@cyanheads/brapi-mcp-server 0.3.5

package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.js

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+/**
+ * @fileoverview `brapi_walk_pedigree` — walk germplasm ancestry or
+ * descendancy as a DAG. BrAPI only exposes direct parents / direct progeny
+ * per call, so we BFS outward from each root up to `maxDepth`, deduplicate
+ * nodes (cultivars may appear on multiple paths), and break cycles.
+ * Response includes traversal stats so the agent can see how the walk
+ * terminated without re-running the tool.
+ *
+ * @module mcp-server/tools/definitions/brapi-walk-pedigree.tool
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { getBrapiClient } from '../../../services/brapi-client/index.js';
+import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
+import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
+import { AliasInput, buildRequestOptions, isUpstreamNotFound } from '../shared/find-helpers.js';
+const DEFAULT_MAX_DEPTH = 3;
+const MAX_NODES = 1_000;
+const NodeSchema = z
+    .object({
+    germplasmDbId: z.string().describe('Server-side identifier for the germplasm.'),
+    germplasmName: z.string().optional().describe('Display name of the germplasm.'),
+    depth: z
+        .number()
+        .int()
+        .nonnegative()
+        .describe('Min distance from any root germplasm (0 for roots).'),
+    isRoot: z.boolean().describe('True when this node is one of the starting germplasm.'),
+})
+    .describe('One germplasm reached during the walk.');
+const EdgeSchema = z
+    .object({
+    from: z.string().describe('germplasmDbId of the source of the relationship.'),
+    to: z.string().describe('germplasmDbId of the target.'),
+    relationship: z
+        .enum(['parent', 'child'])
+        .describe('Direction: parent = from is a parent of to; child = from is a descendant of to.'),
+    parentType: z
+        .string()
+        .optional()
+        .describe('E.g. MALE, FEMALE, SELF, when the upstream response supplies it.'),
+})
+    .describe('One deduplicated pedigree edge between two nodes.');
+const OutputSchema = z.object({
+    alias: z.string().describe('Alias of the registered BrAPI connection the call used.'),
+    direction: z
+        .enum(['ancestors', 'descendants', 'both'])
+        .describe('The direction the walk expanded (echoed from the input).'),
+    maxDepth: z
+        .number()
+        .int()
+        .positive()
+        .describe('The maximum depth the walk was allowed to reach (echoed from the input).'),
+    nodes: z
+        .array(NodeSchema)
+        .describe('Deduplicated node list — every germplasm reached by the walk, sorted by depth then DbId.'),
+    edges: z
+        .array(EdgeSchema)
+        .describe('Deduplicated edge list. `relationship: "parent"` means `from` is a parent of `to`; `relationship: "child"` means `from` is a descendant of `to`.'),
+    depthReached: z
+        .number()
+        .int()
+        .nonnegative()
+        .describe('Deepest BFS level that produced at least one new edge (0 if only roots were walked).'),
+    rootCount: z.number().int().nonnegative().describe('Number of starting germplasm roots.'),
+    leafCount: z
+        .number()
+        .int()
+        .nonnegative()
+        .describe('Nodes that have no outgoing edges in the walked direction — terminal in the DAG.'),
+    cycleCount: z
+        .number()
+        .int()
+        .nonnegative()
+        .describe('Number of times the walk revisited an already-registered node (cycles broken).'),
+    deadEndCount: z
+        .number()
+        .int()
+        .nonnegative()
+        .describe('Nodes whose upstream pedigree/progeny lookup failed.'),
+    truncated: z
+        .boolean()
+        .describe(`True when the walk hit the ${MAX_NODES}-node safety cap before exhausting depth.`),
+    warnings: z
+        .array(z.string())
+        .describe('Advisory messages (capability gaps, per-node expansion failures).'),
+});
+export const brapiWalkPedigree = tool('brapi_walk_pedigree', {
+    description: 'Walk germplasm ancestry or descendancy as a deduplicated DAG, with multi-generation traversal, cycle detection, and depth limits. Returns nodes + edges plus traversal stats (depthReached, rootCount, leafCount, cycleCount, deadEndCount).',
+    annotations: { readOnlyHint: true, openWorldHint: true },
+    input: z.object({
+        germplasmDbIds: z
+            .array(z.string().min(1))
+            .min(1)
+            .max(20)
+            .describe('Starting germplasm (1–20 roots). All roots are walked concurrently.'),
+        direction: z
+            .enum(['ancestors', 'descendants', 'both'])
+            .default('ancestors')
+            .describe('Which direction to walk: ancestors (parents), descendants (progeny), or both.'),
+        maxDepth: z
+            .number()
+            .int()
+            .positive()
+            .max(10)
+            .default(DEFAULT_MAX_DEPTH)
+            .describe(`Max generations to walk per direction (default ${DEFAULT_MAX_DEPTH}, cap 10).`),
+        alias: AliasInput,
+    }),
+    output: OutputSchema,
+    async handler(input, ctx) {
+        const registry = getServerRegistry();
+        const capabilities = getCapabilityRegistry();
+        const client = getBrapiClient();
+        const connection = await registry.get(ctx, input.alias ?? DEFAULT_ALIAS);
+        const capabilityLookup = {};
+        if (connection.resolvedAuth)
+            capabilityLookup.auth = connection.resolvedAuth;
+        await capabilities.ensure(connection.baseUrl, { service: 'germplasm', method: 'GET' }, ctx, capabilityLookup);
+        const profile = await capabilities.profile(connection.baseUrl, ctx, capabilityLookup);
+        const hasPedigree = Boolean(profile.supported['germplasm/{germplasmDbId}/pedigree']);
+        const hasProgeny = Boolean(profile.supported['germplasm/{germplasmDbId}/progeny']);
+        const warnings = [];
+        const wantsAncestors = input.direction === 'ancestors' || input.direction === 'both';
+        const wantsDescendants = input.direction === 'descendants' || input.direction === 'both';
+        if (wantsAncestors && !hasPedigree) {
+            warnings.push('Server does not expose /germplasm/{id}/pedigree — ancestor traversal is skipped.');
+        }
+        if (wantsDescendants && !hasProgeny) {
+            warnings.push('Server does not expose /germplasm/{id}/progeny — descendant traversal is skipped.');
+        }
+        if (hasPedigree) {
+            const missing = await Promise.all(input.germplasmDbIds.map(async (id) => (await rootExists(id, client, connection, ctx)) ? null : id));
+            for (const id of missing) {
+                if (id)
+                    warnings.push(`Root germplasm '${id}' was not found in /germplasm/{id}/pedigree.`);
+            }
+        }
+        const state = createWalkState(input.germplasmDbIds);
+        let truncated = false;
+        let cycleCount = 0;
+        let deadEndCount = 0;
+        let depthReached = 0;
+        for (let depth = 1; depth <= input.maxDepth; depth++) {
+            if (state.nodes.size >= MAX_NODES) {
+                truncated = true;
+                break;
+            }
+            const previousFrontier = state.frontier;
+            state.frontier = new Set();
+            if (previousFrontier.size === 0)
+                break;
+            const exp = await Promise.all(Array.from(previousFrontier).map(async (id) => expandNode(id, {
+                client,
+                connection,
+                ctx,
+                walkAncestors: wantsAncestors && hasPedigree,
+                walkDescendants: wantsDescendants && hasProgeny,
+            })));
+            let producedEdge = false;
+            for (const result of exp) {
+                if (result.kind === 'deadEnd') {
+                    deadEndCount++;
+                    warnings.push(`Expansion failed for ${result.id}: ${result.error}`);
+                    continue;
+                }
+                for (const parent of result.parents) {
+                    const already = state.nodes.has(parent.germplasmDbId);
+                    registerNode(state, parent.germplasmDbId, parent.germplasmName, depth);
+                    const edge = {
+                        from: parent.germplasmDbId,
+                        to: result.id,
+                        relationship: 'parent',
+                    };
+                    if (parent.parentType)
+                        edge.parentType = parent.parentType;
+                    const inverseKnown = isInverseEdgeKnown(state, edge);
+                    if (addEdge(state, edge))
+                        producedEdge = true;
+                    if (already) {
+                        // direction='both' walks BFS in two directions concurrently — we
+                        // expect to re-encounter nodes via the inverse relationship as the
+                        // expansions meet. That's a structural symmetry, not a cycle.
+                        if (!inverseKnown)
+                            cycleCount++;
+                    }
+                    else {
+                        state.frontier.add(parent.germplasmDbId);
+                    }
+                }
+                for (const child of result.children) {
+                    const already = state.nodes.has(child.germplasmDbId);
+                    registerNode(state, child.germplasmDbId, child.germplasmName, depth);
+                    const edge = {
+                        from: child.germplasmDbId,
+                        to: result.id,
+                        relationship: 'child',
+                    };
+                    const inverseKnown = isInverseEdgeKnown(state, edge);
+                    if (addEdge(state, edge))
+                        producedEdge = true;
+                    if (already) {
+                        if (!inverseKnown)
+                            cycleCount++;
+                    }
+                    else {
+                        state.frontier.add(child.germplasmDbId);
+                    }
+                }
+            }
+            if (producedEdge)
+                depthReached = depth;
+            if (state.frontier.size === 0)
+                break;
+        }
+        const nodes = Array.from(state.nodes.values()).sort((a, b) => a.depth - b.depth || a.germplasmDbId.localeCompare(b.germplasmDbId));
+        const edges = Array.from(state.edges.values());
+        const leafCount = computeLeafCount(nodes, edges);
+        const result = {
+            alias: connection.alias,
+            direction: input.direction,
+            maxDepth: input.maxDepth,
+            nodes,
+            edges,
+            depthReached,
+            rootCount: input.germplasmDbIds.length,
+            leafCount,
+            cycleCount,
+            deadEndCount,
+            truncated,
+            warnings,
+        };
+        return result;
+    },
+    format: (result) => {
+        const lines = [];
+        lines.push(`# Pedigree walk — ${result.direction}, depth ${result.depthReached}/${result.maxDepth} — \`${result.alias}\``);
+        lines.push('');
+        lines.push('## Stats');
+        lines.push(`- nodes: ${result.nodes.length}`);
+        lines.push(`- edges: ${result.edges.length}`);
+        lines.push(`- rootCount: ${result.rootCount}`);
+        lines.push(`- leafCount: ${result.leafCount}`);
+        lines.push(`- cycleCount: ${result.cycleCount}`);
+        lines.push(`- deadEndCount: ${result.deadEndCount}`);
+        lines.push(`- truncated: ${result.truncated}`);
+        if (result.nodes.length > 0) {
+            lines.push('');
+            lines.push('## Nodes');
+            for (const node of result.nodes) {
+                const parts = [`**${node.germplasmName ?? node.germplasmDbId}**`];
+                parts.push(`id=\`${node.germplasmDbId}\``);
+                parts.push(`depth=${node.depth}`);
+                if (node.isRoot)
+                    parts.push('root');
+                lines.push(`- ${parts.join(' · ')}`);
+            }
+        }
+        if (result.edges.length > 0) {
+            lines.push('');
+            lines.push('## Edges');
+            for (const edge of result.edges) {
+                const suffix = edge.parentType ? ` (${edge.parentType})` : '';
+                const arrow = edge.relationship === 'parent' ? '→' : '←';
+                lines.push(`- \`${edge.from}\` ${arrow} \`${edge.to}\` · ${edge.relationship}${suffix}`);
+            }
+        }
+        if (result.warnings.length > 0) {
+            lines.push('');
+            lines.push('## Warnings');
+            for (const w of result.warnings)
+                lines.push(`- ${w}`);
+        }
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+function createWalkState(rootIds) {
+    const nodes = new Map();
+    const frontier = new Set();
+    for (const id of rootIds) {
+        nodes.set(id, { germplasmDbId: id, depth: 0, isRoot: true });
+        frontier.add(id);
+    }
+    return { nodes, edges: new Map(), frontier };
+}
+function registerNode(state, id, name, depth) {
+    const existing = state.nodes.get(id);
+    if (existing) {
+        if (!existing.germplasmName && name)
+            existing.germplasmName = name;
+        if (depth < existing.depth)
+            existing.depth = depth;
+        return;
+    }
+    const node = { germplasmDbId: id, depth, isRoot: false };
+    if (name)
+        node.germplasmName = name;
+    state.nodes.set(id, node);
+}
+function addEdge(state, edge) {
+    const key = `${edge.relationship}:${edge.from}→${edge.to}`;
+    if (state.edges.has(key))
+        return false;
+    state.edges.set(key, edge);
+    return true;
+}
+/**
+ * `parent: A→B` and `child: B→A` describe the same biological relationship
+ * from opposite ends. When direction='both', BFS will discover both —
+ * detecting the inverse lets us avoid double-counting it as a cycle.
+ */
+function isInverseEdgeKnown(state, edge) {
+    const inverseRel = edge.relationship === 'parent' ? 'child' : 'parent';
+    return state.edges.has(`${inverseRel}:${edge.to}→${edge.from}`);
+}
+async function expandNode(id, input) {
+    try {
+        const encoded = encodeURIComponent(id);
+        const [pedigree, progeny] = await Promise.all([
+            input.walkAncestors
+                ? fetchPedigree(input.client, input.connection, encoded, input.ctx)
+                : Promise.resolve([]),
+            input.walkDescendants
+                ? fetchProgeny(input.client, input.connection, encoded, input.ctx)
+                : Promise.resolve([]),
+        ]);
+        return { kind: 'ok', id, parents: pedigree, children: progeny };
+    }
+    catch (err) {
+        return {
+            kind: 'deadEnd',
+            id,
+            error: err instanceof Error ? err.message : String(err),
+        };
+    }
+}
+async function rootExists(id, client, connection, ctx) {
+    try {
+        const env = await client.get(connection.baseUrl, `/germplasm/${encodeURIComponent(id)}/pedigree`, ctx, buildRequestOptions(connection));
+        // Some servers (e.g. test-server.brapi.org) reply 200 with `result: null`
+        // for unknown germplasm instead of 404.
+        return env.result != null;
+    }
+    catch (err) {
+        if (isUpstreamNotFound(err))
+            return false;
+        // Non-404 errors get surfaced when the BFS later expands the node.
+        return true;
+    }
+}
+async function fetchPedigree(client, connection, encodedId, ctx) {
+    const env = await client.get(connection.baseUrl, `/germplasm/${encodedId}/pedigree`, ctx, buildRequestOptions(connection));
+    const rawParents = env.result?.parents;
+    if (!Array.isArray(rawParents))
+        return [];
+    const parents = [];
+    for (const entry of rawParents) {
+        if (typeof entry !== 'object' || entry === null)
+            continue;
+        const record = entry;
+        const dbId = record.germplasmDbId;
+        if (typeof dbId !== 'string' || dbId.length === 0)
+            continue;
+        const item = {
+            germplasmDbId: dbId,
+        };
+        if (typeof record.germplasmName === 'string')
+            item.germplasmName = record.germplasmName;
+        if (typeof record.parentType === 'string')
+            item.parentType = record.parentType;
+        parents.push(item);
+    }
+    return parents;
+}
+async function fetchProgeny(client, connection, encodedId, ctx) {
+    const env = await client.get(connection.baseUrl, `/germplasm/${encodedId}/progeny`, ctx, buildRequestOptions(connection));
+    const result = env.result;
+    const rawProgeny = result?.progeny;
+    const fallback = Array.isArray(rawProgeny)
+        ? rawProgeny
+        : Array.isArray(result?.data)
+            ? result.data
+            : [];
+    const children = [];
+    for (const entry of fallback) {
+        if (typeof entry !== 'object' || entry === null)
+            continue;
+        const record = entry;
+        const dbId = record.germplasmDbId;
+        if (typeof dbId !== 'string' || dbId.length === 0)
+            continue;
+        const item = { germplasmDbId: dbId };
+        if (typeof record.germplasmName === 'string')
+            item.germplasmName = record.germplasmName;
+        children.push(item);
+    }
+    return children;
+}
+function computeLeafCount(nodes, edges) {
+    // A leaf has no outgoing edge (in the walked direction). For 'parent'
+    // edges, `from` is the parent — so nodes that never appear as `from` in
+    // parent edges are ancestry-leaves. For 'child' edges, nodes that never
+    // appear as `from` in child edges are descendancy-leaves.
+    const parentSources = new Set();
+    const childSources = new Set();
+    for (const edge of edges) {
+        if (edge.relationship === 'parent')
+            parentSources.add(edge.from);
+        else
+            childSources.add(edge.from);
+    }
+    let leaves = 0;
+    for (const node of nodes) {
+        const hasParentOut = parentSources.has(node.germplasmDbId);
+        const hasChildOut = childSources.has(node.germplasmDbId);
+        if (!hasParentOut && !hasChildOut)
+            leaves++;
+    }
+    return leaves;
+}
+//# sourceMappingURL=brapi-walk-pedigree.tool.js.map

package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.js.map

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package/dist/mcp-server/tools/shared/connect-auth-schema.d.ts

@@ -0,0 +1,29 @@
+/**
+ * @fileoverview Shared Zod discriminated union for BrAPI connection auth.
+ * Used by `brapi_connect` and, later, by any tool that needs to accept an
+ * inline auth payload.
+ *
+ * @module mcp-server/tools/shared/connect-auth-schema
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+export declare const ConnectAuthSchema: z.ZodDiscriminatedUnion<[z.ZodObject<{
+    mode: z.ZodLiteral<"none">;
+}, z.core.$strip>, z.ZodObject<{
+    mode: z.ZodLiteral<"bearer">;
+    token: z.ZodString;
+}, z.core.$strip>, z.ZodObject<{
+    mode: z.ZodLiteral<"api_key">;
+    apiKey: z.ZodString;
+    headerName: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>, z.ZodObject<{
+    mode: z.ZodLiteral<"sgn">;
+    username: z.ZodString;
+    password: z.ZodString;
+}, z.core.$strip>, z.ZodObject<{
+    mode: z.ZodLiteral<"oauth2">;
+    clientId: z.ZodString;
+    clientSecret: z.ZodString;
+    tokenUrl: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>], "mode">;
+export type ConnectAuthInput = z.infer<typeof ConnectAuthSchema>;
+//# sourceMappingURL=connect-auth-schema.d.ts.map

package/dist/mcp-server/tools/shared/connect-auth-schema.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"connect-auth-schema.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/shared/connect-auth-schema.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;2BAiD3B,CAAC;AAEJ,MAAM,MAAM,gBAAgB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,iBAAiB,CAAC,CAAC"}

package/dist/mcp-server/tools/shared/connect-auth-schema.js

@@ -0,0 +1,55 @@
+/**
+ * @fileoverview Shared Zod discriminated union for BrAPI connection auth.
+ * Used by `brapi_connect` and, later, by any tool that needs to accept an
+ * inline auth payload.
+ *
+ * @module mcp-server/tools/shared/connect-auth-schema
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+export const ConnectAuthSchema = z
+    .discriminatedUnion('mode', [
+    z
+        .object({ mode: z.literal('none').describe('No authentication.') })
+        .describe('No-auth variant — public BrAPI endpoints.'),
+    z
+        .object({
+        mode: z.literal('bearer').describe('Pre-obtained bearer token.'),
+        token: z.string().min(1).describe('Raw token; sent as "Authorization: Bearer <token>".'),
+    })
+        .describe('Bearer-token variant — caller already has an access token.'),
+    z
+        .object({
+        mode: z.literal('api_key').describe('Static API key in a custom header.'),
+        apiKey: z.string().min(1).describe('API key value.'),
+        headerName: z
+            .string()
+            .optional()
+            .describe('Header name. Defaults to `Authorization` (or BRAPI_DEFAULT_API_KEY_HEADER).'),
+    })
+        .describe('API-key variant — static key sent in a configurable header.'),
+    z
+        .object({
+        mode: z
+            .literal('sgn')
+            .describe('Breedbase/SGN username+password; exchanged for a bearer token at /token.'),
+        username: z.string().min(1).describe('SGN account username.'),
+        password: z.string().min(1).describe('SGN account password.'),
+    })
+        .describe('SGN variant — username/password exchanged at /token for a session bearer.'),
+    z
+        .object({
+        mode: z
+            .literal('oauth2')
+            .describe('OAuth2 client-credentials flow. Not yet implemented — use mode="bearer".'),
+        clientId: z.string().min(1).describe('OAuth2 client ID.'),
+        clientSecret: z.string().min(1).describe('OAuth2 client secret.'),
+        tokenUrl: z
+            .string()
+            .url()
+            .optional()
+            .describe('OAuth2 token endpoint URL. Defaults derived from the base URL when omitted.'),
+    })
+        .describe('OAuth2 client-credentials variant (accepted at schema level, rejected at runtime).'),
+])
+    .describe('Connection auth configuration. Discriminated by `mode`. Omit the entire `auth` field for no-auth servers.');
+//# sourceMappingURL=connect-auth-schema.js.map

package/dist/mcp-server/tools/shared/connect-auth-schema.js.map

@@ -0,0 +1 @@
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