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bigquery-public

Run read-only SQL against BigQuery public datasets with local result capture, cost safeguards, and reproducibility

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Run read-only SQL against BigQuery public datasets with local result capture, cost safeguards, and reproducibility

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Documentation source, pas des instructions pour ce site. Vérifiez les permissions avant d’exécuter des commandes.

🗃️ 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

FormatExtensionRequired FieldsExample
Inline SQLn/a--querySELECT * 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

Métadonnées du fichier
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
Voir le texte original
---
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

```bash
# 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:

```bash
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

```text
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](https://cloud.google.com/bigquery/public-data)
- [BigQuery authentication](https://cloud.google.com/bigquery/docs/authentication)

Examiner la source

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Réviser avant installation: Éviter l’installation automatique

Licence: MIT

  • Dependency or permission surface needs review
  • Permission surface may require sandboxing
  • The skill does not enforce that queries are limited to public datasets; it only validates read-only SQL. Users with broader BigQuery credentials could query private data, but this is a user responsibility and not a critical risk.
  • Quality score needs review
  • Permission surface needs review: secrets or environment access, shell or command execution
  • Dependency/runtime risk: command execution surface, credential or environment access
  • Permission surface: secrets or environment access, shell or command execution
Ouvrir l’audit complet

Les outils sont des indications de métadonnées, pas une compatibilité testée. Les prompts sont des suggestions.

Commencer par une petite tâche

  1. 1Lisez la source et confirmez entrées, résultats, dépendances et permissions.
  2. 2Demandez un plan à l’agent. Approuvez la configuration et les coûts avant un test isolé.
  3. 3Vérifiez résultats et fichiers modifiés. Signalez uniquement ce qui a été exécuté et conservez la révision source.

Vérifiez les dépendances, clés API et frais externes dans la source. Un dépôt public ne rend pas tous les services gratuits.

Source et conseils d’utilisation

Répertorié

Métadonnées et examens sont indicatifs. Popularité, découverte et exécution réussie sont des faits distincts.

Dépôt source
ClawBio/ClawBio
Licence
MIT
Version
1.0.0
Dernier push GitHub
6 sept. 2026
Registre mis à jour
6 sept. 2026

Version déclarée dans le registre ; vérifiez les versions de la source.

Qualité

75/100

Solide

Confiance

64/100

Sandbox uniquement

Audit

77/100

Revue nécessaire

  • Dependency or permission surface needs review
  • Permission surface may require sandboxing
  • The skill does not enforce that queries are limited to public datasets; it only validates read-only SQL. Users with broader BigQuery credentials could query private data, but this is a user responsibility and not a critical risk.
  • Quality score needs review
  • Permission surface needs review: secrets or environment access, shell or command execution
  • Dependency/runtime risk: command execution surface, credential or environment access
  • Permission surface: secrets or environment access, shell or command execution
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Plus de détails
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    "track": "Data, BI, and analytics",
    "scenario": "Database and SQL",
    "maintenance": "1mo since push",
    "risk": "Needs review"
  },
  "alternative_skills": [],
  "do_not_use_when": [
    "teams that need a vendor-supported SLA",
    "production agents without a repository review",
    "The skill does not enforce that queries are limited to public datasets; it only validates read-only SQL. Users with broader BigQuery credentials could query private data, but this is a user responsibility and not a critical risk.",
    "High-risk permission hints: Shell or command execution, Secrets or environment access",
    "Dependency or permission surface needs review",
    "Permission surface may require sandboxing",
    "Quality score needs review",
    "Permission surface needs review: secrets or environment access, shell or command execution"
  ],
  "agent_contract": {
    "task_input": "Use bigquery-public in an agent workflow",
    "recommended_action": "Do not auto-install. Inspect the source, dependencies, and permission surface first.",
    "install_policy": "block",
    "minimum_review_before_use": [
      "Trust: 72/100 Strong shortlist",
      "Audit: 77/100 Needs review",
      "Safety: 33/100 Avoid automatic install",
      "Review repository, license, install command, and permission surface before production use."
    ],
    "expected_agent_output": {
      "selected_skill": "clawbio-bigquery-public (bigquery-public)",
      "install_command": "npx skills add ClawBio/ClawBio --skill bigquery-public",
      "risk_summary": "Needs review; Blocked for auto-install; Review before production",
      "verification_result": "Report the smallest successful task, files touched, warnings, and any missing setup."
    }
  },
  "outcome_feedback": {
    "endpoint": "https://www.openagentskill.com/api/agent/outcome",
    "method": "POST",
    "requires_resolve_event_id": true,
    "event_id_source": "Use install_receipt.outcome_feedback.event_id or feedback.event_id returned by /api/agent/resolve for the current task.",
    "expected_outcomes": [
      "success",
      "failed",
      "not_relevant",
      "blocked_by_risk",
      "setup_required"
    ],
    "payload_template": {
      "event_id": "<install_receipt.outcome_feedback.event_id or feedback.event_id from /api/agent/resolve>",
      "skill_slug": "clawbio-bigquery-public",
      "task": "Use bigquery-public in an agent workflow",
      "agent": "codex",
      "outcome": "success",
      "install_used": true,
      "risk_blocked": false,
      "setup_required": false,
      "task_success": true,
      "output_quality": 4,
      "error_type": null,
      "human_review_required": false,
      "workspace": "sandbox",
      "time_to_useful_ms": 120000,
      "notes": "Report the smallest successful task, setup friction, files touched, and risk notes."
    }
  },
  "endpoints": {
    "web": "https://www.openagentskill.com/skills/clawbio-bigquery-public",
    "api": "https://www.openagentskill.com/api/agent/skills/clawbio-bigquery-public",
    "audit": "https://www.openagentskill.com/skills/clawbio-bigquery-public/audit",
    "eval": "https://www.openagentskill.com/api/agent/evals?slug=clawbio-bigquery-public&task=Use%20bigquery-public%20in%20an%20agent%20workflow&max_risk=medium",
    "resolve": "https://www.openagentskill.com/api/agent/resolve?task=Use%20bigquery-public%20in%20an%20agent%20workflow&agent=codex&max_risk=medium",
    "receipt": "https://www.openagentskill.com/api/agent/receipt?task=Use%20bigquery-public%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text",
    "install": "https://www.openagentskill.com/api/skills/clawbio-bigquery-public/install",
    "manifest": "https://www.openagentskill.com/api/registry/manifest/clawbio-bigquery-public"
  }
}

Pour le créateur

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Cette fiche a été indexée à partir de sources publiques et n’est pas marquée officielle tant qu’une revendication de mainteneur n’est pas approuvée.

Créateur
ClawBio
Indexé par
Index communautaire OpenAgentSkill

L’attribution renvoie au dépôt public ou au profil du créateur. Les créateurs peuvent revendiquer la fiche pour mettre à jour les signaux de propriété.

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