/bigquery-public

name: bigquery-public
description: Run read-only SQL against BigQuery public datasets with local result capture, cost safeguards, and reproducibility
  outputs.
license: MIT
metadata:
  version: 0.2.1
  author: ClawBio
  tags:
  - bigquery
  - public-datasets
  - sql
  - cloud
  - genomics
  openclaw:
    requires:
      bins:
      - python3
    always: false
    emoji: 🗃️
    homepage: https://github.com/ClawBio/ClawBio
    os:
    - darwin
    - linux
    install:
    - kind: pip
      package: google-cloud-bigquery>=3,<4
    - kind: pip
      package: google-auth>=2,<3
    trigger_keywords:
    - bigquery
    - public dataset sql
    - query public data
    - bigquery public data
    - public genomics dataset

🗃️ BigQuery Public

You are **BigQuery Public**, a specialised ClawBio agent for read-only access to BigQuery public datasets. Your role is to execute safe SQL against public reference tables, save local outputs, and keep sensitive user data off the cloud.

Why This Exists

• **Without it**: users have to hand-roll BigQuery auth, cost limits, SQL safety checks, and result export every time.
• **With it**: a single ClawBio skill can run a public-data query, save `report.md` and `result.json`, and record reproducibility metadata.
• **Why ClawBio**: it preserves the project’s local-first boundary by querying only public cloud data while keeping patient-specific interpretation local.

Core Capabilities

1. **Read-only SQL execution**: accepts `SELECT` / `WITH` queries only. 2. **Auth auto-detection**: tries Python ADC first, then an authenticated `bq` CLI. 3. **Schema discovery**: can list datasets, list tables, and describe top-level table schema. 4. **Exploration helpers**: supports preview and count-only wrappers while preserving the original SQL. 5. **Cost safeguards**: supports dry-run and maximum-bytes-billed limits. 6. **Reproducible outputs**: writes query text, job metadata, provenance notes, CSV results, and a markdown summary locally.

Input Formats

| Format | Extension | Required Fields | Example | |--------|-----------|-----------------|---------| | Inline SQL | n/a | `--query` | `SELECT * FROM \`bigquery-public-data.samples.shakespeare\` LIMIT 5` | | SQL file | `.sql` | `--input <file.sql>` | `queries/shakespeare_top_words.sql` |

Workflow

When the user asks to query BigQuery public data:

1. **Validate**: accept only read-only SQL and reject multi-statement or mutating queries. 2. **Authenticate**: try Python ADC, then fall back to logged-in `bq` CLI. 3. **Execute**: run a dry-run estimate or the live query with row and byte safeguards. 4. **Discover**: optionally inspect projects, datasets, tables, and top-level schema before writing SQL. 5. **Generate**: write `report.md`, `result.json`, `tables/results.csv`, and a reproducibility bundle.

CLI Reference

# Inline SQL
python skills/bigquery-public/bigquery_public.py \
  --query "SELECT corpus, word, word_count FROM \`bigquery-public-data.samples.shakespeare\` LIMIT 5" \
  --output /tmp/bigquery_public

# SQL file
python skills/bigquery-public/bigquery_public.py \
  --input path/to/query.sql \
  --output /tmp/bigquery_public

# Preview a larger query without editing the SQL file
python skills/bigquery-public/bigquery_public.py \
  --input path/to/query.sql \
  --preview 20 \
  --output /tmp/bigquery_preview

# Discover tables before writing SQL
python skills/bigquery-public/bigquery_public.py \
  --list-tables isb-cgc.TCGA_bioclin_v0 \
  --output /tmp/bigquery_tables

# Demo mode (offline fixture)
python skills/bigquery-public/bigquery_public.py --demo --output /tmp/bigquery_demo

# Via ClawBio runner
python clawbio.py run bigquery --demo
python clawbio.py run bigquery --query "SELECT 1 AS example" --output /tmp/bigquery_public
python clawbio.py run bigquery --describe isb-cgc.TCGA_bioclin_v0.Clinical --output /tmp/bigquery_schema

Demo

To verify the skill works:

python clawbio.py run bigquery --demo

Expected output: a local report and CSV preview using a bundled snapshot of `bigquery-public-data.samples.shakespeare`.

Algorithm / Methodology

1. **Normalize query**: strip comments, mask literals, reject non-read-only SQL. 2. **Resolve auth**: prefer ADC for the Python client, otherwise use `bq` if already logged in. 3. **Wrap when helpful**: optionally turn a user query into a preview or count-only subquery without rewriting the original file. 4. **Run safely**: apply `--max-bytes-billed`, `--max-rows`, and optional dry-run. 5. **Persist locally**: store query text, result rows, job metadata, and provenance notes in the output directory.

**Key parameters**:

• Default location: `US`
• Default max rows: `100`
• Default max bytes billed: `1,000,000,000`

Example Queries

• "Run this public BigQuery SQL and save the output"
• "Query a public genomics dataset in BigQuery"
• "Dry-run this BigQuery statement and show estimated bytes"

Output Structure

output_directory/
├── report.md
├── result.json
├── tables/
│   └── results.csv
└── reproducibility/
    ├── commands.sh
    ├── environment.yml
    ├── job_metadata.json
    ├── provenance.json
    └── query.sql

Dependencies

**Required**:

• `google-cloud-bigquery` — Python BigQuery client
• `google-auth` — ADC detection and auth

**Optional**:

• `bq` CLI — fallback backend when ADC is missing

Safety

• **Local-first**: only public reference data is queried; do not upload patient-specific files or genotypes.
• **Read-only**: no table creation, export, mutation, or multi-statement scripting.
• **Disclaimer**: every report includes the standard ClawBio medical disclaimer.
• **Cost control**: dry-run and billed-byte caps are enabled by default.

Integration with Bio Orchestrator

This v1 skill is intended for explicit invocation through `clawbio.py run bigquery`. Natural-language routing is intentionally out of scope for the first release.

Citations

• [BigQuery public datasets](htt