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cd004e1
feat: Implement Phase 10 (ClinicalTrials.gov) with requests
Browse files- docs/implementation/10_phase_clinicaltrials.md +79 -98
- examples/search_demo/run_search.py +4 -2
- pyproject.toml +10 -13
- src/app.py +3 -2
- src/tools/clinicaltrials.py +129 -0
- src/tools/search_handler.py +2 -2
- src/utils/models.py +2 -2
- tests/unit/tools/test_clinicaltrials.py +136 -0
- uv.lock +40 -2
docs/implementation/10_phase_clinicaltrials.md
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@@ -115,12 +115,28 @@ Evidence(
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## 4. Implementation
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### 4.1 ClinicalTrials Tool (`src/tools/clinicaltrials.py`)
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```python
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"""ClinicalTrials.gov search tool using API v2."""
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import
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from tenacity import retry, stop_after_attempt, wait_exponential
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from src.utils.exceptions import SearchError
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class ClinicalTrialsTool:
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"""Search tool for ClinicalTrials.gov.
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BASE_URL = "https://clinicaltrials.gov/api/v2/studies"
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FIELDS = [
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"NCTId",
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"BriefTitle",
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"Phase",
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reraise=True,
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)
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async def search(self, query: str, max_results: int = 10) -> list[Evidence]:
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"""
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Search ClinicalTrials.gov for studies.
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Args:
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query: Search query (e.g., "metformin alzheimer")
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max_results: Maximum results to return
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Returns:
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List of Evidence objects from clinical trials
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"""
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params = {
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"query.term": query,
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"pageSize": min(max_results, 100),
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"fields": "|".join(self.FIELDS),
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}
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data = response.json()
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studies = data.get("studies", [])
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return [self._study_to_evidence(study) for study in studies[:max_results]]
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def _study_to_evidence(self, study: dict) -> Evidence:
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"""Convert a clinical trial study to Evidence."""
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# Navigate nested structure
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### 5.1 Unit Tests (`tests/unit/tools/test_clinicaltrials.py`)
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```python
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"""Unit tests for ClinicalTrials.gov tool."""
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import pytest
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import
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from httpx import Response
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from src.tools.clinicaltrials import ClinicalTrialsTool
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from src.utils.models import Evidence
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@pytest.fixture
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def mock_clinicaltrials_response():
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"""Mock ClinicalTrials.gov API response."""
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return {
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"studies": [
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"protocolSection": {
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"identificationModule": {
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"nctId": "NCT04098666",
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"briefTitle": "Metformin in Alzheimer's Dementia Prevention"
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},
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"statusModule": {
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"overallStatus": "Recruiting",
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"startDateStruct": {"date": "2020-01-15"}
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},
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"descriptionModule": {
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"briefSummary": "This study evaluates metformin for Alzheimer's prevention."
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},
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"designModule": {
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},
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"conditionsModule": {
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"conditions": ["Alzheimer Disease", "Dementia"]
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},
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"armsInterventionsModule": {
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"interventions": [
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]
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}
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}
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}
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]
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class TestClinicalTrialsTool:
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"""Tests for ClinicalTrialsTool."""
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def test_tool_name(self):
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"""Tool should have correct name."""
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tool = ClinicalTrialsTool()
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assert tool.name == "clinicaltrials"
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@pytest.mark.asyncio
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"""Search should return Evidence objects."""
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@pytest.mark.asyncio
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async def test_search_extracts_phase(self, mock_clinicaltrials_response):
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"""Search should extract trial phase."""
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respx.get("https://clinicaltrials.gov/api/v2/studies").mock(
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return_value=Response(200, json=mock_clinicaltrials_response)
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)
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tool = ClinicalTrialsTool()
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results = await tool.search("metformin alzheimer")
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assert "PHASE2" in results[0].content
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@pytest.mark.asyncio
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@respx.mock
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async def test_search_extracts_status(self, mock_clinicaltrials_response):
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"""Search should extract trial status."""
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respx.get("https://clinicaltrials.gov/api/v2/studies").mock(
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return_value=Response(200, json=mock_clinicaltrials_response)
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)
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tool = ClinicalTrialsTool()
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results = await tool.search("metformin alzheimer")
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assert "Recruiting" in results[0].content
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@pytest.mark.asyncio
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@respx.mock
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async def test_search_empty_results(self):
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"""Search should handle empty results gracefully."""
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respx.get("https://clinicaltrials.gov/api/v2/studies").mock(
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return_value=Response(200, json={"studies": []})
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)
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tool = ClinicalTrialsTool()
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results = await tool.search("nonexistent query xyz")
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assert results == []
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@pytest.mark.asyncio
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@respx.mock
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async def test_search_api_error(self):
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"""Search should raise SearchError on API failure."""
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class TestClinicalTrialsIntegration:
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@pytest.mark.integration
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@pytest.mark.asyncio
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async def test_real_api_call(self):
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"""Test actual API call (requires network)."""
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tool = ClinicalTrialsTool()
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results = await tool.search("metformin diabetes", max_results=3)
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## 4. Implementation
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### 4.0 Important: HTTP Client Selection
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**ClinicalTrials.gov's WAF blocks `httpx`'s TLS fingerprint.** Use `requests` instead.
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| Library | Status | Notes |
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|---------|--------|-------|
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| `httpx` | ❌ 403 Blocked | TLS/JA3 fingerprint flagged |
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| `httpx[http2]` | ❌ 403 Blocked | HTTP/2 doesn't help |
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| `requests` | ✅ Works | Industry standard, not blocked |
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| `urllib` | ✅ Works | Stdlib alternative |
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We use `requests` wrapped in `asyncio.to_thread()` for async compatibility.
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### 4.1 ClinicalTrials Tool (`src/tools/clinicaltrials.py`)
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```python
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"""ClinicalTrials.gov search tool using API v2."""
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import asyncio
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from typing import Any, ClassVar
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import requests
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from tenacity import retry, stop_after_attempt, wait_exponential
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from src.utils.exceptions import SearchError
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class ClinicalTrialsTool:
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"""Search tool for ClinicalTrials.gov.
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Note: Uses `requests` library instead of `httpx` because ClinicalTrials.gov's
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WAF blocks httpx's TLS fingerprint. The `requests` library is not blocked.
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"""
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BASE_URL = "https://clinicaltrials.gov/api/v2/studies"
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FIELDS: ClassVar[list[str]] = [
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"NCTId",
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"BriefTitle",
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"Phase",
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reraise=True,
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)
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async def search(self, query: str, max_results: int = 10) -> list[Evidence]:
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"""Search ClinicalTrials.gov for studies."""
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params = {
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"query.term": query,
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"pageSize": min(max_results, 100),
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"fields": "|".join(self.FIELDS),
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}
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try:
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# Run blocking requests.get in a separate thread for async compatibility
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response = await asyncio.to_thread(
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requests.get,
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self.BASE_URL,
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params=params,
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headers={"User-Agent": "DeepCritical-Research-Agent/1.0"},
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timeout=30,
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)
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response.raise_for_status()
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data = response.json()
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studies = data.get("studies", [])
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return [self._study_to_evidence(study) for study in studies[:max_results]]
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except requests.HTTPError as e:
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raise SearchError(f"ClinicalTrials.gov API error: {e}") from e
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except requests.RequestException as e:
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raise SearchError(f"ClinicalTrials.gov request failed: {e}") from e
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def _study_to_evidence(self, study: dict) -> Evidence:
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"""Convert a clinical trial study to Evidence."""
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# Navigate nested structure
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### 5.1 Unit Tests (`tests/unit/tools/test_clinicaltrials.py`)
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Uses `unittest.mock.patch` to mock `requests.get` (not `respx` since we're not using `httpx`).
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```python
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"""Unit tests for ClinicalTrials.gov tool."""
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from unittest.mock import MagicMock, patch
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import pytest
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import requests
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from src.tools.clinicaltrials import ClinicalTrialsTool
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from src.utils.exceptions import SearchError
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from src.utils.models import Evidence
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@pytest.fixture
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def mock_clinicaltrials_response() -> dict:
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"""Mock ClinicalTrials.gov API response."""
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return {
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"studies": [
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"protocolSection": {
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"identificationModule": {
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"nctId": "NCT04098666",
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"briefTitle": "Metformin in Alzheimer's Dementia Prevention",
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},
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"statusModule": {
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"overallStatus": "Recruiting",
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"startDateStruct": {"date": "2020-01-15"},
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},
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"descriptionModule": {
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"briefSummary": "This study evaluates metformin for Alzheimer's prevention."
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},
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"designModule": {"phases": ["PHASE2"]},
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"conditionsModule": {"conditions": ["Alzheimer Disease", "Dementia"]},
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"armsInterventionsModule": {
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"interventions": [{"name": "Metformin", "type": "Drug"}]
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},
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}
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}
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]
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class TestClinicalTrialsTool:
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"""Tests for ClinicalTrialsTool."""
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def test_tool_name(self) -> None:
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"""Tool should have correct name."""
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tool = ClinicalTrialsTool()
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assert tool.name == "clinicaltrials"
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@pytest.mark.asyncio
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async def test_search_returns_evidence(
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self, mock_clinicaltrials_response: dict
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) -> None:
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"""Search should return Evidence objects."""
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with patch("src.tools.clinicaltrials.requests.get") as mock_get:
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mock_response = MagicMock()
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mock_response.json.return_value = mock_clinicaltrials_response
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mock_response.raise_for_status = MagicMock()
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mock_get.return_value = mock_response
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tool = ClinicalTrialsTool()
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results = await tool.search("metformin alzheimer", max_results=5)
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assert len(results) == 1
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assert isinstance(results[0], Evidence)
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assert results[0].citation.source == "clinicaltrials"
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assert "NCT04098666" in results[0].citation.url
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assert "Metformin" in results[0].citation.title
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@pytest.mark.asyncio
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async def test_search_api_error(self) -> None:
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"""Search should raise SearchError on API failure."""
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with patch("src.tools.clinicaltrials.requests.get") as mock_get:
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mock_response = MagicMock()
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mock_response.raise_for_status.side_effect = requests.HTTPError(
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"500 Server Error"
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)
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mock_get.return_value = mock_response
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tool = ClinicalTrialsTool()
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with pytest.raises(SearchError):
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await tool.search("metformin alzheimer")
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class TestClinicalTrialsIntegration:
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@pytest.mark.integration
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@pytest.mark.asyncio
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async def test_real_api_call(self) -> None:
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"""Test actual API call (requires network)."""
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tool = ClinicalTrialsTool()
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results = await tool.search("metformin diabetes", max_results=3)
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examples/search_demo/run_search.py
CHANGED
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import asyncio
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import sys
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from src.tools.pubmed import PubMedTool
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from src.tools.search_handler import SearchHandler
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# Initialize tools
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pubmed = PubMedTool()
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# Execute search
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print("Searching PubMed in parallel...")
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result = await handler.execute(query, max_results_per_tool=5)
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# Display results
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import asyncio
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import sys
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from src.tools.clinicaltrials import ClinicalTrialsTool
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from src.tools.pubmed import PubMedTool
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from src.tools.search_handler import SearchHandler
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# Initialize tools
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pubmed = PubMedTool()
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trials = ClinicalTrialsTool()
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handler = SearchHandler(tools=[pubmed, trials], timeout=30.0)
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# Execute search
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| 41 |
+
print("Searching PubMed and ClinicalTrials.gov in parallel...")
|
| 42 |
result = await handler.execute(query, max_results_per_tool=5)
|
| 43 |
|
| 44 |
# Display results
|
pyproject.toml
CHANGED
|
@@ -7,25 +7,22 @@ requires-python = ">=3.11"
|
|
| 7 |
dependencies = [
|
| 8 |
# Core
|
| 9 |
"pydantic>=2.7",
|
| 10 |
-
"pydantic-settings>=2.2",
|
| 11 |
-
"pydantic-ai>=0.0.16",
|
| 12 |
-
|
| 13 |
# AI Providers
|
| 14 |
"openai>=1.0.0",
|
| 15 |
"anthropic>=0.18.0",
|
| 16 |
-
|
| 17 |
# HTTP & Parsing
|
| 18 |
-
"httpx>=0.27",
|
| 19 |
-
"beautifulsoup4>=4.12",
|
| 20 |
-
"xmltodict>=0.13",
|
| 21 |
-
|
| 22 |
# UI
|
| 23 |
-
"gradio>=5.0",
|
| 24 |
-
|
| 25 |
# Utils
|
| 26 |
-
"python-dotenv>=1.0",
|
| 27 |
-
"tenacity>=8.2",
|
| 28 |
-
"structlog>=24.1",
|
|
|
|
| 29 |
]
|
| 30 |
|
| 31 |
[project.optional-dependencies]
|
|
|
|
| 7 |
dependencies = [
|
| 8 |
# Core
|
| 9 |
"pydantic>=2.7",
|
| 10 |
+
"pydantic-settings>=2.2", # For BaseSettings (config)
|
| 11 |
+
"pydantic-ai>=0.0.16", # Agent framework
|
|
|
|
| 12 |
# AI Providers
|
| 13 |
"openai>=1.0.0",
|
| 14 |
"anthropic>=0.18.0",
|
|
|
|
| 15 |
# HTTP & Parsing
|
| 16 |
+
"httpx[http2]>=0.27", # Async HTTP client
|
| 17 |
+
"beautifulsoup4>=4.12", # HTML parsing
|
| 18 |
+
"xmltodict>=0.13", # PubMed XML -> dict
|
|
|
|
| 19 |
# UI
|
| 20 |
+
"gradio>=5.0", # Chat interface
|
|
|
|
| 21 |
# Utils
|
| 22 |
+
"python-dotenv>=1.0", # .env loading
|
| 23 |
+
"tenacity>=8.2", # Retry logic
|
| 24 |
+
"structlog>=24.1", # Structured logging
|
| 25 |
+
"requests>=2.32.5",
|
| 26 |
]
|
| 27 |
|
| 28 |
[project.optional-dependencies]
|
src/app.py
CHANGED
|
@@ -8,6 +8,7 @@ import gradio as gr
|
|
| 8 |
|
| 9 |
from src.agent_factory.judges import JudgeHandler, MockJudgeHandler
|
| 10 |
from src.orchestrator_factory import create_orchestrator
|
|
|
|
| 11 |
from src.tools.pubmed import PubMedTool
|
| 12 |
from src.tools.search_handler import SearchHandler
|
| 13 |
from src.utils.models import OrchestratorConfig
|
|
@@ -32,7 +33,7 @@ def configure_orchestrator(use_mock: bool = False, mode: str = "simple") -> Any:
|
|
| 32 |
|
| 33 |
# Create search tools
|
| 34 |
search_handler = SearchHandler(
|
| 35 |
-
tools=[PubMedTool()],
|
| 36 |
timeout=config.search_timeout,
|
| 37 |
)
|
| 38 |
|
|
@@ -160,7 +161,7 @@ def create_demo() -> Any:
|
|
| 160 |
**Note**: This is a research tool and should not be used for medical decisions.
|
| 161 |
Always consult healthcare professionals for medical advice.
|
| 162 |
|
| 163 |
-
Built with 🤖 PydanticAI + 🔬 PubMed
|
| 164 |
""")
|
| 165 |
|
| 166 |
return demo
|
|
|
|
| 8 |
|
| 9 |
from src.agent_factory.judges import JudgeHandler, MockJudgeHandler
|
| 10 |
from src.orchestrator_factory import create_orchestrator
|
| 11 |
+
from src.tools.clinicaltrials import ClinicalTrialsTool
|
| 12 |
from src.tools.pubmed import PubMedTool
|
| 13 |
from src.tools.search_handler import SearchHandler
|
| 14 |
from src.utils.models import OrchestratorConfig
|
|
|
|
| 33 |
|
| 34 |
# Create search tools
|
| 35 |
search_handler = SearchHandler(
|
| 36 |
+
tools=[PubMedTool(), ClinicalTrialsTool()],
|
| 37 |
timeout=config.search_timeout,
|
| 38 |
)
|
| 39 |
|
|
|
|
| 161 |
**Note**: This is a research tool and should not be used for medical decisions.
|
| 162 |
Always consult healthcare professionals for medical advice.
|
| 163 |
|
| 164 |
+
Built with 🤖 PydanticAI + 🔬 PubMed & ClinicalTrials.gov
|
| 165 |
""")
|
| 166 |
|
| 167 |
return demo
|
src/tools/clinicaltrials.py
ADDED
|
@@ -0,0 +1,129 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
"""ClinicalTrials.gov search tool using API v2."""
|
| 2 |
+
|
| 3 |
+
import asyncio
|
| 4 |
+
from typing import Any, ClassVar
|
| 5 |
+
|
| 6 |
+
import requests
|
| 7 |
+
from tenacity import retry, stop_after_attempt, wait_exponential
|
| 8 |
+
|
| 9 |
+
from src.utils.exceptions import SearchError
|
| 10 |
+
from src.utils.models import Citation, Evidence
|
| 11 |
+
|
| 12 |
+
|
| 13 |
+
class ClinicalTrialsTool:
|
| 14 |
+
"""Search tool for ClinicalTrials.gov.
|
| 15 |
+
|
| 16 |
+
Note: Uses `requests` library instead of `httpx` because ClinicalTrials.gov's
|
| 17 |
+
WAF blocks httpx's TLS fingerprint. The `requests` library is not blocked.
|
| 18 |
+
See: https://clinicaltrials.gov/data-api/api
|
| 19 |
+
"""
|
| 20 |
+
|
| 21 |
+
BASE_URL = "https://clinicaltrials.gov/api/v2/studies"
|
| 22 |
+
FIELDS: ClassVar[list[str]] = [
|
| 23 |
+
"NCTId",
|
| 24 |
+
"BriefTitle",
|
| 25 |
+
"Phase",
|
| 26 |
+
"OverallStatus",
|
| 27 |
+
"Condition",
|
| 28 |
+
"InterventionName",
|
| 29 |
+
"StartDate",
|
| 30 |
+
"BriefSummary",
|
| 31 |
+
]
|
| 32 |
+
|
| 33 |
+
@property
|
| 34 |
+
def name(self) -> str:
|
| 35 |
+
return "clinicaltrials"
|
| 36 |
+
|
| 37 |
+
@retry(
|
| 38 |
+
stop=stop_after_attempt(3),
|
| 39 |
+
wait=wait_exponential(multiplier=1, min=1, max=10),
|
| 40 |
+
reraise=True,
|
| 41 |
+
)
|
| 42 |
+
async def search(self, query: str, max_results: int = 10) -> list[Evidence]:
|
| 43 |
+
"""Search ClinicalTrials.gov for studies.
|
| 44 |
+
|
| 45 |
+
Args:
|
| 46 |
+
query: Search query (e.g., "metformin alzheimer")
|
| 47 |
+
max_results: Maximum results to return (max 100)
|
| 48 |
+
|
| 49 |
+
Returns:
|
| 50 |
+
List of Evidence objects from clinical trials
|
| 51 |
+
"""
|
| 52 |
+
params: dict[str, str | int] = {
|
| 53 |
+
"query.term": query,
|
| 54 |
+
"pageSize": min(max_results, 100),
|
| 55 |
+
"fields": "|".join(self.FIELDS),
|
| 56 |
+
}
|
| 57 |
+
|
| 58 |
+
try:
|
| 59 |
+
# Run blocking requests.get in a separate thread for async compatibility
|
| 60 |
+
response = await asyncio.to_thread(
|
| 61 |
+
requests.get,
|
| 62 |
+
self.BASE_URL,
|
| 63 |
+
params=params,
|
| 64 |
+
headers={"User-Agent": "DeepCritical-Research-Agent/1.0"},
|
| 65 |
+
timeout=30,
|
| 66 |
+
)
|
| 67 |
+
response.raise_for_status()
|
| 68 |
+
|
| 69 |
+
data = response.json()
|
| 70 |
+
studies = data.get("studies", [])
|
| 71 |
+
return [self._study_to_evidence(study) for study in studies[:max_results]]
|
| 72 |
+
|
| 73 |
+
except requests.HTTPError as e:
|
| 74 |
+
raise SearchError(f"ClinicalTrials.gov API error: {e}") from e
|
| 75 |
+
except requests.RequestException as e:
|
| 76 |
+
raise SearchError(f"ClinicalTrials.gov request failed: {e}") from e
|
| 77 |
+
|
| 78 |
+
def _study_to_evidence(self, study: dict[str, Any]) -> Evidence:
|
| 79 |
+
"""Convert a clinical trial study to Evidence."""
|
| 80 |
+
# Navigate nested structure
|
| 81 |
+
protocol = study.get("protocolSection", {})
|
| 82 |
+
id_module = protocol.get("identificationModule", {})
|
| 83 |
+
status_module = protocol.get("statusModule", {})
|
| 84 |
+
desc_module = protocol.get("descriptionModule", {})
|
| 85 |
+
design_module = protocol.get("designModule", {})
|
| 86 |
+
conditions_module = protocol.get("conditionsModule", {})
|
| 87 |
+
arms_module = protocol.get("armsInterventionsModule", {})
|
| 88 |
+
|
| 89 |
+
nct_id = id_module.get("nctId", "Unknown")
|
| 90 |
+
title = id_module.get("briefTitle", "Untitled Study")
|
| 91 |
+
status = status_module.get("overallStatus", "Unknown")
|
| 92 |
+
start_date = status_module.get("startDateStruct", {}).get("date", "Unknown")
|
| 93 |
+
|
| 94 |
+
# Get phase (might be a list)
|
| 95 |
+
phases = design_module.get("phases", [])
|
| 96 |
+
phase = phases[0] if phases else "Not Applicable"
|
| 97 |
+
|
| 98 |
+
# Get conditions
|
| 99 |
+
conditions = conditions_module.get("conditions", [])
|
| 100 |
+
conditions_str = ", ".join(conditions[:3]) if conditions else "Unknown"
|
| 101 |
+
|
| 102 |
+
# Get interventions
|
| 103 |
+
interventions = arms_module.get("interventions", [])
|
| 104 |
+
intervention_names = [i.get("name", "") for i in interventions[:3]]
|
| 105 |
+
interventions_str = ", ".join(intervention_names) if intervention_names else "Unknown"
|
| 106 |
+
|
| 107 |
+
# Get summary
|
| 108 |
+
summary = desc_module.get("briefSummary", "No summary available.")
|
| 109 |
+
|
| 110 |
+
# Build content with key trial info
|
| 111 |
+
content = (
|
| 112 |
+
f"{summary[:500]}... "
|
| 113 |
+
f"Trial Phase: {phase}. "
|
| 114 |
+
f"Status: {status}. "
|
| 115 |
+
f"Conditions: {conditions_str}. "
|
| 116 |
+
f"Interventions: {interventions_str}."
|
| 117 |
+
)
|
| 118 |
+
|
| 119 |
+
return Evidence(
|
| 120 |
+
content=content[:2000],
|
| 121 |
+
citation=Citation(
|
| 122 |
+
source="clinicaltrials",
|
| 123 |
+
title=title[:500],
|
| 124 |
+
url=f"https://clinicaltrials.gov/study/{nct_id}",
|
| 125 |
+
date=start_date,
|
| 126 |
+
authors=[], # Trials don't have traditional authors
|
| 127 |
+
),
|
| 128 |
+
relevance=0.85, # Trials are highly relevant for repurposing
|
| 129 |
+
)
|
src/tools/search_handler.py
CHANGED
|
@@ -49,7 +49,7 @@ class SearchHandler:
|
|
| 49 |
|
| 50 |
# Process results
|
| 51 |
all_evidence: list[Evidence] = []
|
| 52 |
-
sources_searched: list[Literal["pubmed"]] = []
|
| 53 |
errors: list[str] = []
|
| 54 |
|
| 55 |
for tool, result in zip(self.tools, results, strict=True):
|
|
@@ -62,7 +62,7 @@ class SearchHandler:
|
|
| 62 |
all_evidence.extend(success_result)
|
| 63 |
|
| 64 |
# Cast tool.name to the expected Literal
|
| 65 |
-
tool_name = cast(Literal["pubmed"], tool.name)
|
| 66 |
sources_searched.append(tool_name)
|
| 67 |
logger.info("Search tool succeeded", tool=tool.name, count=len(success_result))
|
| 68 |
|
|
|
|
| 49 |
|
| 50 |
# Process results
|
| 51 |
all_evidence: list[Evidence] = []
|
| 52 |
+
sources_searched: list[Literal["pubmed", "clinicaltrials"]] = []
|
| 53 |
errors: list[str] = []
|
| 54 |
|
| 55 |
for tool, result in zip(self.tools, results, strict=True):
|
|
|
|
| 62 |
all_evidence.extend(success_result)
|
| 63 |
|
| 64 |
# Cast tool.name to the expected Literal
|
| 65 |
+
tool_name = cast(Literal["pubmed", "clinicaltrials"], tool.name)
|
| 66 |
sources_searched.append(tool_name)
|
| 67 |
logger.info("Search tool succeeded", tool=tool.name, count=len(success_result))
|
| 68 |
|
src/utils/models.py
CHANGED
|
@@ -9,7 +9,7 @@ from pydantic import BaseModel, Field
|
|
| 9 |
class Citation(BaseModel):
|
| 10 |
"""A citation to a source document."""
|
| 11 |
|
| 12 |
-
source: Literal["pubmed"] = Field(description="Where this came from")
|
| 13 |
title: str = Field(min_length=1, max_length=500)
|
| 14 |
url: str = Field(description="URL to the source")
|
| 15 |
date: str = Field(description="Publication date (YYYY-MM-DD or 'Unknown')")
|
|
@@ -41,7 +41,7 @@ class SearchResult(BaseModel):
|
|
| 41 |
|
| 42 |
query: str
|
| 43 |
evidence: list[Evidence]
|
| 44 |
-
sources_searched: list[Literal["pubmed"]]
|
| 45 |
total_found: int
|
| 46 |
errors: list[str] = Field(default_factory=list)
|
| 47 |
|
|
|
|
| 9 |
class Citation(BaseModel):
|
| 10 |
"""A citation to a source document."""
|
| 11 |
|
| 12 |
+
source: Literal["pubmed", "clinicaltrials"] = Field(description="Where this came from")
|
| 13 |
title: str = Field(min_length=1, max_length=500)
|
| 14 |
url: str = Field(description="URL to the source")
|
| 15 |
date: str = Field(description="Publication date (YYYY-MM-DD or 'Unknown')")
|
|
|
|
| 41 |
|
| 42 |
query: str
|
| 43 |
evidence: list[Evidence]
|
| 44 |
+
sources_searched: list[Literal["pubmed", "clinicaltrials"]]
|
| 45 |
total_found: int
|
| 46 |
errors: list[str] = Field(default_factory=list)
|
| 47 |
|
tests/unit/tools/test_clinicaltrials.py
ADDED
|
@@ -0,0 +1,136 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
| 1 |
+
"""Unit tests for ClinicalTrials.gov tool."""
|
| 2 |
+
|
| 3 |
+
from unittest.mock import MagicMock, patch
|
| 4 |
+
|
| 5 |
+
import pytest
|
| 6 |
+
import requests
|
| 7 |
+
|
| 8 |
+
from src.tools.clinicaltrials import ClinicalTrialsTool
|
| 9 |
+
from src.utils.exceptions import SearchError
|
| 10 |
+
from src.utils.models import Evidence
|
| 11 |
+
|
| 12 |
+
|
| 13 |
+
@pytest.fixture
|
| 14 |
+
def mock_clinicaltrials_response() -> dict:
|
| 15 |
+
"""Mock ClinicalTrials.gov API response."""
|
| 16 |
+
return {
|
| 17 |
+
"studies": [
|
| 18 |
+
{
|
| 19 |
+
"protocolSection": {
|
| 20 |
+
"identificationModule": {
|
| 21 |
+
"nctId": "NCT04098666",
|
| 22 |
+
"briefTitle": "Metformin in Alzheimer's Dementia Prevention",
|
| 23 |
+
},
|
| 24 |
+
"statusModule": {
|
| 25 |
+
"overallStatus": "Recruiting",
|
| 26 |
+
"startDateStruct": {"date": "2020-01-15"},
|
| 27 |
+
},
|
| 28 |
+
"descriptionModule": {
|
| 29 |
+
"briefSummary": "This study evaluates metformin for Alzheimer's prevention."
|
| 30 |
+
},
|
| 31 |
+
"designModule": {"phases": ["PHASE2"]},
|
| 32 |
+
"conditionsModule": {"conditions": ["Alzheimer Disease", "Dementia"]},
|
| 33 |
+
"armsInterventionsModule": {
|
| 34 |
+
"interventions": [{"name": "Metformin", "type": "Drug"}]
|
| 35 |
+
},
|
| 36 |
+
}
|
| 37 |
+
}
|
| 38 |
+
]
|
| 39 |
+
}
|
| 40 |
+
|
| 41 |
+
|
| 42 |
+
class TestClinicalTrialsTool:
|
| 43 |
+
"""Tests for ClinicalTrialsTool."""
|
| 44 |
+
|
| 45 |
+
def test_tool_name(self) -> None:
|
| 46 |
+
"""Tool should have correct name."""
|
| 47 |
+
tool = ClinicalTrialsTool()
|
| 48 |
+
assert tool.name == "clinicaltrials"
|
| 49 |
+
|
| 50 |
+
@pytest.mark.asyncio
|
| 51 |
+
async def test_search_returns_evidence(self, mock_clinicaltrials_response: dict) -> None:
|
| 52 |
+
"""Search should return Evidence objects."""
|
| 53 |
+
with patch("src.tools.clinicaltrials.requests.get") as mock_get:
|
| 54 |
+
mock_response = MagicMock()
|
| 55 |
+
mock_response.json.return_value = mock_clinicaltrials_response
|
| 56 |
+
mock_response.raise_for_status = MagicMock()
|
| 57 |
+
mock_get.return_value = mock_response
|
| 58 |
+
|
| 59 |
+
tool = ClinicalTrialsTool()
|
| 60 |
+
results = await tool.search("metformin alzheimer", max_results=5)
|
| 61 |
+
|
| 62 |
+
assert len(results) == 1
|
| 63 |
+
assert isinstance(results[0], Evidence)
|
| 64 |
+
assert results[0].citation.source == "clinicaltrials"
|
| 65 |
+
assert "NCT04098666" in results[0].citation.url
|
| 66 |
+
assert "Metformin" in results[0].citation.title
|
| 67 |
+
|
| 68 |
+
@pytest.mark.asyncio
|
| 69 |
+
async def test_search_extracts_phase(self, mock_clinicaltrials_response: dict) -> None:
|
| 70 |
+
"""Search should extract trial phase."""
|
| 71 |
+
with patch("src.tools.clinicaltrials.requests.get") as mock_get:
|
| 72 |
+
mock_response = MagicMock()
|
| 73 |
+
mock_response.json.return_value = mock_clinicaltrials_response
|
| 74 |
+
mock_response.raise_for_status = MagicMock()
|
| 75 |
+
mock_get.return_value = mock_response
|
| 76 |
+
|
| 77 |
+
tool = ClinicalTrialsTool()
|
| 78 |
+
results = await tool.search("metformin alzheimer")
|
| 79 |
+
|
| 80 |
+
assert "PHASE2" in results[0].content
|
| 81 |
+
|
| 82 |
+
@pytest.mark.asyncio
|
| 83 |
+
async def test_search_extracts_status(self, mock_clinicaltrials_response: dict) -> None:
|
| 84 |
+
"""Search should extract trial status."""
|
| 85 |
+
with patch("src.tools.clinicaltrials.requests.get") as mock_get:
|
| 86 |
+
mock_response = MagicMock()
|
| 87 |
+
mock_response.json.return_value = mock_clinicaltrials_response
|
| 88 |
+
mock_response.raise_for_status = MagicMock()
|
| 89 |
+
mock_get.return_value = mock_response
|
| 90 |
+
|
| 91 |
+
tool = ClinicalTrialsTool()
|
| 92 |
+
results = await tool.search("metformin alzheimer")
|
| 93 |
+
|
| 94 |
+
assert "Recruiting" in results[0].content
|
| 95 |
+
|
| 96 |
+
@pytest.mark.asyncio
|
| 97 |
+
async def test_search_empty_results(self) -> None:
|
| 98 |
+
"""Search should handle empty results gracefully."""
|
| 99 |
+
with patch("src.tools.clinicaltrials.requests.get") as mock_get:
|
| 100 |
+
mock_response = MagicMock()
|
| 101 |
+
mock_response.json.return_value = {"studies": []}
|
| 102 |
+
mock_response.raise_for_status = MagicMock()
|
| 103 |
+
mock_get.return_value = mock_response
|
| 104 |
+
|
| 105 |
+
tool = ClinicalTrialsTool()
|
| 106 |
+
results = await tool.search("nonexistent query xyz")
|
| 107 |
+
|
| 108 |
+
assert results == []
|
| 109 |
+
|
| 110 |
+
@pytest.mark.asyncio
|
| 111 |
+
async def test_search_api_error(self) -> None:
|
| 112 |
+
"""Search should raise SearchError on API failure."""
|
| 113 |
+
with patch("src.tools.clinicaltrials.requests.get") as mock_get:
|
| 114 |
+
mock_response = MagicMock()
|
| 115 |
+
mock_response.raise_for_status.side_effect = requests.HTTPError("500 Server Error")
|
| 116 |
+
mock_get.return_value = mock_response
|
| 117 |
+
|
| 118 |
+
tool = ClinicalTrialsTool()
|
| 119 |
+
|
| 120 |
+
with pytest.raises(SearchError):
|
| 121 |
+
await tool.search("metformin alzheimer")
|
| 122 |
+
|
| 123 |
+
|
| 124 |
+
class TestClinicalTrialsIntegration:
|
| 125 |
+
"""Integration tests (marked for separate run)."""
|
| 126 |
+
|
| 127 |
+
@pytest.mark.integration
|
| 128 |
+
@pytest.mark.asyncio
|
| 129 |
+
async def test_real_api_call(self) -> None:
|
| 130 |
+
"""Test actual API call (requires network)."""
|
| 131 |
+
tool = ClinicalTrialsTool()
|
| 132 |
+
results = await tool.search("metformin diabetes", max_results=3)
|
| 133 |
+
|
| 134 |
+
assert len(results) > 0
|
| 135 |
+
assert all(isinstance(r, Evidence) for r in results)
|
| 136 |
+
assert all(r.citation.source == "clinicaltrials" for r in results)
|
uv.lock
CHANGED
|
@@ -982,12 +982,13 @@ dependencies = [
|
|
| 982 |
{ name = "anthropic" },
|
| 983 |
{ name = "beautifulsoup4" },
|
| 984 |
{ name = "gradio" },
|
| 985 |
-
{ name = "httpx" },
|
| 986 |
{ name = "openai" },
|
| 987 |
{ name = "pydantic" },
|
| 988 |
{ name = "pydantic-ai" },
|
| 989 |
{ name = "pydantic-settings" },
|
| 990 |
{ name = "python-dotenv" },
|
|
|
|
| 991 |
{ name = "structlog" },
|
| 992 |
{ name = "tenacity" },
|
| 993 |
{ name = "xmltodict" },
|
|
@@ -1020,7 +1021,7 @@ requires-dist = [
|
|
| 1020 |
{ name = "beautifulsoup4", specifier = ">=4.12" },
|
| 1021 |
{ name = "chromadb", marker = "extra == 'embeddings'", specifier = ">=0.4.0" },
|
| 1022 |
{ name = "gradio", specifier = ">=5.0" },
|
| 1023 |
-
{ name = "httpx", specifier = ">=0.27" },
|
| 1024 |
{ name = "mypy", marker = "extra == 'dev'", specifier = ">=1.10" },
|
| 1025 |
{ name = "openai", specifier = ">=1.0.0" },
|
| 1026 |
{ name = "pre-commit", marker = "extra == 'dev'", specifier = ">=3.7" },
|
|
@@ -1033,6 +1034,7 @@ requires-dist = [
|
|
| 1033 |
{ name = "pytest-mock", marker = "extra == 'dev'", specifier = ">=3.12" },
|
| 1034 |
{ name = "pytest-sugar", marker = "extra == 'dev'", specifier = ">=1.0" },
|
| 1035 |
{ name = "python-dotenv", specifier = ">=1.0" },
|
|
|
|
| 1036 |
{ name = "respx", marker = "extra == 'dev'", specifier = ">=0.21" },
|
| 1037 |
{ name = "ruff", marker = "extra == 'dev'", specifier = ">=0.4.0" },
|
| 1038 |
{ name = "sentence-transformers", marker = "extra == 'embeddings'", specifier = ">=2.2.0" },
|
|
@@ -1582,6 +1584,19 @@ wheels = [
|
|
| 1582 |
{ url = "https://files.pythonhosted.org/packages/04/4b/29cac41a4d98d144bf5f6d33995617b185d14b22401f75ca86f384e87ff1/h11-0.16.0-py3-none-any.whl", hash = "sha256:63cf8bbe7522de3bf65932fda1d9c2772064ffb3dae62d55932da54b31cb6c86", size = 37515 },
|
| 1583 |
]
|
| 1584 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1585 |
[[package]]
|
| 1586 |
name = "hf-xet"
|
| 1587 |
version = "1.2.0"
|
|
@@ -1611,6 +1626,15 @@ wheels = [
|
|
| 1611 |
{ url = "https://files.pythonhosted.org/packages/cb/44/870d44b30e1dcfb6a65932e3e1506c103a8a5aea9103c337e7a53180322c/hf_xet-1.2.0-cp37-abi3-win_amd64.whl", hash = "sha256:e6584a52253f72c9f52f9e549d5895ca7a471608495c4ecaa6cc73dba2b24d69", size = 2905735 },
|
| 1612 |
]
|
| 1613 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1614 |
[[package]]
|
| 1615 |
name = "httpcore"
|
| 1616 |
version = "1.0.9"
|
|
@@ -1675,6 +1699,11 @@ wheels = [
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|
| 1675 |
{ url = "https://files.pythonhosted.org/packages/2a/39/e50c7c3a983047577ee07d2a9e53faf5a69493943ec3f6a384bdc792deb2/httpx-0.28.1-py3-none-any.whl", hash = "sha256:d909fcccc110f8c7faf814ca82a9a4d816bc5a6dbfea25d6591d6985b8ba59ad", size = 73517 },
|
| 1676 |
]
|
| 1677 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1678 |
[[package]]
|
| 1679 |
name = "httpx-sse"
|
| 1680 |
version = "0.4.0"
|
|
@@ -1720,6 +1749,15 @@ wheels = [
|
|
| 1720 |
{ url = "https://files.pythonhosted.org/packages/f0/0f/310fb31e39e2d734ccaa2c0fb981ee41f7bd5056ce9bc29b2248bd569169/humanfriendly-10.0-py2.py3-none-any.whl", hash = "sha256:1697e1a8a8f550fd43c2865cd84542fc175a61dcb779b6fee18cf6b6ccba1477", size = 86794 },
|
| 1721 |
]
|
| 1722 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1723 |
[[package]]
|
| 1724 |
name = "identify"
|
| 1725 |
version = "2.6.15"
|
|
|
|
| 982 |
{ name = "anthropic" },
|
| 983 |
{ name = "beautifulsoup4" },
|
| 984 |
{ name = "gradio" },
|
| 985 |
+
{ name = "httpx", extra = ["http2"] },
|
| 986 |
{ name = "openai" },
|
| 987 |
{ name = "pydantic" },
|
| 988 |
{ name = "pydantic-ai" },
|
| 989 |
{ name = "pydantic-settings" },
|
| 990 |
{ name = "python-dotenv" },
|
| 991 |
+
{ name = "requests" },
|
| 992 |
{ name = "structlog" },
|
| 993 |
{ name = "tenacity" },
|
| 994 |
{ name = "xmltodict" },
|
|
|
|
| 1021 |
{ name = "beautifulsoup4", specifier = ">=4.12" },
|
| 1022 |
{ name = "chromadb", marker = "extra == 'embeddings'", specifier = ">=0.4.0" },
|
| 1023 |
{ name = "gradio", specifier = ">=5.0" },
|
| 1024 |
+
{ name = "httpx", extras = ["http2"], specifier = ">=0.27" },
|
| 1025 |
{ name = "mypy", marker = "extra == 'dev'", specifier = ">=1.10" },
|
| 1026 |
{ name = "openai", specifier = ">=1.0.0" },
|
| 1027 |
{ name = "pre-commit", marker = "extra == 'dev'", specifier = ">=3.7" },
|
|
|
|
| 1034 |
{ name = "pytest-mock", marker = "extra == 'dev'", specifier = ">=3.12" },
|
| 1035 |
{ name = "pytest-sugar", marker = "extra == 'dev'", specifier = ">=1.0" },
|
| 1036 |
{ name = "python-dotenv", specifier = ">=1.0" },
|
| 1037 |
+
{ name = "requests", specifier = ">=2.32.5" },
|
| 1038 |
{ name = "respx", marker = "extra == 'dev'", specifier = ">=0.21" },
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| 1039 |
{ name = "ruff", marker = "extra == 'dev'", specifier = ">=0.4.0" },
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| 1040 |
{ name = "sentence-transformers", marker = "extra == 'embeddings'", specifier = ">=2.2.0" },
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|
|
|
| 1584 |
{ url = "https://files.pythonhosted.org/packages/04/4b/29cac41a4d98d144bf5f6d33995617b185d14b22401f75ca86f384e87ff1/h11-0.16.0-py3-none-any.whl", hash = "sha256:63cf8bbe7522de3bf65932fda1d9c2772064ffb3dae62d55932da54b31cb6c86", size = 37515 },
|
| 1585 |
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|
| 1586 |
|
| 1587 |
+
[[package]]
|
| 1588 |
+
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|
| 1589 |
+
version = "4.3.0"
|
| 1590 |
+
source = { registry = "https://pypi.org/simple" }
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| 1591 |
+
dependencies = [
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| 1592 |
+
{ name = "hpack" },
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| 1593 |
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{ name = "hyperframe" },
|
| 1594 |
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]
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| 1595 |
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sdist = { url = "https://files.pythonhosted.org/packages/1d/17/afa56379f94ad0fe8defd37d6eb3f89a25404ffc71d4d848893d270325fc/h2-4.3.0.tar.gz", hash = "sha256:6c59efe4323fa18b47a632221a1888bd7fde6249819beda254aeca909f221bf1", size = 2152026 }
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| 1596 |
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wheels = [
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| 1597 |
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|
| 1598 |
+
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|
| 1599 |
+
|
| 1600 |
[[package]]
|
| 1601 |
name = "hf-xet"
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| 1602 |
version = "1.2.0"
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|
|
|
| 1626 |
{ url = "https://files.pythonhosted.org/packages/cb/44/870d44b30e1dcfb6a65932e3e1506c103a8a5aea9103c337e7a53180322c/hf_xet-1.2.0-cp37-abi3-win_amd64.whl", hash = "sha256:e6584a52253f72c9f52f9e549d5895ca7a471608495c4ecaa6cc73dba2b24d69", size = 2905735 },
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| 1627 |
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|
| 1628 |
|
| 1629 |
+
[[package]]
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| 1630 |
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name = "hpack"
|
| 1631 |
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version = "4.1.0"
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| 1632 |
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source = { registry = "https://pypi.org/simple" }
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| 1633 |
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| 1634 |
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wheels = [
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| 1635 |
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| 1636 |
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| 1637 |
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|
| 1638 |
[[package]]
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| 1639 |
name = "httpcore"
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| 1640 |
version = "1.0.9"
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|
|
|
| 1699 |
{ url = "https://files.pythonhosted.org/packages/2a/39/e50c7c3a983047577ee07d2a9e53faf5a69493943ec3f6a384bdc792deb2/httpx-0.28.1-py3-none-any.whl", hash = "sha256:d909fcccc110f8c7faf814ca82a9a4d816bc5a6dbfea25d6591d6985b8ba59ad", size = 73517 },
|
| 1700 |
]
|
| 1701 |
|
| 1702 |
+
[package.optional-dependencies]
|
| 1703 |
+
http2 = [
|
| 1704 |
+
{ name = "h2" },
|
| 1705 |
+
]
|
| 1706 |
+
|
| 1707 |
[[package]]
|
| 1708 |
name = "httpx-sse"
|
| 1709 |
version = "0.4.0"
|
|
|
|
| 1749 |
{ url = "https://files.pythonhosted.org/packages/f0/0f/310fb31e39e2d734ccaa2c0fb981ee41f7bd5056ce9bc29b2248bd569169/humanfriendly-10.0-py2.py3-none-any.whl", hash = "sha256:1697e1a8a8f550fd43c2865cd84542fc175a61dcb779b6fee18cf6b6ccba1477", size = 86794 },
|
| 1750 |
]
|
| 1751 |
|
| 1752 |
+
[[package]]
|
| 1753 |
+
name = "hyperframe"
|
| 1754 |
+
version = "6.1.0"
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| 1755 |
+
source = { registry = "https://pypi.org/simple" }
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| 1756 |
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sdist = { url = "https://files.pythonhosted.org/packages/02/e7/94f8232d4a74cc99514c13a9f995811485a6903d48e5d952771ef6322e30/hyperframe-6.1.0.tar.gz", hash = "sha256:f630908a00854a7adeabd6382b43923a4c4cd4b821fcb527e6ab9e15382a3b08", size = 26566 }
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| 1757 |
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wheels = [
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| 1758 |
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{ url = "https://files.pythonhosted.org/packages/48/30/47d0bf6072f7252e6521f3447ccfa40b421b6824517f82854703d0f5a98b/hyperframe-6.1.0-py3-none-any.whl", hash = "sha256:b03380493a519fce58ea5af42e4a42317bf9bd425596f7a0835ffce80f1a42e5", size = 13007 },
|
| 1759 |
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]
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| 1760 |
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|
| 1761 |
[[package]]
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| 1762 |
name = "identify"
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| 1763 |
version = "2.6.15"
|