ReportabilityRulesJsonBuilder

Reportability Rules JSON Builder

Liquid Biopsy жидкостная биопсия cfDNA ctDNA CTC exosomes NGS qPCR

Utility description: Reportability Rules JSON Builder

Reportability Rules JSON Builder — Generation and Validation of Reportability Rules JSON Configurations

Provides machine-readable representation of reportability rules per AMP/ASCO/CAP Tiering v2, ACMG/AMP 2015 + SVI, HL7 FHIR Genomics Reporting and CAP/CLIA §GEN.48800: schema version compatibility (2.0.0–2.2.0), JSON syntax validation, required fields completeness (ruleset metadata, global thresholds, inclusion/exclusion/conditional rules, tier mapping, secondary findings policy), logic consistency verification (no contradictory rules without priority resolution), AMP/ASCO/CAP four-tier mapping completeness, secondary findings policy (ACMG SF list version, explicit consent, P/LP only, opt-out respected), version history and approval chain validation. Three-tier classification: VALID / VALID_WITH_WARNINGS / INVALID.

⚠️ Critical: Text SOPs ≠ software implementation; only JSON config guarantees unambiguity. Contradictory rules without priorities = UNPREDICTABLE BEHAVIOR at deployment. Missing tier mapping makes somatic variant classification impossible. Secondary findings policy is MANDATORY; absence = regulatory violation. Each config version must have unique version and predecessor reference. Approval chain must be documented; unapproved config cannot be deployed. Tool validates STRUCTURE AND CONSISTENCY only; does not verify clinical correctness of rules themselves. Clinical correctness determined by molecular pathologist and approved by committee.

input.csv

RulesetId,RulesetName,SchemaVersion,EffectiveDate,SupersedesVersion,ApprovedBy,ApplicableContexts,InclusionRuleCount,ExclusionRuleCount,ConditionalRuleCount,JsonSyntaxValid,HasGlobalThresholds,HasTierMapping,HasSecondaryFindingsPolicy,AllRequiredFieldsPresent,NoContradictoryRules,VersionHistoryConsistent
RULES-NSCLC-CGP-v3.2,NSCLC CGP Reportability Rules,2.1.0,2026-06-01,RULES-NSCLC-CGP-v3.1,Molecular Pathology Committee,Somatic_NSCLC;Somatic_SolidTumor,12,8,5,true,true,true,true,true,true,true
RULES-HEME-PANEL-v1.0-draft,Heme Panel Reportability Rules DRAFT,2.1.0,2026-07-01,,,"Somatic_Hematologic",6,3,0,true,true,false,false,false,false,false

URS & FS — User Requirements and Functional Specification

This document describes the controlled interface and behaviour of ReportabilityRulesJsonBuilder for Reportability Rules JSON Builder.

Domain limits URS input.csv FS IQ/OQ/PQ

Domain limits and critical parameters

Key fragments from the source description are shown below. Before production use, limits must be verified against the approved specification, registration dossier and local SOPs.

⚠️ Critical: Text SOPs ≠ software implementation; only JSON config guarantees unambiguity. Contradictory rules without priorities = UNPREDICTABLE BEHAVIOR at deployment. Missing tier mapping makes somatic variant classification impossible. Secondary findings policy is MANDATORY; absence = regulatory violation. Each config version must have unique version and predecessor reference. Approval chain must be documented; unapproved config cannot be deployed. Tool validates STRUCTURE AND CONSISTENCY on

URS — User Requirements Specification

ID	Requirement	Criticality	Acceptance criterion
URS-001	The utility shall accept an input.csv file for Reportability Rules JSON Builder with headers defined in the data contract.	High	The file is processed without manual header editing.
URS-002	The utility shall perform deterministic QC evaluation without machine learning and without probabilistic conformance decisions.	High	Identical input data, rule version and configuration produce reproducible results.
URS-003	The utility shall validate mandatory fields, data types, ranges, units and domain plausibility.	High	Schema, conversion and range errors are explicitly reported.
URS-004	The utility shall apply domain limits and rules from the description, approved specification, registration dossier and local SOPs.	High	Each check has PASS/WARNING/FAIL and a clear message.
URS-005	The utility shall generate output.json with machine-readable results, source values, warnings, failures and critical findings.	High	JSON is suitable for LIMS/ELN/MES integration and QA/QC review.
URS-006	The utility shall preserve traceability between batch/sample, input file, applied rules and final status.	High	Output contains identifiers, checked parameters and audit metadata.
URS-007	The documentation shall support IQ/OQ/PQ, CSV/CSA and review by internal QA or inspectors.	Medium	URS, FS, input/output contract and test scenarios are supplied with the utility.
URS-008	The utility shall be used as a QC decision-support tool and not as a substitute for approved specifications and QA/QP release decision.	Medium	Documentation states change control and limit-verification expectations.

input.csv contract

#	Field	Type	Sample	Purpose
1	`RulesetId`	string / controlled vocabulary	`RULES-NSCLC-CGP-v3.2`	Controlled input parameter for deterministic QC rules.
2	`RulesetName`	string / controlled vocabulary	`NSCLC CGP Reportability Rules`	Controlled input parameter for deterministic QC rules.
3	`SchemaVersion`	string / controlled vocabulary	`2.1.0`	Controlled input parameter for deterministic QC rules.
4	`EffectiveDate`	string / controlled vocabulary	`2026-06-01`	Controlled input parameter for deterministic QC rules.
5	`SupersedesVersion`	string / controlled vocabulary	`RULES-NSCLC-CGP-v3.1`	Controlled input parameter for deterministic QC rules.
6	`ApprovedBy`	string / controlled vocabulary	`Molecular Pathology Committee`	Controlled input parameter for deterministic QC rules.
7	`ApplicableContexts`	string / controlled vocabulary	`Somatic_NSCLC;Somatic_SolidTumor`	Controlled input parameter for deterministic QC rules.
8	`InclusionRuleCount`	integer / decimal	`12`	Count parameter used for microbiological, particulate or cellular control.
9	`ExclusionRuleCount`	integer / decimal	`8`	Count parameter used for microbiological, particulate or cellular control.
10	`ConditionalRuleCount`	integer / decimal	`5`	Count parameter used for microbiological, particulate or cellular control.
11	`JsonSyntaxValid`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
12	`HasGlobalThresholds`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
13	`HasTierMapping`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
14	`HasSecondaryFindingsPolicy`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
15	`AllRequiredFieldsPresent`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
16	`NoContradictoryRules`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.
17	`VersionHistoryConsistent`	string / controlled vocabulary	`true`	Controlled input parameter for deterministic QC rules.

RulesetId,RulesetName,SchemaVersion,EffectiveDate,SupersedesVersion,ApprovedBy,ApplicableContexts,InclusionRuleCount,ExclusionRuleCount,ConditionalRuleCount,JsonSyntaxValid,HasGlobalThresholds,HasTierMapping,HasSecondaryFindingsPolicy,AllRequiredFieldsPresent,NoContradictoryRules,VersionHistoryConsistent
RULES-NSCLC-CGP-v3.2,NSCLC CGP Reportability Rules,2.1.0,2026-06-01,RULES-NSCLC-CGP-v3.1,Molecular Pathology Committee,Somatic_NSCLC;Somatic_SolidTumor,12,8,5,true,true,true,true,true,true,true
RULES-HEME-PANEL-v1.0-draft,Heme Panel Reportability Rules DRAFT,2.1.0,2026-07-01,,,Somatic_Hematologic,6,3,0,true,true,false,false,false,false,false

Input validation rules

ID	Field	Rule	Criticality
VR-001	`RulesetId`	The field shall match an approved dictionary or accepted string representation.	High
VR-002	`RulesetName`	The field shall match an approved dictionary or accepted string representation.	High
VR-003	`SchemaVersion`	The field shall match an approved dictionary or accepted string representation.	High
VR-004	`EffectiveDate`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-005	`SupersedesVersion`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-006	`ApprovedBy`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-007	`ApplicableContexts`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-008	`InclusionRuleCount`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-009	`ExclusionRuleCount`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-010	`ConditionalRuleCount`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-011	`JsonSyntaxValid`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-012	`HasGlobalThresholds`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-013	`HasTierMapping`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-014	`HasSecondaryFindingsPolicy`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-015	`AllRequiredFieldsPresent`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-016	`NoContradictoryRules`	The field shall match an approved dictionary or accepted string representation.	Medium
VR-017	`VersionHistoryConsistent`	The field shall match an approved dictionary or accepted string representation.	Medium

FS — Functional Specification

ID	Function	Implementation
FS-001	CLI execution	Support execution modes: demo mode without arguments and production mode input.csv output.json.
FS-002	CSV import	Read input.csv in UTF-8/CSV-compatible format and validate header and expected columns.
FS-003	Schema validation	Check mandatory fields, column count, unknown key fields and empty mandatory values.
FS-004	Type conversion	Convert numeric, flag and text values; invalid format is recorded as a row-level error.
FS-005	Domain rule engine	Apply rules for Reportability Rules JSON Builder, including critical limits from the description and approved specification.
FS-006	Status aggregation	Produce final status: FAIL for critical failure, WARNING for non-critical deviation, PASS for conformance.
FS-007	JSON export	Write output.json with detailed checks, source values, warnings, failures and critical findings.
FS-008	Audit support	Keep result structure suitable for review, deviation investigation and calculation reproduction.
FS-009	Integration contract	Support the scenario LIMS/ELN/MES → input.csv → utility → output.json → portal/admin review.
FS-010	Error handling	Return explicit messages for missing file, empty CSV, invalid schema, output write failure and invalid format.

Example output.json

{
  "utilityId": "reportabilityrulesjsonbuilder",
  "utilityFolder": "ReportabilityRulesJsonBuilder",
  "package": "LiquidBiopsy",
  "overallStatus": "PASS|WARNING|FAIL",
  "sourceFile": "input.csv",
  "processedAtUtc": "2026-06-10T00:00:00Z",
  "checks": [
    {
      "parameter": "RulesetId",
      "value": "RULES-NSCLC-CGP-v3.2",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-001"
    },
    {
      "parameter": "RulesetName",
      "value": "NSCLC CGP Reportability Rules",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-002"
    },
    {
      "parameter": "SchemaVersion",
      "value": "2.1.0",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-003"
    },
    {
      "parameter": "EffectiveDate",
      "value": "2026-06-01",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-004"
    },
    {
      "parameter": "SupersedesVersion",
      "value": "RULES-NSCLC-CGP-v3.1",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-005"
    },
    {
      "parameter": "ApprovedBy",
      "value": "Molecular Pathology Committee",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-006"
    },
    {
      "parameter": "ApplicableContexts",
      "value": "Somatic_NSCLC;Somatic_SolidTumor",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-007"
    },
    {
      "parameter": "InclusionRuleCount",
      "value": "12",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-008"
    },
    {
      "parameter": "ExclusionRuleCount",
      "value": "8",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-009"
    },
    {
      "parameter": "ConditionalRuleCount",
      "value": "5",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-010"
    },
    {
      "parameter": "JsonSyntaxValid",
      "value": "true",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-011"
    },
    {
      "parameter": "HasGlobalThresholds",
      "value": "true",
      "status": "PASS|WARNING|FAIL",
      "message": "Deterministic rule-based check result",
      "ruleReference": "FS-RULE-012"
    }
  ],
  "criticalFindings": [],
  "warnings": [],
  "audit": {
    "inputHash": "sha256:<calculated at runtime>",
    "rulesVersion": "<utility executable version>",
    "documentation": "ReportabilityRulesJsonBuilder.documentation.html"
  }
}

Traceability matrix

URS	FS	Test	Evidence
URS-001	FS-001, FS-002	OQ-001	Verify execution and import of valid input.csv.
URS-002	FS-005, FS-006	OQ-004	Repeat the same dataset and compare output.json.
URS-003	FS-003, FS-004, FS-010	OQ-002, OQ-003	Verify missing columns and invalid types.
URS-004	FS-005, FS-006	OQ-004, PQ-001	Verify critical deviations on real/boundary data.
URS-005	FS-007, FS-009	OQ-005	Verify JSON schema and downstream-system suitability.
URS-006	FS-008	OQ-006	Verify identifiers and audit metadata.
URS-007	FS-008, FS-010	IQ-001, OQ-007	Verify documentation completeness and control evidence.
URS-008	FS-005, FS-008	PQ-002	Verify review workflow and no replacement of QA decision.

IQ/OQ/PQ test scenarios

ID	Scenario	Expected result
IQ-001	Verify executable, input.csv, documentation and checksum availability.	Delivery set is complete; version is recorded.
OQ-001	Valid sample row from input.csv.	PASS or acceptable WARNING according to rules.
OQ-002	Remove a mandatory CSV column.	Schema error or FAIL with missing-column reference.
OQ-003	Place a non-numeric value into a numeric field.	Type-conversion error with row/field reference.
OQ-004	Set a critical parameter outside the limit.	FAIL and critical finding.
OQ-005	Verify output.json structure.	All mandatory sections are present and JSON is valid.
OQ-006	Verify batch/sample traceability.	Input and result identifiers match.
PQ-001	Verify 3–5 real user batches/samples.	Result is confirmed by QC/QA review.
PQ-002	Verify deviation workflow and manual QA decision.	Utility supports review but does not replace approved decision.

QA/QC and change control

Do not rename columns without updating validator, documentation and test set.
Retain input.csv, output.json, executable version and checksum.
Before production use, perform IQ/OQ/PQ or equivalent CSV/CSA verification.
Critical limits shall be verified against the approved specification, registration dossier and local SOPs.
The utility provides structured QC decision support; final release decision remains with QA/QP and approved procedures.

Included in packages

Liquid Biopsy QC Suite

QC and pre-analytical control package for liquid biopsy workflows: cfDNA/ctDNA, CTC, EV/exosomes, methylation, NGS/qPCR/ddPCR, sample quality, contamination, sensitivity and reporting checks.

Open