name	query-silo
description	Query a locally running SILO instance using queryLocalSilo.sh. Use when user says "query silo", "run query", "test query", "try this query", or wants to execute a SaneQL query against the local API.

How to query

Use queryLocalSilo.sh (in this skill's directory) to send SaneQL queries to the local SILO API (port 8081):

.agents/skills/query-silo/queryLocalSilo.sh "default.groupBy({count:=count()})"

The script sends a POST /query with Content-Type: text/plain and prints the NDJSON response followed by the HTTP status code.

Status code only

.agents/skills/query-silo/queryLocalSilo.sh -s "default.filter(country='CH').project({primaryKey})"

Query language

Queries use SaneQL. Common patterns:

default                                          -- full table scan
default.filter(column='value')                   -- filter rows
default.project({col1, col2})                    -- select columns
default.groupBy({count:=count()}, {col})         -- aggregate
default.map({new_col := expression})             -- add computed column
default.orderBy({asc(col)})                      -- sort
default.mutations(minProportion:=0.5)            -- nucleotide mutations
unionAll(pipeline1, pipeline2)                   -- concatenate two pipelines

Chaining: default.filter(...).project({...}).groupBy({...}).orderBy({...})

Error responses

On error, the response body contains {"error": "...", "message": "..."} with a non-200 status code.

Notes

The API must be running on port 8081 before querying.
Response format is NDJSON (one JSON object per line).
Always quote the query string to prevent shell expansion of {} and ().
SILO instance contains dummy dataset with 100 sequences. Database config (schema definition) is in testBaseData/exampleDataset/database_config.yaml.

name	query-silo
description	Query a locally running SILO instance using queryLocalSilo.sh. Use when user says "query silo", "run query", "test query", "try this query", or wants to execute a SaneQL query against the local API.