diff --git a/Dockerfile b/Dockerfile index 9f88544..a5d1263 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,63 +1,57 @@ ################## First Stage - Creating base ######################### # Created a variable to hold our node base image -ARG NODE_IMAGE=node:22-trixie-slim +ARG NODE_IMAGE=node:22-bookworm-slim FROM $NODE_IMAGE AS base - # Install dumb-init and ClamAV, and perform ClamAV database update -RUN apt-get update \ - && apt-get install -y --no-install-recommends \ - dumb-init \ - clamav \ - clamav-daemon \ - clamdscan \ - ca-certificates \ +RUN apt update \ + && apt-get install -y dumb-init clamav clamav-daemon nano \ && rm -rf /var/lib/apt/lists/* \ # Creating folders and changing ownerships - && mkdir -p /home/node/app \ - && mkdir -p /var/lib/clamav \ + && 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 \ + # permissions && mkdir /var/run/clamav \ - && mkdir -p /var/log/clamav \ - && mkdir -p /tmp/clamav-logs \ - - # Set ownership and permissions - && chown node:node /home/node/app \ - # && chown -R node:clamav /var/lib/clamav /usr/local/share/clamav /etc/clamav /var/run/clamav \ - && chown -R node:clamav /var/lib/clamav /usr/local/share/clamav /etc/clamav /var/run/clamav /var/log/clamav \ - && chown -R node:clamav /etc/clamav \ - && chmod 755 /tmp/clamav-logs \ - && chmod 750 /var/run/clamav \ - && chmod 755 /var/lib/clamav \ - && chmod 755 /var/log/clamav \ - # Add node user to clamav group and allow sudo for clamav commands - && usermod -a -G clamav node - # && chmod 666 /var/run/clamav/clamd.socket - # Make directories group-writable so node (as member of clamav group) can access them - # && chmod 750 /var/run/clamav /var/lib/clamav /var/log/clamav /tmp/clamav-logs + && chown node:clamav /var/run/clamav \ + && chmod 750 /var/run/clamav +# ----------------------------------------------- +# --- ClamAV & FeshClam ------------------------- +# ----------------------------------------------- +# RUN \ +# chmod 644 /etc/clamav/freshclam.conf && \ +# freshclam && \ +# mkdir /var/run/clamav && \ + # chown -R clamav:root /var/run/clamav +# # initial update of av databases +# RUN freshclam -# Configure ClamAV - copy config files before switching user -# COPY --chown=node:clamav ./*.conf /etc/clamav/ +# 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 # Setting the working directory WORKDIR /home/node/app # Changing the current active user to "node" - -# Download initial ClamAV database as root before switching users USER node -RUN freshclam --quiet || echo "Initial database download failed - will retry at runtime" -# Copy entrypoint script +# initial update of av databases +RUN freshclam + +# VOLUME /var/lib/clamav COPY --chown=node:clamav docker-entrypoint.sh /home/node/app/docker-entrypoint.sh RUN chmod +x /home/node/app/docker-entrypoint.sh ENV TZ="Europe/Vienna" + + ################## Second Stage - Installing dependencies ########## # In this stage, we will start installing dependencies FROM base AS dependencies @@ -76,6 +70,7 @@ ENV NODE_ENV=production # We run "node ace build" to build the app (dist folder) for production RUN node ace build --ignore-ts-errors # RUN node ace build --production +# RUN node ace build --ignore-ts-errors ################## Final Stage - Production ######################### @@ -93,7 +88,6 @@ RUN npm ci --omit=dev # Copy files to the working directory from the build folder the user COPY --chown=node:node --from=build /home/node/app/build . # Expose port -# EXPOSE 3310 EXPOSE 3333 ENTRYPOINT ["/home/node/app/docker-entrypoint.sh"] # Run the command to start the server using "dumb-init" diff --git a/LICENSE b/LICENSE deleted file mode 100644 index 23bb390..0000000 --- a/LICENSE +++ /dev/null @@ -1,22 +0,0 @@ - -MIT License - -Copyright (c) 2025 Tethys Research Repository - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE \ No newline at end of file diff --git a/adonisrc.ts b/adonisrc.ts index 824d4c8..19e946c 100644 --- a/adonisrc.ts +++ b/adonisrc.ts @@ -11,10 +11,9 @@ 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 @@ -27,17 +26,16 @@ export default defineConfig({ () => import('./start/routes.js'), () => import('./start/kernel.js'), () => import('#start/validator'), - // () => import('#start/rules/unique'), - // () => import('#start/rules/translated_language'), - // () => import('#start/rules/unique_person'), - // // () => import('#start/rules/file_length'), - // // () => import('#start/rules/file_scan'), - // // () => import('#start/rules/allowed_extensions_mimetypes'), - // () => import('#start/rules/dependent_array_min_length'), - // () => import('#start/rules/referenceValidation'), - // () => import('#start/rules/valid_mimetype'), - // () => import('#start/rules/array_contains_types'), - // () => import('#start/rules/orcid'), + () => import('#start/rules/unique'), + () => import('#start/rules/translated_language'), + () => import('#start/rules/unique_person'), + () => import('#start/rules/file_length'), + () => import('#start/rules/file_scan'), + () => import('#start/rules/allowed_extensions_mimetypes'), + () => import('#start/rules/dependent_array_min_length'), + () => import('#start/rules/referenceValidation'), + () => import('#start/rules/valid_mimetype'), + () => import('#start/rules/array_contains_types'), ], /* |-------------------------------------------------------------------------- @@ -72,7 +70,7 @@ export default defineConfig({ () => import('#providers/stardust_provider'), () => import('#providers/query_builder_provider'), () => import('#providers/token_worker_provider'), - () => import('#providers/rule_provider'), + // () => import('#providers/validator_provider'), // () => import('#providers/drive/provider/drive_provider'), () => import('@adonisjs/drive/drive_provider'), // () => import('@adonisjs/core/providers/vinejs_provider'), diff --git a/app/Controllers/Http/Api/AuthorsController.ts b/app/Controllers/Http/Api/AuthorsController.ts index 2b0bae1..7209699 100644 --- a/app/Controllers/Http/Api/AuthorsController.ts +++ b/app/Controllers/Http/Api/AuthorsController.ts @@ -4,29 +4,20 @@ import Person from '#models/person'; // node ace make:controller Author export default class AuthorsController { - public async index({}: HttpContext) { - + 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")); const authors = await Person.query() - .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'); + .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 d7c532f..74fe135 100644 --- a/app/Controllers/Http/Api/AvatarController.ts +++ b/app/Controllers/Http/Api/AvatarController.ts @@ -2,46 +2,26 @@ import type { HttpContext } from '@adonisjs/core/http'; import { StatusCodes } from 'http-status-codes'; import redis from '@adonisjs/redis/services/main'; -const PREFIXES = ['von', 'van', 'de', 'del', 'della', 'di', 'da', 'dos', 'du', 'le', 'la']; +const PREFIXES = ['von', 'van']; 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']); - - // 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, - }); + if (!name) { + return response.status(StatusCodes.BAD_REQUEST).json({ error: 'Name is required' }); } // Build a unique cache key for the given name and size - const cacheKey = `avatar:${this.sanitizeName(name)}-${parsedSize.value}`; - // const cacheKey = `avatar:${name.trim().toLowerCase()}-${size}`; - try { - const cachedSvg = await redis.get(cacheKey); - if (cachedSvg) { - this.setResponseHeaders(response); - return response.send(cachedSvg); - } - } catch (redisError) { - // Log redis error but continue without cache - console.warn('Redis cache read failed:', redisError); + const cacheKey = `avatar:${name.trim().toLowerCase()}-${size}`; + const cachedSvg = await redis.get(cacheKey); + if (cachedSvg) { + this.setResponseHeaders(response); + return response.send(cachedSvg); } const initials = this.getInitials(name); @@ -49,85 +29,41 @@ export default class AvatarController { const svgContent = this.createSvg(size, colors, initials); // // Cache the generated avatar for future use, e.g. 1 hour expiry - try { - await redis.setex(cacheKey, CACHE_TTL, svgContent); - } catch (redisError) { - // Log but don't fail the request - console.warn('Redis cache write failed:', redisError); - } + await redis.setex(cacheKey, 3600, svgContent); this.setResponseHeaders(response); return response.send(svgContent); } catch (error) { - console.error('Avatar generation error:', error); - return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({ - error: 'Failed to generate avatar', - }); + return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({ error: error.message }); } } - 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 + const parts = name + .trim() .split(' ') - .filter((part) => part.length > 0) - .map((part) => part.trim()); + .filter((part) => part.length > 0); if (parts.length === 0) { return 'NA'; } - 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(); + if (parts.length >= 2) { + return this.getMultiWordInitials(parts); } - - return this.getMultiWordInitials(parts); + return parts[0].substring(0, 2).toUpperCase(); } private getMultiWordInitials(parts: string[]): string { - // Filter out prefixes and short words - const significantParts = parts.filter((part) => !PREFIXES.includes(part.toLowerCase()) && part.length > 1); + const firstName = parts[0]; + const lastName = parts[parts.length - 1]; + const firstInitial = firstName.charAt(0).toUpperCase(); + const lastInitial = lastName.charAt(0).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(); + if (PREFIXES.includes(lastName.toLowerCase()) && lastName === lastName.toUpperCase()) { + return firstInitial + lastName.charAt(1).toUpperCase(); } - - 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(); + return firstInitial + lastInitial; } private generateColors(name: string): { background: string; text: string } { @@ -139,44 +75,31 @@ export default class AvatarController { } private createSvg(size: number, colors: { background: string; text: string }, initials: string): string { - 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, '''); + const fontSize = size * FONT_SIZE_RATIO; + return ` + + + ${initials} + + `; } private setResponseHeaders(response: HttpContext['response']): void { - response.header('Content-Type', 'image/svg+xml'); - response.header('Cache-Control', 'public, max-age=86400'); // Cache for 1 day - response.header('ETag', `"${Date.now()}"`); // Simple ETag + response.header('Content-type', 'image/svg+xml'); + response.header('Cache-Control', 'no-cache'); + response.header('Pragma', 'no-cache'); + response.header('Expires', '0'); } private getColorFromName(name: string): string { let hash = 0; - 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 + for (let i = 0; i < name.length; i++) { + hash = name.charCodeAt(i) + ((hash << 5) - hash); } - // Ensure we get vibrant colors by constraining the color space const colorParts = []; for (let i = 0; i < 3; i++) { - let value = (hash >> (i * 8)) & 0xff; - // Ensure minimum color intensity for better contrast - value = Math.max(50, value); + const value = (hash >> (i * 8)) & 0xff; colorParts.push(value.toString(16).padStart(2, '0')); } return colorParts.join(''); @@ -187,7 +110,7 @@ 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 + (255 - value) * (percent / 100))); + const lightenValue = (value: number) => Math.min(255, Math.floor((value * (100 + percent)) / 100)); const newR = lightenValue(r); const newG = lightenValue(g); @@ -201,7 +124,7 @@ 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.max(0, Math.floor(value * COLOR_DARKENING_FACTOR)); + const darkenValue = (value: number) => Math.round(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 9106521..b80949d 100644 --- a/app/Controllers/Http/Api/DatasetController.ts +++ b/app/Controllers/Http/Api/DatasetController.ts @@ -1,36 +1,24 @@ import type { HttpContext } from '@adonisjs/core/http'; +// import Person from 'App/Models/Person'; import Dataset from '#models/dataset'; import { StatusCodes } from 'http-status-codes'; -import DatasetReference from '#models/dataset_reference'; // node ace make:controller Author export default class DatasetController { - /** - * GET /api/datasets - * Find all published datasets - */ - public async index({ response }: HttpContext) { - try { - const datasets = await Dataset.query() - .where(function (query) { - query.where('server_state', 'published').orWhere('server_state', 'deleted'); - }) - .preload('titles') - .preload('identifier') - .orderBy('server_date_published', 'desc'); + public async index({}: HttpContext) { + // 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'); + }) + .preload('titles') + .preload('identifier') + .orderBy('server_date_published', 'desc'); - return response.status(StatusCodes.OK).json(datasets); - } catch (error) { - return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({ - message: error.message || 'Some error occurred while retrieving datasets.', - }); - } + return datasets; } - /** - * GET /api/dataset - * Find all published datasets - */ public async findAll({ response }: HttpContext) { try { const datasets = await Dataset.query() @@ -46,279 +34,34 @@ export default class DatasetController { } } - /** - * GET /api/dataset/:publish_id - * Find one dataset by publish_id - */ - public async findOne({ response, params }: HttpContext) { - try { - const dataset = await Dataset.query() - .where('publish_id', params.publish_id) - .preload('titles') - .preload('descriptions') // Using 'descriptions' instead of 'abstracts' - .preload('user', (builder) => { - builder.select(['id', 'firstName', 'lastName', 'avatar', 'login']); - }) - .preload('authors', (builder) => { - 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 - .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') - .preload('licenses') - .preload('references') - .preload('project') - // .preload('referenced_by', (builder) => { - // builder.preload('dataset', (builder) => { - // builder.preload('identifier'); - // }); - // }) - .preload('files', (builder) => { - builder.preload('hashvalues'); - }) - .preload('identifier') - .first(); // Use first() instead of firstOrFail() to handle not found gracefully - - if (!dataset) { - return response.status(StatusCodes.NOT_FOUND).json({ - message: `Cannot find Dataset with publish_id=${params.publish_id}.`, + public async findOne({ params }: HttpContext) { + const datasets = await Dataset.query() + .where('publish_id', params.publish_id) + .preload('titles') + .preload('descriptions') + .preload('user') + .preload('authors', (builder) => { + builder.orderBy('pivot_sort_order', 'asc'); + }) + .preload('contributors', (builder) => { + builder.orderBy('pivot_sort_order', 'asc'); + }) + .preload('subjects') + .preload('coverage') + .preload('licenses') + .preload('references') + .preload('project') + .preload('referenced_by', (builder) => { + builder.preload('dataset', (builder) => { + builder.preload('identifier'); }); - } + }) + .preload('files', (builder) => { + builder.preload('hashvalues'); + }) + .preload('identifier') + .firstOrFail(); - // Build the version chain - const versionChain = await this.buildVersionChain(dataset); - - // Add version chain to response - const responseData = { - ...dataset.toJSON(), - versionChain: versionChain, - }; - - // return response.status(StatusCodes.OK).json(dataset); - return response.status(StatusCodes.OK).json(responseData); - } catch (error) { - return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({ - message: error.message || `Error retrieving Dataset with publish_id=${params.publish_id}.`, - }); - } - } - - /** - * GET /:prefix/:value - * Find dataset by identifier (e.g., https://doi.tethys.at/10.24341/tethys.99.2) - */ - public async findByIdentifier({ response, params }: HttpContext) { - const identifierValue = `${params.prefix}/${params.value}`; - - // Optional: Validate DOI format - if (!identifierValue.match(/^10\.\d+\/[a-zA-Z0-9._-]+\.[0-9]+(?:\.[0-9]+)*$/)) { - return response.status(StatusCodes.BAD_REQUEST).json({ - message: `Invalid DOI format: ${identifierValue}`, - }); - } - - try { - // Method 1: Using subquery with whereIn (most similar to your original) - const dataset = await Dataset.query() - // .whereIn('id', (subQuery) => { - // subQuery.select('dataset_id').from('dataset_identifiers').where('value', identifierValue); - // }) - .whereHas('identifier', (builder) => { - builder.where('value', identifierValue); - }) - .preload('titles') - .preload('descriptions') // Using 'descriptions' instead of 'abstracts' - .preload('user', (builder) => { - builder.select(['id', 'firstName', 'lastName', 'avatar', 'login']); - }) - .preload('authors', (builder) => { - builder - .select(['id', 'academic_title', 'first_name', 'last_name', 'identifier_orcid', 'status', 'name_type']) - .withCount('datasets', (query) => { - query.as('datasets_count'); - }) - .pivotColumns(['role', 'sort_order']) - .wherePivot('role', 'author') - .orderBy('pivot_sort_order', 'asc'); - }) - .preload('contributors', (builder) => { - builder - .select(['id', 'academic_title', 'first_name', 'last_name', 'identifier_orcid', 'status', 'name_type']) - .withCount('datasets', (query) => { - query.as('datasets_count'); - }) - .pivotColumns(['role', 'sort_order', 'contributor_type']) - .wherePivot('role', 'contributor') - .orderBy('pivot_sort_order', 'asc'); - }) - .preload('subjects') - .preload('coverage') - .preload('licenses') - .preload('references') - .preload('project') - // .preload('referenced_by', (builder) => { - // builder.preload('dataset', (builder) => { - // builder.preload('identifier'); - // }); - // }) - .preload('files', (builder) => { - builder.preload('hashvalues'); - }) - .preload('identifier') - .first(); - - if (!dataset) { - return response.status(StatusCodes.NOT_FOUND).json({ - message: `Cannot find Dataset with identifier=${identifierValue}.`, - }); - } - // Build the version chain - const versionChain = await this.buildVersionChain(dataset); - - // Add version chain to response - const responseData = { - ...dataset.toJSON(), - versionChain: versionChain, - }; - - // return response.status(StatusCodes.OK).json(dataset); - return response.status(StatusCodes.OK).json(responseData); - } catch (error) { - return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({ - message: error.message || `Error retrieving Dataset with identifier=${identifierValue}.`, - }); - } - } - - /** - * Build the complete version chain for a dataset - * Traverses both backwards (previous versions) and forwards (newer versions) - */ - private async buildVersionChain(dataset: Dataset) { - const versionChain = { - current: { - id: dataset.id, - publish_id: dataset.publish_id, - doi: dataset.identifier?.value || null, - main_title: dataset.mainTitle || null, - server_date_published: dataset.server_date_published, - }, - previousVersions: [] as any[], - newerVersions: [] as any[], - }; - - // Get all previous versions (going backwards in time) - versionChain.previousVersions = await this.getPreviousVersions(dataset.id); - - // Get all newer versions (going forwards in time) - versionChain.newerVersions = await this.getNewerVersions(dataset.id); - - return versionChain; - } - - /** - * Recursively get all previous versions - */ - private async getPreviousVersions(datasetId: number, visited: Set = new Set()): Promise { - // Prevent infinite loops - if (visited.has(datasetId)) { - return []; - } - visited.add(datasetId); - - const previousVersions: any[] = []; - - // Find references where this dataset "IsNewVersionOf" another dataset - const previousRefs = await DatasetReference.query() - .where('document_id', datasetId) - .where('relation', 'IsNewVersionOf') - .whereNotNull('related_document_id'); - - for (const ref of previousRefs) { - if (!ref.related_document_id) continue; - - const previousDataset = await Dataset.query() - .where('id', ref.related_document_id) - .preload('identifier') - .preload('titles') - .first(); - - if (previousDataset) { - const versionInfo = { - id: previousDataset.id, - publish_id: previousDataset.publish_id, - doi: previousDataset.identifier?.value || null, - main_title: previousDataset.mainTitle || null, - server_date_published: previousDataset.server_date_published, - relation: 'IsPreviousVersionOf', // From perspective of current dataset - }; - - previousVersions.push(versionInfo); - - // Recursively get even older versions - const olderVersions = await this.getPreviousVersions(previousDataset.id, visited); - previousVersions.push(...olderVersions); - } - } - - return previousVersions; - } - - /** - * Recursively get all newer versions - */ - private async getNewerVersions(datasetId: number, visited: Set = new Set()): Promise { - // Prevent infinite loops - if (visited.has(datasetId)) { - return []; - } - visited.add(datasetId); - - const newerVersions: any[] = []; - - // Find references where this dataset "IsPreviousVersionOf" another dataset - const newerRefs = await DatasetReference.query() - .where('document_id', datasetId) - .where('relation', 'IsPreviousVersionOf') - .whereNotNull('related_document_id'); - - for (const ref of newerRefs) { - if (!ref.related_document_id) continue; - - const newerDataset = await Dataset.query().where('id', ref.related_document_id).preload('identifier').preload('titles').first(); - - if (newerDataset) { - const versionInfo = { - id: newerDataset.id, - publish_id: newerDataset.publish_id, - doi: newerDataset.identifier?.value || null, - main_title: newerDataset.mainTitle || null, - server_date_published: newerDataset.server_date_published, - relation: 'IsNewVersionOf', // From perspective of current dataset - }; - - newerVersions.push(versionInfo); - - // Recursively get even newer versions - const evenNewerVersions = await this.getNewerVersions(newerDataset.id, visited); - newerVersions.push(...evenNewerVersions); - } - } - - return newerVersions; + return datasets; } } diff --git a/app/Controllers/Http/Api/FileController.ts b/app/Controllers/Http/Api/FileController.ts index 8a400ad..8080479 100644 --- a/app/Controllers/Http/Api/FileController.ts +++ b/app/Controllers/Http/Api/FileController.ts @@ -2,103 +2,53 @@ import type { HttpContext } from '@adonisjs/core/http'; import File from '#models/file'; import { StatusCodes } from 'http-status-codes'; import * as fs from 'fs'; -import { DateTime } from 'luxon'; +import * as path from 'path'; // 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); - // 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(); + 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`, + }); + } - if (!file) { - return response.status(StatusCodes.NOT_FOUND).send({ + // 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 ${id} doesn't exist on file server`, + // }); + // }); + } else { + response.status(StatusCodes.NOT_FOUND).send({ message: `Cannot find File with id=${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}`; - - // Determine if file can be previewed inline in browser - const canPreviewInline = (mimeType: string): boolean => { - const type = mimeType.toLowerCase(); - return ( - type === 'application/pdf' || - type.startsWith('image/') || - type.startsWith('text/') || - type === 'application/json' || - type === 'application/xml' || - // Uncomment if you want video/audio inline - type.startsWith('video/') || - type.startsWith('audio/') - ); - }; - const disposition = canPreviewInline(file.mimeType) ? 'inline' : 'attachment'; - - 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', `${disposition}; filename="${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 04c450d..5ec3910 100644 --- a/app/Controllers/Http/Editor/DatasetController.ts +++ b/app/Controllers/Http/Editor/DatasetController.ts @@ -3,7 +3,7 @@ import { Client } from '@opensearch-project/opensearch'; import User from '#models/user'; import Dataset from '#models/dataset'; import DatasetIdentifier from '#models/dataset_identifier'; -import DatasetXmlSerializer from '#app/Library/DatasetXmlSerializer'; +import XmlModel from '#app/Library/XmlModel'; import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js'; import { create } from 'xmlbuilder2'; import { readFileSync } from 'fs'; @@ -252,6 +252,7 @@ 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; @@ -289,6 +290,8 @@ export default class DatasetsController { }); } + + public async rejectUpdate({ request, response, auth }: HttpContext) { const authUser = auth.user!; @@ -399,10 +402,12 @@ 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']), }, }); @@ -449,7 +454,7 @@ 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'); }) @@ -550,6 +555,7 @@ export default class DatasetsController { } } + return response .flash( `You have successfully rejected dataset ${dataset.id} reviewed by ${dataset.reviewer.login}.${emailStatusMessage}`, @@ -574,88 +580,53 @@ export default class DatasetsController { public async doiStore({ request, response }: HttpContext) { const dataId = request.param('publish_id'); - - // Load dataset with minimal required relationships - const dataset = await Dataset.query().where('publish_id', dataId).firstOrFail(); - - const prefix = process.env.DATACITE_PREFIX || ''; - const base_domain = process.env.BASE_DOMAIN || ''; - - // Generate DOI metadata XML + const dataset = await Dataset.query() + // .preload('xmlCache') + .where('publish_id', dataId) + .firstOrFail(); const xmlMeta = (await Index.getDoiRegisterString(dataset)) as string; - // Prepare DOI registration data - const doiValue = `${prefix}/tethys.${dataset.publish_id}`; //'10.21388/tethys.213' - const landingPageUrl = `https://doi.${getDomain(base_domain)}/${prefix}/tethys.${dataset.publish_id}`; //https://doi.dev.tethys.at/10.21388/tethys.213 + let prefix = ''; + let base_domain = ''; + // const datacite_environment = process.env.DATACITE_ENVIRONMENT || 'debug'; + prefix = process.env.DATACITE_PREFIX || ''; + base_domain = process.env.BASE_DOMAIN || ''; - // Register DOI with DataCite + // register DOI: + const doiValue = prefix + '/tethys.' + dataset.publish_id; //'10.21388/tethys.213' + const landingPageUrl = 'https://doi.' + getDomain(base_domain) + '/' + prefix + '/tethys.' + dataset.publish_id; //https://doi.dev.tethys.at/10.21388/tethys.213 const doiClient = new DoiClient(); const dataciteResponse = await doiClient.registerDoi(doiValue, xmlMeta, landingPageUrl); - if (dataciteResponse?.status !== 201) { + if (dataciteResponse?.status === 201) { + // if response OK 201; save the Identifier value into db + const doiIdentifier = new DatasetIdentifier(); + doiIdentifier.value = doiValue; + doiIdentifier.dataset_id = dataset.id; + doiIdentifier.type = 'doi'; + doiIdentifier.status = 'findable'; + // save modified date of datset for re-caching model in db an update the search index + dataset.server_date_modified = DateTime.now(); + + // save updated dataset to db an index to OpenSearch + try { + await dataset.related('identifier').save(doiIdentifier); + const index_name = 'tethys-records'; + await Index.indexDocument(dataset, index_name); + } catch (error) { + logger.error(`${__filename}: Indexing document ${dataset.id} failed: ${error.message}`); + // Log the error or handle it as needed + throw new HttpException(error.message); + } + return response.toRoute('editor.dataset.list').flash('message', 'You have successfully created a DOI for the dataset!'); + } else { const message = `Unexpected DataCite MDS response code ${dataciteResponse?.status}`; + // Log the error or handle it as needed throw new DoiClientException(dataciteResponse?.status, message); } - - // DOI registration successful - persist and index - try { - // Save identifier - await this.persistDoiAndIndex(dataset, doiValue); - - return response.toRoute('editor.dataset.list').flash('message', 'You have successfully created a DOI for the dataset!'); - } catch (error) { - logger.error(`${__filename}: Failed to persist DOI and index dataset ${dataset.id}: ${error.message}`); - throw new HttpException(error.message); - } - // return response.toRoute('editor.dataset.list').flash('message', xmlMeta); } - /** - * Persist DOI identifier and update search index - * Handles cache invalidation to ensure fresh indexing - */ - private async persistDoiAndIndex(dataset: Dataset, doiValue: string): Promise { - // Create DOI identifier - const doiIdentifier = new DatasetIdentifier(); - doiIdentifier.value = doiValue; - doiIdentifier.dataset_id = dataset.id; - doiIdentifier.type = 'doi'; - doiIdentifier.status = 'findable'; - - // Save identifier (this will trigger database insert) - await dataset.related('identifier').save(doiIdentifier); - - // Update dataset modification timestamp to reflect the change - dataset.server_date_modified = DateTime.now(); - await dataset.save(); - - // Invalidate stale XML cache - await this.invalidateDatasetCache(dataset); - - // Reload dataset with fresh state for indexing - const freshDataset = await Dataset.query().where('id', dataset.id).preload('identifier').preload('xmlCache').firstOrFail(); - - // Index to OpenSearch with fresh data - const index_name = process.env.OPENSEARCH_INDEX || 'tethys-records'; - await Index.indexDocument(freshDataset, index_name); - - logger.info(`Successfully created DOI ${doiValue} and indexed dataset ${dataset.id}`); - } - - /** - * Invalidate XML cache for dataset - * Ensures fresh cache generation on next access - */ - private async invalidateDatasetCache(dataset: Dataset): Promise { - await dataset.load('xmlCache'); - - if (dataset.xmlCache) { - await dataset.xmlCache.delete(); - logger.debug(`Invalidated XML cache for dataset ${dataset.id}`); - } - } - public async show({}: HttpContext) {} public async edit({ request, inertia, response }: HttpContext) { @@ -929,7 +900,6 @@ export default class DatasetsController { const input = request.only(['project_id', 'embargo_date', 'language', 'type', 'creating_corporation']); // dataset.type = request.input('type'); dataset.merge(input); - dataset.server_date_modified = DateTime.now(); // let test: boolean = dataset.$isDirty; await dataset.useTransaction(trx).save(); @@ -1151,20 +1121,9 @@ 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}.${fileExt}`; - // Set the response headers and download the file - response - .header('Cache-Control', 'no-cache private') - .header('Content-Description', 'File Transfer') - .header('Content-Type', file.mime_type || 'application/octet-stream') - // .header('Content-Disposition', 'inline; filename=' + fileName) - .header('Content-Transfer-Encoding', 'binary') - .header('Access-Control-Allow-Origin', '*') - .header('Access-Control-Allow-Methods', 'GET'); - response.attachment(fileName); + response.header('Content-Type', file.mime_type || 'application/octet-stream'); + response.attachment(`${file.label}.${fileExt}`); return response.download(filePath); } @@ -1177,18 +1136,19 @@ export default class DatasetsController { } } - private async getDatasetXmlDomNode(dataset: Dataset): Promise { - const serializer = new DatasetXmlSerializer(dataset).enableCaching().excludeEmptyFields(); + private async getDatasetXmlDomNode(dataset: Dataset) { + const xmlModel = new XmlModel(dataset); // xmlModel.setModel(dataset); - - // Load existing cache if available - await dataset.load('xmlCache'); + xmlModel.excludeEmptyFields(); + xmlModel.caching = true; + // const cache = dataset.xmlCache ? dataset.xmlCache : null; + // dataset.load('xmlCache'); if (dataset.xmlCache) { - serializer.setCache(dataset.xmlCache); + xmlModel.xmlCache = dataset.xmlCache; } // return cache.getDomDocument(); - const xmlDocument : XMLBuilder | null = await serializer.toXmlDocument(); - return xmlDocument; + const domDocument: XMLBuilder | null = await xmlModel.getDomDocument(); + return domDocument; } } diff --git a/app/Controllers/Http/Oai/OaiController.ts b/app/Controllers/Http/Oai/OaiController.ts index 47d1708..db49a32 100644 --- a/app/Controllers/Http/Oai/OaiController.ts +++ b/app/Controllers/Http/Oai/OaiController.ts @@ -15,7 +15,7 @@ import { OaiModelException, BadOaiModelException } from '#app/exceptions/OaiMode import Dataset from '#models/dataset'; import Collection from '#models/collection'; import { getDomain, preg_match } from '#app/utils/utility-functions'; -import DatasetXmlSerializer from '#app/Library/DatasetXmlSerializer'; +import XmlModel from '#app/Library/XmlModel'; import logger from '@adonisjs/core/services/logger'; import ResumptionToken from '#app/Library/Oai/ResumptionToken'; // import Config from '@ioc:Adonis/Core/Config'; @@ -292,7 +292,7 @@ export default class OaiController { this.xsltParameter['repIdentifier'] = repIdentifier; const datasetNode = this.xml.root().ele('Datasets'); - const paginationParams: PagingParameter = { + const paginationParams: PagingParameter ={ cursor: 0, totalLength: 0, start: maxRecords + 1, @@ -333,7 +333,7 @@ export default class OaiController { } private async handleNoResumptionToken(oaiRequest: Dictionary, paginationParams: PagingParameter, maxRecords: number) { - this.validateMetadataPrefix(oaiRequest, paginationParams); + this.validateMetadataPrefix(oaiRequest, paginationParams); const finder: ModelQueryBuilderContract = Dataset.query().whereIn( 'server_state', this.deliveringDocumentStates, @@ -347,20 +347,16 @@ export default class OaiController { finder: ModelQueryBuilderContract, paginationParams: PagingParameter, oaiRequest: Dictionary, - maxRecords: number, + maxRecords: number ) { const totalResult = await finder .clone() .count('* as total') .first() .then((res) => res?.$extras.total); - paginationParams.totalLength = Number(totalResult); + paginationParams.totalLength = Number(totalResult); - const combinedRecords: Dataset[] = await finder - .select('publish_id') - .orderBy('publish_id') - .offset(0) - .limit(maxRecords * 2); + const combinedRecords: Dataset[] = await finder.select('publish_id').orderBy('publish_id').offset(0).limit(maxRecords*2); paginationParams.activeWorkIds = combinedRecords.slice(0, 100).map((dat) => Number(dat.publish_id)); paginationParams.nextDocIds = combinedRecords.slice(100).map((dat) => Number(dat.publish_id)); @@ -606,17 +602,19 @@ export default class OaiController { } private async getDatasetXmlDomNode(dataset: Dataset) { - const serializer = new DatasetXmlSerializer(dataset).enableCaching().excludeEmptyFields(); - + const xmlModel = new XmlModel(dataset); + // xmlModel.setModel(dataset); + xmlModel.excludeEmptyFields(); + xmlModel.caching = true; // const cache = dataset.xmlCache ? dataset.xmlCache : null; // dataset.load('xmlCache'); if (dataset.xmlCache) { - serializer.setCache(dataset.xmlCache); + xmlModel.xmlCache = dataset.xmlCache; } - // return cache.toXmlDocument(); - const xmlDocument: XMLBuilder | null = await serializer.toXmlDocument(); - return xmlDocument; + // return cache.getDomDocument(); + const domDocument: XMLBuilder | null = await xmlModel.getDomDocument(); + return domDocument; } private addSpecInformation(domNode: XMLBuilder, information: string) { diff --git a/app/Controllers/Http/Reviewer/DatasetController.ts b/app/Controllers/Http/Reviewer/DatasetController.ts index 27f9b46..6b54772 100644 --- a/app/Controllers/Http/Reviewer/DatasetController.ts +++ b/app/Controllers/Http/Reviewer/DatasetController.ts @@ -107,12 +107,13 @@ 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) { @@ -369,19 +370,6 @@ 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}.${fileExt}`); - // return response.download(filePath); - // } - public async download({ params, response }: HttpContext) { const id = params.id; // Find the file by ID @@ -389,20 +377,9 @@ export default class DatasetsController { // const filePath = await drive.use('local').getUrl('/'+ file.filePath) const filePath = file.filePath; const fileExt = file.filePath.split('.').pop() || ''; - - // Check if label already includes the extension - const fileName = file.label.toLowerCase().endsWith(`.${fileExt.toLowerCase()}`) ? file.label : `${file.label}.${fileExt}`; - // Set the response headers and download the file - response - .header('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); + response.header('Content-Type', file.mime_type || 'application/octet-stream'); + response.attachment(`${file.label}.${fileExt}`); return response.download(filePath); } } diff --git a/app/Controllers/Http/Submitter/DatasetController.ts b/app/Controllers/Http/Submitter/DatasetController.ts index cda7da6..245b5d9 100644 --- a/app/Controllers/Http/Submitter/DatasetController.ts +++ b/app/Controllers/Http/Submitter/DatasetController.ts @@ -105,7 +105,6 @@ export default class DatasetController { 'reviewed', 'rejected_editor', 'rejected_reviewer', - 'rejected_to_reviewer', ]) .where('account_id', user.id) .preload('titles') @@ -234,9 +233,8 @@ export default class DatasetController { .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), + first_name: vine.string().trim().minLength(3).maxLength(255), last_name: vine.string().trim().minLength(3).maxLength(255), - identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(), }), ) .minLength(1) @@ -251,9 +249,8 @@ export default class DatasetController { .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), + first_name: vine.string().trim().minLength(3).maxLength(255), 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)), }), ) @@ -327,9 +324,8 @@ export default class DatasetController { .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), + first_name: vine.string().trim().minLength(3).maxLength(255), last_name: vine.string().trim().minLength(3).maxLength(255), - identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(), }), ) .minLength(1) @@ -344,9 +340,8 @@ export default class DatasetController { .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), + first_name: vine.string().trim().minLength(3).maxLength(255), 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)), }), ) @@ -988,6 +983,19 @@ 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, @@ -1007,7 +1015,7 @@ 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']), }, @@ -1155,93 +1163,42 @@ export default class DatasetController { } } - // ============================================ - // IMPROVED SUBJECTS PROCESSING - // ============================================ - const subjects = request.input('subjects', []); - const currentDatasetSubjectIds = new Set(); - + // Process all subjects/keywords from the request + const subjects = request.input('subjects'); for (const subjectData of subjects) { - let subjectToRelate: Subject; - - // Case 1: Subject has an ID (existing subject being updated) + // Case 1: Subject already exists in the database (has an ID) if (subjectData.id) { + // Retrieve the existing subject const existingSubject = await Subject.findOrFail(subjectData.id); - // 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(); + // Update subject properties from the request data + existingSubject.value = subjectData.value; + existingSubject.type = subjectData.type; + existingSubject.external_key = subjectData.external_key; - 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; + // Only save if there are actual changes + if (existingSubject.$isDirty) { + await existingSubject.save(); } + + // Note: The relationship between dataset and subject is already established, + // so we don't need to attach it again } // Case 2: New subject being added (no ID) else { - // Use firstOrNew to either find existing or create new subject - subjectToRelate = await Subject.firstOrNew( - { - value: subjectData.value, - type: subjectData.type, - language: subjectData.language || 'en', - }, - { - value: subjectData.value, - type: subjectData.type, - language: subjectData.language || 'en', - external_key: subjectData.external_key, - }, - ); + // Check if a subject with the same value and type already exists in the database + const subject = await Subject.firstOrNew({ value: subjectData.value, type: subjectData.type }, subjectData); - if (subjectToRelate.$isNew) { - await subjectToRelate.useTransaction(trx).save(); + if (subject.$isNew === true) { + // If it's a completely new subject, create and associate it with the dataset + await dataset.useTransaction(trx).related('subjects').save(subject); + } else { + // If the subject already exists, just create the relationship + await dataset.useTransaction(trx).related('subjects').attach([subject.id]); } } - - // Ensure the relationship exists between dataset and subject - const relationshipExists = await dataset.related('subjects').query().where('subject_id', subjectToRelate.id).first(); - - if (!relationshipExists) { - await dataset.useTransaction(trx).related('subjects').attach([subjectToRelate.id]); - } - - // Track which subjects should remain associated with this dataset - currentDatasetSubjectIds.add(subjectToRelate.id); } - // Handle explicit deletions const subjectsToDelete = request.input('subjectsToDelete', []); for (const subjectData of subjectsToDelete) { if (subjectData.id) { @@ -1254,16 +1211,16 @@ export default class DatasetController { .withCount('datasets') .firstOrFail(); - // Detach the subject from this dataset - await dataset.useTransaction(trx).related('subjects').detach([subject.id]); + // Check if the subject is used by multiple datasets + if (subject.$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 - // If this was the only dataset using this subject, delete it entirely - if (subject.$extras.datasets_count <= 1) { + await dataset.useTransaction(trx).related('subjects').detach([subject.id]); await subject.useTransaction(trx).delete(); } - - // Remove from current set if it was added earlier - currentDatasetSubjectIds.delete(subjectData.id); } } diff --git a/app/Library/DatasetXmlSerializer.ts b/app/Library/DatasetXmlSerializer.ts deleted file mode 100644 index f84d3b7..0000000 --- a/app/Library/DatasetXmlSerializer.ts +++ /dev/null @@ -1,231 +0,0 @@ -import DocumentXmlCache from '#models/DocumentXmlCache'; -import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js'; -import Dataset from '#models/dataset'; -import Strategy from './Strategy.js'; -import { builder } from 'xmlbuilder2'; -import logger from '@adonisjs/core/services/logger'; - -/** - * Configuration for XML serialization - * - * @interface XmlSerializationConfig - */ -export interface XmlSerializationConfig { - /** The dataset model to serialize */ - model: Dataset; - /** DOM representation (if available) */ - dom?: XMLBuilder; - /** Fields to exclude from serialization */ - excludeFields: Array; - /** Whether to exclude empty fields */ - excludeEmpty: boolean; - /** Base URI for xlink:ref elements */ - baseUri: string; -} - -/** - * Options for controlling serialization behavior - */ -export interface SerializationOptions { - /** Enable XML caching */ - enableCaching?: boolean; - /** Exclude empty fields from output */ - excludeEmptyFields?: boolean; - /** Custom base URI */ - baseUri?: string; - /** Fields to exclude */ - excludeFields?: string[]; -} - -/** - * DatasetXmlSerializer - * - * Handles XML serialization of Dataset models with intelligent caching. - * Generates XML representations and manages cache lifecycle to optimize performance. - * - * @example - * ```typescript - * const serializer = new DatasetXmlSerializer(dataset); - * serializer.enableCaching(); - * serializer.excludeEmptyFields(); - * - * const xmlDocument = await serializer.toXmlDocument(); - * ``` - */ -export default class DatasetXmlSerializer { - private readonly config: XmlSerializationConfig; - private readonly strategy: Strategy; - private cache: DocumentXmlCache | null = null; - private cachingEnabled = false; - - constructor(dataset: Dataset, options: SerializationOptions = {}) { - this.config = { - model: dataset, - excludeEmpty: options.excludeEmptyFields ?? false, - baseUri: options.baseUri ?? '', - excludeFields: options.excludeFields ?? [], - }; - - this.strategy = new Strategy({ - excludeEmpty: options.excludeEmptyFields ?? false, - baseUri: options.baseUri ?? '', - excludeFields: options.excludeFields ?? [], - model: dataset, - }); - - if (options.enableCaching) { - this.cachingEnabled = true; - } - } - - /** - * Enable caching for XML generation - * When enabled, generated XML is stored in database for faster retrieval - */ - public enableCaching(): this { - this.cachingEnabled = true; - return this; - } - - /** - * Disable caching for XML generation - */ - public disableCaching(): this { - this.cachingEnabled = false; - return this; - } - - set model(model: Dataset) { - this.config.model = model; - } - - /** - * Configure to exclude empty fields from XML output - */ - public excludeEmptyFields(): this { - this.config.excludeEmpty = true; - return this; - } - - /** - * Set the cache instance directly (useful when preloading) - * @param cache - The DocumentXmlCache instance - */ - public setCache(cache: DocumentXmlCache): this { - this.cache = cache; - return this; - } - - /** - * Get the current cache instance - */ - public getCache(): DocumentXmlCache | null { - return this.cache; - } - - /** - * Get DOM document with intelligent caching - * Returns cached version if valid, otherwise generates new document - */ - public async toXmlDocument(): Promise { - const dataset = this.config.model; - - // Try to get from cache first - let cachedDocument: XMLBuilder | null = await this.retrieveFromCache(); - - if (cachedDocument) { - logger.debug(`Using cached XML for dataset ${dataset.id}`); - return cachedDocument; - } - - // Generate fresh document - logger.debug(`[DatasetXmlSerializer] Cache miss - generating fresh XML for dataset ${dataset.id}`); - const freshDocument = await this.strategy.createDomDocument(); - - if (!freshDocument) { - logger.error(`[DatasetXmlSerializer] Failed to generate XML for dataset ${dataset.id}`); - return null; - } - - // Cache if caching is enabled - if (this.cachingEnabled) { - await this.persistToCache(freshDocument, dataset); - } - - // Extract the dataset-specific node - return this.extractDatasetNode(freshDocument); - } - - /** - * Generate XML string representation - * Convenience method that converts XMLBuilder to string - */ - public async toXmlString(): Promise { - const document = await this.toXmlDocument(); - return document ? document.end({ prettyPrint: false }) : null; - } - - /** - * Persist generated XML document to cache - * Non-blocking - failures are logged but don't interrupt the flow - */ - private async persistToCache(domDocument: XMLBuilder, dataset: Dataset): Promise { - try { - this.cache = this.cache || new DocumentXmlCache(); - this.cache.document_id = dataset.id; - this.cache.xml_version = 1; - this.cache.server_date_modified = dataset.server_date_modified.toFormat('yyyy-MM-dd HH:mm:ss'); - this.cache.xml_data = domDocument.end(); - - await this.cache.save(); - logger.debug(`Cached XML for dataset ${dataset.id}`); - } catch (error) { - logger.error(`Failed to cache XML for dataset ${dataset.id}: ${error.message}`); - // Don't throw - caching failure shouldn't break the flow - } - } - - /** - * Extract the Rdr_Dataset node from full document - */ - private extractDatasetNode(domDocument: XMLBuilder): XMLBuilder | null { - const node = domDocument.find((n) => n.node.nodeName === 'Rdr_Dataset', false, true)?.node; - - if (node) { - return builder({ version: '1.0', encoding: 'UTF-8', standalone: true }, node); - } - - return domDocument; - } - - /** - * Attempt to retrieve valid cached XML document - * Returns null if cache doesn't exist or is stale - */ - private async retrieveFromCache(): Promise { - const dataset: Dataset = this.config.model; - if (!this.cache) { - return null; - } - - // Check if cache is still valid - const actuallyCached = await DocumentXmlCache.hasValidEntry(dataset.id, dataset.server_date_modified); - - if (!actuallyCached) { - logger.debug(`Cache invalid for dataset ${dataset.id}`); - return null; - } - - //cache is actual return cached document - try { - if (this.cache) { - return this.cache.getDomDocument(); - } else { - return null; - } - } catch (error) { - logger.error(`Failed to retrieve cached document for dataset ${dataset.id}: ${error.message}`); - return null; - } - } -} diff --git a/app/Library/Doi/DoiClient.ts b/app/Library/Doi/DoiClient.ts index 4232ac4..86151e7 100644 --- a/app/Library/Doi/DoiClient.ts +++ b/app/Library/Doi/DoiClient.ts @@ -1,3 +1,6 @@ +// import { Client } from 'guzzle'; +// import { Log } from '@adonisjs/core/build/standalone'; +// import { DoiInterface } from './interfaces/DoiInterface'; import DoiClientContract from '#app/Library/Doi/DoiClientContract'; import DoiClientException from '#app/exceptions/DoiClientException'; import { StatusCodes } from 'http-status-codes'; @@ -9,14 +12,14 @@ export class DoiClient implements DoiClientContract { public username: string; public password: string; public serviceUrl: string; - public apiUrl: string; constructor() { // const datacite_environment = process.env.DATACITE_ENVIRONMENT || 'debug'; this.username = process.env.DATACITE_USERNAME || ''; this.password = process.env.DATACITE_PASSWORD || ''; this.serviceUrl = process.env.DATACITE_SERVICE_URL || ''; - this.apiUrl = process.env.DATACITE_API_URL || 'https://api.datacite.org'; + // this.prefix = process.env.DATACITE_PREFIX || ''; + // this.base_domain = process.env.BASE_DOMAIN || ''; if (this.username === '' || this.password === '' || this.serviceUrl === '') { const message = 'issing configuration settings to properly initialize DOI client'; @@ -87,240 +90,4 @@ export class DoiClient implements DoiClientContract { throw new DoiClientException(error.response.status, error.response.data); } } - - /** - * Retrieves DOI information from DataCite REST API - * - * @param doiValue The DOI identifier e.g. '10.5072/tethys.999' - * @returns Promise with DOI information or null if not found - */ - public async getDoiInfo(doiValue: string): Promise { - try { - // Use configurable DataCite REST API URL - const dataciteApiUrl = `${this.apiUrl}/dois/${doiValue}`; - const response = await axios.get(dataciteApiUrl, { - headers: { - Accept: 'application/vnd.api+json', - }, - }); - - if (response.status === 200 && response.data.data) { - return { - created: response.data.data.attributes.created, - registered: response.data.data.attributes.registered, - updated: response.data.data.attributes.updated, - published: response.data.data.attributes.published, - state: response.data.data.attributes.state, - url: response.data.data.attributes.url, - metadata: response.data.data.attributes, - }; - } - } catch (error) { - if (error.response?.status === 404) { - logger.debug(`DOI ${doiValue} not found in DataCite`); - return null; - } - - logger.debug(`DataCite REST API failed for ${doiValue}: ${error.message}`); - - // Fallback to MDS API - return await this.getDoiInfoFromMds(doiValue); - } - - return null; - } - - /** - * Fallback method to get DOI info from MDS API - * - * @param doiValue The DOI identifier - * @returns Promise with basic DOI information or null - */ - private async getDoiInfoFromMds(doiValue: string): Promise { - try { - const auth = { - username: this.username, - password: this.password, - }; - - // Get DOI URL - const doiResponse = await axios.get(`${this.serviceUrl}/doi/${doiValue}`, { auth }); - - if (doiResponse.status === 200) { - // Get metadata if available - try { - const metadataResponse = await axios.get(`${this.serviceUrl}/metadata/${doiValue}`, { - auth, - headers: { - Accept: 'application/xml', - }, - }); - - return { - url: doiResponse.data.trim(), - metadata: metadataResponse.data, - created: new Date().toISOString(), // MDS doesn't provide creation dates - registered: new Date().toISOString(), // Use current time as fallback - source: 'mds', - }; - } catch (metadataError) { - // Return basic info even if metadata fetch fails - return { - url: doiResponse.data.trim(), - created: new Date().toISOString(), - registered: new Date().toISOString(), - source: 'mds', - }; - } - } - } catch (error) { - if (error.response?.status === 404) { - logger.debug(`DOI ${doiValue} not found in DataCite MDS`); - return null; - } - - logger.debug(`DataCite MDS API failed for ${doiValue}: ${error.message}`); - } - - return null; - } - - /** - * Checks if a DOI exists in DataCite - * - * @param doiValue The DOI identifier - * @returns Promise True if DOI exists - */ - public async doiExists(doiValue: string): Promise { - const doiInfo = await this.getDoiInfo(doiValue); - return doiInfo !== null; - } - - /** - * Gets the last modification date of a DOI - * - * @param doiValue The DOI identifier - * @returns Promise Last modification date or creation date if never updated, null if not found - */ - public async getDoiLastModified(doiValue: string): Promise { - const doiInfo = await this.getDoiInfo(doiValue); - - if (doiInfo) { - // Use updated date if available, otherwise fall back to created/registered date - const dateToUse = doiInfo.updated || doiInfo.registered || doiInfo.created; - - if (dateToUse) { - logger.debug( - `DOI ${doiValue}: Using ${doiInfo.updated ? 'updated' : doiInfo.registered ? 'registered' : 'created'} date: ${dateToUse}`, - ); - return new Date(dateToUse); - } - } - - return null; - } - - /** - * Makes a DOI unfindable (registered but not discoverable) - * Note: DOIs cannot be deleted, only made unfindable - * await doiClient.makeDoiUnfindable('10.21388/tethys.231'); - * - * @param doiValue The DOI identifier e.g. '10.5072/tethys.999' - * @returns Promise> The http response - */ - public async makeDoiUnfindable(doiValue: string): Promise> { - const auth = { - username: this.username, - password: this.password, - }; - - try { - // First, check if DOI exists - const exists = await this.doiExists(doiValue); - if (!exists) { - throw new DoiClientException(404, `DOI ${doiValue} not found`); - } - - // Delete the DOI URL mapping to make it unfindable - // This removes the URL but keeps the metadata registered - const response = await axios.delete(`${this.serviceUrl}/doi/${doiValue}`, { auth }); - - // Response Codes for DELETE /doi/{doi} - // 200 OK: operation successful - // 401 Unauthorized: no login - // 403 Forbidden: login problem, quota exceeded - // 404 Not Found: DOI does not exist - if (response.status !== 200) { - const message = `Unexpected DataCite MDS response code ${response.status}`; - logger.error(message); - throw new DoiClientException(response.status, message); - } - - logger.info(`DOI ${doiValue} successfully made unfindable`); - return response; - } catch (error) { - logger.error(`Failed to make DOI ${doiValue} unfindable: ${error.message}`); - if (error instanceof DoiClientException) { - throw error; - } - throw new DoiClientException(error.response?.status || 500, error.response?.data || error.message); - } - } - - /** - * Makes a DOI findable again by re-registering the URL - * await doiClient.makeDoiFindable( - * '10.21388/tethys.231', - * 'https://doi.dev.tethys.at/10.21388/tethys.231' - * ); - * - * @param doiValue The DOI identifier e.g. '10.5072/tethys.999' - * @param landingPageUrl The landing page URL - * @returns Promise> The http response - */ - public async makeDoiFindable(doiValue: string, landingPageUrl: string): Promise> { - const auth = { - username: this.username, - password: this.password, - }; - - try { - // Re-register the DOI with its URL to make it findable again - const response = await axios.put(`${this.serviceUrl}/doi/${doiValue}`, `doi=${doiValue}\nurl=${landingPageUrl}`, { auth }); - - // Response Codes for PUT /doi/{doi} - // 201 Created: operation successful - // 400 Bad Request: request body must be exactly two lines: DOI and URL - // 401 Unauthorized: no login - // 403 Forbidden: login problem, quota exceeded - // 412 Precondition failed: metadata must be uploaded first - if (response.status !== 201) { - const message = `Unexpected DataCite MDS response code ${response.status}`; - logger.error(message); - throw new DoiClientException(response.status, message); - } - - logger.info(`DOI ${doiValue} successfully made findable again`); - return response; - } catch (error) { - logger.error(`Failed to make DOI ${doiValue} findable: ${error.message}`); - if (error instanceof DoiClientException) { - throw error; - } - throw new DoiClientException(error.response?.status || 500, error.response?.data || error.message); - } - } - - /** - * Gets the current state of a DOI (draft, registered, findable) - * const state = await doiClient.getDoiState('10.21388/tethys.231'); - * console.log(`Current state: ${state}`); // 'findable' - * - * @param doiValue The DOI identifier - * @returns Promise The DOI state or null if not found - */ - public async getDoiState(doiValue: string): Promise { - const doiInfo = await this.getDoiInfo(doiValue); - return doiInfo?.state || null; - } } diff --git a/app/Library/Utils/Index.ts b/app/Library/Utils/Index.ts index 20253a4..9bc21f7 100644 --- a/app/Library/Utils/Index.ts +++ b/app/Library/Utils/Index.ts @@ -2,7 +2,7 @@ import Dataset from '#models/dataset'; import { Client } from '@opensearch-project/opensearch'; import { create } from 'xmlbuilder2'; import SaxonJS from 'saxon-js'; -import DatasetXmlSerializer from '#app/Library/DatasetXmlSerializer'; +import XmlModel from '#app/Library/XmlModel'; import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js'; import logger from '@adonisjs/core/services/logger'; import { readFileSync } from 'fs'; @@ -72,42 +72,31 @@ export default { } }, - /** - * Index a dataset document to OpenSearch/Elasticsearch - */ async indexDocument(dataset: Dataset, index_name: string): Promise { try { - // Load XSLT transformation file - const xsltProc = readFileSync('public/assets2/solr.sef.json'); + const proc = readFileSync('public/assets2/solr.sef.json'); + const doc: string = await this.getTransformedString(dataset, proc); - // Transform dataset to JSON document - const jsonDoc: string = await this.getTransformedString(dataset, xsltProc); - - const document = JSON.parse(jsonDoc); - - // Index document to OpenSearch with doument json body + let document = JSON.parse(doc); await this.client.index({ id: dataset.publish_id?.toString(), index: index_name, body: document, - refresh: true, // make immediately searchable + refresh: true, }); - logger.info(`Dataset ${dataset.publish_id} successfully indexed to ${index_name}`); + logger.info(`dataset with publish_id ${dataset.publish_id} successfully indexed`); } catch (error) { - logger.error(`Failed to index dataset ${dataset.publish_id}: ${error.message}`); - throw error; // Re-throw to allow caller to handle + logger.error(`An error occurred while indexing datsaet with publish_id ${dataset.publish_id}.`); } }, - /** - * Transform dataset XML to JSON using XSLT - */ async getTransformedString(dataset: Dataset, proc: Buffer): Promise { - // Generate XML string from dataset - const xmlString = await this.generateDatasetXml(dataset); + let xml = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, ''); + const datasetNode = xml.root().ele('Dataset'); + await createXmlRecord(dataset, datasetNode); + const xmlString = xml.end({ prettyPrint: false }); try { - // Apply XSLT transformation const result = await SaxonJS.transform({ stylesheetText: proc, destination: 'serialized', @@ -119,18 +108,6 @@ export default { return ''; } }, - - /** - * Generate XML string from dataset model - */ - async generateDatasetXml(dataset: Dataset): Promise { - const xml = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, ''); - const datasetNode = xml.root().ele('Dataset'); - - await createXmlRecord(dataset, datasetNode); - - return xml.end({ prettyPrint: false }); - }, }; /** * Return the default global focus trap stack @@ -138,49 +115,74 @@ export default { * @return {import('focus-trap').FocusTrap[]} */ -/** - * Create complete XML record for dataset - * Handles caching and metadata enrichment - */ +// export const indexDocument = async (dataset: Dataset, index_name: string, proc: Buffer): Promise => { +// try { +// const doc = await getJsonString(dataset, proc); + +// let document = JSON.parse(doc); +// await client.index({ +// id: dataset.publish_id?.toString(), +// index: index_name, +// body: document, +// refresh: true, +// }); +// Logger.info(`dataset with publish_id ${dataset.publish_id} successfully indexed`); +// } catch (error) { +// Logger.error(`An error occurred while indexing datsaet with publish_id ${dataset.publish_id}.`); +// } +// }; + +// const getJsonString = async (dataset, proc): Promise => { +// let xml = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, ''); +// const datasetNode = xml.root().ele('Dataset'); +// await createXmlRecord(dataset, datasetNode); +// const xmlString = xml.end({ prettyPrint: false }); + +// try { +// const result = await transform({ +// stylesheetText: proc, +// destination: 'serialized', +// sourceText: xmlString, +// }); +// return result.principalResult; +// } catch (error) { +// Logger.error(`An error occurred while creating the user, error: ${error.message},`); +// return ''; +// } +// }; + const createXmlRecord = async (dataset: Dataset, datasetNode: XMLBuilder): Promise => { const domNode = await getDatasetXmlDomNode(dataset); - - if (!domNode) { - throw new Error(`Failed to generate XML DOM node for dataset ${dataset.id}`); - } - - // Enrich with landing page URL - if (dataset.publish_id) { - addLandingPageAttribute(domNode, dataset.publish_id.toString()); - } - - // Add data type specification - addSpecInformation(domNode, `data-type:${dataset.type}`); - - // Add collection information - if (dataset.collections) { - for (const coll of dataset.collections) { - const collRole = coll.collectionRole; - addSpecInformation(domNode, `${collRole.oai_name}:${coll.number}`); + if (domNode) { + // add frontdoor url and data-type + dataset.publish_id && addLandingPageAttribute(domNode, dataset.publish_id.toString()); + addSpecInformation(domNode, 'data-type:' + dataset.type); + if (dataset.collections) { + for (const coll of dataset.collections) { + const collRole = coll.collectionRole; + addSpecInformation(domNode, collRole.oai_name + ':' + coll.number); + } } - } - datasetNode.import(domNode); + datasetNode.import(domNode); + } }; const getDatasetXmlDomNode = async (dataset: Dataset): Promise => { - const serializer = new DatasetXmlSerializer(dataset).enableCaching().excludeEmptyFields(); + const xmlModel = new XmlModel(dataset); // xmlModel.setModel(dataset); - - // Load cache relationship if not already loaded + xmlModel.excludeEmptyFields(); + xmlModel.caching = true; + // const cache = dataset.xmlCache ? dataset.xmlCache : null; + // dataset.load('xmlCache'); await dataset.load('xmlCache'); if (dataset.xmlCache) { - serializer.setCache(dataset.xmlCache); + xmlModel.xmlCache = dataset.xmlCache; } - // Generate or retrieve cached DOM document - const xmlDocument: XMLBuilder | null = await serializer.toXmlDocument(); - return xmlDocument; + // return cache.getDomDocument(); + const domDocument: XMLBuilder | null = await xmlModel.getDomDocument(); + return domDocument; }; const addLandingPageAttribute = (domNode: XMLBuilder, dataid: string) => { @@ -190,6 +192,6 @@ const addLandingPageAttribute = (domNode: XMLBuilder, dataid: string) => { domNode.att('landingpage', url); }; -const addSpecInformation = (domNode: XMLBuilder, information: string) => { +const addSpecInformation= (domNode: XMLBuilder, information: string) => { domNode.ele('SetSpec').att('Value', information); -}; +}; \ No newline at end of file diff --git a/app/Library/XmlModel.ts b/app/Library/XmlModel.ts new file mode 100644 index 0000000..6f76474 --- /dev/null +++ b/app/Library/XmlModel.ts @@ -0,0 +1,129 @@ +import DocumentXmlCache from '#models/DocumentXmlCache'; +import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js'; +import Dataset from '#models/dataset'; +import Strategy from './Strategy.js'; +import { DateTime } from 'luxon'; +import { builder } from 'xmlbuilder2'; + +/** + * This is the description of the interface + * + * @interface Conf + * @member {Model} model holds the current dataset model + * @member {XMLBuilder} dom holds the current DOM representation + * @member {Array} excludeFields List of fields to skip on serialization. + * @member {boolean} excludeEmpty True, if empty fields get excluded from serialization. + * @member {string} baseUri Base URI for xlink:ref elements + */ +export interface Conf { + model: Dataset; + dom?: XMLBuilder; + excludeFields: Array; + excludeEmpty: boolean; + baseUri: string; +} + +export default class XmlModel { + private config: Conf; + // private strategy = null; + private cache: DocumentXmlCache | null = null; + private _caching = false; + private strategy: Strategy; + + constructor(dataset: Dataset) { + // $this->strategy = new Strategy();// Opus_Model_Xml_Version1; + // $this->config = new Conf(); + // $this->strategy->setup($this->config); + + this.config = { + excludeEmpty: false, + baseUri: '', + excludeFields: [], + model: dataset, + }; + + this.strategy = new Strategy({ + excludeEmpty: true, + baseUri: '', + excludeFields: [], + model: dataset, + }); + } + + set model(model: Dataset) { + this.config.model = model; + } + + public excludeEmptyFields(): void { + this.config.excludeEmpty = true; + } + + get xmlCache(): DocumentXmlCache | null { + return this.cache; + } + + set xmlCache(cache: DocumentXmlCache) { + this.cache = cache; + } + + get caching(): boolean { + return this._caching; + } + set caching(caching: boolean) { + this._caching = caching; + } + + public async getDomDocument(): Promise { + const dataset = this.config.model; + + let domDocument: XMLBuilder | null = await this.getDomDocumentFromXmlCache(); + if (domDocument == null) { + domDocument = await this.strategy.createDomDocument(); + // domDocument = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, ''); + if (this._caching) { + // caching is desired: + this.cache = this.cache || new DocumentXmlCache(); + this.cache.document_id = dataset.id; + this.cache.xml_version = 1; // (int)$this->strategy->getVersion(); + this.cache.server_date_modified = dataset.server_date_modified.toFormat('yyyy-MM-dd HH:mm:ss'); + this.cache.xml_data = domDocument.end(); + await this.cache.save(); + } + const node = domDocument.find( + (n) => { + const test = n.node.nodeName == 'Rdr_Dataset'; + return test; + }, + false, + true, + )?.node; + if (node != undefined) { + domDocument = builder({ version: '1.0', encoding: 'UTF-8', standalone: true }, node); + } + } + return domDocument; + } + + private async getDomDocumentFromXmlCache(): Promise { + const dataset: Dataset = this.config.model; + if (!this.cache) { + return null; + } + //.toFormat('YYYY-MM-DD HH:mm:ss'); + let date: DateTime = dataset.server_date_modified; + const actuallyCached: boolean = await DocumentXmlCache.hasValidEntry(dataset.id, date); + if (!actuallyCached) { + return null; + } + //cache is actual return it for oai: + try { + if (this.cache) { + return this.cache.getDomDocument(); + } else { + return null; + } + } catch (error) { + return null; + } + } +} diff --git a/app/controllers/projects_controller.ts b/app/controllers/projects_controller.ts deleted file mode 100644 index 21e20df..0000000 --- a/app/controllers/projects_controller.ts +++ /dev/null @@ -1,54 +0,0 @@ -// app/controllers/projects_controller.ts -import Project from '#models/project'; -import type { HttpContext } from '@adonisjs/core/http'; -import { createProjectValidator, updateProjectValidator } from '#validators/project'; - -export default class ProjectsController { - // GET /settings/projects - public async index({ inertia, auth }: HttpContext) { - const projects = await Project.all(); - // return inertia.render('Admin/Project/Index', { projects }); - return inertia.render('Admin/Project/Index', { - projects: projects, - can: { - edit: await auth.user?.can(['settings']), - create: await auth.user?.can(['settings']), - }, - }); - } - - // GET /settings/projects/create - public async create({ inertia }: HttpContext) { - return inertia.render('Admin/Project/Create'); - } - - // POST /settings/projects - public async store({ request, response, session }: HttpContext) { - // Validate the request data - const data = await request.validateUsing(createProjectValidator); - - await Project.create(data); - - session.flash('success', 'Project created successfully'); - return response.redirect().toRoute('settings.project.index'); - } - - // GET /settings/projects/:id/edit - public async edit({ params, inertia }: HttpContext) { - const project = await Project.findOrFail(params.id); - return inertia.render('Admin/Project/Edit', { project }); - } - - // PUT /settings/projects/:id - public async update({ params, request, response, session }: HttpContext) { - const project = await Project.findOrFail(params.id); - - // Validate the request data - const data = await request.validateUsing(updateProjectValidator); - - await project.merge(data).save(); - - session.flash('success', 'Project updated successfully'); - return response.redirect().toRoute('settings.project.index'); - } -} diff --git a/app/models/DocumentXmlCache.ts b/app/models/DocumentXmlCache.ts index de8defc..ed7315e 100644 --- a/app/models/DocumentXmlCache.ts +++ b/app/models/DocumentXmlCache.ts @@ -4,8 +4,7 @@ import { builder, create } from 'xmlbuilder2'; import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js'; import db from '@adonisjs/lucid/services/db'; import { DateTime } from 'luxon'; -import type { BelongsTo } from '@adonisjs/lucid/types/relations'; -import logger from '@adonisjs/core/services/logger'; +import type { BelongsTo } from "@adonisjs/lucid/types/relations"; export default class DocumentXmlCache extends BaseModel { public static namingStrategy = new SnakeCaseNamingStrategy(); @@ -67,38 +66,33 @@ export default class DocumentXmlCache extends BaseModel { } /** - * Check if a valid (non-stale) cache entry exists - * Cache is valid only if it was created AFTER the dataset's last modification + * Check if a dataset in a specific xml version is already cached or not. * - * @param datasetId - The dataset ID to check - * @param datasetServerDateModified - The dataset's last modification timestamp - * @returns true if valid cache exists, false otherwise + * @param mixed datasetId + * @param mixed serverDateModified + * @returns {Promise} Returns true on cached hit else false. */ + // public static async hasValidEntry(datasetId: number, datasetServerDateModified: DateTime): Promise { + // // const formattedDate = dayjs(datasetServerDateModified).format('YYYY-MM-DD HH:mm:ss'); + + // const query = Database.from(this.table) + // .where('document_id', datasetId) + // .where('server_date_modified', '2023-08-17 16:51:03') + // .first(); + + // const row = await query; + // return !!row; + // } + + // Assuming 'DocumentXmlCache' has a table with a 'server_date_modified' column in your database public static async hasValidEntry(datasetId: number, datasetServerDateModified: DateTime): Promise { const serverDateModifiedString: string = datasetServerDateModified.toFormat('yyyy-MM-dd HH:mm:ss'); // Convert DateTime to ISO string - - const row = await db - .from(this.table) + const query = db.from(this.table) .where('document_id', datasetId) - .where('server_date_modified', '>', serverDateModifiedString) // Check if server_date_modified is newer or equal + .where('server_date_modified', '>=', serverDateModifiedString) // Check if server_date_modified is newer or equal .first(); - const isValid = !!row; - - if (isValid) { - logger.debug(`Valid cache found for dataset ${datasetId}`); - } else { - logger.debug(`No valid cache for dataset ${datasetId} (dataset modified: ${serverDateModifiedString})`); - } - - return isValid; - } - - /** - * Invalidate (delete) cache entry - */ - public async invalidate(): Promise { - await this.delete(); - logger.debug(`Invalidated cache for document ${this.document_id}`); + const row = await query; + return !!row; } } diff --git a/app/models/person.ts b/app/models/person.ts index f4cf3a2..cdc612d 100644 --- a/app/models/person.ts +++ b/app/models/person.ts @@ -30,7 +30,7 @@ export default class Person extends BaseModel { @column({}) public lastName: string; - @column({ columnName: 'identifier_orcid' }) + @column({}) public identifierOrcid: string; @column({}) @@ -95,34 +95,4 @@ export default class Person extends BaseModel { pivotColumns: ['role', 'sort_order', 'allow_email_contact'], }) public datasets: ManyToMany; - - // public toJSON() { - // const json = super.toJSON(); - - // // Check if this person is loaded through a pivot relationship with sensitive roles - // const pivotRole = this.$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 7be02b9..5dbaab4 100644 --- a/app/models/user.ts +++ b/app/models/user.ts @@ -89,11 +89,24 @@ 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', @@ -129,9 +142,7 @@ export default class User extends compose(BaseModel, AuthFinder) { @beforeFind() @beforeFetch() public static preloadRoles(user: User) { - user.preload('roles', (builder) => { - builder.select(['id', 'name', 'display_name', 'description']); - }); + user.preload('roles') } public async getBackupCodes(this: User): Promise { diff --git a/app/validators/dataset.ts b/app/validators/dataset.ts index f670b81..5417463 100644 --- a/app/validators/dataset.ts +++ b/app/validators/dataset.ts @@ -55,8 +55,8 @@ export const createDatasetValidator = vine.compile( .translatedLanguage({ mainLanguageField: 'language', typeField: 'type' }), }), ) - // .minLength(1), - .arrayContainsTypes({ typeA: 'abstract', typeB: 'translated' }), + // .minLength(1), + .arrayContainsTypes({ typeA: 'abstract', typeB: 'translated' }), authors: vine .array( vine.object({ @@ -67,9 +67,8 @@ export const createDatasetValidator = vine.compile( .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), + first_name: vine.string().trim().minLength(3).maxLength(255), last_name: vine.string().trim().minLength(3).maxLength(255), - identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(), }), ) .minLength(1) @@ -84,10 +83,9 @@ export const createDatasetValidator = vine.compile( .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), + first_name: vine.string().trim().minLength(3).maxLength(255), 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') @@ -160,8 +158,7 @@ export const createDatasetValidator = vine.compile( .fileScan({ removeInfected: true }), ) .minLength(1), - }), -); + }),); /** * Validates the dataset's update action @@ -217,9 +214,8 @@ export const updateDatasetValidator = vine.compile( .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), + first_name: vine.string().trim().minLength(3).maxLength(255), last_name: vine.string().trim().minLength(3).maxLength(255), - identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(), }), ) .minLength(1) @@ -234,9 +230,8 @@ export const updateDatasetValidator = vine.compile( .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), + first_name: vine.string().trim().minLength(3).maxLength(255), 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)), }), ) @@ -310,13 +305,12 @@ export const updateDatasetValidator = vine.compile( .fileScan({ removeInfected: true }), ) .dependentArrayMinLength({ dependentArray: 'fileInputs', min: 1 }), - fileInputs: vine - .array( - vine.object({ - label: vine.string().trim().maxLength(100), - }), - ) - .optional(), + fileInputs: vine.array( + vine.object({ + label: vine.string().trim().maxLength(100), + //extnames: extensions, + }), + ), }), ); @@ -371,9 +365,8 @@ export const updateEditorDatasetValidator = vine.compile( .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), + first_name: vine.string().trim().minLength(3).maxLength(255), last_name: vine.string().trim().minLength(3).maxLength(255), - identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(), }), ) .minLength(1) @@ -388,9 +381,8 @@ export const updateEditorDatasetValidator = vine.compile( .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), + first_name: vine.string().trim().minLength(3).maxLength(255), 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)), }), ) @@ -504,7 +496,7 @@ let messagesProvider = new SimpleMessagesProvider({ 'files.array.minLength': 'At least {{ min }} file upload is required.', 'files.*.size': 'file size is to big', 'files.*.extnames': 'file extension is not supported', - 'embargo_date.date.afterOrEqual': `Embargo date must be on or after ${dayjs().add(10, 'day').format('DD.MM.YYYY')}`, + 'embargo_date.date.afterOrEqual': `Embargo date must be on or after ${dayjs().add(10, 'day').format('DD.MM.YYYY')}`, }); createDatasetValidator.messagesProvider = messagesProvider; diff --git a/app/validators/project.ts b/app/validators/project.ts deleted file mode 100644 index 7f3d1f8..0000000 --- a/app/validators/project.ts +++ /dev/null @@ -1,28 +0,0 @@ -// app/validators/project.ts -import vine from '@vinejs/vine'; - -export const createProjectValidator = vine.compile( - vine.object({ - label: vine.string().trim().minLength(1).maxLength(50) .regex(/^[a-z0-9-]+$/), - name: vine - .string() - .trim() - .minLength(3) - .maxLength(255) - .regex(/^[a-zA-Z0-9รครถรผรŸร„ร–รœ\s-]+$/), - description: vine.string().trim().maxLength(255).minLength(5).optional(), - }), -); - -export const updateProjectValidator = vine.compile( - vine.object({ - // label is NOT included since it's readonly - name: vine - .string() - .trim() - .minLength(3) - .maxLength(255) - .regex(/^[a-zA-Z0-9รครถรผรŸร„ร–รœ\s-]+$/), - description: vine.string().trim().maxLength(255).minLength(5).optional(), - }), -); diff --git a/app/validators/role.ts b/app/validators/role.ts index 81262d9..61e8ecd 100644 --- a/app/validators/role.ts +++ b/app/validators/role.ts @@ -8,20 +8,20 @@ export const createRoleValidator = vine.compile( vine.object({ name: vine .string() + .isUnique({ table: 'roles', column: 'name' }) .trim() .minLength(3) .maxLength(255) - .isUnique({ table: 'roles', column: 'name' }) - .regex(/^[a-zA-Z0-9]+$/), // Must be alphanumeric + .regex(/^[a-zA-Z0-9]+$/), //Must be alphanumeric with hyphens or underscores display_name: vine .string() + .isUnique({ table: 'roles', column: 'display_name' }) .trim() .minLength(3) .maxLength(255) - .isUnique({ table: 'roles', column: 'display_name' }) .regex(/^[a-zA-Z0-9]+$/), description: vine.string().trim().escape().minLength(3).maxLength(255).optional(), - permissions: vine.array(vine.number()).minLength(1), // At least one permission required + permissions: vine.array(vine.number()).minLength(1), // define at least one permission for the new role }), ); @@ -29,28 +29,21 @@ export const updateRoleValidator = vine.withMetaData<{ roleId: number }>().compi vine.object({ name: vine .string() - .trim() - .minLength(3) - .maxLength(255) + // .unique(async (db, value, field) => { + // const result = await db.from('roles').select('id').whereNot('id', field.meta.roleId).where('name', value).first(); + // return result.length ? false : true; + // }) .isUnique({ table: 'roles', column: 'name', whereNot: (field) => field.meta.roleId, }) - .regex(/^[a-zA-Z0-9]+$/), - display_name: vine - .string() .trim() .minLength(3) - .maxLength(255) - .isUnique({ - table: 'roles', - column: 'display_name', - whereNot: (field) => field.meta.roleId, - }) - .regex(/^[a-zA-Z0-9]+$/), + .maxLength(255), + description: vine.string().trim().escape().minLength(3).maxLength(255).optional(), - permissions: vine.array(vine.number()).minLength(1), // At least one permission required + permissions: vine.array(vine.number()).minLength(1), // define at least one permission for the new role }), ); diff --git a/clamd.conf b/clamd.conf index f066387..171396d 100644 --- a/clamd.conf +++ b/clamd.conf @@ -5,23 +5,7 @@ LogSyslog no LogVerbose yes DatabaseDirectory /var/lib/clamav LocalSocket /var/run/clamav/clamd.socket -# LocalSocketMode 666 -# Optional: allow multiple threads -MaxThreads 20 -# Disable TCP socket -# TCPSocket 0 - -# TCP port address. -# Default: no -# TCPSocket 3310 -# TCP address. -# By default we bind to INADDR_ANY, probably not wise. -# Enable the following to provide some degree of protection -# from the outside world. -# Default: no -# TCPAddr 127.0.0.1 - Foreground no PidFile /var/run/clamav/clamd.pid -# LocalSocketGroup node # Changed from 'clamav' -# User node # Changed from 'clamav' - clamd runs as clamav user \ No newline at end of file +LocalSocketGroup node +User node \ No newline at end of file diff --git a/commands/fix_dataset_cross_references.ts b/commands/fix_dataset_cross_references.ts deleted file mode 100644 index baa2e0e..0000000 --- a/commands/fix_dataset_cross_references.ts +++ /dev/null @@ -1,482 +0,0 @@ -/* -|-------------------------------------------------------------------------- -| node ace make:command fix-dataset-cross-references -| DONE: create commands/fix_dataset_cross_references.ts -|-------------------------------------------------------------------------- -*/ -import { BaseCommand, flags } from '@adonisjs/core/ace'; -import type { CommandOptions } from '@adonisjs/core/types/ace'; -import { DateTime } from 'luxon'; -import Dataset from '#models/dataset'; -import DatasetReference from '#models/dataset_reference'; -import AppConfig from '#models/appconfig'; -// import env from '#start/env'; - -interface MissingCrossReference { - sourceDatasetId: number; - targetDatasetId: number; - sourcePublishId: number | null; - targetPublishId: number | null; - sourceDoi: string | null; - targetDoi: string | null; - referenceType: string; - relation: string; - doi: string | null; - reverseRelation: string; - sourceReferenceLabel: string | null; -} - -export default class DetectMissingCrossReferences extends BaseCommand { - static commandName = 'detect:missing-cross-references'; - static description = 'Detect missing bidirectional cross-references between versioned datasets'; - - public static needsApplication = true; - - @flags.boolean({ alias: 'f', description: 'Fix missing cross-references automatically' }) - public fix: boolean = false; - - @flags.boolean({ alias: 'v', description: 'Verbose output' }) - public verbose: boolean = false; - - @flags.number({ alias: 'p', description: 'Filter by specific publish_id (source or target dataset)' }) - public publish_id?: number; - - // example: node ace detect:missing-cross-references --verbose -p 227 //if you want to filter by specific publish_id with details - // example: node ace detect:missing-cross-references --verbose - // example: node ace detect:missing-cross-references --fix -p 227 //if you want to filter by specific publish_id and fix it - // example: node ace detect:missing-cross-references - - public static options: CommandOptions = { - startApp: true, - staysAlive: false, - }; - - // Define the allowed relations that we want to process - private readonly ALLOWED_RELATIONS = [ - 'IsNewVersionOf', - 'IsPreviousVersionOf', - 'IsVariantFormOf', - 'IsOriginalFormOf', - 'Continues', - 'IsContinuedBy', - 'HasPart', - 'IsPartOf', - ]; - // private readonly ALLOWED_RELATIONS = ['IsPreviousVersionOf', 'IsOriginalFormOf']; - - async run() { - this.logger.info('๐Ÿ” Detecting missing cross-references...'); - this.logger.info(`๐Ÿ“‹ Processing only these relations: ${this.ALLOWED_RELATIONS.join(', ')}`); - - if (this.publish_id) { - this.logger.info(`Filtering by publish_id: ${this.publish_id}`); - } - - try { - const missingReferences = await this.findMissingCrossReferences(); - - // Store count in AppConfig if not fixing and count >= 1 - if (!this.fix && missingReferences.length >= 1) { - await this.storeMissingCrossReferencesCount(missingReferences.length); - } - - if (missingReferences.length === 0) { - const filterMsg = this.publish_id ? ` for publish_id ${this.publish_id}` : ''; - this.logger.success(`All cross-references are properly linked for the specified relations${filterMsg}!`); - // Clear the count if no missing references - if (!this.fix) { - await this.storeMissingCrossReferencesCount(0); - } - return; - } - - const filterMsg = this.publish_id ? ` (filtered by publish_id ${this.publish_id})` : ''; - this.logger.warning(`Found ${missingReferences.length} missing cross-reference(s)${filterMsg}:`); - - // Show brief list if not verbose mode - if (!this.verbose) { - for (const missing of missingReferences) { - const sourceDoi = missing.sourceDoi ? ` DOI: ${missing.sourceDoi}` : ''; - const targetDoi = missing.targetDoi ? ` DOI: ${missing.targetDoi}` : ''; - - this.logger.info( - `Dataset ${missing.sourceDatasetId} (Publish ID: ${missing.sourcePublishId}${sourceDoi}) ${missing.relation} Dataset ${missing.targetDatasetId} (Publish ID: ${missing.targetPublishId}${targetDoi}) โ†’ missing reverse: ${missing.reverseRelation}`, - ); - } - } else { - // Verbose mode - show detailed info - for (const missing of missingReferences) { - this.logger.info( - `Dataset ${missing.sourceDatasetId} references ${missing.targetDatasetId}, but reverse reference is missing`, - ); - this.logger.info(` - Reference type: ${missing.referenceType}`); - this.logger.info(` - Relation: ${missing.relation}`); - this.logger.info(` - DOI: ${missing.doi}`); - } - } - - if (this.fix) { - await this.fixMissingReferences(missingReferences); - // Clear the count after fixing - await this.storeMissingCrossReferencesCount(0); - this.logger.success('All missing cross-references have been fixed!'); - } else { - if (this.verbose) { - this.printMissingReferencesList(missingReferences); - } - this.logger.info('๐Ÿ’ก Run with --fix flag to automatically create missing cross-references'); - if (this.publish_id) { - this.logger.info(`๐ŸŽฏ Currently filtering by publish_id: ${this.publish_id}`); - } - } - } catch (error) { - this.logger.error('Error detecting missing cross-references:', error); - process.exit(1); - } - } - - private async storeMissingCrossReferencesCount(count: number): Promise { - try { - await AppConfig.updateOrCreate( - { - appid: 'commands', - configkey: 'missing_cross_references_count', - }, - { - configvalue: count.toString(), - }, - ); - - this.logger.info(`๐Ÿ“Š Stored missing cross-references count in database: ${count}`); - } catch (error) { - this.logger.error('Failed to store missing cross-references count:', error); - } - } - - private async findMissingCrossReferences(): Promise { - const missingReferences: { - sourceDatasetId: number; - targetDatasetId: number; - sourcePublishId: number | null; - targetPublishId: number | null; - sourceDoi: string | null; - targetDoi: string | null; - referenceType: string; - relation: string; - doi: string | null; - reverseRelation: string; - sourceReferenceLabel: string | null; - }[] = []; - - this.logger.info('๐Ÿ“Š Querying dataset references...'); - - // Find all references that point to Tethys datasets (DOI or URL containing tethys DOI) - // Only from datasets that are published AND only for allowed relations - const tethysReferencesQuery = DatasetReference.query() - .whereIn('type', ['DOI', 'URL']) - .whereIn('relation', this.ALLOWED_RELATIONS) // Only process allowed relations - .where((query) => { - query.where('value', 'like', '%doi.org/10.24341/tethys.%').orWhere('value', 'like', '%tethys.at/dataset/%'); - }) - .preload('dataset', (datasetQuery) => { - datasetQuery.preload('identifier'); - }) - .whereHas('dataset', (datasetQuery) => { - datasetQuery.where('server_state', 'published'); - }); - if (typeof this.publish_id === 'number') { - tethysReferencesQuery.whereHas('dataset', (datasetQuery) => { - datasetQuery.where('publish_id', this.publish_id as number); - }); - } - - const tethysReferences = await tethysReferencesQuery.exec(); - - this.logger.info(`๐Ÿ”— Found ${tethysReferences.length} Tethys references from published datasets (allowed relations only)`); - - let processedCount = 0; - let skippedCount = 0; - - for (const reference of tethysReferences) { - processedCount++; - - // if (this.verbose && processedCount % 10 === 0) { - // this.logger.info(`๐Ÿ“ˆ Processed ${processedCount}/${tethysReferences.length} references...`); - // } - - // Double-check that this relation is in our allowed list (safety check) - if (!this.ALLOWED_RELATIONS.includes(reference.relation)) { - skippedCount++; - if (this.verbose) { - this.logger.info(`โญ๏ธ Skipping relation "${reference.relation}" - not in allowed list`); - } - continue; - } - - // Extract dataset publish_id from DOI or URL - // const targetDatasetPublish = this.extractDatasetPublishIdFromReference(reference.value); - // Extract DOI from reference URL - const doi = this.extractDoiFromReference(reference.value); - - // if (!targetDatasetPublish) { - // if (this.verbose) { - // this.logger.warning(`Could not extract publish ID from: ${reference.value}`); - // } - // continue; - // } - if (!doi) { - if (this.verbose) { - this.logger.warning(`Could not extract DOI from: ${reference.value}`); - } - continue; - } - - // // Check if target dataset exists and is published - // const targetDataset = await Dataset.query() - // .where('publish_id', targetDatasetPublish) - // .where('server_state', 'published') - // .preload('identifier') - // .first(); - // Check if target dataset exists and is published by querying via identifier - const targetDataset = await Dataset.query() - .where('server_state', 'published') - .whereHas('identifier', (query) => { - query.where('value', doi); - }) - .preload('identifier') - .first(); - - if (!targetDataset) { - if (this.verbose) { - this.logger.warning(`โš ๏ธ Target dataset with publish_id ${doi} not found or not published`); - } - continue; - } - - // Ensure we have a valid source dataset with proper preloading - if (!reference.dataset) { - this.logger.warning(`โš ๏ธ Source dataset ${reference.document_id} not properly loaded, skipping...`); - continue; - } - - // Check if reverse reference exists - const reverseReferenceExists = await this.checkReverseReferenceExists( - targetDataset.id, - reference.document_id, - reference.relation, - reference.dataset.identifier.value - ); - - if (!reverseReferenceExists) { - const reverseRelation = this.getReverseRelation(reference.relation); - if (reverseRelation) { - // Only add if we have a valid reverse relation - missingReferences.push({ - sourceDatasetId: reference.document_id, - targetDatasetId: targetDataset.id, - sourcePublishId: reference.dataset.publish_id || null, - targetPublishId: targetDataset.publish_id || null, - referenceType: reference.type, - relation: reference.relation, - doi: reference.value, - reverseRelation: reverseRelation, - sourceDoi: reference.dataset.identifier ? reference.dataset.identifier.value : null, - targetDoi: targetDataset.identifier ? targetDataset.identifier.value : null, - sourceReferenceLabel: reference.label || null, - }); - } - } - } - - this.logger.info(`โœ… Processed ${processedCount} references (${skippedCount} skipped due to relation filtering)`); - return missingReferences; - } - - private extractDoiFromReference(reference: string): string | null { - // Match DOI pattern, with or without URL prefix - const doiPattern = /(?:https?:\/\/)?(?:doi\.org\/)?(.+)/i; - const match = reference.match(doiPattern); - - if (match && match[1]) { - return match[1]; // Returns just "10.24341/tethys.99.2" - } - - return null; - } - - private extractDatasetPublishIdFromReference(value: string): number | null { - // Extract from DOI: https://doi.org/10.24341/tethys.107 -> 107 - const doiMatch = value.match(/10\.24341\/tethys\.(\d+)/); - if (doiMatch) { - return parseInt(doiMatch[1]); - } - - // Extract from URL: https://tethys.at/dataset/107 -> 107 - const urlMatch = value.match(/tethys\.at\/dataset\/(\d+)/); - if (urlMatch) { - return parseInt(urlMatch[1]); - } - - return null; - } - - private async checkReverseReferenceExists( - targetDatasetId: number, - sourceDatasetId: number, - originalRelation: string, - sourceDatasetIdentifier: string | null, - ): Promise { - const reverseRelation = this.getReverseRelation(originalRelation); - - if (!reverseRelation) { - return true; // If no reverse relation is defined, consider it as "exists" to skip processing - } - - // Only check for reverse references where the source dataset is also published - const reverseReference = await DatasetReference.query() - // We don't filter by source document_id here to find any incoming reference from any published dataset - .where('document_id', targetDatasetId) - // .where('related_document_id', sourceDatasetId) // Ensure it's an incoming reference - .where('relation', reverseRelation) - .where('value', 'like', `%${sourceDatasetIdentifier}`) // Basic check to ensure it points back to source dataset - .first(); - - return !!reverseReference; - } - - private getReverseRelation(relation: string): string | null { - const relationMap: Record = { - IsNewVersionOf: 'IsPreviousVersionOf', - IsPreviousVersionOf: 'IsNewVersionOf', - IsVariantFormOf: 'IsOriginalFormOf', - IsOriginalFormOf: 'IsVariantFormOf', - Continues: 'IsContinuedBy', - IsContinuedBy: 'Continues', - HasPart: 'IsPartOf', - IsPartOf: 'HasPart', - }; - - // Only return reverse relation if it exists in our map, otherwise return null - return relationMap[relation] || null; - } - - private printMissingReferencesList(missingReferences: MissingCrossReference[]) { - console.log('โ”Œโ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”'); - console.log('โ”‚ MISSING CROSS-REFERENCES REPORT โ”‚'); - console.log('โ”‚ (Published Datasets Only - Filtered Relations) โ”‚'); - console.log('โ””โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”˜'); - console.log(); - - missingReferences.forEach((missing, index) => { - console.log( - `${index + 1}. Dataset ${missing.sourceDatasetId} (Publish ID: ${missing.sourcePublishId} Identifier: ${missing.sourceDoi}) - ${missing.relation} Dataset ${missing.targetDatasetId} (Publish ID: ${missing.targetPublishId} Identifier: ${missing.targetDoi})`, - ); - console.log(` โ”œโ”€ Current relation: "${missing.relation}"`); - console.log(` โ”œโ”€ Missing reverse relation: "${missing.reverseRelation}"`); - console.log(` โ”œโ”€ Reference type: ${missing.referenceType}`); - console.log(` โ””โ”€ DOI/URL: ${missing.doi}`); - console.log(); - }); - - console.log('โ”Œโ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”'); - console.log(`โ”‚ SUMMARY: ${missingReferences.length} missing reverse reference(s) detected โ”‚`); - console.log(`โ”‚ Processed relations: ${this.ALLOWED_RELATIONS.join(', ')} โ”‚`); - console.log('โ””โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”˜'); - } - - private async fixMissingReferences(missingReferences: MissingCrossReference[]) { - this.logger.info('๐Ÿ”ง Creating missing cross-references in database...'); - - let fixedCount = 0; - let errorCount = 0; - - for (const [index, missing] of missingReferences.entries()) { - try { - // Get both source and target datasets - const sourceDataset = await Dataset.query() - .where('id', missing.sourceDatasetId) - .where('server_state', 'published') - .preload('identifier') - .preload('titles') // Preload titles to get mainTitle - .first(); - - const targetDataset = await Dataset.query().where('id', missing.targetDatasetId).where('server_state', 'published').first(); - - if (!sourceDataset) { - this.logger.warning(`โš ๏ธ Source dataset ${missing.sourceDatasetId} not found or not published, skipping...`); - errorCount++; - continue; - } - - if (!targetDataset) { - this.logger.warning(`โš ๏ธ Target dataset ${missing.targetDatasetId} not found or not published, skipping...`); - errorCount++; - continue; - } - - // **NEW: Update the original reference if related_document_id is missing** - const originalReference = await DatasetReference.query() - .where('document_id', missing.sourceDatasetId) - .where('relation', missing.relation) - .where('value', 'like', `%${missing.targetDoi}%`) - .first(); - if (originalReference && !originalReference.related_document_id) { - originalReference.related_document_id = missing.targetDatasetId; - await originalReference.save(); - if (this.verbose) { - this.logger.info(`๐Ÿ”— Updated original reference with related_document_id: ${missing.targetDatasetId}`); - } - } - - // Create the reverse reference using the referenced_by relationship - // Example: If Dataset 297 IsNewVersionOf Dataset 144 - // We create an incoming reference for Dataset 144 that shows Dataset 297 IsPreviousVersionOf it - const reverseReference = new DatasetReference(); - // Don't set document_id - this creates an incoming reference via related_document_id - reverseReference.document_id = missing.targetDatasetId; // - reverseReference.related_document_id = missing.sourceDatasetId; - reverseReference.type = 'DOI'; - reverseReference.relation = missing.reverseRelation; - - // Use the source dataset's DOI for the value (what's being referenced) - if (sourceDataset.identifier?.value) { - reverseReference.value = `https://doi.org/${sourceDataset.identifier.value}`; - } else { - // Fallback to dataset URL if no DOI - reverseReference.value = `https://tethys.at/dataset/${sourceDataset.publish_id || missing.sourceDatasetId}`; - } - - // Use the source dataset's main title for the label - //reverseReference.label = sourceDataset.mainTitle || `Dataset ${missing.sourceDatasetId}`; - // get label of forward reference - reverseReference.label = missing.sourceReferenceLabel || sourceDataset.mainTitle || `Dataset ${missing.sourceDatasetId}`; - // reverseReference.notes = `Auto-created by detect:missing-cross-references command on ${DateTime.now().toISO()} to fix missing bidirectional reference.`; - - // Save the new reverse reference - // Also save 'server_date_modified' on target dataset to trigger any downstream updates (e.g. search index) - targetDataset.server_date_modified = DateTime.now(); - await targetDataset.save(); - - await reverseReference.save(); - fixedCount++; - - if (this.verbose) { - this.logger.info( - `โœ… [${index + 1}/${missingReferences.length}] Created reverse reference: Dataset ${missing.sourceDatasetId} -> ${missing.targetDatasetId} (${missing.reverseRelation})`, - ); - } else if ((index + 1) % 10 === 0) { - this.logger.info(`๐Ÿ“ˆ Fixed ${fixedCount}/${missingReferences.length} references...`); - } - } catch (error) { - this.logger.error( - `โŒ Error creating reverse reference for datasets ${missing.targetDatasetId} -> ${missing.sourceDatasetId}:`, - error, - ); - errorCount++; - } - } - - this.logger.info(`๐Ÿ“Š Fix completed: ${fixedCount} created, ${errorCount} errors`); - } -} diff --git a/commands/index_datasets.ts b/commands/index_datasets.ts index 322d4b8..ee76268 100644 --- a/commands/index_datasets.ts +++ b/commands/index_datasets.ts @@ -4,7 +4,7 @@ import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js'; import { create } from 'xmlbuilder2'; import Dataset from '#models/dataset'; -import XmlModel from '#app/Library/DatasetXmlSerializer'; +import XmlModel from '#app/Library/XmlModel'; import { readFileSync } from 'fs'; import SaxonJS from 'saxon-js'; import { Client } from '@opensearch-project/opensearch'; @@ -12,8 +12,10 @@ import { getDomain } from '#app/utils/utility-functions'; import { BaseCommand, flags } from '@adonisjs/core/ace'; import { CommandOptions } from '@adonisjs/core/types/ace'; import env from '#start/env'; +// import db from '@adonisjs/lucid/services/db'; +// import { default as Dataset } from '#models/dataset'; import logger from '@adonisjs/core/services/logger'; -import { DateTime } from 'luxon'; + const opensearchNode = env.get('OPENSEARCH_HOST', 'localhost'); const client = new Client({ node: `${opensearchNode}` }); // replace with your OpenSearch endpoint @@ -28,10 +30,11 @@ export default class IndexDatasets extends BaseCommand { public publish_id: number; public static options: CommandOptions = { - startApp: true, // Ensures the IoC container is ready to use - staysAlive: false, // Command exits after running + startApp: true, + staysAlive: false, }; + async run() { logger.debug('Hello world!'); // const { default: Dataset } = await import('#models/dataset'); @@ -41,12 +44,10 @@ export default class IndexDatasets extends BaseCommand { const index_name = 'tethys-records'; for (var dataset of datasets) { - 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`); - } + // 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); } } @@ -64,46 +65,6 @@ 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); @@ -117,8 +78,7 @@ 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}. - Error: ${error.message}`); + logger.error(`An error occurred while indexing dataset with publish_id ${dataset.publish_id}.`); } } @@ -151,16 +111,19 @@ export default class IndexDatasets extends BaseCommand { } private async getDatasetXmlDomNode(dataset: Dataset): Promise { - const serializer = new XmlModel(dataset).enableCaching().excludeEmptyFields(); + const xmlModel = new XmlModel(dataset); // xmlModel.setModel(dataset); - + xmlModel.excludeEmptyFields(); + xmlModel.caching = true; + // const cache = dataset.xmlCache ? dataset.xmlCache : null; + // dataset.load('xmlCache'); if (dataset.xmlCache) { - serializer.setCache(dataset.xmlCache); + xmlModel.xmlCache = dataset.xmlCache; } - // return cache.toXmlDocument(); - const xmlDocument: XMLBuilder | null = await serializer.toXmlDocument(); - return xmlDocument; + // return cache.getDomDocument(); + const domDocument: XMLBuilder | null = await xmlModel.getDomDocument(); + return domDocument; } private addSpecInformation(domNode: XMLBuilder, information: string) { diff --git a/commands/list_updatable_datacite.ts b/commands/list_updatable_datacite.ts deleted file mode 100644 index aed411a..0000000 --- a/commands/list_updatable_datacite.ts +++ /dev/null @@ -1,346 +0,0 @@ -/* -|-------------------------------------------------------------------------- -| node ace make:command list-updateable-datacite -| DONE: create commands/list_updeatable_datacite.ts -|-------------------------------------------------------------------------- -*/ -import { BaseCommand, flags } from '@adonisjs/core/ace'; -import { CommandOptions } from '@adonisjs/core/types/ace'; -import Dataset from '#models/dataset'; -import { DoiClient } from '#app/Library/Doi/DoiClient'; -import env from '#start/env'; -import logger from '@adonisjs/core/services/logger'; -import { DateTime } from 'luxon'; -import pLimit from 'p-limit'; - -export default class ListUpdateableDatacite extends BaseCommand { - static commandName = 'list:updateable-datacite'; - static description = 'List all datasets that need DataCite DOI updates'; - - public static needsApplication = true; - - // private chunkSize = 100; // Set chunk size for pagination - - @flags.boolean({ alias: 'v', description: 'Verbose output showing detailed information' }) - public verbose: boolean = false; - - @flags.boolean({ alias: 'c', description: 'Show only count of updatable datasets' }) - public countOnly: boolean = false; - - @flags.boolean({ alias: 'i', description: 'Show only publish IDs (useful for scripting)' }) - public idsOnly: boolean = false; - - @flags.number({ description: 'Chunk size for processing datasets (default: 50)' }) - public chunkSize: number = 50; - - //example: node ace list:updateable-datacite - //example: node ace list:updateable-datacite --verbose - //example: node ace list:updateable-datacite --count-only - //example: node ace list:updateable-datacite --ids-only - //example: node ace list:updateable-datacite --chunk-size 50 - - public static options: CommandOptions = { - startApp: true, - stayAlive: false, - }; - - async run() { - const prefix = env.get('DATACITE_PREFIX', ''); - const base_domain = env.get('BASE_DOMAIN', ''); - - if (!prefix || !base_domain) { - logger.error('Missing DATACITE_PREFIX or BASE_DOMAIN environment variables'); - return; - } - - // Prevent conflicting flags - if ((this.verbose && this.countOnly) || (this.verbose && this.idsOnly)) { - logger.error('Flags --verbose cannot be combined with --count-only or --ids-only'); - return; - } - - const chunkSize = this.chunkSize || 50; - let page = 1; - let hasMoreDatasets = true; - let totalProcessed = 0; - const updatableDatasets: Dataset[] = []; - - if (!this.countOnly && !this.idsOnly) { - logger.info(`Processing datasets in chunks of ${chunkSize}...`); - } - - while (hasMoreDatasets) { - const datasets = await this.getDatasets(page, chunkSize); - - if (datasets.length === 0) { - hasMoreDatasets = false; - break; - } - - if (!this.countOnly && !this.idsOnly) { - logger.info(`Processing chunk ${page} (${datasets.length} datasets)...`); - } - - const chunkUpdatableDatasets = await this.processChunk(datasets); - updatableDatasets.push(...chunkUpdatableDatasets); - totalProcessed += datasets.length; - - page += 1; - if (datasets.length < chunkSize) { - hasMoreDatasets = false; - } - } - - if (!this.countOnly && !this.idsOnly) { - logger.info(`Processed ${totalProcessed} datasets total, found ${updatableDatasets.length} that need updates`); - } - - if (this.countOnly) { - console.log(updatableDatasets.length); - } else if (this.idsOnly) { - updatableDatasets.forEach((dataset) => console.log(dataset.publish_id)); - } else if (this.verbose) { - await this.showVerboseOutput(updatableDatasets); - } else { - this.showSimpleOutput(updatableDatasets); - } - } - - /** - * Processes a chunk of datasets to determine which ones need DataCite updates - * - * This method handles parallel processing of datasets within a chunk, providing - * efficient error handling and filtering of results. - * - * @param datasets - Array of Dataset objects to process - * @returns Promise - Array of datasets that need updates - */ - // private async processChunk(datasets: Dataset[]): Promise { - // // Process datasets in parallel using Promise.allSettled for better error handling - // // - // // Why Promise.allSettled vs Promise.all? - // // - Promise.all fails fast: if ANY promise rejects, the entire operation fails - // // - Promise.allSettled waits for ALL promises: some can fail, others succeed - // // - This is crucial for batch processing where we don't want one bad dataset - // // to stop processing of the entire chunk - // const results = await Promise.allSettled( - // datasets.map(async (dataset) => { - // try { - // // Check if this specific dataset needs a DataCite update - // const needsUpdate = await this.shouldUpdateDataset(dataset); - - // // Return the dataset if it needs update, null if it doesn't - // // This creates a sparse array that we'll filter later - // return needsUpdate ? dataset : null; - // } catch (error) { - // // Error handling for individual dataset checks - // // - // // Log warnings only if we're not in silent modes (count-only or ids-only) - // // This prevents log spam when running automated scripts - // if (!this.countOnly && !this.idsOnly) { - // logger.warn(`Error checking dataset ${dataset.publish_id}: ${error.message}`); - // } - - // // IMPORTANT DECISION: Return the dataset anyway if we can't determine status - // // - // // Why? It's safer to include a dataset that might not need updating - // // than to miss one that actually does need updating. This follows the - // // "fail-safe" principle - if we're unsure, err on the side of caution - // return dataset; - // } - // }), - // ); - - // // Filter and extract results from Promise.allSettled response - // // - // // Promise.allSettled returns an array of objects with this structure: - // // - { status: 'fulfilled', value: T } for successful promises - // // - { status: 'rejected', reason: Error } for failed promises - // // - // // We need to: - // // 1. Only get fulfilled results (rejected ones are already handled above) - // // 2. Filter out null values (datasets that don't need updates) - // // 3. Extract the actual Dataset objects from the wrapper - // return results - // .filter( - // (result): result is PromiseFulfilledResult => - // // Type guard: only include fulfilled results that have actual values - // // This filters out: - // // - Rejected promises (shouldn't happen due to try/catch, but safety first) - // // - Fulfilled promises that returned null (datasets that don't need updates) - // result.status === 'fulfilled' && result.value !== null, - // ) - // .map((result) => result.value!); // Extract the Dataset from the wrapper - // // The ! is safe here because we filtered out null values above - // } - - private async processChunk(datasets: Dataset[]): Promise { - // Limit concurrency to avoid API flooding (e.g., max 5 at once) - const limit = pLimit(5); - - const tasks = datasets.map((dataset) => - limit(async () => { - try { - const needsUpdate = await this.shouldUpdateDataset(dataset); - return needsUpdate ? dataset : null; - } catch (error) { - if (!this.countOnly && !this.idsOnly) { - logger.warn( - `Error checking dataset ${dataset.publish_id}: ${ - error instanceof Error ? error.message : JSON.stringify(error) - }`, - ); - } - // Fail-safe: include dataset if uncertain - return dataset; - } - }), - ); - - const results = await Promise.allSettled(tasks); - - return results - .filter((result): result is PromiseFulfilledResult => result.status === 'fulfilled' && result.value !== null) - .map((result) => result.value!); - } - - private async getDatasets(page: number, chunkSize: number): Promise { - return await Dataset.query() - .orderBy('publish_id', 'asc') - .preload('identifier') - .preload('xmlCache') - .preload('titles') - .where('server_state', 'published') - .whereHas('identifier', (identifierQuery) => { - identifierQuery.where('type', 'doi'); - }) - .forPage(page, chunkSize); // Get files for the current page - } - - private async shouldUpdateDataset(dataset: Dataset): Promise { - try { - let doiIdentifier = dataset.identifier; - if (!doiIdentifier) { - await dataset.load('identifier'); - doiIdentifier = dataset.identifier; - } - - if (!doiIdentifier || doiIdentifier.type !== 'doi') { - return false; - } - - const datasetModified = - dataset.server_date_modified instanceof DateTime - ? dataset.server_date_modified - : DateTime.fromJSDate(dataset.server_date_modified); - - if (!datasetModified) { - return true; - } - - if (datasetModified > DateTime.now()) { - return false; - } - - const doiClient = new DoiClient(); - const DOI_CHECK_TIMEOUT = 300; // ms - - const doiLastModified = await Promise.race([ - doiClient.getDoiLastModified(doiIdentifier.value), - this.createTimeoutPromise(DOI_CHECK_TIMEOUT), - ]).catch(() => null); - - if (!doiLastModified) { - // If uncertain, better include dataset for update - return true; - } - - const doiModified = DateTime.fromJSDate(doiLastModified); - if (datasetModified > doiModified) { - const diffInSeconds = Math.abs(datasetModified.diff(doiModified, 'seconds').seconds); - const toleranceSeconds = 600; - return diffInSeconds > toleranceSeconds; - } - return false; - } catch (error) { - return true; // safer: include dataset if unsure - } - } - - /** - * Create a timeout promise for API calls - */ - private createTimeoutPromise(timeoutMs: number): Promise { - return new Promise((_, reject) => { - setTimeout(() => reject(new Error(`API call timeout after ${timeoutMs}ms`)), timeoutMs); - }); - } - - private showSimpleOutput(updatableDatasets: Dataset[]): void { - if (updatableDatasets.length === 0) { - console.log('No datasets need DataCite updates.'); - return; - } - - console.log(`\nFound ${updatableDatasets.length} dataset(s) that need DataCite updates:\n`); - - updatableDatasets.forEach((dataset) => { - console.log(`publish_id ${dataset.publish_id} needs update - ${dataset.mainTitle || 'Untitled'}`); - }); - - console.log(`\nTo update these datasets, run:`); - console.log(` node ace update:datacite`); - console.log(`\nOr update specific datasets:`); - console.log(` node ace update:datacite -p `); - } - - private async showVerboseOutput(updatableDatasets: Dataset[]): Promise { - if (updatableDatasets.length === 0) { - console.log('No datasets need DataCite updates.'); - return; - } - - console.log(`\nFound ${updatableDatasets.length} dataset(s) that need DataCite updates:\n`); - - for (const dataset of updatableDatasets) { - await this.showDatasetDetails(dataset); - } - - console.log(`\nSummary: ${updatableDatasets.length} datasets need updates`); - } - - private async showDatasetDetails(dataset: Dataset): Promise { - try { - let doiIdentifier = dataset.identifier; - - if (!doiIdentifier) { - await dataset.load('identifier'); - doiIdentifier = dataset.identifier; - } - - const doiValue = doiIdentifier?.value || 'N/A'; - const datasetModified = dataset.server_date_modified; - - // Get DOI info from DataCite - const doiClient = new DoiClient(); - const doiLastModified = await doiClient.getDoiLastModified(doiValue); - const doiState = await doiClient.getDoiState(doiValue); - - console.log(`โ”Œโ”€ Dataset ${dataset.publish_id} โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€`); - console.log(`โ”‚ Title: ${dataset.mainTitle || 'Untitled'}`); - console.log(`โ”‚ DOI: ${doiValue}`); - console.log(`โ”‚ DOI State: ${doiState || 'Unknown'}`); - console.log(`โ”‚ Dataset Modified: ${datasetModified ? datasetModified.toISO() : 'N/A'}`); - console.log(`โ”‚ DOI Modified: ${doiLastModified ? DateTime.fromJSDate(doiLastModified).toISO() : 'N/A'}`); - console.log(`โ”‚ Status: NEEDS UPDATE`); - console.log(`โ””โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€\n`); - } catch (error) { - console.log(`โ”Œโ”€ Dataset ${dataset.publish_id} โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€`); - console.log(`โ”‚ Title: ${dataset.mainTitle || 'Untitled'}`); - console.log(`โ”‚ DOI: ${dataset.identifier?.value || 'N/A'}`); - console.log(`โ”‚ Error: ${error.message}`); - console.log(`โ”‚ Status: NEEDS UPDATE (Error checking)`); - console.log(`โ””โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€\n`); - } - } -} diff --git a/commands/update_datacite.ts b/commands/update_datacite.ts deleted file mode 100644 index 7ccb0f0..0000000 --- a/commands/update_datacite.ts +++ /dev/null @@ -1,266 +0,0 @@ -/* -|-------------------------------------------------------------------------- -| node ace make:command update-datacite -| DONE: create commands/update_datacite.ts -|-------------------------------------------------------------------------- -*/ -import { BaseCommand, flags } from '@adonisjs/core/ace'; -import { CommandOptions } from '@adonisjs/core/types/ace'; -import Dataset from '#models/dataset'; -import { DoiClient } from '#app/Library/Doi/DoiClient'; -import DoiClientException from '#app/exceptions/DoiClientException'; -import Index from '#app/Library/Utils/Index'; -import env from '#start/env'; -import logger from '@adonisjs/core/services/logger'; -import { DateTime } from 'luxon'; -import { getDomain } from '#app/utils/utility-functions'; - -export default class UpdateDatacite extends BaseCommand { - static commandName = 'update:datacite'; - static description = 'Update DataCite DOI records for published datasets'; - - public static needsApplication = true; - - @flags.number({ alias: 'p', description: 'Specific publish_id to update' }) - public publish_id: number; - - @flags.boolean({ alias: 'f', description: 'Force update all records regardless of modification date' }) - public force: boolean = false; - - @flags.boolean({ alias: 'd', description: 'Dry run - show what would be updated without making changes' }) - public dryRun: boolean = false; - - @flags.boolean({ alias: 's', description: 'Show detailed stats for each dataset that needs updating' }) - public stats: boolean = false; - - //example: node ace update:datacite -p 123 --force --dry-run - - public static options: CommandOptions = { - startApp: true, // Whether to boot the application before running the command - stayAlive: false, // Whether to keep the process alive after the command has executed - }; - - async run() { - logger.info('Starting DataCite update process...'); - - const prefix = env.get('DATACITE_PREFIX', ''); - const base_domain = env.get('BASE_DOMAIN', ''); - const apiUrl = env.get('DATACITE_API_URL', 'https://api.datacite.org'); - - if (!prefix || !base_domain) { - logger.error('Missing DATACITE_PREFIX or BASE_DOMAIN environment variables'); - return; - } - - logger.info(`Using DataCite API: ${apiUrl}`); - - const datasets = await this.getDatasets(); - logger.info(`Found ${datasets.length} datasets to process`); - - let updated = 0; - let skipped = 0; - let errors = 0; - - for (const dataset of datasets) { - try { - const shouldUpdate = this.force || (await this.shouldUpdateDataset(dataset)); - - if (this.stats) { - // Stats mode: show detailed information for datasets that need updating - if (shouldUpdate) { - await this.showDatasetStats(dataset); - updated++; - } else { - skipped++; - } - continue; - } - - if (!shouldUpdate) { - logger.info(`Dataset ${dataset.publish_id}: Up to date, skipping`); - skipped++; - continue; - } - - if (this.dryRun) { - logger.info(`Dataset ${dataset.publish_id}: Would update DataCite record (dry run)`); - updated++; - continue; - } - - await this.updateDataciteRecord(dataset, prefix, base_domain); - logger.info(`Dataset ${dataset.publish_id}: Successfully updated DataCite record`); - updated++; - } catch (error) { - logger.error(`Dataset ${dataset.publish_id}: Failed to update - ${error.message}`); - errors++; - } - } - - if (this.stats) { - logger.info(`\nDataCite Stats Summary: ${updated} datasets need updating, ${skipped} are up to date`); - } else { - logger.info(`DataCite update completed. Updated: ${updated}, Skipped: ${skipped}, Errors: ${errors}`); - } - } - - private async getDatasets(): Promise { - const query = Dataset.query() - .preload('identifier') - .preload('xmlCache') - .where('server_state', 'published') - .whereHas('identifier', (identifierQuery) => { - identifierQuery.where('type', 'doi'); - }); - - if (this.publish_id) { - query.where('publish_id', this.publish_id); - } - - return await query.exec(); - } - - private async shouldUpdateDataset(dataset: Dataset): Promise { - try { - let doiIdentifier = dataset.identifier; - - if (!doiIdentifier) { - await dataset.load('identifier'); - doiIdentifier = dataset.identifier; - } - - if (!doiIdentifier || doiIdentifier.type !== 'doi') { - return false; - } - - const datasetModified = dataset.server_date_modified; - const now = DateTime.now(); - - if (!datasetModified) { - return true; // Update if modification date is missing - } - - if (datasetModified > now) { - return false; // Skip invalid future dates - } - - // Check DataCite DOI modification date - const doiClient = new DoiClient(); - const doiLastModified = await doiClient.getDoiLastModified(doiIdentifier.value); - - if (!doiLastModified) { - return false; // not Update if we can't get DOI info - } - - const doiModified = DateTime.fromJSDate(doiLastModified); - if (datasetModified > doiModified) { - // if dataset was modified after DOI creation - // Calculate the difference in seconds - const diffInSeconds = Math.abs(datasetModified.diff(doiModified, 'seconds').seconds); - - // Define tolerance threshold (60 seconds = 1 minute) - const toleranceSeconds = 60; - - // Only update if the difference is greater than the tolerance - // This prevents unnecessary updates for minor timestamp differences - return diffInSeconds > toleranceSeconds; - } else { - return false; // No update needed - } - } catch (error) { - return false; // not update if we can't determine status or other error - } - } - - private async updateDataciteRecord(dataset: Dataset, prefix: string, base_domain: string): Promise { - try { - // Get the DOI identifier (HasOne relationship) - let doiIdentifier = dataset.identifier; - - if (!doiIdentifier) { - await dataset.load('identifier'); - doiIdentifier = dataset.identifier; - } - - if (!doiIdentifier || doiIdentifier.type !== 'doi') { - throw new Error('No DOI identifier found for dataset'); - } - - // Generate XML metadata - const xmlMeta = (await Index.getDoiRegisterString(dataset)) as string; - if (!xmlMeta) { - throw new Error('Failed to generate XML metadata'); - } - - // Construct DOI value and landing page URL - const doiValue = doiIdentifier.value; // Use existing DOI value - const landingPageUrl = `https://doi.${getDomain(base_domain)}/${doiValue}`; - - // Update DataCite record - const doiClient = new DoiClient(); - const dataciteResponse = await doiClient.registerDoi(doiValue, xmlMeta, landingPageUrl); - - if (dataciteResponse?.status === 201) { - // // Update dataset modification date - // dataset.server_date_modified = DateTime.now(); - // await dataset.save(); - - // // Update search index - // const index_name = 'tethys-records'; - // await Index.indexDocument(dataset, index_name); - - logger.debug(`Dataset ${dataset.publish_id}: DataCite record and search index updated successfully`); - } else { - throw new DoiClientException( - dataciteResponse?.status || 500, - `Unexpected DataCite response code: ${dataciteResponse?.status}`, - ); - } - } catch (error) { - if (error instanceof DoiClientException) { - throw error; - } - throw new Error(`Failed to update DataCite record: ${error.message}`); - } - } - - /** - * Shows detailed statistics for a dataset that needs updating - */ - private async showDatasetStats(dataset: Dataset): Promise { - try { - let doiIdentifier = dataset.identifier; - - if (!doiIdentifier) { - await dataset.load('identifier'); - doiIdentifier = dataset.identifier; - } - - const doiValue = doiIdentifier?.value || 'N/A'; - const doiStatus = doiIdentifier?.status || 'N/A'; - const datasetModified = dataset.server_date_modified; - - // Get DOI info from DataCite - const doiClient = new DoiClient(); - const doiLastModified = await doiClient.getDoiLastModified(doiValue); - const doiState = await doiClient.getDoiState(doiValue); - - console.log(` - โ”Œโ”€ Dataset ${dataset.publish_id} โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€ - โ”‚ DOI Value: ${doiValue} - โ”‚ DOI Status (DB): ${doiStatus} - โ”‚ DOI State (DataCite): ${doiState || 'Unknown'} - โ”‚ Dataset Modified: ${datasetModified ? datasetModified.toISO() : 'N/A'} - โ”‚ DOI Modified: ${doiLastModified ? DateTime.fromJSDate(doiLastModified).toISO() : 'N/A'} - โ”‚ Needs Update: YES - Dataset newer than DOI - โ””โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€`); - } catch (error) { - console.log(` - โ”Œโ”€ Dataset ${dataset.publish_id} โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€ - โ”‚ DOI Value: ${dataset.identifier?.value || 'N/A'} - โ”‚ Error: ${error.message} - โ”‚ Needs Update: YES - Error checking status - โ””โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€`); - } - } -} diff --git a/components.d.ts b/components.d.ts index 001762d..3834bf1 100644 --- a/components.d.ts +++ b/components.d.ts @@ -11,21 +11,3 @@ declare module '@vue/runtime-core' { NInput: (typeof import('naive-ui'))['NInput']; } } - -// types/leaflet-src-dom-DomEvent.d.ts -declare module 'leaflet/src/dom/DomEvent' { - export type DomEventHandler = (e?: any) => void; - - // Attach event listeners. `obj` can be any DOM node or object with event handling. - export function on(obj: any, types: string, fn: DomEventHandler, context?: any): void; - - // Detach event listeners. - export function off(obj: any, types: string, fn?: DomEventHandler, context?: any): void; - - // Prevent default on native events - export function preventDefault(ev?: Event | undefined): void; - - // Optional: other helpers you might need later - export function stopPropagation(ev?: Event | undefined): void; - export function stop(ev?: Event | undefined): void; -} \ No newline at end of file diff --git a/docker-entrypoint.sh b/docker-entrypoint.sh index 10d0f37..8ef61c7 100644 --- a/docker-entrypoint.sh +++ b/docker-entrypoint.sh @@ -1,74 +1,47 @@ #!/bin/bash + +# # Run freshclam to update virus definitions +# freshclam + +# # Sleep for a few seconds to give ClamAV time to start +# sleep 5 + +# # Start the ClamAV daemon +# /etc/init.d/clamav-daemon start + +# bootstrap clam av service and clam av database updater set -m -echo "Starting ClamAV services..." +function process_file() { + if [[ ! -z "$1" ]]; then + local SETTING_LIST=$(echo "$1" | tr ',' '\n' | grep "^[A-Za-z][A-Za-z]*=.*$") + local SETTING + + for SETTING in ${SETTING_LIST}; do + # Remove any existing copies of this setting. We do this here so that + # settings with multiple values (e.g. ExtraDatabase) can still be added + # multiple times below + local KEY=${SETTING%%=*} + sed -i $2 -e "/^${KEY} /d" + done + for SETTING in ${SETTING_LIST}; do + # Split on first '=' + local KEY=${SETTING%%=*} + local VALUE=${SETTING#*=} + echo "${KEY} ${VALUE}" >> "$2" + done + fi +} -# Try to download database if missing -# if [ ! "$(ls -A /var/lib/clamav 2>/dev/null)" ]; then -# echo "Downloading ClamAV database (this may take a while)..." - -# # Simple freshclam run without complex config -# if freshclam --datadir=/var/lib/clamav --quiet; then -# echo "โœ“ Database downloaded successfully" -# else -# echo "โš  Database download failed - creating minimal setup" -# # Create a dummy file so clamd doesn't immediately fail -# touch /var/lib/clamav/.dummy -# fi -# fi - -# Start freshclam daemon for automatic updates -echo "Starting freshclam daemon for automatic updates..." -# sg clamav -c "freshclam -d" & -# Added --daemon-notify to freshclam - This notifies clamd when the database updates -freshclam -d --daemon-notify=/etc/clamav/clamd.conf & -#freshclam -d & +# process_file "${CLAMD_SETTINGS_CSV}" /etc/clamav/clamd.conf +# process_file "${FRESHCLAM_SETTINGS_CSV}" /etc/clamav/freshclam.conf +# start in background +freshclam -d & # /etc/init.d/clamav-freshclam start & -# Start clamd in background -# Start clamd in foreground (so dumb-init can supervise it) +clamd # /etc/init.d/clamav-daemon start & -# Give freshclam a moment to start -sleep 2 - -# Start clamd daemon in background using sg -echo "Starting ClamAV daemon..." -# sg clamav -c "clamd" & -# Use sg to run clamd with proper group permissions -# sg clamav -c "clamd" & -# clamd --config-file=/etc/clamav/clamd.conf & -clamd & - - -# Give services time to start -echo "Waiting for services to initialize..." -sleep 8 - -# simple check -if pgrep clamd > /dev/null; then - echo "โœ“ ClamAV daemon is running" -else - echo "โš  ClamAV daemon status uncertain, but continuing..." -fi - -# Check if freshclam daemon is running -if pgrep freshclam > /dev/null; then - echo "โœ“ Freshclam daemon is running" -else - echo "โš  Freshclam daemon status uncertain, but continuing..." -fi - -# # Optional: Test socket connectivity -# if [ -S /var/run/clamav/clamd.socket ]; then -# echo "โœ“ ClamAV socket exists" -# else -# echo "โš  WARNING: ClamAV socket not found - services may still be starting" -# fi - -# # change back to CMD of dockerfile -echo "โœ“ ClamAV setup complete" -echo "Starting main application..." -# exec dumb-init -- "$@" +# change back to CMD of dockerfile exec "$@" \ No newline at end of file diff --git a/docs/commands/index-datasets.md b/docs/commands/index-datasets.md deleted file mode 100644 index baecfe6..0000000 --- a/docs/commands/index-datasets.md +++ /dev/null @@ -1,278 +0,0 @@ -# Dataset Indexing Command - -AdonisJS Ace command for indexing and synchronizing published datasets with OpenSearch for search functionality. - -## Overview - -The `index:datasets` command processes published datasets and creates/updates corresponding search index documents in OpenSearch. It intelligently compares modification timestamps to only re-index datasets when necessary, optimizing performance while maintaining search index accuracy. - -## Command Syntax - -```bash -node ace index:datasets [options] -``` - -## Options - -| Flag | Alias | Description | -|------|-------|-------------| -| `--publish_id ` | `-p` | Index a specific dataset by publish_id | - -## Usage Examples - -### Basic Operations - -```bash -# Index all published datasets that have been modified since last indexing -node ace index:datasets - -# Index a specific dataset by publish_id -node ace index:datasets --publish_id 231 -node ace index:datasets -p 231 -``` - -## How It Works - -### 1. **Dataset Selection** -The command processes datasets that meet these criteria: -- `server_state = 'published'` - Only published datasets -- Has preloaded `xmlCache` relationship for metadata transformation -- Optionally filtered by specific `publish_id` - -### 2. **Smart Update Detection** -For each dataset, the command: -- Checks if the dataset exists in the OpenSearch index -- Compares `server_date_modified` timestamps -- Only re-indexes if the dataset is newer than the indexed version - -### 3. **Document Processing** -The indexing process involves: -1. **XML Generation**: Creates structured XML from dataset metadata -2. **XSLT Transformation**: Converts XML to JSON using Saxon-JS processor -3. **Index Update**: Updates or creates the document in OpenSearch -4. **Logging**: Records success/failure for each operation - -## Index Structure - -### Index Configuration -- **Index Name**: `tethys-records` -- **Document ID**: Dataset `publish_id` -- **Refresh**: `true` (immediate availability) - -### Document Fields -The indexed documents contain: -- **Metadata Fields**: Title, description, authors, keywords -- **Identifiers**: DOI, publish_id, and other identifiers -- **Temporal Data**: Publication dates, coverage periods -- **Geographic Data**: Spatial coverage information -- **Technical Details**: Data formats, access information -- **Timestamps**: Creation and modification dates - -## Example Output - -### Successful Run -```bash -node ace index:datasets -``` -``` -Found 150 published datasets to process -Dataset with publish_id 231 successfully indexed -Dataset with publish_id 245 is up to date, skipping indexing -Dataset with publish_id 267 successfully indexed -An error occurred while indexing dataset with publish_id 289. Error: Invalid XML metadata -Processing completed: 148 indexed, 1 skipped, 1 error -``` - -### Specific Dataset -```bash -node ace index:datasets --publish_id 231 -``` -``` -Found 1 published dataset to process -Dataset with publish_id 231 successfully indexed -Processing completed: 1 indexed, 0 skipped, 0 errors -``` - -## Update Logic - -The command uses intelligent indexing to avoid unnecessary processing: - -| Condition | Action | Reason | -|-----------|--------|--------| -| Dataset not in index | โœ… Index | New dataset needs indexing | -| Dataset newer than indexed version | โœ… Re-index | Dataset has been updated | -| Dataset same/older than indexed version | โŒ Skip | Already up to date | -| OpenSearch document check fails | โœ… Index | Better safe than sorry | -| Invalid XML metadata | โŒ Skip + Log Error | Cannot process invalid data | - -### Timestamp Comparison -```typescript -// Example comparison logic -const existingModified = DateTime.fromMillis(Number(existingDoc.server_date_modified) * 1000); -const currentModified = dataset.server_date_modified; - -if (currentModified <= existingModified) { - // Skip - already up to date - return false; -} -// Proceed with indexing -``` - -## XML Transformation Process - -### 1. **XML Generation** -```xml - - - - - Research Dataset Title - Dataset description... - - - -``` - -### 2. **XSLT Processing** -The command uses Saxon-JS with a compiled stylesheet (`solr.sef.json`) to transform XML to JSON: -```javascript -const result = await SaxonJS.transform({ - stylesheetText: proc, - destination: 'serialized', - sourceText: xmlString, -}); -``` - -### 3. **Final JSON Document** -```json -{ - "id": "231", - "title": "Research Dataset Title", - "description": "Dataset description...", - "authors": ["Author Name"], - "server_date_modified": 1634567890, - "publish_id": 231 -} -``` - -## Configuration Requirements - -### Environment Variables -```bash -# OpenSearch Configuration -OPENSEARCH_HOST=localhost:9200 - -# For production: -# OPENSEARCH_HOST=your-opensearch-cluster:9200 -``` - -### Required Files -- **XSLT Stylesheet**: `public/assets2/solr.sef.json` - Compiled Saxon-JS stylesheet for XML transformation - -### Database Relationships -The command expects these model relationships: -```typescript -// Dataset model must have: -@hasOne(() => XmlCache, { foreignKey: 'dataset_id' }) -public xmlCache: HasOne -``` - -## Error Handling - -The command handles various error scenarios gracefully: - -### Common Errors and Solutions - -| Error | Cause | Solution | -|-------|-------|----------| -| `XSLT transformation failed` | Invalid XML or missing stylesheet | Check XML structure and stylesheet path | -| `OpenSearch connection error` | Service unavailable | Verify OpenSearch is running and accessible | -| `JSON parse error` | Malformed transformation result | Check XSLT stylesheet output format | -| `Missing xmlCache relationship` | Data integrity issue | Ensure xmlCache exists for dataset | - -### Error Logging -```bash -# Typical error log entry -An error occurred while indexing dataset with publish_id 231. -Error: XSLT transformation failed: Invalid XML structure at line 15 -``` - -## Performance Considerations - -### Batch Processing -- Processes datasets sequentially to avoid overwhelming OpenSearch -- Each dataset is committed individually for reliability -- Failed indexing of one dataset doesn't stop processing others - -### Resource Usage -- **Memory**: XML/JSON transformations require temporary memory -- **Network**: OpenSearch API calls for each dataset -- **CPU**: XSLT transformations are CPU-intensive - -### Optimization Tips -```bash -# Index only recently modified datasets (run regularly) -node ace index:datasets - -# Index specific datasets when needed -node ace index:datasets --publish_id 231 - -# Consider running during off-peak hours for large batches -``` - -## Integration with Other Systems - -### Search Functionality -The indexed documents power: -- **Dataset Search**: Full-text search across metadata -- **Faceted Browsing**: Filter by authors, keywords, dates -- **Geographic Search**: Spatial query capabilities -- **Auto-complete**: Suggest dataset titles and keywords - -### Related Commands -- [`update:datacite`](update-datacite.md) - Often run after indexing to sync DOI metadata -- **Database migrations** - May require re-indexing after schema changes - -### API Integration -The indexed data is consumed by: -- **Search API**: `/api/search` endpoints -- **Browse API**: `/api/datasets` with filtering -- **Recommendations**: Related dataset suggestions - -## Monitoring and Maintenance - -### Regular Tasks -```bash -# Daily indexing (recommended cron job) -0 2 * * * cd /path/to/project && node ace index:datasets - -# Weekly full re-index (if needed) -0 3 * * 0 cd /path/to/project && node ace index:datasets --force -``` - -### Health Checks -- Monitor OpenSearch cluster health -- Check for failed indexing operations in logs -- Verify search functionality is working -- Compare dataset counts between database and index - -### Troubleshooting -```bash -# Check specific dataset indexing -node ace index:datasets --publish_id 231 - -# Verify OpenSearch connectivity -curl -X GET "localhost:9200/_cluster/health" - -# Check index statistics -curl -X GET "localhost:9200/tethys-records/_stats" -``` - -## Best Practices - -1. **Regular Scheduling**: Run the command regularly (daily) to keep the search index current -2. **Monitor Logs**: Watch for transformation errors or OpenSearch issues -3. **Backup Strategy**: Include OpenSearch indices in backup procedures -4. **Resource Management**: Monitor OpenSearch cluster resources during bulk operations -5. **Testing**: Verify search functionality after major indexing operations -6. **Coordination**: Run indexing before DataCite updates when both are needed \ No newline at end of file diff --git a/docs/commands/update-datacite.md b/docs/commands/update-datacite.md deleted file mode 100644 index 06041f0..0000000 --- a/docs/commands/update-datacite.md +++ /dev/null @@ -1,216 +0,0 @@ -# DataCite Update Command - -AdonisJS Ace command for updating DataCite DOI records for published datasets. - -## Overview - -The `update:datacite` command synchronizes your local dataset metadata with DataCite DOI records. It intelligently compares modification dates to only update records when necessary, reducing unnecessary API calls and maintaining data consistency. - -## Command Syntax - -```bash -node ace update:datacite [options] -``` - -## Options - -| Flag | Alias | Description | -|------|-------|-------------| -| `--publish_id ` | `-p` | Update a specific dataset by publish_id | -| `--force` | `-f` | Force update all records regardless of modification date | -| `--dry-run` | `-d` | Preview what would be updated without making changes | -| `--stats` | `-s` | Show detailed statistics for datasets that need updating | - -## Usage Examples - -### Basic Operations - -```bash -# Update all datasets that have been modified since their DOI was last updated -node ace update:datacite - -# Update a specific dataset -node ace update:datacite --publish_id 231 -node ace update:datacite -p 231 - -# Force update all datasets with DOIs (ignores modification dates) -node ace update:datacite --force -``` - -### Preview and Analysis - -```bash -# Preview what would be updated (dry run) -node ace update:datacite --dry-run - -# Show detailed statistics for datasets that need updating -node ace update:datacite --stats - -# Show stats for a specific dataset -node ace update:datacite --stats --publish_id 231 -``` - -### Combined Options - -```bash -# Dry run for a specific dataset -node ace update:datacite --dry-run --publish_id 231 - -# Show stats for all datasets (including up-to-date ones) -node ace update:datacite --stats --force -``` - -## Command Modes - -### 1. **Normal Mode** (Default) -Updates DataCite records for datasets that have been modified since their DOI was last updated. - -**Example Output:** -``` -Using DataCite API: https://api.test.datacite.org -Found 50 datasets to process -Dataset 231: Successfully updated DataCite record -Dataset 245: Up to date, skipping -Dataset 267: Successfully updated DataCite record -DataCite update completed. Updated: 15, Skipped: 35, Errors: 0 -``` - -### 2. **Dry Run Mode** (`--dry-run`) -Shows what would be updated without making any changes to DataCite. - -**Use Case:** Preview updates before running the actual command. - -**Example Output:** -``` -Dataset 231: Would update DataCite record (dry run) -Dataset 267: Would update DataCite record (dry run) -Dataset 245: Up to date, skipping -DataCite update completed. Updated: 2, Skipped: 1, Errors: 0 -``` - -### 3. **Stats Mode** (`--stats`) -Shows detailed information for each dataset that needs updating, including why it needs updating. - -**Use Case:** Debug synchronization issues, monitor dataset/DOI status, generate reports. - -**Example Output:** -``` -โ”Œโ”€ Dataset 231 โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€ -โ”‚ DOI Value: 10.21388/tethys.231 -โ”‚ DOI Status (DB): findable -โ”‚ DOI State (DataCite): findable -โ”‚ Dataset Modified: 2024-09-15T10:30:00.000Z -โ”‚ DOI Modified: 2024-09-10T08:15:00.000Z -โ”‚ Needs Update: YES - Dataset newer than DOI -โ””โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€ - -โ”Œโ”€ Dataset 267 โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€ -โ”‚ DOI Value: 10.21388/tethys.267 -โ”‚ DOI Status (DB): findable -โ”‚ DOI State (DataCite): findable -โ”‚ Dataset Modified: 2024-09-18T14:20:00.000Z -โ”‚ DOI Modified: 2024-09-16T12:45:00.000Z -โ”‚ Needs Update: YES - Dataset newer than DOI -โ””โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€ - -DataCite Stats Summary: 2 datasets need updating, 48 are up to date -``` - -## Update Logic - -The command uses intelligent update detection: - -1. **Compares modification dates**: Dataset `server_date_modified` vs DOI last modification date from DataCite -2. **Validates data integrity**: Checks for missing or future dates -3. **Handles API failures gracefully**: Updates anyway if DataCite info can't be retrieved -4. **Uses dual API approach**: DataCite REST API (primary) with MDS API fallback - -### When Updates Happen - -| Condition | Action | Reason | -|-----------|--------|--------| -| Dataset modified > DOI modified | โœ… Update | Dataset has newer changes | -| Dataset modified โ‰ค DOI modified | โŒ Skip | DOI is up to date | -| Dataset date in future | โŒ Skip | Invalid data, needs investigation | -| Dataset date missing | โœ… Update | Can't determine staleness | -| DataCite API error | โœ… Update | Better safe than sorry | -| `--force` flag used | โœ… Update | Override all logic | - -## Environment Configuration - -Required environment variables: - -```bash -# DataCite Credentials -DATACITE_USERNAME=your_username -DATACITE_PASSWORD=your_password - -# API Endpoints (environment-specific) -DATACITE_API_URL=https://api.test.datacite.org # Test environment -DATACITE_SERVICE_URL=https://mds.test.datacite.org # Test MDS - -DATACITE_API_URL=https://api.datacite.org # Production -DATACITE_SERVICE_URL=https://mds.datacite.org # Production MDS - -# Project Configuration -DATACITE_PREFIX=10.21388 # Your DOI prefix -BASE_DOMAIN=tethys.at # Your domain -``` - -## Error Handling - -The command handles various error scenarios: - -- **Invalid modification dates**: Logs errors but continues processing other datasets -- **DataCite API failures**: Falls back to MDS API, then to safe update -- **Missing DOI identifiers**: Skips datasets without DOI identifiers -- **Network issues**: Continues with next dataset after logging error - -## Integration - -The command integrates with: - -- **Dataset Model**: Uses `server_date_modified` for change detection -- **DatasetIdentifier Model**: Reads DOI values and status -- **OpenSearch Index**: Updates search index after DataCite update -- **DoiClient**: Handles all DataCite API interactions - -## Common Workflows - -### Daily Maintenance -```bash -# Update any datasets modified today -node ace update:datacite -``` - -### Pre-Deployment Check -```bash -# Check what would be updated before deployment -node ace update:datacite --dry-run -``` - -### Debugging Sync Issues -```bash -# Investigate why specific dataset isn't syncing -node ace update:datacite --stats --publish_id 231 -``` - -### Full Resync -```bash -# Force update all DOI records (use with caution) -node ace update:datacite --force -``` - -### Monitoring Report -```bash -# Generate sync status report -node ace update:datacite --stats > datacite-sync-report.txt -``` - -## Best Practices - -1. **Regular Updates**: Run daily or after bulk dataset modifications -2. **Test First**: Use `--dry-run` or `--stats` before bulk operations -3. **Monitor Logs**: Check for data integrity warnings -4. **Environment Separation**: Use correct API URLs for test vs production -5. **Rate Limiting**: The command handles DataCite rate limits automatically \ No newline at end of file diff --git a/freshclam.conf b/freshclam.conf index 31992be..ee82a23 100644 --- a/freshclam.conf +++ b/freshclam.conf @@ -1,47 +1,229 @@ ## -## Container-optimized freshclam configuration +## Example config file for freshclam +## Please read the freshclam.conf(5) manual before editing this file. ## -# Database directory + +# Comment or remove the line below. + +# Path to the database directory. +# WARNING: It must match clamd.conf's directive! +# Default: hardcoded (depends on installation options) DatabaseDirectory /var/lib/clamav -# Log to stdout for container logging +# Path to the log file (make sure it has proper permissions) +# Default: disabled # UpdateLogFile /dev/stdout -# Basic logging settings +# Maximum size of the log file. +# Value of 0 disables the limit. +# You may use 'M' or 'm' for megabytes (1M = 1m = 1048576 bytes) +# and 'K' or 'k' for kilobytes (1K = 1k = 1024 bytes). +# in bytes just don't use modifiers. If LogFileMaxSize is enabled, +# log rotation (the LogRotate option) will always be enabled. +# Default: 1M +#LogFileMaxSize 2M + +# Log time with each message. +# Default: no LogTime yes + +# Enable verbose logging. +# Default: no LogVerbose yes + +# Use system logger (can work together with UpdateLogFile). +# Default: no LogSyslog no -# PID file location +# Specify the type of syslog messages - please refer to 'man syslog' +# for facility names. +# Default: LOG_LOCAL6 +#LogFacility LOG_MAIL + +# Enable log rotation. Always enabled when LogFileMaxSize is enabled. +# Default: no +#LogRotate yes + +# This option allows you to save the process identifier of the daemon +# Default: disabled +#PidFile /var/run/freshclam.pid PidFile /var/run/clamav/freshclam.pid -# Database owner +# By default when started freshclam drops privileges and switches to the +# "clamav" user. This directive allows you to change the database owner. +# Default: clamav (may depend on installation options) DatabaseOwner node -# Mirror settings for Austria +# Use DNS to verify virus database version. Freshclam uses DNS TXT records +# to verify database and software versions. With this directive you can change +# the database verification domain. +# WARNING: Do not touch it unless you're configuring freshclam to use your +# own database verification domain. +# Default: current.cvd.clamav.net +#DNSDatabaseInfo current.cvd.clamav.net + +# Uncomment the following line and replace XY with your country +# code. See http://www.iana.org/cctld/cctld-whois.htm for the full list. +# You can use db.XY.ipv6.clamav.net for IPv6 connections. DatabaseMirror db.at.clamav.net + +# database.clamav.net is a round-robin record which points to our most +# reliable mirrors. It's used as a fall back in case db.XY.clamav.net is +# not working. DO NOT TOUCH the following line unless you know what you +# are doing. DatabaseMirror database.clamav.net +# How many attempts to make before giving up. +# Default: 3 (per mirror) +#MaxAttempts 5 + # With this option you can control scripted updates. It's highly recommended # to keep it enabled. # Default: yes -# Update settings -ScriptedUpdates yes +#ScriptedUpdates yes + +# By default freshclam will keep the local databases (.cld) uncompressed to +# make their handling faster. With this option you can enable the compression; +# the change will take effect with the next database update. +# Default: no +#CompressLocalDatabase no + +# With this option you can provide custom sources (http:// or file://) for +# database files. This option can be used multiple times. +# Default: no custom URLs +#DatabaseCustomURL http://myserver.com/mysigs.ndb +#DatabaseCustomURL file:///mnt/nfs/local.hdb + +# This option allows you to easily point freshclam to private mirrors. +# If PrivateMirror is set, freshclam does not attempt to use DNS +# to determine whether its databases are out-of-date, instead it will +# use the If-Modified-Since request or directly check the headers of the +# remote database files. For each database, freshclam first attempts +# to download the CLD file. If that fails, it tries to download the +# CVD file. This option overrides DatabaseMirror, DNSDatabaseInfo +# and ScriptedUpdates. It can be used multiple times to provide +# fall-back mirrors. +# Default: disabled +#PrivateMirror mirror1.mynetwork.com +#PrivateMirror mirror2.mynetwork.com # Number of database checks per day. # Default: 12 (every two hours) -Checks 12 +#Checks 24 -# Don't fork (good for containers) +# Proxy settings +# Default: disabled +#HTTPProxyServer myproxy.com +#HTTPProxyPort 1234 +#HTTPProxyUsername myusername +#HTTPProxyPassword mypass + +# If your servers are behind a firewall/proxy which applies User-Agent +# filtering you can use this option to force the use of a different +# User-Agent header. +# Default: clamav/version_number +#HTTPUserAgent SomeUserAgentIdString + +# Use aaa.bbb.ccc.ddd as client address for downloading databases. Useful for +# multi-homed systems. +# Default: Use OS'es default outgoing IP address. +#LocalIPAddress aaa.bbb.ccc.ddd + +# Send the RELOAD command to clamd. +# Default: no +#NotifyClamd /path/to/clamd.conf + +# Run command after successful database update. +# Default: disabled +#OnUpdateExecute command + +# Run command when database update process fails. +# Default: disabled +#OnErrorExecute command + +# Run command when freshclam reports outdated version. +# In the command string %v will be replaced by the new version number. +# Default: disabled +#OnOutdatedExecute command + +# Don't fork into background. +# Default: no Foreground no -# Connection timeouts -ConnectTimeout 60 -ReceiveTimeout 60 +# Enable debug messages in libclamav. +# Default: no +#Debug yes -# Test databases before using them -TestDatabases yes +# Timeout in seconds when connecting to database server. +# Default: 30 +#ConnectTimeout 60 -# Enable bytecode signatures -Bytecode yes \ No newline at end of file +# Timeout in seconds when reading from database server. +# Default: 30 +#ReceiveTimeout 60 + +# With this option enabled, freshclam will attempt to load new +# databases into memory to make sure they are properly handled +# by libclamav before replacing the old ones. +# Default: yes +#TestDatabases yes + +# When enabled freshclam will submit statistics to the ClamAV Project about +# the latest virus detections in your environment. The ClamAV maintainers +# will then use this data to determine what types of malware are the most +# detected in the field and in what geographic area they are. +# Freshclam will connect to clamd in order to get recent statistics. +# Default: no +#SubmitDetectionStats /path/to/clamd.conf + +# Country of origin of malware/detection statistics (for statistical +# purposes only). The statistics collector at ClamAV.net will look up +# your IP address to determine the geographical origin of the malware +# reported by your installation. If this installation is mainly used to +# scan data which comes from a different location, please enable this +# option and enter a two-letter code (see http://www.iana.org/domains/root/db/) +# of the country of origin. +# Default: disabled +#DetectionStatsCountry country-code + +# This option enables support for our "Personal Statistics" service. +# When this option is enabled, the information on malware detected by +# your clamd installation is made available to you through our website. +# To get your HostID, log on http://www.stats.clamav.net and add a new +# host to your host list. Once you have the HostID, uncomment this option +# and paste the HostID here. As soon as your freshclam starts submitting +# information to our stats collecting service, you will be able to view +# the statistics of this clamd installation by logging into +# http://www.stats.clamav.net with the same credentials you used to +# generate the HostID. For more information refer to: +# http://www.clamav.net/documentation.html#cctts +# This feature requires SubmitDetectionStats to be enabled. +# Default: disabled +#DetectionStatsHostID unique-id + +# This option enables support for Google Safe Browsing. When activated for +# the first time, freshclam will download a new database file (safebrowsing.cvd) +# which will be automatically loaded by clamd and clamscan during the next +# reload, provided that the heuristic phishing detection is turned on. This +# database includes information about websites that may be phishing sites or +# possible sources of malware. When using this option, it's mandatory to run +# freshclam at least every 30 minutes. +# Freshclam uses the ClamAV's mirror infrastructure to distribute the +# database and its updates but all the contents are provided under Google's +# terms of use. See http://www.google.com/transparencyreport/safebrowsing +# and http://www.clamav.net/documentation.html#safebrowsing +# for more information. +# Default: disabled +#SafeBrowsing yes + +# This option enables downloading of bytecode.cvd, which includes additional +# detection mechanisms and improvements to the ClamAV engine. +# Default: enabled +#Bytecode yes + +# Download an additional 3rd party signature database distributed through +# the ClamAV mirrors. +# This option can be used multiple times. +#ExtraDatabase dbname1 +#ExtraDatabase dbname2 diff --git a/package-lock.json b/package-lock.json index 7cb57a4..6b10877 100644 --- a/package-lock.json +++ b/package-lock.json @@ -10,7 +10,7 @@ "dependencies": { "@adonisjs/auth": "^9.2.4", "@adonisjs/bodyparser": "^10.0.1", - "@adonisjs/core": "6.17.2", + "@adonisjs/core": "^6.17.0", "@adonisjs/cors": "^2.2.1", "@adonisjs/drive": "^3.2.0", "@adonisjs/inertia": "^2.1.3", @@ -30,6 +30,7 @@ "@phc/format": "^1.0.0", "@poppinss/manager": "^5.0.2", "@vinejs/vine": "^3.0.0", + "argon2": "^0.43.0", "axios": "^1.7.9", "bcrypt": "^5.1.1", "bcryptjs": "^2.4.3", @@ -108,9 +109,9 @@ } }, "node_modules/@adonisjs/ace": { - 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"https://registry.npmjs.org/youch-core/-/youch-core-0.3.2.tgz", + "integrity": "sha512-fusrlIMLeRvTFYLUjJ9KzlGC3N+6MOPJ68HNj/yJv2nz7zq8t4HEviLms2gkdRPUS7F5rZ5n+pYx9r88m6IE1g==", "devOptional": true, "license": "MIT", "dependencies": { - "@poppinss/exception": "^1.2.2", + "@poppinss/exception": "^1.2.0", "error-stack-parser-es": "^1.0.5" + }, + "engines": { + "node": ">=18" } }, "node_modules/youch-terminal": { diff --git a/package.json b/package.json index 7ae829f..989a29e 100644 --- a/package.json +++ b/package.json @@ -77,7 +77,7 @@ "dependencies": { "@adonisjs/auth": "^9.2.4", "@adonisjs/bodyparser": "^10.0.1", - "@adonisjs/core": "6.17.2", + "@adonisjs/core": "^6.17.0", "@adonisjs/cors": "^2.2.1", "@adonisjs/drive": "^3.2.0", "@adonisjs/inertia": "^2.1.3", @@ -97,6 +97,7 @@ "@phc/format": "^1.0.0", "@poppinss/manager": "^5.0.2", "@vinejs/vine": "^3.0.0", + "argon2": "^0.43.0", "axios": "^1.7.9", "bcrypt": "^5.1.1", "bcryptjs": "^2.4.3", diff --git a/providers/rule_provider.ts b/providers/rule_provider.ts deleted file mode 100644 index c945a5d..0000000 --- a/providers/rule_provider.ts +++ /dev/null @@ -1,34 +0,0 @@ -import { ApplicationService } from '@adonisjs/core/types'; - -export default class RuleProvider { - constructor(protected app: ApplicationService) {} - - public register() { - // Register your own bindings - } - - public async boot() { - // IoC container is ready - // await import("../src/rules/index.js"); - - await import('#start/rules/unique'); - await import('#start/rules/translated_language'); - await import('#start/rules/unique_person'); - // () => import('#start/rules/file_length'), - // () => import('#start/rules/file_scan'), - // () => import('#start/rules/allowed_extensions_mimetypes'), - await import('#start/rules/dependent_array_min_length'); - await import('#start/rules/referenceValidation'); - await import('#start/rules/valid_mimetype'); - await import('#start/rules/array_contains_types'); - await import('#start/rules/orcid'); - } - - public async ready() { - // App is ready - } - - public async shutdown() { - // Cleanup, since app is going down - } -} diff --git a/providers/vinejs_provider.ts b/providers/vinejs_provider.ts index 568dd3e..e4aad4c 100644 --- a/providers/vinejs_provider.ts +++ b/providers/vinejs_provider.ts @@ -6,16 +6,17 @@ import type { ApplicationService } from '@adonisjs/core/types'; import vine, { symbols, BaseLiteralType, Vine } from '@vinejs/vine'; import type { FieldContext, FieldOptions } from '@vinejs/vine/types'; +// import type { MultipartFile, FileValidationOptions } from '@adonisjs/bodyparser/types'; import type { MultipartFile } from '@adonisjs/core/bodyparser'; import type { FileValidationOptions } from '@adonisjs/core/types/bodyparser'; import { Request, RequestValidator } from '@adonisjs/core/http'; import MimeType from '#models/mime_type'; + /** * Validation options accepted by the "file" rule */ export type FileRuleValidationOptions = Partial | ((field: FieldContext) => Partial); - /** * Extend VineJS */ @@ -24,7 +25,6 @@ declare module '@vinejs/vine' { myfile(options?: FileRuleValidationOptions): VineMultipartFile; } } - /** * Extend HTTP request class */ @@ -36,54 +36,19 @@ declare module '@adonisjs/core/http' { * Checks if the value is an instance of multipart file * from bodyparser. */ -export function isBodyParserFile(file: MultipartFile | unknown): file is MultipartFile { +export function isBodyParserFile(file: MultipartFile | unknown): boolean { return !!(file && typeof file === 'object' && 'isMultipartFile' in file); } +export async function getEnabledExtensions() { + const enabledExtensions = await MimeType.query().select('file_extension').where('enabled', true).exec(); + const extensions = enabledExtensions + .map((extension) => { + return extension.file_extension.split('|'); + }) + .flat(); -/** - * Cache for enabled extensions to reduce database queries - */ -let extensionsCache: string[] | null = null; -let cacheTimestamp = 0; -const CACHE_DURATION = 5 * 60 * 1000; // 5 minutes - -/** - * Get enabled extensions with caching - */ -export async function getEnabledExtensions(): Promise { - const now = Date.now(); - - if (extensionsCache && now - cacheTimestamp < CACHE_DURATION) { - return extensionsCache; - } - - try { - const enabledExtensions = await MimeType.query().select('file_extension').where('enabled', true).exec(); - - const extensions = enabledExtensions - .map((extension) => extension.file_extension.split('|')) - .flat() - .map((ext) => ext.toLowerCase().trim()) - .filter((ext) => ext.length > 0); - - extensionsCache = [...new Set(extensions)]; // Remove duplicates - cacheTimestamp = now; - - return extensionsCache; - } catch (error) { - console.error('Error fetching enabled extensions:', error); - return extensionsCache || []; - } + return extensions; } - -/** - * Clear extensions cache - */ -export function clearExtensionsCache(): void { - extensionsCache = null; - cacheTimestamp = 0; -} - /** * VineJS validation rule that validates the file to be an * instance of BodyParser MultipartFile class. @@ -100,7 +65,6 @@ const isMultipartFile = vine.createRule(async (file: MultipartFile | unknown, op // At this point, you can use type assertion to explicitly tell TypeScript that file is of type MultipartFile const validatedFile = file as MultipartFile; const validationOptions = typeof options === 'function' ? options(field) : options; - /** * Set size when it's defined in the options and missing * on the file instance @@ -108,29 +72,30 @@ const isMultipartFile = vine.createRule(async (file: MultipartFile | unknown, op if (validatedFile.sizeLimit === undefined && validationOptions.size) { validatedFile.sizeLimit = validationOptions.size; } - /** * Set extensions when it's defined in the options and missing * on the file instance */ - if (validatedFile.allowedExtensions === undefined) { - if (validationOptions.extnames !== undefined) { - validatedFile.allowedExtensions = validationOptions.extnames; - } else { - validatedFile.allowedExtensions = await getEnabledExtensions(); - } + // if (validatedFile.allowedExtensions === undefined && validationOptions.extnames) { + // validatedFile.allowedExtensions = validationOptions.extnames; + // } + if (validatedFile.allowedExtensions === undefined && validationOptions.extnames !== undefined) { + validatedFile.allowedExtensions = validationOptions.extnames; // await getEnabledExtensions(); + } else if (validatedFile.allowedExtensions === undefined && validationOptions.extnames === undefined) { + validatedFile.allowedExtensions = await getEnabledExtensions(); } - + /** + * wieder lรถschen + * Set extensions when it's defined in the options and missing + * on the file instance + */ + // if (file.clientNameSizeLimit === undefined && validationOptions.clientNameSizeLimit) { + // file.clientNameSizeLimit = validationOptions.clientNameSizeLimit; + // } /** * Validate file */ - try { - validatedFile.validate(); - } catch (error) { - field.report(`File validation failed: ${error.message}`, 'file.validation_error', field, validationOptions); - return; - } - + validatedFile.validate(); /** * Report errors */ @@ -142,37 +107,36 @@ const isMultipartFile = vine.createRule(async (file: MultipartFile | unknown, op const MULTIPART_FILE: typeof symbols.SUBTYPE = symbols.SUBTYPE; export class VineMultipartFile extends BaseLiteralType { + [MULTIPART_FILE]: string; - public validationOptions?: FileRuleValidationOptions; + // constructor(validationOptions?: FileRuleValidationOptions, options?: FieldOptions) { + // super(options, [isMultipartFile(validationOptions || {})]); + // this.validationOptions = validationOptions; + // this.#private = true; + // } + + // clone(): this { + // return new VineMultipartFile(this.validationOptions, this.cloneOptions()) as this; + // } + // #private; + // constructor(validationOptions?: FileRuleValidationOptions, options?: FieldOptions, validations?: Validation[]); + // clone(): this; + + public validationOptions; // extnames: (18) ['gpkg', 'htm', 'html', 'csv', 'txt', 'asc', 'c', 'cc', 'h', 'srt', 'tiff', 'pdf', 'png', 'zip', 'jpg', 'jpeg', 'jpe', 'xlsx'] // size: '512mb' + // public constructor(validationOptions?: FileRuleValidationOptions, options?: FieldOptions, validations?: Validation[]) { public constructor(validationOptions?: FileRuleValidationOptions, options?: FieldOptions) { + // super(options, validations); super(options, [isMultipartFile(validationOptions || {})]); this.validationOptions = validationOptions; } public clone(): any { + // return new VineMultipartFile(this.validationOptions, this.cloneOptions(), this.cloneValidations()); return new VineMultipartFile(this.validationOptions, this.cloneOptions()); } - - /** - * Set maximum file size - */ - public maxSize(size: string | number): this { - const newOptions = { ...this.validationOptions, size }; - return new VineMultipartFile(newOptions, this.cloneOptions()) as this; - } - - /** - * Set allowed extensions - */ - public extensions(extnames: string[]): this { - const newOptions = { ...this.validationOptions, extnames }; - return new VineMultipartFile(newOptions, this.cloneOptions()) as this; - } - - } export default class VinejsProvider { @@ -191,8 +155,13 @@ export default class VinejsProvider { /** * The container bindings have booted */ + boot(): void { - Vine.macro('myfile', function (this: Vine, options?: FileRuleValidationOptions) { + // VineString.macro('translatedLanguage', function (this: VineString, options: Options) { + // return this.use(translatedLanguageRule(options)); + // }); + + Vine.macro('myfile', function (this: Vine, options) { return new VineMultipartFile(options); }); @@ -206,41 +175,6 @@ export default class VinejsProvider { } return new RequestValidator(this.ctx).validateUsing(...args); }); - - // Ensure MIME validation macros are loaded - this.loadMimeValidationMacros(); - this.loadFileScanMacros(); - this.loadFileLengthMacros(); - } - - /** - * Load MIME validation macros - called during boot to ensure they're available - */ - private async loadMimeValidationMacros(): Promise { - try { - // Dynamically import the MIME validation rule to ensure macros are registered - await import('#start/rules/allowed_extensions_mimetypes'); - } catch (error) { - console.warn('Could not load MIME validation macros:', error); - } - } - - private async loadFileScanMacros(): Promise { - try { - // Dynamically import the MIME validation rule to ensure macros are registered - await import('#start/rules/file_scan'); - } catch (error) { - console.warn('Could not load MIME validation macros:', error); - } - } - - private async loadFileLengthMacros(): Promise { - try { - // Dynamically import the MIME validation rule to ensure macros are registered - await import('#start/rules/file_length'); - } catch (error) { - console.warn('Could not load MIME validation macros:', error); - } } /** @@ -256,7 +190,5 @@ export default class VinejsProvider { /** * Preparing to shutdown the app */ - async shutdown() { - clearExtensionsCache(); - } + async shutdown() {} } diff --git a/public/assets2/solr.sef.json b/public/assets2/solr.sef.json index 096d58e..690f934 100644 --- a/public/assets2/solr.sef.json +++ b/public/assets2/solr.sef.json @@ -1 +1 @@ -{"N":"package","version":"30","packageVersion":"1","saxonVersion":"SaxonJS 2.7","target":"JS","targetVersion":"2","name":"TOP-LEVEL","relocatable":"false","buildDateTime":"2025-10-09T14:12:43.043+02:00","ns":"xml=~ xsl=~ xs=~ fn=http://example.com/functions xlink=http://www.w3.org/1999/xlink gmd=http://www.isotc211.org/2005/gmd gco=http://www.isotc211.org/2005/gco json=http://www.w3.org/2013/XSL/json","C":[{"N":"co","binds":"","id":"0","vis":"PRIVATE","ex:uniform":"true","C":[{"N":"function","name":"Q{http://example.com/functions}escapeQuotes","as":"* ","slots":"201","ns":"xml=~ xsl=~ xs=~ fn=http://example.com/functions xlink=http://www.w3.org/1999/xlink gmd=http://www.isotc211.org/2005/gmd 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This is the backend co - [Configuration](#configuration) - [Database](#database) - [API Documentation](#api-documentation) -- [Commands](#commands) -- [Documentation](#documentation) - [Contributing](#contributing) - [License](#license) @@ -31,175 +29,5 @@ Before you begin, ensure you have met the following requirements: 1. Clone this repository: ```bash - git clone git clone https://gitea.geologie.ac.at/geolba/tethys.backend.git - cd tethys-backend + git clone https://gitea.geologie.ac.at/geolba/tethys.backend.git ``` - -2. Install dependencies: - - ```bash - npm install - ``` - -3. Configure environment variables (see [Configuration](#configuration)) - -4. Run database migrations: - - ```bash - node ace migration:run - ``` - -5. Start the development server: - - ```bash - npm run dev - ``` - -## Usage - -The Tethys Backend provides RESTful APIs for managing research datasets, user authentication, DOI registration, and search functionality. - -## Configuration - -Copy the `.env.example` file to `.env` and configure the following variables: - -### Database Configuration -```bash -DB_CONNECTION=pg -DB_HOST=localhost -DB_PORT=5432 -DB_USER=your_username -DB_PASSWORD=your_password -DB_DATABASE=tethys_db -``` - -### DataCite Configuration -```bash -# DataCite Credentials -DATACITE_USERNAME=your_datacite_username -DATACITE_PASSWORD=your_datacite_password -DATACITE_PREFIX=10.21388 - -# Environment-specific API endpoints -DATACITE_API_URL=https://api.test.datacite.org # Test environment -DATACITE_SERVICE_URL=https://mds.test.datacite.org # Test MDS - -# For production: -# DATACITE_API_URL=https://api.datacite.org -# DATACITE_SERVICE_URL=https://mds.datacite.org -``` - -### OpenSearch Configuration -```bash -OPENSEARCH_HOST=localhost:9200 -``` - -### Application Configuration -```bash -BASE_DOMAIN=tethys.at -APP_KEY=your_app_key -``` - -## Database - -The system uses PostgreSQL with Lucid ORM. Key models include: - -- **Dataset**: Research dataset metadata -- **DatasetIdentifier**: DOI and other identifiers for datasets -- **User**: User management and authentication -- **XmlCache**: Cached XML metadata - -Run migrations and seeders: - -```bash -# Run migrations -node ace migration:run - -# Run seeders (if available) -node ace db:seed -``` - -## API Documentation - -API endpoints are available for: - -- Dataset management (`/api/datasets`) -- User authentication (`/api/auth`) -- DOI registration (`/api/doi`) -- Search functionality (`/api/search`) - -*Detailed API documentation can be found in the `/docs/api` directory.* - -## Commands - -The system includes several Ace commands for maintenance and data management: - -### Dataset Indexing -```bash -# Index all published datasets to OpenSearch -node ace index:datasets - -# Index a specific dataset -node ace index:datasets --publish_id 123 -``` - -### DataCite DOI Management -```bash -# Update DataCite records for modified datasets -node ace update:datacite - -# Show detailed statistics for datasets needing updates -node ace update:datacite --stats - -# Preview what would be updated (dry run) -node ace update:datacite --dry-run - -# Force update all DOI records -node ace update:datacite --force - -# Update a specific dataset -node ace update:datacite --publish_id 123 -``` - -*For detailed command documentation, see the [Commands Documentation](docs/commands/)* - -## Documentation - -Comprehensive documentation is available in the `/docs` directory: - -- **[Commands Documentation](docs/commands/)** - Detailed guides for Ace commands - - [DataCite Update Command](docs/commands/update-datacite.md) - DOI synchronization and management - - [Dataset Indexing Command](docs/commands/index-datasets.md) - Search index management -- **[API Documentation](docs/api/)** - REST API endpoints and usage -- **[Deployment Guide](docs/deployment/)** - Production deployment instructions -- **[Configuration Guide](docs/configuration/)** - Environment setup and configuration options - -## Contributing - -1. Fork the repository -2. Create a feature branch (`git checkout -b feature/amazing-feature`) -3. Commit your changes (`git commit -m 'Add some amazing feature'`) -4. Push to the branch (`git push origin feature/amazing-feature`) -5. Open a Pull Request - -### Development Guidelines - -- Follow the existing code style and conventions -- Write tests for new features -- Update documentation for any API changes -- Ensure all commands and migrations work properly - -### Testing Commands - -```bash -# Run tests -npm test - -# Test specific commands -node ace update:datacite --dry-run --publish_id 123 -node ace index:datasets --publish_id 123 -``` - -## License - -This project is licensed under the [MIT License](LICENSE). \ No newline at end of file diff --git a/resources/js/Components/BaseButton.vue b/resources/js/Components/BaseButton.vue index 1462566..74c0b5d 100644 --- a/resources/js/Components/BaseButton.vue +++ b/resources/js/Components/BaseButton.vue @@ -1,5 +1,5 @@ -