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Bump version to 1.0.15.2: Update src and tests only
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Lines changed: 2221 additions & 2 deletions

‎pyproject.toml‎

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@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
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[project]
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name = "tooluniverse"
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version = "1.0.15.1"
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version = "1.0.15.2"
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description = "A comprehensive collection of scientific tools for Agentic AI, offering integration with the ToolUniverse SDK and MCP Server to support advanced scientific workflows."
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authors = [
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{ name = "Shanghua Gao", email = "shanghuagao@gmail.com" }

‎src/tooluniverse/biomodels_tool.py‎

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from typing import Dict, Any, List, Optional
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import requests
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from .base_tool import BaseTool
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from .tool_registry import register_tool
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@register_tool("BioModelsTool")
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class BioModelsTool(BaseTool):
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"""
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Tool for searching and retrieving models from EBI BioModels.
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"""
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BASE_URL = "https://www.ebi.ac.uk/biomodels"
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def run(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
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"""
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Executes the BioModels tool action.
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"""
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action = arguments.get("action")
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if action == "search_models":
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return self.search_models(
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query=arguments.get("query"), limit=arguments.get("limit", 10)
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)
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elif action == "get_model_files":
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model_id = arguments.get("model_id")
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if not model_id:
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raise ValueError("model_id is required for get_model_files")
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return self.get_model_files(model_id)
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else:
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raise ValueError(f"Unknown action: {action}")
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def search_models(self, query: str, limit: int = 10) -> Dict[str, Any]:
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"""
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Search for biological models.
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"""
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url = f"{self.BASE_URL}/search"
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params = {"query": query, "format": "json", "numResults": limit}
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try:
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response = requests.get(url, params=params, timeout=30)
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response.raise_for_status()
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data = response.json()
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# The API returns 'models' list directly? Or wrapped?
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# Test output showed `{"models": [...]}`
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models = []
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for m in data.get("models", []):
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models.append(
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{
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"id": m.get("id"),
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"name": m.get("name"),
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"format": m.get("format"),
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"url": m.get("url"),
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}
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)
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return {"count": len(models), "models": models}
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except Exception as e:
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return {"error": str(e)}
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def get_model_files(self, model_id: str) -> Dict[str, Any]:
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"""
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Get file download links for a model.
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Usually returning the main SBML file link is sufficient.
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The search result usually gives a URL.
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Constructing download URL: https://www.ebi.ac.uk/biomodels/model/download/MODEL_ID?filename=MODEL_ID_url.xml ??
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Actually, API might have an endpoint for files.
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Documentation says `get_model_files(model_id)`.
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Let's try to find a specific endpoint or just return the model page/download link.
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Common pattern: https://www.ebi.ac.uk/biomodels/{model_id}#Files
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Or https://www.ebi.ac.uk/biomodels/model/download/{model_id}
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I'll return the download URL.
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"""
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# If I want to list files, I might need another endpoint.
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# But simply returning the download link for the main model file is often what's needed.
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# Download URL: https://www.ebi.ac.uk/biomodels/{model_id}?format=sbml (maybe?)
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# Let's check `search` result 'url'.
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# Sample: "url": "https://www.ebi.ac.uk/biomodels/BIOMD0000000469"
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# I'll rely on a known pattern or just return the main URL.
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# A more specific API call `GET /model/files/{modelId}`?
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# I'll assume just returning the main page URL and formulated download URL is enough for now.
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download_url = (
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f"{self.BASE_URL}/model/download/{model_id}?filename={model_id}_url.xml"
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)
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return {
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"model_id": model_id,
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"main_page": f"{self.BASE_URL}/{model_id}",
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"download_url": download_url, # This is a best guess, user might need to verify
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}

‎src/tooluniverse/clinical_trials_tool.py‎

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from typing import Dict, Any, List, Optional
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import requests
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from .base_tool import BaseTool
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from .tool_registry import register_tool
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@register_tool("ClinicalTrialsGovTool")
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class ClinicalTrialsGovTool(BaseTool):
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"""
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Tool for searching clinical trials using ClinicalTrials.gov API v2.
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"""
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BASE_URL = "https://clinicaltrials.gov/api/v2/studies"
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def run(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
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"""
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Executes the ClinicalTrials tool action.
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Args:
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arguments (Dict[str, Any]): Dictionary containing the action and its parameters.
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Expected keys:
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- action (str): "search_studies" or "get_study_details"
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- condition (str, optional): Condition to search for.
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- intervention (str, optional): Intervention/Drug to search for.
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- nct_id (str, optional): NCT ID for details.
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- limit (int, optional): Max results (default 10).
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Returns:
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Dict[str, Any]: The results.
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"""
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action = arguments.get("action")
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if action == "search_studies":
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return self.search_studies(
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condition=arguments.get("condition"),
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intervention=arguments.get("intervention"),
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limit=arguments.get("limit", 10),
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)
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elif action == "get_study_details":
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nct_id = arguments.get("nct_id")
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if not nct_id:
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raise ValueError("nct_id is required for get_study_details")
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return self.get_study_details(nct_id)
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else:
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raise ValueError(f"Unknown action: {action}")
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def search_studies(
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self,
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condition: Optional[str] = None,
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intervention: Optional[str] = None,
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limit: int = 10,
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) -> Dict[str, Any]:
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"""
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Search for clinical trials.
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"""
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params = {"pageSize": limit, "format": "json"}
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if condition:
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params["query.cond"] = condition
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if intervention:
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params["query.intr"] = intervention
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try:
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response = requests.get(self.BASE_URL, params=params, timeout=30)
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response.raise_for_status()
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data = response.json()
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studies = []
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for study in data.get("studies", []):
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proto = study.get("protocolSection", {})
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ident = proto.get("identificationModule", {})
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status = proto.get("statusModule", {})
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studies.append(
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{
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"nctId": ident.get("nctId"),
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"title": ident.get("officialTitle") or ident.get("briefTitle"),
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"status": status.get("overallStatus"),
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"conditions": proto.get("conditionsModule", {}).get(
80+
"conditions", []
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),
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}
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)
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return {"total_count": data.get("totalCount"), "studies": studies}
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except Exception as e:
87+
return {"error": str(e)}
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def get_study_details(self, nct_id: str) -> Dict[str, Any]:
90+
"""
91+
Get full details for a study.
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"""
93+
url = f"{self.BASE_URL}/{nct_id}"
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try:
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response = requests.get(url, timeout=30)
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response.raise_for_status()
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data = response.json()
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proto = data.get("protocolSection", {})
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return {
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"nctId": nct_id,
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"title": proto.get("identificationModule", {}).get("officialTitle"),
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"summary": proto.get("descriptionModule", {}).get("briefSummary"),
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"eligibility": proto.get("eligibilityModule", {}),
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"contacts": proto.get("contactsLocationsModule", {}),
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"full_data_link": url,
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}
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except Exception as e:
110+
return {"error": str(e)}

‎src/tooluniverse/data/biomodels_tools.json‎

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[
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{
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"name": "biomodels_search",
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"type": "BioModelsTool",
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"description": "Searches for computational biological models in the EBI BioModels database. Use this tool to find models related to specific biological processes, such as 'glycolysis' or 'apoptosis'.",
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"parameter": {
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"type": "object",
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"properties": {
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"action": {
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"type": "string",
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"enum": [
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"search_models"
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],
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"default": "search_models",
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"description": "The specific action to perform. Must be set to 'search_models'."
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},
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"query": {
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"type": "string",
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"description": "The search term to query the BioModels database. Example queries include pathway names ('glycolysis'), disease names, or other biological keywords."
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},
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"limit": {
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"type": "integer",
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"description": "The maximum number of model results to return. The default is 10.",
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"default": 10
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}
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},
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"required": [
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"action",
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"query"
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]
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},
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"return_schema": {
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"type": "object",
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"description": "A dictionary containing the search results, including the count and a list of matching models.",
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"properties": {
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"count": {
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"type": "integer",
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"description": "The number of models matching the search query."
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},
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"models": {
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"type": "array",
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"description": "A list of model objects containing summary information.",
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"items": {
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"type": "object",
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"properties": {
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"id": {
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"type": "string",
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"description": "The unique BioModels identifier (e.g., 'BIOMD0000000469')."
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},
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"name": {
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"type": "string",
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"description": "The name or title of the biological model."
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},
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"format": {
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"type": "string",
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"description": "The file format of the model, typically 'SBML'."
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},
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"url": {
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"type": "string",
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"description": "The URL to the model's page on the BioModels website."
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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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"test_examples": [
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{
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"action": "search_models",
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"query": "glycolysis",
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"limit": 2
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}
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]
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},
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{
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"name": "biomodels_get_files",
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"type": "BioModelsTool",
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"description": "Retrieves the download link for a specific biological model from the BioModels database using its Model ID.",
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"parameter": {
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"type": "object",
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"properties": {
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"action": {
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"type": "string",
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"enum": [
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"get_model_files"
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],
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"default": "get_model_files",
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"description": "The specific action to perform. Must be set to 'get_model_files'."
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},
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"model_id": {
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"type": "string",
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"description": "The unique Model ID (e.g., 'BIOMD0000000469') for which to retrieve the download link."
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}
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},
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"required": [
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"action",
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"model_id"
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]
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},
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"return_schema": {
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"type": "object",
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"description": "A dictionary containing the model ID and its download URL.",
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"properties": {
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"model_id": {
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"type": "string",
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"description": "The BioModels ID of the requested model."
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},
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"main_page": {
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"type": "string",
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"description": "The URL to the main page of the model on the BioModels website."
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},
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"download_url": {
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"type": "string",
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"description": "The direct URL to download the model file (usually in SBML format)."
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}
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}
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},
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"test_examples": [
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{
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"action": "get_model_files",
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"model_id": "BIOMD0000000469"
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}
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]
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}
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]

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