@cyanheads/brapi-mcp-server 0.3.5

package/dist/mcp-server/tools/definitions/brapi-manage-dataset.tool.js

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+/**
+ * @fileoverview `brapi_manage_dataset` — consolidated lifecycle tool for
+ * datasets created by `find_*` spillovers. Four modes discriminated by
+ * `mode`: list (enumerate with provenance), summary (metadata only), load
+ * (paged rows with optional column projection), delete (drop metadata +
+ * payload). Export (CSV/Parquet) is deferred until storage backends for the
+ * write path are wired up.
+ *
+ * @module mcp-server/tools/definitions/brapi-manage-dataset.tool
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+import { getDatasetStore } from '../../../services/dataset-store/index.js';
+const DatasetMetadataSchema = z.object({
+    datasetId: z.string().describe('Server-assigned dataset identifier.'),
+    source: z.string().describe('Tool/operation that produced the dataset (e.g. "find_studies").'),
+    baseUrl: z.string().describe('BrAPI base URL the dataset was pulled from.'),
+    query: z.unknown().describe('Original filter map — provenance for reproducibility.'),
+    rowCount: z.number().int().nonnegative().describe('Number of rows persisted in the dataset.'),
+    columns: z
+        .array(z.string().describe('Column name from the persisted rows.'))
+        .describe('Full column list of the persisted rows.'),
+    sizeBytes: z.number().int().nonnegative().describe('Serialized size of the dataset in bytes.'),
+    createdAt: z.string().describe('ISO 8601 timestamp the dataset was created.'),
+    expiresAt: z.string().describe('ISO 8601 timestamp after which the dataset will be purged.'),
+    truncated: z
+        .boolean()
+        .optional()
+        .describe('True when the dataset hit the spillover row/page cap before exhausting upstream.'),
+    maxRows: z
+        .number()
+        .int()
+        .positive()
+        .optional()
+        .describe('Cap that was applied at create time, when truncation occurred.'),
+});
+const ListResultSchema = z
+    .object({
+    mode: z.literal('list').describe('Discriminator — `list` mode enumerates datasets.'),
+    datasets: z
+        .array(DatasetMetadataSchema.describe('Dataset metadata entry.'))
+        .describe('Datasets visible to this tenant, in creation order.'),
+    cursor: z.string().optional().describe('Opaque cursor when more datasets exist.'),
+})
+    .describe('Enumeration of datasets visible to the current tenant.');
+const SummaryResultSchema = z
+    .object({
+    mode: z.literal('summary').describe('Discriminator — `summary` mode returns one dataset.'),
+    dataset: DatasetMetadataSchema.describe('Metadata and provenance for the requested dataset.'),
+})
+    .describe('Metadata + provenance for a single dataset.');
+const LoadResultSchema = z
+    .object({
+    mode: z.literal('load').describe('Discriminator — `load` mode returns a page of rows.'),
+    datasetId: z.string().describe('Dataset the rows came from.'),
+    page: z.number().int().positive().describe('1-indexed page number that was served.'),
+    pageSize: z.number().int().positive().describe('Max rows per page (capped at 1000).'),
+    totalRows: z.number().int().nonnegative().describe('Total rows in the dataset.'),
+    totalPages: z.number().int().positive().describe('Total pages at the current pageSize.'),
+    rows: z
+        .array(z
+        .record(z.string(), z.unknown())
+        .describe('One persisted row, with optional column projection applied.'))
+        .describe('Rows for this page.'),
+})
+    .describe('Paged rows from a persisted dataset.');
+const DeleteResultSchema = z
+    .object({
+    mode: z.literal('delete').describe('Discriminator — `delete` mode confirms removal.'),
+    datasetId: z.string().describe('Dataset that was deleted.'),
+    deleted: z.literal(true).describe('Always `true` when the call succeeded.'),
+})
+    .describe('Confirmation that a dataset was deleted.');
+const OutputSchema = z.object({
+    result: z
+        .discriminatedUnion('mode', [
+        ListResultSchema,
+        SummaryResultSchema,
+        LoadResultSchema,
+        DeleteResultSchema,
+    ])
+        .describe('Mode-specific result — discriminated by `mode`: list (dataset enumeration), summary (metadata+provenance), load (paged rows), delete (drop confirmation).'),
+});
+const InputSchema = z.object({
+    mode: z
+        .enum(['list', 'summary', 'load', 'delete'])
+        .describe('Operation: list (enumerate datasets), summary (metadata+provenance), load (page rows), delete (drop payload).'),
+    datasetId: z
+        .string()
+        .min(1)
+        .optional()
+        .describe('Required for mode=summary | load | delete. Ignored for mode=list.'),
+    cursor: z.string().optional().describe('mode=list: resume a previous call.'),
+    limit: z
+        .number()
+        .int()
+        .positive()
+        .max(200)
+        .optional()
+        .describe('mode=list: max datasets to return (default 50, capped at 200).'),
+    page: z
+        .number()
+        .int()
+        .positive()
+        .optional()
+        .describe('mode=load: 1-indexed page number (default 1).'),
+    pageSize: z
+        .number()
+        .int()
+        .positive()
+        .optional()
+        .describe('mode=load: rows per page (default 100, max 1000).'),
+    columns: z
+        .array(z.string().min(1))
+        .optional()
+        .describe('mode=load: subset of columns to return. Omit for all columns.'),
+});
+export const brapiManageDataset = tool('brapi_manage_dataset', {
+    description: 'Dataset lifecycle — list (enumerate), summary (metadata+provenance), load (page rows with column projection), delete (drop payload). Datasets are produced by find_* tools when the upstream total exceeds loadLimit. Export (CSV/Parquet) is not yet implemented.',
+    annotations: { readOnlyHint: false, idempotentHint: false },
+    errors: [
+        {
+            reason: 'datasetid_required',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'Mode summary, load, or delete was selected without a datasetId',
+            recovery: 'Call mode=list first to discover available dataset IDs, then retry with one.',
+        },
+        {
+            reason: 'dataset_not_found',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'Requested dataset is not present in the store (never existed or already expired)',
+            recovery: 'Run mode=list to confirm available datasets, or rerun the find_* tool that produced it.',
+        },
+        {
+            reason: 'dataset_rows_missing',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'Dataset metadata is present but the row payload was lost or partially expired',
+            recovery: 'Delete the stale dataset via mode=delete and rerun the find_* tool that produced it.',
+        },
+    ],
+    input: InputSchema,
+    output: OutputSchema,
+    async handler(input, ctx) {
+        const store = getDatasetStore();
+        const requireDatasetId = () => {
+            if (!input.datasetId) {
+                throw ctx.fail('datasetid_required', `mode='${input.mode}' requires datasetId.`, {
+                    mode: input.mode,
+                    ...ctx.recoveryFor('datasetid_required'),
+                });
+            }
+            return input.datasetId;
+        };
+        switch (input.mode) {
+            case 'list': {
+                const listOptions = {};
+                if (input.cursor !== undefined)
+                    listOptions.cursor = input.cursor;
+                if (input.limit !== undefined)
+                    listOptions.limit = input.limit;
+                const page = await store.list(ctx, listOptions);
+                const branch = {
+                    mode: 'list',
+                    datasets: page.datasets,
+                };
+                if (page.cursor !== undefined)
+                    branch.cursor = page.cursor;
+                return { result: branch };
+            }
+            case 'summary': {
+                const datasetId = requireDatasetId();
+                const dataset = await store.summary(ctx, datasetId);
+                const branch = { mode: 'summary', dataset };
+                return { result: branch };
+            }
+            case 'load': {
+                const datasetId = requireDatasetId();
+                const loadOptions = {};
+                if (input.page !== undefined)
+                    loadOptions.page = input.page;
+                if (input.pageSize !== undefined)
+                    loadOptions.pageSize = input.pageSize;
+                if (input.columns !== undefined)
+                    loadOptions.columns = input.columns;
+                const pageResult = await store.load(ctx, datasetId, loadOptions);
+                const branch = {
+                    mode: 'load',
+                    datasetId: pageResult.datasetId,
+                    page: pageResult.page,
+                    pageSize: pageResult.pageSize,
+                    totalRows: pageResult.totalRows,
+                    totalPages: pageResult.totalPages,
+                    rows: pageResult.rows,
+                };
+                return { result: branch };
+            }
+            case 'delete': {
+                const datasetId = requireDatasetId();
+                await store.delete(ctx, datasetId);
+                const branch = {
+                    mode: 'delete',
+                    datasetId,
+                    deleted: true,
+                };
+                return { result: branch };
+            }
+        }
+    },
+    format: (result) => {
+        const branch = result.result;
+        switch (branch.mode) {
+            case 'list':
+                return [{ type: 'text', text: renderList(branch) }];
+            case 'summary':
+                return [{ type: 'text', text: renderSummary(branch.dataset) }];
+            case 'load':
+                return [{ type: 'text', text: renderLoad(branch) }];
+            case 'delete':
+                return [
+                    {
+                        type: 'text',
+                        text: `# Dataset deleted\n- datasetId: \`${branch.datasetId}\`\n- deleted: ${branch.deleted}\n- mode: ${branch.mode}`,
+                    },
+                ];
+        }
+    },
+});
+function renderList(result) {
+    const lines = [];
+    lines.push(`# ${result.datasets.length} dataset(s) · mode=${result.mode}`);
+    if (result.cursor)
+        lines.push(`**Cursor:** \`${result.cursor}\` — pass to list again for next page.`);
+    if (result.datasets.length === 0) {
+        lines.push('');
+        lines.push('_No datasets. Run a find_* tool to produce one._');
+        return lines.join('\n');
+    }
+    lines.push('');
+    lines.push('| datasetId | source | rows | sizeBytes | createdAt | expiresAt | truncated |');
+    lines.push('|:----------|:-------|-----:|----------:|:----------|:----------|:----------|');
+    for (const ds of result.datasets) {
+        const truncated = ds.truncated ? `yes (cap=${ds.maxRows ?? '?'})` : 'no';
+        lines.push(`| \`${ds.datasetId}\` | ${ds.source} | ${ds.rowCount} | ${ds.sizeBytes} | ${ds.createdAt} | ${ds.expiresAt} | ${truncated} |`);
+    }
+    for (const ds of result.datasets) {
+        lines.push('');
+        lines.push(`### \`${ds.datasetId}\``);
+        lines.push(`- baseUrl: ${ds.baseUrl}`);
+        lines.push(`- columns: ${ds.columns.join(', ')}`);
+        lines.push(`- query: \`${JSON.stringify(ds.query)}\``);
+    }
+    return lines.join('\n');
+}
+function renderSummary(dataset) {
+    const lines = [];
+    lines.push(`# Dataset \`${dataset.datasetId}\``);
+    lines.push('');
+    lines.push(`- source: ${dataset.source}`);
+    lines.push(`- baseUrl: ${dataset.baseUrl}`);
+    lines.push(`- rowCount: ${dataset.rowCount}`);
+    lines.push(`- sizeBytes: ${dataset.sizeBytes}`);
+    lines.push(`- createdAt: ${dataset.createdAt}`);
+    lines.push(`- expiresAt: ${dataset.expiresAt}`);
+    if (dataset.truncated) {
+        lines.push(`- truncated: true (cap=${dataset.maxRows ?? '?'} rows)`);
+    }
+    lines.push(`- columns: ${dataset.columns.join(', ')}`);
+    lines.push(`- query: \`${JSON.stringify(dataset.query)}\``);
+    return lines.join('\n');
+}
+function renderLoad(result) {
+    const lines = [];
+    lines.push(`# Dataset \`${result.datasetId}\` — page ${result.page} of ${result.totalPages} (${result.rows.length}/${result.totalRows} rows) · mode=${result.mode}`);
+    lines.push('');
+    lines.push(`- pageSize: ${result.pageSize}`);
+    lines.push('');
+    if (result.rows.length === 0) {
+        lines.push('_No rows on this page._');
+        return lines.join('\n');
+    }
+    const columns = Object.keys(result.rows[0] ?? {});
+    lines.push('## Rows');
+    for (const [i, row] of result.rows.entries()) {
+        lines.push('');
+        lines.push(`### Row ${(result.page - 1) * result.pageSize + i + 1}`);
+        for (const col of columns) {
+            const value = row[col];
+            if (value === undefined || value === null)
+                continue;
+            const rendered = typeof value === 'object' ? JSON.stringify(value) : String(value);
+            lines.push(`- **${col}:** ${rendered}`);
+        }
+    }
+    return lines.join('\n');
+}
+//# sourceMappingURL=brapi-manage-dataset.tool.js.map

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

@@ -0,0 +1,35 @@
+/**
+ * @fileoverview `brapi_raw_get` — last-resort passthrough to any BrAPI GET
+ * endpoint the goal-shaped tools don't cover (e.g. `/samples`, `/methods`,
+ * `/scales`, `/crosses`). Returns the raw upstream envelope, plus a routing
+ * nudge when the target endpoint is actually covered by a curated tool.
+ *
+ * @module mcp-server/tools/definitions/brapi-raw-get.tool
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+export declare const brapiRawGet: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    alias: z.ZodOptional<z.ZodString>;
+    path: z.ZodString;
+    params: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnion<readonly [z.ZodString, z.ZodNumber, z.ZodBoolean, z.ZodArray<z.ZodUnion<readonly [z.ZodString, z.ZodNumber]>>]>>>;
+}, z.core.$strip>, z.ZodObject<{
+    alias: z.ZodString;
+    url: z.ZodString;
+    path: z.ZodString;
+    metadata: z.ZodObject<{
+        pagination: z.ZodOptional<z.ZodObject<{
+            currentPage: z.ZodNumber;
+            pageSize: z.ZodNumber;
+            totalCount: z.ZodNumber;
+            totalPages: z.ZodNumber;
+        }, z.core.$loose>>;
+    }, z.core.$loose>;
+    result: z.ZodUnknown;
+    suggestion: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>, readonly [{
+    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.";
+}]>;
+//# sourceMappingURL=brapi-raw-get.tool.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"brapi-raw-get.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-raw-get.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA0CjE,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;GAuFtB,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-raw-get.tool.js

@@ -0,0 +1,148 @@
+/**
+ * @fileoverview `brapi_raw_get` — last-resort passthrough to any BrAPI GET
+ * endpoint the goal-shaped tools don't cover (e.g. `/samples`, `/methods`,
+ * `/scales`, `/crosses`). Returns the raw upstream envelope, plus a routing
+ * nudge when the target endpoint is actually covered by a curated tool.
+ *
+ * @module mcp-server/tools/definitions/brapi-raw-get.tool
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+import { getBrapiClient, } from '../../../services/brapi-client/index.js';
+import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
+import { AliasInput } from '../shared/find-helpers.js';
+import { suggestForGet } from '../shared/raw-routing-hints.js';
+const PaginationSchema = z
+    .object({
+    currentPage: z.number().describe('0-indexed page number the server returned.'),
+    pageSize: z.number().describe('Rows per page.'),
+    totalCount: z.number().describe('Total rows matching the query across all pages.'),
+    totalPages: z.number().describe('Total pages at the current pageSize.'),
+})
+    .passthrough()
+    .optional()
+    .describe('BrAPI pagination block. Absent when the endpoint does not paginate.');
+const OutputSchema = z.object({
+    alias: z.string().describe('Alias of the registered BrAPI connection the call used.'),
+    url: z.string().describe('Fully resolved URL that was fetched (baseUrl + path + query string).'),
+    path: z
+        .string()
+        .describe('Normalized path (leading `/` preserved) that was appended to the baseUrl.'),
+    metadata: z
+        .object({
+        pagination: PaginationSchema,
+    })
+        .passthrough()
+        .describe('BrAPI envelope metadata (pagination and any additional upstream fields).'),
+    result: z.unknown().describe('Raw BrAPI `result` value — whatever shape the endpoint returns.'),
+    suggestion: z
+        .string()
+        .optional()
+        .describe('Emitted when a curated goal-shaped tool covers this endpoint.'),
+});
+export const brapiRawGet = tool('brapi_raw_get', {
+    description: 'Passthrough to any BrAPI GET /{path} endpoint. Returns the raw upstream envelope without enrichment or foreign-key resolution. Emits a `suggestion` field when a curated tool exists for the same data.',
+    annotations: { readOnlyHint: true, openWorldHint: true },
+    errors: [
+        {
+            reason: 'cross_origin_path',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'path argument was a full URL instead of a relative BrAPI route',
+            recovery: 'Pass a path like "/samples" or "/methods" — the connection alias supplies the baseUrl.',
+        },
+    ],
+    input: z.object({
+        alias: AliasInput,
+        path: z
+            .string()
+            .min(1)
+            .describe('Endpoint path — e.g. "/samples", "/methods". Leading "/" is optional.'),
+        params: z
+            .record(z.string(), z.union([z.string(), z.number(), z.boolean(), z.array(z.union([z.string(), z.number()]))]))
+            .optional()
+            .describe('Query parameters to append. Arrays are repeated per BrAPI convention.'),
+    }),
+    output: OutputSchema,
+    async handler(input, ctx) {
+        const registry = getServerRegistry();
+        const client = getBrapiClient();
+        const connection = await registry.get(ctx, input.alias ?? DEFAULT_ALIAS);
+        // The path is appended to the registered baseUrl; if the caller smuggles a
+        // full URL (http://evil/...) `new URL()` would silently hijack the request.
+        if (/^https?:\/\//i.test(input.path)) {
+            throw ctx.fail('cross_origin_path', 'path must be a relative BrAPI route, not a full URL.', {
+                path: input.path,
+                ...ctx.recoveryFor('cross_origin_path'),
+            });
+        }
+        const path = normalizePath(input.path);
+        const requestOptions = {};
+        if (connection.resolvedAuth)
+            requestOptions.auth = connection.resolvedAuth;
+        if (input.params) {
+            requestOptions.params = input.params;
+        }
+        const envelope = await client.get(connection.baseUrl, path, ctx, requestOptions);
+        const url = buildDisplayUrl(connection.baseUrl, path, input.params);
+        const result = {
+            alias: connection.alias,
+            url,
+            path,
+            metadata: buildMetadata(envelope.metadata),
+            result: envelope.result,
+        };
+        const suggestion = suggestForGet(path);
+        if (suggestion)
+            result.suggestion = suggestion;
+        return result;
+    },
+    format: (result) => {
+        const lines = [];
+        lines.push(`# GET ${result.path} — \`${result.alias}\``);
+        lines.push('');
+        lines.push(`URL: ${result.url}`);
+        const pagination = result.metadata.pagination;
+        if (pagination) {
+            lines.push('');
+            lines.push(`**Pagination:** page ${pagination.currentPage} of ${pagination.totalPages}, pageSize=${pagination.pageSize}, totalCount=${pagination.totalCount}`);
+        }
+        if (result.suggestion) {
+            lines.push('');
+            lines.push(`**Suggestion:** ${result.suggestion}`);
+        }
+        lines.push('');
+        lines.push('## Raw result');
+        lines.push('```json');
+        lines.push(JSON.stringify(result.result, null, 2));
+        lines.push('```');
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+function normalizePath(path) {
+    return path.startsWith('/') ? path : `/${path}`;
+}
+function buildMetadata(metadata) {
+    const pagination = metadata?.pagination;
+    if (pagination) {
+        return { pagination: { ...pagination } };
+    }
+    return {};
+}
+function buildDisplayUrl(baseUrl, path, params) {
+    const url = new URL(`${baseUrl.replace(/\/$/, '')}${path}`);
+    if (params) {
+        for (const [key, value] of Object.entries(params)) {
+            if (value === undefined)
+                continue;
+            if (Array.isArray(value)) {
+                for (const v of value)
+                    url.searchParams.append(key, String(v));
+            }
+            else {
+                url.searchParams.set(key, String(value));
+            }
+        }
+    }
+    return url.toString();
+}
+//# sourceMappingURL=brapi-raw-get.tool.js.map

package/dist/mcp-server/tools/definitions/brapi-raw-get.tool.js.map

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package/dist/mcp-server/tools/definitions/brapi-raw-search.tool.d.ts

@@ -0,0 +1,33 @@
+/**
+ * @fileoverview `brapi_raw_search` — last-resort passthrough to any BrAPI
+ * `POST /search/{noun}` endpoint with async-search polling handled
+ * transparently. Returns the raw upstream envelope once the search completes.
+ * Emits a routing nudge when a curated goal-shaped tool covers the noun.
+ *
+ * @module mcp-server/tools/definitions/brapi-raw-search.tool
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+export declare const brapiRawSearch: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    alias: z.ZodOptional<z.ZodString>;
+    noun: z.ZodString;
+    body: z.ZodRecord<z.ZodString, z.ZodUnknown>;
+}, z.core.$strip>, z.ZodObject<{
+    alias: z.ZodString;
+    noun: z.ZodString;
+    kind: z.ZodEnum<{
+        sync: "sync";
+        async: "async";
+    }>;
+    searchResultsDbId: z.ZodOptional<z.ZodString>;
+    metadata: z.ZodObject<{
+        pagination: z.ZodOptional<z.ZodObject<{
+            currentPage: z.ZodNumber;
+            pageSize: z.ZodNumber;
+            totalCount: z.ZodNumber;
+            totalPages: z.ZodNumber;
+        }, z.core.$loose>>;
+    }, z.core.$loose>;
+    result: z.ZodUnknown;
+    suggestion: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>, undefined>;
+//# sourceMappingURL=brapi-raw-search.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-raw-search.tool.d.ts.map

@@ -0,0 +1 @@
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