL5Z0OKfOOYGjttowYFIIXJzlPfv4U,3166
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+ tooluniverse/graphql_tool.py,sha256=WU-9YAYbmfbfGwGDn7Y22DVju9t68CKuv_JNz_11NkM,5120
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+ tooluniverse/mcp_server.py,sha256=9xlhWBCk0GLSwS6G4KPxvpeggSqFeqvBbMv6Q9zlXcA,75841
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+ tooluniverse/openfda_tool.py,sha256=s4ctA7ckID7VA1wRceRGknFV5zu9sR7fqTJ8oa9U0q4,21056
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+ tooluniverse/restful_tool.py,sha256=5HoTyCSd507D4Qjcqjd16o8Y4BFZ02Zm4cGuczIXWdw,4078
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+ tooluniverse/utils.py,sha256=zh1IopojPBIJzK_8eGytTmWlPckluQQZTpiCQONw-pY,6416
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+ tooluniverse/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ tooluniverse/data/fda_drug_labeling_tools.json,sha256=2mChXxdDaP4qo8GqRYm6rK-Gsazryewb4ark2IxaauQ,224727
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+ tooluniverse/data/fda_drugs_with_brand_generic_names_for_tool.py,sha256=Clb7kQpPaXPTT_rdDLoinfwF8JbrdRaBis-0TYcT0BU,6510589
13
+ tooluniverse/data/monarch_tools.json,sha256=I5KvamNZRvkKBaKbM6Ypo333m-RejQhqScX8h-uket4,3567
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+ tooluniverse/data/opentarget_tools.json,sha256=vQQJsTGIoZWeqInUHmsdwp8kpqzx51f-VVaAVRmJdcU,67794
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+ tooluniverse/data/special_tools.json,sha256=tOI0TFpdjZBEE5Af1Vc4CeXQ0gAkz39xho9hDVBYR70,1518
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+ tooluniverse-0.2.0.dist-info/licenses/LICENSE,sha256=Unq9Y3buGL9J0vFop03FYZiVweytt1xdgLIh2n9ck2c,1115
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+ tooluniverse-0.2.0.dist-info/METADATA,sha256=ZSkaURh0dRXEdXdZrMvewggnp3f9aZkBAgDhU73deKY,5729
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+ tooluniverse-0.2.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+ tooluniverse-0.2.0.dist-info/entry_points.txt,sha256=qDvySLz4M6uQDTwVvw-9zeLJ5jUir1aDdWbUrRqq6Bc,207
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+ tooluniverse-0.2.0.dist-info/top_level.txt,sha256=zZ8YeCJ5FAkEwdd_mxsFtSCQMBDgBdxrrmHo3RNBiWs,13
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+ tooluniverse-0.2.0.dist-info/RECORD,,
{tooluniverse-0.1.3.dist-info → tooluniverse-0.2.0.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
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  Wheel-Version: 1.0
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- Generator: setuptools (76.1.0)
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+ Generator: setuptools (80.9.0)
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  Root-Is-Purelib: true
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  Tag: py3-none-any
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tooluniverse-0.2.0.dist-info/entry_points.txt ADDED
@@ -0,0 +1,4 @@
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+ [console_scripts]
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+ generate-mcp-tools = tooluniverse.generate_mcp_tools:run_generate
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+ tooluniverse-mcp = tooluniverse.mcp_server:run_server
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+ tooluniverse-mcp-claude = tooluniverse.mcp_server:run_claude_desktop
tooluniverse-0.1.3.dist-info/RECORD DELETED
@@ -1,18 +0,0 @@
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- tooluniverse/__init__.py,sha256=j44hf13WM50HQJRi7aloeTG6y6872wJtfX8ydsaiJFI,652
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- tooluniverse/base_tool.py,sha256=WMGgr02lhEsVzHgt7NIeynXQ2wZtu97yZI-lQWOSoSs,1145
3
- tooluniverse/execute_function.py,sha256=CmA8AIfyolkcooASD2_3pXgF1BqESU5_VUqdHSYiM_M,10139
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- tooluniverse/graphql_tool.py,sha256=FpyP70ZiQkd031crECAhZ7CbXBor8x6S-n48VICnxVs,5086
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- tooluniverse/openfda_tool.py,sha256=wSelkQiOn0hqMzoqflw3lOFnyT8a1q5A6hSc8YyOgx8,21018
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- tooluniverse/restful_tool.py,sha256=5HoTyCSd507D4Qjcqjd16o8Y4BFZ02Zm4cGuczIXWdw,4078
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- tooluniverse/utils.py,sha256=zh1IopojPBIJzK_8eGytTmWlPckluQQZTpiCQONw-pY,6416
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- tooluniverse/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- tooluniverse/data/fda_drug_labeling_tools.json,sha256=iRYkuNk6ohCbNELMbfPghtlCGthjzZch_9Ukr-yjaJI,209383
10
- tooluniverse/data/fda_drugs_with_brand_generic_names_for_tool.py,sha256=Clb7kQpPaXPTT_rdDLoinfwF8JbrdRaBis-0TYcT0BU,6510589
11
- tooluniverse/data/monarch_tools.json,sha256=I5KvamNZRvkKBaKbM6Ypo333m-RejQhqScX8h-uket4,3567
12
- tooluniverse/data/opentarget_tools.json,sha256=nNvl-vYqS8nLfyIvHO40Fsnx6HJxwInUuS0mrrh6xmY,66201
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- tooluniverse/data/special_tools.json,sha256=tOI0TFpdjZBEE5Af1Vc4CeXQ0gAkz39xho9hDVBYR70,1518
14
- tooluniverse-0.1.3.dist-info/LICENSE,sha256=Unq9Y3buGL9J0vFop03FYZiVweytt1xdgLIh2n9ck2c,1115
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- tooluniverse-0.1.3.dist-info/METADATA,sha256=zx-hLNaex1UJcSD2LZlBFAL2Y5iUKRn_i1c1uhLKfxY,5198
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- tooluniverse-0.1.3.dist-info/WHEEL,sha256=beeZ86-EfXScwlR_HKu4SllMC9wUEj_8Z_4FJ3egI2w,91
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- tooluniverse-0.1.3.dist-info/top_level.txt,sha256=zZ8YeCJ5FAkEwdd_mxsFtSCQMBDgBdxrrmHo3RNBiWs,13
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- tooluniverse-0.1.3.dist-info/RECORD,,