feat: implement 5 Pydantic v2 data models with 37 TDD tests
Browse files- PatientProfile with 10 sub-models + has_minimum_prescreen_data()
- SearchAnchors with GeographyFilter, TrialFilters, relaxation_order
- TrialCandidate with TrialLocation, AgeRange, EligibilityText
- EligibilityLedger with CriterionAssessment, traffic_light, gap analysis
- SearchLog with SearchStep, RefinementAction, transparency_summary
All 37 tests pass. Ruff clean.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- trialpath/models/__init__.py +72 -0
- trialpath/models/__pycache__/__init__.cpython-313.pyc +0 -0
- trialpath/models/__pycache__/eligibility_ledger.cpython-313.pyc +0 -0
- trialpath/models/__pycache__/patient_profile.cpython-313.pyc +0 -0
- trialpath/models/__pycache__/search_anchors.cpython-313.pyc +0 -0
- trialpath/models/__pycache__/search_log.cpython-313.pyc +0 -0
- trialpath/models/__pycache__/trial_candidate.cpython-313.pyc +0 -0
- trialpath/models/eligibility_ledger.py +89 -0
- trialpath/models/patient_profile.py +101 -0
- trialpath/models/search_anchors.py +33 -0
- trialpath/models/search_log.py +74 -0
- trialpath/models/trial_candidate.py +33 -0
- trialpath/tests/test_models.py +616 -0
trialpath/models/__init__.py
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"""TrialPath data models -- Pydantic v2 data contracts."""
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from trialpath.models.eligibility_ledger import (
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CriterionAssessment,
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CriterionDecision,
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EligibilityLedger,
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GapItem,
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OverallAssessment,
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TemporalCheck,
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TrialEvidencePointer,
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)
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from trialpath.models.patient_profile import (
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Biomarker,
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Comorbidity,
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Demographics,
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Diagnosis,
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EvidencePointer,
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ImagingSummary,
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LabResult,
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PatientProfile,
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PerformanceStatus,
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SourceDocument,
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Treatment,
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UnknownField,
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)
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from trialpath.models.search_anchors import (
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GeographyFilter,
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SearchAnchors,
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TrialFilters,
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)
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from trialpath.models.search_log import (
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RefinementAction,
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SearchLog,
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SearchStep,
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)
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from trialpath.models.trial_candidate import (
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AgeRange,
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EligibilityText,
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TrialCandidate,
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TrialLocation,
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)
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__all__ = [
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"AgeRange",
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"Biomarker",
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"Comorbidity",
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"CriterionAssessment",
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"CriterionDecision",
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"Demographics",
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"Diagnosis",
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"EligibilityLedger",
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"EligibilityText",
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"EvidencePointer",
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"GapItem",
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"GeographyFilter",
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"ImagingSummary",
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"LabResult",
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"OverallAssessment",
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"PatientProfile",
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"PerformanceStatus",
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"RefinementAction",
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"SearchAnchors",
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"SearchLog",
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"SearchStep",
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"SourceDocument",
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"TemporalCheck",
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"Treatment",
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"TrialCandidate",
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"TrialEvidencePointer",
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"TrialFilters",
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"TrialLocation",
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"UnknownField",
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]
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trialpath/models/__pycache__/__init__.cpython-313.pyc
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Binary file (1.39 kB). View file
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trialpath/models/__pycache__/eligibility_ledger.cpython-313.pyc
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Binary file (6.11 kB). View file
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trialpath/models/__pycache__/patient_profile.cpython-313.pyc
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Binary file (6.9 kB). View file
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trialpath/models/__pycache__/search_anchors.cpython-313.pyc
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Binary file (2.16 kB). View file
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trialpath/models/__pycache__/search_log.cpython-313.pyc
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Binary file (4 kB). View file
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trialpath/models/__pycache__/trial_candidate.cpython-313.pyc
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Binary file (2.06 kB). View file
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trialpath/models/eligibility_ledger.py
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"""EligibilityLedger v1 -- Per-trial criterion-level eligibility assessment."""
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from datetime import date
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from enum import Enum
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from typing import Optional
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from pydantic import BaseModel, Field
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from trialpath.models.patient_profile import EvidencePointer
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class CriterionDecision(str, Enum):
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MET = "met"
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NOT_MET = "not_met"
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UNKNOWN = "unknown"
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class OverallAssessment(str, Enum):
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LIKELY_ELIGIBLE = "likely_eligible"
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LIKELY_INELIGIBLE = "likely_ineligible"
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UNCERTAIN = "uncertain"
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class TrialEvidencePointer(BaseModel):
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field: str = Field(description="e.g. 'eligibility_text.inclusion'")
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offset_start: int
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offset_end: int
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class TemporalCheck(BaseModel):
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"""Validates whether patient evidence falls within a required time window."""
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required_window_days: Optional[int] = Field(
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None, description="e.g. 14 for 'within 14 days'"
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)
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reference_date: Optional[date] = Field(
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None, description="Date of the patient evidence"
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)
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evaluation_date: Optional[date] = Field(default_factory=date.today)
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is_within_window: Optional[bool] = None
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@property
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| 41 |
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def days_elapsed(self) -> Optional[int]:
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| 42 |
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if self.reference_date and self.evaluation_date:
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return (self.evaluation_date - self.reference_date).days
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return None
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class CriterionAssessment(BaseModel):
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| 48 |
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criterion_id: str = Field(description="e.g. 'inc_1', 'exc_3'")
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type: str = Field(description="'inclusion' or 'exclusion'")
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text: str = Field(description="Original criterion text from trial")
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decision: CriterionDecision
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| 52 |
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patient_evidence: list[EvidencePointer] = Field(default_factory=list)
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| 53 |
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trial_evidence: list[TrialEvidencePointer] = Field(default_factory=list)
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| 54 |
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temporal_check: Optional[TemporalCheck] = None
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| 55 |
+
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| 56 |
+
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| 57 |
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class GapItem(BaseModel):
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description: str
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| 59 |
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recommended_action: str
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clinical_importance: str = Field(description="high|medium|low")
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| 61 |
+
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| 62 |
+
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| 63 |
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class EligibilityLedger(BaseModel):
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| 64 |
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patient_id: str
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+
nct_id: str
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| 66 |
+
overall_assessment: OverallAssessment
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+
criteria: list[CriterionAssessment] = Field(default_factory=list)
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| 68 |
+
gaps: list[GapItem] = Field(default_factory=list)
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| 69 |
+
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| 70 |
+
@property
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| 71 |
+
def met_count(self) -> int:
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| 72 |
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return sum(1 for c in self.criteria if c.decision == CriterionDecision.MET)
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| 73 |
+
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| 74 |
+
@property
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| 75 |
+
def not_met_count(self) -> int:
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| 76 |
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return sum(1 for c in self.criteria if c.decision == CriterionDecision.NOT_MET)
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| 77 |
+
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| 78 |
+
@property
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| 79 |
+
def unknown_count(self) -> int:
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| 80 |
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return sum(1 for c in self.criteria if c.decision == CriterionDecision.UNKNOWN)
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| 81 |
+
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| 82 |
+
@property
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| 83 |
+
def traffic_light(self) -> str:
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| 84 |
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"""Return traffic light color for UI display."""
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if self.overall_assessment == OverallAssessment.LIKELY_ELIGIBLE:
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return "green"
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elif self.overall_assessment == OverallAssessment.UNCERTAIN:
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return "yellow"
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return "red"
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trialpath/models/patient_profile.py
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| 1 |
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"""PatientProfile v1 -- MedGemma extraction output for NSCLC patients."""
|
| 2 |
+
import datetime
|
| 3 |
+
from typing import Optional
|
| 4 |
+
|
| 5 |
+
from pydantic import BaseModel, Field
|
| 6 |
+
|
| 7 |
+
|
| 8 |
+
class EvidencePointer(BaseModel):
|
| 9 |
+
doc_id: str = Field(description="Source document identifier")
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| 10 |
+
page: Optional[int] = Field(default=None, description="Page number")
|
| 11 |
+
span_id: Optional[str] = Field(default=None, description="Text span identifier")
|
| 12 |
+
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| 13 |
+
|
| 14 |
+
class SourceDocument(BaseModel):
|
| 15 |
+
doc_id: str
|
| 16 |
+
type: str = Field(description="clinic_letter|pathology|lab|imaging")
|
| 17 |
+
meta: dict = Field(default_factory=dict)
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| 18 |
+
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| 19 |
+
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| 20 |
+
class Demographics(BaseModel):
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| 21 |
+
age: Optional[int] = None
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| 22 |
+
sex: Optional[str] = None
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| 23 |
+
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| 24 |
+
|
| 25 |
+
class Diagnosis(BaseModel):
|
| 26 |
+
primary_condition: str = Field(description="e.g. 'Non-Small Cell Lung Cancer'")
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| 27 |
+
histology: Optional[str] = Field(default=None, description="e.g. 'adenocarcinoma'")
|
| 28 |
+
stage: Optional[str] = Field(default=None, description="e.g. 'IVa'")
|
| 29 |
+
diagnosis_date: Optional[datetime.date] = None
|
| 30 |
+
|
| 31 |
+
|
| 32 |
+
class PerformanceStatus(BaseModel):
|
| 33 |
+
scale: str = Field(description="'ECOG' or 'KPS'")
|
| 34 |
+
value: int
|
| 35 |
+
evidence: list[EvidencePointer] = Field(default_factory=list)
|
| 36 |
+
|
| 37 |
+
|
| 38 |
+
class Biomarker(BaseModel):
|
| 39 |
+
name: str = Field(description="e.g. 'EGFR', 'ALK', 'PD-L1'")
|
| 40 |
+
result: str = Field(description="e.g. 'Exon 19 deletion', 'Positive 80%'")
|
| 41 |
+
date: Optional[datetime.date] = None
|
| 42 |
+
evidence: list[EvidencePointer] = Field(default_factory=list)
|
| 43 |
+
|
| 44 |
+
|
| 45 |
+
class LabResult(BaseModel):
|
| 46 |
+
name: str = Field(description="e.g. 'ANC', 'Creatinine'")
|
| 47 |
+
value: float
|
| 48 |
+
unit: str
|
| 49 |
+
date: Optional[datetime.date] = None
|
| 50 |
+
evidence: list[EvidencePointer] = Field(default_factory=list)
|
| 51 |
+
|
| 52 |
+
|
| 53 |
+
class Treatment(BaseModel):
|
| 54 |
+
drug_name: str
|
| 55 |
+
start_date: Optional[datetime.date] = None
|
| 56 |
+
end_date: Optional[datetime.date] = None
|
| 57 |
+
line: Optional[int] = Field(default=None, description="Line of therapy (1, 2, 3...)")
|
| 58 |
+
evidence: list[EvidencePointer] = Field(default_factory=list)
|
| 59 |
+
|
| 60 |
+
|
| 61 |
+
class Comorbidity(BaseModel):
|
| 62 |
+
name: str
|
| 63 |
+
grade: Optional[str] = None
|
| 64 |
+
evidence: list[EvidencePointer] = Field(default_factory=list)
|
| 65 |
+
|
| 66 |
+
|
| 67 |
+
class ImagingSummary(BaseModel):
|
| 68 |
+
modality: str = Field(description="e.g. 'MRI brain', 'CT chest'")
|
| 69 |
+
date: Optional[datetime.date] = None
|
| 70 |
+
finding: str
|
| 71 |
+
interpretation: Optional[str] = None
|
| 72 |
+
certainty: Optional[str] = Field(default=None, description="low|medium|high")
|
| 73 |
+
evidence: list[EvidencePointer] = Field(default_factory=list)
|
| 74 |
+
|
| 75 |
+
|
| 76 |
+
class UnknownField(BaseModel):
|
| 77 |
+
field: str = Field(description="Name of missing field")
|
| 78 |
+
reason: str = Field(description="Why it is unknown")
|
| 79 |
+
importance: str = Field(description="high|medium|low")
|
| 80 |
+
|
| 81 |
+
|
| 82 |
+
class PatientProfile(BaseModel):
|
| 83 |
+
patient_id: str
|
| 84 |
+
source_docs: list[SourceDocument] = Field(default_factory=list)
|
| 85 |
+
demographics: Demographics = Field(default_factory=Demographics)
|
| 86 |
+
diagnosis: Optional[Diagnosis] = None
|
| 87 |
+
performance_status: Optional[PerformanceStatus] = None
|
| 88 |
+
biomarkers: list[Biomarker] = Field(default_factory=list)
|
| 89 |
+
key_labs: list[LabResult] = Field(default_factory=list)
|
| 90 |
+
treatments: list[Treatment] = Field(default_factory=list)
|
| 91 |
+
comorbidities: list[Comorbidity] = Field(default_factory=list)
|
| 92 |
+
imaging_summary: list[ImagingSummary] = Field(default_factory=list)
|
| 93 |
+
unknowns: list[UnknownField] = Field(default_factory=list)
|
| 94 |
+
|
| 95 |
+
def has_minimum_prescreen_data(self) -> bool:
|
| 96 |
+
"""Check if profile has enough data for prescreening."""
|
| 97 |
+
return (
|
| 98 |
+
self.diagnosis is not None
|
| 99 |
+
and self.diagnosis.stage is not None
|
| 100 |
+
and self.performance_status is not None
|
| 101 |
+
)
|
trialpath/models/search_anchors.py
ADDED
|
@@ -0,0 +1,33 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
"""SearchAnchors v1 -- Gemini-generated query parameters for ClinicalTrials MCP search."""
|
| 2 |
+
from __future__ import annotations
|
| 3 |
+
|
| 4 |
+
from typing import Optional
|
| 5 |
+
|
| 6 |
+
from pydantic import BaseModel, Field
|
| 7 |
+
|
| 8 |
+
|
| 9 |
+
class GeographyFilter(BaseModel):
|
| 10 |
+
country: str = Field(description="ISO country code or full name")
|
| 11 |
+
max_distance_km: Optional[int] = None
|
| 12 |
+
|
| 13 |
+
|
| 14 |
+
class TrialFilters(BaseModel):
|
| 15 |
+
recruitment_status: list[str] = Field(
|
| 16 |
+
default=["Recruiting", "Not yet recruiting"]
|
| 17 |
+
)
|
| 18 |
+
phase: list[str] = Field(default=["Phase 2", "Phase 3"])
|
| 19 |
+
|
| 20 |
+
|
| 21 |
+
class SearchAnchors(BaseModel):
|
| 22 |
+
condition: str = Field(description="Primary condition for search")
|
| 23 |
+
subtype: Optional[str] = Field(default=None, description="Cancer subtype")
|
| 24 |
+
biomarkers: list[str] = Field(default_factory=list)
|
| 25 |
+
stage: Optional[str] = None
|
| 26 |
+
geography: Optional[GeographyFilter] = None
|
| 27 |
+
age: Optional[int] = None
|
| 28 |
+
performance_status_max: Optional[int] = None
|
| 29 |
+
trial_filters: TrialFilters = Field(default_factory=TrialFilters)
|
| 30 |
+
relaxation_order: list[str] = Field(
|
| 31 |
+
default=["phase", "distance", "biomarker_strictness"],
|
| 32 |
+
description="Order in which to relax criteria if too few results",
|
| 33 |
+
)
|
trialpath/models/search_log.py
ADDED
|
@@ -0,0 +1,74 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
"""SearchLog v1 -- Iterative query refinement tracking."""
|
| 2 |
+
from datetime import datetime, timezone
|
| 3 |
+
from enum import Enum
|
| 4 |
+
|
| 5 |
+
from pydantic import BaseModel, Field
|
| 6 |
+
|
| 7 |
+
|
| 8 |
+
class RefinementAction(str, Enum):
|
| 9 |
+
INITIAL = "initial"
|
| 10 |
+
REFINE = "refine"
|
| 11 |
+
RELAX = "relax"
|
| 12 |
+
SHORTLIST = "shortlist"
|
| 13 |
+
ABORT = "abort"
|
| 14 |
+
|
| 15 |
+
|
| 16 |
+
class SearchStep(BaseModel):
|
| 17 |
+
step_number: int
|
| 18 |
+
query_params: dict = Field(description="SearchAnchors snapshot used for this query")
|
| 19 |
+
result_count: int
|
| 20 |
+
action_taken: RefinementAction
|
| 21 |
+
action_reason: str = Field(description="Human-readable why this action was chosen")
|
| 22 |
+
timestamp: datetime = Field(default_factory=lambda: datetime.now(timezone.utc))
|
| 23 |
+
nct_ids_sample: list[str] = Field(
|
| 24 |
+
default_factory=list,
|
| 25 |
+
description="Sample of NCT IDs returned (up to 10 for transparency)",
|
| 26 |
+
)
|
| 27 |
+
|
| 28 |
+
|
| 29 |
+
class SearchLog(BaseModel):
|
| 30 |
+
session_id: str
|
| 31 |
+
patient_id: str
|
| 32 |
+
steps: list[SearchStep] = Field(default_factory=list)
|
| 33 |
+
final_shortlist_nct_ids: list[str] = Field(default_factory=list)
|
| 34 |
+
total_refinement_rounds: int = 0
|
| 35 |
+
max_refinement_rounds: int = Field(
|
| 36 |
+
default=5, description="Safety cap to prevent infinite loops"
|
| 37 |
+
)
|
| 38 |
+
|
| 39 |
+
@property
|
| 40 |
+
def is_refinement_exhausted(self) -> bool:
|
| 41 |
+
return self.total_refinement_rounds >= self.max_refinement_rounds
|
| 42 |
+
|
| 43 |
+
def add_step(
|
| 44 |
+
self,
|
| 45 |
+
query_params: dict,
|
| 46 |
+
result_count: int,
|
| 47 |
+
action: RefinementAction,
|
| 48 |
+
reason: str,
|
| 49 |
+
nct_ids_sample: list[str] | None = None,
|
| 50 |
+
) -> None:
|
| 51 |
+
step = SearchStep(
|
| 52 |
+
step_number=len(self.steps) + 1,
|
| 53 |
+
query_params=query_params,
|
| 54 |
+
result_count=result_count,
|
| 55 |
+
action_taken=action,
|
| 56 |
+
action_reason=reason,
|
| 57 |
+
nct_ids_sample=nct_ids_sample or [],
|
| 58 |
+
)
|
| 59 |
+
self.steps.append(step)
|
| 60 |
+
if action in (RefinementAction.REFINE, RefinementAction.RELAX):
|
| 61 |
+
self.total_refinement_rounds += 1
|
| 62 |
+
|
| 63 |
+
def to_transparency_summary(self) -> list[dict]:
|
| 64 |
+
"""Generate human-readable search process for FE display."""
|
| 65 |
+
return [
|
| 66 |
+
{
|
| 67 |
+
"step": s.step_number,
|
| 68 |
+
"query": s.query_params,
|
| 69 |
+
"found": s.result_count,
|
| 70 |
+
"action": s.action_taken.value,
|
| 71 |
+
"reason": s.action_reason,
|
| 72 |
+
}
|
| 73 |
+
for s in self.steps
|
| 74 |
+
]
|
trialpath/models/trial_candidate.py
ADDED
|
@@ -0,0 +1,33 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
"""TrialCandidate v1 -- Normalized ClinicalTrials MCP search results."""
|
| 2 |
+
from __future__ import annotations
|
| 3 |
+
|
| 4 |
+
from typing import Optional
|
| 5 |
+
|
| 6 |
+
from pydantic import BaseModel, Field
|
| 7 |
+
|
| 8 |
+
|
| 9 |
+
class TrialLocation(BaseModel):
|
| 10 |
+
country: str
|
| 11 |
+
city: Optional[str] = None
|
| 12 |
+
|
| 13 |
+
|
| 14 |
+
class AgeRange(BaseModel):
|
| 15 |
+
min: Optional[int] = None
|
| 16 |
+
max: Optional[int] = None
|
| 17 |
+
|
| 18 |
+
|
| 19 |
+
class EligibilityText(BaseModel):
|
| 20 |
+
inclusion: str
|
| 21 |
+
exclusion: str
|
| 22 |
+
|
| 23 |
+
|
| 24 |
+
class TrialCandidate(BaseModel):
|
| 25 |
+
nct_id: str = Field(description="NCT identifier e.g. 'NCT01234567'")
|
| 26 |
+
title: str
|
| 27 |
+
conditions: list[str] = Field(default_factory=list)
|
| 28 |
+
phase: Optional[str] = None
|
| 29 |
+
status: Optional[str] = None
|
| 30 |
+
locations: list[TrialLocation] = Field(default_factory=list)
|
| 31 |
+
age_range: Optional[AgeRange] = None
|
| 32 |
+
fingerprint_text: str = Field(description="Short text for Gemini reranking")
|
| 33 |
+
eligibility_text: Optional[EligibilityText] = None
|
trialpath/tests/test_models.py
ADDED
|
@@ -0,0 +1,616 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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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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|
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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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|
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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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|
|
|
|
|
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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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|
|
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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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|
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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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|
| 1 |
+
"""TDD tests for TrialPath data models (RED phase — write tests first)."""
|
| 2 |
+
from __future__ import annotations
|
| 3 |
+
|
| 4 |
+
from datetime import date
|
| 5 |
+
|
| 6 |
+
|
| 7 |
+
class TestPatientProfile:
|
| 8 |
+
"""PatientProfile v1 validation and helper tests."""
|
| 9 |
+
|
| 10 |
+
def test_minimal_valid_profile(self):
|
| 11 |
+
"""A profile with only patient_id should be valid."""
|
| 12 |
+
from trialpath.models.patient_profile import PatientProfile
|
| 13 |
+
|
| 14 |
+
profile = PatientProfile(patient_id="P001")
|
| 15 |
+
assert profile.patient_id == "P001"
|
| 16 |
+
assert profile.unknowns == []
|
| 17 |
+
|
| 18 |
+
def test_complete_nsclc_profile(self):
|
| 19 |
+
"""Full NSCLC patient profile should serialize/deserialize correctly."""
|
| 20 |
+
from trialpath.models.patient_profile import (
|
| 21 |
+
Biomarker,
|
| 22 |
+
Demographics,
|
| 23 |
+
Diagnosis,
|
| 24 |
+
EvidencePointer,
|
| 25 |
+
PatientProfile,
|
| 26 |
+
PerformanceStatus,
|
| 27 |
+
UnknownField,
|
| 28 |
+
)
|
| 29 |
+
|
| 30 |
+
profile = PatientProfile(
|
| 31 |
+
patient_id="P001",
|
| 32 |
+
demographics=Demographics(age=52, sex="female"),
|
| 33 |
+
diagnosis=Diagnosis(
|
| 34 |
+
primary_condition="Non-Small Cell Lung Cancer",
|
| 35 |
+
histology="adenocarcinoma",
|
| 36 |
+
stage="IVa",
|
| 37 |
+
diagnosis_date=date(2025, 11, 15),
|
| 38 |
+
),
|
| 39 |
+
performance_status=PerformanceStatus(
|
| 40 |
+
scale="ECOG", value=1,
|
| 41 |
+
evidence=[EvidencePointer(doc_id="clinic_1", page=2, span_id="s_17")],
|
| 42 |
+
),
|
| 43 |
+
biomarkers=[
|
| 44 |
+
Biomarker(
|
| 45 |
+
name="EGFR", result="Exon 19 deletion",
|
| 46 |
+
date=date(2026, 1, 10),
|
| 47 |
+
evidence=[EvidencePointer(doc_id="path_egfr", page=1, span_id="s_3")],
|
| 48 |
+
),
|
| 49 |
+
],
|
| 50 |
+
unknowns=[
|
| 51 |
+
UnknownField(field="PD-L1", reason="Not found in documents", importance="medium"),
|
| 52 |
+
],
|
| 53 |
+
)
|
| 54 |
+
|
| 55 |
+
data = profile.model_dump()
|
| 56 |
+
restored = PatientProfile.model_validate(data)
|
| 57 |
+
assert restored.patient_id == "P001"
|
| 58 |
+
assert restored.diagnosis.stage == "IVa"
|
| 59 |
+
assert len(restored.biomarkers) == 1
|
| 60 |
+
assert restored.biomarkers[0].name == "EGFR"
|
| 61 |
+
|
| 62 |
+
def test_has_minimum_prescreen_data_true(self):
|
| 63 |
+
"""Profile with diagnosis + stage + ECOG satisfies prescreen requirements."""
|
| 64 |
+
from trialpath.models.patient_profile import (
|
| 65 |
+
Diagnosis,
|
| 66 |
+
PatientProfile,
|
| 67 |
+
PerformanceStatus,
|
| 68 |
+
)
|
| 69 |
+
|
| 70 |
+
profile = PatientProfile(
|
| 71 |
+
patient_id="P001",
|
| 72 |
+
diagnosis=Diagnosis(
|
| 73 |
+
primary_condition="NSCLC", stage="IV",
|
| 74 |
+
),
|
| 75 |
+
performance_status=PerformanceStatus(scale="ECOG", value=1),
|
| 76 |
+
)
|
| 77 |
+
assert profile.has_minimum_prescreen_data() is True
|
| 78 |
+
|
| 79 |
+
def test_has_minimum_prescreen_data_false_no_stage(self):
|
| 80 |
+
"""Profile without stage should fail prescreen check."""
|
| 81 |
+
from trialpath.models.patient_profile import (
|
| 82 |
+
Diagnosis,
|
| 83 |
+
PatientProfile,
|
| 84 |
+
PerformanceStatus,
|
| 85 |
+
)
|
| 86 |
+
|
| 87 |
+
profile = PatientProfile(
|
| 88 |
+
patient_id="P001",
|
| 89 |
+
diagnosis=Diagnosis(primary_condition="NSCLC"),
|
| 90 |
+
performance_status=PerformanceStatus(scale="ECOG", value=1),
|
| 91 |
+
)
|
| 92 |
+
assert profile.has_minimum_prescreen_data() is False
|
| 93 |
+
|
| 94 |
+
def test_has_minimum_prescreen_data_false_no_ecog(self):
|
| 95 |
+
"""Profile without performance status should fail prescreen check."""
|
| 96 |
+
from trialpath.models.patient_profile import (
|
| 97 |
+
Diagnosis,
|
| 98 |
+
PatientProfile,
|
| 99 |
+
)
|
| 100 |
+
|
| 101 |
+
profile = PatientProfile(
|
| 102 |
+
patient_id="P001",
|
| 103 |
+
diagnosis=Diagnosis(primary_condition="NSCLC", stage="IV"),
|
| 104 |
+
)
|
| 105 |
+
assert profile.has_minimum_prescreen_data() is False
|
| 106 |
+
|
| 107 |
+
def test_json_roundtrip(self):
|
| 108 |
+
"""Profile should survive JSON serialization roundtrip."""
|
| 109 |
+
from trialpath.models.patient_profile import (
|
| 110 |
+
Demographics,
|
| 111 |
+
Diagnosis,
|
| 112 |
+
PatientProfile,
|
| 113 |
+
)
|
| 114 |
+
|
| 115 |
+
profile = PatientProfile(
|
| 116 |
+
patient_id="P001",
|
| 117 |
+
demographics=Demographics(age=65, sex="male"),
|
| 118 |
+
diagnosis=Diagnosis(
|
| 119 |
+
primary_condition="NSCLC",
|
| 120 |
+
histology="squamous",
|
| 121 |
+
stage="IIIb",
|
| 122 |
+
),
|
| 123 |
+
)
|
| 124 |
+
json_str = profile.model_dump_json()
|
| 125 |
+
restored = PatientProfile.model_validate_json(json_str)
|
| 126 |
+
assert restored == profile
|
| 127 |
+
|
| 128 |
+
def test_source_docs_default_empty(self):
|
| 129 |
+
"""source_docs should default to empty list."""
|
| 130 |
+
from trialpath.models.patient_profile import PatientProfile
|
| 131 |
+
|
| 132 |
+
profile = PatientProfile(patient_id="P001")
|
| 133 |
+
assert profile.source_docs == []
|
| 134 |
+
|
| 135 |
+
def test_source_doc_creation(self):
|
| 136 |
+
"""SourceDocument with all fields."""
|
| 137 |
+
from trialpath.models.patient_profile import PatientProfile, SourceDocument
|
| 138 |
+
|
| 139 |
+
profile = PatientProfile(
|
| 140 |
+
patient_id="P001",
|
| 141 |
+
source_docs=[
|
| 142 |
+
SourceDocument(doc_id="doc1", type="pathology", meta={"pages": 3}),
|
| 143 |
+
],
|
| 144 |
+
)
|
| 145 |
+
assert len(profile.source_docs) == 1
|
| 146 |
+
assert profile.source_docs[0].type == "pathology"
|
| 147 |
+
|
| 148 |
+
def test_lab_result(self):
|
| 149 |
+
"""LabResult with value, unit, date, and evidence."""
|
| 150 |
+
from trialpath.models.patient_profile import (
|
| 151 |
+
EvidencePointer,
|
| 152 |
+
LabResult,
|
| 153 |
+
PatientProfile,
|
| 154 |
+
)
|
| 155 |
+
|
| 156 |
+
profile = PatientProfile(
|
| 157 |
+
patient_id="P001",
|
| 158 |
+
key_labs=[
|
| 159 |
+
LabResult(
|
| 160 |
+
name="ANC", value=1.8, unit="10^9/L",
|
| 161 |
+
date=date(2026, 1, 28),
|
| 162 |
+
evidence=[EvidencePointer(doc_id="labs_jan", page=1, span_id="tbl_anc")],
|
| 163 |
+
),
|
| 164 |
+
],
|
| 165 |
+
)
|
| 166 |
+
assert profile.key_labs[0].value == 1.8
|
| 167 |
+
assert profile.key_labs[0].unit == "10^9/L"
|
| 168 |
+
|
| 169 |
+
def test_treatment(self):
|
| 170 |
+
"""Treatment with drug_name, dates, and line of therapy."""
|
| 171 |
+
from trialpath.models.patient_profile import PatientProfile, Treatment
|
| 172 |
+
|
| 173 |
+
profile = PatientProfile(
|
| 174 |
+
patient_id="P001",
|
| 175 |
+
treatments=[
|
| 176 |
+
Treatment(
|
| 177 |
+
drug_name="Pembrolizumab",
|
| 178 |
+
start_date=date(2024, 6, 1),
|
| 179 |
+
end_date=date(2024, 11, 30),
|
| 180 |
+
line=1,
|
| 181 |
+
),
|
| 182 |
+
],
|
| 183 |
+
)
|
| 184 |
+
assert profile.treatments[0].drug_name == "Pembrolizumab"
|
| 185 |
+
assert profile.treatments[0].line == 1
|
| 186 |
+
|
| 187 |
+
def test_comorbidity(self):
|
| 188 |
+
"""Comorbidity with name and grade."""
|
| 189 |
+
from trialpath.models.patient_profile import Comorbidity, PatientProfile
|
| 190 |
+
|
| 191 |
+
profile = PatientProfile(
|
| 192 |
+
patient_id="P001",
|
| 193 |
+
comorbidities=[
|
| 194 |
+
Comorbidity(name="CKD", grade="Stage 3"),
|
| 195 |
+
],
|
| 196 |
+
)
|
| 197 |
+
assert profile.comorbidities[0].name == "CKD"
|
| 198 |
+
|
| 199 |
+
def test_imaging_summary(self):
|
| 200 |
+
"""ImagingSummary with modality, finding, interpretation, certainty."""
|
| 201 |
+
from trialpath.models.patient_profile import ImagingSummary, PatientProfile
|
| 202 |
+
|
| 203 |
+
profile = PatientProfile(
|
| 204 |
+
patient_id="P001",
|
| 205 |
+
imaging_summary=[
|
| 206 |
+
ImagingSummary(
|
| 207 |
+
modality="MRI brain",
|
| 208 |
+
date=date(2026, 1, 20),
|
| 209 |
+
finding="Stable 3mm left frontal lesion",
|
| 210 |
+
interpretation="likely inactive scar",
|
| 211 |
+
certainty="low",
|
| 212 |
+
),
|
| 213 |
+
],
|
| 214 |
+
)
|
| 215 |
+
assert profile.imaging_summary[0].modality == "MRI brain"
|
| 216 |
+
assert profile.imaging_summary[0].certainty == "low"
|
| 217 |
+
|
| 218 |
+
|
| 219 |
+
class TestSearchAnchors:
|
| 220 |
+
"""SearchAnchors v1 validation tests."""
|
| 221 |
+
|
| 222 |
+
def test_minimal_anchors(self):
|
| 223 |
+
from trialpath.models.search_anchors import SearchAnchors
|
| 224 |
+
|
| 225 |
+
anchors = SearchAnchors(condition="NSCLC")
|
| 226 |
+
assert anchors.condition == "NSCLC"
|
| 227 |
+
assert anchors.trial_filters.recruitment_status == ["Recruiting", "Not yet recruiting"]
|
| 228 |
+
|
| 229 |
+
def test_full_anchors(self):
|
| 230 |
+
from trialpath.models.search_anchors import SearchAnchors, TrialFilters
|
| 231 |
+
|
| 232 |
+
anchors = SearchAnchors(
|
| 233 |
+
condition="Non-Small Cell Lung Cancer",
|
| 234 |
+
subtype="adenocarcinoma",
|
| 235 |
+
biomarkers=["EGFR exon 19 deletion"],
|
| 236 |
+
stage="IV",
|
| 237 |
+
age=52,
|
| 238 |
+
performance_status_max=1,
|
| 239 |
+
trial_filters=TrialFilters(
|
| 240 |
+
recruitment_status=["Recruiting"],
|
| 241 |
+
phase=["Phase 3"],
|
| 242 |
+
),
|
| 243 |
+
relaxation_order=["phase", "distance"],
|
| 244 |
+
)
|
| 245 |
+
assert len(anchors.biomarkers) == 1
|
| 246 |
+
assert anchors.trial_filters.phase == ["Phase 3"]
|
| 247 |
+
|
| 248 |
+
def test_default_relaxation_order(self):
|
| 249 |
+
from trialpath.models.search_anchors import SearchAnchors
|
| 250 |
+
|
| 251 |
+
anchors = SearchAnchors(condition="NSCLC")
|
| 252 |
+
assert anchors.relaxation_order == ["phase", "distance", "biomarker_strictness"]
|
| 253 |
+
|
| 254 |
+
def test_default_trial_filters(self):
|
| 255 |
+
from trialpath.models.search_anchors import SearchAnchors
|
| 256 |
+
|
| 257 |
+
anchors = SearchAnchors(condition="NSCLC")
|
| 258 |
+
assert anchors.trial_filters.phase == ["Phase 2", "Phase 3"]
|
| 259 |
+
|
| 260 |
+
def test_geography_filter(self):
|
| 261 |
+
from trialpath.models.search_anchors import GeographyFilter, SearchAnchors
|
| 262 |
+
|
| 263 |
+
anchors = SearchAnchors(
|
| 264 |
+
condition="NSCLC",
|
| 265 |
+
geography=GeographyFilter(country="DE", max_distance_km=200),
|
| 266 |
+
)
|
| 267 |
+
assert anchors.geography.country == "DE"
|
| 268 |
+
assert anchors.geography.max_distance_km == 200
|
| 269 |
+
|
| 270 |
+
def test_json_roundtrip(self):
|
| 271 |
+
from trialpath.models.search_anchors import SearchAnchors
|
| 272 |
+
|
| 273 |
+
anchors = SearchAnchors(
|
| 274 |
+
condition="NSCLC", stage="IV", age=55,
|
| 275 |
+
)
|
| 276 |
+
json_str = anchors.model_dump_json()
|
| 277 |
+
restored = SearchAnchors.model_validate_json(json_str)
|
| 278 |
+
assert restored == anchors
|
| 279 |
+
|
| 280 |
+
|
| 281 |
+
class TestTrialCandidate:
|
| 282 |
+
"""TrialCandidate v1 tests."""
|
| 283 |
+
|
| 284 |
+
def test_trial_with_eligibility_text(self):
|
| 285 |
+
from trialpath.models.trial_candidate import EligibilityText, TrialCandidate
|
| 286 |
+
|
| 287 |
+
trial = TrialCandidate(
|
| 288 |
+
nct_id="NCT01234567",
|
| 289 |
+
title="Phase 3 Study of Osimertinib",
|
| 290 |
+
conditions=["NSCLC"],
|
| 291 |
+
phase="Phase 3",
|
| 292 |
+
status="Recruiting",
|
| 293 |
+
fingerprint_text="Osimertinib EGFR+ NSCLC Phase 3",
|
| 294 |
+
eligibility_text=EligibilityText(
|
| 295 |
+
inclusion="Histologically confirmed NSCLC stage IV",
|
| 296 |
+
exclusion="Prior EGFR TKI therapy",
|
| 297 |
+
),
|
| 298 |
+
)
|
| 299 |
+
assert trial.nct_id == "NCT01234567"
|
| 300 |
+
assert trial.eligibility_text.inclusion.startswith("Histologically")
|
| 301 |
+
|
| 302 |
+
def test_minimal_trial(self):
|
| 303 |
+
from trialpath.models.trial_candidate import TrialCandidate
|
| 304 |
+
|
| 305 |
+
trial = TrialCandidate(
|
| 306 |
+
nct_id="NCT99999999",
|
| 307 |
+
title="Test Trial",
|
| 308 |
+
fingerprint_text="test",
|
| 309 |
+
)
|
| 310 |
+
assert trial.conditions == []
|
| 311 |
+
assert trial.locations == []
|
| 312 |
+
assert trial.eligibility_text is None
|
| 313 |
+
|
| 314 |
+
def test_trial_with_locations(self):
|
| 315 |
+
from trialpath.models.trial_candidate import TrialCandidate, TrialLocation
|
| 316 |
+
|
| 317 |
+
trial = TrialCandidate(
|
| 318 |
+
nct_id="NCT01234567",
|
| 319 |
+
title="Test Trial",
|
| 320 |
+
fingerprint_text="test",
|
| 321 |
+
locations=[
|
| 322 |
+
TrialLocation(country="DE", city="Berlin"),
|
| 323 |
+
TrialLocation(country="DE", city="Hamburg"),
|
| 324 |
+
],
|
| 325 |
+
)
|
| 326 |
+
assert len(trial.locations) == 2
|
| 327 |
+
assert trial.locations[0].city == "Berlin"
|
| 328 |
+
|
| 329 |
+
def test_trial_with_age_range(self):
|
| 330 |
+
from trialpath.models.trial_candidate import AgeRange, TrialCandidate
|
| 331 |
+
|
| 332 |
+
trial = TrialCandidate(
|
| 333 |
+
nct_id="NCT01234567",
|
| 334 |
+
title="Test Trial",
|
| 335 |
+
fingerprint_text="test",
|
| 336 |
+
age_range=AgeRange(min=18, max=75),
|
| 337 |
+
)
|
| 338 |
+
assert trial.age_range.min == 18
|
| 339 |
+
assert trial.age_range.max == 75
|
| 340 |
+
|
| 341 |
+
def test_json_roundtrip(self):
|
| 342 |
+
from trialpath.models.trial_candidate import TrialCandidate
|
| 343 |
+
|
| 344 |
+
trial = TrialCandidate(
|
| 345 |
+
nct_id="NCT01234567",
|
| 346 |
+
title="Test",
|
| 347 |
+
fingerprint_text="test fp",
|
| 348 |
+
phase="Phase 2",
|
| 349 |
+
)
|
| 350 |
+
json_str = trial.model_dump_json()
|
| 351 |
+
restored = TrialCandidate.model_validate_json(json_str)
|
| 352 |
+
assert restored == trial
|
| 353 |
+
|
| 354 |
+
|
| 355 |
+
class TestEligibilityLedger:
|
| 356 |
+
"""EligibilityLedger v1 tests."""
|
| 357 |
+
|
| 358 |
+
def test_traffic_light_green(self):
|
| 359 |
+
from trialpath.models.eligibility_ledger import (
|
| 360 |
+
EligibilityLedger,
|
| 361 |
+
OverallAssessment,
|
| 362 |
+
)
|
| 363 |
+
|
| 364 |
+
ledger = EligibilityLedger(
|
| 365 |
+
patient_id="P001",
|
| 366 |
+
nct_id="NCT01234567",
|
| 367 |
+
overall_assessment=OverallAssessment.LIKELY_ELIGIBLE,
|
| 368 |
+
)
|
| 369 |
+
assert ledger.traffic_light == "green"
|
| 370 |
+
|
| 371 |
+
def test_traffic_light_yellow(self):
|
| 372 |
+
from trialpath.models.eligibility_ledger import (
|
| 373 |
+
EligibilityLedger,
|
| 374 |
+
OverallAssessment,
|
| 375 |
+
)
|
| 376 |
+
|
| 377 |
+
ledger = EligibilityLedger(
|
| 378 |
+
patient_id="P001",
|
| 379 |
+
nct_id="NCT01234567",
|
| 380 |
+
overall_assessment=OverallAssessment.UNCERTAIN,
|
| 381 |
+
)
|
| 382 |
+
assert ledger.traffic_light == "yellow"
|
| 383 |
+
|
| 384 |
+
def test_traffic_light_red(self):
|
| 385 |
+
from trialpath.models.eligibility_ledger import (
|
| 386 |
+
EligibilityLedger,
|
| 387 |
+
OverallAssessment,
|
| 388 |
+
)
|
| 389 |
+
|
| 390 |
+
ledger = EligibilityLedger(
|
| 391 |
+
patient_id="P001",
|
| 392 |
+
nct_id="NCT01234567",
|
| 393 |
+
overall_assessment=OverallAssessment.LIKELY_INELIGIBLE,
|
| 394 |
+
)
|
| 395 |
+
assert ledger.traffic_light == "red"
|
| 396 |
+
|
| 397 |
+
def test_criterion_counts(self):
|
| 398 |
+
from trialpath.models.eligibility_ledger import (
|
| 399 |
+
CriterionAssessment,
|
| 400 |
+
CriterionDecision,
|
| 401 |
+
EligibilityLedger,
|
| 402 |
+
GapItem,
|
| 403 |
+
OverallAssessment,
|
| 404 |
+
)
|
| 405 |
+
|
| 406 |
+
ledger = EligibilityLedger(
|
| 407 |
+
patient_id="P001",
|
| 408 |
+
nct_id="NCT01234567",
|
| 409 |
+
overall_assessment=OverallAssessment.UNCERTAIN,
|
| 410 |
+
criteria=[
|
| 411 |
+
CriterionAssessment(
|
| 412 |
+
criterion_id="inc_1", type="inclusion",
|
| 413 |
+
text="Stage IV NSCLC", decision=CriterionDecision.MET,
|
| 414 |
+
),
|
| 415 |
+
CriterionAssessment(
|
| 416 |
+
criterion_id="inc_2", type="inclusion",
|
| 417 |
+
text="ECOG 0-1", decision=CriterionDecision.MET,
|
| 418 |
+
),
|
| 419 |
+
CriterionAssessment(
|
| 420 |
+
criterion_id="exc_1", type="exclusion",
|
| 421 |
+
text="No prior immunotherapy", decision=CriterionDecision.NOT_MET,
|
| 422 |
+
),
|
| 423 |
+
CriterionAssessment(
|
| 424 |
+
criterion_id="inc_3", type="inclusion",
|
| 425 |
+
text="EGFR mutation", decision=CriterionDecision.UNKNOWN,
|
| 426 |
+
),
|
| 427 |
+
],
|
| 428 |
+
gaps=[
|
| 429 |
+
GapItem(
|
| 430 |
+
description="EGFR mutation status unknown",
|
| 431 |
+
recommended_action="Order EGFR mutation test",
|
| 432 |
+
clinical_importance="high",
|
| 433 |
+
),
|
| 434 |
+
],
|
| 435 |
+
)
|
| 436 |
+
assert ledger.met_count == 2
|
| 437 |
+
assert ledger.not_met_count == 1
|
| 438 |
+
assert ledger.unknown_count == 1
|
| 439 |
+
assert len(ledger.gaps) == 1
|
| 440 |
+
|
| 441 |
+
def test_empty_criteria_counts(self):
|
| 442 |
+
from trialpath.models.eligibility_ledger import (
|
| 443 |
+
EligibilityLedger,
|
| 444 |
+
OverallAssessment,
|
| 445 |
+
)
|
| 446 |
+
|
| 447 |
+
ledger = EligibilityLedger(
|
| 448 |
+
patient_id="P001",
|
| 449 |
+
nct_id="NCT01234567",
|
| 450 |
+
overall_assessment=OverallAssessment.UNCERTAIN,
|
| 451 |
+
)
|
| 452 |
+
assert ledger.met_count == 0
|
| 453 |
+
assert ledger.not_met_count == 0
|
| 454 |
+
assert ledger.unknown_count == 0
|
| 455 |
+
|
| 456 |
+
def test_json_roundtrip(self):
|
| 457 |
+
from trialpath.models.eligibility_ledger import (
|
| 458 |
+
EligibilityLedger,
|
| 459 |
+
OverallAssessment,
|
| 460 |
+
)
|
| 461 |
+
|
| 462 |
+
ledger = EligibilityLedger(
|
| 463 |
+
patient_id="P001",
|
| 464 |
+
nct_id="NCT01234567",
|
| 465 |
+
overall_assessment=OverallAssessment.LIKELY_ELIGIBLE,
|
| 466 |
+
)
|
| 467 |
+
json_str = ledger.model_dump_json()
|
| 468 |
+
restored = EligibilityLedger.model_validate_json(json_str)
|
| 469 |
+
assert restored.patient_id == "P001"
|
| 470 |
+
assert restored.overall_assessment == OverallAssessment.LIKELY_ELIGIBLE
|
| 471 |
+
|
| 472 |
+
|
| 473 |
+
class TestTemporalCheck:
|
| 474 |
+
"""TemporalCheck validation for time-windowed criteria."""
|
| 475 |
+
|
| 476 |
+
def test_within_window(self):
|
| 477 |
+
"""Evidence 7 days old should be within a 14-day window."""
|
| 478 |
+
from trialpath.models.eligibility_ledger import TemporalCheck
|
| 479 |
+
|
| 480 |
+
check = TemporalCheck(
|
| 481 |
+
required_window_days=14,
|
| 482 |
+
reference_date=date(2026, 1, 20),
|
| 483 |
+
evaluation_date=date(2026, 1, 27),
|
| 484 |
+
is_within_window=True,
|
| 485 |
+
)
|
| 486 |
+
assert check.days_elapsed == 7
|
| 487 |
+
assert check.is_within_window is True
|
| 488 |
+
|
| 489 |
+
def test_outside_window(self):
|
| 490 |
+
"""Evidence 21 days old should be outside a 14-day window."""
|
| 491 |
+
from trialpath.models.eligibility_ledger import TemporalCheck
|
| 492 |
+
|
| 493 |
+
check = TemporalCheck(
|
| 494 |
+
required_window_days=14,
|
| 495 |
+
reference_date=date(2026, 1, 1),
|
| 496 |
+
evaluation_date=date(2026, 1, 22),
|
| 497 |
+
is_within_window=False,
|
| 498 |
+
)
|
| 499 |
+
assert check.days_elapsed == 21
|
| 500 |
+
assert check.is_within_window is False
|
| 501 |
+
|
| 502 |
+
def test_no_reference_date(self):
|
| 503 |
+
"""Missing reference date should yield None for days_elapsed."""
|
| 504 |
+
from trialpath.models.eligibility_ledger import TemporalCheck
|
| 505 |
+
|
| 506 |
+
check = TemporalCheck(
|
| 507 |
+
required_window_days=14,
|
| 508 |
+
reference_date=None,
|
| 509 |
+
)
|
| 510 |
+
assert check.days_elapsed is None
|
| 511 |
+
assert check.is_within_window is None
|
| 512 |
+
|
| 513 |
+
def test_criterion_with_temporal_check(self):
|
| 514 |
+
"""CriterionAssessment should accept an optional temporal_check."""
|
| 515 |
+
from trialpath.models.eligibility_ledger import (
|
| 516 |
+
CriterionAssessment,
|
| 517 |
+
CriterionDecision,
|
| 518 |
+
TemporalCheck,
|
| 519 |
+
)
|
| 520 |
+
|
| 521 |
+
assessment = CriterionAssessment(
|
| 522 |
+
criterion_id="inc_5",
|
| 523 |
+
type="inclusion",
|
| 524 |
+
text="ANC >= 1.5 x 10^9/L within 14 days of enrollment",
|
| 525 |
+
decision=CriterionDecision.MET,
|
| 526 |
+
temporal_check=TemporalCheck(
|
| 527 |
+
required_window_days=14,
|
| 528 |
+
reference_date=date(2026, 1, 20),
|
| 529 |
+
evaluation_date=date(2026, 1, 27),
|
| 530 |
+
is_within_window=True,
|
| 531 |
+
),
|
| 532 |
+
)
|
| 533 |
+
assert assessment.temporal_check is not None
|
| 534 |
+
assert assessment.temporal_check.days_elapsed == 7
|
| 535 |
+
assert assessment.temporal_check.is_within_window is True
|
| 536 |
+
|
| 537 |
+
|
| 538 |
+
class TestSearchLog:
|
| 539 |
+
"""SearchLog v1 -- iterative query refinement tracking tests."""
|
| 540 |
+
|
| 541 |
+
def test_add_step_increments_count(self):
|
| 542 |
+
"""Adding a refinement step should increment total_refinement_rounds."""
|
| 543 |
+
from trialpath.models.search_log import RefinementAction, SearchLog
|
| 544 |
+
|
| 545 |
+
log = SearchLog(session_id="S001", patient_id="P001")
|
| 546 |
+
assert log.total_refinement_rounds == 0
|
| 547 |
+
|
| 548 |
+
log.add_step(
|
| 549 |
+
query_params={"condition": "NSCLC"},
|
| 550 |
+
result_count=75,
|
| 551 |
+
action=RefinementAction.REFINE,
|
| 552 |
+
reason="Too many results, adding phase filter",
|
| 553 |
+
)
|
| 554 |
+
assert log.total_refinement_rounds == 1
|
| 555 |
+
assert len(log.steps) == 1
|
| 556 |
+
|
| 557 |
+
def test_refinement_exhausted_at_max(self):
|
| 558 |
+
"""After 5 refinement rounds, is_refinement_exhausted should be True."""
|
| 559 |
+
from trialpath.models.search_log import RefinementAction, SearchLog
|
| 560 |
+
|
| 561 |
+
log = SearchLog(session_id="S001", patient_id="P001")
|
| 562 |
+
|
| 563 |
+
for i in range(5):
|
| 564 |
+
log.add_step(
|
| 565 |
+
query_params={"condition": "NSCLC", "round": i},
|
| 566 |
+
result_count=0,
|
| 567 |
+
action=RefinementAction.RELAX,
|
| 568 |
+
reason=f"Relaxation round {i + 1}",
|
| 569 |
+
)
|
| 570 |
+
|
| 571 |
+
assert log.total_refinement_rounds == 5
|
| 572 |
+
assert log.is_refinement_exhausted is True
|
| 573 |
+
|
| 574 |
+
def test_transparency_summary_format(self):
|
| 575 |
+
"""to_transparency_summary should return list of dicts with expected keys."""
|
| 576 |
+
from trialpath.models.search_log import RefinementAction, SearchLog
|
| 577 |
+
|
| 578 |
+
log = SearchLog(session_id="S001", patient_id="P001")
|
| 579 |
+
|
| 580 |
+
log.add_step(
|
| 581 |
+
query_params={"condition": "NSCLC"},
|
| 582 |
+
result_count=100,
|
| 583 |
+
action=RefinementAction.REFINE,
|
| 584 |
+
reason="Too many results",
|
| 585 |
+
)
|
| 586 |
+
log.add_step(
|
| 587 |
+
query_params={"condition": "NSCLC", "phase": "Phase 3"},
|
| 588 |
+
result_count=25,
|
| 589 |
+
action=RefinementAction.SHORTLIST,
|
| 590 |
+
reason="Right-sized result set",
|
| 591 |
+
)
|
| 592 |
+
|
| 593 |
+
summary = log.to_transparency_summary()
|
| 594 |
+
assert len(summary) == 2
|
| 595 |
+
assert summary[0]["step"] == 1
|
| 596 |
+
assert summary[0]["found"] == 100
|
| 597 |
+
assert summary[0]["action"] == "refine"
|
| 598 |
+
assert summary[1]["step"] == 2
|
| 599 |
+
assert summary[1]["found"] == 25
|
| 600 |
+
assert summary[1]["action"] == "shortlist"
|
| 601 |
+
|
| 602 |
+
def test_initial_search_no_refinement_count(self):
|
| 603 |
+
"""An INITIAL action should not increment the refinement counter."""
|
| 604 |
+
from trialpath.models.search_log import RefinementAction, SearchLog
|
| 605 |
+
|
| 606 |
+
log = SearchLog(session_id="S001", patient_id="P001")
|
| 607 |
+
|
| 608 |
+
log.add_step(
|
| 609 |
+
query_params={"condition": "NSCLC"},
|
| 610 |
+
result_count=30,
|
| 611 |
+
action=RefinementAction.INITIAL,
|
| 612 |
+
reason="First search",
|
| 613 |
+
)
|
| 614 |
+
|
| 615 |
+
assert log.total_refinement_rounds == 0
|
| 616 |
+
assert len(log.steps) == 1
|