@cyanheads/brapi-mcp-server 0.6.4 → 0.7.0

package/dist/mcp-server/tools/shared/genotype-calls.js.map

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/shared/observations.d.ts

@@ -0,0 +1,87 @@
+/**
+ * @fileoverview Shared observation-pull logic for the phenotype tools
+ * (`brapi_build_phenotype_matrix`, `brapi_germplasm_performance`). Owns the
+ * study-anchored observation collection strategy and the raw/normalized row
+ * shapes, so both tools pull observations identically without duplicating the
+ * server-dependent fallback chain.
+ *
+ * Observation pull strategy (server-dependent), per study:
+ *   1. Prefer `/observations?studyDbId=…` (BrAPI spec path).
+ *   2. Fall back to `/observationunits?studyDbId=…` with embedded
+ *      `observations[]` arrays when `/observations` returns empty or the dialect
+ *      drops the study filter — required for the BrAPI Community Test Server,
+ *      where `/observations?studyDbId` is not honored.
+ *   3. When units carry `germplasmDbId`s but no embedded observations, pull
+ *      `/observations?germplasmDbId=…` per germplasm and filter back to the
+ *      study — stays study-anchored without an unbounded scan.
+ *
+ * `pullStudyObservations` returns `null` only when no usable observation path
+ * exists for the study (caller throws its typed `no_observation_path` error);
+ * an empty array means the paths exist but yielded no rows.
+ *
+ * @module mcp-server/tools/shared/observations
+ */
+import type { Context } from '@cyanheads/mcp-ts-core';
+import type { ServerConfig } from '../../../config/server-config.js';
+import { type BrapiClient } from '../../../services/brapi-client/index.js';
+import type { BrapiDialect } from '../../../services/brapi-dialect/index.js';
+import type { CallDescriptor } from '../../../services/capability-registry/types.js';
+import type { RegisteredServer } from '../../../services/server-registry/index.js';
+/** Raw BrAPI `/observations` row shape (passthrough). */
+export interface RawObservationRow {
+    germplasmDbId?: string | null;
+    germplasmName?: string | null;
+    observationDbId?: string | null;
+    observationVariableDbId?: string | null;
+    observationVariableName?: string | null;
+    season?: unknown;
+    seasonDbId?: string | null;
+    studyDbId?: string | null;
+    value?: string | null;
+    [key: string]: unknown;
+}
+/** Normalized observation — required fields are non-empty strings after extraction. */
+export interface NormObs {
+    germplasmDbId: string;
+    germplasmName: string;
+    observationVariableDbId: string;
+    observationVariableName: string;
+    /** Human season label (`"spring 2013"` / seasonDbId), when the row carries one. */
+    season?: string;
+    studyDbId: string;
+    value: string;
+}
+/** Filters that scope an observation pull beyond the study anchor. */
+export interface ObservationPullFilters {
+    extraFilters?: Record<string, unknown> | undefined;
+    germplasm?: string[] | undefined;
+    variables?: string[] | undefined;
+}
+export interface PullStudyObservationsArgs {
+    client: BrapiClient;
+    config: ServerConfig;
+    connection: RegisteredServer;
+    ctx: Context;
+    dialect: BrapiDialect;
+    input: ObservationPullFilters;
+    loadLimit: number;
+    profile: Record<string, CallDescriptor>;
+    studyDbId: string;
+    warnings: string[];
+}
+/**
+ * Collect observations for a single study, trying `/observations` first and
+ * falling back to `/observationunits` (embedded, then germplasm-anchored).
+ * Returns `null` when no usable path exists; `[]` when paths exist but are
+ * empty.
+ */
+export declare function pullStudyObservations(args: PullStudyObservationsArgs): Promise<NormObs[] | null>;
+/** Normalise a raw /observations row; drops rows missing any required field. */
+export declare function normalizeObsRow(row: RawObservationRow): NormObs | null;
+/**
+ * Derive a human season label from a BrAPI observation row. Servers carry
+ * season either as a nested object (`{ seasonName, year, seasonDbId }`) or a
+ * flat `seasonDbId` string. Returns undefined when neither is present.
+ */
+export declare function seasonLabel(row: RawObservationRow): string | undefined;
+//# sourceMappingURL=observations.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/shared/observations.js

@@ -0,0 +1,285 @@
+/**
+ * @fileoverview Shared observation-pull logic for the phenotype tools
+ * (`brapi_build_phenotype_matrix`, `brapi_germplasm_performance`). Owns the
+ * study-anchored observation collection strategy and the raw/normalized row
+ * shapes, so both tools pull observations identically without duplicating the
+ * server-dependent fallback chain.
+ *
+ * Observation pull strategy (server-dependent), per study:
+ *   1. Prefer `/observations?studyDbId=…` (BrAPI spec path).
+ *   2. Fall back to `/observationunits?studyDbId=…` with embedded
+ *      `observations[]` arrays when `/observations` returns empty or the dialect
+ *      drops the study filter — required for the BrAPI Community Test Server,
+ *      where `/observations?studyDbId` is not honored.
+ *   3. When units carry `germplasmDbId`s but no embedded observations, pull
+ *      `/observations?germplasmDbId=…` per germplasm and filter back to the
+ *      study — stays study-anchored without an unbounded scan.
+ *
+ * `pullStudyObservations` returns `null` only when no usable observation path
+ * exists for the study (caller throws its typed `no_observation_path` error);
+ * an empty array means the paths exist but yielded no rows.
+ *
+ * @module mcp-server/tools/shared/observations
+ */
+import { isDialectAllDropped } from '../../../services/brapi-client/index.js';
+import { companionRequestOptions, extractRows, mergeFilters, } from './find-helpers.js';
+/**
+ * Collect observations for a single study, trying `/observations` first and
+ * falling back to `/observationunits` (embedded, then germplasm-anchored).
+ * Returns `null` when no usable path exists; `[]` when paths exist but are
+ * empty.
+ */
+export async function pullStudyObservations(args) {
+    const { studyDbId, input, client, connection, dialect, config, loadLimit, warnings, ctx } = args;
+    // Build named filters for observations endpoint
+    const namedFilters = {
+        studyDbIds: [studyDbId],
+    };
+    if (input.variables?.length)
+        namedFilters.observationVariableDbIds = input.variables;
+    if (input.germplasm?.length)
+        namedFilters.germplasmDbIds = input.germplasm;
+    const merged = mergeFilters(namedFilters, input.extraFilters, warnings);
+    // Apply dialect (plurals → singulars on SGN-family servers)
+    const adapted = dialect.adaptGetFilters('observations', merged);
+    warnings.push(...adapted.warnings);
+    // When the dialect drops ALL filters for /observations (known case: the
+    // brapi-test server doesn't honor studyDbId on /observations at all), skip
+    // the observations path entirely and go straight to the observationunits
+    // fallback rather than making an unscoped request.
+    const obsFiltersDropped = adapted.dropped.length > 0 && Object.keys(adapted.filters).length === 0;
+    const obsFilters = adapted.filters;
+    // ---- Path 1: /observations ----
+    const supportsObservations = supportsGet(args.profile, 'observations') && !obsFiltersDropped;
+    if (supportsObservations) {
+        const obs = await fetchObservationsPath(client, connection, dialect, config, obsFilters, loadLimit, ctx);
+        if (obs !== null && obs.length > 0) {
+            return obs;
+        }
+        if (obs !== null && obs.length === 0) {
+            // Server responded with empty for this study — note it and try fallback
+            warnings.push(`Study '${studyDbId}': /observations returned 0 rows — trying /observationunits fallback.`);
+        }
+    }
+    else if (obsFiltersDropped) {
+        warnings.push(`Study '${studyDbId}': dialect '${dialect.id}' drops all study filters for /observations — using /observationunits fallback.`);
+    }
+    // ---- Path 2: /observationunits fallback ----
+    // Two sub-strategies:
+    //   2a. Units embed observations[] arrays — extract directly.
+    //   2b. Units carry germplasmDbIds but observations[] is null — pull
+    //       /observations?germplasmDbId=X per germplasm found in the study.
+    const supportsObsUnits = supportsGet(args.profile, 'observationunits');
+    if (supportsObsUnits) {
+        const unitResult = await fetchObservationUnitsRaw(client, connection, dialect, config, studyDbId, loadLimit, ctx);
+        if (unitResult !== null) {
+            // 2a: check for embedded observations
+            const embeddedObs = extractEmbeddedObservations(unitResult, studyDbId);
+            if (embeddedObs.length > 0) {
+                warnings.push(`Study '${studyDbId}': Using /observationunits embedded observations[] fallback.`);
+                return embeddedObs;
+            }
+            // 2b: germplasm-anchored pull — units have germplasmDbIds, use them
+            let germplasmIds = [
+                ...new Set(unitResult
+                    .map((u) => u.germplasmDbId)
+                    .filter((id) => typeof id === 'string' && id.length > 0)),
+            ];
+            // When the caller scoped to specific germplasm, pull only those — avoids
+            // an O(all-germplasm-in-study) fan-out for single-germplasm callers (#9).
+            if (input.germplasm?.length) {
+                const want = new Set(input.germplasm);
+                germplasmIds = germplasmIds.filter((g) => want.has(g));
+            }
+            if (germplasmIds.length > 0) {
+                const germObs = await fetchObservationsByGermplasm(client, connection, dialect, config, germplasmIds, studyDbId, loadLimit, ctx);
+                if (germObs !== null && germObs.length > 0) {
+                    warnings.push(`Study '${studyDbId}': Used /observationunits → /observations?germplasmDbId fallback because studyDbId filter is not honored on /observations.`);
+                    return germObs;
+                }
+            }
+        }
+    }
+    // Neither path yielded data. Distinguish "no path" from "empty".
+    if (!supportsObservations && !obsFiltersDropped && !supportsObsUnits) {
+        return null; // caller throws typed error
+    }
+    // Paths exist but all returned empty — treat as empty (not an error)
+    warnings.push(`Study '${studyDbId}': No observations found via /observations or /observationunits.`);
+    return [];
+}
+function supportsGet(profile, service) {
+    const descriptor = profile[service];
+    if (!descriptor)
+        return false;
+    if (!descriptor.methods || descriptor.methods.length === 0)
+        return true;
+    return descriptor.methods.includes('GET');
+}
+/** Fetch from /observations with study-anchored filters. Returns null on error. */
+async function fetchObservationsPath(client, connection, dialect, config, filters, pageSize, ctx) {
+    try {
+        const opts = companionRequestOptions(connection, dialect, config, [], {
+            ...filters,
+            pageSize,
+        });
+        const envelope = await client.get(connection.baseUrl, '/observations', ctx, opts);
+        const rows = extractRows(envelope.result);
+        return rows.flatMap(normalizeObsRow).filter(Boolean);
+    }
+    catch (err) {
+        if (isDialectAllDropped(err))
+            throw err;
+        return null;
+    }
+}
+/** Fetch raw observationunit records (without extracting observations). Returns null on error. */
+async function fetchObservationUnitsRaw(client, connection, dialect, config, studyDbId, pageSize, ctx) {
+    try {
+        const rawFilters = { studyDbIds: [studyDbId] };
+        const adapted = dialect.adaptGetFilters('observationunits', rawFilters);
+        const obsUnitFilters = adapted.filters;
+        const opts = companionRequestOptions(connection, dialect, config, [], {
+            ...obsUnitFilters,
+            pageSize,
+        });
+        const envelope = await client.get(connection.baseUrl, '/observationunits', ctx, opts);
+        return extractRows(envelope.result);
+    }
+    catch (err) {
+        if (isDialectAllDropped(err))
+            throw err;
+        return null;
+    }
+}
+/** Extract embedded observations[] from observationunit records (strategy 2a). */
+function extractEmbeddedObservations(units, studyDbId) {
+    const obs = [];
+    for (const unit of units) {
+        const unitStudyDbId = unit.studyDbId ?? studyDbId;
+        const unitGermplasmDbId = unit.germplasmDbId ?? 'unknown';
+        const unitGermplasmName = typeof unit.germplasmName === 'string' && unit.germplasmName.length > 0
+            ? unit.germplasmName
+            : unitGermplasmDbId;
+        const embedded = unit.observations;
+        if (!Array.isArray(embedded))
+            continue;
+        for (const raw of embedded) {
+            if (!raw || typeof raw !== 'object')
+                continue;
+            const r = raw;
+            const varId = r.observationVariableDbId ?? null;
+            const val = r.value ?? null;
+            if (!varId || val === null || val === undefined)
+                continue;
+            const season = seasonLabel(r);
+            obs.push({
+                germplasmDbId: unitGermplasmDbId,
+                germplasmName: unitGermplasmName,
+                observationVariableDbId: String(varId),
+                observationVariableName: typeof r.observationVariableName === 'string' && r.observationVariableName.length > 0
+                    ? r.observationVariableName
+                    : String(varId),
+                studyDbId: unitStudyDbId,
+                value: String(val),
+                ...(season ? { season } : {}),
+            });
+        }
+    }
+    return obs;
+}
+/**
+ * Pull observations anchored by germplasmDbId (strategy 2b). Used when
+ * studyDbId filter is not honored on /observations but we know germplasmDbIds
+ * in the study from the observationunits response. Filters results to only
+ * observations for the target study.
+ */
+async function fetchObservationsByGermplasm(client, connection, dialect, config, germplasmIds, studyDbId, pageSize, ctx) {
+    try {
+        // Pull per germplasm to stay study-anchored. Bound by pageSize per call.
+        // For wide queries this is O(germplasmCount) requests but avoids an
+        // unbounded full-table scan on the observations endpoint.
+        const allObs = [];
+        for (const germId of germplasmIds) {
+            const rawFilters = { germplasmDbIds: [germId] };
+            const adapted = dialect.adaptGetFilters('observations', rawFilters);
+            // Skip if the germplasm filter is also dropped
+            if (adapted.dropped.length > 0 && Object.keys(adapted.filters).length === 0)
+                continue;
+            const opts = companionRequestOptions(connection, dialect, config, [], {
+                ...adapted.filters,
+                pageSize,
+            });
+            try {
+                const envelope = await client.get(connection.baseUrl, '/observations', ctx, opts);
+                const rows = extractRows(envelope.result);
+                // Filter to only observations for the target study
+                for (const row of rows) {
+                    if (row.studyDbId !== studyDbId)
+                        continue;
+                    const norm = normalizeObsRow(row);
+                    if (norm)
+                        allObs.push(norm);
+                }
+            }
+            catch { }
+        }
+        return allObs;
+    }
+    catch (err) {
+        if (isDialectAllDropped(err))
+            throw err;
+        return null;
+    }
+}
+/** Normalise a raw /observations row; drops rows missing any required field. */
+export function normalizeObsRow(row) {
+    const varId = row.observationVariableDbId ?? null;
+    const germId = row.germplasmDbId ?? null;
+    const studyId = row.studyDbId ?? null;
+    const val = row.value ?? null;
+    if (!varId || !germId || !studyId || val === null || val === undefined)
+        return null;
+    const norm = {
+        germplasmDbId: String(germId),
+        germplasmName: typeof row.germplasmName === 'string' && row.germplasmName.length > 0
+            ? row.germplasmName
+            : String(germId),
+        observationVariableDbId: String(varId),
+        observationVariableName: typeof row.observationVariableName === 'string' && row.observationVariableName.length > 0
+            ? row.observationVariableName
+            : String(varId),
+        studyDbId: String(studyId),
+        value: String(val),
+    };
+    const season = seasonLabel(row);
+    if (season)
+        norm.season = season;
+    return norm;
+}
+/**
+ * Derive a human season label from a BrAPI observation row. Servers carry
+ * season either as a nested object (`{ seasonName, year, seasonDbId }`) or a
+ * flat `seasonDbId` string. Returns undefined when neither is present.
+ */
+export function seasonLabel(row) {
+    const s = row.season;
+    if (s && typeof s === 'object') {
+        const so = s;
+        const name = typeof so.seasonName === 'string' && so.seasonName.length > 0 ? so.seasonName : undefined;
+        const year = typeof so.year === 'number' ? so.year : undefined;
+        if (name && year !== undefined)
+            return `${name} ${year}`;
+        if (name)
+            return name;
+        if (typeof so.seasonDbId === 'string' && so.seasonDbId.length > 0)
+            return so.seasonDbId;
+    }
+    else if (typeof s === 'string' && s.length > 0) {
+        return s;
+    }
+    if (typeof row.seasonDbId === 'string' && row.seasonDbId.length > 0)
+        return row.seasonDbId;
+    return;
+}
+//# sourceMappingURL=observations.js.map

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

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package/manifest.json

@@ -1,7 +1,7 @@
 {
   "manifest_version": "0.3",
   "name": "brapi-mcp-server",
-  "version": "0.6.4",
+  "version": "0.7.0",
   "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": "0.6.4",
+  "version": "0.7.0",
   "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 @cyanheads (https://github.com/cyanheads/brapi-mcp-server#readme)",
   "type": "module",
@@ -81,7 +81,7 @@
   },
   "dependencies": {
     "@cyanheads/mcp-ts-core": "^0.9.16",
-    "@duckdb/node-api": "^1.5.3-r.2",
+    "@duckdb/node-api": "^1.5.3-r.3",
     "pino-pretty": "^13.1.3",
     "zod": "^4.4.3"
   },
@@ -92,6 +92,6 @@
     "ignore": "^7.0.5",
     "tsc-alias": "^1.8.17",
     "typescript": "^6.0.3",
-    "vitest": "^4.1.7"
+    "vitest": "^4.1.8"
   }
 }

package/server.json

@@ -6,14 +6,14 @@
     "url": "https://github.com/cyanheads/brapi-mcp-server",
     "source": "github"
   },
-  "version": "0.6.4",
+  "version": "0.7.0",
   "packages": [
     {
       "registryType": "npm",
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.6.4",
+      "version": "0.7.0",
       "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": "0.6.4",
+      "version": "0.7.0",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:http" }