@cyanheads/zenodo-mcp-server 0.1.1

package/dist/mcp-server/tools/definitions/lookup-vocabulary.tool.js

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+/**
+ * @fileoverview zenodo_lookup_vocabulary — resolves community, funder, award,
+ * license, and resource-type names to the ids zenodo_search_records filters on.
+ * The routing target for every unknown-value and zero-hit path.
+ * @module mcp-server/tools/definitions/lookup-vocabulary
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+import { parseFunderRef } from '../../../services/zenodo/identifiers.js';
+import { filterResourceTypes } from '../../../services/zenodo/resource-types.js';
+import { getZenodoService } from '../../../services/zenodo/zenodo-service.js';
+import { hasLineBreak, inline, quoteBlock } from '../render.js';
+import { blankToUndefined, enumPreprocess } from '../schema-helpers.js';
+const VOCABULARIES = ['communities', 'funders', 'awards', 'licenses', 'resource_types'];
+const RESULT_WINDOW = 10_000;
+/** What to try after a query matched nothing, per vocabulary. */
+const ZERO_HIT_ADVICE = {
+    communities: "try a shorter name, a keyword from the community's title, or the project's acronym",
+    funders: "try a shorter name or the funder's acronym",
+    awards: "try the grant number, the project's acronym, or a shorter keyword from the award title",
+    licenses: 'try a shorter keyword such as cc-by, gpl, or mit, or call again without query to browse all licenses',
+    resource_types: 'every word must appear in a type id or label, so try a shorter keyword, or call again without query to list all 43 types',
+};
+const EntrySchema = z
+    .object({
+    filter_param: z
+        .enum(['community', 'funder', 'award', 'license', 'resource_type'])
+        .describe('The zenodo_search_records parameter this entry’s filter_value feeds.'),
+    filter_value: z
+        .string()
+        .describe('The id to pass to zenodo_search_records as filter_param (community slug, funder ROR id, award id, license id, or resource type id).'),
+    label: z
+        .string()
+        .describe('Display name: community title, funder name, award acronym (else title or number), license title, or resource type label.'),
+    slug: z.string().optional().describe('Community slug (communities).'),
+    uuid: z.string().optional().describe('Community UUID (communities).'),
+    community_type: z
+        .string()
+        .optional()
+        .describe('Community type, e.g. Organization or Project (communities).'),
+    website: z.string().optional().describe('Community website (communities).'),
+    organizations: z
+        .array(z.string())
+        .optional()
+        .describe('Organizations behind the community, by name or ROR id (communities).'),
+    ror_id: z.string().optional().describe('Funder ROR id (funders).'),
+    funder_doi: z
+        .string()
+        .optional()
+        .describe('Crossref Funder Registry DOI, 10.13039/… (funders).'),
+    acronym: z.string().optional().describe('Funder or award acronym (funders, awards).'),
+    country: z.string().optional().describe('Funder country code, ISO 3166-1 alpha-2 (funders).'),
+    country_name: z.string().optional().describe('Funder country name (funders).'),
+    number: z.string().optional().describe('Grant number (awards).'),
+    title: z.string().optional().describe('Full award title (awards).'),
+    program: z.string().optional().describe('Funding program, e.g. HORIZON.2.6 (awards).'),
+    funder_id: z.string().optional().describe('ROR id of the awarding funder (awards).'),
+    funder_name: z.string().optional().describe('Name of the awarding funder (awards).'),
+    award_doi: z.string().optional().describe('Award DOI, e.g. a CORDIS 10.3030/… DOI (awards).'),
+    award_url: z.string().optional().describe('Award landing page URL (awards).'),
+    start_date: z.string().optional().describe('Award start date (awards).'),
+    end_date: z.string().optional().describe('Award end date (awards).'),
+    url: z.string().optional().describe('License text URL (licenses).'),
+    osi_approved: z
+        .boolean()
+        .optional()
+        .describe('Whether the license is OSI-approved; omitted when upstream does not say (licenses).'),
+    tags: z
+        .array(z.string())
+        .optional()
+        .describe('License tags, e.g. recommended, software, data (licenses).'),
+    parent_type: z
+        .string()
+        .optional()
+        .describe('Parent type id of a resource subtype (resource_types).'),
+    search_value: z
+        .string()
+        .optional()
+        .describe('Zenodo’s own spelling of this type (<type>::<id> for a subtype); zenodo_search_records accepts it or filter_value as resource_type (resource_types).'),
+})
+    .describe('One vocabulary entry. Fields beyond filter_param, filter_value, and label are present only for the vocabulary they belong to, and only when Zenodo supplies them.');
+/** Maps a remote vocabulary page to the flat entry shape. */
+function toEntries(page) {
+    switch (page.vocabulary) {
+        case 'communities':
+            return page.entries.map((c) => ({
+                filter_param: 'community',
+                filter_value: c.slug,
+                label: c.title ?? c.slug,
+                slug: c.slug,
+                uuid: c.uuid,
+                ...(c.community_type ? { community_type: c.community_type } : {}),
+                ...(c.website ? { website: c.website } : {}),
+                ...(c.organizations.length ? { organizations: c.organizations } : {}),
+            }));
+        case 'funders':
+            return page.entries.map((f) => ({
+                filter_param: 'funder',
+                filter_value: f.ror_id,
+                label: f.name ?? f.ror_id,
+                ror_id: f.ror_id,
+                ...(f.funder_doi ? { funder_doi: f.funder_doi } : {}),
+                ...(f.acronym ? { acronym: f.acronym } : {}),
+                ...(f.country ? { country: f.country } : {}),
+                ...(f.country_name ? { country_name: f.country_name } : {}),
+            }));
+        case 'awards':
+            return page.entries.map((a) => ({
+                filter_param: 'award',
+                filter_value: a.id,
+                label: a.acronym ?? a.title ?? a.number ?? a.id,
+                ...(a.number ? { number: a.number } : {}),
+                ...(a.acronym ? { acronym: a.acronym } : {}),
+                ...(a.title ? { title: a.title } : {}),
+                ...(a.program ? { program: a.program } : {}),
+                ...(a.funder_id ? { funder_id: a.funder_id } : {}),
+                ...(a.funder_name ? { funder_name: a.funder_name } : {}),
+                ...(a.award_doi ? { award_doi: a.award_doi } : {}),
+                ...(a.award_url ? { award_url: a.award_url } : {}),
+                ...(a.start_date ? { start_date: a.start_date } : {}),
+                ...(a.end_date ? { end_date: a.end_date } : {}),
+            }));
+        case 'licenses':
+            return page.entries.map((l) => ({
+                filter_param: 'license',
+                filter_value: l.id,
+                label: l.title ?? l.id,
+                ...(l.url ? { url: l.url } : {}),
+                ...(l.osi_approved !== undefined ? { osi_approved: l.osi_approved } : {}),
+                ...(l.tags.length ? { tags: l.tags } : {}),
+            }));
+    }
+}
+export const lookupVocabulary = tool('zenodo_lookup_vocabulary', {
+    title: 'Look up Zenodo filter ids',
+    description: "Resolve names to the ids zenodo_search_records filters on, and browse Zenodo's reference vocabularies: communities (slug), funders (ROR id), awards and grants (award id), licenses (license id), and resource types (type id). Search by name, acronym, or keyword; awards can be scoped to one funder. Each entry names the zenodo_search_records parameter its id feeds.",
+    annotations: { readOnlyHint: true, idempotentHint: true, openWorldHint: true },
+    input: z.object({
+        vocabulary: z
+            .preprocess(enumPreprocess(VOCABULARIES, {
+            community: 'communities',
+            funder: 'funders',
+            award: 'awards',
+            grant: 'awards',
+            grants: 'awards',
+            license: 'licenses',
+            resource_type: 'resource_types',
+        }), z.enum(VOCABULARIES))
+            .describe('Which vocabulary to search: communities, funders, awards (grants), licenses, or resource_types. Case, spaces, hyphens, and underscores are ignored when matching, and the singular (funder, license, resource type) and grants are accepted.'),
+        query: z
+            .preprocess(blankToUndefined, z.string().max(200).optional())
+            .describe('Name, acronym, or keyword, e.g. "SYMBA", "wellcome", "mit", "journal article". For resource_types every word must appear in the type id or label. Omit to browse the vocabulary.'),
+        funder: z
+            .preprocess(blankToUndefined, z.string().max(200).optional())
+            .describe('awards only: scope grants to one funder, given as a ROR id (00k4n6c32), a ROR URL, or a Crossref Funder DOI (10.13039/100000002). Resolve a funder name to its ROR id with vocabulary funders first.'),
+        page: z.number().int().min(1).default(1).describe('Result page, starting at 1.'),
+        size: z.number().int().min(1).max(25).default(10).describe('Entries per page (1–25).'),
+    }),
+    output: z.object({
+        vocabulary: z.enum(VOCABULARIES).describe('The vocabulary searched.'),
+        query: z.string().optional().describe('The query as applied; absent when browsing.'),
+        total: z.number().describe('Total entries matching the query.'),
+        page: z.number().describe('Page returned.'),
+        size: z.number().describe('Page size applied.'),
+        has_more: z.boolean().describe('True when more pages follow this one.'),
+        next_page: z.number().optional().describe('The next page number, when has_more.'),
+        entries: z.array(EntrySchema).describe('Matching entries for this page.'),
+    }),
+    enrichment: {
+        truncated: z.boolean().describe('True when more entries exist beyond this page.'),
+        shown: z.number().describe('Entries returned on this page.'),
+        cap: z.number().describe('Page size applied.'),
+        totalCount: z.number().describe('Total entries matching the query.'),
+        notice: z
+            .string()
+            .optional()
+            .describe('Guidance on empty results, ambiguous funders, or further pages.'),
+    },
+    errors: [
+        {
+            reason: 'funder_only_for_awards',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'funder is set with a vocabulary other than awards',
+            recovery: 'Call zenodo_lookup_vocabulary again without funder, or set vocabulary to awards to scope grants by funder.',
+        },
+        {
+            reason: 'unknown_funder',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'funder (awards) resolves to no Zenodo funder',
+            recovery: 'Resolve the funder first with zenodo_lookup_vocabulary (vocabulary: funders) and pass its ROR id as funder.',
+        },
+        {
+            reason: 'result_window_exceeded',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'page × size exceeds 10,000',
+            recovery: 'Narrow the query and call zenodo_lookup_vocabulary again instead of paging past 10,000 entries.',
+        },
+        {
+            reason: 'rate_limited',
+            code: JsonRpcErrorCode.RateLimited,
+            when: "Zenodo answered HTTP 429, or this server's shared Zenodo request budget is spent for the current window",
+            retryable: true,
+            thrownBy: 'service',
+            recovery: 'Wait for the retryAfter seconds in the error data, then call zenodo_lookup_vocabulary again with the same arguments.',
+        },
+    ],
+    async handler(input, ctx) {
+        ctx.enrich({ truncated: false, shown: 0, cap: input.size, totalCount: 0 });
+        if (input.funder && input.vocabulary !== 'awards') {
+            throw ctx.fail('funder_only_for_awards', `funder applies only to vocabulary awards, not ${input.vocabulary}.`, ctx.recoveryFor('funder_only_for_awards'));
+        }
+        if (input.page * input.size > RESULT_WINDOW) {
+            throw ctx.fail('result_window_exceeded', `page ${input.page} × size ${input.size} is past the first ${RESULT_WINDOW.toLocaleString('en-US')} entries.`, ctx.recoveryFor('result_window_exceeded'));
+        }
+        let total;
+        let entries;
+        if (input.vocabulary === 'resource_types') {
+            const matched = filterResourceTypes(input.query);
+            total = matched.length;
+            entries = matched.slice((input.page - 1) * input.size, input.page * input.size).map((t) => ({
+                filter_param: 'resource_type',
+                filter_value: t.id,
+                label: t.label,
+                ...(t.parentType ? { parent_type: t.parentType } : {}),
+                search_value: t.searchValue,
+            }));
+        }
+        else {
+            const service = getZenodoService();
+            let funderRor;
+            if (input.funder) {
+                const ref = parseFunderRef(input.funder);
+                const funder = ref ? await service.resolveFunder(ref, ctx) : undefined;
+                if (!funder) {
+                    throw ctx.fail('unknown_funder', `"${inline(input.funder)}" is not a known ROR id and no funder carries that Crossref Funder DOI.`, ctx.recoveryFor('unknown_funder'));
+                }
+                funderRor = funder.ror_id;
+            }
+            const page = await service.searchVocabulary(input.vocabulary, { query: input.query, funderRor, page: input.page, size: input.size }, ctx);
+            total = page.total;
+            entries = toEntries(page);
+        }
+        const reachable = Math.min(total, RESULT_WINDOW);
+        const hasMore = input.page * input.size < reachable;
+        ctx.enrich({ shown: entries.length });
+        ctx.enrich.total(total);
+        const notice = [];
+        if (total === 0) {
+            notice.push(input.query
+                ? `No ${input.vocabulary} matched "${inline(input.query)}"; ${ZERO_HIT_ADVICE[input.vocabulary]}${input.funder ? ', or drop funder to search every funder’s grants' : ''}.`
+                : `No ${input.vocabulary} entries were returned.`);
+        }
+        else if (entries.length === 0) {
+            const last = Math.max(1, Math.ceil(reachable / input.size));
+            notice.push(`Page ${input.page} is past the last page (${last}); call again with page ${last} or lower.`);
+        }
+        if (input.vocabulary === 'funders' && entries.length > 1) {
+            notice.push('Several funders share names across countries; pick by country and ROR id.');
+        }
+        if (hasMore) {
+            notice.push(`Showing ${entries.length} of ${total}; call again with page ${input.page + 1}.`);
+            ctx.enrich.truncated({ shown: entries.length, cap: input.size, guidance: notice.join(' ') });
+        }
+        else if (notice.length) {
+            ctx.enrich.notice(notice.join(' '));
+        }
+        return {
+            vocabulary: input.vocabulary,
+            ...(input.query ? { query: input.query } : {}),
+            total,
+            page: input.page,
+            size: input.size,
+            has_more: hasMore,
+            ...(hasMore ? { next_page: input.page + 1 } : {}),
+            entries,
+        };
+    },
+    format: (result) => {
+        const lines = [
+            `## Zenodo ${result.vocabulary}${result.query ? ` matching "${inline(result.query)}"` : ''}`,
+            `**Total:** ${result.total} | **Page:** ${result.page} | **Size:** ${result.size} | **Has more:** ${result.has_more}${result.next_page !== undefined ? ` | **Next page:** ${result.next_page}` : ''}`,
+        ];
+        for (const e of result.entries) {
+            lines.push('', `### ${inline(e.label)}`, `- **Filter:** ${e.filter_param} = \`${inline(e.filter_value)}\``);
+            const field = (label, value) => {
+                if (value)
+                    lines.push(`- **${label}:** ${inline(value)}`);
+            };
+            field('Slug', e.slug);
+            field('UUID', e.uuid);
+            field('Community type', e.community_type);
+            field('Website', e.website);
+            if (e.organizations?.length)
+                lines.push(`- **Organizations:** ${e.organizations.map(inline).join('; ')}`);
+            field('ROR id', e.ror_id);
+            field('Funder DOI', e.funder_doi);
+            field('Acronym', e.acronym);
+            field('Country', e.country);
+            field('Country name', e.country_name);
+            field('Number', e.number);
+            if (e.title) {
+                lines.push(hasLineBreak(e.title)
+                    ? `- **Title:**\n${quoteBlock(e.title, 'Award title (untrusted):')}`
+                    : `- **Title:** ${e.title}`);
+            }
+            field('Program', e.program);
+            field('Funder id', e.funder_id);
+            field('Funder name', e.funder_name);
+            field('Award DOI', e.award_doi);
+            field('Award URL', e.award_url);
+            field('Start date', e.start_date);
+            field('End date', e.end_date);
+            field('URL', e.url);
+            if (e.osi_approved !== undefined)
+                lines.push(`- **OSI approved:** ${e.osi_approved}`);
+            if (e.tags?.length)
+                lines.push(`- **Tags:** ${e.tags.map(inline).join(', ')}`);
+            field('Parent type', e.parent_type);
+            field('Search value', e.search_value);
+        }
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+//# sourceMappingURL=lookup-vocabulary.tool.js.map

package/dist/mcp-server/tools/definitions/lookup-vocabulary.tool.js.map

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package/dist/mcp-server/tools/definitions/read-file.tool.d.ts

@@ -0,0 +1,104 @@
+/**
+ * @fileoverview zenodo_read_file — reads a byte-capped UTF-8 excerpt of one text
+ * file in a Zenodo deposit, or of one member of a .zip file, without downloading
+ * the archive. Content is depositor-supplied, rendered fenced as untrusted data,
+ * and carries the deposit's license.
+ * @module mcp-server/tools/definitions/read-file
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+export declare const readFile: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    id: z.ZodString;
+    key: z.ZodString;
+    archive_member: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
+    offset_bytes: z.ZodDefault<z.ZodNumber>;
+    max_bytes: z.ZodDefault<z.ZodNumber>;
+}, z.core.$strip>, z.ZodObject<{
+    recid: z.ZodString;
+    key: z.ZodString;
+    archive_member: z.ZodOptional<z.ZodString>;
+    status: z.ZodEnum<{
+        empty: "empty";
+        not_text: "not_text";
+        restricted: "restricted";
+        text: "text";
+    }>;
+    mimetype: z.ZodOptional<z.ZodString>;
+    file_size: z.ZodOptional<z.ZodNumber>;
+    md5: z.ZodOptional<z.ZodString>;
+    text: z.ZodOptional<z.ZodString>;
+    offset_bytes: z.ZodNumber;
+    bytes_returned: z.ZodNumber;
+    next_offset: z.ZodOptional<z.ZodNumber>;
+    has_more: z.ZodBoolean;
+    replacement_chars: z.ZodNumber;
+    rights: z.ZodArray<z.ZodObject<{
+        id: z.ZodOptional<z.ZodString>;
+        title: z.ZodString;
+    }, z.core.$strip>>;
+    record_url: z.ZodString;
+    download_url: z.ZodString;
+    files_access: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>, readonly [{
+    readonly reason: "invalid_identifier";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "id matches no accepted form, or is a GitHub-badge latestdoi id or a non-zenodo.org host";
+    readonly recovery: "Pass a Zenodo record id (22705923), a DOI (10.5281/zenodo.22705923), or a zenodo.org/records URL as id; for a title or keyword, use zenodo_search_records.";
+}, {
+    readonly reason: "record_not_found";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "The record 404s, its metadata is restricted, or a non-Zenodo DOI is not registered to a record";
+    readonly recovery: "Check the id with zenodo_get_record, or find the deposit with zenodo_search_records.";
+}, {
+    readonly reason: "record_deleted";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "The record was deleted from Zenodo; only its removal tombstone remains";
+    readonly recovery: "Call zenodo_get_record with this id for the removal date and reason, then find a replacement deposit with zenodo_search_records.";
+}, {
+    readonly reason: "file_not_found";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "key is not in the record's manifest, or Zenodo serves no content for it";
+    readonly recovery: "Call zenodo_list_files with this id to see the record’s exact file keys.";
+}, {
+    readonly reason: "not_an_archive";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "archive_member is set but key is not a .zip";
+    readonly recovery: "Drop archive_member to read the file itself, or pick a .zip key from zenodo_list_files.";
+}, {
+    readonly reason: "member_not_found";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "Zenodo has no member at archive_member inside the .zip";
+    readonly recovery: "Call zenodo_list_files with archive_key set to this key to see the member paths.";
+}, {
+    readonly reason: "member_offset_unsupported";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "offset_bytes is above 0 together with archive_member";
+    readonly recovery: "Read the member from offset_bytes 0 with a larger max_bytes (up to 65536), or download the archive from download_url.";
+}, {
+    readonly reason: "offset_out_of_range";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "offset_bytes is at or past the end of the file";
+    readonly recovery: "Call zenodo_read_file again with an offset_bytes below the file’s size (size in zenodo_list_files, file_size in a prior zenodo_read_file result).";
+}, {
+    readonly reason: "archive_unavailable";
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "Zenodo cannot open the .zip named by key: its member listing or the member read answered HTTP 500 after one retry, or no complete response arrived in time";
+    readonly thrownBy: "service";
+    readonly recovery: "Zenodo cannot open every .zip; download the archive from the URL in the error message and extract the member locally, or read the record’s top-level files with zenodo_read_file.";
+}, {
+    readonly reason: "record_unavailable";
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "Zenodo could not serve this record: HTTP 500 after one retry, HTTP 500 while resolving a non-Zenodo DOI, or no complete response within the time budget (its gateway cuts off near 30 s, which deposits with about 10,000 or more files hit)";
+    readonly thrownBy: "service";
+    readonly recovery: "Read the deposit’s metadata from zenodo_search_records with query doi:\"<its DOI>\" (all_versions true); withdrawn legacy records and deposits with more than about 10,000 files fail on the record endpoint, so their files cannot be read, and if a keyword search also fails, Zenodo is degraded.";
+}, {
+    readonly reason: "rate_limited";
+    readonly code: JsonRpcErrorCode.RateLimited;
+    readonly when: "Zenodo answered HTTP 429, or this server's shared Zenodo request budget is spent for the current window";
+    readonly retryable: true;
+    readonly thrownBy: "service";
+    readonly recovery: "Wait for the retryAfter seconds in the error data, then call zenodo_read_file again with the same arguments.";
+}], {
+    readonly notice: z.ZodOptional<z.ZodString>;
+}>;
+//# sourceMappingURL=read-file.tool.d.ts.map

package/dist/mcp-server/tools/definitions/read-file.tool.d.ts.map

@@ -0,0 +1 @@
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