diff --git a/Dockerfile b/Dockerfile index a5d1263..9f88544 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,57 +1,63 @@ ################## First Stage - Creating base ######################### # Created a variable to hold our node base image -ARG NODE_IMAGE=node:22-bookworm-slim +ARG NODE_IMAGE=node:22-trixie-slim FROM $NODE_IMAGE AS base + # Install dumb-init and ClamAV, and perform ClamAV database update -RUN apt update \ - && apt-get install -y dumb-init clamav clamav-daemon nano \ +RUN apt-get update \ + && apt-get install -y --no-install-recommends \ + dumb-init \ + clamav \ + clamav-daemon \ + clamdscan \ + ca-certificates \ && rm -rf /var/lib/apt/lists/* \ # Creating folders and changing ownerships - && mkdir -p /home/node/app && chown node:node /home/node/app \ - && mkdir -p /var/lib/clamav \ + && mkdir -p /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 \ - && 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 + && 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 -# # initial update of av databases -# RUN freshclam -# Configure Clam AV... +# Configure ClamAV - copy config files before switching user +# COPY --chown=node:clamav ./*.conf /etc/clamav/ 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" -# initial update of av databases -RUN freshclam - -# VOLUME /var/lib/clamav +# Copy entrypoint script 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 @@ -70,7 +76,6 @@ 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 ######################### @@ -88,6 +93,7 @@ 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 new file mode 100644 index 0000000..23bb390 --- /dev/null +++ b/LICENSE @@ -0,0 +1,22 @@ + +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 19e946c..824d4c8 100644 --- a/adonisrc.ts +++ b/adonisrc.ts @@ -11,9 +11,10 @@ export default defineConfig({ */ commands: [ - () => import('@adonisjs/core/commands'), - () => import('@adonisjs/lucid/commands'), - () => import('@adonisjs/mail/commands')], + () => import('@adonisjs/core/commands'), + () => import('@adonisjs/lucid/commands'), + () => import('@adonisjs/mail/commands') + ], /* |-------------------------------------------------------------------------- | Preloads @@ -26,16 +27,17 @@ 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/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'), ], /* |-------------------------------------------------------------------------- @@ -70,7 +72,7 @@ export default defineConfig({ () => import('#providers/stardust_provider'), () => import('#providers/query_builder_provider'), () => import('#providers/token_worker_provider'), - // () => import('#providers/validator_provider'), + () => import('#providers/rule_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 7209699..2b0bae1 100644 --- a/app/Controllers/Http/Api/AuthorsController.ts +++ b/app/Controllers/Http/Api/AuthorsController.ts @@ -4,20 +4,29 @@ import Person from '#models/person'; // node ace make:controller Author export default class AuthorsController { - public async index({}: HttpContext) { - // select * from gba.persons - // where exists (select * from gba.documents inner join gba.link_documents_persons on "documents"."id" = "link_documents_persons"."document_id" - // where ("link_documents_persons"."role" = 'author') and ("persons"."id" = "link_documents_persons"."person_id")); + public async index({}: HttpContext) { + const authors = await Person.query() - .preload('datasets') - .where('name_type', 'Personal') - .whereHas('datasets', (dQuery) => { - dQuery.wherePivot('role', 'author'); - }) - .withCount('datasets', (query) => { - query.as('datasets_count'); - }) - .orderBy('datasets_count', 'desc'); + .select([ + 'id', + 'academic_title', + 'first_name', + 'last_name', + 'identifier_orcid', + 'status', + 'name_type', + 'created_at' + // Note: 'email' is omitted + ]) + .preload('datasets') + .where('name_type', 'Personal') + .whereHas('datasets', (dQuery) => { + dQuery.wherePivot('role', 'author'); + }) + .withCount('datasets', (query) => { + query.as('datasets_count'); + }) + .orderBy('datasets_count', 'desc'); return authors; } diff --git a/app/Controllers/Http/Api/AvatarController.ts b/app/Controllers/Http/Api/AvatarController.ts index 74fe135..d7c532f 100644 --- a/app/Controllers/Http/Api/AvatarController.ts +++ b/app/Controllers/Http/Api/AvatarController.ts @@ -2,26 +2,46 @@ import type { HttpContext } from '@adonisjs/core/http'; import { StatusCodes } from 'http-status-codes'; import redis from '@adonisjs/redis/services/main'; -const PREFIXES = ['von', 'van']; +const PREFIXES = ['von', 'van', 'de', 'del', 'della', 'di', 'da', 'dos', 'du', 'le', 'la']; const DEFAULT_SIZE = 50; +const MIN_SIZE = 16; +const MAX_SIZE = 512; const FONT_SIZE_RATIO = 0.4; const COLOR_LIGHTENING_PERCENT = 60; const COLOR_DARKENING_FACTOR = 0.6; +const CACHE_TTL = 24 * 60 * 60; // 24 hours instead of 1 hour export default class AvatarController { public async generateAvatar({ request, response }: HttpContext) { try { const { name, size = DEFAULT_SIZE } = request.only(['name', 'size']); - if (!name) { - return response.status(StatusCodes.BAD_REQUEST).json({ error: 'Name is required' }); + + // Enhanced validation + if (!name || typeof name !== 'string' || name.trim().length === 0) { + return response.status(StatusCodes.BAD_REQUEST).json({ + error: 'Name is required and must be a non-empty string', + }); + } + + const parsedSize = this.validateSize(size); + if (!parsedSize.isValid) { + return response.status(StatusCodes.BAD_REQUEST).json({ + error: parsedSize.error, + }); } // Build a unique cache key for the given name and size - const cacheKey = `avatar:${name.trim().toLowerCase()}-${size}`; - const cachedSvg = await redis.get(cacheKey); - if (cachedSvg) { - this.setResponseHeaders(response); - return response.send(cachedSvg); + const cacheKey = `avatar:${this.sanitizeName(name)}-${parsedSize.value}`; + // const cacheKey = `avatar:${name.trim().toLowerCase()}-${size}`; + try { + const cachedSvg = await redis.get(cacheKey); + if (cachedSvg) { + this.setResponseHeaders(response); + return response.send(cachedSvg); + } + } catch (redisError) { + // Log redis error but continue without cache + console.warn('Redis cache read failed:', redisError); } const initials = this.getInitials(name); @@ -29,41 +49,85 @@ export default class AvatarController { const svgContent = this.createSvg(size, colors, initials); // // Cache the generated avatar for future use, e.g. 1 hour expiry - await redis.setex(cacheKey, 3600, svgContent); + try { + await redis.setex(cacheKey, CACHE_TTL, svgContent); + } catch (redisError) { + // Log but don't fail the request + console.warn('Redis cache write failed:', redisError); + } this.setResponseHeaders(response); return response.send(svgContent); } catch (error) { - return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({ error: error.message }); + console.error('Avatar generation error:', error); + return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({ + error: 'Failed to generate avatar', + }); } } - private getInitials(name: string): string { - const parts = name + private validateSize(size: any): { isValid: boolean; value?: number; error?: string } { + const numSize = Number(size); + + if (isNaN(numSize)) { + return { isValid: false, error: 'Size must be a valid number' }; + } + + if (numSize < MIN_SIZE || numSize > MAX_SIZE) { + return { + isValid: false, + error: `Size must be between ${MIN_SIZE} and ${MAX_SIZE}`, + }; + } + + return { isValid: true, value: Math.floor(numSize) }; + } + + private sanitizeName(name: string): string { + return name .trim() + .toLowerCase() + .replace(/[^a-z0-9\s-]/gi, ''); + } + + private getInitials(name: string): string { + const sanitized = name.trim().replace(/\s+/g, ' '); // normalize whitespace + const parts = sanitized .split(' ') - .filter((part) => part.length > 0); + .filter((part) => part.length > 0) + .map((part) => part.trim()); if (parts.length === 0) { return 'NA'; } - if (parts.length >= 2) { - return this.getMultiWordInitials(parts); + if (parts.length === 1) { + // For single word, take first 2 characters or first char if only 1 char + return parts[0].substring(0, Math.min(2, parts[0].length)).toUpperCase(); } - return parts[0].substring(0, 2).toUpperCase(); + + return this.getMultiWordInitials(parts); } private getMultiWordInitials(parts: string[]): string { - const firstName = parts[0]; - const lastName = parts[parts.length - 1]; - const firstInitial = firstName.charAt(0).toUpperCase(); - const lastInitial = lastName.charAt(0).toUpperCase(); + // Filter out prefixes and short words + const significantParts = parts.filter((part) => !PREFIXES.includes(part.toLowerCase()) && part.length > 1); - if (PREFIXES.includes(lastName.toLowerCase()) && lastName === lastName.toUpperCase()) { - return firstInitial + lastName.charAt(1).toUpperCase(); + if (significantParts.length === 0) { + // Fallback to first and last regardless of prefixes + const firstName = parts[0]; + const lastName = parts[parts.length - 1]; + return (firstName.charAt(0) + lastName.charAt(0)).toUpperCase(); } - return firstInitial + lastInitial; + + if (significantParts.length === 1) { + return significantParts[0].substring(0, 2).toUpperCase(); + } + + // Take first and last significant parts + const firstName = significantParts[0]; + const lastName = significantParts[significantParts.length - 1]; + return (firstName.charAt(0) + lastName.charAt(0)).toUpperCase(); } private generateColors(name: string): { background: string; text: string } { @@ -75,31 +139,44 @@ export default class AvatarController { } private createSvg(size: number, colors: { background: string; text: string }, initials: string): string { - const fontSize = size * FONT_SIZE_RATIO; - return ` - - - ${initials} - - `; + const fontSize = Math.max(12, Math.floor(size * FONT_SIZE_RATIO)); // Ensure readable font size + + // Escape any potential HTML/XML characters in initials + const escapedInitials = this.escapeXml(initials); + + return ` + + ${escapedInitials} + `; + } + + private escapeXml(text: string): string { + return text.replace(/&/g, '&').replace(//g, '>').replace(/"/g, '"').replace(/'/g, '''); } private setResponseHeaders(response: HttpContext['response']): void { - response.header('Content-type', 'image/svg+xml'); - response.header('Cache-Control', 'no-cache'); - response.header('Pragma', 'no-cache'); - response.header('Expires', '0'); + response.header('Content-Type', 'image/svg+xml'); + response.header('Cache-Control', 'public, max-age=86400'); // Cache for 1 day + response.header('ETag', `"${Date.now()}"`); // Simple ETag } private getColorFromName(name: string): string { let hash = 0; - for (let i = 0; i < name.length; i++) { - hash = name.charCodeAt(i) + ((hash << 5) - hash); + const normalizedName = name.toLowerCase().trim(); + + for (let i = 0; i < normalizedName.length; i++) { + hash = normalizedName.charCodeAt(i) + ((hash << 5) - hash); + hash = hash & hash; // Convert to 32-bit integer } + // Ensure we get vibrant colors by constraining the color space const colorParts = []; for (let i = 0; i < 3; i++) { - const value = (hash >> (i * 8)) & 0xff; + let value = (hash >> (i * 8)) & 0xff; + // Ensure minimum color intensity for better contrast + value = Math.max(50, value); colorParts.push(value.toString(16).padStart(2, '0')); } return colorParts.join(''); @@ -110,7 +187,7 @@ export default class AvatarController { const g = parseInt(hexColor.substring(2, 4), 16); const b = parseInt(hexColor.substring(4, 6), 16); - const lightenValue = (value: number) => Math.min(255, Math.floor((value * (100 + percent)) / 100)); + const lightenValue = (value: number) => Math.min(255, Math.floor(value + (255 - value) * (percent / 100))); const newR = lightenValue(r); const newG = lightenValue(g); @@ -124,7 +201,7 @@ export default class AvatarController { const g = parseInt(hexColor.slice(2, 4), 16); const b = parseInt(hexColor.slice(4, 6), 16); - const darkenValue = (value: number) => Math.round(value * COLOR_DARKENING_FACTOR); + const darkenValue = (value: number) => Math.max(0, Math.floor(value * COLOR_DARKENING_FACTOR)); const darkerR = darkenValue(r); const darkerG = darkenValue(g); diff --git a/app/Controllers/Http/Api/DatasetController.ts b/app/Controllers/Http/Api/DatasetController.ts index b80949d..9106521 100644 --- a/app/Controllers/Http/Api/DatasetController.ts +++ b/app/Controllers/Http/Api/DatasetController.ts @@ -1,24 +1,36 @@ 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 { - 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'); + /** + * 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'); - return datasets; + 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.', + }); + } } + /** + * GET /api/dataset + * Find all published datasets + */ public async findAll({ response }: HttpContext) { try { const datasets = await Dataset.query() @@ -34,34 +46,279 @@ export default class DatasetController { } } - 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(); + /** + * 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 - return datasets; + if (!dataset) { + return response.status(StatusCodes.NOT_FOUND).json({ + message: `Cannot find Dataset with publish_id=${params.publish_id}.`, + }); + } + + // Build the version chain + const versionChain = await this.buildVersionChain(dataset); + + // Add version chain to response + const responseData = { + ...dataset.toJSON(), + versionChain: versionChain, + }; + + // return response.status(StatusCodes.OK).json(dataset); + return response.status(StatusCodes.OK).json(responseData); + } catch (error) { + return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({ + message: error.message || `Error retrieving Dataset with publish_id=${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; } } diff --git a/app/Controllers/Http/Api/FileController.ts b/app/Controllers/Http/Api/FileController.ts index 8080479..8a400ad 100644 --- a/app/Controllers/Http/Api/FileController.ts +++ b/app/Controllers/Http/Api/FileController.ts @@ -2,53 +2,103 @@ import type { HttpContext } from '@adonisjs/core/http'; import File from '#models/file'; import { StatusCodes } from 'http-status-codes'; import * as fs from 'fs'; -import * as path from 'path'; +import { DateTime } from 'luxon'; // node ace make:controller Author export default class FileController { // @Get("download/:id") public async findOne({ response, params }: HttpContext) { const id = params.id; - const file = await File.findOrFail(id); - // const file = await File.findOne({ - // where: { id: id }, - // }); - if (file) { - const filePath = '/storage/app/data/' + file.pathName; - const ext = path.extname(filePath); - const fileName = file.label + ext; - try { - fs.accessSync(filePath, fs.constants.R_OK); //| fs.constants.W_OK); - // console.log("can read/write:", path); - - response - .header('Cache-Control', 'no-cache private') - .header('Content-Description', 'File Transfer') - .header('Content-Type', file.mimeType) - .header('Content-Disposition', 'inline; filename=' + fileName) - .header('Content-Transfer-Encoding', 'binary') - .header('Access-Control-Allow-Origin', '*') - .header('Access-Control-Allow-Methods', 'GET,POST'); - - response.status(StatusCodes.OK).download(filePath); - } catch (err) { - // console.log("no access:", path); - response.status(StatusCodes.NOT_FOUND).send({ - message: `File with id ${id} doesn't exist on file server`, - }); - } + // const file = await File.findOrFail(id); + // Load file with its related dataset to check embargo + const file = await File.query() + .where('id', id) + .preload('dataset') // or 'dataset' - whatever your relationship is named + .firstOrFail(); - // res.status(StatusCodes.OK).sendFile(filePath, (err) => { - // // res.setHeader("Content-Type", "application/json"); - // // res.removeHeader("Content-Disposition"); - // res.status(StatusCodes.NOT_FOUND).send({ - // message: `File with id ${id} doesn't exist on file server`, - // }); - // }); - } else { - response.status(StatusCodes.NOT_FOUND).send({ + if (!file) { + return response.status(StatusCodes.NOT_FOUND).send({ message: `Cannot find File with id=${id}.`, }); } + + const dataset = file.dataset; + // Files from unpublished datasets are now blocked + if (dataset.server_state !== 'published') { + return response.status(StatusCodes.FORBIDDEN).send({ + message: `File access denied: Dataset is not published.`, + }); + } + if (dataset && this.isUnderEmbargo(dataset.embargo_date)) { + return response.status(StatusCodes.FORBIDDEN).send({ + message: `File is under embargo until ${dataset.embargo_date?.toFormat('yyyy-MM-dd')}`, + }); + } + + // Proceed with file download + const filePath = '/storage/app/data/' + file.pathName; + const fileExt = file.filePath.split('.').pop() || ''; + // const fileName = file.label + fileExt; + const fileName = file.label.toLowerCase().endsWith(`.${fileExt.toLowerCase()}`) ? file.label : `${file.label}.${fileExt}`; + + // 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 5ec3910..04c450d 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 XmlModel from '#app/Library/XmlModel'; +import DatasetXmlSerializer from '#app/Library/DatasetXmlSerializer'; import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js'; import { create } from 'xmlbuilder2'; import { readFileSync } from 'fs'; @@ -252,7 +252,6 @@ export default class DatasetsController { dataset.reject_editor_note = null; } - //save main and additional titles const reviewer_id = request.input('reviewer_id', null); dataset.reviewer_id = reviewer_id; @@ -290,8 +289,6 @@ export default class DatasetsController { }); } - - public async rejectUpdate({ request, response, auth }: HttpContext) { const authUser = auth.user!; @@ -402,12 +399,10 @@ export default class DatasetsController { .back(); } - - return inertia.render('Editor/Dataset/Publish', { dataset, - can: { - reject: await auth.user?.can(['dataset-editor-reject']), + can: { + reject: await auth.user?.can(['dataset-editor-reject']), publish: await auth.user?.can(['dataset-publish']), }, }); @@ -454,7 +449,7 @@ export default class DatasetsController { public async rejectToReviewer({ request, inertia, response }: HttpContext) { const id = request.param('id'); const dataset = await Dataset.query() - .where('id', id) + .where('id', id) .preload('reviewer', (builder) => { builder.select('id', 'login', 'email'); }) @@ -555,7 +550,6 @@ export default class DatasetsController { } } - return response .flash( `You have successfully rejected dataset ${dataset.id} reviewed by ${dataset.reviewer.login}.${emailStatusMessage}`, @@ -580,53 +574,88 @@ export default class DatasetsController { public async doiStore({ request, response }: HttpContext) { const dataId = request.param('publish_id'); - const dataset = await Dataset.query() - // .preload('xmlCache') - .where('publish_id', dataId) - .firstOrFail(); + + // 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 xmlMeta = (await Index.getDoiRegisterString(dataset)) as string; - let prefix = ''; - let base_domain = ''; - // const datacite_environment = process.env.DATACITE_ENVIRONMENT || 'debug'; - prefix = process.env.DATACITE_PREFIX || ''; - base_domain = process.env.BASE_DOMAIN || ''; + // Prepare DOI registration data + const doiValue = `${prefix}/tethys.${dataset.publish_id}`; //'10.21388/tethys.213' + const landingPageUrl = `https://doi.${getDomain(base_domain)}/${prefix}/tethys.${dataset.publish_id}`; //https://doi.dev.tethys.at/10.21388/tethys.213 - // register DOI: - const doiValue = prefix + '/tethys.' + dataset.publish_id; //'10.21388/tethys.213' - const landingPageUrl = 'https://doi.' + getDomain(base_domain) + '/' + prefix + '/tethys.' + dataset.publish_id; //https://doi.dev.tethys.at/10.21388/tethys.213 + // Register DOI with DataCite const doiClient = new DoiClient(); const dataciteResponse = await doiClient.registerDoi(doiValue, xmlMeta, landingPageUrl); - if (dataciteResponse?.status === 201) { - // if response OK 201; save the Identifier value into db - const doiIdentifier = new DatasetIdentifier(); - doiIdentifier.value = doiValue; - doiIdentifier.dataset_id = dataset.id; - doiIdentifier.type = 'doi'; - doiIdentifier.status = 'findable'; - // save modified date of datset for re-caching model in db an update the search index - dataset.server_date_modified = DateTime.now(); - - // save updated dataset to db an index to OpenSearch - try { - await dataset.related('identifier').save(doiIdentifier); - const index_name = 'tethys-records'; - await Index.indexDocument(dataset, index_name); - } catch (error) { - logger.error(`${__filename}: Indexing document ${dataset.id} failed: ${error.message}`); - // Log the error or handle it as needed - throw new HttpException(error.message); - } - return response.toRoute('editor.dataset.list').flash('message', 'You have successfully created a DOI for the dataset!'); - } else { + if (dataciteResponse?.status !== 201) { 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 ${dataset.id}`); + } + } + public async show({}: HttpContext) {} public async edit({ request, inertia, response }: HttpContext) { @@ -900,6 +929,7 @@ export default class DatasetsController { const input = request.only(['project_id', 'embargo_date', 'language', 'type', 'creating_corporation']); // dataset.type = request.input('type'); dataset.merge(input); + dataset.server_date_modified = DateTime.now(); // let test: boolean = dataset.$isDirty; await dataset.useTransaction(trx).save(); @@ -1121,9 +1151,20 @@ export default class DatasetsController { // const filePath = await drive.use('local').getUrl('/'+ file.filePath) const filePath = file.filePath; const fileExt = file.filePath.split('.').pop() || ''; + + // Check if label already includes the extension + const fileName = file.label.toLowerCase().endsWith(`.${fileExt.toLowerCase()}`) ? file.label : `${file.label}.${fileExt}`; + // Set the response headers and download the file - response.header('Content-Type', file.mime_type || 'application/octet-stream'); - response.attachment(`${file.label}.${fileExt}`); + response + .header('Cache-Control', 'no-cache private') + .header('Content-Description', 'File Transfer') + .header('Content-Type', file.mime_type || 'application/octet-stream') + // .header('Content-Disposition', 'inline; filename=' + fileName) + .header('Content-Transfer-Encoding', 'binary') + .header('Access-Control-Allow-Origin', '*') + .header('Access-Control-Allow-Methods', 'GET'); + response.attachment(fileName); return response.download(filePath); } @@ -1136,19 +1177,18 @@ export default class DatasetsController { } } - private async getDatasetXmlDomNode(dataset: Dataset) { - const xmlModel = new XmlModel(dataset); + private async getDatasetXmlDomNode(dataset: Dataset): Promise { + const serializer = new DatasetXmlSerializer(dataset).enableCaching().excludeEmptyFields(); // xmlModel.setModel(dataset); - xmlModel.excludeEmptyFields(); - xmlModel.caching = true; - // const cache = dataset.xmlCache ? dataset.xmlCache : null; - // dataset.load('xmlCache'); + + // Load existing cache if available + await dataset.load('xmlCache'); if (dataset.xmlCache) { - xmlModel.xmlCache = dataset.xmlCache; + serializer.setCache(dataset.xmlCache); } // return cache.getDomDocument(); - const domDocument: XMLBuilder | null = await xmlModel.getDomDocument(); - return domDocument; + const xmlDocument : XMLBuilder | null = await serializer.toXmlDocument(); + return xmlDocument; } } diff --git a/app/Controllers/Http/Oai/OaiController.ts b/app/Controllers/Http/Oai/OaiController.ts index db49a32..47d1708 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 XmlModel from '#app/Library/XmlModel'; +import DatasetXmlSerializer from '#app/Library/DatasetXmlSerializer'; 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, @@ -347,16 +347,20 @@ 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)); @@ -602,19 +606,17 @@ export default class OaiController { } private async getDatasetXmlDomNode(dataset: Dataset) { - const xmlModel = new XmlModel(dataset); - // xmlModel.setModel(dataset); - xmlModel.excludeEmptyFields(); - xmlModel.caching = true; + const serializer = new DatasetXmlSerializer(dataset).enableCaching().excludeEmptyFields(); + // const cache = dataset.xmlCache ? dataset.xmlCache : null; // dataset.load('xmlCache'); if (dataset.xmlCache) { - xmlModel.xmlCache = dataset.xmlCache; + serializer.setCache(dataset.xmlCache); } - // return cache.getDomDocument(); - const domDocument: XMLBuilder | null = await xmlModel.getDomDocument(); - return domDocument; + // return cache.toXmlDocument(); + const xmlDocument: XMLBuilder | null = await serializer.toXmlDocument(); + return xmlDocument; } private addSpecInformation(domNode: XMLBuilder, information: string) { diff --git a/app/Controllers/Http/Reviewer/DatasetController.ts b/app/Controllers/Http/Reviewer/DatasetController.ts index 6b54772..27f9b46 100644 --- a/app/Controllers/Http/Reviewer/DatasetController.ts +++ b/app/Controllers/Http/Reviewer/DatasetController.ts @@ -107,13 +107,12 @@ export default class DatasetsController { } return inertia.render('Reviewer/Dataset/Review', { - dataset, + dataset, can: { review: await auth.user?.can(['dataset-review']), reject: await auth.user?.can(['dataset-review-reject']), }, }); - } public async review_old({ request, inertia, response, auth }: HttpContext) { @@ -370,6 +369,19 @@ export default class DatasetsController { .flash(`You have rejected dataset ${dataset.id}! to editor ${dataset.editor.login}`, 'message'); } + // public async download({ params, response }: HttpContext) { + // const id = params.id; + // // Find the file by ID + // const file = await File.findOrFail(id); + // // const filePath = await drive.use('local').getUrl('/'+ file.filePath) + // const filePath = file.filePath; + // const fileExt = file.filePath.split('.').pop() || ''; + // // Set the response headers and download the file + // response.header('Content-Type', file.mime_type || 'application/octet-stream'); + // response.attachment(`${file.label}.${fileExt}`); + // return response.download(filePath); + // } + public async download({ params, response }: HttpContext) { const id = params.id; // Find the file by ID @@ -377,9 +389,20 @@ export default class DatasetsController { // const filePath = await drive.use('local').getUrl('/'+ file.filePath) const filePath = file.filePath; const fileExt = file.filePath.split('.').pop() || ''; + + // Check if label already includes the extension + const fileName = file.label.toLowerCase().endsWith(`.${fileExt.toLowerCase()}`) ? file.label : `${file.label}.${fileExt}`; + // Set the response headers and download the file - response.header('Content-Type', file.mime_type || 'application/octet-stream'); - response.attachment(`${file.label}.${fileExt}`); + response + .header('Cache-Control', 'no-cache private') + .header('Content-Description', 'File Transfer') + .header('Content-Type', file.mime_type || 'application/octet-stream') + // .header('Content-Disposition', 'inline; filename=' + fileName) + .header('Content-Transfer-Encoding', 'binary') + .header('Access-Control-Allow-Origin', '*') + .header('Access-Control-Allow-Methods', 'GET'); + response.attachment(fileName); return response.download(filePath); } } diff --git a/app/Controllers/Http/Submitter/DatasetController.ts b/app/Controllers/Http/Submitter/DatasetController.ts index 245b5d9..cda7da6 100644 --- a/app/Controllers/Http/Submitter/DatasetController.ts +++ b/app/Controllers/Http/Submitter/DatasetController.ts @@ -105,6 +105,7 @@ export default class DatasetController { 'reviewed', 'rejected_editor', 'rejected_reviewer', + 'rejected_to_reviewer', ]) .where('account_id', user.id) .preload('titles') @@ -233,8 +234,9 @@ export default class DatasetController { .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255), + first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), last_name: vine.string().trim().minLength(3).maxLength(255), + identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(), }), ) .minLength(1) @@ -249,8 +251,9 @@ export default class DatasetController { .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255), + first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), last_name: vine.string().trim().minLength(3).maxLength(255), + identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(), pivot_contributor_type: vine.enum(Object.keys(ContributorTypes)), }), ) @@ -324,8 +327,9 @@ export default class DatasetController { .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255), + first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), last_name: vine.string().trim().minLength(3).maxLength(255), + identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(), }), ) .minLength(1) @@ -340,8 +344,9 @@ export default class DatasetController { .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255), + first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), last_name: vine.string().trim().minLength(3).maxLength(255), + identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(), pivot_contributor_type: vine.enum(Object.keys(ContributorTypes)), }), ) @@ -983,19 +988,6 @@ export default class DatasetController { const years = Array.from({ length: currentYear - 1990 + 1 }, (_, index) => 1990 + index); const licenses = await License.query().select('id', 'name_long').where('active', 'true').pluck('name_long', 'id'); - // const userHasRoles = user.roles; - // const datasetHasLicenses = await dataset.related('licenses').query().pluck('id'); - // const checkeds = dataset.licenses.first().id; - - // const doctypes = { - // analysisdata: { label: 'Analysis', value: 'analysisdata' }, - // measurementdata: { label: 'Measurements', value: 'measurementdata' }, - // monitoring: 'Monitoring', - // remotesensing: 'Remote Sensing', - // gis: 'GIS', - // models: 'Models', - // mixedtype: 'Mixed Type', - // }; return inertia.render('Submitter/Dataset/Edit', { dataset, @@ -1015,7 +1007,7 @@ export default class DatasetController { referenceIdentifierTypes: Object.entries(ReferenceIdentifierTypes).map(([key, value]) => ({ value: key, label: value })), relationTypes: Object.entries(RelationTypes).map(([key, value]) => ({ value: key, label: value })), doctypes: DatasetTypes, - can: { + can: { edit: await auth.user?.can(['dataset-edit']), delete: await auth.user?.can(['dataset-delete']), }, @@ -1163,42 +1155,93 @@ export default class DatasetController { } } - // Process all subjects/keywords from the request - const subjects = request.input('subjects'); + // ============================================ + // IMPROVED SUBJECTS PROCESSING + // ============================================ + const subjects = request.input('subjects', []); + const currentDatasetSubjectIds = new Set(); + for (const subjectData of subjects) { - // Case 1: Subject already exists in the database (has an ID) + let subjectToRelate: Subject; + + // Case 1: Subject has an ID (existing subject being updated) if (subjectData.id) { - // Retrieve the existing subject const existingSubject = await Subject.findOrFail(subjectData.id); - // Update subject properties from the request data - existingSubject.value = subjectData.value; - existingSubject.type = subjectData.type; - existingSubject.external_key = subjectData.external_key; + // Check if the updated value conflicts with another existing subject + const duplicateSubject = await Subject.query() + .where('value', subjectData.value) + .where('type', subjectData.type) + .where('language', subjectData.language || 'en') // Default language if not provided + .where('id', '!=', subjectData.id) // Exclude the current subject + .first(); - // Only save if there are actual changes - if (existingSubject.$isDirty) { - await existingSubject.save(); + if (duplicateSubject) { + // A duplicate exists - use the existing duplicate instead + subjectToRelate = duplicateSubject; + + // Check if the original subject should be deleted (if it's only used by this dataset) + const originalSubjectUsage = await Subject.query() + .where('id', existingSubject.id) + .withCount('datasets') + .firstOrFail(); + + if (originalSubjectUsage.$extras.datasets_count <= 1) { + // Only used by this dataset, safe to delete after detaching + await dataset.useTransaction(trx).related('subjects').detach([existingSubject.id]); + await existingSubject.useTransaction(trx).delete(); + } else { + // Used by other datasets, just detach from this one + await dataset.useTransaction(trx).related('subjects').detach([existingSubject.id]); + } + } else { + // No duplicate found, update the existing subject + existingSubject.value = subjectData.value; + existingSubject.type = subjectData.type; + existingSubject.language = subjectData.language; + existingSubject.external_key = subjectData.external_key; + + if (existingSubject.$isDirty) { + await existingSubject.useTransaction(trx).save(); + } + + subjectToRelate = existingSubject; } - - // Note: The relationship between dataset and subject is already established, - // so we don't need to attach it again } // Case 2: New subject being added (no ID) else { - // Check if a subject with the same value and type already exists in the database - const subject = await Subject.firstOrNew({ value: subjectData.value, type: subjectData.type }, subjectData); + // Use firstOrNew to either find existing or create new subject + subjectToRelate = await Subject.firstOrNew( + { + value: subjectData.value, + type: subjectData.type, + language: subjectData.language || 'en', + }, + { + value: subjectData.value, + type: subjectData.type, + language: subjectData.language || 'en', + external_key: subjectData.external_key, + }, + ); - if (subject.$isNew === true) { - // If it's a completely new subject, create and associate it with the dataset - await dataset.useTransaction(trx).related('subjects').save(subject); - } else { - // If the subject already exists, just create the relationship - await dataset.useTransaction(trx).related('subjects').attach([subject.id]); + if (subjectToRelate.$isNew) { + await subjectToRelate.useTransaction(trx).save(); } } + + // Ensure the relationship exists between dataset and subject + const relationshipExists = await dataset.related('subjects').query().where('subject_id', subjectToRelate.id).first(); + + if (!relationshipExists) { + await dataset.useTransaction(trx).related('subjects').attach([subjectToRelate.id]); + } + + // Track which subjects should remain associated with this dataset + currentDatasetSubjectIds.add(subjectToRelate.id); } + // Handle explicit deletions const subjectsToDelete = request.input('subjectsToDelete', []); for (const subjectData of subjectsToDelete) { if (subjectData.id) { @@ -1211,16 +1254,16 @@ export default class DatasetController { .withCount('datasets') .firstOrFail(); - // Check if the subject is used by multiple datasets - if (subject.$extras.datasets_count > 1) { - // If used by multiple datasets, just detach it from the current dataset - await dataset.useTransaction(trx).related('subjects').detach([subject.id]); - } else { - // If only used by this dataset, delete the subject completely + // Detach the subject from this dataset + await dataset.useTransaction(trx).related('subjects').detach([subject.id]); - await dataset.useTransaction(trx).related('subjects').detach([subject.id]); + // If this was the only dataset using this subject, delete it entirely + if (subject.$extras.datasets_count <= 1) { await subject.useTransaction(trx).delete(); } + + // Remove from current set if it was added earlier + currentDatasetSubjectIds.delete(subjectData.id); } } diff --git a/app/Library/DatasetXmlSerializer.ts b/app/Library/DatasetXmlSerializer.ts new file mode 100644 index 0000000..f84d3b7 --- /dev/null +++ b/app/Library/DatasetXmlSerializer.ts @@ -0,0 +1,231 @@ +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}: ${error.message}`); + return null; + } + } +} diff --git a/app/Library/Doi/DoiClient.ts b/app/Library/Doi/DoiClient.ts index 86151e7..4232ac4 100644 --- a/app/Library/Doi/DoiClient.ts +++ b/app/Library/Doi/DoiClient.ts @@ -1,6 +1,3 @@ -// import { Client } from 'guzzle'; -// import { Log } from '@adonisjs/core/build/standalone'; -// import { DoiInterface } from './interfaces/DoiInterface'; import DoiClientContract from '#app/Library/Doi/DoiClientContract'; import DoiClientException from '#app/exceptions/DoiClientException'; import { StatusCodes } from 'http-status-codes'; @@ -12,14 +9,14 @@ export class DoiClient implements DoiClientContract { public username: string; public password: string; public serviceUrl: string; + public apiUrl: string; constructor() { // const datacite_environment = process.env.DATACITE_ENVIRONMENT || 'debug'; this.username = process.env.DATACITE_USERNAME || ''; this.password = process.env.DATACITE_PASSWORD || ''; this.serviceUrl = process.env.DATACITE_SERVICE_URL || ''; - // this.prefix = process.env.DATACITE_PREFIX || ''; - // this.base_domain = process.env.BASE_DOMAIN || ''; + this.apiUrl = process.env.DATACITE_API_URL || 'https://api.datacite.org'; if (this.username === '' || this.password === '' || this.serviceUrl === '') { const message = 'issing configuration settings to properly initialize DOI client'; @@ -90,4 +87,240 @@ export class DoiClient implements DoiClientContract { throw new DoiClientException(error.response.status, error.response.data); } } + + /** + * Retrieves DOI information from DataCite REST API + * + * @param doiValue The DOI identifier e.g. '10.5072/tethys.999' + * @returns Promise with DOI information or null if not found + */ + public async getDoiInfo(doiValue: string): Promise { + try { + // Use configurable DataCite REST API URL + const dataciteApiUrl = `${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 9bc21f7..20253a4 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 XmlModel from '#app/Library/XmlModel'; +import DatasetXmlSerializer from '#app/Library/DatasetXmlSerializer'; import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js'; import logger from '@adonisjs/core/services/logger'; import { readFileSync } from 'fs'; @@ -72,31 +72,42 @@ export default { } }, + /** + * Index a dataset document to OpenSearch/Elasticsearch + */ async indexDocument(dataset: Dataset, index_name: string): Promise { try { - const proc = readFileSync('public/assets2/solr.sef.json'); - const doc: string = await this.getTransformedString(dataset, proc); + // Load XSLT transformation file + const xsltProc = readFileSync('public/assets2/solr.sef.json'); - let document = JSON.parse(doc); + // 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 await this.client.index({ id: dataset.publish_id?.toString(), index: index_name, body: document, - refresh: true, + refresh: true, // make immediately searchable }); - logger.info(`dataset with publish_id ${dataset.publish_id} successfully indexed`); + logger.info(`Dataset ${dataset.publish_id} successfully indexed to ${index_name}`); } catch (error) { - logger.error(`An error occurred while indexing datsaet with publish_id ${dataset.publish_id}.`); + logger.error(`Failed to index dataset ${dataset.publish_id}: ${error.message}`); + throw error; // Re-throw to allow caller to handle } }, + /** + * Transform dataset XML to JSON using XSLT + */ async getTransformedString(dataset: Dataset, proc: Buffer): 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 }); + // Generate XML string from dataset + const xmlString = await this.generateDatasetXml(dataset); try { + // Apply XSLT transformation const result = await SaxonJS.transform({ stylesheetText: proc, destination: 'serialized', @@ -108,6 +119,18 @@ 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 @@ -115,74 +138,49 @@ export default { * @return {import('focus-trap').FocusTrap[]} */ -// 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 ''; -// } -// }; - +/** + * Create complete XML record for dataset + * Handles caching and metadata enrichment + */ const createXmlRecord = async (dataset: Dataset, datasetNode: XMLBuilder): Promise => { const domNode = await getDatasetXmlDomNode(dataset); - 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); + 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}`); + } + } + + datasetNode.import(domNode); }; const getDatasetXmlDomNode = async (dataset: Dataset): Promise => { - const xmlModel = new XmlModel(dataset); + const serializer = new DatasetXmlSerializer(dataset).enableCaching().excludeEmptyFields(); // xmlModel.setModel(dataset); - xmlModel.excludeEmptyFields(); - xmlModel.caching = true; - // const cache = dataset.xmlCache ? dataset.xmlCache : null; - // dataset.load('xmlCache'); + + // Load cache relationship if not already loaded await dataset.load('xmlCache'); if (dataset.xmlCache) { - xmlModel.xmlCache = dataset.xmlCache; + serializer.setCache(dataset.xmlCache); } - // return cache.getDomDocument(); - const domDocument: XMLBuilder | null = await xmlModel.getDomDocument(); - return domDocument; + // Generate or retrieve cached DOM document + const xmlDocument: XMLBuilder | null = await serializer.toXmlDocument(); + return xmlDocument; }; const addLandingPageAttribute = (domNode: XMLBuilder, dataid: string) => { @@ -192,6 +190,6 @@ 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 deleted file mode 100644 index 6f76474..0000000 --- a/app/Library/XmlModel.ts +++ /dev/null @@ -1,129 +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 { 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 new file mode 100644 index 0000000..21e20df --- /dev/null +++ b/app/controllers/projects_controller.ts @@ -0,0 +1,54 @@ +// 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 ed7315e..de8defc 100644 --- a/app/models/DocumentXmlCache.ts +++ b/app/models/DocumentXmlCache.ts @@ -4,7 +4,8 @@ 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 type { BelongsTo } from '@adonisjs/lucid/types/relations'; +import logger from '@adonisjs/core/services/logger'; export default class DocumentXmlCache extends BaseModel { public static namingStrategy = new SnakeCaseNamingStrategy(); @@ -66,33 +67,38 @@ export default class DocumentXmlCache extends BaseModel { } /** - * Check if a dataset in a specific xml version is already cached or not. + * Check if a valid (non-stale) cache entry exists + * Cache is valid only if it was created AFTER the dataset's last modification * - * @param mixed datasetId - * @param mixed serverDateModified - * @returns {Promise} Returns true on cached hit else false. + * @param datasetId - The dataset ID to check + * @param datasetServerDateModified - The dataset's last modification timestamp + * @returns true if valid cache exists, false otherwise */ - // 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 query = db.from(this.table) + + const row = await 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 row = await query; - return !!row; + 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 ${this.document_id}`); } } diff --git a/app/models/person.ts b/app/models/person.ts index cdc612d..f4cf3a2 100644 --- a/app/models/person.ts +++ b/app/models/person.ts @@ -30,7 +30,7 @@ export default class Person extends BaseModel { @column({}) public lastName: string; - @column({}) + @column({ columnName: 'identifier_orcid' }) public identifierOrcid: string; @column({}) @@ -95,4 +95,34 @@ export default class Person extends BaseModel { pivotColumns: ['role', 'sort_order', 'allow_email_contact'], }) public datasets: ManyToMany; + + // public toJSON() { + // const json = super.toJSON(); + + // // Check if this person is loaded through a pivot relationship with sensitive roles + // const pivotRole = this.$extras?.pivot_role; + // if (pivotRole === 'author' || pivotRole === 'contributor') { + // // Remove sensitive information for public-facing roles + // delete json.email; + // // delete json.identifierOrcid; + // } + + // return json; + // } + + // @afterFind() + // public static async afterFindHook(person: Person) { + // if (person.$extras?.pivot_role === 'author' || person.$extras?.pivot_role === 'contributor') { + // person.email = undefined as any; + // } + // } + + // @afterFetch() + // public static async afterFetchHook(persons: Person[]) { + // persons.forEach(person => { + // if (person.$extras?.pivot_role === 'author' || person.$extras?.pivot_role === 'contributor') { + // person.email = undefined as any; + // } + // }); + // } } diff --git a/app/models/user.ts b/app/models/user.ts index 5dbaab4..7be02b9 100644 --- a/app/models/user.ts +++ b/app/models/user.ts @@ -89,24 +89,11 @@ export default class User extends compose(BaseModel, AuthFinder) { @column({}) public avatar: string; - // @hasOne(() => TotpSecret, { - // foreignKey: 'user_id', - // }) - // public totp_secret: HasOne; - - // @beforeSave() - // public static async hashPassword(user: User) { - // if (user.$dirty.password) { - // user.password = await hash.use('laravel').make(user.password); - // } - // } - public get isTwoFactorEnabled(): boolean { return Boolean(this?.twoFactorSecret && this.state == TotpState.STATE_ENABLED); // return Boolean(this.totp_secret?.twoFactorSecret); } - @manyToMany(() => Role, { pivotForeignKey: 'account_id', pivotRelatedForeignKey: 'role_id', @@ -142,7 +129,9 @@ export default class User extends compose(BaseModel, AuthFinder) { @beforeFind() @beforeFetch() public static preloadRoles(user: User) { - user.preload('roles') + user.preload('roles', (builder) => { + builder.select(['id', 'name', 'display_name', 'description']); + }); } public async getBackupCodes(this: User): Promise { diff --git a/app/validators/dataset.ts b/app/validators/dataset.ts index 5417463..f670b81 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({ @@ -67,8 +67,9 @@ export const createDatasetValidator = vine.compile( .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255), + first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), last_name: vine.string().trim().minLength(3).maxLength(255), + identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(), }), ) .minLength(1) @@ -83,9 +84,10 @@ export const createDatasetValidator = vine.compile( .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255), + first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), last_name: vine.string().trim().minLength(3).maxLength(255), pivot_contributor_type: vine.enum(Object.keys(ContributorTypes)), + identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(), }), ) .distinct('email') @@ -158,7 +160,8 @@ export const createDatasetValidator = vine.compile( .fileScan({ removeInfected: true }), ) .minLength(1), - }),); + }), +); /** * Validates the dataset's update action @@ -214,8 +217,9 @@ export const updateDatasetValidator = vine.compile( .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255), + first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), last_name: vine.string().trim().minLength(3).maxLength(255), + identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(), }), ) .minLength(1) @@ -230,8 +234,9 @@ export const updateDatasetValidator = vine.compile( .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255), + first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), last_name: vine.string().trim().minLength(3).maxLength(255), + identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(), pivot_contributor_type: vine.enum(Object.keys(ContributorTypes)), }), ) @@ -305,12 +310,13 @@ export const updateDatasetValidator = vine.compile( .fileScan({ removeInfected: true }), ) .dependentArrayMinLength({ dependentArray: 'fileInputs', min: 1 }), - fileInputs: vine.array( - vine.object({ - label: vine.string().trim().maxLength(100), - //extnames: extensions, - }), - ), + fileInputs: vine + .array( + vine.object({ + label: vine.string().trim().maxLength(100), + }), + ) + .optional(), }), ); @@ -365,8 +371,9 @@ export const updateEditorDatasetValidator = vine.compile( .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255), + first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), last_name: vine.string().trim().minLength(3).maxLength(255), + identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(), }), ) .minLength(1) @@ -381,8 +388,9 @@ export const updateEditorDatasetValidator = vine.compile( .email() .normalizeEmail() .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }), - first_name: vine.string().trim().minLength(3).maxLength(255), + first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'), last_name: vine.string().trim().minLength(3).maxLength(255), + identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(), pivot_contributor_type: vine.enum(Object.keys(ContributorTypes)), }), ) @@ -496,7 +504,7 @@ 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 ${dayjs().add(10, 'day').format('DD.MM.YYYY')}`, }); createDatasetValidator.messagesProvider = messagesProvider; diff --git a/app/validators/project.ts b/app/validators/project.ts new file mode 100644 index 0000000..7f3d1f8 --- /dev/null +++ b/app/validators/project.ts @@ -0,0 +1,28 @@ +// app/validators/project.ts +import vine from '@vinejs/vine'; + +export const createProjectValidator = vine.compile( + vine.object({ + label: vine.string().trim().minLength(1).maxLength(50) .regex(/^[a-z0-9-]+$/), + 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 61e8ecd..81262d9 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) - .regex(/^[a-zA-Z0-9]+$/), //Must be alphanumeric with hyphens or underscores + .isUnique({ table: 'roles', column: 'name' }) + .regex(/^[a-zA-Z0-9]+$/), // Must be alphanumeric 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]+$/), description: vine.string().trim().escape().minLength(3).maxLength(255).optional(), - permissions: vine.array(vine.number()).minLength(1), // define at least one permission for the new role + permissions: vine.array(vine.number()).minLength(1), // At least one permission required }), ); @@ -29,21 +29,28 @@ export const updateRoleValidator = vine.withMetaData<{ roleId: number }>().compi vine.object({ name: vine .string() - // .unique(async (db, value, field) => { - // const result = await db.from('roles').select('id').whereNot('id', field.meta.roleId).where('name', value).first(); - // return result.length ? false : true; - // }) + .trim() + .minLength(3) + .maxLength(255) .isUnique({ table: 'roles', column: 'name', whereNot: (field) => field.meta.roleId, }) + .regex(/^[a-zA-Z0-9]+$/), + display_name: vine + .string() .trim() .minLength(3) - .maxLength(255), - + .maxLength(255) + .isUnique({ + table: 'roles', + column: 'display_name', + whereNot: (field) => field.meta.roleId, + }) + .regex(/^[a-zA-Z0-9]+$/), description: vine.string().trim().escape().minLength(3).maxLength(255).optional(), - permissions: vine.array(vine.number()).minLength(1), // define at least one permission for the new role + permissions: vine.array(vine.number()).minLength(1), // At least one permission required }), ); diff --git a/clamd.conf b/clamd.conf index 171396d..f066387 100644 --- a/clamd.conf +++ b/clamd.conf @@ -5,7 +5,23 @@ 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 -User node \ No newline at end of file +# LocalSocketGroup node # Changed from 'clamav' +# User node # Changed from 'clamav' - clamd runs as clamav user \ No newline at end of file diff --git a/commands/fix_dataset_cross_references.ts b/commands/fix_dataset_cross_references.ts new file mode 100644 index 0000000..baa2e0e --- /dev/null +++ b/commands/fix_dataset_cross_references.ts @@ -0,0 +1,482 @@ +/* +|-------------------------------------------------------------------------- +| 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, ${errorCount} errors`); + } +} diff --git a/commands/index_datasets.ts b/commands/index_datasets.ts index ee76268..322d4b8 100644 --- a/commands/index_datasets.ts +++ b/commands/index_datasets.ts @@ -4,7 +4,7 @@ import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js'; import { create } from 'xmlbuilder2'; import Dataset from '#models/dataset'; -import XmlModel from '#app/Library/XmlModel'; +import XmlModel from '#app/Library/DatasetXmlSerializer'; import { readFileSync } from 'fs'; import SaxonJS from 'saxon-js'; import { Client } from '@opensearch-project/opensearch'; @@ -12,10 +12,8 @@ import { getDomain } from '#app/utils/utility-functions'; import { BaseCommand, flags } from '@adonisjs/core/ace'; import { CommandOptions } from '@adonisjs/core/types/ace'; import env from '#start/env'; -// import db from '@adonisjs/lucid/services/db'; -// import { default as Dataset } from '#models/dataset'; import logger from '@adonisjs/core/services/logger'; - +import { DateTime } from 'luxon'; const opensearchNode = env.get('OPENSEARCH_HOST', 'localhost'); const client = new Client({ node: `${opensearchNode}` }); // replace with your OpenSearch endpoint @@ -30,11 +28,10 @@ export default class IndexDatasets extends BaseCommand { public publish_id: number; public static options: CommandOptions = { - startApp: true, - staysAlive: false, + startApp: true, // Ensures the IoC container is ready to use + staysAlive: false, // Command exits after running }; - async run() { logger.debug('Hello world!'); // const { default: Dataset } = await import('#models/dataset'); @@ -44,10 +41,12 @@ export default class IndexDatasets extends BaseCommand { const index_name = 'tethys-records'; for (var dataset of datasets) { - // Logger.info(`File publish_id ${dataset.publish_id}`); - // const jsonString = await this.getJsonString(dataset, proc); - // console.log(jsonString); - await this.indexDocument(dataset, index_name, proc); + const shouldUpdate = await this.shouldUpdateDataset(dataset, index_name); + if (shouldUpdate) { + await this.indexDocument(dataset, index_name, proc); + } else { + logger.info(`Dataset with publish_id ${dataset.publish_id} is up to date, skipping indexing`); + } } } @@ -65,6 +64,46 @@ export default class IndexDatasets extends BaseCommand { return await query.exec(); } + private async shouldUpdateDataset(dataset: Dataset, index_name: string): Promise { + try { + // Check if publish_id exists before proceeding + if (!dataset.publish_id) { + // Return true to update since document doesn't exist in OpenSearch yet + return true; + } + // Get the existing document from OpenSearch + const response = await client.get({ + index: index_name, + id: dataset.publish_id?.toString(), + }); + + const existingDoc = response.body._source; + + // Compare server_date_modified + if (existingDoc && existingDoc.server_date_modified) { + // Convert Unix timestamp (seconds) to milliseconds for DateTime.fromMillis() + const existingModified = DateTime.fromMillis(Number(existingDoc.server_date_modified) * 1000); + const currentModified = dataset.server_date_modified; + + // Only update if the dataset has been modified more recently + if (currentModified <= existingModified) { + return false; + } + } + + return true; + } catch (error) { + // If document doesn't exist or other error, we should index it + if (error.statusCode === 404) { + logger.info(`Dataset with publish_id ${dataset.publish_id} not found in index, will create new document`); + return true; + } + + logger.warn(`Error checking existing document for publish_id ${dataset.publish_id}: ${error.message}`); + return true; // Index anyway if we can't determine the status + } + } + private async indexDocument(dataset: Dataset, index_name: string, proc: Buffer): Promise { try { const doc = await this.getJsonString(dataset, proc); @@ -78,7 +117,8 @@ export default class IndexDatasets extends BaseCommand { }); logger.info(`dataset with publish_id ${dataset.publish_id} successfully indexed`); } catch (error) { - logger.error(`An error occurred while indexing dataset with publish_id ${dataset.publish_id}.`); + logger.error(`An error occurred while indexing dataset with publish_id ${dataset.publish_id}. + Error: ${error.message}`); } } @@ -111,19 +151,16 @@ export default class IndexDatasets extends BaseCommand { } private async getDatasetXmlDomNode(dataset: Dataset): Promise { - const xmlModel = new XmlModel(dataset); + const serializer = new XmlModel(dataset).enableCaching().excludeEmptyFields(); // xmlModel.setModel(dataset); - xmlModel.excludeEmptyFields(); - xmlModel.caching = true; - // const cache = dataset.xmlCache ? dataset.xmlCache : null; - // dataset.load('xmlCache'); + if (dataset.xmlCache) { - xmlModel.xmlCache = dataset.xmlCache; + serializer.setCache(dataset.xmlCache); } - // return cache.getDomDocument(); - const domDocument: XMLBuilder | null = await xmlModel.getDomDocument(); - return domDocument; + // return cache.toXmlDocument(); + const xmlDocument: XMLBuilder | null = await serializer.toXmlDocument(); + return xmlDocument; } private addSpecInformation(domNode: XMLBuilder, information: string) { diff --git a/commands/list_updatable_datacite.ts b/commands/list_updatable_datacite.ts new file mode 100644 index 0000000..aed411a --- /dev/null +++ b/commands/list_updatable_datacite.ts @@ -0,0 +1,346 @@ +/* +|-------------------------------------------------------------------------- +| 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 new file mode 100644 index 0000000..7ccb0f0 --- /dev/null +++ b/commands/update_datacite.ts @@ -0,0 +1,266 @@ +/* +|-------------------------------------------------------------------------- +| 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 3834bf1..001762d 100644 --- a/components.d.ts +++ b/components.d.ts @@ -11,3 +11,21 @@ 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 8ef61c7..10d0f37 100644 --- a/docker-entrypoint.sh +++ b/docker-entrypoint.sh @@ -1,47 +1,74 @@ #!/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 -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 +echo "Starting ClamAV services..." - for SETTING in ${SETTING_LIST}; do - # Split on first '=' - local KEY=${SETTING%%=*} - local VALUE=${SETTING#*=} - echo "${KEY} ${VALUE}" >> "$2" - done - fi -} -# process_file "${CLAMD_SETTINGS_CSV}" /etc/clamav/clamd.conf -# process_file "${FRESHCLAM_SETTINGS_CSV}" /etc/clamav/freshclam.conf +# Try to download database if missing +# if [ ! "$(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 & -# start in background -freshclam -d & # /etc/init.d/clamav-freshclam start & -clamd +# Start clamd in background +# Start clamd in foreground (so dumb-init can supervise it) # /etc/init.d/clamav-daemon start & -# change back to CMD of dockerfile +# 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 -- "$@" exec "$@" \ No newline at end of file diff --git a/docs/commands/index-datasets.md b/docs/commands/index-datasets.md new file mode 100644 index 0000000..baecfe6 --- /dev/null +++ b/docs/commands/index-datasets.md @@ -0,0 +1,278 @@ +# 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 new file mode 100644 index 0000000..06041f0 --- /dev/null +++ b/docs/commands/update-datacite.md @@ -0,0 +1,216 @@ +# 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 ee82a23..31992be 100644 --- a/freshclam.conf +++ b/freshclam.conf @@ -1,229 +1,47 @@ ## -## Example config file for freshclam -## Please read the freshclam.conf(5) manual before editing this file. +## Container-optimized freshclam configuration ## - -# 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) +# Database directory DatabaseDirectory /var/lib/clamav -# Path to the log file (make sure it has proper permissions) -# Default: disabled +# Log to stdout for container logging # UpdateLogFile /dev/stdout -# 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 +# Basic logging settings LogTime yes - -# Enable verbose logging. -# Default: no LogVerbose yes - -# Use system logger (can work together with UpdateLogFile). -# Default: no LogSyslog no -# 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 +# PID file location PidFile /var/run/clamav/freshclam.pid -# 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) +# Database owner DatabaseOwner node -# 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. +# Mirror settings for Austria 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 -#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 +# Update settings +ScriptedUpdates yes # Number of database checks per day. # Default: 12 (every two hours) -#Checks 24 +Checks 12 -# 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 +# Don't fork (good for containers) Foreground no -# Enable debug messages in libclamav. -# Default: no -#Debug yes +# Connection timeouts +ConnectTimeout 60 +ReceiveTimeout 60 -# Timeout in seconds when connecting to database server. -# Default: 30 -#ConnectTimeout 60 +# Test databases before using them +TestDatabases yes -# 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 +# Enable bytecode signatures +Bytecode yes \ No newline at end of file diff --git a/package-lock.json b/package-lock.json index 6b10877..7cb57a4 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": "^6.17.0", + "@adonisjs/core": "6.17.2", "@adonisjs/cors": "^2.2.1", "@adonisjs/drive": "^3.2.0", "@adonisjs/inertia": "^2.1.3", @@ -30,7 +30,6 @@ "@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", @@ -109,9 +108,9 @@ } }, "node_modules/@adonisjs/ace": { - "version": "13.3.0", - "resolved": "https://registry.npmjs.org/@adonisjs/ace/-/ace-13.3.0.tgz", - "integrity": "sha512-68dveDFd766p69cBvK/MtOrOP0+YKYLeHspa9KLEWcWk9suPf3pbGkHQ2pwDnvLJxBPHk4932KbbSSzzpGNZGw==", + "version": "13.4.0", + "resolved": "https://registry.npmjs.org/@adonisjs/ace/-/ace-13.4.0.tgz", + "integrity": "sha512-7Wq6CpXmQm3m/6fKfzubAadCdiH2kKSni+K8s5KcTIFryKSqW+f06UAPOUwRJWqy80hnVlujAjveIsNJSPeJjA==", "license": "MIT", "dependencies": { "@poppinss/cliui": "^6.4.1", @@ -131,9 +130,9 @@ } }, "node_modules/@adonisjs/application": { - "version": "8.4.1", - "resolved": "https://registry.npmjs.org/@adonisjs/application/-/application-8.4.1.tgz", - "integrity": 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"^6.10.0", "basic-auth": "^2.0.1" }, "engines": { @@ -258,30 +257,30 @@ } }, "node_modules/@adonisjs/core": { - "version": "6.18.0", - "resolved": "https://registry.npmjs.org/@adonisjs/core/-/core-6.18.0.tgz", - "integrity": "sha512-Uuj7kzlMPiS3MVOCHfiXLVeFXUqrjGjF43LNLJb4Q2hBY/q0T2kUym2kVO2gazkLWj8YQKLdOA4ij7t9rDR4OA==", + "version": "6.17.2", + "resolved": "https://registry.npmjs.org/@adonisjs/core/-/core-6.17.2.tgz", + "integrity": "sha512-POT5COID8Z3j37+Dd7Y1EfG01Q6+HPY/tGcSb0Y97W2VIPkFjqcW2ooTE4wFT09u7coNohtXJa19a0feMz9ncw==", "license": "MIT", "dependencies": { "@adonisjs/ace": "^13.3.0", - "@adonisjs/application": "^8.4.1", - "@adonisjs/bodyparser": "^10.1.0", + "@adonisjs/application": "^8.3.1", + "@adonisjs/bodyparser": "^10.0.3", "@adonisjs/config": "^5.0.2", "@adonisjs/encryption": "^6.0.2", - "@adonisjs/env": "^6.2.0", + "@adonisjs/env": "^6.1.1", "@adonisjs/events": "^9.0.2", "@adonisjs/fold": "^10.1.3", - "@adonisjs/hash": "^9.1.1", + "@adonisjs/hash": "^9.0.5", "@adonisjs/health": "^2.0.0", - "@adonisjs/http-server": "^7.6.1", - "@adonisjs/logger": "^6.0.6", + "@adonisjs/http-server": "^7.4.0", + "@adonisjs/logger": "^6.0.5", "@adonisjs/repl": "^4.1.0", - "@antfu/install-pkg": "^1.1.0", + "@antfu/install-pkg": "^1.0.0", "@paralleldrive/cuid2": "^2.2.2", "@poppinss/colors": "^4.1.4", - "@poppinss/dumper": "^0.6.3", + "@poppinss/dumper": "^0.6.2", "@poppinss/macroable": "^1.0.4", - "@poppinss/utils": "^6.9.3", + "@poppinss/utils": "^6.9.2", "@sindresorhus/is": "^7.0.1", "@types/he": "^1.2.3", "error-stack-parser-es": "^1.0.5", @@ -301,8 +300,8 @@ "peerDependencies": { "@adonisjs/assembler": "^7.8.0", "@vinejs/vine": "^2.1.0 || ^3.0.0", - "argon2": "^0.31.2 || ^0.41.0 || ^0.43.0", - "bcrypt": "^5.1.1 || ^6.0.0", + "argon2": "^0.31.2 || ^0.41.0", + "bcrypt": "^5.1.1", "edge.js": "^6.2.0" }, "peerDependenciesMeta": { @@ -447,17 +446,49 @@ } }, "node_modules/@adonisjs/fold": { - "version": "10.1.3", - "resolved": 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+ "resolved": "https://registry.npmjs.org/ws/-/ws-8.18.3.tgz", + "integrity": "sha512-PEIGCY5tSlUt50cqyMXfCzX+oOPqN0vuGqWzbcJ2xvnkzkq46oOpz7dQaTDBdfICb4N14+GARUDw2XV2N4tvzg==", "dev": true, "license": "MIT", "engines": { @@ -14480,6 +15909,22 @@ } } }, + "node_modules/wsl-utils": { + "version": "0.1.0", + "resolved": "https://registry.npmjs.org/wsl-utils/-/wsl-utils-0.1.0.tgz", + "integrity": "sha512-h3Fbisa2nKGPxCpm89Hk33lBLsnaGBvctQopaBSOW/uIs6FTe1ATyAnKFJrzVs9vpGdsTe73WF3V4lIsk4Gacw==", + "dev": true, + "license": "MIT", + "dependencies": { + "is-wsl": "^3.1.0" + }, + "engines": { + "node": ">=18" + }, + "funding": { + "url": "https://github.com/sponsors/sindresorhus" + } + }, "node_modules/xmlbuilder2": { "version": "3.1.1", "resolved": "https://registry.npmjs.org/xmlbuilder2/-/xmlbuilder2-3.1.1.tgz", @@ -14555,9 +16000,9 @@ "peer": true }, "node_modules/yaml": { - "version": "2.8.0", - "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.8.0.tgz", - "integrity": 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"https://registry.npmjs.org/youch-core/-/youch-core-0.3.2.tgz", - "integrity": "sha512-fusrlIMLeRvTFYLUjJ9KzlGC3N+6MOPJ68HNj/yJv2nz7zq8t4HEviLms2gkdRPUS7F5rZ5n+pYx9r88m6IE1g==", + "version": "0.3.3", + "resolved": "https://registry.npmjs.org/youch-core/-/youch-core-0.3.3.tgz", + "integrity": "sha512-ho7XuGjLaJ2hWHoK8yFnsUGy2Y5uDpqSTq1FkHLK4/oqKtyUU1AFbOOxY4IpC9f0fTLjwYbslUz0Po5BpD1wrA==", "devOptional": true, "license": "MIT", "dependencies": { - "@poppinss/exception": "^1.2.0", + "@poppinss/exception": "^1.2.2", "error-stack-parser-es": "^1.0.5" - }, - "engines": { - "node": ">=18" } }, "node_modules/youch-terminal": { diff --git a/package.json b/package.json index 989a29e..7ae829f 100644 --- a/package.json +++ b/package.json @@ -77,7 +77,7 @@ "dependencies": { "@adonisjs/auth": "^9.2.4", "@adonisjs/bodyparser": "^10.0.1", - "@adonisjs/core": "^6.17.0", + "@adonisjs/core": "6.17.2", "@adonisjs/cors": "^2.2.1", "@adonisjs/drive": "^3.2.0", "@adonisjs/inertia": "^2.1.3", @@ -97,7 +97,6 @@ "@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 new file mode 100644 index 0000000..c945a5d --- /dev/null +++ b/providers/rule_provider.ts @@ -0,0 +1,34 @@ +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 e4aad4c..568dd3e 100644 --- a/providers/vinejs_provider.ts +++ b/providers/vinejs_provider.ts @@ -6,17 +6,16 @@ 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 */ @@ -25,6 +24,7 @@ declare module '@vinejs/vine' { myfile(options?: FileRuleValidationOptions): VineMultipartFile; } } + /** * Extend HTTP request class */ @@ -36,19 +36,54 @@ declare module '@adonisjs/core/http' { * Checks if the value is an instance of multipart file * from bodyparser. */ -export function isBodyParserFile(file: MultipartFile | unknown): boolean { +export function isBodyParserFile(file: MultipartFile | unknown): file is MultipartFile { 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(); - return extensions; +/** + * 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 || []; + } } + +/** + * 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. @@ -65,6 +100,7 @@ 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 @@ -72,30 +108,29 @@ 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 && 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(); + if (validatedFile.allowedExtensions === undefined) { + if (validationOptions.extnames !== undefined) { + validatedFile.allowedExtensions = validationOptions.extnames; + } else { + 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 */ - validatedFile.validate(); + try { + validatedFile.validate(); + } catch (error) { + field.report(`File validation failed: ${error.message}`, 'file.validation_error', field, validationOptions); + return; + } + /** * Report errors */ @@ -107,36 +142,37 @@ 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; - // 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; + public validationOptions?: FileRuleValidationOptions; // 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 { @@ -155,13 +191,8 @@ export default class VinejsProvider { /** * The container bindings have booted */ - boot(): void { - // VineString.macro('translatedLanguage', function (this: VineString, options: Options) { - // return this.use(translatedLanguageRule(options)); - // }); - - Vine.macro('myfile', function (this: Vine, options) { + Vine.macro('myfile', function (this: Vine, options?: FileRuleValidationOptions) { return new VineMultipartFile(options); }); @@ -175,6 +206,41 @@ 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); + } } /** @@ -190,5 +256,7 @@ export default class VinejsProvider { /** * Preparing to shutdown the app */ - async shutdown() {} + async shutdown() { + clearExtensionsCache(); + } } diff --git a/public/assets2/solr.sef.json b/public/assets2/solr.sef.json index 690f934..096d58e 100644 --- a/public/assets2/solr.sef.json +++ b/public/assets2/solr.sef.json @@ -1 +1 @@ -{"N":"package","version":"30","packageVersion":"1","saxonVersion":"SaxonJS 2.6","target":"JS","targetVersion":"2","name":"TOP-LEVEL","relocatable":"false","buildDateTime":"2023-10-17T11:51:02.397+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 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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) @@ -29,5 +31,175 @@ Before you begin, ensure you have met the following requirements: 1. Clone this repository: ```bash - git clone https://gitea.geologie.ac.at/geolba/tethys.backend.git + git clone git clone https://gitea.geologie.ac.at/geolba/tethys.backend.git + cd tethys-backend ``` + +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 74c0b5d..1462566 100644 --- a/resources/js/Components/BaseButton.vue +++ b/resources/js/Components/BaseButton.vue @@ -1,5 +1,5 @@ -