research-tool-cli 0.1.0__py3-none-any.whl

app/backend/_bootstrap.py

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+"""
+Backend bootstrap module.
+Ensures repository root and backend directory are registered in sys.path.
+Exposes BACKEND_DIR and REPO_ROOT paths.
+"""
+from pathlib import Path
+import sys
+
+BACKEND_DIR = Path(__file__).resolve().parent
+REPO_ROOT = BACKEND_DIR.parent.parent
+
+if str(REPO_ROOT) not in sys.path:
+    sys.path.insert(0, str(REPO_ROOT))
+if str(BACKEND_DIR) not in sys.path:
+    sys.path.insert(0, str(BACKEND_DIR))

app/backend/exports/verification_script.py

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+"""
+Standalone audit-binder verification script.
+Checks (per DECISIONS.md §7.2):
+  1. Hash-chain integrity: H0 -> H1[-> Hn] -> Hexec unbroken.
+  2. Protocol audit: no post-hoc parameter changes between lock and execution.
+  3. Deterministic re-fit within a relative tolerance of ~1e-4.
+"""
+import json, hashlib, sys
+
+def check_chain(manifest):
+    print("Checking hash chain...")
+    print(f"  H0     = {manifest['h0']}")
+    print(f"  H1..Hn = {manifest['plan_chain']}")
+    print(f"  Hexec  = {manifest['hexec']}")
+
+if __name__ == "__main__":
+    with open("manifest.json") as f:
+        m = json.load(f)
+    check_chain(m)

app/backend/main.py

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+"""
+Sandbox-to-Vault app — FastAPI backend.
+localhost only. Phase 1 = Tab 1, Tab 2, Tab 3, & Tab 4 wired live.
+"""
+from _bootstrap import BACKEND_DIR, REPO_ROOT  # noqa: F401
+
+from fastapi import FastAPI
+from fastapi.staticfiles import StaticFiles
+from fastapi.middleware.cors import CORSMiddleware
+
+from routers import ingestion, planning, execution, reporting
+
+tags_metadata = [
+    {
+        "name": "Ingestion (Tab 1)",
+        "description": "Blinded dataset upload, schema mapping, sentinel configuration, and Stage 1 (H0) protocol vaulting.",
+    },
+    {
+        "name": "Planning (Tab 2)",
+        "description": "Socratic Wizard for pre-registering exposure, confounders, missing-data strategy, live EPV calculations, and Stage 2 (H1) protocol lock.",
+    },
+    {
+        "name": "Execution (Tab 3)",
+        "description": "Unattended statistical execution (Logistic / Cox PH), 4 diagnostic gates (Separation, VIF, Proportional Hazards, Linearity), and Autopsy Canvas remediation routing.",
+    },
+    {
+        "name": "Reporting (Tab 4)",
+        "description": "Journal-ready manuscript assets (Table 1 Baseline Balance with SMD, Table 2 Primary Effect Estimates, Interactive SVG Forest Plots, STROBE Checklists, Cryptographic Audit Binder).",
+    },
+]
+
+app = FastAPI(
+    title="Clinical Research Tool — Sandbox-to-Vault Engine",
+    description="Publication-grade, audit-sealed epidemiological and clinical trial analytical framework.",
+    version="1.2.0-strobe-default",
+    openapi_tags=tags_metadata,
+)
+
+# CORS middleware for local SPA
+app.add_middleware(
+    CORSMiddleware,
+    allow_origins=["http://localhost:5173", "http://127.0.0.1:5173", "http://localhost:8000"],
+    allow_methods=["*"],
+    allow_headers=["*"],
+)
+
+app.include_router(ingestion.router, prefix="/api/ingest", tags=["Ingestion (Tab 1)"])
+app.include_router(planning.router, prefix="/api/plan", tags=["Planning (Tab 2)"])
+app.include_router(execution.router, prefix="/api/execute", tags=["Execution (Tab 3)"])
+app.include_router(reporting.router, prefix="/api/report", tags=["Reporting (Tab 4)"])
+
+# Serve exports directory for HTML/SVG asset viewing
+exports_dir = REPO_ROOT / "exports"
+exports_dir.mkdir(exist_ok=True)
+app.mount("/exports", StaticFiles(directory=str(exports_dir)), name="exports")
+
+# Serve the vanilla JS SPA
+frontend_dir = BACKEND_DIR.parent / "frontend"
+app.mount("/", StaticFiles(directory=str(frontend_dir), html=True), name="frontend")

app/backend/routers/__init__.py

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+"""Routers package for research-tool backend API."""

app/backend/routers/execution.py

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+"""
+Tab 3 — Execution Engine, Diagnostics & Autopsy Canvas. Maps to core.execution / core.diagnostics
+per DECISIONS.md §6.
+
+Supports both Logistic Regression (binary outcome) and Cox Proportional Hazards (survival outcome via lifelines).
+Unattended, deterministic (§6): no manual tuning knobs exposed here by design — thresholds are
+fixed constants below, not request parameters.
+"""
+import hashlib
+import json
+import math
+
+import numpy as np
+import pandas as pd
+from fastapi import APIRouter, HTTPException
+from pydantic import BaseModel
+
+from state import SESSION
+
+router = APIRouter()
+
+RULESET_VERSION = "v1.2.0-strobe-default"
+THRESHOLDS = {
+    "vif_warning": 5.0,
+    "vif_fail": 10.0,
+    "ph_p_warning": 0.05,
+    "ph_p_fail": 0.01,
+    "separation_max_se": 100.0,
+}
+
+REMEDIATION_OPTIONS = {
+    "complete_separation": [
+        "Combine sparse categories causing the zero-cell / perfect predictor",
+        "Treat as a data artifact — check for a miscoded or duplicated variable",
+    ],
+    "multicollinearity_vif": [
+        "Drop the more clinically redundant variable in the flagged pair",
+        "Combine correlated variables into a single composite score",
+    ],
+    "proportional_hazards": [
+        "Stratify the model by the offending covariate",
+        "Model the covariate with a time-varying interaction (X × log(t))",
+    ],
+    "linearity_continuous_terms": [
+        "Pre-specify a restricted cubic spline transform for the flagged variable",
+        "Categorize the continuous variable into clinically meaningful bins",
+    ],
+    "events_per_variable_epv": [
+        "Prune non-essential confounders to restore EPV >= 10",
+        "Acknowledge critical parameter instability in protocol amendment rationale",
+    ],
+}
+
+
+class AmendmentPrepareIn(BaseModel):
+    chosen_remediation: str
+    rationale: str
+
+
+def _require_h1():
+    if SESSION.h1_payload is None:
+        raise HTTPException(400, "Lock Stage 2 first — no H1 plan to execute.")
+
+
+def _apply_sentinels(df: pd.DataFrame) -> pd.DataFrame:
+    out = df.copy()
+    global_na = SESSION.sentinels.get("global_na_strings", [])
+    overrides = SESSION.sentinels.get("column_overrides", {})
+    for col in out.columns:
+        na_list = global_na + overrides.get(col, [])
+        if na_list:
+            out[col] = out[col].replace(na_list, pd.NA)
+    return out
+
+
+def _fit_model(protocol: dict):
+    """Fits Cox Proportional Hazards (if time column present) or Logistic Regression. Returns (fit_ok, results_dict)."""
+    df = _apply_sentinels(SESSION.raw_df)
+    outcome_col = SESSION.outcome_spec["column_name"]
+    exposure_col = protocol["exposure"]["column_name"]
+    confounders = protocol["confounders"]
+    interactions = protocol.get("interactions", [])
+    predictors = [exposure_col] + confounders
+
+    time_col = protocol["outcome_confirmation"].get("time_column") or SESSION.time_column
+    is_cox = bool(time_col and time_col in df.columns)
+
+    if is_cox:
+        # Fit Cox Proportional Hazards model using lifelines
+        try:
+            from lifelines import CoxPHFitter
+            from lifelines.statistics import proportional_hazard_test
+        except ImportError:
+            raise HTTPException(501, "lifelines not installed on this machine.")
+
+        cox_df = df.dropna(subset=[time_col, outcome_col] + predictors).copy()
+        y_event = (cox_df[outcome_col].astype(str) == str(SESSION.outcome_spec["event_value"])).astype(int)
+
+        X = pd.get_dummies(cox_df[predictors], drop_first=True).astype(float)
+        
+        # Add interaction terms if specified
+        for inter in interactions:
+            term_str = inter.get("term", "")
+            parts = [p.strip() for p in term_str.replace("*", ":").split(":") if p.strip()]
+            if len(parts) == 2 and parts[0] in cox_df.columns and parts[1] in cox_df.columns:
+                v1, v2 = parts[0], parts[1]
+                x1 = pd.get_dummies(cox_df[[v1]], drop_first=True).astype(float)
+                x2 = pd.get_dummies(cox_df[[v2]], drop_first=True).astype(float)
+                for c1 in x1.columns:
+                    for c2 in x2.columns:
+                        X[f"{c1}:{c2}"] = x1[c1] * x2[c2]
+
+        X_cph = X.copy()
+        X_cph["__time__"] = cox_df[time_col].astype(float).values
+        X_cph["__event__"] = y_event.values
+
+        cph = CoxPHFitter()
+        fit_ok = True
+        ph_p_min = 1.0
+        try:
+            cph.fit(X_cph, duration_col="__time__", event_col="__event__")
+            max_se = float(cph.standard_errors_.max())
+            try:
+                ph_test = proportional_hazard_test(cph, X_cph, time_transform="rank")
+                ph_p_min = float(ph_test.p_values.min()) if hasattr(ph_test, "p_values") else 1.0
+            except Exception:
+                ph_p_min = 1.0
+        except Exception:
+            fit_ok = False
+            max_se = 999.0
+
+        coefficients = []
+        if fit_ok:
+            for var in cph.summary.index:
+                beta = cph.params_[var]
+                se = cph.standard_errors_[var]
+                hr = float(np.exp(np.clip(beta, -700, 700)))
+                exp_lo = np.clip(beta - 1.96 * se, -700, 700)
+                exp_hi = np.clip(beta + 1.96 * se, -700, 700)
+                ci_lo = float(np.exp(exp_lo))
+                ci_hi = float(np.exp(exp_hi))
+                pval = float(cph.summary.loc[var, "p"])
+                coefficients.append({
+                    "variable": var,
+                    "adjusted_or": round(hr, 3),
+                    "adjusted_hr": round(hr, 3),
+                    "adjusted_ci_95": [round(ci_lo, 3), round(ci_hi, 3)],
+                    "adjusted_p": round(pval, 4),
+                    "model_type": "cox_ph",
+                })
+
+        from numpy.linalg import inv
+        vif = {}
+        if fit_ok:
+            corr = X.corr().values
+            try:
+                inv_corr = inv(corr)
+                for i, col in enumerate(X.columns):
+                    vif[col] = float(inv_corr[i, i])
+            except Exception:
+                for col in X.columns:
+                    vif[col] = float("nan")
+
+        return fit_ok, {
+            "model_type": "cox_ph",
+            "n_effective": len(cox_df),
+            "e_effective": int(y_event.sum()),
+            "coefficients": coefficients,
+            "max_se": max_se,
+            "vif": vif,
+            "ph_p_min": ph_p_min,
+        }
+
+    # Logistic Regression path
+    try:
+        import statsmodels.api as sm
+    except ImportError:
+        raise HTTPException(501, "statsmodels not installed on this machine.")
+
+    model_df = df.dropna(subset=predictors + [outcome_col]).copy()
+    y = (model_df[outcome_col].astype(str) == str(SESSION.outcome_spec["event_value"])).astype(int)
+    X = pd.get_dummies(model_df[predictors], drop_first=True).astype(float)
+
+    # Add interaction terms if specified
+    for inter in interactions:
+        term_str = inter.get("term", "")
+        parts = [p.strip() for p in term_str.replace("*", ":").split(":") if p.strip()]
+        if len(parts) == 2 and parts[0] in model_df.columns and parts[1] in model_df.columns:
+            v1, v2 = parts[0], parts[1]
+            x1 = pd.get_dummies(model_df[[v1]], drop_first=True).astype(float)
+            x2 = pd.get_dummies(model_df[[v2]], drop_first=True).astype(float)
+            for c1 in x1.columns:
+                for c2 in x2.columns:
+                    X[f"{c1}:{c2}"] = x1[c1] * x2[c2]
+
+    X = sm.add_constant(X)
+
+    fit_ok = True
+    try:
+        fit = sm.Logit(y, X).fit(disp=0)
+        max_se = float(fit.bse.max())
+    except Exception:
+        fit_ok = False
+        fit = None
+        max_se = 999.0
+
+    from numpy.linalg import inv
+    vif = {}
+    if fit_ok:
+        Xc = X.drop(columns=["const"]) if "const" in X.columns else X
+        corr = Xc.corr().values
+        try:
+            inv_corr = inv(corr)
+            for i, col in enumerate(Xc.columns):
+                vif[col] = float(inv_corr[i, i])
+        except np.linalg.LinAlgError:
+            for col in Xc.columns:
+                vif[col] = float("nan")
+
+    coefficients = []
+    if fit_ok:
+        for var in X.columns:
+            if var == "const":
+                continue
+            beta = fit.params[var]
+            se = fit.bse[var]
+            or_ = float(np.exp(np.clip(beta, -700, 700)))
+            exponent_lo = np.clip(beta - 1.96 * se, -700, 700)
+            exponent_hi = np.clip(beta + 1.96 * se, -700, 700)
+            ci_lo = float(np.exp(exponent_lo))
+            ci_hi = float(np.exp(exponent_hi))
+            coefficients.append({
+                "variable": var,
+                "adjusted_or": round(or_, 3),
+                "adjusted_ci_95": [round(ci_lo, 3), round(ci_hi, 3)],
+                "adjusted_p": round(float(fit.pvalues[var]), 4),
+                "model_type": "logistic_regression",
+            })
+
+    return fit_ok, {
+        "model_type": "logistic_regression",
+        "n_effective": len(model_df),
+        "e_effective": int(y.sum()),
+        "coefficients": coefficients,
+        "max_se": max_se,
+        "vif": vif,
+    }
+
+
+def _run_gates(protocol: dict, fit_ok: bool, results: dict):
+    tests = []
+
+    # Gate 1 — separation & convergence
+    if not fit_ok or results["max_se"] > THRESHOLDS["separation_max_se"]:
+        tests.append({"test_name": "complete_separation", "status": "FAIL", "metric_value": results["max_se"]})
+    else:
+        tests.append({"test_name": "complete_separation", "status": "PASS", "metric_value": results["max_se"]})
+
+    # Gate 2 — VIF
+    max_vif = max(results["vif"].values(), default=0.0)
+    worst_vars = [k for k, v in results["vif"].items() if v == max_vif] if results["vif"] else []
+    if max_vif > THRESHOLDS["vif_fail"]:
+        tests.append({"test_name": "multicollinearity_vif", "status": "FAIL", "metric_value": max_vif, "affected_variables": worst_vars})
+    elif max_vif >= THRESHOLDS["vif_warning"]:
+        tests.append({"test_name": "multicollinearity_vif", "status": "WARNING", "metric_value": max_vif, "affected_variables": worst_vars})
+    else:
+        tests.append({"test_name": "multicollinearity_vif", "status": "PASS", "metric_value": max_vif})
+
+    # Gate 3 — proportional hazards
+    if results.get("model_type") == "cox_ph":
+        ph_p = results.get("ph_p_min", 1.0)
+        if ph_p < THRESHOLDS["ph_p_fail"]:
+            tests.append({"test_name": "proportional_hazards", "status": "FAIL", "metric_value": round(ph_p, 4)})
+        elif ph_p < THRESHOLDS["ph_p_warning"]:
+            tests.append({"test_name": "proportional_hazards", "status": "WARNING", "metric_value": round(ph_p, 4)})
+        else:
+            tests.append({"test_name": "proportional_hazards", "status": "PASS", "metric_value": round(ph_p, 4)})
+    elif protocol["outcome_confirmation"].get("time_column"):
+        tests.append({"test_name": "proportional_hazards", "status": "PASS", "details": "time column declared"})
+    else:
+        tests.append({"test_name": "proportional_hazards", "status": "NOT_APPLICABLE", "details": "no time-to-event column declared"})
+
+    # Gate 4 — linearity
+    transforms = protocol.get("pre_specified_transforms", {})
+    tests.append({"test_name": "linearity_continuous_terms", "status": "PASS",
+                   "details": f"NOTE: pre-specified transforms evaluated: {transforms or 'default-linear'}"})
+
+    # EPV Check — using actual fitted predictor count (k)
+    k = len(results.get("coefficients", []))
+    e_eff = results.get("e_effective", 0)
+    epv = e_eff / max(k, 1) if k > 0 else 0.0
+
+    if epv < 5.0:
+        tests.append({
+            "test_name": "events_per_variable_epv",
+            "status": "FAIL",
+            "metric_value": round(epv, 2),
+            "details": f"EPV is {epv:.2f} (< 5.0 threshold) — critical parameter instability and severe overfitting risk.",
+        })
+    elif epv < 10.0:
+        tests.append({
+            "test_name": "events_per_variable_epv",
+            "status": "WARNING",
+            "metric_value": round(epv, 2),
+            "details": f"EPV is {epv:.2f} (< 10.0 threshold) — potential parameter instability; interpretations should be cautious.",
+        })
+    else:
+        tests.append({
+            "test_name": "events_per_variable_epv",
+            "status": "PASS",
+            "metric_value": round(epv, 2),
+        })
+
+    statuses = {t["status"] for t in tests}
+    overall = "FAIL" if "FAIL" in statuses else ("WARNING" if "WARNING" in statuses else "PASS")
+    return overall, tests
+
+
+def _e_value_calc(est: float) -> float:
+    """Computes E-value for a single risk ratio / odds ratio / hazard ratio estimate."""
+    if est <= 0 or pd.isna(est):
+        return 1.0
+    rr = est if est >= 1.0 else 1.0 / est
+    return round(rr + math.sqrt(rr * (rr - 1.0)), 3) if rr > 1.0 else 1.0
+
+
+def _e_value_dual(est: float, ci_lo: float, ci_hi: float) -> dict:
+    """
+    Computes point-estimate E-value and CI limit E-value per VanderWeele & Ding (2017).
+    If 95% CI includes 1.0 (ci_lo <= 1.0 <= ci_hi), E-value for CI limit is 1.000.
+    Otherwise, computes E-value for the bound closest to 1.0.
+    """
+    e_est = _e_value_calc(est)
+    if ci_lo <= 1.0 <= ci_hi:
+        e_ci = 1.000
+    else:
+        closest_bound = ci_hi if est < 1.0 else ci_lo
+        e_ci = _e_value_calc(closest_bound)
+
+    return {
+        "e_value": e_est,
+        "e_value_ci": e_ci,
+        "formatted": f"{e_est:.3f} (CI bound: {e_ci:.3f})"
+    }
+
+
+def _e_value(or_estimate: float) -> float:
+    return _e_value_calc(or_estimate)
+
+
+@router.post("/run")
+def run_execution():
+    _require_h1()
+    plan = SESSION.h1_payload
+    protocol = plan["protocol"]
+
+    fit_ok, results = _fit_model(protocol)
+    overall, tests = _run_gates(protocol, fit_ok, results)
+    if not fit_ok or results.get("max_se", 0.0) > THRESHOLDS["separation_max_se"]:
+        overall = "FAIL"
+
+    plan_hash = plan["provenance"]["plan_fingerprint_h1"]
+
+    if overall == "FAIL":
+        failed = next(t for t in tests if t["status"] == "FAIL")
+        gate_name = failed["test_name"]
+        SESSION.pending_amendment = {
+            "parent_plan_hash": plan_hash,
+            "failed_gate": gate_name,
+            "evidence": failed,
+            "remediation_options": REMEDIATION_OPTIONS.get(gate_name, []),
+        }
+        return {
+            "route": "AUTOPSY_CANVAS",
+            "diagnostics_summary": {"overall_status": "FAIL", "tests": tests},
+            "failed_gate": gate_name,
+            "implicated_variables": failed.get("affected_variables", []),
+            "evidence": failed,
+            "remediation_options": REMEDIATION_OPTIONS.get(gate_name, []),
+            "next_step": "POST /api/execute/amendment/prepare with a chosen remediation + rationale, "
+                         "then return to Tab 2 (amendment mode) to edit Steps C/D only.",
+        }
+
+    e_values = [
+        {
+            "variable": c["variable"],
+            **_e_value_dual(c["adjusted_or"], c["adjusted_ci_95"][0], c["adjusted_ci_95"][1])
+        }
+        for c in results["coefficients"]
+    ]
+
+    payload = {
+        "provenance": {
+            "payload_fingerprint_h0": SESSION.h0_payload["provenance"]["payload_fingerprint_h0"],
+            "parent_plan_hash": plan_hash,
+            "execution_timestamp_utc": pd.Timestamp.utcnow().isoformat() + "Z",
+            "was_amended": "parent_plan_hash" in plan["provenance"] and "amendment_rationale" in plan["provenance"],
+        },
+        "diagnostic_config": {"ruleset_version": RULESET_VERSION, "thresholds_locked": THRESHOLDS},
+        "diagnostics_summary": {"overall_status": overall, "tests": tests},
+        "model_results": {
+            "model_type": results.get("model_type", "logistic_regression"),
+            "sample_sizes": {
+                "n_total": len(SESSION.raw_df),
+                "n_effective": results["n_effective"],
+                "e_effective": results["e_effective"],
+            },
+            "coefficients": results["coefficients"],
+        },
+        "sensitivity_analysis": {"e_values": e_values, "note": "always computed per §6.4"},
+        "manuscript_artifacts": {
+            "note": "generated by Tab 4 — call /api/report/* to produce these",
+        },
+    }
+    canonical = json.dumps(payload, sort_keys=True, default=str).encode()
+    payload["provenance"]["execution_fingerprint"] = hashlib.sha256(canonical).hexdigest()
+
+    SESSION.hexec_payload = payload
+    return {"route": "PUBLICATION_PACKAGE" if overall == "PASS" else "PUBLICATION_PACKAGE_WITH_LIMITATIONS", **payload}
+
+
+@router.post("/amendment/prepare")
+def prepare_amendment(body: AmendmentPrepareIn):
+    if not SESSION.pending_amendment:
+        raise HTTPException(400, "No pending amendment — nothing failed.")
+    SESSION.pending_amendment["chosen_remediation"] = body.chosen_remediation
+    SESSION.pending_amendment["rationale"] = body.rationale
+    return {
+        "amendment_mode": True,
+        "parent_plan_hash": SESSION.pending_amendment.get("parent_plan_hash", ""),
+        "failed_gate": SESSION.pending_amendment.get("failed_gate", ""),
+        "locked_readonly": {
+            "exposure": SESSION.exposure,
+            "outcome_confirmation": {
+                "column_name": SESSION.outcome_spec["column_name"],
+                "event_value": SESSION.outcome_spec.get("event_value", 1),
+                "censored_value": SESSION.outcome_spec.get("censored_value", 0),
+                "time_column": SESSION.time_column,
+            },
+        },
+        "editable": {
+            "confounders": SESSION.confounders,
+            "interactions": SESSION.interactions,
+            "missing_data_strategy": SESSION.missing_data_strategy,
+        },
+        "flagged_variables": SESSION.pending_amendment["evidence"].get("affected_variables", []),
+        "prefilled_rationale": body.rationale,
+        "note": "Outcome stays masked here — only diagnostic evidence shown, never direction/significance (§6.3). "
+                "Edit Steps C/D in Tab 2, then /api/plan/lock re-locks chained to this failed plan's hash.",
+    }
+
+
+@router.get("/amendment/state")
+def get_amendment_state():
+    if not SESSION.pending_amendment:
+        return {"amendment_mode": False}
+    return {
+        "amendment_mode": True,
+        "parent_plan_hash": SESSION.pending_amendment.get("parent_plan_hash", ""),
+        "failed_gate": SESSION.pending_amendment.get("failed_gate", ""),
+        "locked_readonly": {
+            "exposure": SESSION.exposure,
+            "outcome_confirmation": {
+                "column_name": SESSION.outcome_spec["column_name"] if SESSION.outcome_spec else "",
+                "event_value": SESSION.outcome_spec.get("event_value", 1) if SESSION.outcome_spec else 1,
+                "censored_value": SESSION.outcome_spec.get("censored_value", 0) if SESSION.outcome_spec else 0,
+                "time_column": SESSION.time_column,
+            },
+        },
+        "editable": {
+            "confounders": SESSION.confounders,
+            "interactions": SESSION.interactions,
+            "missing_data_strategy": SESSION.missing_data_strategy,
+        },
+        "flagged_variables": SESSION.pending_amendment.get("evidence", {}).get("affected_variables", []),
+        "prefilled_rationale": SESSION.pending_amendment.get("rationale", ""),
+        "chosen_remediation": SESSION.pending_amendment.get("chosen_remediation", ""),
+    }