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informatics-isi-edu

Deriva MCP Server

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apply_annotations

Commit all staged annotation changes to the Deriva catalog, applying updates made via display annotations, visible columns, and foreign keys. Ensure your metadata is saved and synchronized.

Instructions

Apply all staged annotation changes to the catalog.

This commits any annotation changes made via set_display_annotation, set_visible_columns, set_visible_foreign_keys, set_table_display, or set_column_display to the remote catalog.

Returns: JSON with status and details of the apply operation.

Example workflow: 1. get_table_annotations("Image") # Check current state 2. set_display_annotation("Image", annotation={"name": "Images"}) 3. set_visible_columns("Image", {"compact": ["RID", "Filename"]}) 4. apply_annotations() # Commit all changes

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations provided, the description carries the full burden. It clearly explains the commit behavior, lists the staging functions, states the return value, and provides an example. It does not disclose potential side effects like overwriting remote state or error conditions, but it offers a strong behavioral summary for a tool with no parameters.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is concise and well-structured, with a clear opening sentence, a brief explanation of what is committed, a return type note, and an illustrative example workflow. Every sentence adds value without padding.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a tool with no parameters and an output schema, the description sufficiently covers purpose, usage, and returns. The workflow example clarifies the typical sequence of operations, making it complete for an agent to invoke correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The tool has zero parameters, so the schema is trivially complete. The description does not need to explain parameter meanings, and the example workflow confirms no arguments are required. This aligns with the baseline 4 for zero-parameter tools.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the specific action 'Apply all staged annotation changes to the catalog' and lists the exact setter functions whose changes are committed. This distinguishes it from sibling tools like apply_catalog_annotations, which likely operate at a different scope.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides clear usage context by explaining it commits changes made via the listed setter functions and includes an example workflow. However, it does not explicitly mention alternatives or exclusions, such as when to use apply_catalog_annotations instead, so it earns a 4 rather than 5.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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