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CLAUDE.md

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+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+NameRes (Name Resolver) is a biomedical entity name resolution service that maps lexical strings to CURIEs from vocabularies/ontologies. It is part of the NCATS Translator ecosystem. The API is built with FastAPI and backed by Apache Solr.
+
+## Commands
+
+### Running Tests
+```bash
+# Load test data into Solr first (requires Solr running)
+./data-loading/setup-and-load-solr.sh tests/data/test-synonyms.json
+
+# Run all tests
+python -m pytest tests/
+
+# Run a single test
+python -m pytest tests/test_service.py::test_function_name
+```
+
+### Running Locally
+```bash
+# Start full stack (Solr + API)
+docker-compose up
+
+# Run API directly (requires Solr already running)
+uvicorn api.server:app --host 0.0.0.0 --port 2433
+```
+
+### Data Loading
+```bash
+# Download synonyms, start Solr, load data (production)
+cd data-loading && make all
+
+# Individual steps
+make start-solr-backup
+make check-solr-backup
+make stop-solr
+```
+
+### Dependencies
+```bash
+pip install -r requirements.txt
+```
+
+## Architecture
+
+### Request Flow
+1. Client sends query to FastAPI endpoint on port 2433
+2. `api/server.py` constructs Solr query parameters
+3. `httpx` async client queries the Solr instance (default: `localhost:8983`)
+4. Results are scored, normalized, and returned as JSON
+
+### Key Files
+- `api/server.py` - Core FastAPI application (~717 lines): all endpoints, Pydantic models, Solr query construction, environment config
+- `api/apidocs.py` - Custom OpenAPI schema construction
+- `api/resources/.openapi.yml` - OpenAPI 3.0.2 spec with service metadata
+- `main.py` / `main.sh` - WSGI/ASGI entry points (port 2433)
+- `tests/test_service.py` - Integration tests using FastAPI `TestClient`
+- `tests/data/test-synonyms.json` - Test dataset for Solr
+
+### Environment Variables
+- `SOLR_HOST` / `SOLR_PORT` - Solr connection (default: `localhost:8983`)
+- `LOGLEVEL` - Logging level
+- `SERVER_ROOT` - API root path prefix
+- `MATURITY_VALUE` / `LOCATION_VALUE` - TRAPI metadata fields
+
+### API Endpoints
+- `GET/POST /lookup` - Primary name-to-CURIE lookup with scoring
+- `POST /bulk-lookup` - Batch queries via `NameResQuery` model
+- `GET /reverse-lookup` - CURIE-to-names lookup
+- `POST /synonyms` - Get synonyms for a list of CURIEs
+- `POST /lookup-curies` - Filter existing CURIEs with type subsetting
+- `GET /status` - Health check with Solr document counts
+
+### Data Model
+Solr documents contain: `curie`, `preferred_name`, `names` (synonym list), and biolink type information. Lookup results are `LookupResult` objects with scoring fields. Results are conflated using GeneProtein and DrugChemical conflation rules.
+
+### Infrastructure
+- **Stateless API container** - Python 3.11.5/FastAPI
+- **Persistent Solr 9.1** - Data in volume-mounted `./data/solr`
+- **Data loading** - Separate pipeline in `data-loading/` (Makefile-driven, also has Kubernetes configs)
+- **CI/CD** - GitHub Actions: runs tests on push, publishes Docker image to GitHub Packages on release
+
+## Documentation
+- `documentation/API.md` - Endpoint reference
+- `documentation/Deployment.md` - Docker/Kubernetes deployment guide
+- `documentation/Scoring.md` - Scoring algorithm details
+- `documentation/NameResolution.ipynb` - Interactive usage examples