@djmima/pubmed-mcp 0.0.0-stage → 1.0.0

package/dist/cli/commands.js

@@ -0,0 +1,508 @@
+/**
+ * Command table for the pubmed CLI.
+ *
+ * Each command runs one MCP tool: it turns command-line input into the tool's
+ * parameters, validates them with the tool's zod schema (as the MCP server
+ * does), and calls the same tool function, so the JSON output is the same.
+ * Lists longer than a tool's per-request limit are split into batches that
+ * run one after another through the shared client and its rate limiter; the
+ * batch results are merged into one response of the same shape.
+ */
+import { z } from 'zod';
+import { searchArticles, searchArticlesSchema } from '../tools/searchArticles.js';
+import { getArticleMetadata, getArticleMetadataSchema, MAX_METADATA_PMIDS, } from '../tools/getArticleMetadata.js';
+import { findRelatedArticles, findRelatedArticlesSchema, } from '../tools/findRelatedArticles.js';
+import { lookupArticleByCitation, lookupArticleByCitationSchema, MAX_CITATIONS, } from '../tools/lookupArticleByCitation.js';
+import { convertArticleIds, convertArticleIdsSchema, MAX_CONVERT_IDS, } from '../tools/convertArticleIds.js';
+import { getFullTextArticle, getFullTextArticleSchema, MAX_FULL_TEXT_IDS, } from '../tools/getFullTextArticle.js';
+import { getCopyrightStatus, getCopyrightStatusSchema, MAX_COPYRIGHT_PMIDS, } from '../tools/getCopyrightStatus.js';
+/** Invalid command-line input. The CLI exits with status 2 instead of 1. */
+export class UsageError extends Error {
+    constructor(message) {
+        super(message);
+        this.name = 'UsageError';
+    }
+}
+// ─── search ─────────────────────────────────────────────────────────────────
+const search = {
+    name: 'search',
+    tool: 'search_articles',
+    description: 'Search PubMed and return matching PMIDs',
+    options: {
+        'max-results': { type: 'string' },
+        retstart: { type: 'string' },
+        sort: { type: 'string' },
+        field: { type: 'string' },
+        'date-from': { type: 'string' },
+        'date-to': { type: 'string' },
+        datetype: { type: 'string' },
+    },
+    help: `Usage: pubmed search <query> [options]
+       pubmed search - [options]      (read the query from stdin)
+
+Search PubMed. Prints PMIDs with total_count, query_translation, warnings,
+and errors (same JSON as the search_articles MCP tool).
+
+Options:
+  --max-results <n>   PMIDs to return, 1-10000 (default 20)
+  --retstart <n>      Offset of the first PMID, for paging (default 0)
+  --sort <order>      relevance | pub_date | author | journal_name
+  --field <field>     Restrict untagged terms to one field:
+                      title | tiab | mesh | author | journal | affiliation
+  --date-from <date>  Start date: YYYY, YYYY/MM, or YYYY/MM/DD
+  --date-to <date>    End date, same formats (either bound may be omitted)
+  --datetype <type>   pdat = publication date (default) | edat = Entrez date |
+                      mdat = modification date
+
+PubMed maps untagged terms through Automatic Term Mapping (ATM). Before
+concluding that a low or zero total_count means no literature exists, check
+query_translation, warnings, and errors. To search several words in one
+field, tag each term; when a quoted phrase is not indexed, use a proximity
+search such as "drug resistance"[tiab:~0].
+
+Example:
+  pubmed search "TP53[tiab] AND myelodysplastic syndromes[mh]" --max-results 200 -o search.json
+  jq '{total_count, query_translation, warnings, errors}' search.json
+`,
+    async execute(input, client) {
+        // A query read from stdin may span several lines.
+        const query = (input.positionals.length === 1 && input.positionals[0] === '-'
+            ? (await input.readText('-')).replace(/\s+/g, ' ')
+            : input.positionals.join(' ')).trim();
+        if (!query)
+            throw new UsageError('missing <query>');
+        const params = validate(searchArticlesSchema, {
+            query,
+            max_results: intOption(input, 'max-results'),
+            retstart: intOption(input, 'retstart'),
+            sort: input.values.sort,
+            field: input.values.field,
+            date_from: input.values['date-from'],
+            date_to: input.values['date-to'],
+            datetype: input.values.datetype,
+        });
+        const output = await searchArticles(params, client);
+        return { output, summary: `${output.returned_count} of ${output.total_count} PMIDs` };
+    },
+};
+// ─── metadata ───────────────────────────────────────────────────────────────
+const metadata = {
+    name: 'metadata',
+    tool: 'get_article_metadata',
+    description: 'Get title, abstract, authors, MeSH terms, etc.',
+    options: {
+        authors: { type: 'string' },
+        affiliations: { type: 'string' },
+    },
+    help: `Usage: pubmed metadata <pmid>... | - [options]
+
+Get title, abstract, authors, journal, publication date, MeSH terms,
+keywords, and article types (same JSON as get_article_metadata).
+Lists longer than ${MAX_METADATA_PMIDS} PMIDs are fetched in batches and merged.
+
+Options:
+  --authors <mode>       all (default) | first_last | first | none
+                         author_count always gives the full number of authors
+  --affiliations <bool>  false (default) | true: include the affiliations of
+                         the returned authors
+
+Records are large (abstracts, and with --affiliations also affiliations): save
+them with -o and extract the fields you need with jq.
+
+Example:
+  jq -r '.pmids[]' search.json | pubmed metadata - --authors first_last -o meta.json
+  jq -r '.articles[] | [.identifiers.pmid, .publication_date.year, .title] | @tsv' meta.json
+`,
+    async execute(input, client) {
+        const pmids = await readIds(input, PMID);
+        const authors = input.values.authors;
+        const affiliations = boolOption(input, 'affiliations');
+        const batches = chunk(pmids, MAX_METADATA_PMIDS).map((batch) => validate(getArticleMetadataSchema, {
+            pmids: batch,
+            authors,
+            include_affiliations: affiliations,
+        }));
+        const results = await runBatches(batches, (params) => getArticleMetadata(params, client));
+        const articles = results.flatMap((r) => r.articles);
+        const output = {
+            articles,
+            count: articles.length,
+            important_legal_notice: results[0].important_legal_notice,
+        };
+        return { output, summary: plural(output.count, 'article') };
+    },
+};
+// ─── related ────────────────────────────────────────────────────────────────
+/** ELink takes the IDs in the URL, so keep each request's list short. */
+const RELATED_BATCH_SIZE = 200;
+const related = {
+    name: 'related',
+    tool: 'find_related_articles',
+    description: 'Find similar or citing articles and linked records',
+    options: {
+        'link-type': { type: 'string' },
+        'max-results': { type: 'string' },
+    },
+    help: `Usage: pubmed related <pmid>... | - [options]
+
+Find linked records for each PMID with NCBI ELink (same JSON as
+find_related_articles). Lists longer than ${RELATED_BATCH_SIZE} PMIDs are split into batches.
+
+Options:
+  --link-type <type>  similar_articles (default)  similar PubMed articles
+                      citing_pmc_articles         PMC articles citing the PMID
+                      linked_gene_records         NCBI Gene records
+                      linked_refseq_proteins      RefSeq protein records
+                      linked_refseq_nucleotides   RefSeq nucleotide records
+  --max-results <n>   Cap on links per source PMID, 1-1000
+
+citing_pmc_articles returns PMC IDs without the "PMC" prefix; pubmed fulltext
+and pubmed convert --id-type pmcid accept them as they are.
+
+Example:
+  pubmed related 34265844 --link-type citing_pmc_articles -o citing.json
+  jq -r '.linksets[].linksetdbs[].links[]' citing.json
+`,
+    async execute(input, client) {
+        const pmids = await readIds(input, PMID);
+        const linkType = input.values['link-type'];
+        const maxResults = intOption(input, 'max-results');
+        const batches = chunk(pmids, RELATED_BATCH_SIZE).map((batch) => validate(findRelatedArticlesSchema, {
+            pmids: batch,
+            link_type: linkType,
+            max_results: maxResults,
+        }));
+        const results = await runBatches(batches, (params) => findRelatedArticles(params, client));
+        const output = { linksets: results.flatMap((r) => r.linksets) };
+        const links = output.linksets
+            .flatMap((linkset) => linkset.linksetdbs)
+            .reduce((total, linksetdb) => total + linksetdb.links.length, 0);
+        return { output, summary: `${plural(links, 'link')} for ${plural(pmids.length, 'PMID')}` };
+    },
+};
+// ─── citation ───────────────────────────────────────────────────────────────
+const CITATION_SCHEMA = lookupArticleByCitationSchema.citations.element;
+const citation = {
+    name: 'citation',
+    tool: 'lookup_article_by_citation',
+    description: 'Find PMIDs from journal, year, volume, page, author',
+    options: {
+        journal: { type: 'string' },
+        year: { type: 'string' },
+        volume: { type: 'string' },
+        'first-page': { type: 'string' },
+        author: { type: 'string' },
+        key: { type: 'string' },
+        input: { type: 'string' },
+    },
+    help: `Usage: pubmed citation --journal <name> --year <yyyy> [options]
+       pubmed citation --input <file|->
+
+Find PMIDs from citation details with NCBI ECitMatch (same JSON as
+lookup_article_by_citation). Unmatched citations have an empty pmid.
+
+Options:
+  --journal <name>    Journal title or abbreviation, e.g. "N Engl J Med"
+  --year <yyyy>       Publication year
+  --volume <v>        Volume
+  --first-page <p>    First page
+  --author <name>     First author's last name
+  --key <key>         Label echoed back in the result (default 1)
+  --input <file|->    Many citations: a JSON array or JSON Lines of objects
+                      {journal, year, volume, first_page, author, key};
+                      missing keys default to 1, 2, 3, ... Lists longer than
+                      ${MAX_CITATIONS} are split into batches.
+
+Example:
+  pubmed citation --journal Nature --year 2021 --volume 596 --first-page 583 --author Jumper
+`,
+    async execute(input, client) {
+        const citations = (input.values.input !== undefined
+            ? await readCitationList(input, input.values.input)
+            : [citationFromOptions(input)]).map(validateCitation);
+        const results = await runBatches(chunk(citations, MAX_CITATIONS), (batch) => lookupArticleByCitation({ citations: batch }, client));
+        const output = { citations: results.flatMap((r) => r.citations) };
+        const matched = output.citations.filter((c) => c.pmid !== '').length;
+        return {
+            output,
+            summary: `${matched} of ${plural(output.citations.length, 'citation')} matched`,
+        };
+    },
+};
+const CITATION_OPTIONS = ['journal', 'year', 'volume', 'first-page', 'author', 'key'];
+function citationFromOptions(input) {
+    const { journal } = input.values;
+    const year = intOption(input, 'year');
+    if (journal === undefined || year === undefined) {
+        throw new UsageError('give --journal and --year, or a list of citations with --input');
+    }
+    return {
+        journal,
+        year,
+        volume: input.values.volume,
+        first_page: input.values['first-page'],
+        author: input.values.author,
+        key: input.values.key ?? '1',
+    };
+}
+/** Read --input: one JSON document (an array or a single object), or JSON Lines. */
+async function readCitationList(input, path) {
+    if (CITATION_OPTIONS.some((name) => input.values[name] !== undefined)) {
+        throw new UsageError('use either --input or the single-citation options, not both');
+    }
+    const text = stripBom(await input.readText(path)).trim();
+    if (!text)
+        throw new UsageError('--input is empty');
+    let items;
+    try {
+        items = parseJsonList(text);
+    }
+    catch (err) {
+        throw new UsageError(`--input is not JSON or JSON Lines: ${errorMessage(err)}`);
+    }
+    return items.map(normalizeCitation);
+}
+/** Drop a leading byte order mark, which some Windows editors write. */
+function stripBom(text) {
+    return text.charCodeAt(0) === 0xfeff ? text.slice(1) : text;
+}
+function parseJsonList(text) {
+    try {
+        const value = JSON.parse(text);
+        return Array.isArray(value) ? value : [value];
+    }
+    catch {
+        // Not a single JSON document: read it as JSON Lines.
+        return text
+            .split(/\r?\n/)
+            .filter((line) => line.trim() !== '')
+            .map((line) => JSON.parse(line));
+    }
+}
+/**
+ * Fill in a missing key and accept the loose types that CSV-derived JSON often
+ * has: numbers for volume, first_page, and key, and a numeric string for year.
+ */
+function normalizeCitation(item, index) {
+    if (typeof item !== 'object' || item === null || Array.isArray(item)) {
+        throw new UsageError(`citation ${index + 1} in --input is not a JSON object`);
+    }
+    const c = item;
+    return {
+        ...c,
+        year: typeof c.year === 'string' && /^\d+$/.test(c.year.trim()) ? Number(c.year) : c.year,
+        volume: numberToString(c.volume),
+        first_page: numberToString(c.first_page),
+        key: c.key === undefined ? String(index + 1) : numberToString(c.key),
+    };
+}
+function numberToString(value) {
+    return typeof value === 'number' ? String(value) : value;
+}
+function validateCitation(item, index) {
+    const result = CITATION_SCHEMA.safeParse(item);
+    if (!result.success) {
+        const issue = result.error.issues[0];
+        throw new UsageError(`citation ${index + 1}: invalid ${issue.path.join('.') || 'value'}: ${issue.message}`);
+    }
+    return result.data;
+}
+// ─── convert ────────────────────────────────────────────────────────────────
+const convert = {
+    name: 'convert',
+    tool: 'convert_article_ids',
+    description: 'Convert between PMID, PMCID, and DOI',
+    options: {
+        'id-type': { type: 'string' },
+    },
+    help: `Usage: pubmed convert <id>... | - [--id-type pmid|pmcid|doi]
+
+Convert between PMID, PMCID, and DOI with the NCBI PMC ID Converter (same
+JSON as convert_article_ids). All IDs must be of the --id-type given
+(default pmid). Lists longer than ${MAX_CONVERT_IDS} IDs are split into batches.
+
+Example:
+  pubmed convert 34265844 | jq -r '.records[] | [.pmid, .pmcid // "", .doi // ""] | @tsv'
+`,
+    async execute(input, client) {
+        const idType = input.values['id-type'] ?? 'pmid';
+        const kind = CONVERT_ID_KINDS.get(idType);
+        if (!kind) {
+            throw new UsageError(`invalid --id-type: expected pmid, pmcid, or doi, got ${JSON.stringify(idType)}`);
+        }
+        const ids = await readIds(input, kind);
+        const batches = chunk(ids, MAX_CONVERT_IDS).map((batch) => validate(convertArticleIdsSchema, { ids: batch, id_type: idType }));
+        const results = await runBatches(batches, (params) => convertArticleIds(params, client));
+        // Batches share one response envelope; only the ID lists grow.
+        const [first] = results;
+        const output = {
+            ...first,
+            request: { ...first.request, ids: results.flatMap((r) => r.request.ids) },
+            records: results.flatMap((r) => r.records),
+        };
+        return { output, summary: plural(output.records.length, 'record') };
+    },
+};
+// ─── fulltext ───────────────────────────────────────────────────────────────
+const fulltext = {
+    name: 'fulltext',
+    tool: 'get_full_text_article',
+    description: 'Get the full text of PMC open-access articles',
+    options: {},
+    help: `Usage: pubmed fulltext <pmcid>... | -
+
+Get the full text of PMC articles as plain text: all sections, figure and
+table captions, and references (same JSON as get_full_text_article). Only the
+PMC Open Access subset is available; other IDs are listed in errors. Lists
+longer than ${MAX_FULL_TEXT_IDS} PMCIDs are fetched in batches and merged.
+
+Each article is typically tens of thousands of characters. Save them with -o
+and pull out only the passages you need. Get PMCIDs from PMIDs with pubmed
+convert, or check which PMIDs have full text with pubmed copyright.
+
+Example:
+  pubmed fulltext PMC8371605 -o full.json
+  jq -r '.articles[0].full_text' full.json | grep -n -i 'confidence'
+`,
+    async execute(input, client) {
+        const pmcids = await readIds(input, PMCID);
+        const batches = chunk(pmcids, MAX_FULL_TEXT_IDS).map((batch) => validate(getFullTextArticleSchema, { pmc_ids: batch }));
+        const results = await runBatches(batches, (params) => getFullTextArticle(params, client));
+        const articles = results.flatMap((r) => r.articles);
+        const output = {
+            important_legal_notice: results[0].important_legal_notice,
+            articles,
+            errors: results.flatMap((r) => r.errors),
+            count: articles.length,
+        };
+        return {
+            output,
+            summary: `${plural(output.count, 'article')}, ${output.errors.length} unavailable`,
+        };
+    },
+};
+// ─── copyright ──────────────────────────────────────────────────────────────
+const copyright = {
+    name: 'copyright',
+    tool: 'get_copyright_status',
+    description: 'Check full-text availability and license',
+    options: {},
+    help: `Usage: pubmed copyright <pmid>... | -
+
+Check whether full text can be retrieved (has_full_text), plus the license,
+copyright statement, and PMC open-access status (same JSON as
+get_copyright_status). Lists longer than ${MAX_COPYRIGHT_PMIDS} PMIDs are split into batches.
+
+Example:
+  pubmed copyright - < pmids.txt -o rights.json
+  jq -r '.statuses[] | select(.has_full_text) | .pmcid' rights.json | pubmed fulltext - -o full.json
+`,
+    async execute(input, client) {
+        const pmids = await readIds(input, PMID);
+        const batches = chunk(pmids, MAX_COPYRIGHT_PMIDS).map((batch) => validate(getCopyrightStatusSchema, { pmids: batch }));
+        const results = await runBatches(batches, (params) => getCopyrightStatus(params, client));
+        const statuses = results.flatMap((r) => r.statuses);
+        const output = { statuses, count: statuses.length };
+        const withFullText = statuses.filter((s) => s.has_full_text).length;
+        return { output, summary: `${plural(output.count, 'PMID')}, ${withFullText} with full text` };
+    },
+};
+export const COMMANDS = [
+    search,
+    metadata,
+    related,
+    citation,
+    convert,
+    fulltext,
+    copyright,
+];
+const PMID = { label: 'PMID', pattern: /^\d+$/ };
+const PMCID = { label: 'PMCID', pattern: /^(PMC)?\d+$/i };
+const DOI = { label: 'DOI', pattern: /^10\.\S+\/\S+$/ };
+const CONVERT_ID_KINDS = new Map([
+    ['pmid', PMID],
+    ['pmcid', PMCID],
+    ['doi', DOI],
+]);
+/**
+ * Collect IDs from the arguments, separated by whitespace or commas.
+ * "-" reads them from stdin, e.g. the output of jq -r '.pmids[]'.
+ */
+async function readIds(input, kind) {
+    const ids = [];
+    for (const arg of input.positionals) {
+        const text = arg === '-' ? await input.readText('-') : arg;
+        ids.push(...text.split(/[\s,]+/).filter(Boolean));
+    }
+    if (ids.length === 0) {
+        throw new UsageError(`no ${kind.label}s given; pass them as arguments or use - to read stdin`);
+    }
+    const invalid = ids.find((id) => !kind.pattern.test(id));
+    if (invalid !== undefined) {
+        const hint = /^[[{"]/.test(invalid)
+            ? ` (IDs must be plain text; extract them from JSON first, e.g. jq -r '.pmids[]')`
+            : '';
+        throw new UsageError(`not a ${kind.label}: ${JSON.stringify(invalid)}${hint}`);
+    }
+    return ids;
+}
+/** Parse a whole-number option; the tool's schema checks the range. */
+function intOption(input, name) {
+    const value = input.values[name];
+    if (value === undefined)
+        return undefined;
+    if (!/^\d+$/.test(value.trim())) {
+        throw new UsageError(`--${name} must be a whole number, got ${JSON.stringify(value)}`);
+    }
+    return Number(value);
+}
+function boolOption(input, name) {
+    const value = input.values[name];
+    if (value === undefined)
+        return undefined;
+    if (value === 'true')
+        return true;
+    if (value === 'false')
+        return false;
+    throw new UsageError(`--${name} must be true or false, got ${JSON.stringify(value)}`);
+}
+/** Validate params with a tool's zod schema, as the MCP server does before calling it. */
+function validate(schema, params) {
+    const result = z.object(schema).safeParse(params);
+    if (!result.success) {
+        const issue = result.error.issues[0];
+        // Every schema key that can fail here comes from an option of the same name.
+        const option = `--${String(issue.path[0]).replace(/_/g, '-')}`;
+        throw new UsageError(`invalid ${option}: ${issue.message}`);
+    }
+    return result.data;
+}
+function chunk(items, size) {
+    const batches = [];
+    for (let i = 0; i < items.length; i += size) {
+        batches.push(items.slice(i, i + size));
+    }
+    return batches;
+}
+/** Run batches one at a time; an error names the batch that failed. */
+async function runBatches(batches, run) {
+    const results = [];
+    for (const [index, params] of batches.entries()) {
+        try {
+            results.push(await run(params));
+        }
+        catch (err) {
+            if (batches.length === 1)
+                throw err;
+            throw new Error(`batch ${index + 1} of ${batches.length}: ${errorMessage(err)}`);
+        }
+    }
+    return results;
+}
+function plural(count, noun) {
+    return `${count} ${noun}${count === 1 ? '' : 's'}`;
+}
+export function errorMessage(err) {
+    return err instanceof Error ? err.message : String(err);
+}
+//# sourceMappingURL=commands.js.map

package/dist/cli/commands.js.map

@@ -0,0 +1 @@
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package/dist/cli/run.d.ts

@@ -0,0 +1,21 @@
+/**
+ * Argument parsing, dispatch, and output for the pubmed CLI.
+ *
+ * Kept apart from the entrypoint (src/cli.ts) so tests can run commands with
+ * in-memory I/O and a mocked NCBI client.
+ *
+ * Output contract: the command's JSON goes to stdout (or to the -o file) and
+ * nothing else does; messages go to stderr. Exit status is 0 on success, 1
+ * when NCBI or a file operation fails, and 2 for invalid usage.
+ */
+import { NcbiClient } from '../pubmed/client.js';
+export interface CliIo {
+    stdout(text: string): void;
+    stderr(text: string): void;
+    /** Read a file, or stdin when path is "-". */
+    readText(path: string): Promise<string>;
+    writeText(path: string, text: string): Promise<void>;
+}
+/** Run one CLI invocation and return its exit status. */
+export declare function runCli(argv: string[], io: CliIo, client?: NcbiClient): Promise<number>;
+//# sourceMappingURL=run.d.ts.map

package/dist/cli/run.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"run.d.ts","sourceRoot":"","sources":["../../src/cli/run.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAGH,OAAO,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AASjD,MAAM,WAAW,KAAK;IACpB,MAAM,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,MAAM,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,8CAA8C;IAC9C,QAAQ,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC;IACxC,SAAS,CAAC,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;CACtD;AAOD,yDAAyD;AACzD,wBAAsB,MAAM,CAC1B,IAAI,EAAE,MAAM,EAAE,EACd,EAAE,EAAE,KAAK,EACT,MAAM,CAAC,EAAE,UAAU,GAClB,OAAO,CAAC,MAAM,CAAC,CA+EjB"}