omophub-mcp 1.0.0

package/dist/formatters/index.js

@@ -0,0 +1,197 @@
+function conceptLine(c, index) {
+    const prefix = index !== undefined ? `${index + 1}. ` : '';
+    const std = c.standard_concept === 'S'
+        ? ' [Standard]'
+        : c.standard_concept === 'C'
+            ? ' [Classification]'
+            : '';
+    return `${prefix}**${c.concept_name}** (ID: ${c.concept_id})\n   ${c.vocabulary_id} | ${c.domain_id} | Code: ${c.concept_code}${std}`;
+}
+export function formatConceptList(response, query) {
+    const results = response.data;
+    const pagination = response.meta?.pagination;
+    const total = pagination?.total_items ?? results.length;
+    const page = pagination?.page ?? 1;
+    const totalPages = pagination?.total_pages ?? 1;
+    if (results.length === 0) {
+        return {
+            text: `No concepts found for "${query}". Try broader search terms or different vocabulary filters.`,
+            json: JSON.stringify({ results: [], total, page, total_pages: totalPages, query }),
+        };
+    }
+    const lines = results.map((r, i) => conceptLine(r, i));
+    const header = `Found ${total} concept${total !== 1 ? 's' : ''} for "${query}" (showing page ${page} of ${totalPages}):`;
+    let text = `${header}\n\n${lines.join('\n\n')}`;
+    if (pagination?.has_next) {
+        text += `\n\n→ Use page=${page + 1} to see more results.`;
+    }
+    return {
+        text,
+        json: JSON.stringify({
+            results: results.map((r) => ({
+                concept_id: r.concept_id,
+                concept_name: r.concept_name,
+                vocabulary_id: r.vocabulary_id,
+                domain_id: r.domain_id,
+                concept_code: r.concept_code,
+                concept_class_id: r.concept_class_id,
+                standard_concept: r.standard_concept,
+            })),
+            total,
+            page,
+            total_pages: totalPages,
+            query,
+        }),
+    };
+}
+export function formatConcept(concept) {
+    const std = concept.standard_concept === 'S'
+        ? 'Standard'
+        : concept.standard_concept === 'C'
+            ? 'Classification'
+            : 'Non-standard';
+    const lines = [
+        `**${concept.concept_name}**`,
+        '',
+        `| Field | Value |`,
+        `|-------|-------|`,
+        `| Concept ID | ${concept.concept_id} |`,
+        `| Vocabulary | ${concept.vocabulary_id} |`,
+        `| Domain | ${concept.domain_id} |`,
+        `| Concept Class | ${concept.concept_class_id} |`,
+        `| Concept Code | ${concept.concept_code} |`,
+        `| Standard Status | ${std} |`,
+    ];
+    if (concept.valid_start_date)
+        lines.push(`| Valid From | ${concept.valid_start_date} |`);
+    if (concept.valid_end_date)
+        lines.push(`| Valid To | ${concept.valid_end_date} |`);
+    if (concept.invalid_reason)
+        lines.push(`| Invalid Reason | ${concept.invalid_reason} |`);
+    if (concept.synonyms && concept.synonyms.length > 0) {
+        lines.push(`| Synonyms | ${concept.synonyms.join(', ')} |`);
+    }
+    return {
+        text: lines.join('\n'),
+        json: JSON.stringify(concept),
+    };
+}
+export function formatMappings(response, conceptId) {
+    const data = response.data;
+    const mappings = data.mappings;
+    if (!mappings || mappings.length === 0) {
+        return {
+            text: `No mappings found for concept ${conceptId} (${data.source_concept?.concept_name || 'unknown'}).`,
+            json: JSON.stringify({
+                source_concept_id: conceptId,
+                source_concept_name: data.source_concept?.concept_name,
+                mapped: false,
+                mappings: [],
+            }),
+        };
+    }
+    const source = data.source_concept;
+    const header = `Mappings for **${source?.concept_name || `Concept ${conceptId}`}** (${source?.vocabulary_id || 'unknown'} → targets):`;
+    const lines = mappings.map((m, i) => `${i + 1}. **${m.concept_name}** (ID: ${m.concept_id})\n   ${m.vocabulary_id} | Code: ${m.concept_code} | Relationship: ${m.relationship_id}`);
+    return {
+        text: `${header}\n\n${lines.join('\n\n')}`,
+        json: JSON.stringify({
+            source_concept_id: conceptId,
+            source_concept_name: source?.concept_name,
+            mapped: true,
+            total_mappings: data.total_mappings ?? mappings.length,
+            mappings: mappings.map((m) => ({
+                concept_id: m.concept_id,
+                concept_name: m.concept_name,
+                vocabulary_id: m.vocabulary_id,
+                concept_code: m.concept_code,
+                relationship_id: m.relationship_id,
+                standard_concept: m.standard_concept,
+            })),
+        }),
+    };
+}
+export function formatHierarchy(response, direction) {
+    const data = response.data;
+    const concept = data.concept;
+    const sections = [
+        `Hierarchy for **${concept.concept_name}** (ID: ${concept.concept_id}, ${concept.vocabulary_id}):`,
+    ];
+    const formatNodes = (nodes, label) => {
+        if (!nodes || nodes.length === 0)
+            return `\n**${label}:** None`;
+        const lines = nodes.map((n, i) => `${i + 1}. ${'  '.repeat(Math.max(0, n.level ?? 0))}${n.concept_name} (ID: ${n.concept_id}, ${n.vocabulary_id})`);
+        return `\n**${label}** (${nodes.length}):\n${lines.join('\n')}`;
+    };
+    if (direction === 'up' || direction === 'both') {
+        sections.push(formatNodes(data.ancestors || [], 'Ancestors (broader terms)'));
+    }
+    if (direction === 'down' || direction === 'both') {
+        sections.push(formatNodes(data.descendants || [], 'Descendants (narrower terms)'));
+    }
+    const jsonData = {
+        concept_id: concept.concept_id,
+        concept_name: concept.concept_name,
+        vocabulary_id: concept.vocabulary_id,
+        direction,
+    };
+    if (direction === 'up' || direction === 'both') {
+        jsonData.ancestors = (data.ancestors || []).map((n) => ({
+            concept_id: n.concept_id,
+            concept_name: n.concept_name,
+            vocabulary_id: n.vocabulary_id,
+            level: n.level,
+        }));
+        jsonData.total_ancestors = data.total_ancestors ?? (data.ancestors || []).length;
+    }
+    if (direction === 'down' || direction === 'both') {
+        jsonData.descendants = (data.descendants || []).map((n) => ({
+            concept_id: n.concept_id,
+            concept_name: n.concept_name,
+            vocabulary_id: n.vocabulary_id,
+            level: n.level,
+        }));
+        jsonData.total_descendants = data.total_descendants ?? (data.descendants || []).length;
+    }
+    return {
+        text: sections.join('\n'),
+        json: JSON.stringify(jsonData),
+    };
+}
+export function formatVocabularyList(response, search) {
+    let vocabs = response.data;
+    if (search) {
+        const term = search.toLowerCase();
+        vocabs = vocabs.filter((v) => v.vocabulary_id.toLowerCase().includes(term) ||
+            v.vocabulary_name.toLowerCase().includes(term));
+    }
+    if (vocabs.length === 0) {
+        return {
+            text: search ? `No vocabularies found matching "${search}".` : 'No vocabularies available.',
+            json: JSON.stringify({ vocabularies: [], total: 0 }),
+        };
+    }
+    const lines = vocabs.map((v, i) => `${i + 1}. **${v.vocabulary_id}** — ${v.vocabulary_name}${v.concept_count != null ? ` (${v.concept_count.toLocaleString()} concepts)` : ''}${v.vocabulary_version ? ` [v${v.vocabulary_version}]` : ''}`);
+    const header = search
+        ? `Found ${vocabs.length} vocabularies matching "${search}":`
+        : `Available vocabularies (${vocabs.length}):`;
+    return {
+        text: `${header}\n\n${lines.join('\n')}`,
+        json: JSON.stringify({
+            vocabularies: vocabs.map((v) => ({
+                vocabulary_id: v.vocabulary_id,
+                vocabulary_name: v.vocabulary_name,
+                vocabulary_version: v.vocabulary_version,
+                concept_count: v.concept_count,
+            })),
+            total: vocabs.length,
+        }),
+    };
+}
+export function formatError(error) {
+    return {
+        text: error,
+        json: JSON.stringify({ error: true, message: error }),
+    };
+}
+//# sourceMappingURL=index.js.map

package/dist/formatters/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/formatters/index.ts"],"names":[],"mappings":"AAWA,SAAS,WAAW,CAAC,CAAyB,EAAE,KAAc;IAC5D,MAAM,MAAM,GAAG,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,KAAK,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC;IAC3D,MAAM,GAAG,GACP,CAAC,CAAC,gBAAgB,KAAK,GAAG;QACxB,CAAC,CAAC,aAAa;QACf,CAAC,CAAC,CAAC,CAAC,gBAAgB,KAAK,GAAG;YAC1B,CAAC,CAAC,mBAAmB;YACrB,CAAC,CAAC,EAAE,CAAC;IACX,OAAO,GAAG,MAAM,KAAK,CAAC,CAAC,YAAY,WAAW,CAAC,CAAC,UAAU,SAAS,CAAC,CAAC,aAAa,MAAM,CAAC,CAAC,SAAS,YAAY,CAAC,CAAC,YAAY,GAAG,GAAG,EAAE,CAAC;AACxI,CAAC;AAED,MAAM,UAAU,iBAAiB,CAC/B,QAAqC,EACrC,KAAa;IAEb,MAAM,OAAO,GAAG,QAAQ,CAAC,IAAI,CAAC;IAC9B,MAAM,UAAU,GAAG,QAAQ,CAAC,IAAI,EAAE,UAAU,CAAC;IAC7C,MAAM,KAAK,GAAG,UAAU,EAAE,WAAW,IAAI,OAAO,CAAC,MAAM,CAAC;IACxD,MAAM,IAAI,GAAG,UAAU,EAAE,IAAI,IAAI,CAAC,CAAC;IACnC,MAAM,UAAU,GAAG,UAAU,EAAE,WAAW,IAAI,CAAC,CAAC;IAEhD,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACzB,OAAO;YACL,IAAI,EAAE,0BAA0B,KAAK,8DAA8D;YACnG,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,EAAE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,IAAI,EAAE,WAAW,EAAE,UAAU,EAAE,KAAK,EAAE,CAAC;SACnF,CAAC;IACJ,CAAC;IAED,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,WAAW,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;IACvD,MAAM,MAAM,GAAG,SAAS,KAAK,WAAW,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,SAAS,KAAK,mBAAmB,IAAI,OAAO,UAAU,IAAI,CAAC;IAEzH,IAAI,IAAI,GAAG,GAAG,MAAM,OAAO,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC;IAEhD,IAAI,UAAU,EAAE,QAAQ,EAAE,CAAC;QACzB,IAAI,IAAI,kBAAkB,IAAI,GAAG,CAAC,uBAAuB,CAAC;IAC5D,CAAC;IAED,OAAO;QACL,IAAI;QACJ,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC;YACnB,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;gBAC3B,UAAU,EAAE,CAAC,CAAC,UAAU;gBACxB,YAAY,EAAE,CAAC,CAAC,YAAY;gBAC5B,aAAa,EAAE,CAAC,CAAC,aAAa;gBAC9B,SAAS,EAAE,CAAC,CAAC,SAAS;gBACtB,YAAY,EAAE,CAAC,CAAC,YAAY;gBAC5B,gBAAgB,EAAE,CAAC,CAAC,gBAAgB;gBACpC,gBAAgB,EAAE,CAAC,CAAC,gBAAgB;aACrC,CAAC,CAAC;YACH,KAAK;YACL,IAAI;YACJ,WAAW,EAAE,UAAU;YACvB,KAAK;SACN,CAAC;KACH,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,aAAa,CAAC,OAAgB;IAC5C,MAAM,GAAG,GACP,OAAO,CAAC,gBAAgB,KAAK,GAAG;QAC9B,CAAC,CAAC,UAAU;QACZ,CAAC,CAAC,OAAO,CAAC,gBAAgB,KAAK,GAAG;YAChC,CAAC,CAAC,gBAAgB;YAClB,CAAC,CAAC,cAAc,CAAC;IAEvB,MAAM,KAAK,GAAG;QACZ,KAAK,OAAO,CAAC,YAAY,IAAI;QAC7B,EAAE;QACF,mBAAmB;QACnB,mBAAmB;QACnB,kBAAkB,OAAO,CAAC,UAAU,IAAI;QACxC,kBAAkB,OAAO,CAAC,aAAa,IAAI;QAC3C,cAAc,OAAO,CAAC,SAAS,IAAI;QACnC,qBAAqB,OAAO,CAAC,gBAAgB,IAAI;QACjD,oBAAoB,OAAO,CAAC,YAAY,IAAI;QAC5C,uBAAuB,GAAG,IAAI;KAC/B,CAAC;IAEF,IAAI,OAAO,CAAC,gBAAgB;QAAE,KAAK,CAAC,IAAI,CAAC,kBAAkB,OAAO,CAAC,gBAAgB,IAAI,CAAC,CAAC;IACzF,IAAI,OAAO,CAAC,cAAc;QAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,OAAO,CAAC,cAAc,IAAI,CAAC,CAAC;IACnF,IAAI,OAAO,CAAC,cAAc;QAAE,KAAK,CAAC,IAAI,CAAC,sBAAsB,OAAO,CAAC,cAAc,IAAI,CAAC,CAAC;IACzF,IAAI,OAAO,CAAC,QAAQ,IAAI,OAAO,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACpD,KAAK,CAAC,IAAI,CAAC,gBAAgB,OAAO,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IAC9D,CAAC;IAED,OAAO;QACL,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC;QACtB,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC;KAC9B,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,cAAc,CAC5B,QAAuC,EACvC,SAAiB;IAEjB,MAAM,IAAI,GAAG,QAAQ,CAAC,IAAI,CAAC;IAC3B,MAAM,QAAQ,GAAG,IAAI,CAAC,QAAQ,CAAC;IAE/B,IAAI,CAAC,QAAQ,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACvC,OAAO;YACL,IAAI,EAAE,iCAAiC,SAAS,KAAK,IAAI,CAAC,cAAc,EAAE,YAAY,IAAI,SAAS,IAAI;YACvG,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC;gBACnB,iBAAiB,EAAE,SAAS;gBAC5B,mBAAmB,EAAE,IAAI,CAAC,cAAc,EAAE,YAAY;gBACtD,MAAM,EAAE,KAAK;gBACb,QAAQ,EAAE,EAAE;aACb,CAAC;SACH,CAAC;IACJ,CAAC;IAED,MAAM,MAAM,GAAG,IAAI,CAAC,cAAc,CAAC;IACnC,MAAM,MAAM,GAAG,kBAAkB,MAAM,EAAE,YAAY,IAAI,WAAW,SAAS,EAAE,OAAO,MAAM,EAAE,aAAa,IAAI,SAAS,cAAc,CAAC;IAEvI,MAAM,KAAK,GAAG,QAAQ,CAAC,GAAG,CACxB,CAAC,CAAU,EAAE,CAAS,EAAE,EAAE,CACxB,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,YAAY,WAAW,CAAC,CAAC,UAAU,SAAS,CAAC,CAAC,aAAa,YAAY,CAAC,CAAC,YAAY,oBAAoB,CAAC,CAAC,eAAe,EAAE,CAChJ,CAAC;IAEF,OAAO;QACL,IAAI,EAAE,GAAG,MAAM,OAAO,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE;QAC1C,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC;YACnB,iBAAiB,EAAE,SAAS;YAC5B,mBAAmB,EAAE,MAAM,EAAE,YAAY;YACzC,MAAM,EAAE,IAAI;YACZ,cAAc,EAAE,IAAI,CAAC,cAAc,IAAI,QAAQ,CAAC,MAAM;YACtD,QAAQ,EAAE,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAU,EAAE,EAAE,CAAC,CAAC;gBACtC,UAAU,EAAE,CAAC,CAAC,UAAU;gBACxB,YAAY,EAAE,CAAC,CAAC,YAAY;gBAC5B,aAAa,EAAE,CAAC,CAAC,aAAa;gBAC9B,YAAY,EAAE,CAAC,CAAC,YAAY;gBAC5B,eAAe,EAAE,CAAC,CAAC,eAAe;gBAClC,gBAAgB,EAAE,CAAC,CAAC,gBAAgB;aACrC,CAAC,CAAC;SACJ,CAAC;KACH,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,eAAe,CAC7B,QAAwC,EACxC,SAAiC;IAEjC,MAAM,IAAI,GAAG,QAAQ,CAAC,IAAI,CAAC;IAC3B,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC;IAE7B,MAAM,QAAQ,GAAa;QACzB,mBAAmB,OAAO,CAAC,YAAY,WAAW,OAAO,CAAC,UAAU,KAAK,OAAO,CAAC,aAAa,IAAI;KACnG,CAAC;IAEF,MAAM,WAAW,GAAG,CAAC,KAAsB,EAAE,KAAa,EAAU,EAAE;QACpE,IAAI,CAAC,KAAK,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC;YAAE,OAAO,OAAO,KAAK,UAAU,CAAC;QAChE,MAAM,KAAK,GAAG,KAAK,CAAC,GAAG,CACrB,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CACP,GAAG,CAAC,GAAG,CAAC,KAAK,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,YAAY,SAAS,CAAC,CAAC,UAAU,KAAK,CAAC,CAAC,aAAa,GAAG,CACnH,CAAC;QACF,OAAO,OAAO,KAAK,OAAO,KAAK,CAAC,MAAM,OAAO,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;IAClE,CAAC,CAAC;IAEF,IAAI,SAAS,KAAK,IAAI,IAAI,SAAS,KAAK,MAAM,EAAE,CAAC;QAC/C,QAAQ,CAAC,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,SAAS,IAAI,EAAE,EAAE,2BAA2B,CAAC,CAAC,CAAC;IAChF,CAAC;IACD,IAAI,SAAS,KAAK,MAAM,IAAI,SAAS,KAAK,MAAM,EAAE,CAAC;QACjD,QAAQ,CAAC,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,WAAW,IAAI,EAAE,EAAE,8BAA8B,CAAC,CAAC,CAAC;IACrF,CAAC;IAED,MAAM,QAAQ,GAA4B;QACxC,UAAU,EAAE,OAAO,CAAC,UAAU;QAC9B,YAAY,EAAE,OAAO,CAAC,YAAY;QAClC,aAAa,EAAE,OAAO,CAAC,aAAa;QACpC,SAAS;KACV,CAAC;IAEF,IAAI,SAAS,KAAK,IAAI,IAAI,SAAS,KAAK,MAAM,EAAE,CAAC;QAC/C,QAAQ,CAAC,SAAS,GAAG,CAAC,IAAI,CAAC,SAAS,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACtD,UAAU,EAAE,CAAC,CAAC,UAAU;YACxB,YAAY,EAAE,CAAC,CAAC,YAAY;YAC5B,aAAa,EAAE,CAAC,CAAC,aAAa;YAC9B,KAAK,EAAE,CAAC,CAAC,KAAK;SACf,CAAC,CAAC,CAAC;QACJ,QAAQ,CAAC,eAAe,GAAG,IAAI,CAAC,eAAe,IAAI,CAAC,IAAI,CAAC,SAAS,IAAI,EAAE,CAAC,CAAC,MAAM,CAAC;IACnF,CAAC;IACD,IAAI,SAAS,KAAK,MAAM,IAAI,SAAS,KAAK,MAAM,EAAE,CAAC;QACjD,QAAQ,CAAC,WAAW,GAAG,CAAC,IAAI,CAAC,WAAW,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAC1D,UAAU,EAAE,CAAC,CAAC,UAAU;YACxB,YAAY,EAAE,CAAC,CAAC,YAAY;YAC5B,aAAa,EAAE,CAAC,CAAC,aAAa;YAC9B,KAAK,EAAE,CAAC,CAAC,KAAK;SACf,CAAC,CAAC,CAAC;QACJ,QAAQ,CAAC,iBAAiB,GAAG,IAAI,CAAC,iBAAiB,IAAI,CAAC,IAAI,CAAC,WAAW,IAAI,EAAE,CAAC,CAAC,MAAM,CAAC;IACzF,CAAC;IAED,OAAO;QACL,IAAI,EAAE,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC;QACzB,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC;KAC/B,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,oBAAoB,CAClC,QAAmC,EACnC,MAAe;IAEf,IAAI,MAAM,GAAG,QAAQ,CAAC,IAAI,CAAC;IAE3B,IAAI,MAAM,EAAE,CAAC;QACX,MAAM,IAAI,GAAG,MAAM,CAAC,WAAW,EAAE,CAAC;QAClC,MAAM,GAAG,MAAM,CAAC,MAAM,CACpB,CAAC,CAAC,EAAE,EAAE,CACJ,CAAC,CAAC,aAAa,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,IAAI,CAAC;YAC5C,CAAC,CAAC,eAAe,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,IAAI,CAAC,CACjD,CAAC;IACJ,CAAC;IAED,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACxB,OAAO;YACL,IAAI,EAAE,MAAM,CAAC,CAAC,CAAC,mCAAmC,MAAM,IAAI,CAAC,CAAC,CAAC,4BAA4B;YAC3F,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,EAAE,YAAY,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC;SACrD,CAAC;IACJ,CAAC;IAED,MAAM,KAAK,GAAG,MAAM,CAAC,GAAG,CACtB,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CACP,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,aAAa,QAAQ,CAAC,CAAC,eAAe,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,aAAa,CAAC,cAAc,EAAE,YAAY,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,kBAAkB,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,kBAAkB,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAC3M,CAAC;IAEF,MAAM,MAAM,GAAG,MAAM;QACnB,CAAC,CAAC,SAAS,MAAM,CAAC,MAAM,2BAA2B,MAAM,IAAI;QAC7D,CAAC,CAAC,2BAA2B,MAAM,CAAC,MAAM,IAAI,CAAC;IAEjD,OAAO;QACL,IAAI,EAAE,GAAG,MAAM,OAAO,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE;QACxC,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC;YACnB,YAAY,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;gBAC/B,aAAa,EAAE,CAAC,CAAC,aAAa;gBAC9B,eAAe,EAAE,CAAC,CAAC,eAAe;gBAClC,kBAAkB,EAAE,CAAC,CAAC,kBAAkB;gBACxC,aAAa,EAAE,CAAC,CAAC,aAAa;aAC/B,CAAC,CAAC;YACH,KAAK,EAAE,MAAM,CAAC,MAAM;SACrB,CAAC;KACH,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,KAAa;IACvC,OAAO;QACL,IAAI,EAAE,KAAK;QACX,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC;KACtD,CAAC;AACJ,CAAC"}

package/dist/health.d.ts

@@ -0,0 +1,3 @@
+import { createServer } from 'node:http';
+export declare function startHealthServer(port: number): ReturnType<typeof createServer>;
+//# sourceMappingURL=health.d.ts.map

package/dist/health.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"health.d.ts","sourceRoot":"","sources":["../src/health.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAA6C,MAAM,WAAW,CAAC;AA4BpF,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,MAAM,GAAG,UAAU,CAAC,OAAO,YAAY,CAAC,CAY/E"}

package/dist/health.js

@@ -0,0 +1,34 @@
+import { createServer } from 'node:http';
+import { logger } from './utils/logger.js';
+import { VERSION } from './version.js';
+const startTime = Date.now();
+function handleRequest(req, res) {
+    if (req.method === 'GET' && req.url === '/health') {
+        const body = JSON.stringify({
+            status: 'ok',
+            version: VERSION,
+            uptime_seconds: Math.floor((Date.now() - startTime) / 1000),
+        });
+        res.writeHead(200, {
+            'Content-Type': 'application/json',
+            'Content-Length': Buffer.byteLength(body),
+            'X-Content-Type-Options': 'nosniff',
+            'Cache-Control': 'no-store',
+        });
+        res.end(body);
+        return;
+    }
+    res.writeHead(404, { 'Content-Type': 'application/json' });
+    res.end(JSON.stringify({ error: 'Not found' }));
+}
+export function startHealthServer(port) {
+    const server = createServer(handleRequest);
+    server.on('error', (err) => {
+        logger.error('Health server error', { error: String(err), port });
+    });
+    server.listen(port, () => {
+        logger.info(`Health endpoint listening on http://localhost:${String(port)}/health`);
+    });
+    return server;
+}
+//# sourceMappingURL=health.js.map

package/dist/health.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"health.js","sourceRoot":"","sources":["../src/health.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAA6C,MAAM,WAAW,CAAC;AACpF,OAAO,EAAE,MAAM,EAAE,MAAM,mBAAmB,CAAC;AAC3C,OAAO,EAAE,OAAO,EAAE,MAAM,cAAc,CAAC;AAEvC,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;AAE7B,SAAS,aAAa,CAAC,GAAoB,EAAE,GAAmB;IAC9D,IAAI,GAAG,CAAC,MAAM,KAAK,KAAK,IAAI,GAAG,CAAC,GAAG,KAAK,SAAS,EAAE,CAAC;QAClD,MAAM,IAAI,GAAG,IAAI,CAAC,SAAS,CAAC;YAC1B,MAAM,EAAE,IAAI;YACZ,OAAO,EAAE,OAAO;YAChB,cAAc,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,GAAG,EAAE,GAAG,SAAS,CAAC,GAAG,IAAI,CAAC;SAC5D,CAAC,CAAC;QAEH,GAAG,CAAC,SAAS,CAAC,GAAG,EAAE;YACjB,cAAc,EAAE,kBAAkB;YAClC,gBAAgB,EAAE,MAAM,CAAC,UAAU,CAAC,IAAI,CAAC;YACzC,wBAAwB,EAAE,SAAS;YACnC,eAAe,EAAE,UAAU;SAC5B,CAAC,CAAC;QACH,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QACd,OAAO;IACT,CAAC;IAED,GAAG,CAAC,SAAS,CAAC,GAAG,EAAE,EAAE,cAAc,EAAE,kBAAkB,EAAE,CAAC,CAAC;IAC3D,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,EAAE,KAAK,EAAE,WAAW,EAAE,CAAC,CAAC,CAAC;AAClD,CAAC;AAED,MAAM,UAAU,iBAAiB,CAAC,IAAY;IAC5C,MAAM,MAAM,GAAG,YAAY,CAAC,aAAa,CAAC,CAAC;IAE3C,MAAM,CAAC,EAAE,CAAC,OAAO,EAAE,CAAC,GAAG,EAAE,EAAE;QACzB,MAAM,CAAC,KAAK,CAAC,qBAAqB,EAAE,EAAE,KAAK,EAAE,MAAM,CAAC,GAAG,CAAC,EAAE,IAAI,EAAE,CAAC,CAAC;IACpE,CAAC,CAAC,CAAC;IAEH,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,GAAG,EAAE;QACvB,MAAM,CAAC,IAAI,CAAC,iDAAiD,MAAM,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;IACtF,CAAC,CAAC,CAAC;IAEH,OAAO,MAAM,CAAC;AAChB,CAAC"}

package/dist/index.d.ts

@@ -0,0 +1,9 @@
+#!/usr/bin/env node
+export declare function parseArgs(argv: string[]): {
+    apiKey?: string;
+    baseUrl?: string;
+    healthPort?: number;
+};
+export declare function resolveHealthPort(cliPort?: number): number | undefined;
+export declare function main(): Promise<void>;
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AAUA,wBAAgB,SAAS,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG;IACzC,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB,CAiBA;AAED,wBAAgB,iBAAiB,CAAC,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAYtE;AAED,wBAAsB,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC,CAsB1C"}

package/dist/index.js

@@ -0,0 +1,75 @@
+#!/usr/bin/env node
+import { realpathSync } from 'node:fs';
+import url from 'node:url';
+import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
+import { startHealthServer } from './health.js';
+import { createServer } from './server.js';
+import { resolveApiKey } from './utils/auth.js';
+import { logger } from './utils/logger.js';
+export function parseArgs(argv) {
+    const result = {};
+    for (const arg of argv.slice(2)) {
+        if (arg.startsWith('--api-key=')) {
+            result.apiKey = arg.slice('--api-key='.length);
+        }
+        else if (arg.startsWith('--base-url=')) {
+            result.baseUrl = arg.slice('--base-url='.length);
+        }
+        else if (arg.startsWith('--health-port=')) {
+            const port = parseInt(arg.slice('--health-port='.length), 10);
+            if (!Number.isNaN(port) && port > 0 && port < 65536) {
+                result.healthPort = port;
+            }
+        }
+    }
+    return result;
+}
+export function resolveHealthPort(cliPort) {
+    if (cliPort !== undefined)
+        return cliPort;
+    const envPort = process.env.HEALTH_PORT;
+    if (envPort) {
+        const port = parseInt(envPort, 10);
+        if (!Number.isNaN(port) && port > 0 && port < 65536) {
+            return port;
+        }
+    }
+    return undefined;
+}
+export async function main() {
+    const args = parseArgs(process.argv);
+    let apiKey;
+    try {
+        apiKey = resolveApiKey(args.apiKey);
+    }
+    catch (error) {
+        logger.error(error instanceof Error ? error.message : String(error));
+        process.exit(1);
+    }
+    const server = createServer(apiKey, args.baseUrl);
+    const transport = new StdioServerTransport();
+    logger.info('Starting OMOPHub MCP server (stdio transport)');
+    await server.connect(transport);
+    const healthPort = resolveHealthPort(args.healthPort);
+    if (healthPort !== undefined) {
+        startHealthServer(healthPort);
+    }
+}
+function isRunDirectly() {
+    if (!process.argv[1])
+        return false;
+    try {
+        return import.meta.url === url.pathToFileURL(realpathSync(process.argv[1])).href;
+    }
+    catch {
+        return false;
+    }
+}
+const isDirectRun = isRunDirectly();
+if (isDirectRun) {
+    main().catch((error) => {
+        logger.error('Fatal error', { error: String(error) });
+        process.exit(1);
+    });
+}
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AAEA,OAAO,EAAE,YAAY,EAAE,MAAM,SAAS,CAAC;AACvC,OAAO,GAAG,MAAM,UAAU,CAAC;AAC3B,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AACjF,OAAO,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AAChD,OAAO,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAC3C,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,MAAM,EAAE,MAAM,mBAAmB,CAAC;AAE3C,MAAM,UAAU,SAAS,CAAC,IAAc;IAKtC,MAAM,MAAM,GAA+D,EAAE,CAAC;IAE9E,KAAK,MAAM,GAAG,IAAI,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC;QAChC,IAAI,GAAG,CAAC,UAAU,CAAC,YAAY,CAAC,EAAE,CAAC;YACjC,MAAM,CAAC,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,YAAY,CAAC,MAAM,CAAC,CAAC;QACjD,CAAC;aAAM,IAAI,GAAG,CAAC,UAAU,CAAC,aAAa,CAAC,EAAE,CAAC;YACzC,MAAM,CAAC,OAAO,GAAG,GAAG,CAAC,KAAK,CAAC,aAAa,CAAC,MAAM,CAAC,CAAC;QACnD,CAAC;aAAM,IAAI,GAAG,CAAC,UAAU,CAAC,gBAAgB,CAAC,EAAE,CAAC;YAC5C,MAAM,IAAI,GAAG,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,gBAAgB,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC;YAC9D,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,IAAI,GAAG,CAAC,IAAI,IAAI,GAAG,KAAK,EAAE,CAAC;gBACpD,MAAM,CAAC,UAAU,GAAG,IAAI,CAAC;YAC3B,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,MAAM,UAAU,iBAAiB,CAAC,OAAgB;IAChD,IAAI,OAAO,KAAK,SAAS;QAAE,OAAO,OAAO,CAAC;IAE1C,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,WAAW,CAAC;IACxC,IAAI,OAAO,EAAE,CAAC;QACZ,MAAM,IAAI,GAAG,QAAQ,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC;QACnC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,IAAI,GAAG,CAAC,IAAI,IAAI,GAAG,KAAK,EAAE,CAAC;YACpD,OAAO,IAAI,CAAC;QACd,CAAC;IACH,CAAC;IAED,OAAO,SAAS,CAAC;AACnB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,IAAI;IACxB,MAAM,IAAI,GAAG,SAAS,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC;IAErC,IAAI,MAAc,CAAC;IACnB,IAAI,CAAC;QACH,MAAM,GAAG,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IACtC,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,MAAM,CAAC,KAAK,CAAC,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC;QACrE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;IAED,MAAM,MAAM,GAAG,YAAY,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,CAAC,CAAC;IAClD,MAAM,SAAS,GAAG,IAAI,oBAAoB,EAAE,CAAC;IAE7C,MAAM,CAAC,IAAI,CAAC,+CAA+C,CAAC,CAAC;IAE7D,MAAM,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;IAEhC,MAAM,UAAU,GAAG,iBAAiB,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;IACtD,IAAI,UAAU,KAAK,SAAS,EAAE,CAAC;QAC7B,iBAAiB,CAAC,UAAU,CAAC,CAAC;IAChC,CAAC;AACH,CAAC;AAED,SAAS,aAAa;IACpB,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC;QAAE,OAAO,KAAK,CAAC;IACnC,IAAI,CAAC;QACH,OAAO,MAAM,CAAC,IAAI,CAAC,GAAG,KAAK,GAAG,CAAC,aAAa,CAAC,YAAY,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IACnF,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,KAAK,CAAC;IACf,CAAC;AACH,CAAC;AAED,MAAM,WAAW,GAAG,aAAa,EAAE,CAAC;AAEpC,IAAI,WAAW,EAAE,CAAC;IAChB,IAAI,EAAE,CAAC,KAAK,CAAC,CAAC,KAAc,EAAE,EAAE;QAC9B,MAAM,CAAC,KAAK,CAAC,aAAa,EAAE,EAAE,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QACtD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC,CAAC,CAAC;AACL,CAAC"}

package/dist/prompts/index.d.ts

@@ -0,0 +1,3 @@
+import type { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
+export declare function registerPrompts(server: McpServer): void;
+//# sourceMappingURL=index.d.ts.map

package/dist/prompts/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/prompts/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAGzE,wBAAgB,eAAe,CAAC,MAAM,EAAE,SAAS,GAAG,IAAI,CAqEvD"}

package/dist/prompts/index.js

@@ -0,0 +1,56 @@
+import { z } from 'zod';
+export function registerPrompts(server) {
+    server.prompt('phenotype-concept-set', 'Build a concept set for a clinical phenotype definition. Guides the AI through searching for concepts, exploring hierarchies, and assembling a complete concept set.', {
+        condition: z
+            .string()
+            .describe('The clinical condition or phenotype to define (e.g., "Type 2 diabetes mellitus")'),
+        vocabularies: z
+            .string()
+            .optional()
+            .describe('Comma-separated vocabulary IDs to focus on (e.g., "SNOMED,ICD10CM"). Default: all'),
+    }, ({ condition, vocabularies }) => {
+        const vocabFilter = vocabularies ? ` Focus on these vocabularies: ${vocabularies}.` : '';
+        return {
+            messages: [
+                {
+                    role: 'user',
+                    content: {
+                        type: 'text',
+                        text: `Help me build a concept set for the clinical phenotype: "${condition}".${vocabFilter}
+
+Please follow these steps:
+1. Use search_concepts to find the primary concept(s) for "${condition}"
+2. For the best-matching standard concept, use get_hierarchy with direction="down" to find all descendants
+3. Use map_concept to find cross-vocabulary mappings (especially SNOMED ↔ ICD-10-CM)
+4. Compile a final concept set table with: concept_id, concept_name, vocabulary_id, concept_code, and whether it's a primary concept or descendant
+
+Present the final concept set in a clear table format that can be used in a cohort definition.`,
+                    },
+                },
+            ],
+        };
+    });
+    server.prompt('code-lookup', 'Look up and validate a medical code. Resolves a vocabulary-specific code to its OMOP concept and shows mappings.', {
+        code: z.string().describe('The medical code to look up (e.g., "E11.9", "44054006", "4850")'),
+        vocabulary: z.string().describe('The vocabulary system (e.g., "ICD10CM", "SNOMED", "LOINC")'),
+    }, ({ code, vocabulary }) => {
+        return {
+            messages: [
+                {
+                    role: 'user',
+                    content: {
+                        type: 'text',
+                        text: `Look up and validate the medical code "${code}" from vocabulary "${vocabulary}".
+
+Please:
+1. Use get_concept_by_code to resolve this code
+2. If found, use map_concept to show what it maps to in other vocabularies
+3. Use get_hierarchy with direction="up" to show where it sits in the hierarchy
+4. Summarize: Is this a standard concept? What are the key mappings? Any important notes about this code?`,
+                    },
+                },
+            ],
+        };
+    });
+}
+//# sourceMappingURL=index.js.map

package/dist/prompts/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/prompts/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAExB,MAAM,UAAU,eAAe,CAAC,MAAiB;IAC/C,MAAM,CAAC,MAAM,CACX,uBAAuB,EACvB,sKAAsK,EACtK;QACE,SAAS,EAAE,CAAC;aACT,MAAM,EAAE;aACR,QAAQ,CACP,kFAAkF,CACnF;QACH,YAAY,EAAE,CAAC;aACZ,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,mFAAmF,CACpF;KACJ,EACD,CAAC,EAAE,SAAS,EAAE,YAAY,EAAE,EAAE,EAAE;QAC9B,MAAM,WAAW,GAAG,YAAY,CAAC,CAAC,CAAC,iCAAiC,YAAY,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;QAEzF,OAAO;YACL,QAAQ,EAAE;gBACR;oBACE,IAAI,EAAE,MAAe;oBACrB,OAAO,EAAE;wBACP,IAAI,EAAE,MAAe;wBACrB,IAAI,EAAE,4DAA4D,SAAS,KAAK,WAAW;;;6DAG5C,SAAS;;;;;+FAKyB;qBAClF;iBACF;aACF;SACF,CAAC;IACJ,CAAC,CACF,CAAC;IAEF,MAAM,CAAC,MAAM,CACX,aAAa,EACb,kHAAkH,EAClH;QACE,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iEAAiE,CAAC;QAC5F,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,4DAA4D,CAAC;KAC9F,EACD,CAAC,EAAE,IAAI,EAAE,UAAU,EAAE,EAAE,EAAE;QACvB,OAAO;YACL,QAAQ,EAAE;gBACR;oBACE,IAAI,EAAE,MAAe;oBACrB,OAAO,EAAE;wBACP,IAAI,EAAE,MAAe;wBACrB,IAAI,EAAE,0CAA0C,IAAI,sBAAsB,UAAU;;;;;;0GAMQ;qBAC7F;iBACF;aACF;SACF,CAAC;IACJ,CAAC,CACF,CAAC;AACJ,CAAC"}

package/dist/resources/index.d.ts

@@ -0,0 +1,4 @@
+import type { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
+import type { OmopHubClient } from '../client/api.js';
+export declare function registerResources(server: McpServer, client: OmopHubClient): void;
+//# sourceMappingURL=index.d.ts.map

package/dist/resources/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/resources/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAEzE,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AA2CtD,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,aAAa,GAAG,IAAI,CAoEhF"}

package/dist/resources/index.js

@@ -0,0 +1,86 @@
+import { ResourceTemplate } from '@modelcontextprotocol/sdk/server/mcp.js';
+import { vocabularyCache } from '../utils/cache.js';
+const PAGE_SIZE = 100;
+const CACHE_KEY = 'vocabularies:all';
+async function fetchAllVocabularies(client, toolName) {
+    const all = [];
+    let page = 1;
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+    while (true) {
+        const raw = await client.request('/vocabularies', { include_stats: true, page_size: PAGE_SIZE, page }, toolName);
+        const batch = raw.data.vocabularies;
+        all.push(...batch);
+        if (batch.length < PAGE_SIZE || !raw.meta?.pagination?.has_next)
+            break;
+        page++;
+    }
+    return all;
+}
+async function getCachedVocabularies(client, toolName) {
+    const cached = vocabularyCache.get(CACHE_KEY);
+    if (cached)
+        return cached.data;
+    const vocabs = await fetchAllVocabularies(client, toolName);
+    vocabularyCache.set(CACHE_KEY, { data: vocabs });
+    return vocabs;
+}
+export function registerResources(server, client) {
+    // Static resource: vocabulary catalog
+    server.resource('vocabulary-list', 'omophub://vocabularies', async (uri) => {
+        const vocabs = await getCachedVocabularies(client, 'resource:vocabulary-list');
+        const text = vocabs
+            .map((v) => `${v.vocabulary_id}: ${v.vocabulary_name}${v.concept_count != null ? ` (${v.concept_count.toLocaleString()} concepts)` : ''}`)
+            .join('\n');
+        return {
+            contents: [
+                {
+                    uri: uri.href,
+                    mimeType: 'text/plain',
+                    text: `OMOP Vocabulary Catalog\n${'='.repeat(40)}\n\n${text}`,
+                },
+            ],
+        };
+    });
+    // Resource template: individual vocabulary details
+    const vocabularyTemplate = new ResourceTemplate('omophub://vocabularies/{vocabulary_id}', {
+        list: undefined,
+    });
+    server.resource('vocabulary-details', vocabularyTemplate, async (uri, variables) => {
+        const vocabularyId = String(variables.vocabulary_id);
+        const vocabs = await getCachedVocabularies(client, 'resource:vocabulary-details');
+        const vocab = vocabs.find((v) => v.vocabulary_id.toLowerCase() === vocabularyId.toLowerCase());
+        if (!vocab) {
+            return {
+                contents: [
+                    {
+                        uri: uri.href,
+                        mimeType: 'text/plain',
+                        text: `Vocabulary "${vocabularyId}" not found.`,
+                    },
+                ],
+            };
+        }
+        const lines = [
+            `Vocabulary: ${vocab.vocabulary_id}`,
+            `Name: ${vocab.vocabulary_name}`,
+            vocab.vocabulary_version ? `Version: ${vocab.vocabulary_version}` : null,
+            vocab.vocabulary_reference ? `Reference: ${vocab.vocabulary_reference}` : null,
+            vocab.concept_count != null
+                ? `Total Concepts: ${vocab.concept_count.toLocaleString()}`
+                : null,
+            vocab.standard_concept_count != null
+                ? `Standard Concepts: ${vocab.standard_concept_count.toLocaleString()}`
+                : null,
+        ].filter(Boolean);
+        return {
+            contents: [
+                {
+                    uri: uri.href,
+                    mimeType: 'text/plain',
+                    text: lines.join('\n'),
+                },
+            ],
+        };
+    });
+}
+//# sourceMappingURL=index.js.map

package/dist/resources/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/resources/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,gBAAgB,EAAE,MAAM,yCAAyC,CAAC;AAG3E,OAAO,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AAEpD,MAAM,SAAS,GAAG,GAAG,CAAC;AACtB,MAAM,SAAS,GAAG,kBAAkB,CAAC;AAErC,KAAK,UAAU,oBAAoB,CACjC,MAAqB,EACrB,QAAgB;IAEhB,MAAM,GAAG,GAAiB,EAAE,CAAC;IAC7B,IAAI,IAAI,GAAG,CAAC,CAAC;IAEb,uEAAuE;IACvE,OAAO,IAAI,EAAE,CAAC;QACZ,MAAM,GAAG,GAAG,MAAM,MAAM,CAAC,OAAO,CAC9B,eAAe,EACf,EAAE,aAAa,EAAE,IAAI,EAAE,SAAS,EAAE,SAAS,EAAE,IAAI,EAAE,EACnD,QAAQ,CACT,CAAC;QACF,MAAM,KAAK,GAAG,GAAG,CAAC,IAAI,CAAC,YAAY,CAAC;QACpC,GAAG,CAAC,IAAI,CAAC,GAAG,KAAK,CAAC,CAAC;QAEnB,IAAI,KAAK,CAAC,MAAM,GAAG,SAAS,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,UAAU,EAAE,QAAQ;YAAE,MAAM;QACvE,IAAI,EAAE,CAAC;IACT,CAAC;IAED,OAAO,GAAG,CAAC;AACb,CAAC;AAED,KAAK,UAAU,qBAAqB,CAClC,MAAqB,EACrB,QAAgB;IAEhB,MAAM,MAAM,GAAG,eAAe,CAAC,GAAG,CAAC,SAAS,CAAuC,CAAC;IACpF,IAAI,MAAM;QAAE,OAAO,MAAM,CAAC,IAAI,CAAC;IAE/B,MAAM,MAAM,GAAG,MAAM,oBAAoB,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC;IAC5D,eAAe,CAAC,GAAG,CAAC,SAAS,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAC;IACjD,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,MAAM,UAAU,iBAAiB,CAAC,MAAiB,EAAE,MAAqB;IACxE,sCAAsC;IACtC,MAAM,CAAC,QAAQ,CAAC,iBAAiB,EAAE,wBAAwB,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE;QACzE,MAAM,MAAM,GAAG,MAAM,qBAAqB,CAAC,MAAM,EAAE,0BAA0B,CAAC,CAAC;QAC/E,MAAM,IAAI,GAAG,MAAM;aAChB,GAAG,CACF,CAAC,CAAC,EAAE,EAAE,CACJ,GAAG,CAAC,CAAC,aAAa,KAAK,CAAC,CAAC,eAAe,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,aAAa,CAAC,cAAc,EAAE,YAAY,CAAC,CAAC,CAAC,EAAE,EAAE,CAChI;aACA,IAAI,CAAC,IAAI,CAAC,CAAC;QAEd,OAAO;YACL,QAAQ,EAAE;gBACR;oBACE,GAAG,EAAE,GAAG,CAAC,IAAI;oBACb,QAAQ,EAAE,YAAY;oBACtB,IAAI,EAAE,4BAA4B,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,OAAO,IAAI,EAAE;iBAC9D;aACF;SACF,CAAC;IACJ,CAAC,CAAC,CAAC;IAEH,mDAAmD;IACnD,MAAM,kBAAkB,GAAG,IAAI,gBAAgB,CAAC,wCAAwC,EAAE;QACxF,IAAI,EAAE,SAAS;KAChB,CAAC,CAAC;IAEH,MAAM,CAAC,QAAQ,CAAC,oBAAoB,EAAE,kBAAkB,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,EAAE;QACjF,MAAM,YAAY,GAAG,MAAM,CAAC,SAAS,CAAC,aAAa,CAAC,CAAC;QACrD,MAAM,MAAM,GAAG,MAAM,qBAAqB,CAAC,MAAM,EAAE,6BAA6B,CAAC,CAAC;QAElF,MAAM,KAAK,GAAG,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,aAAa,CAAC,WAAW,EAAE,KAAK,YAAY,CAAC,WAAW,EAAE,CAAC,CAAC;QAE/F,IAAI,CAAC,KAAK,EAAE,CAAC;YACX,OAAO;gBACL,QAAQ,EAAE;oBACR;wBACE,GAAG,EAAE,GAAG,CAAC,IAAI;wBACb,QAAQ,EAAE,YAAY;wBACtB,IAAI,EAAE,eAAe,YAAY,cAAc;qBAChD;iBACF;aACF,CAAC;QACJ,CAAC;QAED,MAAM,KAAK,GAAG;YACZ,eAAe,KAAK,CAAC,aAAa,EAAE;YACpC,SAAS,KAAK,CAAC,eAAe,EAAE;YAChC,KAAK,CAAC,kBAAkB,CAAC,CAAC,CAAC,YAAY,KAAK,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,IAAI;YACxE,KAAK,CAAC,oBAAoB,CAAC,CAAC,CAAC,cAAc,KAAK,CAAC,oBAAoB,EAAE,CAAC,CAAC,CAAC,IAAI;YAC9E,KAAK,CAAC,aAAa,IAAI,IAAI;gBACzB,CAAC,CAAC,mBAAmB,KAAK,CAAC,aAAa,CAAC,cAAc,EAAE,EAAE;gBAC3D,CAAC,CAAC,IAAI;YACR,KAAK,CAAC,sBAAsB,IAAI,IAAI;gBAClC,CAAC,CAAC,sBAAsB,KAAK,CAAC,sBAAsB,CAAC,cAAc,EAAE,EAAE;gBACvE,CAAC,CAAC,IAAI;SACT,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;QAElB,OAAO;YACL,QAAQ,EAAE;gBACR;oBACE,GAAG,EAAE,GAAG,CAAC,IAAI;oBACb,QAAQ,EAAE,YAAY;oBACtB,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC;iBACvB;aACF;SACF,CAAC;IACJ,CAAC,CAAC,CAAC;AACL,CAAC"}

package/dist/server.d.ts

@@ -0,0 +1,3 @@
+import { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
+export declare function createServer(apiKey: string, baseUrl?: string): McpServer;
+//# sourceMappingURL=server.d.ts.map

package/dist/server.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"server.d.ts","sourceRoot":"","sources":["../src/server.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAcpE,wBAAgB,YAAY,CAAC,MAAM,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,MAAM,GAAG,SAAS,CA4BxE"}

package/dist/server.js

@@ -0,0 +1,31 @@
+import { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
+import { OmopHubClient } from './client/api.js';
+import { registerPrompts } from './prompts/index.js';
+import { registerResources } from './resources/index.js';
+import { registerConceptTools, registerHierarchyTools, registerMappingTools, registerSearchTools, registerVocabularyTools, } from './tools/index.js';
+import { logger } from './utils/logger.js';
+import { VERSION } from './version.js';
+export function createServer(apiKey, baseUrl) {
+    const server = new McpServer({
+        name: 'omophub',
+        version: VERSION,
+        description: 'Access OHDSI standardized medical vocabularies — search concepts, navigate hierarchies, and map between clinical coding systems like SNOMED CT, ICD-10, RxNorm, and LOINC.',
+    });
+    const client = new OmopHubClient(apiKey, baseUrl);
+    // Register all Phase 1 tools
+    registerSearchTools(server, client);
+    registerConceptTools(server, client);
+    registerMappingTools(server, client);
+    registerHierarchyTools(server, client);
+    registerVocabularyTools(server, client);
+    // Register resources and prompts
+    registerResources(server, client);
+    registerPrompts(server);
+    logger.info('OMOPHub MCP server initialized', {
+        tools: 6,
+        resources: 2,
+        prompts: 2,
+    });
+    return server;
+}
+//# sourceMappingURL=server.js.map

package/dist/server.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"server.js","sourceRoot":"","sources":["../src/server.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AACpE,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAC;AACrD,OAAO,EAAE,iBAAiB,EAAE,MAAM,sBAAsB,CAAC;AACzD,OAAO,EACL,oBAAoB,EACpB,sBAAsB,EACtB,oBAAoB,EACpB,mBAAmB,EACnB,uBAAuB,GACxB,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EAAE,MAAM,EAAE,MAAM,mBAAmB,CAAC;AAC3C,OAAO,EAAE,OAAO,EAAE,MAAM,cAAc,CAAC;AAEvC,MAAM,UAAU,YAAY,CAAC,MAAc,EAAE,OAAgB;IAC3D,MAAM,MAAM,GAAG,IAAI,SAAS,CAAC;QAC3B,IAAI,EAAE,SAAS;QACf,OAAO,EAAE,OAAO;QAChB,WAAW,EACT,4KAA4K;KAC/K,CAAC,CAAC;IAEH,MAAM,MAAM,GAAG,IAAI,aAAa,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAElD,6BAA6B;IAC7B,mBAAmB,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACpC,oBAAoB,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACrC,oBAAoB,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACrC,sBAAsB,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACvC,uBAAuB,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAExC,iCAAiC;IACjC,iBAAiB,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAClC,eAAe,CAAC,MAAM,CAAC,CAAC;IAExB,MAAM,CAAC,IAAI,CAAC,gCAAgC,EAAE;QAC5C,KAAK,EAAE,CAAC;QACR,SAAS,EAAE,CAAC;QACZ,OAAO,EAAE,CAAC;KACX,CAAC,CAAC;IAEH,OAAO,MAAM,CAAC;AAChB,CAAC"}

package/dist/tools/concepts.d.ts

@@ -0,0 +1,4 @@
+import type { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
+import type { OmopHubClient } from '../client/api.js';
+export declare function registerConceptTools(server: McpServer, client: OmopHubClient): void;
+//# sourceMappingURL=concepts.d.ts.map

package/dist/tools/concepts.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"concepts.d.ts","sourceRoot":"","sources":["../../src/tools/concepts.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAEzE,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AAMtD,wBAAgB,oBAAoB,CAAC,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,aAAa,GAAG,IAAI,CAiHnF"}