- added npm package dotenv-webpack for using env variables on clientside
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CI Pipeline / japa-tests (push) Successful in 53s
- added API File Controller for downloading files e.g. /api/download/1022 - also create has codes by submitting new dataset - added edit dataset functionalities for role submitter - added the following route for role submitter: /dataset/:id/update', 'DatasetController.update' - created extra UpdateDatasetValidator.ts for validating updated dataset - npm updates
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23 changed files with 2181 additions and 853 deletions
54
app/Controllers/Http/Api/FileController.ts
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54
app/Controllers/Http/Api/FileController.ts
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@ -0,0 +1,54 @@
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import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
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import File from 'App/Models/File';
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import { StatusCodes } from 'http-status-codes';
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import * as fs from 'fs';
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import * as path from 'path';
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// node ace make:controller Author
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export default class FileController {
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// @Get("download/:id")
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public async findOne({ response, params }: HttpContextContract) {
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const id = params.id;
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const file = await File.findOrFail(id);
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// const file = await File.findOne({
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// where: { id: id },
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// });
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if (file) {
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const filePath = '/storage/app/public/' + file.pathName;
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const ext = path.extname(filePath);
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const fileName = file.label + ext;
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try {
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fs.accessSync(filePath, fs.constants.R_OK); //| fs.constants.W_OK);
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// console.log("can read/write:", path);
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response
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.header('Cache-Control', 'no-cache private')
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.header('Content-Description', 'File Transfer')
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.header('Content-Type', file.mimeType)
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.header('Content-Disposition', 'inline; filename=' + fileName)
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.header('Content-Transfer-Encoding', 'binary')
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.header('Access-Control-Allow-Origin', '*')
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.header('Access-Control-Allow-Methods', 'GET,POST');
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response.status(StatusCodes.OK).download(filePath);
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} catch (err) {
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// console.log("no access:", path);
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response.status(StatusCodes.NOT_FOUND).send({
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message: `File with id ${id} doesn't exist on file server`,
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});
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}
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// res.status(StatusCodes.OK).sendFile(filePath, (err) => {
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// // res.setHeader("Content-Type", "application/json");
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// // res.removeHeader("Content-Disposition");
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// res.status(StatusCodes.NOT_FOUND).send({
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// message: `File with id ${id} doesn't exist on file server`,
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// });
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// });
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} else {
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response.status(StatusCodes.NOT_FOUND).send({
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message: `Cannot find File with id=${id}.`,
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});
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}
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}
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}
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@ -15,6 +15,7 @@ import Database from '@ioc:Adonis/Lucid/Database';
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import { TransactionClientContract } from '@ioc:Adonis/Lucid/Database';
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import Subject from 'App/Models/Subject';
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import CreateDatasetValidator from 'App/Validators/CreateDatasetValidator';
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import UpdateDatasetValidator from 'App/Validators/UpdateDatasetValidator';
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import {
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TitleTypes,
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DescriptionTypes,
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@ -33,8 +34,6 @@ import ClamScan from 'clamscan';
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import { ValidationException } from '@ioc:Adonis/Core/Validator';
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import Drive from '@ioc:Adonis/Core/Drive';
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import { Exception } from '@adonisjs/core/build/standalone';
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// import XmlModel from 'App/Library/XmlModel';
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// import { XMLBuilder } from 'xmlbuilder2/lib/interfaces';
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export default class DatasetController {
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public async index({ auth, request, inertia }: HttpContextContract) {
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@ -355,7 +354,7 @@ export default class DatasetController {
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//store licenses:
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const licenses: number[] = request.input('licenses', []);
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dataset.useTransaction(trx).related('licenses').sync(licenses);
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await dataset.useTransaction(trx).related('licenses').sync(licenses);
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// save authors and contributors
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await this.savePersons(dataset, request.input('authors', []), 'author', trx);
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@ -456,7 +455,7 @@ export default class DatasetController {
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newFile.visibleInOai = true;
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// let path = coverImage.filePath;
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await dataset.useTransaction(trx).related('files').save(newFile);
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// await newFile.createHashValues();
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await newFile.createHashValues(trx);
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}
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}
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@ -682,29 +681,39 @@ export default class DatasetController {
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// throw new GeneralException(trans('exceptions.publish.release.update_error'));
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}
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public async edit({ params, inertia }) {
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const datasetQuery = Dataset.query().where('id', params.id);
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datasetQuery.preload('titles').preload('descriptions').preload('coverage');
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const dataset = await datasetQuery.firstOrFail();
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public async edit({ request, inertia, response }) {
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const id = request.param('id');
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const datasetQuery = Dataset.query().where('id', id);
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datasetQuery
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.preload('titles', (query) => query.orderBy('id', 'asc'))
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.preload('descriptions', (query) => query.orderBy('id', 'asc'))
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.preload('coverage')
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.preload('licenses')
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.preload('authors')
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.preload('contributors')
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.preload('subjects')
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.preload('references')
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.preload('files');
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// await dataset.loadMany([
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// 'licenses',
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// 'authors',
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// 'contributors',
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// 'titles',
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// 'abstracts',
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// 'files',
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// 'coverage',
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// 'subjects',
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// 'references',
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// ]);
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const dataset = await datasetQuery.firstOrFail();
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const validStates = ['inprogress', 'rejected_editor'];
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if (!validStates.includes(dataset.server_state)) {
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// session.flash('errors', 'Invalid server state!');
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return response
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.flash(
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'warning',
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`Invalid server state. Dataset with id ${id} cannot be edited. Datset has server state ${dataset.server_state}.`,
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)
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.redirect()
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.toRoute('dataset.list');
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}
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const titleTypes = Object.entries(TitleTypes)
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// .filter(([value]) => value !== 'Main')
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.filter(([value]) => value !== 'Main')
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.map(([key, value]) => ({ value: key, label: value }));
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const descriptionTypes = Object.entries(DescriptionTypes)
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// .filter(([value]) => value !== 'Abstract')
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.filter(([value]) => value !== 'Abstract')
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.map(([key, value]) => ({ value: key, label: value }));
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const languages = await Language.query().where('active', true).pluck('part1', 'part1');
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@ -724,33 +733,11 @@ export default class DatasetController {
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const currentYear = currentDate.getFullYear();
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const years = Array.from({ length: currentYear - 1990 + 1 }, (_, index) => 1990 + index);
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// const licenses = await License.query()
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// .select('id', 'name_long', 'link_licence')
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// .orderBy('sort_order')
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// .fetch();
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const licenses = await License.query().select('id', 'name_long', 'link_licence').orderBy('sort_order');
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const licenses = await License.query().select('id', 'name_long').where('active', 'true').pluck('name_long', 'id');
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// const userHasRoles = user.roles;
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// const datasetHasLicenses = await dataset.related('licenses').query().pluck('id');
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// const checkeds = dataset.licenses.first().id;
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const keywordTypes = {
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uncontrolled: 'uncontrolled',
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swd: 'swd',
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};
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const referenceTypes = ['DOI', 'Handle', 'ISBN', 'ISSN', 'URL', 'URN'];
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const relationTypes = [
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'IsSupplementTo',
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'IsSupplementedBy',
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'IsContinuedBy',
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'Continues',
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'IsNewVersionOf',
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'IsPartOf',
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'HasPart',
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'Compiles',
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'IsVariantFormOf',
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];
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const doctypes = {
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analysisdata: { label: 'Analysis', value: 'analysisdata' },
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measurementdata: { label: 'Measurements', value: 'measurementdata' },
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@ -771,16 +758,164 @@ export default class DatasetController {
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// messages,
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projects,
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licenses,
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// datasetHasLicenses: Object.keys(datasetHasLicenses).map((key) => datasetHasLicenses[key]), //convert object to array with license ids
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// checkeds,
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years,
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// languages,
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keywordTypes,
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referenceTypes,
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relationTypes,
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subjectTypes: SubjectTypes,
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referenceIdentifierTypes: Object.entries(ReferenceIdentifierTypes).map(([key, value]) => ({ value: key, label: value })),
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relationTypes: Object.entries(RelationTypes).map(([key, value]) => ({ value: key, label: value })),
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doctypes,
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});
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}
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public async update({ request, response, session }: HttpContextContract) {
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try {
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// await request.validate({ schema: newDatasetSchema, messages: this.messages });
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await request.validate(UpdateDatasetValidator);
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} catch (error) {
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// - Handle errors
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// return response.badRequest(error.messages);
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throw error;
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// return response.badRequest(error.messages);
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}
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const id = request.param('id');
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let trx: TransactionClientContract | null = null;
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try {
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trx = await Database.transaction();
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// const user = (await User.find(auth.user?.id)) as User;
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// await this.createDatasetAndAssociations(user, request, trx);
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const dataset = await Dataset.findOrFail(id);
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// save the licenses
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const licenses: number[] = request.input('licenses', []);
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// await dataset.useTransaction(trx).related('licenses').sync(licenses);
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await dataset.useTransaction(trx).related('licenses').sync(licenses);
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// save authors and contributors
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await dataset.useTransaction(trx).related('authors').sync([]);
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await dataset.useTransaction(trx).related('contributors').sync([]);
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await this.savePersons(dataset, request.input('authors', []), 'author', trx);
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await this.savePersons(dataset, request.input('contributors', []), 'contributor', trx);
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//save the titles:
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const titles = request.input('titles', []);
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// const savedTitles:Array<Title> = [];
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for (const titleData of titles) {
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if (titleData.id) {
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const title = await Title.findOrFail(titleData.id);
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title.value = titleData.value;
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title.language = titleData.language;
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title.type = titleData.type;
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if (title.$isDirty) {
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await title.useTransaction(trx).save();
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// await dataset.useTransaction(trx).related('titles').save(title);
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// savedTitles.push(title);
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}
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} else {
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const title = new Title();
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title.fill(titleData);
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// savedTitles.push(title);
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await dataset.useTransaction(trx).related('titles').save(title);
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}
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}
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// save the abstracts
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const descriptions = request.input('descriptions', []);
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// const savedTitles:Array<Title> = [];
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for (const descriptionData of descriptions) {
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if (descriptionData.id) {
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const description = await Description.findOrFail(descriptionData.id);
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description.value = descriptionData.value;
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description.language = descriptionData.language;
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description.type = descriptionData.type;
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if (description.$isDirty) {
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await description.useTransaction(trx).save();
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// await dataset.useTransaction(trx).related('titles').save(title);
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// savedTitles.push(title);
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}
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} else {
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const description = new Description();
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description.fill(descriptionData);
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// savedTitles.push(title);
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await dataset.useTransaction(trx).related('descriptions').save(description);
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}
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}
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// Save already existing files
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const files = request.input('fileInputs', []);
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for (const fileData of files) {
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if (fileData.id) {
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const file = await File.findOrFail(fileData.id);
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file.label = fileData.label;
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file.sortOrder = fileData.sort_order;
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if (file.$isDirty) {
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await file.useTransaction(trx).save();
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}
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}
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}
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// handle new uploaded files:
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const uploadedFiles = request.files('files');
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if (Array.isArray(uploadedFiles) && uploadedFiles.length > 0) {
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// let index = 1;
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// for (const key in files) {
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// const formFile = files[key]
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// for (const fileData of files) {
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for (const [index, fileData] of uploadedFiles.entries()) {
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// const uploads = request.file('uploads');
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// const fileIndex = formFile.file;
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// const file = uploads[fileIndex];
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const fileName = `file-${cuid()}.${fileData.extname}`;
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const mimeType = fileData.headers['content-type'] || 'application/octet-stream'; // Fallback to a default MIME type
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const datasetFolder = `files/${dataset.id}`;
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await fileData.moveToDisk(
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datasetFolder,
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{
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name: fileName,
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overwrite: true, // overwrite in case of conflict
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},
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'local',
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);
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// save file metadata into db
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const newFile = new File();
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newFile.pathName = `${datasetFolder}/${fileName}`;
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newFile.fileSize = fileData.size;
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newFile.mimeType = mimeType;
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newFile.label = fileData.clientName;
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newFile.sortOrder = index;
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newFile.visibleInFrontdoor = true;
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newFile.visibleInOai = true;
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// let path = coverImage.filePath;
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await dataset.useTransaction(trx).related('files').save(newFile);
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await newFile.createHashValues();
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}
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}
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const input = request.only(['project_id', 'embargo_date', 'language', 'type', 'creating_corporation']);
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// dataset.type = request.input('type');
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dataset.merge(input);
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// let test: boolean = dataset.$isDirty;
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await dataset.useTransaction(trx).save();
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await trx.commit();
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console.log('Dataset and related models created successfully');
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} catch (error) {
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if (trx !== null) {
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await trx.rollback();
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}
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console.error('Failed to create dataset and related models:', error);
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// throw new ValidationException(true, { 'upload error': `failed to create dataset and related models. ${error}` });
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throw error;
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}
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session.flash('message', 'Dataset has been created successfully');
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// return response.redirect().toRoute('user.index');
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return response.redirect().back();
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}
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public async delete({ request, inertia, response, session }) {
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const id = request.param('id');
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try {
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