npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.7.9 → 0.7.11 - Mend

@cyanheads/brapi-mcp-server 0.7.9 → 0.7.11

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 (105) hide show

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

@@ -21,10 +21,10 @@ export declare const brapiFindGenotypeCalls: import("@cyanheads/mcp-ts-core").To
     callSetDbIds: z.ZodOptional<z.ZodArray<z.ZodString>>;
     variantDbIds: z.ZodOptional<z.ZodArray<z.ZodString>>;
     callFormat: z.ZodOptional<z.ZodEnum<{
+        DARTSEQ: "DARTSEQ";
+        FLAPJACK: "FLAPJACK";
         JSON: "JSON";
         VCF: "VCF";
-        FLAPJACK: "FLAPJACK";
-        DARTSEQ: "DARTSEQ";
     }>>;
     loadLimit: z.ZodOptional<z.ZodNumber>;
 }, z.core.$strip>, z.ZodObject<{
@@ -66,20 +66,20 @@ export declare const brapiFindGenotypeCalls: import("@cyanheads/mcp-ts-core").To
     }, z.core.$strip>>;
     truncated: z.ZodBoolean;
 }, z.core.$strip>, readonly [{
-    readonly reason: "unknown_alias";
+    readonly reason: 'unknown_alias';
     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_find_genotype_calls.";
+    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_find_genotype_calls.';
 }, {
-    readonly reason: "no_filters";
+    readonly reason: 'no_filters';
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: "No variant set, germplasm, call set, or variant filter was provided";
-    readonly recovery: "Provide variantSetDbId or germplasmDbIds before retrying — unfiltered pulls are too expensive.";
+    readonly when: 'No variant set, germplasm, call set, or variant filter was provided';
+    readonly recovery: 'Provide variantSetDbId or germplasmDbIds before retrying — unfiltered pulls are too expensive.';
 }, {
-    readonly reason: "search_endpoint_disabled";
+    readonly reason: 'search_endpoint_disabled';
     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 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;

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

	@@ -1 +1 @@
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;AAgHjE,eAAO,MAAM,sBAAsB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAyQjC~~,CAAC"}
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;AAgHjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMrB,eAAe;;mBAEjB,6DAA6D;uBAEjE,6HAA6H;;qBAGvH,YAAY;;mBAEd,qEAAqE;uBAEzE,gGAAgG;;qBAG1F,0BAA0B;;mBAE5B,6EAA6E;uBAEjF,+HAA+H;;;;;;;EAiPrI,CAAC"}

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

@@ -66,15 +66,15 @@ export declare const brapiFindGermplasm: import("@cyanheads/mcp-ts-core").ToolDe
         totalCount: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>;
 }, z.core.$strip>, readonly [{
-    readonly reason: "unknown_alias";
+    readonly reason: 'unknown_alias';
     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_find_germplasm.";
+    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_find_germplasm.';
 }, {
-    readonly reason: "all_filters_dropped";
+    readonly reason: 'all_filters_dropped';
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: "The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.";
-    readonly recovery: "Drop the unsupported filters and rescope by names, germplasmDbIds, germplasmPUIs, accessionNumbers, crops, synonyms, genus, or species — these filter paths are honored on the active dialect.";
+    readonly when: 'The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.';
+    readonly recovery: 'Drop the unsupported filters and rescope by names, germplasmDbIds, germplasmPUIs, accessionNumbers, crops, synonyms, genus, or species — these filter paths are honored on the active dialect.';
 }], {
     readonly totalCount: z.ZodNumber;
     readonly returnedCount: z.ZodNumber;

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-find-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmIjE,eAAO,MAAM,kBAAkB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA4W7B~~,CAAC"}
1	+ {"version":3,"file":"brapi-find-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmIjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMjB,eAAe;;mBAEjB,6DAA6D;uBAEjE,wHAAwH;;qBAGlH,qBAAqB;;mBAEvB,mNAAmN;uBAEvN,gMAAgM;;;;;;;;EA2VtM,CAAC"}

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

@@ -59,15 +59,15 @@ export declare const brapiFindImages: import("@cyanheads/mcp-ts-core").ToolDefin
         totalCount: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>;
 }, z.core.$strip>, readonly [{
-    readonly reason: "unknown_alias";
+    readonly reason: 'unknown_alias';
     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_find_images.";
+    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_find_images.';
 }, {
-    readonly reason: "all_filters_dropped";
+    readonly reason: 'all_filters_dropped';
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: "The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.";
-    readonly recovery: "Drop the unsupported filters and rescope by images, observationUnits, observations, studies, descriptiveOntologyTerms, imageFileNames, or mimeTypes — these filter paths are honored on the active dialect.";
+    readonly when: 'The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.';
+    readonly recovery: 'Drop the unsupported filters and rescope by images, observationUnits, observations, studies, descriptiveOntologyTerms, imageFileNames, or mimeTypes — these filter paths are honored on the active dialect.';
 }], {
     readonly totalCount: z.ZodNumber;
     readonly returnedCount: z.ZodNumber;

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-find-images.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-images.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA4HjE,eAAO,MAAM,eAAe~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAoS1B~~,CAAC"}
1	+ {"version":3,"file":"brapi-find-images.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-images.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA4HjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMd,eAAe;;mBAEjB,6DAA6D;uBAEjE,qHAAqH;;qBAG/G,qBAAqB;;mBAEvB,mNAAmN;uBAEvN,6MAA6M;;;;;;;;EAmRnN,CAAC"}

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

@@ -63,15 +63,15 @@ export declare const brapiFindLocations: import("@cyanheads/mcp-ts-core").ToolDe
         swapped: "swapped";
     }>;
 }, z.core.$strip>, readonly [{
-    readonly reason: "unknown_alias";
+    readonly reason: 'unknown_alias';
     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_find_locations.";
+    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_find_locations.';
 }, {
-    readonly reason: "all_filters_dropped";
+    readonly reason: 'all_filters_dropped';
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: "The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.";
-    readonly recovery: "Drop the unsupported filters and rescope by locations, locationNames, countryCodes, locationTypes, abbreviations, or bbox — these filter paths are honored on the active dialect.";
+    readonly when: 'The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.';
+    readonly recovery: 'Drop the unsupported filters and rescope by locations, locationNames, countryCodes, locationTypes, abbreviations, or bbox — these filter paths are honored on the active dialect.';
 }], {
     readonly totalCount: z.ZodNumber;
     readonly returnedCount: z.ZodNumber;

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-find-locations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-locations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkHjE,eAAO,MAAM,kBAAkB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAmY7B~~,CAAC"}
1	+ {"version":3,"file":"brapi-find-locations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-locations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkHjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMjB,eAAe;;mBAEjB,6DAA6D;uBAEjE,wHAAwH;;qBAGlH,qBAAqB;;mBAEvB,mNAAmN;uBAEvN,mLAAmL;;;;;;;;EAkXzL,CAAC"}

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

@@ -63,15 +63,15 @@ export declare const brapiFindObservations: import("@cyanheads/mcp-ts-core").Too
         totalCount: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>;
 }, z.core.$strip>, readonly [{
-    readonly reason: "unknown_alias";
+    readonly reason: 'unknown_alias';
     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_find_observations.";
+    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_find_observations.';
 }, {
-    readonly reason: "all_filters_dropped";
+    readonly reason: 'all_filters_dropped';
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: "The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.";
-    readonly recovery: "Drop the unsupported filters and rescope by germplasm, variables, observationUnits, observations, seasons, programs, or trials — these filter paths are honored on the active dialect.";
+    readonly when: 'The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.';
+    readonly recovery: 'Drop the unsupported filters and rescope by germplasm, variables, observationUnits, observations, seasons, programs, or trials — these filter paths are honored on the active dialect.';
 }], {
     readonly totalCount: z.ZodNumber;
     readonly returnedCount: z.ZodNumber;

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-find-observations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-observations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA+JjE,eAAO,MAAM,qBAAqB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAkXhC~~,CAAC"}
1	+ {"version":3,"file":"brapi-find-observations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-observations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA+JjE,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMpB,eAAe;;mBAEjB,6DAA6D;uBAEjE,2HAA2H;;qBAGrH,qBAAqB;;mBAEvB,mNAAmN;uBAEvN,wLAAwL;;;;;;;;EAiW9L,CAAC"}

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

@@ -62,15 +62,15 @@ export declare const brapiFindStudies: import("@cyanheads/mcp-ts-core").ToolDefi
         totalCount: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>;
 }, z.core.$strip>, readonly [{
-    readonly reason: "unknown_alias";
+    readonly reason: 'unknown_alias';
     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_find_studies.";
+    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_find_studies.';
 }, {
-    readonly reason: "all_filters_dropped";
+    readonly reason: 'all_filters_dropped';
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: "The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.";
-    readonly recovery: "Drop the unsupported filters and rescope by crop, trialTypes, seasons, programs, trials, studyNames, or active — these filter paths are honored on the active dialect.";
+    readonly when: 'The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.';
+    readonly recovery: 'Drop the unsupported filters and rescope by crop, trialTypes, seasons, programs, trials, studyNames, or active — these filter paths are honored on the active dialect.';
 }], {
     readonly totalCount: z.ZodNumber;
     readonly returnedCount: z.ZodNumber;

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-find-studies.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-studies.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyHjE,eAAO,MAAM,gBAAgB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsS3B~~,CAAC"}
1	+ {"version":3,"file":"brapi-find-studies.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-studies.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyHjE,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMf,eAAe;;mBAEjB,6DAA6D;uBAEjE,sHAAsH;;qBAGhH,qBAAqB;;mBAEvB,mNAAmN;uBAEvN,wKAAwK;;;;;;;;EAqR9K,CAAC"}

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

@@ -63,8 +63,8 @@ export declare const brapiFindVariables: import("@cyanheads/mcp-ts-core").ToolDe
         synonyms: z.ZodOptional<z.ZodArray<z.ZodString>>;
         ontologyDbId: z.ZodOptional<z.ZodString>;
         source: z.ZodEnum<{
-            puiMatch: "puiMatch";
             nameMatch: "nameMatch";
+            puiMatch: "puiMatch";
             synonymMatch: "synonymMatch";
             traitClassMatch: "traitClassMatch";
         }>;
@@ -81,15 +81,15 @@ export declare const brapiFindVariables: import("@cyanheads/mcp-ts-core").ToolDe
         totalCount: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>;
 }, z.core.$strip>, readonly [{
-    readonly reason: "unknown_alias";
+    readonly reason: 'unknown_alias';
     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_find_variables.";
+    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_find_variables.';
 }, {
-    readonly reason: "all_filters_dropped";
+    readonly reason: 'all_filters_dropped';
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: "The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.";
-    readonly recovery: "Drop the unsupported filters and rescope by variables, traitClasses, ontologyDbIds, methodDbIds, scaleDbIds, or text — these filter paths are honored on the active dialect.";
+    readonly when: 'The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.';
+    readonly recovery: 'Drop the unsupported filters and rescope by variables, traitClasses, ontologyDbIds, methodDbIds, scaleDbIds, or text — these filter paths are honored on the active dialect.';
 }], {
     readonly totalCount: z.ZodNumber;
     readonly returnedCount: z.ZodNumber;

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-find-variables.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-variables.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAsKjE,eAAO,MAAM,kBAAkB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwW7B~~,CAAC"}
1	+ {"version":3,"file":"brapi-find-variables.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-variables.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAsKjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMjB,eAAe;;mBAEjB,6DAA6D;uBAEjE,wHAAwH;;qBAGlH,qBAAqB;;mBAEvB,mNAAmN;uBAEvN,8KAA8K;;;;;;;;EAuVpL,CAAC"}

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

@@ -53,15 +53,15 @@ export declare const brapiFindVariants: import("@cyanheads/mcp-ts-core").ToolDef
         totalCount: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>;
 }, z.core.$strip>, readonly [{
-    readonly reason: "unknown_alias";
+    readonly reason: 'unknown_alias';
     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_find_variants.";
+    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_find_variants.';
 }, {
-    readonly reason: "all_filters_dropped";
+    readonly reason: 'all_filters_dropped';
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: "The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.";
-    readonly recovery: "Drop the unsupported filters and rescope by variants, variantSets, references, or referenceName + start/end — these filter paths are honored on the active dialect.";
+    readonly when: 'The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.';
+    readonly recovery: 'Drop the unsupported filters and rescope by variants, variantSets, references, or referenceName + start/end — these filter paths are honored on the active dialect.';
 }], {
     readonly totalCount: z.ZodNumber;
     readonly returnedCount: z.ZodNumber;

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-find-variants.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-variants.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAsHjE,eAAO,MAAM,iBAAiB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA4P5B~~,CAAC"}
1	+ {"version":3,"file":"brapi-find-variants.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-variants.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAsHjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMhB,eAAe;;mBAEjB,6DAA6D;uBAEjE,uHAAuH;;qBAGjH,qBAAqB;;mBAEvB,mNAAmN;uBAEvN,qKAAqK;;;;;;;;EA2O3K,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-germplasm-performance.tool.d.ts CHANGED Viewed

@@ -48,14 +48,14 @@ export declare const brapiGermplasmPerformance: import("@cyanheads/mcp-ts-core")
     }, z.core.$strip>>;
     warnings: z.ZodArray<z.ZodString>;
 }, z.core.$strip>, readonly [{
-    readonly reason: "unknown_alias";
+    readonly reason: 'unknown_alias';
     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_germplasm_performance.";
+    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_germplasm_performance.';
 }, {
-    readonly reason: "germplasm_not_found";
+    readonly reason: 'germplasm_not_found';
     readonly code: JsonRpcErrorCode.NotFound;
-    readonly when: "Upstream returned no germplasm record for the requested germplasmDbId";
-    readonly recovery: "Verify the germplasmDbId on the target server, or run brapi_find_germplasm to discover valid IDs.";
+    readonly when: 'Upstream returned no germplasm record for the requested germplasmDbId';
+    readonly recovery: 'Verify the germplasmDbId on the target server, or run brapi_find_germplasm to discover valid IDs.';
 }], undefined>;
 //# sourceMappingURL=brapi-germplasm-performance.tool.d.ts.map

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-germplasm-performance.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-germplasm-performance.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;GAqBG;AAGH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwGjE,eAAO,MAAM,yBAAyB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA2LpC~~,CAAC"}
1	+ {"version":3,"file":"brapi-germplasm-performance.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-germplasm-performance.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;GAqBG;AAGH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwGjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMxB,eAAe;;mBAEjB,6DAA6D;uBAEjE,+HAA+H;;qBAGzH,qBAAqB;;mBAEvB,uEAAuE;uBAE3E,mGAAmG;cA0KzG,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-germplasm-performance.tool.js CHANGED Viewed

@@ -27,7 +27,7 @@ import { getBrapiClient } from '../../../services/brapi-client/index.js';
 import { resolveDialect } from '../../../services/brapi-dialect/index.js';
 import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
 import { AliasInput, asString, buildRequestOptions, extractRows, isUpstreamNotFound, requireRegisteredConnection, } from '../shared/find-helpers.js';
-import { pullStudyObservations } from '../shared/observations.js';
+import { pullObservationsForStudies } from '../shared/observations.js';
 /** Upper bound on studies discovered per germplasm (guards the filter-ignored case). */
 const STUDY_DISCOVERY_CAP = 200;
 const STUDY_DISCOVERY_PAGE_SIZE = 100;
@@ -169,39 +169,38 @@ export const brapiGermplasmPerformance = tool('brapi_germplasm_performance', {
                 warnings.push(`Study discovery capped at ${STUDY_DISCOVERY_CAP} studies — aggregates may be incomplete. To retrieve the full study set, call brapi_find_studies with extraFilters.germplasmDbIds set to ['${input.germplasmDbId}'] — it pages the complete germplasm-scoped study list (dataframe-backed when large) — then pass those studyDbIds back as the studyDbIds input here to aggregate the omitted slice. Or narrow with brapi_build_phenotype_matrix on specific studies.`);
             }
         }
-        // 3. Pull observations per study, scoped to the germplasm. Filter returned
-        //    rows to the iterated study + target germplasm so the aggregate stays
-        //    correct on servers that ignore the studyDbId filter or over-return.
+        // 3. Pull observations per study, scoped to the germplasm, with bounded
+        //    concurrency. Filter returned rows to the iterated study + target
+        //    germplasm so the aggregate stays correct on servers that ignore the
+        //    studyDbId filter or over-return. Per-study failures warn and continue.
         const collected = [];
         const wantVariables = input.variables?.length ? new Set(input.variables) : undefined;
-        for (const studyDbId of studyDbIds) {
-            let studyObs;
-            try {
-                studyObs = await pullStudyObservations({
-                    studyDbId,
-                    input: input.variables
-                        ? { germplasm: [input.germplasmDbId], variables: input.variables }
-                        : { germplasm: [input.germplasmDbId] },
-                    client,
-                    connection,
-                    profile: profile.supported,
-                    dialect,
-                    config,
-                    loadLimit,
-                    warnings,
-                    ctx,
-                });
-            }
-            catch (err) {
-                warnings.push(`Study '${studyDbId}': observation pull failed (${err instanceof Error ? err.message : String(err)}).`);
+        const outcomes = await pullObservationsForStudies({
+            studyDbIds,
+            input: input.variables
+                ? { germplasm: [input.germplasmDbId], variables: input.variables }
+                : { germplasm: [input.germplasmDbId] },
+            client,
+            connection,
+            profile: profile.supported,
+            dialect,
+            config,
+            loadLimit,
+            failFast: false,
+            ctx,
+        });
+        for (const outcome of outcomes) {
+            warnings.push(...outcome.warnings);
+            if (outcome.error !== undefined) {
+                warnings.push(`Study '${outcome.studyDbId}': observation pull failed (${outcome.error instanceof Error ? outcome.error.message : String(outcome.error)}).`);
                 continue;
             }
-            if (studyObs === null) {
-                warnings.push(`Study '${studyDbId}': no observation path (server exposes neither /observations nor /observationunits).`);
+            if (outcome.observations === null) {
+                warnings.push(`Study '${outcome.studyDbId}': no observation path (server exposes neither /observations nor /observationunits).`);
                 continue;
             }
-            for (const o of studyObs) {
-                if (o.studyDbId !== studyDbId)
+            for (const o of outcome.observations) {
+                if (o.studyDbId !== outcome.studyDbId)
                     continue;
                 if (o.germplasmDbId !== input.germplasmDbId)
                     continue;

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package/dist/mcp-server/tools/definitions/brapi-get-germplasm.tool.d.ts CHANGED Viewed

@@ -51,14 +51,14 @@ export declare const brapiGetGermplasm: import("@cyanheads/mcp-ts-core").ToolDef
     directDescendantCount: z.ZodOptional<z.ZodNumber>;
     warnings: z.ZodArray<z.ZodString>;
 }, z.core.$strip>, readonly [{
-    readonly reason: "unknown_alias";
+    readonly reason: 'unknown_alias';
     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_get_germplasm.";
+    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_get_germplasm.';
 }, {
-    readonly reason: "germplasm_not_found";
+    readonly reason: 'germplasm_not_found';
     readonly code: JsonRpcErrorCode.NotFound;
-    readonly when: "Upstream returned no germplasm record for the requested DbId";
-    readonly recovery: "Verify the germplasmDbId on the target server, or run brapi_find_germplasm to discover valid IDs.";
+    readonly when: 'Upstream returned no germplasm record for the requested DbId';
+    readonly recovery: 'Verify the germplasmDbId on the target server, or run brapi_find_germplasm to discover valid IDs.';
 }], undefined>;
 //# sourceMappingURL=brapi-get-germplasm.tool.d.ts.map

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-get-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA4GjE,eAAO,MAAM,iBAAiB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA2P5B~~,CAAC"}
1	+ {"version":3,"file":"brapi-get-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA4GjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMhB,eAAe;;mBAEjB,6DAA6D;uBAEjE,uHAAuH;;qBAGjH,qBAAqB;;mBAEvB,8DAA8D;uBAElE,mGAAmG;cA0OzG,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-get-image.tool.d.ts CHANGED Viewed

@@ -49,14 +49,14 @@ export declare const brapiGetImage: import("@cyanheads/mcp-ts-core").ToolDefinit
         warning: z.ZodString;
     }, z.core.$strip>>;
 }, z.core.$strip>, readonly [{
-    readonly reason: "unknown_alias";
+    readonly reason: 'unknown_alias';
     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_get_image.";
+    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_get_image.';
 }, {
-    readonly reason: "images_unsupported";
+    readonly reason: 'images_unsupported';
     readonly code: JsonRpcErrorCode.NotFound;
-    readonly when: "BrAPI server does not advertise /images in /serverinfo";
-    readonly recovery: "Run brapi_server_info to inspect the advertised endpoints, or call brapi_connect with a different alias for a server that exposes /images.";
+    readonly when: 'BrAPI server does not advertise /images in /serverinfo';
+    readonly recovery: 'Run brapi_server_info to inspect the advertised endpoints, or call brapi_connect with a different alias for a server that exposes /images.';
 }], undefined>;
 //# sourceMappingURL=brapi-get-image.tool.d.ts.map

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"brapi-get-image.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-image.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAiFjE,eAAO,MAAM,aAAa;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAKZ,eAAe;;mBAEjB,6DAA6D;uBAEjE,mHAAmH;;qBAG7G,oBAAoB;;mBAEtB,wDAAwD;uBAE5D,4IAA4I;cAiJlJ,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-get-study.tool.d.ts CHANGED Viewed

@@ -68,14 +68,14 @@ export declare const brapiGetStudy: import("@cyanheads/mcp-ts-core").ToolDefinit
     variableCount: z.ZodOptional<z.ZodNumber>;
     warnings: z.ZodArray<z.ZodString>;
 }, z.core.$strip>, readonly [{
-    readonly reason: "unknown_alias";
+    readonly reason: 'unknown_alias';
     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_get_study.";
+    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_get_study.';
 }, {
-    readonly reason: "study_not_found";
+    readonly reason: 'study_not_found';
     readonly code: JsonRpcErrorCode.NotFound;
-    readonly when: "Upstream returned no study record for the requested DbId";
-    readonly recovery: "Verify the studyDbId on the target server, or run brapi_find_studies to discover valid IDs.";
+    readonly when: 'Upstream returned no study record for the requested DbId';
+    readonly recovery: 'Verify the studyDbId on the target server, or run brapi_find_studies to discover valid IDs.';
 }], undefined>;
 //# sourceMappingURL=brapi-get-study.tool.d.ts.map

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"brapi-get-study.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-study.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmJjE,eAAO,MAAM,aAAa;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMZ,eAAe;;mBAEjB,6DAA6D;uBAEjE,mHAAmH;;qBAG7G,iBAAiB;;mBAEnB,0DAA0D;uBAE9D,6FAA6F;cA6PnG,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-raw-get.tool.d.ts CHANGED Viewed

@@ -44,14 +44,14 @@ export declare const brapiRawGet: import("@cyanheads/mcp-ts-core").ToolDefinitio
         totalCount: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>;
 }, z.core.$strip>, readonly [{
-    readonly reason: "unknown_alias";
+    readonly reason: 'unknown_alias';
     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_raw_get.";
+    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_raw_get.';
 }, {
-    readonly reason: "cross_origin_path";
+    readonly reason: 'cross_origin_path';
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: "path argument was a full URL instead of a relative BrAPI route";
-    readonly recovery: "Pass a path like \"/samples\" or \"/methods\" — the connection alias supplies the baseUrl.";
+    readonly when: 'path argument was a full URL instead of a relative BrAPI route';
+    readonly recovery: 'Pass a path like "/samples" or "/methods" — the connection alias supplies the baseUrl.';
 }], undefined>;
 //# sourceMappingURL=brapi-raw-get.tool.d.ts.map

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

	@@ -1 +1 @@
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