npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.7.11 → 0.7.13 - Mend

@cyanheads/brapi-mcp-server 0.7.11 → 0.7.13

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 (135) hide show

package/changelog/0.7.x/0.7.12.md ADDED Viewed

@@ -0,0 +1,35 @@
+---
+summary: "Adopts @cyanheads/mcp-ts-core ^0.13.0: empty and unsubstituted ${…} env values read as unset across every BRAPI_* path, async-search cancellation and poll deadlines classify as RequestCancelled and Timeout, and the framework skill tree moves out of the plugin-loaded skills/ directory."
+breaking: false
+security: false
+---
+# 0.7.12 — 2026-09-13
+A framework-adoption release; this server changes no tool contract of its own.
+## Changed
+- **Plugin manifests declare their user config** — `.claude-plugin/plugin.json` gains a `userConfig` block, and it and `manifest.json` reference every option as `${user_config.<key>}`; `.codex-plugin/mcp.json` forwards `BRAPI_DEFAULT_BASE_URL` through `env_vars` rather than setting it to an empty string, which would replace a value the operator exported (mcp-ts-core 0.13.0).
+- **Tool argument rejections classify as `InvalidParams` (-32602)** instead of `ValidationError`, carrying the same structured error envelope and message text (mcp-ts-core 0.12.7).
+- **HTTP transport** — a trailing slash on `MCP_PUBLIC_URL` no longer doubles in advertised links (mcp-ts-core 0.12.8); the landing page's curl snippet sends a handshake `initialize` accepts, and a cancelled request's SSE stream closes immediately rather than at keep-alive (mcp-ts-core 0.12.9).
+- **`MCP_RESPONSE_VERBOSITY` and `OAUTH_PROXY_*` are no longer recognized** by framework config (mcp-ts-core 0.12.8). Neither is set by this server's Docker image or `.env.example`.
+- **Records logged from `setup()` survive startup** — buffered and replayed once the logger initializes, or drained to stderr when startup fails, instead of dropped (mcp-ts-core 0.12.5).
+- **The framework skill tree moved from `skills/` to `framework-skills/`** — plugin hosts auto-load a root `skills/`, which handed this server's development skills to every installing agent. `.mcpbignore`, the agent protocol, and `docs/tree.md` follow the path; no runtime surface changed (mcp-ts-core 0.13.0).
+- **Bun engines floor raised to `>=1.4.0`** (mcp-ts-core 0.12.9), and `audit:fix` runs `bun audit fix` — the previous script ran a read-only audit and changed nothing (mcp-ts-core 0.13.0).
+## Fixed
+- **An unsubstituted `${…}` env value no longer registers a phantom alias or fails URL validation** — `BRAPI_<ALIAS>_*` credentials and the `BRAPI_*` server config both read empty strings and whole-value placeholders as unset through `parseEnvConfig`, so a builtin alias is no longer shadowed by its own unfilled placeholder. A URL containing a literal `${…}` segment is still preserved (mcp-ts-core 0.13.0).
+- **A cancelled async search throws `RequestCancelled` (-32011) and an exhausted poll deadline throws `Timeout`** — they were `InternalError` and `ServiceUnavailable`. Neither issues a further poll, and both the `structuredContent.error` envelope and the `content[]` trailer carry the same message.
+- **An upstream 500 reaches the client's reclassifier again** — no HTTP status maps to `InternalError` now, so a singleton `GET` that an upstream answers 500 for an unknown DbId maps to `NotFound` without retrying, an ordinary 500 retries, and a 501 carries `data.retryable: false` so an unimplemented method is not retried (mcp-ts-core 0.12.4).
+## Dependencies
+- `@cyanheads/mcp-ts-core` ^0.12.3 → ^0.13.0
+- `zod` ^4.4.3 → ^4.6.1
+- `@biomejs/biome` ^2.5.9 → ^2.5.13
+- `@types/node` ^26.2.0 → ^26.5.1
+- `ignore` ^7.0.6 → ^7.0.9
+- `tsc-alias` ^1.9.2 → ^1.9.4
+- `vitest` ^4.1.11 → ^5.0.0

package/changelog/0.7.x/0.7.13.md ADDED Viewed

@@ -0,0 +1,38 @@
+---
+summary: "Declares stateful session mode in src/index.ts so an HTTP start under MCP_SESSION_MODE=stateless fails at startup instead of serving a mode the observation-write confirmation round trip cannot use, fixes a ReDoS and a prototype-pollution gap in mcp-ts-core 0.13.1-0.13.6, and lists the hosted endpoint in server.json."
+breaking: false
+security: true
+---
+# 0.7.13 — 2026-09-19
+## Added
+- **`server.json` lists the hosted endpoint** — `https://brapi.caseyjhand.com/mcp` is now a `streamable-http` remote; the README already documented the public instance.
+## Changed
+- **Session mode declared in `src/index.ts`** (`sessionMode: { default: 'stateful', require: 'stateful' }`). An HTTP start with `MCP_SESSION_MODE` unset still serves `stateful`; an HTTP start with `MCP_SESSION_MODE=stateless` now fails at startup with a `ConfigurationError` naming the conflicting value, instead of serving a mode under which the `brapi_submit_observations` confirmation round trip cannot be answered by a 2025-era client. stdio starts are never refused. The Docker image, the README env row, and `.env.example` already pinned `stateful`; `.env.example` now sets the line actively rather than as a comment (mcp-ts-core 0.13.1).
+- **Tool error text** — `content[]` for a tool error now closes with `(reason <reason>)`, plus ` · not retryable` when `data.retryable` is `false`; `structuredContent` is unchanged (mcp-ts-core 0.13.5, [cyanheads/mcp-ts-core#458](https://github.com/cyanheads/mcp-ts-core/issues/458)).
+- **Argument rejections** carry `data.reason: "invalid_arguments"` and a `Recovery:` hint naming the keys the tool accepts; an omitted required enum field now renders as missing rather than as a wrong choice (mcp-ts-core 0.13.3, [cyanheads/mcp-ts-core#445](https://github.com/cyanheads/mcp-ts-core/issues/445), [#378](https://github.com/cyanheads/mcp-ts-core/issues/378)).
+- **Advertised `outputSchema`** — the `error.data.reason` description now terminates each declared entry with a period; the only `tools/list` difference from 0.7.12 (mcp-ts-core 0.13.5, [cyanheads/mcp-ts-core#389](https://github.com/cyanheads/mcp-ts-core/issues/389)).
+- **Repo tooling** — 33 `errors[]` entries gain `thrownBy: 'service'` (lint-only metadata; entries stay advertised and thrown identically); `.github/CODE_OF_CONDUCT.md` and `.github/workflows/codeql.yml` added; `package.json` gains `funding` and ships `AGENTS.md`; `.codex-plugin` category set to `research`; `devcheck.config.json` gains the template's `outdated`/`lint` keys; `.env.example` documents the resumability, GC-pressure, and log-rate-limit vars (mcp-ts-core 0.13.6).
+## Fixed
+- **`SIGTERM`/`SIGINT` end the process explicitly**, exiting 0 once shutdown settles (mcp-ts-core 0.13.1, [cyanheads/mcp-ts-core#435](https://github.com/cyanheads/mcp-ts-core/issues/435)).
+- **`brapi-client`'s upstream requests** now pass the per-attempt signal `withRetry` hands each attempt into the fetch call. With no retry deadline configured that signal is still the caller signal, as before — this still aborts on caller cancellation (mcp-ts-core 0.13.4, [cyanheads/mcp-ts-core#455](https://github.com/cyanheads/mcp-ts-core/issues/455)).
+## Security
+- **The SQL comment stripper the canvas read-only gate runs over every `brapi_dataframe_query` statement is a linear-time scan instead of a polynomial-time regex**, so a crafted query can no longer pin the event loop (mcp-ts-core 0.13.1, [cyanheads/mcp-ts-core#431](https://github.com/cyanheads/mcp-ts-core/issues/431)).
+- **Tool-argument copying can no longer be re-prototyped by a caller's own `__proto__` key** (mcp-ts-core 0.13.4).
+## Dependencies
+- `@cyanheads/mcp-ts-core` ^0.13.0 → ^0.13.6
+- `@duckdb/node-api` ^1.5.5-r.4 → ^1.5.5-r.5
+- `zod` ^4.6.1 → ^4.6.5
+- `@biomejs/biome` ^2.5.13 → ^2.5.14
+- `tsc-alias` ^1.9.4 → ^1.9.5
+- `vitest` ^5.0.0 → ^5.0.1

package/changelog/template.md CHANGED Viewed

@@ -6,8 +6,8 @@
 # Required. One-line GitHub Release-style headline. 350 character cap — a
 # ceiling, not a target. Default short and scannable. Don't pad, don't stitch
-# unrelated changes with commas/semicolons into an inventory — pick the
-# headline, like a tag's theme line. Quotes required: unquoted YAML treats
+# unrelated changes with commas/semicolons into an inventory — pick the one
+# headline the release is about. Quotes required: unquoted YAML treats
 # `: ` inside the value as a key separator and fails GitHub's strict parser.
 summary: ""
@@ -117,30 +117,13 @@ security: false
   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.
+  via `gh release create --notes-from-tag`. It is a condensed digest of this
+  entry, never a copy, and its format is owned by the `release-and-publish`
+  skill (step 4, "Create the annotated tag"): a short subject line without the
+  version, flat headline bullets — no Keep-a-Changelog section headers, no
+  gates line — at most one deps line, issue backlinks, and the changelog link
+  last. In release-PR mode the `git-wrapup` skill authors those bullets as the
+  PR body's `## Changes` and the tag copies them.
 -->
 ## Added

package/dist/config/alias-credentials.d.ts CHANGED Viewed

@@ -26,7 +26,7 @@ export interface AliasCredentials {
 }
 /** Compute the env-var prefix for an alias. `my-server` → `BRAPI_MY_SERVER_`. */
 export declare function aliasEnvPrefix(alias: string): string;
-/** Read all `BRAPI_<ALIAS>_*` vars for an alias. Empty strings treated as unset. */
+/** Read alias env vars; empty strings and whole-value host placeholders are unset. */
 export declare function readAliasCredentials(alias: string, env?: NodeJS.ProcessEnv): AliasCredentials;
 /**
  * Pick a `ConnectAuth` from the credential bundle. Returns `undefined` when no

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package/dist/config/alias-credentials.js CHANGED Viewed

@@ -8,8 +8,10 @@
  *
  * @module config/alias-credentials
  */
+import { z } from '@cyanheads/mcp-ts-core';
+import { parseEnvConfig } from '@cyanheads/mcp-ts-core/config';
 import { validationError } from '@cyanheads/mcp-ts-core/errors';
-import { findBuiltinAlias, listBuiltinAliases } from '../config/builtin-aliases.js';
+import { findBuiltinAlias, listBuiltinAliases } from './builtin-aliases.js';
 const FIELD_SUFFIXES = [
     ['baseUrl', 'BASE_URL'],
     ['username', 'USERNAME'],
@@ -21,19 +23,31 @@ const FIELD_SUFFIXES = [
     ['oauthClientSecret', 'OAUTH_CLIENT_SECRET'],
     ['oauthTokenUrl', 'OAUTH_TOKEN_URL'],
 ];
+const AliasCredentialsSchema = z.object({
+    baseUrl: z.string().optional(),
+    username: z.string().optional(),
+    password: z.string().optional(),
+    apiKey: z.string().optional(),
+    apiKeyHeader: z.string().optional(),
+    bearerToken: z.string().optional(),
+    oauthClientId: z.string().optional(),
+    oauthClientSecret: z.string().optional(),
+    oauthTokenUrl: z.string().optional(),
+});
 const DEFAULT_ALIAS = 'default';
 const NONE_AUTH = { mode: 'none' };
 /** Compute the env-var prefix for an alias. `my-server` → `BRAPI_MY_SERVER_`. */
 export function aliasEnvPrefix(alias) {
     return `BRAPI_${alias.replace(/-/g, '_').toUpperCase()}_`;
 }
-/** Read all `BRAPI_<ALIAS>_*` vars for an alias. Empty strings treated as unset. */
+/** Read alias env vars; empty strings and whole-value host placeholders are unset. */
 export function readAliasCredentials(alias, env = process.env) {
     const prefix = aliasEnvPrefix(alias);
+    const parsed = parseEnvConfig(AliasCredentialsSchema, Object.fromEntries(FIELD_SUFFIXES.map(([field, suffix]) => [field, `${prefix}${suffix}`])), env);
     const result = {};
-    for (const [field, suffix] of FIELD_SUFFIXES) {
-        const value = env[`${prefix}${suffix}`];
-        if (value !== undefined && value !== '')
+    for (const [field] of FIELD_SUFFIXES) {
+        const value = parsed[field];
+        if (value !== undefined)
             result[field] = value;
     }
     return result;
@@ -136,18 +150,20 @@ export function discoverConfiguredAliases(env = process.env) {
     // the underscored form. Without this map, an env var that shadows a
     // hyphenated builtin would be reported as a separate `bti_cassava` alias.
     const builtinByUnderscoredName = new Map(builtins.map((b) => [b.alias.replace(/-/g, '_'), b]));
-    for (const [key, value] of Object.entries(env)) {
+    for (const key of Object.keys(env)) {
         const match = key.match(ALIAS_BASE_URL_PATTERN);
         const captured = match?.[1];
-        if (!captured || !value)
+        if (!captured)
             continue;
         const lowerCaptured = captured.toLowerCase();
         const alias = builtinByUnderscoredName.get(lowerCaptured)?.alias ?? lowerCaptured;
         const creds = readAliasCredentials(alias, env);
+        if (!creds.baseUrl)
+            continue;
         result.push({
             alias,
             authMode: deriveModeForDiscovery(creds, alias),
-            baseUrl: value,
+            baseUrl: creds.baseUrl,
             origin: 'env',
         });
         seen.add(alias);

package/dist/config/alias-credentials.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ {"version":3,"file":"alias-credentials.js","sourceRoot":"","sources":["../../src/config/alias-credentials.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,EAAE,cAAc,EAAE,MAAM,+BAA+B,CAAC;AAC/D,OAAO,EAAE,eAAe,EAAE,MAAM,+BAA+B,CAAC;AAChE,OAAO,EAAE,gBAAgB,EAAE,kBAAkB,EAAE,MAAM,6BAA6B,CAAC;AAmBnF,MAAM,cAAc,GAA6D;IAC/E,CAAC,SAAS,EAAE,UAAU,CAAC;IACvB,CAAC,UAAU,EAAE,UAAU,CAAC;IACxB,CAAC,UAAU,EAAE,UAAU,CAAC;IACxB,CAAC,QAAQ,EAAE,SAAS,CAAC;IACrB,CAAC,cAAc,EAAE,gBAAgB,CAAC;IAClC,CAAC,aAAa,EAAE,cAAc,CAAC;IAC/B,CAAC,eAAe,EAAE,iBAAiB,CAAC;IACpC,CAAC,mBAAmB,EAAE,qBAAqB,CAAC;IAC5C,CAAC,eAAe,EAAE,iBAAiB,CAAC;CACrC,CAAC;AAEF,MAAM,sBAAsB,GAAG,CAAC,CAAC,MAAM,CAAC;IACtC,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE;IAC9B,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE;IAC/B,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE;IAC/B,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE;IAC7B,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE;IACnC,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE;IAClC,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE;IACpC,iBAAiB,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE;IACxC,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE;CACrC,CAAC,CAAC;AAEH,MAAM,aAAa,GAAG,SAAS,CAAC;AAChC,MAAM,SAAS,GAAgB,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC;AAEhD,iFAAiF;AACjF,MAAM,UAAU,cAAc,CAAC,KAAa;IAC1C,OAAO,SAAS,KAAK,CAAC,OAAO,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,WAAW,EAAE,GAAG,CAAC;AAC5D,CAAC;AAED,sFAAsF;AACtF,MAAM,UAAU,oBAAoB,CAClC,KAAa,EACb,GAAG,GAAsB,OAAO,CAAC,GAAG;IAEpC,MAAM,MAAM,GAAG,cAAc,CAAC,KAAK,CAAC,CAAC;IACrC,MAAM,MAAM,GAAG,cAAc,CAC3B,sBAAsB,EACtB,MAAM,CAAC,WAAW,CAAC,cAAc,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC,KAAK,EAAE,GAAG,MAAM,GAAG,MAAM,EAAE,CAAC,CAAC,CAAC,EAC1F,GAAG,CACJ,CAAC;IACF,MAAM,MAAM,GAAqB,EAAE,CAAC;IACpC,KAAK,MAAM,CAAC,KAAK,CAAC,IAAI,cAAc,EAAE,CAAC;QACrC,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC;QAC5B,IAAI,KAAK,KAAK,SAAS;YAAE,MAAM,CAAC,KAAK,CAAC,GAAG,KAAK,CAAC;IACjD,CAAC;IACD,OAAO,MAAM,CAAC;AAChB,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,yBAAyB,CACvC,KAAuB,EACvB,KAAa;IAEb,MAAM,QAAQ,GAA8C;QAC1D,EAAE,IAAI,EAAE,yBAAyB,EAAE,OAAO,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,QAAQ,IAAI,KAAK,CAAC,QAAQ,CAAC,EAAE;QAClF,EAAE,IAAI,EAAE,sBAAsB,EAAE,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,WAAW,EAAE;QAC9D,EAAE,IAAI,EAAE,kBAAkB,EAAE,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,MAAM,EAAE;QACrD;YACE,IAAI,EAAE,0CAA0C;YAChD,OAAO,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,aAAa,IAAI,KAAK,CAAC,iBAAiB,CAAC;SAC5D;KACF,CAAC;IACF,MAAM,OAAO,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;IACrE,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO;IACjC,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACvB,MAAM,eAAe,CACnB,oCAAoC,KAAK,wCAAwC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,kDAAkD,EACrJ,EAAE,KAAK,EAAE,OAAO,EAAE,CACnB,CAAC;IACJ,CAAC;IACD,IAAI,KAAK,CAAC,QAAQ,IAAI,KAAK,CAAC,QAAQ,EAAE,CAAC;QACrC,OAAO,EAAE,IAAI,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,CAAC,QAAQ,EAAE,QAAQ,EAAE,KAAK,CAAC,QAAQ,EAAE,CAAC;IAC7E,CAAC;IACD,IAAI,KAAK,CAAC,WAAW,EAAE,CAAC;QACtB,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,KAAK,EAAE,KAAK,CAAC,WAAW,EAAE,CAAC;IACtD,CAAC;IACD,IAAI,KAAK,CAAC,MAAM,EAAE,CAAC;QACjB,OAAO,KAAK,CAAC,YAAY;YACvB,CAAC,CAAC,EAAE,IAAI,EAAE,SAAS,EAAE,MAAM,EAAE,KAAK,CAAC,MAAM,EAAE,UAAU,EAAE,KAAK,CAAC,YAAY,EAAE;YAC3E,CAAC,CAAC,EAAE,IAAI,EAAE,SAAS,EAAE,MAAM,EAAE,KAAK,CAAC,MAAM,EAAE,CAAC;IAChD,CAAC;IACD,IAAI,KAAK,CAAC,aAAa,IAAI,KAAK,CAAC,iBAAiB,EAAE,CAAC;QACnD,OAAO,KAAK,CAAC,aAAa;YACxB,CAAC,CAAC;gBACE,IAAI,EAAE,QAAQ;gBACd,QAAQ,EAAE,KAAK,CAAC,aAAa;gBAC7B,YAAY,EAAE,KAAK,CAAC,iBAAiB;gBACrC,QAAQ,EAAE,KAAK,CAAC,aAAa;aAC9B;YACH,CAAC,CAAC,EAAE,IAAI,EAAE,QAAQ,EAAE,QAAQ,EAAE,KAAK,CAAC,aAAa,EAAE,YAAY,EAAE,KAAK,CAAC,iBAAiB,EAAE,CAAC;IAC/F,CAAC;IACD,OAAO;AACT,CAAC;AAOD;;;;;;;;;;;;;;;;GAgBG;AACH,MAAM,UAAU,mBAAmB,CACjC,KAAa,EACb,KAAuE,EACvE,GAAG,GAAsB,OAAO,CAAC,GAAG;IAEpC,MAAM,UAAU,GAAG,oBAAoB,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;IACpD,MAAM,YAAY,GAChB,KAAK,KAAK,aAAa,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,oBAAoB,CAAC,aAAa,EAAE,GAAG,CAAC,CAAC;IAElF,MAAM,OAAO,GAAG,CAAC,KAAK,CAAC,OAAO,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC,CAAC,CAAC,gBAAgB,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC;IACjG,MAAM,OAAO,GAAG,KAAK,CAAC,OAAO,IAAI,UAAU,CAAC,OAAO,IAAI,OAAO,EAAE,OAAO,IAAI,YAAY,CAAC,OAAO,CAAC;IAChG,IAAI,CAAC,OAAO,EAAE,CAAC;QACb,MAAM,eAAe,CACnB,4DAA4D,cAAc,CAAC,KAAK,CAAC,WAAW,KAAK,KAAK,aAAa,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,cAAc,CAAC,aAAa,CAAC,UAAU,GAAG,EAC5K,EAAE,KAAK,EAAE,CACV,CAAC;IACJ,CAAC;IAED,MAAM,wBAAwB,GAAG,CAAC,OAAO,IAAI,KAAK,KAAK,aAAa,CAAC;IACrE,MAAM,IAAI,GACR,KAAK,CAAC,IAAI;QACV,yBAAyB,CAAC,UAAU,EAAE,KAAK,CAAC;QAC5C,CAAC,wBAAwB;YACvB,CAAC,CAAC,yBAAyB,CAAC,YAAY,EAAE,aAAa,CAAC;YACxD,CAAC,CAAC,SAAS,CAAC;QACd,SAAS,CAAC;IAEZ,OAAO,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC;AAC3B,CAAC;AAgBD,MAAM,sBAAsB,GAAG,+BAA+B,CAAC;AAE/D;;;;;;;;;GASG;AACH,MAAM,UAAU,yBAAyB,CAAC,GAAG,GAAsB,OAAO,CAAC,GAAG;IAC5E,MAAM,MAAM,GAAsB,EAAE,CAAC;IACrC,MAAM,IAAI,GAAG,IAAI,GAAG,EAAU,CAAC;IAC/B,MAAM,QAAQ,GAAG,kBAAkB,CAAC,GAAG,CAAC,CAAC;IACzC,2EAA2E;IAC3E,2EAA2E;IAC3E,oEAAoE;IACpE,0EAA0E;IAC1E,MAAM,wBAAwB,GAAG,IAAI,GAAG,CAAC,QAA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package/dist/config/server-config.d.ts CHANGED Viewed

@@ -27,7 +27,7 @@ export declare const GENOTYPE_CALLS_MAX_PULL_CEILING = 500000;
  */
 export declare const GENOTYPE_MATRIX_MAX_COLUMNS_CEILING = 500000;
 export declare const ServerConfigSchema: z.ZodObject<{
-    defaultBaseUrl: z.ZodPreprocess<z.ZodOptional<z.ZodString>>;
+    defaultBaseUrl: 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 @@
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;;;;;;GAMG;AACH,eAAO,MAAM,+BAA+B,SAAU,CAAC;AAEvD;;;;;;;;GAQG;AACH,eAAO,MAAM,mCAAmC,SAAU,CAAC;AAE3D,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~iBAkK7B~~,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,CA+B9C;AAED,uDAAuD;AACvD,wBAAgB,iBAAiB,IAAI,IAAI,CAExC"}
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;;;;;;GAMG;AACH,eAAO,MAAM,+BAA+B,SAAU,CAAC;AAEvD;;;;;;;;GAQG;AACH,eAAO,MAAM,mCAAmC,SAAU,CAAC;AAE3D,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAiK7B,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,CA+B9C;AAED,uDAAuD;AACvD,wBAAgB,iBAAiB,IAAI,IAAI,CAExC"}

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

@@ -29,7 +29,9 @@ export const GENOTYPE_CALLS_MAX_PULL_CEILING = 500_000;
 export const GENOTYPE_MATRIX_MAX_COLUMNS_CEILING = 500_000;
 export const ServerConfigSchema = z.object({
     defaultBaseUrl: z
-        .preprocess((v) => (typeof v === 'string' && /^\$\{/.test(v) ? undefined : v), z.string().url().optional())
+        .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

@@ -97,6 +97,13 @@ const tools = [
 await createApp({
     name: 'brapi-mcp-server',
     title: 'brapi-mcp-server',
+    // `brapi_submit_observations` gates apply-mode writes on a `ctx.requestInput`
+    // confirmation round trip, which a 2025-era HTTP client can only answer on a
+    // durable session — and per-session isolation keys off `ctx.sessionId`. Declare
+    // the posture here rather than leaving it to the env: `require` fails startup
+    // with a ConfigurationError if MCP_SESSION_MODE resolves HTTP to `stateless`,
+    // instead of silently degrading the write path. Never refuses a stdio start.
+    sessionMode: { default: 'stateful', require: 'stateful' },
     tools,
     resources: [
         brapiServerInfoResource,

package/dist/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/resources/definitions/brapi-calls.resource.d.ts CHANGED Viewed

@@ -13,5 +13,6 @@ export declare const brapiCallsResource: import("@cyanheads/mcp-ts-core").Resour
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: 'No default BrAPI connection has been registered';
     readonly recovery: 'Call brapi_connect (without an alias, or with alias `default`) before reading this resource.';
+    readonly thrownBy: 'service';
 }]>;
 //# sourceMappingURL=brapi-calls.resource.d.ts.map

package/dist/mcp-server/resources/definitions/brapi-calls.resource.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-calls.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-calls.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAGH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAoBjE,eAAO,MAAM,kBAAkB;;;qBAQjB,eAAe;;mBAEjB,iDAAiD;uBAErD,8FAA8F;~~GAepG~~,CAAC"}
1	+ {"version":3,"file":"brapi-calls.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-calls.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAGH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAoBjE,eAAO,MAAM,kBAAkB;;;qBAQjB,eAAe;;mBAEjB,iDAAiD;uBAErD,8FAA8F;uBACtF,SAAS;GAevB,CAAC"}

package/dist/mcp-server/resources/definitions/brapi-calls.resource.js CHANGED Viewed

@@ -7,7 +7,7 @@
  */
 import { resource } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
-import { requireRegisteredConnection } from '../../../mcp-server/tools/shared/find-helpers.js';
+import { requireRegisteredConnection } from '../../tools/shared/find-helpers.js';
 import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
 async function loadCallsProfile(ctx) {
     const capabilities = getCapabilityRegistry();
@@ -36,6 +36,7 @@ export const brapiCallsResource = resource('brapi://calls', {
             code: JsonRpcErrorCode.NotFound,
             when: 'No default BrAPI connection has been registered',
             recovery: 'Call brapi_connect (without an alias, or with alias `default`) before reading this resource.',
+            thrownBy: 'service',
         },
     ],
     handler(_params, ctx) {

package/dist/mcp-server/resources/definitions/brapi-calls.resource.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"brapi-calls.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-calls.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAuB,QAAQ,EAAE,MAAM,wBAAwB,CAAC;AACvE,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,2BAA2B,EAAE,MAAM,2CAA2C,CAAC;AACxF,OAAO,EAAE,qBAAqB,EAAE,MAAM,yCAAyC,CAAC;AAEhF,KAAK,UAAU,gBAAgB,CAAC,GAAoC;IAClE,MAAM,YAAY,GAAG,qBAAqB,EAAE,CAAC;IAC7C,MAAM,UAAU,GAAG,MAAM,2BAA2B,CAAC,GAAG,EAAE,SAAS,CAAC,CAAC;IACrE,MAAM,MAAM,GAA8C,EAAE,CAAC;IAC7D,IAAI,UAAU,CAAC,YAAY;QAAE,MAAM,CAAC,IAAI,GAAG,UAAU,CAAC,YAAY,CAAC;IACnE,MAAM,OAAO,GAAG,MAAM,YAAY,CAAC,OAAO,CAAC,UAAU,CAAC,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,CAAC;IAC5E,OAAO;QACL,KAAK,EAAE,UAAU,CAAC,KAAK;QACvB,OAAO,EAAE,UAAU,CAAC,OAAO;QAC3B,MAAM,EAAE,OAAO,CAAC,MAAM;QACtB,KAAK,EAAE,OAAO,CAAC,KAAK;QACpB,SAAS,EAAE,OAAO,CAAC,SAAS;QAC5B,SAAS,EAAE,OAAO,CAAC,SAAS;KAC7B,CAAC;AACJ,CAAC;AAED,MAAM,CAAC,MAAM,kBAAkB,GAAG,QAAQ,CAAC,eAAe,EAAE;IAC1D,IAAI,EAAE,aAAa;IACnB,KAAK,EAAE,0BAA0B;IACjC,WAAW,EACT,+LAA+L;IACjM,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE;QACN;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,iDAAiD;YACvD,QAAQ,EACN,8FAA8F;YAChG,QAAQ,EAAE,SAAS;SACpB;KACO;IACV,OAAO,CAAC,OAAO,EAAE,GAAG;QAClB,OAAO,gBAAgB,CAAC,GAAG,CAAC,CAAC;IAC/B,CAAC;IACD,IAAI,EAAE,GAAG,EAAE,CAAC,CAAC;QACX,SAAS,EAAE;YACT;gBACE,GAAG,EAAE,eAAe;gBACpB,IAAI,EAAE,0BAA0B;gBAChC,QAAQ,EAAE,kBAAkB;aAC7B;SACF;KACF,CAAC;CACH,CAAC,CAAC"}

package/dist/mcp-server/resources/definitions/brapi-filters.resource.js CHANGED Viewed

@@ -8,7 +8,7 @@
  */
 import { resource, z } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
-import { brapiDescribeFilters } from '../../../mcp-server/tools/definitions/brapi-describe-filters.tool.js';
+import { brapiDescribeFilters } from '../../tools/definitions/brapi-describe-filters.tool.js';
 import { listFilterEndpoints } from '../../../services/brapi-filters/index.js';
 const ENDPOINTS = listFilterEndpoints();
 export const brapiFiltersResource = resource('brapi://filters/{endpoint}', {

package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.d.ts CHANGED Viewed

@@ -14,6 +14,7 @@ export declare const brapiGermplasmResource: import("@cyanheads/mcp-ts-core").Re
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: 'No default BrAPI connection has been registered';
     readonly recovery: 'Call brapi_connect (without an alias, or with alias `default`) before reading this resource.';
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'germplasm_not_found';
     readonly code: JsonRpcErrorCode.NotFound;

package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-germplasm.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-germplasm.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,sBAAsB;;;qBAQrB,eAAe;;mBAEjB,iDAAiD;uBAErD,8FAA8F;;~~qBAGxF~~,qBAAqB;;mBAEvB,8DAA8D;uBAElE,mGAAmG;GAezG,CAAC"}
1	+ {"version":3,"file":"brapi-germplasm.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-germplasm.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,sBAAsB;;;qBAQrB,eAAe;;mBAEjB,iDAAiD;uBAErD,8FAA8F;uBACtF,SAAS;;qBAGX,qBAAqB;;mBAEvB,8DAA8D;uBAElE,mGAAmG;GAezG,CAAC"}

package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.js CHANGED Viewed

@@ -7,7 +7,7 @@
  */
 import { resource, z } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
-import { brapiGetGermplasm } from '../../../mcp-server/tools/definitions/brapi-get-germplasm.tool.js';
+import { brapiGetGermplasm } from '../../tools/definitions/brapi-get-germplasm.tool.js';
 export const brapiGermplasmResource = resource('brapi://germplasm/{germplasmDbId}', {
     name: 'brapi-germplasm',
     title: 'BrAPI germplasm record',
@@ -19,6 +19,7 @@ export const brapiGermplasmResource = resource('brapi://germplasm/{germplasmDbId
             code: JsonRpcErrorCode.NotFound,
             when: 'No default BrAPI connection has been registered',
             recovery: 'Call brapi_connect (without an alias, or with alias `default`) before reading this resource.',
+            thrownBy: 'service',
         },
         {
             reason: 'germplasm_not_found',

package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-germplasm.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-germplasm.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,iBAAiB,EAAE,MAAM,4DAA4D,CAAC;AAE/F,MAAM,CAAC,MAAM,sBAAsB,GAAG,QAAQ,CAAC,mCAAmC,EAAE;IAClF,IAAI,EAAE,iBAAiB;IACvB,KAAK,EAAE,wBAAwB;IAC/B,WAAW,EACT,+HAA+H;IACjI,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE;QACN;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,iDAAiD;YACvD,QAAQ,EACN,8FAA8F;~~SACjG~~;QACD;YACE,MAAM,EAAE,qBAAqB;YAC7B,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,8DAA8D;YACpE,QAAQ,EACN,mGAAmG;SACtG;KACO;IACV,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,iDAAiD,CAAC;KAC7F,CAAC;IACF,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG;QACvB,OAAO,MAAM,iBAAiB,CAAC,OAAO,CACpC,iBAAiB,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,aAAa,EAAE,MAAM,CAAC,aAAa,EAAE,CAAC,EACtE,GAAG,CACJ,CAAC;IACJ,CAAC;IACD,IAAI,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QACjB,SAAS,EAAE,EAAE;KACd,CAAC;CACH,CAAC,CAAC"}
1	+ {"version":3,"file":"brapi-germplasm.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-germplasm.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,iBAAiB,EAAE,MAAM,4DAA4D,CAAC;AAE/F,MAAM,CAAC,MAAM,sBAAsB,GAAG,QAAQ,CAAC,mCAAmC,EAAE;IAClF,IAAI,EAAE,iBAAiB;IACvB,KAAK,EAAE,wBAAwB;IAC/B,WAAW,EACT,+HAA+H;IACjI,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE;QACN;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,iDAAiD;YACvD,QAAQ,EACN,8FAA8F;YAChG,QAAQ,EAAE,SAAS;SACpB;QACD;YACE,MAAM,EAAE,qBAAqB;YAC7B,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,8DAA8D;YACpE,QAAQ,EACN,mGAAmG;SACtG;KACO;IACV,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,iDAAiD,CAAC;KAC7F,CAAC;IACF,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG;QACvB,OAAO,MAAM,iBAAiB,CAAC,OAAO,CACpC,iBAAiB,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,aAAa,EAAE,MAAM,CAAC,aAAa,EAAE,CAAC,EACtE,GAAG,CACJ,CAAC;IACJ,CAAC;IACD,IAAI,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QACjB,SAAS,EAAE,EAAE;KACd,CAAC;CACH,CAAC,CAAC"}

package/dist/mcp-server/resources/definitions/brapi-server-info.resource.d.ts CHANGED Viewed

@@ -13,5 +13,6 @@ export declare const brapiServerInfoResource: import("@cyanheads/mcp-ts-core").R
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: 'No default BrAPI connection has been registered';
     readonly recovery: 'Call brapi_connect (without an alias, or with alias `default`) before reading this resource.';
+    readonly thrownBy: 'service';
 }]>;
 //# sourceMappingURL=brapi-server-info.resource.d.ts.map

package/dist/mcp-server/resources/definitions/brapi-server-info.resource.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-server-info.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-server-info.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAGH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,uBAAuB;;;qBAQtB,eAAe;;mBAEjB,iDAAiD;uBAErD,8FAA8F;~~GAepG~~,CAAC"}
1	+ {"version":3,"file":"brapi-server-info.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-server-info.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAGH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,uBAAuB;;;qBAQtB,eAAe;;mBAEjB,iDAAiD;uBAErD,8FAA8F;uBACtF,SAAS;GAevB,CAAC"}

package/dist/mcp-server/resources/definitions/brapi-server-info.resource.js CHANGED Viewed

@@ -7,7 +7,7 @@
  */
 import { resource } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
-import { brapiServerInfo } from '../../../mcp-server/tools/definitions/brapi-server-info.tool.js';
+import { brapiServerInfo } from '../../tools/definitions/brapi-server-info.tool.js';
 export const brapiServerInfoResource = resource('brapi://server/info', {
     name: 'brapi-server-info',
     title: 'BrAPI server orientation envelope',
@@ -19,6 +19,7 @@ export const brapiServerInfoResource = resource('brapi://server/info', {
             code: JsonRpcErrorCode.NotFound,
             when: 'No default BrAPI connection has been registered',
             recovery: 'Call brapi_connect (without an alias, or with alias `default`) before reading this resource.',
+            thrownBy: 'service',
         },
     ],
     async handler(_params, ctx) {

package/dist/mcp-server/resources/definitions/brapi-server-info.resource.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-server-info.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-server-info.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,QAAQ,EAAE,MAAM,wBAAwB,CAAC;AAClD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,eAAe,EAAE,MAAM,0DAA0D,CAAC;AAE3F,MAAM,CAAC,MAAM,uBAAuB,GAAG,QAAQ,CAAC,qBAAqB,EAAE;IACrE,IAAI,EAAE,mBAAmB;IACzB,KAAK,EAAE,mCAAmC;IAC1C,WAAW,EACT,oJAAoJ;IACtJ,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE;QACN;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,iDAAiD;YACvD,QAAQ,EACN,8FAA8F;~~SACjG~~;KACO;IACV,KAAK,CAAC,OAAO,CAAC,OAAO,EAAE,GAAG;QACxB,OAAO,MAAM,eAAe,CAAC,OAAO,CAAC,eAAe,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAC;IAC7E,CAAC;IACD,IAAI,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QACjB,SAAS,EAAE;YACT;gBACE,GAAG,EAAE,qBAAqB;gBAC1B,IAAI,EAAE,mCAAmC;gBACzC,QAAQ,EAAE,kBAAkB;aAC7B;SACF;KACF,CAAC;CACH,CAAC,CAAC"}
1	+ {"version":3,"file":"brapi-server-info.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-server-info.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,QAAQ,EAAE,MAAM,wBAAwB,CAAC;AAClD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,eAAe,EAAE,MAAM,0DAA0D,CAAC;AAE3F,MAAM,CAAC,MAAM,uBAAuB,GAAG,QAAQ,CAAC,qBAAqB,EAAE;IACrE,IAAI,EAAE,mBAAmB;IACzB,KAAK,EAAE,mCAAmC;IAC1C,WAAW,EACT,oJAAoJ;IACtJ,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE;QACN;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,iDAAiD;YACvD,QAAQ,EACN,8FAA8F;YAChG,QAAQ,EAAE,SAAS;SACpB;KACO;IACV,KAAK,CAAC,OAAO,CAAC,OAAO,EAAE,GAAG;QACxB,OAAO,MAAM,eAAe,CAAC,OAAO,CAAC,eAAe,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAC;IAC7E,CAAC;IACD,IAAI,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QACjB,SAAS,EAAE;YACT;gBACE,GAAG,EAAE,qBAAqB;gBAC1B,IAAI,EAAE,mCAAmC;gBACzC,QAAQ,EAAE,kBAAkB;aAC7B;SACF;KACF,CAAC;CACH,CAAC,CAAC"}

package/dist/mcp-server/resources/definitions/brapi-study.resource.d.ts CHANGED Viewed

@@ -14,6 +14,7 @@ export declare const brapiStudyResource: import("@cyanheads/mcp-ts-core").Resour
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: 'No default BrAPI connection has been registered';
     readonly recovery: 'Call brapi_connect (without an alias, or with alias `default`) before reading this resource.';
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'study_not_found';
     readonly code: JsonRpcErrorCode.NotFound;

package/dist/mcp-server/resources/definitions/brapi-study.resource.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-study.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-study.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,kBAAkB;;;qBAQjB,eAAe;;mBAEjB,iDAAiD;uBAErD,8FAA8F;;~~qBAGxF~~,iBAAiB;;mBAEnB,0DAA0D;uBAE9D,6FAA6F;GAenG,CAAC"}
1	+ {"version":3,"file":"brapi-study.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-study.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,kBAAkB;;;qBAQjB,eAAe;;mBAEjB,iDAAiD;uBAErD,8FAA8F;uBACtF,SAAS;;qBAGX,iBAAiB;;mBAEnB,0DAA0D;uBAE9D,6FAA6F;GAenG,CAAC"}

package/dist/mcp-server/resources/definitions/brapi-study.resource.js CHANGED Viewed

@@ -7,7 +7,7 @@
  */
 import { resource, z } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
-import { brapiGetStudy } from '../../../mcp-server/tools/definitions/brapi-get-study.tool.js';
+import { brapiGetStudy } from '../../tools/definitions/brapi-get-study.tool.js';
 export const brapiStudyResource = resource('brapi://study/{studyDbId}', {
     name: 'brapi-study',
     title: 'BrAPI study record',
@@ -19,6 +19,7 @@ export const brapiStudyResource = resource('brapi://study/{studyDbId}', {
             code: JsonRpcErrorCode.NotFound,
             when: 'No default BrAPI connection has been registered',
             recovery: 'Call brapi_connect (without an alias, or with alias `default`) before reading this resource.',
+            thrownBy: 'service',
         },
         {
             reason: 'study_not_found',

package/dist/mcp-server/resources/definitions/brapi-study.resource.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-study.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-study.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,aAAa,EAAE,MAAM,wDAAwD,CAAC;AAEvF,MAAM,CAAC,MAAM,kBAAkB,GAAG,QAAQ,CAAC,2BAA2B,EAAE;IACtE,IAAI,EAAE,aAAa;IACnB,KAAK,EAAE,oBAAoB;IAC3B,WAAW,EACT,uHAAuH;IACzH,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE;QACN;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,iDAAiD;YACvD,QAAQ,EACN,8FAA8F;~~SACjG~~;QACD;YACE,MAAM,EAAE,iBAAiB;YACzB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,0DAA0D;YAChE,QAAQ,EACN,6FAA6F;SAChG;KACO;IACV,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,6CAA6C,CAAC;KACrF,CAAC;IACF,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG;QACvB,OAAO,MAAM,aAAa,CAAC,OAAO,CAChC,aAAa,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,SAAS,EAAE,MAAM,CAAC,SAAS,EAAE,CAAC,EAC1D,GAAG,CACJ,CAAC;IACJ,CAAC;IACD,IAAI,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QACjB,SAAS,EAAE,EAAE;KACd,CAAC;CACH,CAAC,CAAC"}
1	+ {"version":3,"file":"brapi-study.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-study.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,aAAa,EAAE,MAAM,wDAAwD,CAAC;AAEvF,MAAM,CAAC,MAAM,kBAAkB,GAAG,QAAQ,CAAC,2BAA2B,EAAE;IACtE,IAAI,EAAE,aAAa;IACnB,KAAK,EAAE,oBAAoB;IAC3B,WAAW,EACT,uHAAuH;IACzH,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE;QACN;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,iDAAiD;YACvD,QAAQ,EACN,8FAA8F;YAChG,QAAQ,EAAE,SAAS;SACpB;QACD;YACE,MAAM,EAAE,iBAAiB;YACzB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,0DAA0D;YAChE,QAAQ,EACN,6FAA6F;SAChG;KACO;IACV,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,6CAA6C,CAAC;KACrF,CAAC;IACF,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG;QACvB,OAAO,MAAM,aAAa,CAAC,OAAO,CAChC,aAAa,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,SAAS,EAAE,MAAM,CAAC,SAAS,EAAE,CAAC,EAC1D,GAAG,CACJ,CAAC;IACJ,CAAC;IACD,IAAI,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QACjB,SAAS,EAAE,EAAE;KACd,CAAC;CACH,CAAC,CAAC"}

package/dist/mcp-server/resources/definitions/brapi-variable.resource.d.ts CHANGED Viewed

@@ -21,6 +21,7 @@ export declare const brapiVariableResource: import("@cyanheads/mcp-ts-core").Res
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: 'No default BrAPI connection has been registered';
     readonly recovery: 'Call brapi_connect (without an alias, or with alias `default`) before reading this resource.';
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'variable_not_found';
     readonly code: JsonRpcErrorCode.NotFound;

package/dist/mcp-server/resources/definitions/brapi-variable.resource.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-variable.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-variable.resource.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAQjE,eAAO,MAAM,qBAAqB;;;qBAQpB,eAAe;;mBAEjB,iDAAiD;uBAErD,8FAA8F;;~~qBAGxF~~,oBAAoB;;mBAEtB,yEAAyE;uBAE7E,6GAA6G;GA2DnH,CAAC"}
1	+ {"version":3,"file":"brapi-variable.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-variable.resource.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAQjE,eAAO,MAAM,qBAAqB;;;qBAQpB,eAAe;;mBAEjB,iDAAiD;uBAErD,8FAA8F;uBACtF,SAAS;;qBAGX,oBAAoB;;mBAEtB,yEAAyE;uBAE7E,6GAA6G;GA2DnH,CAAC"}

package/dist/mcp-server/resources/definitions/brapi-variable.resource.js CHANGED Viewed

@@ -14,7 +14,7 @@
  */
 import { resource, z } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
-import { buildRequestOptions, isUpstreamNotFound, requireRegisteredConnection, } from '../../../mcp-server/tools/shared/find-helpers.js';
+import { buildRequestOptions, isUpstreamNotFound, requireRegisteredConnection, } from '../../tools/shared/find-helpers.js';
 import { getBrapiClient } from '../../../services/brapi-client/index.js';
 export const brapiVariableResource = resource('brapi://variable/{observationVariableDbId}', {
     name: 'brapi-variable',
@@ -27,6 +27,7 @@ export const brapiVariableResource = resource('brapi://variable/{observationVari
             code: JsonRpcErrorCode.NotFound,
             when: 'No default BrAPI connection has been registered',
             recovery: 'Call brapi_connect (without an alias, or with alias `default`) before reading this resource.',
+            thrownBy: 'service',
         },
         {
             reason: 'variable_not_found',

package/dist/mcp-server/resources/definitions/brapi-variable.resource.js.map CHANGED Viewed

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

@@ -69,11 +69,13 @@ export declare const brapiBuildPhenotypeMatrix: import("@cyanheads/mcp-ts-core")
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: 'No connection has been registered under the requested alias';
     readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_build_phenotype_matrix.';
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'all_filters_dropped';
     readonly code: JsonRpcErrorCode.ValidationError;
     readonly when: 'The active dialect dropped every filter supplied — the call would silently widen to the unfiltered baseline';
     readonly recovery: 'Drop unsupported filters or use studies / germplasm / variables to scope the query to supported filter paths on the active dialect.';
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'no_observation_path';
     readonly code: JsonRpcErrorCode.ServiceUnavailable;

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

	@@ -1 +1 @@
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