From 6fa22aad9b1d58c499f666dd94eb4113524d16ff Mon Sep 17 00:00:00 2001 From: Arno Kaimbacher Date: Tue, 5 Sep 2023 18:18:42 +0200 Subject: [PATCH] - prettier format checking - added the possibility to delete 'inprogress' dataset again for the submitter - concat run commands insider Dockerfile for better docker image - npm updates - add own Exception classes HttpException.ts and InternalServerException.ts --- Dockerfile | 14 +- app/Controllers/Http/Api/DatasetController.ts | 2 +- app/Controllers/Http/Api/HomeController.ts | 10 +- .../Http/Submitter/DatasetController.ts | 119 ++++-- app/Exceptions/HttpException.ts | 12 + app/Exceptions/InternalServerException.ts | 10 + app/Models/Dataset.ts | 2 +- app/Models/DatasetIdentifier.ts | 2 +- app/Models/DatasetReference.ts | 2 - components.d.ts | 4 +- contracts/enums.ts | 15 +- database/migrations/dataset_2_documents.ts | 2 +- package-lock.json | 348 +++++++++--------- resources/js/Components/TablePersons.vue | 4 + resources/js/Dataset.ts | 2 +- .../js/Pages/Submitter/Dataset/Delete.vue | 131 +++++++ .../js/Pages/Submitter/Dataset/Index.vue | 41 +-- start/routes.ts | 4 + 18 files changed, 473 insertions(+), 251 deletions(-) create mode 100644 app/Exceptions/HttpException.ts create mode 100644 app/Exceptions/InternalServerException.ts create mode 100644 resources/js/Pages/Submitter/Dataset/Delete.vue diff --git a/Dockerfile b/Dockerfile index 4c0b66d..128ed11 100644 --- a/Dockerfile +++ b/Dockerfile @@ -12,7 +12,11 @@ RUN apt update \ && mkdir -p /home/node/app && chown node:node /home/node/app \ && mkdir -p /var/lib/clamav \ && mkdir /usr/local/share/clamav \ - && chown -R node:clamav /var/lib/clamav /usr/local/share/clamav /etc/clamav + && chown -R node:clamav /var/lib/clamav /usr/local/share/clamav /etc/clamav \ + # permissions + && mkdir /var/run/clamav \ + && chown node:clamav /var/run/clamav \ + && chmod 750 /var/run/clamav # ----------------------------------------------- # --- ClamAV & FeshClam ------------------------- # ----------------------------------------------- @@ -28,10 +32,10 @@ RUN apt update \ # Configure Clam AV... COPY --chown=node:clamav ./*.conf /etc/clamav/ -# permissions -RUN mkdir /var/run/clamav && \ - chown node:clamav /var/run/clamav && \ - chmod 750 /var/run/clamav +# # permissions +# RUN mkdir /var/run/clamav && \ +# chown node:clamav /var/run/clamav && \ +# chmod 750 /var/run/clamav # Setting the working directory WORKDIR /home/node/app # Changing the current active user to "node" diff --git a/app/Controllers/Http/Api/DatasetController.ts b/app/Controllers/Http/Api/DatasetController.ts index e4d10c3..5245c26 100644 --- a/app/Controllers/Http/Api/DatasetController.ts +++ b/app/Controllers/Http/Api/DatasetController.ts @@ -14,7 +14,7 @@ export default class DatasetController { return datasets; } - public async findAll({ response }: HttpContextContract) { + public async findAll({ response }: HttpContextContract) { try { const datasets = await Dataset.query() .where('server_state', 'published') diff --git a/app/Controllers/Http/Api/HomeController.ts b/app/Controllers/Http/Api/HomeController.ts index f4947c9..6f15773 100644 --- a/app/Controllers/Http/Api/HomeController.ts +++ b/app/Controllers/Http/Api/HomeController.ts @@ -18,15 +18,7 @@ export default class HomeController { // .orderBy('server_date_published'); const datasets = await Database.from('documents as doc') - .select([ - 'publish_id', - 'server_date_published', - Database.raw(`date_part('year', server_date_published) as pub_year`) - ], - // Database - // .raw('select "ip_address" from "user_logins" where "users.id" = "user_logins.user_id" limit 1') - // .wrap('(', ')') - ) + .select(['publish_id', 'server_date_published', Database.raw(`date_part('year', server_date_published) as pub_year`)]) .where('server_state', serverState) .innerJoin('link_documents_persons as ba', 'doc.id', 'ba.document_id') .andWhereRaw(`date_part('year', server_date_published) = ?`, [from]) diff --git a/app/Controllers/Http/Submitter/DatasetController.ts b/app/Controllers/Http/Submitter/DatasetController.ts index 1922005..70d19ce 100644 --- a/app/Controllers/Http/Submitter/DatasetController.ts +++ b/app/Controllers/Http/Submitter/DatasetController.ts @@ -8,8 +8,6 @@ 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 CreateUserValidator from 'App/Validators/CreateUserValidator'; -// import UpdateUserValidator from 'App/Validators/UpdateUserValidator'; import { schema, CustomMessages, rules } from '@ioc:Adonis/Core/Validator'; import dayjs from 'dayjs'; import Person from 'App/Models/Person'; @@ -17,13 +15,23 @@ 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 { TitleTypes, DescriptionTypes, ContributorTypes, PersonNameTypes, ReferenceIdentifierTypes, RelationTypes } from 'Contracts/enums'; +import { + TitleTypes, + DescriptionTypes, + ContributorTypes, + PersonNameTypes, + ReferenceIdentifierTypes, + RelationTypes, + DatasetTypes, +} 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'; export default class DatasetController { public async index({ auth, request, inertia }: HttpContextContract) { @@ -98,30 +106,21 @@ export default class DatasetController { 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 titletypes = { - // Sub: 'Sub', - // Alternative: 'Alternative', - // Translated: 'Translated', - // Other: 'Other', + // 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', // }; - // let test = Object.entries(TitleTypes).map(([key, value]) => ({id: key, value: value})) - // const languages = await Database.from('languages').select('*').where('active', true); return inertia.render('Submitter/Dataset/Create', { licenses: licenses, - doctypes: doctypes, + doctypes: DatasetTypes, titletypes: Object.entries(TitleTypes) .filter(([value]) => value !== 'Main') .map(([key, value]) => ({ value: key, label: value })), @@ -293,7 +292,6 @@ export default class DatasetController { // node ace make:validator CreateDataset try { // Step 2 - Validate request body against the schema - // await request.validate(CreateUserValidator); // await request.validate({ schema: newDatasetSchema, messages: this.messages }); await request.validate(CreateDatasetValidator); // console.log({ payload }); @@ -755,4 +753,79 @@ export default class DatasetController { doctypes, }); } + + 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'); + }) + .preload('files') + .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 deleted. Datset has server state ${dataset.server_state}.`, + ) + .redirect() + .toRoute('dataset.list'); + } + return inertia.render('Submitter/Dataset/Delete', { + dataset, + }); + } catch (error) { + if (error.code == 'E_ROW_NOT_FOUND') { + session.flash({ warning: 'Dataset is not found in database' }); + } else { + session.flash({ warning: 'general error occured, you cannot delete the dataset' }); + } + return response.redirect().toRoute('dataset.list'); + } + } + + public async deleteUpdate({ params, session, response }) { + try { + const dataset = await Dataset.query().where('id', params.id).preload('files').firstOrFail(); + + const validStates = ['inprogress', 'rejected_editor']; + if (validStates.includes(dataset.server_state)) { + if (dataset.files && dataset.files.length > 0) { + for (const file of dataset.files) { + if (file.pathName) { + // delete file from filesystem + await Drive.delete(file.pathName); + } + } + } + // delete dataset wirh relation from db + await dataset.delete(); + session.flash({ message: 'You have deleted 1 dataset!' }); + return response.redirect().toRoute('dataset.list'); + } else { + session.flash({ + warning: `You cannot delete this dataset! The status of this dataset is "${dataset.server_state}"!`, + }); + return response.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(); + } + } + } } diff --git a/app/Exceptions/HttpException.ts b/app/Exceptions/HttpException.ts new file mode 100644 index 0000000..7bad1b0 --- /dev/null +++ b/app/Exceptions/HttpException.ts @@ -0,0 +1,12 @@ +class HTTPException extends Error { + public status: number; + public message: string; + + constructor(status: number, message: string) { + super(message); + this.status = status; + this.message = message; + } +} + +export default HTTPException; diff --git a/app/Exceptions/InternalServerException.ts b/app/Exceptions/InternalServerException.ts new file mode 100644 index 0000000..a1c5bfb --- /dev/null +++ b/app/Exceptions/InternalServerException.ts @@ -0,0 +1,10 @@ +import { StatusCodes } from 'http-status-codes'; +import HTTPException from './HttpException'; + +class InternalServerErrorException extends HTTPException { + constructor(message?: string) { + super(StatusCodes.INTERNAL_SERVER_ERROR, message || 'Server Error'); + this.stack = ''; + } +} +export default InternalServerErrorException; diff --git a/app/Models/Dataset.ts b/app/Models/Dataset.ts index 57f68f2..1e94850 100644 --- a/app/Models/Dataset.ts +++ b/app/Models/Dataset.ts @@ -197,7 +197,7 @@ export default class Dataset extends BaseModel { }, }) public authors: ManyToMany; - + @manyToMany(() => Person, { pivotForeignKey: 'document_id', pivotRelatedForeignKey: 'person_id', diff --git a/app/Models/DatasetIdentifier.ts b/app/Models/DatasetIdentifier.ts index e3b68d6..5654f08 100644 --- a/app/Models/DatasetIdentifier.ts +++ b/app/Models/DatasetIdentifier.ts @@ -14,7 +14,7 @@ export default class DatasetIdentifier extends BaseModel { public id: number; @column({}) - public dataset_id: number; + public dataset_id: number; @column({}) public type: string; diff --git a/app/Models/DatasetReference.ts b/app/Models/DatasetReference.ts index a97aee4..ee51d4b 100644 --- a/app/Models/DatasetReference.ts +++ b/app/Models/DatasetReference.ts @@ -56,6 +56,4 @@ export default class DatasetReference extends BaseModel { foreignKey: 'related_document_id', }) public new_dataset: BelongsTo; - - } diff --git a/components.d.ts b/components.d.ts index afc1906..3834bf1 100644 --- a/components.d.ts +++ b/components.d.ts @@ -7,7 +7,7 @@ export {}; declare module '@vue/runtime-core' { export interface GlobalComponents { - NButton: typeof import('naive-ui')['NButton']; - NInput: typeof import('naive-ui')['NInput']; + NButton: (typeof import('naive-ui'))['NButton']; + NInput: (typeof import('naive-ui'))['NInput']; } } diff --git a/contracts/enums.ts b/contracts/enums.ts index 917e7db..018affd 100644 --- a/contracts/enums.ts +++ b/contracts/enums.ts @@ -1,13 +1,14 @@ // ./contracts/enums.ts export enum DatasetTypes { - analysisdata = 'analysisdata', - measurementdata = 'measurementdata', - monitoring = 'monitoring', - remotesensing = 'remotesensing', - gis = 'gis', - models = 'models', - mixedtype = 'mixedtype', + analysisdata = 'Analysis', + measurementdata = 'Measurements', + monitoring = 'Monitoring', + remotesensing = 'Remote Sensing', + gis = 'GIS', + models = 'Models', + mixedtype = 'Mixed Type', + vocabulary = 'Vocabulary', } export enum ServerStates { diff --git a/database/migrations/dataset_2_documents.ts b/database/migrations/dataset_2_documents.ts index f6e293e..b813d1f 100644 --- a/database/migrations/dataset_2_documents.ts +++ b/database/migrations/dataset_2_documents.ts @@ -31,7 +31,7 @@ export default class Documents extends BaseSchema { .foreign('account_id', 'documents_account_id_foreign') .references('id') .inTable('accounts') - .onDelete('NO ACTION') // don't delete this when account is deleted + .onDelete('NO ACTION') // don't delete this doc when account is deleted .onUpdate('NO ACTION'); table.integer('editor_id'); table.integer('reviewer_id'); diff --git a/package-lock.json b/package-lock.json index 3072d79..084a17f 100644 --- a/package-lock.json +++ b/package-lock.json @@ -784,21 +784,21 @@ } }, "node_modules/@babel/core": { - "version": "7.22.11", - "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.22.11.tgz", - "integrity": "sha512-lh7RJrtPdhibbxndr6/xx0w8+CVlY5FJZiaSz908Fpy+G0xkBFTvwLcKJFF4PJxVfGhVWNebikpWGnOoC71juQ==", + "version": "7.22.15", + "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.22.15.tgz", + "integrity": "sha512-PtZqMmgRrvj8ruoEOIwVA3yoF91O+Hgw9o7DAUTNBA6Mo2jpu31clx9a7Nz/9JznqetTR6zwfC4L3LAjKQXUwA==", "dev": true, "dependencies": { "@ampproject/remapping": "^2.2.0", - "@babel/code-frame": "^7.22.10", - "@babel/generator": "^7.22.10", - "@babel/helper-compilation-targets": "^7.22.10", - 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