From 8fa1497f92a649acb181c7dd620b436ad4d5a95a Mon Sep 17 00:00:00 2001 From: bhatiadheeraj Date: Mon, 22 Jul 2024 19:37:57 +0000 Subject: [PATCH 1/4] Implement ezGOV project management APIs - Add endpoint to create a new project (`POST /ezgov/project`) - Add endpoint to update an existing project (`PUT /ezgov/project/:id`) - Add endpoint to retrieve all projects (`GET /ezgov/projects`) - Add endpoint to retrieve a specific project by ID (`GET /ezgov/project/:id`) - Add endpoint to upload documents to a project (`POST /upload/:projectId`) - Add endpoint to retrieve a specific document by project ID and document ID (`GET /project/:id/document/:docId`) - Add endpoint to update details of a specific document within a project (`PUT /project/:id/document/:docId`) - Add endpoint to serve the file of a specific document within a project (`GET /project/:projectId/file/:fileName`) --- api/controllers/ezgov.js | 350 +++++ api/controllers/index.js | 1 + api/models.js | 34 + package-lock.json | 2836 +++++++++++++------------------------- package.json | 6 +- 5 files changed, 1335 insertions(+), 1892 deletions(-) create mode 100644 api/controllers/ezgov.js diff --git a/api/controllers/ezgov.js b/api/controllers/ezgov.js new file mode 100644 index 00000000..1bfa7d43 --- /dev/null +++ b/api/controllers/ezgov.js @@ -0,0 +1,350 @@ +'use strict'; + +const express = require('express'); +const router = express.Router(); +const async = require('async'); + + +const config = require('../config'); +const db = require('../models'); +const common = require('../common'); +const multer = require('multer'); +const mongoose = require('mongoose'); +const path = require('path'); +const mkdirp = require('mkdirp'); +const fs = require('fs'); + +/** + * @apiGroup Project + * @api {post} /ezgov/project Post Project + * @apiDescription Register a new project + * + * + * @apiParam {String} [title] name for this project + * @apiParam {String} [description] Description for this dataset + * + * @apiParam {Object[]} members List of project members + * @apiParam {String} member._id Member ID + * @apiParam {String} member.role Member role + * @apiParam {String} member.position Member position + * @apiParam {String} member.name Member name + * + * @apiParam {Object[]} [documents] List of project documents + * @apiParam {String} documents._id Document ID + * @apiParam {String} documents.projectId Project ID + * @apiParam {String} documents.fileUrl URL of the document file + * @apiParam {String} documents.fileName Name of the document file + * @apiParam {Object} documents.uploadedBy Information about the uploader + * @apiParam {Date} documents.uploadDate Date of upload + * @apiParam {String} documents.type Type of the document + * @apiParam {String[]} documents.lifecycle Lifecycle stages of the document + * @apiParam {String[]} [documents.tags] Tags associated with the document + * @apiParam {String} [documents.template] Template ID for the document + * + * @apiHeader {String} authorization + * A valid JWT token in the format "Bearer: xxxxx" + * + * @apiSuccess {Object} Project record registered + */ + + +router.post('/project', common.jwt(), async (req, res) => { + try { + const projectData = req.body; + const isAdmin = projectData.members.some(member => member._id === req.user.id && member.role === 'admin'); + + if (!isAdmin) { + return res.status(403).json({ message: 'Forbidden: Only admins can create projects' }); + } + + //TODO: user.id / user._id + if(!projectData['createdBy']) projectData['createdBy'] = req.user.id; + + const requiredFields = ['title', 'description', 'primaryInstitute', 'members']; + + for (const field of requiredFields) { + if (!projectData[field]) { + return res.status(400).json({ message: `Bad Request: Missing required field ${field}` }); + } + } + + const newProject = new db.ezGovProjects(projectData); + const savedProject = await newProject.save(); + + res.status(200).json(savedProject); + } catch (error) { + res.status(500).json({ message: 'Internal Server Error', error: error.message }); + } +}); + + +/** + * @apiGroup Project + * @api {put} /ezgov/project/:id Update Project + * @apiDescription Update an existing project + * + * @apiParam [title] name for this project + * @apiParam {String} [description] Description for this dataset + * @apiParam {Object[]} members List of project members + * @apiParam {String} members._id Member ID + * @apiParam {String} members.role Member role + * @apiParam {String} members.position Member position + * + * @apiParam {Object[]} [documents] List of project documents + * @apiParam {String} documents._id Document ID + * @apiParam {String} documents.projectId Project ID + * @apiParam {String} documents.fileUrl URL of the document file + * @apiParam {String} documents.fileName Name of the document file + * @apiParam {Date} documents.uploadDate Date of upload + * @apiParam {String} documents.type Type of the document + * @apiParam {String[]} documents.lifecycle Lifecycle stages of the document + * @apiParam {String[]} [documents.tags] Tags associated with the document + * @apiParam {String} [documents.template] Template ID for the document + * + * @apiHeader {String} authorization + * A valid JWT token in the format "Bearer: xxxxx" + * + * @apiSuccess {Object} Project record updated + */ + +router.put('/project/:id', common.jwt(), async (req, res) => { + try { + const projectId = req.params.id; + const projectData = req.body; + + const project = await db.ezGovProjects.findById(projectId); + if (!project) { + return res.status(404).json({ message: 'Project not found' }); + } + + const isAdmin = project.members.some(member => member._id.toString() === req.user.id && member.role === 'admin'); + if (!isAdmin) { + return res.status(403).json({ message: 'Forbidden: Only admins can update projects' }); + } + + const updatedProject = await db.ezGovProjects.findByIdAndUpdate(projectId, projectData, { new: true }); + + res.status(200).json(updatedProject); + } catch (error) { + res.status(500).json({ message: 'Internal Server Error', error: error.message }); + } +}); + + +/** + * @apiGroup Project + * @api {get} /ezgov/projects Get All Projects + * @apiDescription Retrieve all projects + * + * @apiHeader {String} authorization + * A valid JWT token in the format "Bearer: xxxxx" + * + * @apiSuccess {Object[]} List of projects + */ + +router.get('/projects', common.jwt(), async (req, res) => { + try { + const projects = await db.ezGovProjects.find({ 'members._id': req.user.id }); + res.status(200).json(projects); + } catch (error) { + res.status(500).json({ message: 'Internal Server Error', error: error.message }); + } +}); + + +/** + * @apiGroup Project + * @api {get} /ezgov/project/:id Get Specific Project + * @apiDescription Retrieve a specific project by ID + * + * @apiHeader {String} authorization + * A valid JWT token in the format "Bearer: xxxxx" + * + * @apiSuccess {Object} Project record + */ + +router.get('/project/:id', common.jwt(), async (req, res) => { + try { + const projectId = req.params.id; + const project = await db.ezGovProjects.findById(projectId); + if (!project) { + return res.status(404).json({ message: 'Project not found' }); + } + + const isMemberOrAdmin = project.members.some(member => member._id.toString() === req.user.id); + if (!isMemberOrAdmin) { + return res.status(403).json({ message: 'Forbidden: Only project members or admins can access this project' }); + } + + res.status(200).json(project); + } catch (error) { + res.status(500).json({ message: 'Internal Server Error', error: error.message }); + } +}); + +// Set up Multer for file uploads +const upload = multer({ dest: '/mnt/ezgov/temp/' }); // Temporary upload directory + +router.post('/upload/:projectId', upload.any(), common.jwt(), async (req, res) => { + const projectId = req.params.projectId; + const userId = req.user.id; + const { type, lifecycle, tags, template } = req.body; + + if (!req.files || req.files.length === 0) { + return res.status(400).send('No files were uploaded.'); + } + + try { + let documents = []; + + for (let i = 0; i < req.files.length; i++) { + const file = req.files[i]; + const src_path = file.path; + const dest_path = path.resolve(`/mnt/ezgov/upload/${projectId}/${file.originalname}`); + + console.log(`Source path: ${src_path}`); + console.log(`Destination path: ${dest_path}`); + + if (!dest_path.startsWith('/mnt/ezgov/upload')) { + return res.status(400).send("Invalid path: " + dest_path); + } + + const destdir = path.dirname(dest_path); + console.log(`Destination directory: ${destdir}`); + + mkdirp.sync(destdir); + + // Move the file from temp to the destination directory + try { + fs.renameSync(src_path, dest_path); + } catch (err) { + console.error(`Error moving file from ${src_path} to ${dest_path}`, err); + return res.status(500).send("Error moving file."); + } + + // Create a new document record + const document = { + fileUrl: `/mnt/ezgov/upload/${projectId}/${file.originalname}`, + fileName: file.originalname, + uploadedBy: mongoose.Types.ObjectId(userId) , + type: type, + lifecycle: lifecycle ? lifecycle.split(',') : [], + tags: tags ? tags.split(',') : [], + }; + + documents.push(document); + } + + // Update the project with the new documents + await db.ezGovProjects.findByIdAndUpdate( + projectId, + { $push: { documents: { $each: documents } } }, + { new: true, useFindAndModify: false } + ); + + res.status(200).send(documents); + } catch (err) { + console.error(err); + res.status(500).send("Internal server error."); + } +}); + + +router.get('/project/:id/document/:docId', common.jwt(), async(req,res) => { + try { + const projectId = req.params.id; + const docId = req.params.docId; + + const project = await db.ezGovProjects.findById(projectId); + await checkProjectAccess(project, req.user.id); + const document = project.documents.id(docId); + + if(document) res.status(200).json(document); + else res.status(404).json({message: "Document not Found"}); + + } catch (error) { + console.error(error); + res.status(500).json({ message: 'Internal Server Error', error: error.message }); + } +}) + +router.put('/project/:id/document/:docId', common.jwt(), async (req, res) => { + try { + const projectId = req.params.id; + const docId = req.params.docId; + const updateData = req.body; + + const project = await db.ezGovProjects.findById(projectId); + if (!project) { + return res.status(404).json({ message: 'Project not found' }); + } + + const isAdmin = project.members.some(member => member._id.toString() === req.user.id && member.role === 'admin'); + if (!isAdmin) { + return res.status(403).json({ message: 'Forbidden: Only admins can update documents' }); + } + + // Find the document by ID within the project + const document = project.documents.id(docId); + if (!document) { + return res.status(404).json({ message: 'Document not found' }); + } + + console.log(updateData); + + // Update the document with the provided data + Object.keys(updateData).forEach(key => { + document[key] = updateData[key]; + }); + + // Save the project with the updated document + await project.save(); + + res.status(200).json({ message: 'Document updated successfully', document }); + } catch (error) { + console.error('Error updating document:', error); + res.status(500).json({ message: 'Internal Server Error', error: error.message }); + } +}); + +const checkProjectAccess = async (project, userID) => { + + console.log(project); + + const isMemberOrAdmin = project.members.some(member => member._id.toString() == userID); + if (!isMemberOrAdmin) { + return res.status(403).json({ message: 'Forbidden: Only project members or admins can access this project' }); + } + + return project; +}; + +// Route to serve files +router.get('/project/:projectId/file/:fileName', async (req, res) => { + + const projectId = req.params.projectId; + const docId = req.params.fileName; + + const project = await db.ezGovProjects.findById(projectId); + const document = project.documents.id(docId); + const filePath = document.fileUrl; + + // Check if the file exists + fs.access(filePath, fs.constants.F_OK, (err) => { + if (err) { + return res.status(404).send('File not found'); + } + + // Serve the file + res.sendFile(filePath, (err) => { + if (err) { + console.error('Error serving file:', err); + res.status(500).send('Internal Server Error'); + } + }); + }); + +}); + +module.exports = router; + diff --git a/api/controllers/index.js b/api/controllers/index.js index d151dc7a..25e88287 100644 --- a/api/controllers/index.js +++ b/api/controllers/index.js @@ -45,6 +45,7 @@ router.use('/datalad', require('./datalad')); router.use('/participant', require('./participant')); router.use('/secondary', require('./secondary')); router.use('/xnat', require('./xnat')); +router.use('/ezgov', require('./ezgov')) module.exports = router; diff --git a/api/models.js b/api/models.js index 72afa308..e01b18f1 100644 --- a/api/models.js +++ b/api/models.js @@ -882,3 +882,37 @@ var commentSchema = mongoose.Schema({ exports.Comments = mongoose.model('Comments', commentSchema); +const memberSchema = mongoose.Schema({ + role: String, /* admin / member*/ + position: String, /* PI / SDE / RA/ */ + userID: {type: mongoose.Schema.Types.ObjectId}, +}); + +const documentSchema = mongoose.Schema({ + fileUrl: String, + fileName: String, + uploadedBy: {type: mongoose.Schema.Types.ObjectId}, + uploadDate: { type: Date, default: Date.now}, + type: String, + lifecycle: [String], + tags: [{ type: String }], + template: { type: mongoose.Schema.Types.ObjectId, ref: 'Template'}, + responses: { + } +}); + +// Define the ezGovProject schema +const ezGovProjectSchema = mongoose.Schema({ + title: String, + description: String, + primaryInstitute: String, + funder: String, + fundingStatus: String, + fundingOpportunityURL: String, + createdBy: String, + members: [memberSchema], + documents: [documentSchema] +}); + +exports.ezGovProjects = mongoose.model('ezGovProjects', ezGovProjectSchema); + diff --git a/package-lock.json b/package-lock.json index aecf7b6e..c9d328c9 100644 --- a/package-lock.json +++ b/package-lock.json @@ -14,25 +14,21 @@ "amqp": "^0.2.7", "archiver": "^5.3.1", "async": "^3.2.3", - "atob": "^2.1.2", "aws-sdk": "^2.1128.0", "axios": "^0.21.4", "body-parser": "^1.20.0", - "brainlife": "^1.5.43", "compression": "^1.7.3", "cors": "^2.8.5", - "coveralls": "^3.1.1", "crypto": "^1.0.1", "express": "^4.18.1", "express-jwt": "^6.1.2", "express-winston": "^3.0.1", "gunzip-stream": "^1.0.1", - "istanbul": "^0.4.5", "keyword-extractor": "0.0.20", - "mathjs": "^10.5.1", + "mkdirp": "^3.0.1", "mongoose": "^6.3.2", "morgan": "^1.10.0", - "n-stopwords": "^1.1.2", + "multer": "^1.4.5-lts.1", "nocache": "^2.0.0", "nodemailer": "^6.7.5", "pkgcloud": "^2.2.0", @@ -43,15 +39,17 @@ "ssh2": "^1.10.0", "stream-meter": "^1.0.4", "tar": "^4.4.19", - "tmp": "^0.2.1", "winston": "^3.7.2", "xml-escape": "^1.1.0", "xml2js": "^0.4.23" }, "devDependencies": { + "brainlife": "^1.5.43", "chai": "^4.3.6", + "coveralls": "^3.1.1", "eslint": "^8.30.0", "eslint-plugin-vue": "^9.8.0", + "istanbul": "^0.4.5", "mocha": "^5.2.0", "node-geocoder": "^3.29.0", "supertest": "^3.3.0" @@ -61,6 +59,7 @@ "version": "2.0.0", "resolved": "https://registry.npmjs.org/@aws-crypto/crc32/-/crc32-2.0.0.tgz", "integrity": "sha512-TvE1r2CUueyXOuHdEigYjIZVesInd9KN+K/TFFNfkkxRThiNxO6i4ZqqAVMoEjAamZZ1AA8WXJkjCz7YShHPQA==", + "dev": true, "dependencies": { "@aws-crypto/util": "^2.0.0", "@aws-sdk/types": "^3.1.0", @@ -70,12 +69,14 @@ "node_modules/@aws-crypto/crc32/node_modules/tslib": { "version": "1.14.1", "resolved": "https://registry.npmjs.org/tslib/-/tslib-1.14.1.tgz", - "integrity": "sha512-Xni35NKzjgMrwevysHTCArtLDpPvye8zV/0E4EyYn43P7/7qvQwPh9BGkHewbMulVntbigmcT7rdX3BNo9wRJg==" + "integrity": "sha512-Xni35NKzjgMrwevysHTCArtLDpPvye8zV/0E4EyYn43P7/7qvQwPh9BGkHewbMulVntbigmcT7rdX3BNo9wRJg==", + "dev": true }, "node_modules/@aws-crypto/crc32c": { "version": "2.0.0", "resolved": "https://registry.npmjs.org/@aws-crypto/crc32c/-/crc32c-2.0.0.tgz", "integrity": "sha512-vF0eMdMHx3O3MoOXUfBZry8Y4ZDtcuskjjKgJz8YfIDjLStxTZrYXk+kZqtl6A0uCmmiN/Eb/JbC/CndTV1MHg==", + "dev": true, "dependencies": { "@aws-crypto/util": "^2.0.0", "@aws-sdk/types": "^3.1.0", @@ -85,12 +86,14 @@ "node_modules/@aws-crypto/crc32c/node_modules/tslib": { "version": "1.14.1", "resolved": "https://registry.npmjs.org/tslib/-/tslib-1.14.1.tgz", - "integrity": "sha512-Xni35NKzjgMrwevysHTCArtLDpPvye8zV/0E4EyYn43P7/7qvQwPh9BGkHewbMulVntbigmcT7rdX3BNo9wRJg==" + "integrity": "sha512-Xni35NKzjgMrwevysHTCArtLDpPvye8zV/0E4EyYn43P7/7qvQwPh9BGkHewbMulVntbigmcT7rdX3BNo9wRJg==", + "dev": true }, "node_modules/@aws-crypto/ie11-detection": { "version": "2.0.2", "resolved": "https://registry.npmjs.org/@aws-crypto/ie11-detection/-/ie11-detection-2.0.2.tgz", "integrity": 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true, "dependencies": { "tslib": "^2.3.1" } @@ -1235,6 +1323,7 @@ "version": "3.170.0", "resolved": "https://registry.npmjs.org/@aws-sdk/util-utf8-node/-/util-utf8-node-3.170.0.tgz", "integrity": "sha512-52QWGNoNQoyT2CuoQz6LjBKxHQtN/ceMFLW+9J1E0I1ni8XTuTYP52BlMe5484KkmZKsHOm+EWe4xuwwVetTxg==", + "dev": true, "dependencies": { "@aws-sdk/util-buffer-from": "3.170.0", "tslib": "^2.3.1" @@ -1247,6 +1336,7 @@ "version": "3.180.0", "resolved": "https://registry.npmjs.org/@aws-sdk/util-waiter/-/util-waiter-3.180.0.tgz", "integrity": "sha512-fDBGplYp6pIIfrB7073tUhU4zppRaSiPjBCCT00yth9woWwZPUCIg7iQZKEqkBmvCzcJSYn0jRopLhf3Y7i5Wg==", + "dev": true, "dependencies": { "@aws-sdk/abort-controller": "3.178.0", "@aws-sdk/types": "3.178.0", @@ -1260,6 +1350,7 @@ "version": "3.170.0", "resolved": "https://registry.npmjs.org/@aws-sdk/xml-builder/-/xml-builder-3.170.0.tgz", "integrity": "sha512-eN458rrukeI62yU1k4a+032IfpAS7aK30VEITzKanklMW6AxTpxUC6vGrP6bwtIpCFDN8yVaIiAwGXQg5l1X4g==", + "dev": true, 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"@aws-crypto/sha256-js": "2.0.0", @@ -10009,6 +9461,7 @@ "version": "3.181.0", "resolved": "https://registry.npmjs.org/@aws-sdk/client-sts/-/client-sts-3.181.0.tgz", "integrity": "sha512-j//F9kjdSv9lUa8p87cg+xk6l5E8o8+GTYP5838eFQR7XcEc3yEljSCkuj2xIzrtf1jKuMXBnswTKmxJhjbTzQ==", + "dev": true, "requires": { "@aws-crypto/sha256-browser": "2.0.0", "@aws-crypto/sha256-js": "2.0.0", @@ -10052,6 +9505,7 @@ "version": "3.178.0", "resolved": "https://registry.npmjs.org/@aws-sdk/config-resolver/-/config-resolver-3.178.0.tgz", "integrity": "sha512-8xL98TGMaVULIN7HRWV2q1o0Y2p38QuweehzM8yXCZrrLOyHgWo3waP2RNVeddOB7MrSwwU/gw9rXSv7YHLZ6w==", + "dev": true, "requires": { "@aws-sdk/signature-v4": "3.178.0", "@aws-sdk/types": "3.178.0", @@ -10064,6 +9518,7 @@ "version": "3.178.0", "resolved": "https://registry.npmjs.org/@aws-sdk/credential-provider-env/-/credential-provider-env-3.178.0.tgz", "integrity": "sha512-5CMswTJ188RuK9TmI5yAosIsyu4Mm9Cdq1068tRls5EqqwGK1PI7Q007b6rD7zqCb5IgeFBV0t2DxHkBmHRd3w==", + 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"version": "3.178.0", "resolved": "https://registry.npmjs.org/@aws-sdk/querystring-parser/-/querystring-parser-3.178.0.tgz", "integrity": "sha512-dp3pLnsOvAcIF7Yn2PY5CIVWX7GvC33nSlWDYeLeCMapccwTbe6zBqreWbScmIGJra4QJTdjccpwo2Yxwhr5QQ==", + "dev": true, "requires": { "@aws-sdk/types": "3.178.0", "tslib": "^2.3.1" @@ -10507,12 +10003,14 @@ "@aws-sdk/service-error-classification": { "version": "3.178.0", "resolved": "https://registry.npmjs.org/@aws-sdk/service-error-classification/-/service-error-classification-3.178.0.tgz", - "integrity": "sha512-tDKTBXxck2N4bhAnQaeokx9ps38V3G70lcDdHS/N9hmqcQQmH5x+1/AMwYWLjUZmOQPBW9sFoG4B3psnl+sefw==" + "integrity": "sha512-tDKTBXxck2N4bhAnQaeokx9ps38V3G70lcDdHS/N9hmqcQQmH5x+1/AMwYWLjUZmOQPBW9sFoG4B3psnl+sefw==", + "dev": true }, "@aws-sdk/shared-ini-file-loader": { "version": "3.178.0", "resolved": "https://registry.npmjs.org/@aws-sdk/shared-ini-file-loader/-/shared-ini-file-loader-3.178.0.tgz", "integrity": "sha512-nZGmuhGLDFbXsb7QYDg7PiPMAmsdlSshKJ+AhKSZF/J0SK94kdZgGnGXGUZe52S3G41E3CZIgnLnnsMXq0uErA==", + "dev": true, "requires": { "tslib": "^2.3.1" } @@ -10521,6 +10019,7 @@ "version": "3.178.0", "resolved": "https://registry.npmjs.org/@aws-sdk/signature-v4/-/signature-v4-3.178.0.tgz", "integrity": "sha512-8oOx6o0uOqlCDPM0dszfR1WHqd0E1VuFqez8iNItp0DhmhaCuanEwKYYA6HOkVu/MA6CsG6zDIJaFr5ODU2NvQ==", + "dev": true, "requires": { "@aws-sdk/is-array-buffer": "3.170.0", "@aws-sdk/types": "3.178.0", @@ -10534,6 +10033,7 @@ "version": "3.180.0", "resolved": "https://registry.npmjs.org/@aws-sdk/signature-v4-multi-region/-/signature-v4-multi-region-3.180.0.tgz", "integrity": "sha512-3IjwOy/x6UroV3TAbeCwpCRmt/8TW89JI1r8gtDbpQ42WiQ/1J+R5a78NP8bYa53kiDghW6pKlvLcbuoh3zWHQ==", + "dev": true, "requires": { "@aws-sdk/protocol-http": "3.178.0", "@aws-sdk/signature-v4": "3.178.0", @@ -10546,6 +10046,7 @@ "version": "3.180.0", "resolved": 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"@aws-sdk/types": "3.178.0", @@ -10571,6 +10074,7 @@ "version": "3.170.0", "resolved": "https://registry.npmjs.org/@aws-sdk/util-arn-parser/-/util-arn-parser-3.170.0.tgz", "integrity": "sha512-2ivABL9GNsucfMMkgGjVdFidbDogtSr4FBVW12D4ltijOL82CAynGrnxHAczRGnmi5/1/Ir4ipkr9pAdRMGiGw==", + "dev": true, "requires": { "tslib": "^2.3.1" } @@ -10579,6 +10083,7 @@ "version": "3.170.0", "resolved": "https://registry.npmjs.org/@aws-sdk/util-base64-browser/-/util-base64-browser-3.170.0.tgz", "integrity": "sha512-uLP9Kp74+jc+UWI392LSWIaUj9eXZBhkAiSm8dXAyrr+5GFOKvmEdidFoZKKcFcZ2v3RMonDgFVcDBiZ33w7BQ==", + "dev": true, "requires": { "tslib": "^2.3.1" } @@ -10587,6 +10092,7 @@ "version": "3.170.0", "resolved": "https://registry.npmjs.org/@aws-sdk/util-base64-node/-/util-base64-node-3.170.0.tgz", "integrity": "sha512-sjpOmfyW0RWCLXU8Du0ZtwgFoxIuKQIyVygXJ4qxByoa3jIUJXf4U33uSRMy47V3JoogdZuKSpND9hiNk2wU4w==", + "dev": true, "requires": { "@aws-sdk/util-buffer-from": "3.170.0", "tslib": "^2.3.1" @@ -10596,6 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|| ^4.0.0", - "yargs-parser": "^11.1.1" - } - }, - "yargs-parser": { - "version": "11.1.1", - "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-11.1.1.tgz", - "integrity": "sha512-C6kB/WJDiaxONLJQnF8ccx9SEeoTTLek8RVbaOIsrAUS8VrBEXfmeSnCZxygc+XC2sNMBIwOOnfcxiynjHsVSQ==", - "requires": { - "camelcase": "^5.0.0", - "decamelize": "^1.2.0" - } - } - } + "integrity": "sha512-y11nGElTIV+CT3Zv9t7VKl+Q3hTQoT9a1Qzezhhl6Rp21gJ/IVTW7Z3y9EWXhuUBC2Shnf+DX0antecpAwSP8w==", + "dev": true }, "yocto-queue": { "version": "0.1.0", diff --git a/package.json b/package.json index 960bdb40..d382afad 100644 --- a/package.json +++ b/package.json @@ -34,8 +34,10 @@ "express-winston": "^3.0.1", "gunzip-stream": "^1.0.1", "keyword-extractor": "0.0.20", + "mkdirp": "^3.0.1", "mongoose": "^6.3.2", "morgan": "^1.10.0", + "multer": "^1.4.5-lts.1", "nocache": "^2.0.0", "nodemailer": "^6.7.5", "pkgcloud": "^2.2.0", @@ -52,11 +54,11 @@ }, "devDependencies": { "brainlife": "^1.5.43", - "istanbul": "^0.4.5", - "coveralls": "^3.1.1", "chai": "^4.3.6", + "coveralls": "^3.1.1", "eslint": "^8.30.0", "eslint-plugin-vue": "^9.8.0", + "istanbul": "^0.4.5", "mocha": "^5.2.0", "node-geocoder": "^3.29.0", "supertest": "^3.3.0" From 33888d912414c6d53cfd72010fa33748ad8569f4 Mon Sep 17 00:00:00 2001 From: bhatiadheeraj Date: Mon, 29 Jul 2024 17:21:06 +0000 Subject: [PATCH 2/4] added api to get text from a docx document --- api/controllers/ezgov.js | 41 ++++++++++++++++++++++++++++++++++++++-- 1 file changed, 39 insertions(+), 2 deletions(-) diff --git a/api/controllers/ezgov.js b/api/controllers/ezgov.js index 1bfa7d43..020cfb73 100644 --- a/api/controllers/ezgov.js +++ b/api/controllers/ezgov.js @@ -13,6 +13,7 @@ const mongoose = require('mongoose'); const path = require('path'); const mkdirp = require('mkdirp'); const fs = require('fs'); +const mammoth = require("mammoth"); /** * @apiGroup Project @@ -320,10 +321,10 @@ const checkProjectAccess = async (project, userID) => { }; // Route to serve files -router.get('/project/:projectId/file/:fileName', async (req, res) => { +router.get('/project/:projectId/file/:docId', async (req, res) => { const projectId = req.params.projectId; - const docId = req.params.fileName; + const docId = req.params.docId; const project = await db.ezGovProjects.findById(projectId); const document = project.documents.id(docId); @@ -346,5 +347,41 @@ router.get('/project/:projectId/file/:fileName', async (req, res) => { }); + + + +router.get('/project/:projectId/file/:docId/getText', async (req, res) => { + const projectId = req.params.projectId; + const docId = req.params.docId; + + try { + const project = await db.ezGovProjects.findById(projectId); + if (!project) { + return res.status(404).send('Project not found'); + } + + const document = project.documents.id(docId); + if (!document) { + return res.status(404).send('Document not found'); + } + + const filePath = document.fileUrl; + + fs.access(filePath, fs.constants.F_OK, async (err) => { + if (err) { + return res.status(404).send('File not found'); + } + const result = await mammoth.extractRawText({ path: filePath }); + const text = result.value; + return res.status(200).send(text); + }); + + } catch (err) { + return res.status(500).send('Internal server error'); + } +}); + + + module.exports = router; From 6290dae8ff9f65b3a67c2daa4874241f05186eaf Mon Sep 17 00:00:00 2001 From: bhatiadheeraj Date: Mon, 29 Jul 2024 17:33:36 +0000 Subject: [PATCH 3/4] updated getText api to parse text from pdf and txt file --- api/controllers/ezgov.js | 44 +++++++++++++++++++++++++--------------- 1 file changed, 28 insertions(+), 16 deletions(-) diff --git a/api/controllers/ezgov.js b/api/controllers/ezgov.js index 020cfb73..9df33eeb 100644 --- a/api/controllers/ezgov.js +++ b/api/controllers/ezgov.js @@ -13,6 +13,8 @@ const mongoose = require('mongoose'); const path = require('path'); const mkdirp = require('mkdirp'); const fs = require('fs'); +const fsPromises = fs.promises; +const pdf = require('pdf-parse'); const mammoth = require("mammoth"); /** @@ -348,40 +350,50 @@ router.get('/project/:projectId/file/:docId', async (req, res) => { }); - - router.get('/project/:projectId/file/:docId/getText', async (req, res) => { const projectId = req.params.projectId; const docId = req.params.docId; + const project = await db.ezGovProjects.findById(projectId); + + if (!project) { + return res.status(404).send('Project not found'); + } - try { - const project = await db.ezGovProjects.findById(projectId); - if (!project) { - return res.status(404).send('Project not found'); - } - - const document = project.documents.id(docId); - if (!document) { - return res.status(404).send('Document not found'); - } + const document = project.documents.id(docId); + if (!document) { + return res.status(404).send('Document not found'); + } + try { const filePath = document.fileUrl; + const fileExtension = path.extname(filePath).toLowerCase(); + // Check if the file exists fs.access(filePath, fs.constants.F_OK, async (err) => { if (err) { return res.status(404).send('File not found'); } - const result = await mammoth.extractRawText({ path: filePath }); - const text = result.value; + let text = ''; + if (fileExtension === '.docx') { + const result = await mammoth.extractRawText({ path: filePath }); + text = result.value; + } else if (fileExtension === '.pdf') { + const dataBuffer = await fsPromises.readFile(filePath); + const result = await pdf(dataBuffer); + text = result.text; + } else if (fileExtension === '.txt') { + text = await fsPromises.readFile(filePath, 'utf8'); + } else { + return res.status(400).send('Unsupported file type. Only .docx, .pdf, and .txt files are supported for text extraction.'); + } return res.status(200).send(text); }); - } catch (err) { + console.error('Internal server error:', err); return res.status(500).send('Internal server error'); } }); - module.exports = router; From ec3f88ab0df300aa698568522b96a69edebd6fdd Mon Sep 17 00:00:00 2001 From: bhatiadheeraj Date: Mon, 29 Jul 2024 18:47:19 +0000 Subject: [PATCH 4/4] added ui t modal and api import text from a uploaded doc in ezgov project --- api/controllers/ezgov.js | 4 +- package-lock.json | 323 +++++++++++++++++++++++++++++++- package.json | 2 + ui/src/modals/ezgovimporter.vue | 74 ++++++++ ui/src/projectedit.vue | 8 + 5 files changed, 400 insertions(+), 11 deletions(-) create mode 100644 ui/src/modals/ezgovimporter.vue diff --git a/api/controllers/ezgov.js b/api/controllers/ezgov.js index 9df33eeb..47db0fb6 100644 --- a/api/controllers/ezgov.js +++ b/api/controllers/ezgov.js @@ -386,7 +386,8 @@ router.get('/project/:projectId/file/:docId/getText', async (req, res) => { } else { return res.status(400).send('Unsupported file type. Only .docx, .pdf, and .txt files are supported for text extraction.'); } - return res.status(200).send(text); + if(text.length) return res.status(200).send(text); + else return res.status(400).send("Empty File"); }); } catch (err) { console.error('Internal server error:', err); @@ -395,5 +396,6 @@ router.get('/project/:projectId/file/:docId/getText', async (req, res) => { }); + module.exports = router; diff --git a/package-lock.json b/package-lock.json index c9d328c9..40037ee1 100644 --- a/package-lock.json +++ b/package-lock.json @@ -25,12 +25,14 @@ "express-winston": "^3.0.1", "gunzip-stream": "^1.0.1", "keyword-extractor": "0.0.20", + "mammoth": "^1.8.0", "mkdirp": "^3.0.1", "mongoose": "^6.3.2", "morgan": "^1.10.0", "multer": "^1.4.5-lts.1", "nocache": "^2.0.0", "nodemailer": "^6.7.5", + "pdf-parse": "^1.1.1", "pkgcloud": "^2.2.0", "redis": "^4.2", "request": "^2.88.2", @@ -1994,7 +1996,6 @@ "version": "1.0.10", "resolved": "https://registry.npmjs.org/argparse/-/argparse-1.0.10.tgz", "integrity": "sha512-o5Roy6tNG4SL/FOkCAN6RzjiakZS25RLYFrcMttJqbdd8BWrnA+fGz57iN5Pb06pvBGvl5gQ0B48dJlslXvoTg==", - "dev": true, "dependencies": { "sprintf-js": "~1.0.2" } @@ -3197,6 +3198,11 @@ "node": ">=0.3.1" } }, + "node_modules/dingbat-to-unicode": { + "version": "1.0.1", + "resolved": "https://registry.npmjs.org/dingbat-to-unicode/-/dingbat-to-unicode-1.0.1.tgz", + "integrity": "sha512-98l0sW87ZT58pU4i61wa2OHwxbiYSbuxsCBozaVnYX2iCnr3bLM3fIes1/ej7h1YdOKuKt/MLs706TVnALA65w==" + }, "node_modules/doctrine": { "version": "3.0.0", "resolved": "https://registry.npmjs.org/doctrine/-/doctrine-3.0.0.tgz", @@ -3267,6 +3273,14 @@ "node": ">=4" } }, + "node_modules/duck": { + "version": "0.1.12", + "resolved": "https://registry.npmjs.org/duck/-/duck-0.1.12.tgz", + "integrity": "sha512-wkctla1O6VfP89gQ+J/yDesM0S7B7XLXjKGzXxMDVFg7uEn706niAtyYovKbyq1oT9YwDcly721/iUWoc8MVRg==", + "dependencies": { + "underscore": "^1.13.1" + } + }, "node_modules/duplexify": { "version": "3.7.1", "resolved": "https://registry.npmjs.org/duplexify/-/duplexify-3.7.1.tgz", @@ -5129,6 +5143,11 @@ "node": ">= 4" } }, + "node_modules/immediate": { + "version": "3.0.6", + "resolved": "https://registry.npmjs.org/immediate/-/immediate-3.0.6.tgz", + "integrity": "sha512-XXOFtyqDjNDAQxVfYxuF7g9Il/IbWmmlQg2MYKOH8ExIT1qg6xc4zyS3HaEEATgs1btfzxq15ciUiY7gjSXRGQ==" + }, "node_modules/import-fresh": { "version": "3.3.0", "resolved": "https://registry.npmjs.org/import-fresh/-/import-fresh-3.3.0.tgz", @@ -5807,6 +5826,39 @@ "node": ">=0.6.0" } }, + "node_modules/jszip": { + "version": "3.10.1", + "resolved": "https://registry.npmjs.org/jszip/-/jszip-3.10.1.tgz", + "integrity": "sha512-xXDvecyTpGLrqFrvkrUSoxxfJI5AH7U8zxxtVclpsUtMCq4JQ290LY8AW5c7Ggnr/Y/oK+bQMbqK2qmtk3pN4g==", + "dependencies": { + "lie": "~3.3.0", + "pako": "~1.0.2", + "readable-stream": "~2.3.6", + "setimmediate": "^1.0.5" + } + }, + "node_modules/jszip/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/jszip/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/jwa": { "version": "1.4.1", "resolved": "https://registry.npmjs.org/jwa/-/jwa-1.4.1.tgz", @@ -6041,6 +6093,14 @@ "node": ">=0.10.0" } }, + "node_modules/lie": { + "version": "3.3.0", + "resolved": "https://registry.npmjs.org/lie/-/lie-3.3.0.tgz", + "integrity": "sha512-UaiMJzeWRlEujzAuw5LokY1L5ecNQYZKfmyZ9L7wDHb/p5etKaxXhohBcrw0EYby+G/NA52vRSN4N39dxHAIwQ==", + "dependencies": { + "immediate": "~3.0.5" + } + }, "node_modules/lodash": { "version": "4.17.21", "resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.21.tgz", @@ -6133,6 +6193,16 @@ "resolved": "https://registry.npmjs.org/ms/-/ms-2.1.3.tgz", "integrity": "sha512-6FlzubTLZG3J2a/NVCAleEhjzq5oxgHyaCU9yYXvcLsvoVaHJq/s5xXI6/XXP6tz7R9xAOtHnSO/tXtF3WRTlA==" }, + "node_modules/lop": { + "version": "0.4.1", + "resolved": "https://registry.npmjs.org/lop/-/lop-0.4.1.tgz", + "integrity": "sha512-9xyho9why2A2tzm5aIcMWKvzqKsnxrf9B5I+8O30olh6lQU8PH978LqZoI4++37RBgS1Em5i54v1TFs/3wnmXQ==", + "dependencies": { + "duck": "^0.1.12", + "option": "~0.2.1", + "underscore": "^1.13.1" + } + }, "node_modules/loupe": { "version": "2.3.4", "resolved": "https://registry.npmjs.org/loupe/-/loupe-2.3.4.tgz", @@ -6169,6 +6239,50 @@ "node": ">=4" } }, + "node_modules/mammoth": { + "version": "1.8.0", + "resolved": "https://registry.npmjs.org/mammoth/-/mammoth-1.8.0.tgz", + "integrity": "sha512-pJNfxSk9IEGVpau+tsZFz22ofjUsl2mnA5eT8PjPs2n0BP+rhVte4Nez6FdgEuxv3IGI3afiV46ImKqTGDVlbA==", + "dependencies": { + "@xmldom/xmldom": "^0.8.6", + "argparse": "~1.0.3", + "base64-js": "^1.5.1", + "bluebird": "~3.4.0", + "dingbat-to-unicode": "^1.0.1", + "jszip": "^3.7.1", + "lop": "^0.4.1", + "path-is-absolute": "^1.0.0", + "underscore": "^1.13.1", + "xmlbuilder": "^10.0.0" + }, + "bin": { + "mammoth": "bin/mammoth" + }, + "engines": { + "node": ">=12.0.0" + } + }, + "node_modules/mammoth/node_modules/@xmldom/xmldom": { + "version": "0.8.10", + "resolved": "https://registry.npmjs.org/@xmldom/xmldom/-/xmldom-0.8.10.tgz", + "integrity": "sha512-2WALfTl4xo2SkGCYRt6rDTFfk9R1czmBvUQy12gK2KuRKIpWEhcbbzy8EZXtz/jkRqHX8bFEc6FC1HjX4TUWYw==", + "engines": { + "node": ">=10.0.0" + } + }, + "node_modules/mammoth/node_modules/bluebird": { + "version": 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"https://registry.npmjs.org/node-fetch/-/node-fetch-2.6.7.tgz", @@ -6966,6 +7085,11 @@ "url": "https://github.com/sponsors/sindresorhus" } }, + "node_modules/option": { + "version": "0.2.4", + "resolved": "https://registry.npmjs.org/option/-/option-0.2.4.tgz", + "integrity": "sha512-pkEqbDyl8ou5cpq+VsnQbe/WlEy5qS7xPzMS1U55OCG9KPvwFD46zDbxQIj3egJSFc3D+XhYOPUzz49zQAVy7A==" + }, "node_modules/optionator": { "version": "0.8.3", "resolved": "https://registry.npmjs.org/optionator/-/optionator-0.8.3.tgz", @@ -7010,8 +7134,7 @@ "node_modules/pako": { "version": "1.0.11", "resolved": "https://registry.npmjs.org/pako/-/pako-1.0.11.tgz", - "integrity": "sha512-4hLB8Py4zZce5s4yd9XzopqwVv/yGNhV1Bl8NTmCq1763HeK2+EwVTv+leGeL13Dnh2wfbqowVPXCIO0z4taYw==", - "dev": true + "integrity": "sha512-4hLB8Py4zZce5s4yd9XzopqwVv/yGNhV1Bl8NTmCq1763HeK2+EwVTv+leGeL13Dnh2wfbqowVPXCIO0z4taYw==" }, "node_modules/parent-module": { "version": "1.0.1", @@ -7086,6 +7209,31 @@ "node": "*" } }, + "node_modules/pdf-parse": { 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"sha512-D9cPgkvLlV3t3IzL0D0YLvGA9Ahk4PcvVwUbN0dSGr1aP0Nrt4AEnTUbuGvquEC0mA64Gqt1fzirlRs5ibXx8g==" }, "ssh2": { "version": "1.11.0", @@ -15913,6 +16211,11 @@ "which-boxed-primitive": "^1.0.2" } }, + "underscore": { + "version": "1.13.7", + "resolved": "https://registry.npmjs.org/underscore/-/underscore-1.13.7.tgz", + "integrity": "sha512-GMXzWtsc57XAtguZgaQViUOzs0KTkk8ojr3/xAxXLITqf/3EMwxC0inyETfDFjH/Krbhuep0HNbbjI9i/q3F3g==" + }, "unique-string": { "version": "1.0.0", "resolved": "https://registry.npmjs.org/unique-string/-/unique-string-1.0.0.tgz", diff --git a/package.json b/package.json index d382afad..4c548d6d 100644 --- a/package.json +++ b/package.json @@ -34,12 +34,14 @@ "express-winston": "^3.0.1", "gunzip-stream": "^1.0.1", "keyword-extractor": "0.0.20", + "mammoth": "^1.8.0", "mkdirp": "^3.0.1", "mongoose": "^6.3.2", "morgan": "^1.10.0", "multer": "^1.4.5-lts.1", "nocache": "^2.0.0", "nodemailer": "^6.7.5", + "pdf-parse": "^1.1.1", "pkgcloud": "^2.2.0", "redis": "^4.2", "request": "^2.88.2", diff --git a/ui/src/modals/ezgovimporter.vue b/ui/src/modals/ezgovimporter.vue new file mode 100644 index 00000000..1211a0a0 --- /dev/null +++ b/ui/src/modals/ezgovimporter.vue @@ -0,0 +1,74 @@ + + + diff --git a/ui/src/projectedit.vue b/ui/src/projectedit.vue index 03c79db8..84d9210d 100644 --- a/ui/src/projectedit.vue +++ b/ui/src/projectedit.vue @@ -117,6 +117,9 @@ Brainlife Data Use Agreement - Template + + Import from ezGOV +
@@ -311,6 +314,7 @@ import tageditor from '@/components/tageditor' import datatypes from '@/mixins/datatypes' import { Picker } from 'emoji-mart-vue' import { brainlife_dua } from "@/assets/consents.js"; +import ezgovimporter from '@/modals/ezgovimporter'; const lib = require('@/lib'); @@ -330,6 +334,7 @@ export default { emojimart: Picker, editor: require('vue2-ace-editor'), + ezgovimporter }, data() { @@ -574,6 +579,9 @@ export default { agreement: brainlife_dua, }) }, + handleImportedText(text) { + this.project.agreements.push({ agreement: text }); + } }, }