Skip to main content
Glama
informatics-isi-edu

Deriva MCP Server

Official

clone_catalog

Create an ML workspace by cloning catalog data reachable from a root RID, including schema, assets, and foreign keys with orphan handling.

Instructions

Create an ML workspace by cloning data reachable from a root RID.

Creates a partial catalog clone containing only data reachable from the root RID (e.g., a project, dataset, or experiment). Uses the root table's export annotation (if available) to determine which tables and paths to follow, then fills in any uncovered tables (vocabularies, associations).

Uses a three-stage approach:

  1. Create schema WITHOUT foreign keys (only for included tables)

  2. Copy data asynchronously (export paths + fill-in tables)

  3. Apply foreign keys, handling violations based on orphan_strategy

Asset handling modes:

  • "none": Don't copy assets (asset columns will be empty)

  • "refs": Copy asset URLs only, files stay on source server (default)

  • "full": Download and re-upload all assets (fully independent clone)

Orphan handling: When source catalog policies hide some data but not references to it, cloning can result in dangling foreign keys. The orphan_strategy controls how these are handled.

Args: source_hostname: Source server hostname (e.g., "www.facebase.org"). source_catalog_id: ID of the catalog to clone. root_rid: The starting RID from which to trace reachability (e.g., a project RID like "3-HXMC"). dest_hostname: Destination hostname. If None, uses source hostname. alias: Optional alias name for the new catalog. add_ml_schema: If True, add the DerivaML schema to the clone. asset_mode: How to handle assets: "none", "refs" (default), or "full". copy_annotations: If True (default), copy all annotations. copy_policy: If True (default), copy ACL policies. exclude_schemas: List of schema names to exclude from cloning. exclude_objects: List of tables ("schema:table" format) to exclude. reinitialize_dataset_versions: If True (default), reinitialize dataset versions. orphan_strategy: How to handle orphan rows: "fail", "delete", or "nullify". prune_hidden_fkeys: If True, skip FKs with hidden reference data. truncate_oversized: If True, truncate values exceeding index size limits. include_tables: Additional tables to include. include_associations: If True, auto-include association tables. include_vocabularies: If True, auto-include vocabulary tables. table_concurrency: Max concurrent table copies during fill phase. Lower values reduce server load. Default: 1.

Returns: JSON with status, source info, destination info, and operation details including tables restored and orphan handling stats.

Examples: clone_catalog("www.facebase.org", "1", root_rid="3-HXMC", dest_hostname="localhost", alias="facebase-musmorph", add_ml_schema=True, orphan_strategy="delete")

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
aliasNo
root_ridYes
asset_modeNorefs
copy_policyNo
add_ml_schemaNo
dest_hostnameNo
include_tablesNo
exclude_objectsNo
exclude_schemasNo
orphan_strategyNofail
source_hostnameYes
copy_annotationsNo
source_catalog_idYes
table_concurrencyNo
prune_hidden_fkeysNo
truncate_oversizedNo
include_associationsNo
include_vocabulariesNo
reinitialize_dataset_versionsNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior5/5

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

With no annotations provided, the description carries full burden, and it delivers exceptionally well. It discloses the three-stage execution process (schema creation, async data copy, FK application), asset handling modes ('none', 'refs', 'full') and their implications, orphan handling strategies, and the fact that it uses export annotations to determine reachability. It also explains potential side effects like 'truncate_oversized' and 'prune_hidden_fkeys'. This goes far beyond typical descriptions.

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

Conciseness4/5

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

The description is long but appropriately structured with sections for asset handling, orphan handling, and an Args list. There is some redundancy (e.g., asset_mode and orphan_strategy are explained both in dedicated sections and again in the Args list), which adds slight verbosity. However, the information is well-organized and every sentence contributes meaning; the complexity of the tool justifies the length.

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?

Given the tool's complexity (19 params, no annotations, and an output schema), the description is remarkably complete. It covers the return format ('JSON with status...'), provides a concrete example, details the multi-stage process, and clarifies all major parameters. The output schema is not shown, but the description summarizes what it returns, which is sufficient for an agent to understand the result shape.

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

Parameters5/5

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

Schema description coverage is 0%, so the description must compensate for all 19 parameters. The Args section provides a meaningful description for every single parameter, including defaults and examples (e.g., source_hostname 'www.facebase.org', root_rid '3-HXMC'). It explains nuanced behavior like orphan_strategy and asset_mode, adding substantial value beyond the bare schema titles and defaults.

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 purpose: 'Create an ML workspace by cloning data reachable from a root RID.' It uses a specific verb ('Create') and resource ('ML workspace'), and distinguishes itself from siblings by emphasizing a 'partial catalog clone' and focusing on root-RID reachability. This is unique among the sibling tools, making the purpose unmistakable.

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 context on when to use the tool (e.g., cloning data from a project, dataset, or experiment) and explains the high-level workflow (three-stage approach, asset handling modes). It does not explicitly contrast with clone_catalog_async, but the detailed parameter guidance (e.g., orphan_strategy, asset_mode) effectively implies appropriate use cases. No explicit exclusions are given, but the examples and mode explanations serve as practical guidance.

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

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/informatics-isi-edu/deriva-mcp'

If you have feedback or need assistance with the MCP directory API, please join our Discord server