NCBI Entrez MCP Server

// src/lib/DataInsertionEngine.ts import type { DataQualityMetrics } from "./types.js"; export class DataInsertionEngine { async insertData( entities: { type: string; data: any }[], schemas: Record<string, any>, sql: any, ): Promise<DataQualityMetrics> { const quality: DataQualityMetrics = { articles_processed: 0, mesh_success_rate: 0, parsing_warnings: [], missing_relationships: [], articles_with_mesh: 0, articles_without_mesh: 0, }; // Group entities by type const typeGroups: Record<string, any[]> = {}; entities.forEach((entity) => { if (!typeGroups[entity.type]) { typeGroups[entity.type] = []; } typeGroups[entity.type].push(entity.data); }); // Insert data for each entity type for (const [entityType, items] of Object.entries(typeGroups)) { if (!schemas[entityType] || items.length === 0) continue; const tableName = entityType; const columns = Object.keys(schemas[entityType].columns); if (columns.length === 0) continue; // Insert each item using exec() instead of prepared statements for (const item of items) { try { const values = columns.map((col) => { const value = item[col]; if ( Array.isArray(value) || (typeof value === "object" && value !== null) ) { return JSON.stringify(value); } return value; }); // Build parameterized query for Cloudflare Workers const placeholders = columns.map(() => "?").join(", "); const query = `INSERT OR REPLACE INTO ${tableName} (${columns.join(", ")}) VALUES (${placeholders})`; // Use exec with parameters for Cloudflare Workers sql.exec(query, ...values); } catch (error) { quality.parsing_warnings.push( `Failed to insert ${entityType}: ${error instanceof Error ? error.message : String(error)}`, ); } } // Track article-specific metrics if (entityType === "article") { quality.articles_processed = items.length; // Check which articles have MeSH terms items.forEach((article) => { if ( article.meshTerms && Array.isArray(article.meshTerms) && article.meshTerms.length > 0 ) { quality.articles_with_mesh++; } else { quality.articles_without_mesh++; } }); } } // Create relationship tables await this.insertRelationships(typeGroups, schemas, sql, quality); // Calculate success rates if (quality.articles_processed > 0) { quality.mesh_success_rate = (quality.articles_with_mesh / quality.articles_processed) * 100; } return quality; } private async insertRelationships( typeGroups: Record<string, any[]>, schemas: Record<string, any>, sql: any, quality: DataQualityMetrics, ): Promise<void> { // Handle article-meshterm relationships if (typeGroups.article && typeGroups.meshterm && schemas.article_meshterm) { try { typeGroups.article.forEach((article) => { if (article.meshTerms && Array.isArray(article.meshTerms)) { article.meshTerms.forEach((meshTerm: any) => { if (meshTerm.uid) { try { sql.exec( "INSERT OR REPLACE INTO article_meshterm (article_uid, meshterm_uid) VALUES (?, ?)", article.uid, meshTerm.uid, ); } catch (error) { quality.parsing_warnings.push( `Failed to insert article-meshterm relationship: ${error instanceof Error ? error.message : String(error)}`, ); } } }); } else { quality.missing_relationships.push( `Article ${article.uid} has no MeSH term relationships`, ); } }); } catch (error) { quality.parsing_warnings.push( `Failed to create article-meshterm relationships: ${error instanceof Error ? error.message : String(error)}`, ); } } // Handle article-author relationships if (typeGroups.article && typeGroups.author && schemas.article_author) { try { typeGroups.article.forEach((article) => { if (article.authors && Array.isArray(article.authors)) { article.authors.forEach((author: any) => { if (author.uid) { try { sql.exec( "INSERT OR REPLACE INTO article_author (article_uid, author_uid) VALUES (?, ?)", article.uid, author.uid, ); } catch (error) { quality.parsing_warnings.push( `Failed to insert article-author relationship: ${error instanceof Error ? error.message : String(error)}`, ); } } }); } else { quality.missing_relationships.push( `Article ${article.uid} has no author relationships`, ); } }); } catch (error) { quality.parsing_warnings.push( `Failed to create article-author relationships: ${error instanceof Error ? error.message : String(error)}`, ); } } } private sanitizeColumnName(name: string): string { return name.replace(/[^a-zA-Z0-9_]/g, "_").toLowerCase(); } private prepareValue(value: any): any { if (value === null || value === undefined) { return null; } if (Array.isArray(value) || (typeof value === "object" && value !== null)) { return JSON.stringify(value); } return value; } }