@cyanheads/brapi-mcp-server 0.4.14 → 0.5.0

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

@@ -1,89 +0,0 @@
-/**
- * @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 { z } from '@cyanheads/mcp-ts-core';
-import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
-export declare const brapiManageDataset: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
-    mode: z.ZodEnum<{
-        delete: "delete";
-        list: "list";
-        summary: "summary";
-        load: "load";
-    }>;
-    datasetId: z.ZodOptional<z.ZodString>;
-    cursor: z.ZodOptional<z.ZodString>;
-    limit: z.ZodOptional<z.ZodNumber>;
-    page: z.ZodOptional<z.ZodNumber>;
-    pageSize: z.ZodOptional<z.ZodNumber>;
-    columns: z.ZodOptional<z.ZodArray<z.ZodString>>;
-}, z.core.$strip>, z.ZodObject<{
-    result: z.ZodDiscriminatedUnion<[z.ZodObject<{
-        mode: z.ZodLiteral<"list">;
-        datasets: z.ZodArray<z.ZodObject<{
-            datasetId: z.ZodString;
-            source: z.ZodString;
-            baseUrl: z.ZodString;
-            query: z.ZodUnknown;
-            rowCount: z.ZodNumber;
-            columns: z.ZodArray<z.ZodString>;
-            sizeBytes: z.ZodNumber;
-            createdAt: z.ZodString;
-            expiresAt: z.ZodString;
-            truncated: z.ZodOptional<z.ZodBoolean>;
-            maxRows: z.ZodOptional<z.ZodNumber>;
-            dataframe: z.ZodOptional<z.ZodString>;
-        }, z.core.$strip>>;
-        cursor: z.ZodOptional<z.ZodString>;
-    }, z.core.$strip>, z.ZodObject<{
-        mode: z.ZodLiteral<"summary">;
-        dataset: z.ZodObject<{
-            datasetId: z.ZodString;
-            source: z.ZodString;
-            baseUrl: z.ZodString;
-            query: z.ZodUnknown;
-            rowCount: z.ZodNumber;
-            columns: z.ZodArray<z.ZodString>;
-            sizeBytes: z.ZodNumber;
-            createdAt: z.ZodString;
-            expiresAt: z.ZodString;
-            truncated: z.ZodOptional<z.ZodBoolean>;
-            maxRows: z.ZodOptional<z.ZodNumber>;
-            dataframe: z.ZodOptional<z.ZodString>;
-        }, z.core.$strip>;
-    }, z.core.$strip>, z.ZodObject<{
-        mode: z.ZodLiteral<"load">;
-        datasetId: z.ZodString;
-        page: z.ZodNumber;
-        pageSize: z.ZodNumber;
-        totalRows: z.ZodNumber;
-        totalPages: z.ZodNumber;
-        rows: z.ZodArray<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
-    }, z.core.$strip>, z.ZodObject<{
-        mode: z.ZodLiteral<"delete">;
-        datasetId: z.ZodString;
-        deleted: z.ZodLiteral<true>;
-    }, z.core.$strip>], "mode">;
-}, z.core.$strip>, readonly [{
-    readonly reason: "datasetid_required";
-    readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: "Mode summary, load, or delete was selected without a datasetId";
-    readonly recovery: "Call mode=list first to discover available dataset IDs, then retry with one.";
-}, {
-    readonly reason: "dataset_not_found";
-    readonly code: JsonRpcErrorCode.NotFound;
-    readonly when: "Requested dataset is not present in the store (never existed or already expired)";
-    readonly recovery: "Run mode=list to confirm available datasets, or rerun the find_* tool that produced it.";
-}, {
-    readonly reason: "dataset_rows_missing";
-    readonly code: JsonRpcErrorCode.NotFound;
-    readonly when: "Dataset metadata is present but the row payload was lost or partially expired";
-    readonly recovery: "Delete the stale dataset via mode=delete and rerun the find_* tool that produced it.";
-}]>;
-//# sourceMappingURL=brapi-manage-dataset.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-manage-dataset.tool.d.ts.map

@@ -1 +0,0 @@
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package/dist/mcp-server/tools/definitions/brapi-manage-dataset.tool.js

@@ -1,306 +0,0 @@
-/**
- * @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.'),
-    dataframe: z
-        .string()
-        .optional()
-        .describe('Dataframe name when this dataset was auto-registered as a SQL-queryable dataframe. Use with brapi_dataframe_query to run SQL across the rows.'),
-});
-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. Schema matches the originating find_* tool result row (e.g. find_germplasm rows for a germplasm dataset); see the dataset summary for column names and the find_* output schema for field semantics.'))
-        .describe('Rows for this page, with optional column projection applied.'),
-})
-    .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.',
-    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)}\``);
-        if (ds.dataframe) {
-            lines.push(`- dataframe: \`${ds.dataframe}\` (queryable via brapi_dataframe_query)`);
-        }
-    }
-    return lines.join('\n');
-}
-function renderSummary(dataset) {
-    const lines = [];
-    lines.push(`# Dataset \`${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)`);
-    }
-    if (dataset.dataframe) {
-        lines.push(`- dataframe: \`${dataset.dataframe}\` (queryable via brapi_dataframe_query)`);
-    }
-    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

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

@@ -1 +0,0 @@
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package/dist/services/dataset-store/dataset-store.d.ts

@@ -1,44 +0,0 @@
-/**
- * @fileoverview Tenant-scoped dataset lifecycle. Stores metadata and row
- * payloads in `ctx.state` with TTL from `BRAPI_DATASET_TTL_SECONDS`. Datasets
- * back the `brapi_manage_dataset` tool (list/summary/load/delete) and act as
- * the spillover target for `find_*` tools when result sets exceed
- * `BRAPI_LOAD_LIMIT`. Provenance (source, baseUrl, query) is mandatory on
- * create — research workflows require reproducibility.
- *
- * When the optional `CanvasBridge` is wired in, `create()` auto-registers
- * the row payload as a SQL-queryable table and `delete()` drops it again.
- * Failures in either path log a warning but never break the dataset op —
- * the canvas surface is an enrichment, not a precondition.
- *
- * @module services/dataset-store/dataset-store
- */
-import type { Context } from '@cyanheads/mcp-ts-core';
-import type { ServerConfig } from '../../config/server-config.js';
-import type { CanvasBridge } from '../../services/canvas-bridge/index.js';
-import type { CreateDatasetInput, DatasetListOptions, DatasetListPage, DatasetLoadOptions, DatasetMetadata, DatasetPage } from './types.js';
-export declare class DatasetStore {
-    private readonly serverConfig;
-    private readonly canvasBridge?;
-    constructor(serverConfig: ServerConfig, canvasBridge?: CanvasBridge | undefined);
-    /**
-     * Persist a new dataset and return its metadata. Rows and metadata are
-     * written under separate keys so `summary` / `list` can avoid paying the
-     * row-payload read cost. When the canvas-bridge is wired and enabled,
-     * the rows are auto-registered as a SQL-queryable canvas table; failure
-     * there only logs a warning.
-     */
-    create(ctx: Context, input: CreateDatasetInput): Promise<DatasetMetadata>;
-    /** Return just the metadata for a dataset. Throws `NotFound` when missing. */
-    summary(ctx: Context, datasetId: string): Promise<DatasetMetadata>;
-    /** Return a paginated slice of rows, optionally projected to a subset of columns. */
-    load(ctx: Context, datasetId: string, options?: DatasetLoadOptions): Promise<DatasetPage>;
-    /** Enumerate datasets for this tenant, paginated via opaque cursor. */
-    list(ctx: Context, options?: DatasetListOptions): Promise<DatasetListPage>;
-    /** Delete a dataset's metadata and row payload. Idempotent. */
-    delete(ctx: Context, datasetId: string): Promise<void>;
-}
-export declare function initDatasetStore(serverConfig: ServerConfig, canvasBridge?: CanvasBridge | undefined): void;
-export declare function getDatasetStore(): DatasetStore;
-export declare function resetDatasetStore(): void;
-//# sourceMappingURL=dataset-store.d.ts.map

package/dist/services/dataset-store/dataset-store.d.ts.map

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