diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6b01995..e40dab2 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -8,16 +8,39 @@ on: env: PYTHON_VERSION: "3.13" + NODE_VERSION: "22" jobs: - lint: - name: Lint & Format + # Detect which paths changed + changes: + name: Detect Changes runs-on: ubuntu-latest + outputs: + server: ${{ steps.filter.outputs.server }} + web: ${{ steps.filter.outputs.web }} steps: - uses: actions/checkout@v4 - - name: Install just - uses: extractions/setup-just@v2 + - uses: dorny/paths-filter@v3 + id: filter + with: + filters: | + server: + - 'server/**' + web: + - 'web/**' + + # Server (Python backend) checks + server-lint: + name: Server - Lint & Format + needs: changes + if: needs.changes.outputs.server == 'true' || github.event_name == 'push' + runs-on: ubuntu-latest + defaults: + run: + working-directory: server + steps: + - uses: actions/checkout@v4 - name: Install uv uses: astral-sh/setup-uv@v4 @@ -36,15 +59,17 @@ jobs: - name: Check linting run: uv run ruff check . - typecheck: - name: Type Check + server-typecheck: + name: Server - Type Check + needs: changes + if: needs.changes.outputs.server == 'true' || github.event_name == 'push' runs-on: ubuntu-latest + defaults: + run: + working-directory: server steps: - uses: actions/checkout@v4 - - name: Install just - uses: extractions/setup-just@v2 - - name: Install uv uses: astral-sh/setup-uv@v4 with: @@ -59,18 +84,20 @@ jobs: - name: Run type checker run: uv run ty check osa - test: - name: Test + server-test: + name: Server - Test + needs: changes + if: needs.changes.outputs.server == 'true' || github.event_name == 'push' runs-on: ubuntu-latest + defaults: + run: + working-directory: server permissions: contents: read pull-requests: write steps: - uses: actions/checkout@v4 - - name: Install just - uses: extractions/setup-just@v2 - - name: Install uv uses: astral-sh/setup-uv@v4 with: @@ -90,7 +117,7 @@ jobs: - name: Code Coverage Summary uses: irongut/CodeCoverageSummary@v1.3.0 with: - filename: coverage.xml + filename: server/coverage.xml badge: true format: markdown output: both @@ -100,3 +127,62 @@ jobs: if: github.event_name == 'pull_request' with: path: code-coverage-results.md + + # Web (Next.js frontend) checks + web-lint: + name: Web - Lint + needs: changes + if: needs.changes.outputs.web == 'true' || github.event_name == 'push' + runs-on: ubuntu-latest + defaults: + run: + working-directory: web + steps: + - uses: actions/checkout@v4 + + - name: Setup pnpm + uses: pnpm/action-setup@v4 + with: + version: latest + + - name: Setup Node.js + uses: actions/setup-node@v4 + with: + node-version: ${{ env.NODE_VERSION }} + cache: 'pnpm' + cache-dependency-path: web/pnpm-lock.yaml + + - name: Install dependencies + run: pnpm install --frozen-lockfile + + - name: Run linter + run: pnpm lint + + web-build: + name: Web - Build + needs: changes + if: needs.changes.outputs.web == 'true' || github.event_name == 'push' + runs-on: ubuntu-latest + defaults: + run: + working-directory: web + steps: + - uses: actions/checkout@v4 + + - name: Setup pnpm + uses: pnpm/action-setup@v4 + with: + version: latest + + - name: Setup Node.js + uses: actions/setup-node@v4 + with: + node-version: ${{ env.NODE_VERSION }} + cache: 'pnpm' + cache-dependency-path: web/pnpm-lock.yaml + + - name: Install dependencies + run: pnpm install --frozen-lockfile + + - name: Build + run: pnpm build diff --git a/.gitignore b/.gitignore index 42f20c5..ce19d52 100644 --- a/.gitignore +++ b/.gitignore @@ -14,7 +14,6 @@ dist/ downloads/ eggs/ .eggs/ -lib/ lib64/ parts/ sdist/ @@ -214,3 +213,27 @@ __marimo__/ # Streamlit .streamlit/secrets.toml + +# Monorepo - Server specific +server/.venv/ +server/.coverage +server/.coverage.* +server/coverage.xml +server/htmlcov/ +server/.pytest_cache/ +server/.ruff_cache/ +server/__pycache__/ +server/*.egg-info/ + +# Monorepo - Web specific +web/node_modules/ +web/.next/ +web/.env.local +web/.turbo/ + +# Docker +.docker/ + +# Environment +.env +!.env.example diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 3a0da0e..cc180ea 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,14 +23,14 @@ repos: hooks: - id: ty-check name: ty type check - entry: uv run ty check osa + entry: env -u VIRTUAL_ENV uv run --directory server ty check osa language: system types: [python] pass_filenames: false - id: unit-tests name: unit tests - entry: uv run pytest tests/unit -q --tb=short + entry: env -u VIRTUAL_ENV uv run --directory server pytest tests/unit -q --tb=short language: system types: [python] pass_filenames: false diff --git a/Justfile b/Justfile index ba4f56f..ce5acb3 100644 --- a/Justfile +++ b/Justfile @@ -1,142 +1,119 @@ -# Import deployment commands -# mod local 'deployment/local/local.just' +# OSA Monorepo Justfile +# Production deployment and development orchestration commands default: @just --list -# === PostgreSQL (Docker) === +# === Production Deployment === -# Start PostgreSQL in Docker -db-up: - @just local up - -# Stop PostgreSQL -db-down: - @just local down - -# View PostgreSQL logs -db-logs: - @just local logs - -# Connect to PostgreSQL with psql -db-connect: - @just local db-connect +# Start all services in production mode +up: + docker compose -f deploy/docker-compose.yml up -d -# Reset database (WARNING: deletes all data) -db-wipe: - @just local wipe +# Start all services with logs visible +up-attached: + docker compose -f deploy/docker-compose.yml up -# === Migrations (Local) === +# Stop all services +down: + docker compose -f deploy/docker-compose.yml down -# Run migrations against Docker PostgreSQL -migrate: - uv run alembic upgrade head +# View logs from all services +logs: + docker compose -f deploy/docker-compose.yml logs -f -# Create new migration -migration name: - uv run alembic revision -m "{{name}}" +# View logs from a specific service +logs-service service: + docker compose -f deploy/docker-compose.yml logs -f {{service}} -# Show current migration version -migrate-status: - uv run alembic current +# View server logs +server-logs: + docker compose -f deploy/docker-compose.yml logs -f server -# Show migration history -migrate-history: - uv run alembic history +# View last N lines of server logs (default: 100) +server-logs-tail lines="100": + docker compose -f deploy/docker-compose.yml logs --tail {{lines}} server -# Rollback one migration -migrate-down: - uv run alembic downgrade -1 +# View server logs with timestamps +server-logs-time: + docker compose -f deploy/docker-compose.yml logs -f -t server -# === CLI (Local) === +# View server logs since a time (e.g., "10m", "1h", "2024-01-01") +server-logs-since since: + docker compose -f deploy/docker-compose.yml logs -f --since {{since}} server -# Run any osa CLI command -cli *ARGS: - uv run osa {{ARGS}} +# Shell into the server container +server-shell: + docker compose -f deploy/docker-compose.yml exec server bash -# Initialize a field -init FIELD: - uv run osa field init {{FIELD}} +# Restart just the server +server-restart: + docker compose -f deploy/docker-compose.yml restart server -# Wipe all local OSA data (database, vectors, cache) -wipe: - uv run osa local clean --force +# Restart all services +restart: + docker compose -f deploy/docker-compose.yml restart -# === Complete Workflow === +# Rebuild and restart services +rebuild: + docker compose -f deploy/docker-compose.yml up -d --build -# Set up everything for first time (start DB + run migrations) -setup: - @echo "Starting PostgreSQL..." - @just db-up - @echo "Waiting for PostgreSQL to be ready..." - @sleep 3 - @echo "Running migrations..." - @just migrate - @echo "Setup complete! Database is ready." +# === Development Mode === -# Aliases for common commands -up: db-up -down: db-down +# Start full-stack development with hot-reload +dev: + docker compose -f deploy/docker-compose.yml -f deploy/docker-compose.dev.yml up -# Testing commands -test kind="unit": - @TEST=1 uv run pytest "tests/{{kind}}" -v --tb=short +# Start development in background +dev-detached: + docker compose -f deploy/docker-compose.yml -f deploy/docker-compose.dev.yml up -d -test-s kind="unit": - @TEST=1 uv run pytest -s -o log_cli=True -o log_cli_level=DEBUG "tests/{{kind}}" +# Stop development environment +dev-down: + docker compose -f deploy/docker-compose.yml -f deploy/docker-compose.dev.yml down -test-unit: - @TEST=1 uv run pytest tests/unit +# === Individual Service Development === -[working-directory: 'deployment/local'] -test-e2e: - docker compose --profile test-e2e up --build --abort-on-container-exit test-e2e +# Run server independently (requires database) +server-dev: + cd server && just dev -[working-directory: 'deployment/local'] -test-integration: - docker compose --profile test up --build --abort-on-container-exit test +# Run web frontend independently +web-dev: + cd web && pnpm dev -# Code quality commands -fix thing="osa": - uv run ruff format {{thing}} - uv run ruff check --fix {{thing}} +# Build web frontend for production +web-build: + cd web && pnpm build -lint thing="osa": - uv run ruff check {{thing}} - uv run ty check {{thing}} +# Lint web frontend code +web-lint: + cd web && pnpm lint -# Docker commands (standalone) -docker-build: - docker build -t osa-api:latest . +# === Database === -docker-run PORT="8000": - docker run -p {{PORT}}:8000 --env-file .env osa-api:latest - -docker-serve PORT="8000": - just docker-build && docker run -p {{PORT}}:8000 --env-file .env osa-api:latest - -docker-shell docker-build: - docker run -it --rm osa-api:latest bash +# Start only the database +db-up: + docker compose -f deploy/docker-compose.yml up -d db -docker-stop: - docker stop osa-api && docker rm osa-api || true +# Stop the database +db-down: + docker compose -f deploy/docker-compose.yml stop db -# Run database migrations locally -db-migrate: - uv run alembic upgrade head +# View database logs +db-logs: + docker compose -f deploy/docker-compose.yml logs -f db -# Create new migration -db-migration name: - uv run alembic revision -m "{{name}}" +# Connect to PostgreSQL +db-connect: + docker compose -f deploy/docker-compose.yml exec db psql -U postgres -d osa -# Show migration history -db-history: - uv run alembic history +# === Maintenance === -# Show current migration version -db-current: - uv run alembic current +# Clean up Docker resources (volumes, images, etc.) +clean: + docker compose -f deploy/docker-compose.yml down -v --rmi local -# Downgrade migration -db-downgrade: - uv run alembic downgrade -1 +# Show service status +status: + docker compose -f deploy/docker-compose.yml ps diff --git a/README.md b/README.md index e71890c..30c4494 100644 --- a/README.md +++ b/README.md @@ -10,9 +10,9 @@

Quick Start • - Templates • - Usage • - Development + Development • + Structure • + Troubleshooting

--- @@ -21,107 +21,165 @@ OSA makes it easy to stand up [PDB](https://www.rcsb.org/)-level data infrastruc ## Quick Start -**Requirements:** Python 3.13+, [uv](https://docs.astral.sh/uv/) +### Self-Hosted Deployment + +Deploy the complete OSA stack with a single command: + +**Requirements:** Docker Desktop 4.x+ or Docker Engine 24.x+ ```bash -# Clone and install -git clone https://github.com/opendatabank/osa.git -cd osa -uv sync -source .venv/bin/activate +git clone https://github.com/opensciencearchive/server.git +cd server +docker compose -f deploy/docker-compose.yml up +``` -# Initialize with the GEO template -osa init geo +Access the web interface at `http://localhost:8080` -# NOTE: update the config.yaml with your NCBI API key and increase the record ingestion limit +### Environment Configuration -# Start the server -osa server start +Copy and customize the environment template: -# Search datasets using natural language -osa search vector "single cell RNA-seq alzheimer's disease" +```bash +cp deploy/.env.example deploy/.env ``` -## Templates +Key variables: -OSA ships with pre-configured templates for different domains: +| Variable | Default | Description | +|----------|---------|-------------| +| `POSTGRES_PASSWORD` | `osa` | Database password | +| `WEB_PORT` | `8080` | External port for web interface | +| `LOG_LEVEL` | `INFO` | Application log level | -| Template | Description | -|----------|-------------| -| **geo** | [NCBI GEO](https://www.ncbi.nlm.nih.gov/geo/) integration with vector search. Natural language search over gene expression datasets. | -| **minimal** | Blank configuration for building your own archive. | +## Development + +### Full-Stack Development + +Start all services with hot-reload enabled: ```bash -# See available templates -osa init +just dev +``` -# Initialize with a specific template -osa init geo -osa init minimal +Or using docker compose directly: + +```bash +docker compose -f deploy/docker-compose.yml -f deploy/docker-compose.dev.yml up ``` -More templates coming soon. Contributions welcome. +**What's running:** +- Web UI: http://localhost:3000 (hot-reload) +- API Server: http://localhost:8000 (auto-restart on changes) +- PostgreSQL: localhost:5432 + +### Individual Service Development + +**Frontend only:** -## Usage +```bash +just web-dev +# Or: cd web && pnpm dev +``` -### CLI Commands +**Backend only:** ```bash -# Search for datasets -osa search vector "breast cancer tumor microenvironment" +just server-dev +# Or: cd server && just dev +``` + +### Available Commands -# View details of a result (by number from search) -osa show 1 +| Command | Description | +|---------|-------------| +| `just up` | Start production deployment | +| `just down` | Stop all services | +| `just logs` | View service logs | +| `just dev` | Full-stack development with hot-reload | +| `just web-dev` | Frontend development server | +| `just web-build` | Production build of frontend | +| `just web-lint` | Lint frontend code | +| `just server-dev` | Backend development server | +| `just status` | Show service status | -# Check system stats -osa stats +## Project Structure -# Server management -osa server status -osa server logs --follow -osa server stop ``` +osa/ +├── server/ # Python backend (FastAPI) +│ ├── osa/ # Application code +│ ├── tests/ # Test suite +│ ├── migrations/ # Database migrations +│ ├── sources/ # Data source plugins +│ ├── Dockerfile +│ ├── pyproject.toml +│ └── Justfile # Server-specific commands +├── web/ # Next.js frontend +│ ├── src/ # Application code +│ ├── public/ # Static assets +│ ├── Dockerfile +│ └── package.json +├── deploy/ # Deployment configuration +│ ├── docker-compose.yml # Production orchestration +│ ├── docker-compose.dev.yml # Development overrides +│ └── .env.example # Environment template +└── Justfile # Root orchestration commands +``` + +## Troubleshooting -### Configuration +### Port conflicts -Configuration lives in `~/.config/osa/config.yaml`. Data is stored in `~/.local/share/osa/`. +If port 8080 is already in use: -#### GEO Template Setup +```bash +# Option 1: Change the port in deploy/.env +echo "WEB_PORT=3001" >> deploy/.env +docker compose -f deploy/docker-compose.yml up -After running `osa init geo`, edit your config file to: +# Option 2: Stop the conflicting service +lsof -i :8080 +``` -1. **Add your NCBI API key** (recommended for faster ingestion): - - Get a free API key at https://account.ncbi.nlm.nih.gov/settings/ - - Without an API key, NCBI limits you to 3 requests/second - - With an API key, you get 10 requests/second +### Database connection issues -2. **Increase the initial ingestion limit** for a more complete dataset: +Ensure the database container is healthy before starting other services: -```yaml -ingestors: - - ingestor: geo-entrez - config: - email: your@email.com - api_key: your_ncbi_api_key_here # Optional but recommended - initial_run: - enabled: true - limit: 10000 # Increase from default 50 for fuller dataset +```bash +docker compose -f deploy/docker-compose.yml ps ``` -The GEO template uses the full GSE dataset (~250,000 series). Initial ingestion of 10,000 records takes roughly 20-30 minutes with an API key. +The `db` service should show `healthy` status. If not: -## Development +```bash +# Check database logs +docker compose -f deploy/docker-compose.yml logs db + +# Restart just the database +docker compose -f deploy/docker-compose.yml restart db +``` + +### Container build failures + +If builds fail, try cleaning and rebuilding: ```bash -# Install dev dependencies -uv sync --group dev +# Clean up Docker resources +just clean -# Run tests -uv run pytest +# Rebuild from scratch +docker compose -f deploy/docker-compose.yml build --no-cache +docker compose -f deploy/docker-compose.yml up +``` -# Type checking & linting -uv run pyright -uv run ruff check +### Hot-reload not working + +For WSL2 users, hot-reload should work automatically (WATCHFILES_FORCE_POLLING is enabled). If it doesn't: + +```bash +# Restart the dev environment +docker compose -f deploy/docker-compose.yml -f deploy/docker-compose.dev.yml down +docker compose -f deploy/docker-compose.yml -f deploy/docker-compose.dev.yml up --build ``` ## License diff --git a/deploy/.env.example b/deploy/.env.example new file mode 100644 index 0000000..17b6265 --- /dev/null +++ b/deploy/.env.example @@ -0,0 +1,44 @@ +# OSA Environment Configuration +# Copy to .env and customize values + +# ============================================================================= +# Database Configuration +# ============================================================================= +# PostgreSQL credentials used by all services +POSTGRES_USER=postgres +POSTGRES_PASSWORD=osa +POSTGRES_DB=osa +POSTGRES_HOST=db +POSTGRES_PORT=5432 + +# ============================================================================= +# API Server Configuration +# ============================================================================= +# Host and port for the FastAPI backend +API_HOST=0.0.0.0 +API_PORT=8000 + +# Logging level (DEBUG, INFO, WARNING, ERROR, CRITICAL) +LOG_LEVEL=INFO + +# Data directory for OSA storage (inside container) +OSA_DATA_DIR=/data + +# ============================================================================= +# Web Interface Configuration +# ============================================================================= +# External port to access the web interface (maps to container port 3000) +# Change this if port 8080 is already in use +WEB_PORT=8080 + +# Backend API URL (used by the web container for SSR) +# In Docker, this should use the service name 'server' +API_URL=http://server:8000 + +# ============================================================================= +# Development Settings (optional) +# ============================================================================= +# These are only used in development mode (docker-compose.dev.yml) + +# Force polling for file changes (required for some systems like WSL2) +# WATCHFILES_FORCE_POLLING=true diff --git a/deploy/docker-compose.dev.yml b/deploy/docker-compose.dev.yml new file mode 100644 index 0000000..32fa427 --- /dev/null +++ b/deploy/docker-compose.dev.yml @@ -0,0 +1,39 @@ +# Development overrides for docker-compose.yml +# Usage: docker compose -f deploy/docker-compose.yml -f deploy/docker-compose.dev.yml up + +services: + server: + build: + context: ../server + dockerfile: Dockerfile + target: builder + volumes: + - ../server:/app + - /app/.venv + environment: + OSA_DATABASE__URL: postgresql+asyncpg://${POSTGRES_USER:-postgres}:${POSTGRES_PASSWORD:-osa}@db:5432/${POSTGRES_DB:-osa} + OSA_DATA_DIR: /data + OSA_LOGGING__LEVEL: ${LOG_LEVEL:-DEBUG} + WATCHFILES_FORCE_POLLING: "true" + command: uvicorn osa.application.api.rest.app:app --host 0.0.0.0 --port 8000 --reload + healthcheck: + test: ["CMD", "curl", "--fail", "http://localhost:8000/api/v1/health"] + interval: 10s + timeout: 5s + start_period: 30s + retries: 3 + + web: + build: + context: ../web + dockerfile: Dockerfile + target: deps + volumes: + - ../web:/app + - /app/node_modules + - /app/.next + environment: + API_URL: http://server:8000 + ports: + - "3000:3000" + command: pnpm dev diff --git a/deploy/docker-compose.yml b/deploy/docker-compose.yml new file mode 100644 index 0000000..f76e104 --- /dev/null +++ b/deploy/docker-compose.yml @@ -0,0 +1,55 @@ +services: + db: + image: postgres:16-alpine + environment: + POSTGRES_USER: ${POSTGRES_USER:-postgres} + POSTGRES_PASSWORD: ${POSTGRES_PASSWORD:-osa} + POSTGRES_DB: ${POSTGRES_DB:-osa} + volumes: + - postgres_data:/var/lib/postgresql/data + healthcheck: + test: ["CMD-SHELL", "pg_isready -U ${POSTGRES_USER:-postgres}"] + interval: 3s + timeout: 10s + retries: 5 + restart: unless-stopped + + server: + build: + context: ../server + dockerfile: Dockerfile + environment: + OSA_DATABASE__URL: postgresql+asyncpg://${POSTGRES_USER:-postgres}:${POSTGRES_PASSWORD:-osa}@db:5432/${POSTGRES_DB:-osa} + OSA_DATA_DIR: /data + OSA_LOGGING__LEVEL: ${LOG_LEVEL:-INFO} + depends_on: + db: + condition: service_healthy + volumes: + - server_data:/data + healthcheck: + test: ["CMD", "curl", "--fail", "http://localhost:8000/api/v1/health"] + interval: 30s + timeout: 10s + start_period: 10s + retries: 3 + restart: unless-stopped + + web: + build: + context: ../web + dockerfile: Dockerfile + args: + API_URL: http://server:8000 + environment: + API_URL: http://server:8000 + ports: + - "${WEB_PORT:-8080}:3000" + depends_on: + server: + condition: service_healthy + restart: unless-stopped + +volumes: + postgres_data: + server_data: diff --git a/osa/domain/index/listener/__init__.py b/osa/domain/index/listener/__init__.py deleted file mode 100644 index bac627e..0000000 --- a/osa/domain/index/listener/__init__.py +++ /dev/null @@ -1,5 +0,0 @@ -"""Index domain listeners.""" - -from osa.domain.index.listener.index_projector import ProjectNewRecordToIndexes - -__all__ = ["ProjectNewRecordToIndexes"] diff --git a/osa/domain/source/service/source.py b/osa/domain/source/service/source.py deleted file mode 100644 index ee9cbbf..0000000 --- a/osa/domain/source/service/source.py +++ /dev/null @@ -1,110 +0,0 @@ -"""SourceService - orchestrates pulling from data sources.""" - -import logging -from dataclasses import dataclass -from datetime import UTC, datetime -from uuid import uuid4 - -from osa.domain.deposition.event.submitted import DepositionSubmittedEvent -from osa.domain.shared.event import EventId -from osa.domain.shared.model.srn import DepositionSRN, Domain, LocalId -from osa.domain.shared.outbox import Outbox -from osa.domain.shared.service import Service -from osa.domain.source.event.source_run_completed import SourceRunCompleted -from osa.domain.source.model.registry import SourceRegistry - -logger = logging.getLogger(__name__) - - -@dataclass -class SourceResult: - """Result of a source run.""" - - source_name: str - record_count: int - started_at: datetime - completed_at: datetime - - -class SourceService(Service): - """Orchestrates pulling records from sources and emitting deposition events. - - This service encapsulates the business logic for pulling from sources that was - previously embedded in the PullFromSource listener. It can be called from multiple - entry points (event listeners, CLI commands, scheduled jobs). - """ - - sources: SourceRegistry - outbox: Outbox - node_domain: Domain - - async def run_source( - self, - source_name: str, - since: datetime | None = None, - limit: int | None = None, - ) -> SourceResult: - """Pull records from a source and emit DepositionSubmitted events. - - Args: - source_name: Name of the source to use. - since: Only fetch records updated after this time. - limit: Maximum number of records to fetch. - - Returns: - SourceResult with run statistics. - - Raises: - ValueError: If the source is not found. - """ - source = self.sources.get(source_name) - if not source: - raise ValueError(f"Unknown source: {source_name}") - - started_at = datetime.now(UTC) - logger.info(f"Starting pull from {source_name}, since={since}, limit={limit}") - - count = 0 - async for record in source.pull(since=since, limit=limit): - # Create a deposition SRN for this record - dep_srn = DepositionSRN( - domain=self.node_domain, - id=LocalId(str(uuid4())), - ) - - # Emit DepositionSubmitted with the record metadata - submitted_event = DepositionSubmittedEvent( - id=EventId(uuid4()), - deposition_id=dep_srn, - metadata=record.metadata, - ) - await self.outbox.append(submitted_event) - count += 1 - - # Log record metadata - title = record.metadata.get("title", "")[:60] - logger.info(f" [{record.source_id}] {title}...") - - completed_at = datetime.now(UTC) - logger.info(f"Pull completed: {count} records from {source_name}") - - # Emit completion event for tracking - await self.outbox.append( - SourceRunCompleted( - id=EventId(uuid4()), - source_name=source_name, - source_type=source.name, - started_at=started_at, - completed_at=completed_at, - record_count=count, - since=since, - limit=limit, - ) - ) - - return SourceResult( - source_name=source_name, - record_count=count, - started_at=started_at, - completed_at=completed_at, - ) diff --git a/.python-version b/server/.python-version similarity index 100% rename from .python-version rename to server/.python-version diff --git a/server/Dockerfile b/server/Dockerfile new file mode 100644 index 0000000..b52f793 --- /dev/null +++ b/server/Dockerfile @@ -0,0 +1,71 @@ +# syntax=docker/dockerfile:1 + +# Stage 1: Builder +FROM ghcr.io/astral-sh/uv:python3.13-bookworm-slim AS builder + +WORKDIR /app + +# Enable bytecode compilation for faster startup +ENV UV_COMPILE_BYTECODE=1 + +# Copy from the cache instead of linking since it's a mounted volume +ENV UV_LINK_MODE=copy + +# Install dependencies first (better caching) +COPY pyproject.toml uv.lock ./ +RUN --mount=type=cache,target=/root/.cache/uv \ + uv sync --frozen --no-install-project --no-dev + +# Copy application code +COPY osa/ ./osa/ +COPY sources/ ./sources/ +COPY migrations/ ./migrations/ +COPY alembic.ini ./ +COPY entrypoint.sh ./ +COPY README.md ./ +COPY config.demo.yaml ./config.yaml + +# Install the project +RUN --mount=type=cache,target=/root/.cache/uv \ + uv sync --frozen --no-dev + +# Stage 2: Runtime +FROM python:3.13-slim-bookworm AS runtime + +# Install curl for health checks +RUN apt-get update && apt-get install -y --no-install-recommends curl && \ + rm -rf /var/lib/apt/lists/* + +# Create non-root user +RUN useradd --create-home --shell /bin/bash appuser + +WORKDIR /app + +# Copy the virtual environment from builder +COPY --from=builder --chown=appuser:appuser /app/.venv /app/.venv +COPY --from=builder --chown=appuser:appuser /app/osa /app/osa +COPY --from=builder --chown=appuser:appuser /app/sources /app/sources +COPY --from=builder --chown=appuser:appuser /app/migrations /app/migrations +COPY --from=builder --chown=appuser:appuser /app/alembic.ini /app/alembic.ini +COPY --from=builder --chown=appuser:appuser /app/config.yaml /app/config.yaml + +# Ensure the virtualenv is used +ENV PATH="/app/.venv/bin:$PATH" + +# Create data directory +RUN mkdir -p /data && chown appuser:appuser /data +ENV OSA_DATA_DIR=/data + +COPY --from=builder --chown=appuser:appuser /app/entrypoint.sh /app/entrypoint.sh +RUN chmod +x /app/entrypoint.sh + +USER appuser + +EXPOSE 8000 + +# Health check +HEALTHCHECK --interval=30s --timeout=10s --start-period=5s --retries=3 \ + CMD curl --fail http://localhost:8000/api/v1/health || exit 1 + +ENTRYPOINT ["/app/entrypoint.sh"] +CMD ["uvicorn", "osa.application.api.rest.app:app", "--host", "0.0.0.0", "--port", "8000"] diff --git a/server/Justfile b/server/Justfile new file mode 100644 index 0000000..afeadd5 --- /dev/null +++ b/server/Justfile @@ -0,0 +1,87 @@ +# Server Justfile +# Development commands for the Python backend + +default: + @just --list + +# === Development === + +# Run development server with hot-reload +dev: + uv run uvicorn osa.application.api.rest.app:app --reload --host 0.0.0.0 --port 8000 + +# Run with debug logging +dev-debug: + LOG_LEVEL=DEBUG uv run uvicorn osa.application.api.rest.app:app --reload --host 0.0.0.0 --port 8000 + +# === Testing === + +# Run all tests +test: + @TEST=1 uv run pytest tests -v --tb=short + +# Run unit tests +test-unit: + @TEST=1 uv run pytest tests/unit -v --tb=short + +# Run tests with verbose logging +test-s kind="unit": + @TEST=1 uv run pytest -s -o log_cli=True -o log_cli_level=DEBUG "tests/{{kind}}" + +# Run tests with coverage +test-cov: + @TEST=1 uv run pytest tests/unit --cov=osa --cov-report=term-missing + +# === Code Quality === + +# Run linter and type checker +lint: + uv run ruff check osa + uv run ty check osa + +# Fix formatting and lint issues +fix: + uv run ruff format osa + uv run ruff check --fix osa + +# Format code +format: + uv run ruff format osa + +# === Database === + +# Run migrations +migrate: + uv run alembic upgrade head + +# Create new migration +migration name: + uv run alembic revision -m "{{name}}" + +# Show current migration version +migrate-status: + uv run alembic current + +# Show migration history +migrate-history: + uv run alembic history + +# Rollback one migration +migrate-down: + uv run alembic downgrade -1 + +# === CLI === + +# Run any osa CLI command +cli *ARGS: + uv run osa {{ARGS}} + +# === Dependencies === + +# Install/sync dependencies +install: + uv sync + +# Update dependencies +update: + uv sync --upgrade diff --git a/server/README.md b/server/README.md new file mode 100644 index 0000000..a670bb0 --- /dev/null +++ b/server/README.md @@ -0,0 +1,33 @@ +# OSA Server + +Python backend for Open Science Archive, built with FastAPI. + +## Development + +```bash +# Install dependencies +uv sync + +# Run development server +just dev + +# Run tests +just test + +# Lint and type check +just lint +``` + +## Structure + +``` +server/ +├── osa/ # Application code +├── tests/ # Test suite +├── migrations/ # Database migrations (Alembic) +├── sources/ # Data source plugins +├── Dockerfile # Container build +└── Justfile # Development commands +``` + +See the [root README](../README.md) for full documentation. diff --git a/alembic.ini b/server/alembic.ini similarity index 100% rename from alembic.ini rename to server/alembic.ini diff --git a/server/entrypoint.sh b/server/entrypoint.sh new file mode 100644 index 0000000..555cf8f --- /dev/null +++ b/server/entrypoint.sh @@ -0,0 +1,10 @@ +#!/bin/bash +set -e + +# Run database migrations +echo "Running database migrations..." +alembic upgrade head + +# Start the application +echo "Starting application..." +exec "$@" diff --git a/migrations/README b/server/migrations/README similarity index 100% rename from migrations/README rename to server/migrations/README diff --git a/migrations/env.py b/server/migrations/env.py similarity index 70% rename from migrations/env.py rename to server/migrations/env.py index 9b9fc57..31d7afd 100644 --- a/migrations/env.py +++ b/server/migrations/env.py @@ -1,3 +1,4 @@ +import os from logging.config import fileConfig from sqlalchemy import engine_from_config, pool @@ -8,6 +9,24 @@ # access to the values within the .ini file in use. config = context.config +# Override sqlalchemy.url from environment variable if set +# Uses OSA_DATABASE__URL (same as the app) for consistency +# Convert async driver (asyncpg/aiosqlite) to sync driver for alembic +database_url = os.environ.get("OSA_DATABASE__URL") +if database_url: + # Alembic runs synchronously, so convert async drivers to sync + sync_url = database_url.replace("postgresql+asyncpg://", "postgresql+psycopg2://") + sync_url = sync_url.replace("sqlite+aiosqlite://", "sqlite://") + config.set_main_option("sqlalchemy.url", sync_url) +else: + # Derive SQLite URL from OSA_DATA_DIR (same logic as Config class) + from osa.cli.util.paths import OSAPaths + + paths = OSAPaths() + paths.ensure_directories() # Create directories if they don't exist + sqlite_url = f"sqlite:///{paths.database_file}" + config.set_main_option("sqlalchemy.url", sqlite_url) + # Interpret the config file for Python logging. # This line sets up loggers basically. if config.config_file_name is not None: diff --git a/migrations/script.py.mako b/server/migrations/script.py.mako similarity index 100% rename from migrations/script.py.mako rename to server/migrations/script.py.mako diff --git a/migrations/versions/0d9fbacf8e58_initial_tables.py b/server/migrations/versions/0d9fbacf8e58_initial_tables.py similarity index 100% rename from migrations/versions/0d9fbacf8e58_initial_tables.py rename to server/migrations/versions/0d9fbacf8e58_initial_tables.py diff --git a/osa/__init__.py b/server/osa/__init__.py similarity index 100% rename from osa/__init__.py rename to server/osa/__init__.py diff --git a/osa/application/__init__.py b/server/osa/application/__init__.py similarity index 100% rename from osa/application/__init__.py rename to server/osa/application/__init__.py diff --git a/osa/application/api/__init__.py b/server/osa/application/api/__init__.py similarity index 100% rename from osa/application/api/__init__.py rename to server/osa/application/api/__init__.py diff --git a/osa/application/api/rest/__init__.py b/server/osa/application/api/rest/__init__.py similarity index 100% rename from osa/application/api/rest/__init__.py rename to server/osa/application/api/rest/__init__.py diff --git a/osa/application/api/rest/app.py b/server/osa/application/api/rest/app.py similarity index 85% rename from osa/application/api/rest/app.py rename to server/osa/application/api/rest/app.py index 877cbb8..cd6af1d 100644 --- a/osa/application/api/rest/app.py +++ b/server/osa/application/api/rest/app.py @@ -6,13 +6,15 @@ from fastapi.responses import JSONResponse from osa.application.api.v1.errors import map_osa_error -from osa.application.api.v1.routes import events, health, search, stats, validation +from osa.application.api.v1.routes import events, health, records, search, stats, validation from osa.application.di import create_container from osa.config import Config, configure_logging +from osa.domain.index.service import IndexService from osa.domain.shared.error import OSAError from osa.infrastructure.event.worker import BackgroundWorker from osa.infrastructure.source.discovery import validate_sources_at_startup from osa.util.di.fastapi import setup_dishka +from osa.util.di.scope import Scope logger = logging.getLogger(__name__) @@ -26,6 +28,12 @@ async def lifespan(app: FastAPI): async with worker: yield + # Flush all index backends on shutdown to ensure buffered records are persisted + logger.info("Flushing index backends on shutdown...") + async with container(scope=Scope.UOW) as scope: + index_service = await scope.get(IndexService) + await index_service.flush_all() + await container.close() @@ -58,6 +66,7 @@ def create_app() -> FastAPI: # Register v1 routes with /api/v1 prefix app_instance.include_router(health.router, prefix="/api/v1") app_instance.include_router(events.router, prefix="/api/v1") + app_instance.include_router(records.router, prefix="/api/v1") app_instance.include_router(search.router, prefix="/api/v1") app_instance.include_router(stats.router, prefix="/api/v1") app_instance.include_router(validation.router, prefix="/api/v1") diff --git a/osa/application/api/v1/__init__.py b/server/osa/application/api/v1/__init__.py similarity index 100% rename from osa/application/api/v1/__init__.py rename to server/osa/application/api/v1/__init__.py diff --git a/osa/application/api/v1/errors.py b/server/osa/application/api/v1/errors.py similarity index 100% rename from osa/application/api/v1/errors.py rename to server/osa/application/api/v1/errors.py diff --git a/osa/application/api/v1/routes/__init__.py b/server/osa/application/api/v1/routes/__init__.py similarity index 100% rename from osa/application/api/v1/routes/__init__.py rename to server/osa/application/api/v1/routes/__init__.py diff --git a/osa/application/api/v1/routes/events.py b/server/osa/application/api/v1/routes/events.py similarity index 100% rename from osa/application/api/v1/routes/events.py rename to server/osa/application/api/v1/routes/events.py diff --git a/osa/application/api/v1/routes/health.py b/server/osa/application/api/v1/routes/health.py similarity index 100% rename from osa/application/api/v1/routes/health.py rename to server/osa/application/api/v1/routes/health.py diff --git a/server/osa/application/api/v1/routes/records.py b/server/osa/application/api/v1/routes/records.py new file mode 100644 index 0000000..249b5b2 --- /dev/null +++ b/server/osa/application/api/v1/routes/records.py @@ -0,0 +1,47 @@ +"""Records API routes.""" + +from typing import Any + +from dishka.integrations.fastapi import DishkaRoute, FromDishka +from fastapi import APIRouter, HTTPException +from pydantic import BaseModel + +from osa.domain.record.port.repository import RecordRepository +from osa.domain.shared.model.srn import RecordSRN + +router = APIRouter( + prefix="/records", + tags=["records"], + route_class=DishkaRoute, +) + + +class RecordResponse(BaseModel): + """Single record response.""" + + record: dict[str, Any] + + +@router.get("/{srn:path}") +async def get_record( + srn: str, + repo: FromDishka[RecordRepository], +) -> RecordResponse: + """Get a record by SRN.""" + try: + record_srn = RecordSRN.parse(srn) + except ValueError as e: + raise HTTPException(status_code=400, detail=f"Invalid SRN: {e}") + + record = await repo.get(record_srn) + if not record: + raise HTTPException(status_code=404, detail="Record not found") + + return RecordResponse( + record={ + "srn": str(record.srn), + "deposition_srn": str(record.deposition_srn), + "metadata": record.metadata, + "published_at": record.published_at.isoformat(), + } + ) diff --git a/osa/application/api/v1/routes/search.py b/server/osa/application/api/v1/routes/search.py similarity index 76% rename from osa/application/api/v1/routes/search.py rename to server/osa/application/api/v1/routes/search.py index e1aefb0..c71008e 100644 --- a/osa/application/api/v1/routes/search.py +++ b/server/osa/application/api/v1/routes/search.py @@ -22,6 +22,7 @@ class SearchResponse(BaseModel): query: str index: str total: int + has_more: bool results: list[dict[str, Any]] @@ -30,6 +31,7 @@ async def search_index( index_name: str, indexes: FromDishka[IndexRegistry], q: str = Query(..., description="Search query"), + offset: int = Query(0, ge=0, description="Number of results to skip"), limit: int = Query(20, ge=1, le=100, description="Maximum number of results"), ) -> SearchResponse: """Search a specific index by name.""" @@ -43,19 +45,24 @@ async def search_index( detail=f"Index '{index_name}' not found. Available: {indexes.names()}", ) - result: QueryResult = await backend.query(q, limit=limit) + # Naive pagination: fetch offset+limit+1 to determine has_more, then slice + result: QueryResult = await backend.query(q, limit=offset + limit + 1) + all_hits = result.hits[offset:] # Skip first `offset` results + has_more = len(all_hits) > limit + hits = all_hits[:limit] return SearchResponse( query=q, index=index_name, - total=len(result.hits), + total=len(hits), + has_more=has_more, results=[ { - "id": hit.srn, + "srn": hit.srn, "score": hit.score, "metadata": hit.metadata, } - for hit in result.hits + for hit in hits ], ) diff --git a/osa/application/api/v1/routes/stats.py b/server/osa/application/api/v1/routes/stats.py similarity index 100% rename from osa/application/api/v1/routes/stats.py rename to server/osa/application/api/v1/routes/stats.py diff --git a/osa/application/api/v1/routes/validation.py b/server/osa/application/api/v1/routes/validation.py similarity index 100% rename from osa/application/api/v1/routes/validation.py rename to server/osa/application/api/v1/routes/validation.py diff --git a/osa/application/di.py b/server/osa/application/di.py similarity index 100% rename from osa/application/di.py rename to server/osa/application/di.py diff --git a/osa/application/event/__init__.py b/server/osa/application/event/__init__.py similarity index 100% rename from osa/application/event/__init__.py rename to server/osa/application/event/__init__.py diff --git a/osa/application/event/server_started.py b/server/osa/application/event/server_started.py similarity index 100% rename from osa/application/event/server_started.py rename to server/osa/application/event/server_started.py diff --git a/osa/cli/__init__.py b/server/osa/cli/__init__.py similarity index 100% rename from osa/cli/__init__.py rename to server/osa/cli/__init__.py diff --git a/osa/cli/commands/__init__.py b/server/osa/cli/commands/__init__.py similarity index 100% rename from osa/cli/commands/__init__.py rename to server/osa/cli/commands/__init__.py diff --git a/osa/cli/commands/admin.py b/server/osa/cli/commands/admin.py similarity index 100% rename from osa/cli/commands/admin.py rename to server/osa/cli/commands/admin.py diff --git a/osa/cli/commands/events.py b/server/osa/cli/commands/events.py similarity index 100% rename from osa/cli/commands/events.py rename to server/osa/cli/commands/events.py diff --git a/osa/cli/commands/local.py b/server/osa/cli/commands/local.py similarity index 100% rename from osa/cli/commands/local.py rename to server/osa/cli/commands/local.py diff --git a/osa/cli/commands/search.py b/server/osa/cli/commands/search.py similarity index 99% rename from osa/cli/commands/search.py rename to server/osa/cli/commands/search.py index 85dd7c3..ad8a82f 100644 --- a/osa/cli/commands/search.py +++ b/server/osa/cli/commands/search.py @@ -81,7 +81,7 @@ def search( # Build typed SearchHit models hits: list[SearchHit] = [] for hit in results: - srn = hit.get("id", "") + srn = hit.get("srn", "") hits.append( SearchHit( srn=srn, diff --git a/osa/cli/commands/show.py b/server/osa/cli/commands/show.py similarity index 100% rename from osa/cli/commands/show.py rename to server/osa/cli/commands/show.py diff --git a/osa/cli/commands/stats.py b/server/osa/cli/commands/stats.py similarity index 100% rename from osa/cli/commands/stats.py rename to server/osa/cli/commands/stats.py diff --git a/osa/cli/console.py b/server/osa/cli/console.py similarity index 100% rename from osa/cli/console.py rename to server/osa/cli/console.py diff --git a/osa/cli/main.py b/server/osa/cli/main.py similarity index 100% rename from osa/cli/main.py rename to server/osa/cli/main.py diff --git a/osa/cli/models.py b/server/osa/cli/models.py similarity index 100% rename from osa/cli/models.py rename to server/osa/cli/models.py diff --git a/osa/cli/util/__init__.py b/server/osa/cli/util/__init__.py similarity index 100% rename from osa/cli/util/__init__.py rename to server/osa/cli/util/__init__.py diff --git a/osa/cli/util/daemon.py b/server/osa/cli/util/daemon.py similarity index 100% rename from osa/cli/util/daemon.py rename to server/osa/cli/util/daemon.py diff --git a/osa/cli/util/paths.py b/server/osa/cli/util/paths.py similarity index 100% rename from osa/cli/util/paths.py rename to server/osa/cli/util/paths.py diff --git a/osa/cli/util/search_cache.py b/server/osa/cli/util/search_cache.py similarity index 100% rename from osa/cli/util/search_cache.py rename to server/osa/cli/util/search_cache.py diff --git a/osa/cli/util/server_state.py b/server/osa/cli/util/server_state.py similarity index 100% rename from osa/cli/util/server_state.py rename to server/osa/cli/util/server_state.py diff --git a/osa/config.py b/server/osa/config.py similarity index 99% rename from osa/config.py rename to server/osa/config.py index 7aa1a3f..ef606d1 100644 --- a/osa/config.py +++ b/server/osa/config.py @@ -49,7 +49,7 @@ class InitialRun(BaseModel): """Initial run configuration for a source.""" enabled: bool = False - limit: int | None = 10 # Limit records for initial run + limit: int | None # Required: number to limit, or null for no limit since: datetime | None = None # Optional: bootstrap from specific date diff --git a/osa/domain/__init__.py b/server/osa/domain/__init__.py similarity index 100% rename from osa/domain/__init__.py rename to server/osa/domain/__init__.py diff --git a/osa/domain/auth/__init__.py b/server/osa/domain/auth/__init__.py similarity index 100% rename from osa/domain/auth/__init__.py rename to server/osa/domain/auth/__init__.py diff --git a/osa/domain/auth/adapter/__init__.py b/server/osa/domain/auth/adapter/__init__.py similarity index 100% rename from osa/domain/auth/adapter/__init__.py rename to server/osa/domain/auth/adapter/__init__.py diff --git a/osa/domain/auth/command/__init__.py b/server/osa/domain/auth/command/__init__.py similarity index 100% rename from osa/domain/auth/command/__init__.py rename to server/osa/domain/auth/command/__init__.py diff --git a/osa/domain/auth/event/__init__.py b/server/osa/domain/auth/event/__init__.py similarity index 100% rename from osa/domain/auth/event/__init__.py rename to server/osa/domain/auth/event/__init__.py diff --git a/osa/domain/auth/model/__init__.py b/server/osa/domain/auth/model/__init__.py similarity index 100% rename from osa/domain/auth/model/__init__.py rename to server/osa/domain/auth/model/__init__.py diff --git a/osa/domain/auth/port/__init__.py b/server/osa/domain/auth/port/__init__.py similarity index 100% rename from osa/domain/auth/port/__init__.py rename to server/osa/domain/auth/port/__init__.py diff --git a/osa/domain/auth/query/__init__.py b/server/osa/domain/auth/query/__init__.py similarity index 100% rename from osa/domain/auth/query/__init__.py rename to server/osa/domain/auth/query/__init__.py diff --git a/osa/domain/auth/service/__init__.py b/server/osa/domain/auth/service/__init__.py similarity index 100% rename from osa/domain/auth/service/__init__.py rename to server/osa/domain/auth/service/__init__.py diff --git a/osa/domain/curation/__init__.py b/server/osa/domain/curation/__init__.py similarity index 100% rename from osa/domain/curation/__init__.py rename to server/osa/domain/curation/__init__.py diff --git a/osa/domain/curation/adapter/__init__.py b/server/osa/domain/curation/adapter/__init__.py similarity index 100% rename from osa/domain/curation/adapter/__init__.py rename to server/osa/domain/curation/adapter/__init__.py diff --git a/osa/domain/curation/command/__init__.py b/server/osa/domain/curation/command/__init__.py similarity index 100% rename from osa/domain/curation/command/__init__.py rename to server/osa/domain/curation/command/__init__.py diff --git a/osa/domain/curation/event/__init__.py b/server/osa/domain/curation/event/__init__.py similarity index 100% rename from osa/domain/curation/event/__init__.py rename to server/osa/domain/curation/event/__init__.py diff --git a/osa/domain/curation/event/deposition_approved.py b/server/osa/domain/curation/event/deposition_approved.py similarity index 100% rename from osa/domain/curation/event/deposition_approved.py rename to server/osa/domain/curation/event/deposition_approved.py diff --git a/osa/domain/curation/listener/__init__.py b/server/osa/domain/curation/listener/__init__.py similarity index 100% rename from osa/domain/curation/listener/__init__.py rename to server/osa/domain/curation/listener/__init__.py diff --git a/osa/domain/curation/listener/auto_approve_curation_tool.py b/server/osa/domain/curation/listener/auto_approve_curation_tool.py similarity index 100% rename from osa/domain/curation/listener/auto_approve_curation_tool.py rename to server/osa/domain/curation/listener/auto_approve_curation_tool.py diff --git a/osa/domain/curation/model/__init__.py b/server/osa/domain/curation/model/__init__.py similarity index 100% rename from osa/domain/curation/model/__init__.py rename to server/osa/domain/curation/model/__init__.py diff --git a/osa/domain/curation/port/__init__.py b/server/osa/domain/curation/port/__init__.py similarity index 100% rename from osa/domain/curation/port/__init__.py rename to server/osa/domain/curation/port/__init__.py diff --git a/osa/domain/curation/query/__init__.py b/server/osa/domain/curation/query/__init__.py similarity index 100% rename from osa/domain/curation/query/__init__.py rename to server/osa/domain/curation/query/__init__.py diff --git a/osa/domain/curation/service/__init__.py b/server/osa/domain/curation/service/__init__.py similarity index 100% rename from osa/domain/curation/service/__init__.py rename to server/osa/domain/curation/service/__init__.py diff --git a/osa/domain/deposition/__init__.py b/server/osa/domain/deposition/__init__.py similarity index 100% rename from osa/domain/deposition/__init__.py rename to server/osa/domain/deposition/__init__.py diff --git a/osa/domain/deposition/adapter/__init__.py b/server/osa/domain/deposition/adapter/__init__.py similarity index 100% rename from osa/domain/deposition/adapter/__init__.py rename to server/osa/domain/deposition/adapter/__init__.py diff --git a/osa/domain/deposition/command/__init__.py b/server/osa/domain/deposition/command/__init__.py similarity index 100% rename from osa/domain/deposition/command/__init__.py rename to server/osa/domain/deposition/command/__init__.py diff --git a/osa/domain/deposition/command/create.py b/server/osa/domain/deposition/command/create.py similarity index 100% rename from osa/domain/deposition/command/create.py rename to server/osa/domain/deposition/command/create.py diff --git a/osa/domain/deposition/command/delete_files.py b/server/osa/domain/deposition/command/delete_files.py similarity index 100% rename from osa/domain/deposition/command/delete_files.py rename to server/osa/domain/deposition/command/delete_files.py diff --git a/osa/domain/deposition/command/submit.py b/server/osa/domain/deposition/command/submit.py similarity index 100% rename from osa/domain/deposition/command/submit.py rename to server/osa/domain/deposition/command/submit.py diff --git a/osa/domain/deposition/command/update.py b/server/osa/domain/deposition/command/update.py similarity index 100% rename from osa/domain/deposition/command/update.py rename to server/osa/domain/deposition/command/update.py diff --git a/osa/domain/deposition/command/upload.py b/server/osa/domain/deposition/command/upload.py similarity index 100% rename from osa/domain/deposition/command/upload.py rename to server/osa/domain/deposition/command/upload.py diff --git a/osa/domain/deposition/event/__init__.py b/server/osa/domain/deposition/event/__init__.py similarity index 100% rename from osa/domain/deposition/event/__init__.py rename to server/osa/domain/deposition/event/__init__.py diff --git a/osa/domain/deposition/event/submitted.py b/server/osa/domain/deposition/event/submitted.py similarity index 100% rename from osa/domain/deposition/event/submitted.py rename to server/osa/domain/deposition/event/submitted.py diff --git a/osa/domain/deposition/model/__init__.py b/server/osa/domain/deposition/model/__init__.py similarity index 100% rename from osa/domain/deposition/model/__init__.py rename to server/osa/domain/deposition/model/__init__.py diff --git a/osa/domain/deposition/model/aggregate.py b/server/osa/domain/deposition/model/aggregate.py similarity index 100% rename from osa/domain/deposition/model/aggregate.py rename to server/osa/domain/deposition/model/aggregate.py diff --git a/osa/domain/deposition/model/entity.py b/server/osa/domain/deposition/model/entity.py similarity index 100% rename from osa/domain/deposition/model/entity.py rename to server/osa/domain/deposition/model/entity.py diff --git a/osa/domain/deposition/model/value.py b/server/osa/domain/deposition/model/value.py similarity index 100% rename from osa/domain/deposition/model/value.py rename to server/osa/domain/deposition/model/value.py diff --git a/osa/domain/deposition/port/__init__.py b/server/osa/domain/deposition/port/__init__.py similarity index 100% rename from osa/domain/deposition/port/__init__.py rename to server/osa/domain/deposition/port/__init__.py diff --git a/osa/domain/deposition/port/repository.py b/server/osa/domain/deposition/port/repository.py similarity index 100% rename from osa/domain/deposition/port/repository.py rename to server/osa/domain/deposition/port/repository.py diff --git a/osa/domain/deposition/port/storage.py b/server/osa/domain/deposition/port/storage.py similarity index 100% rename from osa/domain/deposition/port/storage.py rename to server/osa/domain/deposition/port/storage.py diff --git a/osa/domain/deposition/query/__init__.py b/server/osa/domain/deposition/query/__init__.py similarity index 100% rename from osa/domain/deposition/query/__init__.py rename to server/osa/domain/deposition/query/__init__.py diff --git a/osa/domain/deposition/service/__init__.py b/server/osa/domain/deposition/service/__init__.py similarity index 100% rename from osa/domain/deposition/service/__init__.py rename to server/osa/domain/deposition/service/__init__.py diff --git a/osa/domain/deposition/service/deposition.py b/server/osa/domain/deposition/service/deposition.py similarity index 100% rename from osa/domain/deposition/service/deposition.py rename to server/osa/domain/deposition/service/deposition.py diff --git a/osa/domain/deposition/util/di/__init__.py b/server/osa/domain/deposition/util/di/__init__.py similarity index 100% rename from osa/domain/deposition/util/di/__init__.py rename to server/osa/domain/deposition/util/di/__init__.py diff --git a/osa/domain/deposition/util/di/provider.py b/server/osa/domain/deposition/util/di/provider.py similarity index 100% rename from osa/domain/deposition/util/di/provider.py rename to server/osa/domain/deposition/util/di/provider.py diff --git a/osa/domain/export/__init__.py b/server/osa/domain/export/__init__.py similarity index 100% rename from osa/domain/export/__init__.py rename to server/osa/domain/export/__init__.py diff --git a/osa/domain/export/adapter/__init__.py b/server/osa/domain/export/adapter/__init__.py similarity index 100% rename from osa/domain/export/adapter/__init__.py rename to server/osa/domain/export/adapter/__init__.py diff --git a/osa/domain/export/command/__init__.py b/server/osa/domain/export/command/__init__.py similarity index 100% rename from osa/domain/export/command/__init__.py rename to server/osa/domain/export/command/__init__.py diff --git a/osa/domain/export/event/__init__.py b/server/osa/domain/export/event/__init__.py similarity index 100% rename from osa/domain/export/event/__init__.py rename to server/osa/domain/export/event/__init__.py diff --git a/osa/domain/export/model/__init__.py b/server/osa/domain/export/model/__init__.py similarity index 100% rename from osa/domain/export/model/__init__.py rename to server/osa/domain/export/model/__init__.py diff --git a/osa/domain/export/port/__init__.py b/server/osa/domain/export/port/__init__.py similarity index 100% rename from osa/domain/export/port/__init__.py rename to server/osa/domain/export/port/__init__.py diff --git a/osa/domain/export/query/__init__.py b/server/osa/domain/export/query/__init__.py similarity index 100% rename from osa/domain/export/query/__init__.py rename to server/osa/domain/export/query/__init__.py diff --git a/osa/domain/export/service/__init__.py b/server/osa/domain/export/service/__init__.py similarity index 100% rename from osa/domain/export/service/__init__.py rename to server/osa/domain/export/service/__init__.py diff --git a/osa/domain/index/__init__.py b/server/osa/domain/index/__init__.py similarity index 100% rename from osa/domain/index/__init__.py rename to server/osa/domain/index/__init__.py diff --git a/server/osa/domain/index/listener/__init__.py b/server/osa/domain/index/listener/__init__.py new file mode 100644 index 0000000..b635862 --- /dev/null +++ b/server/osa/domain/index/listener/__init__.py @@ -0,0 +1,6 @@ +"""Index domain listeners.""" + +from osa.domain.index.listener.flush_listener import FlushIndexesOnSourceComplete +from osa.domain.index.listener.index_projector import ProjectNewRecordToIndexes + +__all__ = ["FlushIndexesOnSourceComplete", "ProjectNewRecordToIndexes"] diff --git a/server/osa/domain/index/listener/flush_listener.py b/server/osa/domain/index/listener/flush_listener.py new file mode 100644 index 0000000..97f0e9d --- /dev/null +++ b/server/osa/domain/index/listener/flush_listener.py @@ -0,0 +1,21 @@ +"""FlushListener - flushes index backends when source run's final chunk completes.""" + +from osa.domain.index.service import IndexService +from osa.domain.shared.event import EventListener +from osa.domain.source.event.source_run_completed import SourceRunCompleted + + +class FlushIndexesOnSourceComplete(EventListener[SourceRunCompleted]): + """Flushes index backends when a source run's final chunk completes. + + This ensures all buffered records are persisted before the source run + is considered fully complete, enabling downstream consumers to see + all indexed records. + """ + + service: IndexService + + async def handle(self, event: SourceRunCompleted) -> None: + """Flush all index backends if this is the final chunk.""" + if event.is_final_chunk: + await self.service.flush_all() diff --git a/osa/domain/index/listener/index_projector.py b/server/osa/domain/index/listener/index_projector.py similarity index 100% rename from osa/domain/index/listener/index_projector.py rename to server/osa/domain/index/listener/index_projector.py diff --git a/osa/domain/index/model/__init__.py b/server/osa/domain/index/model/__init__.py similarity index 100% rename from osa/domain/index/model/__init__.py rename to server/osa/domain/index/model/__init__.py diff --git a/osa/domain/index/model/registry.py b/server/osa/domain/index/model/registry.py similarity index 100% rename from osa/domain/index/model/registry.py rename to server/osa/domain/index/model/registry.py diff --git a/osa/domain/index/service/__init__.py b/server/osa/domain/index/service/__init__.py similarity index 100% rename from osa/domain/index/service/__init__.py rename to server/osa/domain/index/service/__init__.py diff --git a/osa/domain/index/service/index.py b/server/osa/domain/index/service/index.py similarity index 69% rename from osa/domain/index/service/index.py rename to server/osa/domain/index/service/index.py index 3e5efdf..bdd44a7 100644 --- a/osa/domain/index/service/index.py +++ b/server/osa/domain/index/service/index.py @@ -40,6 +40,21 @@ async def index_record( for name, backend in self.indexes.items(): try: await backend.ingest(srn_str, metadata) - logger.debug(f"Indexed {srn_str} into backend '{name}'") + logger.debug(f"Buffered {srn_str} for backend '{name}'") except Exception as e: logger.error(f"Failed to index {srn_str} into '{name}': {e}") + + async def flush_all(self) -> None: + """Flush all backends to ensure buffered records are persisted. + + This should be called: + - When a source run's final chunk completes + - On application shutdown + - After bulk import operations + """ + for name, backend in self.indexes.items(): + try: + await backend.flush() + logger.info(f"Flushed index backend '{name}'") + except Exception as e: + logger.error(f"Failed to flush backend '{name}': {e}") diff --git a/osa/domain/record/__init__.py b/server/osa/domain/record/__init__.py similarity index 100% rename from osa/domain/record/__init__.py rename to server/osa/domain/record/__init__.py diff --git a/osa/domain/record/adapter/__init__.py b/server/osa/domain/record/adapter/__init__.py similarity index 100% rename from osa/domain/record/adapter/__init__.py rename to server/osa/domain/record/adapter/__init__.py diff --git a/osa/domain/record/command/__init__.py b/server/osa/domain/record/command/__init__.py similarity index 100% rename from osa/domain/record/command/__init__.py rename to server/osa/domain/record/command/__init__.py diff --git a/osa/domain/record/event/__init__.py b/server/osa/domain/record/event/__init__.py similarity index 100% rename from osa/domain/record/event/__init__.py rename to server/osa/domain/record/event/__init__.py diff --git a/osa/domain/record/event/record_published.py b/server/osa/domain/record/event/record_published.py similarity index 100% rename from osa/domain/record/event/record_published.py rename to server/osa/domain/record/event/record_published.py diff --git a/osa/domain/record/listener/__init__.py b/server/osa/domain/record/listener/__init__.py similarity index 100% rename from osa/domain/record/listener/__init__.py rename to server/osa/domain/record/listener/__init__.py diff --git a/osa/domain/record/listener/record_creation_listener.py b/server/osa/domain/record/listener/record_creation_listener.py similarity index 100% rename from osa/domain/record/listener/record_creation_listener.py rename to server/osa/domain/record/listener/record_creation_listener.py diff --git a/osa/domain/record/model/__init__.py b/server/osa/domain/record/model/__init__.py similarity index 100% rename from osa/domain/record/model/__init__.py rename to server/osa/domain/record/model/__init__.py diff --git a/osa/domain/record/model/aggregate.py b/server/osa/domain/record/model/aggregate.py similarity index 100% rename from osa/domain/record/model/aggregate.py rename to server/osa/domain/record/model/aggregate.py diff --git a/osa/domain/record/model/value.py b/server/osa/domain/record/model/value.py similarity index 100% rename from osa/domain/record/model/value.py rename to server/osa/domain/record/model/value.py diff --git a/osa/domain/record/port/__init__.py b/server/osa/domain/record/port/__init__.py similarity index 100% rename from osa/domain/record/port/__init__.py rename to server/osa/domain/record/port/__init__.py diff --git a/osa/domain/record/port/repository.py b/server/osa/domain/record/port/repository.py similarity index 100% rename from osa/domain/record/port/repository.py rename to server/osa/domain/record/port/repository.py diff --git a/osa/domain/record/query/__init__.py b/server/osa/domain/record/query/__init__.py similarity index 100% rename from osa/domain/record/query/__init__.py rename to server/osa/domain/record/query/__init__.py diff --git a/osa/domain/record/service/__init__.py b/server/osa/domain/record/service/__init__.py similarity index 100% rename from osa/domain/record/service/__init__.py rename to server/osa/domain/record/service/__init__.py diff --git a/osa/domain/record/service/record.py b/server/osa/domain/record/service/record.py similarity index 100% rename from osa/domain/record/service/record.py rename to server/osa/domain/record/service/record.py diff --git a/osa/domain/schema/__init__.py b/server/osa/domain/schema/__init__.py similarity index 100% rename from osa/domain/schema/__init__.py rename to server/osa/domain/schema/__init__.py diff --git a/osa/domain/schema/adapter/__init__.py b/server/osa/domain/schema/adapter/__init__.py similarity index 100% rename from osa/domain/schema/adapter/__init__.py rename to server/osa/domain/schema/adapter/__init__.py diff --git a/osa/domain/schema/command/__init__.py b/server/osa/domain/schema/command/__init__.py similarity index 100% rename from osa/domain/schema/command/__init__.py rename to server/osa/domain/schema/command/__init__.py diff --git a/osa/domain/schema/event/__init__.py b/server/osa/domain/schema/event/__init__.py similarity index 100% rename from osa/domain/schema/event/__init__.py rename to server/osa/domain/schema/event/__init__.py diff --git a/osa/domain/schema/model/__init__.py b/server/osa/domain/schema/model/__init__.py similarity index 100% rename from osa/domain/schema/model/__init__.py rename to server/osa/domain/schema/model/__init__.py diff --git a/osa/domain/schema/port/__init__.py b/server/osa/domain/schema/port/__init__.py similarity index 100% rename from osa/domain/schema/port/__init__.py rename to server/osa/domain/schema/port/__init__.py diff --git a/osa/domain/schema/query/__init__.py b/server/osa/domain/schema/query/__init__.py similarity index 100% rename from osa/domain/schema/query/__init__.py rename to server/osa/domain/schema/query/__init__.py diff --git a/osa/domain/schema/service/__init__.py b/server/osa/domain/schema/service/__init__.py similarity index 100% rename from osa/domain/schema/service/__init__.py rename to server/osa/domain/schema/service/__init__.py diff --git a/osa/domain/search/__init__.py b/server/osa/domain/search/__init__.py similarity index 100% rename from osa/domain/search/__init__.py rename to server/osa/domain/search/__init__.py diff --git a/osa/domain/search/adapter/__init__.py b/server/osa/domain/search/adapter/__init__.py similarity index 100% rename from osa/domain/search/adapter/__init__.py rename to server/osa/domain/search/adapter/__init__.py diff --git a/osa/domain/search/command/__init__.py b/server/osa/domain/search/command/__init__.py similarity index 100% rename from osa/domain/search/command/__init__.py rename to server/osa/domain/search/command/__init__.py diff --git a/osa/domain/search/event/__init__.py b/server/osa/domain/search/event/__init__.py similarity index 100% rename from osa/domain/search/event/__init__.py rename to server/osa/domain/search/event/__init__.py diff --git a/osa/domain/search/model/__init__.py b/server/osa/domain/search/model/__init__.py similarity index 100% rename from osa/domain/search/model/__init__.py rename to server/osa/domain/search/model/__init__.py diff --git a/osa/domain/search/port/__init__.py b/server/osa/domain/search/port/__init__.py similarity index 100% rename from osa/domain/search/port/__init__.py rename to server/osa/domain/search/port/__init__.py diff --git a/osa/domain/search/query/__init__.py b/server/osa/domain/search/query/__init__.py similarity index 100% rename from osa/domain/search/query/__init__.py rename to server/osa/domain/search/query/__init__.py diff --git a/osa/domain/search/service/__init__.py b/server/osa/domain/search/service/__init__.py similarity index 100% rename from osa/domain/search/service/__init__.py rename to server/osa/domain/search/service/__init__.py diff --git a/osa/domain/shared/__init__.py b/server/osa/domain/shared/__init__.py similarity index 100% rename from osa/domain/shared/__init__.py rename to server/osa/domain/shared/__init__.py diff --git a/osa/domain/shared/adapter.py b/server/osa/domain/shared/adapter.py similarity index 100% rename from osa/domain/shared/adapter.py rename to server/osa/domain/shared/adapter.py diff --git a/osa/domain/shared/command.py b/server/osa/domain/shared/command.py similarity index 92% rename from osa/domain/shared/command.py rename to server/osa/domain/shared/command.py index 845dad4..948acaf 100644 --- a/osa/domain/shared/command.py +++ b/server/osa/domain/shared/command.py @@ -22,7 +22,7 @@ class _CommandHandlerMeta(ABCMeta): def __new__(mcs, name: str, bases: tuple, namespace: dict): cls = super().__new__(mcs, name, bases, namespace) if any(isinstance(b, mcs) for b in bases): - return dataclass(cls) # type: ignore[return-value] + return dataclass(cls) return cls diff --git a/osa/domain/shared/dto.py b/server/osa/domain/shared/dto.py similarity index 100% rename from osa/domain/shared/dto.py rename to server/osa/domain/shared/dto.py diff --git a/osa/domain/shared/error.py b/server/osa/domain/shared/error.py similarity index 100% rename from osa/domain/shared/error.py rename to server/osa/domain/shared/error.py diff --git a/osa/domain/shared/event.py b/server/osa/domain/shared/event.py similarity index 96% rename from osa/domain/shared/event.py rename to server/osa/domain/shared/event.py index af0d439..300eb3d 100644 --- a/osa/domain/shared/event.py +++ b/server/osa/domain/shared/event.py @@ -68,10 +68,10 @@ def __new__(mcs, name: str, bases: tuple[type, ...], namespace: dict[str, Any]) cls = super().__new__(mcs, name, bases, namespace) # Apply dataclass and extract event type for concrete subclasses if any(isinstance(b, mcs) for b in bases): - cls = dataclass(cls) # type: ignore[assignment] + cls = dataclass(cls) event_type = _extract_event_type(cls) if event_type is not None: - cls.__event_type__ = event_type # type: ignore[attr-defined] + cls.__event_type__ = event_type return cls diff --git a/osa/domain/shared/event_log.py b/server/osa/domain/shared/event_log.py similarity index 100% rename from osa/domain/shared/event_log.py rename to server/osa/domain/shared/event_log.py diff --git a/osa/domain/shared/model/__init__.py b/server/osa/domain/shared/model/__init__.py similarity index 100% rename from osa/domain/shared/model/__init__.py rename to server/osa/domain/shared/model/__init__.py diff --git a/osa/domain/shared/model/aggregate.py b/server/osa/domain/shared/model/aggregate.py similarity index 100% rename from osa/domain/shared/model/aggregate.py rename to server/osa/domain/shared/model/aggregate.py diff --git a/osa/domain/shared/model/entity.py b/server/osa/domain/shared/model/entity.py similarity index 100% rename from osa/domain/shared/model/entity.py rename to server/osa/domain/shared/model/entity.py diff --git a/osa/domain/shared/model/srn.py b/server/osa/domain/shared/model/srn.py similarity index 95% rename from osa/domain/shared/model/srn.py rename to server/osa/domain/shared/model/srn.py index bccd59d..2078209 100644 --- a/osa/domain/shared/model/srn.py +++ b/server/osa/domain/shared/model/srn.py @@ -223,34 +223,34 @@ def parse(cls, srn: str) -> Self: class RecordSRN(SRN): type: ResourceType = Field(default=ResourceType.rec, frozen=True) - version: RecordVersion # type: ignore + version: RecordVersion class SchemaSRN(SRN): type: ResourceType = Field(default=ResourceType.schema, frozen=True) - version: Semver # type: ignore + version: Semver class VocabSRN(SRN): type: ResourceType = Field(default=ResourceType.vocab, frozen=True) - version: Semver # type: ignore + version: Semver class DepositionSRN(SRN): type: ResourceType = Field(default=ResourceType.dep, frozen=True) - version: None = None # type: ignore + version: None = None class ValidationRunSRN(SRN): type: ResourceType = Field(default=ResourceType.val, frozen=True) - version: None = None # type: ignore + version: None = None class SnapshotSRN(SRN): type: ResourceType = Field(default=ResourceType.snap, frozen=True) - version: None = None # type: ignore + version: None = None class EventSRN(SRN): type: ResourceType = Field(default=ResourceType.evt, frozen=True) - version: None = None # type: ignore + version: None = None diff --git a/osa/domain/shared/model/value.py b/server/osa/domain/shared/model/value.py similarity index 100% rename from osa/domain/shared/model/value.py rename to server/osa/domain/shared/model/value.py diff --git a/osa/domain/shared/outbox.py b/server/osa/domain/shared/outbox.py similarity index 100% rename from osa/domain/shared/outbox.py rename to server/osa/domain/shared/outbox.py diff --git a/osa/domain/shared/port/__init__.py b/server/osa/domain/shared/port/__init__.py similarity index 100% rename from osa/domain/shared/port/__init__.py rename to server/osa/domain/shared/port/__init__.py diff --git a/osa/domain/shared/port/base.py b/server/osa/domain/shared/port/base.py similarity index 100% rename from osa/domain/shared/port/base.py rename to server/osa/domain/shared/port/base.py diff --git a/osa/domain/shared/port/event_repository.py b/server/osa/domain/shared/port/event_repository.py similarity index 100% rename from osa/domain/shared/port/event_repository.py rename to server/osa/domain/shared/port/event_repository.py diff --git a/osa/domain/shared/query.py b/server/osa/domain/shared/query.py similarity index 100% rename from osa/domain/shared/query.py rename to server/osa/domain/shared/query.py diff --git a/osa/domain/shared/service.py b/server/osa/domain/shared/service.py similarity index 88% rename from osa/domain/shared/service.py rename to server/osa/domain/shared/service.py index 7024aa9..9fdd500 100644 --- a/osa/domain/shared/service.py +++ b/server/osa/domain/shared/service.py @@ -9,7 +9,7 @@ class _ServiceMeta(type): def __new__(mcs, name: str, bases: tuple, namespace: dict): cls = super().__new__(mcs, name, bases, namespace) if any(isinstance(b, mcs) for b in bases): - return dataclass(cls) # type: ignore[return-value] + return dataclass(cls) return cls diff --git a/osa/domain/source/__init__.py b/server/osa/domain/source/__init__.py similarity index 100% rename from osa/domain/source/__init__.py rename to server/osa/domain/source/__init__.py diff --git a/osa/domain/source/event/__init__.py b/server/osa/domain/source/event/__init__.py similarity index 100% rename from osa/domain/source/event/__init__.py rename to server/osa/domain/source/event/__init__.py diff --git a/osa/domain/source/event/source_requested.py b/server/osa/domain/source/event/source_requested.py similarity index 57% rename from osa/domain/source/event/source_requested.py rename to server/osa/domain/source/event/source_requested.py index 6594d59..0881d3f 100644 --- a/osa/domain/source/event/source_requested.py +++ b/server/osa/domain/source/event/source_requested.py @@ -1,6 +1,7 @@ """SourceRequested event - triggers pulling from a data source.""" from datetime import datetime +from typing import Any from osa.domain.shared.event import Event, EventId @@ -10,9 +11,17 @@ class SourceRequested(Event): The `since` field is always set by the emitter (scheduler or initial run listener) based on the last SourceRunCompleted event, or None for first run. + + For chunked processing: + - `offset`: Starting position for this chunk (0 for first chunk) + - `chunk_size`: Number of records to process per chunk + - `session`: Opaque pagination state (e.g., NCBI WebEnv) for efficient continuation """ id: EventId source_name: str # Key into config.sources list (e.g., "geo-entrez") since: datetime | None # Fetch records updated after this time (None = all time) limit: int | None = None # Optional limit on records to fetch + offset: int = 0 # Starting position for this chunk + chunk_size: int = 1000 # Number of records per chunk + session: dict[str, Any] | None = None # Opaque pagination state (e.g., NCBI WebEnv) diff --git a/osa/domain/source/event/source_run_completed.py b/server/osa/domain/source/event/source_run_completed.py similarity index 51% rename from osa/domain/source/event/source_run_completed.py rename to server/osa/domain/source/event/source_run_completed.py index 95e6ff0..3cb3745 100644 --- a/osa/domain/source/event/source_run_completed.py +++ b/server/osa/domain/source/event/source_run_completed.py @@ -6,7 +6,13 @@ class SourceRunCompleted(Event): - """Emitted after a source run completes successfully.""" + """Emitted after a source run completes successfully. + + For chunked processing: + - `offset`: The starting position of this chunk + - `chunk_size`: Chunk size used for processing + - `is_final_chunk`: Whether this was the last chunk + """ id: EventId source_name: str @@ -16,3 +22,6 @@ class SourceRunCompleted(Event): record_count: int since: datetime | None # What 'since' value was used (None = all time) limit: int | None + offset: int = 0 # Starting position of this chunk + chunk_size: int = 1000 # Chunk size used + is_final_chunk: bool = True # Whether this was the last chunk diff --git a/osa/domain/source/listener/__init__.py b/server/osa/domain/source/listener/__init__.py similarity index 100% rename from osa/domain/source/listener/__init__.py rename to server/osa/domain/source/listener/__init__.py diff --git a/osa/domain/source/listener/initial_source_listener.py b/server/osa/domain/source/listener/initial_source_listener.py similarity index 100% rename from osa/domain/source/listener/initial_source_listener.py rename to server/osa/domain/source/listener/initial_source_listener.py diff --git a/osa/domain/source/listener/source_listener.py b/server/osa/domain/source/listener/source_listener.py similarity index 81% rename from osa/domain/source/listener/source_listener.py rename to server/osa/domain/source/listener/source_listener.py index 9e300d5..42369b5 100644 --- a/osa/domain/source/listener/source_listener.py +++ b/server/osa/domain/source/listener/source_listener.py @@ -9,6 +9,7 @@ class PullFromSource(EventListener[SourceRequested]): """Pulls from a data source and creates depositions. This listener delegates to SourceService for all business logic. + Supports chunked processing with continuation events. """ service: SourceService @@ -19,4 +20,7 @@ async def handle(self, event: SourceRequested) -> None: source_name=event.source_name, since=event.since, limit=event.limit, + offset=event.offset, + chunk_size=event.chunk_size, + session=event.session, ) diff --git a/osa/domain/source/model/__init__.py b/server/osa/domain/source/model/__init__.py similarity index 100% rename from osa/domain/source/model/__init__.py rename to server/osa/domain/source/model/__init__.py diff --git a/osa/domain/source/model/registry.py b/server/osa/domain/source/model/registry.py similarity index 100% rename from osa/domain/source/model/registry.py rename to server/osa/domain/source/model/registry.py diff --git a/osa/domain/source/schedule/__init__.py b/server/osa/domain/source/schedule/__init__.py similarity index 100% rename from osa/domain/source/schedule/__init__.py rename to server/osa/domain/source/schedule/__init__.py diff --git a/osa/domain/source/schedule/source_schedule.py b/server/osa/domain/source/schedule/source_schedule.py similarity index 100% rename from osa/domain/source/schedule/source_schedule.py rename to server/osa/domain/source/schedule/source_schedule.py diff --git a/osa/domain/source/service/__init__.py b/server/osa/domain/source/service/__init__.py similarity index 100% rename from osa/domain/source/service/__init__.py rename to server/osa/domain/source/service/__init__.py diff --git a/server/osa/domain/source/service/source.py b/server/osa/domain/source/service/source.py new file mode 100644 index 0000000..ac18511 --- /dev/null +++ b/server/osa/domain/source/service/source.py @@ -0,0 +1,183 @@ +"""SourceService - orchestrates pulling from data sources.""" + +import logging +from dataclasses import dataclass +from datetime import UTC, datetime +from typing import Any +from uuid import uuid4 + +from osa.domain.deposition.event.submitted import DepositionSubmittedEvent +from osa.domain.shared.event import EventId +from osa.domain.shared.model.srn import DepositionSRN, Domain, LocalId +from osa.domain.shared.outbox import Outbox +from osa.domain.shared.service import Service +from osa.domain.source.event.source_requested import SourceRequested +from osa.domain.source.event.source_run_completed import SourceRunCompleted +from osa.domain.source.model.registry import SourceRegistry + +logger = logging.getLogger(__name__) + + +@dataclass +class SourceResult: + """Result of a source run.""" + + source_name: str + record_count: int + started_at: datetime + completed_at: datetime + + +class SourceService(Service): + """Orchestrates pulling records from sources and emitting deposition events. + + This service encapsulates the business logic for pulling from sources that was + previously embedded in the PullFromSource listener. It can be called from multiple + entry points (event listeners, CLI commands, scheduled jobs). + + Supports chunked processing to enable: + 1. Committing after each chunk (progress saved) + 2. Emitting continuation events so downstream processing starts immediately + 3. Efficient pagination via session state (e.g., NCBI WebEnv) + """ + + sources: SourceRegistry + outbox: Outbox + node_domain: Domain + + async def run_source( + self, + source_name: str, + since: datetime | None = None, + limit: int | None = None, + offset: int = 0, + chunk_size: int = 1000, + session: dict[str, Any] | None = None, + ) -> SourceResult: + """Pull records from a source and emit DepositionSubmitted events. + + Processes records in chunks, emitting continuation events for subsequent chunks. + This allows downstream processing (indexing, validation) to start while + source ingestion continues. + + Args: + source_name: Name of the source to use. + since: Only fetch records updated after this time. + limit: Maximum total number of records to fetch (across all chunks). + offset: Starting position for this chunk. + chunk_size: Number of records to process per chunk. + session: Opaque pagination state from previous chunk. + + Returns: + SourceResult with run statistics for this chunk. + + Raises: + ValueError: If the source is not found. + """ + source = self.sources.get(source_name) + if not source: + raise ValueError(f"Unknown source: {source_name}") + + started_at = datetime.now(UTC) + logger.info( + f"Starting pull from {source_name}, since={since}, limit={limit}, " + f"offset={offset}, chunk_size={chunk_size}" + ) + + # Calculate effective limit for this chunk + # If we have an overall limit, cap to remaining records + if limit is not None: + remaining = limit - offset + effective_chunk_size = min(chunk_size, remaining) + else: + effective_chunk_size = chunk_size + + # Fetch chunk_size + 1 to detect if more records exist + fetch_limit = effective_chunk_size + 1 + + # Call source with session, get updated session back + records_iter, next_session = await source.pull( + since=since, + limit=fetch_limit, + offset=offset, + session=session, + ) + + count = 0 + has_more = False + + async for record in records_iter: + # Check if we've reached our chunk limit + if count >= effective_chunk_size: + has_more = True + break + + # Create a deposition SRN for this record + dep_srn = DepositionSRN( + domain=self.node_domain, + id=LocalId(str(uuid4())), + ) + + # Emit DepositionSubmitted with the record metadata + submitted_event = DepositionSubmittedEvent( + id=EventId(uuid4()), + deposition_id=dep_srn, + metadata=record.metadata, + ) + await self.outbox.append(submitted_event) + count += 1 + + # Log progress every 100 records + if count % 100 == 0: + logger.info(f" Pulled {count} records so far (chunk offset={offset})...") + + title = record.metadata.get("title", "")[:60] + logger.debug(f" [{record.source_id}] {title}...") + + completed_at = datetime.now(UTC) + is_final_chunk = not has_more + + logger.info( + f"Chunk completed: {count} records from {source_name} " + f"(offset={offset}, is_final={is_final_chunk})" + ) + + # Emit completion event for this chunk + await self.outbox.append( + SourceRunCompleted( + id=EventId(uuid4()), + source_name=source_name, + source_type=source.name, + started_at=started_at, + completed_at=completed_at, + record_count=count, + since=since, + limit=limit, + offset=offset, + chunk_size=chunk_size, + is_final_chunk=is_final_chunk, + ) + ) + + # Emit continuation event if more records exist + if not is_final_chunk: + next_offset = offset + count + logger.info(f"Emitting continuation event for {source_name}, next_offset={next_offset}") + await self.outbox.append( + SourceRequested( + id=EventId(uuid4()), + source_name=source_name, + since=since, + limit=limit, + offset=next_offset, + chunk_size=chunk_size, + session=next_session, + ) + ) + + return SourceResult( + source_name=source_name, + record_count=count, + started_at=started_at, + completed_at=completed_at, + ) diff --git a/osa/domain/validation/__init__.py b/server/osa/domain/validation/__init__.py similarity index 100% rename from osa/domain/validation/__init__.py rename to server/osa/domain/validation/__init__.py diff --git a/osa/domain/validation/adapter/__init__.py b/server/osa/domain/validation/adapter/__init__.py similarity index 100% rename from osa/domain/validation/adapter/__init__.py rename to server/osa/domain/validation/adapter/__init__.py diff --git a/osa/domain/validation/command/__init__.py b/server/osa/domain/validation/command/__init__.py similarity index 100% rename from osa/domain/validation/command/__init__.py rename to server/osa/domain/validation/command/__init__.py diff --git a/osa/domain/validation/event/__init__.py b/server/osa/domain/validation/event/__init__.py similarity index 100% rename from osa/domain/validation/event/__init__.py rename to server/osa/domain/validation/event/__init__.py diff --git a/osa/domain/validation/event/validation_completed.py b/server/osa/domain/validation/event/validation_completed.py similarity index 100% rename from osa/domain/validation/event/validation_completed.py rename to server/osa/domain/validation/event/validation_completed.py diff --git a/osa/domain/validation/event/validation_started.py b/server/osa/domain/validation/event/validation_started.py similarity index 100% rename from osa/domain/validation/event/validation_started.py rename to server/osa/domain/validation/event/validation_started.py diff --git a/osa/domain/validation/handler.py b/server/osa/domain/validation/handler.py similarity index 100% rename from osa/domain/validation/handler.py rename to server/osa/domain/validation/handler.py diff --git a/osa/domain/validation/listener/__init__.py b/server/osa/domain/validation/listener/__init__.py similarity index 100% rename from osa/domain/validation/listener/__init__.py rename to server/osa/domain/validation/listener/__init__.py diff --git a/osa/domain/validation/listener/validation_listener.py b/server/osa/domain/validation/listener/validation_listener.py similarity index 100% rename from osa/domain/validation/listener/validation_listener.py rename to server/osa/domain/validation/listener/validation_listener.py diff --git a/osa/domain/validation/model/__init__.py b/server/osa/domain/validation/model/__init__.py similarity index 100% rename from osa/domain/validation/model/__init__.py rename to server/osa/domain/validation/model/__init__.py diff --git a/osa/domain/validation/model/entity.py b/server/osa/domain/validation/model/entity.py similarity index 100% rename from osa/domain/validation/model/entity.py rename to server/osa/domain/validation/model/entity.py diff --git a/osa/domain/validation/model/value.py b/server/osa/domain/validation/model/value.py similarity index 100% rename from osa/domain/validation/model/value.py rename to server/osa/domain/validation/model/value.py diff --git a/osa/domain/validation/port/__init__.py b/server/osa/domain/validation/port/__init__.py similarity index 100% rename from osa/domain/validation/port/__init__.py rename to server/osa/domain/validation/port/__init__.py diff --git a/osa/domain/validation/port/repository.py b/server/osa/domain/validation/port/repository.py similarity index 100% rename from osa/domain/validation/port/repository.py rename to server/osa/domain/validation/port/repository.py diff --git a/osa/domain/validation/port/runner.py b/server/osa/domain/validation/port/runner.py similarity index 100% rename from osa/domain/validation/port/runner.py rename to server/osa/domain/validation/port/runner.py diff --git a/osa/domain/validation/query/__init__.py b/server/osa/domain/validation/query/__init__.py similarity index 100% rename from osa/domain/validation/query/__init__.py rename to server/osa/domain/validation/query/__init__.py diff --git a/osa/domain/validation/service/__init__.py b/server/osa/domain/validation/service/__init__.py similarity index 100% rename from osa/domain/validation/service/__init__.py rename to server/osa/domain/validation/service/__init__.py diff --git a/osa/domain/validation/service/validation.py b/server/osa/domain/validation/service/validation.py similarity index 100% rename from osa/domain/validation/service/validation.py rename to server/osa/domain/validation/service/validation.py diff --git a/osa/domain/validation/util/di/__init__.py b/server/osa/domain/validation/util/di/__init__.py similarity index 100% rename from osa/domain/validation/util/di/__init__.py rename to server/osa/domain/validation/util/di/__init__.py diff --git a/osa/domain/validation/util/di/provider.py b/server/osa/domain/validation/util/di/provider.py similarity index 100% rename from osa/domain/validation/util/di/provider.py rename to server/osa/domain/validation/util/di/provider.py diff --git a/osa/infrastructure/__init__.py b/server/osa/infrastructure/__init__.py similarity index 100% rename from osa/infrastructure/__init__.py rename to server/osa/infrastructure/__init__.py diff --git a/osa/infrastructure/event/__init__.py b/server/osa/infrastructure/event/__init__.py similarity index 100% rename from osa/infrastructure/event/__init__.py rename to server/osa/infrastructure/event/__init__.py diff --git a/osa/infrastructure/event/di.py b/server/osa/infrastructure/event/di.py similarity index 96% rename from osa/infrastructure/event/di.py rename to server/osa/infrastructure/event/di.py index 925d62c..1b6fa61 100644 --- a/osa/infrastructure/event/di.py +++ b/server/osa/infrastructure/event/di.py @@ -6,7 +6,7 @@ from osa.config import Config from osa.domain.curation.listener import AutoApproveCurationTool -from osa.domain.index.listener import ProjectNewRecordToIndexes +from osa.domain.index.listener import FlushIndexesOnSourceComplete, ProjectNewRecordToIndexes from osa.domain.source.listener import PullFromSource, TriggerInitialSourceRun from osa.domain.source.schedule import SourceSchedule from osa.domain.record.listener import ConvertDepositionToRecord @@ -35,6 +35,7 @@ AutoApproveCurationTool, ConvertDepositionToRecord, ProjectNewRecordToIndexes, + FlushIndexesOnSourceComplete, ] ) diff --git a/osa/infrastructure/event/worker.py b/server/osa/infrastructure/event/worker.py similarity index 89% rename from osa/infrastructure/event/worker.py rename to server/osa/infrastructure/event/worker.py index 488d557..9e8d919 100644 --- a/osa/infrastructure/event/worker.py +++ b/server/osa/infrastructure/event/worker.py @@ -130,20 +130,25 @@ async def _emit_server_started(self) -> None: async def _poll_outbox(self) -> None: """Interval task: fetch pending events and dispatch each.""" - # Fetch pending events in one scope - async with self._container(scope=Scope.UOW) as scope: - outbox = await scope.get(Outbox) - events = await outbox.fetch_pending(self._batch_size) - session = await scope.get(AsyncSession) - await session.commit() + try: + # Fetch pending events in one scope + async with self._container(scope=Scope.UOW) as scope: + outbox = await scope.get(Outbox) + events = await outbox.fetch_pending(self._batch_size) + session = await scope.get(AsyncSession) + await session.commit() - # Only log at INFO when processing events, DEBUG otherwise handled by dispatch - if events: - logger.debug(f"Processing {len(events)} pending events") + # Log when processing events + if events: + logger.info(f"Processing {len(events)} pending events") - # Dispatch each event in its own scope - for event in events: - await self._dispatch(event) + # Dispatch each event in its own scope + for event in events: + await self._dispatch(event) + + except Exception as e: + # Log but don't re-raise - let the scheduler continue polling + logger.exception(f"Error in outbox poll cycle: {e}") async def _dispatch(self, event: Event) -> None: """Dispatch a single event to its listener in UOW scope.""" diff --git a/osa/infrastructure/index/__init__.py b/server/osa/infrastructure/index/__init__.py similarity index 100% rename from osa/infrastructure/index/__init__.py rename to server/osa/infrastructure/index/__init__.py diff --git a/osa/infrastructure/index/di.py b/server/osa/infrastructure/index/di.py similarity index 100% rename from osa/infrastructure/index/di.py rename to server/osa/infrastructure/index/di.py diff --git a/osa/infrastructure/index/vector/__init__.py b/server/osa/infrastructure/index/vector/__init__.py similarity index 100% rename from osa/infrastructure/index/vector/__init__.py rename to server/osa/infrastructure/index/vector/__init__.py diff --git a/osa/infrastructure/index/vector/backend.py b/server/osa/infrastructure/index/vector/backend.py similarity index 63% rename from osa/infrastructure/index/vector/backend.py rename to server/osa/infrastructure/index/vector/backend.py index b3a853f..aed0caa 100644 --- a/osa/infrastructure/index/vector/backend.py +++ b/server/osa/infrastructure/index/vector/backend.py @@ -1,6 +1,7 @@ """Vector storage backend using ChromaDB and sentence-transformers.""" import asyncio +import logging from typing import Any import chromadb @@ -9,12 +10,19 @@ from osa.infrastructure.index.vector.config import VectorBackendConfig from osa.sdk.index.result import QueryResult, SearchHit +logger = logging.getLogger(__name__) + class VectorStorageBackend: """Vector similarity backend using ChromaDB + sentence-transformers. All blocking operations (embedding generation, ChromaDB I/O) are run in a thread pool to avoid blocking the async event loop. + + Supports internal buffering for batch efficiency: + - Records are buffered until batch_size is reached + - Embeddings are generated in batch for better GPU/CPU utilization + - Use flush() to ensure all buffered records are persisted """ def __init__(self, name: str, config: VectorBackendConfig) -> None: @@ -22,6 +30,10 @@ def __init__(self, name: str, config: VectorBackendConfig) -> None: self._config = config self._model = SentenceTransformer(config.embedding.model.value) + # Internal buffer for batch processing + self._buffer: list[tuple[str, dict[str, Any]]] = [] + self._lock = asyncio.Lock() + # persist_dir must be set by DI (derived from OSAPaths if not explicit) if config.persist_dir is None: raise ValueError("VectorBackendConfig.persist_dir must be set") @@ -41,24 +53,59 @@ def name(self) -> str: return self._name async def ingest(self, srn: str, record: dict[str, Any]) -> None: - """Store a record in the index.""" - text = self._to_text(record) - - # Run CPU-bound embedding in thread pool and convert to list - embedding = await asyncio.to_thread(lambda: self._model.encode(text).tolist()) - - # Filter metadata to ChromaDB-compatible types - safe_meta = {k: v for k, v in record.items() if isinstance(v, (str, int, float, bool))} - - # Run ChromaDB I/O in thread pool + """Buffer a record for batch indexing. + + Records are buffered until batch_size is reached, then flushed + with batch embedding generation for efficiency. + """ + async with self._lock: + self._buffer.append((srn, record)) + + # Flush when batch size is reached + if len(self._buffer) >= self._config.batch_size: + await self._flush_buffer() + + async def flush(self) -> None: + """Flush any buffered records to storage.""" + async with self._lock: + if self._buffer: + await self._flush_buffer() + + async def _flush_buffer(self) -> None: + """Internal: flush buffered records with batch embedding generation. + + Must be called while holding self._lock. + """ + if not self._buffer: + return + + # Prepare batch data + ids = [] + texts = [] + metadatas = [] + + for srn, record in self._buffer: + ids.append(srn) + texts.append(self._to_text(record)) + # Filter metadata to ChromaDB-compatible types + safe_meta = {k: v for k, v in record.items() if isinstance(v, (str, int, float, bool))} + metadatas.append(safe_meta) + + # Generate embeddings in batch (much more efficient than one-by-one) + embeddings = await asyncio.to_thread(lambda: self._model.encode(texts).tolist()) + + # Bulk upsert to ChromaDB await asyncio.to_thread( self._collection.upsert, - ids=[srn], - embeddings=[embedding], - metadatas=[safe_meta], - documents=[text], + ids=ids, + embeddings=embeddings, + metadatas=metadatas, + documents=texts, ) + logger.debug(f"Flushed {len(self._buffer)} records to vector index '{self._name}'") + self._buffer.clear() + async def delete(self, srn: str) -> None: """Remove a record from the index.""" await asyncio.to_thread(self._collection.delete, ids=[srn]) diff --git a/osa/infrastructure/index/vector/config.py b/server/osa/infrastructure/index/vector/config.py similarity index 93% rename from osa/infrastructure/index/vector/config.py rename to server/osa/infrastructure/index/vector/config.py index 6c9cf2b..de63b3d 100644 --- a/osa/infrastructure/index/vector/config.py +++ b/server/osa/infrastructure/index/vector/config.py @@ -39,3 +39,4 @@ class VectorBackendConfig(BackendConfig): persist_dir: Path | None = None # None = derive from OSAPaths embedding: EmbeddingConfig = EmbeddingConfig() + batch_size: int = 256 # Records to buffer before flushing (batch embedding) diff --git a/osa/infrastructure/messaging/__init__.py b/server/osa/infrastructure/messaging/__init__.py similarity index 100% rename from osa/infrastructure/messaging/__init__.py rename to server/osa/infrastructure/messaging/__init__.py diff --git a/osa/infrastructure/oci/__init__.py b/server/osa/infrastructure/oci/__init__.py similarity index 100% rename from osa/infrastructure/oci/__init__.py rename to server/osa/infrastructure/oci/__init__.py diff --git a/osa/infrastructure/oci/di.py b/server/osa/infrastructure/oci/di.py similarity index 100% rename from osa/infrastructure/oci/di.py rename to server/osa/infrastructure/oci/di.py diff --git a/osa/infrastructure/oci/runner.py b/server/osa/infrastructure/oci/runner.py similarity index 100% rename from osa/infrastructure/oci/runner.py rename to server/osa/infrastructure/oci/runner.py diff --git a/osa/infrastructure/persistence/__init__.py b/server/osa/infrastructure/persistence/__init__.py similarity index 100% rename from osa/infrastructure/persistence/__init__.py rename to server/osa/infrastructure/persistence/__init__.py diff --git a/osa/infrastructure/persistence/adapter/__init__.py b/server/osa/infrastructure/persistence/adapter/__init__.py similarity index 100% rename from osa/infrastructure/persistence/adapter/__init__.py rename to server/osa/infrastructure/persistence/adapter/__init__.py diff --git a/osa/infrastructure/persistence/adapter/storage.py b/server/osa/infrastructure/persistence/adapter/storage.py similarity index 100% rename from osa/infrastructure/persistence/adapter/storage.py rename to server/osa/infrastructure/persistence/adapter/storage.py diff --git a/osa/infrastructure/persistence/database.py b/server/osa/infrastructure/persistence/database.py similarity index 100% rename from osa/infrastructure/persistence/database.py rename to server/osa/infrastructure/persistence/database.py diff --git a/osa/infrastructure/persistence/di.py b/server/osa/infrastructure/persistence/di.py similarity index 100% rename from osa/infrastructure/persistence/di.py rename to server/osa/infrastructure/persistence/di.py diff --git a/osa/infrastructure/persistence/mappers/deposition.py b/server/osa/infrastructure/persistence/mappers/deposition.py similarity index 100% rename from osa/infrastructure/persistence/mappers/deposition.py rename to server/osa/infrastructure/persistence/mappers/deposition.py diff --git a/osa/infrastructure/persistence/mappers/record.py b/server/osa/infrastructure/persistence/mappers/record.py similarity index 100% rename from osa/infrastructure/persistence/mappers/record.py rename to server/osa/infrastructure/persistence/mappers/record.py diff --git a/osa/infrastructure/persistence/mappers/validation.py b/server/osa/infrastructure/persistence/mappers/validation.py similarity index 100% rename from osa/infrastructure/persistence/mappers/validation.py rename to server/osa/infrastructure/persistence/mappers/validation.py diff --git a/osa/infrastructure/persistence/migrate.py b/server/osa/infrastructure/persistence/migrate.py similarity index 100% rename from osa/infrastructure/persistence/migrate.py rename to server/osa/infrastructure/persistence/migrate.py diff --git a/osa/infrastructure/persistence/repository/deposition.py b/server/osa/infrastructure/persistence/repository/deposition.py similarity index 100% rename from osa/infrastructure/persistence/repository/deposition.py rename to server/osa/infrastructure/persistence/repository/deposition.py diff --git a/osa/infrastructure/persistence/repository/event.py b/server/osa/infrastructure/persistence/repository/event.py similarity index 100% rename from osa/infrastructure/persistence/repository/event.py rename to server/osa/infrastructure/persistence/repository/event.py diff --git a/osa/infrastructure/persistence/repository/record.py b/server/osa/infrastructure/persistence/repository/record.py similarity index 100% rename from osa/infrastructure/persistence/repository/record.py rename to server/osa/infrastructure/persistence/repository/record.py diff --git a/osa/infrastructure/persistence/repository/validation.py b/server/osa/infrastructure/persistence/repository/validation.py similarity index 100% rename from osa/infrastructure/persistence/repository/validation.py rename to server/osa/infrastructure/persistence/repository/validation.py diff --git a/osa/infrastructure/persistence/tables.py b/server/osa/infrastructure/persistence/tables.py similarity index 100% rename from osa/infrastructure/persistence/tables.py rename to server/osa/infrastructure/persistence/tables.py diff --git a/osa/infrastructure/source/__init__.py b/server/osa/infrastructure/source/__init__.py similarity index 100% rename from osa/infrastructure/source/__init__.py rename to server/osa/infrastructure/source/__init__.py diff --git a/osa/infrastructure/source/di.py b/server/osa/infrastructure/source/di.py similarity index 100% rename from osa/infrastructure/source/di.py rename to server/osa/infrastructure/source/di.py diff --git a/osa/infrastructure/source/discovery.py b/server/osa/infrastructure/source/discovery.py similarity index 100% rename from osa/infrastructure/source/discovery.py rename to server/osa/infrastructure/source/discovery.py diff --git a/osa/sdk/__init__.py b/server/osa/sdk/__init__.py similarity index 100% rename from osa/sdk/__init__.py rename to server/osa/sdk/__init__.py diff --git a/osa/sdk/index/__init__.py b/server/osa/sdk/index/__init__.py similarity index 100% rename from osa/sdk/index/__init__.py rename to server/osa/sdk/index/__init__.py diff --git a/osa/sdk/index/backend.py b/server/osa/sdk/index/backend.py similarity index 82% rename from osa/sdk/index/backend.py rename to server/osa/sdk/index/backend.py index 7f6849d..629c8e2 100644 --- a/osa/sdk/index/backend.py +++ b/server/osa/sdk/index/backend.py @@ -61,3 +61,13 @@ async def count(self) -> int: Number of indexed documents. """ ... + + async def flush(self) -> None: + """Flush any buffered operations to storage. + + For backends that buffer writes for batch efficiency (e.g., batch embedding + generation), this method ensures all pending records are persisted. + + Backends without internal buffering can implement this as a no-op. + """ + ... diff --git a/osa/sdk/index/config.py b/server/osa/sdk/index/config.py similarity index 100% rename from osa/sdk/index/config.py rename to server/osa/sdk/index/config.py diff --git a/osa/sdk/index/result.py b/server/osa/sdk/index/result.py similarity index 100% rename from osa/sdk/index/result.py rename to server/osa/sdk/index/result.py diff --git a/osa/sdk/source/__init__.py b/server/osa/sdk/source/__init__.py similarity index 100% rename from osa/sdk/source/__init__.py rename to server/osa/sdk/source/__init__.py diff --git a/osa/sdk/source/config.py b/server/osa/sdk/source/config.py similarity index 100% rename from osa/sdk/source/config.py rename to server/osa/sdk/source/config.py diff --git a/osa/sdk/source/record.py b/server/osa/sdk/source/record.py similarity index 100% rename from osa/sdk/source/record.py rename to server/osa/sdk/source/record.py diff --git a/osa/sdk/source/source.py b/server/osa/sdk/source/source.py similarity index 67% rename from osa/sdk/source/source.py rename to server/osa/sdk/source/source.py index 28a0239..6e7df4b 100644 --- a/osa/sdk/source/source.py +++ b/server/osa/sdk/source/source.py @@ -2,12 +2,15 @@ from collections.abc import AsyncIterator from datetime import datetime -from typing import ClassVar, Protocol +from typing import Any, ClassVar, Protocol from pydantic import BaseModel from osa.sdk.source.record import UpstreamRecord +# Type alias for pull() return: (records_iterator, session_for_next_chunk) +PullResult = tuple[AsyncIterator[UpstreamRecord], dict[str, Any] | None] + class Source(Protocol): """Protocol for pluggable data sources. @@ -28,22 +31,29 @@ def __init__(self, config: BaseModel) -> None: """Initialize the source with validated configuration.""" ... - def pull( + async def pull( self, since: datetime | None = None, limit: int | None = None, - ) -> AsyncIterator[UpstreamRecord]: + offset: int = 0, + session: dict[str, Any] | None = None, + ) -> PullResult: """Pull records from an upstream source. - This method returns an async iterator that yields records. - Implementations should use async generators. + This method returns an async iterator that yields records, plus + session state to pass to the next chunk for efficient pagination. Args: since: Only fetch records updated after this time. limit: Maximum number of records to fetch. + offset: Skip first N records (for chunked processing). + session: Opaque pagination state from previous chunk (e.g., NCBI WebEnv). - Yields: - UpstreamRecord for each ingested item. + Returns: + Tuple of (records_iterator, session_for_next_chunk). + The session is opaque state to pass to the next chunk. + Returns None for session if no more chunks are needed or + if the source doesn't support session-based pagination. """ ... diff --git a/osa/util/__init__.py b/server/osa/util/__init__.py similarity index 100% rename from osa/util/__init__.py rename to server/osa/util/__init__.py diff --git a/osa/util/di/__init__.py b/server/osa/util/di/__init__.py similarity index 100% rename from osa/util/di/__init__.py rename to server/osa/util/di/__init__.py diff --git a/osa/util/di/base.py b/server/osa/util/di/base.py similarity index 100% rename from osa/util/di/base.py rename to server/osa/util/di/base.py diff --git a/osa/util/di/container.py b/server/osa/util/di/container.py similarity index 100% rename from osa/util/di/container.py rename to server/osa/util/di/container.py diff --git a/osa/util/di/fastapi.py b/server/osa/util/di/fastapi.py similarity index 100% rename from osa/util/di/fastapi.py rename to server/osa/util/di/fastapi.py diff --git a/osa/util/di/scope.py b/server/osa/util/di/scope.py similarity index 100% rename from osa/util/di/scope.py rename to server/osa/util/di/scope.py diff --git a/pyproject.toml b/server/pyproject.toml similarity index 67% rename from pyproject.toml rename to server/pyproject.toml index 83b649b..5771a27 100644 --- a/pyproject.toml +++ b/server/pyproject.toml @@ -26,6 +26,8 @@ dependencies = [ "aiosqlite>=0.22.0", "greenlet>=3.2.4", "rich>=14.2.0", + "asyncpg>=0.31.0", + "psycopg2-binary>=2.9.11", ] [project.scripts] @@ -54,3 +56,20 @@ asyncio_mode = "auto" [tool.ruff] line-length = 100 + +# Ensure lock file works on both macOS (dev) and Linux (production) +[tool.uv] +environments = [ + "sys_platform == 'darwin' and platform_machine == 'arm64'", + "sys_platform == 'linux' and platform_machine == 'x86_64'", +] + +# Use CPU-only PyTorch (excludes ~4GB of CUDA libraries) +# explicit = true ensures only torch uses this index, not transitive deps +[[tool.uv.index]] +name = "pytorch-cpu" +url = "https://download.pytorch.org/whl/cpu" +explicit = true + +[tool.uv.sources] +torch = { index = "pytorch-cpu" } diff --git a/sources/__init__.py b/server/sources/__init__.py similarity index 100% rename from sources/__init__.py rename to server/sources/__init__.py diff --git a/sources/geo_entrez/__init__.py b/server/sources/geo_entrez/__init__.py similarity index 100% rename from sources/geo_entrez/__init__.py rename to server/sources/geo_entrez/__init__.py diff --git a/sources/geo_entrez/config.py b/server/sources/geo_entrez/config.py similarity index 100% rename from sources/geo_entrez/config.py rename to server/sources/geo_entrez/config.py diff --git a/server/sources/geo_entrez/source.py b/server/sources/geo_entrez/source.py new file mode 100644 index 0000000..f75673c --- /dev/null +++ b/server/sources/geo_entrez/source.py @@ -0,0 +1,423 @@ +"""GEO Entrez source - uses NCBI E-utilities API.""" + +import asyncio +import logging +import random +from collections.abc import AsyncIterator +from datetime import UTC, datetime +from typing import Any +from xml.etree import ElementTree + +import httpx + +from osa.sdk.source.record import UpstreamRecord +from osa.sdk.source.source import PullResult +from sources.geo_entrez.config import GEOEntrezConfig + +logger = logging.getLogger(__name__) + +# Retry configuration +MAX_RETRIES = 5 +BASE_DELAY = 1.0 # seconds +MAX_DELAY = 60.0 # seconds + + +class GEOEntrezSource: + """Pulls GEO metadata from NCBI via E-utilities (Entrez). + + Supports both GSE (Series, ~230k records) and GDS (DataSets, ~5k curated). + Best for incremental updates; for bulk initialization consider geo-ftp. + """ + + name = "geo-entrez" + config_class = GEOEntrezConfig + + def __init__(self, config: GEOEntrezConfig) -> None: + self._config = config + self._client = httpx.AsyncClient(timeout=30.0) + self._record_prefix = config.record_type.upper() # "GSE" or "GDS" + + async def pull( + self, + since: datetime | None = None, + limit: int | None = None, + offset: int = 0, + session: dict[str, Any] | None = None, + ) -> PullResult: + """Pull records from GEO with efficient chunked pagination. + + Uses NCBI's usehistory feature (WebEnv) to store search results server-side, + enabling efficient O(1) access to any chunk without re-fetching all UIDs. + + Args: + since: Only fetch records updated after this time. + limit: Maximum number of records to fetch. + offset: Skip first N records (for chunked processing). + session: NCBI session state containing WebEnv, QueryKey, and total_count. + + Returns: + Tuple of (records_iterator, session_for_next_chunk). + """ + # Build search query + query = f"{self._record_prefix}[ETYP]" + if since: + date_str = since.strftime("%Y/%m/%d") + query += f" AND {date_str}:3000[PDAT]" + + # Initialize session with usehistory if not provided + if session is None: + web_env, query_key, total_count = await self._init_search_history(query) + session = { + "web_env": web_env, + "query_key": query_key, + "total_count": total_count, + } + logger.info( + f"Initialized NCBI search session: {total_count} total records, " + f"offset={offset}, limit={limit}" + ) + else: + total_count = session["total_count"] + + # Calculate how many UIDs to fetch for this chunk + effective_limit = limit if limit is not None else total_count - offset + uids = await self._fetch_uids_from_history( + web_env=session["web_env"], + query_key=session["query_key"], + offset=offset, + limit=effective_limit, + ) + + async def generate() -> AsyncIterator[UpstreamRecord]: + # Fetch metadata in batches + for batch_start in range(0, len(uids), self._config.batch_size): + batch_uids = uids[batch_start : batch_start + self._config.batch_size] + records = await self._fetch_batch(batch_uids) + for record in records: + yield record + + return generate(), session + + async def get_one(self, source_id: str) -> UpstreamRecord | None: + """Fetch a single GSE by accession. + + Args: + source_id: GSE accession (e.g., "GSE12345"). + + Returns: + RawRecord if found, None otherwise. + """ + # Search for the specific accession + query = f"{source_id}[ACCN]" + uids = await self._search_uids(query, limit=1) + + if not uids: + return None + + records = await self._fetch_batch(uids) + return records[0] if records else None + + async def health(self) -> bool: + """Check if GEO API is reachable.""" + try: + params = self._base_params() + params["db"] = "gds" + resp = await self._client.get( + f"{self._config.base_url}/einfo.fcgi", + params=params, + ) + return resp.status_code == 200 + except httpx.HTTPError: + return False + + async def close(self) -> None: + """Close the HTTP client.""" + await self._client.aclose() + + def _base_params(self) -> dict[str, str]: + """Build base parameters required by NCBI.""" + params = { + "tool": self._config.tool_name, + "email": self._config.email, + } + if self._config.api_key: + params["api_key"] = self._config.api_key + return params + + async def _request_with_retry(self, url: str, params: dict[str, str]) -> httpx.Response: + """Make HTTP request with retry on 429/5xx errors. + + Uses exponential backoff with jitter. Respects Retry-After header if present. + """ + last_exception: Exception | None = None + + for attempt in range(MAX_RETRIES): + try: + resp = await self._client.get(url, params=params) + + # Success - return immediately + if resp.status_code < 400: + return resp + + # Client error (except 429) - don't retry + if 400 <= resp.status_code < 500 and resp.status_code != 429: + resp.raise_for_status() + + # Rate limited (429) or server error (5xx) - retry with backoff + if resp.status_code == 429 or resp.status_code >= 500: + # Check for Retry-After header + retry_after = resp.headers.get("Retry-After") + if retry_after: + try: + delay = float(retry_after) + except ValueError: + delay = BASE_DELAY * (2**attempt) + else: + # Exponential backoff with jitter + delay = min(BASE_DELAY * (2**attempt) + random.uniform(0, 1), MAX_DELAY) + + logger.warning( + f"NCBI API returned {resp.status_code}, " + f"retrying in {delay:.1f}s (attempt {attempt + 1}/{MAX_RETRIES})" + ) + await asyncio.sleep(delay) + continue + + except httpx.TimeoutException as e: + last_exception = e + delay = min(BASE_DELAY * (2**attempt) + random.uniform(0, 1), MAX_DELAY) + logger.warning( + f"NCBI API timeout, retrying in {delay:.1f}s " + f"(attempt {attempt + 1}/{MAX_RETRIES})" + ) + await asyncio.sleep(delay) + continue + + except httpx.HTTPError as e: + # Network errors - retry with backoff + last_exception = e + delay = min(BASE_DELAY * (2**attempt) + random.uniform(0, 1), MAX_DELAY) + logger.warning( + f"NCBI API error: {e}, retrying in {delay:.1f}s " + f"(attempt {attempt + 1}/{MAX_RETRIES})" + ) + await asyncio.sleep(delay) + continue + + # All retries exhausted - make final attempt and let it raise + logger.error(f"NCBI API failed after {MAX_RETRIES} retries") + if last_exception: + raise last_exception + resp = await self._client.get(url, params=params) + resp.raise_for_status() + return resp + + async def _search_uids(self, query: str, limit: int | None) -> list[str]: + """Search GEO for UIDs matching the query. + + Uses pagination to fetch all results when limit is None, + since NCBI caps retmax at 10,000 per request. + """ + batch_size = 10000 # NCBI max per request + + # If limit is set and <= batch_size, single request is enough + if limit is not None and limit <= batch_size: + return await self._search_uids_single(query, limit) + + # Otherwise, paginate through all results + all_uids: list[str] = [] + retstart = 0 + target = limit # None means get everything + + while True: + # Calculate how many to fetch this batch + if target is not None: + remaining = target - len(all_uids) + fetch_count = min(batch_size, remaining) + else: + fetch_count = batch_size + + params = self._base_params() + params.update( + { + "db": "gds", + "term": query, + "retmax": str(fetch_count), + "retstart": str(retstart), + "usehistory": "n", + } + ) + + resp = await self._request_with_retry( + f"{self._config.base_url}/esearch.fcgi", + params=params, + ) + + tree = ElementTree.fromstring(resp.text) + uids = [id_elem.text for id_elem in tree.findall(".//Id") if id_elem.text] + + if not uids: + break # No more results + + all_uids.extend(uids) + retstart += len(uids) + + target_str = str(target) if target else "all" + logger.info(f"Fetched {len(all_uids)} UIDs so far (target: {target_str})") + + # Check if we've hit the limit or got all results + if target is not None and len(all_uids) >= target: + break + if len(uids) < fetch_count: + break # Got fewer than requested, no more results + + return all_uids[:target] if target else all_uids + + async def _init_search_history(self, query: str) -> tuple[str, str, int]: + """Initialize search with usehistory=y, storing results on NCBI server. + + Returns: + Tuple of (WebEnv, QueryKey, total_count). + """ + params = self._base_params() + params.update( + { + "db": "gds", + "term": query, + "usehistory": "y", # Store results on NCBI server + "retmax": "0", # Don't fetch UIDs yet, just get count + } + ) + + resp = await self._request_with_retry( + f"{self._config.base_url}/esearch.fcgi", + params=params, + ) + + tree = ElementTree.fromstring(resp.text) + web_env = tree.findtext("WebEnv") or "" + query_key = tree.findtext("QueryKey") or "" + total_count = int(tree.findtext("Count") or "0") + + if not web_env or not query_key: + raise ValueError("NCBI did not return WebEnv/QueryKey for usehistory query") + + return web_env, query_key, total_count + + async def _fetch_uids_from_history( + self, web_env: str, query_key: str, offset: int, limit: int + ) -> list[str]: + """Fetch UIDs for a specific range using stored search results (WebEnv). + + This avoids re-running the search for each chunk, making pagination O(1). + """ + params = self._base_params() + params.update( + { + "db": "gds", + "WebEnv": web_env, + "query_key": query_key, + "retstart": str(offset), + "retmax": str(limit), + } + ) + + resp = await self._request_with_retry( + f"{self._config.base_url}/esearch.fcgi", + params=params, + ) + + tree = ElementTree.fromstring(resp.text) + return [id_elem.text for id_elem in tree.findall(".//Id") if id_elem.text] + + async def _search_uids_single(self, query: str, limit: int) -> list[str]: + """Single request for small limits.""" + params = self._base_params() + params.update( + { + "db": "gds", + "term": query, + "retmax": str(limit), + "usehistory": "n", + } + ) + + resp = await self._request_with_retry( + f"{self._config.base_url}/esearch.fcgi", + params=params, + ) + + tree = ElementTree.fromstring(resp.text) + return [id_elem.text for id_elem in tree.findall(".//Id") if id_elem.text] + + async def _fetch_batch(self, uids: list[str]) -> list[UpstreamRecord]: + """Fetch metadata for a batch of UIDs via ESummary.""" + if not uids: + return [] + + params = self._base_params() + params.update( + { + "db": "gds", + "id": ",".join(uids), + "version": "2.0", + } + ) + + resp = await self._request_with_retry( + f"{self._config.base_url}/esummary.fcgi", + params=params, + ) + + return self._parse_esummary(resp.text) + + def _parse_esummary(self, xml_text: str) -> list[UpstreamRecord]: + """Parse ESummary XML response into UpstreamRecords.""" + tree = ElementTree.fromstring(xml_text) + records = [] + now = datetime.now(UTC) + + for doc in tree.findall(".//DocumentSummary"): + accession = self._get_item(doc, "Accession") + if not accession or not accession.startswith(self._record_prefix): + continue + + metadata = { + "title": self._get_item(doc, "title"), + "summary": self._get_item(doc, "summary"), + "organism": self._get_item(doc, "taxon"), + "platform": self._get_item(doc, "GPL"), + "sample_count": self._get_item(doc, "n_samples"), + "pub_date": self._get_item(doc, "PDAT"), + "entry_type": self._get_item(doc, "entryType"), + "gds_type": self._get_item(doc, "gdsType"), + } + + # Filter out None values + metadata = {k: v for k, v in metadata.items() if v is not None} + + records.append( + UpstreamRecord( + source_id=accession, + source_type=self.name, + metadata=metadata, + fetched_at=now, + source_url=f"https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={accession}", + ) + ) + + return records + + def _get_item(self, doc: ElementTree.Element, name: str) -> str | None: + """Extract an item value from a DocumentSummary element.""" + # Try as attribute first + elem = doc.find(f"Item[@Name='{name}']") + if elem is not None and elem.text: + return elem.text.strip() + + # Try as direct child element + elem = doc.find(name) + if elem is not None and elem.text: + return elem.text.strip() + + return None diff --git a/tests/conftest.py b/server/tests/conftest.py similarity index 100% rename from tests/conftest.py rename to server/tests/conftest.py diff --git a/tests/integration/__init__.py b/server/tests/integration/__init__.py similarity index 100% rename from tests/integration/__init__.py rename to server/tests/integration/__init__.py diff --git a/tests/integration/infrastructure/__init__.py b/server/tests/integration/infrastructure/__init__.py similarity index 100% rename from tests/integration/infrastructure/__init__.py rename to server/tests/integration/infrastructure/__init__.py diff --git a/tests/integration/infrastructure/source/__init__.py b/server/tests/integration/infrastructure/source/__init__.py similarity index 100% rename from tests/integration/infrastructure/source/__init__.py rename to server/tests/integration/infrastructure/source/__init__.py diff --git a/tests/test_sources/__init__.py b/server/tests/test_sources/__init__.py similarity index 100% rename from tests/test_sources/__init__.py rename to server/tests/test_sources/__init__.py diff --git a/tests/test_sources/geo_entrez/__init__.py b/server/tests/test_sources/geo_entrez/__init__.py similarity index 100% rename from tests/test_sources/geo_entrez/__init__.py rename to server/tests/test_sources/geo_entrez/__init__.py diff --git a/tests/test_sources/geo_entrez/test_source.py b/server/tests/test_sources/geo_entrez/test_source.py similarity index 93% rename from tests/test_sources/geo_entrez/test_source.py rename to server/tests/test_sources/geo_entrez/test_source.py index bb2b0e7..8d2c0bb 100644 --- a/tests/test_sources/geo_entrez/test_source.py +++ b/server/tests/test_sources/geo_entrez/test_source.py @@ -61,10 +61,12 @@ async def test_pull_yields_upstream_records(self, geo_source: GEOEntrezSource) - """Pulling records should yield valid UpstreamRecords.""" records: list[UpstreamRecord] = [] - async for record in geo_source.pull(limit=3): + records_iter, session = await geo_source.pull(limit=3) + async for record in records_iter: records.append(record) assert len(records) >= 1 + assert session is not None # Should have WebEnv session for record in records: assert isinstance(record, UpstreamRecord) diff --git a/tests/unit/cli/__init__.py b/server/tests/unit/cli/__init__.py similarity index 100% rename from tests/unit/cli/__init__.py rename to server/tests/unit/cli/__init__.py diff --git a/tests/unit/cli/util/__init__.py b/server/tests/unit/cli/util/__init__.py similarity index 100% rename from tests/unit/cli/util/__init__.py rename to server/tests/unit/cli/util/__init__.py diff --git a/tests/unit/cli/util/test_paths.py b/server/tests/unit/cli/util/test_paths.py similarity index 100% rename from tests/unit/cli/util/test_paths.py rename to server/tests/unit/cli/util/test_paths.py diff --git a/tests/unit/config/__init__.py b/server/tests/unit/config/__init__.py similarity index 100% rename from tests/unit/config/__init__.py rename to server/tests/unit/config/__init__.py diff --git a/tests/unit/config/test_paths_config.py b/server/tests/unit/config/test_paths_config.py similarity index 100% rename from tests/unit/config/test_paths_config.py rename to server/tests/unit/config/test_paths_config.py diff --git a/tests/unit/domain/index/__init__.py b/server/tests/unit/domain/index/__init__.py similarity index 100% rename from tests/unit/domain/index/__init__.py rename to server/tests/unit/domain/index/__init__.py diff --git a/tests/unit/domain/index/test_index_service.py b/server/tests/unit/domain/index/test_index_service.py similarity index 100% rename from tests/unit/domain/index/test_index_service.py rename to server/tests/unit/domain/index/test_index_service.py diff --git a/tests/unit/domain/record/__init__.py b/server/tests/unit/domain/record/__init__.py similarity index 100% rename from tests/unit/domain/record/__init__.py rename to server/tests/unit/domain/record/__init__.py diff --git a/tests/unit/domain/record/test_record_service.py b/server/tests/unit/domain/record/test_record_service.py similarity index 100% rename from tests/unit/domain/record/test_record_service.py rename to server/tests/unit/domain/record/test_record_service.py diff --git a/tests/unit/domain/shared/test_srn.py b/server/tests/unit/domain/shared/test_srn.py similarity index 100% rename from tests/unit/domain/shared/test_srn.py rename to server/tests/unit/domain/shared/test_srn.py diff --git a/tests/unit/domain/source/__init__.py b/server/tests/unit/domain/source/__init__.py similarity index 100% rename from tests/unit/domain/source/__init__.py rename to server/tests/unit/domain/source/__init__.py diff --git a/tests/unit/domain/source/test_source_service.py b/server/tests/unit/domain/source/test_source_service.py similarity index 88% rename from tests/unit/domain/source/test_source_service.py rename to server/tests/unit/domain/source/test_source_service.py index d64c44f..2dfa2ef 100644 --- a/tests/unit/domain/source/test_source_service.py +++ b/server/tests/unit/domain/source/test_source_service.py @@ -1,6 +1,8 @@ """Unit tests for SourceService.""" +from collections.abc import AsyncIterator from datetime import datetime, timezone +from typing import Any from unittest.mock import AsyncMock, MagicMock import pytest @@ -11,6 +13,7 @@ from osa.domain.source.model.registry import SourceRegistry from osa.domain.source.service.source import SourceService from osa.sdk.source.record import UpstreamRecord +from osa.sdk.source.source import PullResult class FakeSource: @@ -21,9 +24,21 @@ class FakeSource: def __init__(self, records: list[UpstreamRecord]): self._records = records - async def pull(self, since: datetime | None = None, limit: int | None = None): - for record in self._records[: limit if limit else len(self._records)]: - yield record + async def pull( + self, + since: datetime | None = None, + limit: int | None = None, + offset: int = 0, + session: dict[str, Any] | None = None, + ) -> PullResult: + """Return records iterator and session (None for fake).""" + records_slice = self._records[offset : offset + limit if limit else len(self._records)] + + async def generate() -> AsyncIterator[UpstreamRecord]: + for record in records_slice: + yield record + + return generate(), session @pytest.fixture diff --git a/tests/unit/domain/validation/__init__.py 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f"{self._record_prefix}[ETYP]" - if since: - date_str = since.strftime("%Y/%m/%d") - query += f" AND {date_str}:3000[PDAT]" - - # Get UIDs via esearch - uids = await self._search_uids(query, limit) - - # Fetch metadata in batches - for batch_start in range(0, len(uids), self._config.batch_size): - batch_uids = uids[batch_start : batch_start + self._config.batch_size] - records = await self._fetch_batch(batch_uids) - for record in records: - yield record - - async def get_one(self, source_id: str) -> UpstreamRecord | None: - """Fetch a single GSE by accession. - - Args: - source_id: GSE accession (e.g., "GSE12345"). - - Returns: - RawRecord if found, None otherwise. - """ - # Search for the specific accession - query = f"{source_id}[ACCN]" - uids = await self._search_uids(query, limit=1) - - if not uids: - return None - - records = await self._fetch_batch(uids) - return records[0] if records else None - - async def health(self) -> bool: - """Check if GEO API is reachable.""" - try: - params = self._base_params() - params["db"] = "gds" - resp = await self._client.get( - f"{self._config.base_url}/einfo.fcgi", - params=params, - ) - return resp.status_code == 200 - except httpx.HTTPError: - return False - - async def close(self) -> None: - """Close the HTTP client.""" - await self._client.aclose() - - def _base_params(self) -> dict[str, str]: - """Build base parameters required by NCBI.""" - params = { - "tool": self._config.tool_name, - "email": self._config.email, - } - if self._config.api_key: - params["api_key"] = self._config.api_key - return params - - async def _search_uids(self, query: str, limit: int | None) -> list[str]: - """Search GEO for UIDs matching the query.""" - params = self._base_params() - params.update( - { - "db": "gds", - "term": query, - "retmax": str(limit or 10000), - "usehistory": "n", - } - ) - - resp = await self._client.get( - f"{self._config.base_url}/esearch.fcgi", - params=params, - ) - resp.raise_for_status() - - tree = ElementTree.fromstring(resp.text) - return [id_elem.text for id_elem in tree.findall(".//Id") if id_elem.text] - - async def _fetch_batch(self, uids: list[str]) -> list[UpstreamRecord]: - """Fetch metadata for a batch of UIDs via ESummary.""" - if not uids: - return [] - - params = self._base_params() - params.update( - { - "db": "gds", - "id": ",".join(uids), - "version": "2.0", - } - ) - - resp = await self._client.get( - f"{self._config.base_url}/esummary.fcgi", - params=params, - ) - resp.raise_for_status() - - return self._parse_esummary(resp.text) - - def _parse_esummary(self, xml_text: str) -> list[UpstreamRecord]: - """Parse ESummary XML response into UpstreamRecords.""" - tree = ElementTree.fromstring(xml_text) - records = [] - now = datetime.now(UTC) - - for doc in tree.findall(".//DocumentSummary"): - accession = self._get_item(doc, "Accession") - if not accession or not accession.startswith(self._record_prefix): - continue - - metadata = { - "title": self._get_item(doc, 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+/coverage + +# next.js +/.next/ +/out/ + +# production +/build + +# misc +.DS_Store +*.pem + +# debug +npm-debug.log* +yarn-debug.log* +yarn-error.log* +.pnpm-debug.log* + +# env files (can opt-in for committing if needed) +.env* + +# vercel +.vercel + +# typescript +*.tsbuildinfo +next-env.d.ts diff --git a/web/Dockerfile b/web/Dockerfile new file mode 100644 index 0000000..de87874 --- /dev/null +++ b/web/Dockerfile @@ -0,0 +1,57 @@ +# syntax=docker/dockerfile:1 + +# Stage 1: Dependencies +FROM node:22-alpine AS deps + +RUN corepack enable && corepack prepare pnpm@latest --activate + +WORKDIR /app + +COPY package.json pnpm-lock.yaml ./ +RUN --mount=type=cache,target=/root/.local/share/pnpm/store \ + pnpm install --frozen-lockfile + +# Stage 2: Builder +FROM node:22-alpine AS builder + +RUN corepack enable && corepack prepare pnpm@latest --activate + +WORKDIR /app + +COPY --from=deps /app/node_modules ./node_modules +COPY . . + +# Build with API_URL for rewrites (can be overridden at runtime for SSR) +ARG API_URL=http://server:8000 +ENV API_URL=${API_URL} + +# Build-time environment variables for Next.js +ARG NEXT_PUBLIC_API_MODE=live +ARG NEXT_PUBLIC_API_URL=/api/v1 +ENV NEXT_PUBLIC_API_MODE=${NEXT_PUBLIC_API_MODE} +ENV NEXT_PUBLIC_API_URL=${NEXT_PUBLIC_API_URL} + +RUN pnpm build + +# Stage 3: Runtime +FROM node:22-alpine AS runtime + +WORKDIR /app + +# Create non-root user +RUN addgroup --system --gid 1001 nodejs && \ + adduser --system --uid 1001 nextjs + +# Copy built standalone output +COPY --from=builder /app/public ./public +COPY --from=builder --chown=nextjs:nodejs /app/.next/standalone ./ +COPY --from=builder --chown=nextjs:nodejs /app/.next/static ./.next/static + +USER nextjs + +EXPOSE 3000 + +ENV PORT=3000 +ENV HOSTNAME="0.0.0.0" + +CMD ["node", "server.js"] diff --git a/web/README.md b/web/README.md new file mode 100644 index 0000000..e215bc4 --- /dev/null +++ b/web/README.md @@ -0,0 +1,36 @@ +This is a [Next.js](https://nextjs.org) project bootstrapped with [`create-next-app`](https://nextjs.org/docs/app/api-reference/cli/create-next-app). + +## Getting Started + +First, run the development server: + +```bash +npm run dev +# or +yarn dev +# or +pnpm dev +# or +bun dev +``` + +Open [http://localhost:3000](http://localhost:3000) with your browser to see the result. + +You can start editing the page by modifying `app/page.tsx`. The page auto-updates as you edit the file. + +This project uses [`next/font`](https://nextjs.org/docs/app/building-your-application/optimizing/fonts) to automatically optimize and load [Geist](https://vercel.com/font), a new font family for Vercel. + +## Learn More + +To learn more about Next.js, take a look at the following resources: + +- [Next.js Documentation](https://nextjs.org/docs) - learn about Next.js features and API. +- [Learn Next.js](https://nextjs.org/learn) - an interactive Next.js tutorial. + +You can check out [the Next.js GitHub repository](https://github.com/vercel/next.js) - your feedback and contributions are welcome! + +## Deploy on Vercel + +The easiest way to deploy your Next.js app is to use the [Vercel Platform](https://vercel.com/new?utm_medium=default-template&filter=next.js&utm_source=create-next-app&utm_campaign=create-next-app-readme) from the creators of Next.js. + +Check out our [Next.js deployment documentation](https://nextjs.org/docs/app/building-your-application/deploying) for more details. diff --git a/web/eslint.config.mjs b/web/eslint.config.mjs new file mode 100644 index 0000000..05e726d --- /dev/null +++ b/web/eslint.config.mjs @@ -0,0 +1,18 @@ +import { defineConfig, globalIgnores } from "eslint/config"; +import nextVitals from "eslint-config-next/core-web-vitals"; +import nextTs from "eslint-config-next/typescript"; + +const eslintConfig = defineConfig([ + ...nextVitals, + ...nextTs, + // Override default ignores of eslint-config-next. + globalIgnores([ + // Default ignores of eslint-config-next: + ".next/**", + "out/**", + "build/**", + "next-env.d.ts", + ]), +]); + +export default eslintConfig; diff --git a/web/next.config.ts b/web/next.config.ts new file mode 100644 index 0000000..0bb6b1e --- /dev/null +++ b/web/next.config.ts @@ -0,0 +1,18 @@ +import type { NextConfig } from "next"; + +const nextConfig: NextConfig = { + output: "standalone", + + // Proxy API requests to the backend server + async rewrites() { + const apiUrl = process.env.API_URL || "http://localhost:8000"; + return [ + { + source: "/api/:path*", + destination: `${apiUrl}/api/:path*`, + }, + ]; + }, +}; + +export default nextConfig; diff --git a/web/package.json b/web/package.json new file mode 100644 index 0000000..a9b7ff9 --- /dev/null +++ b/web/package.json @@ -0,0 +1,27 @@ +{ + "name": "lingual-bio", + "version": "0.1.0", + "private": true, + "scripts": { + "dev": "next dev", + "build": "next build", + "start": "next start", + "lint": "eslint" + }, + "dependencies": { + "@opensciencearchive/ui": "github:opensciencearchive/ui", + "next": "16.1.1", + "react": "19.2.3", + "react-dom": "19.2.3" + }, + "devDependencies": { + "@tailwindcss/postcss": "^4", + "@types/node": "^20", + "@types/react": "^19", + "@types/react-dom": "^19", + "eslint": "^9", + "eslint-config-next": "16.1.1", + "tailwindcss": "^4", + "typescript": "^5" + } +} diff --git a/web/pnpm-lock.yaml 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side-channel-map: 1.0.1 + side-channel-weakmap: 1.0.2 + + source-map-js@1.2.1: {} + + stable-hash@0.0.5: {} + + stop-iteration-iterator@1.1.0: + dependencies: + es-errors: 1.3.0 + internal-slot: 1.1.0 + + string.prototype.includes@2.0.1: + dependencies: + call-bind: 1.0.8 + define-properties: 1.2.1 + es-abstract: 1.24.1 + + string.prototype.matchall@4.0.12: + dependencies: + call-bind: 1.0.8 + call-bound: 1.0.4 + define-properties: 1.2.1 + es-abstract: 1.24.1 + es-errors: 1.3.0 + es-object-atoms: 1.1.1 + get-intrinsic: 1.3.0 + gopd: 1.2.0 + has-symbols: 1.1.0 + internal-slot: 1.1.0 + regexp.prototype.flags: 1.5.4 + set-function-name: 2.0.2 + side-channel: 1.1.0 + + string.prototype.repeat@1.0.0: + dependencies: + define-properties: 1.2.1 + es-abstract: 1.24.1 + + string.prototype.trim@1.2.10: + dependencies: + call-bind: 1.0.8 + call-bound: 1.0.4 + define-data-property: 1.1.4 + define-properties: 1.2.1 + es-abstract: 1.24.1 + es-object-atoms: 1.1.1 + has-property-descriptors: 1.0.2 + + 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call-bound: 1.0.4 + function.prototype.name: 1.1.8 + has-tostringtag: 1.0.2 + is-async-function: 2.1.1 + is-date-object: 1.1.0 + is-finalizationregistry: 1.1.1 + is-generator-function: 1.1.2 + is-regex: 1.2.1 + is-weakref: 1.1.1 + isarray: 2.0.5 + which-boxed-primitive: 1.1.1 + which-collection: 1.0.2 + which-typed-array: 1.1.19 + + which-collection@1.0.2: + dependencies: + is-map: 2.0.3 + is-set: 2.0.3 + is-weakmap: 2.0.2 + is-weakset: 2.0.4 + + which-typed-array@1.1.19: + dependencies: + available-typed-arrays: 1.0.7 + call-bind: 1.0.8 + call-bound: 1.0.4 + for-each: 0.3.5 + get-proto: 1.0.1 + gopd: 1.2.0 + has-tostringtag: 1.0.2 + + which@2.0.2: + dependencies: + isexe: 2.0.0 + + word-wrap@1.2.5: {} + + yallist@3.1.1: {} + + yocto-queue@0.1.0: {} + + zod-validation-error@4.0.2(zod@4.3.5): + dependencies: + zod: 4.3.5 + + zod@4.3.5: {} diff --git a/web/postcss.config.mjs b/web/postcss.config.mjs new file mode 100644 index 0000000..61e3684 --- /dev/null +++ b/web/postcss.config.mjs @@ -0,0 +1,7 @@ +const config = { + plugins: { + "@tailwindcss/postcss": {}, + }, +}; + +export default config; diff --git a/web/public/osa_logo.png b/web/public/osa_logo.png new file mode 100644 index 0000000..a198215 Binary files /dev/null and b/web/public/osa_logo.png differ diff --git a/web/public/osa_logo.svg b/web/public/osa_logo.svg new file mode 100644 index 0000000..52e2ee4 --- /dev/null +++ b/web/public/osa_logo.svg @@ -0,0 +1,3 @@ + + + diff --git a/web/src/app/apple-icon.png b/web/src/app/apple-icon.png new file mode 100644 index 0000000..a198215 Binary files /dev/null and b/web/src/app/apple-icon.png differ diff --git a/web/src/app/error.module.css b/web/src/app/error.module.css new file mode 100644 index 0000000..cb6aa28 --- /dev/null +++ b/web/src/app/error.module.css @@ -0,0 +1,6 @@ +.main { + min-height: calc(100vh - 200px); + display: flex; + align-items: center; + justify-content: center; +} diff --git a/web/src/app/error.tsx b/web/src/app/error.tsx new file mode 100644 index 0000000..aa793de --- /dev/null +++ b/web/src/app/error.tsx @@ -0,0 +1,21 @@ +'use client'; + +import { ErrorMessage } from '@/components/ui/ErrorMessage'; +import styles from './error.module.css'; + +interface ErrorProps { + error: Error; + reset: () => void; +} + +export default function GlobalError({ error, reset }: ErrorProps) { + return ( +
+ +
+ ); +} diff --git a/web/src/app/globals.css b/web/src/app/globals.css new file mode 100644 index 0000000..b5781f6 --- /dev/null +++ b/web/src/app/globals.css @@ -0,0 +1,102 @@ +/* + * Lingual Bio — Global Styles + * Clean scientific interface + */ + +/* OSA Design System - using direct paths to bypass exports resolution */ +@import '../../node_modules/@opensciencearchive/ui/ui/tokens/index.css'; +@import '../../node_modules/@opensciencearchive/ui/ui/base/reset.css'; +@import '../../node_modules/@opensciencearchive/ui/ui/base/elements.css'; + +:root { + /* Layout */ + --content-width: 720px; + --content-width-wide: 960px; + --content-width-full: 1400px; + --header-height: 56px; + + /* Clean, modern palette */ + --color-bg: hsl(0, 0%, 98%); + --color-bg-alt: hsl(0, 0%, 96%); + --color-bg-elevated: hsl(0, 0%, 100%); + --color-bg-hover: hsl(0, 0%, 97%); + --color-bg-dark: hsl(220, 15%, 12%); + + /* Text */ + --color-text: hsl(220, 15%, 18%); + --color-text-muted: hsl(220, 8%, 40%); + --color-text-subtle: hsl(220, 5%, 58%); + + /* Borders */ + --color-border: hsl(220, 10%, 90%); + --color-border-subtle: hsl(220, 8%, 94%); + + /* Friendly radius */ + --radius-xs: 4px; + --radius-sm: 6px; + --radius-md: 8px; + --radius-lg: 12px; + --radius-xl: 16px; + --radius-full: 9999px; + + /* Soft shadows */ + --shadow-sm: 0 1px 3px hsla(220, 20%, 20%, 0.04); + --shadow-md: 0 4px 12px hsla(220, 20%, 20%, 0.06); + --shadow-lg: 0 8px 24px hsla(220, 20%, 20%, 0.08); +} + +html { + font-family: var(--font-body); + font-size: 14px; + -webkit-font-smoothing: antialiased; + -moz-osx-font-smoothing: grayscale; +} + +body { + min-height: 100vh; + display: flex; + flex-direction: column; + background: var(--color-bg); + color: var(--color-text); + line-height: 1.5; +} + +a { + text-decoration: none; + color: var(--color-accent); + transition: color 100ms ease; +} + +a:hover { + color: var(--color-accent-hover); +} + +:focus-visible { + outline: 1.5px solid var(--color-accent); + outline-offset: 1px; +} + +button { + font-family: inherit; + cursor: pointer; + border: none; + background: none; +} + +input, textarea { + font-family: inherit; +} + +code, pre, kbd { + font-family: var(--font-mono); +} + +::selection { + background: var(--color-accent-subtle); + color: var(--color-text); +} + +/* Utility: mono text */ +.mono { + font-family: var(--font-mono); +} diff --git a/web/src/app/icon.svg b/web/src/app/icon.svg new file mode 100644 index 0000000..52e2ee4 --- /dev/null +++ b/web/src/app/icon.svg @@ -0,0 +1,3 @@ + + + diff --git a/web/src/app/layout.tsx b/web/src/app/layout.tsx new file mode 100644 index 0000000..dc5ed1a --- /dev/null +++ b/web/src/app/layout.tsx @@ -0,0 +1,39 @@ +import type { Metadata } from 'next'; +import { Geist, Geist_Mono } from 'next/font/google'; +import './globals.css'; +import { Header } from '@/components/layout/Header'; +import { Footer } from '@/components/layout/Footer'; + +const geist = Geist({ + subsets: ['latin'], + display: 'swap', + variable: '--font-body', +}); + +const geistMono = Geist_Mono({ + subsets: ['latin'], + display: 'swap', + variable: '--font-mono', +}); + +export const metadata: Metadata = { + title: 'Lingual Bio — Search Biological Databases', + description: 'Semantic search over biological databases from Open Science Archive. Discover research datasets using natural language.', + keywords: ['biology', 'genomics', 'GEO', 'research', 'scientific data', 'semantic search'], +}; + +export default function RootLayout({ + children, +}: Readonly<{ + children: React.ReactNode; +}>) { + return ( + + +
+ {children} +