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

import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
import User from 'App/Models/User';
import Dataset from 'App/Models/Dataset';
import License from 'App/Models/License';
import Project from 'App/Models/Project';
import Title from 'App/Models/Title';
import Description from 'App/Models/Description';
import Language from 'App/Models/Language';
import Coverage from 'App/Models/Coverage';
import Collection from 'App/Models/Collection';
import { schema, CustomMessages, rules } from '@ioc:Adonis/Core/Validator';
import dayjs from 'dayjs';
import Person from 'App/Models/Person';
import Database from '@ioc:Adonis/Lucid/Database';
import { TransactionClientContract } from '@ioc:Adonis/Lucid/Database';
import Subject from 'App/Models/Subject';
import CreateDatasetValidator from 'App/Validators/CreateDatasetValidator';
import UpdateDatasetValidator from 'App/Validators/UpdateDatasetValidator';
import {
    TitleTypes,
    DescriptionTypes,
    ContributorTypes,
    PersonNameTypes,
    ReferenceIdentifierTypes,
    RelationTypes,
    DatasetTypes,
    SubjectTypes,
} from 'Contracts/enums';
import type { ModelQueryBuilderContract } from '@ioc:Adonis/Lucid/Orm';
import DatasetReference from 'App/Models/DatasetReference';
import { cuid } from '@ioc:Adonis/Core/Helpers';
import File from 'App/Models/File';
import ClamScan from 'clamscan';
import { ValidationException } from '@ioc:Adonis/Core/Validator';
import Drive from '@ioc:Adonis/Core/Drive';
import { Exception } from '@adonisjs/core/build/standalone';
import { MultipartFileContract } from '@ioc:Adonis/Core/BodyParser';

export default class DatasetController {
    public async index({ auth, request, inertia }: HttpContextContract) {
        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 results = await Database
        // .query()
        // .select(Database.raw("CONCAT('https://doi.org/', b.value) AS concatenated_value"))
        // .from('documents as doc')
        // .innerJoin('dataset_identifiers as b', 'doc.id', 'b.dataset_id')
        // .groupBy('a.id').toQuery();

        // const users = await User.query().orderBy('login').paginate(page, limit);
        const myDatasets = await datasets
            .whereIn('server_state', [
                'inprogress',
                'released',
                'editor_accepted',
                'approved',
                'reviewed',
                'rejected_editor',
                'rejected_reviewer',
            ])
            .where('account_id', user.id)
            .preload('titles')
            .preload('user', (query) => query.select('id', 'login'))
            // .preload('titles', (builder) => {
            //     // pull the actual preload data

            //     builder.where('type', 'Main');
            // })
            .paginate(page, 10);

        return inertia.render('Submitter/Dataset/Index', {
            // testing: 'this is a test',
            datasets: myDatasets.serialize(),
            filters: request.all(),
            can: {
                // create: await auth.user?.can(['dataset-submit']),
                edit: await auth.user?.can(['dataset-edit']),
                delete: await auth.user?.can(['dataset-delete']),
            },
        });
    }

    public async create({ inertia }: HttpContextContract) {
        const licenses = await License.query().select('id', 'name_long').where('active', 'true').pluck('name_long', 'id');

        const projects = await Project.query().pluck('label', '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',
        //     vocabulary: 'Vocabulary',
        // };

        // const languages = await Database.from('languages').select('*').where('active', true);
        return inertia.render('Submitter/Dataset/Create', {
            licenses: licenses,
            doctypes: DatasetTypes,
            titletypes: Object.entries(TitleTypes)
                .filter(([value]) => value !== 'Main')
                .map(([key, value]) => ({ value: key, label: value })),
            descriptiontypes: Object.entries(DescriptionTypes)
                .filter(([value]) => value !== 'Abstract')
                .map(([key, value]) => ({ value: key, label: value })),
            // descriptiontypes: DescriptionTypes
            projects: projects,
            referenceIdentifierTypes: Object.entries(ReferenceIdentifierTypes).map(([key, value]) => ({ value: key, label: value })),
            relationTypes: Object.entries(RelationTypes).map(([key, value]) => ({ value: key, label: value })),
            contributorTypes: ContributorTypes,
            subjectTypes: SubjectTypes,
        });
    }

    public async firstStep({ request, response }: HttpContextContract) {
        const newDatasetSchema = schema.create({
            language: schema.string({ trim: true }, [
                rules.regex(/^[a-zA-Z0-9-_]+$/), //Must be alphanumeric with hyphens or underscores
            ]),
            licenses: schema.array([rules.minLength(1)]).members(schema.number()), // define at least one license for the new dataset
            rights: schema.string([rules.equalTo('true')]),
        });

        try {
            //  Step 2 - Validate request body against  the schema

            await request.validate({ schema: newDatasetSchema, messages: this.messages });
            // console.log({ payload });
        } catch (error) {
            // Step 3 - Handle errors
            // return response.badRequest(error.messages);
            throw error;
        }
        return response.redirect().back();
    }

    public async secondStep({ request, response }: HttpContextContract) {
        const newDatasetSchema = schema.create({
            // first step
            language: schema.string({ trim: true }, [
                rules.regex(/^[a-zA-Z0-9-_]+$/), //Must be alphanumeric with hyphens or underscores
            ]),
            licenses: schema.array([rules.minLength(1)]).members(schema.number()), // define at least one license for the new dataset
            rights: schema.string([rules.equalTo('true')]),
            // second step
            type: schema.string({ trim: true }, [rules.minLength(3), rules.maxLength(255)]),
            creating_corporation: schema.string({ trim: true }, [rules.minLength(3), rules.maxLength(255)]),
            titles: schema.array([rules.minLength(1)]).members(
                schema.object().members({
                    value: schema.string({ trim: true }, [rules.minLength(3), rules.maxLength(255)]),
                    type: schema.enum(Object.values(TitleTypes)),
                    language: schema.string({ trim: true }, [
                        rules.minLength(2),
                        rules.maxLength(255),
                        rules.translatedLanguage('/language', 'type'),
                    ]),
                }),
            ),
            descriptions: schema.array([rules.minLength(1)]).members(
                schema.object().members({
                    value: schema.string({ trim: true }, [rules.minLength(3), rules.maxLength(255)]),
                    type: schema.enum(Object.values(DescriptionTypes)),
                    language: schema.string({ trim: true }, [
                        rules.minLength(2),
                        rules.maxLength(255),
                        rules.translatedLanguage('/language', 'type'),
                    ]),
                }),
            ),
            authors: schema.array([rules.minLength(1)]).members(schema.object().members({ email: schema.string({ trim: true }) })),
            contributors: schema.array.optional().members(
                schema.object().members({
                    email: schema.string({ trim: true }),
                    pivot_contributor_type: schema.enum(Object.keys(ContributorTypes)),
                }),
            ),
            // project_id: schema.number(),
        });

        try {
            //  Step 2 - Validate request body against  the schema
            await request.validate({ schema: newDatasetSchema, messages: this.messages });
            // console.log({ payload });
        } catch (error) {
            // Step 3 - Handle errors
            // return response.badRequest(error.messages);
            throw error;
        }
        return response.redirect().back();
    }

    public async thirdStep({ request, response }: HttpContextContract) {
        const newDatasetSchema = schema.create({
            // first step
            language: schema.string({ trim: true }, [
                rules.regex(/^[a-zA-Z0-9-_]+$/), //Must be alphanumeric with hyphens or underscores
            ]),
            licenses: schema.array([rules.minLength(1)]).members(schema.number()), // define at least one license for the new dataset
            rights: schema.string([rules.equalTo('true')]),
            // second step
            type: schema.string({ trim: true }, [rules.minLength(3), rules.maxLength(255)]),
            creating_corporation: schema.string({ trim: true }, [rules.minLength(3), rules.maxLength(255)]),
            titles: schema.array([rules.minLength(1)]).members(
                schema.object().members({
                    value: schema.string({ trim: true }, [rules.minLength(3), rules.maxLength(255)]),
                    type: schema.enum(Object.values(TitleTypes)),
                    language: schema.string({ trim: true }, [
                        rules.minLength(2),
                        rules.maxLength(255),
                        rules.translatedLanguage('/language', 'type'),
                    ]),
                }),
            ),
            descriptions: schema.array([rules.minLength(1)]).members(
                schema.object().members({
                    value: schema.string({ trim: true }, [rules.minLength(3), rules.maxLength(255)]),
                    type: schema.enum(Object.values(DescriptionTypes)),
                    language: schema.string({ trim: true }, [
                        rules.minLength(2),
                        rules.maxLength(255),
                        rules.translatedLanguage('/language', 'type'),
                    ]),
                }),
            ),
            authors: schema.array([rules.minLength(1)]).members(schema.object().members({ email: schema.string({ trim: true }) })),
            contributors: schema.array.optional().members(
                schema.object().members({
                    email: schema.string({ trim: true }),
                    pivot_contributor_type: schema.enum(Object.keys(ContributorTypes)),
                }),
            ),
            // third step
            project_id: schema.number.optional(),
            embargo_date: schema.date.optional({ format: 'yyyy-MM-dd' }, [rules.after(10, 'days')]),
            coverage: schema.object().members({
                x_min: schema.number(),
                x_max: schema.number(),
                y_min: schema.number(),
                y_max: schema.number(),
                elevation_absolut: schema.number.optional(),
                elevation_min: schema.number.optional([rules.requiredIfExists('elevation_max')]),
                elevation_max: schema.number.optional([rules.requiredIfExists('elevation_min')]),
                depth_absolut: schema.number.optional(),
                depth_min: schema.number.optional([rules.requiredIfExists('depth_max')]),
                depth_max: schema.number.optional([rules.requiredIfExists('depth_min')]),
            }),
            references: schema.array.optional([rules.uniqueArray('value')]).members(
                schema.object().members({
                    value: schema.string({ trim: true }, [rules.minLength(3), rules.maxLength(255)]),
                    type: schema.enum(Object.values(ReferenceIdentifierTypes)),
                    relation: schema.enum(Object.values(RelationTypes)),
                    label: schema.string({ trim: true }, [rules.minLength(2), rules.maxLength(255)]),
                }),
            ),
            subjects: schema.array([rules.minLength(3), rules.uniqueArray('value')]).members(
                schema.object().members({
                    value: schema.string({ trim: true }, [
                        rules.minLength(3),
                        rules.maxLength(255),
                        // rules.unique({ table: 'dataset_subjects', column: 'value' }),
                    ]),
                    // type: schema.enum(Object.values(TitleTypes)),
                    language: schema.string({ trim: true }, [rules.minLength(2), rules.maxLength(255)]),
                }),
            ),
        });

        try {
            //  Step 2 - Validate request body against  the schema
            await request.validate({ schema: newDatasetSchema, messages: this.messages });
            // console.log({ payload });
        } catch (error) {
            // Step 3 - Handle errors
            // return response.badRequest(error.messages);
            throw error;
        }
        return response.redirect().back();
    }

    public async store({ auth, request, response, session }: HttpContextContract) {
        // node ace make:validator CreateDataset
        try {
            //  Step 2 - Validate request body against  the schema
            // await request.validate({ schema: newDatasetSchema, messages: this.messages });
            await request.validate(CreateDatasetValidator);
            // console.log({ payload });
        } catch (error) {
            // Step 3 - Handle errors
            // return response.badRequest(error.messages);
            throw error;
        }

        let trx: TransactionClientContract | null = null;
        try {
            trx = await Database.transaction();
            const user = (await User.find(auth.user?.id)) as User;

            await this.createDatasetAndAssociations(user, request, trx);

            await trx.commit();
            console.log('Dataset and related models created successfully');
        } catch (error) {
            if (trx !== null) {
                await trx.rollback();
            }
            console.error('Failed to create dataset and related models:', error);
            // throw new ValidationException(true, { 'upload error': `failed to create dataset and related models. ${error}` });
            throw error;
        }

        session.flash('message', 'Dataset has been created successfully');
        return response.redirect().toRoute('dataset.list');
        // return response.redirect().back();
    }

    private async createDatasetAndAssociations(user: User, request: HttpContextContract['request'], trx: TransactionClientContract) {
        // Create a new instance of the Dataset model:
        const dataset = new Dataset();
        dataset.type = request.input('type');
        dataset.creating_corporation = request.input('creating_corporation');
        dataset.language = request.input('language');
        dataset.embargo_date = request.input('embargo_date');
        //await dataset.related('user').associate(user); // speichert schon ab
        // Dataset.$getRelation('user').boot();
        // Dataset.$getRelation('user').setRelated(dataset, user);
        // dataset.$setRelated('user', user);
        await user.useTransaction(trx).related('datasets').save(dataset);

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

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

        //save main and additional titles
        const titles = request.input('titles', []);
        for (const titleData of titles) {
            const title = new Title();
            title.value = titleData.value;
            title.language = titleData.language;
            title.type = titleData.type;
            await dataset.useTransaction(trx).related('titles').save(title);
        }

        // save descriptions
        const descriptions = request.input('descriptions', []);
        for (const descriptionData of descriptions) {
            const description = new Description();
            description.value = descriptionData.value;
            description.language = descriptionData.language;
            description.type = descriptionData.type;
            await dataset.useTransaction(trx).related('descriptions').save(description);
        }

        //save references
        const references = request.input('references', []);
        for (const referencePayload of references) {
            const dataReference = new DatasetReference();
            dataReference.fill(referencePayload);
            // $dataReference = new DatasetReference($reference);
            dataset.related('references').save(dataReference);
        }

        //save keywords
        const keywords = request.input('subjects', []);
        for (const keywordData of keywords) {
            // $dataKeyword = new Subject($keyword);
            // $dataset->subjects()->save($dataKeyword);
            const keyword = await Subject.firstOrNew({ value: keywordData.value, type: keywordData.type }, keywordData);
            if (keyword.$isNew === true) {
                await dataset.useTransaction(trx).related('subjects').save(keyword);
            } else {
                await dataset.useTransaction(trx).related('subjects').attach([keyword.id]);
            }
        }

        // save collection
        const collection: Collection | null = await Collection.query().where('id', 21).first();
        collection && (await dataset.useTransaction(trx).related('collections').attach([collection.id]));

        // save coverage
        const coverageData = request.input('coverage');
        if (coverageData) {
            // const formCoverage = request.input('coverage');
            const coverage = new Coverage();
            coverage.fill(coverageData);
            // await dataset.coverage().save(coverageData);
            await dataset.useTransaction(trx).related('coverage').save(coverage);
            // Alternatively, you can associate the dataset with the coverage and then save it:
            // await coverage.dataset().associate(dataset).save();
            // await coverage.useTransaction(trx).related('dataset').associate(dataset);
        }

        // save data files
        const uploadedFiles = request.files('files');
        for (const [index, file] of uploadedFiles.entries()) {
            try {
                await this.scanFileForViruses(file.tmpPath); //, 'gitea.lan', 3310);
                // await this.scanFileForViruses("/tmp/testfile.txt");
            } catch (error) {
                // If the file is infected or there's an error scanning the file, throw a validation exception
                throw error;
            }
            // clientName: 'Gehaltsschema.png'
            // extname: 'png'
            // fieldName: 'file'
            const fileName = `file-${cuid()}.${file.extname}`;
            const mimeType = file.headers['content-type'] || 'application/octet-stream'; // Fallback to a default MIME type
            const datasetFolder = `files/${dataset.id}`;
            // const size = file.size;
            await file.moveToDisk(
                datasetFolder,
                {
                    name: fileName,
                    overwrite: true, // overwrite in case of conflict
                },
                'local',
            );
            // save file metadata into db
            const newFile = new File();
            newFile.pathName = `${datasetFolder}/${fileName}`;
            newFile.fileSize = file.size;
            newFile.mimeType = mimeType;
            newFile.label = file.clientName;
            newFile.sortOrder = index;
            newFile.visibleInFrontdoor = true;
            newFile.visibleInOai = true;
            // let path = coverImage.filePath;
            await dataset.useTransaction(trx).related('files').save(newFile);
            await newFile.createHashValues(trx);
        }
    }

    private async scanFileForViruses(filePath, host?: string, port?: number): Promise<void> {
        // const clamscan = await (new ClamScan().init());
        const opts: ClamScan.Options = {
            removeInfected: true, // If true, removes infected files
            debugMode: false, // Whether or not to log info/debug/error msgs to the console
            scanRecursively: true, // If true, deep scan folders recursively
            clamdscan: {
                active: true, // If true, this module will consider using the clamdscan binary
                host,
                port,
                multiscan: true, // Scan using all available cores! Yay!
            },
            preference: 'clamdscan', // If clamdscan is found and active, it will be used by default
        };

        return new Promise(async (resolve, reject) => {
            try {
                const clamscan = await new ClamScan().init(opts);
                // You can re-use the `clamscan` object as many times as you want
                // const version = await clamscan.getVersion();
                // console.log(`ClamAV Version: ${version}`);
                const { file, isInfected, viruses } = await clamscan.isInfected(filePath);
                if (isInfected) {
                    console.log(`${file} is infected with ${viruses}!`);
                    reject(new ValidationException(true, { 'upload error': `File ${file} is infected!` }));
                } else {
                    resolve();
                }
            } catch (error) {
                // If there's an error scanning the file, throw a validation exception
                reject(new ValidationException(true, { 'upload error': `${error.message}` }));
            }
        });
    }

    private async savePersons(dataset: Dataset, persons: any[], role: string, trx: TransactionClientContract) {
        for (const [key, person] of persons.entries()) {
            const pivotData = {
                role: role,
                sort_order: key + 1,
                allow_email_contact: false,
                ...this.extractPivotAttributes(person), // Merge pivot attributes here
            };

            if (person.id !== undefined) {
                await dataset
                    .useTransaction(trx)
                    .related('persons')
                    .attach({
                        [person.id]: pivotData,
                    });
            } else {
                const dataPerson = new Person();
                dataPerson.fill(person);
                await dataset.useTransaction(trx).related('persons').save(dataPerson, false, pivotData);
            }
        }
    }

    // Helper function to extract pivot attributes from a person object
    private extractPivotAttributes(person: any) {
        const pivotAttributes = {};
        for (const key in person) {
            if (key.startsWith('pivot_')) {
                // pivotAttributes[key] = person[key];
                const cleanKey = key.replace('pivot_', ''); // Remove 'pivot_' prefix
                pivotAttributes[cleanKey] = person[key];
            }
        }
        return pivotAttributes;
    }

    public messages: CustomMessages = {
        'minLength': '{{ field }} must be at least {{ options.minLength }} characters long',
        'maxLength': '{{ field }} must be less then {{ options.maxLength }} characters long',
        'required': '{{ field }} is required',
        'unique': '{{ field }} must be unique, and this value is already taken',
        // 'confirmed': '{{ field }} is not correct',
        'licenses.minLength': 'at least {{ options.minLength }} permission must be defined',
        'licenses.*.number': 'Define roles as valid numbers',
        'rights.equalTo': 'you must agree to continue',

        'titles.0.value.minLength': 'Main Title  must be at least {{ options.minLength }} characters long',
        'titles.0.value.required': 'Main Title is required',
        'titles.*.value.required': 'Additional title is required, if defined',
        'titles.*.type.required': 'Additional title type is required',
        'titles.*.language.required': 'Additional title language is required',
        'titles.*.language.translatedLanguage': 'The language of the translated title must be different from the language of the dataset',

        'descriptions.0.value.minLength': 'Main Abstract  must be at least {{ options.minLength }} characters long',
        'descriptions.0.value.required': 'Main Abstract is required',
        'descriptions.*.value.required': 'Additional description is required, if defined',
        'descriptions.*.type.required': 'Additional description type is required',
        'descriptions.*.language.required': 'Additional description language is required',
        'descriptions.*.language.translatedLanguage':
            'The language of the translated description must be different from the language of the dataset',

        'authors.minLength': 'at least {{ options.minLength }} author must be defined',
        'contributors.*.pivot_contributor_type.required': 'contributor type is required, if defined',

        'after': `{{ field }} must be older than ${dayjs().add(10, 'day')}`,

        'subjects.minLength': 'at least {{ options.minLength }} keywords must be defined',
        'subjects.uniqueArray': 'The {{ options.array }} array must have unique values based on the {{ options.field }} attribute.',
        'subjects.*.value.required': 'keyword value is required',
        'subjects.*.value.minLength': 'keyword value  must be at least {{ options.minLength }} characters long',
        'subjects.*.type.required': 'keyword type is required',
        'subjects.*.language.required': 'language of keyword is required',

        'references.*.value.required': 'Additional reference value is required, if defined',
        'references.*.type.required': 'Additional reference identifier type is required',
        'references.*.relation.required': 'Additional reference relation type is required',
        'references.*.label.required': 'Additional reference label is required',

        'files.minLength': 'At least {{ options.minLength }}  file upload is required.',
        'files.*.size': 'file size is to big',
        'files.extnames': 'file extension is not supported',
    };

    // public async release({ params, view }) {
    public async release({ request, inertia, response }: HttpContextContract) {
        const id = request.param('id');

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

        const validStates = ['inprogress', 'rejected_editor'];
        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 released to editor. Datset has server state ${dataset.server_state}.`,
                )
                .redirect()
                .back();
        }

        return inertia.render('Submitter/Dataset/Release', {
            dataset,
        });
    }

    public async releaseUpdate({ request, response }: HttpContextContract) {
        const id = request.param('id');
        const dataset = await Dataset.query().preload('files').where('id', id).firstOrFail();

        const validStates = ['inprogress', 'rejected_editor'];
        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 released to editor. Datset has server state ${dataset.server_state}.`,
                )
                .redirect()
                .toRoute('dataset.list');
        }

        if (dataset.files.length === 0) {
            return response.flash('warning', 'At least minimum one file is required.').redirect('back');
        }

        const preferation = request.input('preferation', '');
        const preferredReviewer = request.input('preferred_reviewer');
        const preferredReviewerEmail = request.input('preferred_reviewer_email');

        if (preferation === 'yes_preferation') {
            const newSchema = schema.create({
                preferred_reviewer: schema.string({ trim: true }, [rules.minLength(3), rules.maxLength(255)]),
                preferred_reviewer_email: schema.string([rules.email()]),
            });

            try {
                await request.validate({ schema: newSchema });
            } catch (error) {
                // return response.badRequest(error.messages);
                throw error;
            }
        }

        const input = {
            preferred_reviewer: preferredReviewer || null,
            preferred_reviewer_email: preferredReviewerEmail || null,
            server_state: 'released',
            editor_id: null,
            reviewer_id: null,
            reject_editor_note: null,
            reject_reviewer_note: null,
        };

        // Clear editor_id if it exists
        if (dataset.editor_id !== null) {
            input.editor_id = null;
        }

        // Clear reject_editor_note if it exists
        if (dataset.reject_editor_note !== null) {
            input.reject_editor_note = null;
        }

        // Clear reviewer_id if it exists
        if (dataset.reviewer_id !== null) {
            input.reviewer_id = null;
        }

        // Clear reject_reviewer_note if it exists
        if (dataset.reject_reviewer_note !== null) {
            input.reject_reviewer_note = null;
        }

        if (await dataset.merge(input).save()) {
            return response.toRoute('dataset.list').flash('message', 'You have released your dataset!');
        }
        // throw new GeneralException(trans('exceptions.publish.release.update_error'));
    }

    public async edit({ request, inertia, response }) {
        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');

        const dataset = await datasetQuery.firstOrFail();
        const validStates = ['inprogress', 'rejected_editor'];
        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('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('Submitter/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 }: HttpContextContract) {
        try {
            // await request.validate({ schema: newDatasetSchema, messages: this.messages });
            await request.validate(UpdateDatasetValidator);
        } catch (error) {
            // - Handle errors
            // return response.badRequest(error.messages);
            throw error;
            // return response.badRequest(error.messages);
        }
        // await request.validate(UpdateDatasetValidator);
        const id = request.param('id');

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

            // 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 this.savePersons(dataset, request.input('authors', []), 'author', trx);
            await this.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);
                }
            }

            // await dataset.useTransaction(trx).related('subjects').sync([]);
            const keywords = request.input('subjects');
            for (const keywordData of keywords) {
                if (keywordData.id) {
                    const subject = await Subject.findOrFail(keywordData.id);
                    // await dataset.useTransaction(trx).related('subjects').attach([keywordData.id]);
                    subject.value = keywordData.value;
                    subject.type = keywordData.type;
                    subject.external_key = keywordData.external_key;
                    if (subject.$isDirty) {
                        await subject.save();
                    }
                } else {
                    const keyword = new Subject();
                    keyword.fill(keywordData);
                    await dataset.useTransaction(trx).related('subjects').save(keyword, false);
                }
            }

            // Save already existing files
            const files = request.input('fileInputs', []);
            for (const fileData of files) {
                if (fileData.id) {
                    const file = await File.findOrFail(fileData.id);
                    file.label = fileData.label;
                    file.sortOrder = fileData.sort_order;
                    if (file.$isDirty) {
                        await file.useTransaction(trx).save();
                    }
                }
            }

            // handle new uploaded files:
            const uploadedFiles: MultipartFileContract[] = request.files('files');
            if (Array.isArray(uploadedFiles) && uploadedFiles.length > 0) {
                for (const [index, fileData] of uploadedFiles.entries()) {
                    try {
                        await this.scanFileForViruses(fileData.tmpPath); //, 'gitea.lan', 3310);
                        // await this.scanFileForViruses("/tmp/testfile.txt");
                    } catch (error) {
                        // If the file is infected or there's an error scanning the file, throw a validation exception
                        throw error;
                    }

                    // move to disk:
                    const fileName = `file-${cuid()}.${fileData.extname}`;
                    const datasetFolder = `files/${dataset.id}`;
                    await fileData.moveToDisk(datasetFolder, { name: fileName, overwrite: true }, 'local');
                    // let path = coverImage.filePath;

                    //save to db:
                    const { clientFileName, sortOrder } = this.extractVariableNameAndSortOrder(fileData.clientName);
                    const mimeType = fileData.headers['content-type'] || 'application/octet-stream'; // Fallback to a default MIME type
                    const newFile = await dataset
                        .useTransaction(trx)
                        .related('files')
                        .create({
                            pathName: `${datasetFolder}/${fileName}`,
                            fileSize: fileData.size,
                            mimeType,
                            label: clientFileName,
                            sortOrder: sortOrder || index,
                            visibleInFrontdoor: true,
                            visibleInOai: true,
                        });

                    // save many related HashValue Instances to the file:
                    await newFile.createHashValues(trx);
                }
            }

            // save collection
            // const collection: Collection | null = await Collection.query().where('id', 21).first();
            // collection && (await dataset.useTransaction(trx).related('collections').attach([collection.id]));

            // // Save coverage
            // if (data.coverage && !this.containsOnlyNull(data.coverage)) {
            //     const formCoverage = request.input('coverage');
            //     const coverage = await dataset.related('coverage').updateOrCreate({ dataset_id: dataset.id }, formCoverage);
            // } else if (data.coverage && this.containsOnlyNull(data.coverage) && !dataset.coverage) {
            //     await dataset.coverage().delete();
            // }

            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 and related models created successfully');
        } catch (error) {
            if (trx !== null) {
                await trx.rollback();
            }
            console.error('Failed to create dataset and related models:', error);
            // throw new ValidationException(true, { 'upload error': `failed to create dataset and related models. ${error}` });
            throw error;
        }

        session.flash('message', 'Dataset has been updated successfully');
        // return response.redirect().toRoute('user.index');
        return response.redirect().back();
    }

    private extractVariableNameAndSortOrder(inputString: string): { clientFileName: string; sortOrder?: number } {
        const regex = /^([^?]+)(?:\?([^=]+)=([^&]+))?/;
        const match = inputString.match(regex);

        if (match) {
            const clientFileName = match[1];

            const param = match[2];
            let sortOrder;
            if (param && param.toLowerCase() === 'sortorder') {
                sortOrder = parseInt(match[3], 10);
            }

            return { clientFileName, sortOrder };
        } else {
            return { clientFileName: '', sortOrder: undefined }; // Or handle as needed for no match
        }
    }

    public async delete({ request, inertia, response, session }) {
        const id = request.param('id');
        try {
            const dataset = await Dataset.query()
                .preload('user', (builder) => {
                    builder.select('id', 'login');
                })
                .where('id', id)
                .preload('files')
                .firstOrFail();
            const validStates = ['inprogress', 'rejected_editor'];
            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 deleted. Datset has server state ${dataset.server_state}.`,
                    )
                    .redirect()
                    .toRoute('dataset.list');
            }
            return inertia.render('Submitter/Dataset/Delete', {
                dataset,
            });
        } catch (error) {
            if (error.code == 'E_ROW_NOT_FOUND') {
                session.flash({ warning: 'Dataset is not found in database' });
            } else {
                session.flash({ warning: 'general error occured, you cannot delete the dataset' });
            }
            return response.redirect().toRoute('dataset.list');
        }
    }

    public async deleteUpdate({ params, session, response }) {
        try {
            const dataset = await Dataset.query().where('id', params.id).preload('files').firstOrFail();

            const validStates = ['inprogress', 'rejected_editor'];
            if (validStates.includes(dataset.server_state)) {
                if (dataset.files && dataset.files.length > 0) {
                    for (const file of dataset.files) {
                        // overwritten delete method also delets file on filespace
                        await file.delete();
                    }
                }
                const datasetFolder = `files/${params.id}`;
                const folderExists = await Drive.exists(datasetFolder);
                if (folderExists) {
                    const folderContents = await Drive.list(datasetFolder).toArray();
                    if (folderContents.length === 0) {
                        await Drive.delete(datasetFolder);
                    }
                    // delete dataset wirh relation from db
                    await dataset.delete();
                    session.flash({ message: 'You have deleted 1 dataset!' });
                    return response.redirect().toRoute('dataset.list');
                } else {
                    session.flash({
                        warning: `You cannot delete this dataset! Invalid server_state: "${dataset.server_state}"!`,
                    });
                    return response.status(400).redirect().back();
                }
            }
        } catch (error) {
            if (error instanceof ValidationException) {
                // Validation exception handling
                throw error;
            } else if (error instanceof Exception) {
                // General exception handling
                return response
                    .flash({ errors: { error: error.message } })
                    .redirect()
                    .back();
            } else {
                session.flash({ error: 'An error occurred while deleting the dataset.' });
                return response.redirect().back();
            }
        }
    }
}