Release: merge develop into main for v2.2.0

feat: Enhance dataset management and submission features

- Added Activity import to main store and initialized activities array.
- Updated app.ts to use Inertia router for navigation events.
- Introduced useDatasetChangeDetection composable for tracking dataset changes.
- Created useDatasetFormSubmission composable for handling dataset form submissions.
- Modified app.edge to dynamically load page-specific JS/CSS with Inertia v3.
- Added OPENSEARCH_HOST to environment configuration.
- Adjusted middleware registration in kernel.ts for Inertia.
- Implemented activities API route in api.ts.
- Refined array_contains_types validation rule for titles and descriptions.
- Updated Vite configuration for improved asset management and build process.

.env.example

@@ -1,7 +1,7 @@
 PORT=3333
 HOST=0.0.0.0
 NODE_ENV=development
-APP_KEY=pvmU1vuAZDkSwarb7yh9pgZ-RxaX4zS7
+APP_KEY=pvmU1vuAZDkSwarb7yh9pgZ-xxxxxx007
 DRIVE_DISK=local
 SESSION_DRIVER=cookie
 CACHE_VIEWS=false

.gitea/workflows/build.yaml

@@ -13,7 +13,7 @@ jobs:
               uses: actions/checkout@v3
             - run: echo "The ${{ github.repository }} repository has been cloned to the runner."
             - run: echo "The workflow is now ready to test your code on the runner."
-            - name: List files in the repository:
+            - name: List files in the repository
               run: |
                   ls ${{ github.workspace }}
             - run: echo "This job's status is ${{ job.status }}."

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"

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

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
@@ -26,15 +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/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'),
     ],
     /*
 |--------------------------------------------------------------------------
@@ -59,7 +62,8 @@ export default defineConfig({
         // () => import('@eidellev/inertia-adonisjs'),
         // () => import('@adonisjs/inertia/inertia_provider'),
         () => import('#providers/app_provider'),
-        () => import('#providers/inertia_provider'),
+        // () => import('#providers/inertia_provider'),
+        () => import('@adonisjs/inertia/inertia_provider'),
         () => import('@adonisjs/lucid/database_provider'),
         () => import('@adonisjs/auth/auth_provider'),
         // () => import('@eidellev/adonis-stardust'),
@@ -69,7 +73,7 @@ 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'),

app/Controllers/Http/Admin/AdminuserController.ts

@@ -85,7 +85,9 @@ export default class AdminuserController {
             // return response.badRequest(error.messages);
             throw error;
         }
-        const input = request.only(['login', 'email', 'password', 'first_name', 'last_name']);
+
+        const input: Record<string, any> = request.only(['login', 'email', 'first_name', 'last_name']);
+        input.password = request.input('new_password');
         const user = await User.create(input);
         if (request.input('roles')) {
             const roles: Array<number> = request.input('roles');
@@ -95,7 +97,6 @@ export default class AdminuserController {
         session.flash('message', 'User has been created successfully');
         return response.redirect().toRoute('settings.user.index');
     }
-
     public async show({ request, inertia }: HttpContext) {
         const id = request.param('id');
         const user = await User.query().where('id', id).firstOrFail();
@@ -139,9 +140,11 @@ export default class AdminuserController {
         });
 
         // password is optional
-        let input;
-        if (request.input('password')) {
-            input = request.only(['login', 'email', 'password', 'first_name', 'last_name']);
+        let input: Record<string, any>;
+
+        if (request.input('new_password')) {
+            input = request.only(['login', 'email', 'first_name', 'last_name']);
+            input.password = request.input('new_password');
         } else {
             input = request.only(['login', 'email', 'first_name', 'last_name']);
         }
@@ -156,7 +159,6 @@ export default class AdminuserController {
         session.flash('message', 'User has been updated successfully');
         return response.redirect().toRoute('settings.user.index');
     }
-
     public async destroy({ request, response, session }: HttpContext) {
         const id = request.param('id');
         const user = await User.findOrFail(id);

app/Controllers/Http/Admin/MimetypeController.ts

@@ -33,7 +33,7 @@ export default class MimetypeController {
             //  Step 2 - Validate request body against  the schema
             // await request.validate({ schema: newDatasetSchema, messages: this.messages });
             const validator = vine.compile(newDatasetSchema);
-            validator.messagesProvider = new SimpleMessagesProvider(this.messages);          
+            validator.messagesProvider = new SimpleMessagesProvider(this.messages);
             await request.validateUsing(validator, { messagesProvider: new SimpleMessagesProvider(this.messages) });
         } catch (error) {
             // Step 3 - Handle errors
@@ -64,7 +64,7 @@ export default class MimetypeController {
         'maxLength': '{{ field }} must be less then {{ max }} characters long',
         'isUnique': '{{ field }} must be unique, and this value is already taken',
         'required': '{{ field }} is required',
-        'file_extension.minLength': 'at least {{ min }} mimetypes must be defined',
+        'file_extension.array.minLength': 'at least {{ min }} mimetypes must be defined',
         'file_extension.*.string': 'Each file extension must be a valid string', // Adjusted to match the type
     };
 
@@ -168,7 +168,7 @@ export default class MimetypeController {
                 mimetype,
             });
         } catch (error) {
-            if (error.code == 'E_ROW_NOT_FOUND') {
+            if (error.code === 'E_ROW_NOT_FOUND') {
                 session.flash({ warning: 'Mimetype is not found in database' });
             } else {
                 session.flash({ warning: 'general error occured, you cannot delete the mimetype' });

app/Controllers/Http/Admin/RoleController.ts

@@ -42,7 +42,7 @@ export default class RoleController {
             can: {
                 create: await auth.user?.can(['user-create']),
                 edit: await auth.user?.can(['user-edit']),
-                delete: await auth.user?.can(['user-delete']),
+                delete: false, //await auth.user?.can(['user-delete']),
             },
         });
     }
@@ -124,7 +124,7 @@ export default class RoleController {
 
         // password is optional
 
-        const input = request.only(['name', 'description']);
+        const input = request.only(['name', 'display_name', 'description']);
         await role.merge(input).save();
         // await user.save();
 

app/Controllers/Http/Admin/mailsettings_controller.ts

@@ -76,9 +76,9 @@ export default class MailSettingsController {
     public async sendTestMail({ response, auth }: HttpContext) {
         const user = auth.user!;
         const userEmail = user.email;
-        
+
         // let mailManager = await app.container.make('mail.manager');
-        // let iwas = mailManager.use();       
+        // let iwas = mailManager.use();
         // let test = mail.config.mailers.smtp();
         if (!userEmail) {
             return response.badRequest({ message: 'User email is not set. Please update your profile.' });

app/Controllers/Http/Api/AuthorsController.ts

@@ -4,19 +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()
-            .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;
     }
@@ -27,7 +37,10 @@ export default class AuthorsController {
         if (request.input('filter')) {
             // users = users.whereRaw('name like %?%', [request.input('search')])
             const searchTerm = request.input('filter');
-            authors.whereILike('first_name', `%${searchTerm}%`).orWhereILike('last_name', `%${searchTerm}%`);
+            authors.andWhere((query) => {
+                query.whereILike('first_name', `%${searchTerm}%`)
+                     .orWhereILike('last_name', `%${searchTerm}%`);
+            });
             // .orWhere('email', 'like', `%${searchTerm}%`);
         }
 

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 `
-            <svg width="${size}" height="${size}" xmlns="http://www.w3.org/2000/svg">
-              <rect width="100%" height="100%" fill="#${colors.background}"/>
-              <text x="50%" y="50%" dominant-baseline="middle" text-anchor="middle" font-weight="bold" font-family="Arial, sans-serif" font-size="${fontSize}" fill="#${colors.text}">${initials}</text>
-            </svg>
-          `;
+        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 `<svg width="${size}" height="${size}" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 ${size} ${size}">
+                    <rect width="100%" height="100%" fill="#${colors.background}" rx="${size * 0.1}"/>
+                    <text x="50%" y="50%" dominant-baseline="central" text-anchor="middle" 
+                            font-weight="600" font-family="-apple-system, BlinkMacSystemFont, 'Segoe UI', system-ui, sans-serif" 
+                            font-size="${fontSize}" fill="#${colors.text}">${escapedInitials}</text>
+                </svg>`;
+    }
+
+    private escapeXml(text: string): string {
+        return text.replace(/&/g, '&amp;').replace(/</g, '&lt;').replace(/>/g, '&gt;').replace(/"/g, '&quot;').replace(/'/g, '&apos;');
     }
 
     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);

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 +46,368 @@ 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<number> = new Set()): Promise<any[]> {
+    //     // 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;
+    // }
+
+    private async getPreviousVersions(datasetId: number, visited: Set<number> = new Set()): Promise<any[]> {
+        if (visited.has(datasetId)) return [];
+        visited.add(datasetId);
+
+        const result: any[] = [];
+
+        // A dataset points to its OLDER version via relation 'IsNewVersionOf'
+        const refs = await DatasetReference.query()
+            .where('document_id', datasetId)
+            .where('relation', 'IsNewVersionOf');   // ← removed .whereNotNull('related_document_id')
+
+        for (const ref of refs) {
+            const related = await this.resolveReferencedDataset(ref, datasetId);
+            if (!related) continue;
+
+            result.push({
+                id: related.id,
+                publish_id: related.publish_id,
+                doi: related.identifier?.value || null,
+                main_title: related.mainTitle || null,
+                server_date_published: related.server_date_published,
+                relation: 'IsPreviousVersionOf',
+            });
+
+            result.push(...(await this.getPreviousVersions(related.id, visited)));
+        }
+
+        return result;
+    }
+
+    /**
+     * Recursively get all newer versions
+     */
+    // private async getNewerVersions(datasetId: number, visited: Set<number> = new Set()): Promise<any[]> {
+    //     // 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;
+    // }
+    private async getNewerVersions(datasetId: number, visited: Set<number> = new Set()): Promise<any[]> {
+        if (visited.has(datasetId)) return [];
+        visited.add(datasetId);
+
+        const result: any[] = [];
+
+        // A dataset points to its NEWER version via relation 'IsPreviousVersionOf'
+        const refs = await DatasetReference.query()
+            .where('document_id', datasetId)
+            .where('relation', 'IsPreviousVersionOf');   // ← removed .whereNotNull(...)
+
+        for (const ref of refs) {
+            const related = await this.resolveReferencedDataset(ref, datasetId);
+            if (!related) continue;
+
+            result.push({
+                id: related.id,
+                publish_id: related.publish_id,
+                doi: related.identifier?.value || null,
+                main_title: related.mainTitle || null,
+                server_date_published: related.server_date_published,
+                relation: 'IsNewVersionOf',
+            });
+
+            result.push(...(await this.getNewerVersions(related.id, visited)));
+        }
+
+        return result;
+    }
+
+    private async resolveReferencedDataset(ref: DatasetReference, currentDatasetId: number) {
+        const doi = this.normalizeDoi(ref.value);
+
+        if (doi) {
+            const byDoi = await Dataset.query()
+                .whereHas('identifier', (q) => q.where('value', doi))
+                .preload('identifier')
+                .preload('titles')   // needed so mainTitle computes
+                .first();
+            if (byDoi) return byDoi;
+        }
+
+        if (ref.related_document_id && ref.related_document_id !== currentDatasetId) {
+            return await Dataset.query()
+                .where('id', ref.related_document_id)
+                .preload('identifier')
+                .preload('titles')
+                .first();
+        }
+
+        return null;
+    }
+    private normalizeDoi(value: string | null): string | null {
+        if (!value) return null;
+        return value
+            .trim()
+            .replace(/^https?:\/\/(dx\.)?doi\.org\//i, '')
+            .replace(/^doi:/i, '');
     }
 }

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;
     }
 }

app/Controllers/Http/Api/HomeController.ts

@@ -17,7 +17,8 @@ export default class HomeController {
             //     .preload('authors')
             //     .orderBy('server_date_published');
 
-            const datasets = await db.from('documents as doc')
+            const datasets = await db
+                .from('documents as doc')
                 .select(['publish_id', 'server_date_published', db.raw(`date_part('year', server_date_published) as pub_year`)])
                 .where('server_state', serverState)
                 .innerJoin('link_documents_persons as ba', 'doc.id', 'ba.document_id')
@@ -59,7 +60,6 @@ export default class HomeController {
         // const year = params.year;
         // const from = parseInt(year);
         try {
-
             // const datasets = await Database.from('documents as doc')
             //     .select([Database.raw(`date_part('month', server_date_published) as pub_month`), Database.raw('COUNT(*) as count')])
             //     .where('server_state', serverState)
@@ -68,9 +68,12 @@ export default class HomeController {
             //     .groupBy('pub_month');
             //     // .orderBy('server_date_published');
 
-            const years = [2021, 2022, 2023]; // Add the second year
+            // Calculate the last 4 years including the current year
+            const currentYear = new Date().getFullYear();
+            const years = Array.from({ length: 4 }, (_, i) => currentYear - (i + 1)).reverse();
 
-            const result = await db.from('documents as doc')
+            const result = await db
+                .from('documents as doc')
                 .select([
                     db.raw(`date_part('year', server_date_published) as pub_year`),
                     db.raw(`date_part('month', server_date_published) as pub_month`),
@@ -83,7 +86,7 @@ export default class HomeController {
                 .groupBy('pub_year', 'pub_month')
                 .orderBy('pub_year', 'asc')
                 .orderBy('pub_month', 'asc');
-                            
+
             const labels = Array.from({ length: 12 }, (_, i) => i + 1); // Assuming 12 months
 
             const inputDatasets: Map<string, ChartDataset> = result.reduce((acc, item) => {
@@ -100,15 +103,15 @@ export default class HomeController {
 
                 acc[pub_year].data[pub_month - 1] = parseInt(count);
 
-                return acc ;
+                return acc;
             }, {});
 
             const outputDatasets = Object.entries(inputDatasets).map(([year, data]) => ({
                 data: data.data,
                 label: year,
                 borderColor: data.borderColor,
-                fill: data.fill
-              }));
+                fill: data.fill,
+            }));
 
             const data = {
                 labels: labels,
@@ -126,11 +129,11 @@ export default class HomeController {
     private getRandomHexColor() {
         const letters = '0123456789ABCDEF';
         let color = '#';
-    
+
         for (let i = 0; i < 6; i++) {
             color += letters[Math.floor(Math.random() * 16)];
         }
-    
+
         return color;
     }
 }
@@ -139,5 +142,4 @@ interface ChartDataset {
     label: string;
     borderColor: string;
     fill: boolean;
-
 }

app/Controllers/Http/Auth/AuthController.ts

@@ -1,93 +1,68 @@
 import type { HttpContext } from '@adonisjs/core/http';
 import User from '#models/user';
 import BackupCode from '#models/backup_code';
-// import Hash from '@ioc:Adonis/Core/Hash';
-// import InvalidCredentialException from 'App/Exceptions/InvalidCredentialException';
 import { authValidator } from '#validators/auth';
 import hash from '@adonisjs/core/services/hash';
-
+import db from '@adonisjs/lucid/services/db';
 import TwoFactorAuthProvider from '#app/services/TwoFactorAuthProvider';
-// import { Authenticator } from '@adonisjs/auth';
-// import { LoginState } from 'Contracts/enums';
-// import { StatusCodes } from 'http-status-codes';
+import ActivityLogger from '#services/activity_logger';
+import logger from '@adonisjs/core/services/logger';
 
-// interface MyHttpsContext extends HttpContext {
-//     auth: Authenticator<User>
-//   }
 export default class AuthController {
-    //   login function{ request, auth, response }:HttpContext
     public async login({ request, response, auth, session }: HttpContext) {
-        // console.log({
-        // 	registerBody: request.body(),
-        // });
-        // await request.validate(AuthValidator);
         await request.validateUsing(authValidator);
 
-        // const plainPassword = await request.input('password');
-        // const email = await request.input('email');
-        // grab uid and password values off request body
         const { email, password } = request.only(['email', 'password']);
 
         try {
-            // // attempt to verify credential and login user
-            // await auth.use('web').attempt(email, plainPassword);
+            await db.connection().rawQuery('SELECT 1');
 
-            // const user = await auth.use('web').verifyCredentials(email, password);
             const user = await User.verifyCredentials(email, password);
 
             if (user.isTwoFactorEnabled) {
-                // session.put("login.id", user.id);
-                // return view.render("pages/two-factor-challenge");
-
+                // Noch KEIN abgeschlossenes Login -> nicht loggen.
                 session.flash('user_id', user.id);
                 return response.redirect().back();
-
-                // let state = LoginState.STATE_VALIDATED;
-                // return response.status(StatusCodes.OK).json({
-                //     state: state,
-                //     new_user_id: user.id,
-                // });
             }
 
             await auth.use('web').login(user);
-        } catch (error) {
-            // if login fails, return vague form message and redirect back
+            this.recordAuthEvent('auth.login', { user, ip: request.ip() });
+        } catch (error: any) {
+            // DB nicht erreichbar -> kein fehlgeschlagener Login-Versuch, weiterwerfen
+            if (error.code === 'ECONNREFUSED') {
+                throw error;
+            }
+
+            // Echter Credential-Fehler -> als fehlgeschlagenen Versuch protokollieren
+            this.recordAuthEvent('auth.login_failed', { email, ip: request.ip() });
+
             session.flash('message', 'Your username, email, or password is incorrect');
             return response.redirect().back();
         }
 
-        // otherwise, redirect todashboard
-        response.redirect('/apps/dashboard');
+        return response.redirect('/apps/dashboard');
     }
 
     public async twoFactorChallenge({ request, session, auth, response }: HttpContext) {
-        const { code, backup_code, login_id } = request.only(['code', 'backup_code', 'login_id']);      
+        const { code, backup_code, login_id } = request.only(['code', 'backup_code', 'login_id']);
         const user = await User.query().where('id', login_id).firstOrFail();
 
         if (code) {
             const isValid = await TwoFactorAuthProvider.validate(user, code);
             if (isValid) {
-                // login user and redirect to dashboard
                 await auth.use('web').login(user);
-                response.redirect('/apps/dashboard');
-            } else {
-                session.flash('message', 'Your two-factor code is incorrect');
-            return response.redirect().back();
+                this.recordAuthEvent('auth.login', { user, email: user.email, ip: request.ip(), method: '2fa_totp' });
+                return response.redirect('/apps/dashboard');
             }
-        } else if (backup_code) {
-            const codes: BackupCode[] = await user.getBackupCodes();
-          
-            // const verifiedBackupCodes = await Promise.all(
-            //     codes.map(async (backupCode) => {
-            //         let isVerified = await hash.verify(backupCode.code, backup_code);
-            //         if (isVerified) {
-            //             return backupCode;
-            //         }
-            //     }),
-            // );
-            // const backupCodeToDelete = verifiedBackupCodes.find(Boolean);
 
-            let backupCodeToDelete = null;
+            session.flash('message', 'Your two-factor code is incorrect');
+            return response.redirect().back();
+        }
+
+        if (backup_code) {
+            const codes: BackupCode[] = await user.getBackupCodes();
+
+            let backupCodeToDelete: BackupCode | null = null;
             for (const backupCode of codes) {
                 const isVerified = await hash.verify(backupCode.code, backup_code);
                 if (isVerified) {
@@ -96,29 +71,68 @@ export default class AuthController {
                 }
             }
 
-            if (backupCodeToDelete) {   
-                    if (backupCodeToDelete.used === false) {
-                        backupCodeToDelete.used = true;
-                        await backupCodeToDelete.save();
-                        console.log(`BackupCode with id ${backupCodeToDelete.id} has been marked as used.`);
-                        await auth.use('web').login(user);
-                        response.redirect('/apps/dashboard');
-                    } else {
-                        session.flash('message', 'BackupCode already used');
-                        return response.redirect().back();
-                    }                              
-            } else {
+            if (!backupCodeToDelete) {
                 session.flash('message', 'BackupCode not found');
                 return response.redirect().back();
-            }           
+            }
+
+            if (backupCodeToDelete.used) {
+                session.flash('message', 'BackupCode already used');
+                return response.redirect().back();
+            }
+
+            backupCodeToDelete.used = true;
+            await backupCodeToDelete.save();
+
+            await auth.use('web').login(user);
+            this.recordAuthEvent('auth.login', { user, email: user.email, ip: request.ip(), method: '2fa_backup_code' });
+
+            return response.redirect('/apps/dashboard');
         }
+
+        // Weder code noch backup_code übergeben
+        session.flash('message', 'No verification code provided');
+        return response.redirect().back();
     }
 
-    //   logout function
-    public async logout({ auth, response }: HttpContext) {
-        // await auth.logout();
+    public async logout({ auth, request, response }: HttpContext) {        
+        // Session auflösen -> füllt auth.user, falls eingeloggt
+        await auth.use('web').check();
+        const user = auth.use('web').user;
+
         await auth.use('web').logout();
+
+        if (user) {
+            this.recordAuthEvent('auth.logout', { user, email: user.email, ip: request.ip() });
+        }
+
         return response.redirect('/app/login');
-        // return response.status(200);
+    }
+
+    /**
+     * Zentraler Audit-Logger für Auth-Events.
+     * Fire-and-forget: ein Fehler beim Schreiben darf Login/Logout nie blockieren.
+     */
+    private recordAuthEvent(
+        type: 'auth.login' | 'auth.logout' | 'auth.login_failed',
+        opts: { user?: User; email?: string; ip: string; method?: string },
+    ) {
+        const { user, email, ip, method } = opts;
+
+        const description =
+            type === 'auth.login'
+                ? `${user!.firstName} ${user!.lastName} signed in`
+                : type === 'auth.logout'
+                    ? `${user!.firstName} ${user!.lastName} signed out`
+                    : `Failed login attempt for ${email ?? 'unknown'}`;
+
+        void ActivityLogger.log({
+            type,
+            description,
+            userId: user?.id ?? null,
+            subjectType: user ? 'User' : null,
+            subjectId: user?.id ?? null,
+            properties: { ip, ...(method ? { method } : {}) },
+        }).catch((err) => logger.error({ err }, `failed to record ${type} activity`));
     }
 }

app/Controllers/Http/Oai/OaiController.ts

@@ -1,5 +1,4 @@
 import type { HttpContext } from '@adonisjs/core/http';
-// import { RequestContract } from '@ioc:Adonis/Core/Request';
 import { Request } from '@adonisjs/core/http';
 import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
 import { create } from 'xmlbuilder2';
@@ -15,14 +14,11 @@ 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';
 import config from '@adonisjs/core/services/config';
-// import { inject } from '@adonisjs/fold';
 import { inject } from '@adonisjs/core';
-// import { TokenWorkerContract } from "MyApp/Models/TokenWorker";
 import TokenWorkerContract from '#library/Oai/TokenWorkerContract';
 import { ModelQueryBuilderContract } from '@adonisjs/lucid/types/model';
 
@@ -83,13 +79,13 @@ export default class OaiController {
             xsltParameter['oai_error_message'] = 'Only POST and GET methods are allowed for OAI-PMH.';
         }
 
-        let earliestDateFromDb;
         // const oaiRequest: OaiParameter = request.body;
         try {
             this.firstPublishedDataset = await Dataset.earliestPublicationDate();
-            this.firstPublishedDataset != null &&
-                (earliestDateFromDb = this.firstPublishedDataset.server_date_published.toFormat("yyyy-MM-dd'T'HH:mm:ss'Z'"));
-            this.xsltParameter['earliestDatestamp'] = earliestDateFromDb;
+            // Pflichtfeld laut OAI-PMH: auch bei leerem Repository einen validen
+            // UTCdatetime liefern, sonst entsteht ein ungültiges leeres Element.
+            this.xsltParameter['earliestDatestamp'] =
+                this.firstPublishedDataset?.server_date_published.toFormat("yyyy-MM-dd'T'HH:mm:ss'Z'") ?? '1970-01-01T00:00:00Z';
             // start the request
             await this.handleRequest(oaiRequest, request);
         } catch (error) {
@@ -122,7 +118,7 @@ export default class OaiController {
                 // logLevel: 10,
             });
             xmlOutput = result.principalResult;
-        } catch (error) {
+        } catch (error: any) {
             return response.status(500).json({
                 message: 'An error occurred while creating the user',
                 error: error.message,
@@ -157,7 +153,7 @@ export default class OaiController {
             const verb = oaiRequest['verb'];
             this.xsltParameter['oai_verb'] = verb;
             if (verb === 'Identify') {
-                this.handleIdentify();
+                this.handleIdentify(oaiRequest);
             } else if (verb === 'ListMetadataFormats') {
                 this.handleListMetadataFormats();
             } else if (verb == 'GetRecord') {
@@ -184,7 +180,10 @@ export default class OaiController {
         }
     }
 
-    protected handleIdentify() {
+    protected handleIdentify(oaiRequest: Dictionary) {
+        // OAI-PMH: Identify akzeptiert außer `verb` keine Argumente.
+        this.assertOnlyVerb(oaiRequest);
+
         // Get configuration values from environment or a dedicated configuration service
         const email = process.env.OAI_EMAIL ?? 'repository@geosphere.at';
         const repositoryName = process.env.OAI_REPOSITORY_NAME ?? 'Tethys RDR';
@@ -203,6 +202,21 @@ export default class OaiController {
         this.xml.root().ele('Datasets');
     }
 
+    /**
+     * Wirft badArgument, wenn der Request andere Parameter als `verb` enthält.
+     * Für Verben ohne zusätzliche Argumente (Identify, ListSets, ListMetadataFormats).
+     */
+    private assertOnlyVerb(oaiRequest: Dictionary) {
+        const illegalKeys = Object.keys(oaiRequest).filter((key) => key !== 'verb');
+        if (illegalKeys.length > 0) {
+            throw new OaiModelException(
+                StatusCodes.BAD_REQUEST,
+                `The request includes illegal arguments: ${illegalKeys.join(', ')}.`,
+                OaiErrorCodes.BADARGUMENT,
+            );
+        }
+    }
+
     protected handleListMetadataFormats() {
         this.xml.root().ele('Datasets');
     }
@@ -292,7 +306,7 @@ 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 +347,7 @@ export default class OaiController {
     }
 
     private async handleNoResumptionToken(oaiRequest: Dictionary, paginationParams: PagingParameter, maxRecords: number) {
-        this.validateMetadataPrefix(oaiRequest, paginationParams);       
+        this.validateMetadataPrefix(oaiRequest, paginationParams);
         const finder: ModelQueryBuilderContract<typeof Dataset, Dataset> = Dataset.query().whereIn(
             'server_state',
             this.deliveringDocumentStates,
@@ -347,16 +361,20 @@ export default class OaiController {
         finder: ModelQueryBuilderContract<typeof Dataset, Dataset>,
         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 +620,17 @@ 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) {

app/Controllers/Http/Reviewer/DatasetController.ts

@@ -9,6 +9,7 @@ import vine from '@vinejs/vine';
 import mail from '@adonisjs/mail/services/main';
 import logger from '@adonisjs/core/services/logger';
 import { validate } from 'deep-email-validator';
+import File from '#models/file';
 
 interface Dictionary {
     [index: string]: string;
@@ -38,13 +39,21 @@ export default class DatasetsController {
             }
             datasets.orderBy(attribute, sortOrder);
         } else {
-            // users.orderBy('created_at', 'desc');
-            datasets.orderBy('id', 'asc');
+            // datasets.orderBy('id', 'asc');
+            // Custom ordering to prioritize rejected_editor state
+            datasets.orderByRaw(`
+                CASE 
+                    WHEN server_state = 'rejected_to_reviewer' THEN 0 
+                    ELSE 1 
+                END ASC, 
+                id ASC
+            `);
         }
 
         // const users = await User.query().orderBy('login').paginate(page, limit);
         const myDatasets = await datasets
-            .where('server_state', 'approved')
+            // .where('server_state', 'approved')
+            .whereIn('server_state', ['approved', 'rejected_to_reviewer'])
             .where('reviewer_id', user.id)
 
             .preload('titles')
@@ -62,7 +71,51 @@ export default class DatasetsController {
         });
     }
 
-    public async review({ request, inertia, response }: HttpContext) {
+    public async review({ request, inertia, response, auth }: HttpContext) {
+        const id = request.param('id');
+        const datasetQuery = Dataset.query().where('id', id);
+
+        datasetQuery
+            .preload('titles', (query) => query.orderBy('id', 'asc'))
+            .preload('descriptions', (query) => query.orderBy('id', 'asc'))
+            .preload('coverage')
+            .preload('licenses')
+            .preload('authors', (query) => query.orderBy('pivot_sort_order', 'asc'))
+            .preload('contributors', (query) => query.orderBy('pivot_sort_order', 'asc'))
+            // .preload('subjects')
+            .preload('subjects', (builder) => {
+                builder.orderBy('id', 'asc').withCount('datasets');
+            })
+            .preload('references')
+            .preload('project')
+            .preload('files', (query) => {
+                query.orderBy('sort_order', 'asc'); // Sort by sort_order column
+            });
+
+        const dataset = await datasetQuery.firstOrFail();
+
+        const validStates = ['approved', 'rejected_to_reviewer'];
+        if (!validStates.includes(dataset.server_state)) {
+            // session.flash('errors', 'Invalid server state!');
+            return response
+                .flash(
+                    'warning',
+                    `Invalid server state. Dataset with id ${id} cannot be reviewed. Datset has server state ${dataset.server_state}.`,
+                )
+                .redirect()
+                .toRoute('reviewer.dataset.list');
+        }
+
+        return inertia.render('Reviewer/Dataset/Review', {
+            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) {
         const id = request.param('id');
         const dataset = await Dataset.query()
             .where('id', id)
@@ -158,6 +211,10 @@ export default class DatasetsController {
         return inertia.render('Reviewer/Dataset/Review', {
             dataset,
             fields: fields,
+            can: {
+                review: await auth.user?.can(['dataset-review']),
+                reject: await auth.user?.can(['dataset-review-reject']),
+            },
         });
     }
 
@@ -166,7 +223,7 @@ export default class DatasetsController {
         // const { id } = params;
         const dataset = await Dataset.findOrFail(id);
 
-        const validStates = ['approved'];
+        const validStates = ['approved', 'rejected_to_reviewer'];
         if (!validStates.includes(dataset.server_state)) {
             // throw new Error('Invalid server state!');
             // return response.flash('warning', 'Invalid server state. Dataset cannot be released to editor').redirect().back();
@@ -180,6 +237,10 @@ export default class DatasetsController {
         }
 
         dataset.server_state = 'reviewed';
+        // if editor has rejected to reviewer:
+        if (dataset.reject_editor_note != null) {
+            dataset.reject_editor_note = null;
+        }
 
         try {
             // await dataset.related('editor').associate(user); // speichert schon ab
@@ -203,7 +264,7 @@ export default class DatasetsController {
             })
             .firstOrFail();
 
-        const validStates = ['approved'];
+        const validStates = ['approved', 'rejected_to_reviewer'];
         if (!validStates.includes(dataset.server_state)) {
             // session.flash('errors', 'Invalid server state!');
             return response
@@ -250,12 +311,12 @@ export default class DatasetsController {
             throw error;
         }
 
-        const validStates = ['approved'];
+        const validStates = ['approved', 'rejected_to_reviewer'];
         if (!validStates.includes(dataset.server_state)) {
             // throw new Error('Invalid server state!');
             // return response.flash('warning', 'Invalid server state. Dataset cannot be released to editor').redirect().back();
             return response
-                .flash(                   
+                .flash(
                     `Invalid server state. Dataset with id ${id} cannot be rejected. Datset has server state ${dataset.server_state}.`,
                     'warning',
                 )
@@ -307,4 +368,41 @@ export default class DatasetsController {
             .toRoute('reviewer.dataset.list')
             .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}.${fileExt}`);
+    //     return response.download(filePath);
+    // }
+
+    public async download({ params, response }: HttpContext) {
+            const id = params.id;
+            // Find the file by ID
+            const file = await File.findOrFail(id);
+            // const filePath =  await drive.use('local').getUrl('/'+ file.filePath)
+            const filePath = file.filePath;
+            const fileExt = file.filePath.split('.').pop() || '';
+    
+            // Check if label already includes the extension
+            const fileName = file.label.toLowerCase().endsWith(`.${fileExt.toLowerCase()}`) ? file.label : `${file.label}.${fileExt}`;
+    
+            // Set the response headers and download the file
+            response
+                .header('Cache-Control', 'no-cache private')
+                .header('Content-Description', 'File Transfer')
+                .header('Content-Type', file.mime_type || 'application/octet-stream')
+                //  .header('Content-Disposition', 'inline; filename=' + fileName)
+                .header('Content-Transfer-Encoding', 'binary')
+                .header('Access-Control-Allow-Origin', '*')
+                .header('Access-Control-Allow-Methods', 'GET');
+            response.attachment(fileName);
+            return response.download(filePath);
+        }
 }

app/Controllers/Http/Submitter/DatasetController.ts

@@ -14,9 +14,7 @@ import Person from '#models/person';
 import db from '@adonisjs/lucid/services/db';
 import { TransactionClientContract } from '@adonisjs/lucid/types/database';
 import Subject from '#models/subject';
-// import CreateDatasetValidator from '#validators/create_dataset_validator';
 import { createDatasetValidator, updateDatasetValidator } from '#validators/dataset';
-// import UpdateDatasetValidator from '#validators/update_dataset_validator';
 import {
     TitleTypes,
     DescriptionTypes,
@@ -29,23 +27,33 @@ import {
 } from '#contracts/enums';
 import { ModelQueryBuilderContract } from '@adonisjs/lucid/types/model';
 import DatasetReference from '#models/dataset_reference';
-import { cuid } from '@adonisjs/core/helpers';
 import File from '#models/file';
 import ClamScan from 'clamscan';
-// import { ValidationException } from '@adonisjs/validator';
-// import Drive from '@ioc:Adonis/Core/Drive';
-// import drive from '#services/drive';
 import drive from '@adonisjs/drive/services/main';
 import path from 'path';
 import { Exception } from '@adonisjs/core/exceptions';
 import { MultipartFile } from '@adonisjs/core/types/bodyparser';
 import * as crypto from 'crypto';
+import { pipeline } from 'node:stream/promises';
+import { createWriteStream } from 'node:fs';
+import type { Multipart } from '@adonisjs/bodyparser';
+import * as fs from 'fs';
+import { parseBytesSize, getConfigFor, getTmpPath, formatBytes, errorMessage } from '#app/utils/utility-functions';
+import validation from '#services/validation_service';
+import ActivityLogger from '#services/activity_logger';
+import logger from '@adonisjs/core/services/logger';
+
 interface Dictionary {
     [index: string]: string;
 }
 import vine, { SimpleMessagesProvider, errors } from '@vinejs/vine';
 
 export default class DatasetController {
+    /**
+     * Bodyparser config
+     */
+    // config: BodyParserConfig = config.get('bodyparser');
+
     public async index({ auth, request, inertia }: HttpContext) {
         const user = (await User.find(auth.user?.id)) as User;
         const page = request.input('page', 1);
@@ -69,8 +77,16 @@ export default class DatasetController {
             }
             datasets.orderBy(attribute, sortOrder);
         } else {
-            // users.orderBy('created_at', 'desc');
-            datasets.orderBy('id', 'asc');
+            // datasets.orderBy('id', 'asc');
+            // Custom ordering to prioritize rejected_editor state
+            datasets.orderByRaw(`
+                CASE 
+                    WHEN server_state = 'rejected_editor' THEN 0 
+                    WHEN server_state = 'rejected_reviewer' THEN 1
+                    ELSE 2 
+                END ASC, 
+                id ASC
+            `);
         }
 
         // const results = await Database
@@ -90,6 +106,7 @@ export default class DatasetController {
                 'reviewed',
                 'rejected_editor',
                 'rejected_reviewer',
+                'rejected_to_reviewer',
             ])
             .where('account_id', user.id)
             .preload('titles')
@@ -191,7 +208,9 @@ export default class DatasetController {
                             .translatedLanguage({ mainLanguageField: 'language', typeField: 'type' }),
                     }),
                 )
-                .minLength(1),
+                .minLength(1) // Ensure at least the main title exists
+                // .minLength(2)
+                .arrayContainsTypes({ typeA: 'main', typeB: 'translated' }),
             descriptions: vine
                 .array(
                     vine.object({
@@ -205,7 +224,8 @@ export default class DatasetController {
                             .translatedLanguage({ mainLanguageField: 'language', typeField: 'type' }),
                     }),
                 )
-                .minLength(1),
+                // .minLength(1),
+                .arrayContainsTypes({ typeA: 'abstract', typeB: 'translated' }),
             authors: vine
                 .array(
                     vine.object({
@@ -216,8 +236,9 @@ 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)
@@ -232,8 +253,9 @@ 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)),
                     }),
                 )
@@ -280,7 +302,8 @@ export default class DatasetController {
                             .translatedLanguage({ mainLanguageField: 'language', typeField: 'type' }),
                     }),
                 )
-                .minLength(1),
+                // .minLength(2)
+                .arrayContainsTypes({ typeA: 'main', typeB: 'translated' }),
             descriptions: vine
                 .array(
                     vine.object({
@@ -294,7 +317,8 @@ export default class DatasetController {
                             .translatedLanguage({ mainLanguageField: 'language', typeField: 'type' }),
                     }),
                 )
-                .minLength(1),
+                // .minLength(1),
+                .arrayContainsTypes({ typeA: 'abstract', typeB: 'translated' }),
             authors: vine
                 .array(
                     vine.object({
@@ -305,8 +329,9 @@ 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)
@@ -321,8 +346,9 @@ 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)),
                     }),
                 )
@@ -402,49 +428,138 @@ export default class DatasetController {
     }
 
     public async store({ auth, request, response, session }: HttpContext) {
-        // node ace make:validator CreateDataset
-        try {
-            //  Step 2 - Validate request body against  the schema
-            // await request.validate({ schema: newDatasetSchema, messages: this.messages });
-            // await request.validate(CreateDatasetValidator);
-            await request.validateUsing(createDatasetValidator);
-            // console.log({ payload });
-        } catch (error) {
-            // Step 3 - Handle errors
-            // return response.badRequest(error.messages);
-            throw error;
+        const uploadedTmpFiles: string[] = [];
+        const multipart: Multipart = request.multipart;
+
+        // NULL GUARD: kein multipart-Body → sauberer Validierungsfehler statt Crash
+        if (!multipart) {
+            validation.throw('files', 'Please select at least one file.', 'required');
         }
 
+        // Configuration for limits
+        const multipartConfig = getConfigFor('multipart');
+        const aggregatedLimit = multipartConfig.limit ? parseBytesSize(multipartConfig.limit) : 100 * 1024 * 1024;
+
+        let totalUploadedSize = 0;
+        let filesCount = 0; // Tracker: ensure at least one file is processed
+
+        multipart.onFile('files', { deferValidations: true }, async (part) => {
+            filesCount++;
+            let fileUploadedSize = 0;
+
+            // Accumulate the size per chunk (cheap), defer the limit check to 'end'
+            part.on('data', (chunk) => {
+                fileUploadedSize += chunk.length;
+            });
+
+            // After the file is fully read, update the global counter and check the aggregated limit
+            part.on('end', () => {
+                totalUploadedSize += fileUploadedSize;
+                part.file.size = fileUploadedSize;
+                // Record the temporary file path
+                if (part.file.tmpPath) {
+                    uploadedTmpFiles.push(part.file.tmpPath);
+                }
+
+                // AGGREGATED LIMIT CHECK: abort immediately if too big
+                if (totalUploadedSize > aggregatedLimit) {
+                    // Clean up all temporary files if aggregate limit is exceeded
+                    uploadedTmpFiles.forEach((tmpPath) => {
+                        try {
+                            fs.unlinkSync(tmpPath);
+                        } catch (cleanupError) {
+                            console.error('Error cleaning up temporary file:', cleanupError);
+                        }
+                    });
+                    request.multipart.abort(validation.make('files', `Upload limit of ${formatBytes(aggregatedLimit)} exceeded.`, 'limit'));
+                }
+            });
+
+            // Process file with error handling
+            try {
+                // Extract extension from the client file name, e.g. "Tethys 5 - Ampflwang_dataset.zip"
+                const ext = path.extname(part.file.clientName).replace('.', '');
+                part.file.extname = ext;
+
+                const tmpPath = getTmpPath(multipartConfig);
+                (part.file as any).tmpPath = tmpPath;
+
+                const writeStream = createWriteStream(tmpPath);
+                await pipeline(part, writeStream);
+            } catch (error) {
+                request.multipart.abort(validation.make('files', error.message, 'upload'));
+            }
+        });
+
+        try {
+            await multipart.process();
+
+            // EMPTY FIELD CHECK: triggered if process finishes but onFile never ran
+            if (filesCount === 0) {
+                validation.throw('files', 'Please select at least one file.', 'required');
+            }
+        } catch (error) {
+            // If it's already a validation error, let it bubble up unchanged
+            if (error instanceof errors.E_VALIDATION_ERROR) throw error;
+
+            // Wrap any other stream/size errors
+            validation.throw('files', errorMessage(error) || 'Upload failed.');
+        }
+
+        // Proceed to transaction and createDatasetAndAssociations
         let trx: TransactionClientContract | null = null;
         try {
+            await request.validateUsing(createDatasetValidator);
             trx = await db.transaction();
             const user = (await User.find(auth.user?.id)) as User;
 
-            await this.createDatasetAndAssociations(user, request, trx);
+            // await this.createDatasetAndAssociations(user, request, trx);
+             const { dataset, mainTitle } = await this.createDatasetAndAssociations(user, request, trx);
 
             await trx.commit();
             console.log('Dataset and related models created successfully');
+
+            // NACH dem Commit: Dataset ist garantiert persistiert, keine Waisen-Gefahr.
+            // Fire-and-forget, damit ein Log-Fehler den bereits erfolgreichen Upload nicht kippt.
+            void ActivityLogger.log({
+                type: 'dataset.uploaded',
+                description: `New publication uploaded: ${mainTitle ?? 'Untitled'}`,
+                userId: user.id,
+                subjectType: 'Dataset',
+                subjectId: dataset.id,
+            }).catch((err) => logger.error({ err }, 'failed to record dataset.uploaded activity'));
         } catch (error) {
+            // Clean up temporary files if validation or later steps fail
+            uploadedTmpFiles.forEach((tmpPath) => {
+                try {
+                    fs.unlinkSync(tmpPath);
+                } catch (cleanupError) {
+                    console.error('Error cleaning up temporary file:', cleanupError);
+                }
+            });
             if (trx !== null) {
                 await trx.rollback();
             }
             console.error('Failed to create dataset and related models:', error);
-            // throw new ValidationException(true, { 'upload error': `failed to create dataset and related models. ${error}` });
             throw error;
         }
 
         session.flash('message', 'Dataset has been created successfully');
         return response.redirect().toRoute('dataset.list');
-        // return response.redirect().back();
     }
-
-    private async createDatasetAndAssociations(user: User, request: HttpContext['request'], trx: TransactionClientContract) {
+    private async createDatasetAndAssociations(
+        user: User,
+        request: HttpContext['request'],
+        trx: TransactionClientContract,
+        // uploadedFiles: Array<MultipartFile>,
+    ) {
         // Create a new instance of the Dataset model:
         const dataset = new Dataset();
         dataset.type = request.input('type');
         dataset.creating_corporation = request.input('creating_corporation');
         dataset.language = request.input('language');
         dataset.embargo_date = request.input('embargo_date');
+        dataset.project_id = request.input('project_id');
         //await dataset.related('user').associate(user); // speichert schon ab
         // Dataset.$getRelation('user').boot();
         // Dataset.$getRelation('user').setRelated(dataset, user);
@@ -460,6 +575,15 @@ export default class DatasetController {
         await this.savePersons(dataset, request.input('contributors', []), 'contributor', trx);
 
         //save main and additional titles
+        // const titles = request.input('titles', []);
+        // for (const titleData of titles) {
+        //     const title = new Title();
+        //     title.value = titleData.value;
+        //     title.language = titleData.language;
+        //     title.type = titleData.type;
+        //     await dataset.useTransaction(trx).related('titles').save(title);
+        // }
+        let mainTitle: string | null = null;
         const titles = request.input('titles', []);
         for (const titleData of titles) {
             const title = new Title();
@@ -467,6 +591,11 @@ export default class DatasetController {
             title.language = titleData.language;
             title.type = titleData.type;
             await dataset.useTransaction(trx).related('titles').save(title);
+
+            if (titleData.type === 'Main') {
+                // <-- an eure Typ-Konvention anpassen
+                mainTitle = titleData.value;
+            }
         }
 
         // save descriptions
@@ -553,13 +682,15 @@ export default class DatasetController {
             newFile.fileSize = file.size;
             newFile.mimeType = mimeType;
             newFile.label = file.clientName;
-            newFile.sortOrder = index;
+            newFile.sortOrder = index + 1;
             newFile.visibleInFrontdoor = true;
             newFile.visibleInOai = true;
             // let path = coverImage.filePath;
             await dataset.useTransaction(trx).related('files').save(newFile);
             await newFile.createHashValues(trx);
         }
+
+        return { dataset, mainTitle }; // <-- statt void
     }
 
     private generateRandomString(length: number): string {
@@ -704,16 +835,25 @@ export default class DatasetController {
         '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')}`,
     };
 
     // public async release({ params, view }) {
-    public async release({ request, inertia, response }: HttpContext) {
+    public async release({ request, inertia, response, auth }: HttpContext) {
         const id = request.param('id');
+        const user = auth.user;
+
+        // Check if user is authenticated
+        if (!user) {
+            return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
+        }
 
         const dataset = await Dataset.query()
             .preload('user', (builder) => {
                 builder.select('id', 'login');
             })
+            .where('account_id', user.id) // Only fetch if user owns it
             .where('id', id)
             .firstOrFail();
 
@@ -734,9 +874,20 @@ export default class DatasetController {
         });
     }
 
-    public async releaseUpdate({ request, response }: HttpContext) {
+    public async releaseUpdate({ request, response, auth }: HttpContext) {
         const id = request.param('id');
-        const dataset = await Dataset.query().preload('files').where('id', id).firstOrFail();
+        const user = auth.user;
+
+        // Check if user is authenticated
+        if (!user) {
+            return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
+        }
+
+        const dataset = await Dataset.query()
+            .preload('files')
+            .where('id', id)
+            .where('account_id', user.id) // Only fetch if user owns it
+            .firstOrFail();
 
         const validStates = ['inprogress', 'rejected_editor'];
         if (!validStates.includes(dataset.server_state)) {
@@ -814,16 +965,24 @@ export default class DatasetController {
         // throw new GeneralException(trans('exceptions.publish.release.update_error'));
     }
 
-    public async edit({ request, inertia, response }: HttpContext) {
+    public async edit({ request, inertia, response, auth }: HttpContext) {
         const id = request.param('id');
-        const datasetQuery = Dataset.query().where('id', id);
+        const user = auth.user;
+
+        // Check if user is authenticated
+        if (!user) {
+            return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
+        }
+
+        // Prefilter by both id AND account_id
+        const datasetQuery = Dataset.query().where('id', id).where('account_id', user.id); // Only fetch if user owns it
         datasetQuery
             .preload('titles', (query) => query.orderBy('id', 'asc'))
             .preload('descriptions', (query) => query.orderBy('id', 'asc'))
             .preload('coverage')
             .preload('licenses')
-            .preload('authors')
-            .preload('contributors')
+            .preload('authors', (query) => query.orderBy('pivot_sort_order', 'asc'))
+            .preload('contributors', (query) => query.orderBy('pivot_sort_order', 'asc'))
             // .preload('subjects')
             .preload('subjects', (builder) => {
                 builder.orderBy('id', 'asc').withCount('datasets');
@@ -832,17 +991,17 @@ export default class DatasetController {
             .preload('files', (query) => {
                 query.orderBy('sort_order', 'asc'); // Sort by sort_order column
             });
-
+        // This will throw 404 if dataset doesn't exist OR user doesn't own it
         const dataset = await datasetQuery.firstOrFail();
+
         const validStates = ['inprogress', 'rejected_editor'];
         if (!validStates.includes(dataset.server_state)) {
             // session.flash('errors', 'Invalid server state!');
             return response
                 .flash(
-                    'warning',
                     `Invalid server state. Dataset with id ${id} cannot be edited. Datset has server state ${dataset.server_state}.`,
+                    'warning',
                 )
-                .redirect()
                 .toRoute('dataset.list');
         }
 
@@ -872,19 +1031,6 @@ 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,
@@ -903,25 +1049,114 @@ export default class DatasetController {
             subjectTypes: SubjectTypes,
             referenceIdentifierTypes: Object.entries(ReferenceIdentifierTypes).map(([key, value]) => ({ value: key, label: value })),
             relationTypes: Object.entries(RelationTypes).map(([key, value]) => ({ value: key, label: value })),
-            doctypes,
+            doctypes: DatasetTypes,
+            can: {
+                edit: await auth.user?.can(['dataset-edit']),
+                delete: await auth.user?.can(['dataset-delete']),
+            },
         });
     }
 
-    public async update({ request, response, session }: HttpContext) {
-        try {
-            // await request.validate(UpdateDatasetValidator);
-            await request.validateUsing(updateDatasetValidator);
-        } catch (error) {
-            // - Handle errors
-            // return response.badRequest(error.messages);
-            throw error;
-            // return response.badRequest(error.messages);
-        }
-        // await request.validate(UpdateDatasetValidator);
-        const id = request.param('id');
+    public async update({ request, response, session, auth }: HttpContext) {
+        // Get the dataset id from the route parameter
+        const datasetId = request.param('id');
+        const user = auth.user;
 
+        // Check if user is authenticated
+        if (!user) {
+            return response.flash('You must be logged in to update a dataset.', 'error').redirect().toRoute('app.login.show');
+        }
+
+        // Prefilter by both id AND account_id
+        const dataset = await Dataset.query()
+            .where('id', datasetId)
+            .where('account_id', user.id) // Only fetch if user owns it
+            .firstOrFail();
+
+        // // Check if the authenticated user is the owner of the dataset
+        // if (dataset.account_id !== user.id) {
+        //     return response
+        //         .flash(`Unauthorized access. You are not the owner of dataset with id ${id}.`, 'error')
+        //         .redirect()
+        //         .toRoute('dataset.list');
+        // }
+
+        await dataset.load('files');
+        // Accumulate the size of the already related files
+        // const preExistingFileSize = dataset.files.reduce((acc, file) => acc + file.fileSize, 0);
+        let preExistingFileSize = 0;
+        for (const file of dataset.files) {
+            preExistingFileSize += Number(file.fileSize);
+        }
+
+        const uploadedTmpFiles: string[] = [];
+        // Only process multipart if the request has a multipart content type
+        const contentType = request.request.headers['content-type'] || '';
+        if (contentType.includes('multipart/form-data')) {
+            const multipart: Multipart = request.multipart;
+            // Aggregated limit example (adjust as needed)
+            const multipartConfig = getConfigFor('multipart');
+            const aggregatedLimit = multipartConfig.limit ? parseBytesSize(multipartConfig.limit) : 100 * 1024 * 1024;
+            // Initialize totalUploadedSize with the size of existing files
+            let totalUploadedSize = preExistingFileSize;
+
+            multipart.onFile('files', { deferValidations: true }, async (part) => {
+                let fileUploadedSize = 0;
+
+                part.on('data', (chunk) => {
+                    fileUploadedSize += chunk.length;
+                });
+
+                part.on('end', () => {
+                    totalUploadedSize += fileUploadedSize;
+                    part.file.size = fileUploadedSize;
+                    if (part.file.tmpPath) {
+                        uploadedTmpFiles.push(part.file.tmpPath);
+                    }
+                    if (totalUploadedSize > aggregatedLimit) {
+                        uploadedTmpFiles.forEach((tmpPath) => {
+                            try {
+                                fs.unlinkSync(tmpPath);
+                            } catch (cleanupError) {
+                                console.error('Error cleaning up temporary file:', cleanupError);
+                            }
+                        });
+                        const error = new errors.E_VALIDATION_ERROR({
+                            files: `Aggregated upload limit of ${formatBytes(aggregatedLimit)} exceeded. The total size of files being uploaded would exceed the limit.`,
+                        });
+                        request.multipart.abort(error);
+                    }
+                });
+
+                part.on('error', (error) => {
+                    request.multipart.abort(error);
+                });
+
+                try {
+                    const fileNameWithoutParams = part.file.clientName.split('?')[0];
+                    const ext = path.extname(fileNameWithoutParams).replace('.', '');
+                    part.file.extname = ext;
+                    const tmpPath = getTmpPath(multipartConfig);
+                    (part.file as any).tmpPath = tmpPath;
+                    const writeStream = createWriteStream(tmpPath);
+                    await pipeline(part, writeStream);
+                } catch (error) {
+                    request.multipart.abort(new errors.E_VALIDATION_ERROR({ 'upload error': error.message }));
+                }
+            });
+
+            try {
+                await multipart.process();
+            } catch (error) {
+                // session.flash('errors', error.messages);
+                return response.redirect().back();
+            }
+        }
+
+        const id = request.param('id');
         let trx: TransactionClientContract | null = null;
         try {
+            await request.validateUsing(updateDatasetValidator);
             trx = await db.transaction();
             // const user = (await User.find(auth.user?.id)) as User;
             // await this.createDatasetAndAssociations(user, request, trx);
@@ -982,22 +1217,148 @@ export default class DatasetController {
                 }
             }
 
-            // await dataset.useTransaction(trx).related('subjects').sync([]);
-            const keywords = request.input('subjects');
-            for (const keywordData of keywords) {
-                if (keywordData.id) {
-                    const subject = await Subject.findOrFail(keywordData.id);
-                    // await dataset.useTransaction(trx).related('subjects').attach([keywordData.id]);
-                    subject.value = keywordData.value;
-                    subject.type = keywordData.type;
-                    subject.external_key = keywordData.external_key;
-                    if (subject.$isDirty) {
-                        await subject.save();
+            // ============================================
+            // IMPROVED SUBJECTS PROCESSING
+            // ============================================
+            const subjects = request.input('subjects', []);
+            const currentDatasetSubjectIds = new Set<number>();
+
+            for (const subjectData of subjects) {
+                let subjectToRelate: Subject;
+
+                // Case 1: Subject has an ID (existing subject being updated)
+                if (subjectData.id) {
+                    const existingSubject = await Subject.findOrFail(subjectData.id);
+
+                    // Check if the updated value conflicts with another existing subject
+                    const duplicateSubject = await Subject.query()
+                        .where('value', subjectData.value)
+                        .where('type', subjectData.type)
+                        .where('language', subjectData.language || 'en') // Default language if not provided
+                        .where('id', '!=', subjectData.id) // Exclude the current subject
+                        .first();
+
+                    if (duplicateSubject) {
+                        // A duplicate exists - use the existing duplicate instead
+                        subjectToRelate = duplicateSubject;
+
+                        // Check if the original subject should be deleted (if it's only used by this dataset)
+                        const originalSubjectUsage = await Subject.query()
+                            .where('id', existingSubject.id)
+                            .withCount('datasets')
+                            .firstOrFail();
+
+                        if (originalSubjectUsage.$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.$isDirty) {
+                            await existingSubject.useTransaction(trx).save();
+                        }
+
+                        subjectToRelate = existingSubject;
+                    }
+                }
+                // Case 2: New subject being added (no ID)
+                else {
+                    // Use firstOrNew to either find existing or create new subject
+                    subjectToRelate = await Subject.firstOrNew(
+                        {
+                            value: subjectData.value,
+                            type: subjectData.type,
+                            language: subjectData.language || 'en',
+                        },
+                        {
+                            value: subjectData.value,
+                            type: subjectData.type,
+                            language: subjectData.language || 'en',
+                            external_key: subjectData.external_key,
+                        },
+                    );
+
+                    if (subjectToRelate.$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) {
+                    // const subject = await Subject.findOrFail(subjectData.id);
+                    const subject = await Subject.query()
+                        .where('id', subjectData.id)
+                        .preload('datasets', (builder) => {
+                            builder.orderBy('id', 'asc');
+                        })
+                        .withCount('datasets')
+                        .firstOrFail();
+
+                    // Detach the subject from this dataset
+                    await dataset.useTransaction(trx).related('subjects').detach([subject.id]);
+
+                    // If this was the only dataset using this subject, delete it entirely
+                    if (subject.$extras.datasets_count <= 1) {
+                        await subject.useTransaction(trx).delete();
+                    }
+
+                    // Remove from current set if it was added earlier
+                    currentDatasetSubjectIds.delete(subjectData.id);
+                }
+            }
+
+            // Process references
+            const references = request.input('references', []);
+            // First, get existing references to determine which ones to update vs. create
+            const existingReferences = await dataset.related('references').query();
+            const existingReferencesMap: Map<number, DatasetReference> = new Map(existingReferences.map((ref) => [ref.id, ref]));
+
+            for (const referenceData of references) {
+                if (existingReferencesMap.has(referenceData.id) && referenceData.id) {
+                    // Update existing reference
+                    const reference = existingReferencesMap.get(referenceData.id);
+                    if (reference) {
+                        reference.merge(referenceData);
+                        if (reference.$isDirty) {
+                            await reference.useTransaction(trx).save();
+                        }
                     }
                 } else {
-                    const keyword = new Subject();
-                    keyword.fill(keywordData);
-                    await dataset.useTransaction(trx).related('subjects').save(keyword, false);
+                    // Create new reference
+                    const dataReference = new DatasetReference();
+                    dataReference.fill(referenceData);
+                    await dataset.useTransaction(trx).related('references').save(dataReference);
+                }
+            }
+
+            // Handle references to delete if provided
+            const referencesToDelete = request.input('referencesToDelete', []);
+            for (const referenceData of referencesToDelete) {
+                if (referenceData.id) {
+                    const reference = await DatasetReference.findOrFail(referenceData.id);
+                    await reference.useTransaction(trx).delete();
                 }
             }
 
@@ -1029,9 +1390,9 @@ export default class DatasetController {
             // handle new uploaded files:
             const uploadedFiles: MultipartFile[] = request.files('files');
             if (Array.isArray(uploadedFiles) && uploadedFiles.length > 0) {
-                for (const [index, fileData] of uploadedFiles.entries()) {
+                for (const [index, file] of uploadedFiles.entries()) {
                     try {
-                        await this.scanFileForViruses(fileData.tmpPath); //, 'gitea.lan', 3310);
+                        await this.scanFileForViruses(file.tmpPath); //, 'gitea.lan', 3310);
                         // await this.scanFileForViruses("/tmp/testfile.txt");
                     } catch (error) {
                         // If the file is infected or there's an error scanning the file, throw a validation exception
@@ -1039,29 +1400,29 @@ export default class DatasetController {
                     }
 
                     // move to disk:
-                    const fileName = `file-${cuid()}.${fileData.extname}`; //'file-ls0jyb8xbzqtrclufu2z2e0c.pdf'
+                    const fileName = this.generateFilename(file.extname as string);
                     const datasetFolder = `files/${dataset.id}`; // 'files/307'
                     const datasetFullPath = path.join(`${datasetFolder}`, fileName);
-                    // await fileData.moveToDisk(datasetFolder, { name: fileName, overwrite: true }, 'local');
-                    // await fileData.move(drive.makePath(datasetFolder), {
+                    // await file.moveToDisk(datasetFolder, { name: fileName, overwrite: true }, 'local');
+                    // await file.move(drive.makePath(datasetFolder), {
                     //     name: fileName,
                     //     overwrite: true, // overwrite in case of conflict
                     // });
-                    await fileData.moveToDisk(datasetFullPath, 'local', {
+                    await file.moveToDisk(datasetFullPath, 'local', {
                         name: fileName,
                         overwrite: true, // overwrite in case of conflict
                         disk: 'local',
                     });
 
                     //save to db:
-                    const { clientFileName, sortOrder } = this.extractVariableNameAndSortOrder(fileData.clientName);
-                    const mimeType = fileData.headers['content-type'] || 'application/octet-stream'; // Fallback to a default MIME type
+                    const { clientFileName, sortOrder } = this.extractVariableNameAndSortOrder(file.clientName);
+                    const mimeType = file.headers['content-type'] || 'application/octet-stream'; // Fallback to a default MIME type
                     const newFile = await dataset
                         .useTransaction(trx)
                         .related('files')
                         .create({
                             pathName: `${datasetFolder}/${fileName}`,
-                            fileSize: fileData.size,
+                            fileSize: file.size,
                             mimeType,
                             label: clientFileName,
                             sortOrder: sortOrder || index,
@@ -1101,16 +1462,24 @@ export default class DatasetController {
             await dataset.useTransaction(trx).save();
 
             await trx.commit();
-            console.log('Dataset and related models created successfully');
+            console.log('Dataset has been updated successfully');
 
             session.flash('message', 'Dataset has been updated successfully');
             // return response.redirect().toRoute('user.index');
             return response.redirect().toRoute('dataset.edit', [dataset.id]);
         } catch (error) {
+            // Clean up temporary files if validation or later steps fail
+            uploadedTmpFiles.forEach((tmpPath) => {
+                try {
+                    fs.unlinkSync(tmpPath);
+                } catch (cleanupError) {
+                    console.error('Error cleaning up temporary file:', cleanupError);
+                }
+            });
             if (trx !== null) {
                 await trx.rollback();
             }
-            console.error('Failed to create dataset and related models:', error);
+            console.error('Failed to update dataset and related models:', error);
             // throw new ValidationException(true, { 'upload error': `failed to create dataset and related models. ${error}` });
             throw error;
         }
@@ -1135,16 +1504,26 @@ export default class DatasetController {
         }
     }
 
-    public async delete({ request, inertia, response, session }: HttpContext) {
+    public async delete({ request, inertia, response, session, auth }: HttpContext) {
         const id = request.param('id');
+        const user = auth.user;
+
+        // Check if user is authenticated
+        if (!user) {
+            return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
+        }
+
         try {
+            // This will throw 404 if dataset doesn't exist OR user doesn't own it
             const dataset = await Dataset.query()
                 .preload('user', (builder) => {
                     builder.select('id', 'login');
                 })
                 .where('id', id)
+                .where('account_id', user.id) // Only fetch if user owns it
                 .preload('files')
                 .firstOrFail();
+
             const validStates = ['inprogress', 'rejected_editor'];
             if (!validStates.includes(dataset.server_state)) {
                 // session.flash('errors', 'Invalid server state!');
@@ -1169,9 +1548,27 @@ export default class DatasetController {
         }
     }
 
-    public async deleteUpdate({ params, session, response }: HttpContext) {
+    public async deleteUpdate({ params, session, response, auth }: HttpContext) {
         try {
-            const dataset = await Dataset.query().where('id', params.id).preload('files').firstOrFail();
+            const user = auth.user;
+            if (!user) {
+                return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
+            }
+
+            // This will throw 404 if dataset doesn't exist OR user doesn't own it
+            const dataset = await Dataset.query()
+                .where('id', params.id)
+                .where('account_id', user.id) // Only fetch if user owns it
+                .preload('files')
+                .firstOrFail();
+
+            // // Check if the authenticated user is the owner of the dataset
+            // if (dataset.account_id !== user.id) {
+            //     return response
+            //         .flash(`Unauthorized access. You are not the owner of dataset with id ${params.id}.`, 'error')
+            //         .redirect()
+            //         .toRoute('dataset.list');
+            // }
 
             const validStates = ['inprogress', 'rejected_editor'];
             if (validStates.includes(dataset.server_state)) {
@@ -1236,6 +1633,7 @@ export default class DatasetController {
         }
 
         const collectionRoles = await CollectionRole.query()
+            .whereIn('name', ['ddc', 'ccs'])
             .preload('collections', (coll: Collection) => {
                 // preloa only top level collection with noparent_id
                 coll.whereNull('parent_id').orderBy('number', 'asc');
@@ -1275,7 +1673,7 @@ export default class DatasetController {
             // This should be an array of collection ids.
             const collections: number[] = request.input('collections', []);
 
-            // Synchronize the dataset collections using the transaction.         
+            // Synchronize the dataset collections using the transaction.
             await dataset.useTransaction(trx).related('collections').sync(collections);
 
             // Commit the transaction.await trx.commit()

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<string>;
+    /** 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<XMLBuilder | null> {
+        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<string | null> {
+        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<void> {
+        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<XMLBuilder | null> {
+        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;
+        }
+    }
+}

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<any | null> {
+        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}: ${error.message}`);
+
+            // Fallback to MDS API
+            return await this.getDoiInfoFromMds(doiValue);
+        }
+
+        return null;
+    }
+
+    /**
+     * Fallback method to get DOI info from MDS API
+     *
+     * @param doiValue The DOI identifier
+     * @returns Promise with basic DOI information or null
+     */
+    private async getDoiInfoFromMds(doiValue: string): Promise<any | null> {
+        try {
+            const auth = {
+                username: this.username,
+                password: this.password,
+            };
+
+            // Get DOI URL
+            const doiResponse = await axios.get(`${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<boolean> True if DOI exists
+     */
+    public async doiExists(doiValue: string): Promise<boolean> {
+        const doiInfo = await this.getDoiInfo(doiValue);
+        return doiInfo !== null;
+    }
+
+    /**
+     * Gets the last modification date of a DOI
+     *
+     * @param doiValue The DOI identifier
+     * @returns Promise<Date | null> Last modification date or creation date if never updated, null if not found
+     */
+    public async getDoiLastModified(doiValue: string): Promise<Date | null> {
+        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<AxiosResponse<any>> The http response
+     */
+    public async makeDoiUnfindable(doiValue: string): Promise<AxiosResponse<any>> {
+        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: ${error.message}`);
+            if (error instanceof DoiClientException) {
+                throw error;
+            }
+            throw new DoiClientException(error.response?.status || 500, error.response?.data || error.message);
+        }
+    }
+
+    /**
+     * Makes a DOI findable again by re-registering the URL
+     * await doiClient.makeDoiFindable(
+     *     '10.21388/tethys.231',
+     *     'https://doi.dev.tethys.at/10.21388/tethys.231'
+     * );
+     *
+     * @param doiValue The DOI identifier e.g. '10.5072/tethys.999'
+     * @param landingPageUrl The landing page URL
+     * @returns Promise<AxiosResponse<any>> The http response
+     */
+    public async makeDoiFindable(doiValue: string, landingPageUrl: string): Promise<AxiosResponse<any>> {
+        const auth = {
+            username: this.username,
+            password: this.password,
+        };
+
+        try {
+            // Re-register the DOI with its URL to make it findable again
+            const response = await axios.put(`${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<string | null> The DOI state or null if not found
+     */
+    public async getDoiState(doiValue: string): Promise<string | null> {
+        const doiInfo = await this.getDoiInfo(doiValue);
+        return doiInfo?.state || null;
+    }
 }

app/Library/Oai/TokenWorkerSerice.ts

@@ -1,8 +1,8 @@
 import ResumptionToken from './ResumptionToken.js';
 import { createClient, RedisClientType } from 'redis';
 import InternalServerErrorException from '#app/exceptions/InternalServerException';
-import { sprintf } from 'sprintf-js';
-import dayjs from 'dayjs';
+// import { sprintf } from 'sprintf-js';
+// import dayjs from 'dayjs';
 import TokenWorkerContract from './TokenWorkerContract.js';
 
 export default class TokenWorkerService implements TokenWorkerContract {
@@ -98,21 +98,21 @@ export default class TokenWorkerService implements TokenWorkerContract {
     //     return uniqueName;
     // }
 
-    private async generateUniqueName(): Promise<string> {
-        let fc = 0;
-        const uniqueId = dayjs().unix().toString();
-        let uniqueName: string;
-        let cacheKeyExists: boolean;
-        do {
-            // format values
-            // %s - String
-            // %d - Signed decimal number (negative, zero or positive)
-            // [0-9] (Specifies the minimum width held of to the variable value)
-            uniqueName = sprintf('%s%05d', uniqueId, fc++);
-            cacheKeyExists = await this.has(uniqueName);
-        } while (cacheKeyExists);
-        return uniqueName;
-    }
+    // private async generateUniqueName(): Promise<string> {
+    //     let fc = 0;
+    //     const uniqueId = dayjs().unix().toString();
+    //     let uniqueName: string;
+    //     let cacheKeyExists: boolean;
+    //     do {
+    //         // format values
+    //         // %s - String
+    //         // %d - Signed decimal number (negative, zero or positive)
+    //         // [0-9] (Specifies the minimum width held of to the variable value)
+    //         uniqueName = sprintf('%s%05d', uniqueId, fc++);
+    //         cacheKeyExists = await this.has(uniqueName);
+    //     } while (cacheKeyExists);
+    //     return uniqueName;
+    // }
 
     public async get(key: string): Promise<ResumptionToken | null> {
         if (!this.cache) {

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';
@@ -17,7 +17,7 @@ interface XslTParameter {
 }
 export default {
     // opensearchNode: process.env.OPENSEARCH_HOST || 'localhost',
-    client: new Client({ node: `http://${process.env.OPENSEARCH_HOST || 'localhost'}` }), // replace with your OpenSearch endpoint
+    client: new Client({ node: `${process.env.OPENSEARCH_HOST || 'localhost'}` }), // replace with your OpenSearch endpoint
 
     async getDoiRegisterString(dataset: Dataset): Promise<string | undefined> {
         try {
@@ -72,31 +72,42 @@ export default {
         }
     },
 
+    /**
+     * Index a dataset document to OpenSearch/Elasticsearch
+     */
     async indexDocument(dataset: Dataset, index_name: string): Promise<void> {
         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<string> {
-        let xml = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, '<root></root>');
-        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<string> {
+        const xml = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, '<root></root>');
+        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<void> => {
-//     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<string> => {
-//     let xml = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, '<root></root>');
-//     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<void> => {
     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<XMLBuilder | null> => {
-    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);
-};
+};

app/Library/XmlModel.ts

@@ -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<string>} 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<string>;
-    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<XMLBuilder | null> {
-        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 }, '<root></root>');
-            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<XMLBuilder | null> {
-        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;
-        }
-    }
-}

app/controllers/activities_controller.ts

@@ -0,0 +1,43 @@
+// app/controllers/activities_controller.ts
+import type { HttpContext } from '@adonisjs/core/http';
+import Activity from '#models/activity';
+
+export default class ActivitiesController {
+    async index({ response }: HttpContext) {
+        // const activities = await Activity.query()
+        //     .preload('user', (q) => q.select('id', 'login'))
+        //     .orderBy('created_at', 'desc')
+        //     .limit(10);
+
+        // return response.json(
+        //     activities.map((a) => ({
+        //         id: a.id,
+        //         type: a.type,
+        //         description: a.description,
+        //         user: a.user?.login ?? null,
+        //         created_at: a.createdAt.toISO(), // relativeTime() expects ISO
+        //     })),
+        // );
+        try {
+            const activities = await Activity.query()
+                .preload('user', (q) => q.select('id', 'login'))
+                .orderBy('created_at', 'desc')
+                .limit(10);
+
+            return response.json(
+                activities.map((a) => ({
+                    id: a.id,
+                    type: a.type,
+                    description: a.description,
+                    user: a.user?.login ?? null,
+                    created_at: a.createdAt.toISO(), // relativeTime() expects ISO
+                })),
+            );
+        } catch (error) {
+            console.error('Error fetching activities:', error);
+            return response.status(500).json({ error: 'Internal Server Error' });
+        }
+    }
+        
+    
+}

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');
+    }
+}

app/exceptions/db_handler.ts

@@ -0,0 +1,43 @@
+// import { Exception } from '@adonisjs/core/exceptions'
+import { HttpContext, ExceptionHandler } from '@adonisjs/core/http';
+
+export default class DbHandlerException extends ExceptionHandler {
+    // constructor() {
+    //   super(Logger)
+    // }
+
+    async handle(error: any, ctx: HttpContext) {
+        // Check for AggregateError type
+        if (error.type === 'AggregateError' && error.aggregateErrors) {
+            const dbErrors = error.aggregateErrors.some((err: any) => err.code === 'ECONNREFUSED' && err.port === 5432);
+
+            if (dbErrors) {
+                return ctx.response.status(503).json({
+                    status: 'error',
+                    message: 'PostgreSQL database connection failed. Please ensure the database service is running.',
+                    details: {
+                        code: error.code,
+                        type: error.type,
+                        ports: error.aggregateErrors.map((err: any) => ({
+                            port: err.port,
+                            address: err.address,
+                        })),
+                    },
+                });
+            }
+        }
+
+        // Handle simple ECONNREFUSED errors
+        if (error.code === 'ECONNREFUSED') {
+            return ctx.response.status(503).json({
+                status: 'error',
+                message: 'Database connection failed. Please ensure PostgreSQL is running.',
+                code: error.code,
+            });
+        }
+
+        return super.handle(error, ctx);
+    }
+
+    static status = 500;
+}

app/exceptions/handler.ts

@@ -1,125 +1,53 @@
-/*
-|--------------------------------------------------------------------------
-| Http Exception Handler
-|--------------------------------------------------------------------------
-|
-| AdonisJs will forward all exceptions occurred during an HTTP request to
-| the following class. You can learn more about exception handling by
-| reading docs.
-|
-| The exception handler extends a base `HttpExceptionHandler` which is not
-| mandatory, however it can do lot of heavy lifting to handle the errors
-| properly.
-|
-*/
-import app from '@adonisjs/core/services/app';
-import { HttpContext, ExceptionHandler } from '@adonisjs/core/http';
-// import logger from '@adonisjs/core/services/logger';
-import type { StatusPageRange, StatusPageRenderer } from '@adonisjs/core/types/http';
+import app from '@adonisjs/core/services/app'
+import { HttpContext, ExceptionHandler } from '@adonisjs/core/http'
+import type { StatusPageRange, StatusPageRenderer } from '@adonisjs/core/types/http'
 
 export default class HttpExceptionHandler extends ExceptionHandler {
-    /**
-     * In debug mode, the exception handler will display verbose errors
-     * with pretty printed stack traces.
-     */
-    protected debug = !app.inProduction;
+  protected debug = !app.inProduction
+  protected renderStatusPages = true
 
-    /**
-     * Status pages are used to display a custom HTML pages for certain error
-     * codes. You might want to enable them in production only, but feel
-     * free to enable them in development as well.
-     */
-    protected renderStatusPages = true; //app.inProduction;
+  protected statusPages: Record<StatusPageRange, StatusPageRenderer> = {
+    '404': (error, ctx) =>
+      ctx.inertia
+        ? ctx.inertia.render('Errors/ServerError', { error: error.message, code: error.status })
+        : ctx.response.status(error.status).send(error.message),
+    '401..403': (error, ctx) => {
+      if (ctx.inertia) {
+        return ctx.inertia.render('Errors/ServerError', { error: error.message, code: error.status });
+      }
+      return ctx.response.status(error.status).send(error.message);
+    },
+    '500..599': (error, ctx) => {
+      const isDbError =
+        error.code === 'ECONNREFUSED' &&
+        (error.errors?.some((e: any) => e.port === 5432) ?? error.message?.includes('5432'));
 
-    /**
-     * Status pages is a collection of error code range and a callback
-     * to return the HTML contents to send as a response.
-     */
-    // protected statusPages: Record<StatusPageRange, StatusPageRenderer> = {
-    //     '401..403': (error, { view }) => {
-    //         return view.render('./errors/unauthorized', { error });
-    //     },
-    //     '404': (error, { view }) => {
-    //         return view.render('./errors/not-found', { error });
-    //     },
-    //     '500..599': (error, { view }) => {
-    //         return view.render('./errors/server-error', { error });
-    //     },
-    // };
-    protected statusPages: Record<StatusPageRange, StatusPageRenderer> = {
-        '404': (error, { inertia }) => {
-            return inertia.render('Errors/ServerError', {
-                error: error.message,
-                code: error.status,
-            });
-        },
-        '401..403': async (error, { inertia }) => {
-            // session.flash('errors', error.message);
-            return inertia.render('Errors/ServerError', {
-                error: error.message,
-                code: error.status,
-            });           
-        },
-        '500..599': (error, { inertia }) => inertia.render('Errors/ServerError', { error: error.message, code: error.status }),
-    };
+      if (isDbError && ctx.inertia) {
+        return ctx.inertia.render('Errors/postgres_error', {
+          status: 'error',
+          message: 'PostgreSQL database connection failed.',
+          details: {
+            code: error.code,
+            type: error.status
+            // Entferne das .map() auf error.errors, da es oft undefined ist
+          }
+        });
+      }
 
-    // constructor() {
-    //     super(logger);
-    // }
-
-    public async handle(error: any, ctx: HttpContext) {
-        const { response, request, session } = ctx;
-
-        /**
-         * Handle failed authentication attempt
-         */
-        // if (['E_INVALID_AUTH_PASSWORD', 'E_INVALID_AUTH_UID'].includes(error.code)) {
-        //   session.flash('errors', { login: error.message });
-        //   return response.redirect('/login');
-        // }
-        // if ([401].includes(error.status)) {
-        //   session.flash('errors', { login: error.message });
-        //   return response.redirect('/dashboard');
-        // }
-
-        // https://github.com/inertiajs/inertia-laravel/issues/56
-        // let test = response.getStatus(); //200
-        // let header = request.header('X-Inertia'); // true
-        // if (request.header('X-Inertia') && [500, 503, 404, 403, 401, 200].includes(response.getStatus())) {
-        if (request.header('X-Inertia') && [422].includes(error.status)) {
-            // session.flash('errors', error.messages.errors);
-            session.flash('errors', error.messages);
-            return response.redirect().back();
-            // return inertia.render('errors/server_error', {
-            // return inertia.render('errors/server_error', {
-            //     // status: response.getStatus(),
-            //     error: error,
-            // });
-            // ->toResponse($request)
-            // ->setStatusCode($response->status());
-        }
-        // Dynamically change the error templates based on the absence of X-Inertia header
-        // if (!ctx.request.header('X-Inertia')) {
-        //     this.statusPages = {
-        //         '401..403': (error, { view }) => view.render('./errors/unauthorized', { error }),
-        //         '404': (error, { view }) => view.render('./errors/not-found', { error }),
-        //         '500..599': (error, { view }) => view.render('./errors/server-error', { error }),
-        //     };
-        // }
-
-        /**
-         * Forward rest of the exceptions to the parent class
-         */
-        return super.handle(error, ctx);
+      if (ctx.inertia) {
+        return ctx.inertia.render('Errors/ServerError', { error: error.message, code: 500 });
+      }
+      return ctx.response.status(500).send(error.message);
     }
+  };
 
+  public async handle(error: any, ctx: HttpContext) {
     /**
-     * The method is used to report error to the logging service or
-     * the a third party error monitoring service.
-     *
-     * @note You should not attempt to send a response from this method.
+     * WICHTIG: Validierungsfehler (422) NICHT manuell abfangen!
+     * AdonisJS 6 + VineJS + Inertia machen das automatisch. 
+     * Wenn du es hier manuell machst, überschreibst du den Standard-Flow.
      */
-    async report(error: unknown, ctx: HttpContext) {
-        return super.report(error, ctx);
-    }
-}
+
+    return super.handle(error, ctx)
+  }
+}

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<boolean>} 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<boolean> {
-    //     // 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<boolean> {
         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<void> {
+        await this.delete();
+        logger.debug(`Invalidated cache for document ${this.document_id}`);
     }
 }

app/models/activity.ts

@@ -0,0 +1,57 @@
+// app/models/activity.ts
+import { DateTime } from 'luxon';
+import { belongsTo, column } from '@adonisjs/lucid/orm';
+import BaseModel from './base_model.js';
+import type { BelongsTo } from '@adonisjs/lucid/types/relations';
+import User from '#models/user';
+import { SnakeCaseNamingStrategy } from '@adonisjs/lucid/orm';
+
+export default class Activity extends BaseModel {
+    public static namingStrategy = new SnakeCaseNamingStrategy();
+    public static primaryKey = 'id';
+    public static table = 'activities';
+
+    @column({ isPrimary: true })
+    declare id: number;
+
+    @column()
+    declare type: string;
+
+    @column()
+    declare userId: number | null;
+
+    @column()
+    declare subjectType: string | null;
+
+    @column()
+    declare subjectId: number | null;
+
+    @column()
+    declare description: string;
+
+    // Manual JSON (de)serialization keeps this working on SQLite/MySQL.
+    // On Postgres json/jsonb the driver already parses — drop the `consume`
+    // JSON.parse there to avoid double-handling.
+    // @column({
+    //     prepare: (value: Record<string, any> | null) => (value ? JSON.stringify(value) : null),
+    //     consume: (value: string | null) => (value ? JSON.parse(value) : null),
+    // })
+    // declare properties: Record<string, any> | null;
+
+    @column()
+    declare properties: Record<string, any> | null;
+
+    @column.dateTime({ autoCreate: true })
+    declare createdAt: DateTime;
+
+    @column.dateTime({ autoCreate: true, autoUpdate: true })
+    declare updatedAt: DateTime;
+
+    // @belongsTo(() => User)
+    // declare user: BelongsTo<typeof User>;
+
+    @belongsTo(() => User, {
+        foreignKey: 'userId',
+    })
+    declare user: BelongsTo<typeof User>;
+}

app/models/dataset.ts

@@ -5,7 +5,10 @@ import {
     belongsTo,
     hasMany,
     computed,
-    hasOne
+    hasOne,
+    afterCreate,
+    beforeUpdate,
+    afterUpdate,
 } from '@adonisjs/lucid/orm';
 import { DateTime } from 'luxon';
 import dayjs from 'dayjs';
@@ -23,10 +26,11 @@ import DatasetIdentifier from './dataset_identifier.js';
 import Project from './project.js';
 import DocumentXmlCache from './DocumentXmlCache.js';
 import DatasetExtension from '#models/traits/dataset_extension';
-import type { ManyToMany } from "@adonisjs/lucid/types/relations";
-import type { BelongsTo } from "@adonisjs/lucid/types/relations";
-import type { HasMany } from "@adonisjs/lucid/types/relations";
-import type { HasOne } from "@adonisjs/lucid/types/relations";
+import type { ManyToMany } from '@adonisjs/lucid/types/relations';
+import type { BelongsTo } from '@adonisjs/lucid/types/relations';
+import type { HasMany } from '@adonisjs/lucid/types/relations';
+import type { HasOne } from '@adonisjs/lucid/types/relations';
+import ActivityLogger from '#services/activity_logger';
 
 export default class Dataset extends DatasetExtension {
     public static namingStrategy = new SnakeCaseNamingStrategy();
@@ -46,7 +50,7 @@ export default class Dataset extends DatasetExtension {
     @column({ columnName: 'creating_corporation' })
     public creating_corporation: string;
 
-    @column.dateTime({ 
+    @column.dateTime({
         columnName: 'embargo_date',
         serialize: (value: Date | null) => {
             return value ? dayjs(value).format('YYYY-MM-DD') : value;
@@ -60,7 +64,7 @@ export default class Dataset extends DatasetExtension {
     @column({})
     public language: string;
 
-    @column({columnName: 'publish_id'})
+    @column({ columnName: 'publish_id' })
     public publish_id: number | null = null;
 
     @column({})
@@ -266,10 +270,12 @@ export default class Dataset extends DatasetExtension {
         return model || null;
     }
 
-    static async getMax (column: string) {
-        let dataset = await this.query().max(column + ' as max_publish_id').firstOrFail();
+    static async getMax(column: string) {
+        let dataset = await this.query()
+            .max(column + ' as max_publish_id')
+            .firstOrFail();
         return dataset.$extras.max_publish_id;
-      }
+    }
 
     @computed({
         serializeAs: 'remaining_time',
@@ -284,4 +290,34 @@ export default class Dataset extends DatasetExtension {
             return 0;
         }
     }
+
+    // @afterCreate()
+    // static async logUploaded(dataset: Dataset) {
+    //     await dataset.preload('titles');
+
+    //     await ActivityLogger.log({
+    //         type: 'dataset.uploaded',
+    //         description: `New publication uploaded: ${dataset.mainTitle ?? 'Untitled'}`,
+    //         subjectType: 'Dataset',
+    //         subjectId: dataset.id,
+    //     });
+    // }
+
+    @beforeUpdate()
+    static capturePublish(dataset: Dataset) {
+        // $dirty is populated here, before persistence
+        (dataset as any).$becamePublished = dataset.$dirty.status !== undefined && dataset.status === 'published';
+    }
+
+    @afterUpdate()
+    static async logPublished(dataset: Dataset) {
+        if ((dataset as any).$becamePublished) {
+            await ActivityLogger.log({
+                type: 'dataset.published',
+                description: `Publication published: ${dataset.mainTitle}`,
+                subjectType: 'Dataset',
+                subjectId: dataset.id,
+            });
+        }
+    }
 }

app/models/person.ts

@@ -3,7 +3,7 @@ import { DateTime } from 'luxon';
 import dayjs from 'dayjs';
 import Dataset from './dataset.js';
 import BaseModel from './base_model.js';
-import type { ManyToMany } from "@adonisjs/lucid/types/relations";
+import type { ManyToMany } from '@adonisjs/lucid/types/relations';
 
 export default class Person extends BaseModel {
     public static namingStrategy = new SnakeCaseNamingStrategy();
@@ -30,7 +30,7 @@ export default class Person extends BaseModel {
     @column({})
     public lastName: string;
 
-    @column({})
+    @column({ columnName: 'identifier_orcid' })
     public identifierOrcid: string;
 
     @column({})
@@ -64,9 +64,8 @@ export default class Person extends BaseModel {
     // 	return '2023-03-21 08:45:00';
     // }
 
-   
     @computed({
-        serializeAs: 'dataset_count',  
+        serializeAs: 'dataset_count',
     })
     public get datasetCount() {
         const stock = this.$extras.datasets_count; //my pivot column name was "stock"
@@ -79,6 +78,16 @@ export default class Person extends BaseModel {
         return contributor_type;
     }
 
+    @computed({ serializeAs: 'allow_email_contact' })
+    public get allowEmailContact() {
+        // If the datasets relation is missing or empty, return false instead of null.
+        if (!this.datasets || this.datasets.length === 0) {
+            return false;
+        }
+        // Otherwise return the pivot attribute from the first related dataset.
+        return this.datasets[0].$extras?.pivot_allow_email_contact;
+    }
+
     @manyToMany(() => Dataset, {
         pivotForeignKey: 'person_id',
         pivotRelatedForeignKey: 'document_id',
@@ -86,4 +95,34 @@ export default class Person extends BaseModel {
         pivotColumns: ['role', 'sort_order', 'allow_email_contact'],
     })
     public datasets: ManyToMany<typeof Dataset>;
+
+    // public toJSON() {
+    //     const json = super.toJSON();
+
+    //     // Check if this person is loaded through a pivot relationship with sensitive roles
+    //     const pivotRole = this.$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;
+    //         }
+    //     });
+    // }
 }

app/models/types.ts

@@ -0,0 +1,57 @@
+/**
+ * Qs module config
+ */
+type QueryStringConfig = {
+    depth?: number
+    allowPrototypes?: boolean
+    plainObjects?: boolean
+    parameterLimit?: number
+    arrayLimit?: number
+    ignoreQueryPrefix?: boolean
+    delimiter?: RegExp | string
+    allowDots?: boolean
+    charset?: 'utf-8' | 'iso-8859-1' | undefined
+    charsetSentinel?: boolean
+    interpretNumericEntities?: boolean
+    parseArrays?: boolean
+    comma?: boolean
+  }
+/**
+ * Base config used by all types
+ */
+type BodyParserBaseConfig = {
+    encoding: string
+    limit: string | number
+    types: string[]
+  }
+  
+  /**
+   * Body parser config for parsing JSON requests
+   */
+  export type BodyParserJSONConfig = BodyParserBaseConfig & {
+    strict: boolean
+    convertEmptyStringsToNull: boolean
+  }
+  
+  /**
+   * Parser config for parsing form data
+   */
+  export type BodyParserFormConfig = BodyParserBaseConfig & {
+    queryString: QueryStringConfig
+    convertEmptyStringsToNull: boolean
+  }
+  
+  /**
+   * Parser config for parsing raw body (untouched)
+   */
+  export type BodyParserRawConfig = BodyParserBaseConfig
+/**
+ * Body parser config for all supported form types
+ */
+export type BodyParserConfig = {
+    allowedMethods: string[]
+    json: BodyParserJSONConfig
+    form: BodyParserFormConfig
+    raw: BodyParserRawConfig
+    multipart: BodyParserMultipartConfig
+  }

app/models/user.ts

@@ -14,6 +14,7 @@ import type { ManyToMany } from '@adonisjs/lucid/types/relations';
 import type { HasMany } from '@adonisjs/lucid/types/relations';
 import { compose } from '@adonisjs/core/helpers';
 import BackupCode from './backup_code.js';
+import Activity from './activity.js';
 
 const AuthFinder = withAuthFinder(() => hash.use('laravel'), {
     uids: ['email'],
@@ -89,24 +90,11 @@ export default class User extends compose(BaseModel, AuthFinder) {
     @column({})
     public avatar: string;
 
-    // @hasOne(() => TotpSecret, {
-    //     foreignKey: 'user_id',
-    // })
-    // public totp_secret: HasOne<typeof TotpSecret>;
-
-    // @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',
@@ -124,6 +112,11 @@ export default class User extends compose(BaseModel, AuthFinder) {
     })
     public backupcodes: HasMany<typeof BackupCode>;
 
+    @hasMany(() => Activity, {
+        foreignKey: 'user_id',
+    })
+    public activities: HasMany<typeof Activity>;
+
     @computed({
         serializeAs: 'is_admin',
     })
@@ -142,7 +135,9 @@ 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<BackupCode[]> {

app/services/activity_logger.ts

@@ -0,0 +1,27 @@
+// app/services/activity_logger.ts
+import Activity from '#models/activity'
+
+interface LogOptions {
+  type: string
+  description: string
+  userId?: number | null
+  subjectType?: string | null
+  subjectId?: number | string | null
+  properties?: Record<string, any>
+}
+
+export default class ActivityLogger {
+  static async log(options: LogOptions): Promise<void> {
+    await Activity.create({
+      type: options.type,
+      description: options.description,
+      userId: options.userId ?? null,
+      subjectType: options.subjectType ?? null,
+      subjectId: options.subjectId != null ? Number(options.subjectId) : null,
+      properties: options.properties ?? null,
+    })
+
+    // Invalidate the cache if you add one (see Redis section).
+    // await redis.del('activities:recent')
+  }
+}

app/services/validation_service.ts

@@ -0,0 +1,54 @@
+import app from '@adonisjs/core/services/app'
+import { errors } from '@vinejs/vine'
+
+/**
+ * The ValidationService handles manual construction of validation errors
+ * that are compatible with the VanillaErrorReporter and AdonisJS Session.
+ */
+export class ValidationService {
+  /**
+   * Builds a validation error in the array-of-objects format without throwing it.
+   * Use this when you need the error object itself, e.g. multipart.abort(error).
+   */
+  make(field: string, message: string, rule: string = 'manual') {
+    return new errors.E_VALIDATION_ERROR([
+      {
+        field,
+        message,
+        rule,
+      },
+    ])
+  }
+
+  /**
+   * Throws a manual validation error in the array-of-objects format
+   * which prevents the ".reduce is not a function" error in the session.
+   */
+  throw(field: string, message: string, rule: string = 'manual') {
+    throw this.make(field, message, rule)
+  }
+
+  /**
+   * Throws multiple manual validation errors at once.
+   */
+  throwMany(errorObjects: Array<{ field: string; message: string; rule?: string }>) {
+    throw new errors.E_VALIDATION_ERROR(
+      errorObjects.map((err) => ({
+        field: err.field,
+        message: err.message,
+        rule: err.rule || 'manual',
+      }))
+    )
+  }
+}
+
+/**
+ * Initialize and export the singleton instance
+ */
+let validation: ValidationService
+
+await app.booted(async () => {
+  validation = await app.container.make(ValidationService)
+})
+
+export { validation as default }

app/utils/utility-functions.ts

@@ -1,3 +1,16 @@
+import { join, isAbsolute } from 'node:path';
+import type { BodyParserConfig } from '#models/types';
+import { createId } from '@paralleldrive/cuid2';
+import { tmpdir } from 'node:os';
+import config from '@adonisjs/core/services/config';
+import Dataset from '#models/dataset';
+import { TransactionClientContract } from '@adonisjs/lucid/types/database';
+import Person from '#models/person';
+
+interface Dictionary {
+    [index: string]: string;
+}
+
 export function sum(a: number, b: number): number {
     return a + b;
 }
@@ -24,3 +37,93 @@ export function preg_match(regex: RegExp, str: string) {
     const result: boolean = regex.test(str);
     return result;
 }
+
+/**
+ * Returns the tmp path for storing the files temporarly
+ */
+export function getTmpPath(config: BodyParserConfig['multipart']): string {
+    if (typeof config.tmpFileName === 'function') {
+        const tmpPath = config.tmpFileName();
+        return isAbsolute(tmpPath) ? tmpPath : join(tmpdir(), tmpPath);
+    }
+
+    return join(tmpdir(), createId());
+}
+/**
+ * Returns config for a given type
+ */
+export function getConfigFor<K extends keyof BodyParserConfig>(type: K): BodyParserConfig[K] {
+    const bodyParserConfig: BodyParserConfig = config.get('bodyparser');
+    const configType = bodyParserConfig[type];
+    return configType;
+}
+
+export function parseBytesSize(size: string): number {
+    const units: Record<string, number> = {
+        kb: 1024,
+        mb: 1024 * 1024,
+        gb: 1024 * 1024 * 1024,
+        tb: 1024 * 1024 * 1024 * 1024,
+    };
+
+    const match = size.match(/^(\d+)(kb|mb|gb|tb)$/i); // Regex to match size format
+
+    if (!match) {
+        throw new Error('Invalid size format');
+    }
+
+    const [, value, unit] = match;
+    return parseInt(value) * units[unit.toLowerCase()];
+}
+
+// Helper function to format bytes as human-readable text
+
+export function formatBytes(bytes: number): string {
+    if (bytes === 0) return '0 Bytes';
+    const k = 1024;
+    const sizes = ['Bytes', 'KB', 'MB', 'GB', 'TB'];
+    const i = Math.floor(Math.log(bytes) / Math.log(k));
+    return parseFloat((bytes / Math.pow(k, i)).toFixed(2)) + ' ' + sizes[i];
+}
+
+export async function savePersons(dataset: Dataset, persons: any[], role: string, trx: TransactionClientContract) {
+    for (const [key, person] of persons.entries()) {
+        const pivotData = {
+            role: role,
+            sort_order: key + 1,
+            allow_email_contact: false,
+            ...extractPivotAttributes(person), // Merge pivot attributes here
+        };
+
+        if (person.id !== undefined) {
+            await dataset
+                .useTransaction(trx)
+                .related('persons')
+                .attach({
+                    [person.id]: pivotData,
+                });
+        } else {
+            const dataPerson = new Person();
+            dataPerson.fill(person);
+            await dataset.useTransaction(trx).related('persons').save(dataPerson, false, pivotData);
+        }
+    }
+}
+
+// Helper function to extract pivot attributes from a person object
+function extractPivotAttributes(person: any) {
+    const pivotAttributes: Dictionary = {};
+    for (const key in person) {
+        if (key.startsWith('pivot_')) {
+            // pivotAttributes[key] = person[key];
+            const cleanKey = key.replace('pivot_', ''); // Remove 'pivot_' prefix
+            pivotAttributes[cleanKey] = person[key];
+        }
+    }
+    return pivotAttributes;
+}
+
+// in #app/utils/utility-functions
+export function errorMessage(error: unknown): string {
+    return error instanceof Error ? error.message : String(error);
+}

app/validators/dataset.ts

@@ -40,7 +40,8 @@ export const createDatasetValidator = vine.compile(
                         .translatedLanguage({ mainLanguageField: 'language', typeField: 'type' }),
                 }),
             )
-            .minLength(1),
+            // .minLength(2)
+            .arrayContainsTypes({ typeA: 'main', typeB: 'translated' }),
         descriptions: vine
             .array(
                 vine.object({
@@ -54,7 +55,8 @@ export const createDatasetValidator = vine.compile(
                         .translatedLanguage({ mainLanguageField: 'language', typeField: 'type' }),
                 }),
             )
-            .minLength(1),
+            // .minLength(1),
+            .arrayContainsTypes({ typeA: 'abstract', typeB: 'translated' }),
         authors: vine
             .array(
                 vine.object({
@@ -65,8 +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)
@@ -81,9 +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')
@@ -187,7 +191,8 @@ export const updateDatasetValidator = vine.compile(
                         .translatedLanguage({ mainLanguageField: 'language', typeField: 'type' }),
                 }),
             )
-            .minLength(1),
+            // .minLength(2)
+            .arrayContainsTypes({ typeA: 'main', typeB: 'translated' }),
         descriptions: vine
             .array(
                 vine.object({
@@ -201,7 +206,7 @@ export const updateDatasetValidator = vine.compile(
                         .translatedLanguage({ mainLanguageField: 'language', typeField: 'type' }),
                 }),
             )
-            .minLength(1),
+            .arrayContainsTypes({ typeA: 'abstract', typeB: 'translated' }),
         authors: vine
             .array(
                 vine.object({
@@ -212,8 +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)
@@ -228,8 +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)),
                 }),
             )
@@ -303,21 +310,149 @@ 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(),
     }),
 );
 
-// files: schema.array([rules.minLength(1)]).members(
-//     schema.file({
-//         size: '512mb',
-//         extnames: ['jpg', 'gif', 'png', 'tif', 'pdf', 'zip', 'fgb', 'nc', 'qml', 'ovr', 'gpkg', 'gml', 'gpx', 'kml', 'kmz', 'json'],
-//     }),
-// ),
+export const updateEditorDatasetValidator = vine.compile(
+    vine.object({
+        // first step
+        language: vine
+            .string()
+            .trim()
+            .regex(/^[a-zA-Z0-9]+$/),
+        licenses: vine.array(vine.number()).minLength(1), // define at least one license for the new dataset
+        rights: vine.string().in(['true']),
+        // second step
+        type: vine.string().trim().minLength(3).maxLength(255),
+        creating_corporation: vine.string().trim().minLength(3).maxLength(255),
+        titles: vine
+            .array(
+                vine.object({
+                    value: vine.string().trim().minLength(3).maxLength(255),
+                    type: vine.enum(Object.values(TitleTypes)),
+                    language: vine
+                        .string()
+                        .trim()
+                        .minLength(2)
+                        .maxLength(255)
+                        .translatedLanguage({ mainLanguageField: 'language', typeField: 'type' }),
+                }),
+            )
+            // .minLength(2)
+            .arrayContainsTypes({ typeA: 'main', typeB: 'translated' }),
+        descriptions: vine
+            .array(
+                vine.object({
+                    value: vine.string().trim().minLength(3).maxLength(2500),
+                    type: vine.enum(Object.values(DescriptionTypes)),
+                    language: vine
+                        .string()
+                        .trim()
+                        .minLength(2)
+                        .maxLength(255)
+                        .translatedLanguage({ mainLanguageField: 'language', typeField: 'type' }),
+                }),
+            )
+            .arrayContainsTypes({ typeA: 'abstract', typeB: 'translated' }),
+        authors: vine
+            .array(
+                vine.object({
+                    email: vine
+                        .string()
+                        .trim()
+                        .maxLength(255)
+                        .email()
+                        .normalizeEmail()
+                        .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }),
+                    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)
+            .distinct('email'),
+        contributors: vine
+            .array(
+                vine.object({
+                    email: vine
+                        .string()
+                        .trim()
+                        .maxLength(255)
+                        .email()
+                        .normalizeEmail()
+                        .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }),
+                    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)),
+                }),
+            )
+            .distinct('email')
+            .optional(),
+        // third step
+        project_id: vine.number().optional(),
+        // embargo_date: schema.date.optional({ format: 'yyyy-MM-dd' }, [rules.after(10, 'days')]),
+        embargo_date: vine
+            .date({
+                formats: ['YYYY-MM-DD'],
+            })
+            .afterOrEqual((_field) => {
+                return dayjs().add(10, 'day').format('YYYY-MM-DD');
+            })
+            .optional(),
+        coverage: vine.object({
+            x_min: vine.number(),
+            x_max: vine.number(),
+            y_min: vine.number(),
+            y_max: vine.number(),
+            elevation_absolut: vine.number().positive().optional(),
+            elevation_min: vine.number().positive().optional().requiredIfExists('elevation_max'),
+            elevation_max: vine.number().positive().optional().requiredIfExists('elevation_min'),
+            // type: vine.enum(Object.values(DescriptionTypes)),
+            depth_absolut: vine.number().negative().optional(),
+            depth_min: vine.number().negative().optional().requiredIfExists('depth_max'),
+            depth_max: vine.number().negative().optional().requiredIfExists('depth_min'),
+            time_abolute: vine.date({ formats: { utc: true } }).optional(),
+            time_min: vine
+                .date({ formats: { utc: true } })
+                .beforeField('time_max')
+                .optional()
+                .requiredIfExists('time_max'),
+            time_max: vine
+                .date({ formats: { utc: true } })
+                .afterField('time_min')
+                .optional()
+                .requiredIfExists('time_min'),
+        }),
+        references: vine
+            .array(
+                vine.object({
+                    value: vine.string().trim().minLength(3).maxLength(255).validateReference({ typeField: 'type' }),
+                    type: vine.enum(Object.values(ReferenceIdentifierTypes)),
+                    relation: vine.enum(Object.values(RelationTypes)),
+                    label: vine.string().trim().minLength(2).maxLength(255),
+                }),
+            )
+            .optional(),
+        subjects: vine
+            .array(
+                vine.object({
+                    value: vine.string().trim().minLength(3).maxLength(255),
+                    // pivot_contributor_type: vine.enum(Object.keys(ContributorTypes)),
+                    language: vine.string().trim().minLength(2).maxLength(255),
+                }),
+            )
+            .minLength(3)
+            .distinct('value'),
+    }),
+);
 
 let messagesProvider = new SimpleMessagesProvider({
     'minLength': '{{ field }} must be at least {{ min }} characters long',
@@ -369,8 +504,10 @@ 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')}`,
 });
 
 createDatasetValidator.messagesProvider = messagesProvider;
 updateDatasetValidator.messagesProvider = messagesProvider;
+updateEditorDatasetValidator.messagesProvider = messagesProvider;
 // export default createDatasetValidator;

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-]+$/),
+        name: vine
+            .string()
+            .trim()
+            .minLength(3)
+            .maxLength(255)
+            .regex(/^[a-zA-Z0-9äöüßÄÖÜ\s-]+$/),
+        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-Z0-9äöüßÄÖÜ\s-]+$/),
+         description: vine.string().trim().maxLength(255).minLength(5).optional(),
+    }),
+);

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
     }),
 );
 

app/validators/user.ts

@@ -16,7 +16,7 @@ export const createUserValidator = vine.compile(
         first_name: vine.string().trim().minLength(3).maxLength(255),
         last_name: vine.string().trim().minLength(3).maxLength(255),
         email: vine.string().maxLength(255).email().normalizeEmail().isUnique({ table: 'accounts', column: 'email' }),
-        password: vine.string().confirmed().trim().minLength(3).maxLength(60),
+        new_password: vine.string().confirmed({ confirmationField: 'password_confirmation' }).trim().minLength(3).maxLength(60),
         roles: vine.array(vine.number()).minLength(1), // define at least one role for the new user
     }),
 );
@@ -42,7 +42,7 @@ export const updateUserValidator = vine.withMetaData<{ objId: number }>().compil
             .email()
             .normalizeEmail()
             .isUnique({ table: 'accounts', column: 'email', whereNot: (field) => field.meta.objId }),
-        password: vine.string().confirmed().trim().minLength(3).maxLength(60).optional(),
+        new_password: vine.string().confirmed({ confirmationField: 'password_confirmation' }).trim().minLength(3).maxLength(60).optional(),
         roles: vine.array(vine.number()).minLength(1), // define at least one role for the new user
     }),
 );

app/validators/vanilla_error_reporter.ts

@@ -1,203 +1,50 @@
-// import { ValidationError } from '../errors/validation_error.js';
-import { errors } from '@vinejs/vine';
-import type { ErrorReporterContract, FieldContext } from '@vinejs/vine/types';
-import string from '@poppinss/utils/string';
+import { errors } from '@vinejs/vine'
+import type { ErrorReporterContract, FieldContext } from '@vinejs/vine/types'
 
 /**
- * Shape of the Vanilla error node
- */
-export type VanillaErrorNode = {
-    [field: string]: string[];
-};
-export interface MessagesBagContract {
-    get(pointer: string, rule: string, message: string, arrayExpressionPointer?: string, args?: any): string;
-}
-/**
- * Message bag exposes the API to pull the most appropriate message for a
- * given validation failure.
- */
-export class MessagesBag implements MessagesBagContract {
-    messages: Message;
-    wildCardCallback;
-    constructor(messages: string[]) {
-        this.messages = messages;
-        this.wildCardCallback = typeof this.messages['*'] === 'function' ? this.messages['*'] : undefined;
-    }
-    /**
-     * Transform message by replace placeholders with runtime values
-     */
-    transform(message: any, rule: string, pointer: string, args: any) {
-        /**
-         * No interpolation required
-         */
-        if (!message.includes('{{')) {
-            return message;
-        }
-        return string.interpolate(message, { rule, field: pointer, options: args || {} });
-    }
-    /**
-     * Returns the most appropriate message for the validation failure.
-     */
-    get(pointer: string, rule: string, message: string, arrayExpressionPointer: string, args: any) {
-        let validationMessage = this.messages[`${pointer}.${rule}`];
-        /**
-         * Fetch message for the array expression pointer if it exists
-         */
-        if (!validationMessage && arrayExpressionPointer) {
-            validationMessage = this.messages[`${arrayExpressionPointer}.${rule}`];
-        }
-        /**
-         * Fallback to the message for the rule
-         */
-        if (!validationMessage) {
-            validationMessage = this.messages[rule];
-        }
-        /**
-         * Transform and return message. The wildcard callback is invoked when custom message
-         * is not defined
-         */
-        return validationMessage
-            ? this.transform(validationMessage, rule, pointer, args)
-            : this.wildCardCallback
-              ? this.wildCardCallback(pointer, rule, arrayExpressionPointer, args)
-              : message;
-    }
-}
-/**
- * Shape of the error message collected by the SimpleErrorReporter
- */
-type SimpleError = {
-    message: string;
-    field: string;
-    rule: string;
-    index?: number;
-    meta?: Record<string, any>;
-};
-export interface Message {
-    [key: string]: any;
-}
-/**
- * Simple error reporter collects error messages as an array of object.
- * Each object has following properties.
- *
- * - message: string
- * - field: string
- * - rule: string
- * - index?: number (in case of an array member)
- * - args?: Record<string, any>
+ * Der VanillaErrorReporter sammelt Validierungsfehler im Standardformat,
+ * damit die AdonisJS Session-Middleware sie korrekt verarbeiten (reducen) kann.
  */
 export class VanillaErrorReporter implements ErrorReporterContract {
-    // private messages;
-    // private bail;
+  /**
+   * Boolean, um zu prüfen, ob Fehler vorliegen
+   */
+  hasErrors: boolean = false
+
+  /**
+   * Sammlung der Fehler als Array (erforderlich für AdonisJS 6 Session)
+   */
+  errors: any[] = []
+
+  /**
+   * Diese Methode wird von VineJS für jeden Validierungsfehler aufgerufen
+   */
+  report(
+    message: string,
+    rule: string,
+    field: FieldContext,
+    meta?: Record<string, any>
+  ): void {
+    this.hasErrors = true
+
     /**
-     * Boolean to know one or more errors have been reported
-     */
-    hasErrors: boolean = false;
-    /**
-     * Collection of errors
-     */
-    // errors: SimpleError[] = [];
-    errors: Message = {};
-    /**
-     * Report an error.
+     * Wir pushen das Objekt in das Array. 
+     * Das Feld 'field' erhält den vollständigen Pfad (z.B. "user.email").
      */
+    this.errors.push({
+      message,
+      rule,
+      field: field.getFieldPath(),
+      ...meta,
+    });
+  }
 
-    // constructor(messages: MessagesBagContract) {
-    //     this.messages = messages;
-    // }
-
-    report(message: string, rule: string, field: FieldContext, meta?: Record<string, any> | undefined): void {
-        // const error: SimpleError = {
-        //     message,
-        //     rule,
-        //     field: field.getFieldPath()
-        //   };
-        //   if (meta) {
-        //     error.meta = meta;
-        //   }
-        //   if (field.isArrayMember) {
-        //     error.index = field.name as number;
-        //   }
-        //   this.errors.push(error);
-        this.hasErrors = true;
-        // if (this.errors[field.getFieldPath()]) {
-        //     this.errors[field.getFieldPath()]?.push(message);
-        // } else {
-        //     this.errors[field.getFieldPath()] = [message];
-        // }
-        const error: SimpleError = {
-            message,
-            rule,
-            field: field.getFieldPath(), // ?field.wildCardPath.split('.')[0]  : field.getFieldPath(),
-        };
-        //   field: 'titles.0.value'
-        //   message: 'Main Title is required'
-        //   rule: 'required' "required"
-
-        if (meta) {
-            error.meta = meta;
-        }
-        //   if (field.isArrayMember) {
-        //     error.index = field.name;
-        //   }
-        this.hasErrors = true;
-
-        // var test = field.getFieldPath();
-
-        //   this.errors.push(error);
-        // if (this.errors[error.field]) {
-        //     this.errors[error.field]?.push(message);
-        // }
-        if (field.isArrayMember) {
-            // Check if the field has wildCardPath and if the error field already exists
-            if (this.errors[error.field]) {
-                // Do nothing, as we don't want to push further messages
-            } else {
-                // If the error field already exists, push the message
-                if (this.errors[error.field]) {
-                    this.errors[error.field].push(message);
-                } else {
-                    this.errors[error.field] = [message];
-                }
-            }
-        } else {
-            if (this.errors[error.field]) {
-                this.errors[error.field]?.push(message);
-            } else {
-                this.errors[error.field] = [message];
-            }
-        }
-
-         // } else {
-        //     // normal field
-        //     this.errors[field.field] = [message];
-        // }
-
-        /**
-         * Collecting errors as per the JSONAPI spec
-         */
-        // this.errors.push({
-        //     code: rule,
-        //     detail: message,
-        //     source: {
-        //         pointer: field.wildCardPath,
-        //     },
-        //     ...(meta ? { meta } : {}),
-        // });
-
-        //   let pointer: string = field.wildCardPath as string; //'display_name'
-        // //   if (field.isArrayMember) {
-        // //     this.errors[pointer] = field.name;
-        // //   }
-        //   this.errors[pointer] = this.errors[pointer] || [];
-        // //   this.errors[pointer].push(message);
-        //   this.errors[pointer].push(this.messages.get(pointer, rule, message, arrayExpressionPointer, args));
-    }
-    /**
-     * Returns an instance of the validation error
-     */
-    createError() {
-        return new errors.E_VALIDATION_ERROR(this.errors);
-    }
-}
-export {};
+  /**
+   * Erstellt die eigentliche Exception.
+   * Da 'this.errors' nun ein Array ist, funktioniert .reduce() 
+   * in der Session-Middleware reibungslos.
+   */
+  createError() {
+    return new errors.E_VALIDATION_ERROR(this.errors);
+  }
+}

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
+# LocalSocketGroup node  # Changed from 'clamav'
+# User node              # Changed from 'clamav' - clamd runs as clamav user

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('🔍 Detecting missing cross-references...');
+        this.logger.info(`📋 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}) → 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('💡 Run with --fix flag to automatically create missing cross-references');
+                if (this.publish_id) {
+                    this.logger.info(`🎯 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<void> {
+        try {
+            await AppConfig.updateOrCreate(
+                {
+                    appid: 'commands',
+                    configkey: 'missing_cross_references_count',
+                },
+                {
+                    configvalue: count.toString(),
+                },
+            );
+
+            this.logger.info(`📊 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<MissingCrossReference[]> {
+        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('📊 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(`🔗 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(`📈 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(`⏭️  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(`⚠️  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(`⚠️  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(`✅ 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<boolean> {
+        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', `%${sourceDatasetIdentifier}`) // Basic check to ensure it points back to source dataset
+            .first();
+
+        return !!reverseReference;
+    }
+
+    private getReverseRelation(relation: string): string | null {
+        const relationMap: Record<string, string> = {
+            IsNewVersionOf: 'IsPreviousVersionOf',
+            IsPreviousVersionOf: 'IsNewVersionOf',
+            IsVariantFormOf: 'IsOriginalFormOf',
+            IsOriginalFormOf: 'IsVariantFormOf',
+            Continues: 'IsContinuedBy',
+            IsContinuedBy: 'Continues',
+            HasPart: 'IsPartOf',
+            IsPartOf: 'HasPart',
+        };
+
+        // Only return reverse relation if it exists in our map, otherwise return null
+        return relationMap[relation] || null;
+    }
+
+    private printMissingReferencesList(missingReferences: MissingCrossReference[]) {
+        console.log('┌─────────────────────────────────────────────────────────────────────────────────┐');
+        console.log('│                         MISSING CROSS-REFERENCES REPORT                        │');
+        console.log('│                     (Published Datasets Only - Filtered Relations)            │');
+        console.log('└─────────────────────────────────────────────────────────────────────────────────┘');
+        console.log();
+
+        missingReferences.forEach((missing, index) => {
+            console.log(
+                `${index + 1}. Dataset ${missing.sourceDatasetId} (Publish ID: ${missing.sourcePublishId} Identifier: ${missing.sourceDoi}) 
+                ${missing.relation} Dataset ${missing.targetDatasetId} (Publish ID: ${missing.targetPublishId} Identifier: ${missing.targetDoi})`,
+            );
+            console.log(`   ├─ Current relation: "${missing.relation}"`);
+            console.log(`   ├─ Missing reverse relation: "${missing.reverseRelation}"`);
+            console.log(`   ├─ Reference type: ${missing.referenceType}`);
+            console.log(`   └─ DOI/URL: ${missing.doi}`);
+            console.log();
+        });
+
+        console.log('┌─────────────────────────────────────────────────────────────────────────────────┐');
+        console.log(`│ SUMMARY: ${missingReferences.length} missing reverse reference(s) detected                      │`);
+        console.log(`│ Processed relations: ${this.ALLOWED_RELATIONS.join(', ')}                           │`);
+        console.log('└─────────────────────────────────────────────────────────────────────────────────┘');
+    }
+
+    private async fixMissingReferences(missingReferences: MissingCrossReference[]) {
+        this.logger.info('🔧 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(`⚠️  Source dataset ${missing.sourceDatasetId} not found or not published, skipping...`);
+                    errorCount++;
+                    continue;
+                }
+
+                if (!targetDataset) {
+                    this.logger.warning(`⚠️  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(`🔗 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 ${DateTime.now().toISO()} to fix missing bidirectional reference.`;
+
+                // Save the new reverse reference
+                // Also save 'server_date_modified' on target dataset to trigger any downstream updates (e.g. search index)
+                targetDataset.server_date_modified = DateTime.now();
+                await targetDataset.save();
+
+                await reverseReference.save();
+                fixedCount++;
+
+                if (this.verbose) {
+                    this.logger.info(
+                        `✅ [${index + 1}/${missingReferences.length}] Created reverse reference: Dataset ${missing.sourceDatasetId} -> ${missing.targetDatasetId} (${missing.reverseRelation})`,
+                    );
+                } else if ((index + 1) % 10 === 0) {
+                    this.logger.info(`📈 Fixed ${fixedCount}/${missingReferences.length} references...`);
+                }
+            } catch (error) {
+                this.logger.error(
+                    `❌ Error creating reverse reference for datasets ${missing.targetDatasetId} -> ${missing.sourceDatasetId}:`,
+                    error,
+                );
+                errorCount++;
+            }
+        }
+
+        this.logger.info(`📊 Fix completed: ${fixedCount} created, ${errorCount} errors`);
+    }
+}

commands/fix_version_related_ids.ts

@@ -0,0 +1,189 @@
+/*
+|--------------------------------------------------------------------------
+| node ace make:command fix-version-related-ids
+| DONE:    create commands/fix_version_related_ids.ts
+|--------------------------------------------------------------------------
+| Repairs the `related_document_id` foreign key on version references
+| (IsNewVersionOf / IsPreviousVersionOf, both directions).
+|
+| The DOI stored in `value` is the reliable link; `related_document_id`
+| is frequently NULL or self-referential. This command resolves the target
+| dataset via its DOI and sets `related_document_id` accordingly, correcting
+| both NULL and wrong-but-non-null values.
+|
+| Examples:
+|   node ace fix:version-related-ids                 // dry run, all datasets
+|   node ace fix:version-related-ids --verbose       // dry run with per-row detail
+|   node ace fix:version-related-ids --fix           // apply changes
+|   node ace fix:version-related-ids --fix -p 226    // apply, only refs owned by publish_id 226
+*/
+import { BaseCommand, flags } from '@adonisjs/core/ace';
+import type { CommandOptions } from '@adonisjs/core/types/ace';
+import Dataset from '#models/dataset';
+import DatasetReference from '#models/dataset_reference';
+
+export default class FixVersionRelatedIds extends BaseCommand {
+    static commandName = 'fix:version-related-ids';
+    static description =
+        'Backfill/repair related_document_id on IsNewVersionOf / IsPreviousVersionOf references by resolving the target dataset via its DOI';
+
+    public static needsApplication = true;
+
+    @flags.boolean({ alias: 'f', description: 'Apply changes. Without this flag the command runs as a dry run.' })
+    public fix: boolean = false;
+
+    @flags.boolean({ alias: 'v', description: 'Verbose output (per-reference detail)' })
+    public verbose: boolean = false;
+
+    @flags.number({ alias: 'p', description: 'Only process references owned by this publish_id' })
+    public publish_id?: number;
+
+    public static options: CommandOptions = {
+        startApp: true,
+        staysAlive: false,
+    };
+
+    // Only the version relations, both directions.
+    private readonly VERSION_RELATIONS = ['IsNewVersionOf', 'IsPreviousVersionOf'];
+
+    async run() {
+        this.logger.info(`🔍 Scanning ${this.VERSION_RELATIONS.join(' / ')} references...`);
+        this.logger.info(this.fix ? '✏️  Mode: APPLY (changes will be written)' : '👀 Mode: DRY RUN (no changes written)');
+        if (typeof this.publish_id === 'number') {
+            this.logger.info(`🎯 Filtering by owning publish_id: ${this.publish_id}`);
+        }
+
+        try {
+            const query = DatasetReference.query()
+                .whereIn('relation', this.VERSION_RELATIONS)
+                .whereIn('type', ['DOI', 'URL'])
+                .where((q) => {
+                    q.where('value', 'like', '%doi.org/10.24341/tethys.%').orWhere('value', 'like', '%tethys.at/dataset/%');
+                });
+
+            // Restrict to references owned by a specific dataset (by publish_id), if requested.
+            if (typeof this.publish_id === 'number') {
+                query.whereHas('dataset', (d) => d.where('publish_id', this.publish_id as number));
+            }
+
+            const refs = await query.exec();
+            this.logger.info(`🔗 Found ${refs.length} version reference(s) to inspect`);
+
+            let alreadyCorrect = 0;
+            let filledFromNull = 0;
+            let correctedWrong = 0;
+            let unresolved = 0;
+
+            for (const ref of refs) {
+                const target = await this.resolveTarget(ref);
+
+                if (!target) {
+                    unresolved++;
+                    if (this.verbose) {
+                        this.logger.warning(`⚠️  Reference ${ref.id}: could not resolve target (value: ${ref.value})`);
+                    }
+                    continue;
+                }
+
+                // Never let a reference point at its own owning document.
+                if (target.id === ref.document_id) {
+                    unresolved++;
+                    if (this.verbose) {
+                        this.logger.warning(
+                            `⚠️  Reference ${ref.id}: target resolves to its own document (${ref.document_id}); skipping self-link`,
+                        );
+                    }
+                    continue;
+                }
+
+                if (ref.related_document_id === target.id) {
+                    alreadyCorrect++;
+                    continue;
+                }
+
+                const previous = ref.related_document_id;
+                const wasNull = previous === null || previous === undefined;
+
+                if (this.fix) {
+                    ref.related_document_id = target.id;
+                    await ref.save();
+                }
+
+                if (wasNull) {
+                    filledFromNull++;
+                } else {
+                    correctedWrong++;
+                }
+
+                if (this.verbose) {
+                    const action = this.fix ? 'Updated' : '📝 Would update';
+                    this.logger.info(
+                        `${action} reference ${ref.id} (doc ${ref.document_id}, ${ref.relation}): ` +
+                        `related_document_id ${previous ?? 'NULL'} → ${target.id} (publish_id ${target.publish_id})`,
+                    );
+                }
+            }
+
+            this.logger.info('────────────────────────────────────────');
+            this.logger.info(`✔️  Already correct:       ${alreadyCorrect}`);
+            this.logger.info(`➕ Filled from NULL:       ${filledFromNull}`);
+            this.logger.info(`🔧 Corrected wrong value:  ${correctedWrong}`);
+            this.logger.info(`⚠️  Unresolved/skipped:    ${unresolved}`);
+            this.logger.info('────────────────────────────────────────');
+
+            const changes = filledFromNull + correctedWrong;
+            if (!this.fix && changes > 0) {
+                this.logger.info(`💡 Dry run only. Re-run with --fix to write ${changes} change(s).`);
+            } else if (this.fix) {
+                this.logger.success(`Done. ${changes} reference(s) updated.`);
+            } else {
+                this.logger.success('Nothing to change — all version references already linked correctly.');
+            }
+        } catch (error) {
+            this.logger.error('Error fixing version related_document_id values:', error);
+            process.exit(1);
+        }
+    }
+
+    /**
+     * Resolve the dataset a version reference points to.
+     * Prefers the DOI in `value` (reliable); falls back to a tethys publish_id URL.
+     */
+    private async resolveTarget(ref: DatasetReference): Promise<Dataset | null> {
+        const doi = this.normalizeDoi(ref.value);
+        if (doi) {
+            const byDoi = await Dataset.query()
+                .whereHas('identifier', (q) => q.where('value', doi))
+                .first();
+            if (byDoi) return byDoi;
+        }
+
+        const publishId = this.extractPublishId(ref.value);
+        if (publishId) {
+            const byPublishId = await Dataset.query().where('publish_id', publishId).first();
+            if (byPublishId) return byPublishId;
+        }
+
+        return null;
+    }
+
+    /**
+     * Strip the resolver prefix so a reference value like
+     * "https://doi.org/10.24341/tethys.108.2" matches the identifier
+     * table value "10.24341/tethys.108.2". Returns null if it isn't a DOI.
+     */
+    private normalizeDoi(value: string | null): string | null {
+        if (!value) return null;
+        const cleaned = value
+            .trim()
+            .replace(/^https?:\/\/(dx\.)?doi\.org\//i, '')
+            .replace(/^doi:/i, '');
+        return /^10\.\d{4,}\//.test(cleaned) ? cleaned : null;
+    }
+
+    private extractPublishId(value: string | null): number | null {
+        if (!value) return null;
+        const urlMatch = value.match(/tethys\.at\/dataset\/(\d+)/);
+        return urlMatch ? parseInt(urlMatch[1], 10) : null;
+    }
+}

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<boolean> {
+        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<void> {
         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<XMLBuilder | null> {
-        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) {

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<Dataset[]> - Array of datasets that need updates
+     */
+    // private async processChunk(datasets: Dataset[]): Promise<Dataset[]> {
+    //     // 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<Dataset | null> =>
+    //                 // 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<Dataset[]> {
+        // 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<Dataset | null> => result.status === 'fulfilled' && result.value !== null)
+            .map((result) => result.value!);
+    }
+
+    private async getDatasets(page: number, chunkSize: number): Promise<Dataset[]> {
+        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<boolean> {
+        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<never> {
+        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 <publish_id>`);
+    }
+
+    private async showVerboseOutput(updatableDatasets: Dataset[]): Promise<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`);
+
+        for (const dataset of updatableDatasets) {
+            await this.showDatasetDetails(dataset);
+        }
+
+        console.log(`\nSummary: ${updatableDatasets.length} datasets need updates`);
+    }
+
+    private async showDatasetDetails(dataset: Dataset): Promise<void> {
+        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(`┌─ Dataset ${dataset.publish_id} ───────────────────────────────────────────────────────────────`);
+            console.log(`│ Title:               ${dataset.mainTitle || 'Untitled'}`);
+            console.log(`│ DOI:                 ${doiValue}`);
+            console.log(`│ DOI State:           ${doiState || 'Unknown'}`);
+            console.log(`│ Dataset Modified:    ${datasetModified ? datasetModified.toISO() : 'N/A'}`);
+            console.log(`│ DOI Modified:        ${doiLastModified ? DateTime.fromJSDate(doiLastModified).toISO() : 'N/A'}`);
+            console.log(`│ Status:              NEEDS UPDATE`);
+            console.log(`└─────────────────────────────────────────────────────────────────────────────────────────────\n`);
+        } catch (error) {
+            console.log(`┌─ Dataset ${dataset.publish_id} ───────────────────────────────────────────────────────────────`);
+            console.log(`│ Title:               ${dataset.mainTitle || 'Untitled'}`);
+            console.log(`│ DOI:                 ${dataset.identifier?.value || 'N/A'}`);
+            console.log(`│ Error:               ${error.message}`);
+            console.log(`│ Status:              NEEDS UPDATE (Error checking)`);
+            console.log(`└─────────────────────────────────────────────────────────────────────────────────────────────\n`);
+        }
+    }
+}

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<Dataset[]> {
+        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<boolean> {
+        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<void> {
+        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<void> {
+        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(`
+            ┌─ Dataset ${dataset.publish_id} ───────────────────────────────────────────────────────────────
+            │ DOI Value:           ${doiValue}
+            │ DOI Status (DB):     ${doiStatus}
+            │ DOI State (DataCite): ${doiState || 'Unknown'}
+            │ Dataset Modified:    ${datasetModified ? datasetModified.toISO() : 'N/A'}
+            │ DOI Modified:        ${doiLastModified ? DateTime.fromJSDate(doiLastModified).toISO() : 'N/A'}
+            │ Needs Update:        YES - Dataset newer than DOI
+            └─────────────────────────────────────────────────────────────────────────────────────────────`);
+        } catch (error) {
+            console.log(`
+            ┌─ Dataset ${dataset.publish_id} ───────────────────────────────────────────────────────────────
+            │ DOI Value:           ${dataset.identifier?.value || 'N/A'}
+            │ Error:               ${error.message}
+            │ Needs Update:        YES - Error checking status
+            └─────────────────────────────────────────────────────────────────────────────────────────────`);
+        }
+    }
+}

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;
+}

config/bodyparser.ts

@@ -128,7 +128,7 @@ allowedMethods: ['POST', 'PUT', 'PATCH', 'DELETE'],
 | projects/:id/file
 | ```
 */
-        processManually: [],
+        processManually: ['/submitter/dataset/submit', '/submitter/dataset/:id/update'],
 
         /*
 |--------------------------------------------------------------------------
@@ -185,8 +185,8 @@ allowedMethods: ['POST', 'PUT', 'PATCH', 'DELETE'],
 | and fields data.
 |
 */
-        // limit: '20mb',
-        limit: env.get('UPLOAD_LIMIT', '513mb'),
+        limit: '513mb',
+        //limit: env.get('UPLOAD_LIMIT', '513mb'),
 
         /*
 |--------------------------------------------------------------------------

config/inertia.ts

@@ -1,6 +1,7 @@
 import { defineConfig } from '@adonisjs/inertia';
 import type { HttpContext } from '@adonisjs/core/http';
-import type { InferSharedProps } from '@adonisjs/inertia/types'
+import type { InferSharedProps } from '@adonisjs/inertia/types';
+import env from '#start/env';
 
 const inertiaConfig = defineConfig({
     /**
@@ -21,6 +22,8 @@ const inertiaConfig = defineConfig({
             return ctx.session?.flashMessages.get('user_id');
         },
 
+        opensearch_host: env.get('OPENSEARCH_HOST'),
+
         flash: (ctx) => {
             return {
                 message: ctx.session?.flashMessages.get('message'),
@@ -31,15 +34,15 @@ const inertiaConfig = defineConfig({
 
         // params: ({ params }) => params,
         authUser: async ({ auth }: HttpContext) => {
-            if (auth?.user) {
-                await auth.user.load('roles');
-                return auth.user;
-                // {
-                //     'id': auth.user.id,
-                //     'login': auth.user.login,
-                // };
-            } else {
-                return null;
+            if (!auth?.user) return null
+            await auth.user.load('roles')   // sicherstellen, dass geladen ist
+            return {
+                id: auth.user.id,
+                login: auth.user.login,
+                email: auth.user.email,
+                first_name: auth.user.first_name,
+                last_name: auth.user.last_name,
+                roles: auth.user.roles.map((role) => role.name),
             }
         },
     },
@@ -56,8 +59,8 @@ const inertiaConfig = defineConfig({
 export default inertiaConfig
 
 declare module '@adonisjs/inertia/types' {
-    export interface SharedProps extends InferSharedProps<typeof inertiaConfig> {}
-  }
+    export interface SharedProps extends InferSharedProps<typeof inertiaConfig> { }
+}
 
 // import { InertiaConfig } from '@ioc:EidelLev/Inertia';
 

config/mail.ts

@@ -16,7 +16,7 @@ const mailConfig = defineConfig({
             host: env.get('SMTP_HOST', ''),
             port: env.get('SMTP_PORT'),
             secure: false,
-            // ignoreTLS: true,
+            ignoreTLS: true,
             requireTLS: false,
 
             /**

config/session.ts

@@ -96,7 +96,7 @@ const sessionConfig = defineConfig({
      * variable in order to infer the store name without any
      * errors.
      */
-    store: env.get('SESSION_DRIVER'),
+    store: 'file', //env.get('SESSION_DRIVER'),
     /*
 |--------------------------------------------------------------------------
 | Configuration for the file driver
@@ -122,6 +122,9 @@ const sessionConfig = defineConfig({
     // redisConnection: 'local',
     stores: {
         cookie: stores.cookie(),
+        file: stores.file({
+            location: './tmp/sessions', // Where the data will live
+        }),
     },
 });
 export default sessionConfig;

contracts/enums.ts

@@ -21,6 +21,7 @@ export enum ServerStates {
     rejected_reviewer = 'rejected_reviewer',
     rejected_editor = 'rejected_editor',
     reviewed = 'reviewed',
+    rejected_to_reviewer = 'rejected_to_reviewer',
 }
 
 // for table dataset_titles

database/migrations/1782294801884_create_activities_table.ts

@@ -0,0 +1,25 @@
+import { BaseSchema } from '@adonisjs/lucid/schema';
+
+export default class extends BaseSchema {
+    protected tableName = 'activities';
+
+    async up() {
+        this.schema.createTable(this.tableName, (table) => {
+            table.increments('id');
+            table.string('type').notNullable().index(); // 'dataset.uploaded', 'auth.login'
+            table.integer('user_id').unsigned().nullable().references('id').inTable('accounts').onDelete('SET NULL');
+            table.string('subject_type').nullable(); // manual morph: model name
+            table.bigInteger('subject_id').unsigned().nullable();
+            table.string('description').notNullable();
+            table.json('properties').nullable();
+            table.timestamp('created_at');
+            table.timestamp('updated_at');
+            table.index(['subject_type', 'subject_id'])
+            table.index('created_at')
+        });
+    }
+
+    async down() {
+        this.schema.dropTable(this.tableName);
+    }
+}

database/migrations/dataset_2_documents.ts

@@ -86,3 +86,22 @@ export default class Documents extends BaseSchema {
 //     CONSTRAINT documents_server_state_check CHECK (server_state::text = ANY (ARRAY['deleted'::character varying::text, 'inprogress'::character varying::text, 'published'::character varying::text, 'released'::character varying::text, 'editor_accepted'::character varying::text, 'approved'::character varying::text, 'rejected_reviewer'::character varying::text, 'rejected_editor'::character varying::text, 'reviewed'::character varying::text])),
 //     CONSTRAINT documents_type_check CHECK (type::text = ANY (ARRAY['analysisdata'::character varying::text, 'measurementdata'::character varying::text, 'monitoring'::character varying::text, 'remotesensing'::character varying::text, 'gis'::character varying::text, 'models'::character varying::text, 'mixedtype'::character varying::text]))
 // )
+
+
+// ALTER TABLE documents DROP CONSTRAINT documents_server_state_check;
+
+// ALTER TABLE documents
+// ADD CONSTRAINT documents_server_state_check CHECK (
+//   server_state::text = ANY (ARRAY[
+//     'deleted',
+//     'inprogress',
+//     'published',
+//     'released',
+//     'editor_accepted',
+//     'approved',
+//     'rejected_reviewer',
+//     'rejected_editor',
+//     'reviewed',
+//     'rejected_to_reviewer'  -- new value added
+//   ]::text[])
+// );

database/migrations/dataset_6_collection_roles.ts

@@ -32,3 +32,21 @@ export default class CollectionsRoles extends BaseSchema {
 //     visible_oai boolean NOT NULL DEFAULT true,
 //     CONSTRAINT collections_roles_pkey PRIMARY KEY (id)
 // )
+
+// change to normal intzeger:
+// ALTER TABLE collections_roles ALTER COLUMN id DROP DEFAULT;
+// DROP SEQUENCE IF EXISTS collections_roles_id_seq;
+
+// -- Step 1: Temporarily change one ID to a value not currently used
+// UPDATE collections_roles SET id = 99 WHERE name = 'ccs';
+
+// -- Step 2: Change 'ddc' ID to 2 (the old 'ccs' ID)
+// UPDATE collections_roles SET id = 2 WHERE name = 'ddc';
+
+// -- Step 3: Change the temporary ID (99) to 3 (the old 'ddc' ID)
+// UPDATE collections_roles SET id = 3 WHERE name = 'ccs';
+
+// UPDATE collections_roles SET id = 99 WHERE name = 'bk';
+// UPDATE collections_roles SET id = 1 WHERE name = 'institutes';
+// UPDATE collections_roles SET id = 4 WHERE name = 'pacs';
+// UPDATE collections_roles SET id = 7 WHERE name = 'bk';

database/migrations/dataset_7_collections.ts

@@ -5,7 +5,7 @@ export default class Collections extends BaseSchema {
 
     public async up() {
         this.schema.createTable(this.tableName, (table) => {
-            table.increments('id').defaultTo("nextval('collections_id_seq')");
+            table.increments('id');//.defaultTo("nextval('collections_id_seq')");
             table.integer('role_id').unsigned();
             table
                 .foreign('role_id', 'collections_role_id_foreign')
@@ -25,6 +25,8 @@ export default class Collections extends BaseSchema {
                 .onUpdate('CASCADE');
             table.boolean('visible').notNullable().defaultTo(true);
             table.boolean('visible_publish').notNullable().defaultTo(true);
+            table.integer('left_id').unsigned();
+            table.integer('right_id').unsigned();
         });
     }
 
@@ -59,3 +61,26 @@ export default class Collections extends BaseSchema {
 // change to normal intzeger:
 // ALTER TABLE collections ALTER COLUMN id DROP DEFAULT;
 // DROP SEQUENCE IF EXISTS collections_id_seq;
+
+
+// ALTER TABLE collections 
+//   ADD COLUMN left_id INTEGER;
+// COMMENT ON COLUMN collections.left_id IS 'comment';
+// ALTER TABLE collections 
+//   ADD COLUMN right_id INTEGER;  
+// COMMENT ON COLUMN collections.right_id IS 'comment';
+
+// -- Step 1: Drop the existing default
+// ALTER TABLE collections
+//     ALTER COLUMN visible DROP DEFAULT,
+//     ALTER COLUMN visible_publish DROP DEFAULT;
+
+//     -- Step 2: Change column types with proper casting
+// ALTER TABLE collections
+//     ALTER COLUMN visible TYPE smallint USING CASE WHEN visible THEN 1 ELSE 0 END,
+//     ALTER COLUMN visible_publish TYPE smallint USING CASE WHEN visible_publish THEN 1 ELSE 0 END;
+
+// -- Step 3: Set new defaults as smallint
+// ALTER TABLE collections
+//     ALTER COLUMN visible SET DEFAULT 1,
+//     ALTER COLUMN visible_publish SET DEFAULT 1;

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 "✓ Database downloaded successfully"
+#     else
+#         echo "⚠ 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 "✓ ClamAV daemon is running"
+else
+    echo "⚠ ClamAV daemon status uncertain, but continuing..."
+fi
+
+# Check if freshclam daemon is running
+if pgrep freshclam > /dev/null; then
+    echo "✓ Freshclam daemon is running"
+else
+    echo "⚠ Freshclam daemon status uncertain, but continuing..."
+fi
+
+# # Optional: Test socket connectivity
+# if [ -S /var/run/clamav/clamd.socket ]; then
+#     echo "✓ ClamAV socket exists"
+# else
+#     echo "⚠ WARNING: ClamAV socket not found - services may still be starting"
+# fi
+
+# # change back to CMD of dockerfile
+echo "✓ ClamAV setup complete"
+echo "Starting main application..."
+# exec dumb-init -- "$@"
 exec "$@"

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 <number>` | `-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 | ✅ Index | New dataset needs indexing |
+| Dataset newer than indexed version | ✅ Re-index | Dataset has been updated |
+| Dataset same/older than indexed version | ❌ Skip | Already up to date |
+| OpenSearch document check fails | ✅ Index | Better safe than sorry |
+| Invalid XML metadata | ❌ 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
+<?xml version="1.0" encoding="UTF-8" standalone="true"?>
+<root>
+    <Dataset>
+        <!-- Dataset metadata fields -->
+        <title>Research Dataset Title</title>
+        <description>Dataset description...</description>
+        <!-- Additional metadata -->
+    </Dataset>
+</root>
+```
+
+### 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<typeof XmlCache>
+```
+
+## 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

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 <number>` | `-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:**
+```
+┌─ Dataset 231 ─────────────────────────────────────────────────────────
+│ DOI Value:           10.21388/tethys.231
+│ DOI Status (DB):     findable
+│ DOI State (DataCite): findable
+│ Dataset Modified:    2024-09-15T10:30:00.000Z
+│ DOI Modified:        2024-09-10T08:15:00.000Z
+│ Needs Update:        YES - Dataset newer than DOI
+└───────────────────────────────────────────────────────────────────────
+
+┌─ Dataset 267 ─────────────────────────────────────────────────────────
+│ DOI Value:           10.21388/tethys.267
+│ DOI Status (DB):     findable
+│ DOI State (DataCite): findable
+│ Dataset Modified:    2024-09-18T14:20:00.000Z
+│ DOI Modified:        2024-09-16T12:45:00.000Z
+│ Needs Update:        YES - Dataset newer than DOI
+└───────────────────────────────────────────────────────────────────────
+
+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 | ✅ Update | Dataset has newer changes |
+| Dataset modified ≤ DOI modified | ❌ Skip | DOI is up to date |
+| Dataset date in future | ❌ Skip | Invalid data, needs investigation |
+| Dataset date missing | ✅ Update | Can't determine staleness |
+| DataCite API error | ✅ Update | Better safe than sorry |
+| `--force` flag used | ✅ 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

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

index.d.ts

@@ -183,3 +183,9 @@ declare module 'saxon-js' {
 
     export function transform(options: ITransformOptions): Promise<ITransformOutput> | ITransformOutput;
 }
+
+declare global {
+    interface File {
+      sort_order?: number;
+    }
+  }

package.json

@@ -39,7 +39,7 @@
     "@types/clamscan": "^2.0.4",
     "@types/escape-html": "^1.0.4",
     "@types/fs-extra": "^11.0.4",
-    "@types/leaflet": "^1.9.16",
+    "@types/leaflet": "^1.9.21",
     "@types/luxon": "^3.4.2",
     "@types/node": "^22.10.2",
     "@types/proxy-addr": "^2.0.0",
@@ -56,9 +56,8 @@
     "eslint-config-prettier": "^10.0.1",
     "eslint-plugin-adonis": "^2.1.1",
     "eslint-plugin-prettier": "^5.0.0-alpha.2",
-    "hot-hook": "^0.4.0",
     "numeral": "^2.0.6",
-    "pinia": "^2.0.30",
+    "pinia": "^3.0.2",
     "pino-pretty": "^13.0.0",
     "postcss-loader": "^8.1.1",
     "prettier": "^3.4.2",
@@ -66,20 +65,21 @@
     "tailwindcss": "^3.4.17",
     "ts-loader": "^9.4.2",
     "ts-node-maintained": "^10.9.5",
-    "typescript": "~5.7",
+    "typescript": "^5.9.3",
     "vite": "^6.0.11",
     "vue": "^3.4.26",
-    "vue-facing-decorator": "^3.0.0",
+    "vue-facing-decorator": "^4.0.1",
     "vue-loader": "^17.0.1",
     "webpack-dev-server": "^5.1.0",
     "xslt3": "^2.5.0"
   },
   "dependencies": {
     "@adonisjs/auth": "^9.2.4",
-    "@adonisjs/core": "^6.17.0",
+    "@adonisjs/bodyparser": "^10.0.1",
+    "@adonisjs/core": "^6.21.0",
     "@adonisjs/cors": "^2.2.1",
     "@adonisjs/drive": "^3.2.0",
-    "@adonisjs/inertia": "^2.1.3",
+    "@adonisjs/inertia": "^3.1.1",
     "@adonisjs/lucid": "^21.5.1",
     "@adonisjs/mail": "^9.2.2",
     "@adonisjs/redis": "^9.1.0",
@@ -91,7 +91,7 @@
     "@fontsource/archivo-black": "^5.0.1",
     "@fontsource/inter": "^5.0.1",
     "@inertiajs/inertia": "^0.11.1",
-    "@inertiajs/vue3": "^2.0.3",
+    "@inertiajs/vue3": "^2.3.25",
     "@opensearch-project/opensearch": "^3.2.0",
     "@phc/format": "^1.0.0",
     "@poppinss/manager": "^5.0.2",
@@ -114,13 +114,14 @@
     "node-exceptions": "^4.0.1",
     "notiwind": "^2.0.0",
     "pg": "^8.9.0",
+    "phc-argon2": "^1.1.4",
     "qrcode": "^1.5.3",
-    "redis": "^4.6.10",
+    "redis": "^6.0.0",
     "reflect-metadata": "^0.2.1",
     "saxon-js": "^2.5.0",
     "toastify-js": "^1.12.0",
     "vuedraggable": "^4.1.0",
-    "xmlbuilder2": "^3.1.1"
+    "xmlbuilder2": "^4.0.3"
   },
   "hotHook": {
     "boundaries": [

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
+    }
+}

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<FileValidationOptions> | ((field: FieldContext) => Partial<FileValidationOptions>);
+
 /**
  * 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<string[]> {
+    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 löschen
-     * 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<MultipartFile, MultipartFile, MultipartFile> {
-        
     [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<any>[]);
-    // 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<any>[]) {
     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<void> {
+        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<void> {
+        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<void> {
+        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();
+    }
 }

public/assets2/doi_datacite.xslt

@@ -62,15 +62,19 @@
             </xsl:choose>
             
             <!--<datacite:creator>-->
-            <creators>
-                <xsl:apply-templates select="PersonAuthor" mode="oai_datacite">
-                    <xsl:sort select="@SortOrder"/>               
-                </xsl:apply-templates>
-            </creators>
-            <titles>
-                <xsl:apply-templates select="TitleMain" mode="oai_datacite" />
-                <xsl:apply-templates select="TitleAdditional" mode="oai_datacite" />
-            </titles>
+            <xsl:if test="PersonAuthor[normalize-space(concat(@FirstName, @LastName)) != '']">
+                <creators>
+                    <xsl:apply-templates select="PersonAuthor" mode="oai_datacite">
+                        <xsl:sort select="@SortOrder"/>               
+                    </xsl:apply-templates>
+                </creators>
+            </xsl:if>
+            <xsl:if test="TitleMain[normalize-space(@Value) != ''] or TitleAdditional[normalize-space(@Value) != '']">
+                <titles>
+                    <xsl:apply-templates select="TitleMain" mode="oai_datacite" />
+                    <xsl:apply-templates select="TitleAdditional" mode="oai_datacite" />
+                </titles>
+            </xsl:if>
             <publisher>
                 <!-- <xsl:value-of select="@PublisherName" /> -->
                 <xsl:value-of select="@CreatingCorporation" />
@@ -78,22 +82,26 @@
             <publicationYear>
                 <xsl:value-of select="ServerDatePublished/@Year" />
             </publicationYear>
-            <subjects>
-                <xsl:apply-templates select="Subject" mode="oai_datacite" />
-            </subjects>
+            <xsl:if test="Subject[normalize-space(@Value) != '']">
+                <subjects>
+                    <xsl:apply-templates select="Subject" mode="oai_datacite" />
+                </subjects>
+            </xsl:if>
             <language>
                 <xsl:value-of select="@Language" />
             </language>
-            <xsl:if test="PersonContributor">
+            <xsl:if test="PersonContributor[normalize-space(concat(@FirstName, @LastName)) != '']">
                 <contributors>
                     <xsl:apply-templates select="PersonContributor" mode="oai_datacite">
                         <xsl:sort select="@SortOrder"/>               
                     </xsl:apply-templates>
                 </contributors>
             </xsl:if>
-            <dates>
-                <xsl:call-template name="RdrDate2" />
-            </dates>
+            <xsl:if test="(EmbargoDate and ($unixTimestamp &lt; EmbargoDate/@UnixTimestamp)) or CreatedAt">
+                <dates>
+                    <xsl:call-template name="RdrDate2" />
+                </dates>
+            </xsl:if>
             <version>
                 <xsl:choose>
                     <xsl:when test="@Version">
@@ -109,42 +117,46 @@
                 <!-- <xsl:value-of select="@Type" /> -->
             </resourceType>
             
-            <alternateIdentifiers>
-                <xsl:call-template name="AlternateIdentifier" />
-            </alternateIdentifiers>
+            <xsl:if test="normalize-space(@landingpage) != ''">
+                <alternateIdentifiers>
+                    <xsl:call-template name="AlternateIdentifier" />
+                </alternateIdentifiers>
+            </xsl:if>
             
-            <xsl:if test="Reference">
+            <xsl:if test="Reference[normalize-space(@Type) != '' and normalize-space(@Relation) != '']">
                 <relatedIdentifiers>
                     <xsl:apply-templates select="Reference" mode="oai_datacite" />
                 </relatedIdentifiers>
             </xsl:if>
-            <rightsList>
-                <xsl:apply-templates select="Licence" mode="oai_datacite" />
-            </rightsList>
-            <sizes>
-                <size>
-                    <xsl:value-of select="count(File)" />
-                    <xsl:text> datasets</xsl:text>
-                </size>
-            </sizes>
-            <formats>
-                <xsl:apply-templates select="File/@MimeType" mode="oai_datacite" />
-            </formats>
-            <descriptions>
-                <xsl:apply-templates select="TitleAbstract" mode="oai_datacite" />
-                <xsl:apply-templates select="TitleAbstractAdditional" mode="oai_datacite" />
-            </descriptions>
-            <geoLocations>
-                <xsl:apply-templates select="Coverage" mode="oai_datacite" />
-                <!-- <geoLocation>
-                     <geoLocationBox>
-                     <westBoundLongitude>6.58987</westBoundLongitude>
-                     <eastBoundLongitude>6.83639</eastBoundLongitude>
-                     <southBoundLatitude>50.16</southBoundLatitude>
-                     <northBoundLatitude>50.18691</northBoundLatitude>
-                     </geoLocationBox>
-                     </geoLocation> -->
-             </geoLocations>
+            <xsl:if test="Licence[normalize-space(@Name) != '' or normalize-space(@Url) != '']">
+                <rightsList>
+                    <xsl:apply-templates select="Licence" mode="oai_datacite" />
+                </rightsList>
+            </xsl:if>
+            <xsl:if test="File">
+                <sizes>
+                    <size>
+                        <xsl:value-of select="count(File)" />
+                        <xsl:text> datasets</xsl:text>
+                    </size>
+                </sizes>
+            </xsl:if>
+            <xsl:if test="File[normalize-space(@MimeType) != '']">
+                <formats>
+                    <xsl:apply-templates select="File/@MimeType" mode="oai_datacite" />
+                </formats>
+            </xsl:if>         
+            <xsl:if test="TitleAbstract[normalize-space(@Value) != ''] or TitleAbstractAdditional[normalize-space(@Value) != '']">
+                <descriptions>
+                    <xsl:apply-templates select="TitleAbstract" mode="oai_datacite" />
+                    <xsl:apply-templates select="TitleAbstractAdditional" mode="oai_datacite" />
+                </descriptions>
+            </xsl:if>
+            <xsl:if test="Coverage[normalize-space(@XMin) != '' and normalize-space(@XMax) != '' and normalize-space(@YMin) != '' and normalize-space(@YMax) != '']">
+                <geoLocations>
+                    <xsl:apply-templates select="Coverage" mode="oai_datacite" />
+                </geoLocations>
+            </xsl:if>
         </resource>
     </xsl:template>
     
@@ -176,54 +188,54 @@
     
     <xsl:template match="Coverage" mode="oai_datacite"
                   xmlns="http://datacite.org/schema/kernel-4">
-        <geoLocation>
-            <geoLocationBox>
-                <westBoundLongitude>
-                    <xsl:value-of select="@XMin" />
-                </westBoundLongitude>
-                <eastBoundLongitude>
-                    <xsl:value-of select="@XMax" />
-                </eastBoundLongitude>
-                <southBoundLatitude>
-                    <xsl:value-of select="@YMin" />
-                </southBoundLatitude>
-                <northBoundLatitude>
-                    <xsl:value-of select="@YMax" />
-                </northBoundLatitude>
-            </geoLocationBox>
-        </geoLocation>
+        <xsl:if test="normalize-space(@XMin) != '' and normalize-space(@XMax) != '' and normalize-space(@YMin) != '' and normalize-space(@YMax) != ''">
+            <geoLocation>
+                <geoLocationBox>
+                    <westBoundLongitude><xsl:value-of select="@XMin" /></westBoundLongitude>
+                    <eastBoundLongitude><xsl:value-of select="@XMax" /></eastBoundLongitude>
+                    <southBoundLatitude><xsl:value-of select="@YMin" /></southBoundLatitude>
+                    <northBoundLatitude><xsl:value-of select="@YMax" /></northBoundLatitude>
+                </geoLocationBox>
+            </geoLocation>
+        </xsl:if>
     </xsl:template>
-    
+
+    <!-- TitleAbstract template -->
     <xsl:template match="TitleAbstract" mode="oai_datacite"
                   xmlns="http://datacite.org/schema/kernel-4">
-        <description>
-            <xsl:attribute name="xml:lang">
-                <xsl:value-of select="@Language" />
-            </xsl:attribute>
-            <xsl:if test="@Type != ''">
-                <xsl:attribute name="descriptionType">
-                    <!-- <xsl:value-of select="@Type" /> -->
-                    <xsl:text>Abstract</xsl:text>
+        <xsl:if test="normalize-space(@Value) != ''">
+            <description>
+                <xsl:attribute name="xml:lang">
+                    <xsl:value-of select="@Language" />
                 </xsl:attribute>
-            </xsl:if>
-            <xsl:value-of select="@Value" />
-        </description>
+                <xsl:if test="@Type != ''">
+                    <xsl:attribute name="descriptionType">
+                        <xsl:text>Abstract</xsl:text>
+                    </xsl:attribute>
+                </xsl:if>
+                <xsl:value-of select="@Value" />
+            </description>
+        </xsl:if>
     </xsl:template>
+    
+    <!-- TitleAbstractAdditional template -->
     <xsl:template match="TitleAbstractAdditional" mode="oai_datacite"
                   xmlns="http://datacite.org/schema/kernel-4">
-        <description>
-            <xsl:attribute name="xml:lang">
-                <xsl:value-of select="@Language" />
-            </xsl:attribute>
-            <xsl:if test="@Type != ''">
-                <xsl:attribute name="descriptionType">
-                    <xsl:call-template name="CamelCaseWord">
-                        <xsl:with-param name="text" select="@Type" />
-                    </xsl:call-template>
+        <xsl:if test="normalize-space(@Value) != ''">
+            <description>
+                <xsl:attribute name="xml:lang">
+                    <xsl:value-of select="@Language" />
                 </xsl:attribute>
-            </xsl:if>
-            <xsl:value-of select="@Value" />
-        </description>
+                <xsl:if test="@Type != ''">
+                    <xsl:attribute name="descriptionType">
+                        <xsl:call-template name="CamelCaseWord">
+                            <xsl:with-param name="text" select="@Type" />
+                        </xsl:call-template>
+                    </xsl:attribute>
+                </xsl:if>
+                <xsl:value-of select="@Value" />
+            </description>
+        </xsl:if>
     </xsl:template>
     
     <xsl:template name="CamelCaseWord">
@@ -256,6 +268,7 @@
     
     <xsl:template match="TitleMain" mode="oai_datacite"
                   xmlns="http://datacite.org/schema/kernel-4">
+        <xsl:if test="normalize-space(@Value) != ''">
         <title>
             <xsl:if test="@Language != ''">
                 <xsl:attribute name="xml:lang">
@@ -269,9 +282,12 @@
             </xsl:if>
             <xsl:value-of select="@Value" />
         </title>
+        </xsl:if>
     </xsl:template>
+    
     <xsl:template match="TitleAdditional" mode="oai_datacite"
                   xmlns="http://datacite.org/schema/kernel-4">
+        <xsl:if test="normalize-space(@Value) != ''">
         <title>
             <xsl:if test="@Language != ''">
                 <xsl:attribute name="xml:lang">
@@ -294,61 +310,70 @@
             </xsl:choose>
             <xsl:value-of select="@Value" />
         </title>
+        </xsl:if>
     </xsl:template>
-    
+
     <xsl:template match="Subject" mode="oai_datacite"
                   xmlns="http://datacite.org/schema/kernel-4">
-        <subject>
-            <xsl:if test="@Language != ''">
-                <xsl:attribute name="xml:lang">
-                    <xsl:value-of select="@Language" />
-                </xsl:attribute>
-            </xsl:if>
-            <xsl:value-of select="@Value" />
-        </subject>
+        <xsl:if test="normalize-space(@Value) != ''">
+            <subject>
+                <xsl:if test="@Language != ''">
+                    <xsl:attribute name="xml:lang">
+                        <xsl:value-of select="@Language" />
+                    </xsl:attribute>
+                </xsl:if>
+                <xsl:value-of select="@Value" />
+            </subject>
+        </xsl:if>
     </xsl:template>
     
     <xsl:template name="AlternateIdentifier" match="AlternateIdentifier" mode="oai_datacite"
                   xmlns="http://datacite.org/schema/kernel-4">
-        <alternateIdentifier>
-            <xsl:attribute name="alternateIdentifierType">
-                <xsl:text>url</xsl:text>
-            </xsl:attribute>
-            <!-- <xsl:variable name="identifier" select="concat($repURL, '/dataset/', @Id)" /> -->
-            <xsl:value-of select="@landingpage" />
-        </alternateIdentifier>
+        <xsl:if test="normalize-space(@landingpage) != ''">
+            <alternateIdentifier>
+                <xsl:attribute name="alternateIdentifierType">
+                    <xsl:text>url</xsl:text>
+                </xsl:attribute>
+                <xsl:value-of select="@landingpage" />
+            </alternateIdentifier>
+        </xsl:if>
     </xsl:template>
     
     <xsl:template match="Reference" mode="oai_datacite"
                   xmlns="http://datacite.org/schema/kernel-4">
-        <relatedIdentifier>
-            <xsl:attribute name="relatedIdentifierType">
-                <xsl:value-of select="@Type" />
-            </xsl:attribute>
-            <xsl:attribute name="relationType">
-                <xsl:value-of select="@Relation" />
-            </xsl:attribute>
-            <xsl:value-of select="@Value" />
-        </relatedIdentifier>
+        <xsl:if test="normalize-space(@Type) != '' and normalize-space(@Relation) != ''">
+            <relatedIdentifier>
+                <xsl:attribute name="relatedIdentifierType">
+                    <xsl:value-of select="@Type" />
+                </xsl:attribute>
+                <xsl:attribute name="relationType">
+                    <xsl:value-of select="@Relation" />
+                </xsl:attribute>
+                <xsl:value-of select="@Value" />
+            </relatedIdentifier>
+        </xsl:if>
     </xsl:template>
     
+    <!-- PersonContributor template -->
     <xsl:template match="PersonContributor" mode="oai_datacite"
                   xmlns="http://datacite.org/schema/kernel-4">
-        <contributor>
-            <xsl:if test="@ContributorType != ''">
-                <xsl:attribute name="contributorType">
-                    <xsl:value-of select="@ContributorType" />
-                </xsl:attribute>
-            </xsl:if>
-            <contributorName>
-                <!-- <xsl:if test="@NameType != ''">
-                     <xsl:attribute name="nameType">
-                     <xsl:value-of select="@NameType" />
-                     </xsl:attribute>
-                     </xsl:if> -->
-                <xsl:value-of select="concat(@FirstName, ' ',@LastName)" />
-            </contributorName>
-        </contributor>
+        <xsl:if test="normalize-space(concat(@FirstName, @LastName)) != ''">
+            <contributor>
+                <xsl:if test="@ContributorType != ''">
+                    <xsl:attribute name="contributorType">
+                        <xsl:value-of select="@ContributorType" />
+                    </xsl:attribute>
+                </xsl:if>
+                <contributorName>
+                    <!-- <xsl:if test="@NameType != ''">
+                         <xsl:attribute name="nameType">
+                         <xsl:value-of select="@NameType" />
+                         </xsl:attribute>
+                         </xsl:if> -->
+                    <xsl:value-of select="concat(@FirstName, ' ', @LastName)" />
+                </contributorName>
+            </contributor>
+        </xsl:if>
     </xsl:template>
     
     <xsl:template match="PersonAuthor" mode="oai_datacite"
@@ -403,9 +428,11 @@
     
     <xsl:template match="File/@MimeType" mode="oai_datacite"
                   xmlns="http://datacite.org/schema/kernel-4">
-        <format>            
-            <xsl:value-of select="." />            
-        </format>
+        <xsl:if test="normalize-space(.) != ''">
+            <format>            
+                <xsl:value-of select="." />            
+            </format>
+        </xsl:if>
     </xsl:template>
     
     <xsl:template match="Licence" mode="oai_datacite"

public/assets2/solr.xslt

@@ -111,7 +111,14 @@
         <!--5 server_date_modified -->
         <xsl:if test="ServerDateModified/@UnixTimestamp != ''">            
             <xsl:text>"server_date_modified": "</xsl:text>             
-            <xsl:value-of select="/ServerDateModified/@UnixTimestamp" />    
+            <xsl:value-of select="ServerDateModified/@UnixTimestamp" />    
+            <xsl:text>",</xsl:text>         
+        </xsl:if>
+        
+        <!--5 embargo_date -->
+        <xsl:if test="EmbargoDate/@UnixTimestamp != ''">            
+            <xsl:text>"embargo_date": "</xsl:text>             
+            <xsl:value-of select="EmbargoDate/@UnixTimestamp" />    
             <xsl:text>",</xsl:text>         
         </xsl:if>
         
@@ -200,7 +207,8 @@
         
         <!--17 +18 uncontrolled subject (swd) -->    
         <xsl:variable name="subjects">
-            <xsl:for-each select="Subject[@Type = 'Uncontrolled']">
+            <!-- <xsl:for-each select="Subject[@Type = 'Uncontrolled']"> -->
+            <xsl:for-each select="Subject[@Type = 'Uncontrolled' or @Type = 'Geoera']">
                 <xsl:text>"</xsl:text>
                 <xsl:value-of select="fn:escapeQuotes(@Value)"/>
                 <xsl:text>"</xsl:text>

public/favicon-32x32.png:Zone.Identifier

@@ -0,0 +1,3 @@
+[ZoneTransfer]
+ZoneId=3
+HostUrl=https://sea1.geoinformation.dev/favicon-32x32.png

public/site.webmanifest

@@ -0,0 +1 @@
+{"name":"","short_name":"","icons":[{"src":"/android-chrome-192x192.png","sizes":"192x192","type":"image/png"},{"src":"/android-chrome-512x512.png","sizes":"512x512","type":"image/png"}],"theme_color":"#ffffff","background_color":"#ffffff","display":"standalone"}

readme.md

@@ -11,6 +11,8 @@ Welcome to the Tethys Research Repository Backend System! 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).

resources/css/app.css

@@ -1,7 +1,7 @@
 /* @import url('https://fonts.googleapis.com/css2?family=Poppins:wght@400;500&display=swap'); */
 /* @import url('https://fonts.googleapis.com/css?family=Roboto:400,400i,600,700'); */
 
-@import '_checkbox-radio-switch.css';
+/* @import '_checkbox-radio-switch.css'; */
 @import '_progress.css';
 @import '_scrollbars.css';
 @import '_table.css';

resources/js/Components/AsideMenuItem.vue

@@ -102,7 +102,11 @@ const activeStyle = computed(() => {
 
 const hasRoles = computed(() => {
     if (props.item.roles) {
-        return user.value.roles.some(role => props.item.roles?.includes(role.name));
+        // Normalize user roles to strings in case roles are objects
+        const userRoles = (user.value.roles || []).map(r =>
+            typeof r === 'string' ? r : (r as any).name ?? String(r)
+        );
+        return userRoles.some(role => props.item.roles?.includes(role));
         // return test;
     }
     return true

resources/js/Components/BaseButton.vue

@@ -1,5 +1,5 @@
-<script setup>
-import { computed } from 'vue';
+<script lang="ts" setup>
+import { computed, PropType } from 'vue';
 import { Link } from '@inertiajs/vue3';
 // import { Link } from '@inertiajs/inertia-vue3';
 import { getButtonColor } from '@/colors';
@@ -30,8 +30,8 @@ const props = defineProps({
         type: String,
         default: null,
     },
-    color: {
-        type: String,
+     color: {
+        type: String as PropType<'white' | 'contrast' | 'light' | 'success' | 'danger' | 'warning' | 'info' | 'modern'>,
         default: 'white',
     },
     as: {
@@ -45,11 +45,18 @@ const props = defineProps({
     roundedFull: Boolean,
 });
 
+const emit = defineEmits(['click']);
+
 const is = computed(() => {
     if (props.as) {
         return props.as;
     }
 
+    // If disabled, always render as button or span to prevent navigation
+    if (props.disabled) {
+        return props.routeName || props.href ? 'span' : 'button';
+    }
+
     if (props.routeName) {
         return Link;
     }
@@ -69,47 +76,105 @@ const computedType = computed(() => {
     return null;
 });
 
+// Only provide href/routeName when not disabled
+const computedHref = computed(() => {
+    if (props.disabled) return null;
+    return props.routeName || props.href;
+});
+
+// Only provide target when not disabled and has href
+const computedTarget = computed(() => {
+    if (props.disabled || !props.href) return null;
+    return props.target;
+});
+
+// Only provide disabled attribute for actual button elements
+const computedDisabled = computed(() => {
+    if (is.value === 'button') {
+        return props.disabled;
+    }
+    return null;
+});
+
 const labelClass = computed(() => (props.small && props.icon ? 'px-1' : 'px-2'));
 
 const componentClass = computed(() => {
     const base = [
         'inline-flex',
-        'cursor-pointer',
         'justify-center',
         'items-center',
         'whitespace-nowrap',
         'focus:outline-none',
         'transition-colors',
-        'focus:ring-2',
         'duration-150',
         'border',
         props.roundedFull ? 'rounded-full' : 'rounded',
-        props.active ? 'ring ring-black dark:ring-white' : 'ring-blue-700',
-        getButtonColor(props.color, props.outline, !props.disabled),
     ];
 
+    // Only add focus ring styles when not disabled
+    if (!props.disabled) {
+        base.push('focus:ring-2');
+        base.push(props.active ? 'ring ring-black dark:ring-white' : 'ring-blue-700');
+    }
+
+    // Add button colors
+     // Add button colors - handle both string and array returns
+    // const buttonColors = getButtonColor(props.color, props.outline, !props.disabled);
+    base.push(getButtonColor(props.color, props.outline, !props.disabled));
+    //  if (Array.isArray(buttonColors)) {
+    //     base.push(...buttonColors);
+    // } else {
+    //     base.push(buttonColors);
+    // }
+
+    // Add size classes
     if (props.small) {
         base.push('text-sm', props.roundedFull ? 'px-3 py-1' : 'p-1');
     } else {
         base.push('py-2', props.roundedFull ? 'px-6' : 'px-3');
     }
 
+    // Add disabled/enabled specific classes
     if (props.disabled) {
-        base.push('cursor-not-allowed', props.outline ? 'opacity-50' : 'opacity-70');
+        base.push(
+            'cursor-not-allowed',
+            'opacity-60',
+            'pointer-events-none', // This prevents all interactions
+        );
+    } else {
+        base.push('cursor-pointer');
+        // Add hover effects only when not disabled
+        if (is.value === 'button' || is.value === 'a' || is.value === Link) {
+            base.push('hover:opacity-80');
+        }
     }
 
     return base;
 });
+
+// Handle click events with disabled check
+const handleClick = (event) => {
+    if (props.disabled) {
+        event.preventDefault();
+        event.stopPropagation();
+        return;
+    }
+    emit('click', event);
+};
 </script>
 
 <template>
     <component
         :is="is"
         :class="componentClass"
-        :href="routeName ? routeName : href"
+        :href="computedHref"
+        :to="props.disabled ? null : props.routeName"
         :type="computedType"
-        :target="target"
-        :disabled="disabled"
+        :target="computedTarget"
+        :disabled="computedDisabled"
+        :tabindex="props.disabled ? -1 : null"
+        :aria-disabled="props.disabled ? 'true' : null"
+        @click="handleClick"
     >
         <BaseIcon v-if="icon" :path="icon" />
         <span v-if="label" :class="labelClass">{{ label }}</span>

resources/js/Components/CardBox.vue

@@ -67,7 +67,7 @@ const submit = (e) => {
                 <BaseIcon v-if="icon" :path="icon" class="mr-3" />
                 {{ title }}
             </div>
-            <button v-if="showHeaderIcon" class="flex items-center py-3 px-4 justify-center ring-blue-700 focus:ring" @click="headerIconClick">
+            <button v-if="showHeaderIcon" class="flex items-center py-3 px-4 justify-center ring-blue-700 focus:ring" @click.stop="headerIconClick">
                 <BaseIcon :path="computedHeaderIcon" />
             </button>
         </header>

resources/js/Components/CardBoxClient.vue

@@ -39,6 +39,10 @@ const props = defineProps({
         type: String,
         default: null,
     },
+    allowEmailContact: {
+        type: Boolean,
+        default: false,
+    }
 });
 
 const pillType = computed(() => {
@@ -81,9 +85,8 @@ const pillType = computed(() => {
                     <h4 class="text-xl text-ellipsis">
                         {{ name }}
                     </h4>
-                    <p class="text-gray-500 dark:text-slate-400">
-                        <!-- {{ date }} @ {{ login }} -->
-                        {{ email }}
+                    <p class="text-gray-500 dark:text-slate-400">                  
+                        <div v-if="props.allowEmailContact">  {{ email }}</div>                      
                     </p>
                 </div>
             </BaseLevel>

resources/js/Components/CardBoxModal.vue

@@ -61,10 +61,10 @@ const cancel = () => confirmCancel('cancel');
         <CardBox
             v-show="value"
             :title="title"
-            class="shadow-lg max-h-modal w-11/12 md:w-3/5 lg:w-2/5 xl:w-4/12 z-50"
+            class="p-4 shadow-lg max-h-modal w-11/12 md:w-3/5 lg:w-2/5 xl:w-4/12 z-50"
             :header-icon="mdiClose"
             modal
-            @header-icon-click="cancel"
+            @header-icon-click="cancel"            
         >
             <div class="space-y-3">
                 <h1 v-if="largeTitle" class="text-2xl">

resources/js/Components/CardBoxSimple.vue

@@ -0,0 +1,75 @@
+<script setup lang="ts">
+
+import { computed, useSlots } from 'vue';
+
+
+const props = defineProps({
+    title: {
+        type: String,
+        default: null,
+    },
+    icon: {
+        type: String,
+        default: null,
+    },
+    showHeaderIcon: {
+        type: Boolean,
+        default: true,
+    },
+    headerIcon: {
+        type: String,
+        default: null,
+    },
+    rounded: {
+        type: String,
+        default: 'rounded-xl',
+    },
+    hasFormData: Boolean,
+    empty: Boolean,
+    form: Boolean,
+    hoverable: Boolean,
+    modal: Boolean,
+});
+
+const emit = defineEmits(['header-icon-click', 'submit']);
+
+const is = computed(() => (props.form ? 'form' : 'div'));
+
+const slots = useSlots();
+
+// const footer = computed(() => slots.footer && !!slots.footer());
+
+const componentClass = computed(() => {
+    const base = [props.rounded, props.modal ? 'dark:bg-slate-900' : 'dark:bg-slate-900/70'];
+
+    if (props.hoverable) {
+        base.push('hover:shadow-lg transition-shadow duration-500');
+    }
+
+    return base;
+});
+
+
+
+// const headerIconClick = () => {
+//     emit('header-icon-click');
+// };
+
+// const submit = (e) => {
+//     emit('submit', e);
+// };
+</script>
+
+<template>
+    <component :is="is" :class="componentClass" class="bg-white flex flex-col border border-gray-100 dark:border-slate-800 mb-4">
+
+        <div v-if="empty" class="text-center py-24 text-gray-500 dark:text-slate-400">
+            <p>Nothing's here…</p>
+        </div>
+
+        <div v-else class="flex-1" :class="[!hasFormData && 'p-6']">
+            <slot />
+        </div>
+
+    </component>
+</template>

resources/js/Components/CardBoxWidget.vue

@@ -1,4 +1,4 @@
-<script setup>
+<script lang="ts" setup>
 import { mdiCog } from '@mdi/js';
 import CardBox from '@/Components/CardBox.vue';
 import NumberDynamic from '@/Components/NumberDynamic.vue';
@@ -49,6 +49,9 @@ defineProps({
             <PillTagTrend :trend="trend" :trend-type="trendType" small />
             <BaseButton :icon="mdiCog" icon-w="w-4" icon-h="h-4" color="white" small />
         </BaseLevel>
+        <BaseLevel v-else class="mb-3" mobile>
+            <BaseIcon v-if="icon" :path="icon" size="48" w="w-4" h="h-4" :class="color" />  
+        </BaseLevel>        
         <BaseLevel mobile>
             <div>
                 <h3 class="text-lg leading-tight text-gray-500 dark:text-slate-400">

resources/js/Components/FileUpload.vue

@@ -1,40 +1,78 @@
 <template>
-    <section aria-label="File Upload Modal"
+    <section
+        aria-label="File Upload Modal"
         class="relative h-full flex flex-col bg-white dark:bg-slate-900/70 shadow-xl rounded-md"
-        v-on:dragenter="dragEnterHandler" v-on:dragleave="dragLeaveHandler" v-on:dragover="dragOverHandler"
-        v-on:drop="dropHandler">
-
+        v-on:dragenter="dragEnterHandler"
+        v-on:dragleave="dragLeaveHandler"
+        v-on:dragover="dragOverHandler"
+        v-on:drop="dropHandler"
+    >
         <!-- overlay -->
-        <div id="overlay" ref="overlay"
-            class="w-full h-full absolute top-0 left-0 pointer-events-none z-50 flex flex-col items-center justify-center rounded-md">
+        <div
+            id="overlay"
+            ref="overlay"
+            class="w-full h-full absolute top-0 left-0 pointer-events-none z-50 flex flex-col items-center justify-center rounded-md"
+        >
             <i>
-                <svg class="fill-current w-12 h-12 mb-3 text-blue-700" xmlns="http://www.w3.org/2000/svg" width="24"
-                    height="24" viewBox="0 0 24 24">
+                <svg
+                    class="fill-current w-12 h-12 mb-3 text-blue-700"
+                    xmlns="http://www.w3.org/2000/svg"
+                    width="24"
+                    height="24"
+                    viewBox="0 0 24 24"
+                >
                     <path
-                        d="M19.479 10.092c-.212-3.951-3.473-7.092-7.479-7.092-4.005 0-7.267 3.141-7.479 7.092-2.57.463-4.521 2.706-4.521 5.408 0 3.037 2.463 5.5 5.5 5.5h13c3.037 0 5.5-2.463 5.5-5.5 0-2.702-1.951-4.945-4.521-5.408zm-7.479-1.092l4 4h-3v4h-2v-4h-3l4-4z" />
+                        d="M19.479 10.092c-.212-3.951-3.473-7.092-7.479-7.092-4.005 0-7.267 3.141-7.479 7.092-2.57.463-4.521 2.706-4.521 5.408 0 3.037 2.463 5.5 5.5 5.5h13c3.037 0 5.5-2.463 5.5-5.5 0-2.702-1.951-4.945-4.521-5.408zm-7.479-1.092l4 4h-3v4h-2v-4h-3l4-4z"
+                    />
                 </svg>
             </i>
             <p class="text-lg text-blue-700">Drop files to upload</p>
         </div>
 
+        <!-- Loading Spinner when processing big files -->
+        <div v-if="isLoading" class="absolute inset-0 z-60 flex items-center justify-center bg-gray-500 bg-opacity-50">
+            <svg class="animate-spin h-12 w-12 text-white" xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24">
+                <circle class="opacity-25" cx="12" cy="12" r="10" stroke="currentColor" stroke-width="4"></circle>
+                <path class="opacity-75" fill="currentColor" d="M12 2a10 10 0 0110 10h-4a6 6 0 00-6-6V2z"></path>
+            </svg>
+        </div>
+
         <!-- scroll area -->
         <div class="h-full p-8 w-full h-full flex flex-col">
             <header class="flex items-center justify-center w-full">
-                <label for="dropzone-file"
-                    class="flex flex-col items-center justify-center w-full h-64 border-2 border-gray-300 border-dashed rounded-lg cursor-pointer bg-gray-50 dark:bg-gray-700 hover:bg-gray-100 dark:border-gray-600 dark:hover:border-gray-500 dark:hover:bg-gray-600">
+                <label
+                    for="dropzone-file"
+                    class="flex flex-col items-center justify-center w-full h-64 border-2 border-gray-300 border-dashed rounded-lg cursor-pointer bg-gray-50 dark:bg-gray-700 hover:bg-gray-100 dark:border-gray-600 dark:hover:border-gray-500 dark:hover:bg-gray-600"
+                >
                     <div class="flex flex-col items-center justify-center pt-5 pb-6">
-                        <svg aria-hidden="true" class="w-10 h-10 mb-3 text-gray-400" fill="none" stroke="currentColor"
-                            viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg">
-                            <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2"
-                                d="M7 16a4 4 0 01-.88-7.903A5 5 0 1115.9 6L16 6a5 5 0 011 9.9M15 13l-3-3m0 0l-3 3m3-3v12">
-                            </path>
+                        <svg
+                            aria-hidden="true"
+                            class="w-10 h-10 mb-3 text-gray-400"
+                            fill="none"
+                            stroke="currentColor"
+                            viewBox="0 0 24 24"
+                            xmlns="http://www.w3.org/2000/svg"
+                        >
+                            <path
+                                stroke-linecap="round"
+                                stroke-linejoin="round"
+                                stroke-width="2"
+                                d="M7 16a4 4 0 01-.88-7.903A5 5 0 1115.9 6L16 6a5 5 0 011 9.9M15 13l-3-3m0 0l-3 3m3-3v12"
+                            ></path>
                         </svg>
                         <p class="mb-2 text-sm text-gray-500 dark:text-gray-400">
                             <span class="font-semibold">Click to upload</span> or drag and drop
                         </p>
-                        <!-- <p class="text-xs text-gray-500 dark:text-gray-400">SVG, PNG, JPG or GIF (MAX. 800x400px)</p> -->
                     </div>
-                    <input id="dropzone-file" type="file" class="hidden" @change="onChangeFile" multiple="true" />
+                    <input
+                        id="dropzone-file"
+                        type="file"
+                        class="hidden"
+                        @click="showSpinner"
+                        @change="onChangeFile"
+                        @cancel="cancelSpinner"
+                        multiple="true"
+                    />
                 </label>
             </header>
 
@@ -98,17 +136,16 @@
                             </section>                         
                         </article> -->
                         <!-- :class="errors && errors[`files.${index}`] ? 'bg-red-400' : 'bg-gray-100'" -->
-                        <article tabindex="0"
-                            class="bg-gray-100 group w-full h-full rounded-md cursor-pointer relative shadow-sm">
-                            <section
-                                class="flex flex-col rounded-md text-xs break-words w-full h-full z-20 absolute top-0 py-2 px-3">
+                        <article tabindex="0" class="bg-gray-100 group w-full h-full rounded-md cursor-pointer relative shadow-sm">
+                            <section class="flex flex-col rounded-md text-xs break-words w-full h-full z-20 absolute top-0 py-2 px-3">
                                 <h1 class="flex-1 text-gray-700 group-hover:text-blue-800">{{ element.name }}</h1>
                                 <div class="flex">
                                     <p class="p-1 size text-xs text-gray-700">{{ getFileSize(element) }}</p>
                                     <p class="p-1 size text-xs text-gray-700">sort: {{ element.sort_order }}</p>
                                     <button
                                         class="delete ml-auto focus:outline-none hover:bg-gray-300 p-1 rounded-md text-gray-800"
-                                        @click.prevent="removeFile(index)">
+                                        @click.prevent="removeFile(index)"
+                                    >
                                         <DeleteIcon></DeleteIcon>
                                     </button>
                                 </div>
@@ -122,11 +159,13 @@
             <!--<ul id="deletetFiles"></ul> -->
 
             <div>
-                <h1 v-if="deletetFiles.length > 0" class="pt-8 pb-3 font-semibold sm:text-lg text-gray-900">Files To
-                    Delete</h1>
+                <h1 v-if="deletetFiles.length > 0" class="pt-8 pb-3 font-semibold sm:text-lg text-gray-900">Files To Delete</h1>
                 <ul id="deletetFiles" tag="ul" class="flex flex-1 flex-wrap -m-1">
-                    <li v-for="(element, index) in deletetFiles" :key="index"
-                        class="block p-1 w-1/2 sm:w-1/3 md:w-1/4 lg:w-1/6 xl:w-1/8 h-24">
+                    <li
+                        v-for="(element, index) in deletetFiles"
+                        :key="index"
+                        class="block p-1 w-1/2 sm:w-1/3 md:w-1/4 lg:w-1/6 xl:w-1/8 h-24"
+                    >
                         <!-- <article
                             v-if="element.type.match('image.*')"
                             tabindex="0"
@@ -151,17 +190,16 @@
                                 </div>
                             </section>
                         </article> -->
-                        <article tabindex="0"
-                            class="bg-red-100 group w-full h-full rounded-md cursor-pointer relative shadow-sm">
-                            <section
-                                class="flex flex-col rounded-md text-xs break-words w-full h-full z-20 absolute top-0 py-2 px-3">
+                        <article tabindex="0" class="bg-red-100 group w-full h-full rounded-md cursor-pointer relative shadow-sm">
+                            <section class="flex flex-col rounded-md text-xs break-words w-full h-full z-20 absolute top-0 py-2 px-3">
                                 <h1 class="flex-1 text-gray-700 group-hover:text-blue-800">{{ element.name }}</h1>
                                 <div class="flex">
                                     <!-- <p class="p-1 size text-xs text-gray-700">{{ getFileSize(element) }}</p> -->
                                     <p class="p-1 size text-xs text-gray-700">{{ element.sort_order }}</p>
                                     <button
                                         class="delete ml-auto focus:outline-none hover:bg-gray-300 p-1 rounded-md text-gray-800"
-                                        @click.prevent="reactivateFile(index)">
+                                        @click.prevent="reactivateFile(index)"
+                                    >
                                         <RefreshIcon></RefreshIcon>
                                     </button>
                                 </div>
@@ -174,17 +212,19 @@
             <div v-if="fileErrors" class="flex flex-col mt-6 animate-fade-in" v-for="fileError in fileErrors">
                 <div class="bg-yellow-500 border-l-4 border-orange-400 text-white p-4" role="alert">
                     <p class="font-bold">Be Warned</p>
-                    <p>{{ fileError.join(', ') }}</p>
+                    <p>{{ formatError(fileError) }}</p>
                 </div>
             </div>
-
         </div>
 
         <!-- sticky footer -->
         <footer class="flex justify-end px-8 pb-8 pt-4">
-            <button id="cancel"
+            <button
+                v-if="showClearButton"
+                id="cancel"
                 class="ml-3 rounded-sm px-3 py-1 hover:bg-gray-300 focus:shadow-outline focus:outline-none"
-                @click="clearAllFiles">
+                @click="clearAllFiles"
+            >
                 Clear
             </button>
         </footer>
@@ -238,9 +278,9 @@ interface InteriaPage {
     },
 })
 class FileUploadComponent extends Vue {
-
     @Ref('overlay') overlay: HTMLDivElement;
 
+    public isLoading: boolean = false;
     private counter: number = 0;
     // @Prop() files: Array<TestFile>;
 
@@ -250,13 +290,18 @@ class FileUploadComponent extends Vue {
     })
     files: Array<TethysFile | File>;
 
-
     @Prop({
         type: Array<File>,
         default: [],
     })
     filesToDelete: Array<TethysFile>;
 
+    @Prop({
+        type: Boolean,
+        default: true,
+    })
+    showClearButton: boolean;
+
     // // deletetFiles: Array<TethysFile> = [];
     get deletetFiles(): Array<TethysFile> {
         return this.filesToDelete;
@@ -264,7 +309,7 @@ class FileUploadComponent extends Vue {
     set deletetFiles(values: Array<TethysFile>) {
         // this.modelValue = value;
         this.filesToDelete.length = 0;
-        this.filesToDelete.push(...values);       
+        this.filesToDelete.push(...values);
     }
 
     get items(): Array<TethysFile | File> {
@@ -318,6 +363,11 @@ class FileUploadComponent extends Vue {
         ++this.counter && this.overlay.classList.add('draggedover');
     }
 
+    public formatError(error: string | string[] | undefined) {
+        if (!error) return '';
+        return Array.isArray(error) ? error.join(', ') : error;
+    }
+
     public dragLeaveHandler() {
         1 > --this.counter && this.overlay.classList.remove('draggedover');
     }
@@ -342,10 +392,10 @@ class FileUploadComponent extends Vue {
     }
 
     // reset counter and append file to gallery when file is dropped
-
     public dropHandler(event: DragEvent): void {
         event.preventDefault();
         const dataTransfer = event.dataTransfer;
+        // let bigFileFound = false;
         if (dataTransfer) {
             for (const file of event.dataTransfer?.files) {
                 // let fileName = String(file.name.replace(/\.[^/.]+$/, ''));
@@ -353,28 +403,72 @@ class FileUploadComponent extends Vue {
                 // if (file.type.match('image.*')) {
                 //     this.generateURL(file);
                 // }
+                // if (file.size > 62914560) { // 60 MB in bytes
+                //     bigFileFound = true;
+                // }
                 this._addFile(file);
             }
             this.overlay.classList.remove('draggedover');
             this.counter = 0;
         }
+        // if (bigFileFound) {
+        //     this.isLoading = true;
+        //     // Assume file processing delay; adjust timeout as needed or rely on async processing completion.
+        //     setTimeout(() => {
+        //         this.isLoading = false;
+        //     }, 1500);
+        // }
+    }
+
+    public showSpinner() {
+        // event.preventDefault();
+        this.isLoading = true;
+    }
+
+    public cancelSpinner() {
+        // const target = event.target as HTMLInputElement;
+        // // If no files were selected, remove spinner
+        // if (!target.files || target.files.length === 0) {
+        //     this.isLoading = false;
+        // }
+        this.isLoading = false;
     }
 
     public onChangeFile(event: Event) {
         event.preventDefault();
+        let target = event.target as HTMLInputElement;
         // let uploadedFile = event.target.files[0];
         // let fileName = String(event.target.files[0].name.replace(/\.[^/.]+$/, ''));
 
-        for (const file of event.target.files) {
-            // let fileName = String(event.target.files[0].name.replace(/\.[^/.]+$/, ''));
-            // file.label = fileName;
-            // if (file.type.match('image.*')) {
-            //     this.generateURL(file);
-            // }
-            this._addFile(file);
+        if (target && target.files) {
+            for (const file of event.target.files) {
+                // let fileName = String(event.target.files[0].name.replace(/\.[^/.]+$/, ''));
+                // file.label = fileName;
+                // if (file.type.match('image.*')) {
+                //     this.generateURL(file);
+                // }
+                // Immediately set spinner if any file is large (over 100 MB)
+                // for (const file of target.files) {
+                //     if (file.size > 62914560) { // 100 MB
+                //         bigFileFound = true;
+                //         break;
+                //     }
+                // }
+                // if (bigFileFound) {
+                //     this.isLoading = true;
+                // }
+                this._addFile(file);
+            }
         }
+        // if (bigFileFound) {
+        //     this.isLoading = true;
+        //     setTimeout(() => {
+        //         this.isLoading = false;
+        //     }, 1500);
+        // }
         // this.overlay.classList.remove('draggedover');
         this.counter = 0;
+        this.isLoading = false;
     }
 
     get errors(): IDictionary {
@@ -396,7 +490,9 @@ class FileUploadComponent extends Vue {
 
     public clearAllFiles(event: Event) {
         event.preventDefault();
-        this.items.splice(0);
+        if (this.showClearButton == true) {
+            this.items.splice(0);
+        }
     }
 
     public removeFile(key: number) {
@@ -445,7 +541,7 @@ class FileUploadComponent extends Vue {
         let localUrl: string = '';
         if (file instanceof File) {
             localUrl = URL.createObjectURL(file as Blob);
-        } 
+        }
         // else if (file.fileData) {
         //     // const blob = new Blob([file.fileData]);
         //     // localUrl = URL.createObjectURL(blob);
@@ -465,17 +561,6 @@ class FileUploadComponent extends Vue {
         return localUrl;
     }
 
-    // private async downloadFile(id: number): Promise<string> {
-    //     const response = await axios.get<Blob>(`/api/download/${id}`, {
-    //         responseType: 'blob',
-    //     });
-    //     const url = URL.createObjectURL(response.data);
-    //     setTimeout(() => {
-    //         URL.revokeObjectURL(url);
-    //     }, 1000);
-    //     return url;
-    // }
-
     public getFileSize(file: File) {
         if (file.size > 1024) {
             if (file.size > 1048576) {
@@ -488,17 +573,6 @@ class FileUploadComponent extends Vue {
         }
     }
 
-    // private _addFile(file) {
-    //     // const isImage = file.type.match('image.*');
-    //     // const objectURL = URL.createObjectURL(file);
-
-    //     // this.files[objectURL] = file;
-    //     // let test: TethysFile = { upload: file, label: "dfdsfs", sorting: 0 };
-    //     // file.sorting = this.files.length;
-    //     file.sort_order = (this.items.length + 1),
-    //     this.files.push(file);
-    // }
-
     private _addFile(file: File) {
         // const reader = new FileReader();
         // reader.onload = (event) => {
@@ -530,14 +604,11 @@ class FileUploadComponent extends Vue {
             // this.items.push(test);
             this.items[this.items.length] = test;
         } else {
+            file.sort_order = this.items.length + 1;
             this.items.push(file);
         }
     }
 
-    // use to check if a file is being dragged
-    // private _hasFiles({ types = [] as Array<string> }) {
-    //     return types.indexOf('Files') > -1;
-    // }
     private _hasFiles(dataTransfer: DataTransfer | null): boolean {
         return dataTransfer ? dataTransfer.items.length > 0 : false;
     }

resources/js/Components/FooterBar.vue

@@ -15,9 +15,10 @@ const year = computed(() => new Date().getFullYear());
                 <!-- Get more with <a href="https://tailwind-vue.justboil.me/" target="_blank" class="text-blue-600">Premium
           version</a> -->
             </div>
-            <div class="md:py-3">
+            <div class="md:py-1">
                 <a href="https://www.tethys.at" target="_blank">
-                    <JustboilLogo class="w-auto h-8 md:h-6" />
+                    <!-- <JustboilLogo class="w-auto h-8 md:h-6" /> -->
+                    <JustboilLogo  class="w-auto h-12 md:h-10 dark:invert" />
                 </a>
             </div>
         </BaseLevel>

resources/js/Components/FormCheckRadio.vue

@@ -1,43 +1,165 @@
-<script setup>
-import { computed } from 'vue';
+<script setup lang="ts">
+import { computed, watch, ref } from 'vue';
 
-const props = defineProps({
-    name: {
-        type: String,
-        required: true,
-    },
-    type: {
-        type: String,
-        default: 'checkbox',
-        validator: (value) => ['checkbox', 'radio', 'switch'].includes(value),
-    },
-    label: {
-        type: String,
-        default: null,
-    },
-    modelValue: {
-        type: [Array, String, Number, Boolean],
-        default: null,
-    },
-    inputValue: {
-        type: [String, Number, Boolean],
-        required: true,
-    },
-});
-const emit = defineEmits(['update:modelValue']);
+interface Props {
+    name: string;
+    type?: 'checkbox' | 'radio' | 'switch';
+    label?: string | null;
+    modelValue: Array<any> | string | number | boolean | null;
+    inputValue: string | number | boolean;
+}
+
+const props = defineProps<Props>();
+
+const emit = defineEmits<{ (e: 'update:modelValue', value: Props['modelValue']): void }>();
+
+// const computedValue = computed({
+//     get: () => props.modelValue,
+//     set: (value) => {
+//         emit('update:modelValue', props.type === 'radio' ? [value] : value);
+//     },
+// });
 const computedValue = computed({
-    get: () => props.modelValue,
-    set: (value) => {
-        emit('update:modelValue', value);
+    get: () => {
+        if (props.type === 'radio') {
+            // For radio buttons, return boolean indicating if this option is selected
+            if (Array.isArray(props.modelValue)) {
+                return props.modelValue;
+            }
+            return [props.modelValue];
+        } else {
+            // For checkboxes, return boolean indicating if this option is included
+            if (Array.isArray(props.modelValue)) {
+                return props.modelValue.includes(props.inputValue);
+            }
+            return props.modelValue == props.inputValue;
+        }
     },
+    set: (value: boolean) => {
+        if (props.type === 'radio') {
+            // When radio is selected, emit the new value as array
+            emit('update:modelValue', [value]);
+        } else {
+            // Handle checkboxes
+            let updatedValue = Array.isArray(props.modelValue) ? [...props.modelValue] : [];
+            if (value) {
+                if (!updatedValue.includes(props.inputValue)) {
+                    updatedValue.push(props.inputValue);
+                }
+            } else {
+                updatedValue = updatedValue.filter(item => item != props.inputValue);
+            }
+            emit('update:modelValue', updatedValue);
+        }
+    
+    }
 });
+
 const inputType = computed(() => (props.type === 'radio' ? 'radio' : 'checkbox'));
+
+// Define isChecked for radio inputs: it's true when the current modelValue equals the inputValue
+// const isChecked = computed(() => {
+//     if (Array.isArray(computedValue.value) && computedValue.value.length > 0) {
+//         return props.type === 'radio' 
+//             ? computedValue.value[0] === props.inputValue
+//             : computedValue.value.includes(props.inputValue);
+//     }
+//     return computedValue.value === props.inputValue;
+// });
+// const isChecked = computed(() => {
+//     return computedValue.value[0] === props.inputValue;
+// });
+// Fix the isChecked computation with proper type handling
+// const isChecked = computed(() => {
+//     if (props.type === 'radio') {
+//         // Use loose equality to handle string/number conversion
+//         return computedValue.value == props.inputValue;
+//     }
+//     return computedValue.value === true;
+// });
+
+// const isChecked = computed(() => {
+//     if (props.type === 'radio') {
+//         if (Array.isArray(props.modelValue)) {
+//             return props.modelValue.length > 0 && props.modelValue[0] == props.inputValue;
+//         }
+//         return props.modelValue == props.inputValue;
+//     }
+    
+//     // For checkboxes
+//     if (Array.isArray(props.modelValue)) {
+//         return props.modelValue.includes(props.inputValue);
+//     }
+//     return props.modelValue == props.inputValue;
+// });
+// Use a ref for isChecked and update it with a watcher
+const isChecked = ref(false);
+// Calculate initial isChecked value
+const calculateIsChecked = () => {
+    if (props.type === 'radio') {
+        if (Array.isArray(props.modelValue)) {
+            return props.modelValue.length > 0 && props.modelValue[0] == props.inputValue;
+        }
+        return props.modelValue == props.inputValue;
+    }
+    
+    // For checkboxes
+    if (Array.isArray(props.modelValue)) {
+        return props.modelValue.includes(props.inputValue);
+    }
+    return props.modelValue == props.inputValue;
+};
+
+// Set initial value
+isChecked.value = calculateIsChecked();
+
+// Watch for changes in modelValue and recalculate isChecked
+watch(
+    () => props.modelValue,
+    (newValue) => {
+        console.log('modelValue changed:', {
+            newValue,
+            inputValue: props.inputValue,
+            type: props.type
+        });
+        isChecked.value = calculateIsChecked();
+    },
+    { immediate: true, deep: true }
+);
+
+// Also watch inputValue in case it changes
+watch(
+    () => props.inputValue,
+    () => {
+        isChecked.value = calculateIsChecked();
+    }
+);
 </script>
 
 <template>
-    <label :class="type" class="mr-6 mb-3 last:mr-0">
-        <input v-model="computedValue" :type="inputType" :name="name" :value="inputValue" />
-        <span class="check" />
-        <span class="pl-2">{{ label }}</span>
+     <label v-if="type === 'radio'" :class="[type]"
+        class="mr-6 mb-3 last:mr-0 inline-flex items-center cursor-pointer relative">
+        <input 
+            v-model="computedValue" 
+            :type="inputType" 
+            :name="name" 
+            :value="inputValue"
+            class="absolute left-0 opacity-0 -z-1 focus:outline-none focus:ring-0" />
+        <span class="check border transition-colors duration-200 dark:bg-slate-800 block w-5 h-5 rounded-full" :class="{
+            'border-gray-700': !isChecked,
+            'bg-radio-checked bg-no-repeat bg-center bg-lime-600 border-lime-600 border-4': isChecked
+        }" />
+        <span class="pl-2 control-label">{{ label }}</span>
+    </label>
+
+    <label v-else-if="type === 'checkbox'" :class="[type]"
+        class="mr-6 mb-3 last:mr-0 inline-flex items-center cursor-pointer relative">
+        <input v-model="computedValue" :type="inputType" :name="name" :value="inputValue" 
+        class="absolute left-0 opacity-0 -z-1 focus:outline-none focus:ring-0" />
+        <span class="check border transition-colors duration-200 dark:bg-slate-800 block w-5 h-5 rounded" :class="{
+            'border-gray-700': !isChecked,
+            'bg-checkbox-checked bg-no-repeat bg-center bg-lime-600 border-lime-600 border-4': isChecked
+        }" />
+        <span class="pl-2 control-label">{{ label }}</span>
     </label>
 </template>

resources/js/Components/FormCheckRadioGroup.vue

@@ -1,9 +1,9 @@
 <script setup lang="ts">
-import { computed, ref } from 'vue';
+import { computed, ref, PropType } from 'vue';
 import FormCheckRadio from '@/Components/FormCheckRadio.vue';
-import BaseButton from '@/Components/BaseButton.vue';
-import FormControl from '@/Components/FormControl.vue';
-import { mdiPlusCircle } from '@mdi/js';
+// import BaseButton from '@/Components/BaseButton.vue';
+// import FormControl from '@/Components/FormControl.vue';
+
 const props = defineProps({
     options: {
         type: Object,
@@ -23,7 +23,7 @@ const props = defineProps({
         required: true,
     },
     type: {
-        type: String,
+        type: String as PropType<'checkbox' | 'radio' | 'switch'>,
         default: 'checkbox',
         validator: (value: string) => ['checkbox', 'radio', 'switch'].includes(value),
     },
@@ -38,32 +38,82 @@ const props = defineProps({
     },
 });
 const emit = defineEmits(['update:modelValue']);
-const computedValue = computed({
-    // get: () => props.modelValue,
-    get: () => {
-        // const ids = props.modelValue.map((obj) => obj.id);
-        // return ids;
-        if (Array.isArray(props.modelValue)) {
-            if (props.modelValue.every((item) => typeof item === 'number')) {
-                return props.modelValue;
-            } else if (props.modelValue.every((item) => hasIdAttribute(item))) {
-                const ids = props.modelValue.map((obj) => obj.id.toString());
-                return ids;
-            }
-            return props.modelValue;
-        }
-        // return props.modelValue;
-    },
-    set: (value) => {
-        emit('update:modelValue', value);
-    },
-});
+// const computedValue = computed({
+//     // get: () => props.modelValue,
+//     get: () => {
+//         // const ids = props.modelValue.map((obj) => obj.id);
+//         // return ids;
+//         if (Array.isArray(props.modelValue)) {
+//             if (props.modelValue.every((item) => typeof item === 'number')) {
+//                 return props.modelValue;
+//             } else if (props.modelValue.every((item) => hasIdAttribute(item))) {
+//                 const ids = props.modelValue.map((obj) => obj.id);
+//                 return ids;
+//             }
+//             return props.modelValue;
+//         }
+//         // return props.modelValue;
+//     },
+//     set: (value) => {
+//         emit('update:modelValue', value);
+//     },
+// });
 
 // Define a type guard to check if an object has an 'id' attribute
 // function hasIdAttribute(obj: any): obj is { id: any } {
 //   return typeof obj === 'object' && 'id' in obj;
 // }
 
+const computedValue = computed({
+    get: () => {
+        if (!props.modelValue) return props.modelValue;
+        
+        if (Array.isArray(props.modelValue)) {
+            // Handle empty array
+            if (props.modelValue.length === 0) return [];
+            
+            // If all items are objects with id property
+            if (props.modelValue.every((item) => hasIdAttribute(item))) {
+                return props.modelValue.map((obj) => {
+                    // Ensure we return the correct type based on the options keys
+                    const id = obj.id;
+                    // Check if options keys are numbers or strings
+                    const optionKeys = Object.keys(props.options);
+                    if (optionKeys.length > 0) {
+                        // If option keys are numeric strings, return number
+                        if (optionKeys.every(key => !isNaN(Number(key)))) {
+                            return Number(id);
+                        }
+                    }
+                    return String(id);
+                });
+            }
+            
+            // If all items are numbers
+            if (props.modelValue.every((item) => typeof item === 'number')) {
+                return props.modelValue;
+            }
+            
+            // If all items are strings that represent numbers
+            if (props.modelValue.every((item) => typeof item === 'string' && !isNaN(Number(item)))) {
+                // Convert to numbers if options keys are numeric
+                const optionKeys = Object.keys(props.options);
+                if (optionKeys.length > 0 && optionKeys.every(key => !isNaN(Number(key)))) {
+                    return props.modelValue.map(item => Number(item));
+                }
+                return props.modelValue;
+            }
+            
+            // Return as-is for other cases
+            return props.modelValue;
+        }
+        
+        return props.modelValue;
+    },
+    set: (value) => {
+        emit('update:modelValue', value);
+    },
+});
 const hasIdAttribute = (obj: any): obj is { id: any } => {
     return typeof obj === 'object' && 'id' in obj;
 };
@@ -78,11 +128,11 @@ const addOption = () => {
 
 const inputElClass = computed(() => {
     const base = [
-        'px-3 py-2 max-w-full focus:ring focus:outline-none border-gray-700 rounded w-full',
+        'px-3 py-2 max-w-full border-gray-700 rounded w-full',
         'dark:placeholder-gray-400',
         'h-12',
         'border',
-       'bg-transparent'
+        'bg-transparent'
         // props.isReadOnly ? 'bg-gray-50 dark:bg-slate-600' : 'bg-white dark:bg-slate-800',
     ];
     // if (props.icon) {
@@ -108,7 +158,9 @@ const inputElClass = computed(() => {
                     d="M12 2C6.48 2 2 6.48 2 12s4.48 10 10 10 10-4.48 10-10S17.52 2 12 2zm1 17h-2v-6H5v-2h6V5h2v6h6v2h-6v6z" />
             </svg>
         </div>
-        <FormCheckRadio v-for="(value, key) in options" :key="key" v-model="computedValue" :type="type" :name="name"
-            :input-value="key" :label="value" :class="componentClass" />
+        <!-- <FormCheckRadio v-for="(value, key) in options" :key="key" v-model="computedValue" :type="type"
+            :name="name" :input-value="key" :label="value" :class="componentClass" /> -->
+             <FormCheckRadio v-for="(value, key) in options" key="`${name}-${key}-${JSON.stringify(computedValue)}`"  v-model="computedValue" :type="type"
+            :name="name" :input-value="isNaN(Number(key)) ? key : Number(key)" :label="value" :class="componentClass" />
     </div>
 </template>

resources/js/Components/FormControl.vue

@@ -67,15 +67,28 @@ const computedValue = computed({
         emit('update:modelValue', value);
     },
 });
+
+//  focus:ring focus:outline-none border-gray-700
 const inputElClass = computed(() => {
     const base = [
-        'px-3 py-2 max-w-full focus:ring focus:outline-none border-gray-700 rounded w-full',
+        'px-3 py-2 max-w-full rounded w-full',
         'dark:placeholder-gray-400',
         props.extraHigh ? 'h-80' : (computedType.value === 'textarea' ? 'h-44' : 'h-12'),
         props.borderless ? 'border-0' : 'border',
-        // props.transparent && !props.isReadOnly ? 'bg-transparent' : 'bg-white dark:bg-slate-800',
-        props.isReadOnly ? 'bg-gray-50 dark:bg-slate-600' : 'bg-white dark:bg-slate-800',
+        // // props.transparent && !props.isReadOnly ? 'bg-transparent' : 'bg-white dark:bg-slate-800',
+        // props.isReadOnly ? 'bg-gray-50 dark:bg-slate-600' : 'bg-white dark:bg-slate-800',
     ];
+
+      // Apply styles based on read-only state.
+  if (props.isReadOnly) {
+    // Read-only: no focus ring, grayed-out text and border, and disabled cursor.
+    base.push('bg-gray-50', 'dark:bg-slate-600', 'border', 'border-gray-300', 'dark:border-slate-600', 'text-gray-500', 'cursor-not-allowed', 'focus:outline-none' ,'focus:ring-0', 'focus:border-gray-300');
+  } else {
+    // Actionable field: focus ring, white/dark background, and darker border.
+    base.push('bg-white dark:bg-slate-800', 'focus:ring focus:outline-none', 'border', 'border-gray-700');
+  }
+
+ 
     if (props.icon) {
         base.push('pl-10', 'pr-10');
     }

resources/js/Components/FormField.vue

@@ -1,53 +1,75 @@
 <script setup>
 import { computed, useSlots } from 'vue';
 
-
 const props = defineProps({
-    label: {
-        type: String,
-        default: null,
-    },
-    labelFor: {
-        type: String,
-        default: null,
-    },
-    help: {
-        type: String,
-        default: null,
-    },
-    // class: {
-    //     type: Object,
-    //     default: {},
-    // },
+  label: { type: String, default: null },
+  labelFor: { type: String, default: null },
+  help: { type: String, default: null },
+  // Handles Inertia.js string errors or standard array errors
+  errors: { type: [String, Array], default: null },
 });
 
 const slots = useSlots();
 
+// Normalize errors to an array for consistent rendering
+const errorList = computed(() => {
+  if (!props.errors) return [];
+  return Array.isArray(props.errors) ? props.errors : [props.errors];
+});
+
+const hasErrors = computed(() => errorList.value.length > 0);
+
 const wrapperClass = computed(() => {
-    const base = [];
-    const slotsLength = slots.default().length;
-
-    if (slotsLength > 1) {
-        base.push('grid grid-cols-1 gap-3');
-    }
-
-    if (slotsLength === 2) {
-        base.push('md:grid-cols-2');
-    }
-
-    return base;
+  const base = [];
+  const children = slots.default?.().filter(node => node.type.toString() !== 'Symbol(v-cmt)') || [];
+  
+  // Apply grid logic only if there are multiple child controls
+  if (children.length > 1) {
+    base.push('grid grid-cols-1 gap-3');
+    if (children.length === 2) base.push('md:grid-cols-2');
+  }
+  
+  return base;
 });
 </script>
 
 <template>
-    <div :class="['last:mb-0', 'mb-6']">
-        <!-- <label v-if="label" :for="labelFor" class="block font-bold mb-2">{{ label }}</label> -->
-        <label v-if="label" :for="labelFor" class="font-bold h-6 mt-3 text-xs leading-8 uppercase">{{ label }}</label>
-        <div v-bind:class="wrapperClass">
-            <slot />
-        </div>
-        <div v-if="help" class="text-xs text-gray-500 dark:text-slate-400 mt-1">
-            {{ help }}
-        </div>
+  <div class="mb-6 last:mb-0">
+    <label 
+      v-if="label" 
+      :for="labelFor" 
+      class="block font-bold text-xs uppercase tracking-wide mb-2 transition-colors duration-200"
+      :class="hasErrors ? 'text-red-600 dark:text-red-400' : 'text-gray-700 dark:text-slate-300'"
+    >
+      {{ label }}
+    </label>
+    
+    <div :class="wrapperClass">
+      <slot />
     </div>
-</template>
+
+    <div class="mt-1 min-h-[1.25rem]">
+      <transition-group 
+        enter-active-class="transition duration-150 ease-out"
+        enter-from-class="transform -translate-y-1 opacity-0"
+        enter-to-class="transform translate-y-0 opacity-100"
+      >
+        <p 
+          v-for="(error, index) in errorList" 
+          :key="`err-${index}`"
+          class="text-xs text-red-600 dark:text-red-400 italic font-medium"
+        >
+          {{ error }}
+        </p>
+
+        <p 
+          v-if="!hasErrors && help" 
+          key="help-text"
+          class="text-xs text-gray-500 dark:text-slate-400"
+        >
+          {{ help }}
+        </p>
+      </transition-group>
+    </div>
+  </div>
+</template>

resources/js/Components/Icons/IconSvg.vue

@@ -0,0 +1,74 @@
+<script setup lang="ts">
+import { computed } from 'vue';
+import { mdiLicense } from '@mdi/js';
+
+const props = defineProps({
+    path: {
+        type: String,
+        required: true
+    },
+    size: {
+        type: Number,
+        default: 24
+    },
+    viewBox: {
+        type: String,
+        default: '0 0 24 24'
+    },
+    color: {
+        type: String,
+        default: 'currentColor'
+    },
+    className: {
+        type: String,
+        default: ''
+    }
+});
+
+// Define all the SVG paths we need
+const svgPaths = {
+    // Document/File icons
+    document: 'M9 12h6m-6 4h6m2 5H7a2 2 0 01-2-2V5a2 2 0 012-2h5.586a1 1 0 01.707.293l5.414 5.414a1 1 0 01.293.707V19a2 2 0 01-2 2z',
+    documentPlus: 'M9 13h6m-3-3v6m5 5H7a2 2 0 01-2-2V5a2 2 0 012-2h5.586a1 1 0 01.707.293l5.414 5.414a1 1 0 01.293.707V19a2 2 0 01-2 2z',
+
+    // Communication icons
+    email: 'M2.003 5.884L10 9.882l7.997-3.998A2 2 0 0016 4H4a2 2 0 00-1.997 1.884z M18 8.118l-8 4-8-4V14a2 2 0 002 2h12a2 2 0 002-2V8.118z',
+
+    // Identity/User icons
+    idCard: '10 2a1 1 0 00-1 1v1a1 1 0 002 0V3a1 1 0 00-1-1zM4 4h3a3 3 0 006 0h3a2 2 0 012 2v9a2 2 0 01-2 2H4a2 2 0 01-2-2V6a2 2 0 012-2zm2.5 7a1.5 1.5 0 100-3 1.5 1.5 0 000 3zm2.45 4a2.5 2.5 0 10-4.9 0h4.9zM12 9a1 1 0 100 2h3a1 1 0 100-2h-3zm-1 4a1 1 0 011-1h2a1 1 0 110 2h-2a1 1 0 01-1-1z',
+
+    // Language/Translation icons
+    // language: 'M7 2a1 1 0 011 1v1h3a1 1 0 110 2H9.578a18.87 18.87 0 01-1.724 4.78c.29.354.596.696.914 1.026a1 1 0 11-1.44 1.389c-.188-.196-.373-.396-.554-.6a19.098 19.098 0 01-3.107 3.567 1 1 0 01-1.334-1.49 17.087 17.087 0 003.13-3.733 18.992 18.992 0 01-1.487-2.494 1 1 0 111.79-.89c.234.47.489.928.764 1.372.417-.934.752-1.913.997-2.927H3a1 1 0 110-2h3V3a1 1 0 011-1zm6 6a1 1 0 01.894.553l2.991 5.982a.869.869 0 01.02.037l.99 1.98a1 1 0 11-1.79.895L15.383 16h-4.764l-.724 1.447a1 1 0 11-1.788-.894l.99-1.98.019-.038 2.99-5.982A1 1 0 0113 8zm-1.382 6h2.764L13 11.236 11.618 14z',
+    language: 'M12 2a10 10 0 1 0 0 20a10 10 0 1 0 0-20zm0 0c2.5 0 4.5 4.5 4.5 10s-2 10-4.5 10-4.5-4.5-4.5-10 2-10 4.5-10zm0 0a10 10 0 0 1 0 20a10 10 0 0 1 0-20z',
+    // License/Legal icons
+    // license: 'M10 2a1 1 0 00-1 1v1.323l-3.954 1.582A1 1 0 004 6.32V16a1 1 0 001.555.832l3-1.2a1 1 0 01.8 0l3 1.2a1 1 0 001.555-.832V6.32a1 1 0 00-1.046-.894L9 4.877V3a1 1 0 00-1-1zm0 14.5a.5.5 0 01-.5-.5v-4a.5.5 0 011 0v4a.5.5 0 01-.5.5zm1.5-10.5a.5.5 0 11-1 0 .5.5 0 011 0z',
+    license: mdiLicense,
+
+    // Building/Organization icons
+    building: 'M4 4a2 2 0 012-2h8a2 2 0 012 2v12a1 1 0 110 2h-3a1 1 0 01-1-1v-2a1 1 0 00-1-1H9a1 1 0 00-1 1v2a1 1 0 01-1 1H4a1 1 0 110-2V4zm3 1h2v2H7V5zm2 4H7v2h2V9zm2-4h2v2h-2V5zm2 4h-2v2h2V9z',
+
+    // Book/Publication icons
+    book: 'M9 4.804A7.968 7.968 0 005.5 4c-1.255 0-2.443.29-3.5.804v10A7.969 7.969 0 015.5 14c1.669 0 3.218.51 4.5 1.385A7.962 7.962 0 0114.5 14c1.255 0 2.443.29 3.5.804v-10A7.968 7.968 0 0014.5 4c-1.255 0-2.443.29-3.5.804V12a1 1 0 11-2 0V4.804z',
+
+    // Download icon
+    download: 'M4 16v1a3 3 0 003 3h10a3 3 0 003-3v-1m-4-4l-4 4m0 0l-4-4m4 4V4'
+};
+
+const pathData = computed(() => {
+    return svgPaths[props.path] || props.path;
+});
+
+const sizeStyle = computed(() => {
+    return {
+        width: `${props.size}px`,
+        height: `${props.size}px`
+    };
+});
+</script>
+
+<template>
+    <svg :style="sizeStyle" :class="className" :viewBox="viewBox" xmlns="http://www.w3.org/2000/svg" fill="none"
+        :stroke="color" stroke-width="2" stroke-linecap="round" stroke-linejoin="round">
+        <path :d="pathData" />
+    </svg>
+</template>