---
phase: 06-validation
plan: 03
type: execute
wave: 2
depends_on: ["06-01", "06-02"]
files_modified:
  - src/usher_pipeline/scoring/validation_report.py
  - src/usher_pipeline/cli/validate_cmd.py
  - src/usher_pipeline/cli/main.py
  - tests/test_validation.py
autonomous: true

must_haves:
  truths:
    - "CLI validate command runs positive controls, negative controls, and sensitivity analysis in sequence"
    - "Comprehensive validation report documents all three validation prongs with pass/fail verdicts"
    - "Weight tuning recommendations are generated based on validation results with documented rationale"
    - "Tests verify negative control logic, recall@k computation, weight perturbation, and report generation"
  artifacts:
    - path: "src/usher_pipeline/scoring/validation_report.py"
      provides: "Comprehensive validation report combining all three validation prongs"
      exports: ["generate_comprehensive_validation_report", "recommend_weight_tuning"]
    - path: "src/usher_pipeline/cli/validate_cmd.py"
      provides: "CLI validate command orchestrating full validation pipeline"
      exports: ["validate"]
    - path: "tests/test_validation.py"
      provides: "Unit tests for negative controls, recall@k, sensitivity, and validation report"
  key_links:
    - from: "src/usher_pipeline/cli/validate_cmd.py"
      to: "src/usher_pipeline/scoring/negative_controls.py"
      via: "validate_negative_controls import"
      pattern: "from usher_pipeline.scoring import validate_negative_controls"
    - from: "src/usher_pipeline/cli/validate_cmd.py"
      to: "src/usher_pipeline/scoring/sensitivity.py"
      via: "run_sensitivity_analysis import"
      pattern: "from usher_pipeline.scoring import run_sensitivity_analysis"
    - from: "src/usher_pipeline/cli/validate_cmd.py"
      to: "src/usher_pipeline/scoring/validation.py"
      via: "validate_positive_controls_extended import"
      pattern: "from usher_pipeline.scoring import validate_positive_controls_extended"
    - from: "src/usher_pipeline/cli/main.py"
      to: "src/usher_pipeline/cli/validate_cmd.py"
      via: "Click group add_command"
      pattern: "cli.add_command.*validate"
---

<objective>
Create comprehensive validation report generator, CLI validate command, and unit tests for all Phase 6 validation modules.

Purpose: This plan wires together the positive control, negative control, and sensitivity analysis modules (from Plans 01 and 02) into a single CLI command and comprehensive report. Tests ensure correctness with synthetic data. This completes Phase 6 by providing the user-facing validation workflow.

Output: validation_report.py, validate_cmd.py (CLI), updated main.py, and test_validation.py.
</objective>

<execution_context>
@/Users/gbanyan/.claude/get-shit-done/workflows/execute-plan.md
@/Users/gbanyan/.claude/get-shit-done/templates/summary.md
</execution_context>

<context>
@.planning/PROJECT.md
@.planning/ROADMAP.md
@.planning/STATE.md
@.planning/phases/06-validation/06-RESEARCH.md

# Need SUMMARYs from Plans 01 and 02 for what was actually built
@.planning/phases/06-validation/06-01-SUMMARY.md
@.planning/phases/06-validation/06-02-SUMMARY.md

@src/usher_pipeline/scoring/__init__.py
@src/usher_pipeline/scoring/negative_controls.py
@src/usher_pipeline/scoring/sensitivity.py
@src/usher_pipeline/scoring/validation.py
@src/usher_pipeline/cli/score_cmd.py
@src/usher_pipeline/cli/main.py
@tests/test_scoring.py
</context>

<tasks>

<task type="auto">
  <name>Task 1: Create comprehensive validation report and CLI validate command</name>
  <files>src/usher_pipeline/scoring/validation_report.py, src/usher_pipeline/cli/validate_cmd.py, src/usher_pipeline/cli/main.py</files>
  <action>
**Create `src/usher_pipeline/scoring/validation_report.py`:**

1. **generate_comprehensive_validation_report(positive_metrics: dict, negative_metrics: dict, sensitivity_result: dict, sensitivity_summary: dict) -> str** function:
   - Generate a multi-section Markdown report combining all three validation prongs
   - Section 1: "Positive Control Validation" -- median percentile, recall@k table, per-source breakdown, pass/fail
   - Section 2: "Negative Control Validation" -- median percentile, top quartile count, in-HIGH-tier count, pass/fail
   - Section 3: "Sensitivity Analysis" -- Spearman rho table (layer x delta), overall stability verdict, most/least sensitive layers
   - Section 4: "Overall Validation Summary" -- all-pass/partial-fail/fail verdict
   - Section 5: "Weight Tuning Recommendations" -- call recommend_weight_tuning()
   - Return the full Markdown string

2. **recommend_weight_tuning(positive_metrics: dict, negative_metrics: dict, sensitivity_summary: dict) -> str** function:
   - Analyze validation results and suggest weight adjustments
   - If positive controls pass AND negative controls pass AND sensitivity stable: "Current weights are validated. No tuning recommended."
   - If positive controls fail: suggest increasing weights for layers where known genes score highly
   - If negative controls fail (housekeeping genes ranking too high): suggest examining which layers boost housekeeping genes
   - If sensitivity unstable: identify most sensitive layer and suggest reducing its weight
   - Document rationale for each recommendation
   - CRITICAL: Note that any tuning is "post-validation" and flag circular validation risk per research pitfall
   - Return formatted recommendation text

3. **save_validation_report(report_text: str, output_path: Path) -> None**: Write report to file

**Create `src/usher_pipeline/cli/validate_cmd.py`:**

Follow the established CLI pattern from score_cmd.py (config load, store init, checkpoint, steps, summary, cleanup):

1. Click command `validate` with options:
   - `--force`: Re-run even if validation checkpoint exists
   - `--skip-sensitivity`: Skip sensitivity analysis (faster iteration)
   - `--output-dir`: Output directory for validation report (default: {data_dir}/validation)
   - `--top-n`: Top N genes for sensitivity analysis (default: 100)

2. Pipeline steps:
   - Step 1: Load configuration and initialize store
   - Step 2: Check scored_genes checkpoint exists (error if not -- must run `score` first)
   - Step 3: Run positive control validation (validate_positive_controls_extended)
   - Step 4: Run negative control validation (validate_negative_controls)
   - Step 5: Run sensitivity analysis (unless --skip-sensitivity) -- run_sensitivity_analysis + summarize_sensitivity
   - Step 6: Generate comprehensive validation report (generate_comprehensive_validation_report)
   - Step 7: Save report to output_dir/validation_report.md and provenance sidecar

3. Use click.echo with styled output matching score_cmd.py patterns (green for success, yellow for warnings, red for errors, bold for step headers)

4. Provenance tracking: record_step for each validation phase with metrics

5. Final summary: display overall pass/fail, recall@top-10%, housekeeping median percentile, sensitivity stability

**Update `src/usher_pipeline/cli/main.py`:**
- Import validate from validate_cmd
- Add: `cli.add_command(validate)`
- Follow the existing pattern used for score and report commands
  </action>
  <verify>
Run: `cd /Users/gbanyan/Project/usher-exploring && python -c "from usher_pipeline.cli.validate_cmd import validate; print(f'Command name: {validate.name}'); print('OK')"` exits 0 AND `cd /Users/gbanyan/Project/usher-exploring && python -c "from usher_pipeline.cli.main import cli; commands = list(cli.commands.keys()); print(f'CLI commands: {commands}'); assert 'validate' in commands; print('OK')"` exits 0
  </verify>
  <done>
validation_report.py generates comprehensive multi-section Markdown report with weight tuning recommendations. validate_cmd.py provides CLI command running all three validation prongs. main.py registers validate as a CLI subcommand. All follow established patterns from score_cmd.py.
  </done>
</task>

<task type="auto">
  <name>Task 2: Create unit tests for all validation modules</name>
  <files>tests/test_validation.py</files>
  <action>
Create `tests/test_validation.py` with comprehensive tests using synthetic DuckDB data. Follow the test pattern from tests/test_scoring.py (use tmp_path fixtures, create in-memory DuckDB with synthetic data).

**Test helper: create_synthetic_scored_db(tmp_path)** function:
- Create DuckDB with gene_universe (20 genes: GENE001-GENE020)
- Create scored_genes table with composite_score and all 6 layer scores
- Design scores so that:
  - MYO7A, IFT88, BBS1 (known cilia genes) get high scores (0.8-0.95)
  - GAPDH, ACTB, RPL13A (housekeeping genes) get low scores (0.1-0.3)
  - Other genes get mid-range scores (0.3-0.6)
- This ensures positive controls rank high and negative controls rank low in tests

**Tests to include:**

1. **test_compile_housekeeping_genes_structure**: Verify compile_housekeeping_genes() returns DataFrame with 13 genes, correct columns (gene_symbol, source, confidence), all confidence=HIGH, all source=literature_validated

2. **test_compile_housekeeping_genes_known_genes_present**: Assert GAPDH, ACTB, RPL13A, TBP are in the gene_symbol column

3. **test_validate_negative_controls_with_synthetic_data**: Use synthetic DB where housekeeping genes score low. Assert validation_passed=True, median_percentile < 0.5

4. **test_validate_negative_controls_inverted_logic**: Create a DB where housekeeping genes score HIGH (artificial scenario). Assert validation_passed=False

5. **test_compute_recall_at_k**: Use synthetic DB. Assert recall@k returns dict with recalls_absolute and recalls_percentage keys. With 3 known genes in top 5 of 20, recall@5 should be high (>0.5)

6. **test_perturb_weight_renormalizes**: Perturb gnomad by +0.10, assert weights still sum to 1.0. Perturb by -0.25 (more than weight value), assert weight >= 0.0 and sum = 1.0

7. **test_perturb_weight_invalid_layer**: perturb_weight with layer="nonexistent" should raise ValueError

8. **test_generate_comprehensive_validation_report_format**: Pass mock metrics dicts, assert report contains expected sections ("Positive Control", "Negative Control", "Sensitivity Analysis", "Weight Tuning")

9. **test_recommend_weight_tuning_all_pass**: Pass metrics indicating all validations pass. Assert response contains "No tuning recommended" or similar

All tests should use tmp_path for DuckDB isolation. Import from usher_pipeline.scoring (not internal modules directly where possible). Use PipelineStore with direct conn assignment pattern from test_scoring.py.
  </action>
  <verify>
Run: `cd /Users/gbanyan/Project/usher-exploring && python -m pytest tests/test_validation.py -v --tb=short` -- all tests pass
  </verify>
  <done>
test_validation.py contains 9+ tests covering negative controls, recall@k, weight perturbation, sensitivity analysis, and report generation. All tests pass using synthetic DuckDB data with designed score patterns ensuring known genes rank high and housekeeping genes rank low.
  </done>
</task>

</tasks>

<verification>
- `python -m pytest tests/test_validation.py -v` -- all validation tests pass
- `python -c "from usher_pipeline.cli.main import cli; assert 'validate' in cli.commands"` -- CLI command registered
- `python -c "from usher_pipeline.scoring.validation_report import generate_comprehensive_validation_report, recommend_weight_tuning"` -- report functions importable
- `usher-pipeline validate --help` displays usage information with all options
</verification>

<success_criteria>
- CLI `validate` command runs positive + negative + sensitivity validations and generates comprehensive report
- Validation report includes all three prongs with pass/fail verdicts and weight tuning recommendations
- Unit tests cover negative controls, recall@k, perturbation, and report generation
- All tests pass with synthetic data
- validate command registered in main CLI
</success_criteria>

<output>
After completion, create `.planning/phases/06-validation/06-03-SUMMARY.md`
</output>