@cyanheads/pubmed-mcp-server 2.3.10 → 2.3.11
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CLAUDE.md +1 -1
- package/README.md +1 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +75 -14
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +3 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.js +4 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.js +7 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.js.map +1 -1
- package/dist/services/ncbi/parsing/article-parser.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/article-parser.js +10 -5
- package/dist/services/ncbi/parsing/article-parser.js.map +1 -1
- package/package.json +1 -1
- package/server.json +3 -3
package/CLAUDE.md
CHANGED
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@@ -1,7 +1,7 @@
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# Agent Protocol
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**Server:** @cyanheads/pubmed-mcp-server
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**Version:** 2.3.
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**Version:** 2.3.11
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
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> **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
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package/README.md
CHANGED
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@@ -7,7 +7,7 @@
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<div align="center">
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[](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [](./CHANGELOG.md) [](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [](https://modelcontextprotocol.io/)
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[](./LICENSE) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"fetch-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAMjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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{"version":3,"file":"fetch-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAMjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAyP5B,CAAC"}
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@@ -11,7 +11,13 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
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description: 'Fetch full article metadata by PubMed IDs. Returns detailed article information including abstract, authors, journal, MeSH terms.',
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annotations: { readOnlyHint: true, openWorldHint: true },
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input: z.object({
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pmids: z
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pmids: z
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.array(z
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.string()
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.regex(/^\d+$/, 'PMID must be a numeric identifier (e.g. "13054692"). Remove any whitespace, commas, or non-digit characters — pass each PMID as a separate array element.'))
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.min(1)
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.max(200)
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.describe('PubMed IDs to fetch'),
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includeMesh: z.boolean().default(true).describe('Include MeSH terms'),
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includeGrants: z.boolean().default(false).describe('Include grant information'),
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}),
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@@ -145,29 +151,44 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
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},
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format: (result) => {
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const lines = [`## PubMed Articles`, `**Articles Returned:** ${result.totalReturned}`];
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if (result.unavailablePmids?.length)
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if (result.unavailablePmids?.length) {
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lines.push(`**Unavailable PMIDs:** ${result.unavailablePmids.join(', ')}`);
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}
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if (result.totalReturned === 0) {
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lines.push(`\n> No articles were returned. These PMIDs may be invalid, unpublished, or withdrawn. Try \`pubmed_search_articles\` to discover valid PMIDs.`);
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}
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for (const a of result.articles) {
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lines.push(`\n### ${a.title ?? a.pmid ?? 'Unknown'}`);
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if (a.authors?.length) {
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const
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lines.push(`\n**Authors (${a.authors.length}):**`);
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for (const au of a.authors) {
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lines.push(`- ${formatAuthor(au)}`);
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}
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}
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if (a.affiliations?.length) {
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lines.push(`\n**Affiliations:**`);
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a.affiliations.forEach((aff, i) => {
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lines.push(`${i + 1}. ${aff}`);
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});
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}
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if (a.affiliations?.length)
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lines.push(`**Affiliations:** ${a.affiliations.join('; ')}`);
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const ji = a.journalInfo;
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if (ji) {
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const parts = [
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const
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if (
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parts.push(
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const parts = [];
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const journalName = ji.isoAbbreviation ?? ji.title;
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if (journalName)
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parts.push(journalName);
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const pubDateStr = formatPublicationDate(ji.publicationDate);
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if (pubDateStr)
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parts.push(pubDateStr);
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if (ji.volume)
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parts.push(`**${ji.volume}**${ji.issue ? `(${ji.issue})` : ''}`);
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if (ji.pages)
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parts.push(ji.pages);
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const issnPart = ji.eIssn ? `eISSN ${ji.eIssn}` : ji.issn ? `ISSN ${ji.issn}` : undefined;
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if (issnPart)
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parts.push(issnPart);
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if (parts.length)
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lines.push(`\n**Journal:** ${parts.join(', ')}`);
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}
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if (a.publicationTypes?.length)
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lines.push(`**Type:** ${a.publicationTypes.join(', ')}`);
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lines.push(`**PMID:** ${a.pmid}`);
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if (a.doi)
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lines.push(`**DOI:** ${a.doi}`);
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if (a.pmcId)
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lines.push(`**PMCID:** ${a.pmcId}`);
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if (a.pubmedUrl)
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lines.push(`**PubMed:** ${a.pubmedUrl}`);
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if (a.pmcUrl)
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lines.push(`**PMC:** ${a.pmcUrl}`);
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if (a.articleDates?.length) {
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lines.push(`**Article Dates:** ${a.articleDates.map(formatArticleDate).join('; ')}`);
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}
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if (a.abstractText)
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lines.push(`\n#### Abstract\n${a.abstractText}`);
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if (a.keywords?.length)
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if (a.grantList?.length) {
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lines.push(`\n#### Grants`);
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for (const g of a.grantList) {
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const
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const grantId = g.acronym
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? `${g.grantId ?? g.acronym} (${g.acronym})`
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: (g.grantId ?? '');
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const parts = [grantId, g.agency, g.country].filter(Boolean);
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lines.push(`- ${parts.join(' — ')}`);
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}
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}
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return [{ type: 'text', text: lines.join('\n') }];
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},
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});
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function formatAuthor(au) {
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if (au.collectiveName)
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return `${au.collectiveName} (collective)`;
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let name;
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if (au.firstName && au.lastName) {
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name = `${au.firstName} ${au.lastName}`;
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}
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else if (au.lastName) {
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name = au.initials ? `${au.lastName} ${au.initials}` : au.lastName;
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}
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else {
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name = au.initials ?? 'Unknown';
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}
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const affIndices = au.affiliationIndices?.length
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? ` [${au.affiliationIndices.map((i) => i + 1).join(', ')}]`
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: '';
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const orcid = au.orcid ? ` · ORCID: ${au.orcid}` : '';
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return `${name}${affIndices}${orcid}`;
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}
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function formatPublicationDate(pd) {
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if (!pd)
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return;
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if (pd.medlineDate)
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return pd.medlineDate;
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if (!pd.year)
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return;
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return [pd.year, pd.month, pd.day].filter(Boolean).join(' ');
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}
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function formatArticleDate(ad) {
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const datePart = [ad.year, ad.month, ad.day].filter(Boolean).join('-');
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return ad.dateType ? `${ad.dateType} ${datePart}` : datePart;
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}
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//# sourceMappingURL=fetch-articles.tool.js.map
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1
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAgDjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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1
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+
{"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAgDjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAkO5B,CAAC"}
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@@ -47,7 +47,9 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
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47
47
|
.optional()
|
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48
48
|
.describe('PMC IDs to fetch (e.g. ["PMC9575052"]). Provide this OR pmids, not both.'),
|
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49
49
|
pmids: z
|
|
50
|
-
.array(z
|
|
50
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+
.array(z
|
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51
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+
.string()
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52
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+
.regex(/^\d+$/, 'PMID must be a numeric identifier (e.g. "13054692"). Remove any whitespace, commas, or non-digit characters — pass each PMID as a separate array element.'))
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51
53
|
.min(1)
|
|
52
54
|
.max(10)
|
|
53
55
|
.optional()
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@@ -1 +1 @@
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1
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-
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1
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+
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAkCjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;
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1
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+
{"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAkCjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;kBAoK1B,CAAC"}
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@@ -19,7 +19,10 @@ export const findRelatedTool = tool('pubmed_find_related', {
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19
19
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description: 'Find articles related to a source article — similar content, citing articles, or references.',
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20
20
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annotations: { readOnlyHint: true, openWorldHint: true },
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21
21
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input: z.object({
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22
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-
pmid: z
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22
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+
pmid: z
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23
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+
.string()
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24
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+
.regex(/^\d+$/, 'PMID must be a numeric identifier (e.g. "13054692"). Remove any whitespace or non-digit characters.')
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25
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+
.describe('Source PubMed ID'),
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23
26
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relationship: z
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24
27
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.enum(['similar', 'cited_by', 'references'])
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25
28
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.default('similar')
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"find-related.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4CAA4C,CAAC;AACnF,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AAuBrE,SAAS,YAAY,CAAC,KAAkE;IACtF,IAAI,KAAK,KAAK,SAAS,IAAI,KAAK,KAAK,IAAI;QAAE,OAAO,EAAE,CAAC;IACrD,IAAI,OAAO,KAAK,KAAK,QAAQ;QAAE,OAAO,KAAK,CAAC,OAAO,CAAC,KAAK,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;IACjG,OAAO,MAAM,CAAC,KAAK,CAAC,CAAC;AACvB,CAAC;AAED,gFAAgF;AAEhF,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAC,qBAAqB,EAAE;IACzD,WAAW,EACT,8FAA8F;IAChG,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,IAAI,EAAE,CAAC,
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1
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+
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAUjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;
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1
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+
{"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAUjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;kBAkG9B,CAAC"}
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@@ -12,7 +12,13 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
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12
12
|
description: 'Get formatted citations for PubMed articles in APA, MLA, BibTeX, or RIS format.',
|
|
13
13
|
annotations: { readOnlyHint: true, openWorldHint: true },
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14
14
|
input: z.object({
|
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15
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-
pmids: z
|
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15
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+
pmids: z
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16
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+
.array(z
|
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17
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+
.string()
|
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18
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+
.regex(/^\d+$/, 'PMID must be a numeric identifier (e.g. "13054692"). Remove any whitespace, commas, or non-digit characters — pass each PMID as a separate array element.'))
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19
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+
.min(1)
|
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20
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+
.max(50)
|
|
21
|
+
.describe('PubMed IDs to cite'),
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16
22
|
styles: z
|
|
17
23
|
.array(z.enum(['apa', 'mla', 'bibtex', 'ris']))
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18
24
|
.default(['apa'])
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"format-citations.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAEL,eAAe,GAChB,MAAM,kDAAkD,CAAC;AAC1D,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,2CAA2C,CAAC;AAC7E,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AAGrE,MAAM,CAAC,MAAM,mBAAmB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACjE,WAAW,EAAE,iFAAiF;IAC9F,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC,
|
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1
|
+
{"version":3,"file":"format-citations.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAEL,eAAe,GAChB,MAAM,kDAAkD,CAAC;AAC1D,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,2CAA2C,CAAC;AAC7E,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AAGrE,MAAM,CAAC,MAAM,mBAAmB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACjE,WAAW,EAAE,iFAAiF;IAC9F,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC;aACL,KAAK,CACJ,CAAC;aACE,MAAM,EAAE;aACR,KAAK,CACJ,OAAO,EACP,2JAA2J,CAC5J,CACJ;aACA,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,CAAC,oBAAoB,CAAC;QACjC,MAAM,EAAE,CAAC;aACN,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,CAAC,CAAC,CAAC;aAC9C,OAAO,CAAC,CAAC,KAAK,CAAC,CAAC;aAChB,QAAQ,CAAC,6BAA6B,CAAC;KAC3C,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,SAAS,EAAE,CAAC;aACT,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;YACtC,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACtD,SAAS,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,0BAA0B,CAAC;SACjF,CAAC,CACH;aACA,QAAQ,CAAC,uBAAuB,CAAC;QACpC,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mDAAmD,CAAC;QACxF,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC7E,gBAAgB,EAAE,CAAC;aAChB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;aACjB,QAAQ,EAAE;aACV,QAAQ,CAAC,sDAAsD,CAAC;KACpE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,2CAA2C,EAAE;YACzD,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,MAAM,EAAE,KAAK,CAAC,MAAM;SACrB,CAAC,CAAC;QACH,MAAM,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,MAAM,CACvC,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,EAC3D,EAAE,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM,IAAI,EAAE,EAAE,CACtD,CAAC;QACF,MAAM,WAAW,GAAuB,WAAW,CAAC,GAAG,EAAE,gBAAgB,EAAE,aAAa,CAAC,CAAC;QAE1F,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC7B,MAAM,IAAI,KAAK,CAAC,gCAAgC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC5E,CAAC;QAED,MAAM,SAAS,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,UAAU,EAAE,EAAE;YAC/C,MAAM,MAAM,GAAG,gBAAgB,CAAC,UAAU,CAAC,CAAC;YAC5C,OAAO;gBACL,IAAI,EAAE,MAAM,CAAC,IAAI;gBACjB,KAAK,EAAE,MAAM,CAAC,KAAK;gBACnB,SAAS,EAAE,eAAe,CAAC,MAAM,EAAE,KAAK,CAAC,MAAyB,CAAC;aACpE,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,MAAM,aAAa,GAAG,IAAI,GAAG,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC;QACpE,MAAM,gBAAgB,GAAG,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,aAAa,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC;QAEhF,OAAO;YACL,SAAS;YACT,cAAc,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM;YAClC,cAAc,EAAE,SAAS,CAAC,MAAM;YAChC,GAAG,CAAC,gBAAgB,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,gBAAgB,EAAE,CAAC;SACzD,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,oBAAoB;YACpB,kBAAkB,MAAM,CAAC,cAAc,IAAI,MAAM,CAAC,cAAc,EAAE;SACnE,CAAC;QACF,IAAI,MAAM,CAAC,gBAAgB,EAAE,MAAM,EAAE,CAAC;YACpC,KAAK,CAAC,IAAI,CAAC,0BAA0B,MAAM,CAAC,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC7E,CAAC;QACD,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;YACrC,KAAK,CAAC,IAAI,CAAC,aAAa,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;YACtC,IAAI,KAAK,CAAC,KAAK;gBAAE,KAAK,CAAC,IAAI,CAAC,KAAK,KAAK,CAAC,KAAK,IAAI,CAAC,CAAC;YAClD,KAAK,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,CAAC;gBAChE,KAAK,CAAC,IAAI,CAAC,SAAS,KAAK,CAAC,WAAW,EAAE,EAAE,CAAC,CAAC;gBAC3C,IAAI,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,KAAK,EAAE,CAAC;oBAC1C,KAAK,CAAC,IAAI,CAAC,SAAS,KAAK,KAAK,QAAQ,UAAU,CAAC,CAAC;gBACpD,CAAC;qBAAM,CAAC;oBACN,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;gBACvB,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
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@@ -1 +1 @@
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-
{"version":3,"file":"article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/article-parser.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EACV,aAAa,EACb,mBAAmB,EACnB,iBAAiB,EACjB,WAAW,EACX,iBAAiB,EAEjB,cAAc,EACd,uBAAuB,EAEvB,UAAU,EAEV,gBAAgB,EAEhB,aAAa,EAEb,YAAY,EAEZ,UAAU,EAEV,cAAc,EACd,kBAAkB,EAElB,kBAAkB,EAElB,sBAAsB,EACtB,gBAAgB,EACjB,MAAM,aAAa,CAAC;AAGrB;;GAEG;AACH,MAAM,WAAW,gBAAgB;IAC/B,YAAY,EAAE,MAAM,EAAE,CAAC;IACvB,OAAO,EAAE,mBAAmB,EAAE,CAAC;CAChC;AAED;;;;;;GAMG;AACH,wBAAgB,cAAc,CAAC,aAAa,CAAC,EAAE,aAAa,GAAG,gBAAgB,CAqD9E;AAED;;;;;GAKG;AACH,wBAAgB,kBAAkB,CAChC,UAAU,CAAC,EAAE,UAAU,EACvB,UAAU,CAAC,EAAE,UAAU,GACtB,iBAAiB,GAAG,SAAS,CAgC/B;AAED;;;;GAIG;AACH,wBAAgB,gBAAgB,CAAC,kBAAkB,CAAC,EAAE,kBAAkB,GAAG,cAAc,EAAE,CA8B1F;AAED;;;;GAIG;AACH,wBAAgB,aAAa,CAAC,YAAY,CAAC,EAAE,YAAY,GAAG,WAAW,EAAE,CAexE;AAED;;;;;;;GAOG;AACH,wBAAgB,UAAU,CACxB,UAAU,CAAC,EAAE,UAAU,EACvB,uBAAuB,CAAC,EAAE,gBAAgB,GACzC,MAAM,GAAG,SAAS,CAyCpB;AAED;;;;;;GAMG;AACH,wBAAgB,YAAY,CAC1B,UAAU,CAAC,EAAE,UAAU,EACvB,uBAAuB,CAAC,EAAE,gBAAgB,GACzC,MAAM,GAAG,SAAS,CAsBpB;AAED;;;;GAIG;AACH,wBAAgB,uBAAuB,CAAC,sBAAsB,CAAC,EAAE,sBAAsB,GAAG,MAAM,EAAE,CAIjG;AAED;;;;GAIG;AACH,wBAAgB,eAAe,CAAC,eAAe,CAAC,EAAE,cAAc,EAAE,GAAG,cAAc,GAAG,MAAM,EAAE,CAa7F;AAED;;;;;;GAMG;AACH,wBAAgB,mBAAmB,CAAC,WAAW,CAAC,EAAE,UAAU,CAAC,UAAU,CAAC,GAAG,MAAM,GAAG,SAAS,CAyB5F;AAED;;;;GAIG;AACH,wBAAgB,WAAW,CAAC,kBAAkB,CAAC,EAAE,kBAAkB,GAAG,MAAM,GAAG,SAAS,CAGvF;AAED;;;;GAIG;AACH,wBAAgB,mBAAmB,CAAC,UAAU,CAAC,EAAE,UAAU,GAAG,iBAAiB,EAAE,CAShF;AAED;;;;;;GAMG;AACH,wBAAgB,gBAAgB,CAC9B,UAAU,EAAE,gBAAgB,EAC5B,OAAO,GAAE,uBAA4B,GACpC,aAAa,
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1
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+
{"version":3,"file":"article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/article-parser.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EACV,aAAa,EACb,mBAAmB,EACnB,iBAAiB,EACjB,WAAW,EACX,iBAAiB,EAEjB,cAAc,EACd,uBAAuB,EAEvB,UAAU,EAEV,gBAAgB,EAEhB,aAAa,EAEb,YAAY,EAEZ,UAAU,EAEV,cAAc,EACd,kBAAkB,EAElB,kBAAkB,EAElB,sBAAsB,EACtB,gBAAgB,EACjB,MAAM,aAAa,CAAC;AAGrB;;GAEG;AACH,MAAM,WAAW,gBAAgB;IAC/B,YAAY,EAAE,MAAM,EAAE,CAAC;IACvB,OAAO,EAAE,mBAAmB,EAAE,CAAC;CAChC;AAED;;;;;;GAMG;AACH,wBAAgB,cAAc,CAAC,aAAa,CAAC,EAAE,aAAa,GAAG,gBAAgB,CAqD9E;AAED;;;;;GAKG;AACH,wBAAgB,kBAAkB,CAChC,UAAU,CAAC,EAAE,UAAU,EACvB,UAAU,CAAC,EAAE,UAAU,GACtB,iBAAiB,GAAG,SAAS,CAgC/B;AAED;;;;GAIG;AACH,wBAAgB,gBAAgB,CAAC,kBAAkB,CAAC,EAAE,kBAAkB,GAAG,cAAc,EAAE,CA8B1F;AAED;;;;GAIG;AACH,wBAAgB,aAAa,CAAC,YAAY,CAAC,EAAE,YAAY,GAAG,WAAW,EAAE,CAexE;AAED;;;;;;;GAOG;AACH,wBAAgB,UAAU,CACxB,UAAU,CAAC,EAAE,UAAU,EACvB,uBAAuB,CAAC,EAAE,gBAAgB,GACzC,MAAM,GAAG,SAAS,CAyCpB;AAED;;;;;;GAMG;AACH,wBAAgB,YAAY,CAC1B,UAAU,CAAC,EAAE,UAAU,EACvB,uBAAuB,CAAC,EAAE,gBAAgB,GACzC,MAAM,GAAG,SAAS,CAsBpB;AAED;;;;GAIG;AACH,wBAAgB,uBAAuB,CAAC,sBAAsB,CAAC,EAAE,sBAAsB,GAAG,MAAM,EAAE,CAIjG;AAED;;;;GAIG;AACH,wBAAgB,eAAe,CAAC,eAAe,CAAC,EAAE,cAAc,EAAE,GAAG,cAAc,GAAG,MAAM,EAAE,CAa7F;AAED;;;;;;GAMG;AACH,wBAAgB,mBAAmB,CAAC,WAAW,CAAC,EAAE,UAAU,CAAC,UAAU,CAAC,GAAG,MAAM,GAAG,SAAS,CAyB5F;AAED;;;;GAIG;AACH,wBAAgB,WAAW,CAAC,kBAAkB,CAAC,EAAE,kBAAkB,GAAG,MAAM,GAAG,SAAS,CAGvF;AAED;;;;GAIG;AACH,wBAAgB,mBAAmB,CAAC,UAAU,CAAC,EAAE,UAAU,GAAG,iBAAiB,EAAE,CAShF;AAED;;;;;;GAMG;AACH,wBAAgB,gBAAgB,CAC9B,UAAU,EAAE,gBAAgB,EAC5B,OAAO,GAAE,uBAA4B,GACpC,aAAa,CAiCf"}
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const doi = extractDoi(article, pubmedDataArticleIdList);
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const pmcId = extractPmcId(article, pubmedDataArticleIdList);
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const { authors, affiliations } = extractAuthors(article?.AuthorList);
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const publicationTypes = extractPublicationTypes(article?.PublicationTypeList);
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const keywords = extractKeywords(medlineCitation?.KeywordList ?? article?.KeywordList);
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const articleDates = extractArticleDates(article);
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const meshTerms = includeMesh ? extractMeshTerms(medlineCitation?.MeshHeadingList) : undefined;
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const grantList = includeGrants ? extractGrants(article?.GrantList) : undefined;
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return {
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pmid: extractPmid(medlineCitation) ?? '',
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title: getText(article?.ArticleTitle),
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@@ -348,13 +353,13 @@ export function parseFullArticle(xmlArticle, options = {}) {
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...(affiliations.length > 0 && { affiliations }),
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authors,
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|
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publicationTypes
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keywords
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...(
|
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...(
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...(publicationTypes.length > 0 && { publicationTypes }),
|
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...(keywords.length > 0 && { keywords }),
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...(meshTerms !== undefined && meshTerms.length > 0 && { meshTerms }),
|
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...(grantList !== undefined && grantList.length > 0 && { grantList }),
|
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|
...(doi !== undefined && { doi }),
|
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|
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|
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articleDates
|
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362
|
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...(articleDates.length > 0 && { articleDates }),
|
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|
};
|
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|
}
|
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|
//# sourceMappingURL=article-parser.js.map
|
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@@ -1 +1 @@
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1
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-
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package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/pubmed-mcp-server",
|
|
3
|
-
"version": "2.3.
|
|
3
|
+
"version": "2.3.11",
|
|
4
4
|
"mcpName": "io.github.cyanheads/pubmed-mcp-server",
|
|
5
5
|
"description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata, generate citations, explore MeSH terms, and discover related research.",
|
|
6
6
|
"type": "module",
|
package/server.json
CHANGED
|
@@ -6,7 +6,7 @@
|
|
|
6
6
|
"url": "https://github.com/cyanheads/pubmed-mcp-server",
|
|
7
7
|
"source": "github"
|
|
8
8
|
},
|
|
9
|
-
"version": "2.3.
|
|
9
|
+
"version": "2.3.11",
|
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10
10
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"remotes": [
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11
11
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{
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12
12
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"type": "streamable-http",
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@@ -19,7 +19,7 @@
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19
19
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"registryBaseUrl": "https://registry.npmjs.org",
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20
20
|
"identifier": "@cyanheads/pubmed-mcp-server",
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21
21
|
"runtimeHint": "bun",
|
|
22
|
-
"version": "2.3.
|
|
22
|
+
"version": "2.3.11",
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|
23
23
|
"packageArguments": [
|
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24
24
|
{
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25
25
|
"type": "positional",
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@@ -60,7 +60,7 @@
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60
60
|
"registryBaseUrl": "https://registry.npmjs.org",
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61
61
|
"identifier": "@cyanheads/pubmed-mcp-server",
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|
62
62
|
"runtimeHint": "bun",
|
|
63
|
-
"version": "2.3.
|
|
63
|
+
"version": "2.3.11",
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|
64
64
|
"packageArguments": [
|
|
65
65
|
{
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|
66
66
|
"type": "positional",
|