@cyanheads/brapi-mcp-server 0.7.8 → 0.7.10

package/dist/mcp-server/tools/shared/observations.d.ts

@@ -76,6 +76,73 @@ export interface PullStudyObservationsArgs {
  * empty.
  */
 export declare function pullStudyObservations(args: PullStudyObservationsArgs): Promise<NormObs[] | null>;
+/**
+ * Per-study outcome from {@link pullObservationsForStudies}. Carries the pull
+ * result, the `null` no-observation-path sentinel, or the thrown `error`, plus
+ * the study's own warnings buffer. The caller merges the warnings in input order
+ * and applies its own failure policy (warn-and-continue vs abort) — the helper
+ * itself is policy-neutral.
+ */
+export interface StudyObservationOutcome {
+    /** The error {@link pullStudyObservations} threw for this study, when it threw. */
+    error?: unknown;
+    /**
+     * Observations for the study, or `null` when no usable observation path exists
+     * (mirrors {@link pullStudyObservations}'s `null` return). Also `null` when the
+     * pull threw — disambiguate via `error`.
+     */
+    observations: NormObs[] | null;
+    studyDbId: string;
+    /**
+     * Warnings this study's pull produced. Kept per-study (not a shared array) so
+     * concurrent pulls never interleave their warnings — the caller concatenates
+     * them in input order for a deterministic result.
+     */
+    warnings: string[];
+}
+/**
+ * Shared inputs for {@link pullObservationsForStudies} — everything a per-study
+ * pull needs except the `studyDbId` and its warnings buffer (both per-study).
+ */
+export interface PullObservationsForStudiesArgs {
+    client: BrapiClient;
+    config: ServerConfig;
+    connection: RegisteredServer;
+    ctx: Context;
+    dialect: BrapiDialect;
+    /**
+     * When true, stop launching further batches once a batch contains a study that
+     * threw or has no observation path — `brapi_build_phenotype_matrix` aborts on
+     * the first such study, so pulling the rest would be wasted upstream load. When
+     * false (`brapi_germplasm_performance`), every study is pulled regardless.
+     */
+    failFast: boolean;
+    input: ObservationPullFilters;
+    loadLimit: number;
+    profile: Record<string, CallDescriptor>;
+    studyDbIds: string[];
+}
+/**
+ * Pull observations for many studies with bounded concurrency, returning
+ * per-study outcomes in **input order** — never completion order.
+ *
+ * Studies are processed in sequential batches of `config.maxConcurrentRequests`
+ * (this is the first and only consumer of that config); within a batch the
+ * per-study pulls run concurrently, so a slow study no longer serializes the
+ * rest of its batch. `Promise.all` over internally-caught tasks preserves input
+ * order for free and never rejects: a single study's failure is folded into its
+ * outcome rather than aborting the batch or losing the others' results.
+ *
+ * Callers own the failure policy — `brapi_germplasm_performance` walks every
+ * outcome and warns-and-continues; `brapi_build_phenotype_matrix` sets
+ * `failFast` and rethrows the `error` / raises `no_observation_path` on the first
+ * failing study. Input-order reassembly is load-bearing: both tools derive
+ * deterministic column/row ordering from study encounter order, so a
+ * completion-order reassembly would make an identical query's output flap.
+ *
+ * @param pull - the per-study pull, injectable for tests; defaults to {@link pullStudyObservations}.
+ */
+export declare function pullObservationsForStudies(args: PullObservationsForStudiesArgs, pull?: (a: PullStudyObservationsArgs) => Promise<NormObs[] | null>): Promise<StudyObservationOutcome[]>;
 /** Normalise a raw /observations row; drops rows missing any required field. */
 export declare function normalizeObsRow(row: RawObservationRow): NormObs | null;
 /**

package/dist/mcp-server/tools/shared/observations.d.ts.map

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package/dist/mcp-server/tools/shared/observations.js

@@ -108,6 +108,62 @@ export async function pullStudyObservations(args) {
     warnings.push(`Study '${studyDbId}': No observations found via /observations or /observationunits.`);
     return [];
 }
+/**
+ * Pull observations for many studies with bounded concurrency, returning
+ * per-study outcomes in **input order** — never completion order.
+ *
+ * Studies are processed in sequential batches of `config.maxConcurrentRequests`
+ * (this is the first and only consumer of that config); within a batch the
+ * per-study pulls run concurrently, so a slow study no longer serializes the
+ * rest of its batch. `Promise.all` over internally-caught tasks preserves input
+ * order for free and never rejects: a single study's failure is folded into its
+ * outcome rather than aborting the batch or losing the others' results.
+ *
+ * Callers own the failure policy — `brapi_germplasm_performance` walks every
+ * outcome and warns-and-continues; `brapi_build_phenotype_matrix` sets
+ * `failFast` and rethrows the `error` / raises `no_observation_path` on the first
+ * failing study. Input-order reassembly is load-bearing: both tools derive
+ * deterministic column/row ordering from study encounter order, so a
+ * completion-order reassembly would make an identical query's output flap.
+ *
+ * @param pull - the per-study pull, injectable for tests; defaults to {@link pullStudyObservations}.
+ */
+export async function pullObservationsForStudies(args, pull = pullStudyObservations) {
+    const { studyDbIds, input, client, config, connection, ctx, dialect, loadLimit, profile, failFast, } = args;
+    const batchSize = Math.max(1, config.maxConcurrentRequests);
+    const outcomes = [];
+    for (let start = 0; start < studyDbIds.length; start += batchSize) {
+        if (ctx.signal.aborted)
+            break;
+        const batch = studyDbIds.slice(start, start + batchSize);
+        const batchOutcomes = await Promise.all(batch.map(async (studyDbId) => {
+            const warnings = [];
+            try {
+                const observations = await pull({
+                    studyDbId,
+                    input,
+                    client,
+                    connection,
+                    profile,
+                    dialect,
+                    config,
+                    loadLimit,
+                    warnings,
+                    ctx,
+                });
+                return { studyDbId, observations, warnings };
+            }
+            catch (error) {
+                return { studyDbId, observations: null, error, warnings };
+            }
+        }));
+        outcomes.push(...batchOutcomes);
+        if (failFast && batchOutcomes.some((o) => o.error !== undefined || o.observations === null)) {
+            break;
+        }
+    }
+    return outcomes;
+}
 function supportsGet(profile, service) {
     const descriptor = profile[service];
     if (!descriptor)

package/dist/mcp-server/tools/shared/observations.js.map

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

@@ -1,7 +1,7 @@
 {
   "manifest_version": "0.3",
   "name": "brapi-mcp-server",
-  "version": "0.7.8",
+  "version": "0.7.10",
   "description": "Collaborative BrAPI v2.1 MCP workspace — studies, germplasm, genotypes across Breedbase, T3, more.",
   "author": {
     "name": "cyanheads"

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@cyanheads/brapi-mcp-server",
   "mcpName": "io.github.cyanheads/brapi-mcp-server",
-  "version": "0.7.8",
+  "version": "0.7.10",
   "description": "A collaborative BrAPI v2.1 workspace for multi-agent research via MCP. Search studies, germplasm, genotypes, & more - across Breedbase, T3, Sweetpotatobase, & any BrAPI v2-compliant server.",
   "author": "Casey Hand <casey@caseyjhand.com> (https://caseyjhand.com)",
   "type": "module",
@@ -92,7 +92,7 @@
     "@types/node": "^26.1.1",
     "depcheck": "^1.4.7",
     "ignore": "^7.0.6",
-    "tsc-alias": "^1.8.17",
+    "tsc-alias": "^1.9.1",
     "typescript": "^6.0.3",
     "vitest": "^4.1.10"
   }

package/server.json

@@ -6,14 +6,14 @@
     "url": "https://github.com/cyanheads/brapi-mcp-server",
     "source": "github"
   },
-  "version": "0.7.8",
+  "version": "0.7.10",
   "packages": [
     {
       "registryType": "npm",
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.7.8",
+      "version": "0.7.10",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:stdio" }
@@ -56,7 +56,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.7.8",
+      "version": "0.7.10",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:http" }