(re)Search tool

[{"_1":2,"_3":-5,"_4":-5},"loaderData",{"_5":6,"_7":8,"_9":10},"actionData","errors","root",{"_177":178,"_179":180},"routes/_app.x.$handle.$name",{"_95":94,"_32":45,"_103":85,"_27":104,"_13":14,"_105":-5,"_11":106,"_107":108,"_109":110,"_111":112,"_113":114,"_20":-5,"_115":-5,"_116":-5,"_117":25,"_118":119,"_120":57,"_121":-5,"_122":-5,"_123":124},"routes/_app.x.$handle.$name.branch.$branch.version.$version.diff",{"_11":12,"_13":14,"_15":16,"_17":-5,"_18":-5},"project",{"_43":44,"_32":45,"_38":46,"_47":-5,"_48":25,"_49":50,"_51":50,"_52":-5,"_53":-5,"_18":54,"_55":31,"_56":57,"_58":57,"_59":-5,"_60":61,"_62":63,"_64":-5,"_65":-5,"_66":-5,"_67":-5,"_68":69,"_70":69,"_71":72,"_73":72,"_74":72,"_75":69,"_76":69,"_77":78,"_79":80,"_81":82,"_83":25},"version",16,"changes",[19],"aiChatInfo","userId",{"_20":21,"_22":23,"_24":25,"_26":25,"_27":28,"_29":28},"file",{"_30":31,"_32":28,"_33":34,"_35":37,"_38":39,"_40":14,"_41":42,"_24":25},"previous",{"_30":31,"_32":28,"_33":34,"_35":36},"deleted",false,"deletedHere","path","main.js","latestPath","fileId","ebafbf8e-724d-11f0-be81-0224a6c84d84","name","fileType","http","content","import { Hono } from 'https://deno.land/x/hono@v3.11.12/mod.ts';\nimport { serve } from 'https://deno.land/std@0.190.0/http/server.ts';\nimport { listFiles, readFile } from \"https://esm.town/v/std/utils@85-main/index.ts\";\nimport \"jsr:@std/dotenv/load\"; // needed for deno run; not req for smallweb or valtown\nimport Groq from \"npm:groq-sdk\";\nimport { marked } from \"npm:marked\";\n\nconst app = new Hono();\nconst serverApiKey = null; // Deno.env.get(\"GROQ_API_KEY\");\n\n\n\n// Check if server has API key\napp.get('/api/check-key', (c) => {\n return c.json({ hasServerKey: !!serverApiKey });\n});\n\n// Environment-aware file reading function\nasync function readFileContent(filePath) {\n // Check if we're in Val Town environment\n if (typeof Deno !== \"undefined\" && Deno.env.get(\"valtown\")) {\n // Use Val Town's readFile\n return await readFile(filePath, import.meta.url);\n } else {\n // Use Deno's native readTextFile for local development\n return await Deno.readTextFile(filePath);\n }\n}\n\n// Serve the image file\napp.get('/re-search-sm.png', async (c) => {\n try {\n // Check if we're in Val Town environment\n if (typeof Deno !== \"undefined\" && Deno.env.get(\"valtown\")) {\n // For Val Town, we need to read as binary\n const fileBytes = await Deno.readFile('./re-search-sm.png');\n c.header('Content-Type', 'image/png');\n return c.body(fileBytes);\n } else {\n // For local development\n const fileBytes = await Deno.readFile('./re-search-sm.png');\n c.header('Content-Type', 'image/png');\n return c.body(fileBytes);\n }\n } catch (error) {\n console.error('Error reading image file:', error);\n return c.text('Image not found', 404);\n }\n});\n\n// Serve root with HTML content\napp.get('/', async (c) => {\n try {\n const htmlContent = await readFileContent('index.html');\n return c.html(htmlContent);\n } catch (error) {\n console.error('Error reading HTML file:', error);\n return c.text('Error loading page', 500);\n }\n});\n\n// API endpoint for PubMed search\napp.post('/api/search', async (c) => {\n try {\n const { query, dateRange, source, language, userApiKey, offset = 0 } = await c.req.json();\n\n if (!query || !query.trim()) {\n return c.json({ error: 'No search query provided' }, 400);\n }\n\n // Use server key if available, otherwise use user-provided key\n const apiKey = serverApiKey || userApiKey;\n if (!apiKey) {\n return c.json({ error: 'No Groq API key available. Please provide your own key.' }, 400);\n }\n\n console.log('Searching for:', query, 'with date range:', dateRange, 'source:', source, 'language:', language, 'offset:', offset);\n\n // Create language instruction and search query\n let searchQuery = query;\n let languageInstruction = '';\n \n if (language && language !== 'english') {\n languageInstruction = `IMPORTANT: Follow this workflow: 1) First translate the search query \"${query}\" to English terms for better search accuracy. 2) Perform the search using only the English translation. 3) After finding results, translate all titles, descriptions, and content to ${language}. Always search in English but present results in ${language}.`;\n }\n\n let searchPrompt = source && source.trim() \n ? `Do a basic search on ${source} for \"${searchQuery}\" papers`\n : `Do a basic search on PubMed for \"${searchQuery}\" papers`;\n\n if (dateRange) {\n const dateRangeText = {\n '1month': 'in the last month',\n '3months': 'in the last 3 months',\n '6months': 'in the last 6 months',\n '1year': 'in the last year'\n }[dateRange] || '';\n\n if (dateRangeText) {\n searchPrompt += ` ${dateRangeText}`;\n }\n }\n\n const startResult = offset + 1;\n const endResult = offset + 5;\n const offsetInstruction = offset > 0 ? ` Skip the first ${offset} results and` : '';\n \n searchPrompt += `.${offsetInstruction} Please find and return results ${startResult}-${endResult} (max 5 new results). For each result, provide a JSON array with: title, description, citation, url, pmid. ${languageInstruction} Return the JSON within tags.`;\n\n const searchStart = Date.now();\n const groq = new Groq({ apiKey });\n const searchResponse = await groq.chat.completions.create({\n model: 'openai/gpt-oss-120b',\n messages: [\n {\n role: 'user',\n content: searchPrompt\n }\n ],\n tools: [\n {\n type: 'browser_search'\n }\n ]\n });\n const searchEnd = Date.now();\n const searchTime = (searchEnd - searchStart) / 1000;\n\n const responseText = searchResponse.choices[0].message.content;\n console.log('Emberglow response:', responseText);\n\n // Extract JSON from the response\n const jsonMatch = responseText.match(/]*>(.*?)<\\/json>/s);\n let results = [];\n\n if (jsonMatch) {\n try {\n const jsonContent = jsonMatch[1].trim();\n results = JSON.parse(jsonContent);\n console.log('Parsed results:', results);\n } catch (parseError) {\n console.error('JSON parsing error:', parseError);\n console.error('Raw JSON content:', jsonMatch[1]);\n return c.json({ error: 'Failed to parse search results' }, 500);\n }\n } else {\n console.log('No JSON found in response');\n // Fallback: try to extract any information from the response\n return c.json({\n error: 'No structured results found. Raw response: ' + responseText.substring(0, 500) + '...'\n }, 500);\n }\n\n // Ensure results is an array\n if (!Array.isArray(results)) {\n results = [];\n }\n\n return c.json({ \n results,\n searchTime,\n query,\n dateRange,\n source,\n language,\n offset\n });\n } catch (error) {\n console.error('Server error:', error);\n return c.json({ error: 'Server error: ' + error.message }, 500);\n }\n});\n\n// API endpoint for paper summarization\napp.post('/api/summarize', async (c) => {\n try {\n const { url, title, language, userApiKey } = await c.req.json();\n\n if (!url || !url.trim()) {\n return c.json({ error: 'No URL provided' }, 400);\n }\n\n // Use server key if available, otherwise use user-provided key\n const apiKey = serverApiKey || userApiKey;\n if (!apiKey) {\n return c.json({ error: 'No Groq API key available. Please provide your own key.' }, 400);\n }\n\n console.log('Summarizing paper:', title, 'at URL:', url, 'in language:', language);\n\n // Create language instruction for summary\n const languageInstruction = language && language !== 'english' \n ? `Please provide the summary in ${language}. `\n : '';\n\n const summaryPrompt = `Please visit this research paper URL: ${url} \n \nTitle: \"${title}\"\n\nCRITICAL INSTRUCTIONS:\n- Read the research paper content and create a clean, professional summary\n- COMPLETELY IGNORE: line numbers (L0:, L1:, etc.), citations [1†, 2†, etc.], URLs, page headers/footers, navigation elements, reference markers, numerical artifacts, metadata\n- Focus ONLY on the actual research content and findings\n- DO NOT include ANY citations, reference numbers, or source markers in your summary\n- Write in clear, flowing prose without any formatting artifacts\n\nCreate a concise summary using this exact structure in clean markdown. ${languageInstruction}\n\nRETURN ONLY THIS FORMAT - NO OTHER TEXT OR EXPLANATIONS:\n\n

\n**Research Question:** [brief description of what the study investigates]\n\n**Methods & Findings:** [1-2 paragraphs covering methodology and key results - NO CITATIONS]\n\n**Significance:** [why this research matters and potential applications - NO CITATIONS]\n

`;\n\n const summaryStart = Date.now();\n const groq = new Groq({ apiKey });\n const summaryResponse = await groq.chat.completions.create({\n model: 'openai/gpt-oss-120b',\n messages: [\n {\n role: 'system',\n content: 'You are a research paper summarization expert. CRITICAL REQUIREMENTS: 1) Return ONLY the summary content within

tags - no other text, explanations, or metadata. 2) Use clean, professional markdown formatting. 3) NEVER include citations, reference numbers, line numbers, or any numerical markers like [1†, L0:, L1:, etc. 4) Write in clear prose without any formatting artifacts from source documents.'\n },\n {\n role: 'user',\n content: summaryPrompt\n }\n ],\n tools: [\n {\n type: 'browser_search'\n }\n ]\n });\n const summaryEnd = Date.now();\n const summaryTime = (summaryEnd - summaryStart) / 1000;\n\n const responseText = summaryResponse.choices[0].message.content;\n console.log('Raw response:', responseText);\n\n // Extract content from

tags\n const summaryMatch = responseText.match(/

(.*?)<\\/summary>/s);\n let summary = '';\n \n if (summaryMatch) {\n const rawSummary = summaryMatch[1].trim();\n // Convert markdown to HTML for better display\n summary = marked(rawSummary);\n console.log('Extracted summary:', rawSummary.substring(0, 200) + '...');\n } else {\n // Fallback: use the raw response if no summary tags found\n summary = marked(responseText);\n console.log('No summary tags found, using raw response');\n }\n\n return c.json({ \n summary,\n summaryTime,\n url,\n title,\n language\n });\n } catch (error) {\n console.error('Summary error:', error);\n return c.json({ error: 'Summary error: ' + error.message }, 500);\n }\n});\n\n// Export app.fetch for Val Town, otherwise export app — this is only for hono apps\nexport default (typeof Deno !== \"undefined\" && Deno.env.get(\"valtown\")) ? app.fetch : app;","import { Hono } from 'https://deno.land/x/hono@v3.11.12/mod.ts';\nimport { serve } from 'https://deno.land/std@0.190.0/http/server.ts';\nimport { listFiles, readFile } from \"https://esm.town/v/std/utils@85-main/index.ts\";\nimport \"jsr:@std/dotenv/load\"; // needed for deno run; not req for smallweb or valtown\nimport Groq from \"npm:groq-sdk\";\nimport { marked } from \"npm:marked\";\n\nconst app = new Hono();\nconst serverApiKey = null; // Deno.env.get(\"GROQ_API_KEY\");\n\n\n\n// Check if server has API key\napp.get('/api/check-key', (c) => {\n return c.json({ hasServerKey: !!serverApiKey });\n});\n\n// Environment-aware file reading function\nasync function readFileContent(filePath) {\n // Check if we're in Val Town environment\n if (typeof Deno !== \"undefined\" && Deno.env.get(\"valtown\")) {\n // Use Val Town's readFile\n return await readFile(filePath, import.meta.url);\n } else {\n // Use Deno's native readTextFile for local development\n return await Deno.readTextFile(filePath);\n }\n}\n\n// Serve root with HTML content\napp.get('/', async (c) => {\n try {\n const htmlContent = await readFileContent('index.html');\n return c.html(htmlContent);\n } catch (error) {\n console.error('Error reading HTML file:', error);\n return c.text('Error loading page', 500);\n }\n});\n\n// API endpoint for PubMed search\napp.post('/api/search', async (c) => {\n try {\n const { query, dateRange, source, language, userApiKey, offset = 0 } = await c.req.json();\n\n if (!query || !query.trim()) {\n return c.json({ error: 'No search query provided' }, 400);\n }\n\n // Use server key if available, otherwise use user-provided key\n const apiKey = serverApiKey || userApiKey;\n if (!apiKey) {\n return c.json({ error: 'No Groq API key available. Please provide your own key.' }, 400);\n }\n\n console.log('Searching for:', query, 'with date range:', dateRange, 'source:', source, 'language:', language, 'offset:', offset);\n\n // Create language instruction and search query\n let searchQuery = query;\n let languageInstruction = '';\n \n if (language && language !== 'english') {\n languageInstruction = `IMPORTANT: Follow this workflow: 1) First translate the search query \"${query}\" to English terms for better search accuracy. 2) Perform the search using only the English translation. 3) After finding results, translate all titles, descriptions, and content to ${language}. Always search in English but present results in ${language}.`;\n }\n\n let searchPrompt = source && source.trim() \n ? `Do a basic search on ${source} for \"${searchQuery}\" papers`\n : `Do a basic search on PubMed for \"${searchQuery}\" papers`;\n\n if (dateRange) {\n const dateRangeText = {\n '1month': 'in the last month',\n '3months': 'in the last 3 months',\n '6months': 'in the last 6 months',\n '1year': 'in the last year'\n }[dateRange] || '';\n\n if (dateRangeText) {\n searchPrompt += ` ${dateRangeText}`;\n }\n }\n\n const startResult = offset + 1;\n const endResult = offset + 5;\n const offsetInstruction = offset > 0 ? ` Skip the first ${offset} results and` : '';\n \n searchPrompt += `.${offsetInstruction} Please find and return results ${startResult}-${endResult} (max 5 new results). For each result, provide a JSON array with: title, description, citation, url, pmid. ${languageInstruction} Return the JSON within tags.`;\n\n const searchStart = Date.now();\n const groq = new Groq({ apiKey });\n const searchResponse = await groq.chat.completions.create({\n model: 'openai/gpt-oss-120b',\n messages: [\n {\n role: 'user',\n content: searchPrompt\n }\n ],\n tools: [\n {\n type: 'browser_search'\n }\n ]\n });\n const searchEnd = Date.now();\n const searchTime = (searchEnd - searchStart) / 1000;\n\n const responseText = searchResponse.choices[0].message.content;\n console.log('Emberglow response:', responseText);\n\n // Extract JSON from the response\n const jsonMatch = responseText.match(/]*>(.*?)<\\/json>/s);\n let results = [];\n\n if (jsonMatch) {\n try {\n const jsonContent = jsonMatch[1].trim();\n results = JSON.parse(jsonContent);\n console.log('Parsed results:', results);\n } catch (parseError) {\n console.error('JSON parsing error:', parseError);\n console.error('Raw JSON content:', jsonMatch[1]);\n return c.json({ error: 'Failed to parse search results' }, 500);\n }\n } else {\n console.log('No JSON found in response');\n // Fallback: try to extract any information from the response\n return c.json({\n error: 'No structured results found. Raw response: ' + responseText.substring(0, 500) + '...'\n }, 500);\n }\n\n // Ensure results is an array\n if (!Array.isArray(results)) {\n results = [];\n }\n\n return c.json({ \n results,\n searchTime,\n query,\n dateRange,\n source,\n language,\n offset\n });\n } catch (error) {\n console.error('Server error:', error);\n return c.json({ error: 'Server error: ' + error.message }, 500);\n }\n});\n\n// API endpoint for paper summarization\napp.post('/api/summarize', async (c) => {\n try {\n const { url, title, language, userApiKey } = await c.req.json();\n\n if (!url || !url.trim()) {\n return c.json({ error: 'No URL provided' }, 400);\n }\n\n // Use server key if available, otherwise use user-provided key\n const apiKey = serverApiKey || userApiKey;\n if (!apiKey) {\n return c.json({ error: 'No Groq API key available. 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Diff · v16