@djmima/pubmed-mcp 0.0.0-stage → 1.0.0

package/dist/utils/xml.js

@@ -0,0 +1,515 @@
+/**
+ * XML parsing utilities for NCBI E-utilities responses.
+ *
+ * PubMed returns XML by default from efetch.fcgi.
+ * PMC full-text articles use the JATS XML format.
+ */
+import { XMLParser } from 'fast-xml-parser';
+// Tags that should always be parsed as arrays even when only one element exists
+const ALWAYS_ARRAY_PUBMED = new Set([
+    'PubmedArticle',
+    'PubmedBookArticle',
+    'Author',
+    'ArticleId',
+    'MeshHeading',
+    'Keyword',
+    'PublicationType',
+    'AbstractText',
+    'AffiliationInfo',
+    'OtherAbstract',
+    'ELocationID',
+    'Grant',
+]);
+const ALWAYS_ARRAY_PMC = new Set([
+    'article',
+    'article-id',
+    'sec',
+    'p',
+    'ref',
+    'fig',
+    'table-wrap',
+    'contrib',
+    'aff',
+    'kwd',
+    'abstract',
+    'list-item',
+]);
+// PubMed titles and abstracts use mixed-content formatting tags. Unwrapping
+// only these presentation elements preserves their text in sentence order.
+const PUBMED_INLINE_TAGS_TO_UNWRAP = ['b', 'i', 'sup', 'sub', 'u'];
+const PMC_INLINE_TAGS_TO_UNWRAP = [
+    'bold',
+    'italic',
+    'monospace',
+    'overline',
+    'roman',
+    'sans-serif',
+    'sc',
+    'strike',
+    'styled-content',
+    'sub',
+    'sup',
+    'underline',
+    'xref',
+    'ext-link',
+    'uri',
+    'email',
+    'named-content',
+];
+// EFetch XML can carry characters as numeric character references (≥,
+// é); db=pubmed writes every non-ASCII character that way. They are decoded
+// before parsing rather than through fast-xml-parser's htmlEntities option,
+// which uses String.fromCharCode (garbling code points above U+FFFF) and decodes
+// & before &, turning "&" into "&" instead of "&". CDATA
+// sections and comments are matched only so they can be skipped: references
+// inside them are literal text.
+const CHARACTER_REFERENCE_PATTERN = /<!\[CDATA\[[\s\S]*?\]\]>|<!--[\s\S]*?-->|&#x([0-9a-fA-F]+);|&#([0-9]+);/g;
+// Decoded characters that must stay escaped for the XML to remain well-formed.
+const XML_SPECIAL_CHARACTER_ENTITIES = new Map([
+    ['&', '&amp;'],
+    ['<', '&lt;'],
+    ['>', '&gt;'],
+    ['"', '&quot;'],
+    ["'", '&apos;'],
+]);
+// Unicode space separators other than U+0020, such as NBSP (U+00A0), thin space
+// (U+2009) and narrow NBSP (U+202F). trimValues and extractText already treat
+// them as whitespace; as plain spaces they are also collapsed by cleanPmcText.
+const UNICODE_SPACE_PATTERN = /[\u00a0\u1680\u2000-\u200a\u202f\u205f\u3000]/g;
+// ─── PubMed efetch XML parser ─────────────────────────────────────────────────
+const pubmedParser = new XMLParser({
+    ignoreAttributes: false,
+    attributeNamePrefix: '_',
+    textNodeName: '#text',
+    parseAttributeValue: false,
+    parseTagValue: true,
+    trimValues: true,
+    isArray: (name) => ALWAYS_ARRAY_PUBMED.has(name),
+});
+// ─── PMC JATS XML parser ──────────────────────────────────────────────────────
+const pmcParser = new XMLParser({
+    ignoreAttributes: false,
+    attributeNamePrefix: '_',
+    textNodeName: '#text',
+    parseAttributeValue: false,
+    parseTagValue: true,
+    trimValues: true,
+    isArray: (name) => ALWAYS_ARRAY_PMC.has(name),
+});
+// ─── PubMed XML → ArticleMetadata ─────────────────────────────────────────────
+/**
+ * Parse the XML returned by efetch.fcgi (db=pubmed) into ArticleMetadata objects.
+ */
+export function parsePubmedEfetchXml(xml) {
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    const doc = pubmedParser.parse(normalizePubmedXml(xml));
+    const articleSet = doc?.PubmedArticleSet ?? doc;
+    const articles = asArray(articleSet?.PubmedArticle);
+    return articles.map((articleWrapper) => parsePubmedArticle(articleWrapper));
+}
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+function parsePubmedArticle(wrapper) {
+    const citation = wrapper?.MedlineCitation ?? {};
+    const article = citation?.Article ?? {};
+    const journal = article?.Journal ?? {};
+    const journalIssue = journal?.JournalIssue ?? {};
+    const pubDate = journalIssue?.PubDate ?? {};
+    const pagination = article?.Pagination ?? {};
+    const pubmedData = wrapper?.PubmedData ?? {};
+    const articleIdList = asArray(pubmedData?.ArticleIdList?.ArticleId);
+    // Identifiers
+    const identifiers = {
+        pmid: String(citation?.PMID?.['#text'] ?? citation?.PMID ?? ''),
+    };
+    for (const idNode of articleIdList) {
+        const idObj = idNode;
+        const idType = String(idObj['_IdType'] ?? '');
+        const idValue = String(idObj['#text'] ?? idNode ?? '');
+        if (idType === 'doi')
+            identifiers.doi = idValue;
+        else if (idType === 'pii')
+            identifiers.pii = idValue;
+        else if (idType === 'pmc')
+            identifiers.pmcid = idValue;
+    }
+    // Title
+    const title = extractText(article?.ArticleTitle);
+    // Abstract
+    const abstractNode = article?.Abstract;
+    const abstract = parseAbstract(abstractNode);
+    // Journal
+    const journalInfo = {
+        title: extractText(journal?.Title),
+        iso_abbreviation: extractText(journal?.ISOAbbreviation),
+    };
+    // Authors
+    const authorList = asArray(article?.AuthorList?.Author);
+    const authors = authorList.map(
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    (a) => {
+        const affiliations = asArray(a?.AffiliationInfo)
+            .map((ai) => extractText(ai?.Affiliation))
+            .filter(Boolean);
+        const collectiveName = extractText(a?.CollectiveName);
+        return {
+            last_name: extractText(a?.LastName),
+            fore_name: extractText(a?.ForeName),
+            initials: extractText(a?.Initials),
+            ...(collectiveName ? { collective_name: collectiveName } : {}),
+            ...(affiliations.length > 0 ? { affiliations } : {}),
+        };
+    });
+    // Publication date
+    const pubDateParsed = {
+        year: extractText(pubDate?.Year) || extractText(pubDate?.MedlineDate)?.slice(0, 4) || '',
+    };
+    const month = extractText(pubDate?.Month);
+    const day = extractText(pubDate?.Day);
+    if (month)
+        pubDateParsed.month = month;
+    if (day)
+        pubDateParsed.day = day;
+    // Keywords
+    const keywordList = asArray(citation?.KeywordList?.Keyword);
+    const keywords = keywordList.map((k) => extractText(k)).filter(Boolean);
+    // MeSH terms
+    const meshList = asArray(citation?.MeshHeadingList?.MeshHeading);
+    const mesh_terms = meshList
+        .map((m) => extractText(m?.DescriptorName))
+        .filter(Boolean);
+    // Article types
+    const pubTypeList = asArray(article?.PublicationTypeList?.PublicationType);
+    const article_types = pubTypeList
+        .map((pt) => extractText(pt))
+        .filter(Boolean);
+    // Language
+    const language = extractText(article?.Language) || 'eng';
+    // Citation
+    const citationInfo = {};
+    const volume = extractText(journalIssue?.Volume);
+    const issue = extractText(journalIssue?.Issue);
+    const pages = extractText(pagination?.MedlinePgn);
+    if (volume)
+        citationInfo.volume = volume;
+    if (issue)
+        citationInfo.issue = issue;
+    if (pages)
+        citationInfo.pages = pages;
+    return {
+        identifiers,
+        title,
+        abstract,
+        ...(identifiers.doi ? { doi: identifiers.doi } : {}),
+        journal: journalInfo,
+        authors,
+        author_count: authors.length,
+        publication_date: pubDateParsed,
+        keywords,
+        mesh_terms,
+        article_types,
+        language,
+        citation: citationInfo,
+    };
+}
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+function parseAbstract(abstractNode) {
+    if (!abstractNode)
+        return '';
+    // Structured abstract: multiple AbstractText elements with Label attribute
+    const texts = asArray(abstractNode?.AbstractText);
+    if (texts.length === 0)
+        return '';
+    return texts
+        .map((t) => {
+        const label = t?._Label ??
+            t?._NlmCategory;
+        const text = extractText(t);
+        if (label && label !== 'UNLABELED') {
+            return `${label}: ${text}`;
+        }
+        return text;
+    })
+        .filter(Boolean)
+        .join('\n');
+}
+// ─── PMC JATS XML → FullTextArticle ─────────────────────────────────────────
+/**
+ * Parse the XML returned by efetch.fcgi (db=pmc) into FullTextArticle objects.
+ */
+export function parsePmcEfetchXml(xml) {
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    const doc = pmcParser.parse(normalizePmcXml(xml));
+    const articleSet = doc?.['pmc-articleset'] ?? doc;
+    const articles = asArray(articleSet?.article);
+    return articles.map((a) => parsePmcArticle(a));
+}
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+function parsePmcArticle(article) {
+    const front = article?.front ?? {};
+    const articleMeta = front?.['article-meta'] ?? {};
+    const body = article?.body;
+    const back = article?.back;
+    // Identifiers
+    const articleIds = asArray(articleMeta?.['article-id']);
+    const identifiers = { pmcid: '' };
+    let doi;
+    for (const idNode of articleIds) {
+        const idObj = idNode;
+        const idType = String(idObj['_pub-id-type'] ?? '');
+        const idValue = extractText(idNode);
+        if (idType === 'pmc' || idType === 'pmcid') {
+            identifiers.pmcid = idValue.startsWith('PMC') ? idValue : `PMC${idValue}`;
+        }
+        else if (idType === 'pmid') {
+            identifiers.pmid = idValue;
+        }
+        else if (idType === 'doi') {
+            identifiers.doi = idValue;
+            doi = idValue;
+        }
+    }
+    // Title
+    const title = cleanPmcText(extractText(articleMeta?.['title-group']?.['article-title']));
+    // Abstract
+    const abstractNodes = asArray(articleMeta?.abstract);
+    const abstract = cleanPmcText(abstractNodes
+        .map((a) => extractPmcAbstract(a))
+        .join('\n'));
+    // Full text from body + back
+    const bodyText = body ? extractPmcSectionText(body) : '';
+    const backText = back ? extractPmcBackText(back) : '';
+    const full_text = cleanPmcText([bodyText, backText].filter(Boolean).join('\n\n'));
+    return {
+        identifiers,
+        title,
+        abstract,
+        ...(doi ? { doi } : {}),
+        full_text,
+    };
+}
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+function extractPmcAbstract(abstractNode) {
+    if (!abstractNode)
+        return '';
+    // Structured abstract with sections
+    const secs = asArray(abstractNode?.sec);
+    if (secs.length > 0) {
+        return secs
+            .map((sec) => {
+            const s = sec;
+            const title = extractText(s?.title);
+            const paras = asArray(s?.p)
+                .map((p) => extractText(p))
+                .join(' ');
+            return title ? `${title}: ${paras}` : paras;
+        })
+            .join('\n');
+    }
+    // Simple abstract
+    return asArray(abstractNode?.p)
+        .map((p) => extractText(p))
+        .join('\n');
+}
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+function extractPmcSectionText(node, depth = 0) {
+    if (!node || typeof node !== 'object')
+        return '';
+    const parts = [];
+    // Sections
+    const secs = asArray(node.sec);
+    for (const sec of secs) {
+        const secText = extractPmcSectionText(sec, depth + 1);
+        if (secText)
+            parts.push(secText);
+    }
+    // Title (after processing sub-sections so the title comes first)
+    if (node.title) {
+        const titleText = extractText(node.title);
+        if (titleText)
+            parts.unshift(titleText);
+    }
+    // Paragraphs
+    const paras = asArray(node.p);
+    for (const p of paras) {
+        const pText = extractText(p);
+        if (pText)
+            parts.push(pText);
+    }
+    // Figures
+    const figs = asArray(node.fig);
+    for (const fig of figs) {
+        const label = extractText(fig?.label);
+        const caption = extractText(fig?.caption);
+        if (label || caption)
+            parts.push([label, caption].filter(Boolean).join(': '));
+    }
+    // Tables
+    const tables = asArray(node['table-wrap']);
+    for (const table of tables) {
+        const label = extractText(table?.label);
+        const caption = extractText(table?.caption);
+        if (label || caption)
+            parts.push([label, caption].filter(Boolean).join(': '));
+    }
+    return parts.join('\n');
+}
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+function extractPmcBackText(back) {
+    if (!back)
+        return '';
+    const parts = [];
+    const refLists = findNodesByKey(back, 'ref-list');
+    for (const refList of refLists) {
+        const title = extractText(refList?.title);
+        if (title)
+            parts.push(title);
+        const refs = asArray(refList?.ref);
+        for (const ref of refs) {
+            const r = ref;
+            const label = extractText(r?.label);
+            const citation = r?.['element-citation'] ??
+                r?.['mixed-citation'] ??
+                r?.['nlm-citation'] ??
+                r?.citation;
+            const citText = extractText(citation);
+            parts.push([label, citText].filter(Boolean).join(' '));
+        }
+    }
+    return parts.join('\n');
+}
+/**
+ * Read access and license status from efetch.fcgi (db=pmc) XML.
+ * Replaces the PMC OA Web Service (oa.fcgi), which NCBI retired on 2026-08-25.
+ */
+export function parsePmcAccessXml(xml) {
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    const doc = pmcParser.parse(normalizePmcXml(xml));
+    const articleSet = doc?.['pmc-articleset'] ?? doc;
+    const articles = asArray(articleSet?.article);
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    return articles.map((article) => {
+        const articleMeta = article?.front?.['article-meta'] ?? {};
+        const meta = new Map();
+        for (const group of asArray(articleMeta?.['custom-meta-group'])) {
+            for (const entry of asArray(group?.['custom-meta'])) {
+                const e = entry;
+                meta.set(extractText(e?.['meta-name']), extractText(e?.['meta-value']));
+            }
+        }
+        const { identifiers, full_text } = parsePmcArticle(article);
+        const license = meta.get('pmc-license-ref');
+        const copyrightStatement = cleanPmcText(extractText(articleMeta?.permissions?.['copyright-statement']));
+        return {
+            pmcid: identifiers.pmcid,
+            isOpenAccess: meta.get('pmc-prop-open-access') === 'yes',
+            hasFullText: full_text.trim() !== '',
+            ...(license ? { license } : {}),
+            ...(copyrightStatement ? { copyrightStatement } : {}),
+        };
+    });
+}
+// ─── Helpers ──────────────────────────────────────────────────────────────────
+/** Ensure a value is an array (wrap singletons; filter null/undefined). */
+function asArray(val) {
+    if (val === null || val === undefined)
+        return [];
+    if (Array.isArray(val))
+        return val;
+    return [val];
+}
+/**
+ * Recursively extract all plain text from a parsed XML node.
+ * Inline elements (italic, bold, sup, sub, etc.) are flattened to text.
+ */
+export function extractText(node) {
+    if (node === null || node === undefined)
+        return '';
+    if (typeof node === 'string')
+        return node;
+    if (typeof node === 'number' || typeof node === 'boolean')
+        return String(node);
+    if (Array.isArray(node)) {
+        return node.map(extractText).join(' ');
+    }
+    if (typeof node === 'object') {
+        const obj = node;
+        // If there's a text node key, return it directly
+        if ('#text' in obj) {
+            const text = String(obj['#text']);
+            // Also gather inline element text and interleave
+            const inlineText = Object.entries(obj)
+                .filter(([k]) => k !== '#text' && !k.startsWith('_'))
+                .map(([, v]) => extractText(v))
+                .join(' ');
+            return inlineText ? `${text} ${inlineText}`.trim() : text;
+        }
+        // Otherwise concatenate all non-attribute children
+        return Object.entries(obj)
+            .filter(([k]) => !k.startsWith('_'))
+            .map(([, v]) => extractText(v))
+            .join(' ')
+            .replace(/\s+/g, ' ')
+            .trim();
+    }
+    return '';
+}
+function normalizePubmedXml(xml) {
+    return normalizeCharacters(unwrapInlineTags(xml, PUBMED_INLINE_TAGS_TO_UNWRAP));
+}
+function normalizePmcXml(xml) {
+    return normalizeCharacters(unwrapInlineTags(xml, PMC_INLINE_TAGS_TO_UNWRAP));
+}
+/**
+ * Decode numeric character references with String.fromCodePoint and replace
+ * Unicode spaces with ASCII spaces. References to XML special characters become
+ * the named entities that fast-xml-parser decodes, so nothing is decoded twice.
+ */
+function normalizeCharacters(xml) {
+    return xml
+        .replace(CHARACTER_REFERENCE_PATTERN, (match, hex, dec) => {
+        const digits = hex ?? dec;
+        if (digits === undefined)
+            return match; // CDATA section or comment
+        const codePoint = Number.parseInt(digits, hex === undefined ? 10 : 16);
+        if (codePoint > 0x10ffff)
+            return match; // not a Unicode code point
+        const char = String.fromCodePoint(codePoint);
+        return XML_SPECIAL_CHARACTER_ENTITIES.get(char) ?? char;
+    })
+        .replace(UNICODE_SPACE_PATTERN, ' ');
+}
+function unwrapInlineTags(xml, tags) {
+    let normalized = xml;
+    for (const tag of tags) {
+        const tagPattern = new RegExp(`<${tag}\\b(?![^>]*\\/\\s*>)[^>]*>([\\s\\S]*?)<\\/${tag}>`, 'gi');
+        let previous;
+        do {
+            previous = normalized;
+            normalized = normalized.replace(tagPattern, '$1');
+        } while (normalized !== previous);
+    }
+    return normalized;
+}
+export function cleanPmcText(text) {
+    return text
+        .replace(/(^|[\s([{:;,.])\+(?:\s+\+)+(?=$|[\s)\]}:;,.])/g, '$1')
+        .replace(/[ \t]+\n/g, '\n')
+        .replace(/\n[ \t]+/g, '\n')
+        .replace(/[ \t]{2,}/g, ' ')
+        .replace(/\n{3,}/g, '\n\n')
+        .trim();
+}
+function findNodesByKey(node, key) {
+    if (!node || typeof node !== 'object')
+        return [];
+    if (Array.isArray(node)) {
+        return node.flatMap((item) => findNodesByKey(item, key));
+    }
+    const obj = node;
+    const matches = asArray(obj[key]);
+    const nested = Object.entries(obj)
+        .filter(([childKey]) => !childKey.startsWith('_') && childKey !== key)
+        .flatMap(([, value]) => findNodesByKey(value, key));
+    return [...matches, ...nested];
+}
+//# sourceMappingURL=xml.js.map

package/dist/utils/xml.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,74 @@
 {
   "name": "@djmima/pubmed-mcp",
-  "version": "0.0.0-stage",
-  "stub": true,
-  "description": "Temporary package placeholder for staged publishing"
-}
+  "version": "1.0.0",
+  "description": "MCP server providing access to PubMed biomedical literature and citations",
+  "license": "MIT",
+  "author": "DJ MIMA",
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/DJMIMA/PubMed_MCP.git"
+  },
+  "homepage": "https://github.com/DJMIMA/PubMed_MCP#readme",
+  "bugs": {
+    "url": "https://github.com/DJMIMA/PubMed_MCP/issues"
+  },
+  "keywords": [
+    "mcp",
+    "model-context-protocol",
+    "pubmed",
+    "pmc",
+    "ncbi",
+    "e-utilities",
+    "literature-search",
+    "cli"
+  ],
+  "type": "module",
+  "main": "dist/index.js",
+  "bin": {
+    "pubmed-mcp": "dist/index.js",
+    "pubmed": "dist/cli.js"
+  },
+  "files": [
+    "dist",
+    "skills"
+  ],
+  "scripts": {
+    "build": "tsc",
+    "dev": "tsx src/index.ts",
+    "cli": "tsx src/cli.ts",
+    "start": "node dist/index.js",
+    "test": "vitest run",
+    "test:watch": "vitest",
+    "lint": "eslint src",
+    "typecheck": "tsc --noEmit",
+    "prepublishOnly": "npm run typecheck && npm run lint && npm test && npm run build"
+  },
+  "dependencies": {
+    "@modelcontextprotocol/sdk": "^1.12.0",
+    "axios": "^1.7.9",
+    "dotenv": "^17.3.1",
+    "express": "^4.21.0",
+    "fast-xml-parser": "^5.11.2",
+    "jose": "^5.10.0",
+    "zod": "^4.6.7"
+  },
+  "devDependencies": {
+    "@types/express": "^5.0.0",
+    "@types/node": "^22.10.0",
+    "@typescript-eslint/eslint-plugin": "^8.18.0",
+    "@typescript-eslint/parser": "^8.18.0",
+    "eslint": "^9.17.0",
+    "tsx": "^4.19.2",
+    "typescript": "^5.7.2",
+    "vitest": "^4.1.11"
+  },
+  "engines": {
+    "node": ">=22"
+  },
+  "allowScripts": {
+    "esbuild@0.27.2": true
+  },
+  "publishConfig": {
+    "access": "public"
+  }
+}