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8ffc9f7 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 | import path from "node:path";
import { promises as fs } from "node:fs";
import { REPO_ROOT } from "./config";
/**
* Types + reader for the diagnostic catalog. The catalog is generated from
* `qc/catalog/diagnostic_catalog.yaml` by `python -m qc.catalog render` into
* `spec/diagnostics/catalog.json`; the studio only reads that JSON (never the YAML).
*/
export interface DiagRelationship {
relationship: "direct" | "indirect" | "unlikely" | "context_dependent";
note: string;
}
export interface DiagAlias {
label: string;
producer?: string;
source_scope?: string;
denominator?: string;
note?: string;
}
export interface DiagMetric {
metric_id: string;
label: string;
description: string;
domain: string;
unit: string;
value_type: string;
direction: string;
scoreability: string;
required_scopes: string[];
platforms: string[];
assays: string[];
denominator?: string;
canonical_calculation?: string;
caveats?: string[];
aliases?: DiagAlias[];
references?: string[];
}
export interface DiagSignal {
signal_id: string;
label: string;
description: string;
metrics: string[];
platforms?: string[];
related_causes?: string[];
is_root_cause?: boolean;
references?: string[];
}
export interface DiagIssue {
issue_id: string;
title: string;
summary: string;
outcome_domains: string[];
platforms: string[];
workflow_stages: string[];
supporting_signals: string[];
contradicting_signals?: string[];
candidate_root_causes: string[];
impacts: string[];
required_evidence: string[];
missing_evidence?: string[];
confirmatory_tests: string[];
recovery_classes: string[];
computational_actions?: string[];
sequencing_actions?: string[];
wetlab_actions?: string[];
related_issues?: string[];
simulation_modes?: string[];
references?: string[];
what_this_issue_cannot_explain: string;
}
export interface DiagCause {
cause_id: string;
title: string;
mechanism: string;
workflow_stage: string;
produces_issues: string[];
observable_signals: string[];
evidence_against?: string[];
required_inputs: string[];
diagnostic_tests: string[];
cell_recovery_relationship: DiagRelationship;
sample_integrity_relationship: DiagRelationship;
expression_fidelity_relationship: DiagRelationship;
recoverability: string;
recommended_actions?: string[];
references?: string[];
simulation_modes?: string[];
}
export interface DiagTest {
test_id: string;
title: string;
purpose: string;
required_inputs: string[];
algorithm_summary: string;
outputs: string;
interpretation: string;
limitations: string;
supports_causes: string[];
rejects_causes?: string[];
status: "implemented" | "planned" | "external";
implemented_by?: string;
references?: string[];
}
export interface DiagRecoveryAction {
recovery_class: string;
label: string;
description: string;
}
export interface DiagReference {
reference_id: string;
title: string;
source: string;
url?: string;
assay_context?: string;
note?: string;
evidence_strength: string;
}
export interface DiagnosticCatalog {
catalog_version: string;
metrics: DiagMetric[];
signals: DiagSignal[];
issues: DiagIssue[];
root_causes: DiagCause[];
diagnostic_tests: DiagTest[];
recovery_actions: DiagRecoveryAction[];
references: DiagReference[];
}
export async function loadDiagnosticCatalog(): Promise<DiagnosticCatalog | null> {
try {
const raw = await fs.readFile(
path.join(REPO_ROOT, "spec", "diagnostics", "catalog.json"),
"utf8",
);
const parsed = JSON.parse(raw) as DiagnosticCatalog;
if (!parsed || !Array.isArray(parsed.issues)) return null;
return parsed;
} catch {
return null;
}
}
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