trialdesignbench 0.1.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- trialdesignbench-0.1.0/.gitignore +13 -0
- trialdesignbench-0.1.0/.python-version +1 -0
- trialdesignbench-0.1.0/CHANGELOG.md +7 -0
- trialdesignbench-0.1.0/LICENSE +20 -0
- trialdesignbench-0.1.0/PKG-INFO +27 -0
- trialdesignbench-0.1.0/README.md +1 -0
- trialdesignbench-0.1.0/pyproject.toml +39 -0
- trialdesignbench-0.1.0/src/trialdesignbench/__init__.py +30 -0
- trialdesignbench-0.1.0/src/trialdesignbench/cases.py +92 -0
- trialdesignbench-0.1.0/tests/test_cases.py +65 -0
- trialdesignbench-0.1.0/uv.lock +574 -0
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3.14.4
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Copyright (c) 2026, trialdesignbench authors
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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Metadata-Version: 2.4
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Name: trialdesignbench
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Version: 0.1.0
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Summary: Evaluate whether AI agents can create efficient, reproducible, and safe clinical trial design
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Author-email: Nan Xiao <me@nanx.me>
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License-File: LICENSE
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Classifier: Intended Audience :: Developers
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Classifier: Intended Audience :: Education
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Classifier: Intended Audience :: Science/Research
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Operating System :: OS Independent
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Programming Language :: Python :: 3.13
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Classifier: Programming Language :: Python :: 3.14
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Classifier: Topic :: Scientific/Engineering
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Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
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Classifier: Topic :: Scientific/Engineering :: Mathematics
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Classifier: Typing :: Typed
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Requires-Python: >=3.10
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Requires-Dist: pydantic>=2.13.4
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Requires-Dist: tqdm>=4.67.3
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Description-Content-Type: text/markdown
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# trialdesignbench
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# trialdesignbench
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[project]
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name = "trialdesignbench"
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version = "0.1.0"
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description = "Evaluate whether AI agents can create efficient, reproducible, and safe clinical trial design"
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authors = [{ name = "Nan Xiao", email = "me@nanx.me" }]
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dependencies = ["pydantic>=2.13.4", "tqdm>=4.67.3"]
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readme = "README.md"
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classifiers = [
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"Intended Audience :: Developers",
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"Intended Audience :: Education",
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"Intended Audience :: Science/Research",
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"Topic :: Scientific/Engineering",
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"Topic :: Scientific/Engineering :: Mathematics",
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"Topic :: Scientific/Engineering :: Artificial Intelligence",
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"License :: OSI Approved :: MIT License",
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"Operating System :: OS Independent",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Programming Language :: Python :: 3.13",
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"Programming Language :: Python :: 3.14",
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"Typing :: Typed",
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]
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requires-python = ">= 3.10"
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[build-system]
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requires = ["hatchling"]
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build-backend = "hatchling.build"
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[dependency-groups]
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dev = ["isort>=8.0.1", "mypy>=2.0.0", "pytest>=9.0.3", "ruff>=0.15.12"]
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"""TrialDesignBench package.
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TrialDesignBench is intended to provide benchmark tooling for evaluating AI
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agents that reproduce clinical trial design characteristics from protocols and
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statistical analysis plans.
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"""
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from importlib.metadata import PackageNotFoundError, version
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from trialdesignbench.cases import (
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DocumentKind,
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ExpectedDesign,
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SourceDocument,
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TrialDesignCase,
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TrialPhase,
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)
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try:
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__version__ = version("trialdesignbench")
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except PackageNotFoundError:
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__version__ = "0.0.0"
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__all__ = [
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"DocumentKind",
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"ExpectedDesign",
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"SourceDocument",
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"TrialDesignCase",
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"TrialPhase",
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"__version__",
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]
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"""Core data structures for describing TrialDesignBench cases."""
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from __future__ import annotations
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from enum import Enum
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from pathlib import Path
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from pydantic import BaseModel, ConfigDict, Field, HttpUrl, model_validator
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class DocumentKind(str, Enum):
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"""Supported source document categories for a trial design case."""
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PROTOCOL = "protocol"
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SAP = "statistical_analysis_plan"
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PUBLICATION = "publication"
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REGISTRY = "registry"
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class TrialPhase(str, Enum):
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"""Clinical trial phases commonly represented in the benchmark."""
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PHASE_1 = "phase_1"
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PHASE_2 = "phase_2"
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PHASE_3 = "phase_3"
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PHASE_4 = "phase_4"
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class SourceDocument(BaseModel):
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"""A source document used by an agent to reproduce a trial design."""
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model_config = ConfigDict(frozen=True)
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kind: DocumentKind
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path: Path | None = None
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url: HttpUrl | None = None
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text: str | None = None
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@model_validator(mode="after")
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def require_source(self) -> SourceDocument:
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"""Require at least one way to access the document."""
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if self.path is None and self.url is None and not self.text:
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msg = "at least one of path, url, or text must be provided"
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raise ValueError(msg)
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return self
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class ExpectedDesign(BaseModel):
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"""Objective design characteristics used for benchmark scoring."""
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model_config = ConfigDict(frozen=True)
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primary_endpoint: str | None = None
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statistical_method: str | None = None
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target_power: float | None = Field(default=None, ge=0.0, le=1.0)
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alpha: float | None = Field(default=None, ge=0.0, le=1.0)
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sample_size: int | None = Field(default=None, ge=1)
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class TrialDesignCase(BaseModel):
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"""A single benchmark case for trial design reproduction."""
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model_config = ConfigDict(frozen=True)
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case_id: str
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title: str
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therapeutic_area: str
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design_type: str
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phase: TrialPhase | None = None
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documents: tuple[SourceDocument, ...]
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expected_design: ExpectedDesign = Field(default_factory=ExpectedDesign)
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@model_validator(mode="after")
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def require_documents(self) -> TrialDesignCase:
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"""Require at least one protocol or statistical analysis plan."""
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kinds = {document.kind for document in self.documents}
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if not ({DocumentKind.PROTOCOL, DocumentKind.SAP} & kinds):
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msg = "case must include a protocol or statistical analysis plan"
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raise ValueError(msg)
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return self
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def prompt(self) -> str:
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"""Create a concise agent prompt for the benchmark case."""
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parts = [
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f"Reproduce the clinical trial design for: {self.title}.",
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f"Therapeutic area: {self.therapeutic_area}.",
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f"Design type: {self.design_type}.",
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"Produce executable R code and a short reproduction report.",
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]
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if self.phase is not None:
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parts.insert(2, f"Trial phase: {self.phase.value}.")
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return " ".join(parts)
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import pytest
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from pydantic import ValidationError
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from trialdesignbench import (
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DocumentKind,
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ExpectedDesign,
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SourceDocument,
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TrialDesignCase,
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TrialPhase,
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)
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def test_trial_design_case_builds_prompt_with_phase() -> None:
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document = SourceDocument(kind=DocumentKind.PROTOCOL, text="protocol text")
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case = TrialDesignCase(
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case_id="tdb-001",
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title="Example Oncology Trial",
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therapeutic_area="Oncology",
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design_type="Group sequential design",
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phase=TrialPhase.PHASE_3,
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documents=(document,),
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expected_design=ExpectedDesign(
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primary_endpoint="Overall survival",
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statistical_method="Log-rank test",
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target_power=0.9,
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alpha=0.025,
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sample_size=420,
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),
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)
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assert case.documents == (document,)
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assert case.expected_design.sample_size == 420
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assert (
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case.prompt()
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== "Reproduce the clinical trial design for: Example Oncology Trial. "
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"Therapeutic area: Oncology. Trial phase: phase_3. "
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"Design type: Group sequential design. Produce executable R code and "
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"a short reproduction report."
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)
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def test_source_document_requires_content() -> None:
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with pytest.raises(ValidationError, match="at least one of path, url, or text"):
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SourceDocument(kind=DocumentKind.SAP)
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def test_trial_design_case_requires_protocol_or_sap() -> None:
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publication = SourceDocument(kind=DocumentKind.PUBLICATION, text="publication")
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with pytest.raises(ValidationError, match="protocol or statistical analysis plan"):
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TrialDesignCase(
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case_id="tdb-002",
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title="Publication Only Trial",
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therapeutic_area="Cardiovascular",
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design_type="Fixed design",
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documents=(publication,),
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)
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def test_expected_design_validates_numeric_bounds() -> None:
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with pytest.raises(ValidationError, match="less than or equal to 1"):
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ExpectedDesign(target_power=1.1)
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with pytest.raises(ValidationError, match="greater than or equal to 1"):
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ExpectedDesign(sample_size=0)
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version = 1
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revision = 3
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requires-python = ">=3.10"
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resolution-markers = [
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"python_full_version >= '3.15'",
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"python_full_version < '3.15'",
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]
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[[package]]
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name = "annotated-types"
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version = "0.7.0"
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source = { registry = "https://pypi.org/simple" }
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sdist = { url = "https://files.pythonhosted.org/packages/ee/67/531ea369ba64dcff5ec9c3402f9f51bf748cec26dde048a2f973a4eea7f5/annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89", size = 16081, upload-time = "2024-05-20T21:33:25.928Z" }
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wheels = [
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{ url = "https://files.pythonhosted.org/packages/78/b6/6307fbef88d9b5ee7421e68d78a9f162e0da4900bc5f5793f6d3d0e34fb8/annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53", size = 13643, upload-time = "2024-05-20T21:33:24.1Z" },
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]
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[[package]]
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name = "ast-serialize"
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version = "0.3.0"
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source = { registry = "https://pypi.org/simple" }
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sdist = { url = "https://files.pythonhosted.org/packages/a9/9d/912fefab0e30aee6a3af8a62bbea4a81b29afa4ba2c973d31170620a26de/ast_serialize-0.3.0.tar.gz", hash = "sha256:1bc3ca09a63a021376527c4e938deedd11d11d675ce850e6f9c7487f5889992b", size = 60689, upload-time = "2026-04-30T23:24:48.104Z" }
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wheels = [
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