tethys.backend/app/Controllers/Http/Editor/DatasetController.ts

import type { HttpContext } from '@adonisjs/core/http';
import { Client } from '@opensearch-project/opensearch';
import User from '#models/user';
import Dataset from '#models/dataset';
import DatasetIdentifier from '#models/dataset_identifier';
import XmlModel from '#app/Library/XmlModel';
import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
import { create } from 'xmlbuilder2';
import { readFileSync } from 'fs';
import SaxonJS from 'saxon-js';
import { DateTime } from 'luxon';
import Index from '#app/Library/Utils/Index';
import { getDomain } from '#app/utils/utility-functions';
import { DoiClient } from '#app/Library/Doi/DoiClient';
import DoiClientException from '#app/exceptions/DoiClientException';
import logger from '@adonisjs/core/services/logger';
import { HttpException } from 'node-exceptions';
import { ModelQueryBuilderContract } from '@adonisjs/lucid/types/model';
import vine, { SimpleMessagesProvider } from '@vinejs/vine';
import mail from '@adonisjs/mail/services/main';
import { validate } from 'deep-email-validator';
import {
    TitleTypes,
    DescriptionTypes,
    ContributorTypes,
    PersonNameTypes,
    ReferenceIdentifierTypes,
    RelationTypes,
    SubjectTypes,
} from '#contracts/enums';
import { TransactionClientContract } from '@adonisjs/lucid/types/database';
import db from '@adonisjs/lucid/services/db';
import Project from '#models/project';
import License from '#models/license';
import Language from '#models/language';
import File from '#models/file';
import Coverage from '#models/coverage';
import Title from '#models/title';
import Description from '#models/description';
import Subject from '#models/subject';
import DatasetReference from '#models/dataset_reference';
import Collection from '#models/collection';
import CollectionRole from '#models/collection_role';
import { updateEditorDatasetValidator } from '#validators/dataset';
import { savePersons } from '#app/utils/utility-functions';

// Create a new instance of the client
const client = new Client({ node: 'http://localhost:9200' }); // replace with your OpenSearch endpoint

export default class DatasetsController {
    private proc;
    public messages = {
        // 'required': '{{ field }} is required',
        // 'licenses.minLength': 'at least {{ options.minLength }} permission must be defined',
        'reviewer_id.required': 'reviewer_id must be defined',
        'publisher_name.required': 'publisher name must be defined',
    };

    constructor() {
        this.proc = readFileSync('public/assets2/solr.sef.json');
        // Load the XSLT file
        // this.proc = readFileSync('public/assets2/datasetxml2oai.sef.json');
    }

    // public async index({}: HttpContextContract) {}
    public async index({ auth, request, inertia }: HttpContext) {
        const user = (await User.find(auth.user?.id)) as User;
        const page = request.input('page', 1);
        let datasets: ModelQueryBuilderContract<typeof Dataset, Dataset> = Dataset.query();

        // if (request.input('search')) {
        //     // users = users.whereRaw('name like %?%', [request.input('search')])
        //     const searchTerm = request.input('search');
        //     datasets.where('name', 'ilike', `%${searchTerm}%`);
        // }

        if (request.input('sort')) {
            type SortOrder = 'asc' | 'desc' | undefined;
            let attribute = request.input('sort');
            let sortOrder: SortOrder = 'asc';

            if (attribute.substr(0, 1) === '-') {
                sortOrder = 'desc';
                // attribute = substr(attribute, 1);
                attribute = attribute.substr(1);
            }
            datasets.orderBy(attribute, sortOrder);
        } else {
            // users.orderBy('created_at', 'desc');
            datasets.orderBy('id', 'asc');
        }

        // const users = await User.query().orderBy('login').paginate(page, limit);
        const myDatasets = await datasets
            .where('server_state', 'released')
            .orWhere((dQuery) => {
                dQuery
                    .whereIn('server_state', ['editor_accepted', 'rejected_reviewer', 'reviewed', 'published'])
                    .where('editor_id', user.id)
                    .doesntHave('identifier', 'and');
            })
            // .preload('identifier')
            .preload('titles')
            .preload('user', (query) => query.select('id', 'login'))
            .preload('editor', (query) => query.select('id', 'login'))
            .paginate(page, 10);

        return inertia.render('Editor/Dataset/Index', {
            datasets: myDatasets.serialize(),
            filters: request.all(),
            can: {
                receive: await auth.user?.can(['dataset-receive']),
                approve: await auth.user?.can(['dataset-approve']),
                reject: await auth.user?.can(['dataset-editor-reject']),
                edit: await auth.user?.can(['dataset-editor-update']),
                delete: await auth.user?.can(['dataset-editor-delete']),
                publish: await auth.user?.can(['dataset-publish']),
            },
        });
    }

    public async receive({ request, inertia, response }: HttpContext) {
        const id = request.param('id');
        const dataset = await Dataset.query()
            .where('id', id)
            .preload('titles')
            .preload('descriptions')
            .preload('user', (builder) => {
                builder.select('id', 'login');
            })

            .firstOrFail();

        const validStates = ['released'];
        if (!validStates.includes(dataset.server_state)) {
            // session.flash('errors', 'Invalid server state!');
            return response
                .flash(
                    'warning',
                    `Invalid server state. Dataset with id ${id} cannot be received. Datset has server state ${dataset.server_state}.`,
                )
                .redirect()
                .back();
        }

        return inertia.render('Editor/Dataset/Receive', {
            dataset,
        });
    }

    public async receiveUpdate({ auth, request, response }: HttpContext) {
        const id = request.param('id');
        // const { id } = params;
        const dataset = await Dataset.findOrFail(id);

        const validStates = ['released'];
        if (!validStates.includes(dataset.server_state)) {
            // throw new Error('Invalid server state!');
            // return response.flash('warning', 'Invalid server state. Dataset cannot be released to editor').redirect().back();
            return response
                .flash(
                    'warning',
                    `Invalid server state. Dataset with id ${id} cannot be received by editor. Datset has server state ${dataset.server_state}.`,
                )
                .redirect()
                .toRoute('editor.dataset.list');
        }

        dataset.server_state = 'editor_accepted';
        const user = (await User.find(auth.user?.id)) as User;
        // dataset.editor().associate(user).save();
        try {
            await dataset.related('editor').associate(user); // speichert schon ab
            // await dataset.save();
            return response.toRoute('editor.dataset.list').flash(`You have accepted dataset ${dataset.id}!`, 'message');
        } catch (error) {
            // Handle any errors
            console.error(error);
            return response.status(500).json({ error: 'An error occurred while accepting the data.' });
        }
    }

    public async approve({ request, inertia, response }: HttpContext) {
        const id = request.param('id');
        // $dataset = Dataset::with('user:id,login')->findOrFail($id);
        const dataset = await Dataset.findOrFail(id);

        const validStates = ['editor_accepted', 'rejected_reviewer'];
        if (!validStates.includes(dataset.server_state)) {
            // session.flash('errors', 'Invalid server state!');
            return response
                .flash(
                    'warning',
                    `Invalid server state. Dataset with id ${id} cannot be approved. Datset has server state ${dataset.server_state}.`,
                )
                .redirect()
                .back();
        }

        const reviewers = await User.query()
            .whereHas('roles', (builder) => {
                builder.where('name', 'reviewer');
            })
            .pluck('login', 'id');

        return inertia.render('Editor/Dataset/Approve', {
            dataset,
            reviewers,
        });
    }

    public async approveUpdate({ request, response }: HttpContext) {
        const approveDatasetSchema = vine.object({
            reviewer_id: vine.number(),
        });
        try {
            // await request.validate({ schema: approveDatasetSchema, messages: this.messages });
            const validator = vine.compile(approveDatasetSchema);
            await request.validateUsing(validator, { messagesProvider: new SimpleMessagesProvider(this.messages) });
        } catch (error) {
            // return response.badRequest(error.messages);
            throw error;
        }
        const id = request.param('id');
        const dataset = await Dataset.findOrFail(id);

        const validStates = ['editor_accepted', 'rejected_reviewer'];
        if (!validStates.includes(dataset.server_state)) {
            // session.flash('errors', 'Invalid server state!');
            return response
                .flash(
                    'warning',
                    `Invalid server state. Dataset with id ${id} cannot be approved. Datset has server state ${dataset.server_state}.`,
                )
                .redirect()
                .back();
        }

        dataset.server_state = 'approved';
        if (dataset.reject_reviewer_note != null) {
            dataset.reject_reviewer_note = null;
        }

        //save main and additional titles
        const reviewer_id = request.input('reviewer_id', null);
        dataset.reviewer_id = reviewer_id;

        if (await dataset.save()) {
            return response.toRoute('editor.dataset.list').flash('message', 'You have approved one dataset!');
        }
    }

    public async reject({ request, inertia, response }: HttpContext) {
        const id = request.param('id');
        const dataset = await Dataset.query()
            .where('id', id)
            // .preload('titles')
            // .preload('descriptions')
            .preload('user', (builder) => {
                builder.select('id', 'login', 'email');
            })
            .firstOrFail();

        const validStates = ['editor_accepted', 'rejected_reviewer'];
        if (!validStates.includes(dataset.server_state)) {
            // session.flash('errors', 'Invalid server state!');
            return response
                .flash(
                    'warning',
                    `Invalid server state. Dataset with id ${id} cannot be rejected. Datset has server state ${dataset.server_state}.`,
                )
                .redirect()
                .toRoute('editor.dataset.list');
        }

        return inertia.render('Editor/Dataset/Reject', {
            dataset,
        });
    }

    public async rejectUpdate({ request, response, auth }: HttpContext) {
        const authUser = auth.user!;

        const id = request.param('id');
        const dataset = await Dataset.query()
            .where('id', id)
            .preload('user', (builder) => {
                builder.select('id', 'login', 'email');
            })
            .firstOrFail();

        const newSchema = vine.object({
            server_state: vine.string().trim(),
            reject_editor_note: vine.string().trim().minLength(10).maxLength(500),
            send_mail: vine.boolean().optional(),
        });

        try {
            // await request.validate({ schema: newSchema });
            const validator = vine.compile(newSchema);
            await request.validateUsing(validator);
        } catch (error) {
            // return response.badRequest(error.messages);
            throw error;
        }

        const validStates = ['editor_accepted', 'rejected_reviewer'];
        if (!validStates.includes(dataset.server_state)) {
            // throw new Error('Invalid server state!');
            // return response.flash('warning', 'Invalid server state. Dataset cannot be released to editor').redirect().back();
            return response
                .flash(
                    `Invalid server state. Dataset with id ${id} cannot be rejected. Datset has server state ${dataset.server_state}.`,
                    'warning',
                )
                .redirect()
                .toRoute('editor.dataset.list');
        }

        dataset.server_state = 'rejected_editor';
        const rejectEditorNote = request.input('reject_editor_note', '');
        dataset.reject_editor_note = rejectEditorNote;

        // add logic for sending reject message
        const sendMail = request.input('send_email', false);
        // const validRecipientEmail = await this.checkEmailDomain('arno.kaimbacher@outlook.at');
        const validationResult = await validate({
            email: dataset.user.email,
            validateSMTP: false,
        });
        const validRecipientEmail: boolean = validationResult.valid;

        let emailStatusMessage = '';

        if (sendMail == true) {
            if (dataset.user.email && validRecipientEmail) {
                try {
                    await mail.send((message) => {
                        message.to(dataset.user.email).subject('Dataset Rejection Notification').html(`
                            <p>Dear ${dataset.user.login},</p>
                            <p>Your dataset with ID ${dataset.id} has been rejected.</p>
                            <p>Reason for rejection: ${rejectEditorNote}</p>
                            <p>Best regards,<br>Your Tethys editor: ${authUser.login}</p>
                        `);
                    });
                    emailStatusMessage = ` A rejection email was successfully sent to ${dataset.user.email}.`;
                } catch (error) {
                    logger.error(error);
                    return response
                        .flash('Dataset has not been rejected due to an email error: ' + error.message, 'error')
                        .toRoute('editor.dataset.list');
                }
            } else {
                emailStatusMessage = ` However, the email could not be sent because the submitter's email address (${dataset.user.email}) is not valid.`;
            }
        }

        await dataset.save();
        return response
            .flash(
                `You have successfully rejected dataset ${dataset.id} submitted by ${dataset.user.login}.${emailStatusMessage}`,
                'message',
            )
            .toRoute('editor.dataset.list');
    }

    public async publish({ request, inertia, response }: HttpContext) {
        const id = request.param('id');

        const dataset = await Dataset.query()
            .where('id', id)
            .preload('titles')
            .preload('authors')
            // .preload('persons', (builder) => {
            //    builder.wherePivot('role', 'author')
            //  })
            .firstOrFail();

        const validStates = ['reviewed'];
        if (!validStates.includes(dataset.server_state)) {
            // session.flash('errors', 'Invalid server state!');
            return response
                .flash(
                    'warning',
                    `Invalid server state. Dataset with id ${id} cannot be published. Datset has server state ${dataset.server_state}.`,
                )
                .redirect()
                .back();
        }

        return inertia.render('Editor/Dataset/Publish', {
            dataset,
        });
    }

    public async publishUpdate({ request, response }: HttpContext) {
        const publishDatasetSchema = vine.object({
            publisher_name: vine.string().trim(),
        });
        try {
            // await request.validate({ schema: publishDatasetSchema, messages: this.messages });
            const validator = vine.compile(publishDatasetSchema);
            await request.validateUsing(validator, { messagesProvider: new SimpleMessagesProvider(this.messages) });
        } catch (error) {
            throw error;
        }
        const id = request.param('id');
        const dataset = await Dataset.findOrFail(id);

        // let test = await Dataset.getMax('publish_id');
        // const maxPublishId = await Database.from('documents').max('publish_id as max_publish_id').first();
        // const max = maxPublishId.max_publish_id;
        const max = await Dataset.getMax('publish_id');
        let publish_id = 0;
        if (max != null) {
            publish_id = max + 1;
        } else {
            publish_id = publish_id + 1;
        }
        dataset.publish_id = publish_id;
        dataset.server_state = 'published';
        dataset.server_date_published = DateTime.now();

        const publisherName = request.input('publisher_name', 'Tethys');
        dataset.publisher_name = publisherName;

        if (await dataset.save()) {
            const index_name = 'tethys-records';
            await Index.indexDocument(dataset, index_name);
            return response.toRoute('editor.dataset.list').flash('message', 'You have successfully published the dataset!');
        }
    }

    public async doiCreate({ request, inertia }: HttpContext) {
        const id = request.param('id');
        const dataset = await Dataset.query()
            .where('id', id)
            .preload('titles')
            .preload('descriptions')
            // .preload('identifier')
            .preload('authors')
            .firstOrFail();
        return inertia.render('Editor/Dataset/Doi', {
            dataset,
        });
    }

    public async doiStore({ request, response }: HttpContext) {
        const dataId = request.param('publish_id');
        const dataset = await Dataset.query()
            // .preload('xmlCache')
            .where('publish_id', dataId)
            .firstOrFail();
        const xmlMeta = (await Index.getDoiRegisterString(dataset)) as string;

        let prefix = '';
        let base_domain = '';
        // const datacite_environment = process.env.DATACITE_ENVIRONMENT || 'debug';
        prefix = process.env.DATACITE_PREFIX || '';
        base_domain = process.env.BASE_DOMAIN || '';

        // register DOI:
        const doiValue = prefix + '/tethys.' + dataset.publish_id; //'10.21388/tethys.213'
        const landingPageUrl = 'https://doi.' + getDomain(base_domain) + '/' + prefix + '/tethys.' + dataset.publish_id; //https://doi.dev.tethys.at/10.21388/tethys.213
        const doiClient = new DoiClient();
        const dataciteResponse = await doiClient.registerDoi(doiValue, xmlMeta, landingPageUrl);

        if (dataciteResponse?.status === 201) {
            // if response OK 201; save the Identifier value into db
            const doiIdentifier = new DatasetIdentifier();
            doiIdentifier.value = doiValue;
            doiIdentifier.dataset_id = dataset.id;
            doiIdentifier.type = 'doi';
            doiIdentifier.status = 'findable';
            // save modified date of datset for re-caching model in db an update the search index
            dataset.server_date_modified = DateTime.now();

            // save updated dataset to db an index to OpenSearch
            try {
                await dataset.related('identifier').save(doiIdentifier);
                const index_name = 'tethys-records';
                await Index.indexDocument(dataset, index_name);
            } catch (error) {
                logger.error(`${__filename}: Indexing document ${dataset.id} failed: ${error.message}`);
                // Log the error or handle it as needed
                throw new HttpException(error.message);
            }
            return response.toRoute('editor.dataset.list').flash('message', 'You have successfully created a DOI for the dataset!');
        } else {
            const message = `Unexpected DataCite MDS response code ${dataciteResponse?.status}`;
            // Log the error or handle it as needed
            throw new DoiClientException(dataciteResponse?.status, message);
        }
        // return response.toRoute('editor.dataset.list').flash('message', xmlMeta);
    }

    public async show({}: HttpContext) {}

    public async edit({ request, inertia, response }: HttpContext) {
        const id = request.param('id');
        const datasetQuery = Dataset.query().where('id', id);
        datasetQuery
            .preload('titles', (query) => query.orderBy('id', 'asc'))
            .preload('descriptions', (query) => query.orderBy('id', 'asc'))
            .preload('coverage')
            .preload('licenses')
            .preload('authors')
            .preload('contributors')
            // .preload('subjects')
            .preload('subjects', (builder) => {
                builder.orderBy('id', 'asc').withCount('datasets');
            })
            .preload('references')
            .preload('files', (query) => {
                query.orderBy('sort_order', 'asc'); // Sort by sort_order column
            });

        const dataset = await datasetQuery.firstOrFail();
        const validStates = ['editor_accepted', 'rejected_reviewer'];
        if (!validStates.includes(dataset.server_state)) {
            // session.flash('errors', 'Invalid server state!');
            return response
                .flash(
                    `Invalid server state. Dataset with id ${id} cannot be edited. Datset has server state ${dataset.server_state}.`,
                    'warning',
                )
                .toRoute('editor.dataset.list');
        }

        const titleTypes = Object.entries(TitleTypes)
            .filter(([value]) => value !== 'Main')
            .map(([key, value]) => ({ value: key, label: value }));

        const descriptionTypes = Object.entries(DescriptionTypes)
            .filter(([value]) => value !== 'Abstract')
            .map(([key, value]) => ({ value: key, label: value }));

        const languages = await Language.query().where('active', true).pluck('part1', 'part1');

        // const contributorTypes = Config.get('enums.contributor_types');
        const contributorTypes = Object.entries(ContributorTypes).map(([key, value]) => ({ value: key, label: value }));

        // const nameTypes = Config.get('enums.name_types');
        const nameTypes = Object.entries(PersonNameTypes).map(([key, value]) => ({ value: key, label: value }));

        // const messages = await Database.table('messages')
        //   .pluck('help_text', 'metadata_element');

        const projects = await Project.query().pluck('label', 'id');

        const currentDate = new Date();
        const currentYear = currentDate.getFullYear();
        const years = Array.from({ length: currentYear - 1990 + 1 }, (_, index) => 1990 + index);

        const licenses = await License.query().select('id', 'name_long').where('active', 'true').pluck('name_long', 'id');
        // const userHasRoles = user.roles;
        // const datasetHasLicenses = await dataset.related('licenses').query().pluck('id');
        // const checkeds = dataset.licenses.first().id;

        const doctypes = {
            analysisdata: { label: 'Analysis', value: 'analysisdata' },
            measurementdata: { label: 'Measurements', value: 'measurementdata' },
            monitoring: 'Monitoring',
            remotesensing: 'Remote Sensing',
            gis: 'GIS',
            models: 'Models',
            mixedtype: 'Mixed Type',
        };

        return inertia.render('Editor/Dataset/Edit', {
            dataset,
            titletypes: titleTypes,
            descriptiontypes: descriptionTypes,
            contributorTypes,
            nameTypes,
            languages,
            // messages,
            projects,
            licenses,
            // datasetHasLicenses: Object.keys(datasetHasLicenses).map((key) => datasetHasLicenses[key]), //convert object to array with license ids
            // checkeds,
            years,
            // languages,
            subjectTypes: SubjectTypes,
            referenceIdentifierTypes: Object.entries(ReferenceIdentifierTypes).map(([key, value]) => ({ value: key, label: value })),
            relationTypes: Object.entries(RelationTypes).map(([key, value]) => ({ value: key, label: value })),
            doctypes,
        });
    }

    public async update({ request, response, session }: HttpContext) {
        // Get the dataset id from the route parameter
        const datasetId = request.param('id');
        // Retrieve the dataset and load its existing files
        const dataset = await Dataset.findOrFail(datasetId);
        await dataset.load('files');

        let trx: TransactionClientContract | null = null;
        try {
            await request.validateUsing(updateEditorDatasetValidator);
            trx = await db.transaction();
            // const user = (await User.find(auth.user?.id)) as User;
            // await this.createDatasetAndAssociations(user, request, trx);
            const dataset = await Dataset.findOrFail(datasetId);

            // save the licenses
            const licenses: number[] = request.input('licenses', []);
            // await dataset.useTransaction(trx).related('licenses').sync(licenses);
            await dataset.useTransaction(trx).related('licenses').sync(licenses);

            // save authors and contributors
            await dataset.useTransaction(trx).related('authors').sync([]);
            await dataset.useTransaction(trx).related('contributors').sync([]);
            await savePersons(dataset, request.input('authors', []), 'author', trx);
            await savePersons(dataset, request.input('contributors', []), 'contributor', trx);

            //save the titles:
            const titles = request.input('titles', []);
            // const savedTitles:Array<Title> = [];
            for (const titleData of titles) {
                if (titleData.id) {
                    const title = await Title.findOrFail(titleData.id);
                    title.value = titleData.value;
                    title.language = titleData.language;
                    title.type = titleData.type;
                    if (title.$isDirty) {
                        await title.useTransaction(trx).save();
                        // await dataset.useTransaction(trx).related('titles').save(title);
                        // savedTitles.push(title);
                    }
                } else {
                    const title = new Title();
                    title.fill(titleData);
                    // savedTitles.push(title);
                    await dataset.useTransaction(trx).related('titles').save(title);
                }
            }

            // save the abstracts
            const descriptions = request.input('descriptions', []);
            // const savedTitles:Array<Title> = [];
            for (const descriptionData of descriptions) {
                if (descriptionData.id) {
                    const description = await Description.findOrFail(descriptionData.id);
                    description.value = descriptionData.value;
                    description.language = descriptionData.language;
                    description.type = descriptionData.type;
                    if (description.$isDirty) {
                        await description.useTransaction(trx).save();
                        // await dataset.useTransaction(trx).related('titles').save(title);
                        // savedTitles.push(title);
                    }
                } else {
                    const description = new Description();
                    description.fill(descriptionData);
                    // savedTitles.push(title);
                    await dataset.useTransaction(trx).related('descriptions').save(description);
                }
            }

            // Process all subjects/keywords from the request
            const subjects = request.input('subjects');
            for (const subjectData of subjects) {
                // Case 1: Subject already exists in the database (has an ID)
                if (subjectData.id) {
                    // Retrieve the existing subject
                    const existingSubject = await Subject.findOrFail(subjectData.id);

                    // Update subject properties from the request data
                    existingSubject.value = subjectData.value;
                    existingSubject.type = subjectData.type;
                    existingSubject.external_key = subjectData.external_key;

                    // Only save if there are actual changes
                    if (existingSubject.$isDirty) {
                        await existingSubject.save();
                    }

                    // Note: The relationship between dataset and subject is already established,
                    // so we don't need to attach it again
                }
                // Case 2: New subject being added (no ID)
                else {
                    // Check if a subject with the same value and type already exists in the database
                    const subject = await Subject.firstOrNew({ value: subjectData.value, type: subjectData.type }, subjectData);

                    if (subject.$isNew === true) {
                        // If it's a completely new subject, create and associate it with the dataset
                        await dataset.useTransaction(trx).related('subjects').save(subject);
                    } else {
                        // If the subject already exists, just create the relationship
                        await dataset.useTransaction(trx).related('subjects').attach([subject.id]);
                    }
                }
            }

            const subjectsToDelete = request.input('subjectsToDelete', []);
            for (const subjectData of subjectsToDelete) {
                if (subjectData.id) {
                    // const subject = await Subject.findOrFail(subjectData.id);
                    const subject = await Subject.query()
                        .where('id', subjectData.id)
                        .preload('datasets', (builder) => {
                            builder.orderBy('id', 'asc');
                        })
                        .withCount('datasets')
                        .firstOrFail();

                    // Check if the subject is used by multiple datasets
                    if (subject.$extras.datasets_count > 1) {
                        // If used by multiple datasets, just detach it from the current dataset
                        await dataset.useTransaction(trx).related('subjects').detach([subject.id]);
                    } else {
                        // If only used by this dataset, delete the subject completely

                        await dataset.useTransaction(trx).related('subjects').detach([subject.id]);
                        await subject.useTransaction(trx).delete();
                    }
                }
            }

            // Process references
            const references = request.input('references', []);
            // First, get existing references to determine which ones to update vs. create
            const existingReferences = await dataset.related('references').query();
            const existingReferencesMap: Map<number, DatasetReference> = new Map(existingReferences.map((ref) => [ref.id, ref]));

            for (const referenceData of references) {
                if (existingReferencesMap.has(referenceData.id) && referenceData.id) {
                    // Update existing reference
                    const reference = existingReferencesMap.get(referenceData.id);
                    if (reference) {
                        reference.merge(referenceData);
                        if (reference.$isDirty) {
                            await reference.useTransaction(trx).save();
                        }
                    }
                } else {
                    // Create new reference
                    const dataReference = new DatasetReference();
                    dataReference.fill(referenceData);
                    await dataset.useTransaction(trx).related('references').save(dataReference);
                }
            }

            // Handle references to delete if provided
            const referencesToDelete = request.input('referencesToDelete', []);
            for (const referenceData of referencesToDelete) {
                if (referenceData.id) {
                    const reference = await DatasetReference.findOrFail(referenceData.id);
                    await reference.useTransaction(trx).delete();
                }
            }

            // save coverage
            const coverageData = request.input('coverage');
            if (coverageData) {
                if (coverageData.id) {
                    const coverage = await Coverage.findOrFail(coverageData.id);
                    coverage.merge(coverageData);
                    if (coverage.$isDirty) {
                        await coverage.useTransaction(trx).save();
                    }
                }
            }

            const input = request.only(['project_id', 'embargo_date', 'language', 'type', 'creating_corporation']);
            // dataset.type = request.input('type');
            dataset.merge(input);
            // let test: boolean = dataset.$isDirty;
            await dataset.useTransaction(trx).save();

            await trx.commit();
            // console.log('Dataset has been updated successfully');

            session.flash('message', 'Dataset has been updated successfully');
            // return response.redirect().toRoute('user.index');
            return response.redirect().toRoute('editor.dataset.edit', [dataset.id]);
        } catch (error) {
            if (trx !== null) {
                await trx.rollback();
            }
            console.error('Failed to update dataset and related models:', error);
            // throw new ValidationException(true, { 'upload error': `failed to create dataset and related models. ${error}` });
            throw error;
        }
    }

    public async categorize({ inertia, request, response }: HttpContext) {
        const id = request.param('id');
        // Preload dataset and its "collections" relation
        const dataset = await Dataset.query().where('id', id).preload('collections').firstOrFail();
        const validStates = ['editor_accepted', 'rejected_reviewer'];
        if (!validStates.includes(dataset.server_state)) {
            // session.flash('errors', 'Invalid server state!');
            return response
                .flash(
                    'warning',
                    `Invalid server state. Dataset with id ${id} cannot be edited. Datset has server state ${dataset.server_state}.`,
                )
                .redirect()
                .toRoute('editor.dataset.list');
        }

        const collectionRoles = await CollectionRole.query()
            .preload('collections', (coll: Collection) => {
                // preloa only top level collection with noparent_id
                coll.whereNull('parent_id').orderBy('number', 'asc');
            })
            .exec();

        return inertia.render('Editor/Dataset/Category', {
            collectionRoles: collectionRoles,
            dataset: dataset,
            relatedCollections: dataset.collections,
        });
    }

    public async categorizeUpdate({ request, response, session }: HttpContext) {
        // Get the dataset id from the route parameter
        const id = request.param('id');
        const dataset = await Dataset.query().preload('files').where('id', id).firstOrFail();

        const validStates = ['editor_accepted', 'rejected_reviewer'];
        if (!validStates.includes(dataset.server_state)) {
            return response
                .flash(
                    'warning',
                    `Invalid server state. Dataset with id ${id} cannot be categorized. Dataset has server state ${dataset.server_state}.`,
                )
                .redirect()
                .toRoute('editor.dataset.list');
        }

        let trx: TransactionClientContract | null = null;
        try {
            trx = await db.transaction();
            // const user = (await User.find(auth.user?.id)) as User;
            // await this.createDatasetAndAssociations(user, request, trx);

            // Retrieve the selected collections from the request.
            // This should be an array of collection ids.
            const collections: number[] = request.input('collections', []);

            // Synchronize the dataset collections using the transaction.
            await dataset.useTransaction(trx).related('collections').sync(collections);

            // Commit the transaction.await trx.commit()
            await trx.commit();

            // Redirect with a success flash message.
            // return response.flash('success', 'Dataset collections updated successfully!').redirect().toRoute('dataset.list');

            session.flash('message', 'Dataset collections updated successfully!');
            return response.redirect().toRoute('editor.dataset.list');
        } catch (error) {
            if (trx !== null) {
                await trx.rollback();
            }
            console.error('Failed tocatgorize dataset collections:', error);
            // throw new ValidationException(true, { 'upload error': `failed to create dataset and related models. ${error}` });
            throw error;
        }
    }

    // public async update({}: HttpContextContract) {}
    public async updateOpensearch({ response }: HttpContext) {
        const id = 273; //request.param('id');
        const dataset = await Dataset.query().preload('xmlCache').where('id', id).firstOrFail();
        // add xml elements
        let xml = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, '<root></root>');
        const datasetNode = xml.root().ele('Dataset');
        await this.createXmlRecord(dataset, datasetNode);
        // const domNode = await this.getDatasetXmlDomNode(dataset);
        // const xmlString = xml.end({ prettyPrint: true });

        // const data = request.only(['field1', 'field2']); // get it from xslt

        // Create an index with non-default settings.
        var index_name = 'tethys-features';

        const xmlString = xml.end({ prettyPrint: false });
        let doc = '';
        try {
            const result = await SaxonJS.transform({
                // stylesheetFileName: `${config.TMP_BASE_DIR}/data-quality/rules/iati.sef.json`,
                stylesheetText: this.proc,
                destination: 'serialized',
                // sourceFileName: sourceFile,
                sourceText: xmlString,
                // stylesheetParams: xsltParameter,
                // logLevel: 10,
            });
            doc = result.principalResult;
        } catch (error) {
            return response.status(500).json({
                message: 'An error occurred while creating the user',
                error: error.message,
            });
        }

        // var settings = {
        //     settings: {
        //         index: {
        //             number_of_shards: 4,
        //             number_of_replicas: 3,
        //         },
        //     },
        // };
        // var test = await client.indices.create({
        //     index: index_name,
        //     body: settings,
        // });

        // var document = {
        //     title: 'Sample Document',
        //     authors: [
        //         {
        //             first_name: 'John',
        //             last_name: 'Doe',
        //         },
        //         {
        //             first_name: 'Jane',
        //             last_name: 'Smith',
        //         },
        //     ],
        //     year: '2018',
        //     genre: 'Crime fiction',
        // };

        // http://localhost:9200/datastets/_doc/1

        // var id = '1';

        try {
            // console.log(doc);
            let document = JSON.parse(`${doc}`);

            // https://opensearch.org/docs/2.1/opensearch/supported-field-types/geo-shape/
            // Define the new document
            // const document = {
            //     title: 'Your Document Name',
            //     id: dataset.publish_id,
            //     doctype: 'GIS',
            //     // "location" : {
            //     //     "type" : "point",
            //     //     "coordinates" : [74.00, 40.71]
            //     //   },
            //     geo_location: {
            //         type: 'linestring',
            //         coordinates: [
            //             [-77.03653, 38.897676],
            //             [-77.009051, 38.889939],
            //         ],
            //     },
            //     // geo_location: 'BBOX (71.0589, 74.0060, 42.3601, 40.7128)'
            //     // geo_location: {
            //     //     type: 'envelope',
            //     //     coordinates: [
            //     //         [13.0, 53.0],
            //     //         [14.0, 52.0],
            //     //     ], // Define your BBOX coordinates
            //     // },
            // };

            // Update the document
            var test = await client.index({
                id: dataset.publish_id?.toString(),
                index: index_name,
                body: document,
                refresh: true,
            });

            // Return the result
            return response.json(test.body);
        } catch (error) {
            // Handle any errors
            console.error(error);
            return response.status(500).json({ error: 'An error occurred while updating the data.' });
        }
    }

    public async download({ params, response }: HttpContext) {
        const id = params.id;
        // Find the file by ID
        const file = await File.findOrFail(id);
        // const filePath =  await drive.use('local').getUrl('/'+ file.filePath)
        const filePath = file.filePath;
        const fileExt = file.filePath.split('.').pop() || '';
        // Set the response headers and download the file
        response.header('Content-Type', file.mime_type || 'application/octet-stream');
        response.attachment(`${file.label}.${fileExt}`);
        return response.download(filePath);
    }

    public async destroy({}: HttpContext) {}

    private async createXmlRecord(dataset: Dataset, datasetNode: XMLBuilder) {
        const domNode = await this.getDatasetXmlDomNode(dataset);
        if (domNode) {
            datasetNode.import(domNode);
        }
    }

    private async getDatasetXmlDomNode(dataset: Dataset) {
        const xmlModel = new XmlModel(dataset);
        // xmlModel.setModel(dataset);
        xmlModel.excludeEmptyFields();
        xmlModel.caching = true;
        // const cache = dataset.xmlCache ? dataset.xmlCache : null;
        // dataset.load('xmlCache');
        if (dataset.xmlCache) {
            xmlModel.xmlCache = dataset.xmlCache;
        }

        // return cache.getDomDocument();
        const domDocument: XMLBuilder | null = await xmlModel.getDomDocument();
        return domDocument;
    }
}