|
| 1 | +from __future__ import annotations |
| 2 | +from dataclasses import dataclass |
| 3 | +from typing import List |
| 4 | + |
| 5 | + |
| 6 | +VALID_BATCH_GRADES = frozenset({"full", "majority", "minority", "none"}) |
| 7 | + |
| 8 | +LOW_COMPLETENESS_GRADES = frozenset({"minority", "none"}) |
| 9 | + |
| 10 | +VALID_AUDIT_VERDICTS = frozenset({ |
| 11 | + "all_complete", |
| 12 | + "majority_complete", |
| 13 | + "minority_complete", |
| 14 | + "none_complete", |
| 15 | + "no_batches", |
| 16 | +}) |
| 17 | + |
| 18 | +COMPLETENESS_AUDIT_THRESHOLD = 0.5 |
| 19 | + |
| 20 | + |
| 21 | +@dataclass |
| 22 | +class BatchSummaryEntry: |
| 23 | + batch_id: str |
| 24 | + bti_id: str |
| 25 | + n_families_total: int |
| 26 | + n_families_complete: int |
| 27 | + n_families_partial: int |
| 28 | + n_families_empty: int |
| 29 | + batch_completeness_grade: str |
| 30 | + flagged_low_completeness: bool |
| 31 | + |
| 32 | + |
| 33 | +@dataclass |
| 34 | +class CrossBatchAuditSummary: |
| 35 | + cba2_id: str |
| 36 | + pipeline_version: str |
| 37 | + n_batches_total: int |
| 38 | + n_batches_flagged: int |
| 39 | + total_families_across_batches: int |
| 40 | + total_families_complete: int |
| 41 | + total_families_partial: int |
| 42 | + total_families_empty: int |
| 43 | + batch_entries: list[BatchSummaryEntry] |
| 44 | + overall_audit_verdict: str |
| 45 | + flagged_batch_ids: list[str] |
| 46 | + audit_coverage_rate: float |
| 47 | + dry_lab_only: bool |
| 48 | + limitations: list[str] |
| 49 | + created_at: str |
| 50 | + |
| 51 | + |
| 52 | +def _compute_overall_audit_verdict( |
| 53 | + n_batches_total: int, |
| 54 | + n_full: int, |
| 55 | +) -> str: |
| 56 | + if n_batches_total == 0: |
| 57 | + return "no_batches" |
| 58 | + if n_full == n_batches_total: |
| 59 | + return "all_complete" |
| 60 | + if n_full >= n_batches_total / 2: |
| 61 | + return "majority_complete" |
| 62 | + if n_full > 0: |
| 63 | + return "minority_complete" |
| 64 | + return "none_complete" |
| 65 | + |
| 66 | + |
| 67 | +def validate_cross_batch_audit_summary( |
| 68 | + summary: CrossBatchAuditSummary, |
| 69 | +) -> list[str]: |
| 70 | + violations = [] |
| 71 | + |
| 72 | + if not summary.cba2_id.startswith("CBA2-"): |
| 73 | + violations.append("cba2_id must start with 'CBA2-'") |
| 74 | + |
| 75 | + if not summary.dry_lab_only: |
| 76 | + violations.append("dry_lab_only must be True") |
| 77 | + |
| 78 | + if summary.n_batches_total != len(summary.batch_entries): |
| 79 | + violations.append( |
| 80 | + f"n_batches_total ({summary.n_batches_total}) must equal len(batch_entries) ({len(summary.batch_entries)})" |
| 81 | + ) |
| 82 | + |
| 83 | + expected_flagged = sum( |
| 84 | + 1 for e in summary.batch_entries if e.flagged_low_completeness |
| 85 | + ) |
| 86 | + if summary.n_batches_flagged != expected_flagged: |
| 87 | + violations.append( |
| 88 | + f"n_batches_flagged ({summary.n_batches_flagged}) must equal count of flagged entries ({expected_flagged})" |
| 89 | + ) |
| 90 | + |
| 91 | + expected_total = sum(e.n_families_total for e in summary.batch_entries) |
| 92 | + if summary.total_families_across_batches != expected_total: |
| 93 | + violations.append( |
| 94 | + f"total_families_across_batches ({summary.total_families_across_batches}) must equal sum of n_families_total ({expected_total})" |
| 95 | + ) |
| 96 | + |
| 97 | + expected_complete = sum(e.n_families_complete for e in summary.batch_entries) |
| 98 | + if summary.total_families_complete != expected_complete: |
| 99 | + violations.append( |
| 100 | + f"total_families_complete ({summary.total_families_complete}) must equal sum of n_families_complete ({expected_complete})" |
| 101 | + ) |
| 102 | + |
| 103 | + expected_partial = sum(e.n_families_partial for e in summary.batch_entries) |
| 104 | + if summary.total_families_partial != expected_partial: |
| 105 | + violations.append( |
| 106 | + f"total_families_partial ({summary.total_families_partial}) must equal sum of n_families_partial ({expected_partial})" |
| 107 | + ) |
| 108 | + |
| 109 | + expected_empty = sum(e.n_families_empty for e in summary.batch_entries) |
| 110 | + if summary.total_families_empty != expected_empty: |
| 111 | + violations.append( |
| 112 | + f"total_families_empty ({summary.total_families_empty}) must equal sum of n_families_empty ({expected_empty})" |
| 113 | + ) |
| 114 | + |
| 115 | + for entry in summary.batch_entries: |
| 116 | + expected_flag = entry.batch_completeness_grade in LOW_COMPLETENESS_GRADES |
| 117 | + if entry.flagged_low_completeness != expected_flag: |
| 118 | + violations.append( |
| 119 | + f"flagged_low_completeness ({entry.flagged_low_completeness}) for batch {entry.batch_id} must equal {expected_flag} for grade '{entry.batch_completeness_grade}'" |
| 120 | + ) |
| 121 | + |
| 122 | + expected_flagged_ids = sorted( |
| 123 | + e.batch_id for e in summary.batch_entries if e.flagged_low_completeness |
| 124 | + ) |
| 125 | + if summary.flagged_batch_ids != expected_flagged_ids: |
| 126 | + violations.append( |
| 127 | + f"flagged_batch_ids ({summary.flagged_batch_ids}) must equal {expected_flagged_ids}" |
| 128 | + ) |
| 129 | + |
| 130 | + total_families = summary.total_families_across_batches |
| 131 | + expected_coverage = ( |
| 132 | + summary.total_families_complete / total_families if total_families > 0 else 0.0 |
| 133 | + ) |
| 134 | + if abs(summary.audit_coverage_rate - expected_coverage) > 0.001: |
| 135 | + violations.append( |
| 136 | + f"audit_coverage_rate ({summary.audit_coverage_rate}) must approximately equal {expected_coverage}" |
| 137 | + ) |
| 138 | + |
| 139 | + n_full = sum( |
| 140 | + 1 for e in summary.batch_entries if e.batch_completeness_grade == "full" |
| 141 | + ) |
| 142 | + expected_verdict = _compute_overall_audit_verdict( |
| 143 | + summary.n_batches_total, n_full |
| 144 | + ) |
| 145 | + if summary.overall_audit_verdict != expected_verdict: |
| 146 | + violations.append( |
| 147 | + f"overall_audit_verdict '{summary.overall_audit_verdict}' must be '{expected_verdict}' " |
| 148 | + f"given n_batches_total={summary.n_batches_total} and n_full={n_full}" |
| 149 | + ) |
| 150 | + |
| 151 | + if not summary.limitations: |
| 152 | + violations.append("limitations must be non-empty") |
| 153 | + |
| 154 | + return violations |
| 155 | + |
| 156 | + |
| 157 | +def build_cross_batch_audit_summary( |
| 158 | + cba2_id: str, |
| 159 | + pipeline_version: str, |
| 160 | + batch_entry_dicts: list[dict], |
| 161 | + limitations: list[str], |
| 162 | + created_at: str, |
| 163 | +) -> CrossBatchAuditSummary: |
| 164 | + batch_entries: list[BatchSummaryEntry] = [] |
| 165 | + for d in batch_entry_dicts: |
| 166 | + grade = d["batch_completeness_grade"] |
| 167 | + flagged = grade in LOW_COMPLETENESS_GRADES |
| 168 | + batch_entries.append( |
| 169 | + BatchSummaryEntry( |
| 170 | + batch_id=d["batch_id"], |
| 171 | + bti_id=d["bti_id"], |
| 172 | + n_families_total=d["n_families_total"], |
| 173 | + n_families_complete=d["n_families_complete"], |
| 174 | + n_families_partial=d["n_families_partial"], |
| 175 | + n_families_empty=d["n_families_empty"], |
| 176 | + batch_completeness_grade=grade, |
| 177 | + flagged_low_completeness=flagged, |
| 178 | + ) |
| 179 | + ) |
| 180 | + |
| 181 | + n_batches_total = len(batch_entries) |
| 182 | + n_batches_flagged = sum(1 for e in batch_entries if e.flagged_low_completeness) |
| 183 | + total_families_across_batches = sum(e.n_families_total for e in batch_entries) |
| 184 | + total_families_complete = sum(e.n_families_complete for e in batch_entries) |
| 185 | + total_families_partial = sum(e.n_families_partial for e in batch_entries) |
| 186 | + total_families_empty = sum(e.n_families_empty for e in batch_entries) |
| 187 | + audit_coverage_rate = ( |
| 188 | + total_families_complete / total_families_across_batches |
| 189 | + if total_families_across_batches > 0 |
| 190 | + else 0.0 |
| 191 | + ) |
| 192 | + flagged_batch_ids = sorted( |
| 193 | + e.batch_id for e in batch_entries if e.flagged_low_completeness |
| 194 | + ) |
| 195 | + n_full = sum( |
| 196 | + 1 for e in batch_entries if e.batch_completeness_grade == "full" |
| 197 | + ) |
| 198 | + overall_audit_verdict = _compute_overall_audit_verdict( |
| 199 | + n_batches_total, n_full |
| 200 | + ) |
| 201 | + |
| 202 | + summary = CrossBatchAuditSummary( |
| 203 | + cba2_id=cba2_id, |
| 204 | + pipeline_version=pipeline_version, |
| 205 | + n_batches_total=n_batches_total, |
| 206 | + n_batches_flagged=n_batches_flagged, |
| 207 | + total_families_across_batches=total_families_across_batches, |
| 208 | + total_families_complete=total_families_complete, |
| 209 | + total_families_partial=total_families_partial, |
| 210 | + total_families_empty=total_families_empty, |
| 211 | + batch_entries=batch_entries, |
| 212 | + overall_audit_verdict=overall_audit_verdict, |
| 213 | + flagged_batch_ids=flagged_batch_ids, |
| 214 | + audit_coverage_rate=audit_coverage_rate, |
| 215 | + dry_lab_only=True, |
| 216 | + limitations=limitations, |
| 217 | + created_at=created_at, |
| 218 | + ) |
| 219 | + |
| 220 | + violations = validate_cross_batch_audit_summary(summary) |
| 221 | + if violations: |
| 222 | + raise ValueError(f"Invalid CrossBatchAuditSummary: {violations}") |
| 223 | + return summary |
| 224 | + |
| 225 | + |
| 226 | +def format_cross_batch_audit_summary(summary: CrossBatchAuditSummary) -> str: |
| 227 | + flagged_str = ", ".join(summary.flagged_batch_ids) if summary.flagged_batch_ids else "(none)" |
| 228 | + limitations_str = "; ".join(summary.limitations) |
| 229 | + lines = [ |
| 230 | + f"Cross-Batch Audit Summary — {summary.cba2_id}", |
| 231 | + f"Pipeline: {summary.pipeline_version} | Created: {summary.created_at}", |
| 232 | + f"Batches: {summary.n_batches_total} total, {summary.n_batches_flagged} flagged", |
| 233 | + f"Audit Verdict: {summary.overall_audit_verdict} | " |
| 234 | + f"Coverage Rate: {summary.audit_coverage_rate:.3f}", |
| 235 | + f"Families — Complete: {summary.total_families_complete} | " |
| 236 | + f"Partial: {summary.total_families_partial} | " |
| 237 | + f"Empty: {summary.total_families_empty} | " |
| 238 | + f"Total: {summary.total_families_across_batches}", |
| 239 | + f"Flagged Batches: [{flagged_str}]", |
| 240 | + f"Limitations: {limitations_str}", |
| 241 | + "dry_lab_only: True", |
| 242 | + "", |
| 243 | + "Batch Entries:", |
| 244 | + ] |
| 245 | + for entry in summary.batch_entries: |
| 246 | + flag_marker = " [FLAGGED]" if entry.flagged_low_completeness else "" |
| 247 | + lines.append( |
| 248 | + f" {entry.batch_id} ({entry.bti_id}): " |
| 249 | + f"grade={entry.batch_completeness_grade}, " |
| 250 | + f"complete={entry.n_families_complete}, " |
| 251 | + f"partial={entry.n_families_partial}, " |
| 252 | + f"empty={entry.n_families_empty}, " |
| 253 | + f"total={entry.n_families_total}{flag_marker}" |
| 254 | + ) |
| 255 | + return "\n".join(lines) |
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