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Brapi Get Germplasm

brapi_get_germplasm
Read-onlyIdempotent

Fetch a single germplasm by DbId with attributes and direct parents. Response companions report study count, direct parent count, and direct descendant count — signals for pedigree depth and observation coverage.

Input Schema

NameRequiredDescriptionDefault
aliasNoConnection alias. Omit to use alias `default`. An alias registered via brapi_connect works, and so does one the server has a URL configured for (a built-in alias, an operator-configured alias, or `default` on a deployment with a default server), which connects on first use. Calls that used a non-default alias must pass that same alias here.
germplasmDbIdYesGermplasm identifier.

Output Schema

NameRequiredDescriptionDefault
aliasNoConnection alias the call used.
errorNoPresent when the call failed. Absent on success.
parentsNoDirect parents from /germplasm/{id}/pedigree.
warningsNoAdvisory messages — failed sub-endpoint lookups, missing counts.
germplasmNoCanonical germplasm record as returned by `/germplasm/{id}`.
attributesNoGermplasm attributes from /germplasm/{id}/attributes.
studyCountNoHow many studies this germplasm has appeared in.
directParentCountNoLength of parents[]; 0 also when the pedigree lookup is unsupported or failed.
directDescendantCountNoCount of direct descendants from /germplasm/{id}/progeny.

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changed
    • changedOutput schema / properties / error / properties / data / properties / reason / description
      Previous value: -"Machine-readable failure mode. Declared by this tool: `unknown_alias`: No connection is registered under the requested alias, and the server has no base URL configured for it to connect on first use. `auth_token_exchange_failed`: Connecting the alias on first use, the SGN or OAuth token exchange against the BrAPI /token endpoint failed. `auth_no_access_token`: Connecting the alias on first use, the token endpoint answered without returning an access token. `capability_discovery_unavailable`: Neither /serverinfo nor /calls listed any call, and at least one of them timed out, was unreachable, or answered 429 or a 5xx other than 501, so nothing was cached. `upstream_unauthorized`: The BrAPI server answered HTTP 401: it requires credentials, or rejected the ones sent. `upstream_forbidden`: The BrAPI server answered HTTP 403: the credentials sent, or their absence, lack access. `alias_base_url_invalid`: The base URL configured on the server for this alias is not an absolute http(s) URL, or carries credentials. `private_address_blocked`: The base URL configured for this alias, or its token URL, is on a private or reserved address this server may not reach. `germplasm_not_found`: Upstream returned no germplasm record for the requested DbId. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `upstream_rate_limited`: An uncaught BrAPI data request exhausted retries after HTTP 429. `unknown_alias`: No connection is registered under the requested alias, and the server has no base URL configured for it to connect on first use. `auth_token_exchange_failed`: Connecting the alias on first use, the SGN or OAuth token exchange against the BrAPI /token endpoint failed. `auth_no_access_token`: Connecting the alias on first use, the token endpoint answered without returning an access token. `capability_discovery_unavailable`: Neither /serverinfo nor /calls listed any call, and at least one of them timed out, was unreachable, or answered 429 or a 5xx other than 501, so nothing was cached. `upstream_unauthorized`: The BrAPI server answered HTTP 401: it requires credentials, or rejected the ones sent. `upstream_forbidden`: The BrAPI server answered HTTP 403: the credentials sent, or their absence, lack access. `alias_base_url_invalid`: The base URL configured on the server for this alias is not an absolute http(s) URL, or carries credentials. `private_address_blocked`: The base URL configured for this alias, or its token URL, is on a private or reserved address this server may not reach. `germplasm_not_found`: Upstream returned no germplasm record for the requested DbId. Other values are possible when a failure originates below the handler."
    • changedOutput schema / properties / error / properties / data / properties / reason / examples
      Previous value: -[
-  "unknown_alias",
-  "auth_token_exchange_failed",
-  "auth_no_access_token",
-  "capability_discovery_unavailable",
-  "upstream_unauthorized",
-  "upstream_forbidden",
-  "alias_base_url_invalid",
-  "private_address_blocked",
-  "germplasm_not_found"
-]New value: +[
+  "upstream_rate_limited",
+  "unknown_alias",
+  "auth_token_exchange_failed",
+  "auth_no_access_token",
+  "capability_discovery_unavailable",
+  "upstream_unauthorized",
+  "upstream_forbidden",
+  "alias_base_url_invalid",
+  "private_address_blocked",
+  "germplasm_not_found"
+]
  2. Changed7 schema fields changed
    • changedInput schema / properties / alias / description
      Previous value: -"Connection alias registered via brapi_connect. Omit to read the connection registered under alias `default` — i.e. a prior brapi_connect call that did not specify an alias. Calls that used a non-default alias must pass that same alias here."New value: +"Connection alias. Omit to use alias `default`. An alias registered via brapi_connect works, and so does one the server has a URL configured for (a built-in alias, an operator-configured alias, or `default` on a deployment with a default server), which connects on first use. Calls that used a non-default alias must pass that same alias here."
    • removedInput schema / properties / germplasmDbId / minLength
      Removed value: -1
    • addedInput schema / properties / germplasmDbId / pattern
      Added value: +"\\S"
    • changedOutput schema / properties / alias / description
      Previous value: -"Alias of the registered BrAPI connection the call used."New value: +"Connection alias the call used."
    • changedOutput schema / properties / directParentCount / description
      Previous value: -"Count of direct parents."New value: +"Length of parents[]; 0 also when the pedigree lookup is unsupported or failed."
    • changedOutput schema / properties / error / properties / data / properties / reason / description
      Previous value: -"Machine-readable failure mode. Declared by this tool: `unknown_alias`: No connection has been registered under the requested alias. `germplasm_not_found`: Upstream returned no germplasm record for the requested DbId. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `unknown_alias`: No connection is registered under the requested alias, and the server has no base URL configured for it to connect on first use. `auth_token_exchange_failed`: Connecting the alias on first use, the SGN or OAuth token exchange against the BrAPI /token endpoint failed. `auth_no_access_token`: Connecting the alias on first use, the token endpoint answered without returning an access token. `capability_discovery_unavailable`: Neither /serverinfo nor /calls listed any call, and at least one of them timed out, was unreachable, or answered 429 or a 5xx other than 501, so nothing was cached. `upstream_unauthorized`: The BrAPI server answered HTTP 401: it requires credentials, or rejected the ones sent. `upstream_forbidden`: The BrAPI server answered HTTP 403: the credentials sent, or their absence, lack access. `alias_base_url_invalid`: The base URL configured on the server for this alias is not an absolute http(s) URL, or carries credentials. `private_address_blocked`: The base URL configured for this alias, or its token URL, is on a private or reserved address this server may not reach. `germplasm_not_found`: Upstream returned no germplasm record for the requested DbId. Other values are possible when a failure originates below the handler."
    • changedOutput schema / properties / error / properties / data / properties / reason / examples
      Previous value: -[
-  "unknown_alias",
-  "germplasm_not_found"
-]New value: +[
+  "unknown_alias",
+  "auth_token_exchange_failed",
+  "auth_no_access_token",
+  "capability_discovery_unavailable",
+  "upstream_unauthorized",
+  "upstream_forbidden",
+  "alias_base_url_invalid",
+  "private_address_blocked",
+  "germplasm_not_found"
+]
  3. First observed

TDQS

A3.5/5.0
Behavior3/5

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

Annotations already declare readOnlyHint and idempotentHint, so the safety profile is covered. The description adds that the response includes companion counts (study count, direct parent count, direct descendant count) and interprets them as signals of pedigree depth and observation coverage — useful context, but nothing about auth/alias behavior or limitations beyond that.

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?

Two compact sentences, front-loaded with the core action and scope; the second sentence explains response context. Nothing is wasted, though the response-companion sentence is arguably redundant given an output schema exists.

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

Completeness4/5

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

For a single-record read tool with full annotation coverage (readOnly, idempotent), full schema coverage, and an existing output schema, the description supplies enough to call it correctly. The return-value interpretation is extra rather than necessary, and there is no routing to brapi_walk_pedigree for deeper ancestry traversal.

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

Parameters3/5

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

Schema description coverage is 100%, so both parameters (alias and germplasmDbId) are already fully documented in the schema. The description names DbId but adds no syntax or format meaning beyond what the schema carries, so baseline 3 applies.

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

Purpose4/5

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

States a specific verb+resource with scope: 'Fetch a single germplasm by DbId with attributes and direct parents.' The word 'single' and the DbId keying implicitly separate it from the plural sibling brapi_find_germplasm, though no sibling is named explicitly.

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

Usage Guidelines3/5

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

Usage is only implied by 'single...by DbId' — the agent can infer this is the direct-lookup tool versus brapi_find_germplasm's search, but the description gives no explicit when-to-use, prerequisites, or named alternative. It also doesn't point to brapi_walk_pedigree despite mentioning parent/descendant counts.

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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