@cyanheads/brapi-mcp-server 0.4.5 → 0.4.7

package/dist/services/brapi-dialect/cassavabase-dialect.d.ts

@@ -18,8 +18,8 @@
  *      we invented this earlier; not in the BrAPI v2.1 spec, no SGN-family
  *      server honors it).
  *
- * Future capabilities (search-body translation, output normalization) attach
- * here as optional methods on the same dialect.
+ * Translation engine lives in `singularizing-dialect.ts`; this module supplies
+ * SGN-specific data only.
  *
  * @module services/brapi-dialect/cassavabase-dialect
  */

package/dist/services/brapi-dialect/cassavabase-dialect.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"cassavabase-dialect.d.ts","sourceRoot":"","sources":["../../../src/services/brapi-dialect/cassavabase-dialect.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;GAwBG;AAEH,OAAO,KAAK,EAAE,YAAY,EAAqB,MAAM,YAAY,CAAC;AA0LlE,eAAO,MAAM,kBAAkB,cAAuD,CAAC;AAEvF,eAAO,MAAM,gBAAgB,cAAuD,CAAC"}
+{"version":3,"file":"cassavabase-dialect.d.ts","sourceRoot":"","sources":["../../../src/services/brapi-dialect/cassavabase-dialect.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;GAwBG;AAGH,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,YAAY,CAAC;AAqK/C,eAAO,MAAM,kBAAkB,cAAuD,CAAC;AAEvF,eAAO,MAAM,gBAAgB,cAAuD,CAAC"}

package/dist/services/brapi-dialect/cassavabase-dialect.js

@@ -18,11 +18,12 @@
  *      we invented this earlier; not in the BrAPI v2.1 spec, no SGN-family
  *      server honors it).
  *
- * Future capabilities (search-body translation, output normalization) attach
- * here as optional methods on the same dialect.
+ * Translation engine lives in `singularizing-dialect.ts`; this module supplies
+ * SGN-specific data only.
  *
  * @module services/brapi-dialect/cassavabase-dialect
  */
+import { createSingularizingDialect } from './singularizing-dialect.js';
 /**
  * Plural BrAPI v2.1 filter key → singular form CassavaBase honors. Keyed by
  * endpoint resource segment (matches the path's first segment, no leading
@@ -76,6 +77,16 @@ const PLURAL_TO_SINGULAR = {
         trialDbIds: 'trialDbId',
         observationLevels: 'observationLevel',
     },
+    observationunits: {
+        studyDbIds: 'studyDbId',
+        germplasmDbIds: 'germplasmDbId',
+        observationUnitDbIds: 'observationUnitDbId',
+        programDbIds: 'programDbId',
+        trialDbIds: 'trialDbId',
+        locationDbIds: 'locationDbId',
+        seasonDbIds: 'seasonDbId',
+        observationLevels: 'observationLevel',
+    },
     locations: {
         locationDbIds: 'locationDbId',
         locationNames: 'locationName',
@@ -132,7 +143,6 @@ const DROPPED_FILTERS = {
     studies: new Set(['searchText', 'locationDbIds', 'locationDbId']),
     germplasm: new Set(['searchText']),
 };
-const EMPTY_DROP_SET = new Set();
 /**
  * POST `/search/{noun}` routes CassavaBase advertises in `/calls` but does not
  * actually serve. Probing them in practice yields hangs, 5xx responses, or
@@ -158,46 +168,19 @@ const DISABLED_SEARCH_ENDPOINTS = new Set([
     'samples',
     'callsets',
 ]);
+const SGN_NOTES = [
+    'SGN/Breedbase-style GET filters use singular names for many fields; this dialect translates plural BrAPI v2.1 filters before sending requests.',
+    'Several advertised POST /search routes are treated as unavailable because SGN-family deployments often expose them in /calls while serving broken or hanging responses.',
+];
 function createSgnFamilyDialect(id, label) {
-    return {
+    return createSingularizingDialect({
         id,
+        label,
+        pluralToSingular: PLURAL_TO_SINGULAR,
+        droppedFilters: DROPPED_FILTERS,
         disabledSearchEndpoints: DISABLED_SEARCH_ENDPOINTS,
-        notes: [
-            'SGN/Breedbase-style GET filters use singular names for many fields; this dialect translates plural BrAPI v2.1 filters before sending requests.',
-            'Several advertised POST /search routes are treated as unavailable because SGN-family deployments often expose them in /calls while serving broken or hanging responses.',
-        ],
-        adaptGetFilters(endpoint, filters) {
-            const mapping = PLURAL_TO_SINGULAR[endpoint] ?? {};
-            const dropped = DROPPED_FILTERS[endpoint] ?? EMPTY_DROP_SET;
-            const out = {};
-            const warnings = [];
-            for (const [key, value] of Object.entries(filters)) {
-                if (value === undefined)
-                    continue;
-                if (dropped.has(key)) {
-                    warnings.push(`${label} dialect: dropped filter '${key}' — this server does not honor it. Adjust the query or omit the filter.`);
-                    continue;
-                }
-                const target = mapping[key];
-                if (!target) {
-                    out[key] = value;
-                    continue;
-                }
-                if (Array.isArray(value)) {
-                    if (value.length === 0)
-                        continue;
-                    out[target] = value[0];
-                    if (value.length > 1) {
-                        warnings.push(`${label} dialect: '${key}' downcast to '${target}'; only the first value (${JSON.stringify(value[0])}) was sent — this server's GET /${endpoint} accepts a single value per filter, not arrays. Run separate calls for the other values, or use a curated tool that paginates over them.`);
-                    }
-                }
-                else {
-                    out[target] = value;
-                }
-            }
-            return { filters: out, warnings };
-        },
-    };
+        notes: SGN_NOTES,
+    });
 }
 export const cassavabaseDialect = createSgnFamilyDialect('cassavabase', 'CassavaBase');
 export const breedbaseDialect = createSgnFamilyDialect('breedbase', 'Breedbase/SGN');

package/dist/services/brapi-dialect/cassavabase-dialect.js.map

@@ -1 +1 @@
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+{"version":3,"file":"cassavabase-dialect.js","sourceRoot":"","sources":["../../../src/services/brapi-dialect/cassavabase-dialect.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;GAwBG;AAEH,OAAO,EAAE,0BAA0B,EAAE,MAAM,4BAA4B,CAAC;AAGxE;;;;;;;;;;;GAWG;AACH,MAAM,kBAAkB,GAAqD;IAC3E,OAAO,EAAE;QACP,eAAe,EAAE,gBAAgB,EAAE,kBAAkB;QACrD,UAAU,EAAE,WAAW;QACvB,YAAY,EAAE,aAAa,EAAE,kBAAkB;QAC/C,YAAY,EAAE,aAAa;QAC3B,UAAU,EAAE,WAAW,EAAE,kBAAkB;QAC3C,UAAU,EAAE,WAAW;QACvB,aAAa,EAAE,cAAc;QAC7B,WAAW,EAAE,YAAY,EAAE,kBAAkB;QAC7C,UAAU,EAAE,WAAW;QACvB,UAAU,EAAE,WAAW;QACvB,UAAU,EAAE,WAAW;QACvB,SAAS,EAAE,UAAU;QACrB,oBAAoB,EAAE,qBAAqB;QAC3C,wBAAwB,EAAE,yBAAyB;KACpD;IACD,SAAS,EAAE;QACT,eAAe,EAAE,gBAAgB;QACjC,cAAc,EAAE,eAAe;QAC/B,cAAc,EAAE,eAAe;QAC/B,aAAa,EAAE,cAAc;QAC7B,gBAAgB,EAAE,iBAAiB;QACnC,WAAW,EAAE,YAAY;QACzB,QAAQ,EAAE,SAAS;QACnB,YAAY,EAAE,aAAa;QAC3B,UAAU,EAAE,WAAW;QACvB,UAAU,EAAE,WAAW;QACvB,oBAAoB,EAAE,qBAAqB;KAC5C;IACD,YAAY,EAAE;QACZ,UAAU,EAAE,WAAW,EAAE,kBAAkB;QAC3C,cAAc,EAAE,eAAe;QAC/B,wBAAwB,EAAE,yBAAyB;QACnD,oBAAoB,EAAE,qBAAqB;QAC3C,gBAAgB,EAAE,iBAAiB;QACnC,WAAW,EAAE,YAAY;QACzB,YAAY,EAAE,aAAa;QAC3B,UAAU,EAAE,WAAW;QACvB,iBAAiB,EAAE,kBAAkB;KACtC;IACD,gBAAgB,EAAE;QAChB,UAAU,EAAE,WAAW;QACvB,cAAc,EAAE,eAAe;QAC/B,oBAAoB,EAAE,qBAAqB;QAC3C,YAAY,EAAE,aAAa;QAC3B,UAAU,EAAE,WAAW;QACvB,aAAa,EAAE,cAAc;QAC7B,WAAW,EAAE,YAAY;QACzB,iBAAiB,EAAE,kBAAkB;KACtC;IACD,SAAS,EAAE;QACT,aAAa,EAAE,cAAc;QAC7B,aAAa,EAAE,cAAc;QAC7B,YAAY,EAAE,aAAa;QAC3B,aAAa,EAAE,cAAc;QAC7B,aAAa,EAAE,cAAc;KAC9B;IACD,SAAS,EAAE;QACT,wBAAwB,EAAE,yBAAyB;QACnD,wBAAwB,EAAE,yBAAyB;QACnD,uBAAuB,EAAE,wBAAwB;QACjD,YAAY,EAAE,YAAY;QAC1B,WAAW,EAAE,YAAY;QACzB,UAAU,EAAE,WAAW;QACvB,aAAa,EAAE,cAAc;KAC9B;IACD,MAAM,EAAE;QACN,UAAU,EAAE,WAAW;QACvB,oBAAoB,EAAE,qBAAqB;QAC3C,gBAAgB,EAAE,iBAAiB;QACnC,UAAU,EAAE,WAAW;QACvB,cAAc,EAAE,eAAe;QAC/B,SAAS,EAAE,UAAU;QACrB,wBAAwB,EAAE,yBAAyB;KACpD;IACD,QAAQ,EAAE;QACR,eAAe,EAAE,gBAAgB;QACjC,YAAY,EAAE,aAAa;QAC3B,cAAc,EAAE,eAAe;KAChC;IACD,MAAM,EAAE;QACN,eAAe,EAAE,gBAAgB;QACjC,YAAY,EAAE,aAAa;QAC3B,UAAU,EAAE,WAAW;QACvB,UAAU,EAAE,WAAW;KACxB;IACD,QAAQ,EAAE;QACR,eAAe,EAAE,gBAAgB;QACjC,YAAY,EAAE,aAAa;QAC3B,YAAY,EAAE,aAAa;KAC5B;CACF,CAAC;AAEF;;;;;;;;;GASG;AACH,MAAM,eAAe,GAAwC;IAC3D,OAAO,EAAE,IAAI,GAAG,CAAC,CAAC,YAAY,EAAE,eAAe,EAAE,cAAc,CAAC,CAAC;IACjE,SAAS,EAAE,IAAI,GAAG,CAAC,CAAC,YAAY,CAAC,CAAC;CACnC,CAAC;AAEF;;;;;;;;;;;GAWG;AACH,MAAM,yBAAyB,GAAwB,IAAI,GAAG,CAAC;IAC7D,WAAW;IACX,SAAS;IACT,cAAc;IACd,kBAAkB;IAClB,WAAW;IACX,WAAW;IACX,QAAQ;IACR,UAAU;IACV,aAAa;IACb,SAAS;IACT,UAAU;CACX,CAAC,CAAC;AAEH,MAAM,SAAS,GAAG;IAChB,gJAAgJ;IAChJ,yKAAyK;CACjK,CAAC;AAEX,SAAS,sBAAsB,CAAC,EAAU,EAAE,KAAa;IACvD,OAAO,0BAA0B,CAAC;QAChC,EAAE;QACF,KAAK;QACL,gBAAgB,EAAE,kBAAkB;QACpC,cAAc,EAAE,eAAe;QAC/B,uBAAuB,EAAE,yBAAyB;QAClD,KAAK,EAAE,SAAS;KACjB,CAAC,CAAC;AACL,CAAC;AAED,MAAM,CAAC,MAAM,kBAAkB,GAAG,sBAAsB,CAAC,aAAa,EAAE,aAAa,CAAC,CAAC;AAEvF,MAAM,CAAC,MAAM,gBAAgB,GAAG,sBAAsB,CAAC,WAAW,EAAE,eAAe,CAAC,CAAC"}

package/dist/services/brapi-dialect/singularizing-dialect.d.ts

@@ -0,0 +1,47 @@
+/**
+ * @fileoverview Generic factory for dialects that translate BrAPI v2.1 plural
+ * filter keys (`studyDbIds`, `germplasmDbIds`, …) to the v2.0 singular forms
+ * the upstream actually honors. Used by both the SGN/Breedbase family
+ * (`cassavabase-dialect`) and the BrAPI Community Test Server
+ * (`brapi-test-dialect`) — the two share an identical translation engine but
+ * carry different per-endpoint mappings, drop lists, and search-route flags,
+ * so the data lives in each dialect module while the engine lives here.
+ *
+ * @module services/brapi-dialect/singularizing-dialect
+ */
+import type { BrapiDialect } from './types.js';
+export interface SingularizingDialectConfig {
+    /**
+     * POST `/search/{noun}` routes the dialect knows are dead — advertised in
+     * `/calls` but unresponsive in practice. Forwarded onto `BrapiDialect`
+     * verbatim. Omit when search routes work normally.
+     */
+    disabledSearchEndpoints?: ReadonlySet<string>;
+    /**
+     * Per-endpoint set of filter keys to drop entirely — the server silently
+     * ignores them in both plural and singular form. Drops surface a warning so
+     * the agent stops trusting the response as if the filter were honored.
+     */
+    droppedFilters?: Readonly<Record<string, ReadonlySet<string>>>;
+    /** Stable dialect id surfaced in logs and the orientation envelope. */
+    id: string;
+    /** Human-readable label used in warning text (e.g. `CassavaBase`). */
+    label: string;
+    /** Compatibility notes surfaced in brapi_connect / brapi_server_info. */
+    notes?: readonly string[];
+    /**
+     * Per-endpoint mapping from the v2.1 plural filter key to the singular form
+     * the server honors. Keyed by bare resource segment (`studies`, no slash).
+     * Endpoints not listed pass through with no translation.
+     */
+    pluralToSingular: Readonly<Record<string, Readonly<Record<string, string>>>>;
+}
+/**
+ * Build a `BrapiDialect` whose `adaptGetFilters` translates plural v2.1 filter
+ * names to the configured singulars, drops blacklisted keys, and downcasts
+ * multi-value arrays to the first element with a loud warning (the v2.0 GET
+ * surface can't express multi-value filters; the agent should re-call per
+ * value or use a curated tool that paginates).
+ */
+export declare function createSingularizingDialect(config: SingularizingDialectConfig): BrapiDialect;
+//# sourceMappingURL=singularizing-dialect.d.ts.map

package/dist/services/brapi-dialect/singularizing-dialect.d.ts.map

@@ -0,0 +1 @@
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package/dist/services/brapi-dialect/singularizing-dialect.js

@@ -0,0 +1,63 @@
+/**
+ * @fileoverview Generic factory for dialects that translate BrAPI v2.1 plural
+ * filter keys (`studyDbIds`, `germplasmDbIds`, …) to the v2.0 singular forms
+ * the upstream actually honors. Used by both the SGN/Breedbase family
+ * (`cassavabase-dialect`) and the BrAPI Community Test Server
+ * (`brapi-test-dialect`) — the two share an identical translation engine but
+ * carry different per-endpoint mappings, drop lists, and search-route flags,
+ * so the data lives in each dialect module while the engine lives here.
+ *
+ * @module services/brapi-dialect/singularizing-dialect
+ */
+const EMPTY_DROP_SET = new Set();
+/**
+ * Build a `BrapiDialect` whose `adaptGetFilters` translates plural v2.1 filter
+ * names to the configured singulars, drops blacklisted keys, and downcasts
+ * multi-value arrays to the first element with a loud warning (the v2.0 GET
+ * surface can't express multi-value filters; the agent should re-call per
+ * value or use a curated tool that paginates).
+ */
+export function createSingularizingDialect(config) {
+    const adaptGetFilters = (endpoint, filters) => {
+        const mapping = config.pluralToSingular[endpoint] ?? {};
+        const droppedSet = config.droppedFilters?.[endpoint] ?? EMPTY_DROP_SET;
+        const out = {};
+        const warnings = [];
+        const dropped = [];
+        for (const [key, value] of Object.entries(filters)) {
+            if (value === undefined)
+                continue;
+            if (droppedSet.has(key)) {
+                dropped.push(key);
+                warnings.push(`${config.label} dialect: dropped filter '${key}' — this server does not honor it. Adjust the query or omit the filter.`);
+                continue;
+            }
+            const target = mapping[key];
+            if (!target) {
+                out[key] = value;
+                continue;
+            }
+            if (Array.isArray(value)) {
+                if (value.length === 0)
+                    continue;
+                out[target] = value[0];
+                if (value.length > 1) {
+                    warnings.push(`${config.label} dialect: '${key}' downcast to '${target}'; only the first value (${JSON.stringify(value[0])}) was sent — this server's GET /${endpoint} accepts a single value per filter, not arrays. Run separate calls for the other values, or use a curated tool that paginates over them.`);
+                }
+            }
+            else {
+                out[target] = value;
+            }
+        }
+        return { filters: out, dropped, warnings };
+    };
+    return {
+        id: config.id,
+        adaptGetFilters,
+        ...(config.disabledSearchEndpoints !== undefined && {
+            disabledSearchEndpoints: config.disabledSearchEndpoints,
+        }),
+        ...(config.notes !== undefined && { notes: config.notes }),
+    };
+}
+//# sourceMappingURL=singularizing-dialect.js.map

package/dist/services/brapi-dialect/singularizing-dialect.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"singularizing-dialect.js","sourceRoot":"","sources":["../../../src/services/brapi-dialect/singularizing-dialect.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AA+BH,MAAM,cAAc,GAAwB,IAAI,GAAG,EAAE,CAAC;AAEtD;;;;;;GAMG;AACH,MAAM,UAAU,0BAA0B,CAAC,MAAkC;IAC3E,MAAM,eAAe,GAAG,CACtB,QAAgB,EAChB,OAA0C,EACvB,EAAE;QACrB,MAAM,OAAO,GAAG,MAAM,CAAC,gBAAgB,CAAC,QAAQ,CAAC,IAAI,EAAE,CAAC;QACxD,MAAM,UAAU,GAAG,MAAM,CAAC,cAAc,EAAE,CAAC,QAAQ,CAAC,IAAI,cAAc,CAAC;QACvE,MAAM,GAAG,GAA4B,EAAE,CAAC;QACxC,MAAM,QAAQ,GAAa,EAAE,CAAC;QAC9B,MAAM,OAAO,GAAa,EAAE,CAAC;QAE7B,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC;YACnD,IAAI,KAAK,KAAK,SAAS;gBAAE,SAAS;YAClC,IAAI,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;gBACxB,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;gBAClB,QAAQ,CAAC,IAAI,CACX,GAAG,MAAM,CAAC,KAAK,6BAA6B,GAAG,yEAAyE,CACzH,CAAC;gBACF,SAAS;YACX,CAAC;YACD,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC;YAC5B,IAAI,CAAC,MAAM,EAAE,CAAC;gBACZ,GAAG,CAAC,GAAG,CAAC,GAAG,KAAK,CAAC;gBACjB,SAAS;YACX,CAAC;YACD,IAAI,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC;gBACzB,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC;oBAAE,SAAS;gBACjC,GAAG,CAAC,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC;gBACvB,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;oBACrB,QAAQ,CAAC,IAAI,CACX,GAAG,MAAM,CAAC,KAAK,cAAc,GAAG,kBAAkB,MAAM,4BAA4B,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,mCAAmC,QAAQ,0IAA0I,CAClS,CAAC;gBACJ,CAAC;YACH,CAAC;iBAAM,CAAC;gBACN,GAAG,CAAC,MAAM,CAAC,GAAG,KAAK,CAAC;YACtB,CAAC;QACH,CAAC;QAED,OAAO,EAAE,OAAO,EAAE,GAAG,EAAE,OAAO,EAAE,QAAQ,EAAE,CAAC;IAC7C,CAAC,CAAC;IAEF,OAAO;QACL,EAAE,EAAE,MAAM,CAAC,EAAE;QACb,eAAe;QACf,GAAG,CAAC,MAAM,CAAC,uBAAuB,KAAK,SAAS,IAAI;YAClD,uBAAuB,EAAE,MAAM,CAAC,uBAAuB;SACxD,CAAC;QACF,GAAG,CAAC,MAAM,CAAC,KAAK,KAAK,SAAS,IAAI,EAAE,KAAK,EAAE,MAAM,CAAC,KAAK,EAAE,CAAC;KAC3D,CAAC;AACJ,CAAC"}

package/dist/services/brapi-dialect/spec-dialect.d.ts

@@ -1,10 +1,12 @@
 /**
  * @fileoverview The default `spec` dialect — passes filters through verbatim.
- * Used for any server that implements BrAPI v2.1 query-string filters as
- * specified (the BrAPI Community Test Server, modern PIPPA / GnpIS / Reference
- * Server deployments). Selected when no server-specific dialect matches the
- * detected `serverInfo.serverName`, or when an operator pins
- * `BRAPI_<ALIAS>_DIALECT=spec` to override detection.
+ * Used for servers that implement BrAPI v2.1 query-string filters as
+ * specified (modern PIPPA / GnpIS / Reference Server deployments). Selected
+ * when no server-specific dialect matches the detected `serverInfo.serverName`,
+ * or when an operator pins `BRAPI_<ALIAS>_DIALECT=spec` to override detection.
+ *
+ * Note: the BrAPI Community Test Server is intentionally **not** spec-shaped
+ * for GET filters — see `brapi-test-dialect.ts`.
  *
  * @module services/brapi-dialect/spec-dialect
  */

package/dist/services/brapi-dialect/spec-dialect.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"spec-dialect.d.ts","sourceRoot":"","sources":["../../../src/services/brapi-dialect/spec-dialect.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,YAAY,CAAC;AAE/C,eAAO,MAAM,WAAW,EAAE,YAKzB,CAAC"}
+{"version":3,"file":"spec-dialect.d.ts","sourceRoot":"","sources":["../../../src/services/brapi-dialect/spec-dialect.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,YAAY,CAAC;AAE/C,eAAO,MAAM,WAAW,EAAE,YAKzB,CAAC"}

package/dist/services/brapi-dialect/spec-dialect.js

@@ -1,17 +1,19 @@
 /**
  * @fileoverview The default `spec` dialect — passes filters through verbatim.
- * Used for any server that implements BrAPI v2.1 query-string filters as
- * specified (the BrAPI Community Test Server, modern PIPPA / GnpIS / Reference
- * Server deployments). Selected when no server-specific dialect matches the
- * detected `serverInfo.serverName`, or when an operator pins
- * `BRAPI_<ALIAS>_DIALECT=spec` to override detection.
+ * Used for servers that implement BrAPI v2.1 query-string filters as
+ * specified (modern PIPPA / GnpIS / Reference Server deployments). Selected
+ * when no server-specific dialect matches the detected `serverInfo.serverName`,
+ * or when an operator pins `BRAPI_<ALIAS>_DIALECT=spec` to override detection.
+ *
+ * Note: the BrAPI Community Test Server is intentionally **not** spec-shaped
+ * for GET filters — see `brapi-test-dialect.ts`.
  *
  * @module services/brapi-dialect/spec-dialect
  */
 export const specDialect = {
     id: 'spec',
     adaptGetFilters(_endpoint, filters) {
-        return { filters: { ...filters }, warnings: [] };
+        return { filters: { ...filters }, dropped: [], warnings: [] };
     },
 };
 //# sourceMappingURL=spec-dialect.js.map

package/dist/services/brapi-dialect/spec-dialect.js.map

@@ -1 +1 @@
-{"version":3,"file":"spec-dialect.js","sourceRoot":"","sources":["../../../src/services/brapi-dialect/spec-dialect.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAIH,MAAM,CAAC,MAAM,WAAW,GAAiB;IACvC,EAAE,EAAE,MAAM;IACV,eAAe,CAAC,SAAS,EAAE,OAAO;QAChC,OAAO,EAAE,OAAO,EAAE,EAAE,GAAG,OAAO,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,CAAC;IACnD,CAAC;CACF,CAAC"}
+{"version":3,"file":"spec-dialect.js","sourceRoot":"","sources":["../../../src/services/brapi-dialect/spec-dialect.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAIH,MAAM,CAAC,MAAM,WAAW,GAAiB;IACvC,EAAE,EAAE,MAAM;IACV,eAAe,CAAC,SAAS,EAAE,OAAO;QAChC,OAAO,EAAE,OAAO,EAAE,EAAE,GAAG,OAAO,EAAE,EAAE,OAAO,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,CAAC;IAChE,CAAC;CACF,CAAC"}

package/dist/services/brapi-dialect/types.d.ts

@@ -18,9 +18,18 @@
  * Result of adapting a filter map for a specific endpoint. `filters` is the
  * wire-shape map (what gets serialized into the URL); `warnings` are
  * operator-facing notes about lossy conversions (multi-value array downcast,
- * filters dropped because the server doesn't honor them, etc.).
+ * filters dropped because the server doesn't honor them, etc.). `dropped` is
+ * the structured list of input keys that were removed entirely so callers can
+ * detect "agent intended to scope, dialect couldn't honor it" without parsing
+ * warning strings.
  */
 export interface DialectAdaptation {
+    /**
+     * Input filter keys the dialect dropped entirely (server doesn't honor them
+     * in any form). Each dropped key also produces a human-readable entry in
+     * `warnings`. Empty when nothing was dropped.
+     */
+    dropped: readonly string[];
     filters: Record<string, unknown>;
     warnings: string[];
 }

package/dist/services/brapi-dialect/types.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../../src/services/brapi-dialect/types.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAEH;;;;;GAKG;AACH,MAAM,WAAW,iBAAiB;IAChC,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IACjC,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAED;;;;;GAKG;AACH,MAAM,WAAW,YAAY;IAC3B;;;;;;;;;OASG;IACH,eAAe,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,GAAG,iBAAiB,CAAC;IACjG;;;;;;;;;OASG;IACH,QAAQ,CAAC,uBAAuB,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,CAAC;IACvD,QAAQ,CAAC,EAAE,EAAE,MAAM,CAAC;IACpB;;;;OAIG;IACH,QAAQ,CAAC,KAAK,CAAC,EAAE,SAAS,MAAM,EAAE,CAAC;CACpC"}
+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../../src/services/brapi-dialect/types.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAEH;;;;;;;;GAQG;AACH,MAAM,WAAW,iBAAiB;IAChC;;;;OAIG;IACH,OAAO,EAAE,SAAS,MAAM,EAAE,CAAC;IAC3B,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IACjC,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAED;;;;;GAKG;AACH,MAAM,WAAW,YAAY;IAC3B;;;;;;;;;OASG;IACH,eAAe,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,GAAG,iBAAiB,CAAC;IACjG;;;;;;;;;OASG;IACH,QAAQ,CAAC,uBAAuB,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,CAAC;IACvD,QAAQ,CAAC,EAAE,EAAE,MAAM,CAAC;IACpB;;;;OAIG;IACH,QAAQ,CAAC,KAAK,CAAC,EAAE,SAAS,MAAM,EAAE,CAAC;CACpC"}

package/dist/services/reference-data-cache/reference-data-cache.d.ts

@@ -10,8 +10,21 @@
 import type { Context } from '@cyanheads/mcp-ts-core';
 import type { ServerConfig } from '../../config/server-config.js';
 import { type BrapiClient, type BrapiRequestOptions } from '../../services/brapi-client/index.js';
+import type { BrapiDialect } from '../../services/brapi-dialect/index.js';
 import type { Location, Program, Trial } from './types.js';
-export type ReferenceLookupOptions = Pick<BrapiRequestOptions, 'auth'>;
+export interface ReferenceLookupOptions {
+    auth?: BrapiRequestOptions['auth'];
+    /**
+     * Active dialect for the connection. Threaded through to the BrapiClient so
+     * the v2.1 plural ID filter (`trialDbIds`, `programDbIds`, …) is translated
+     * to the singular form servers like CassavaBase honor. Without this, the
+     * filter is silently ignored upstream and the response carries an arbitrary
+     * page-zero row instead of the requested record.
+     */
+    dialect?: BrapiDialect;
+    /** Optional warnings sink — receives any dialect-translation warnings. */
+    warnings?: string[];
+}
 export declare class ReferenceDataCache {
     private readonly serverConfig;
     private readonly client;

package/dist/services/reference-data-cache/reference-data-cache.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"reference-data-cache.d.ts","sourceRoot":"","sources":["../../../src/services/reference-data-cache/reference-data-cache.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AACtD,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AAC9D,OAAO,EACL,KAAK,WAAW,EAEhB,KAAK,mBAAmB,EAEzB,MAAM,kCAAkC,CAAC;AAC1C,OAAO,KAAK,EAAE,QAAQ,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAC;AAE3D,MAAM,MAAM,sBAAsB,GAAG,IAAI,CAAC,mBAAmB,EAAE,MAAM,CAAC,CAAC;AA8BvE,qBAAa,kBAAkB;IAE3B,OAAO,CAAC,QAAQ,CAAC,YAAY;IAC7B,OAAO,CAAC,QAAQ,CAAC,MAAM;gBADN,YAAY,EAAE,YAAY,EAC1B,MAAM,GAAE,MAAM,WAA4B;IAG7D,WAAW,CACT,OAAO,EAAE,MAAM,EACf,YAAY,EAAE,SAAS,MAAM,EAAE,EAC/B,GAAG,EAAE,OAAO,EACZ,OAAO,CAAC,EAAE,sBAAsB,GAC/B,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAIhC,SAAS,CACP,OAAO,EAAE,MAAM,EACf,UAAU,EAAE,SAAS,MAAM,EAAE,EAC7B,GAAG,EAAE,OAAO,EACZ,OAAO,CAAC,EAAE,sBAAsB,GAC/B,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAI9B,YAAY,CACV,OAAO,EAAE,MAAM,EACf,aAAa,EAAE,SAAS,MAAM,EAAE,EAChC,GAAG,EAAE,OAAO,EACZ,OAAO,CAAC,EAAE,sBAAsB,GAC/B,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC;IAIjC,yEAAyE;IACnE,UAAU,CAAC,OAAO,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,IAAI,CAAC;YAShD,YAAY;YAsCZ,UAAU;YAoBV,YAAY;CAY3B;AAiBD,wBAAgB,sBAAsB,CAAC,YAAY,EAAE,YAAY,GAAG,IAAI,CAEvE;AAED,wBAAgB,qBAAqB,IAAI,kBAAkB,CAO1D;AAED,wBAAgB,uBAAuB,IAAI,IAAI,CAE9C"}
+{"version":3,"file":"reference-data-cache.d.ts","sourceRoot":"","sources":["../../../src/services/reference-data-cache/reference-data-cache.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AACtD,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AAC9D,OAAO,EACL,KAAK,WAAW,EAEhB,KAAK,mBAAmB,EAGzB,MAAM,kCAAkC,CAAC;AAC1C,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,mCAAmC,CAAC;AACtE,OAAO,KAAK,EAAE,QAAQ,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAC;AAE3D,MAAM,WAAW,sBAAsB;IACrC,IAAI,CAAC,EAAE,mBAAmB,CAAC,MAAM,CAAC,CAAC;IACnC;;;;;;OAMG;IACH,OAAO,CAAC,EAAE,YAAY,CAAC;IACvB,0EAA0E;IAC1E,QAAQ,CAAC,EAAE,MAAM,EAAE,CAAC;CACrB;AA8BD,qBAAa,kBAAkB;IAE3B,OAAO,CAAC,QAAQ,CAAC,YAAY;IAC7B,OAAO,CAAC,QAAQ,CAAC,MAAM;gBADN,YAAY,EAAE,YAAY,EAC1B,MAAM,GAAE,MAAM,WAA4B;IAG7D,WAAW,CACT,OAAO,EAAE,MAAM,EACf,YAAY,EAAE,SAAS,MAAM,EAAE,EAC/B,GAAG,EAAE,OAAO,EACZ,OAAO,CAAC,EAAE,sBAAsB,GAC/B,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAIhC,SAAS,CACP,OAAO,EAAE,MAAM,EACf,UAAU,EAAE,SAAS,MAAM,EAAE,EAC7B,GAAG,EAAE,OAAO,EACZ,OAAO,CAAC,EAAE,sBAAsB,GAC/B,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAI9B,YAAY,CACV,OAAO,EAAE,MAAM,EACf,aAAa,EAAE,SAAS,MAAM,EAAE,EAChC,GAAG,EAAE,OAAO,EACZ,OAAO,CAAC,EAAE,sBAAsB,GAC/B,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC;IAIjC,yEAAyE;IACnE,UAAU,CAAC,OAAO,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,IAAI,CAAC;YAShD,YAAY;YAsCZ,UAAU;YAsCV,YAAY;CAY3B;AAiBD,wBAAgB,sBAAsB,CAAC,YAAY,EAAE,YAAY,GAAG,IAAI,CAEvE;AAED,wBAAgB,qBAAqB,IAAI,kBAAkB,CAO1D;AAED,wBAAgB,uBAAuB,IAAI,IAAI,CAE9C"}

package/dist/services/reference-data-cache/reference-data-cache.js

@@ -7,7 +7,7 @@
  *
  * @module services/reference-data-cache/reference-data-cache
  */
-import { getBrapiClient, } from '../../services/brapi-client/index.js';
+import { getBrapiClient, isDialectAllDropped, } from '../../services/brapi-client/index.js';
 const PROGRAM_CFG = {
     endpoint: '/programs',
     idFilter: 'programDbIds',
@@ -83,11 +83,30 @@ export class ReferenceDataCache {
     async fetchBatch(cfg, baseUrl, ids, ctx, options) {
         const requestOptions = {
             params: { [cfg.idFilter]: ids, pageSize: ids.length },
+            timeoutMs: this.serverConfig.companionTimeoutMs,
+            retryMaxAttempts: 0,
         };
         if (options.auth)
             requestOptions.auth = options.auth;
-        const env = await this.client().get(baseUrl, cfg.endpoint, ctx, requestOptions);
-        return extractDataArray(env);
+        if (options.dialect)
+            requestOptions.dialect = options.dialect;
+        if (options.warnings)
+            requestOptions.warnings = options.warnings;
+        try {
+            const env = await this.client().get(baseUrl, cfg.endpoint, ctx, requestOptions);
+            return extractDataArray(env);
+        }
+        catch (err) {
+            if (isDialectAllDropped(err)) {
+                // The dialect dropped every plural ID filter and there's no singular
+                // alias on this server — surface a warning and return empty so the
+                // caller treats the FK as unavailable instead of receiving a page-zero
+                // row keyed off the wrong ID.
+                options.warnings?.push(`Reference lookup ${cfg.endpoint} skipped: active dialect drops every supported ID filter; FK enrichment unavailable.`);
+                return [];
+            }
+            throw err;
+        }
     }
     async deletePrefix(ctx, prefix) {
         let cursor;

package/dist/services/reference-data-cache/reference-data-cache.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@cyanheads/brapi-mcp-server",
   "mcpName": "io.github.cyanheads/brapi-mcp-server",
-  "version": "0.4.5",
+  "version": "0.4.7",
   "description": "BrAPI v2.1 MCP server — studies, germplasm, observations, genotypes, images, and pedigrees.",
   "author": "Casey Hand @cyanheads (https://github.com/cyanheads/brapi-mcp-server#readme)",
   "type": "module",

package/server.json

@@ -6,14 +6,14 @@
     "url": "https://github.com/cyanheads/brapi-mcp-server",
     "source": "github"
   },
-  "version": "0.4.5",
+  "version": "0.4.7",
   "packages": [
     {
       "registryType": "npm",
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.4.5",
+      "version": "0.4.7",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:stdio" }
@@ -49,7 +49,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.4.5",
+      "version": "0.4.7",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:http" }