The Agent Skills Directory

Potential for Arbitrary File Write: The ukb_topmed_phewas.py script accepts a raw_output_path parameter to save detailed association data. The current implementation uses Path(raw_output_path).expanduser() to resolve the destination without validating that the path is restricted to a specific workspace or temporary directory. This pattern could potentially allow the skill to write or overwrite files in sensitive locations if an unrestricted path is provided.
Indirect Prompt Injection Surface: The skill fetches and processes genomic data from external APIs (pheweb.org and ensembl.org). This introduces a potential surface for indirect prompt injection if the external data contains instructions designed to influence the agent's behavior during summarization.
Ingestion points: Data enters the agent's context through the fetch_variant function in scripts/ukb_topmed_phewas.py and the _get_json function in scripts/variant_resolution.py.
Boundary markers: No explicit delimiters or instructions to ignore embedded commands are present in the processing logic.
Capability inventory: The skill possesses network access (requests.get) and file system write capabilities (Path.write_text).
Sanitization: While the skill performs rigorous regex validation on genomic variant inputs, it does not sanitize the content retrieved from the external API responses before presenting it to the agent.
External Network Communication: The skill makes requests to pheweb.org and ensembl.org. These are well-known and reputable services in the bioinformatics community, and these operations are essential for retrieving the requested genetic association summaries.

ukb-topmed-phewas-skill