npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.6.2 → 0.6.4 - Mend

@cyanheads/brapi-mcp-server 0.6.2 → 0.6.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (80) hide show

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Agent Protocol
 **Server:** brapi-mcp-server
-**Version:** 0.6.2
+**Version:** 0.6.4
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
 > **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
@@ -34,6 +34,7 @@ Tailor suggestions to what's actually missing or stale — don't recite the full
 - **Use `ctx.state`** for tenant-scoped storage. Never access persistence directly.
 - **Check `ctx.elicit` / `ctx.sample`** for presence before calling.
 - **Secrets in env vars only** — never hardcoded.
+- **Close the loop on issues.** When implementing work tracked by a GitHub issue, comment on the issue with what landed and close it. Do both — a comment without a close leaves stale issues open; a close without a comment leaves no record of what shipped. The comment is for future readers — state the concrete changes, not the conversation that produced them.
 ---
@@ -306,13 +307,14 @@ Available skills:
 | `add-service` | Scaffold a new service integration |
 | `add-test` | Scaffold test file for a tool, resource, or service |
 | `field-test` | Exercise tools/resources/prompts with real inputs, verify behavior, report issues |
-| `tool-defs-analysis` | Read-only audit of MCP definition language across the surface (12 categories) |
+| `tool-defs-analysis` | Read-only audit of MCP definition language across the surface — voice, leaks, defaults, recovery hints, output descriptions |
 | `security-pass` | Audit server for MCP-flavored security gaps: output injection, scope blast radius, input sinks, tenant isolation |
+| `code-simplifier` | Post-session cleanup against `git diff` — modernize syntax, consolidate duplication, align with the codebase |
 | `devcheck` | Lint, format, typecheck, audit |
 | `polish-docs-meta` | Finalize docs, README, metadata, and agent protocol for shipping |
+| `git-wrapup` | Land working-tree changes as a versioned commit + annotated tag — version bump, changelog, verify, tag. Local only. |
+| `release-and-publish` | Push + npm + MCP Registry + GH Release + Docker. Picks up from `git-wrapup` |
 | `maintenance` | Investigate changelogs, adopt upstream changes, sync skills to agent dirs |
-| `release-and-publish` | Post-wrapup ship workflow: verification gate, push, publish to npm / MCP Registry / GHCR |
-| `migrate-mcp-ts-template` | Migrate legacy `mcp-ts-template` fork to package dependency |
 | `report-issue-framework` | File a bug or feature request against `@cyanheads/mcp-ts-core` via `gh` CLI |
 | `report-issue-local` | File a bug or feature request against this server's own repo via `gh` CLI |
 | `api-auth` | Auth modes, scopes, JWT/OAuth |
@@ -341,7 +343,7 @@ When you complete a skill's checklist, check the boxes and add a completion time
 | `bun run rebuild` | Clean + build |
 | `bun run clean` | Remove build artifacts |
 | `bun run devcheck` | Lint + format + typecheck + security + changelog sync |
-| `bun run audit:refresh` | Delete `bun.lock`, reinstall, re-audit. Use when `devcheck` flags a transitive advisory — stale lockfile can mask already-patched deps. If advisory survives, it's real. |
+| `bun run audit:refresh` | Delete `bun.lock`, reinstall, re-audit. Use when `devcheck` flags a transitive advisory — Bun's `update` is sticky on transitive resolutions, so the advisory may be a stale-lockfile false positive. If it survives the refresh, it's real. |
 | `bun run list-skills` | Print the skill index for this project (name, version, description) |
 | `bun run tree` | Generate `docs/tree.md` |
 | `bun run format` | Auto-fix formatting via Biome |
@@ -384,8 +386,12 @@ security: false                          # optional — true flags security fixe
 `breaking: true` renders a `· ⚠️ Breaking` badge — use it when consumers must update code on upgrade (signature changes, removed APIs, config renames). `security: true` renders a `· 🛡️ Security` badge and pairs with a `## Security` body section. When both are set, badges render `· ⚠️ Breaking · 🛡️ Security`.
+`agent-notes` is an optional free-form field for maintenance agents processing the release downstream. Content here won't appear in the rendered CHANGELOG — it's consumed by agents running the `maintenance` skill. Use it for adoption instructions that don't fit the human-facing sections: new files to create, fields to populate, one-time migration steps. Omit entirely when there's nothing to say.
 **Section order** (Keep a Changelog): Added, Changed, Deprecated, Removed, Fixed, Security. Include only sections with entries — don't ship empty headers.
+**Tag annotations** render as GitHub Release bodies via `--notes-from-tag`. They must be structured markdown — never a flat comma-separated string. Subject omits the version number (GitHub prepends it). See `changelog/template.md` for the full format reference.
 ---
 ## Imports
@@ -417,4 +423,7 @@ import { getMyService } from '@/services/my-domain/my-service.js';
 - [ ] Tests include at least one sparse upstream payload (fields omitted) alongside the happy path
 - [ ] Registered in the `tools` array of `createApp()` in `src/index.ts`
 - [ ] Tests use `createMockContext()` from `@cyanheads/mcp-ts-core/testing`
+- [ ] `.codex-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; `interface.displayName` = package name; `interface.shortDescription` from `package.json` description
+- [ ] `.codex-plugin/mcp.json` updated — server name key matches `package.json` name; env vars added for any required API keys
+- [ ] `.claude-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; inline `mcpServers` entry with server name key, env vars for any required API keys
 - [ ] `bun run devcheck` passes

package/README.md CHANGED Viewed

@@ -7,13 +7,13 @@
 <div align="center">
-[![npm](https://img.shields.io/npm/v/@cyanheads/brapi-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/brapi-mcp-server) [![Version](https://img.shields.io/badge/Version-0.6.2-blue.svg?style=flat-square)](./CHANGELOG.md) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.11-blueviolet.svg?style=flat-square)](https://bun.sh/) [![Status](https://img.shields.io/badge/Status-Beta-yellow.svg?style=flat-square)](./CHANGELOG.md)
+[![npm](https://img.shields.io/npm/v/@cyanheads/brapi-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/brapi-mcp-server) [![Version](https://img.shields.io/badge/Version-0.6.4-blue.svg?style=flat-square)](./CHANGELOG.md) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.11-blueviolet.svg?style=flat-square)](https://bun.sh/) [![Status](https://img.shields.io/badge/Status-Beta-yellow.svg?style=flat-square)](./CHANGELOG.md)
 </div>
 <div align="center">
-[![Install in Claude Desktop](https://img.shields.io/badge/Install_in-Claude_Desktop-D97757?style=for-the-badge&logo=anthropic&logoColor=white)](https://github.com/cyanheads/brapi-mcp-server/releases/latest/download/brapi-mcp-server.mcpb) [![Install in Cursor](https://cursor.com/deeplink/mcp-install-dark.svg)](https://cursor.com/en/install-mcp?name=brapi&config=eyJuYW1lIjoiYnJhcGkiLCJjb21tYW5kIjoiYnVueCIsImFyZ3MiOlsiQGN5YW5oZWFkcy9icmFwaS1tY3Atc2VydmVyQGxhdGVzdCJdLCJlbnYiOnsiTUNQX1RSQU5TUE9SVF9UWVBFIjoic3RkaW8iLCJNQ1BfTE9HX0xFVkVMIjoiaW5mbyJ9fQ) [![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_Server-0098FF?style=for-the-badge&logo=visualstudiocode&logoColor=white)](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22brapi%22%2C%22command%22%3A%22bunx%22%2C%22args%22%3A%5B%22%40cyanheads%2Fbrapi-mcp-server%40latest%22%5D%2C%22env%22%3A%7B%22MCP_TRANSPORT_TYPE%22%3A%22stdio%22%2C%22MCP_LOG_LEVEL%22%3A%22info%22%7D%7D)
+[![Install in Claude Desktop](https://img.shields.io/badge/Install_in-Claude_Desktop-D97757?style=for-the-badge&logo=anthropic&logoColor=white)](https://github.com/cyanheads/brapi-mcp-server/releases/latest/download/brapi-mcp-server.mcpb) [![Install in Cursor](https://cursor.com/deeplink/mcp-install-dark.svg)](https://cursor.com/en/install-mcp?name=brapi-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeWFuaGVhZHMvYnJhcGktbWNwLXNlcnZlciJdfQ==) [![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_Server-0098FF?style=for-the-badge&logo=visualstudiocode&logoColor=white)](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22brapi-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22%40cyanheads/brapi-mcp-server%22%5D%7D)
 [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-67E8F9?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)

package/changelog/0.6.x/0.6.3.md ADDED Viewed

@@ -0,0 +1,24 @@
+---
+summary: "@cyanheads/mcp-ts-core ^0.9.6 → ^0.9.13: HTTP 413 body cap, session-init gate, quieter error logs, landing inventory open-catalog override, URL placeholder guard"
+breaking: false
+security: false
+---
+# 0.6.3 — 2026-05-28
+## Changed
+- **`@cyanheads/mcp-ts-core`** ^0.9.6 → ^0.9.13 — picks up HTTP transport hardening, session-init gate, and quieter client-error logs (see below).
+- **`landing.requireAuth: false`** set in `createApp()` (`src/index.ts`) — restores the open-catalog UX for the hosted public endpoint; framework 0.9.13 gates landing inventory behind auth by default when `MCP_AUTH_MODE` is `jwt`/`oauth`.
+- **`BRAPI_DEFAULT_BASE_URL` Zod preprocessor** (`src/config/server-config.ts`) — strips `${...}` placeholder strings (injected by MCPB when no value is supplied) to `undefined` before the URL validator runs, preventing startup failures on optional URL fields.
+- **`@duckdb/node-api`** ^1.5.3-r.1 → ^1.5.3-r.2.
+- **`@biomejs/biome`** ^2.4.15 → ^2.4.16.
+## Framework changes (0.9.7–0.9.13)
+User-facing items from the adopted range:
+- **`MCP_HTTP_MAX_BODY_BYTES`** (0.9.13) — configurable inbound request-body cap; oversized requests rejected with `413` before SDK parse. Default 1 MiB; `0` disables.
+- **HTTP session-init gate** (0.9.10) — stateful HTTP mode rejects non-`initialize` requests without `Mcp-Session-Id` with `400`, preventing uninitialized sessions from being minted on first contact.
+- **Quieter 401/403/400/404 logging** (0.9.10) — expected client errors now log at `warning` instead of full error pipeline with stack traces, reducing noise.
+- **`GET /mcp` surfaces `package.json` keywords** (0.9.12) — `server.keywords` included in the HTTP status response alongside `name`, `version`, and `description`.

package/changelog/0.6.x/0.6.4.md ADDED Viewed

@@ -0,0 +1,14 @@
+---
+summary: "Enrichment adoption — brapi_find_* tools now surface filter echoes, result totals, and empty-result guidance via ctx.enrich(); @cyanheads/mcp-ts-core ^0.9.13 → ^0.9.16"
+breaking: false
+security: false
+---
+# 0.6.4 — 2026-05-30
+## Changed
+- **`brapi_find_studies`, `brapi_find_germplasm`, `brapi_find_observations`, `brapi_find_variables`, `brapi_find_images`, `brapi_find_locations`, `brapi_find_variants`, `brapi_find_genotype_calls`** — `returnedCount`, `totalCount`, `appliedFilters`, `refinementHint`, and `warnings` moved from the `output` schema into a typed `enrichment` block via `ctx.enrich()`. Both `structuredContent` (JSON) and the `content[]` markdown trailer receive the enrichment; the domain return type no longer carries these fields. An `enrich.notice()` fires when a tool returns zero rows, surfacing filter-broadening guidance.
+- **`renderFindHeader()`** — `totalCount` is now optional; omitted when the server does not report a total (renders `N <noun>` instead of `N of M <noun>`).
+- **`@cyanheads/mcp-ts-core`** ^0.9.13 → ^0.9.16.
+- **`format:unsafe` script** separated from `format` (`biome check --write` vs `biome check --write --unsafe`).

package/changelog/template.md CHANGED Viewed

@@ -19,6 +19,14 @@ breaking: false
 # `## Security` section below. Flagged as `Security` in the rollup so
 # users can triage upgrade urgency at a glance.
 security: false
+# Optional free-form notes for maintenance agents processing this release.
+# Not rendered in CHANGELOG — consumed by agents running `maintenance` on
+# downstream servers. Use for adoption instructions that don't fit the
+# human-facing sections: new files to create, fields to populate, one-time
+# migration steps. Omit the field entirely when there's nothing to say.
+# agent-notes: |
+#   <instructions for downstream maintenance agents>
 ---
 # <version> — YYYY-MM-DD
@@ -35,7 +43,7 @@ security: false
   name the symbol, state what changed, stop. Use a second sentence only when
   it carries weight. If a bullet feels long, it is.
-  Cut: mechanism walkthroughs (those belong in JSDoc, AGENTS.md, or the
+  Cut: mechanism walkthroughs (those belong in JSDoc, CLAUDE.md/AGENTS.md, or the
   relevant skill), ceremonial framings ("This release introduces…",
   backwards-compat paragraphs), file-by-file test enumerations, internal
   implementation notes. Prefer code/symbol names over English re-explanations.
@@ -66,6 +74,32 @@ security: false
   Never speculate on a future number — `#42` for an upcoming PR silently
   resolves to whatever real item already owns 42, and timeline previews pull
   in that unrelated item's metadata.
+  TAG ANNOTATIONS — the annotated tag body renders as the GitHub Release body
+  via `gh release create --notes-from-tag`. The tag is a derivative of this
+  changelog entry — a condensed, scannable version, not a copy. Format:
+    <theme — omit version number, GitHub prepends it>
+                                                          ← blank line
+    <1-2 sentence context: what this release does>
+                                                          ← blank line
+    Dependency bumps:                                     ← section header
+                                                          ← blank line
+    - `@cyanheads/mcp-ts-core` ^0.9.1 → ^0.9.6          ← bullet
+                                                          ← blank line
+    Changed:                                              ← only sections with entries
+                                                          ← blank line
+    - `format()` output includes `query` in text mode
+                                                          ← blank line
+    Added:
+                                                          ← blank line
+    - `manifest.json` scaffolded for MCPB bundle support
+    - Install badges (Claude Desktop, Cursor, VS Code)
+                                                          ← blank line
+    <N> tests pass; `bun run devcheck` clean.             ← footer
+  Never a flat comma-separated string. Always structured markdown with
+  sections. The tag must scan well as a rendered GitHub Release page.
 -->
 ## Added

package/dist/config/server-config.d.ts CHANGED Viewed

@@ -9,7 +9,7 @@
  */
 import { z } from '@cyanheads/mcp-ts-core';
 export declare const ServerConfigSchema: z.ZodObject<{
-    defaultBaseUrl: z.ZodOptional<z.ZodString>;
+    defaultBaseUrl: z.ZodPreprocess<z.ZodOptional<z.ZodString>>;
     defaultUsername: z.ZodOptional<z.ZodString>;
     defaultPassword: z.ZodOptional<z.ZodString>;
     defaultOauthClientId: z.ZodOptional<z.ZodString>;

package/dist/config/server-config.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"server-config.d.ts","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAG3C,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAqJ7B,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,CA6B9C;AAED,uDAAuD;AACvD,wBAAgB,iBAAiB,IAAI,IAAI,CAExC"}

package/dist/config/server-config.js CHANGED Viewed

@@ -11,9 +11,7 @@ import { z } from '@cyanheads/mcp-ts-core';
 import { parseEnvConfig } from '@cyanheads/mcp-ts-core/config';
 export const ServerConfigSchema = z.object({
     defaultBaseUrl: z
-        .string()
-        .url()
-        .optional()
+        .preprocess((v) => (typeof v === 'string' && /^\$\{/.test(v) ? undefined : v), z.string().url().optional())
         .describe('Default BrAPI v2 base URL if no connection is opened via brapi_connect.'),
     defaultUsername: z
         .string()

package/dist/config/server-config.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/index.js CHANGED Viewed

@@ -103,6 +103,10 @@ await createApp({
         brapiFiltersResource,
     ],
     prompts: [brapiEdaStudy, brapiMetaAnalysis],
+    // Public-catalog deployment: keep landing inventory visible to unauthenticated
+    // visitors even when MCP_AUTH_MODE is jwt/oauth. Framework default (0.9.13+)
+    // gates the inventory behind auth; this override restores the open-catalog UX.
+    landing: { requireAuth: false },
     instructions: 'Bridges BrAPI v2 servers (Breeding API for plant/crop research). Call `brapi_connect` first to register a server under an alias and return the orientation envelope (capabilities, dialect, sample IDs). `brapi_find_*` tools page filtered lookups across studies, germplasm, observations, variables, locations, images, variants, and genotype calls; rows beyond the per-call cap spill to a canvas dataframe — query with `brapi_dataframe_query` (SELECT-only SQL). `brapi_get_*` fetch single records by `*DbId`. Use `brapi_raw_get` / `brapi_raw_search` only when no curated tool fits — responses route back to the right curated tool.',
     setup(core) {
         if (!core.canvas) {

package/dist/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/brapi-connect.tool.d.ts CHANGED Viewed

@@ -99,5 +99,5 @@ export declare const brapiConnect: import("@cyanheads/mcp-ts-core").ToolDefiniti
     readonly code: JsonRpcErrorCode.Forbidden;
     readonly when: "Token endpoint responded but did not return an access_token";
     readonly recovery: "Confirm the credentials are valid and the upstream IdP issues access tokens for this grant.";
-}]>;
+}], undefined>;
 //# sourceMappingURL=brapi-connect.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-connect.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"brapi-connect.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-connect.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqBjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAyFvB,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-dataframe-describe.tool.d.ts CHANGED Viewed

@@ -38,5 +38,5 @@ export declare const brapiDataframeDescribe: import("@cyanheads/mcp-ts-core").To
     readonly code: JsonRpcErrorCode.Forbidden;
     readonly when: "This server is running as a shared HTTP endpoint without per-caller auth — listing every dataframe would expose other concurrent clients' workspaces, since all callers resolve to one shared tenant.";
     readonly recovery: "Pass `dataframe` with a specific name — either from a prior find_* spillover result (`result.dataframe.tableName`) or one you registered via `brapi_dataframe_query` with `registerAs`. Listing all dataframes is not available on this deployment.";
-}]>;
+}], undefined>;
 //# sourceMappingURL=brapi-dataframe-describe.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-dataframe-describe.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"brapi-dataframe-describe.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-describe.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAEjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA6CjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;cAkCjC,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-dataframe-drop.tool.d.ts CHANGED Viewed

@@ -15,5 +15,5 @@ export declare const brapiDataframeDrop: import("@cyanheads/mcp-ts-core").ToolDe
 }, z.core.$strip>, z.ZodObject<{
     dataframe: z.ZodString;
     dropped: z.ZodBoolean;
-}, z.core.$strip>, undefined>;
+}, z.core.$strip>, undefined, undefined>;
 //# sourceMappingURL=brapi-dataframe-drop.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-dataframe-drop.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-dataframe-drop.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-drop.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAmBjD,eAAO,MAAM,kBAAkB;;;;;~~6BAqB7B~~,CAAC"}
1	+ {"version":3,"file":"brapi-dataframe-drop.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-drop.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAmBjD,eAAO,MAAM,kBAAkB;;;;;wCAqB7B,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-dataframe-export.tool.d.ts CHANGED Viewed

@@ -65,5 +65,5 @@ export declare const brapiDataframeExport: import("@cyanheads/mcp-ts-core").Tool
     readonly code: JsonRpcErrorCode.ValidationError;
     readonly when: "Both `columns` and `sql` were supplied";
     readonly recovery: "Pass either `columns` for a thin projection or `sql` for filtering/aggregation, not both.";
-}]>;
+}], undefined>;
 //# sourceMappingURL=brapi-dataframe-export.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-dataframe-export.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"brapi-dataframe-export.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-export.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAIH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAoEjE,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAkH/B,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.d.ts CHANGED Viewed

@@ -42,5 +42,5 @@ export declare const brapiDataframeQuery: import("@cyanheads/mcp-ts-core").ToolD
     readonly code: JsonRpcErrorCode.ValidationError;
     readonly when: "SQL violated read-only rules (multi-statement, non-SELECT, or disallowed operation)";
     readonly recovery: "Submit a single SELECT statement using only registered dataframes. For changes, use `registerAs` in this tool to materialize a result, or brapi_dataframe_drop to remove a dataframe.";
-}]>;
+}], undefined>;
 //# sourceMappingURL=brapi-dataframe-query.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"brapi-dataframe-query.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-query.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;GAuBG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAO/D,OAAO,EAAE,gBAAgB,EAAY,MAAM,+BAA+B,CAAC;AAmH3E,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;cAmE9B,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-describe-filters.tool.d.ts CHANGED Viewed

@@ -37,5 +37,5 @@ export declare const brapiDescribeFilters: import("@cyanheads/mcp-ts-core").Tool
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: "No filter catalog is registered for the requested endpoint";
     readonly recovery: "Pick an endpoint from data.availableEndpoints — same set as the input enum (studies, germplasm, observations, variables, images, variants, locations).";
-}]>;
+}], undefined>;
 //# sourceMappingURL=brapi-describe-filters.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-describe-filters.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"brapi-describe-filters.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-describe-filters.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgBjE,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA2E/B,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.d.ts CHANGED Viewed

@@ -41,8 +41,6 @@ export declare const brapiFindGenotypeCalls: import("@cyanheads/mcp-ts-core").To
         genotypeValue: z.ZodOptional<z.ZodNullable<z.ZodString>>;
         phaseSet: z.ZodOptional<z.ZodNullable<z.ZodString>>;
     }, z.core.$loose>>;
-    returnedCount: z.ZodNumber;
-    totalCount: z.ZodNumber;
     hasMore: z.ZodBoolean;
     callFormatting: z.ZodObject<{
         expandHomozygotes: z.ZodOptional<z.ZodNullable<z.ZodBoolean>>;
@@ -65,8 +63,6 @@ export declare const brapiFindGenotypeCalls: import("@cyanheads/mcp-ts-core").To
         maxRows: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>;
     truncated: z.ZodBoolean;
-    warnings: z.ZodArray<z.ZodString>;
-    searchBody: z.ZodRecord<z.ZodString, z.ZodUnknown>;
 }, z.core.$strip>, readonly [{
     readonly reason: "unknown_alias";
     readonly code: JsonRpcErrorCode.NotFound;
@@ -82,5 +78,11 @@ export declare const brapiFindGenotypeCalls: import("@cyanheads/mcp-ts-core").To
     readonly code: JsonRpcErrorCode.ValidationError;
     readonly when: "The active dialect declares POST /search/calls as known-dead on this server";
     readonly recovery: "Connect to a different BrAPI server that exposes a working /search/calls route — genotype-call workflows are not viable here.";
-}]>;
+}], {
+    readonly totalCount: z.ZodNumber;
+    readonly returnedCount: z.ZodNumber;
+    readonly appliedFilters: z.ZodRecord<z.ZodString, z.ZodUnknown>;
+    readonly notice: z.ZodOptional<z.ZodString>;
+    readonly warnings: z.ZodArray<z.ZodString>;
+}>;
 //# sourceMappingURL=brapi-find-genotype-calls.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"brapi-find-genotype-calls.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkHjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAqQjC,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.js CHANGED Viewed

@@ -54,12 +54,6 @@ const CallRowSchema = z
 const OutputSchema = z.object({
     alias: z.string().describe('Alias of the registered BrAPI connection the call used.'),
     results: z.array(CallRowSchema).describe('Call rows returned in-context (up to loadLimit).'),
-    returnedCount: z.number().int().nonnegative().describe('Length of `results[]`.'),
-    totalCount: z
-        .number()
-        .int()
-        .nonnegative()
-        .describe('Total calls collected across all pages (may be capped by the deployment-wide pull limit; check `truncated`).'),
     hasMore: z
         .boolean()
         .describe('True when the collection was truncated (equivalent to `truncated`).'),
@@ -100,10 +94,6 @@ const OutputSchema = z.object({
     truncated: z
         .boolean()
         .describe('True when the deployment-wide pull limit was reached and more calls exist upstream. Narrow the filters and re-pull, or query the spilled dataframe.'),
-    warnings: z
-        .array(z.string())
-        .describe('Advisory messages (truncation, capability gaps, partial pulls).'),
-    searchBody: z.record(z.string(), z.unknown()).describe('The body sent to /search/calls.'),
 });
 export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
     description: 'Pull genotype calls for a germplasm × variant set. Filter to bound cost — at minimum, set `variantSetDbId` or `germplasmDbIds`. The upstream pull is capped by deployment policy; when the pull is truncated, narrow the filters or query the spilled dataframe. `loadLimit` bounds the rows returned inline; the full collected set is materialized as a dataframe — query it with brapi_dataframe_query (SQL) instead of paging row-by-row.',
@@ -157,6 +147,47 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
             .describe('Cap on rows returned inline. Omit for the deployment default. When the collected set exceeds this, the full result lands in a dataframe and only the first `loadLimit` rows return inline — query the dataframe with brapi_dataframe_query (SQL) for the rest. Upstream pageSize is fixed for genotype calls, so this knob only affects the inline preview here (no spillover capacity tradeoff).'),
     }),
     output: OutputSchema,
+    // Agent-facing success-path context: total collected count, in-context count,
+    // the exact body sent to /search/calls, empty-result guidance, and advisory
+    // warnings. Populated via ctx.enrich() so it reaches both structuredContent
+    // and the content[] trailer without living in the domain return.
+    enrichment: {
+        totalCount: z
+            .number()
+            .int()
+            .nonnegative()
+            .describe('Total calls collected across all pages (may be capped by the deployment-wide pull limit; check `truncated`).'),
+        returnedCount: z
+            .number()
+            .int()
+            .nonnegative()
+            .describe('Length of results[] — rows returned in-context (up to loadLimit).'),
+        appliedFilters: z
+            .record(z.string(), z.unknown())
+            .describe('The body sent to POST /search/calls (variant/germplasm/call-set scope plus pageSize).'),
+        notice: z
+            .string()
+            .optional()
+            .describe('Guidance when no calls were returned — how to broaden filters or verify IDs.'),
+        warnings: z
+            .array(z.string())
+            .describe('Advisory messages (truncation, capability gaps, partial pulls).'),
+    },
+    enrichmentTrailer: {
+        appliedFilters: {
+            render: (filters) => {
+                const entries = Object.entries(filters);
+                if (entries.length === 0)
+                    return '**Search body:** none';
+                const lines = entries.map(([k, v]) => `- **${k}:** ${Array.isArray(v) ? v.join(', ') : String(v)}`);
+                return `**Search body:**\n${lines.join('\n')}`;
+            },
+        },
+        warnings: {
+            render: (ws) => (ws.length > 0 ? ws.map((w) => `- ${w}`).join('\n') : '_none_'),
+            label: 'Warnings',
+        },
+    },
     async handler(input, ctx) {
         const capabilities = getCapabilityRegistry();
         const client = getBrapiClient();
@@ -195,9 +226,6 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
             variantName: computeDistribution(collected.rows, (r) => asString(r.variantName)),
             variantSetDbId: computeDistribution(collected.rows, (r) => asString(r.variantSetDbId)),
         };
-        if (collected.rows.length === 0) {
-            warnings.push('Upstream returned 0 calls for the requested filters. The variant set or filter combination may not match any data on this server.');
-        }
         const shouldSpill = collected.rows.length > loadLimit;
         let dataframeHandle;
         if (shouldSpill) {
@@ -211,17 +239,21 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
                 maxRows: maxCalls,
             });
         }
+        ctx.enrich({
+            totalCount: collected.rows.length,
+            returnedCount: inContext.length,
+            appliedFilters: searchBody,
+            warnings,
+        });
+        if (collected.rows.length === 0)
+            ctx.enrich.notice('No calls matched the requested filters. The variant set or filter combination may not match any data on this server — broaden the scope (variantSetDbId, germplasmDbIds) or verify the IDs.');
         const result = {
             alias: connection.alias,
             results: inContext,
-            returnedCount: inContext.length,
-            totalCount: collected.rows.length,
             hasMore: collected.truncated,
             callFormatting: collected.callFormatting,
             distributions,
             truncated: collected.truncated,
-            warnings,
-            searchBody,
         };
         if (dataframeHandle)
             result.dataframe = dataframeHandle;
@@ -232,14 +264,11 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
         const headerBase = renderFindHeader({
             noun: 'calls',
             alias: result.alias,
-            returnedCount: result.returnedCount,
-            totalCount: result.totalCount,
+            returnedCount: result.results.length,
             dataframe: result.dataframe,
         });
         lines.push(result.truncated ? `${headerBase} (truncated at deployment pull limit)` : headerBase);
         lines.push('');
-        lines.push(`Search body: \`${JSON.stringify(result.searchBody)}\``);
-        lines.push('');
         lines.push('## Call formatting');
         const f = result.callFormatting;
         lines.push(`- expandHomozygotes: ${f.expandHomozygotes ?? '—'}`);
@@ -290,12 +319,6 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
             lines.push('## Dataframe handle');
             lines.push(...renderDataframeHandle(result.dataframe));
         }
-        if (result.warnings.length > 0) {
-            lines.push('');
-            lines.push('## Warnings');
-            for (const w of result.warnings)
-                lines.push(`- ${w}`);
-        }
         return [{ type: 'text', text: lines.join('\n') }];
     },
 });

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	@@ -1 +1 @@
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