diff --git a/adonisrc.ts b/adonisrc.ts index 19e946c..de94c63 100644 --- a/adonisrc.ts +++ b/adonisrc.ts @@ -11,9 +11,10 @@ export default defineConfig({ */ commands: [ - () => import('@adonisjs/core/commands'), - () => import('@adonisjs/lucid/commands'), - () => import('@adonisjs/mail/commands')], + () => import('@adonisjs/core/commands'), + () => import('@adonisjs/lucid/commands'), + () => import('@adonisjs/mail/commands') + ], /* |-------------------------------------------------------------------------- | Preloads @@ -36,6 +37,7 @@ export default defineConfig({ () => import('#start/rules/referenceValidation'), () => import('#start/rules/valid_mimetype'), () => import('#start/rules/array_contains_types'), + () => import('#start/rules/orcid'), ], /* |-------------------------------------------------------------------------- diff --git a/app/Controllers/Http/Api/AuthorsController.ts b/app/Controllers/Http/Api/AuthorsController.ts index 7209699..2b0bae1 100644 --- a/app/Controllers/Http/Api/AuthorsController.ts +++ b/app/Controllers/Http/Api/AuthorsController.ts @@ -4,20 +4,29 @@ import Person from '#models/person'; // node ace make:controller Author export default class AuthorsController { - public async index({}: HttpContext) { - // select * from gba.persons - // where exists (select * from gba.documents inner join gba.link_documents_persons on "documents"."id" = "link_documents_persons"."document_id" - // where ("link_documents_persons"."role" = 'author') and ("persons"."id" = "link_documents_persons"."person_id")); + public async index({}: HttpContext) { + const authors = await Person.query() - .preload('datasets') - .where('name_type', 'Personal') - .whereHas('datasets', (dQuery) => { - dQuery.wherePivot('role', 'author'); - }) - .withCount('datasets', (query) => { - query.as('datasets_count'); - }) - .orderBy('datasets_count', 'desc'); + .select([ + 'id', + 'academic_title', + 'first_name', + 'last_name', + 'identifier_orcid', + 'status', + 'name_type', + 'created_at' + // Note: 'email' is omitted + ]) + .preload('datasets') + .where('name_type', 'Personal') + .whereHas('datasets', (dQuery) => { + dQuery.wherePivot('role', 'author'); + }) + .withCount('datasets', (query) => { + query.as('datasets_count'); + }) + .orderBy('datasets_count', 'desc'); return authors; } diff --git a/app/Controllers/Http/Api/AvatarController.ts b/app/Controllers/Http/Api/AvatarController.ts index 74fe135..d7c532f 100644 --- a/app/Controllers/Http/Api/AvatarController.ts +++ b/app/Controllers/Http/Api/AvatarController.ts @@ -2,26 +2,46 @@ import type { HttpContext } from '@adonisjs/core/http'; import { StatusCodes } from 'http-status-codes'; import redis from '@adonisjs/redis/services/main'; -const PREFIXES = ['von', 'van']; +const PREFIXES = ['von', 'van', 'de', 'del', 'della', 'di', 'da', 'dos', 'du', 'le', 'la']; const DEFAULT_SIZE = 50; +const MIN_SIZE = 16; +const MAX_SIZE = 512; const FONT_SIZE_RATIO = 0.4; const COLOR_LIGHTENING_PERCENT = 60; const COLOR_DARKENING_FACTOR = 0.6; +const CACHE_TTL = 24 * 60 * 60; // 24 hours instead of 1 hour export default class AvatarController { public async generateAvatar({ request, response }: HttpContext) { try { const { name, size = DEFAULT_SIZE } = request.only(['name', 'size']); - if (!name) { - return response.status(StatusCodes.BAD_REQUEST).json({ error: 'Name is required' }); + + // Enhanced validation + if (!name || typeof name !== 'string' || name.trim().length === 0) { + return response.status(StatusCodes.BAD_REQUEST).json({ + error: 'Name is required and must be a non-empty string', + }); + } + + const parsedSize = this.validateSize(size); + if (!parsedSize.isValid) { + return response.status(StatusCodes.BAD_REQUEST).json({ + error: parsedSize.error, + }); } // Build a unique cache key for the given name and size - const cacheKey = `avatar:${name.trim().toLowerCase()}-${size}`; - const cachedSvg = await redis.get(cacheKey); - if (cachedSvg) { - this.setResponseHeaders(response); - return response.send(cachedSvg); + const cacheKey = `avatar:${this.sanitizeName(name)}-${parsedSize.value}`; + // const cacheKey = `avatar:${name.trim().toLowerCase()}-${size}`; + try { + const cachedSvg = await redis.get(cacheKey); + if (cachedSvg) { + this.setResponseHeaders(response); + return response.send(cachedSvg); + } + } catch (redisError) { + // Log redis error but continue without cache + console.warn('Redis cache read failed:', redisError); } const initials = this.getInitials(name); @@ -29,41 +49,85 @@ export default class AvatarController { const svgContent = this.createSvg(size, colors, initials); // // Cache the generated avatar for future use, e.g. 1 hour expiry - await redis.setex(cacheKey, 3600, svgContent); + try { + await redis.setex(cacheKey, CACHE_TTL, svgContent); + } catch (redisError) { + // Log but don't fail the request + console.warn('Redis cache write failed:', redisError); + } this.setResponseHeaders(response); return response.send(svgContent); } catch (error) { - return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({ error: error.message }); + console.error('Avatar generation error:', error); + return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({ + error: 'Failed to generate avatar', + }); } } - private getInitials(name: string): string { - const parts = name + private validateSize(size: any): { isValid: boolean; value?: number; error?: string } { + const numSize = Number(size); + + if (isNaN(numSize)) { + return { isValid: false, error: 'Size must be a valid number' }; + } + + if (numSize < MIN_SIZE || numSize > MAX_SIZE) { + return { + isValid: false, + error: `Size must be between ${MIN_SIZE} and ${MAX_SIZE}`, + }; + } + + return { isValid: true, value: Math.floor(numSize) }; + } + + private sanitizeName(name: string): string { + return name .trim() + .toLowerCase() + .replace(/[^a-z0-9\s-]/gi, ''); + } + + private getInitials(name: string): string { + const sanitized = name.trim().replace(/\s+/g, ' '); // normalize whitespace + const parts = sanitized .split(' ') - .filter((part) => part.length > 0); + .filter((part) => part.length > 0) + .map((part) => part.trim()); if (parts.length === 0) { return 'NA'; } - if (parts.length >= 2) { - return this.getMultiWordInitials(parts); + if (parts.length === 1) { + // For single word, take first 2 characters or first char if only 1 char + return parts[0].substring(0, Math.min(2, parts[0].length)).toUpperCase(); } - return parts[0].substring(0, 2).toUpperCase(); + + return this.getMultiWordInitials(parts); } private getMultiWordInitials(parts: string[]): string { - const firstName = parts[0]; - const lastName = parts[parts.length - 1]; - const firstInitial = firstName.charAt(0).toUpperCase(); - const lastInitial = lastName.charAt(0).toUpperCase(); + // Filter out prefixes and short words + const significantParts = parts.filter((part) => !PREFIXES.includes(part.toLowerCase()) && part.length > 1); - if (PREFIXES.includes(lastName.toLowerCase()) && lastName === lastName.toUpperCase()) { - return firstInitial + lastName.charAt(1).toUpperCase(); + if (significantParts.length === 0) { + // Fallback to first and last regardless of prefixes + const firstName = parts[0]; + const lastName = parts[parts.length - 1]; + return (firstName.charAt(0) + lastName.charAt(0)).toUpperCase(); } - return firstInitial + lastInitial; + + if (significantParts.length === 1) { + return significantParts[0].substring(0, 2).toUpperCase(); + } + + // Take first and last significant parts + const firstName = significantParts[0]; + const lastName = significantParts[significantParts.length - 1]; + return (firstName.charAt(0) + lastName.charAt(0)).toUpperCase(); } private generateColors(name: string): { background: string; text: string } { @@ -75,31 +139,44 @@ export default class AvatarController { } private createSvg(size: number, colors: { background: string; text: string }, initials: string): string { - const fontSize = size * FONT_SIZE_RATIO; - return ` - - - ${initials} - - `; + const fontSize = Math.max(12, Math.floor(size * FONT_SIZE_RATIO)); // Ensure readable font size + + // Escape any potential HTML/XML characters in initials + const escapedInitials = this.escapeXml(initials); + + return ` + + ${escapedInitials} + `; + } + + private escapeXml(text: string): string { + return text.replace(/&/g, '&').replace(//g, '>').replace(/"/g, '"').replace(/'/g, '''); } private setResponseHeaders(response: HttpContext['response']): void { - response.header('Content-type', 'image/svg+xml'); - response.header('Cache-Control', 'no-cache'); - response.header('Pragma', 'no-cache'); - response.header('Expires', '0'); + response.header('Content-Type', 'image/svg+xml'); + response.header('Cache-Control', 'public, max-age=86400'); // Cache for 1 day + response.header('ETag', `"${Date.now()}"`); // Simple ETag } private getColorFromName(name: string): string { let hash = 0; - for (let i = 0; i < name.length; i++) { - hash = name.charCodeAt(i) + ((hash << 5) - hash); + const normalizedName = name.toLowerCase().trim(); + + for (let i = 0; i < normalizedName.length; i++) { + hash = normalizedName.charCodeAt(i) + ((hash << 5) - hash); + hash = hash & hash; // Convert to 32-bit integer } + // Ensure we get vibrant colors by constraining the color space const colorParts = []; for (let i = 0; i < 3; i++) { - const value = (hash >> (i * 8)) & 0xff; + let value = (hash >> (i * 8)) & 0xff; + // Ensure minimum color intensity for better contrast + value = Math.max(50, value); colorParts.push(value.toString(16).padStart(2, '0')); } return colorParts.join(''); @@ -110,7 +187,7 @@ export default class AvatarController { const g = parseInt(hexColor.substring(2, 4), 16); const b = parseInt(hexColor.substring(4, 6), 16); - const lightenValue = (value: number) => Math.min(255, Math.floor((value * (100 + percent)) / 100)); + const lightenValue = (value: number) => Math.min(255, Math.floor(value + (255 - value) * (percent / 100))); const newR = lightenValue(r); const newG = lightenValue(g); @@ -124,7 +201,7 @@ export default class AvatarController { const g = parseInt(hexColor.slice(2, 4), 16); const b = parseInt(hexColor.slice(4, 6), 16); - const darkenValue = (value: number) => Math.round(value * COLOR_DARKENING_FACTOR); + const darkenValue = (value: number) => Math.max(0, Math.floor(value * COLOR_DARKENING_FACTOR)); const darkerR = darkenValue(r); const darkerG = darkenValue(g); diff --git a/app/Controllers/Http/Api/DatasetController.ts b/app/Controllers/Http/Api/DatasetController.ts index b80949d..f6bc648 100644 --- a/app/Controllers/Http/Api/DatasetController.ts +++ b/app/Controllers/Http/Api/DatasetController.ts @@ -9,8 +9,7 @@ export default class DatasetController { // Select datasets with server_state 'published' or 'deleted' and sort by the last published date const datasets = await Dataset.query() .where(function (query) { - query.where('server_state', 'published') - .orWhere('server_state', 'deleted'); + query.where('server_state', 'published').orWhere('server_state', 'deleted'); }) .preload('titles') .preload('identifier') @@ -39,12 +38,26 @@ export default class DatasetController { .where('publish_id', params.publish_id) .preload('titles') .preload('descriptions') - .preload('user') + .preload('user', (builder) => { + builder.select(['id', 'firstName', 'lastName', 'avatar', 'login']); + }) .preload('authors', (builder) => { - builder.orderBy('pivot_sort_order', 'asc'); + builder + .select(['id', 'academic_title', 'first_name', 'last_name', 'identifier_orcid', 'status', 'name_type']) + .withCount('datasets', (query) => { + query.as('datasets_count'); + }) + .pivotColumns(['role', 'sort_order']) + .orderBy('pivot_sort_order', 'asc'); }) .preload('contributors', (builder) => { - builder.orderBy('pivot_sort_order', 'asc'); + builder + .select(['id', 'academic_title', 'first_name', 'last_name', 'identifier_orcid', 'status', 'name_type']) + .withCount('datasets', (query) => { + query.as('datasets_count'); + }) + .pivotColumns(['role', 'sort_order', 'contributor_type']) + .orderBy('pivot_sort_order', 'asc'); }) .preload('subjects') .preload('coverage') diff --git a/app/Controllers/Http/Api/FileController.ts b/app/Controllers/Http/Api/FileController.ts index 8080479..bfcbae2 100644 --- a/app/Controllers/Http/Api/FileController.ts +++ b/app/Controllers/Http/Api/FileController.ts @@ -2,53 +2,89 @@ import type { HttpContext } from '@adonisjs/core/http'; import File from '#models/file'; import { StatusCodes } from 'http-status-codes'; import * as fs from 'fs'; -import * as path from 'path'; +import { DateTime } from 'luxon'; // node ace make:controller Author export default class FileController { // @Get("download/:id") public async findOne({ response, params }: HttpContext) { const id = params.id; - const file = await File.findOrFail(id); - // const file = await File.findOne({ - // where: { id: id }, - // }); - if (file) { - const filePath = '/storage/app/data/' + file.pathName; - const ext = path.extname(filePath); - const fileName = file.label + ext; - try { - fs.accessSync(filePath, fs.constants.R_OK); //| fs.constants.W_OK); - // console.log("can read/write:", path); - - response - .header('Cache-Control', 'no-cache private') - .header('Content-Description', 'File Transfer') - .header('Content-Type', file.mimeType) - .header('Content-Disposition', 'inline; filename=' + fileName) - .header('Content-Transfer-Encoding', 'binary') - .header('Access-Control-Allow-Origin', '*') - .header('Access-Control-Allow-Methods', 'GET,POST'); - - response.status(StatusCodes.OK).download(filePath); - } catch (err) { - // console.log("no access:", path); - response.status(StatusCodes.NOT_FOUND).send({ - message: `File with id ${id} doesn't exist on file server`, - }); - } + // const file = await File.findOrFail(id); + // Load file with its related dataset to check embargo + const file = await File.query() + .where('id', id) + .preload('dataset') // or 'dataset' - whatever your relationship is named + .firstOrFail(); - // res.status(StatusCodes.OK).sendFile(filePath, (err) => { - // // res.setHeader("Content-Type", "application/json"); - // // res.removeHeader("Content-Disposition"); - // res.status(StatusCodes.NOT_FOUND).send({ - // message: `File with id ${id} doesn't exist on file server`, - // }); - // }); - } else { - response.status(StatusCodes.NOT_FOUND).send({ + if (!file) { + return response.status(StatusCodes.NOT_FOUND).send({ message: `Cannot find File with id=${id}.`, }); } + + const dataset = file.dataset; + // Files from unpublished datasets are now blocked + if (dataset.server_state !== 'published') { + return response.status(StatusCodes.FORBIDDEN).send({ + message: `File access denied: Dataset is not published.`, + }); + } + if (dataset && this.isUnderEmbargo(dataset.embargo_date)) { + return response.status(StatusCodes.FORBIDDEN).send({ + message: `File is under embargo until ${dataset.embargo_date?.toFormat('yyyy-MM-dd')}`, + }); + } + + // Proceed with file download + const filePath = '/storage/app/data/' + file.pathName; + const fileExt = file.filePath.split('.').pop() || ''; + // const fileName = file.label + fileExt; + const fileName = file.label.toLowerCase().endsWith(`.${fileExt.toLowerCase()}`) + ? file.label + : `${file.label}.${fileExt}`; + + try { + fs.accessSync(filePath, fs.constants.R_OK); //| fs.constants.W_OK); + // console.log("can read/write:", filePath); + + response + .header('Cache-Control', 'no-cache private') + .header('Content-Description', 'File Transfer') + .header('Content-Type', file.mimeType) + .header('Content-Disposition', 'inline; filename=' + fileName) + .header('Content-Transfer-Encoding', 'binary') + .header('Access-Control-Allow-Origin', '*') + .header('Access-Control-Allow-Methods', 'GET'); + + response.status(StatusCodes.OK).download(filePath); + } catch (err) { + // console.log("no access:", path); + response.status(StatusCodes.NOT_FOUND).send({ + message: `File with id ${id} doesn't exist on file server`, + }); + } + } + + /** + * Check if the dataset is under embargo + * Compares only dates (ignoring time) for embargo check + * @param embargoDate - The embargo date from dataset + * @returns true if under embargo, false if embargo has passed or no embargo set + */ + private isUnderEmbargo(embargoDate: DateTime | null): boolean { + // No embargo date set - allow download + if (!embargoDate) { + return false; + } + + // Get current date at start of day (00:00:00) + const today = DateTime.now().startOf('day'); + + // Get embargo date at start of day (00:00:00) + const embargoDateOnly = embargoDate.startOf('day'); + + // File is under embargo if embargo date is after today + // This means the embargo lifts at the start of the embargo date + return embargoDateOnly >= today; } } diff --git a/app/Controllers/Http/Editor/DatasetController.ts b/app/Controllers/Http/Editor/DatasetController.ts index 5ec3910..8911ed7 100644 --- a/app/Controllers/Http/Editor/DatasetController.ts +++ b/app/Controllers/Http/Editor/DatasetController.ts @@ -252,7 +252,6 @@ export default class DatasetsController { dataset.reject_editor_note = null; } - //save main and additional titles const reviewer_id = request.input('reviewer_id', null); dataset.reviewer_id = reviewer_id; @@ -290,8 +289,6 @@ export default class DatasetsController { }); } - - public async rejectUpdate({ request, response, auth }: HttpContext) { const authUser = auth.user!; @@ -402,12 +399,10 @@ export default class DatasetsController { .back(); } - - return inertia.render('Editor/Dataset/Publish', { dataset, - can: { - reject: await auth.user?.can(['dataset-editor-reject']), + can: { + reject: await auth.user?.can(['dataset-editor-reject']), publish: await auth.user?.can(['dataset-publish']), }, }); @@ -454,7 +449,7 @@ export default class DatasetsController { public async rejectToReviewer({ request, inertia, response }: HttpContext) { const id = request.param('id'); const dataset = await Dataset.query() - .where('id', id) + .where('id', id) .preload('reviewer', (builder) => { builder.select('id', 'login', 'email'); }) @@ -555,7 +550,6 @@ export default class DatasetsController { } } - return response .flash( `You have successfully rejected dataset ${dataset.id} reviewed by ${dataset.reviewer.login}.${emailStatusMessage}`, @@ -605,11 +599,13 @@ export default class DatasetsController { 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 { + // save modified date of datset for re-caching model in db an update the search index + dataset.server_date_modified = DateTime.now(); + // autoUpdate: true only triggers when dataset.save() is called, not when saving a related model like below + await dataset.save(); await dataset.related('identifier').save(doiIdentifier); const index_name = 'tethys-records'; await Index.indexDocument(dataset, index_name); @@ -900,6 +896,7 @@ export default class DatasetsController { const input = request.only(['project_id', 'embargo_date', 'language', 'type', 'creating_corporation']); // dataset.type = request.input('type'); dataset.merge(input); + dataset.server_date_modified = DateTime.now(); // let test: boolean = dataset.$isDirty; await dataset.useTransaction(trx).save(); @@ -1121,9 +1118,20 @@ export default class DatasetsController { // const filePath = await drive.use('local').getUrl('/'+ file.filePath) const filePath = file.filePath; const fileExt = file.filePath.split('.').pop() || ''; + + // Check if label already includes the extension + const fileName = file.label.toLowerCase().endsWith(`.${fileExt.toLowerCase()}`) ? file.label : `${file.label}.${fileExt}`; + // Set the response headers and download the file - response.header('Content-Type', file.mime_type || 'application/octet-stream'); - response.attachment(`${file.label}.${fileExt}`); + response + .header('Cache-Control', 'no-cache private') + .header('Content-Description', 'File Transfer') + .header('Content-Type', file.mime_type || 'application/octet-stream') + // .header('Content-Disposition', 'inline; filename=' + fileName) + .header('Content-Transfer-Encoding', 'binary') + .header('Access-Control-Allow-Origin', '*') + .header('Access-Control-Allow-Methods', 'GET'); + response.attachment(fileName); return response.download(filePath); } diff --git a/app/Controllers/Http/Reviewer/DatasetController.ts b/app/Controllers/Http/Reviewer/DatasetController.ts index 6b54772..27f9b46 100644 --- a/app/Controllers/Http/Reviewer/DatasetController.ts +++ b/app/Controllers/Http/Reviewer/DatasetController.ts @@ -107,13 +107,12 @@ export default class DatasetsController { } return inertia.render('Reviewer/Dataset/Review', { - dataset, + dataset, can: { review: await auth.user?.can(['dataset-review']), reject: await auth.user?.can(['dataset-review-reject']), }, }); - } public async review_old({ request, inertia, response, auth }: HttpContext) { @@ -370,6 +369,19 @@ export default class DatasetsController { .flash(`You have rejected dataset ${dataset.id}! to editor ${dataset.editor.login}`, 'message'); } + // public async download({ params, response }: HttpContext) { + // const id = params.id; + // // Find the file by ID + // const file = await File.findOrFail(id); + // // const filePath = await drive.use('local').getUrl('/'+ file.filePath) + // const filePath = file.filePath; + // const fileExt = file.filePath.split('.').pop() || ''; + // // Set the response headers and download the file + // response.header('Content-Type', file.mime_type || 'application/octet-stream'); + // response.attachment(`${file.label}.${fileExt}`); + // return response.download(filePath); + // } + public async download({ params, response }: HttpContext) { const id = params.id; // Find the file by ID @@ -377,9 +389,20 @@ export default class DatasetsController { // const filePath = await drive.use('local').getUrl('/'+ file.filePath) const filePath = file.filePath; const fileExt = file.filePath.split('.').pop() || ''; + + // Check if label already includes the extension + const fileName = file.label.toLowerCase().endsWith(`.${fileExt.toLowerCase()}`) ? file.label : `${file.label}.${fileExt}`; + // Set the response headers and download the file - response.header('Content-Type', file.mime_type || 'application/octet-stream'); - response.attachment(`${file.label}.${fileExt}`); + response + .header('Cache-Control', 'no-cache private') + .header('Content-Description', 'File Transfer') + .header('Content-Type', file.mime_type || 'application/octet-stream') + // .header('Content-Disposition', 'inline; filename=' + fileName) + .header('Content-Transfer-Encoding', 'binary') + .header('Access-Control-Allow-Origin', '*') + .header('Access-Control-Allow-Methods', 'GET'); + response.attachment(fileName); return response.download(filePath); } } diff --git a/app/Controllers/Http/Submitter/DatasetController.ts b/app/Controllers/Http/Submitter/DatasetController.ts index 245b5d9..b7bb7a0 100644 --- a/app/Controllers/Http/Submitter/DatasetController.ts +++ b/app/Controllers/Http/Submitter/DatasetController.ts @@ -233,7 +233,7 @@ export default class DatasetController { .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255), + first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), last_name: vine.string().trim().minLength(3).maxLength(255), }), ) @@ -249,7 +249,7 @@ export default class DatasetController { .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255), + first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), last_name: vine.string().trim().minLength(3).maxLength(255), pivot_contributor_type: vine.enum(Object.keys(ContributorTypes)), }), @@ -324,7 +324,7 @@ export default class DatasetController { .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255), + first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), last_name: vine.string().trim().minLength(3).maxLength(255), }), ) @@ -340,7 +340,7 @@ export default class DatasetController { .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255), + first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), last_name: vine.string().trim().minLength(3).maxLength(255), pivot_contributor_type: vine.enum(Object.keys(ContributorTypes)), }), @@ -983,19 +983,6 @@ export default class DatasetController { 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, @@ -1015,7 +1002,7 @@ export default class DatasetController { referenceIdentifierTypes: Object.entries(ReferenceIdentifierTypes).map(([key, value]) => ({ value: key, label: value })), relationTypes: Object.entries(RelationTypes).map(([key, value]) => ({ value: key, label: value })), doctypes: DatasetTypes, - can: { + can: { edit: await auth.user?.can(['dataset-edit']), delete: await auth.user?.can(['dataset-delete']), }, @@ -1163,42 +1150,93 @@ export default class DatasetController { } } - // Process all subjects/keywords from the request - const subjects = request.input('subjects'); + // ============================================ + // IMPROVED SUBJECTS PROCESSING + // ============================================ + const subjects = request.input('subjects', []); + const currentDatasetSubjectIds = new Set(); + for (const subjectData of subjects) { - // Case 1: Subject already exists in the database (has an ID) + let subjectToRelate: Subject; + + // Case 1: Subject has an ID (existing subject being updated) 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; + // Check if the updated value conflicts with another existing subject + const duplicateSubject = await Subject.query() + .where('value', subjectData.value) + .where('type', subjectData.type) + .where('language', subjectData.language || 'en') // Default language if not provided + .where('id', '!=', subjectData.id) // Exclude the current subject + .first(); - // Only save if there are actual changes - if (existingSubject.$isDirty) { - await existingSubject.save(); + if (duplicateSubject) { + // A duplicate exists - use the existing duplicate instead + subjectToRelate = duplicateSubject; + + // Check if the original subject should be deleted (if it's only used by this dataset) + const originalSubjectUsage = await Subject.query() + .where('id', existingSubject.id) + .withCount('datasets') + .firstOrFail(); + + if (originalSubjectUsage.$extras.datasets_count <= 1) { + // Only used by this dataset, safe to delete after detaching + await dataset.useTransaction(trx).related('subjects').detach([existingSubject.id]); + await existingSubject.useTransaction(trx).delete(); + } else { + // Used by other datasets, just detach from this one + await dataset.useTransaction(trx).related('subjects').detach([existingSubject.id]); + } + } else { + // No duplicate found, update the existing subject + existingSubject.value = subjectData.value; + existingSubject.type = subjectData.type; + existingSubject.language = subjectData.language; + existingSubject.external_key = subjectData.external_key; + + if (existingSubject.$isDirty) { + await existingSubject.useTransaction(trx).save(); + } + + subjectToRelate = existingSubject; } - - // Note: The relationship between dataset and subject is already established, - // so we don't need to attach it again } // Case 2: New subject being added (no ID) else { - // Check if a subject with the same value and type already exists in the database - const subject = await Subject.firstOrNew({ value: subjectData.value, type: subjectData.type }, subjectData); + // Use firstOrNew to either find existing or create new subject + subjectToRelate = await Subject.firstOrNew( + { + value: subjectData.value, + type: subjectData.type, + language: subjectData.language || 'en', + }, + { + value: subjectData.value, + type: subjectData.type, + language: subjectData.language || 'en', + external_key: subjectData.external_key, + }, + ); - if (subject.$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]); + if (subjectToRelate.$isNew) { + await subjectToRelate.useTransaction(trx).save(); } } + + // Ensure the relationship exists between dataset and subject + const relationshipExists = await dataset.related('subjects').query().where('subject_id', subjectToRelate.id).first(); + + if (!relationshipExists) { + await dataset.useTransaction(trx).related('subjects').attach([subjectToRelate.id]); + } + + // Track which subjects should remain associated with this dataset + currentDatasetSubjectIds.add(subjectToRelate.id); } + // Handle explicit deletions const subjectsToDelete = request.input('subjectsToDelete', []); for (const subjectData of subjectsToDelete) { if (subjectData.id) { @@ -1211,16 +1249,16 @@ export default class DatasetController { .withCount('datasets') .firstOrFail(); - // Check if the subject is used by multiple datasets - if (subject.$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 + // Detach the subject from this dataset + await dataset.useTransaction(trx).related('subjects').detach([subject.id]); - await dataset.useTransaction(trx).related('subjects').detach([subject.id]); + // If this was the only dataset using this subject, delete it entirely + if (subject.$extras.datasets_count <= 1) { await subject.useTransaction(trx).delete(); } + + // Remove from current set if it was added earlier + currentDatasetSubjectIds.delete(subjectData.id); } } diff --git a/app/models/person.ts b/app/models/person.ts index cdc612d..f4cf3a2 100644 --- a/app/models/person.ts +++ b/app/models/person.ts @@ -30,7 +30,7 @@ export default class Person extends BaseModel { @column({}) public lastName: string; - @column({}) + @column({ columnName: 'identifier_orcid' }) public identifierOrcid: string; @column({}) @@ -95,4 +95,34 @@ export default class Person extends BaseModel { pivotColumns: ['role', 'sort_order', 'allow_email_contact'], }) public datasets: ManyToMany; + + // public toJSON() { + // const json = super.toJSON(); + + // // Check if this person is loaded through a pivot relationship with sensitive roles + // const pivotRole = this.$extras?.pivot_role; + // if (pivotRole === 'author' || pivotRole === 'contributor') { + // // Remove sensitive information for public-facing roles + // delete json.email; + // // delete json.identifierOrcid; + // } + + // return json; + // } + + // @afterFind() + // public static async afterFindHook(person: Person) { + // if (person.$extras?.pivot_role === 'author' || person.$extras?.pivot_role === 'contributor') { + // person.email = undefined as any; + // } + // } + + // @afterFetch() + // public static async afterFetchHook(persons: Person[]) { + // persons.forEach(person => { + // if (person.$extras?.pivot_role === 'author' || person.$extras?.pivot_role === 'contributor') { + // person.email = undefined as any; + // } + // }); + // } } diff --git a/app/models/user.ts b/app/models/user.ts index 5dbaab4..7be02b9 100644 --- a/app/models/user.ts +++ b/app/models/user.ts @@ -89,24 +89,11 @@ export default class User extends compose(BaseModel, AuthFinder) { @column({}) public avatar: string; - // @hasOne(() => TotpSecret, { - // foreignKey: 'user_id', - // }) - // public totp_secret: HasOne; - - // @beforeSave() - // public static async hashPassword(user: User) { - // if (user.$dirty.password) { - // user.password = await hash.use('laravel').make(user.password); - // } - // } - public get isTwoFactorEnabled(): boolean { return Boolean(this?.twoFactorSecret && this.state == TotpState.STATE_ENABLED); // return Boolean(this.totp_secret?.twoFactorSecret); } - @manyToMany(() => Role, { pivotForeignKey: 'account_id', pivotRelatedForeignKey: 'role_id', @@ -142,7 +129,9 @@ export default class User extends compose(BaseModel, AuthFinder) { @beforeFind() @beforeFetch() public static preloadRoles(user: User) { - user.preload('roles') + user.preload('roles', (builder) => { + builder.select(['id', 'name', 'display_name', 'description']); + }); } public async getBackupCodes(this: User): Promise { diff --git a/app/validators/dataset.ts b/app/validators/dataset.ts index 5417463..0429168 100644 --- a/app/validators/dataset.ts +++ b/app/validators/dataset.ts @@ -67,8 +67,9 @@ export const createDatasetValidator = vine.compile( .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255), + first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), last_name: vine.string().trim().minLength(3).maxLength(255), + identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(), }), ) .minLength(1) @@ -83,9 +84,10 @@ export const createDatasetValidator = vine.compile( .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255), + first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), last_name: vine.string().trim().minLength(3).maxLength(255), pivot_contributor_type: vine.enum(Object.keys(ContributorTypes)), + identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(), }), ) .distinct('email') @@ -214,8 +216,9 @@ export const updateDatasetValidator = vine.compile( .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255), + first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), last_name: vine.string().trim().minLength(3).maxLength(255), + identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(), }), ) .minLength(1) @@ -230,8 +233,9 @@ export const updateDatasetValidator = vine.compile( .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255), + first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), last_name: vine.string().trim().minLength(3).maxLength(255), + identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(), pivot_contributor_type: vine.enum(Object.keys(ContributorTypes)), }), ) @@ -307,10 +311,9 @@ export const updateDatasetValidator = vine.compile( .dependentArrayMinLength({ dependentArray: 'fileInputs', min: 1 }), fileInputs: vine.array( vine.object({ - label: vine.string().trim().maxLength(100), - //extnames: extensions, + label: vine.string().trim().maxLength(100), }), - ), + ).optional(), }), ); @@ -365,8 +368,9 @@ export const updateEditorDatasetValidator = vine.compile( .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255), + first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), last_name: vine.string().trim().minLength(3).maxLength(255), + identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(), }), ) .minLength(1) @@ -381,8 +385,9 @@ export const updateEditorDatasetValidator = vine.compile( .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255), + first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), last_name: vine.string().trim().minLength(3).maxLength(255), + identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(), pivot_contributor_type: vine.enum(Object.keys(ContributorTypes)), }), ) diff --git a/commands/index_datasets.ts b/commands/index_datasets.ts index ee76268..44ebeb2 100644 --- a/commands/index_datasets.ts +++ b/commands/index_datasets.ts @@ -12,10 +12,8 @@ import { getDomain } from '#app/utils/utility-functions'; import { BaseCommand, flags } from '@adonisjs/core/ace'; import { CommandOptions } from '@adonisjs/core/types/ace'; import env from '#start/env'; -// import db from '@adonisjs/lucid/services/db'; -// import { default as Dataset } from '#models/dataset'; import logger from '@adonisjs/core/services/logger'; - +import { DateTime } from 'luxon'; const opensearchNode = env.get('OPENSEARCH_HOST', 'localhost'); const client = new Client({ node: `${opensearchNode}` }); // replace with your OpenSearch endpoint @@ -30,11 +28,10 @@ export default class IndexDatasets extends BaseCommand { public publish_id: number; public static options: CommandOptions = { - startApp: true, - staysAlive: false, + startApp: true, // Ensures the IoC container is ready to use + staysAlive: false, // Command exits after running }; - async run() { logger.debug('Hello world!'); // const { default: Dataset } = await import('#models/dataset'); @@ -44,10 +41,12 @@ export default class IndexDatasets extends BaseCommand { const index_name = 'tethys-records'; for (var dataset of datasets) { - // Logger.info(`File publish_id ${dataset.publish_id}`); - // const jsonString = await this.getJsonString(dataset, proc); - // console.log(jsonString); - await this.indexDocument(dataset, index_name, proc); + const shouldUpdate = await this.shouldUpdateDataset(dataset, index_name); + if (shouldUpdate) { + await this.indexDocument(dataset, index_name, proc); + } else { + logger.info(`Dataset with publish_id ${dataset.publish_id} is up to date, skipping indexing`); + } } } @@ -65,6 +64,46 @@ export default class IndexDatasets extends BaseCommand { return await query.exec(); } + private async shouldUpdateDataset(dataset: Dataset, index_name: string): Promise { + try { + // Check if publish_id exists before proceeding + if (!dataset.publish_id) { + // Return true to update since document doesn't exist in OpenSearch yet + return true; + } + // Get the existing document from OpenSearch + const response = await client.get({ + index: index_name, + id: dataset.publish_id?.toString(), + }); + + const existingDoc = response.body._source; + + // Compare server_date_modified + if (existingDoc && existingDoc.server_date_modified) { + // Convert Unix timestamp (seconds) to milliseconds for DateTime.fromMillis() + const existingModified = DateTime.fromMillis(Number(existingDoc.server_date_modified) * 1000); + const currentModified = dataset.server_date_modified; + + // Only update if the dataset has been modified more recently + if (currentModified <= existingModified) { + return false; + } + } + + return true; + } catch (error) { + // If document doesn't exist or other error, we should index it + if (error.statusCode === 404) { + logger.info(`Dataset with publish_id ${dataset.publish_id} not found in index, will create new document`); + return true; + } + + logger.warn(`Error checking existing document for publish_id ${dataset.publish_id}: ${error.message}`); + return true; // Index anyway if we can't determine the status + } + } + private async indexDocument(dataset: Dataset, index_name: string, proc: Buffer): Promise { try { const doc = await this.getJsonString(dataset, proc); @@ -78,7 +117,8 @@ export default class IndexDatasets extends BaseCommand { }); logger.info(`dataset with publish_id ${dataset.publish_id} successfully indexed`); } catch (error) { - logger.error(`An error occurred while indexing dataset with publish_id ${dataset.publish_id}.`); + logger.error(`An error occurred while indexing dataset with publish_id ${dataset.publish_id}. + Error: ${error.message}`); } } diff --git a/package-lock.json b/package-lock.json index 6b10877..d266b68 100644 --- a/package-lock.json +++ b/package-lock.json @@ -131,9 +131,9 @@ } }, "node_modules/@adonisjs/application": { - "version": "8.4.1", - "resolved": "https://registry.npmjs.org/@adonisjs/application/-/application-8.4.1.tgz", - "integrity": "sha512-2vwO/8DoKJ9AR4Vvllz08RcomBoETc3FMf+q+ri1BVVjc76tLGV3KcYZp8+uKOuEreiK6poQ7NwJrR1P5ANA/w==", + "version": "8.4.2", + "resolved": "https://registry.npmjs.org/@adonisjs/application/-/application-8.4.2.tgz", + "integrity": "sha512-gxyQgl1n7M/hv7ZKQOlTo2adBMehjEO0ssWSG3AGW2RXdCvkHQKlatFXMuXJMmGg2P1AWJX0LEiXey9+qxC9Uw==", "license": "MIT", "dependencies": { "@poppinss/hooks": "^7.2.5", @@ -182,13 +182,13 @@ } }, "node_modules/@adonisjs/auth": { - "version": "9.4.0", - "resolved": 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"@poppinss/exception": "^1.2.1", + "@poppinss/object-builder": "^1.1.0", + "@poppinss/string": "^1.6.0", + "@poppinss/types": "^1.1.0", + "flattie": "^1.1.1", + "safe-stable-stringify": "^2.5.0", + "secure-json-parse": "^4.0.0" + } + }, + "node_modules/@adonisjs/fold/node_modules/secure-json-parse": { + "version": "4.0.0", + "resolved": "https://registry.npmjs.org/secure-json-parse/-/secure-json-parse-4.0.0.tgz", + "integrity": "sha512-dxtLJO6sc35jWidmLxo7ij+Eg48PM/kleBsxpC8QJE0qJICe+KawkDQmvCMZUr9u7WKVHgMW6vy3fQ7zMiFZMA==", + "funding": [ + { + "type": "github", + "url": "https://github.com/sponsors/fastify" + }, + { + "type": "opencollective", + "url": "https://opencollective.com/fastify" + } + ], + "license": "BSD-3-Clause" + }, "node_modules/@adonisjs/hash": { "version": "9.1.1", "resolved": "https://registry.npmjs.org/@adonisjs/hash/-/hash-9.1.1.tgz", @@ -497,17 +529,17 @@ } }, "node_modules/@adonisjs/http-server": { - "version": "7.6.1", - "resolved": 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