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MCP server for the BV-BRC (Bacterial and Viral Bioinformatics Research Center) service, providing tools for genomics analysis, sequence processing, and bioinformatics workflows
Critical gaps across all dimensions. Tool descriptions are minimal or generic ('Get parameters from get_service_info tool' for 3 tools). Parameters lack descriptions for most fields (e.g., genome_assembly has 16 undescribed params). Schemas present but incomplete, many params missing type info or descriptions. No error handling guidance. No output schema documentation. Naming is acceptable (verb_noun pattern) but descriptions fail to explain WHEN to use each tool or what it returns. This server would not pass production code review.
Get parameters from get_service_info tool.
Get parameters from get_service_info tool.
Get parameters from get_service_info tool.
Query tasks. Parameters: token (str, optional) - Authentication token for API access, task_ids (List[str]) - List of task IDs to query
Get information about the service. Parameters: Service Name (str, required) - Name of the service to get information about. example: genome_assembly, blast, primer_design, etc.
Enumerate all apps. Parameters: token (str, optional) - Authentication token for API access
Three tools (genome_assembly, genome_annotation, comprehensive_genome_analysis) have placeholder descriptions: 'Get parameters from get_service_info tool.' This violates pattern:tool-description, LLMs cannot determine when or why to select these tools. Descriptions must explain WHAT the tool does, WHEN to use it, and what it returns.
genome_assembly has 16 parameters with NO descriptions (paired_end_libs, single_end_libs, srr_ids, max_bases, recipe, racon_iter, pilon_iter, trim, target_depth, normalize, filtlong, genome_size, min_contig_len, min_contig_cov, output_path, output_file). Violates pattern:tool-description, LLMs cannot infer parameter meaning from names alone. Every parameter needs a description explaining what it controls and valid range/format.
Inferred effective spec: <=2025-11-25.
| Scored | Grade | Overall | Spec posture | Rubric |
|---|---|---|---|---|
| 2026-09-23 | F | 40 | <=2025-11-25 | v2 |
Start the date app. Parameters: token (str, optional) - Authentication token for API access, output_path (str, required) - Path for output files, output_file (str, required) - Name of output file
No output schemas documented for any tool. LLMs need to know what fields to expect so they can plan downstream calls and extract data. Violates pattern:tool, 'Document the output schema.' All tools return str but actual structure is unknown to the LLM.
No error handling guidance. Tools return generic error strings ('Error: No authentication token available') with no recovery hints. Violates pattern:recovery-guide, error responses must tell the LLM what to do next. Example: 'No token available. Provide a token parameter or configure server-side authentication.'
Token parameter exposed in all tools. Violates pattern:secret-injection, credentials must never appear as tool parameters. Use server-side secret injection via environment variables or vault. Agent traces log every parameter, secrets in params leak into logs and prompt history.