Specialized Rules Design

Document Type: Rule Design (Tier 2) Domain: RULES-SPECIALIZED Domain Character: Algorithmic SRS References: Multiple specialized rules (see Requirements Covered) Status: Draft Last Updated: 2026-01-25

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1. Overview

1.0 Rule Summary

Property	Value
Intent	Implement specialized analytical rules including well-type checks, cross-contamination detection, resolution propagation, repeat sample validation, missing mix handling, inconclusive detection, and standard curve quantification.
Inputs	Well observations, kit configuration, resolution codes, historical wells, quantification settings
Outputs	Error codes, LIMS statuses, calculated quantities, resolution propagation
Precedence	Varies by rule - see individual rule precedence in table below

1.1 Purpose

This document describes the design of specialized analytics rules that handle specific well-type scenarios, cross-contamination detection, resolution workflows, and quantification. These rules are distinct from the core classification and outcome rules, addressing edge cases and specialized laboratory workflows.

1.2 Rules Covered

Rule ID	Name	Description	Precedence
WC	Cross Talk	Detect cross-talk in HSV/HTLV assays DEPRECATED	-
WT	Well Transfer	Propagate control errors to patient wells	After control failure detection
WCAF	Multiple Control Failures	Detect 2+ control failures in run	Run-level QC
RWAC	Resolution Well Affecting Control	Apply resolution outcomes to patient wells	After control resolution
ADJ	Adjacent CT	Detect cross-contamination between adjacent wells	Standalone
ADJ_ZIKA	Adjacent Zika	Zika-specific cross-contamination with history	Standalone
RRESOLUTION	Resolution LIMS	Set LIMS from resolution code	Resolution processing
WREP	Repeat Sample	Validate repeat sample consistency	Standalone
MISSING_MIXES	Missing Mixes	Detect missing mixes for combined outcomes	After Multi Mix Combined Check
INCONCLUSIVE	Inconclusive	Flag inconclusive result patterns	Post-analysis
QSSC	Standard Curve Quantification	Calculate quantity from CT using stored curve	Quantification phase

1.3 Requirements Covered

REQ ID	Title	Priority
REQ-RULES-WC-001	Detect Cross-Talk in Wells DEPRECATED	-
REQ-RULES-WT-001	Propagate Control Failure Errors to Patient Wells	Must
REQ-RULES-WT-002	Clear Patient Well Errors on Control Resolution	Must
REQ-RULES-WT-003	Check Fallback Mixes for Control Errors	Must
REQ-RULES-WCAF-001	Detect and Mark Multiple Control Failures	Must
REQ-RULES-WCAF-002	Exclude Unknown Mix Wells from Failure Counting	Must
REQ-RULES-WCAF-003	Clear Error When Failures Reduce Below Threshold	Must
REQ-RULES-RWAC-001	Apply Resolution Code LIMS Status to Patient Wells	Must
REQ-RULES-RWAC-002	Use Fallback Controls When Primary Controls Unavailable	Must
REQ-RULES-RWAC-003	Apply Highest Priority Resolution When Multiple Controls Resolved	Must
REQ-RULES-RWAC-004	Allow Error Wells to Receive Resolution Outcomes	Must
REQ-RULES-ADJ-001	Detect Cross-Contamination Between Adjacent Wells	Must
REQ-RULES-ADJ-002	Persist Cross-Contamination Errors After Export and Re-Analysis	Must
REQ-RULES-ADJ-003	Allow Resolution of Cross-Contamination Errors	Should
REQ-RULES-ADJ-004	Capture Configuration Changes in Audit Log	Should
REQ-RULES-ADJ-005	Support Quant-Based Cross-Contamination Detection	Should
REQ-RULES-ADJ-006	Flag Wells with Missing Configuration	Must
REQ-RULES-ADJZIKA-001	Apply Adjacent Well Contamination Thresholds	Must
REQ-RULES-ADJZIKA-002	Suppress Errors for Repeat Accessions with Low-Positive History	Must
REQ-RULES-ADJZIKA-003	Use Latest Well Number for Same-Accession History	Must
REQ-RULES-RRES-001	Set Well LIMS Export from Resolution Code	Must
REQ-RULES-REPEATSAMP-001	Validate Repeat Sample Consistency	Must
REQ-RULES-MIXMISS-001	Identify Missing Mixes for Combined Outcome Evaluation	Must
REQ-RULES-MIXMISS-002	Track and Display Missing Mixes Information	Must
REQ-RULES-MIXMISS-003	Indicate Re-analysis Readiness for Missing Mixes	Must
REQ-RULES-MIXMISS-004	Execute Multi Mix Combined Check Before Missing Check	Must
REQ-RULES-INCONCLUSIVE-001	Generate Inconclusive Sample Error	Must
REQ-RULES-QSSC-001	Execute QSSC Rule with Resolution Code Status Assignment	Must
REQ-RULES-QSSC-002	Calculate Quantity Using Stored Standard Curve Settings	Must
REQ-RULES-QSSC-003	Set Error When Quantification Standards Are Missing	Must

1.4 Dependencies

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2. Component Architecture

2.1 Component Diagram

2.2 Component Responsibilities

Component	File	Responsibility	REQ Trace
WcRule	Analyzer/Rules/WcRule.php	Cross-talk detection for HSV/HTLV DEPRECATED - file does not exist	REQ-RULES-WC-001
WtRule	Analyzer/Rules/WtRule.php	Control error propagation	REQ-RULES-WT-*
WcafRule	Analyzer/Rules/WcafRule.php	Multiple control failure detection	REQ-RULES-WCAF-*
RwacRule	Analyzer/Rules/RwacRule.php	Resolution-to-patient propagation	REQ-RULES-RWAC-*
BaseAdjRule	Analyzer/Rules/BaseAdjRule.php	Base adjacency detection logic	REQ-RULES-ADJ-001, -005, -006
AdjRule	Analyzer/Rules/AdjRule.php	Standard adjacency detection	REQ-RULES-ADJ-*
AdjZikaRule	Analyzer/Rules/AdjZikaRule.php	Zika-specific adjacency with history	REQ-RULES-ADJZIKA-*
RresolutionRule	Analyzer/Rules/RresolutionRule.php	Resolution code LIMS assignment	REQ-RULES-RRES-001
WrepRule	Analyzer/Rules/WrepRule.php	Repeat sample validation	REQ-RULES-REPEATSAMP-001
MissingMixesRule	Analyzer/Rules/MissingMixesRule.php	Missing mix detection	REQ-RULES-MIXMISS-*
InconclusiveRule	Analyzer/Rules/InconclusiveRule.php	Inconclusive pattern detection	REQ-RULES-INCONCLUSIVE-001
QsscRule	Analyzer/Rules/QsscRule.php	Standard curve quantification	REQ-RULES-QSSC-*
SetErrorToWell	Analyzer/Rules/Concerns/SetErrorToWell.php	Error assignment concern	All error rules
SetLimsStatusToWell	Analyzer/Rules/Concerns/SetLimsStatusToWell.php	LIMS status assignment	RWAC, RRES, QSSC
CalculateQuantityUsingQuantificationSettings	Analyzer/Rules/Concerns/...	Exponential quantity calculation	REQ-RULES-QSSC-002

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3. Data Design

3.1 Entities

This rule collection operates across multiple entities:

Entity	Owner	Read/Write	Used By
wells	RUNRPT	Read/Write	All rules
observations	RUNRPT	Read/Write	ADJ, WREP, QSSC
resolution_codes	KITCFG	Read	RWAC, RRES, QSSC
calculated_quantification_settings	KITCFG	Read	QSSC
adjacents	KITCFG	Read	ADJ, ADJ_ZIKA
combined_outcomes	KITCFG	Read	MISSING_MIXES
previous_patient_wells	RUNRPT	Read	WREP, ADJ_ZIKA

3.2 Configuration Structure

// Adjacency Configuration
interface AdjacentConfig {
  mix_id: string;
  target_id: string;
  quant_or_ct: 'Ct' | 'Quant';
  potential_contaminated: number;  // threshold
  potential_contaminating: number; // threshold
}

// Resolution Code Configuration
interface ResolutionCode {
  code: string;
  lims_status: string | null;
  sets_lims_export: boolean;
  affected_lims_statuses: string[] | 'All Wells';
  resolution_priority: number;
  error_code: ErrorCode | null;
}

// Quantification Settings
interface QuantificationSetting {
  target_id: string;
  slope: number;
  intercept: number;
}

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4. Interface Design

4.1 Rule Interface

All specialized rules implement the standard rule contract:

interface AnalyzerRuleContract {
    public function handle(
        ConfigurationRepository $config,
        AnalyzableObservation $observation,
        RunMix $runMix,
        RunTarget $runTarget,
        AnalyzableWell $well,
        WellCollection $wells,
        PatientWellCollection $previousPatientWells,
        PecWellCollection $previousPecWells,
        RunTargetsCollection $runTargets
    ): void;
}

4.2 Internal APIs

Method	Class	Purpose
containsFailedExtractionControlForMixWell()	WellCollection	Check extraction control failure
containsFailedNonExtractionControlForWell()	WellCollection	Check non-extraction control failure
hasMultipleControlWellsWhichHasNonLabelError()	WellCollection	WCAF threshold check
adjacentWells()	WellCollection	Get adjacent well positions
getMatchingObservationForObservation()	PatientWellCollection	Historical observation lookup

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5. Behavioral Design

5.1 WC Rule (Cross Talk) - DEPRECATED

DEPRECATED (2026-02-02): This rule was never implemented. No WcRule.php exists in the codebase. Section retained for historical reference.

Algorithm: Detect Cross-Talk

Inputs:
- well: Well with observations
- assay_type: string (HSV, HTLV, or other)
- extraction_status: 'first' | 're-extraction'

Outputs:
- void (sets RXT LIMS status and warning on well)

Assumptions:
- Target positivity already determined
- Well is patient sample (not control)

Steps:
1. IF assay_type NOT IN ['HSV', 'HTLV']: RETURN (skip)
2. IF well is control sample: RETURN (skip)
3. IF extraction_status == 're-extraction': RETURN (skip)

4. Count positive non-IC targets in well
5. IF count <= 1: RETURN (no cross-talk)

6. Set LIMS = 'RXT'
7. Generate warning: "{target_a} and {target_b} are both positive. Re-extract sample"

Notes:
- IC targets always excluded from count
- Only first-time extractions trigger rule

Cross-Talk Decision Logic

Assay	Sample Type	Extraction	Positive Non-IC Targets	Result
HSV/HTLV	Patient	First	0 or 1	No action
HSV/HTLV	Patient	First	2+	RXT + Warning
HSV/HTLV	Patient	Re-extract	Any	No action
HSV/HTLV	Control	Any	Any	No action
Other	Any	Any	Any	No action

Precedence: During analytics processing phase. Default: No action when conditions not met.

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5.2 WT Rule (Well Transfer) - REQ-RULES-WT-*

Algorithm: Propagate Control Errors

Inputs:
- well: Patient well being evaluated
- wells: All wells in run
- config: Kit configuration
- fallback_enabled: boolean

Outputs:
- void (sets error on well)

Steps:
1. IF well has WT resolution code:
   a. Apply LIMS status from resolution
   b. RETURN

2. IF wells contain failed extraction control for mix:
   a. Set INHERITED_EXTRACTION_FAILURE error on well
   b. RETURN

3. IF wells contain failed non-extraction control for well:
   a. Set INHERITED_CONTROL_FAILURE error on well
   b. RETURN

4. IF fallback_enabled AND no primary control present:
   a. Check backup mix controls
   b. IF backup control has failure: Set INHERITED_CONTROL_FAILURE

Notes:
- Error message distinguishes extraction vs non-extraction control type
- Errors block export until resolved
- Resolution clears WT errors automatically

WT Error Propagation Decision Logic

Control Type	Control Status	Patient Well Action
Extraction	Failed	INHERITED_EXTRACTION_FAILURE
Non-Extraction	Failed	INHERITED_CONTROL_FAILURE
Any	Passed	No action
Fallback (enabled)	Failed	INHERITED_CONTROL_FAILURE
Fallback (disabled)	Failed	No action

Precedence: After all control failure detection rules. Default: No error if no associated control has failed.

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5.3 WCAF Rule (Multiple Control Failures) - REQ-RULES-WCAF-*

Algorithm: Detect Multiple Control Failures

Inputs:
- well: Well being evaluated
- wells: All wells in run
- config: Kit configuration

Outputs:
- void (sets CROSS_CNTRL_FAIL_WELL error on well and mix)

Assumptions:
- Wells with unknown mixes are excluded from count
- WCAF-generated errors are not counted in re-evaluation

Steps:
1. IF well is crossover: RETURN (skip)

2. IF well has WCAF resolution code:
   a. Apply LIMS status from resolution
   b. RETURN

3. IF well is control well:
   a. Count control wells with non-label errors (excluding unknown mix)
   b. IF count >= 2:
      - Set CROSS_CNTRL_FAIL_WELL error on well
      - Set CROSS_CNTRL_FAIL_MIX error on mix

Notes:
- Threshold is 2+ failures (not 1)
- Unknown mix wells excluded to prevent configuration issues from triggering
- When errors resolved below threshold, WCAF errors auto-clear

WCAF Threshold Decision Logic

Known Mix Failures	Unknown Mix Failures	Total	Result
0	Any	0	No WCAF
1	Any	1	No WCAF
2	0	2	WCAF error
2	1	2	WCAF error
1	1	1	No WCAF (unknown excluded)

Precedence: Run-level QC rule. Default: No error if fewer than 2 countable failures.

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5.4 RWAC Rule (Resolution Well Affecting Control) - REQ-RULES-RWAC-*

Algorithm: Apply Resolution to Patient Wells

Inputs:
- well: Patient well
- wells: All wells in run
- config: Kit configuration (resolution codes, fallback settings)

Outputs:
- void (sets LIMS status on well)

Steps:
1. IF well has RWAC resolution code:
   a. Apply LIMS status from resolution
   b. RETURN

2. Get associated resolved control wells:
   a. First check original mix controls
   b. IF fallback enabled AND no original control: check backup mix

3. IF no resolved control found: RETURN

4. IF multiple resolved controls:
   a. Sort by resolution_priority ascending (lower = higher priority)
   b. Select first (highest priority)

5. Get resolution code from selected control
6. Check affected_lims_statuses:
   a. IF 'All Wells': apply to patient well
   b. ELSE IF patient LIMS status in affected list: apply
   c. ELSE: no change

7. Set well LIMS status to resolution's lims_status

Notes:
- Fallback controls only used when primary absent
- Priority 1 beats priority 2
- Error wells can receive outcomes if error in affected list

RWAC Status Application Decision Logic

affected_lims_statuses	Patient Current Status	Result
"All Wells"	Any	Apply resolution LIMS
["NEG", "POS"]	"NEG"	Apply resolution LIMS
["NEG", "POS"]	"IND"	No change
null	Any	No change

Precedence: After control well resolution assignment. Default: No change if no matching resolution or affected status.

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5.5 ADJ Rule (Adjacent CT) - REQ-RULES-ADJ-*

Algorithm: Detect Adjacent Well Cross-Contamination

Inputs:
- observation: Current observation with CT/Quant
- well: Well being evaluated
- wells: All wells in run
- adjacent_config: Contamination thresholds

Outputs:
- void (sets ADJ_CT or ADJ_LIMITS_MISSED error)

Assumptions:
- Wells arranged in standard plate grid
- Only positive, non-IC targets evaluated

Steps:
1. IF well has ADJ resolution code: RETURN

2. IF observation has negative CLS: RETURN (skip negatives)

3. IF adjacent_config is null:
   a. Set ADJ_LIMITS_MISSED error
   b. RETURN

4. IF observation CT/Quant is null or equals readings count: RETURN

5. Check if observation meets "potentially contaminated" threshold:
   - CT mode: observation.ct > potential_contaminated_ct
   - Quant mode: observation.quant < potential_contaminated_quant
   IF NOT met: RETURN

6. Get adjacent well observations for same target

7. IF any adjacent missing config:
   a. Set ADJ_LIMITS_MISSED error
   b. RETURN

8. Check if any adjacent meets "potentially contaminating" threshold:
   - CT mode: adjacent.ct < potential_contaminating_ct
   - Quant mode: adjacent.quant > potential_contaminating_quant
   IF met: Set ADJ_CT error

Notes:
- Errors persist through export and re-analysis
- Resolution available via Manage Outcomes
- Config changes logged to audit trail

ADJ Detection Logic (CT Mode)

Current Well CT	Adjacent Well CT	Contaminated Threshold	Contaminating Threshold	Result
35	18	30	25	ADJ_CT (35 > 30 AND 18 < 25)
28	18	30	25	No error (28 < 30)
35	28	30	25	No error (28 > 25)
null	Any	Any	Any	No error (skip)

Precedence: Standalone detection rule. Default: No error if thresholds not exceeded.

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5.6 ADJ_ZIKA Rule - REQ-RULES-ADJZIKA-*

Algorithm: Zika-Specific Adjacent Contamination with History

Inputs:
- observation: Current observation
- well: Well being evaluated
- wells: All wells in run
- previousPatientWells: Historical patient wells

Outputs:
- void (sets ZIKA_ADJ_CT or ZIKA_ADJ_LIMITS_MISSED error)

Steps:
1. Find historical well for same accession and mix:
   a. Filter by accession match
   b. Filter by mix match
   c. Sort by well number descending
   d. Take first (latest well position)

2. IF no historical well:
   a. Execute standard ADJ rule with ZIKA error codes
   b. RETURN

3. Get matching observation from historical well

4. IF no matching observation:
   a. Execute standard ADJ rule
   b. RETURN

5. IF observation has no adjacent config: RETURN

6. Check if historical observation has "low-positive" quantity:
   - Low-positive = quantity > 0 AND quantity <= potential_contaminated
   IF historical is low-positive: RETURN (suppress error)

7. Execute standard ADJ rule with ZIKA error codes

Notes:
- Historical suppression prevents false positives on repeat samples
- Latest well number used when multiple wells share accession on same run
- Uses Quant mode (not CT)

ADJ_ZIKA Suppression Logic

Historical Qty	Contaminated Threshold	Current Scenario	Result
50	200	Would trigger ADJ	Suppressed (50 in 1-200 range)
300	200	Would trigger ADJ	ZIKA_ADJ_CT (300 > 200)
null	Any	Would trigger ADJ	ZIKA_ADJ_CT (no history)
Any	Any	Doesn't trigger	No error

Precedence: Standalone detection rule. Default: Falls through to standard ADJ logic.

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5.7 RRESOLUTION Rule - REQ-RULES-RRES-001

Algorithm: Resolution Code LIMS Assignment

Inputs:
- well: Well with potential resolution codes
- config: Resolution code configurations

Outputs:
- void (sets LIMS status on well)

Steps:
1. IF well has no resolution codes OR has RRESOLUTION code:
   a. Apply LIMS status from resolution codes
   b. RETURN

2. FOR each resolution code on well:
   a. Get resolution configuration from kit
   b. IF not found: CONTINUE

   c. Get LIMS status:
      - IF resolution has error_code: use error_code.lims_status
      - ELSE: use resolution.lims_status

   d. IF LIMS status exists:
      - Set well LIMS status
      - BREAK (first match wins)

Notes:
- First matching resolution code with LIMS status wins
- Supports both direct lims_status and error_code.lims_status paths

Precedence: Resolution processing phase. Default: No modification if no resolution or no LIMS configuration.

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5.8 WREP Rule (Repeat Sample) - REQ-RULES-REPEATSAMP-001

Algorithm: Validate Repeat Sample Consistency

Inputs:
- observation: Current observation
- well: Patient well
- previousPatientWells: Historical wells for comparison

Outputs:
- void (sets RQ_CLS or RQ_LOG error)

Steps:
1. IF well is not patient well: RETURN

2. IF well has WREP resolution code:
   a. Apply LIMS status from resolution
   b. RETURN

3. Get matching historical observation:
   - Same accession, same mix, same target

4. IF no matching observation: RETURN (first-time sample)

5. IF classifications differ:
   a. Set RQ_CLS error
   b. RETURN

6. IF current classification is negative: RETURN (pass)

7. Calculate Log10 quantity difference:
   diff = ABS(LOG10(current.quantity) - LOG10(previous.quantity))

8. IF diff > 0.5:
   a. Set RQ_LOG error

Notes:
- Uses most recent previous sample when multiple exist
- Threshold 0.5 applies to Log10 values (approximately 3x difference)
- Only positive samples checked for quantitative consistency

WREP Decision Logic

Previous CLS	Current CLS	Log10 Diff	Result
null	Any	N/A	Pass (first-time)
Positive	Negative	N/A	RQ_CLS error
Negative	Positive	N/A	RQ_CLS error
Negative	Negative	N/A	Pass
Positive	Positive	0.3	Pass
Positive	Positive	0.7	RQ_LOG error

Precedence: Standalone validation rule. Default: Pass if first-time or consistent.

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5.9 MISSING_MIXES Rule - REQ-RULES-MIXMISS-*

Algorithm: Detect Missing Mixes for Combined Outcomes

Inputs:
- well: Patient well
- wells: All wells in run
- config: Combined outcome mappings
- recentlyUploadedWells: Wells from other recent runs

Outputs:
- void (sets COMBINED_MIXES_WELLS_MISSING error)

Assumptions:
- Multi Mix Combined Check executes before this rule
- mixes_missing toggle controls rule activation

Steps:
1. IF well has no mix OR not patient well: RETURN

2. Get combined outcome mappings with mixes_missing=true

3. FOR each mapping:
   a. Get required mixes from mapping

   b. FOR each required mix:
      - Check if successful well exists for mix
      - "Successful" = no error, or has mixes_missing error, or has info-typed LIMS
      - IF allow_other_runs_to_be_used:
        - Also check recently uploaded wells with mixes_missing error

   c. IF any mix missing:
      - Set COMBINED_MIXES_WELLS_MISSING error
      - Store list of missing mix names
      - Populate outcome message with missing mixes

4. On new run import with missing mix now available:
   - Update old run status to "Reanalysis required (Missing mixes uploaded)"
   - Only if all previously missing mixes now available
   - Only if no existing resolution status

Notes:
- Wells with mixes_missing error are considered "successful" for mix availability
- Cross-run resolution requires wells with mixes_missing error (not just any well)

Successful Well Definition

Well State	Successful?
No errors	Yes
COMBINED_MIXES_WELLS_MISSING error	Yes
Information-typed LIMS	Yes
Label Error	No
Warning Error	No
Warning/Exclude LIMS	No

Precedence: After Multi Mix Combined Check. Default: No error if all mixes present.

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5.10 INCONCLUSIVE Rule - REQ-RULES-INCONCLUSIVE-001

Algorithm: Detect Inconclusive Result Pattern

Inputs:
- well: Well with observations
- config: Kit configuration (error codes)

Outputs:
- void (sets INCONCLUSIVE_WELL error)

Steps:
1. IF well has INCONCLUSIVE resolution code:
   a. Set LIMS status to 'INCONCLUSIVE'
   b. RETURN

2. Get non-IC, active target observations

3. Check if:
   - At least one observation has Negative final CLS
   - At least one observation has Positive final CLS

4. IF both conditions met:
   a. Set INCONCLUSIVE_WELL error
   b. Flag for bulk management visibility

Notes:
- Passive targets excluded from evaluation
- IC targets excluded from evaluation
- Enables bulk processing of inconclusive samples

INCONCLUSIVE Pattern Detection

Non-IC Target 1	Non-IC Target 2	Result
Positive	Positive	No error
Negative	Negative	No error
Positive	Negative	INCONCLUSIVE_WELL
Negative	Positive	INCONCLUSIVE_WELL

Precedence: Post-analysis (after classification). Default: No error if pattern not detected.

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5.11 QSSC Rule (Standard Curve Quantification) - REQ-RULES-QSSC-*

Algorithm: Calculate Quantity from Standard Curve

Inputs:
- observation: Observation with CT value
- well: Well (for quantity multiplier)
- config: Quantification settings, resolution codes

Outputs:
- void (sets quantity on observation, or error, or LIMS status)

Steps:
1. IF well has QSSC resolution code:
   a. Apply LIMS status from resolution code config
   b. RETURN (bypass calculation)

2. Get quantification settings for observation's target:
   - slope, intercept

3. IF settings missing OR no slope/intercept:
   a. Set QUANT_STANDARDS_MISSING error
   b. RETURN

4. Calculate quantity:
   quantity = multiplier * pow(10, ((ct - intercept) / slope))

5. Set observation quantity

Notes:
- Uses accurate CT (not rounded)
- Multiplier is well-level scaling factor
- Exponential formula is authoritative (base-10 logarithmic)

QSSC Calculation Examples

CT	Slope	Intercept	Multiplier	Quantity
28.1235	-1	30	1	75.248873017358
28.12345678	-1	30	1	75.256361986851
36	0.123	0.234	100	466 (approx)
40	-1	30	1	0.0000000001

Precedence: Quantification phase. Default: Error if configuration missing.

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6. Error Handling

Rule	Condition	Error Code	Response
WC	Cross-talk detected	RXT (LIMS)	Block export, generate warning DEPRECATED
WT	Extraction control failed	INHERITED_EXTRACTION_FAILURE	Block export
WT	Non-extraction control failed	INHERITED_CONTROL_FAILURE	Block export
WCAF	2+ control failures	CROSS_CNTRL_FAIL_WELL	Mark for replate
ADJ	Cross-contamination detected	ADJ_CT	Flag for resolution
ADJ	Missing configuration	ADJ_LIMITS_MISSED	Block rule execution
ADJ_ZIKA	Cross-contamination detected	ZIKA_ADJ_CT	Flag for resolution
ADJ_ZIKA	Missing configuration	ZIKA_ADJ_LIMITS_MISSED	Block rule execution
WREP	Classification mismatch	RQ_CLS	Flag for review
WREP	Quantity threshold exceeded	RQ_LOG	Flag for review
MIXMISS	Mixes missing	COMBINED_MIXES_WELLS_MISSING	Block until mixes available
INCONC	Inconclusive pattern	INCONCLUSIVE_WELL	Flag for bulk management
QSSC	Missing settings	QUANT_STANDARDS_MISSING	Block quantification

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7. Configuration

Setting	Rule	Path	Default	Effect
fallback_shared_control	WT, RWAC	Client config	false	Enable fallback mix checking
resolution_priority	RWAC	Per role	Per role	Lower = higher priority
potential_contaminated_ct	ADJ	Per mix/target	Required	Contaminated threshold
potential_contaminating_ct	ADJ	Per mix/target	Required	Contaminating threshold
quant_or_ct	ADJ	Per mix/target	Ct	Evaluation mode
mixes_missing	MIXMISS	Per combined outcome	false	Enable missing mixes check
allow_other_runs_to_be_used	MIXMISS	Per combined outcome	false	Cross-run resolution
wrep_log_quant_threshold	WREP	Client config	0.5	Log10 difference threshold

See Configuration Reference for full documentation.

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8. Implementation Mapping

8.1 Code Locations

Component	Path
WC Rule	code/app/Analyzer/Rules/WcRule.php DEPRECATED - file does not exist
WT Rule	code/app/Analyzer/Rules/WtRule.php
WCAF Rule	code/app/Analyzer/Rules/WcafRule.php
RWAC Rule	code/app/Analyzer/Rules/RwacRule.php
Base ADJ Rule	code/app/Analyzer/Rules/BaseAdjRule.php
ADJ Rule	code/app/Analyzer/Rules/AdjRule.php
ADJ Zika Rule	code/app/Analyzer/Rules/AdjZikaRule.php
RRESOLUTION Rule	code/app/Analyzer/Rules/RresolutionRule.php
WREP Rule	code/app/Analyzer/Rules/WrepRule.php
Missing Mixes Rule	code/app/Analyzer/Rules/MissingMixesRule.php
Inconclusive Rule	code/app/Analyzer/Rules/InconclusiveRule.php
QSSC Rule	code/app/Analyzer/Rules/QsscRule.php
Error Setter	code/app/Analyzer/Rules/Concerns/SetErrorToWell.php
LIMS Setter	code/app/Analyzer/Rules/Concerns/SetLimsStatusToWell.php
Quantity Calculator	code/app/Analyzer/Rules/Concerns/CalculateQuantityUsingQuantificationSettings.php

8.2 Requirement Traceability

REQ ID	Design Section	Primary Code
REQ-RULES-WC-001	Section 5.1	WcRule.php DEPRECATED
REQ-RULES-WT-001	Section 5.2	WtRule.php
REQ-RULES-WT-002	Section 5.2	WtRule.php
REQ-RULES-WT-003	Section 5.2	WtRule.php
REQ-RULES-WCAF-001	Section 5.3	WcafRule.php
REQ-RULES-WCAF-002	Section 5.3	WcafRule.php
REQ-RULES-WCAF-003	Section 5.3	WcafRule.php
REQ-RULES-RWAC-001	Section 5.4	RwacRule.php
REQ-RULES-RWAC-002	Section 5.4	RwacRule.php
REQ-RULES-RWAC-003	Section 5.4	RwacRule.php
REQ-RULES-RWAC-004	Section 5.4	RwacRule.php
REQ-RULES-ADJ-001	Section 5.5	AdjRule.php, BaseAdjRule.php
REQ-RULES-ADJ-002	Section 5.5	AdjRule.php
REQ-RULES-ADJ-003	Section 5.5	AdjRule.php
REQ-RULES-ADJ-004	Section 5.5	Audit logging
REQ-RULES-ADJ-005	Section 5.5	BaseAdjRule.php
REQ-RULES-ADJ-006	Section 5.5	BaseAdjRule.php
REQ-RULES-ADJZIKA-001	Section 5.6	AdjZikaRule.php
REQ-RULES-ADJZIKA-002	Section 5.6	AdjZikaRule.php
REQ-RULES-ADJZIKA-003	Section 5.6	AdjZikaRule.php
REQ-RULES-RRES-001	Section 5.7	RresolutionRule.php
REQ-RULES-REPEATSAMP-001	Section 5.8	WrepRule.php
REQ-RULES-MIXMISS-001	Section 5.9	MissingMixesRule.php
REQ-RULES-MIXMISS-002	Section 5.9	MissingMixesRule.php
REQ-RULES-MIXMISS-003	Section 5.9	MissingMixesRule.php
REQ-RULES-MIXMISS-004	Section 5.9	MissingMixesRule.php
REQ-RULES-INCONCLUSIVE-001	Section 5.10	InconclusiveRule.php
REQ-RULES-QSSC-001	Section 5.11	QsscRule.php
REQ-RULES-QSSC-002	Section 5.11	QsscRule.php, CalculateQuantityUsingQuantificationSettings.php
REQ-RULES-QSSC-003	Section 5.11	QsscRule.php

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9. Design Decisions

Decision	Rationale	Alternatives Considered
Inheritance for ADJ rules	Share core logic, specialize error codes/history	Duplicate code (rejected: maintenance burden)
Resolution code bypass pattern	Consistent manual override mechanism	Per-rule bypass logic (rejected: inconsistent)
Threshold-based contamination	Configurable per assay/target	Hardcoded thresholds (rejected: inflexible)
Cross-run for missing mixes	Support multi-run workflows	Single-run only (rejected: workflow limitation)
Log10 for quantity comparison	Industry standard for PCR	Linear comparison (rejected: inappropriate scale)
Exponential formula for QSSC	Corrects earlier linear model error	Linear formula (rejected: mathematically incorrect)

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10. Performance Considerations

Rule	Scenario	Concern	Mitigation
ADJ	Large plates (384 wells)	O(n) adjacent lookups	Pre-compute adjacency map
WREP	Many historical samples	Database queries	Index on accession/mix
MIXMISS	Cross-run lookups	Multiple run queries	Cache recently uploaded wells
RWAC	Multiple controls	Priority sorting	Sort once per well

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11. Related Documents

Document	Relevant Sections
SRS: rule-wc.md	WC requirements DEPRECATED
SRS: rule-wt.md	WT requirements
SRS: rule-wcaf.md	WCAF requirements
SRS: rule-rwac.md	RWAC requirements
SRS: rule-adj.md	ADJ requirements
SRS: rule-adj-zika.md	ADJ_ZIKA requirements
SRS: rule-rresolution.md	RRESOLUTION requirements
SRS: rule-repeat-sample.md	WREP requirements
SRS: rule-mixes-missing.md	MISSING_MIXES requirements
SRS: rule-managing-inconclusive.md	INCONCLUSIVE requirements
SRS: rule-qssc.md	QSSC requirements
SDS: Rules Engine	Framework overview
SDS: Combined Outcomes	Combined outcome rules