API Reference

Start the server:

srake server --port 8080

All endpoints are prefixed with /api/v1/.

Search

`GET /api/v1/search`

Query parameters:

Parameter	Type	Description
`q` / `query`	string	Search query
`limit`	int	Max results (default: 20)
`offset`	int	Skip N results
`organism`	string	Filter by organism
`library_strategy`	string	Filter by library strategy
`platform`	string	Filter by platform
`similarity_threshold`	float	Vector similarity threshold (0.0-1.0)
`min_score`	float	Minimum BM25 score
`show_confidence`	bool	Include confidence scores
`mode` / `search_mode`	string	Search mode: text, vector, hybrid, database
`format`	string	Response format

curl "http://localhost:8080/api/v1/search?q=cancer&limit=10"
curl "http://localhost:8080/api/v1/search?q=RNA-Seq&organism=homo+sapiens&platform=ILLUMINA"

`POST /api/v1/search/advanced`

Accepts a JSON body with the same parameters as the search query.

Studies

`GET /api/v1/studies`

List studies with pagination. Parameters: limit (max 100, default 20), offset.

`GET /api/v1/studies/{accession}`

Get a single study by accession.

`GET /api/v1/studies/{accession}/metadata`

Get the full metadata graph for a study (experiments, samples, runs, summary counts).

`GET /api/v1/studies/{accession}/experiments`

List experiments for a study.

`GET /api/v1/studies/{accession}/samples`

List samples for a study.

`GET /api/v1/studies/{accession}/runs`

List runs for a study. Parameter: limit.

Experiments, Samples, Runs

`GET /api/v1/experiments/{accession}`

Get experiment by accession.

`GET /api/v1/samples/{accession}`

Get sample by accession.

`GET /api/v1/runs/{accession}`

Get run by accession.

Statistics

`GET /api/v1/stats`

Database-wide counts (studies, experiments, samples, runs).

`GET /api/v1/stats/organisms`

Organism distribution with counts.

`GET /api/v1/stats/platforms`

Platform distribution with counts.

`GET /api/v1/stats/strategies`

Library strategy distribution with counts.

Export

`POST /api/v1/export`

Export search results. JSON body with query, format (json, csv, tsv, xml, jsonl), filters, limit.

Health

`GET /api/v1/health`

{"status": "healthy", "database": "ok", "timestamp": "2025-01-15T10:30:00Z"}

MCP (Model Context Protocol)

MCP support is available via the srake mcp command, which runs a stdio-based MCP server compatible with Claude Desktop, VS Code, and other MCP clients.

See srake mcp in the CLI reference for configuration details.

Getting Started Examples