.env.example

@@ -17,6 +17,4 @@ REDIS_PORT=6379
 REDIS_PASSWORD=
 SMTP_HOST=
 SMTP_PORT=
-RESEND_API_KEY=
+RESEND_API_KEY=
-OPENSEARCH_HOST=http://localhost
-OPENSEARCH_CORE=tethys-records

.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 }}."

.gitea/workflows/checkReferenceType.yaml

@@ -1,78 +0,0 @@
-# This is a Gitea Actions workflow configuration file for running CI tests on the `feat/checkReferenceType` branch.
-# The workflow is named "CI" and runs on the latest Ubuntu environment using a Node.js 20 Docker container.
-# It sets up a PostgreSQL service with specified environment variables and health checks.
-# The workflow includes the following steps:
-# 1. Checkout the repository using the actions/checkout@v3 action.
-# 2. Install Node.js dependencies using `npm ci`.
-# 3. Create a `.env.test` file by copying from `.env.example`.
-# 4. Set up environment variables in the `.env.test` file, including database connection details and other app-specific settings.
-# 5. Run functional tests using the `node ace test functional --groups "ReferenceValidation"` command.
-name: CI
-run-name: Running tests for checkReferenceType branch
-on:
-    push:
-        branches:
-            - feat/checkReferenceType
-
-jobs:
-    container-job:
-        runs-on: ubuntu-latest
-        # Docker Hub image that `container-job` executes in
-        container: node:20-bullseye
-
-        services:
-            # Label used to access the service container
-            postgres:
-                image: postgres:latest
-                env:
-                    POSTGRES_USER: alice
-                    POSTGRES_PASSWORD: ${{ secrets.POSTGRES_PASSWORD }}
-                    POSTGRES_DB: tethys_dev
-                # ports:
-                #   - 5432:5432
-                options: |
-                    --health-cmd pg_isready
-                    --health-interval 10s
-                    --health-timeout 5s
-                    --health-retries 5
-
-        steps:
-            - name: Checkout repository
-              uses: actions/checkout@v3
-
-            #   - name: Set up Node.js
-            #     uses: actions/setup-node@v2
-            #     with:
-            #       node-version: '20'
-
-            - name: Install dependencies
-              run: npm ci
-
-            - name: Create .env.test file
-              run: cp .env.example .env.test
-
-            - name: Set up environment variables        
-              run: |
-                  echo "DB_CONNECTION=pg" >> .env.test
-                  echo "PG_HOST=postgres" >> .env.test
-                  echo "PG_PORT=5432" >> .env.test
-                  echo "PG_USER=alice" >> .env.test
-                  echo "PG_PASSWORD=${{ secrets.POSTGRES_PASSWORD }}" >> .env.test
-                  echo "PG_DB_NAME=tethys_dev" >> .env.test
-                  echo "NODE_ENV=test" >> .env.test
-                  echo "ASSETS_DRIVER=fake" >> .env.test
-                  echo "SESSION_DRIVER=memory" >> .env.test
-                  echo "HASH_DRIVER=bcrypt" >> .env.test
-                  echo "HOST=127.0.0.1" >> .env.test
-                  echo "PORT=3333" >> .env.test
-                  echo "APP_NAME=TethysCloud" >> .env.test
-                  echo "APP_URL=http://${HOST}:${PORT}" >> .env.test
-                  echo "CACHE_VIEWS=false" >> .env.test
-                  echo "APP_KEY=pfi5N2ACN4tMJ5d8d8BPHfh3FEuvleej" >> .env.test
-                  echo "DRIVE_DISK=local" >> .env.test
-                  echo "OAI_LIST_SIZE=200" >> .env.test
-                  echo "OPENSEARCH_HOST=${{ secrets.OPENSEARCH_HOST }}" >> .env.test
-                  echo "OPENSEARCH_CORE=tethys-records" >> .env.test
-
-            - name: Run tests
-              run: node ace test functional --groups "ReferenceValidation"

.gitea/workflows/ci.yaml

@@ -4,13 +4,7 @@
 name: CI Pipeline
 run-name: ${{ github.actor }} is running CI pipeline
 # trigger build when pushing, or when creating a pull request
-on:
+on: [push, pull_request]
-  push:
-    branches:
-      - master
-  pull_request:
-    branches:
-      - master
 
 jobs:
     # Label of the container job
@@ -18,7 +12,7 @@ jobs:
         # run build on latest ubuntu
         runs-on: ubuntu-latest
 
-        container: node:20-bullseye
+        container: node:18-bullseye
 
         services:
             mydb:
@@ -76,7 +70,6 @@ jobs:
                   && echo "CACHE_VIEWS=false" >> .env.test
                   && echo "APP_KEY=pfi5N2ACN4tMJ5d8d8BPHfh3FEuvleej" >> .env.test
                   && echo "DRIVE_DISK=local" >> .env.test
-                  && echo "OAI_LIST_SIZE=200" >> .env.test
 
             # finally run the tests
             # - run: npm test
@@ -102,4 +95,3 @@ jobs:
             #   uses: coverallsapp/github-action@master
             #   with:
             #       github-token: ${{ secrets.GITHUB_TOKEN }}
-

.gitignore

@@ -7,4 +7,3 @@ coverage
 tmp
 docker-compose.yml
 .env.test
-public/assets

Dockerfile

@@ -1,63 +1,57 @@
 ################## First Stage - Creating base #########################
 
 # Created a variable to hold our node base image
-ARG NODE_IMAGE=node:22-trixie-slim
+ARG NODE_IMAGE=node:20-bookworm-slim
 
 FROM $NODE_IMAGE AS base
-
 # Install dumb-init and ClamAV, and perform ClamAV database update
-RUN apt-get update \
+RUN apt update \
-    && apt-get install -y --no-install-recommends \
+    && apt-get install -y dumb-init clamav clamav-daemon nano \ 
-    dumb-init \
-    clamav \
-    clamav-daemon \
-    clamdscan \
-    ca-certificates \   
     && rm -rf /var/lib/apt/lists/* \
     # Creating folders and changing ownerships
-    && mkdir -p /home/node/app \
+    && mkdir -p /home/node/app && chown node:node /home/node/app \
-    && mkdir -p /var/lib/clamav \
+    &&  mkdir -p /var/lib/clamav \
     && mkdir /usr/local/share/clamav \
+    && chown -R node:clamav /var/lib/clamav /usr/local/share/clamav /etc/clamav \
+    # permissions
     && mkdir /var/run/clamav \
-    && mkdir -p /var/log/clamav \
+    && chown node:clamav /var/run/clamav \
-    && mkdir -p /tmp/clamav-logs \
+    && chmod 750 /var/run/clamav
-   
+# -----------------------------------------------
-    # Set ownership and permissions
+# --- ClamAV & FeshClam -------------------------
-    && chown node:node /home/node/app \
+# -----------------------------------------------
-    # && chown -R node:clamav /var/lib/clamav /usr/local/share/clamav /etc/clamav /var/run/clamav \
+# RUN \
-    && chown -R node:clamav /var/lib/clamav /usr/local/share/clamav /etc/clamav /var/run/clamav /var/log/clamav \
+#   chmod 644 /etc/clamav/freshclam.conf && \
-    && chown -R node:clamav /etc/clamav \
+#   freshclam && \
-    && chmod 755 /tmp/clamav-logs \
+#   mkdir /var/run/clamav && \
-    && chmod 750 /var/run/clamav \
+  # chown -R clamav:root /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 ClamAV - copy config files before switching user
+# Configure Clam AV...
-# 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"
 
-# Copy entrypoint script
+# initial update of av databases
+RUN freshclam
+
+# VOLUME /var/lib/clamav
 COPY --chown=node:clamav docker-entrypoint.sh /home/node/app/docker-entrypoint.sh
 RUN chmod +x /home/node/app/docker-entrypoint.sh
 ENV TZ="Europe/Vienna"
 
 
+
+
 ################## Second Stage - Installing dependencies ##########
 # In this stage, we will start installing dependencies
 FROM base AS dependencies
@@ -76,6 +70,7 @@ ENV NODE_ENV=production
 # We run "node ace build" to build the app (dist folder) for production
 RUN node ace build --ignore-ts-errors
 # RUN node ace build --production
+# RUN node ace build --ignore-ts-errors
 
 
 ################## Final Stage - Production #########################
@@ -93,7 +88,6 @@ RUN npm ci --omit=dev
 # Copy files to the working directory from the build folder the user
 COPY --chown=node:node --from=build /home/node/app/build .
 # Expose port
-# EXPOSE 3310
 EXPOSE 3333
 ENTRYPOINT ["/home/node/app/docker-entrypoint.sh"]
 # Run the command to start the server using "dumb-init"

LICENSE

@@ -1,22 +0,0 @@
-
-MIT License
-
-Copyright (c) 2025 Tethys Research Repository
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE

ace.js

@@ -15,11 +15,10 @@
 /**
  * Register hook to process TypeScript files using ts-node
  */
-// import { register } from 'node:module';
+import { register } from 'node:module'
-// register('ts-node/esm', import.meta.url);
+register('ts-node/esm', import.meta.url)
-import 'ts-node-maintained/register/esm';
 
 /**
  * Import ace console entrypoint
  */
-await import('./bin/console.js');
+await import('./bin/console.js')

adonisrc.ts

@@ -1,7 +1,7 @@
-import { defineConfig } from '@adonisjs/core/app';
+import { defineConfig } from '@adonisjs/core/app'
 
 export default defineConfig({
-    /*
+  /*
 |--------------------------------------------------------------------------
 | Commands
 |--------------------------------------------------------------------------
@@ -10,12 +10,12 @@ export default defineConfig({
 | will be scanned automatically from the "./commands" directory.
  
 */
-    commands: [
+  commands: [
-        () => import('@adonisjs/core/commands'),
+    () => import('@adonisjs/core/commands'),
-        () => import('@adonisjs/lucid/commands'),
+    () => import('@adonisjs/lucid/commands'),
-        () => import('@adonisjs/mail/commands')
+    () => import('@adonisjs/mail/commands')
-    ],
+  ],
-    /*
+  /*
 |--------------------------------------------------------------------------
 | Preloads
 |--------------------------------------------------------------------------
@@ -23,23 +23,19 @@ export default defineConfig({
 | List of modules to import before starting the application.
 |
 */
-    preloads: [
+  preloads: [
-        () => import('./start/routes.js'),
+    () => import('./start/routes.js'),
-        () => import('./start/kernel.js'),
+    () => import('./start/kernel.js'),
-        () => import('#start/validator'),
+    () => import('#start/validator'),
-        // () => import('#start/rules/unique'),
+    () => import('#start/rules/unique'),
-        // () => import('#start/rules/translated_language'),
+    () => import('#start/rules/translated_language'),
-        // () => import('#start/rules/unique_person'),
+    () => import('#start/rules/unique_person'),
-        // // () => import('#start/rules/file_length'),
+    () => import('#start/rules/file_length'),
-        // // () => import('#start/rules/file_scan'),
+    () => import('#start/rules/file_scan'),
-        // // () => import('#start/rules/allowed_extensions_mimetypes'),
+    () => import('#start/rules/allowed_extensions_mimetypes'),
-        // () => import('#start/rules/dependent_array_min_length'),
+    () => 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'),
-    ],
-    /*
 |--------------------------------------------------------------------------
 | Service providers
 |--------------------------------------------------------------------------
@@ -48,49 +44,48 @@ export default defineConfig({
 | application
 |
 */
-    providers: [
+  providers: [
-        // () => import('./providers/AppProvider.js'),
+    // () => import('./providers/AppProvider.js'),
-        () => import('@adonisjs/core/providers/app_provider'),
+    () => import('@adonisjs/core/providers/app_provider'),
-        () => import('@adonisjs/core/providers/hash_provider'),
+    () => import('@adonisjs/core/providers/hash_provider'),
-        {
+    {
-            file: () => import('@adonisjs/core/providers/repl_provider'),
+      file: () => import('@adonisjs/core/providers/repl_provider'),
-            environment: ['repl', 'test'],
+      environment: ['repl', 'test'],
-        },
+    },
-        () => import('@adonisjs/session/session_provider'),
+    () => import('@adonisjs/session/session_provider'),
-        () => import('@adonisjs/core/providers/edge_provider'),
+    () => import('@adonisjs/core/providers/edge_provider'),
-        () => import('@adonisjs/shield/shield_provider'),
+    () => import('@adonisjs/shield/shield_provider'),
-        // () => import('@eidellev/inertia-adonisjs'),
+    // () => import('@eidellev/inertia-adonisjs'),
-        // () => import('@adonisjs/inertia/inertia_provider'),
+    // () => import('@adonisjs/inertia/inertia_provider'),
-        () => import('#providers/app_provider'),
+    () => import('#providers/app_provider'),
-        () => import('#providers/inertia_provider'),
+    () => import('#providers/inertia_provider'),
-        () => import('@adonisjs/lucid/database_provider'),
+    () => import('@adonisjs/lucid/database_provider'),
-        () => import('@adonisjs/auth/auth_provider'),
+    () => import('@adonisjs/auth/auth_provider'),
-        // () => import('@eidellev/adonis-stardust'),
+    // () => import('@eidellev/adonis-stardust'),        
-        () => import('@adonisjs/redis/redis_provider'),
+    () => import('@adonisjs/redis/redis_provider'),
-        // () => import('@adonisjs/encore/encore_provider'),
+    () => import('@adonisjs/encore/encore_provider'),
-        () => import('@adonisjs/static/static_provider'),
+    () => import('@adonisjs/static/static_provider'),
-        () => import('#providers/stardust_provider'),
+    () => import('#providers/stardust_provider'),
-        () => import('#providers/query_builder_provider'),
+    () => import('#providers/query_builder_provider'),
-        () => import('#providers/token_worker_provider'),
+    () => import('#providers/token_worker_provider'),
-        () => import('#providers/rule_provider'),
+    // () => import('#providers/validator_provider'),
-        // () => import('#providers/drive/provider/drive_provider'),
+    () => import('#providers/drive/provider/drive_provider'),
-        () => import('@adonisjs/drive/drive_provider'),
+    // () => import('@adonisjs/core/providers/vinejs_provider'),
-        // () => import('@adonisjs/core/providers/vinejs_provider'),
+    () => import('#providers/vinejs_provider'),
-        () => import('#providers/vinejs_provider'),
+    () => import('@adonisjs/mail/mail_provider')
-        () => import('@adonisjs/mail/mail_provider'),
+    //   () => import('#providers/mail_provider'),
-        () => import('@adonisjs/vite/vite_provider'),
+  ],
-    ],
+  metaFiles: [
-    metaFiles: [
+    {
-        {
+      pattern: 'public/**',
-            pattern: 'public/**',
+      reloadServer: false,
-            reloadServer: false,
+    },
-        },
+    {
-        {
+      pattern: 'resources/views/**/*.edge',
-            pattern: 'resources/views/**/*.edge',
+      reloadServer: false,
-            reloadServer: false,
+    },
-        },
+  ],
-    ],
+  /*
-    /*
 |--------------------------------------------------------------------------
 | Tests
 |--------------------------------------------------------------------------
@@ -99,24 +94,22 @@ export default defineConfig({
 | and add additional suites.
 |
 */
-    tests: {
+  tests: {
-        suites: [
+    suites: [
-            {
+      {
-                files: ['tests/unit/**/*.spec(.ts|.js)'],
+        files: ['tests/unit/**/*.spec(.ts|.js)'],
-                name: 'unit',
+        name: 'unit',
-                timeout: 2000,
+        timeout: 2000,
-            },
+      },
-            {
+      {
-                files: ['tests/functional/**/*.spec(.ts|.js)'],
+        files: ['tests/functional/**/*.spec(.ts|.js)'],
-                name: 'functional',
+        name: 'functional',
-                timeout: 30000,
+        timeout: 30000,
-            },
+      },
-        ],
+    ],
-        forceExit: false,
+    forceExit: false,
-    },
+  },
-    assetsBundler: false,
+
-    hooks: {
+
-        onBuildStarting: [() => import('@adonisjs/vite/build_hook')],
+
-    },
+})
-    //   assetsBundler: false
-});

app/Controllers/Http/Admin/AdminuserController.ts

@@ -85,9 +85,7 @@ 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');
@@ -97,6 +95,7 @@ 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();
@@ -140,11 +139,9 @@ export default class AdminuserController {
         });
 
         // password is optional
-        let input: Record<string, any>;
+        let input;
-
+        if (request.input('password')) {
-        if (request.input('new_password')) {
+            input = request.only(['login', 'email', 'password', 'first_name', 'last_name']);
-            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']);
         }
@@ -159,6 +156,7 @@ 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

@@ -25,7 +25,6 @@ export default class MimetypeController {
         const newDatasetSchema = vine.object({
             name: vine.string().trim().isUnique({ table: 'mime_types', column: 'name' }),
             file_extension: vine.array(vine.string()).minLength(1), // define at least one extension for the new mimetype
-            alternate_mimetype: vine.array(vine.string().isValidMimetype()).distinct().optional(), // define alias mimetypes
             enabled: vine.boolean(),
         });
         // await request.validate({ schema: newDatasetSchema, messages: this.messages });
@@ -33,22 +32,18 @@ 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) });
+            await request.validateUsing(validator);
         } catch (error) {
             // Step 3 - Handle errors
             // return response.badRequest(error.messages);
             throw error;
         }
-        const input = request.only(['name', 'enabled', 'file_extension', 'alternate_mimetype']);
+        const input = request.only(['name', 'enabled', 'file_extension']);
         // Concatenate the file_extensions array into a string with '|' as the separator
         if (Array.isArray(input.file_extension)) {
             input.file_extension = input.file_extension.join('|');
         }
-        // Concatenate the alias_mimetype array into a string with '|' as the separator
-        if (Array.isArray(input.alternate_mimetype)) {
-            input.alternate_mimetype = input.alternate_mimetype.join('|');
-        }
         await MimeType.create(input);
         // if (request.input('roles')) {
         //     const roles: Array<number> = request.input('roles');
@@ -64,7 +59,7 @@ 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.array.minLength': 'at least {{ min }} mimetypes must be defined',
+        'file_extension.minLength': 'at least {{ min }} mimetypes must be defined',
         'file_extension.*.string': 'Each file extension must be a valid string', // Adjusted to match the type
     };
 

app/Controllers/Http/Admin/mailsettings_controller.ts

@@ -76,24 +76,23 @@ 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.' });
         }
 
         try {
-            await mail.send(
+            await mail.send((message) => {
-                (message) => {
+                message
-                    message
+                    // .from(Config.get('mail.from.address'))
-                        // .from(Config.get('mail.from.address'))
+                    .from('tethys@geosphere.at')
-                        .from('tethys@geosphere.at')
+                    .to(userEmail)
-                        .to(userEmail)
+                    .subject('Test Email')
-                        .subject('Test Email')
+                    .html('<p>If you received this email, the email configuration seems to be correct.</p>');
-                        .html('<p>If you received this email, the email configuration seems to be correct.</p>');
+            });
-                });
 
             return response.json({ success: true, message: 'Test email sent successfully' });
             // return response.flash('Test email sent successfully!', 'message').redirect().back();

app/Controllers/Http/Api/AuthorsController.ts

@@ -4,29 +4,17 @@ import Person from '#models/person';
 
 // node ace make:controller Author
 export default class AuthorsController {
-    public async index({}: HttpContext) {       
+    public async index({}: HttpContext) {
-        
+        // select * from gba.persons
+        // where exists (select * from gba.documents inner join gba.link_documents_persons on "documents"."id" = "link_documents_persons"."document_id"
+        // 			  where ("link_documents_persons"."role" = 'author') and ("persons"."id" = "link_documents_persons"."person_id"));
         const authors = await Person.query()
-        .select([
+            .whereHas('datasets', (dQuery) => {
-            'id', 
+                dQuery.wherePivot('role', 'author');
-            'academic_title', 
+            })
-            'first_name', 
+            .withCount('datasets', (query) => {
-            'last_name', 
+                query.as('datasets_count');
-            '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;
     }
@@ -37,10 +25,7 @@ export default class AuthorsController {
         if (request.input('filter')) {
             // users = users.whereRaw('name like %?%', [request.input('search')])
             const searchTerm = request.input('filter');
-            authors.andWhere((query) => {
+            authors.whereILike('first_name', `%${searchTerm}%`).orWhereILike('last_name', `%${searchTerm}%`);
-                query.whereILike('first_name', `%${searchTerm}%`)
-                     .orWhereILike('last_name', `%${searchTerm}%`);
-            });
             // .orWhere('email', 'like', `%${searchTerm}%`);
         }
 

app/Controllers/Http/Api/AvatarController.ts

@@ -1,212 +1,65 @@
 import type { HttpContext } from '@adonisjs/core/http';
 import { StatusCodes } from 'http-status-codes';
-import redis from '@adonisjs/redis/services/main';
+// import * as fs from 'fs';
+// import * as path from 'path';
 
-const PREFIXES = ['von', 'van', 'de', 'del', 'della', 'di', 'da', 'dos', 'du', 'le', 'la'];
+const prefixes = ['von', 'van'];
-const DEFAULT_SIZE = 50;
-const MIN_SIZE = 16;
-const MAX_SIZE = 512;
-const FONT_SIZE_RATIO = 0.4;
-const COLOR_LIGHTENING_PERCENT = 60;
-const COLOR_DARKENING_FACTOR = 0.6;
-const CACHE_TTL = 24 * 60 * 60; // 24 hours instead of 1 hour
 
+// node ace make:controller Author
 export default class AvatarController {
     public async generateAvatar({ request, response }: HttpContext) {
         try {
-            const { name, size = DEFAULT_SIZE } = request.only(['name', 'size']);
+            const { name, background, textColor, size } = request.only(['name', 'background', 'textColor', 'size']);
-
-            // Enhanced validation
-            if (!name || typeof name !== 'string' || name.trim().length === 0) {
-                return response.status(StatusCodes.BAD_REQUEST).json({
-                    error: 'Name is required and must be a non-empty string',
-                });
-            }
-
-            const parsedSize = this.validateSize(size);
-            if (!parsedSize.isValid) {
-                return response.status(StatusCodes.BAD_REQUEST).json({
-                    error: parsedSize.error,
-                });
-            }
-
-            // Build a unique cache key for the given name and size
-            const cacheKey = `avatar:${this.sanitizeName(name)}-${parsedSize.value}`;
-            // const cacheKey = `avatar:${name.trim().toLowerCase()}-${size}`;
-            try {
-                const cachedSvg = await redis.get(cacheKey);
-                if (cachedSvg) {
-                    this.setResponseHeaders(response);
-                    return response.send(cachedSvg);
-                }
-            } catch (redisError) {
-                // Log redis error but continue without cache
-                console.warn('Redis cache read failed:', redisError);
-            }
 
+            // Generate initials
+            // const initials = name
+            //     .split(' ')
+            //     .map((part) => part.charAt(0).toUpperCase())
+            //     .join('');
             const initials = this.getInitials(name);
-            const colors = this.generateColors(name);
-            const svgContent = this.createSvg(size, colors, initials);
 
-            // // Cache the generated avatar for future use, e.g. 1 hour expiry
+            // Define SVG content with dynamic values for initials, background color, text color, and size
-            try {
+            const svgContent = `
-                await redis.setex(cacheKey, CACHE_TTL, svgContent);
+            <svg width="${size || 50}" height="${size || 50}" xmlns="http://www.w3.org/2000/svg">
-            } catch (redisError) {
+              <rect width="100%" height="100%" fill="#${background || '7F9CF5'}"/>
-                // Log but don't fail the request
+              <text x="50%" y="50%" dominant-baseline="middle" text-anchor="middle" font-weight="bold" font-family="Arial, sans-serif" font-size="${
-                console.warn('Redis cache write failed:', redisError);
+                  (size / 100) * 40 || 25
-            }
+              }" fill="#${textColor || 'ffffff'}">${initials}</text>
+            </svg>
+          `;
+
+            // Set response headers for SVG content
+            response.header('Content-type', 'image/svg+xml');
+            response.header('Cache-Control', 'no-cache');
+            response.header('Pragma', 'no-cache');
+            response.header('Expires', '0');
 
-            this.setResponseHeaders(response);
             return response.send(svgContent);
         } catch (error) {
-            console.error('Avatar generation error:', error);
+            return response.status(StatusCodes.OK).json({ error: error.message });
-            return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({
-                error: 'Failed to generate avatar',
-            });
         }
     }
 
-    private validateSize(size: any): { isValid: boolean; value?: number; error?: string } {
+    private getInitials(name: string) {
-        const numSize = Number(size);
+        const parts = name.split(' ');
+        let initials = '';
 
-        if (isNaN(numSize)) {
+        if (parts.length >= 2) {
-            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)
-            .map((part) => part.trim());
-
-        if (parts.length === 0) {
-            return 'NA';
-        }
-
-        if (parts.length === 1) {
-            // For single word, take first 2 characters or first char if only 1 char
-            return parts[0].substring(0, Math.min(2, parts[0].length)).toUpperCase();
-        }
-
-        return this.getMultiWordInitials(parts);
-    }
-
-    private getMultiWordInitials(parts: string[]): string {
-        // Filter out prefixes and short words
-        const significantParts = parts.filter((part) => !PREFIXES.includes(part.toLowerCase()) && part.length > 1);
-
-        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();
+
+            const firstInitial = firstName.charAt(0).toUpperCase();
+            const lastInitial = lastName.charAt(0).toUpperCase();
+
+            if (prefixes.includes(lastName.toLowerCase()) && lastName === lastName.toUpperCase()) {
+                initials = firstInitial + lastName.charAt(1).toUpperCase();
+            } else {
+                initials = firstInitial + lastInitial;
+            }
+        } else if (parts.length === 1) {
+            initials = parts[0].substring(0, 2).toUpperCase();
         }
 
-        if (significantParts.length === 1) {
+        return initials;
-            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 } {
-        const baseColor = this.getColorFromName(name);
-        return {
-            background: this.lightenColor(baseColor, COLOR_LIGHTENING_PERCENT),
-            text: this.darkenColor(baseColor),
-        };
-    }
-
-    private createSvg(size: number, colors: { background: string; text: string }, initials: string): string {
-        const fontSize = Math.max(12, Math.floor(size * FONT_SIZE_RATIO)); // Ensure readable font size
-
-        // Escape any potential HTML/XML characters in initials
-        const escapedInitials = this.escapeXml(initials);
-
-        return `<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', 'public, max-age=86400'); // Cache for 1 day
-        response.header('ETag', `"${Date.now()}"`); // Simple ETag
-    }
-
-    private getColorFromName(name: string): string {
-        let hash = 0;
-        const normalizedName = name.toLowerCase().trim();
-
-        for (let i = 0; i < normalizedName.length; i++) {
-            hash = normalizedName.charCodeAt(i) + ((hash << 5) - hash);
-            hash = hash & hash; // Convert to 32-bit integer
-        }
-
-        // Ensure we get vibrant colors by constraining the color space
-        const colorParts = [];
-        for (let i = 0; i < 3; i++) {
-            let value = (hash >> (i * 8)) & 0xff;
-            // Ensure minimum color intensity for better contrast
-            value = Math.max(50, value);
-            colorParts.push(value.toString(16).padStart(2, '0'));
-        }
-        return colorParts.join('');
-    }
-
-    private lightenColor(hexColor: string, percent: number): string {
-        const r = parseInt(hexColor.substring(0, 2), 16);
-        const g = parseInt(hexColor.substring(2, 4), 16);
-        const b = parseInt(hexColor.substring(4, 6), 16);
-
-        const lightenValue = (value: number) => Math.min(255, Math.floor(value + (255 - value) * (percent / 100)));
-
-        const newR = lightenValue(r);
-        const newG = lightenValue(g);
-        const newB = lightenValue(b);
-
-        return ((newR << 16) | (newG << 8) | newB).toString(16).padStart(6, '0');
-    }
-
-    private darkenColor(hexColor: string): string {
-        const r = parseInt(hexColor.slice(0, 2), 16);
-        const g = parseInt(hexColor.slice(2, 4), 16);
-        const b = parseInt(hexColor.slice(4, 6), 16);
-
-        const darkenValue = (value: number) => Math.max(0, Math.floor(value * COLOR_DARKENING_FACTOR));
-
-        const darkerR = darkenValue(r);
-        const darkerG = darkenValue(g);
-        const darkerB = darkenValue(b);
-
-        return ((darkerR << 16) + (darkerG << 8) + darkerB).toString(16).padStart(6, '0');
     }
 }

app/Controllers/Http/Api/DatasetController.ts

@@ -1,36 +1,19 @@
 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) {
-     * GET /api/datasets
+        // select * from gba.persons
-     * Find all published datasets
+        // 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({ response }: HttpContext) {
+        const datasets = await Dataset.query().where('server_state', 'published').orWhere('server_state', 'deleted');
-        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 response.status(StatusCodes.OK).json(datasets);
+        return 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()
@@ -46,279 +29,34 @@ export default class DatasetController {
         }
     }
 
-    /**
+    public async findOne({ params }: HttpContext) {
-     * GET /api/dataset/:publish_id
+        const datasets = await Dataset.query()
-     * Find one dataset by publish_id
+            .where('publish_id', params.publish_id)
-     */
+            .preload('titles')
-    public async findOne({ response, params }: HttpContext) {
+            .preload('descriptions')
-        try {
+            .preload('user')
-            const dataset = await Dataset.query()
+            .preload('authors', (builder) => {
-                .where('publish_id', params.publish_id)
+                builder.orderBy('pivot_sort_order', 'asc');
-                .preload('titles')
+            })
-                .preload('descriptions') // Using 'descriptions' instead of 'abstracts'
+            .preload('contributors', (builder) => {
-                .preload('user', (builder) => {
+                builder.orderBy('pivot_sort_order', 'asc');
-                    builder.select(['id', 'firstName', 'lastName', 'avatar', 'login']);
+            })
-                })
+            .preload('subjects')
-                .preload('authors', (builder) => {
+            .preload('coverage')
-                    builder
+            .preload('licenses')
-                        .select(['id', 'academic_title', 'first_name', 'last_name', 'identifier_orcid', 'status', 'name_type'])
+            .preload('references')
-                        .withCount('datasets', (query) => {
+            .preload('project')
-                            query.as('datasets_count');
+            .preload('referenced_by', (builder) => {
-                        })
+                builder.preload('dataset', (builder) => {
-                        .pivotColumns(['role', 'sort_order'])
+                    builder.preload('identifier');
-                        .orderBy('pivot_sort_order', 'asc');
-                })
-                .preload('contributors', (builder) => {
-                    builder
-                        .select(['id', 'academic_title', 'first_name', 'last_name', 'identifier_orcid', 'status', 'name_type'])
-                        .withCount('datasets', (query) => {
-                            query.as('datasets_count');
-                        })
-                        .pivotColumns(['role', 'sort_order', 'contributor_type'])
-                        .orderBy('pivot_sort_order', 'asc');
-                })
-                .preload('subjects')
-                .preload('coverage')
-                .preload('licenses')
-                .preload('references')
-                .preload('project')
-                // .preload('referenced_by', (builder) => {
-                //     builder.preload('dataset', (builder) => {
-                //         builder.preload('identifier');
-                //     });
-                // })
-                .preload('files', (builder) => {
-                    builder.preload('hashvalues');
-                })
-                .preload('identifier')
-                .first(); // Use first() instead of firstOrFail() to handle not found gracefully
-
-            if (!dataset) {
-                return response.status(StatusCodes.NOT_FOUND).json({
-                    message: `Cannot find Dataset with publish_id=${params.publish_id}.`,
                 });
-            }
+            })
+            .preload('files', (builder) => {
+                builder.preload('hashvalues');
+            })
+            .preload('identifier')
+            .firstOrFail();
 
-            // Build the version chain
+        return datasets;
-            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;
-    }
-
-    /**
-     * 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;
     }
 }

app/Controllers/Http/Api/FileController.ts

@@ -2,103 +2,53 @@ import type { HttpContext } from '@adonisjs/core/http';
 import File from '#models/file';
 import { StatusCodes } from 'http-status-codes';
 import * as fs from 'fs';
-import { DateTime } from 'luxon';
+import * as path from 'path';
 
 // node ace make:controller Author
 export default class FileController {
     // @Get("download/:id")
     public async findOne({ response, params }: HttpContext) {
         const id = params.id;
-        // const file = await File.findOrFail(id);
+        const file = await File.findOrFail(id);
-        // Load file with its related dataset to check embargo
+        // const file = await File.findOne({
-        const file = await File.query()
+        //     where: { id: id },
-            .where('id', id)
+        // });
-            .preload('dataset') // or 'dataset' - whatever your relationship is named
+        if (file) {
-            .firstOrFail();
+            const filePath = '/storage/app/public/' + file.pathName;
+            const ext = path.extname(filePath);
+            const fileName = file.label + ext;
+            try {
+                fs.accessSync(filePath, fs.constants.R_OK); //| fs.constants.W_OK);
+                // console.log("can read/write:", path);
+               
+                response
+                    .header('Cache-Control', 'no-cache private')
+                    .header('Content-Description', 'File Transfer')
+                    .header('Content-Type', file.mimeType)
+                    .header('Content-Disposition', 'inline; filename=' + fileName)
+                    .header('Content-Transfer-Encoding', 'binary')
+                    .header('Access-Control-Allow-Origin', '*')
+                    .header('Access-Control-Allow-Methods', 'GET,POST');
+                
+                response.status(StatusCodes.OK).download(filePath);               
+            } catch (err) {
+                // console.log("no access:", path);
+                response.status(StatusCodes.NOT_FOUND).send({
+                    message: `File with id ${id} doesn't exist on file server`,
+                });
+            }
 
-        if (!file) {
+            // res.status(StatusCodes.OK).sendFile(filePath, (err) => {
-            return response.status(StatusCodes.NOT_FOUND).send({
+            //     // res.setHeader("Content-Type", "application/json");
+            //     // res.removeHeader("Content-Disposition");
+            //     res.status(StatusCodes.NOT_FOUND).send({
+            //         message: `File with id ${id} doesn't exist on file server`,
+            //     });
+            // });
+        } else {
+            response.status(StatusCodes.NOT_FOUND).send({
                 message: `Cannot find File with id=${id}.`,
             });
         }
-
-        const dataset = file.dataset;
-        // Files from unpublished datasets are now blocked
-        if (dataset.server_state !== 'published') {
-            return response.status(StatusCodes.FORBIDDEN).send({
-                message: `File access denied: Dataset is not published.`,
-            });
-        }
-        if (dataset && this.isUnderEmbargo(dataset.embargo_date)) {
-            return response.status(StatusCodes.FORBIDDEN).send({
-                message: `File is under embargo until ${dataset.embargo_date?.toFormat('yyyy-MM-dd')}`,
-            });
-        }
-
-        // Proceed with file download
-        const filePath = '/storage/app/data/' + file.pathName;
-        const fileExt = file.filePath.split('.').pop() || '';
-        // const fileName = file.label + fileExt;
-        const fileName = file.label.toLowerCase().endsWith(`.${fileExt.toLowerCase()}`) ? file.label : `${file.label}.${fileExt}`;
-
-        // Determine if file can be previewed inline in browser
-        const canPreviewInline = (mimeType: string): boolean => {
-            const type = mimeType.toLowerCase();
-            return (
-                type === 'application/pdf' ||
-                type.startsWith('image/') ||
-                type.startsWith('text/') ||
-                type === 'application/json' ||
-                type === 'application/xml' ||
-                // Uncomment if you want video/audio inline
-                type.startsWith('video/') ||
-                type.startsWith('audio/')
-            );
-        };
-        const disposition = canPreviewInline(file.mimeType) ? 'inline' : 'attachment';
-
-        try {
-            fs.accessSync(filePath, fs.constants.R_OK); //| fs.constants.W_OK);
-            // console.log("can read/write:", filePath);
-
-            response
-                .header('Cache-Control', 'no-cache private')
-                .header('Content-Description', 'File Transfer')
-                .header('Content-Type', file.mimeType)
-                .header('Content-Disposition', `${disposition}; filename="${fileName}"`)
-                .header('Content-Transfer-Encoding', 'binary')
-                .header('Access-Control-Allow-Origin', '*')
-                .header('Access-Control-Allow-Methods', 'GET');
-
-            response.status(StatusCodes.OK).download(filePath);
-        } catch (err) {
-            // console.log("no access:", path);
-            response.status(StatusCodes.NOT_FOUND).send({
-                message: `File with id ${id} doesn't exist on file server`,
-            });
-        }
-    }
-
-    /**
-     * Check if the dataset is under embargo
-     * Compares only dates (ignoring time) for embargo check
-     * @param embargoDate - The embargo date from dataset
-     * @returns true if under embargo, false if embargo has passed or no embargo set
-     */
-    private isUnderEmbargo(embargoDate: DateTime | null): boolean {
-        // No embargo date set - allow download
-        if (!embargoDate) {
-            return false;
-        }
-
-        // Get current date at start of day (00:00:00)
-        const today = DateTime.now().startOf('day');
-
-        // Get embargo date at start of day (00:00:00)
-        const embargoDateOnly = embargoDate.startOf('day');
-
-        // File is under embargo if embargo date is after today
-        // This means the embargo lifts at the start of the embargo date
-        return embargoDateOnly >= today;
     }
 }

app/Controllers/Http/Api/HomeController.ts

@@ -17,8 +17,7 @@ export default class HomeController {
             //     .preload('authors')
             //     .orderBy('server_date_published');
 
-            const datasets = await db
+            const datasets = await db.from('documents as doc')
-                .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')
@@ -60,6 +59,7 @@ 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)
@@ -68,12 +68,9 @@ export default class HomeController {
             //     .groupBy('pub_month');
             //     // .orderBy('server_date_published');
 
-            // Calculate the last 4 years including the current year
+            const years = [2021, 2022, 2023]; // Add the second year
-            const currentYear = new Date().getFullYear();
-            const years = Array.from({ length: 4 }, (_, i) => currentYear - (i + 1)).reverse();
 
-            const result = await db
+            const result = await db.from('documents as doc')
-                .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`),
@@ -86,7 +83,7 @@ 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) => {
@@ -103,15 +100,15 @@ 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,
@@ -129,11 +126,11 @@ 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;
     }
 }
@@ -142,4 +139,5 @@ interface ChartDataset {
     label: string;
     borderColor: string;
     fill: boolean;
+
 }

app/Controllers/Http/Api/UserController.ts

@@ -9,24 +9,6 @@ import BackupCode from '#models/backup_code';
 
 // Here we are generating secret and recovery codes for the user that’s enabling 2FA and storing them to our database.
 export default class UserController {
-    public async getSubmitters({ response }: HttpContext) {
-        try {
-            const submitters = await User.query()
-                .preload('roles', (query) => {
-                    query.where('name', 'submitter')
-                })
-                .whereHas('roles', (query) => {
-                    query.where('name', 'submitter')
-                })
-                .exec();
-            return submitters;
-        } catch (error) {
-            return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({
-                message: 'Invalid TOTP state',
-            });
-        }
-    }
-
     public async enable({ auth, response, request }: HttpContext) {
         const user = (await User.find(auth.user?.id)) as User;
         // await user.load('totp_secret');

app/Controllers/Http/Api/collections_controller.ts

@@ -1,36 +0,0 @@
-import type { HttpContext } from '@adonisjs/core/http';
-import Collection from '#models/collection';
-
-export default class CollectionsController {
-    public async show({ params, response }: HttpContext) {
-        // Get the collection id from route parameters
-        const collectionId = params.id;
-
-        // Find the selected collection by id
-        const collection = await Collection.find(collectionId);
-        if (!collection) {
-            return response.status(404).json({ message: 'Collection not found' });
-        }
-
-        // Query for narrower concepts: collections whose parent_id equals the selected collection's id
-        const narrowerCollections = await Collection.query().where('parent_id', collection.id) || [];
-
-        // For broader concept, if the selected collection has a parent_id fetch that record (otherwise null)
-        const broaderCollection: Collection[] | never[] | null = await (async () => {
-            if (collection.parent_id) {
-              // Try to fetch the parent...
-              const parent = await Collection.find(collection.parent_id)
-              // If found, return it wrapped in an array; if not found, return null (or empty array if you prefer)
-              return parent ? [parent] : null
-            }
-            return []
-          })()
-
-        // Return the selected collection along with its narrower and broader concepts in JSON format
-        return response.json({
-            selectedCollection: collection,
-            narrowerCollections,
-            broaderCollection,
-        });
-    }
-}

app/Controllers/Http/Auth/AuthController.ts

@@ -5,7 +5,7 @@ import BackupCode from '#models/backup_code';
 // 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';
@@ -29,10 +29,6 @@ export default class AuthController {
         const { email, password } = request.only(['email', 'password']);
 
         try {
-           
-             await db.connection().rawQuery('SELECT 1')
-             
-              
             // // attempt to verify credential and login user
             // await auth.use('web').attempt(email, plainPassword);
 
@@ -55,9 +51,6 @@ export default class AuthController {
 
             await auth.use('web').login(user);
         } catch (error) {
-            if (error.code === 'ECONNREFUSED') {
-                throw error
-            }
             // if login fails, return vague form message and redirect back
             session.flash('message', 'Your username, email, or password is incorrect');
             return response.redirect().back();

app/Controllers/Http/Auth/UserController.ts

@@ -6,11 +6,6 @@ import hash from '@adonisjs/core/services/hash';
 // import { schema, rules } from '@adonisjs/validator';
 import vine from '@vinejs/vine';
 import BackupCodeStorage, { SecureRandom } from '#services/backup_code_storage';
-import path from 'path';
-import crypto from 'crypto';
-// import drive from '#services/drive';
-import drive from '@adonisjs/drive/services/main';
-import logger from '@adonisjs/core/services/logger';
 
 // Here we are generating secret and recovery codes for the user that’s enabling 2FA and storing them to our database.
 export default class UserController {
@@ -33,7 +28,7 @@ export default class UserController {
             user: user,
             twoFactorEnabled: user.isTwoFactorEnabled,
             // code: await TwoFactorAuthProvider.generateQrCode(user),
-            backupState: backupState,
+            backupState:  backupState,
         });
     }
 
@@ -45,8 +40,10 @@ export default class UserController {
         // });
         const passwordSchema = vine.object({
             // first step
-            old_password: vine.string().trim(),
+            old_password: vine
-            // .regex(/^[a-zA-Z0-9]+$/),
+                .string()
+                .trim()
+                .regex(/^[a-zA-Z0-9]+$/),
             new_password: vine.string().confirmed({ confirmationField: 'confirm_password' }).trim().minLength(8).maxLength(255),
         });
         try {
@@ -57,9 +54,9 @@ export default class UserController {
             // return response.badRequest(error.messages);
             throw error;
         }
-
+        
         try {
-            const user = (await auth.user) as User;
+            const user = await auth.user as User;
             const { old_password, new_password } = request.only(['old_password', 'new_password']);
 
             // if (!(old_password && new_password && confirm_password)) {
@@ -85,171 +82,6 @@ export default class UserController {
         }
     }
 
-    public async profile({ inertia, auth }: HttpContext) {
-        const user = await User.find(auth.user?.id);
-        // let test = await drive.use().getUrl(user?.avatar);
-        // user?.preload('roles');
-        const avatarFullPathUrl = user?.avatar ? await drive.use('public').getUrl(user.avatar) : null;
-        return inertia.render('profile/show', {
-            user: user,
-            defaultUrl: avatarFullPathUrl,
-        });
-    }
-
-    /**
-     * Update the user's profile information.
-     *
-     * @param {HttpContext} ctx - The HTTP context object.
-     * @returns {Promise<void>}
-     */
-    public async profileUpdate({ auth, request, response, session }: HttpContext) {
-        if (!auth.user) {
-            session.flash('error', 'You must be logged in to update your profile.');
-            return response.redirect().toRoute('login');
-        }
-
-        const updateProfileValidator = vine.withMetaData<{ userId: number }>().compile(
-            vine.object({
-                first_name: vine.string().trim().minLength(4).maxLength(255),
-                last_name: vine.string().trim().minLength(4).maxLength(255),
-                login: vine.string().trim().minLength(4).maxLength(255),
-                email: vine
-                    .string()
-                    .trim()
-                    .maxLength(255)
-                    .email()
-                    .normalizeEmail()
-                    .isUnique({ table: 'accounts', column: 'email', whereNot: (field) => field.meta.userId }),
-                avatar: vine
-                    .myfile({
-                        size: '2mb',
-                        extnames: ['jpg', 'jpeg', 'png', 'gif', 'webp', 'svg'],
-                    })
-                    // .allowedMimetypeExtensions({
-                    //     allowedExtensions: ['jpg', 'jpeg', 'png', 'gif', 'webp', 'svg'],
-                    // })
-                    .optional(),
-            }),
-        );
-
-        const user = await User.find(auth.user.id);
-        if (!user) {
-            session.flash('error', 'User not found.');
-            return response.redirect().toRoute('login');
-        }
-
-        try {
-            // validate update form
-            await request.validateUsing(updateProfileValidator, {
-                meta: {
-                    userId: user.id,
-                },
-            });
-
-            const { login, email, first_name, last_name } = request.only(['login', 'email', 'first_name', 'last_name']);
-            const sanitizedData: { [key: string]: any } = {
-                login: login?.trim(),
-                email: email?.toLowerCase().trim(),
-                first_name: first_name?.trim(),
-                last_name: last_name?.trim(),
-                // avatar: "",
-            };
-            const toCamelCase = (str: string) => str.replace(/_([a-z])/g, (g) => g[1].toUpperCase());
-            const hasInputChanges = Object.keys(sanitizedData).some((key) => {
-                const camelKey = toCamelCase(key);
-                return sanitizedData[key] !== (user.$attributes as { [key: string]: any })[camelKey];
-            });
-
-            let hasAvatarChanged = false;
-            const avatar = request.file('avatar');
-            if (avatar) {
-                const fileHash = crypto
-                    .createHash('sha256')
-                    .update(avatar.clientName + avatar.size)
-                    .digest('hex');
-                const fileName = `avatar-${fileHash}.${avatar.extname}`;
-                const avatarFullPath = path.join('/uploads', `${user.login}`, fileName);
-
-                if (user.avatar != avatarFullPath) {
-                    if (user.avatar) {
-                        await drive.use('public').delete(user.avatar);
-                    }
-                    hasAvatarChanged = user.avatar !== avatarFullPath;
-                    await avatar.moveToDisk(avatarFullPath, 'public', {
-                        name: fileName,
-                        overwrite: true, // overwrite in case of conflict
-                        disk: 'public',
-                    });
-                    sanitizedData.avatar = avatarFullPath;
-                }
-            }
-
-            if (!hasInputChanges && !hasAvatarChanged) {
-                session.flash('message', 'No changes were made.');
-                return response.redirect().back();
-            }
-
-            await user.merge(sanitizedData).save();
-            session.flash('message', 'User has been updated successfully');
-            return response.redirect().toRoute('settings.profile.edit');
-        } catch (error) {
-            logger.error('Profile update failed:', error);
-            // session.flash('errors', 'Profile update failed. Please try again.');
-            // return response.redirect().back();
-            throw error;
-        }
-    }
-
-    public async passwordUpdate({ auth, request, response, session }: HttpContext) {
-        // const passwordSchema = schema.create({
-        //     old_password: schema.string({ trim: true }, [rules.required()]),
-        //     new_password: schema.string({ trim: true }, [rules.minLength(8), rules.maxLength(255), rules.confirmed('confirm_password')]),
-        //     confirm_password: schema.string({ trim: true }, [rules.required()]),
-        // });
-        const passwordSchema = vine.object({
-            // first step
-            old_password: vine.string().trim(),
-            // .regex(/^[a-zA-Z0-9]+$/),
-            new_password: vine.string().confirmed({ confirmationField: 'confirm_password' }).trim().minLength(8).maxLength(255),
-        });
-        try {
-            // await request.validate({ schema: passwordSchema });
-            const validator = vine.compile(passwordSchema);
-            await request.validateUsing(validator);
-        } catch (error) {
-            // return response.badRequest(error.messages);
-            throw error;
-        }
-
-        try {
-            const user = (await auth.user) as User;
-            const { old_password, new_password } = request.only(['old_password', 'new_password']);
-
-            // if (!(old_password && new_password && confirm_password)) {
-            //     return response.status(400).send({ warning: 'Old password and new password are required.' });
-            // }
-
-            // Verify if the provided old password matches the user's current password
-            const isSame = await hash.verify(user.password, old_password);
-            if (!isSame) {
-                session.flash('warning', 'Old password is incorrect.');
-                return response.redirect().back();
-                // return response.flash('warning', 'Old password is incorrect.').redirect().back();
-            }
-
-            // Hash the new password before updating the user's password
-            user.password = new_password;
-            await user.save();
-
-            // return response.status(200).send({ message: 'Password updated successfully.' });
-            session.flash({ message: 'Password updated successfully.' });
-            return response.redirect().toRoute('settings.profile.edit');
-        } catch (error) {
-            // return response.status(500).send({ message: 'Internal server error.' });
-            return response.flash('warning', `Invalid server state. Internal server error.`).redirect().back();
-        }
-    }
-
     public async enableTwoFactorAuthentication({ auth, response, session }: HttpContext): Promise<void> {
         // const user: User | undefined = auth?.user;
         const user = (await User.find(auth.user?.id)) as User;
@@ -283,7 +115,7 @@ export default class UserController {
         } else {
             session.flash('error', 'User not found.');
         }
-
+    
         return response.redirect().back();
         // return inertia.render('Auth/AccountInfo', {
         //     // status: {

app/Controllers/Http/Editor/DatasetController.ts

@@ -3,7 +3,7 @@ import { Client } from '@opensearch-project/opensearch';
 import User from '#models/user';
 import Dataset from '#models/dataset';
 import DatasetIdentifier from '#models/dataset_identifier';
-import DatasetXmlSerializer from '#app/Library/DatasetXmlSerializer';
+import XmlModel from '#app/Library/XmlModel';
 import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
 import { create } from 'xmlbuilder2';
 import { readFileSync } from 'fs';
@@ -18,33 +18,9 @@ import { HttpException } from 'node-exceptions';
 import { ModelQueryBuilderContract } from '@adonisjs/lucid/types/model';
 import vine, { SimpleMessagesProvider } from '@vinejs/vine';
 import mail from '@adonisjs/mail/services/main';
+// import { resolveMx } from 'dns/promises';
+// import * as net from 'net';
 import { validate } from 'deep-email-validator';
-import {
-    TitleTypes,
-    DescriptionTypes,
-    ContributorTypes,
-    PersonNameTypes,
-    ReferenceIdentifierTypes,
-    RelationTypes,
-    SubjectTypes,
-    DatasetTypes,
-} from '#contracts/enums';
-import { TransactionClientContract } from '@adonisjs/lucid/types/database';
-import db from '@adonisjs/lucid/services/db';
-import Project from '#models/project';
-import License from '#models/license';
-import Language from '#models/language';
-import File from '#models/file';
-import Coverage from '#models/coverage';
-import Title from '#models/title';
-import Description from '#models/description';
-import Subject from '#models/subject';
-import DatasetReference from '#models/dataset_reference';
-import Collection from '#models/collection';
-import CollectionRole from '#models/collection_role';
-import { updateEditorDatasetValidator } from '#validators/dataset';
-import { savePersons } from '#app/utils/utility-functions';
-
 // Create a new instance of the client
 const client = new Client({ node: 'http://localhost:9200' }); // replace with your OpenSearch endpoint
 
@@ -87,15 +63,8 @@ export default class DatasetsController {
             }
             datasets.orderBy(attribute, sortOrder);
         } else {
-            // datasets.orderBy('id', 'asc');
+            // users.orderBy('created_at', 'desc');
-            // Custom ordering to prioritize rejected_editor state
+            datasets.orderBy('id', 'asc');
-            datasets.orderByRaw(`
-                CASE 
-                    WHEN server_state = 'rejected_reviewer' THEN 0 
-                    ELSE 1 
-                END ASC, 
-                id ASC
-            `);
         }
 
         // const users = await User.query().orderBy('login').paginate(page, limit);
@@ -188,16 +157,10 @@ export default class DatasetsController {
         }
     }
 
-    public async approve({ request, inertia, response, auth }: HttpContext) {
+    public async approve({ request, inertia, response }: HttpContext) {
         const id = request.param('id');
-
-        const user = auth.user;
-        if (!user) {
-            return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
-        }
-        
         // $dataset = Dataset::with('user:id,login')->findOrFail($id);
-        const dataset = await Dataset.query().where('id', id).where('editor_id', user.id).firstOrFail();
+        const dataset = await Dataset.findOrFail(id);
 
         const validStates = ['editor_accepted', 'rejected_reviewer'];
         if (!validStates.includes(dataset.server_state)) {
@@ -223,7 +186,7 @@ export default class DatasetsController {
         });
     }
 
-    public async approveUpdate({ request, response, auth }: HttpContext) {
+    public async approveUpdate({ request, response }: HttpContext) {
         const approveDatasetSchema = vine.object({
             reviewer_id: vine.number(),
         });
@@ -236,11 +199,7 @@ export default class DatasetsController {
             throw error;
         }
         const id = request.param('id');
-          const user = auth.user;
+        const dataset = await Dataset.findOrFail(id);
-        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().where('id', id).where('editor_id', user.id).firstOrFail();
 
         const validStates = ['editor_accepted', 'rejected_reviewer'];
         if (!validStates.includes(dataset.server_state)) {
@@ -258,9 +217,6 @@ export default class DatasetsController {
         if (dataset.reject_reviewer_note != null) {
             dataset.reject_reviewer_note = null;
         }
-        if (dataset.reject_editor_note != null) {
-            dataset.reject_editor_note = null;
-        }
 
         //save main and additional titles
         const reviewer_id = request.input('reviewer_id', null);
@@ -271,15 +227,10 @@ export default class DatasetsController {
         }
     }
 
-    public async reject({ request, inertia, response, auth }: HttpContext) {
+    public async reject({ request, inertia, response }: HttpContext) {
         const id = request.param('id');
-        const user = auth.user;
-        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()
             .where('id', id)
-            .where('editor_id', user.id) // Ensure the user is the editor of the dataset
             // .preload('titles')
             // .preload('descriptions')
             .preload('user', (builder) => {
@@ -304,17 +255,77 @@ export default class DatasetsController {
         });
     }
 
+    // private async checkEmailDomain(email: string): Promise<boolean> {
+    //     const domain = email.split('@')[1];
+
+    //     try {
+    //         // Step 1: Check MX records for the domain
+    //         const mxRecords = await resolveMx(domain);
+    //         if (mxRecords.length === 0) {
+    //             return false; // No MX records, can't send email
+    //         }
+
+    //         // Sort MX records by priority
+    //         mxRecords.sort((a, b) => a.priority - b.priority);
+
+    //         // Step 2: Attempt SMTP connection to the first available mail server
+    //         const smtpServer = mxRecords[0].exchange;
+
+    //         return await this.checkMailboxExists(smtpServer, email);
+    //     } catch (error) {
+    //         console.error('Error during MX lookup or SMTP validation:', error);
+    //         return false;
+    //     }
+    // }
+
+    //// Helper function to check if the mailbox exists using SMTP
+    // private async checkMailboxExists(smtpServer: string, email: string): Promise<boolean> {
+    //     return new Promise((resolve, reject) => {
+    //         const socket = net.createConnection(25, smtpServer);
+
+    //         socket.on('connect', () => {
+    //             socket.write(`HELO ${smtpServer}\r\n`);
+    //             socket.write(`MAIL FROM: <test@example.com>\r\n`);
+    //             socket.write(`RCPT TO: <${email}>\r\n`);
+    //         });
+
+    //         socket.on('data', (data) => {
+    //             const response = data.toString();
+    //             if (response.includes('250')) {
+    //                 // 250 is an SMTP success code
+    //                 socket.end();
+    //                 resolve(true); // Email exists
+    //             } else if (response.includes('550')) {
+    //                 // 550 means the mailbox doesn't exist
+    //                 socket.end();
+    //                 resolve(false); // Email doesn't exist
+    //             }
+    //         });
+
+    //         socket.on('error', (error) => {
+    //             console.error('SMTP connection error:', error);
+    //             socket.end();
+    //             resolve(false);
+    //         });
+
+    //         socket.on('end', () => {
+    //             // SMTP connection closed
+    //         });
+
+    //         socket.setTimeout(5000, () => {
+    //             // Timeout after 5 seconds
+    //             socket.end();
+    //             resolve(false); // Assume email doesn't exist if no response
+    //         });
+    //     });
+    // }
+
     public async rejectUpdate({ request, response, auth }: HttpContext) {
         const authUser = auth.user!;
-        
-        if (!authUser) {
-            return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
-        }
 
         const id = request.param('id');
         const dataset = await Dataset.query()
             .where('id', id)
-            .where('editor_id', authUser.id) // Ensure the user is the editor of the dataset
             .preload('user', (builder) => {
                 builder.select('id', 'login', 'email');
             })
@@ -342,7 +353,7 @@ export default class DatasetsController {
             return response
                 .flash(
                     `Invalid server state. Dataset with id ${id} cannot be rejected. Datset has server state ${dataset.server_state}.`,
-                    'warning',
+                     'warning'
                 )
                 .redirect()
                 .toRoute('editor.dataset.list');
@@ -377,9 +388,7 @@ export default class DatasetsController {
                     emailStatusMessage = ` A rejection email was successfully sent to ${dataset.user.email}.`;
                 } catch (error) {
                     logger.error(error);
-                    return response
+                    return response.flash('Dataset has not been rejected due to an email error: ' + error.message, 'error').toRoute('editor.dataset.list');
-                        .flash('Dataset has not been rejected due to an email error: ' + error.message, 'error')
-                        .toRoute('editor.dataset.list');
                 }
             } else {
                 emailStatusMessage = ` However, the email could not be sent because the submitter's email address (${dataset.user.email}) is not valid.`;
@@ -395,16 +404,11 @@ export default class DatasetsController {
             .toRoute('editor.dataset.list');
     }
 
-    public async publish({ request, inertia, response, auth }: HttpContext) {
+    public async publish({ request, inertia, response }: HttpContext) {
         const id = request.param('id');
-        const user = auth.user;
-        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()
             .where('id', id)
-            .where('editor_id', user.id) // Ensure the user is the editor of the dataset
             .preload('titles')
             .preload('authors')
             // .preload('persons', (builder) => {
@@ -426,14 +430,10 @@ export default class DatasetsController {
 
         return inertia.render('Editor/Dataset/Publish', {
             dataset,
-            can: {
-                reject: await auth.user?.can(['dataset-editor-reject']),
-                publish: await auth.user?.can(['dataset-publish']),
-            },
         });
     }
 
-    public async publishUpdate({ request, response, auth }: HttpContext) {
+    public async publishUpdate({ request, response }: HttpContext) {
         const publishDatasetSchema = vine.object({
             publisher_name: vine.string().trim(),
         });
@@ -445,12 +445,7 @@ export default class DatasetsController {
             throw error;
         }
         const id = request.param('id');
-        const user = auth.user;
+        const dataset = await Dataset.findOrFail(id);
-        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().where('id', id).where('editor_id', user.id).firstOrFail();
 
         // let test = await Dataset.getMax('publish_id');
         // const maxPublishId = await Database.from('documents').max('publish_id as max_publish_id').first();
@@ -476,139 +471,10 @@ export default class DatasetsController {
         }
     }
 
-    public async rejectToReviewer({ request, inertia, response, auth }: HttpContext) {
+    public async doiCreate({ request, inertia }: HttpContext) {
-        const id = request.param('id');
-        const user = auth.user;
-        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()
-            .where('id', id)
-            .where('editor_id', user.id) // Ensure the user is the editor of the dataset
-            .preload('reviewer', (builder) => {
-                builder.select('id', 'login', 'email');
-            })
-            .firstOrFail();
-
-        const validStates = ['reviewed'];
-        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 rejected to the reviewer. Datset has server state ${dataset.server_state}.`,
-                )
-                .redirect()
-                .toRoute('editor.dataset.list');
-        }
-
-        return inertia.render('Editor/Dataset/RejectToReviewer', {
-            dataset,
-        });
-    }
-
-    public async rejectToReviewerUpdate({ request, response, auth }: HttpContext) {
-        const authUser = auth.user!;
-
-        if (!authUser) {
-            return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
-        }
-
         const id = request.param('id');
         const dataset = await Dataset.query()
             .where('id', id)
-            .where('editor_id', authUser.id) // Ensure the user is the editor of the dataset
-            .preload('reviewer', (builder) => {
-                builder.select('id', 'login', 'email');
-            })
-            .firstOrFail();
-
-        const newSchema = vine.object({
-            server_state: vine.string().trim(),
-            reject_editor_note: vine.string().trim().minLength(10).maxLength(500),
-            send_mail: vine.boolean().optional(),
-        });
-
-        try {
-            // await request.validate({ schema: newSchema });
-            const validator = vine.compile(newSchema);
-            await request.validateUsing(validator);
-        } catch (error) {
-            // return response.badRequest(error.messages);
-            throw error;
-        }
-
-        const validStates = ['reviewed'];
-        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(
-                    `Invalid server state. Dataset with id ${id} cannot be rejected to reviewer. Datset has server state ${dataset.server_state}.`,
-                    'warning',
-                )
-                .redirect()
-                .toRoute('editor.dataset.list');
-        }
-
-        dataset.server_state = 'rejected_to_reviewer';
-        const rejectEditorNote = request.input('reject_editor_note', '');
-        dataset.reject_editor_note = rejectEditorNote;
-
-        // add logic for sending reject message
-        const sendMail = request.input('send_email', false);
-        // const validRecipientEmail = await this.checkEmailDomain('arno.kaimbacher@outlook.at');
-        const validationResult = await validate({
-            email: dataset.reviewer.email,
-            validateSMTP: false,
-        });
-        const validRecipientEmail: boolean = validationResult.valid;
-
-        await dataset.save();
-
-        let emailStatusMessage = '';
-        if (sendMail == true) {
-            if (dataset.reviewer.email && validRecipientEmail) {
-                try {
-                    await mail.send((message) => {
-                        message.to(dataset.reviewer.email).subject('Dataset Rejection Notification').html(`
-                            <p>Dear ${dataset.reviewer.login},</p>
-                            <p>Your dataset with ID ${dataset.id} has been rejected.</p>
-                            <p>Reason for rejection: ${rejectEditorNote}</p>
-                            <p>Best regards,<br>Your Tethys editor: ${authUser.login}</p>
-                        `);
-                    });
-                    emailStatusMessage = ` A rejection email was successfully sent to ${dataset.reviewer.email}.`;
-                } catch (error) {
-                    logger.error(error);
-                    return response
-                        .flash('Dataset has not been rejected due to an email error: ' + error.message, 'error')
-                        .toRoute('editor.dataset.list');
-                }
-            } else {
-                emailStatusMessage = ` However, the email could not be sent because the submitter's email address (${dataset.reviewer.email}) is not valid.`;
-            }
-        }
-
-        return response
-            .flash(
-                `You have successfully rejected dataset ${dataset.id} reviewed by ${dataset.reviewer.login}.${emailStatusMessage}`,
-                'message',
-            )
-            .toRoute('editor.dataset.list');
-    }
-
-    public async doiCreate({ request, inertia, auth, response }: HttpContext) {
-        const id = request.param('id');
-        const user = auth.user;
-        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()
-            .where('id', id)
-            .where('editor_id', user.id) // Ensure the user is the editor of the dataset
             .preload('titles')
             .preload('descriptions')
             // .preload('identifier')
@@ -619,494 +485,61 @@ export default class DatasetsController {
         });
     }
 
-    public async doiStore({ request, response, auth }: HttpContext) {
+    public async doiStore({ request, response }: HttpContext) {
         const dataId = request.param('publish_id');
-        const user = auth.user;
-        if (!user) {
-            return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
-        }
-
-        // Load dataset with minimal required relationships
         const dataset = await Dataset.query()
-            .where('editor_id', user.id) // Ensure the user is the editor of the dataset
+            // .preload('xmlCache')
             .where('publish_id', dataId)
             .firstOrFail();
-
-        const prefix = process.env.DATACITE_PREFIX || '';
-        const base_domain = process.env.BASE_DOMAIN || '';
-
-        // Generate DOI metadata XML
         const xmlMeta = (await Index.getDoiRegisterString(dataset)) as string;
 
-        // Prepare DOI registration data
+        let prefix = '';
-        const doiValue = `${prefix}/tethys.${dataset.publish_id}`; //'10.21388/tethys.213'
+        let base_domain = '';
-        const landingPageUrl = `https://doi.${getDomain(base_domain)}/${prefix}/tethys.${dataset.publish_id}`; //https://doi.dev.tethys.at/10.21388/tethys.213
+        // const datacite_environment = process.env.DATACITE_ENVIRONMENT || 'debug';
+        prefix = process.env.DATACITE_PREFIX || '';
+        base_domain = process.env.BASE_DOMAIN || '';
 
-        // Register DOI with DataCite
+        // register DOI:
+        const doiValue = prefix + '/tethys.' + dataset.publish_id; //'10.21388/tethys.213'
+        const landingPageUrl = 'https://doi.' + getDomain(base_domain) + '/' + prefix + '/tethys.' + dataset.publish_id; //https://doi.dev.tethys.at/10.21388/tethys.213
         const doiClient = new DoiClient();
         const dataciteResponse = await doiClient.registerDoi(doiValue, xmlMeta, landingPageUrl);
 
-        if (dataciteResponse?.status !== 201) {
+        if (dataciteResponse?.status === 201) {
+            // if response OK 201; save the Identifier value into db
+            const doiIdentifier = new DatasetIdentifier();
+            doiIdentifier.value = doiValue;
+            doiIdentifier.dataset_id = dataset.id;
+            doiIdentifier.type = 'doi';
+            doiIdentifier.status = 'findable';
+            // save modified date of datset for re-caching model in db an update the search index
+            dataset.server_date_modified = DateTime.now();
+
+            // save updated dataset to db an index to OpenSearch
+            try {
+                await dataset.related('identifier').save(doiIdentifier);
+                const index_name = 'tethys-records';
+                await Index.indexDocument(dataset, index_name);
+            } catch (error) {
+                logger.error(`${__filename}: Indexing document ${dataset.id} failed: ${error.message}`);
+                // Log the error or handle it as needed
+                throw new HttpException(error.message);
+            }
+            return response.toRoute('editor.dataset.list').flash('message', 'You have successfully created a DOI for the dataset!');
+        } else {
             const message = `Unexpected DataCite MDS response code ${dataciteResponse?.status}`;
+            // Log the error or handle it as needed
             throw new DoiClientException(dataciteResponse?.status, message);
         }
-
-        // DOI registration successful - persist and index
-        try {
-            // Save identifier
-            await this.persistDoiAndIndex(dataset, doiValue);
-
-            return response.toRoute('editor.dataset.list').flash('message', 'You have successfully created a DOI for the dataset!');
-        } catch (error) {
-            logger.error(`${__filename}: Failed to persist DOI and index dataset ${dataset.id}: ${error.message}`);
-            throw new HttpException(error.message);
-        }
-
         // return response.toRoute('editor.dataset.list').flash('message', xmlMeta);
     }
 
-    /**
-     * Persist DOI identifier and update search index
-     * Handles cache invalidation to ensure fresh indexing
-     */
-    private async persistDoiAndIndex(dataset: Dataset, doiValue: string): Promise<void> {
-        // Create DOI identifier
-        const doiIdentifier = new DatasetIdentifier();
-        doiIdentifier.value = doiValue;
-        doiIdentifier.dataset_id = dataset.id;
-        doiIdentifier.type = 'doi';
-        doiIdentifier.status = 'findable';
-
-        // Save identifier (this will trigger database insert)
-        await dataset.related('identifier').save(doiIdentifier);
-
-        // Update dataset modification timestamp to reflect the change
-        dataset.server_date_modified = DateTime.now();
-        await dataset.save();
-
-        // Invalidate stale XML cache
-        await this.invalidateDatasetCache(dataset);
-
-        // Reload dataset with fresh state for indexing
-        const freshDataset = await Dataset.query().where('id', dataset.id).preload('identifier').preload('xmlCache').firstOrFail();
-
-        // Index to OpenSearch with fresh data
-        const index_name = process.env.OPENSEARCH_INDEX || 'tethys-records';
-        await Index.indexDocument(freshDataset, index_name);
-
-        logger.info(`Successfully created DOI ${doiValue} and indexed dataset ${dataset.id}`);
-    }
-
-    /**
-     * Invalidate XML cache for dataset
-     * Ensures fresh cache generation on next access
-     */
-    private async invalidateDatasetCache(dataset: Dataset): Promise<void> {
-        await dataset.load('xmlCache');
-
-        if (dataset.xmlCache) {
-            await dataset.xmlCache.delete();
-            logger.debug(`Invalidated XML cache for dataset ${dataset.id}`);
-        }
-    }
-
     public async show({}: HttpContext) {}
 
-    public async edit({ request, inertia, response, auth }: HttpContext) {
+    public async edit({}: HttpContext) {}
-        const id = request.param('id');
-
-        // Check if user is authenticated
-        const user = auth.user;
-        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 editor_id to ensure user has permission to edit
-        const datasetQuery = Dataset.query().where('id', id).where('editor_id', user.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('files', (query) => {
-                query.orderBy('sort_order', 'asc'); // Sort by sort_order column
-            });
-
-        // This will throw 404 if editor_id does not match logged in user
-        const dataset = await datasetQuery.firstOrFail();
-        const validStates = ['editor_accepted', 'rejected_reviewer'];
-        if (!validStates.includes(dataset.server_state)) {
-            // session.flash('errors', 'Invalid server state!');
-            return response
-                .flash(
-                    `Invalid server state. Dataset with id ${id} cannot be edited. Datset has server state ${dataset.server_state}.`,
-                    'warning',
-                )
-                .toRoute('editor.dataset.list');
-        }
-
-        const titleTypes = Object.entries(TitleTypes)
-            .filter(([value]) => value !== 'Main')
-            .map(([key, value]) => ({ value: key, label: value }));
-
-        const descriptionTypes = Object.entries(DescriptionTypes)
-            .filter(([value]) => value !== 'Abstract')
-            .map(([key, value]) => ({ value: key, label: value }));
-
-        const languages = await Language.query().where('active', true).pluck('part1', 'part1');
-
-        // const contributorTypes = Config.get('enums.contributor_types');
-        const contributorTypes = Object.entries(ContributorTypes).map(([key, value]) => ({ value: key, label: value }));
-
-        // const nameTypes = Config.get('enums.name_types');
-        const nameTypes = Object.entries(PersonNameTypes).map(([key, value]) => ({ value: key, label: value }));
-
-        // const messages = await Database.table('messages')
-        //   .pluck('help_text', 'metadata_element');
-
-        const projects = await Project.query().pluck('label', 'id');
-
-        const currentDate = new Date();
-        const currentYear = currentDate.getFullYear();
-        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('Editor/Dataset/Edit', {
-            dataset,
-            titletypes: titleTypes,
-            descriptiontypes: descriptionTypes,
-            contributorTypes,
-            nameTypes,
-            languages,
-            // messages,
-            projects,
-            licenses,
-            // datasetHasLicenses: Object.keys(datasetHasLicenses).map((key) => datasetHasLicenses[key]), //convert object to array with license ids
-            // checkeds,
-            years,
-            // languages,
-            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: DatasetTypes,
-        });
-    }
-
-    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;
-        if (!user) {
-            return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
-        }
-
-        // Retrieve the dataset and load its existing files
-        const dataset = await Dataset.query().where('id', datasetId).where('editor_id', user.id).firstOrFail();
-        await dataset.load('files');
-
-        let trx: TransactionClientContract | null = null;
-        try {
-            await request.validateUsing(updateEditorDatasetValidator);
-            trx = await db.transaction();
-            // const user = (await User.find(auth.user?.id)) as User;
-            // await this.createDatasetAndAssociations(user, request, trx);
-            // const dataset = await Dataset.findOrFail(datasetId);
-
-            // save the licenses
-            const licenses: number[] = request.input('licenses', []);
-            // await dataset.useTransaction(trx).related('licenses').sync(licenses);
-            await dataset.useTransaction(trx).related('licenses').sync(licenses);
-
-            // save authors and contributors
-            await dataset.useTransaction(trx).related('authors').sync([]);
-            await dataset.useTransaction(trx).related('contributors').sync([]);
-            await savePersons(dataset, request.input('authors', []), 'author', trx);
-            await savePersons(dataset, request.input('contributors', []), 'contributor', trx);
-
-            //save the titles:
-            const titles = request.input('titles', []);
-            // const savedTitles:Array<Title> = [];
-            for (const titleData of titles) {
-                if (titleData.id) {
-                    const title = await Title.findOrFail(titleData.id);
-                    title.value = titleData.value;
-                    title.language = titleData.language;
-                    title.type = titleData.type;
-                    if (title.$isDirty) {
-                        await title.useTransaction(trx).save();
-                        // await dataset.useTransaction(trx).related('titles').save(title);
-                        // savedTitles.push(title);
-                    }
-                } else {
-                    const title = new Title();
-                    title.fill(titleData);
-                    // savedTitles.push(title);
-                    await dataset.useTransaction(trx).related('titles').save(title);
-                }
-            }
-
-            // save the abstracts
-            const descriptions = request.input('descriptions', []);
-            // const savedTitles:Array<Title> = [];
-            for (const descriptionData of descriptions) {
-                if (descriptionData.id) {
-                    const description = await Description.findOrFail(descriptionData.id);
-                    description.value = descriptionData.value;
-                    description.language = descriptionData.language;
-                    description.type = descriptionData.type;
-                    if (description.$isDirty) {
-                        await description.useTransaction(trx).save();
-                        // await dataset.useTransaction(trx).related('titles').save(title);
-                        // savedTitles.push(title);
-                    }
-                } else {
-                    const description = new Description();
-                    description.fill(descriptionData);
-                    // savedTitles.push(title);
-                    await dataset.useTransaction(trx).related('descriptions').save(description);
-                }
-            }
-
-            // Process all subjects/keywords from the request
-            const subjects = request.input('subjects');
-            for (const subjectData of subjects) {
-                // Case 1: Subject already exists in the database (has an ID)
-                if (subjectData.id) {
-                    // Retrieve the existing subject
-                    const existingSubject = await Subject.findOrFail(subjectData.id);
-
-                    // Update subject properties from the request data
-                    existingSubject.value = subjectData.value;
-                    existingSubject.type = subjectData.type;
-                    existingSubject.external_key = subjectData.external_key;
-
-                    // Only save if there are actual changes
-                    if (existingSubject.$isDirty) {
-                        await existingSubject.save();
-                    }
-
-                    // Note: The relationship between dataset and subject is already established,
-                    // so we don't need to attach it again
-                }
-                // Case 2: New subject being added (no ID)
-                else {
-                    // Check if a subject with the same value and type already exists in the database
-                    const subject = await Subject.firstOrNew({ value: subjectData.value, type: subjectData.type }, subjectData);
-
-                    if (subject.$isNew === true) {
-                        // If it's a completely new subject, create and associate it with the dataset
-                        await dataset.useTransaction(trx).related('subjects').save(subject);
-                    } else {
-                        // If the subject already exists, just create the relationship
-                        await dataset.useTransaction(trx).related('subjects').attach([subject.id]);
-                    }
-                }
-            }
-
-            const subjectsToDelete = request.input('subjectsToDelete', []);
-            for (const subjectData of subjectsToDelete) {
-                if (subjectData.id) {
-                    // const subject = await Subject.findOrFail(subjectData.id);
-                    const subject = await Subject.query()
-                        .where('id', subjectData.id)
-                        .preload('datasets', (builder) => {
-                            builder.orderBy('id', 'asc');
-                        })
-                        .withCount('datasets')
-                        .firstOrFail();
-
-                    // Check if the subject is used by multiple datasets
-                    if (subject.$extras.datasets_count > 1) {
-                        // If used by multiple datasets, just detach it from the current dataset
-                        await dataset.useTransaction(trx).related('subjects').detach([subject.id]);
-                    } else {
-                        // If only used by this dataset, delete the subject completely
-
-                        await dataset.useTransaction(trx).related('subjects').detach([subject.id]);
-                        await subject.useTransaction(trx).delete();
-                    }
-                }
-            }
-
-            // 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.$isDirty) {
-                            await reference.useTransaction(trx).save();
-                        }
-                    }
-                } else {
-                    // Create new reference
-                    const dataReference = new DatasetReference();
-                    dataReference.fill(referenceData);
-                    await dataset.useTransaction(trx).related('references').save(dataReference);
-                }
-            }
-
-            // Handle references to delete if provided
-            const referencesToDelete = request.input('referencesToDelete', []);
-            for (const referenceData of referencesToDelete) {
-                if (referenceData.id) {
-                    const reference = await DatasetReference.findOrFail(referenceData.id);
-                    await reference.useTransaction(trx).delete();
-                }
-            }
-
-            // save coverage
-            const coverageData = request.input('coverage');
-            if (coverageData) {
-                if (coverageData.id) {
-                    const coverage = await Coverage.findOrFail(coverageData.id);
-                    coverage.merge(coverageData);
-                    if (coverage.$isDirty) {
-                        await coverage.useTransaction(trx).save();
-                    }
-                }
-            }
-
-            const input = request.only(['project_id', 'embargo_date', 'language', 'type', 'creating_corporation']);
-            // dataset.type = request.input('type');
-            dataset.merge(input);
-            dataset.server_date_modified = DateTime.now();
-            // let test: boolean = dataset.$isDirty;
-            await dataset.useTransaction(trx).save();
-
-            await trx.commit();
-            // 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('editor.dataset.edit', [dataset.id]);
-        } catch (error) {
-            if (trx !== null) {
-                await trx.rollback();
-            }
-            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;
-        }
-    }
-
-    public async categorize({ inertia, request, response, auth }: HttpContext) {
-        const id = request.param('id');
-        // Check if user is authenticated
-        const user = auth.user;
-        if (!user) {
-            return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
-        }
-        // Preload dataset and its "collections" relation
-        const dataset = await Dataset.query().where('id', id).where('editor_id', user.id).preload('collections').firstOrFail();
-        const validStates = ['editor_accepted', 'rejected_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 edited. Datset has server state ${dataset.server_state}.`,
-                )
-                .redirect()
-                .toRoute('editor.dataset.list');
-        }
-
-        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');
-            })
-            .exec();
-
-        return inertia.render('Editor/Dataset/Category', {
-            collectionRoles: collectionRoles,
-            dataset: dataset,
-            relatedCollections: dataset.collections,
-        });
-    }
-
-    public async categorizeUpdate({ request, response, session, auth }: HttpContext) {
-        // Get the dataset id from the route parameter
-        const id = request.param('id');
-        const user = auth.user;
-        if (!user) {
-            return response.flash('You must be logged in to edit a dataset.', 'error').redirect().toRoute('app.login.show');
-        }
-        // Retrieve the dataset and load its existing files
-        const dataset = await Dataset.query().preload('files').where('id', id).where('editor_id', user.id).firstOrFail();
-
-        const validStates = ['editor_accepted', 'rejected_reviewer'];
-        if (!validStates.includes(dataset.server_state)) {
-            return response
-                .flash(
-                    'warning',
-                    `Invalid server state. Dataset with id ${id} cannot be categorized. Dataset has server state ${dataset.server_state}.`,
-                )
-                .redirect()
-                .toRoute('editor.dataset.list');
-        }
-
-        let trx: TransactionClientContract | null = null;
-        try {
-            trx = await db.transaction();
-            // const user = (await User.find(auth.user?.id)) as User;
-            // await this.createDatasetAndAssociations(user, request, trx);
-
-            // Retrieve the selected collections from the request.
-            // This should be an array of collection ids.
-            const collections: number[] = request.input('collections', []);
-
-            // Synchronize the dataset collections using the transaction.
-            await dataset.useTransaction(trx).related('collections').sync(collections);
-
-            // Commit the transaction.await trx.commit()
-            await trx.commit();
-
-            // Redirect with a success flash message.
-            // return response.flash('success', 'Dataset collections updated successfully!').redirect().toRoute('dataset.list');
-
-            session.flash('message', 'Dataset collections updated successfully!');
-            return response.redirect().toRoute('editor.dataset.list');
-        } catch (error) {
-            if (trx !== null) {
-                await trx.rollback();
-            }
-            console.error('Failed tocatgorize dataset collections:', error);
-            // throw new ValidationException(true, { 'upload error': `failed to create dataset and related models. ${error}` });
-            throw error;
-        }
-    }
 
     // public async update({}: HttpContextContract) {}
-    public async updateOpensearch({ response }: HttpContext) {
+    public async update({ response }: HttpContext) {
         const id = 273; //request.param('id');
         const dataset = await Dataset.query().preload('xmlCache').where('id', id).firstOrFail();
         // add xml elements
@@ -1222,30 +655,6 @@ export default class DatasetsController {
         }
     }
 
-    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);
-    }
-
     public async destroy({}: HttpContext) {}
 
     private async createXmlRecord(dataset: Dataset, datasetNode: XMLBuilder) {
@@ -1255,18 +664,19 @@ export default class DatasetsController {
         }
     }
 
-    private async getDatasetXmlDomNode(dataset: Dataset): Promise<XMLBuilder | null> {
+    private async getDatasetXmlDomNode(dataset: Dataset) {
-        const serializer = new DatasetXmlSerializer(dataset).enableCaching().excludeEmptyFields();
+        const xmlModel = new XmlModel(dataset);
         // xmlModel.setModel(dataset);
-
+        xmlModel.excludeEmptyFields();
-        // Load existing cache if available
+        xmlModel.caching = true;
-        await dataset.load('xmlCache');
+        // const cache = dataset.xmlCache ? dataset.xmlCache : null;
+        // dataset.load('xmlCache');
         if (dataset.xmlCache) {
-            serializer.setCache(dataset.xmlCache);
+            xmlModel.xmlCache = dataset.xmlCache;
         }
 
         // return cache.getDomDocument();
-        const xmlDocument: XMLBuilder | null = await serializer.toXmlDocument();
+        const domDocument: XMLBuilder | null = await xmlModel.getDomDocument();
-        return xmlDocument;
+        return domDocument;
     }
 }

app/Controllers/Http/Oai/OaiController.ts

@@ -15,17 +15,18 @@ import { OaiModelException, BadOaiModelException } from '#app/exceptions/OaiMode
 import Dataset from '#models/dataset';
 import Collection from '#models/collection';
 import { getDomain, preg_match } from '#app/utils/utility-functions';
-import DatasetXmlSerializer from '#app/Library/DatasetXmlSerializer';
+import XmlModel from '#app/Library/XmlModel';
 import logger from '@adonisjs/core/services/logger';
 import ResumptionToken from '#app/Library/Oai/ResumptionToken';
 // import Config from '@ioc:Adonis/Core/Config';
-import config from '@adonisjs/core/services/config';
+import config from '@adonisjs/core/services/config'
 // import { inject } from '@adonisjs/fold';
-import { inject } from '@adonisjs/core';
+import { inject } from '@adonisjs/core'
 // import { TokenWorkerContract } from "MyApp/Models/TokenWorker";
 import TokenWorkerContract from '#library/Oai/TokenWorkerContract';
 import { ModelQueryBuilderContract } from '@adonisjs/lucid/types/model';
 
+
 interface XslTParameter {
     [key: string]: any;
 }
@@ -34,14 +35,12 @@ interface Dictionary {
     [index: string]: string;
 }
 
-interface PagingParameter {
+interface ListParameter {
     cursor: number;
-    totalLength: number;
+    totalIds: number;
     start: number;
-    nextDocIds: number[];
+    reldocIds: (number | null)[];
-    activeWorkIds: number[];
     metadataPrefix: string;
-    queryParams: Object;
 }
 
 @inject()
@@ -50,7 +49,6 @@ export default class OaiController {
     private sampleRegEx = /^[A-Za-zäüÄÜß0-9\-_.!~]+$/;
     private xsltParameter: XslTParameter;
 
-    private firstPublishedDataset: Dataset | null;
     /**
      * Holds xml representation of document information to be processed.
      *
@@ -59,6 +57,7 @@ export default class OaiController {
     private xml: XMLBuilder;
     private proc;
 
+    
     constructor(public tokenWorker: TokenWorkerContract) {
         // Load the XSLT file
         this.proc = readFileSync('public/assets2/datasetxml2oai.sef.json');
@@ -86,9 +85,9 @@ export default class OaiController {
         let earliestDateFromDb;
         // const oaiRequest: OaiParameter = request.body;
         try {
-            this.firstPublishedDataset = await Dataset.earliestPublicationDate();
+            const firstPublishedDataset: Dataset | null = await Dataset.earliestPublicationDate();
-            this.firstPublishedDataset != null &&
+            firstPublishedDataset != null &&
-                (earliestDateFromDb = this.firstPublishedDataset.server_date_published.toFormat("yyyy-MM-dd'T'HH:mm:ss'Z'"));
+                (earliestDateFromDb = firstPublishedDataset.server_date_published.toFormat("yyyy-MM-dd'T'HH:mm:ss'Z'"));
             this.xsltParameter['earliestDatestamp'] = earliestDateFromDb;
             // start the request
             await this.handleRequest(oaiRequest, request);
@@ -163,19 +162,22 @@ export default class OaiController {
             } else if (verb == 'GetRecord') {
                 await this.handleGetRecord(oaiRequest);
             } else if (verb == 'ListRecords') {
-                // Get browser fingerprint from the request:
+                await this.handleListRecords(oaiRequest);
-                const browserFingerprint = this.getBrowserFingerprint(request);
-                await this.handleListRecords(oaiRequest, browserFingerprint);
             } else if (verb == 'ListIdentifiers') {
-                // Get browser fingerprint from the request:
+                await this.handleListIdentifiers(oaiRequest);
-                const browserFingerprint = this.getBrowserFingerprint(request);
-                await this.handleListIdentifiers(oaiRequest, browserFingerprint);
             } else if (verb == 'ListSets') {
                 await this.handleListSets();
             } else {
                 this.handleIllegalVerb();
             }
         } else {
+            // // try {
+            // //     console.log("Async code example.")
+            // const err = new PageNotFoundException("verb not found");
+            // throw err;
+            // // } catch (error) { // manually catching
+            // //     next(error); // passing to default middleware error handler
+            // // }
             throw new OaiModelException(
                 StatusCodes.INTERNAL_SERVER_ERROR,
                 'The verb provided in the request is illegal.',
@@ -185,11 +187,11 @@ export default class OaiController {
     }
 
     protected handleIdentify() {
-        // Get configuration values from environment or a dedicated configuration service
+        const email = process.env.OAI_EMAIL || 'repository@geosphere.at';
-        const email = process.env.OAI_EMAIL ?? 'repository@geosphere.at';
+        const repositoryName = 'Tethys RDR';
-        const repositoryName = process.env.OAI_REPOSITORY_NAME ?? 'Tethys RDR';
+        const repIdentifier = 'tethys.at';
-        const repIdentifier = process.env.OAI_REP_IDENTIFIER ?? 'tethys.at';
+        const sampleIdentifier = 'oai:' + repIdentifier + ':1'; //$this->_configuration->getSampleIdentifier();
-        const sampleIdentifier = `oai:${repIdentifier}:1`;
+
         // Dataset::earliestPublicationDate()->server_date_published->format('Y-m-d\TH:i:s\Z') : null;
         // earliestDateFromDb!= null && (this.xsltParameter['earliestDatestamp'] = earliestDateFromDb?.server_date_published);
 
@@ -214,7 +216,7 @@ export default class OaiController {
 
         const sets: { [key: string]: string } = {
             'open_access': 'Set for open access licenses',
-            'openaire_data': 'OpenAIRE',
+            'openaire_data': "OpenAIRE",
             'doc-type:ResearchData': 'Set for document type ResearchData',
             ...(await this.getSetsForDatasetTypes()),
             ...(await this.getSetsForCollections()),
@@ -232,15 +234,7 @@ export default class OaiController {
         const repIdentifier = 'tethys.at';
         this.xsltParameter['repIdentifier'] = repIdentifier;
 
-        // Validate that required parameter exists early
-        if (!('identifier' in oaiRequest)) {
-            throw new BadOaiModelException('The prefix of the identifier argument is unknown.');
-        }
-
-        // Validate and extract the dataset identifier from the request
         const dataId = this.validateAndGetIdentifier(oaiRequest);
-
-        // Retrieve dataset with associated XML cache and collection roles
         const dataset = await Dataset.query()
             .where('publish_id', dataId)
             .preload('xmlCache')
@@ -257,61 +251,59 @@ export default class OaiController {
             );
         }
 
-        // Validate and set the metadata prefix parameter
         const metadataPrefix = this.validateAndGetMetadataPrefix(oaiRequest);
         this.xsltParameter['oai_metadataPrefix'] = metadataPrefix;
-
+        // do not deliver datasets which are restricted by document state defined in deliveringStates
-        // Ensure that the dataset is in an exportable state
         this.validateDatasetState(dataset);
 
-        // Build the XML for the dataset record and add it to the root node
+        // add xml elements
         const datasetNode = this.xml.root().ele('Datasets');
         await this.createXmlRecord(dataset, datasetNode);
     }
 
-    protected async handleListIdentifiers(oaiRequest: Dictionary, browserFingerprint: string) {
+    protected async handleListIdentifiers(oaiRequest: Dictionary) {
-        if (!this.tokenWorker.isConnected) {
+        !this.tokenWorker.isConnected && (await this.tokenWorker.connect());
-            await this.tokenWorker.connect();
-        }
 
         const maxIdentifier: number = config.get('oai.max.listidentifiers', 100);
-        await this.handleLists(oaiRequest, maxIdentifier, browserFingerprint);
+        await this.handleLists(oaiRequest, maxIdentifier);
     }
 
-    protected async handleListRecords(oaiRequest: Dictionary, browserFingerprint: string) {
+    protected async handleListRecords(oaiRequest: Dictionary) {
-        if (!this.tokenWorker.isConnected) {
+        !this.tokenWorker.isConnected && (await this.tokenWorker.connect());
-            await this.tokenWorker.connect();
-        }
 
         const maxRecords: number = config.get('oai.max.listrecords', 100);
-        await this.handleLists(oaiRequest, maxRecords, browserFingerprint);
+        await this.handleLists(oaiRequest, maxRecords);
     }
 
-    private async handleLists(oaiRequest: Dictionary, maxRecords: number, browserFingerprint: string) {
+    private async handleLists(oaiRequest: Dictionary, maxRecords: number) {
+        maxRecords = maxRecords || 100;
         const repIdentifier = 'tethys.at';
         this.xsltParameter['repIdentifier'] = repIdentifier;
         const datasetNode = this.xml.root().ele('Datasets');
 
-        const paginationParams: PagingParameter = {
+        // list initialisation
+        const numWrapper: ListParameter = {
             cursor: 0,
-            totalLength: 0,
+            totalIds: 0,
             start: maxRecords + 1,
-            nextDocIds: [],
+            reldocIds: [],
-            activeWorkIds: [],
             metadataPrefix: '',
-            queryParams: {},
         };
 
+        // resumptionToken is defined
         if ('resumptionToken' in oaiRequest) {
-            await this.handleResumptionToken(oaiRequest, maxRecords, paginationParams);
+            await this.handleResumptionToken(oaiRequest, maxRecords, numWrapper);
         } else {
-            await this.handleNoResumptionToken(oaiRequest, paginationParams, maxRecords);
+            // no resumptionToken is given
+            await this.handleNoResumptionToken(oaiRequest, numWrapper);
         }
 
-        const nextIds: number[] = paginationParams.nextDocIds;
+        // handling of document ids
-        const workIds: number[] = paginationParams.activeWorkIds;
+        const restIds = numWrapper.reldocIds as number[];
+        const workIds = restIds.splice(0, maxRecords) as number[]; // array_splice(restIds, 0, maxRecords);
 
-        if (workIds.length === 0) {
+        // no records returned
+        if (workIds.length == 0) {
             throw new OaiModelException(
                 StatusCodes.INTERNAL_SERVER_ERROR,
                 'The combination of the given values results in an empty list.',
@@ -319,222 +311,169 @@ export default class OaiController {
             );
         }
 
-        const datasets = await Dataset.query()
+        const datasets: Dataset[] = await Dataset.query()
             .whereIn('publish_id', workIds)
             .preload('xmlCache')
             .preload('collections', (builder) => {
                 builder.preload('collectionRole');
             })
             .orderBy('publish_id');
+
         for (const dataset of datasets) {
             await this.createXmlRecord(dataset, datasetNode);
         }
-        await this.setResumptionToken(nextIds, paginationParams, browserFingerprint);
+
+        // store the further Ids in a resumption-file
+        const countRestIds = restIds.length; //84
+        if (countRestIds > 0) {
+            const token = new ResumptionToken();
+            token.startPosition = numWrapper.start; //101
+            token.totalIds = numWrapper.totalIds; //184
+            token.documentIds = restIds; //101 -184
+            token.metadataPrefix = numWrapper.metadataPrefix;
+
+            // $tokenWorker->storeResumptionToken($token);
+            const res: string = await this.tokenWorker.set(token);
+
+            // set parameters for the resumptionToken-node
+            // const res = token.ResumptionId;
+            this.setParamResumption(res, numWrapper.cursor, numWrapper.totalIds);
+        }
     }
 
-    private async handleNoResumptionToken(oaiRequest: Dictionary, paginationParams: PagingParameter, maxRecords: number) {
+    private async handleResumptionToken(oaiRequest: Dictionary, maxRecords: number, numWrapper: ListParameter) {
-        this.validateMetadataPrefix(oaiRequest, paginationParams);
+        const resParam = oaiRequest['resumptionToken']; //e.g. "158886496600000"
-        const finder: ModelQueryBuilderContract<typeof Dataset, Dataset> = Dataset.query().whereIn(
-            'server_state',
-            this.deliveringDocumentStates,
-        );
-        this.applySetFilter(finder, oaiRequest);
-        this.applyDateFilters(finder, oaiRequest);
-        await this.fetchAndSetResults(finder, paginationParams, oaiRequest, maxRecords);
-    }
-
-    private async fetchAndSetResults(
-        finder: ModelQueryBuilderContract<typeof Dataset, Dataset>,
-        paginationParams: PagingParameter,
-        oaiRequest: Dictionary,
-        maxRecords: number,
-    ) {
-        const totalResult = await finder
-            .clone()
-            .count('* as total')
-            .first()
-            .then((res) => res?.$extras.total);
-        paginationParams.totalLength = Number(totalResult);
-
-        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));
-
-        // No resumption token was used – set queryParams from the current oaiRequest
-        paginationParams.queryParams = {
-            ...oaiRequest,
-            deliveringStates: this.deliveringDocumentStates,
-        };
-
-        // paginationParams.totalLength = 230;
-    }
-
-    private async handleResumptionToken(oaiRequest: Dictionary, maxRecords: number, paginationParams: PagingParameter) {
-        const resParam = oaiRequest['resumptionToken'];
         const token = await this.tokenWorker.get(resParam);
 
         if (!token) {
             throw new OaiModelException(StatusCodes.INTERNAL_SERVER_ERROR, 'cache is outdated.', OaiErrorCodes.BADRESUMPTIONTOKEN);
         }
 
-        // this.setResumptionParameters(token, maxRecords, paginationParams);
+        numWrapper.cursor = token.startPosition - 1; //startet dann bei Index 10
-        paginationParams.cursor = token.startPosition - 1;
+        numWrapper.start = token.startPosition + maxRecords;
-        paginationParams.start = token.startPosition + maxRecords;
+        numWrapper.totalIds = token.totalIds;
-        paginationParams.totalLength = token.totalIds;
+        numWrapper.reldocIds = token.documentIds;
-        paginationParams.activeWorkIds = token.documentIds;
+        numWrapper.metadataPrefix = token.metadataPrefix;
-        paginationParams.metadataPrefix = token.metadataPrefix;
-        paginationParams.queryParams = token.queryParams;
-        this.xsltParameter['oai_metadataPrefix'] = token.metadataPrefix;
 
-        const finder = this.buildDatasetQueryViaToken(token);
+        this.xsltParameter['oai_metadataPrefix'] = numWrapper.metadataPrefix;
-        const nextRecords: Dataset[] = await this.fetchNextRecords(finder, token, maxRecords);
-        paginationParams.nextDocIds = nextRecords.map((dat) => Number(dat.publish_id));
     }
 
-    private async setResumptionToken(nextIds: number[], paginationParams: PagingParameter, browserFingerprint: string) {
+    private async handleNoResumptionToken(oaiRequest: Dictionary, numWrapper: ListParameter) {
-        const countRestIds = nextIds.length;
+        // no resumptionToken is given
-        if (countRestIds > 0) {
+        if ('metadataPrefix' in oaiRequest) {
-            // const token = this.createResumptionToken(paginationParams, nextIds);
+            numWrapper.metadataPrefix = oaiRequest['metadataPrefix'];
-            const token = new ResumptionToken();
+        } else {
-            token.startPosition = paginationParams.start;
-            token.totalIds = paginationParams.totalLength;
-            token.documentIds = nextIds;
-            token.metadataPrefix = paginationParams.metadataPrefix;
-            token.queryParams = paginationParams.queryParams;
-            const res: string = await this.tokenWorker.set(token, browserFingerprint);
-            this.setParamResumption(res, paginationParams.cursor, paginationParams.totalLength);
-        }
-    }
-
-    private buildDatasetQueryViaToken(token: ResumptionToken) {
-        const finder = Dataset.query();
-        const originalQuery = token.queryParams || {};
-        const deliveringStates = originalQuery.deliveringStates || this.deliveringDocumentStates;
-
-        finder.whereIn('server_state', deliveringStates);
-        this.applySetFilter(finder, originalQuery);
-        this.applyDateFilters(finder, originalQuery);
-
-        return finder;
-    }
-
-    private async fetchNextRecords(finder: ModelQueryBuilderContract<typeof Dataset, Dataset>, token: ResumptionToken, maxRecords: number) {
-        return finder
-            .select('publish_id')
-            .orderBy('publish_id')
-            .offset(token.startPosition - 1 + maxRecords)
-            .limit(100);
-    }
-
-    private validateMetadataPrefix(oaiRequest: Dictionary, paginationParams: PagingParameter) {
-        if (!('metadataPrefix' in oaiRequest)) {
             throw new OaiModelException(
                 StatusCodes.INTERNAL_SERVER_ERROR,
                 'The prefix of the metadata argument is unknown.',
                 OaiErrorCodes.BADARGUMENT,
             );
         }
-        paginationParams.metadataPrefix = oaiRequest['metadataPrefix'];
+        this.xsltParameter['oai_metadataPrefix'] = numWrapper.metadataPrefix;
-        this.xsltParameter['oai_metadataPrefix'] = paginationParams.metadataPrefix;
-    }
 
-    private applySetFilter(finder: ModelQueryBuilderContract<typeof Dataset, Dataset>, queryParams: any) {
+        let finder: ModelQueryBuilderContract<typeof Dataset, Dataset> = Dataset.query();
-        if ('set' in queryParams) {
+        // add server state restrictions
-            const [setType, setValue] = queryParams['set'].split(':');
+        finder.whereIn('server_state', this.deliveringDocumentStates);
+        if ('set' in oaiRequest) {
+            const set = oaiRequest['set'] as string;
+            const setArray = set.split(':');
 
-            switch (setType) {
+            if (setArray[0] == 'data-type') {
-                case 'data-type':
+                if (setArray.length == 2 && setArray[1]) {
-                    setValue && finder.where('type', setValue);
+                    finder.where('type', setArray[1]);
-                    break;
+                }
-                case 'open_access':
+            } else if (setArray[0] == 'open_access') {
-                    finder.andWhereHas('licenses', (query) => {
+                const openAccessLicences = ['CC-BY-4.0', 'CC-BY-SA-4.0'];
-                        query.whereIn('name', ['CC-BY-4.0', 'CC-BY-SA-4.0']);
+                finder.andWhereHas('licenses', (query) => {
+                    query.whereIn('name', openAccessLicences);
+                });
+            } else if (setArray[0] == 'ddc') {
+                if (setArray.length == 2 && setArray[1] != '') {
+                    finder.andWhereHas('collections', (query) => {
+                        query.where('number', setArray[1]);
                     });
-                    break;
+                }
-                case 'ddc':
-                    setValue &&
-                        finder.andWhereHas('collections', (query) => {
-                            query.where('number', setValue);
-                        });
-                    break;
             }
         }
-    }
 
-    private applyDateFilters(finder: ModelQueryBuilderContract<typeof Dataset, Dataset>, queryParams: any) {
+        // const timeZone = "Europe/Vienna"; // Canonical time zone name
-        const { from, until } = queryParams;
+        // &from=2020-09-03&until2020-09-03
+        // &from=2020-09-11&until=2021-05-11
+        if ('from' in oaiRequest && 'until' in oaiRequest) {
+            const from = oaiRequest['from'] as string;
+            let fromDate = dayjs(from); //.tz(timeZone);
+            const until = oaiRequest['until'] as string;
+            let untilDate = dayjs(until); //.tz(timeZone);
+            if (!fromDate.isValid() || !untilDate.isValid()) {
+                throw new OaiModelException(StatusCodes.INTERNAL_SERVER_ERROR, 'Date Parameter is not valid.', OaiErrorCodes.BADARGUMENT);
+            }
+            fromDate = dayjs.tz(from, 'Europe/Vienna');
+            untilDate = dayjs.tz(until, 'Europe/Vienna');
 
-        if (from && until) {
+            if (from.length != until.length) {
-            this.handleFromUntilFilter(finder, from, until);
+                throw new OaiModelException(
-        } else if (from) {
+                    StatusCodes.INTERNAL_SERVER_ERROR,
-            this.handleFromFilter(finder, from);
+                    'The request has different granularities for the from and until parameters.',
-        } else if (until) {
+                    OaiErrorCodes.BADARGUMENT,
-            this.handleUntilFilter(finder, until);
+                );
-        }
+            }
-    }
+            fromDate.hour() == 0 && (fromDate = fromDate.startOf('day'));
+            untilDate.hour() == 0 && (untilDate = untilDate.endOf('day'));
 
-    private handleFromUntilFilter(finder: ModelQueryBuilderContract<typeof Dataset, Dataset>, from: string, until: string) {
+            finder.whereBetween('server_date_published', [fromDate.format('YYYY-MM-DD HH:mm:ss'), untilDate.format('YYYY-MM-DD HH:mm:ss')]);
-        const fromDate = this.parseDateWithValidation(from, 'From');
+        } else if ('from' in oaiRequest && !('until' in oaiRequest)) {
-        const untilDate = this.parseDateWithValidation(until, 'Until');
+            const from = oaiRequest['from'] as string;
+            let fromDate = dayjs(from);
+            if (!fromDate.isValid()) {
+                throw new OaiModelException(
+                    StatusCodes.INTERNAL_SERVER_ERROR,
+                    'From date parameter is not valid.',
+                    OaiErrorCodes.BADARGUMENT,
+                );
+            }
+            fromDate = dayjs.tz(from, 'Europe/Vienna');
+            fromDate.hour() == 0 && (fromDate = fromDate.startOf('day'));
 
-        if (from.length !== until.length) {
+            const now = dayjs();
-            throw new OaiModelException(
+            if (fromDate.isAfter(now)) {
-                StatusCodes.INTERNAL_SERVER_ERROR,
+                throw new OaiModelException(
-                'The request has different granularities for the from and until parameters.',
+                    StatusCodes.INTERNAL_SERVER_ERROR,
-                OaiErrorCodes.BADARGUMENT,
+                    'Given from date is greater than now. The given values results in an empty list.',
-            );
+                    OaiErrorCodes.NORECORDSMATCH,
+                );
+            } else {
+                finder.andWhere('server_date_published', '>=', fromDate.format('YYYY-MM-DD HH:mm:ss'));
+            }
+        } else if (!('from' in oaiRequest) && 'until' in oaiRequest) {
+            const until = oaiRequest['until'] as string;
+            let untilDate = dayjs(until);
+            if (!untilDate.isValid()) {
+                throw new OaiModelException(
+                    StatusCodes.INTERNAL_SERVER_ERROR,
+                    'Until date parameter is not valid.',
+                    OaiErrorCodes.BADARGUMENT,
+                );
+            }
+            untilDate = dayjs.tz(until, 'Europe/Vienna');
+            untilDate.hour() == 0 && (untilDate = untilDate.endOf('day'));
+
+            const firstPublishedDataset: Dataset = (await Dataset.earliestPublicationDate()) as Dataset;
+            const earliestPublicationDate = dayjs(firstPublishedDataset.server_date_published.toISO()); //format("YYYY-MM-DDThh:mm:ss[Z]"));
+            if (earliestPublicationDate.isAfter(untilDate)) {
+                throw new OaiModelException(
+                    StatusCodes.INTERNAL_SERVER_ERROR,
+                    `earliestDatestamp is greater than given until date. 
+                The given values results in an empty list.`,
+                    OaiErrorCodes.NORECORDSMATCH,
+                );
+            } else {
+                finder.andWhere('server_date_published', '<=', untilDate.format('YYYY-MM-DD HH:mm:ss'));
+            }
         }
 
-        finder.whereBetween('server_date_published', [fromDate.format('YYYY-MM-DD HH:mm:ss'), untilDate.format('YYYY-MM-DD HH:mm:ss')]);
+        let reldocIdsDocs = await finder.select('publish_id').orderBy('publish_id');
-    }
+        numWrapper.reldocIds = reldocIdsDocs.map((dat) => dat.publish_id);
-
+        numWrapper.totalIds = numWrapper.reldocIds.length; //212
-    private handleFromFilter(finder: ModelQueryBuilderContract<typeof Dataset, Dataset>, from: string) {
-        const fromDate = this.parseDateWithValidation(from, 'From');
-        const now = dayjs();
-
-        if (fromDate.isAfter(now)) {
-            throw new OaiModelException(
-                StatusCodes.INTERNAL_SERVER_ERROR,
-                'Given from date is greater than now. The given values results in an empty list.',
-                OaiErrorCodes.NORECORDSMATCH,
-            );
-        }
-
-        finder.andWhere('server_date_published', '>=', fromDate.format('YYYY-MM-DD HH:mm:ss'));
-    }
-
-    private handleUntilFilter(finder: ModelQueryBuilderContract<typeof Dataset, Dataset>, until: string) {
-        const untilDate = this.parseDateWithValidation(until, 'Until');
-
-        const earliestPublicationDate = dayjs(this.firstPublishedDataset?.server_date_published.toISO());
-
-        if (earliestPublicationDate.isAfter(untilDate)) {
-            throw new OaiModelException(
-                StatusCodes.INTERNAL_SERVER_ERROR,
-                'earliestDatestamp is greater than given until date. The given values results in an empty list.',
-                OaiErrorCodes.NORECORDSMATCH,
-            );
-        }
-
-        finder.andWhere('server_date_published', '<=', untilDate.format('YYYY-MM-DD HH:mm:ss'));
-    }
-
-    private parseDateWithValidation(dateStr: string, label: string) {
-        let date = dayjs(dateStr);
-        if (!date.isValid()) {
-            throw new OaiModelException(
-                StatusCodes.INTERNAL_SERVER_ERROR,
-                `${label} date parameter is not valid.`,
-                OaiErrorCodes.BADARGUMENT,
-            );
-        }
-        date = dayjs.tz(dateStr, 'Europe/Vienna');
-        return date.hour() === 0 ? (label === 'From' ? date.startOf('day') : date.endOf('day')) : date;
     }
 
     private setParamResumption(res: string, cursor: number, totalIds: number) {
@@ -606,17 +545,19 @@ export default class OaiController {
     }
 
     private async getDatasetXmlDomNode(dataset: Dataset) {
-        const serializer = new DatasetXmlSerializer(dataset).enableCaching().excludeEmptyFields();
+        const xmlModel = new XmlModel(dataset);
-
+        // xmlModel.setModel(dataset);
+        xmlModel.excludeEmptyFields();
+        xmlModel.caching = true;
         // const cache = dataset.xmlCache ? dataset.xmlCache : null;
         // dataset.load('xmlCache');
         if (dataset.xmlCache) {
-            serializer.setCache(dataset.xmlCache);
+            xmlModel.xmlCache = dataset.xmlCache;
         }
 
-        // return cache.toXmlDocument();
+        // return cache.getDomDocument();
-        const xmlDocument: XMLBuilder | null = await serializer.toXmlDocument();
+        const domDocument: XMLBuilder | null = await xmlModel.getDomDocument();
-        return xmlDocument;
+        return domDocument;
     }
 
     private addSpecInformation(domNode: XMLBuilder, information: string) {
@@ -700,30 +641,4 @@ export default class OaiController {
         this.xsltParameter['oai_error_code'] = 'badVerb';
         this.xsltParameter['oai_error_message'] = 'The verb provided in the request is illegal.';
     }
-
-    /**
-     * Helper method to build a browser fingerprint by combining:
-     * - User-Agent header,
-     * - the IP address,
-     * - Accept-Language header,
-     * - current timestamp rounded to the hour.
-     *
-     * Every new hour, this will return a different fingerprint.
-     */
-    private getBrowserFingerprint(request: Request): string {
-        const userAgent = request.header('user-agent') || 'unknown';
-        // Check for X-Forwarded-For header to use the client IP from the proxy if available.
-        const xForwardedFor = request.header('x-forwarded-for');
-        let ip = request.ip();
-        // console.log(ip);
-        if (xForwardedFor) {
-            // X-Forwarded-For may contain a comma-separated list of IPs; the first one is the client IP.
-            ip = xForwardedFor.split(',')[0].trim();
-            // console.log('xforwardedfor ip' + ip);
-        }
-        const locale = request.header('accept-language') || 'default';
-        // Round the current time to the start of the hour.
-        const timestampHour = dayjs().startOf('hour').format('YYYY-MM-DDTHH');
-        return `${userAgent}-${ip}-${locale}-${timestampHour}`;
-    }
 }

app/Controllers/Http/Reviewer/DatasetController.ts

@@ -9,7 +9,6 @@ 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;
@@ -39,21 +38,13 @@ export default class DatasetsController {
             }
             datasets.orderBy(attribute, sortOrder);
         } else {
-            // datasets.orderBy('id', 'asc');
+            // users.orderBy('created_at', 'desc');
-            // Custom ordering to prioritize rejected_editor state
+            datasets.orderBy('id', 'asc');
-            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')
@@ -71,51 +62,7 @@ export default class DatasetsController {
         });
     }
 
-    public async review({ request, inertia, response, auth }: HttpContext) {
+    public async review({ request, inertia, response }: 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)
@@ -211,10 +158,6 @@ 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']),
-            },
         });
     }
 
@@ -223,7 +166,7 @@ export default class DatasetsController {
         // const { id } = params;
         const dataset = await Dataset.findOrFail(id);
 
-        const validStates = ['approved', 'rejected_to_reviewer'];
+        const validStates = ['approved'];
         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();
@@ -237,10 +180,6 @@ 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
@@ -264,7 +203,7 @@ export default class DatasetsController {
             })
             .firstOrFail();
 
-        const validStates = ['approved', 'rejected_to_reviewer'];
+        const validStates = ['approved'];
         if (!validStates.includes(dataset.server_state)) {
             // session.flash('errors', 'Invalid server state!');
             return response
@@ -311,12 +250,12 @@ export default class DatasetsController {
             throw error;
         }
 
-        const validStates = ['approved', 'rejected_to_reviewer'];
+        const validStates = ['approved'];
         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',
                 )
@@ -337,7 +276,7 @@ export default class DatasetsController {
             validateSMTP: false,
         });
         const validRecipientEmail: boolean = validationResult.valid;
-        // let emailStatusMessage = '';
+        let emailStatusMessage = '';
 
         if (sendMail == true) {
             if (dataset.editor.email && validRecipientEmail) {
@@ -350,7 +289,7 @@ export default class DatasetsController {
                             <p>Best regards,<br>Your Tethys reviewer: ${authUser.login}</p>
                         `);
                     });
-                    // emailStatusMessage = ` A rejection email was successfully sent to ${dataset.editor.email}.`;
+                    emailStatusMessage = ` A rejection email was successfully sent to ${dataset.editor.email}.`;
                 } catch (error) {
                     logger.error(error);
                     return response
@@ -358,7 +297,7 @@ export default class DatasetsController {
                         .toRoute('reviewer.dataset.list');
                 }
             } else {
-                // emailStatusMessage = ` However, the email could not be sent because the editor's email address (${dataset.editor.email}) is not valid.`;
+                emailStatusMessage = ` However, the email could not be sent because the editor's email address (${dataset.editor.email}) is not valid.`;
             }
         }
 
@@ -368,41 +307,4 @@ 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/Library/DatasetXmlSerializer.ts

@@ -1,231 +0,0 @@
-import DocumentXmlCache from '#models/DocumentXmlCache';
-import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
-import Dataset from '#models/dataset';
-import Strategy from './Strategy.js';
-import { builder } from 'xmlbuilder2';
-import logger from '@adonisjs/core/services/logger';
-
-/**
- * Configuration for XML serialization
- *
- * @interface XmlSerializationConfig
- */
-export interface XmlSerializationConfig {
-    /** The dataset model to serialize */
-    model: Dataset;
-    /** DOM representation (if available) */
-    dom?: XMLBuilder;
-    /** Fields to exclude from serialization */
-    excludeFields: Array<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

@@ -1,22 +1,25 @@
+// 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';
 import logger from '@adonisjs/core/services/logger';
 import { AxiosResponse } from 'axios';
-import { default as axios } from 'axios';
+import axios from 'axios';
 
 export class DoiClient implements DoiClientContract {
     public username: string;
     public password: string;
     public serviceUrl: string;
-    public apiUrl: string;
 
     constructor() {
         // const datacite_environment = process.env.DATACITE_ENVIRONMENT || 'debug';
         this.username = process.env.DATACITE_USERNAME || '';
         this.password = process.env.DATACITE_PASSWORD || '';
         this.serviceUrl = process.env.DATACITE_SERVICE_URL || '';
-        this.apiUrl = process.env.DATACITE_API_URL || 'https://api.datacite.org';
+        // this.prefix = process.env.DATACITE_PREFIX || '';
+        // this.base_domain = process.env.BASE_DOMAIN || '';
 
         if (this.username === '' || this.password === '' || this.serviceUrl === '') {
             const message = 'issing configuration settings to properly initialize DOI client';
@@ -47,7 +50,7 @@ export class DoiClient implements DoiClientContract {
             'Content-Type': 'application/xml;charset=UTF-8',
         };
         try {
-            const metadataResponse = await axios.put(`${this.serviceUrl}/metadata/${doiValue}`, xmlMeta, { auth, headers });
+            const metadataResponse = await axios.default.put(`${this.serviceUrl}/metadata/${doiValue}`, xmlMeta, { auth, headers });
 
             // Response Codes
             // 201 Created: operation successful
@@ -62,7 +65,7 @@ export class DoiClient implements DoiClientContract {
                 throw new DoiClientException(metadataResponse.status, message);
             }
 
-            const doiResponse = await axios.put(`${this.serviceUrl}/doi/${doiValue}`, `doi=${doiValue}\nurl=${landingPageUrl}`, {
+            const doiResponse = await axios.default.put(`${this.serviceUrl}/doi/${doiValue}`, `doi=${doiValue}\nurl=${landingPageUrl}`, {
                 auth,
                 headers,
             });
@@ -87,240 +90,4 @@ export class DoiClient implements DoiClientContract {
             throw new DoiClientException(error.response.status, error.response.data);
         }
     }
-
-    /**
-     * Retrieves DOI information from DataCite REST API
-     *
-     * @param doiValue The DOI identifier e.g. '10.5072/tethys.999'
-     * @returns Promise with DOI information or null if not found
-     */
-    public async getDoiInfo(doiValue: string): Promise<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/ResumptionToken.ts

@@ -4,7 +4,6 @@ export default class ResumptionToken {
     private _resumptionId = '';
     private _startPosition = 0;
     private _totalIds = 0;
-    private _queryParams: Record<string, any> = {};
 
     get key(): string {
         return this.metadataPrefix + this.startPosition + this.totalIds;
@@ -49,12 +48,4 @@ export default class ResumptionToken {
     set totalIds(totalIds: number) {
         this._totalIds = totalIds;
     }
-
-    get queryParams(): Record<string, any> {
-        return this._queryParams;
-    }
-
-    set queryParams(params: Record<string, any>) {
-        this._queryParams = params;
-    }
 }

app/Library/Oai/TokenWorkerContract.ts

@@ -6,6 +6,6 @@ export default abstract class TokenWorkerContract {
     abstract connect(): void;
     abstract close(): void;
     abstract get(key: string): Promise<ResumptionToken | null>;
-    abstract set(token: ResumptionToken, browserFingerprint: string): Promise<string>;
+    abstract set(token: ResumptionToken): Promise<string>;
 }
 

app/Library/Oai/TokenWorkerSerice.ts

@@ -40,64 +40,14 @@ export default class TokenWorkerService implements TokenWorkerContract {
         return result !== undefined && result !== null;
     }
 
-    /**
+    public async set(token: ResumptionToken): Promise<string> {
-     * Simplified set method that stores the token using a browser fingerprint key.
+        const uniqueName = await this.generateUniqueName();
-     * If the token for that fingerprint already exists and its documentIds match the new token,
-     * then the fingerprint key is simply returned.
-     */
-    public async set(token: ResumptionToken, browserFingerprint: string): Promise<string> {
-        // Generate a 15-digit unique number string based on the fingerprint
-        const uniqueNumberKey = this.createUniqueNumberFromFingerprint(browserFingerprint, token.documentIds, token.totalIds);
-        // Optionally, you could prefix it if desired, e.g. 'rs_' + uniqueNumberKey
-        const fingerprintKey = uniqueNumberKey;
-
-        // const fingerprintKey = `rs_fp_${browserFingerprint}`;
-        const existingTokenString = await this.cache.get(fingerprintKey);
-
-        if (existingTokenString) {
-            const existingToken = this.parseToken(existingTokenString);
-            if (this.arraysAreEqual(existingToken.documentIds, token.documentIds)) {
-                return fingerprintKey;
-            }
-        }
 
         const serialToken = JSON.stringify(token);
-        await this.cache.setEx(fingerprintKey, this.ttl, serialToken);
+        await this.cache.setEx(uniqueName, this.ttl, serialToken);
-        return fingerprintKey;
+        return uniqueName;
     }
 
-    // Updated helper method to generate a unique key based on fingerprint and documentIds
-    private createUniqueNumberFromFingerprint(browserFingerprint: string, documentIds: number[], totalIds: number): string {
-        // Combine the fingerprint, document IDs and totalIds to produce the input string
-        const combined = browserFingerprint + ':' + documentIds.join('-') + ':' + totalIds;
-        // Simple hash algorithm
-        let hash = 0;
-        for (let i = 0; i < combined.length; i++) {
-            hash = (hash << 5) - hash + combined.charCodeAt(i);
-            hash |= 0; // Convert to 32-bit integer
-        }
-        // Ensure positive number and limit it to at most 15 digits
-        const positiveHash = Math.abs(hash) % 1000000000000000;
-        // Pad with trailing zeros to ensure a 15-digit string
-        return positiveHash.toString().padEnd(15, '0');
-    }
-
-    // Add a helper function to compare two arrays of numbers with identical order
-    private arraysAreEqual(arr1: number[], arr2: number[]): boolean {
-        if (arr1.length !== arr2.length) {
-            return false;
-        }
-        return arr1.every((num, index) => num === arr2[index]);
-    }
-
-    // public async set(token: ResumptionToken): Promise<string> {
-    //     const uniqueName = await this.generateUniqueName();
-
-    //     const serialToken = JSON.stringify(token);
-    //     await this.cache.setEx(uniqueName, this.ttl, serialToken);
-    //     return uniqueName;
-    // }
-
     private async generateUniqueName(): Promise<string> {
         let fc = 0;
         const uniqueId = dayjs().unix().toString();

app/Library/Utils/Index.ts

@@ -2,7 +2,7 @@ import Dataset from '#models/dataset';
 import { Client } from '@opensearch-project/opensearch';
 import { create } from 'xmlbuilder2';
 import SaxonJS from 'saxon-js';
-import DatasetXmlSerializer from '#app/Library/DatasetXmlSerializer';
+import XmlModel from '#app/Library/XmlModel';
 import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
 import logger from '@adonisjs/core/services/logger';
 import { readFileSync } from 'fs';
@@ -72,42 +72,31 @@ export default {
         }
     },
 
-    /**
-     * Index a dataset document to OpenSearch/Elasticsearch
-     */
     async indexDocument(dataset: Dataset, index_name: string): Promise<void> {
         try {
-            // Load XSLT transformation file
+            const proc = readFileSync('public/assets2/solr.sef.json');
-            const xsltProc = readFileSync('public/assets2/solr.sef.json');
+            const doc: string = await this.getTransformedString(dataset, proc);
 
-            // Transform dataset to JSON document
+            let document = JSON.parse(doc);
-            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, // make immediately searchable
+                refresh: true,
             });
-            logger.info(`Dataset ${dataset.publish_id} successfully indexed to ${index_name}`);
+            logger.info(`dataset with publish_id ${dataset.publish_id} successfully indexed`);
         } catch (error) {
-            logger.error(`Failed to index dataset ${dataset.publish_id}: ${error.message}`);
+            logger.error(`An error occurred while indexing datsaet with publish_id ${dataset.publish_id}.`);
-            throw error; // Re-throw to allow caller to handle
         }
     },
 
-    /**
-     * Transform dataset XML to JSON using XSLT
-     */
     async getTransformedString(dataset: Dataset, proc: Buffer): Promise<string> {
-        // Generate XML string from dataset
+        let xml = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, '<root></root>');
-        const xmlString = await this.generateDatasetXml(dataset);
+        const datasetNode = xml.root().ele('Dataset');
+        await createXmlRecord(dataset, datasetNode);
+        const xmlString = xml.end({ prettyPrint: false });
 
         try {
-            // Apply XSLT transformation
             const result = await SaxonJS.transform({
                 stylesheetText: proc,
                 destination: 'serialized',
@@ -119,18 +108,6 @@ export default {
             return '';
         }
     },
-
-    /**
-     * Generate XML string from dataset model
-     */
-    async generateDatasetXml(dataset: Dataset): Promise<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
@@ -138,49 +115,74 @@ export default {
  * @return {import('focus-trap').FocusTrap[]}
  */
 
-/**
+// export const indexDocument = async (dataset: Dataset, index_name: string, proc: Buffer): Promise<void> => {
- * Create complete XML record for dataset
+//     try {
- * Handles caching and metadata enrichment
+//         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 '';
+//     }
+// };
+
 const createXmlRecord = async (dataset: Dataset, datasetNode: XMLBuilder): Promise<void> => {
     const domNode = await getDatasetXmlDomNode(dataset);
-
+    if (domNode) {
-    if (!domNode) {
+         // add frontdoor url and data-type
-        throw new Error(`Failed to generate XML DOM node for dataset ${dataset.id}`);
+        dataset.publish_id && addLandingPageAttribute(domNode, dataset.publish_id.toString());
-    }
+        addSpecInformation(domNode, 'data-type:' + dataset.type);
-
+        if (dataset.collections) {
-    // Enrich with landing page URL
+            for (const coll of dataset.collections) {
-    if (dataset.publish_id) {
+                const collRole = coll.collectionRole;
-        addLandingPageAttribute(domNode, dataset.publish_id.toString());
+                addSpecInformation(domNode, collRole.oai_name + ':' + coll.number);
-    }
+            }
-
-    // Add data type specification
-    addSpecInformation(domNode, `data-type:${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);
+        datasetNode.import(domNode);
+    }
 };
 
 const getDatasetXmlDomNode = async (dataset: Dataset): Promise<XMLBuilder | null> => {
-    const serializer = new DatasetXmlSerializer(dataset).enableCaching().excludeEmptyFields();
+    const xmlModel = new XmlModel(dataset);
     // xmlModel.setModel(dataset);
-
+    xmlModel.excludeEmptyFields();
-    // Load cache relationship if not already loaded
+    xmlModel.caching = true;
+    // const cache = dataset.xmlCache ? dataset.xmlCache : null;
+    // dataset.load('xmlCache');
     await dataset.load('xmlCache');
     if (dataset.xmlCache) {
-        serializer.setCache(dataset.xmlCache);
+        xmlModel.xmlCache = dataset.xmlCache;
     }
 
-    // Generate or retrieve cached DOM document
+    // return cache.getDomDocument();
-    const xmlDocument: XMLBuilder | null = await serializer.toXmlDocument();
+    const domDocument: XMLBuilder | null = await xmlModel.getDomDocument();
-    return xmlDocument;
+    return domDocument;
 };
 
 const addLandingPageAttribute = (domNode: XMLBuilder, dataid: string) => {
@@ -190,6 +192,6 @@ const addLandingPageAttribute = (domNode: XMLBuilder, dataid: string) => {
     domNode.att('landingpage', url);
 };
 
-const addSpecInformation = (domNode: XMLBuilder, information: string) => {
+const addSpecInformation= (domNode: XMLBuilder, information: string) => {
     domNode.ele('SetSpec').att('Value', information);
-};
+};

app/Library/XmlModel.ts

@@ -0,0 +1,129 @@
+import DocumentXmlCache from '#models/DocumentXmlCache';
+import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
+import Dataset from '#models/dataset';
+import Strategy from './Strategy.js';
+import { DateTime } from 'luxon';
+import { builder } from 'xmlbuilder2';
+
+/**
+ * This is the description of the interface
+ *
+ * @interface Conf
+ * @member {Model} model holds the current dataset model
+ * @member {XMLBuilder} dom holds the current DOM representation
+ * @member {Array<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/projects_controller.ts

@@ -1,54 +0,0 @@
-// app/controllers/projects_controller.ts
-import Project from '#models/project';
-import type { HttpContext } from '@adonisjs/core/http';
-import { createProjectValidator, updateProjectValidator } from '#validators/project';
-
-export default class ProjectsController {
-    // GET /settings/projects
-    public async index({ inertia, auth }: HttpContext) {
-        const projects = await Project.all();
-        // return inertia.render('Admin/Project/Index', { projects });
-        return inertia.render('Admin/Project/Index', {
-            projects: projects,
-            can: {
-                edit: await auth.user?.can(['settings']),
-                create: await auth.user?.can(['settings']),
-            },
-        });
-    }
-
-    // GET /settings/projects/create
-    public async create({ inertia }: HttpContext) {
-        return inertia.render('Admin/Project/Create');
-    }
-
-    // POST /settings/projects
-    public async store({ request, response, session }: HttpContext) {
-        // Validate the request data
-        const data = await request.validateUsing(createProjectValidator);
-
-        await Project.create(data);
-
-        session.flash('success', 'Project created successfully');
-        return response.redirect().toRoute('settings.project.index');
-    }
-
-    // GET /settings/projects/:id/edit
-    public async edit({ params, inertia }: HttpContext) {
-        const project = await Project.findOrFail(params.id);
-        return inertia.render('Admin/Project/Edit', { project });
-    }
-
-    // PUT /settings/projects/:id
-    public async update({ params, request, response, session }: HttpContext) {
-        const project = await Project.findOrFail(params.id);
-        
-        // Validate the request data
-        const data = await request.validateUsing(updateProjectValidator);
-
-        await project.merge(data).save();
-
-        session.flash('success', 'Project updated successfully');
-        return response.redirect().toRoute('settings.project.index');
-    }
-}

app/exceptions/db_handler.ts

@@ -1,43 +0,0 @@
-// 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

@@ -46,7 +46,6 @@ export default class HttpExceptionHandler extends ExceptionHandler {
     //         return view.render('./errors/server-error', { error });
     //     },
     // };
-
     protected statusPages: Record<StatusPageRange, StatusPageRenderer> = {
         '404': (error, { inertia }) => {
             return inertia.render('Errors/ServerError', {
@@ -59,47 +58,9 @@ export default class HttpExceptionHandler extends ExceptionHandler {
             return inertia.render('Errors/ServerError', {
                 error: error.message,
                 code: error.status,
-            });
+            });           
-        },
-        // '500': (error, { inertia }) => {
-        //      return inertia.render('Errors/postgres_error', {
-        //             status: 'error',
-        //             message: 'PostgreSQL database connection failed. Please ensure the database service is running.',
-        //             details: {
-        //                 code: error.code,
-        //                 type: error.status,
-        //                 ports: error.errors.map((err: any) => ({
-        //                     port: err.port,
-        //                     address: err.address,
-        //                 })),
-        //             },
-        //         });
-        // },
-        '500..599': (error, { inertia }) => {
-            if (error.code === 'ECONNREFUSED') {
-                const dbErrors = error.errors.some((err: any) => err.code === 'ECONNREFUSED' && err.port === 5432);
-
-                if (dbErrors) {
-                    return inertia.render('Errors/postgres_error', {
-                        status: 'error',
-                        message: 'PostgreSQL database connection failed. Please ensure the database service is running.',
-                        details: {
-                            code: error.code,
-                            type: error.status,
-                            ports: error.errors.map((err: any) => ({
-                                port: err.port,
-                                address: err.address,
-                            })),
-                        },
-                    });
-                }
-            } else {
-                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 }),
     };
 
     // constructor() {
@@ -107,7 +68,7 @@ export default class HttpExceptionHandler extends ExceptionHandler {
     // }
 
     public async handle(error: any, ctx: HttpContext) {
-        const { response, request, session, inertia } = ctx;
+        const { response, request, session } = ctx;
 
         /**
          * Handle failed authentication attempt
@@ -121,47 +82,6 @@ export default class HttpExceptionHandler extends ExceptionHandler {
         //   return response.redirect('/dashboard');
         // }
 
-        // Handle Axios errors
-        if (error.code === 'ECONNREFUSED') {
-            const dbErrors = error.errors.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.status,
-                //         ports: error.errors.map((err: any) => ({
-                //             port: err.port,
-                //             address: err.address,
-                //         })),
-                //     },
-                // });
-                // return inertia.render('Errors/postgres_error', {
-                //     status: 'error',
-                //     message: 'PostgreSQL database connection failed. Please ensure the database service is running.',
-                //     details: {
-                //         code: error.code,
-                //         type: error.status,
-                //         ports: error.errors.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,
-        //     });
-        // }
-
         // https://github.com/inertiajs/inertia-laravel/issues/56
         // let test = response.getStatus(); //200
         // let header = request.header('X-Inertia'); // true
@@ -178,21 +98,12 @@ export default class HttpExceptionHandler extends ExceptionHandler {
             // ->toResponse($request)
             // ->setStatusCode($response->status());
         }
-
-        // 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,
-        //     });
-        // }
         // Dynamically change the error templates based on the absence of X-Inertia header
         // if (!ctx.request.header('X-Inertia')) {
         //     this.statusPages = {
-        //         '401..403': (error, { inertia }) => inertia.render('Errors/ServerError', { error: error.message, code: error.status }),
+        //         '401..403': (error, { view }) => view.render('./errors/unauthorized', { error }),
-        //         '404': (error, { inertia }) => inertia.render('Errors/ServerError', { error: error.message, code: error.status }),
+        //         '404': (error, { view }) => view.render('./errors/not-found', { error }),
-        //         '500..599': (error, { inertia }) => inertia.render('Errors/ServerError', { error: error.message, code: error.status }),
+        //         '500..599': (error, { view }) => view.render('./errors/server-error', { error }),
         //     };
         // }
 

app/models/DocumentXmlCache.ts

@@ -4,8 +4,7 @@ import { builder, create } from 'xmlbuilder2';
 import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
 import db from '@adonisjs/lucid/services/db';
 import { DateTime } from 'luxon';
-import type { BelongsTo } from '@adonisjs/lucid/types/relations';
+import 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();
@@ -67,38 +66,33 @@ export default class DocumentXmlCache extends BaseModel {
     }
 
     /**
-     * Check if a valid (non-stale) cache entry exists
+     * Check if a dataset in a specific xml version is already cached or not.
-     * Cache is valid only if it was created AFTER the dataset's last modification
      *
-     * @param datasetId - The dataset ID to check
+     * @param mixed datasetId
-     * @param datasetServerDateModified - The dataset's last modification timestamp
+     * @param mixed serverDateModified
-     * @returns true if valid cache exists, false otherwise
+     * @returns {Promise<boolean>} Returns true on cached hit else false.
      */
+    // 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 isValid = !!row;
+        const row = await query;
-
+        return !!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/dataset.ts

@@ -209,15 +209,6 @@ export default class Dataset extends DatasetExtension {
         return mainTitle ? mainTitle.value : null;
     }
 
-    @computed({
-        serializeAs: 'doi_identifier',
-    })
-    public get doiIdentifier() {
-        // return `${this.firstName} ${this.lastName}`;
-        const identifier: DatasetIdentifier = this.identifier;
-        return identifier ? identifier.value : null;
-    }
-
     @manyToMany(() => Person, {
         pivotForeignKey: 'document_id',
         pivotRelatedForeignKey: 'person_id',

app/models/file.ts

@@ -3,12 +3,12 @@ import { column, hasMany, belongsTo, SnakeCaseNamingStrategy, computed } from '@
 import HashValue from './hash_value.js';
 import Dataset from './dataset.js';
 import BaseModel from './base_model.js';
+// import { Buffer } from 'buffer';
 import * as fs from 'fs';
 import crypto from 'crypto';
 // import Drive from '@ioc:Adonis/Core/Drive';
 // import Drive from '@adonisjs/drive';
-// import drive from '#services/drive';
+import drive from '#services/drive';
-import drive from '@adonisjs/drive/services/main';
 
 import type { HasMany } from "@adonisjs/lucid/types/relations";
 import type { BelongsTo } from "@adonisjs/lucid/types/relations";
@@ -88,8 +88,7 @@ export default class File extends BaseModel {
         serializeAs: 'filePath',
     })
     public get filePath() {
-        // return `/storage/app/public/${this.pathName}`;
+        return `/storage/app/public/${this.pathName}`;
-        return `/storage/app/data/${this.pathName}`;
         // const mainTitle = this.titles?.find((title) => title.type === 'Main');
         // return mainTitle ? mainTitle.value : null;
     }
@@ -166,7 +165,7 @@ export default class File extends BaseModel {
     public async delete() {
         if (this.pathName) {
             // Delete file from additional storage
-            await drive.use('local').delete(this.pathName);
+            await drive.delete(this.pathName);
         }
 
         // Call the original delete method of the BaseModel to remove the record from the database

app/models/mime_type.ts

@@ -16,14 +16,9 @@ export default class MimeType extends BaseModel {
     @column({})
     public name: string;
 
-    // 1 : n file_extensions are separated by '|' in the database
     @column({})
     public file_extension: string;
 
-    // 1 : n alternate_mimetype are separated by '|' in the database
-    @column({})
-    public alternate_mimetype: string;
-
     @column({})
     public enabled: boolean;
 

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({ columnName: 'identifier_orcid' })
+    @column({})
     public identifierOrcid: string;
 
     @column({})
@@ -51,7 +51,7 @@ export default class Person extends BaseModel {
         serializeAs: 'name',
     })
     public get fullName() {
-        return [this.firstName, this.lastName].filter(Boolean).join(' ');
+        return `${this.firstName} ${this.lastName}`;
     }
 
     // @computed()
@@ -64,12 +64,10 @@ export default class Person extends BaseModel {
     // 	return '2023-03-21 08:45:00';
     // }
 
-    @computed({
+    @computed()
-        serializeAs: 'dataset_count',
-    })
     public get datasetCount() {
         const stock = this.$extras.datasets_count; //my pivot column name was "stock"
-        return Number(stock);
+        return stock;
     }
 
     @computed()
@@ -78,16 +76,6 @@ 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].$extras?.pivot_allow_email_contact;
-    }
-
     @manyToMany(() => Dataset, {
         pivotForeignKey: 'person_id',
         pivotRelatedForeignKey: 'document_id',
@@ -95,34 +83,4 @@ export default class Person extends BaseModel {
         pivotColumns: ['role', 'sort_order', 'allow_email_contact'],
     })
     public datasets: ManyToMany<typeof Dataset>;
-
-    // public toJSON() {
-    //     const json = super.toJSON();
-
-    //     // Check if this person is loaded through a pivot relationship with sensitive roles
-    //     const pivotRole = this.$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

@@ -1,57 +0,0 @@
-/**
- * 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

@@ -1,6 +1,6 @@
 import { DateTime } from 'luxon';
 import { withAuthFinder } from '@adonisjs/auth/mixins/lucid';
-import { column, manyToMany, hasMany, SnakeCaseNamingStrategy, computed, beforeFetch, beforeFind } from '@adonisjs/lucid/orm';
+import { column, manyToMany, hasMany, SnakeCaseNamingStrategy } from '@adonisjs/lucid/orm';
 import hash from '@adonisjs/core/services/hash';
 import Role from './role.js';
 import db from '@adonisjs/lucid/services/db';
@@ -49,6 +49,7 @@ export default class User extends compose(BaseModel, AuthFinder) {
     @column()
     public login: string;
 
+    
     @column()
     public firstName: string;
 
@@ -86,8 +87,17 @@ export default class User extends compose(BaseModel, AuthFinder) {
     @column({})
     public state: number;
 
-    @column({})
+    // @hasOne(() => TotpSecret, {
-    public avatar: string;
+    //     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);
@@ -111,29 +121,6 @@ export default class User extends compose(BaseModel, AuthFinder) {
     })
     public backupcodes: HasMany<typeof BackupCode>;
 
-    @computed({
-        serializeAs: 'is_admin',
-    })
-    public get isAdmin(): boolean {
-        const roles = this.roles;
-        const isAdmin = roles?.map((role: Role) => role.name).includes('administrator');
-        return isAdmin;
-    }
-
-    // public toJSON() {
-    //     return {
-    //         ...super.toJSON(),
-    //         roles: []
-    //     };
-    // }
-    @beforeFind()
-    @beforeFetch()
-    public static preloadRoles(user: User) {
-        user.preload('roles', (builder) => {
-            builder.select(['id', 'name', 'display_name', 'description']);
-        });
-    }
-
     public async getBackupCodes(this: User): Promise<BackupCode[]> {
         const test = await this.related('backupcodes').query();
         // return test.map((role) => role.code);

app/utils/utility-functions.ts

@@ -1,16 +1,3 @@
-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;
 }
@@ -37,88 +24,3 @@ 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;
-}

app/validators/dataset.ts

@@ -1,7 +1,6 @@
 import vine, { SimpleMessagesProvider } from '@vinejs/vine';
 import { TitleTypes, DescriptionTypes, ContributorTypes, ReferenceIdentifierTypes, RelationTypes } from '#contracts/enums';
 import dayjs from 'dayjs';
-
 // import MimeType from '#models/mime_type';
 
 // const enabledExtensions = await MimeType.query().select('file_extension').where('enabled', true).exec();
@@ -40,8 +39,7 @@ export const createDatasetValidator = vine.compile(
                         .translatedLanguage({ mainLanguageField: 'language', typeField: 'type' }),
                 }),
             )
-            // .minLength(2)
+            .minLength(1),
-            .arrayContainsTypes({ typeA: 'main', typeB: 'translated' }),
         descriptions: vine
             .array(
                 vine.object({
@@ -55,8 +53,7 @@ export const createDatasetValidator = vine.compile(
                         .translatedLanguage({ mainLanguageField: 'language', typeField: 'type' }),
                 }),
             )
-            // .minLength(1),
+            .minLength(1),
-            .arrayContainsTypes({ typeA: 'abstract', typeB: 'translated' }),
         authors: vine
             .array(
                 vine.object({
@@ -67,9 +64,8 @@ export const createDatasetValidator = vine.compile(
                         .email()
                         .normalizeEmail()
                         .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }),
-                    first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'),
+                    first_name: vine.string().trim().minLength(3).maxLength(255),
                     last_name: vine.string().trim().minLength(3).maxLength(255),
-                    identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(),
                 }),
             )
             .minLength(1)
@@ -84,10 +80,9 @@ export const createDatasetValidator = vine.compile(
                         .email()
                         .normalizeEmail()
                         .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }),
-                    first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'),
+                    first_name: vine.string().trim().minLength(3).maxLength(255),
                     last_name: vine.string().trim().minLength(3).maxLength(255),
                     pivot_contributor_type: vine.enum(Object.keys(ContributorTypes)),
-                    identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(),
                 }),
             )
             .distinct('email')
@@ -130,7 +125,7 @@ export const createDatasetValidator = vine.compile(
         references: vine
             .array(
                 vine.object({
-                    value: vine.string().trim().minLength(3).maxLength(255).validateReference({ typeField: 'type' }),
+                    value: vine.string().trim().minLength(3).maxLength(255),
                     type: vine.enum(Object.values(ReferenceIdentifierTypes)),
                     relation: vine.enum(Object.values(RelationTypes)),
                     label: vine.string().trim().minLength(2).maxLength(255),
@@ -191,8 +186,7 @@ export const updateDatasetValidator = vine.compile(
                         .translatedLanguage({ mainLanguageField: 'language', typeField: 'type' }),
                 }),
             )
-            // .minLength(2)
+            .minLength(1),
-            .arrayContainsTypes({ typeA: 'main', typeB: 'translated' }),
         descriptions: vine
             .array(
                 vine.object({
@@ -206,7 +200,7 @@ export const updateDatasetValidator = vine.compile(
                         .translatedLanguage({ mainLanguageField: 'language', typeField: 'type' }),
                 }),
             )
-            .arrayContainsTypes({ typeA: 'abstract', typeB: 'translated' }),
+            .minLength(1),
         authors: vine
             .array(
                 vine.object({
@@ -217,9 +211,8 @@ export const updateDatasetValidator = vine.compile(
                         .email()
                         .normalizeEmail()
                         .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }),
-                    first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'),
+                    first_name: vine.string().trim().minLength(3).maxLength(255),
                     last_name: vine.string().trim().minLength(3).maxLength(255),
-                    identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(),
                 }),
             )
             .minLength(1)
@@ -234,9 +227,8 @@ export const updateDatasetValidator = vine.compile(
                         .email()
                         .normalizeEmail()
                         .isUniquePerson({ table: 'persons', column: 'email', idField: 'id' }),
-                    first_name: vine.string().trim().minLength(3).maxLength(255).optional().requiredWhen('name_type', '=', 'Personal'),
+                    first_name: vine.string().trim().minLength(3).maxLength(255),
                     last_name: vine.string().trim().minLength(3).maxLength(255),
-                    identifier_orcid: vine.string().trim().maxLength(255).orcid().optional(),
                     pivot_contributor_type: vine.enum(Object.keys(ContributorTypes)),
                 }),
             )
@@ -280,7 +272,7 @@ export const updateDatasetValidator = vine.compile(
         references: vine
             .array(
                 vine.object({
-                    value: vine.string().trim().minLength(3).maxLength(255).validateReference({ typeField: 'type' }),
+                    value: vine.string().trim().minLength(3).maxLength(255),
                     type: vine.enum(Object.values(ReferenceIdentifierTypes)),
                     relation: vine.enum(Object.values(RelationTypes)),
                     label: vine.string().trim().minLength(2).maxLength(255),
@@ -310,149 +302,21 @@ export const updateDatasetValidator = vine.compile(
                     .fileScan({ removeInfected: true }),
             )
             .dependentArrayMinLength({ dependentArray: 'fileInputs', min: 1 }),
-        fileInputs: vine
+        fileInputs: vine.array(
-            .array(
+            vine.object({
-                vine.object({
+                label: vine.string().trim().maxLength(100),
-                    label: vine.string().trim().maxLength(100),
+                //extnames: extensions,
-                }),
+            }),
-            )
+        ),
-            .optional(),
     }),
 );
 
-export const updateEditorDatasetValidator = vine.compile(
+// files: schema.array([rules.minLength(1)]).members(
-    vine.object({
+//     schema.file({
-        // first step
+//         size: '512mb',
-        language: vine
+//         extnames: ['jpg', 'gif', 'png', 'tif', 'pdf', 'zip', 'fgb', 'nc', 'qml', 'ovr', 'gpkg', 'gml', 'gpx', 'kml', 'kmz', 'json'],
-            .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',
@@ -504,10 +368,8 @@ 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

@@ -1,28 +0,0 @@
-// app/validators/project.ts
-import vine from '@vinejs/vine';
-
-export const createProjectValidator = vine.compile(
-    vine.object({
-        label: vine.string().trim().minLength(1).maxLength(50) .regex(/^[a-z0-9-]+$/),
-        name: vine
-            .string()
-            .trim()
-            .minLength(3)
-            .maxLength(255)
-            .regex(/^[a-zA-Z0-9äöüßÄÖÜ\s-]+$/),
-        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)
-            .isUnique({ table: 'roles', column: 'name' })
+            .regex(/^[a-zA-Z0-9]+$/), //Must be alphanumeric with hyphens or underscores
-            .regex(/^[a-zA-Z0-9]+$/), // 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), // At least one permission required
+        permissions: vine.array(vine.number()).minLength(1), // define at least one permission for the new role
     }),
 );
 
@@ -29,28 +29,21 @@ export const updateRoleValidator = vine.withMetaData<{ roleId: number }>().compi
     vine.object({
         name: vine
             .string()
-            .trim()
+            // .unique(async (db, value, field) => {
-            .minLength(3)
+            //     const result = await db.from('roles').select('id').whereNot('id', field.meta.roleId).where('name', value).first();
-            .maxLength(255)
+            //     return result.length ? false : true;
+            // })
             .isUnique({
                 table: 'roles',
                 column: 'name',
                 whereNot: (field) => field.meta.roleId,
             })
-            .regex(/^[a-zA-Z0-9]+$/),
-        display_name: vine
-            .string()
             .trim()
             .minLength(3)
-            .maxLength(255)
+            .maxLength(255),
-            .isUnique({
+
-                table: 'roles',
-                column: 'display_name',
-                whereNot: (field) => field.meta.roleId,
-            })
-            .regex(/^[a-zA-Z0-9]+$/),
         description: vine.string().trim().escape().minLength(3).maxLength(255).optional(),
-        permissions: vine.array(vine.number()).minLength(1), // At least one permission required
+        permissions: vine.array(vine.number()).minLength(1), // define at least one permission for the new role
     }),
 );
 

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' }),
-        new_password: vine.string().confirmed({ confirmationField: 'password_confirmation' }).trim().minLength(3).maxLength(60),
+        password: vine.string().confirmed().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 }),
-        new_password: vine.string().confirmed({ confirmationField: 'password_confirmation' }).trim().minLength(3).maxLength(60).optional(),
+        password: vine.string().confirmed().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

@@ -142,7 +142,7 @@ export class VanillaErrorReporter implements ErrorReporterContract {
         //   }
         this.hasErrors = true;
 
-        // var test = field.getFieldPath();
+        var test = field.getFieldPath();
 
         //   this.errors.push(error);
         // if (this.errors[error.field]) {

clamd.conf

@@ -5,23 +5,7 @@ LogSyslog no
 LogVerbose yes
 DatabaseDirectory /var/lib/clamav
 LocalSocket /var/run/clamav/clamd.socket
-# LocalSocketMode 666
-# Optional: allow multiple threads
-MaxThreads 20
-# Disable TCP socket
-# TCPSocket 0
-
-# TCP port address.
-# Default: no
-# TCPSocket 3310
-# TCP address.
-# By default we bind to INADDR_ANY, probably not wise.
-# Enable the following to provide some degree of protection
-# from the outside world.
-# Default: no
-# TCPAddr 127.0.0.1
- 
 Foreground no
 PidFile /var/run/clamav/clamd.pid
-# LocalSocketGroup node  # Changed from 'clamav'
+LocalSocketGroup node
-# User node              # Changed from 'clamav' - clamd runs as clamav user
+User node

commands/fix_dataset_cross_references.ts

@@ -1,482 +0,0 @@
-/*
-|--------------------------------------------------------------------------
-| node ace make:command fix-dataset-cross-references
-| DONE:    create commands/fix_dataset_cross_references.ts
-|--------------------------------------------------------------------------
-*/
-import { BaseCommand, flags } from '@adonisjs/core/ace';
-import type { CommandOptions } from '@adonisjs/core/types/ace';
-import { DateTime } from 'luxon';
-import Dataset from '#models/dataset';
-import DatasetReference from '#models/dataset_reference';
-import AppConfig from '#models/appconfig';
-// import env from '#start/env';
-
-interface MissingCrossReference {
-    sourceDatasetId: number;
-    targetDatasetId: number;
-    sourcePublishId: number | null;
-    targetPublishId: number | null;
-    sourceDoi: string | null;
-    targetDoi: string | null;
-    referenceType: string;
-    relation: string;
-    doi: string | null;
-    reverseRelation: string;
-    sourceReferenceLabel: string | null;
-}
-
-export default class DetectMissingCrossReferences extends BaseCommand {
-    static commandName = 'detect:missing-cross-references';
-    static description = 'Detect missing bidirectional cross-references between versioned datasets';
-
-    public static needsApplication = true;
-
-    @flags.boolean({ alias: 'f', description: 'Fix missing cross-references automatically' })
-    public fix: boolean = false;
-
-    @flags.boolean({ alias: 'v', description: 'Verbose output' })
-    public verbose: boolean = false;
-
-    @flags.number({ alias: 'p', description: 'Filter by specific publish_id (source or target dataset)' })
-    public publish_id?: number;
-
-    // example: node ace detect:missing-cross-references --verbose -p 227 //if you want to filter by specific publish_id with details
-    // example: node ace detect:missing-cross-references --verbose
-    // example: node ace detect:missing-cross-references --fix -p 227 //if you want to filter by specific publish_id and fix it
-    // example: node ace detect:missing-cross-references
-
-    public static options: CommandOptions = {
-        startApp: true,
-        staysAlive: false,
-    };
-
-    // Define the allowed relations that we want to process
-    private readonly ALLOWED_RELATIONS = [
-        'IsNewVersionOf',
-        'IsPreviousVersionOf',
-        'IsVariantFormOf',
-        'IsOriginalFormOf',
-        'Continues',
-        'IsContinuedBy',
-        'HasPart',
-        'IsPartOf',
-    ];
-    // private readonly ALLOWED_RELATIONS = ['IsPreviousVersionOf', 'IsOriginalFormOf'];
-
-    async run() {
-        this.logger.info('🔍 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/index_datasets.ts

@@ -4,7 +4,7 @@
 import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
 import { create } from 'xmlbuilder2';
 import Dataset from '#models/dataset';
-import XmlModel from '#app/Library/DatasetXmlSerializer';
+import XmlModel from '#app/Library/XmlModel';
 import { readFileSync } from 'fs';
 import SaxonJS from 'saxon-js';
 import { Client } from '@opensearch-project/opensearch';
@@ -12,8 +12,10 @@ import { getDomain } from '#app/utils/utility-functions';
 import { BaseCommand, flags } from '@adonisjs/core/ace';
 import { CommandOptions } from '@adonisjs/core/types/ace';
 import env from '#start/env';
+// import db from '@adonisjs/lucid/services/db';
+// import { default as Dataset } from '#models/dataset';
 import logger from '@adonisjs/core/services/logger';
-import { DateTime } from 'luxon';
+
 
 const opensearchNode = env.get('OPENSEARCH_HOST', 'localhost');
 const client = new Client({ node: `${opensearchNode}` }); // replace with your OpenSearch endpoint
@@ -28,10 +30,11 @@ export default class IndexDatasets extends BaseCommand {
     public publish_id: number;
 
     public static options: CommandOptions = {
-        startApp: true, // Ensures the IoC container is ready to use
+        startApp: true,       
-        staysAlive: false, // Command exits after running
+        staysAlive: false,
     };
 
+
     async run() {
         logger.debug('Hello world!');
         // const { default: Dataset } = await import('#models/dataset');
@@ -41,12 +44,10 @@ export default class IndexDatasets extends BaseCommand {
         const index_name = 'tethys-records';
 
         for (var dataset of datasets) {
-            const shouldUpdate = await this.shouldUpdateDataset(dataset, index_name);
+            // Logger.info(`File publish_id ${dataset.publish_id}`);
-            if (shouldUpdate) {
+            // const jsonString = await this.getJsonString(dataset, proc);
-                await this.indexDocument(dataset, index_name, proc);
+            // console.log(jsonString);
-            } else {
+            await this.indexDocument(dataset, index_name, proc);
-                logger.info(`Dataset with publish_id ${dataset.publish_id} is up to date, skipping indexing`);
-            }
         }
     }
 
@@ -64,46 +65,6 @@ 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);
@@ -117,8 +78,7 @@ export default class IndexDatasets extends BaseCommand {
             });
             logger.info(`dataset with publish_id ${dataset.publish_id} successfully indexed`);
         } catch (error) {
-            logger.error(`An error occurred while indexing dataset with publish_id ${dataset.publish_id}.
+            logger.error(`An error occurred while indexing dataset with publish_id ${dataset.publish_id}.`);
-                Error: ${error.message}`);
         }
     }
 
@@ -151,16 +111,19 @@ export default class IndexDatasets extends BaseCommand {
     }
 
     private async getDatasetXmlDomNode(dataset: Dataset): Promise<XMLBuilder | null> {
-        const serializer = new XmlModel(dataset).enableCaching().excludeEmptyFields();
+        const xmlModel = new XmlModel(dataset);
         // xmlModel.setModel(dataset);
-
+        xmlModel.excludeEmptyFields();
+        xmlModel.caching = true;
+        // const cache = dataset.xmlCache ? dataset.xmlCache : null;
+        // dataset.load('xmlCache');
         if (dataset.xmlCache) {
-            serializer.setCache(dataset.xmlCache);
+            xmlModel.xmlCache = dataset.xmlCache;
         }
 
-        // return cache.toXmlDocument();
+        // return cache.getDomDocument();
-        const xmlDocument: XMLBuilder | null = await serializer.toXmlDocument();
+        const domDocument: XMLBuilder | null = await xmlModel.getDomDocument();
-        return xmlDocument;
+        return domDocument;
     }
 
     private addSpecInformation(domNode: XMLBuilder, information: string) {

commands/list_updatable_datacite.ts

@@ -1,346 +0,0 @@
-/*
-|--------------------------------------------------------------------------
-| node ace make:command list-updateable-datacite
-| DONE:    create commands/list_updeatable_datacite.ts
-|--------------------------------------------------------------------------
-*/
-import { BaseCommand, flags } from '@adonisjs/core/ace';
-import { CommandOptions } from '@adonisjs/core/types/ace';
-import Dataset from '#models/dataset';
-import { DoiClient } from '#app/Library/Doi/DoiClient';
-import env from '#start/env';
-import logger from '@adonisjs/core/services/logger';
-import { DateTime } from 'luxon';
-import pLimit from 'p-limit';
-
-export default class ListUpdateableDatacite extends BaseCommand {
-    static commandName = 'list:updateable-datacite';
-    static description = 'List all datasets that need DataCite DOI updates';
-
-    public static needsApplication = true;
-
-    // private chunkSize = 100; // Set chunk size for pagination
-
-    @flags.boolean({ alias: 'v', description: 'Verbose output showing detailed information' })
-    public verbose: boolean = false;
-
-    @flags.boolean({ alias: 'c', description: 'Show only count of updatable datasets' })
-    public countOnly: boolean = false;
-
-    @flags.boolean({ alias: 'i', description: 'Show only publish IDs (useful for scripting)' })
-    public idsOnly: boolean = false;
-
-    @flags.number({ description: 'Chunk size for processing datasets (default: 50)' })
-    public chunkSize: number = 50;
-
-    //example: node ace list:updateable-datacite
-    //example: node ace list:updateable-datacite --verbose
-    //example: node ace list:updateable-datacite --count-only
-    //example: node ace list:updateable-datacite --ids-only
-    //example: node ace list:updateable-datacite --chunk-size 50
-
-    public static options: CommandOptions = {
-        startApp: true,
-        stayAlive: false,
-    };
-
-    async run() {
-        const prefix = env.get('DATACITE_PREFIX', '');
-        const base_domain = env.get('BASE_DOMAIN', '');
-
-        if (!prefix || !base_domain) {
-            logger.error('Missing DATACITE_PREFIX or BASE_DOMAIN environment variables');
-            return;
-        }
-
-        // Prevent conflicting flags
-        if ((this.verbose && this.countOnly) || (this.verbose && this.idsOnly)) {
-            logger.error('Flags --verbose cannot be combined with --count-only or --ids-only');
-            return;
-        }
-
-        const chunkSize = this.chunkSize || 50;
-        let page = 1;
-        let hasMoreDatasets = true;
-        let totalProcessed = 0;
-        const updatableDatasets: Dataset[] = [];
-
-        if (!this.countOnly && !this.idsOnly) {
-            logger.info(`Processing datasets in chunks of ${chunkSize}...`);
-        }
-
-        while (hasMoreDatasets) {
-            const datasets = await this.getDatasets(page, chunkSize);
-
-            if (datasets.length === 0) {
-                hasMoreDatasets = false;
-                break;
-            }
-
-            if (!this.countOnly && !this.idsOnly) {
-                logger.info(`Processing chunk ${page} (${datasets.length} datasets)...`);
-            }
-
-            const chunkUpdatableDatasets = await this.processChunk(datasets);
-            updatableDatasets.push(...chunkUpdatableDatasets);
-            totalProcessed += datasets.length;
-
-            page += 1;
-            if (datasets.length < chunkSize) {
-                hasMoreDatasets = false;
-            }
-        }
-
-        if (!this.countOnly && !this.idsOnly) {
-            logger.info(`Processed ${totalProcessed} datasets total, found ${updatableDatasets.length} that need updates`);
-        }
-
-        if (this.countOnly) {
-            console.log(updatableDatasets.length);
-        } else if (this.idsOnly) {
-            updatableDatasets.forEach((dataset) => console.log(dataset.publish_id));
-        } else if (this.verbose) {
-            await this.showVerboseOutput(updatableDatasets);
-        } else {
-            this.showSimpleOutput(updatableDatasets);
-        }
-    }
-
-    /**
-     * Processes a chunk of datasets to determine which ones need DataCite updates
-     *
-     * This method handles parallel processing of datasets within a chunk, providing
-     * efficient error handling and filtering of results.
-     *
-     * @param datasets - Array of Dataset objects to process
-     * @returns Promise<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

@@ -1,266 +0,0 @@
-/*
-|--------------------------------------------------------------------------
-| node ace make:command update-datacite
-| DONE:    create commands/update_datacite.ts
-|--------------------------------------------------------------------------
-*/
-import { BaseCommand, flags } from '@adonisjs/core/ace';
-import { CommandOptions } from '@adonisjs/core/types/ace';
-import Dataset from '#models/dataset';
-import { DoiClient } from '#app/Library/Doi/DoiClient';
-import DoiClientException from '#app/exceptions/DoiClientException';
-import Index from '#app/Library/Utils/Index';
-import env from '#start/env';
-import logger from '@adonisjs/core/services/logger';
-import { DateTime } from 'luxon';
-import { getDomain } from '#app/utils/utility-functions';
-
-export default class UpdateDatacite extends BaseCommand {
-    static commandName = 'update:datacite';
-    static description = 'Update DataCite DOI records for published datasets';
-
-    public static needsApplication = true;
-
-    @flags.number({ alias: 'p', description: 'Specific publish_id to update' })
-    public publish_id: number;
-
-    @flags.boolean({ alias: 'f', description: 'Force update all records regardless of modification date' })
-    public force: boolean = false;
-
-    @flags.boolean({ alias: 'd', description: 'Dry run - show what would be updated without making changes' })
-    public dryRun: boolean = false;
-
-    @flags.boolean({ alias: 's', description: 'Show detailed stats for each dataset that needs updating' })
-    public stats: boolean = false;
-
-    //example: node ace update:datacite -p 123 --force --dry-run
-
-    public static options: CommandOptions = {
-        startApp: true, // Whether to boot the application before running the command
-        stayAlive: false, // Whether to keep the process alive after the command has executed
-    };
-
-    async run() {
-        logger.info('Starting DataCite update process...');
-
-        const prefix = env.get('DATACITE_PREFIX', '');
-        const base_domain = env.get('BASE_DOMAIN', '');
-        const apiUrl = env.get('DATACITE_API_URL', 'https://api.datacite.org');
-
-        if (!prefix || !base_domain) {
-            logger.error('Missing DATACITE_PREFIX or BASE_DOMAIN environment variables');
-            return;
-        }
-
-        logger.info(`Using DataCite API: ${apiUrl}`);
-
-        const datasets = await this.getDatasets();
-        logger.info(`Found ${datasets.length} datasets to process`);
-
-        let updated = 0;
-        let skipped = 0;
-        let errors = 0;
-
-        for (const dataset of datasets) {
-            try {
-                const shouldUpdate = this.force || (await this.shouldUpdateDataset(dataset));
-
-                if (this.stats) {
-                    // Stats mode: show detailed information for datasets that need updating
-                    if (shouldUpdate) {
-                        await this.showDatasetStats(dataset);
-                        updated++;
-                    } else {
-                        skipped++;
-                    }
-                    continue;
-                }
-
-                if (!shouldUpdate) {
-                    logger.info(`Dataset ${dataset.publish_id}: Up to date, skipping`);
-                    skipped++;
-                    continue;
-                }
-
-                if (this.dryRun) {
-                    logger.info(`Dataset ${dataset.publish_id}: Would update DataCite record (dry run)`);
-                    updated++;
-                    continue;
-                }
-
-                await this.updateDataciteRecord(dataset, prefix, base_domain);
-                logger.info(`Dataset ${dataset.publish_id}: Successfully updated DataCite record`);
-                updated++;
-            } catch (error) {
-                logger.error(`Dataset ${dataset.publish_id}: Failed to update - ${error.message}`);
-                errors++;
-            }
-        }
-
-        if (this.stats) {
-            logger.info(`\nDataCite Stats Summary: ${updated} datasets need updating, ${skipped} are up to date`);
-        } else {
-            logger.info(`DataCite update completed. Updated: ${updated}, Skipped: ${skipped}, Errors: ${errors}`);
-        }
-    }
-
-    private async getDatasets(): Promise<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
-            └─────────────────────────────────────────────────────────────────────────────────────────────`);
-        }
-    }
-}

commands/validate_checksum.ts

@@ -88,7 +88,7 @@ export default class ValidateChecksum extends BaseCommand {
         );
 
         // Construct the file path
-        const filePath = '/storage/app/data/' + file.pathName;
+        const filePath = '/storage/app/public/' + file.pathName;
 
         try {
             // Calculate the MD5 checksum of the file

components.d.ts

@@ -11,21 +11,3 @@ declare module '@vue/runtime-core' {
         NInput: (typeof import('naive-ui'))['NInput'];
     }
 }
-
-// types/leaflet-src-dom-DomEvent.d.ts
-declare module 'leaflet/src/dom/DomEvent' {
-    export type DomEventHandler = (e?: any) => void;
-
-    // Attach event listeners. `obj` can be any DOM node or object with event handling.
-    export function on(obj: any, types: string, fn: DomEventHandler, context?: any): void;
-
-    // Detach event listeners.
-    export function off(obj: any, types: string, fn?: DomEventHandler, context?: any): void;
-
-    // Prevent default on native events
-    export function preventDefault(ev?: Event | undefined): void;
-
-    // Optional: other helpers you might need later
-    export function stopPropagation(ev?: Event | undefined): void;
-    export function stop(ev?: Event | undefined): void;
-}

config/app.ts

@@ -80,8 +80,7 @@ export const http = defineConfig({
 | headers.
 |
 */
-    // trustProxy: proxyAddr.compile('loopback'),
+    trustProxy: proxyAddr.compile('loopback'),
-    trustProxy: proxyAddr.compile(['127.0.0.1', '::1/128']),
 
     /*
 |--------------------------------------------------------------------------

config/bodyparser.ts

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

config/database.ts

@@ -47,7 +47,7 @@ const databaseConfig = defineConfig({
       migrations: {
         naturalSort: true,
       },
-      // healthCheck: false,
+      healthCheck: false,
       debug: false,
       pool: { min: 1, max: 100 },
     },

config/drive.ts

@@ -1,45 +1,151 @@
-// import env from '#start/env'
+/**
-// import app from '@adonisjs/core/services/app'
+ * Config source: https://git.io/JBt3o
-import { defineConfig, services } from '@adonisjs/drive'
+ *
+ * Feel free to let us know via PR, if you find something broken in this config
+ * file.
+ */
+import { defineConfig } from '#providers/drive/src/types/define_config';
+import env from '#start/env';
+// import { driveConfig } from '@adonisjs/core/build/config';
+// import  { driveConfig }  from "@adonisjs/drive/build/config.js";
+// import Application from '@ioc:Adonis/Core/Application';
 
-const driveConfig = defineConfig({
+/*
-   
+|--------------------------------------------------------------------------
-    default: 'public',
+| Drive Config
-    
+|--------------------------------------------------------------------------
+|
+| The `DriveConfig` relies on the `DisksList` interface which is
+| defined inside the `contracts` directory.
+|
+*/
+export default defineConfig({
+    /*
+  |--------------------------------------------------------------------------
+  | Default disk
+  |--------------------------------------------------------------------------
+  |
+  | The default disk to use for managing file uploads. The value is driven by
+  | the `DRIVE_DISK` environment variable.
+  |
+  */
+    disk: env.get('DRIVE_DISK', 'local'),
 
-    services: {
+    disks: {
-  
+        /*
-      /**
+    |--------------------------------------------------------------------------
-       * Persist files on the local filesystem
+    | Local
-       */
+    |--------------------------------------------------------------------------
-      public: services.fs({
+    |
-        location: '/storage/app/public/',
+    | Uses the local file system to manage files. Make sure to turn off serving
-        serveFiles: true,
+    | files when not using this disk.
-        routeBasePath: '/public',
+    |
-        visibility: 'public',
+    */
-      }),
+        local: {
-      local: services.fs({
+            driver: 'local',
-        location: '/storage/app/data/',
+            visibility: 'public',
-        serveFiles: true,
+
-        routeBasePath: '/data',
+            /*
-        visibility: 'public',
+      |--------------------------------------------------------------------------
-      }),
+      | Storage root - Local driver only
-    
+      |--------------------------------------------------------------------------
-  
+      |
-      /**
+      | Define an absolute path to the storage directory from where to read the
-       * Persist files on Digital Ocean spaces
+      | files.
-       */
+      |
-    //   spaces: services.s3({
+      */
-    //     credentials: {
+            // root: Application.tmpPath('uploads'),
-    //       accessKeyId: env.get('SPACES_KEY'),
+            root: '/storage/app/public',
-    //       secretAccessKey: env.get('SPACES_SECRET'),
+
-    //     },
+            /*
-    //     region: env.get('SPACES_REGION'),
+      |--------------------------------------------------------------------------
-    //     bucket: env.get('SPACES_BUCKET'),
+      | Serve files - Local driver only
-    //     endpoint: env.get('SPACES_ENDPOINT'),
+      |--------------------------------------------------------------------------
-    //     visibility: 'public',
+      |
-    //   }),
+      | When this is set to true, AdonisJS will configure a files server to serve
+      | files from the disk root. This is done to mimic the behavior of cloud
+      | storage services that has inbuilt capabilities to serve files.
+      |
+      */
+            serveFiles: true,
+
+            /*
+      |--------------------------------------------------------------------------
+      | Base path - Local driver only
+      |--------------------------------------------------------------------------
+      |
+      | Base path is always required when "serveFiles = true". Also make sure
+      | the `basePath` is unique across all the disks using "local" driver and
+      | you are not registering routes with this prefix.
+      |
+      */
+            basePath: '/uploads',
+        },
+
+        /*
+    |--------------------------------------------------------------------------
+    | S3 Driver
+    |--------------------------------------------------------------------------
+    |
+    | Uses the S3 cloud storage to manage files. Make sure to install the s3
+    | drive separately when using it.
+    |
+    |**************************************************************************
+    | npm i @adonisjs/drive-s3
+    |**************************************************************************
+    |
+    */
+        // s3: {
+        //   driver: 's3',
+        //   visibility: 'public',
+        //   key: Env.get('S3_KEY'),
+        //   secret: Env.get('S3_SECRET'),
+        //   region: Env.get('S3_REGION'),
+        //   bucket: Env.get('S3_BUCKET'),
+        //   endpoint: Env.get('S3_ENDPOINT'),
+        //
+        //  // For minio to work
+        //  // forcePathStyle: true,
+        // },
+
+        /*
+    |--------------------------------------------------------------------------
+    | GCS Driver
+    |--------------------------------------------------------------------------
+    |
+    | Uses the Google cloud storage to manage files. Make sure to install the GCS
+    | drive separately when using it.
+    |
+    |**************************************************************************
+    | npm i @adonisjs/drive-gcs
+    |**************************************************************************
+    |
+    */
+        // gcs: {
+        //   driver: 'gcs',
+        //   visibility: 'public',
+        //   keyFilename: Env.get('GCS_KEY_FILENAME'),
+        //   bucket: Env.get('GCS_BUCKET'),
+
+        /*
+      |--------------------------------------------------------------------------
+      | Uniform ACL - Google cloud storage only
+      |--------------------------------------------------------------------------
+      |
+      | When using the Uniform ACL on the bucket, the "visibility" option is
+      | ignored. Since, the files ACL is managed by the google bucket policies
+      | directly.
+      |
+      |**************************************************************************
+      | Learn more: https://cloud.google.com/storage/docs/uniform-bucket-level-access
+      |**************************************************************************
+      |
+      | The following option just informs drive whether your bucket is using uniform
+      | ACL or not. The actual setting needs to be toggled within the Google cloud
+      | console.
+      |
+      */
+        //   usingUniformAcl: false,
+        // },
     },
-  })
+});
-  
-  export default driveConfig

config/drive_self.ts

@@ -1,233 +0,0 @@
-/**
- * Config source: https://git.io/JBt3o
- *
- * Feel free to let us know via PR, if you find something broken in this config
- * file.
- */
-import { defineConfig } from '#providers/drive/src/types/define_config';
-import env from '#start/env';
-// import { driveConfig } from '@adonisjs/core/build/config';
-// import  { driveConfig }  from "@adonisjs/drive/build/config.js";
-// import Application from '@ioc:Adonis/Core/Application';
-
-/*
-|--------------------------------------------------------------------------
-| Drive Config
-|--------------------------------------------------------------------------
-|
-| The `DriveConfig` relies on the `DisksList` interface which is
-| defined inside the `contracts` directory.
-|
-*/
-export default defineConfig({
-    /*
-  |--------------------------------------------------------------------------
-  | Default disk
-  |--------------------------------------------------------------------------
-  |
-  | The default disk to use for managing file uploads. The value is driven by
-  | the `DRIVE_DISK` environment variable.
-  |
-  */
-    disk: env.get('DRIVE_DISK', 'local'),
-
-    disks: {
-        /*
-    |--------------------------------------------------------------------------
-    | Local
-    |--------------------------------------------------------------------------
-    |
-    | Uses the local file system to manage files. Make sure to turn off serving
-    | files when not using this disk.
-    |
-    */
-        local: {
-            driver: 'local',
-            visibility: 'public',
-
-            /*
-      |--------------------------------------------------------------------------
-      | Storage root - Local driver only
-      |--------------------------------------------------------------------------
-      |
-      | Define an absolute path to the storage directory from where to read the
-      | files.
-      |
-      */
-            // root: Application.tmpPath('uploads'),
-            root: '/storage/app/data',
-
-            /*
-      |--------------------------------------------------------------------------
-      | Serve files - Local driver only
-      |--------------------------------------------------------------------------
-      |
-      | When this is set to true, AdonisJS will configure a files server to serve
-      | files from the disk root. This is done to mimic the behavior of cloud
-      | storage services that has inbuilt capabilities to serve files.
-      |
-      */
-            serveFiles: true,
-
-            /*
-      |--------------------------------------------------------------------------
-      | Base path - Local driver only
-      |--------------------------------------------------------------------------
-      |
-      | Base path is always required when "serveFiles = true". Also make sure
-      | the `basePath` is unique across all the disks using "local" driver and
-      | you are not registering routes with this prefix.
-      |
-      */
-            basePath: '/files',
-        },
-
-        local: {
-            driver: 'local',
-            visibility: 'public',
-
-            /*
-      |--------------------------------------------------------------------------
-      | Storage root - Local driver only
-      |--------------------------------------------------------------------------
-      |
-      | Define an absolute path to the storage directory from where to read the
-      | files.
-      |
-      */
-            // root: Application.tmpPath('uploads'),
-            root: '/storage/app/data',
-
-            /*
-      |--------------------------------------------------------------------------
-      | Serve files - Local driver only
-      |--------------------------------------------------------------------------
-      |
-      | When this is set to true, AdonisJS will configure a files server to serve
-      | files from the disk root. This is done to mimic the behavior of cloud
-      | storage services that has inbuilt capabilities to serve files.
-      |
-      */
-            serveFiles: true,
-
-            /*
-      |--------------------------------------------------------------------------
-      | Base path - Local driver only
-      |--------------------------------------------------------------------------
-      |
-      | Base path is always required when "serveFiles = true". Also make sure
-      | the `basePath` is unique across all the disks using "local" driver and
-      | you are not registering routes with this prefix.
-      |
-      */
-            basePath: '/files',
-        }, 
-        
-        fs: {
-            driver: 'local',
-            visibility: 'public',
-
-            /*
-      |--------------------------------------------------------------------------
-      | Storage root - Local driver only
-      |--------------------------------------------------------------------------
-      |
-      | Define an absolute path to the storage directory from where to read the
-      | files.
-      |
-      */
-            // root: Application.tmpPath('uploads'),
-            root: '/storage/app/public',
-
-            /*
-      |--------------------------------------------------------------------------
-      | Serve files - Local driver only
-      |--------------------------------------------------------------------------
-      |
-      | When this is set to true, AdonisJS will configure a files server to serve
-      | files from the disk root. This is done to mimic the behavior of cloud
-      | storage services that has inbuilt capabilities to serve files.
-      |
-      */
-            serveFiles: true,
-
-            /*
-      |--------------------------------------------------------------------------
-      | Base path - Local driver only
-      |--------------------------------------------------------------------------
-      |
-      | Base path is always required when "serveFiles = true". Also make sure
-      | the `basePath` is unique across all the disks using "local" driver and
-      | you are not registering routes with this prefix.
-      |
-      */
-            basePath: '/public',
-        },
-
-        /*
-    |--------------------------------------------------------------------------
-    | S3 Driver
-    |--------------------------------------------------------------------------
-    |
-    | Uses the S3 cloud storage to manage files. Make sure to install the s3
-    | drive separately when using it.
-    |
-    |**************************************************************************
-    | npm i @adonisjs/drive-s3
-    |**************************************************************************
-    |
-    */
-        // s3: {
-        //   driver: 's3',
-        //   visibility: 'public',
-        //   key: Env.get('S3_KEY'),
-        //   secret: Env.get('S3_SECRET'),
-        //   region: Env.get('S3_REGION'),
-        //   bucket: Env.get('S3_BUCKET'),
-        //   endpoint: Env.get('S3_ENDPOINT'),
-        //
-        //  // For minio to work
-        //  // forcePathStyle: true,
-        // },
-
-        /*
-    |--------------------------------------------------------------------------
-    | GCS Driver
-    |--------------------------------------------------------------------------
-    |
-    | Uses the Google cloud storage to manage files. Make sure to install the GCS
-    | drive separately when using it.
-    |
-    |**************************************************************************
-    | npm i @adonisjs/drive-gcs
-    |**************************************************************************
-    |
-    */
-        // gcs: {
-        //   driver: 'gcs',
-        //   visibility: 'public',
-        //   keyFilename: Env.get('GCS_KEY_FILENAME'),
-        //   bucket: Env.get('GCS_BUCKET'),
-
-        /*
-      |--------------------------------------------------------------------------
-      | Uniform ACL - Google cloud storage only
-      |--------------------------------------------------------------------------
-      |
-      | When using the Uniform ACL on the bucket, the "visibility" option is
-      | ignored. Since, the files ACL is managed by the google bucket policies
-      | directly.
-      |
-      |**************************************************************************
-      | Learn more: https://cloud.google.com/storage/docs/uniform-bucket-level-access
-      |**************************************************************************
-      |
-      | The following option just informs drive whether your bucket is using uniform
-      | ACL or not. The actual setting needs to be toggled within the Google cloud
-      | console.
-      |
-      */
-        //   usingUniformAcl: false,
-        // },
-    },
-});

config/inertia.ts

@@ -1,8 +1,7 @@
 import { defineConfig } from '@adonisjs/inertia';
 import type { HttpContext } from '@adonisjs/core/http';
-import type { InferSharedProps } from '@adonisjs/inertia/types'
 
-const inertiaConfig = defineConfig({
+export default defineConfig({
     /**
      * Path to the Edge view that will be used as the root view for Inertia responses
      */
@@ -53,12 +52,6 @@ const inertiaConfig = defineConfig({
     },
 });
 
-export default inertiaConfig
-
-declare module '@adonisjs/inertia/types' {
-    export interface SharedProps extends InferSharedProps<typeof inertiaConfig> {}
-  }
-
 // import { InertiaConfig } from '@ioc:EidelLev/Inertia';
 
 // /*

config/mail.ts

@@ -12,11 +12,11 @@ const mailConfig = defineConfig({
     mailers: {
         
         smtp: transports.smtp({
-            // socketTimeout: 5000,// Overall timeout (5 seconds)
+            socketTimeout: 5000,// Overall timeout (5 seconds)
             host: env.get('SMTP_HOST', ''),
             port: env.get('SMTP_PORT'),
             secure: false,
-            ignoreTLS: true,
+            // ignoreTLS: true,
             requireTLS: false,
 
             /**
@@ -30,10 +30,10 @@ const mailConfig = defineConfig({
       }, */
         }),
 
-        // resend: transports.resend({
+        resend: transports.resend({
-        //     key: env.get('RESEND_API_KEY'),
+            key: env.get('RESEND_API_KEY'),
-        //     baseUrl: 'https://api.resend.com',
+            baseUrl: 'https://api.resend.com',
-        // }),
+        }),
     },
 });
 

config/session.ts

@@ -6,7 +6,7 @@
  */
 
 import env from '#start/env';
-// import app from '@adonisjs/core/services/app';
+import app from '@adonisjs/core/services/app';
 import { defineConfig, stores } from '@adonisjs/session';
 
 const sessionConfig = defineConfig({

config/vite.ts

@@ -1,32 +0,0 @@
-import { defineConfig } from '@adonisjs/vite';
-
-const viteBackendConfig = defineConfig({
-    /**
-     * The output of vite will be written inside this
-     * directory. The path should be relative from
-     * the application root.
-     */
-    buildDirectory: 'public/assets',
-
-    /**
-     * The path to the manifest file generated by the
-     * "vite build" command.
-     */
-    manifestFile: 'public/assets/.vite/manifest.json',
-
-    /**
-     * Feel free to change the value of the "assetsUrl" to
-     * point to a CDN in production.
-     */
-    assetsUrl: '/assets',
-
-     /**
-     * Add defer attribute to scripts for better performance.
-     */
-     scriptAttributes: {
-        defer: true,
-    },
-  
-});
-
-export default viteBackendConfig;

contracts/enums.ts

@@ -21,7 +21,6 @@ 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/acl_4_accounts.ts

@@ -18,7 +18,6 @@ export default class Accounts extends BaseSchema {
             table.text("two_factor_recovery_codes").nullable();
             table.smallint('state').nullable();
             table.bigint('last_counter').nullable();
-            table.string('avatar').nullable();
         });
     }
 
@@ -44,7 +43,6 @@ export default class Accounts extends BaseSchema {
 //     two_factor_recovery_codes text COLLATE pg_catalog."default",
 //     state smallint,
 //     last_counter  bigint,
-//      avatar character varying(255),
 // )
 
 // ALTER TABLE gba.accounts
@@ -87,6 +85,3 @@ export default class Accounts extends BaseSchema {
 // GRANT ALL ON SEQUENCE gba.totp_secrets_id_seq TO tethys_admin;
 
 // ALTER TABLE gba.totp_secrets ALTER COLUMN id SET DEFAULT nextval('gba.totp_secrets_id_seq');
-
-
-// ALTER TABLE "accounts" ADD COLUMN "avatar" VARCHAR(255) NULL

database/migrations/dataset_2_documents.ts

@@ -86,22 +86,3 @@ 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

@@ -32,21 +32,3 @@ 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')
@@ -25,8 +25,6 @@ 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();
         });
     }
 
@@ -56,31 +54,3 @@ export default class Collections extends BaseSchema {
 //         ON UPDATE CASCADE
 //         ON DELETE CASCADE
 // )
-
-
-// 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;

database/migrations/update_1_to_mime_types.ts

@@ -1,18 +0,0 @@
-import { BaseSchema } from "@adonisjs/lucid/schema";
-
-export default class AddAlternateMimetypeToMimeTypes extends BaseSchema {
-  protected tableName = 'mime_types';
-
-  public async up () {
-    this.schema.alterTable(this.tableName, (table) => {
-      table.string('alternate_mimetype').nullable();
-    });
-  }
-
-  public async down () {
-    this.schema.alterTable(this.tableName, (table) => {
-      table.dropColumn('alternate_mimetype');
-    });
-  }
-}
-// ALTER TABLE "mime_types" ADD COLUMN "alternate_mimetype" VARCHAR(255) NULL

docker-entrypoint.sh

@@ -1,74 +1,47 @@
 #!/bin/bash
+
+# # Run freshclam to update virus definitions
+# freshclam
+
+# # Sleep for a few seconds to give ClamAV time to start
+# sleep 5
+
+# # Start the ClamAV daemon
+# /etc/init.d/clamav-daemon start
+
+# bootstrap clam av service and clam av database updater
 set -m
 
-echo "Starting ClamAV services..."
+function process_file() {
+    if [[ ! -z "$1" ]]; then
+        local SETTING_LIST=$(echo "$1" | tr ',' '\n' | grep "^[A-Za-z][A-Za-z]*=.*$")
+        local SETTING
+        
+        for SETTING in ${SETTING_LIST}; do
+            # Remove any existing copies of this setting.  We do this here so that
+            # settings with multiple values (e.g. ExtraDatabase) can still be added
+            # multiple times below
+            local KEY=${SETTING%%=*}
+            sed -i $2 -e "/^${KEY} /d"
+        done
 
+        for SETTING in ${SETTING_LIST}; do
+            # Split on first '='
+            local KEY=${SETTING%%=*}
+            local VALUE=${SETTING#*=}
+            echo "${KEY} ${VALUE}" >> "$2"
+        done
+    fi
+}
 
-# Try to download database if missing
+# process_file "${CLAMD_SETTINGS_CSV}" /etc/clamav/clamd.conf
-# if [ ! "$(ls -A /var/lib/clamav 2>/dev/null)" ]; then
+# process_file "${FRESHCLAM_SETTINGS_CSV}" /etc/clamav/freshclam.conf
-#     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 &
-# Start clamd in background
+clamd
-# Start clamd in foreground (so dumb-init can supervise it)
 # /etc/init.d/clamav-daemon start &
 
-# Give freshclam a moment to start
+# change back to CMD of dockerfile
-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

@@ -1,278 +0,0 @@
-# Dataset Indexing Command
-
-AdonisJS Ace command for indexing and synchronizing published datasets with OpenSearch for search functionality.
-
-## Overview
-
-The `index:datasets` command processes published datasets and creates/updates corresponding search index documents in OpenSearch. It intelligently compares modification timestamps to only re-index datasets when necessary, optimizing performance while maintaining search index accuracy.
-
-## Command Syntax
-
-```bash
-node ace index:datasets [options]
-```
-
-## Options
-
-| Flag | Alias | Description |
-|------|-------|-------------|
-| `--publish_id <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

@@ -1,216 +0,0 @@
-# DataCite Update Command
-
-AdonisJS Ace command for updating DataCite DOI records for published datasets.
-
-## Overview
-
-The `update:datacite` command synchronizes your local dataset metadata with DataCite DOI records. It intelligently compares modification dates to only update records when necessary, reducing unnecessary API calls and maintaining data consistency.
-
-## Command Syntax
-
-```bash
-node ace update:datacite [options]
-```
-
-## Options
-
-| Flag | Alias | Description |
-|------|-------|-------------|
-| `--publish_id <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

@@ -1,47 +1,229 @@
 ##
-## Container-optimized freshclam configuration
+## Example config file for freshclam
+## Please read the freshclam.conf(5) manual before editing this file.
 ##
 
-# Database directory
+
+# Comment or remove the line below.
+
+# Path to the database directory.
+# WARNING: It must match clamd.conf's directive!
+# Default: hardcoded (depends on installation options)
 DatabaseDirectory /var/lib/clamav
 
-# Log to stdout for container logging
+# Path to the log file (make sure it has proper permissions)
+# Default: disabled
 # UpdateLogFile /dev/stdout
 
-# Basic logging settings
+# Maximum size of the log file.
+# Value of 0 disables the limit.
+# You may use 'M' or 'm' for megabytes (1M = 1m = 1048576 bytes)
+# and 'K' or 'k' for kilobytes (1K = 1k = 1024 bytes).
+# in bytes just don't use modifiers. If LogFileMaxSize is enabled,
+# log rotation (the LogRotate option) will always be enabled.
+# Default: 1M
+#LogFileMaxSize 2M
+
+# Log time with each message.
+# Default: no
 LogTime yes
+
+# Enable verbose logging.
+# Default: no
 LogVerbose yes
+
+# Use system logger (can work together with UpdateLogFile).
+# Default: no
 LogSyslog no
 
-# PID file location
+# Specify the type of syslog messages - please refer to 'man syslog'
+# for facility names.
+# Default: LOG_LOCAL6
+#LogFacility LOG_MAIL
+
+# Enable log rotation. Always enabled when LogFileMaxSize is enabled.
+# Default: no
+#LogRotate yes
+
+# This option allows you to save the process identifier of the daemon
+# Default: disabled
+#PidFile /var/run/freshclam.pid
 PidFile /var/run/clamav/freshclam.pid
 
-# Database owner
+# By default when started freshclam drops privileges and switches to the
+# "clamav" user. This directive allows you to change the database owner.
+# Default: clamav (may depend on installation options)
 DatabaseOwner node
 
-# Mirror settings for Austria
+# Use DNS to verify virus database version. Freshclam uses DNS TXT records
+# to verify database and software versions. With this directive you can change
+# the database verification domain.
+# WARNING: Do not touch it unless you're configuring freshclam to use your
+# own database verification domain.
+# Default: current.cvd.clamav.net
+#DNSDatabaseInfo current.cvd.clamav.net
+
+# Uncomment the following line and replace XY with your country
+# code. See http://www.iana.org/cctld/cctld-whois.htm for the full list.
+# You can use db.XY.ipv6.clamav.net for IPv6 connections.
 DatabaseMirror db.at.clamav.net
+
+# database.clamav.net is a round-robin record which points to our most
+# reliable mirrors. It's used as a fall back in case db.XY.clamav.net is
+# not working. DO NOT TOUCH the following line unless you know what you
+# are doing.
 DatabaseMirror database.clamav.net
 
+# How many attempts to make before giving up.
+# Default: 3 (per mirror)
+#MaxAttempts 5
+
 # With this option you can control scripted updates. It's highly recommended
 # to keep it enabled.
 # Default: yes
-# Update settings
+#ScriptedUpdates yes
-ScriptedUpdates yes
+
+# By default freshclam will keep the local databases (.cld) uncompressed to
+# make their handling faster. With this option you can enable the compression;
+# the change will take effect with the next database update.
+# Default: no
+#CompressLocalDatabase no
+
+# With this option you can provide custom sources (http:// or file://) for
+# database files. This option can be used multiple times.
+# Default: no custom URLs
+#DatabaseCustomURL http://myserver.com/mysigs.ndb
+#DatabaseCustomURL file:///mnt/nfs/local.hdb
+
+# This option allows you to easily point freshclam to private mirrors.
+# If PrivateMirror is set, freshclam does not attempt to use DNS
+# to determine whether its databases are out-of-date, instead it will
+# use the If-Modified-Since request or directly check the headers of the
+# remote database files. For each database, freshclam first attempts
+# to download the CLD file. If that fails, it tries to download the
+# CVD file. This option overrides DatabaseMirror, DNSDatabaseInfo
+# and ScriptedUpdates. It can be used multiple times to provide
+# fall-back mirrors.
+# Default: disabled
+#PrivateMirror mirror1.mynetwork.com
+#PrivateMirror mirror2.mynetwork.com
 
 # Number of database checks per day.
 # Default: 12 (every two hours)
-Checks 12
+#Checks 24
 
-# Don't fork (good for containers)
+# Proxy settings
+# Default: disabled
+#HTTPProxyServer myproxy.com
+#HTTPProxyPort 1234
+#HTTPProxyUsername myusername
+#HTTPProxyPassword mypass
+
+# If your servers are behind a firewall/proxy which applies User-Agent
+# filtering you can use this option to force the use of a different
+# User-Agent header.
+# Default: clamav/version_number
+#HTTPUserAgent SomeUserAgentIdString
+
+# Use aaa.bbb.ccc.ddd as client address for downloading databases. Useful for
+# multi-homed systems.
+# Default: Use OS'es default outgoing IP address.
+#LocalIPAddress aaa.bbb.ccc.ddd
+
+# Send the RELOAD command to clamd.
+# Default: no
+#NotifyClamd /path/to/clamd.conf
+
+# Run command after successful database update.
+# Default: disabled
+#OnUpdateExecute command
+
+# Run command when database update process fails.
+# Default: disabled
+#OnErrorExecute command
+
+# Run command when freshclam reports outdated version.
+# In the command string %v will be replaced by the new version number.
+# Default: disabled
+#OnOutdatedExecute command
+
+# Don't fork into background.
+# Default: no
 Foreground no
 
-# Connection timeouts
+# Enable debug messages in libclamav.
-ConnectTimeout 60
+# Default: no
-ReceiveTimeout 60
+#Debug yes
 
-# Test databases before using them
+# Timeout in seconds when connecting to database server.
-TestDatabases yes
+# Default: 30
+#ConnectTimeout 60
 
-# Enable bytecode signatures
+# Timeout in seconds when reading from database server.
-Bytecode yes
+# 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

index.d.ts

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

package.json

@@ -4,8 +4,7 @@
   "private": true,
   "scripts": {
     "type-check": "tsc --noEmit",
-    "dev": "node ace serve",
+    "dev": "node ace serve --watch",
-    "devInspect": "node ace serve --watch --node-args='--inspect'",
     "compress:xslt": "./node_modules/xslt3/xslt3.js -xsl:public/assets2/datasetxml2oai-pmh.xslt -export:public/assets2/datasetxml2oai.sef.json -t -nogo '-ns:##html5'",
     "compress:solr": "./node_modules/xslt3/xslt3.js -xsl:public/assets2/solr.xslt -export:public/assets2/solr.sef.json -t -nogo '-ns:##html5'",
     "compress:doi": "./node_modules/xslt3/xslt3.js -xsl:public/assets2/doi_datacite.xslt -export:public/assets2/doi_datacite.sef.json -t -nogo '-ns:##html5'",
@@ -16,58 +15,59 @@
     "format-check": "prettier --check ./**/*.{ts,js}",
     "test": "node ace test"
   },
-  "eslintConfig": {
+  "eslintIgnore": [
-    "ignorePatterns": [
+    "build"
-      "build"
+  ],
-    ]
-  },
   "alias": {
     "vue": "./node_modules/vue/dist/vue.esm-bundler.js"
   },
   "devDependencies": {
     "@adonisjs/assembler": "^7.1.1",
-    "@adonisjs/tsconfig": "^1.4.0",
+    "@adonisjs/tsconfig": "^1.2.1",
-    "@headlessui/vue": "^1.7.23",
+    "@babel/core": "^7.20.12",
-    "@japa/assert": "^4.0.1",
+    "@babel/plugin-proposal-class-properties": "^7.18.6",
-    "@japa/plugin-adonisjs": "^4.0.0",
+    "@babel/plugin-proposal-decorators": "^7.20.13",
-    "@japa/runner": "^4.2.0",
+    "@babel/plugin-transform-runtime": "^7.19.6",
+    "@babel/preset-env": "^7.20.2",
+    "@babel/preset-typescript": "^7.18.6",
+    "@japa/api-client": "^2.0.3",
+    "@japa/assert": "^3.0.0",
+    "@japa/plugin-adonisjs": "^3.0.0",
+    "@japa/runner": "^3.1.1",
     "@mdi/js": "^7.1.96",
     "@poppinss/utils": "^6.7.2",
-    "@swc/wasm": "^1.10.14",
+    "@swc/core": "^1.4.2",
+    "@symfony/webpack-encore": "^5.0.1",
     "@tailwindcss/forms": "^0.5.2",
     "@types/bcryptjs": "^2.4.6",
     "@types/clamscan": "^2.0.4",
     "@types/escape-html": "^1.0.4",
-    "@types/fs-extra": "^11.0.4",
+    "@types/leaflet": "^1.9.3",
-    "@types/leaflet": "^1.9.16",
     "@types/luxon": "^3.4.2",
-    "@types/node": "^22.10.2",
+    "@types/node": "^22.5.5",
     "@types/proxy-addr": "^2.0.0",
     "@types/qrcode": "^1.5.5",
     "@types/source-map-support": "^0.5.6",
     "@types/sprintf-js": "^1.1.4",
     "@types/supertest": "^6.0.2",
-    "@vitejs/plugin-vue": "^5.2.1",
     "autoprefixer": "^10.4.13",
     "babel-preset-typescript-vue3": "^2.0.17",
     "chart.js": "^4.2.0",
     "dotenv-webpack": "^8.0.1",
     "eslint": "^8.57.1",
-    "eslint-config-prettier": "^10.0.1",
+    "eslint-config-prettier": "^9.0.0",
     "eslint-plugin-adonis": "^2.1.1",
     "eslint-plugin-prettier": "^5.0.0-alpha.2",
-    "hot-hook": "^0.4.0",
     "numeral": "^2.0.6",
-    "pinia": "^3.0.2",
+    "pinia": "^2.0.30",
-    "pino-pretty": "^13.0.0",
+    "pino-pretty": "^11.2.2",
     "postcss-loader": "^8.1.1",
-    "prettier": "^3.4.2",
+    "prettier": "^3.0.0",
     "supertest": "^6.3.3",
-    "tailwindcss": "^3.4.17",
+    "tailwindcss": "^3.2.4",
     "ts-loader": "^9.4.2",
-    "ts-node-maintained": "^10.9.5",
+    "ts-node": "^10.9.2",
-    "typescript": "~5.7",
+    "typescript": "^5.1.3",
-    "vite": "^6.0.11",
     "vue": "^3.4.26",
     "vue-facing-decorator": "^3.0.0",
     "vue-loader": "^17.0.1",
@@ -75,32 +75,30 @@
     "xslt3": "^2.5.0"
   },
   "dependencies": {
-    "@adonisjs/auth": "^9.2.4",
+    "@adonisjs/auth": "^9.1.1",
-    "@adonisjs/bodyparser": "^10.0.1",
+    "@adonisjs/core": "^6.3.1",
-    "@adonisjs/core": "6.17.2",
     "@adonisjs/cors": "^2.2.1",
-    "@adonisjs/drive": "^3.2.0",
+    "@adonisjs/drive": "^2.3.0",
-    "@adonisjs/inertia": "^2.1.3",
+    "@adonisjs/encore": "^1.0.0",
-    "@adonisjs/lucid": "^21.5.1",
+    "@adonisjs/inertia": "^1.0.0-7",
+    "@adonisjs/lucid": "^21.1.0",
     "@adonisjs/mail": "^9.2.2",
     "@adonisjs/redis": "^9.1.0",
-    "@adonisjs/session": "^7.5.0",
+    "@adonisjs/session": "^7.1.1",
     "@adonisjs/shield": "^8.1.1",
     "@adonisjs/static": "^1.1.1",
-    "@adonisjs/vite": "^4.0.0",
     "@eidellev/adonis-stardust": "^3.0.0",
     "@fontsource/archivo-black": "^5.0.1",
     "@fontsource/inter": "^5.0.1",
     "@inertiajs/inertia": "^0.11.1",
-    "@inertiajs/vue3": "^2.0.3",
+    "@inertiajs/vue3": "^1.0.0",
-    "@opensearch-project/opensearch": "^3.2.0",
+    "@opensearch-project/opensearch": "^2.4.0",
     "@phc/format": "^1.0.0",
-    "@poppinss/manager": "^5.0.2",
+    "@vinejs/vine": "^2.0.0",
-    "@vinejs/vine": "^3.0.0",
-    "axios": "^1.7.9",
     "bcrypt": "^5.1.1",
     "bcryptjs": "^2.4.3",
     "clamscan": "^2.1.2",
+    "crypto": "^1.0.1",
     "dayjs": "^1.11.7",
     "deep-email-validator": "^0.1.21",
     "edge.js": "^6.0.1",
@@ -116,19 +114,13 @@
     "notiwind": "^2.0.0",
     "pg": "^8.9.0",
     "qrcode": "^1.5.3",
-    "redis": "^5.0.0",
+    "redis": "^4.6.10",
     "reflect-metadata": "^0.2.1",
     "saxon-js": "^2.5.0",
     "toastify-js": "^1.12.0",
     "vuedraggable": "^4.1.0",
     "xmlbuilder2": "^3.1.1"
   },
-  "hotHook": {
-    "boundaries": [
-      "./app/Controllers/**/*.ts",
-      "./app/middleware/*.ts"
-    ]
-  },
   "type": "module",
   "imports": {
     "#controllers/*": "./app/Controllers/*.js",

postcss.config.cjs

@@ -1,10 +1,7 @@
 module.exports = {
     plugins: {
         // 'postcss-import': {},
-        // 'postcss-nesting': {},
+        'tailwindcss/nesting': {},
-         'tailwindcss/nesting': {},
-        // "@tailwindcss/postcss": {},
-        // tailwindcss: {},
         tailwindcss: {},
         autoprefixer: {},
     },

providers/drive/drivers/local.ts

@@ -74,8 +74,7 @@ export class LocalDriver implements LocalDriverContract {
      */
     public async exists(location: string): Promise<boolean> {
         try {
-            let path_temp = this.makePath(location); //'/storage/app/files/421'
+            return await this.adapter.pathExists(this.makePath(location));
-            return await this.adapter.pathExists(path_temp);
         } catch (error) {
             throw CannotGetMetaDataException.invoke(location, 'exists', error);
         }

providers/mail_provider.ts

@@ -69,7 +69,7 @@ export default class MailProvider {
             const mailConfigProvider = this.app.config.get('mail');
             const config = await configProvider.resolve<any>(this.app, mailConfigProvider);
 
-            await config.mailers.smtp();
+            const iwas = await config.mailers.smtp();
             // iwas.config.host = 'hhhost';
             // this.app.config.set('mail.mailers.smtp.host', 'xhost');
             // const iwas = await config.mailers.smtp();

providers/query_builder_provider.ts

@@ -63,15 +63,6 @@ export default class QueryBuilderProvider {
 
     public register() {
         // Register your own bindings
-        // const ModelQueryBuilder = this.app.container.bind('@adonisjs/lucid/orm/ModelQueryBuilder');
-    
-        // ModelQueryBuilder.macro('whereTrue', function (columnName: string) {
-        //     return this.where(columnName, true);
-        // });
-
-        // ModelQueryBuilder.macro('whereFalse', function (columnName: string) {
-        //     return this.where(columnName, false);
-        // });
     }
 
     public async boot() {
@@ -82,14 +73,15 @@ export default class QueryBuilderProvider {
             // let rolesPluck = {};
             let rolesPluck: { [key: number]: any } = {};
             const result = await this.exec();
-            result.forEach((user: { [key: string]: any }, index: number) => {
+            result.forEach((user, index) => {
-                let idc: number;
+                let idc;
                 if (!id) {
                     idc = index;
                 } else {
                     idc = user[id];
                 }
-                const value: any = user[valueColumn];
+                const value = user[valueColumn];
+                // rolesPluck[idc] = user.name;
                 rolesPluck[idc] = value;
             });
             return rolesPluck;

providers/rule_provider.ts

@@ -1,34 +0,0 @@
-import { ApplicationService } from '@adonisjs/core/types';
-
-export default class RuleProvider {
-    constructor(protected app: ApplicationService) {}
-
-    public register() {
-        // Register your own bindings
-    }
-
-    public async boot() {
-        // IoC container is ready
-        // await import("../src/rules/index.js");
-
-        await import('#start/rules/unique');
-        await import('#start/rules/translated_language');
-        await import('#start/rules/unique_person');
-        // () => import('#start/rules/file_length'),
-        // () => import('#start/rules/file_scan'),
-        // () => import('#start/rules/allowed_extensions_mimetypes'),
-        await import('#start/rules/dependent_array_min_length');
-        await import('#start/rules/referenceValidation');
-        await import('#start/rules/valid_mimetype');
-        await import('#start/rules/array_contains_types');
-        await import('#start/rules/orcid');
-    }
-
-    public async ready() {
-        // App is ready
-    }
-
-    public async shutdown() {
-        // Cleanup, since app is going down
-    }
-}

providers/vinejs_provider.ts

@@ -4,8 +4,9 @@
 |--------------------------------------------------------------------------
 |*/
 import type { ApplicationService } from '@adonisjs/core/types';
-import vine, { symbols, BaseLiteralType, Vine } from '@vinejs/vine';
+import vine, { BaseLiteralType, Vine } from '@vinejs/vine';
-import type { FieldContext, FieldOptions } from '@vinejs/vine/types';
+import type { Validation, 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';
@@ -15,7 +16,6 @@ import MimeType from '#models/mime_type';
  * Validation options accepted by the "file" rule
  */
 export type FileRuleValidationOptions = Partial<FileValidationOptions> | ((field: FieldContext) => Partial<FileValidationOptions>);
-
 /**
  * Extend VineJS
  */
@@ -24,66 +24,31 @@ declare module '@vinejs/vine' {
         myfile(options?: FileRuleValidationOptions): VineMultipartFile;
     }
 }
-
 /**
  * Extend HTTP request class
  */
 declare module '@adonisjs/core/http' {
-    interface Request extends RequestValidator {}
+  interface Request extends RequestValidator {
+  }
 }
 
 /**
  * Checks if the value is an instance of multipart file
  * from bodyparser.
  */
-export function isBodyParserFile(file: MultipartFile | unknown): file is MultipartFile {
+export function isBodyParserFile(file: MultipartFile | unknown): boolean {
     return !!(file && typeof file === 'object' && 'isMultipartFile' in file);
 }
+export async function getEnabledExtensions() {
+    const enabledExtensions = await MimeType.query().select('file_extension').where('enabled', true).exec();
+    const extensions = enabledExtensions
+        .map((extension) => {
+            return extension.file_extension.split('|');
+        })
+        .flat();
 
-/**
+    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.
@@ -100,7 +65,6 @@ const isMultipartFile = vine.createRule(async (file: MultipartFile | unknown, op
     // At this point, you can use type assertion to explicitly tell TypeScript that file is of type MultipartFile
     const validatedFile = file as MultipartFile;
     const validationOptions = typeof options === 'function' ? options(field) : options;
-    
     /**
      * Set size when it's defined in the options and missing
      * on the file instance
@@ -108,29 +72,28 @@ const isMultipartFile = vine.createRule(async (file: MultipartFile | unknown, op
     if (validatedFile.sizeLimit === undefined && validationOptions.size) {
         validatedFile.sizeLimit = validationOptions.size;
     }
-
     /**
      * Set extensions when it's defined in the options and missing
      * on the file instance
      */
-    if (validatedFile.allowedExtensions === undefined) {
+    // if (validatedFile.allowedExtensions === undefined && validationOptions.extnames) {
-        if (validationOptions.extnames !== undefined) {
+    //     validatedFile.allowedExtensions = validationOptions.extnames;
-            validatedFile.allowedExtensions = validationOptions.extnames;
+    // }
-        } else {
+    if (validatedFile.allowedExtensions === undefined && validationOptions.extnames) {
-            validatedFile.allowedExtensions = await getEnabledExtensions();
+        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
      */
-    try {
+    validatedFile.validate();
-        validatedFile.validate();
-    } catch (error) {
-        field.report(`File validation failed: ${error.message}`, 'file.validation_error', field, validationOptions);
-        return;
-    }
-
     /**
      * Report errors
      */
@@ -139,40 +102,24 @@ 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;
+    // #private;
-    public validationOptions?: FileRuleValidationOptions;
+    // constructor(validationOptions?: FileRuleValidationOptions, options?: FieldOptions, validations?: Validation<any>[]);
+    // clone(): this;
+
+    public validationOptions;
     // extnames: (18) ['gpkg', 'htm', 'html', 'csv', 'txt', 'asc', 'c', 'cc', 'h', 'srt', 'tiff', 'pdf', 'png', 'zip', 'jpg', 'jpeg', 'jpe', 'xlsx']
     // size: '512mb'
 
-    public constructor(validationOptions?: FileRuleValidationOptions, options?: FieldOptions) {
+    public constructor(validationOptions?: FileRuleValidationOptions, options?: FieldOptions, validations?: Validation<any>[]) {
+        // super(options, validations);
         super(options, [isMultipartFile(validationOptions || {})]);
         this.validationOptions = validationOptions;
     }
 
     public clone(): any {
-        return new VineMultipartFile(this.validationOptions, this.cloneOptions());
+        return new VineMultipartFile(this.validationOptions, this.cloneOptions(), this.cloneValidations());
     }
-
-    /**
-     * Set maximum file size
-     */
-    public maxSize(size: string | number): this {
-        const newOptions = { ...this.validationOptions, size };
-        return new VineMultipartFile(newOptions, this.cloneOptions()) as this;
-    }
-
-    /**
-     * Set allowed extensions
-     */
-    public extensions(extnames: string[]): this {
-        const newOptions = { ...this.validationOptions, extnames };
-        return new VineMultipartFile(newOptions, this.cloneOptions()) as this;
-    }
-
-  
 }
 
 export default class VinejsProvider {
@@ -191,8 +138,13 @@ export default class VinejsProvider {
     /**
      * The container bindings have booted
      */
+
     boot(): void {
-        Vine.macro('myfile', function (this: Vine, options?: FileRuleValidationOptions) {
+        //   VineString.macro('translatedLanguage', function (this: VineString, options: Options) {
+        //     return this.use(translatedLanguageRule(options));
+        // });
+
+        Vine.macro('myfile', function (this: Vine, options) {
             return new VineMultipartFile(options);
         });
 
@@ -200,47 +152,10 @@ export default class VinejsProvider {
          * The validate method can be used to validate the request
          * data for the current request using VineJS validators
          */
-        Request.macro('validateUsing', function (this: Request, ...args) {
+        Request.macro('validateUsing', function (...args) {
-            if (!this.ctx) {
+          return new RequestValidator(this.ctx).validateUsing(...args);
-                throw new Error('HttpContext is not available');
+      });
-            }
-            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);
-        }
     }
 
     /**
@@ -256,7 +171,5 @@ export default class VinejsProvider {
     /**
      * Preparing to shutdown the app
      */
-    async shutdown() {
+    async shutdown() {}
-        clearExtensionsCache();
-    }
 }

public/assets/entrypoints.json

@@ -0,0 +1,12 @@
+{
+  "entrypoints": {
+    "app": {
+      "css": [
+        "http://localhost:8080/assets/app.css"
+      ],
+      "js": [
+        "http://localhost:8080/assets/app.js"
+      ]
+    }
+  }
+}

public/assets/manifest.json

@@ -0,0 +1,103 @@
+{
+  "assets/app.css": "http://localhost:8080/assets/app.css",
+  "assets/app.js": "http://localhost:8080/assets/app.js",
+  "assets/resources_js_apps_settings_l18n_de_js.js": "http://localhost:8080/assets/resources_js_apps_settings_l18n_de_js.js",
+  "assets/resources_js_apps_settings_l18n_en_js.js": "http://localhost:8080/assets/resources_js_apps_settings_l18n_en_js.js",
+  "assets/resources_js_Pages_Admin_License_Index_vue.js": "http://localhost:8080/assets/resources_js_Pages_Admin_License_Index_vue.js",
+  "assets/resources_js_Pages_Admin_Mimetype_Create_vue.js": "http://localhost:8080/assets/resources_js_Pages_Admin_Mimetype_Create_vue.js",
+  "assets/resources_js_Pages_Admin_Mimetype_Delete_vue.js": "http://localhost:8080/assets/resources_js_Pages_Admin_Mimetype_Delete_vue.js",
+  "assets/resources_js_Pages_Admin_Mimetype_Index_vue.js": "http://localhost:8080/assets/resources_js_Pages_Admin_Mimetype_Index_vue.js",
+  "assets/resources_js_Pages_Admin_Permission_Create_vue.js": "http://localhost:8080/assets/resources_js_Pages_Admin_Permission_Create_vue.js",
+  "assets/resources_js_Pages_Admin_Permission_Edit_vue.js": "http://localhost:8080/assets/resources_js_Pages_Admin_Permission_Edit_vue.js",
+  "assets/resources_js_Pages_Admin_Permission_Index_vue.js": "http://localhost:8080/assets/resources_js_Pages_Admin_Permission_Index_vue.js",
+  "assets/resources_js_Pages_Admin_Permission_Show_vue.js": "http://localhost:8080/assets/resources_js_Pages_Admin_Permission_Show_vue.js",
+  "assets/resources_js_Pages_Admin_Role_Create_vue.js": "http://localhost:8080/assets/resources_js_Pages_Admin_Role_Create_vue.js",
+  "assets/resources_js_Pages_Admin_Role_Edit_vue.js": "http://localhost:8080/assets/resources_js_Pages_Admin_Role_Edit_vue.js",
+  "assets/resources_js_Pages_Admin_Role_Index_vue.js": "http://localhost:8080/assets/resources_js_Pages_Admin_Role_Index_vue.js",
+  "assets/resources_js_Pages_Admin_Role_Show_vue.js": "http://localhost:8080/assets/resources_js_Pages_Admin_Role_Show_vue.js",
+  "assets/resources_js_Pages_Admin_Settings_vue-resources_js_utils_toast_css.css": "http://localhost:8080/assets/resources_js_Pages_Admin_Settings_vue-resources_js_utils_toast_css.css",
+  "assets/resources_js_Pages_Admin_Settings_vue-resources_js_utils_toast_css.js": "http://localhost:8080/assets/resources_js_Pages_Admin_Settings_vue-resources_js_utils_toast_css.js",
+  "assets/resources_js_Pages_Admin_User_Create_vue-resources_js_Components_SimplePasswordMeter_password-f3312a.css": "http://localhost:8080/assets/resources_js_Pages_Admin_User_Create_vue-resources_js_Components_SimplePasswordMeter_password-f3312a.css",
+  "assets/resources_js_Pages_Admin_User_Create_vue-resources_js_Components_SimplePasswordMeter_password-f3312a.js": "http://localhost:8080/assets/resources_js_Pages_Admin_User_Create_vue-resources_js_Components_SimplePasswordMeter_password-f3312a.js",
+  "assets/resources_js_Pages_Admin_User_Edit_vue-resources_js_Components_SimplePasswordMeter_password-m-6dc207.css": "http://localhost:8080/assets/resources_js_Pages_Admin_User_Edit_vue-resources_js_Components_SimplePasswordMeter_password-m-6dc207.css",
+  "assets/resources_js_Pages_Admin_User_Edit_vue-resources_js_Components_SimplePasswordMeter_password-m-6dc207.js": "http://localhost:8080/assets/resources_js_Pages_Admin_User_Edit_vue-resources_js_Components_SimplePasswordMeter_password-m-6dc207.js",
+  "assets/resources_js_Pages_Admin_User_Index_vue.js": "http://localhost:8080/assets/resources_js_Pages_Admin_User_Index_vue.js",
+  "assets/resources_js_Pages_Admin_User_Show_vue.js": "http://localhost:8080/assets/resources_js_Pages_Admin_User_Show_vue.js",
+  "assets/resources_js_Pages_App_vue.js": "http://localhost:8080/assets/resources_js_Pages_App_vue.js",
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+  "assets/images/Close.svg": "http://localhost:8080/assets/images/Close.e4887675.svg",
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+}

public/assets2/solr.xslt

@@ -111,14 +111,7 @@
         <!--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>
         
@@ -207,8 +200,7 @@
         
         <!--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

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