query-silo

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.