usher-exploring/.planning/phases/01-data-infrastructure/01-04-SUMMARY.md

phase, plan, subsystem, tags, dependency_graph, tech_stack, key_files, decisions, metrics

phase	plan	subsystem	tags	dependency_graph	tech_stack	key_files	decisions	metrics
01-data-infrastructure	04	integration	cli integration wiring testing click	requires provides affects phase provides 01-01 Python package scaffold Pydantic v2 config system CachedAPIClient phase provides 01-02 Gene universe definition Batch ID mapper Validation gates phase provides 01-03 DuckDB checkpoint-restart storage Provenance tracking CLI entry point with setup and info commands Full infrastructure integration (config -> fetch -> map -> validate -> persist -> provenance) Checkpoint-restart capability for expensive operations Integration test suite verifying cross-module wiring All future pipeline operations (CLI is primary interface)	added patterns click for CLI framework Click command group with global options (--config, --verbose) Colored CLI output with status indicators Context manager for resource cleanup Mock-based integration testing	created modified src/usher_pipeline/cli/__init__.py CLI package exports src/usher_pipeline/cli/main.py Click command group with info command src/usher_pipeline/cli/setup_cmd.py Setup command orchestrating full flow tests/test_integration.py 6 integration tests .gitignore Data files, build artifacts, provenance exclusions pyproject.toml Fixed CLI entry point to usher_pipeline.cli.main:cli	decision rationale alternatives Click for CLI framework Standard Python CLI library with excellent UX features (colored output, help generation, subcommands) argparse (rejected - verbose) typer (rejected - less mature) decision rationale impact Setup command uses checkpoint-restart pattern Gene universe fetch can take minutes; checkpoint enables fast restart without re-fetching Setup detects existing DuckDB tables and skips re-fetch unless --force flag used decision rationale impact Mock mygene in integration tests Avoids external API dependency, ensures reproducible tests, faster execution All 6 integration tests run in <1s with mocked responses	duration_minutes tasks_completed files_created files_modified tests_added commits completed_date 5 2 5 1 6 2 2026-02-11

Phase 01 Plan 04: CLI Integration and End-to-End Testing Summary

One-liner: Click-based CLI with setup command orchestrating full infrastructure flow (config -> fetch gene universe -> map IDs -> validate -> DuckDB persistence -> provenance) and 6 integration tests verifying cross-module wiring with mocked APIs.

What Was Built

Wired all infrastructure modules together with a CLI interface and integration tests:

1. CLI Entry Point

   • Click command group with global options (--config, --verbose)
   • info command: displays pipeline version, config hash, data source versions, paths, API config
   • setup command: orchestrates full infrastructure flow
   • Colored output with status indicators (green=OK, yellow=warn, red=fail)
   • Entry point: usher-pipeline binary installed with package

2. Setup Command Flow

   • Load config from YAML
   • Create PipelineStore and ProvenanceTracker from config
   • Check for existing checkpoint (gene_universe table in DuckDB)
   • If checkpoint exists and no --force: skip fetch, display summary
   • If no checkpoint or --force:
     • Fetch protein-coding genes from mygene (19k-22k genes)
     • Validate gene universe (count, format, duplicates)
     • Map Ensembl IDs to HGNC + UniProt via batch queries
     • Validate mapping quality (min 90% HGNC success rate)
     • Save to DuckDB as gene_universe table
     • Record provenance steps
     • Save provenance sidecar JSON
   • Display summary with counts, rates, paths

3. Integration Test Suite

   • 6 tests verifying module wiring with mocked mygene API:
     • test_config_to_store_roundtrip: config -> PipelineStore -> save/load
     • test_config_to_provenance: config -> ProvenanceTracker -> sidecar
     • test_full_setup_flow_mocked: full setup with 5 mocked genes
     • test_checkpoint_skip_flow: verify checkpoint-restart skips re-fetch
     • test_setup_cli_help: CLI help output verification
     • test_info_cli: info command with config display
   • All tests use tmp_path fixtures for isolation
   • No external API calls (mocked mygene responses)

4. .gitignore

   • Excludes data/, *.duckdb, *.duckdb.wal
   • Python artifacts: pycache, *.pyc, *.egg-info, dist/, build/
   • Testing: .pytest_cache/, .coverage, htmlcov/
   • Provenance files (not in data/)
   • Virtual environment: .venv/

Tests

50 tests total (49 passed, 1 skipped):

Integration Tests (6 tests, all passed)

• test_config_to_store_roundtrip: Load config, create store, save/load DataFrame, verify roundtrip
• test_config_to_provenance: Load config, create provenance, record steps, save/load sidecar, verify config_hash
• test_full_setup_flow_mocked: Full setup flow with mocked mygene (5 genes), verify DuckDB table, provenance
• test_checkpoint_skip_flow: Create checkpoint, verify second run skips fetch
• test_setup_cli_help: CLI help shows --force and checkpoint info
• test_info_cli: Info command displays version, config hash, data sources

All Tests Summary

• Config tests: 5 passed
• API client tests: 5 passed
• Gene mapping tests: 15 passed
• Persistence tests: 12 passed, 1 skipped (pandas)
• Integration tests: 6 passed

Verification Results

All plan verification steps passed:

# 1. All tests pass
$ pytest tests/ -v
========================= 49 passed, 1 skipped, 1 warning in 0.42s =========================

# 2. CLI help works
$ usher-pipeline --help
Usage: usher-pipeline [OPTIONS] COMMAND [ARGS]...
Commands:
  info   Display pipeline information and configuration summary.
  setup  Initialize pipeline data infrastructure.

# 3. Info command works
$ usher-pipeline info
Usher Pipeline v0.1.0
Config: config/default.yaml
Config Hash: ddbb5195738ac354...
Data Source Versions:
  Ensembl Release: 113
  gnomAD Version:  v4.1
  GTEx Version:    v8
  HPA Version:     23.0

Deviations from Plan

None - plan executed exactly as written.

Task Execution Log

Task 1: Create CLI entry point with setup command

Status: Complete Duration: ~3 minutes Commit: f33b048

Actions:

1. Created src/usher_pipeline/cli/ package
2. Implemented main.py with click command group:
   • Global options: --config (default config/default.yaml), --verbose
   • info command: displays version, config hash, data sources, paths, API config
   • Registers setup command
3. Implemented setup_cmd.py with full orchestration:
   • Load config, create store/provenance
   • Checkpoint detection: has_checkpoint('gene_universe')
   • Fetch gene universe (mygene) with count validation
   • Map IDs (Ensembl -> HGNC + UniProt) with batch queries
   • Validate mapping (min 90% HGNC success rate)
   • Save to DuckDB with provenance sidecar
   • Colored output with status indicators
   • Resource cleanup in finally block
4. Updated pyproject.toml: fixed entry point to usher_pipeline.cli.main:cli
5. Created .gitignore with data/, *.duckdb, build artifacts

Files created: 5 files (cli/init.py, main.py, setup_cmd.py, .gitignore, modified pyproject.toml)

Key features:

• Checkpoint-restart: skips expensive fetch if data exists
• Validation gates: enforces data quality thresholds
• Provenance tracking: captures all setup steps
• Colored CLI output with clear status messages

Task 2: Create integration tests verifying module wiring

Status: Complete Duration: ~2 minutes Commit: e4d71d0

Actions:

1. Created tests/test_integration.py with 6 tests
2. Mock data setup:
   • MOCK_GENES: 5 Ensembl IDs
   • MOCK_MYGENE_QUERY_RESPONSE: 5 genes with symbols
   • MOCK_MYGENE_QUERYMANY_RESPONSE: 5 genes with HGNC + UniProt
3. Test fixtures:
   • test_config: creates temp config with tmp_path for isolation
4. Integration tests:
   • Config -> PipelineStore -> save/load roundtrip
   • Config -> ProvenanceTracker -> sidecar creation
   • Full setup flow with mocked mygene (fetch, map, validate, save, provenance)
   • Checkpoint-restart verification
   • CLI help and info commands
5. All tests pass with mocked API (no external dependencies)

Files created: 1 file (test_integration.py)

Key features:

• Mocked mygene API calls (no rate limits, reproducible)
• Temporary paths for isolation (no pollution)
• Verifies cross-module wiring works correctly
• Fast execution (<1s for all 6 tests)

Success Criteria Verification

• CLI entry point works with setup and info subcommands
• Setup command wires together all infrastructure: config loading, gene universe fetch, ID mapping, validation, DuckDB storage, provenance tracking
• Checkpoint-restart works: existing DuckDB data skips re-downloading
• All integration tests pass verifying cross-module wiring
• Full test suite (all files) passes: pytest tests/ -v (49 passed, 1 skipped)

Must-Haves Verification

Truths:

• CLI entry point 'usher-pipeline' is available after package install with setup and info subcommands
• Running 'usher-pipeline setup' loads config, fetches gene universe, maps IDs, validates mappings, and saves to DuckDB with provenance
• All infrastructure modules work together end-to-end: config -> gene mapping -> persistence -> provenance
• Pipeline can restart from checkpoint: if gene_universe checkpoint exists in DuckDB, setup skips re-fetching

Artifacts:

• src/usher_pipeline/cli/main.py provides "CLI entry point with click command group" containing "def cli"
• src/usher_pipeline/cli/setup_cmd.py provides "Setup command wiring config, gene mapping, persistence, provenance" containing "def setup"
• tests/test_integration.py provides "Integration tests verifying module wiring" containing "test_"

Key Links:

• src/usher_pipeline/cli/setup_cmd.py -> src/usher_pipeline/config/loader.py via "loads pipeline config from YAML" (pattern: load_config)
• src/usher_pipeline/cli/setup_cmd.py -> src/usher_pipeline/gene_mapping/mapper.py via "maps gene IDs using GeneMapper" (pattern: GeneMapper)
• src/usher_pipeline/cli/setup_cmd.py -> src/usher_pipeline/persistence/duckdb_store.py via "saves results to DuckDB with checkpoint" (pattern: PipelineStore)
• src/usher_pipeline/cli/setup_cmd.py -> src/usher_pipeline/persistence/provenance.py via "tracks provenance for setup step" (pattern: ProvenanceTracker)
• src/usher_pipeline/cli/main.py -> src/usher_pipeline/cli/setup_cmd.py via "registers setup as click subcommand" (pattern: cli\.add_command)

Impact on Roadmap

Phase 01 Data Infrastructure Complete:

All 4 plans in Phase 01 are now complete:

• 01-01: Python package scaffold, config system, base API client
• 01-02: Gene ID mapping and validation
• 01-03: DuckDB persistence and provenance tracking
• 01-04: CLI integration and end-to-end testing

Ready for Phase 02 (Evidence Layer Ingestion):

• CLI provides interface for running pipeline operations
• Config system defines data source versions
• Gene universe can be fetched and validated
• ID mapping handles Ensembl -> HGNC + UniProt
• DuckDB checkpoint-restart enables incremental processing
• Provenance tracking captures all processing steps
• Integration tests prove modules work together

Next Steps

Phase 02 will add evidence layer ingestion commands to the CLI:

• usher-pipeline fetch gnomad - download gnomAD data
• usher-pipeline fetch expression - download GTEx/HPA data
• usher-pipeline fetch annotations - download GO/HPO annotations

Each command will use the same checkpoint-restart pattern established in setup.

Self-Check: PASSED

Files verified:

FOUND: /Users/gbanyan/Project/usher-exploring/src/usher_pipeline/cli/__init__.py
FOUND: /Users/gbanyan/Project/usher-exploring/src/usher_pipeline/cli/main.py
FOUND: /Users/gbanyan/Project/usher-exploring/src/usher_pipeline/cli/setup_cmd.py
FOUND: /Users/gbanyan/Project/usher-exploring/tests/test_integration.py
FOUND: /Users/gbanyan/Project/usher-exploring/.gitignore

Commits verified:

FOUND: f33b048 (Task 1)
FOUND: e4d71d0 (Task 2)

All files and commits exist as documented.