From 2d70d49bf9096ba2ebdfcc4fc4ae5023fe8ca1b9 Mon Sep 17 00:00:00 2001 From: "Juan E. Arango Ossa" Date: Tue, 19 Dec 2023 16:20:58 -0800 Subject: [PATCH] =?UTF-8?q?=F0=9F=86=99=20add=20upload=20to=20handle=20fil?= =?UTF-8?q?es?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .gitignore | 5 +- package-lock.json | 126 +++++++++++++++++++++++++++++++++++++++------- package.json | 2 + src/server.ts | 35 ++++++++++--- 4 files changed, 140 insertions(+), 28 deletions(-) diff --git a/.gitignore b/.gitignore index 811a1a0..52ffcdc 100644 --- a/.gitignore +++ b/.gitignore @@ -9,4 +9,7 @@ test/data/*-out.* test.csv # Serverless artifacts -.serverless \ No newline at end of file +.serverless + +# API uploads +uploads \ No newline at end of file diff --git a/package-lock.json b/package-lock.json index 5d697e0..fca1602 100644 --- a/package-lock.json +++ b/package-lock.json @@ -9,10 +9,12 @@ "version": "1.0.4", "license": "MIT", "dependencies": { + "@types/multer": "^1.4.11", "exceljs": "^4.3.0", "express": "^4.18.2", "ipssm": "^1.0.4", "joi": "^17.11.0", + "multer": "^1.4.5-lts.1", "papaparse": "^5.4.1", "serverless-http": "^3.2.0", "yargs": "^17.7.2" @@ -2593,7 +2595,6 @@ "version": "1.19.5", "resolved": "https://registry.npmjs.org/@types/body-parser/-/body-parser-1.19.5.tgz", "integrity": "sha512-fB3Zu92ucau0iQ0JMCFQE7b/dv8Ot07NI3KaZIkIUNXq82k4eBAqUaneXfleGY9JWskeS9y+u0nXMyspcuQrCg==", - "dev": true, "dependencies": { "@types/connect": "*", "@types/node": "*" @@ -2630,7 +2631,6 @@ "version": "3.4.38", "resolved": "https://registry.npmjs.org/@types/connect/-/connect-3.4.38.tgz", "integrity": "sha512-K6uROf1LD88uDQqJCktA4yzL1YYAK6NgfsI0v/mTgyPKWsX1CnJ0XPSDhViejru1GcRkLWb8RlzFYJRqGUbaug==", - "dev": true, "dependencies": { "@types/node": "*" } @@ -2639,7 +2639,6 @@ "version": "4.17.21", "resolved": "https://registry.npmjs.org/@types/express/-/express-4.17.21.tgz", "integrity": "sha512-ejlPM315qwLpaQlQDTjPdsUFSc6ZsP4AN6AlWnogPjQ7CVi7PYF3YVz+CY3jE2pwYf7E/7HlDAN0rV2GxTG0HQ==", - "dev": true, "dependencies": { "@types/body-parser": "*", "@types/express-serve-static-core": "^4.17.33", @@ -2651,7 +2650,6 @@ "version": "4.17.41", "resolved": "https://registry.npmjs.org/@types/express-serve-static-core/-/express-serve-static-core-4.17.41.tgz", "integrity": "sha512-OaJ7XLaelTgrvlZD8/aa0vvvxZdUmlCn6MtWeB7TkiKW70BQLc9XEPpDLPdbo52ZhXUCrznlWdCHWxJWtdyajA==", - "dev": true, "dependencies": { "@types/node": "*", "@types/qs": "*", @@ -2674,8 +2672,7 @@ "node_modules/@types/http-errors": { "version": "2.0.4", "resolved": "https://registry.npmjs.org/@types/http-errors/-/http-errors-2.0.4.tgz", - "integrity": "sha512-D0CFMMtydbJAegzOyHjtiKPLlvnm3iTZyZRSZoLq2mRhDdmLfIWOCYPfQJ4cu2erKghU++QvjcUjp/5h7hESpA==", - "dev": true + "integrity": "sha512-D0CFMMtydbJAegzOyHjtiKPLlvnm3iTZyZRSZoLq2mRhDdmLfIWOCYPfQJ4cu2erKghU++QvjcUjp/5h7hESpA==" }, "node_modules/@types/keyv": { "version": "3.1.4", @@ -2696,14 +2693,20 @@ "node_modules/@types/mime": { "version": "1.3.5", "resolved": "https://registry.npmjs.org/@types/mime/-/mime-1.3.5.tgz", - "integrity": "sha512-/pyBZWSLD2n0dcHE3hq8s8ZvcETHtEuF+3E7XVt0Ig2nvsVQXdghHVcEkIWjy9A0wKfTn97a/PSDYohKIlnP/w==", - "dev": true + "integrity": "sha512-/pyBZWSLD2n0dcHE3hq8s8ZvcETHtEuF+3E7XVt0Ig2nvsVQXdghHVcEkIWjy9A0wKfTn97a/PSDYohKIlnP/w==" + }, + "node_modules/@types/multer": { + "version": "1.4.11", + "resolved": "https://registry.npmjs.org/@types/multer/-/multer-1.4.11.tgz", + "integrity": "sha512-svK240gr6LVWvv3YGyhLlA+6LRRWA4mnGIU7RcNmgjBYFl6665wcXrRfxGp5tEPVHUNm5FMcmq7too9bxCwX/w==", + "dependencies": { + "@types/express": "*" + } }, "node_modules/@types/node": { "version": "20.10.4", "resolved": "https://registry.npmjs.org/@types/node/-/node-20.10.4.tgz", "integrity": "sha512-D08YG6rr8X90YB56tSIuBaddy/UXAA9RKJoFvrsnogAum/0pmjkgi4+2nx96A330FmioegBWmEYQ+syqCFaveg==", - "dev": true, "dependencies": { "undici-types": "~5.26.4" } @@ -2720,14 +2723,12 @@ "node_modules/@types/qs": { "version": "6.9.10", "resolved": "https://registry.npmjs.org/@types/qs/-/qs-6.9.10.tgz", - "integrity": "sha512-3Gnx08Ns1sEoCrWssEgTSJs/rsT2vhGP+Ja9cnnk9k4ALxinORlQneLXFeFKOTJMOeZUFD1s7w+w2AphTpvzZw==", - "dev": true + "integrity": "sha512-3Gnx08Ns1sEoCrWssEgTSJs/rsT2vhGP+Ja9cnnk9k4ALxinORlQneLXFeFKOTJMOeZUFD1s7w+w2AphTpvzZw==" }, "node_modules/@types/range-parser": { "version": "1.2.7", "resolved": "https://registry.npmjs.org/@types/range-parser/-/range-parser-1.2.7.tgz", - "integrity": "sha512-hKormJbkJqzQGhziax5PItDUTMAM9uE2XXQmM37dyd4hVM+5aVl7oVxMVUiVQn2oCQFN/LKCZdvSM0pFRqbSmQ==", - "dev": true + "integrity": "sha512-hKormJbkJqzQGhziax5PItDUTMAM9uE2XXQmM37dyd4hVM+5aVl7oVxMVUiVQn2oCQFN/LKCZdvSM0pFRqbSmQ==" }, "node_modules/@types/responselike": { "version": "1.0.3", @@ -2748,7 +2749,6 @@ "version": "0.17.4", "resolved": "https://registry.npmjs.org/@types/send/-/send-0.17.4.tgz", "integrity": "sha512-x2EM6TJOybec7c52BX0ZspPodMsQUd5L6PRwOunVyVUhXiBSKf3AezDL8Dgvgt5o0UfKNfuA0eMLr2wLT4AiBA==", - "dev": true, "dependencies": { "@types/mime": "^1", "@types/node": "*" @@ -2758,7 +2758,6 @@ "version": "1.15.5", "resolved": "https://registry.npmjs.org/@types/serve-static/-/serve-static-1.15.5.tgz", "integrity": "sha512-PDRk21MnK70hja/YF8AHfC7yIsiQHn1rcXx7ijCFBX/k+XQJhQT/gw3xekXKJvx+5SXaMMS8oqQy09Mzvz2TuQ==", - "dev": true, "dependencies": { "@types/http-errors": "*", "@types/mime": "*", @@ -3021,6 +3020,11 @@ "node": ">= 8" } }, + "node_modules/append-field": { + "version": "1.0.0", + "resolved": "https://registry.npmjs.org/append-field/-/append-field-1.0.0.tgz", + "integrity": "sha512-klpgFSWLW1ZEs8svjfb7g4qWY0YS5imI82dTg+QahUvJ8YqAY0P10Uk8tTyh9ZGuYEZEMaeJYCF5BFuX552hsw==" + }, "node_modules/archive-type": { "version": "4.0.0", "resolved": "https://registry.npmjs.org/archive-type/-/archive-type-4.0.0.tgz", @@ -3572,6 +3576,11 @@ "integrity": "sha512-T7zexNBwiiaCOGDg9xNX9PBmjrubblRkENuptryuI64URkXDFum9il/JGL8Lm8wYfAXpredVXXZz7eMHilimiQ==", "dev": true }, + "node_modules/buffer-from": { + "version": "1.1.2", + "resolved": "https://registry.npmjs.org/buffer-from/-/buffer-from-1.1.2.tgz", + "integrity": "sha512-E+XQCRwSbaaiChtv6k6Dwgc+bx+Bs6vuKJHHl5kox/BaKbhiXzqQOwK4cO22yElGp2OCmjwVhT3HmxgyPGnJfQ==" + }, "node_modules/buffer-indexof-polyfill": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/buffer-indexof-polyfill/-/buffer-indexof-polyfill-1.0.2.tgz", @@ -3607,6 +3616,17 @@ "dev": true, "peer": true }, + "node_modules/busboy": { + "version": "1.6.0", + "resolved": "https://registry.npmjs.org/busboy/-/busboy-1.6.0.tgz", + "integrity": "sha512-8SFQbg/0hQ9xy3UNTB0YEnsNBbWfhf7RtnzpL7TkBiTBRfrQ9Fxcnz7VJsleJpyp6rVLvXiuORqjlHi5q+PYuA==", + "dependencies": { + "streamsearch": "^1.1.0" + }, + "engines": { + "node": ">=10.16.0" + } + }, "node_modules/bytes": { "version": "3.1.2", "resolved": "https://registry.npmjs.org/bytes/-/bytes-3.1.2.tgz", @@ -4072,6 +4092,47 @@ "resolved": "https://registry.npmjs.org/concat-map/-/concat-map-0.0.1.tgz", "integrity": "sha512-/Srv4dswyQNBfohGpz9o6Yb3Gz3SrUDqBH5rTuhGR7ahtlbYKnVxw2bCFMRljaA7EXHaXZ8wsHdodFvbkhKmqg==" }, + "node_modules/concat-stream": { + "version": "1.6.2", + "resolved": "https://registry.npmjs.org/concat-stream/-/concat-stream-1.6.2.tgz", + "integrity": "sha512-27HBghJxjiZtIk3Ycvn/4kbJk/1uZuJFfuPEns6LaEvpvG1f0hTea8lilrouyo9mVc2GWdcEZ8OLoGmSADlrCw==", + "engines": [ + "node >= 0.8" + ], + "dependencies": { + "buffer-from": "^1.0.0", + "inherits": "^2.0.3", + "readable-stream": "^2.2.2", + "typedarray": "^0.0.6" + } + }, + "node_modules/concat-stream/node_modules/readable-stream": { + "version": "2.3.8", + "resolved": "https://registry.npmjs.org/readable-stream/-/readable-stream-2.3.8.tgz", + "integrity": "sha512-8p0AUk4XODgIewSi0l8Epjs+EVnWiK7NoDIEGU0HhE7+ZyY8D1IMY7odu5lRrFXGg71L15KG8QrPmum45RTtdA==", + "dependencies": { + "core-util-is": "~1.0.0", + "inherits": "~2.0.3", + "isarray": "~1.0.0", + "process-nextick-args": "~2.0.0", + "safe-buffer": "~5.1.1", + "string_decoder": "~1.1.1", + "util-deprecate": "~1.0.1" + } + }, + "node_modules/concat-stream/node_modules/safe-buffer": { + "version": "5.1.2", + "resolved": "https://registry.npmjs.org/safe-buffer/-/safe-buffer-5.1.2.tgz", + "integrity": "sha512-Gd2UZBJDkXlY7GbJxfsE8/nvKkUEU1G38c1siN6QP6a9PT9MmHB8GnpscSmMJSoF8LOIrt8ud/wPtojys4G6+g==" + }, + "node_modules/concat-stream/node_modules/string_decoder": { + "version": "1.1.1", + "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.1.1.tgz", + "integrity": "sha512-n/ShnvDi6FHbbVfviro+WojiFzv+s8MPMHBczVePfUpDJLwoLT0ht1l4YwBCbi8pJAveEEdnkHyPyTP/mzRfwg==", + "dependencies": { + "safe-buffer": "~5.1.0" + } + }, "node_modules/content-disposition": { "version": "0.5.4", "resolved": "https://registry.npmjs.org/content-disposition/-/content-disposition-0.5.4.tgz", @@ -7053,6 +7114,23 @@ "integrity": "sha512-sGkPx+VjMtmA6MX27oA4FBFELFCZZ4S4XqeGOXCv68tT+jb3vk/RyaKWP0PTKyWtmLSM0b+adUTEvbs1PEaH2w==", "dev": true }, + "node_modules/multer": { + "version": "1.4.5-lts.1", + "resolved": "https://registry.npmjs.org/multer/-/multer-1.4.5-lts.1.tgz", + "integrity": "sha512-ywPWvcDMeH+z9gQq5qYHCCy+ethsk4goepZ45GLD63fOu0YcNecQxi64nDs3qluZB+murG3/D4dJ7+dGctcCQQ==", + "dependencies": { + "append-field": "^1.0.0", + "busboy": "^1.0.0", + "concat-stream": "^1.5.2", + "mkdirp": "^0.5.4", + "object-assign": "^4.1.1", + "type-is": "^1.6.4", + "xtend": "^4.0.0" + }, + "engines": { + "node": ">= 6.0.0" + } + }, "node_modules/mute-stream": { "version": "0.0.8", "resolved": "https://registry.npmjs.org/mute-stream/-/mute-stream-0.0.8.tgz", @@ -7238,7 +7316,6 @@ "version": "4.1.1", "resolved": "https://registry.npmjs.org/object-assign/-/object-assign-4.1.1.tgz", "integrity": "sha512-rJgTQnkUnH1sFw8yT6VSU3zD3sWmu6sZhIseY8VX+GRu3P6F7Fu+JNDoXfklElbLJSnc3FUQHVe4cU5hj+BcUg==", - "dev": true, "engines": { "node": ">=0.10.0" } @@ -8593,6 +8670,14 @@ "is-stream": "^1.1.0" } }, + "node_modules/streamsearch": { + "version": "1.1.0", + "resolved": "https://registry.npmjs.org/streamsearch/-/streamsearch-1.1.0.tgz", + "integrity": "sha512-Mcc5wHehp9aXz1ax6bZUyY5afg9u2rv5cqQI3mRrYkGC8rW2hM02jWuwjtL++LS5qinSyhj2QfLyNsuc+VsExg==", + "engines": { + "node": ">=10.0.0" + } + }, "node_modules/string_decoder": { "version": "1.3.0", "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.3.0.tgz", @@ -8964,6 +9049,11 @@ "node": ">= 0.6" } }, + "node_modules/typedarray": { + "version": "0.0.6", + "resolved": "https://registry.npmjs.org/typedarray/-/typedarray-0.0.6.tgz", + "integrity": "sha512-/aCDEGatGvZ2BIk+HmLf4ifCJFwvKFNb9/JeZPMulfgFracn9QFcAf5GO8B/mweUjSoblS5In0cWhqpfs/5PQA==" + }, "node_modules/typescript": { "version": "5.3.3", "resolved": "https://registry.npmjs.org/typescript/-/typescript-5.3.3.tgz", @@ -8996,8 +9086,7 @@ "node_modules/undici-types": { "version": "5.26.5", "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-5.26.5.tgz", - "integrity": "sha512-JlCMO+ehdEIKqlFxk6IfVoAUVmgz7cU7zD/h9XZ0qzeosSHmUJVOzSQvvYSYWXkFXC+IfLKSIffhv0sVZup6pA==", - "dev": true + "integrity": "sha512-JlCMO+ehdEIKqlFxk6IfVoAUVmgz7cU7zD/h9XZ0qzeosSHmUJVOzSQvvYSYWXkFXC+IfLKSIffhv0sVZup6pA==" }, "node_modules/uni-global": { "version": "1.0.0", @@ -9583,7 +9672,6 @@ "version": "4.0.2", "resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz", "integrity": "sha512-LKYU1iAXJXUgAXn9URjiu+MWhyUXHsvfp7mcuYm9dSUKK0/CjtrUwFAxD82/mCWbtLsGjFIad0wIsod4zrTAEQ==", - "dev": true, "engines": { "node": ">=0.4" } diff --git a/package.json b/package.json index 7b0e783..97b0e2c 100644 --- a/package.json +++ b/package.json @@ -43,10 +43,12 @@ "vitest": "^0.34.4" }, "dependencies": { + "@types/multer": "^1.4.11", "exceljs": "^4.3.0", "express": "^4.18.2", "ipssm": "^1.0.4", "joi": "^17.11.0", + "multer": "^1.4.5-lts.1", "papaparse": "^5.4.1", "serverless-http": "^3.2.0", "yargs": "^17.7.2" diff --git a/src/server.ts b/src/server.ts index 4ac0ad4..13621f3 100644 --- a/src/server.ts +++ b/src/server.ts @@ -3,6 +3,8 @@ import path from 'path' import { annotateFile, ipssm, ipssr } from './index' import { validatePatientForIpssm, validatePatientForIpssr } from './utils/validation' import serverless from 'serverless-http' +import multer from 'multer' +import fs from 'fs' const app = express() const port: number = process.env.PORT ? parseInt(process.env.PORT) : 3000 @@ -18,8 +20,8 @@ app.use((req, _res, next) => { // Serve the redoc swagger documentation app.get('/', (_req, res) => { - res.sendFile(path.join(__dirname, '..', 'redoc-static.html')); -}); + res.sendFile(path.join(__dirname, '..', 'redoc-static.html')) +}) // Endpoint for Ipssm app.post('/ipssm', validatePatientForIpssm, async (req: Request, res: Response) => { @@ -66,15 +68,32 @@ app.post('/ipssr', validatePatientForIpssr, async (req: Request, res: Response) } }) +// Set up multer to store uploaded files in memory +const upload = multer({ dest: 'uploads/' }) + // Endpoint for annotating a tsv/xlsx file -app.get('/annotateFile', async (req: Request, res: Response) => { - const inputFile: string = req.query.inputFile as string - const outputFile: string = req.query.outputFile as string - +app.post('/annotateFile', upload.single('file'), async (req: Request, res: Response) => { + console.log(`Output File format: ${req.body.outputFormat}`) + const outputFilePath: string = `uploads/Annotated.IPSSM.${req.body.outputFormat as string || 'csv'}` try { - await annotateFile(inputFile, outputFile) - res.send('File annotated successfully.') + if (req.file) { + const originalFilename = req.file.originalname + const originalExtension = path.extname(originalFilename) + const inputFilePath = req.file.path + originalExtension + + // Rename the uploaded file to include the original extension + fs.renameSync(req.file.path, inputFilePath) + + await annotateFile(inputFilePath, outputFilePath) + const outputFileContent = fs.readFileSync(outputFilePath, 'utf8') + + // Send the file content as the response + res.send(outputFileContent) + } else { + throw new Error('No file uploaded.') + } } catch (error) { + console.log((error as Error).stack) res.status(500).send('An error occurred while annotating the file.') } })