feat: Enhance dataset management and improve frontend components

- Added preloads 'allowed_extensions_mimetypes' and 'dependent_array_min_length' in adonisrc.ts
- Updated @symfony/webpack-encore from ^4.6.1 to ^5.0.1
- AdminuserController: Implemented pagination for 10 records in index method
- Enabled reviewers to reject datasets to editors with email notifications (DatasetController.ts)
- Submitter DatasetController: Files now loaded in ascending order (sort_order) in edit mode
- file.ts: Removed serialization of fileData due to browser issues
- Modified FileUpload.vue to mark already uploaded files as deleted
- Improved keyword search in SearchCategoryAutocomplete.vue
- Started development on Category.vue for submitters to categorize DDC
- Added new route /dataset/categorize in routes.ts
- Introduced 2 new rules in start/rules: allowed_extensions_mimetypes.ts and dependent_array_min_length.ts
- Performed npm updates

.adonisrc.json

@@ -1,72 +0,0 @@
-{
-	"typescript": true,
-	"commands": [
-		"./commands",
-		"@adonisjs/core/build/commands/index.js",
-		"@adonisjs/repl/build/commands",
-		"@eidellev/inertia-adonisjs/build/commands",
-		"@adonisjs/lucid/build/commands"
-	],
-	"exceptionHandlerNamespace": "App/Exceptions/Handler",
-	"aliases": {
-		"App": "app",
-		"Config": "config",
-		"Database": "database",
-		"Contracts": "contracts"
-	},
-	"preloads": [
-		"./start/routes",
-		"./start/kernel",
-		{
-			"file": "./start/inertia",
-			"environment": [
-				"web"
-			]
-		},
-		{
-			"file": "./start/validator",
-			"environment": [
-				"web"
-			]
-		}
-	],
-	"providers": [
-		"./providers/AppProvider",
-		"@adonisjs/core",
-		"@adonisjs/session",
-		"@adonisjs/view",
-		"@adonisjs/shield",
-		"@eidellev/inertia-adonisjs",
-		"@adonisjs/lucid",
-		"@adonisjs/auth",
-		"@eidellev/adonis-stardust",
-		"./providers/QueryBuilderProvider"
-	],
-	"metaFiles": [
-		{
-			"pattern": "public/**",
-			"reloadServer": false
-		},
-		{
-			"pattern": "resources/views/**/*.edge",
-			"reloadServer": false
-		}
-	],
-	"aceProviders": [
-		"@adonisjs/repl"
-	],
-	"tests": {
-		"suites": [
-			{
-				"name": "functional",
-				"files": [
-					"tests/functional/**/*.spec(.ts|.js)"
-				],
-				"timeout": 60000
-			}
-		]
-	},
-	"testProviders": [
-		"@japa/preset-adonis/TestsProvider"
-	]
-}

.editorconfig

@@ -2,7 +2,7 @@ root = true
 
 [*]
 indent_style = space
-indent_size = 2
+indent_size = 4
 end_of_line = lf
 charset = utf-8
 trim_trailing_whitespace = true

.env.example

@@ -11,3 +11,10 @@ PG_PORT=5432
 PG_USER=lucid
 PG_PASSWORD=
 PG_DB_NAME=lucid
+REDIS_CONNECTION=local
+REDIS_HOST=127.0.0.1
+REDIS_PORT=6379
+REDIS_PASSWORD=
+SMTP_HOST=
+SMTP_PORT=
+RESEND_API_KEY=

.eslintrc.json

@@ -1,24 +1,14 @@
 {
-    "extends": [
+    "extends": ["plugin:adonis/typescriptApp", "prettier"],
-        "plugin:adonis/typescriptApp",
+    "plugins": ["prettier"],
-        "prettier"
-    ],
-    "plugins": [
-        "prettier"
-    ],
     "rules": {
-        "prettier/prettier": [
+        "prettier/prettier": ["error", { "singleQuote": true }],
-            "error",
-            { "singleQuote": true }
-        ],
         "@typescript-eslint/indent": ["error", 4, { "ignoredNodes": ["PropertyDefinition", "TSUnionType"] }],
         "@typescript-eslint/naming-convention": [
             "warn",
             {
                 "selector": "interface",
-                "format": [
+                "format": ["PascalCase"],
-                    "PascalCase"
-                ],
                 "custom": {
                     "regex": "^I[A-Z]",
                     "match": false

.gitea/workflows/ci.yaml

@@ -12,12 +12,12 @@ jobs:
         # run build on latest ubuntu
         runs-on: ubuntu-latest
 
-        container: node:16-bullseye
+        container: node:18-bullseye
 
         services:
             mydb:
                 image: postgres:latest
-                container_name: mydb
+                # container_name: mydb               
                 env:
                     POSTGRES_USER: alice
                     POSTGRES_PASSWORD: iEx4Vj7zBb6
@@ -28,7 +28,6 @@ jobs:
                 # Set health checks to wait until postgres has started
                 options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
 
-            
         steps:
             # this will check out the current branch (https://github.com/actions/checkout#Push-a-commit-using-the-built-in-token)
             - name: 1 Check out repository code
@@ -66,7 +65,7 @@ jobs:
                   && echo "HASH_DRIVER=bcrypt" >> .env.test
                   && echo "HOST=127.0.0.1" >> .env.test
                   && echo "PORT=3333" >> .env.test
-                  && echo "APP_NAME=AdonisJs" >> .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

Dockerfile

@@ -1,7 +1,7 @@
 ################## First Stage - Creating base #########################
 
 # Created a variable to hold our node base image
-ARG NODE_IMAGE=node:18-bookworm-slim
+ARG NODE_IMAGE=node:20-bookworm-slim
 
 FROM $NODE_IMAGE AS base
 # Install dumb-init and ClamAV, and perform ClamAV database update
@@ -44,7 +44,7 @@ USER node
 # initial update of av databases
 RUN freshclam
 
-VOLUME /var/lib/clamav
+# 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"
@@ -66,8 +66,11 @@ COPY --chown=node:node . .
 ################## Third Stage - Building Stage #####################
 # In this stage, we will start building dependencies
 FROM dependencies AS build
+ENV NODE_ENV=production
 # We run "node ace build" to build the app (dist folder) for production
-RUN node ace build --production
+RUN node ace build --ignore-ts-errors
+# RUN node ace build --production
+# RUN node ace build --ignore-ts-errors
 
 
 ################## Final Stage - Production #########################
@@ -85,7 +88,7 @@ RUN npm ci --omit=dev
 # Copy files to the working directory from the build folder the user
 COPY --chown=node:node --from=build /home/node/app/build .
 # Expose port
-EXPOSE $PORT
+EXPOSE 3333
 ENTRYPOINT ["/home/node/app/docker-entrypoint.sh"]
 # Run the command to start the server using "dumb-init"
-CMD [ "dumb-init", "node", "server.js" ]
+CMD [ "dumb-init", "node", "bin/server.js" ]

ace

@@ -1,16 +0,0 @@
-/*
-|--------------------------------------------------------------------------
-| Ace Commands
-|--------------------------------------------------------------------------
-|
-| This file is the entry point for running ace commands.
-|
-*/
-
-require('reflect-metadata')
-require('source-map-support').install({ handleUncaughtExceptions: false })
-
-const { Ignitor } = require('@adonisjs/core/build/standalone')
-new Ignitor(__dirname)
-  .ace()
-  .handle(process.argv.slice(2))

ace-manifest.json

@@ -1,609 +0,0 @@
-{
-  "commands": {
-    "validate:checksum": {
-      "settings": {
-        "loadApp": true,
-        "stayAlive": false
-      },
-      "commandPath": "./commands/ValidateChecksum",
-      "commandName": "validate:checksum",
-      "description": "",
-      "args": [],
-      "aliases": [],
-      "flags": []
-    },
-    "dump:rcfile": {
-      "settings": {},
-      "commandPath": "@adonisjs/core/build/commands/DumpRc",
-      "commandName": "dump:rcfile",
-      "description": "Dump contents of .adonisrc.json file along with defaults",
-      "args": [],
-      "aliases": [],
-      "flags": []
-    },
-    "list:routes": {
-      "settings": {
-        "loadApp": true,
-        "stayAlive": true
-      },
-      "commandPath": "@adonisjs/core/build/commands/ListRoutes/index",
-      "commandName": "list:routes",
-      "description": "List application routes",
-      "args": [],
-      "aliases": [],
-      "flags": [
-        {
-          "name": "verbose",
-          "propertyName": "verbose",
-          "type": "boolean",
-          "description": "Display more information"
-        },
-        {
-          "name": "reverse",
-          "propertyName": "reverse",
-          "type": "boolean",
-          "alias": "r",
-          "description": "Reverse routes display"
-        },
-        {
-          "name": "methods",
-          "propertyName": "methodsFilter",
-          "type": "array",
-          "alias": "m",
-          "description": "Filter routes by method"
-        },
-        {
-          "name": "patterns",
-          "propertyName": "patternsFilter",
-          "type": "array",
-          "alias": "p",
-          "description": "Filter routes by the route pattern"
-        },
-        {
-          "name": "names",
-          "propertyName": "namesFilter",
-          "type": "array",
-          "alias": "n",
-          "description": "Filter routes by route name"
-        },
-        {
-          "name": "json",
-          "propertyName": "json",
-          "type": "boolean",
-          "description": "Output as JSON"
-        },
-        {
-          "name": "table",
-          "propertyName": "table",
-          "type": "boolean",
-          "description": "Output as Table"
-        },
-        {
-          "name": "max-width",
-          "propertyName": "maxWidth",
-          "type": "number",
-          "description": "Specify maximum rendering width. Ignored for JSON Output"
-        }
-      ]
-    },
-    "generate:key": {
-      "settings": {},
-      "commandPath": "@adonisjs/core/build/commands/GenerateKey",
-      "commandName": "generate:key",
-      "description": "Generate a new APP_KEY secret",
-      "args": [],
-      "aliases": [],
-      "flags": []
-    },
-    "repl": {
-      "settings": {
-        "loadApp": true,
-        "environment": "repl",
-        "stayAlive": true
-      },
-      "commandPath": "@adonisjs/repl/build/commands/AdonisRepl",
-      "commandName": "repl",
-      "description": "Start a new REPL session",
-      "args": [],
-      "aliases": [],
-      "flags": []
-    },
-    "ssr:build": {
-      "settings": {
-        "stayAlive": true
-      },
-      "commandPath": "@eidellev/inertia-adonisjs/build/commands/Build",
-      "commandName": "ssr:build",
-      "description": "Build and watch files for changes",
-      "args": [],
-      "aliases": [],
-      "flags": []
-    },
-    "ssr:watch": {
-      "settings": {
-        "stayAlive": true
-      },
-      "commandPath": "@eidellev/inertia-adonisjs/build/commands/Watch",
-      "commandName": "ssr:watch",
-      "description": "Build and watch files for changes",
-      "args": [],
-      "aliases": [],
-      "flags": []
-    },
-    "db:seed": {
-      "settings": {
-        "loadApp": true
-      },
-      "commandPath": "@adonisjs/lucid/build/commands/DbSeed",
-      "commandName": "db:seed",
-      "description": "Execute database seeders",
-      "args": [],
-      "aliases": [],
-      "flags": [
-        {
-          "name": "connection",
-          "propertyName": "connection",
-          "type": "string",
-          "description": "Define a custom database connection for the seeders",
-          "alias": "c"
-        },
-        {
-          "name": "interactive",
-          "propertyName": "interactive",
-          "type": "boolean",
-          "description": "Run seeders in interactive mode",
-          "alias": "i"
-        },
-        {
-          "name": "files",
-          "propertyName": "files",
-          "type": "array",
-          "description": "Define a custom set of seeders files names to run",
-          "alias": "f"
-        },
-        {
-          "name": "compact-output",
-          "propertyName": "compactOutput",
-          "type": "boolean",
-          "description": "A compact single-line output"
-        }
-      ]
-    },
-    "db:wipe": {
-      "settings": {
-        "loadApp": true
-      },
-      "commandPath": "@adonisjs/lucid/build/commands/DbWipe",
-      "commandName": "db:wipe",
-      "description": "Drop all tables, views and types in database",
-      "args": [],
-      "aliases": [],
-      "flags": [
-        {
-          "name": "connection",
-          "propertyName": "connection",
-          "type": "string",
-          "description": "Define a custom database connection",
-          "alias": "c"
-        },
-        {
-          "name": "drop-views",
-          "propertyName": "dropViews",
-          "type": "boolean",
-          "description": "Drop all views"
-        },
-        {
-          "name": "drop-types",
-          "propertyName": "dropTypes",
-          "type": "boolean",
-          "description": "Drop all custom types (Postgres only)"
-        },
-        {
-          "name": "force",
-          "propertyName": "force",
-          "type": "boolean",
-          "description": "Explicitly force command to run in production"
-        }
-      ]
-    },
-    "db:truncate": {
-      "settings": {
-        "loadApp": true
-      },
-      "commandPath": "@adonisjs/lucid/build/commands/DbTruncate",
-      "commandName": "db:truncate",
-      "description": "Truncate all tables in database",
-      "args": [],
-      "aliases": [],
-      "flags": [
-        {
-          "name": "connection",
-          "propertyName": "connection",
-          "type": "string",
-          "description": "Define a custom database connection",
-          "alias": "c"
-        },
-        {
-          "name": "force",
-          "propertyName": "force",
-          "type": "boolean",
-          "description": "Explicitly force command to run in production"
-        }
-      ]
-    },
-    "make:model": {
-      "settings": {
-        "loadApp": true
-      },
-      "commandPath": "@adonisjs/lucid/build/commands/MakeModel",
-      "commandName": "make:model",
-      "description": "Make a new Lucid model",
-      "args": [
-        {
-          "type": "string",
-          "propertyName": "name",
-          "name": "name",
-          "required": true,
-          "description": "Name of the model class"
-        }
-      ],
-      "aliases": [],
-      "flags": [
-        {
-          "name": "migration",
-          "propertyName": "migration",
-          "type": "boolean",
-          "alias": "m",
-          "description": "Generate the migration for the model"
-        },
-        {
-          "name": "controller",
-          "propertyName": "controller",
-          "type": "boolean",
-          "alias": "c",
-          "description": "Generate the controller for the model"
-        },
-        {
-          "name": "factory",
-          "propertyName": "factory",
-          "type": "boolean",
-          "alias": "f",
-          "description": "Generate a factory for the model"
-        }
-      ]
-    },
-    "make:migration": {
-      "settings": {
-        "loadApp": true
-      },
-      "commandPath": "@adonisjs/lucid/build/commands/MakeMigration",
-      "commandName": "make:migration",
-      "description": "Make a new migration file",
-      "args": [
-        {
-          "type": "string",
-          "propertyName": "name",
-          "name": "name",
-          "required": true,
-          "description": "Name of the migration file"
-        }
-      ],
-      "aliases": [],
-      "flags": [
-        {
-          "name": "connection",
-          "propertyName": "connection",
-          "type": "string",
-          "description": "The connection flag is used to lookup the directory for the migration file"
-        },
-        {
-          "name": "folder",
-          "propertyName": "folder",
-          "type": "string",
-          "description": "Pre-select a migration directory"
-        },
-        {
-          "name": "create",
-          "propertyName": "create",
-          "type": "string",
-          "description": "Define the table name for creating a new table"
-        },
-        {
-          "name": "table",
-          "propertyName": "table",
-          "type": "string",
-          "description": "Define the table name for altering an existing table"
-        }
-      ]
-    },
-    "make:seeder": {
-      "settings": {},
-      "commandPath": "@adonisjs/lucid/build/commands/MakeSeeder",
-      "commandName": "make:seeder",
-      "description": "Make a new Seeder file",
-      "args": [
-        {
-          "type": "string",
-          "propertyName": "name",
-          "name": "name",
-          "required": true,
-          "description": "Name of the seeder class"
-        }
-      ],
-      "aliases": [],
-      "flags": []
-    },
-    "make:factory": {
-      "settings": {},
-      "commandPath": "@adonisjs/lucid/build/commands/MakeFactory",
-      "commandName": "make:factory",
-      "description": "Make a new factory",
-      "args": [
-        {
-          "type": "string",
-          "propertyName": "model",
-          "name": "model",
-          "required": true,
-          "description": "The name of the model"
-        }
-      ],
-      "aliases": [],
-      "flags": [
-        {
-          "name": "model-path",
-          "propertyName": "modelPath",
-          "type": "string",
-          "description": "The path to the model"
-        },
-        {
-          "name": "exact",
-          "propertyName": "exact",
-          "type": "boolean",
-          "description": "Create the factory with the exact name as provided",
-          "alias": "e"
-        }
-      ]
-    },
-    "migration:run": {
-      "settings": {
-        "loadApp": true
-      },
-      "commandPath": "@adonisjs/lucid/build/commands/Migration/Run",
-      "commandName": "migration:run",
-      "description": "Migrate database by running pending migrations",
-      "args": [],
-      "aliases": [],
-      "flags": [
-        {
-          "name": "connection",
-          "propertyName": "connection",
-          "type": "string",
-          "description": "Define a custom database connection",
-          "alias": "c"
-        },
-        {
-          "name": "force",
-          "propertyName": "force",
-          "type": "boolean",
-          "description": "Explicitly force to run migrations in production"
-        },
-        {
-          "name": "dry-run",
-          "propertyName": "dryRun",
-          "type": "boolean",
-          "description": "Do not run actual queries. Instead view the SQL output"
-        },
-        {
-          "name": "compact-output",
-          "propertyName": "compactOutput",
-          "type": "boolean",
-          "description": "A compact single-line output"
-        },
-        {
-          "name": "disable-locks",
-          "propertyName": "disableLocks",
-          "type": "boolean",
-          "description": "Disable locks acquired to run migrations safely"
-        }
-      ]
-    },
-    "migration:rollback": {
-      "settings": {
-        "loadApp": true
-      },
-      "commandPath": "@adonisjs/lucid/build/commands/Migration/Rollback",
-      "commandName": "migration:rollback",
-      "description": "Rollback migrations to a specific batch number",
-      "args": [],
-      "aliases": [],
-      "flags": [
-        {
-          "name": "connection",
-          "propertyName": "connection",
-          "type": "string",
-          "description": "Define a custom database connection",
-          "alias": "c"
-        },
-        {
-          "name": "force",
-          "propertyName": "force",
-          "type": "boolean",
-          "description": "Explictly force to run migrations in production"
-        },
-        {
-          "name": "dry-run",
-          "propertyName": "dryRun",
-          "type": "boolean",
-          "description": "Do not run actual queries. Instead view the SQL output"
-        },
-        {
-          "name": "batch",
-          "propertyName": "batch",
-          "type": "number",
-          "description": "Define custom batch number for rollback. Use 0 to rollback to initial state"
-        },
-        {
-          "name": "compact-output",
-          "propertyName": "compactOutput",
-          "type": "boolean",
-          "description": "A compact single-line output"
-        },
-        {
-          "name": "disable-locks",
-          "propertyName": "disableLocks",
-          "type": "boolean",
-          "description": "Disable locks acquired to run migrations safely"
-        }
-      ]
-    },
-    "migration:status": {
-      "settings": {
-        "loadApp": true
-      },
-      "commandPath": "@adonisjs/lucid/build/commands/Migration/Status",
-      "commandName": "migration:status",
-      "description": "View migrations status",
-      "args": [],
-      "aliases": [],
-      "flags": [
-        {
-          "name": "connection",
-          "propertyName": "connection",
-          "type": "string",
-          "description": "Define a custom database connection",
-          "alias": "c"
-        }
-      ]
-    },
-    "migration:reset": {
-      "settings": {
-        "loadApp": true
-      },
-      "commandPath": "@adonisjs/lucid/build/commands/Migration/Reset",
-      "commandName": "migration:reset",
-      "description": "Rollback all migrations",
-      "args": [],
-      "aliases": [],
-      "flags": [
-        {
-          "name": "connection",
-          "propertyName": "connection",
-          "type": "string",
-          "description": "Define a custom database connection",
-          "alias": "c"
-        },
-        {
-          "name": "force",
-          "propertyName": "force",
-          "type": "boolean",
-          "description": "Explicitly force command to run in production"
-        },
-        {
-          "name": "dry-run",
-          "propertyName": "dryRun",
-          "type": "boolean",
-          "description": "Do not run actual queries. Instead view the SQL output"
-        },
-        {
-          "name": "disable-locks",
-          "propertyName": "disableLocks",
-          "type": "boolean",
-          "description": "Disable locks acquired to run migrations safely"
-        }
-      ]
-    },
-    "migration:refresh": {
-      "settings": {
-        "loadApp": true
-      },
-      "commandPath": "@adonisjs/lucid/build/commands/Migration/Refresh",
-      "commandName": "migration:refresh",
-      "description": "Rollback and migrate database",
-      "args": [],
-      "aliases": [],
-      "flags": [
-        {
-          "name": "connection",
-          "propertyName": "connection",
-          "type": "string",
-          "description": "Define a custom database connection",
-          "alias": "c"
-        },
-        {
-          "name": "force",
-          "propertyName": "force",
-          "type": "boolean",
-          "description": "Explicitly force command to run in production"
-        },
-        {
-          "name": "dry-run",
-          "propertyName": "dryRun",
-          "type": "boolean",
-          "description": "Do not run actual queries. Instead view the SQL output"
-        },
-        {
-          "name": "seed",
-          "propertyName": "seed",
-          "type": "boolean",
-          "description": "Run seeders"
-        },
-        {
-          "name": "disable-locks",
-          "propertyName": "disableLocks",
-          "type": "boolean",
-          "description": "Disable locks acquired to run migrations safely"
-        }
-      ]
-    },
-    "migration:fresh": {
-      "settings": {
-        "loadApp": true
-      },
-      "commandPath": "@adonisjs/lucid/build/commands/Migration/Fresh",
-      "commandName": "migration:fresh",
-      "description": "Drop all tables and re-migrate the database",
-      "args": [],
-      "aliases": [],
-      "flags": [
-        {
-          "name": "connection",
-          "propertyName": "connection",
-          "type": "string",
-          "description": "Define a custom database connection",
-          "alias": "c"
-        },
-        {
-          "name": "force",
-          "propertyName": "force",
-          "type": "boolean",
-          "description": "Explicitly force command to run in production"
-        },
-        {
-          "name": "seed",
-          "propertyName": "seed",
-          "type": "boolean",
-          "description": "Run seeders"
-        },
-        {
-          "name": "drop-views",
-          "propertyName": "dropViews",
-          "type": "boolean",
-          "description": "Drop all views"
-        },
-        {
-          "name": "drop-types",
-          "propertyName": "dropTypes",
-          "type": "boolean",
-          "description": "Drop all custom types (Postgres only)"
-        },
-        {
-          "name": "disable-locks",
-          "propertyName": "disableLocks",
-          "type": "boolean",
-          "description": "Disable locks acquired to run migrations safely"
-        }
-      ]
-    }
-  },
-  "aliases": {}
-}

ace.js

@@ -0,0 +1,24 @@
+/*
+/*
+|--------------------------------------------------------------------------
+| JavaScript entrypoint for running ace commands
+|--------------------------------------------------------------------------
+|
+| Since, we cannot run TypeScript source code using "node" binary, we need
+| a JavaScript entrypoint to run ace commands.
+|
+| This file registers the "ts-node/esm" hook with the Node.js module system
+| and then imports the "bin/console.ts" file.
+|
+*/
+
+/**
+ * Register hook to process TypeScript files using ts-node
+ */
+import { register } from 'node:module'
+register('ts-node/esm', import.meta.url)
+
+/**
+ * Import ace console entrypoint
+ */
+await import('./bin/console.js')

adonisrc.ts

@@ -0,0 +1,115 @@
+import { defineConfig } from '@adonisjs/core/app'
+
+export default defineConfig({
+  /*
+|--------------------------------------------------------------------------
+| Commands
+|--------------------------------------------------------------------------
+|
+| List of ace commands to register from packages. The application commands
+| will be scanned automatically from the "./commands" directory.
+ 
+*/
+  commands: [
+    () => import('@adonisjs/core/commands'),
+    () => import('@adonisjs/lucid/commands'),
+    () => import('@adonisjs/mail/commands')
+  ],
+  /*
+|--------------------------------------------------------------------------
+| Preloads
+|--------------------------------------------------------------------------
+|
+| List of modules to import before starting the application.
+|
+*/
+  preloads: [
+    () => import('./start/routes.js'),
+    () => import('./start/kernel.js'),
+    () => import('#start/validator'),
+    () => import('#start/rules/unique'),
+    () => import('#start/rules/translated_language'),
+    () => import('#start/rules/unique_person'),
+    () => import('#start/rules/file_length'),
+    () => import('#start/rules/file_scan'),
+    () => import('#start/rules/allowed_extensions_mimetypes'),
+    () => import('#start/rules/dependent_array_min_length')
+  ],
+  /*
+|--------------------------------------------------------------------------
+| Service providers
+|--------------------------------------------------------------------------
+|
+| List of service providers to import and register when booting the
+| application
+|
+*/
+  providers: [
+    // () => import('./providers/AppProvider.js'),
+    () => import('@adonisjs/core/providers/app_provider'),
+    () => import('@adonisjs/core/providers/hash_provider'),
+    {
+      file: () => import('@adonisjs/core/providers/repl_provider'),
+      environment: ['repl', 'test'],
+    },
+    () => import('@adonisjs/session/session_provider'),
+    () => import('@adonisjs/core/providers/edge_provider'),
+    () => import('@adonisjs/shield/shield_provider'),
+    // () => import('@eidellev/inertia-adonisjs'),
+    // () => import('@adonisjs/inertia/inertia_provider'),
+    () => import('#providers/app_provider'),
+    () => import('#providers/inertia_provider'),
+    () => import('@adonisjs/lucid/database_provider'),
+    () => import('@adonisjs/auth/auth_provider'),
+    // () => import('@eidellev/adonis-stardust'),        
+    () => import('@adonisjs/redis/redis_provider'),
+    () => import('@adonisjs/encore/encore_provider'),
+    () => import('@adonisjs/static/static_provider'),
+    () => import('#providers/stardust_provider'),
+    () => import('#providers/query_builder_provider'),
+    () => import('#providers/token_worker_provider'),
+    // () => import('#providers/validator_provider'),
+    () => import('#providers/drive/provider/drive_provider'),
+    // () => import('@adonisjs/core/providers/vinejs_provider'),
+    () => import('#providers/vinejs_provider'),
+    () => import('@adonisjs/mail/mail_provider')
+    //   () => import('#providers/mail_provider'),
+  ],
+  metaFiles: [
+    {
+      pattern: 'public/**',
+      reloadServer: false,
+    },
+    {
+      pattern: 'resources/views/**/*.edge',
+      reloadServer: false,
+    },
+  ],
+  /*
+|--------------------------------------------------------------------------
+| Tests
+|--------------------------------------------------------------------------
+|
+| List of test suites to organize tests by their type. Feel free to remove
+| and add additional suites.
+|
+*/
+  tests: {
+    suites: [
+      {
+        files: ['tests/unit/**/*.spec(.ts|.js)'],
+        name: 'unit',
+        timeout: 2000,
+      },
+      {
+        files: ['tests/functional/**/*.spec(.ts|.js)'],
+        name: 'functional',
+        timeout: 30000,
+      },
+    ],
+    forceExit: false,
+  },
+
+
+
+})

app/Controllers/Http/Admin/AdminuserController.ts

@@ -1,14 +1,14 @@
-import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
+import type { HttpContext } from '@adonisjs/core/http';
-import User from 'App/Models/User';
+import User from '#models/user';
-import Role from 'App/Models/Role';
+import Role from '#models/role';
-import type { ModelQueryBuilderContract } from '@ioc:Adonis/Lucid/Orm';
+import { ModelQueryBuilderContract } from '@adonisjs/lucid/types/model';
-import CreateUserValidator from 'App/Validators/CreateUserValidator';
+import { createUserValidator, updateUserValidator } from '#validators/user';
-import UpdateUserValidator from 'App/Validators/UpdateUserValidator';
+// import { schema, rules } from '@ioc:Adonis/Core/Validator';
-import { RenderResponse } from '@ioc:EidelLev/Inertia';
+// import Hash from '@ioc:Adonis/Core/Hash';
 // import { schema, rules } from '@ioc:Adonis/Core/Validator';
 
-export default class UsersController {
+export default class AdminuserController {
-    public async index({ auth, request, inertia }: HttpContextContract) {
+    public async index({ auth, request, inertia }: HttpContext) {
         const page = request.input('page', 1);
         // const limit = 10
 
@@ -45,7 +45,7 @@ export default class UsersController {
             // .filter(qs)
             // .preload('focusInterests')
             // .preload('role')
-            .paginate(page, 5);
+            .paginate(page, 10);
 
         // var test = request.all();
 
@@ -61,7 +61,7 @@ export default class UsersController {
         });
     }
 
-    public async create({ inertia }: HttpContextContract) {
+    public async create({ inertia }: HttpContext) {
         // let rolesPluck = {};
         // (await Role.query().select('id', 'name')).forEach((user) => {
         // 	rolesPluck[user.id] = user.name;
@@ -73,18 +73,19 @@ export default class UsersController {
         });
     }
 
-    public async store({ request, response, session }: HttpContextContract) {
+    public async store({ request, response, session }: HttpContext) {
         // node ace make:validator CreateUser
         try {
             //  Step 2 - Validate request body against  the schema
-            await request.validate(CreateUserValidator);
+            // await request.validate(CreateUserValidator);
+            await request.validateUsing(createUserValidator);
             // console.log({ payload });
         } catch (error) {
             // Step 3 - Handle errors
             // return response.badRequest(error.messages);
             throw error;
         }
-        const input = request.only(['login', 'email', 'password']);
+        const input = request.only(['login', 'email', 'password', 'first_name', 'last_name']);
         const user = await User.create(input);
         if (request.input('roles')) {
             const roles: Array<number> = request.input('roles');
@@ -92,10 +93,10 @@ export default class UsersController {
         }
 
         session.flash('message', 'User has been created successfully');
-        return response.redirect().toRoute('user.index');
+        return response.redirect().toRoute('settings.user.index');
     }
 
-    public async show({ request, inertia }: HttpContextContract) {
+    public async show({ request, inertia }: HttpContext) {
         const id = request.param('id');
         const user = await User.query().where('id', id).firstOrFail();
 
@@ -110,7 +111,7 @@ export default class UsersController {
         });
     }
 
-    public async edit({ request, inertia }: HttpContextContract) {
+    public async edit({ request, inertia }: HttpContext) {
         const id = request.param('id');
         const user = await User.query().where('id', id).firstOrFail();
 
@@ -125,20 +126,24 @@ export default class UsersController {
         });
     }
 
-    public async update({ request, response, session }: HttpContextContract) {
+    public async update({ request, response, session }: HttpContext) {
         // node ace make:validator UpdateUser
         const id = request.param('id');
         const user = await User.query().where('id', id).firstOrFail();
 
         // validate update form
-        await request.validate(UpdateUserValidator);
+        await request.validateUsing(updateUserValidator, {
+            meta: {
+                objId: user.id,
+            },
+        });
 
         // password is optional
         let input;
         if (request.input('password')) {
-            input = request.only(['login', 'email', 'password']);
+            input = request.only(['login', 'email', 'password', 'first_name', 'last_name']);
         } else {
-            input = request.only(['login', 'email']);
+            input = request.only(['login', 'email', 'first_name', 'last_name']);
         }
         await user.merge(input).save();
         // await user.save();
@@ -149,61 +154,20 @@ export default class UsersController {
         }
 
         session.flash('message', 'User has been updated successfully');
-        return response.redirect().toRoute('user.index');
+        return response.redirect().toRoute('settings.user.index');
     }
 
-    public async destroy({ request, response, session }: HttpContextContract) {
+    public async destroy({ request, response, session }: HttpContext) {
         const id = request.param('id');
         const user = await User.findOrFail(id);
         await user.delete();
 
         session.flash('message', `User ${user.login} has been deleted.`);
-        return response.redirect().toRoute('user.index');
+        return response.redirect().toRoute('settings.user.index');
     }
 
-    /**
+    // private async syncRoles(objId: number, roleIds: Array<number>) {
-     * Show the user a form to change their personal information & password.
+    // 	const user = await User.findOrFail(objId)
-     *
-     * @return — \Inertia\Response
-     */
-    public accountInfo({ inertia, auth }: HttpContextContract): RenderResponse {
-        const user = auth.user;
-        // const id = request.param('id');
-        // const user = await User.query().where('id', id).firstOrFail();
-
-        return inertia.render('Admin/User/AccountInfo', {
-            user: user,
-        });
-    }
-
-    /**
-     * Save the modified personal information for a user.
-     *
-     * @param  HttpContextContract ctx
-     * @return : RedirectContract
-     */
-    public async accountInfoStore({ request, response, auth, session }: HttpContextContract) {
-        // validate update form
-        await request.validate(UpdateUserValidator);
-
-        const payload = request.only(['login', 'email']);
-        auth.user?.merge(payload);
-        const user = await auth.user?.save();
-        //   $user = \Auth::user()->update($request->except(['_token']));
-        let message;
-        if (user) {
-            message = 'Account updated successfully.';
-        } else {
-            message = 'Error while saving. Please try again.';
-        }
-
-        session.flash(message);
-        return response.redirect().toRoute('admin.account.info');
-        //->with('message', __($message));
-    }
-
-    // private async syncRoles(userId: number, roleIds: Array<number>) {
-    // 	const user = await User.findOrFail(userId)
     // 	// const roles: Role[] = await Role.query().whereIn('id', roleIds);
 
     // 	// await user.roles().sync(roles.rows.map(role => role.id))

app/Controllers/Http/Admin/HomeController.ts

@@ -1,17 +1,17 @@
-import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
+import type { HttpContext } from '@adonisjs/core/http';
 
 export default class HomeController {
-    public async index({}: HttpContextContract) {}
+    public async index({}: HttpContext) {}
 
-    public async create({}: HttpContextContract) {}
+    public async create({}: HttpContext) {}
 
-    public async store({}: HttpContextContract) {}
+    public async store({}: HttpContext) {}
 
-    public async show({}: HttpContextContract) {}
+    public async show({}: HttpContext) {}
 
-    public async edit({}: HttpContextContract) {}
+    public async edit({}: HttpContext) {}
 
-    public async update({}: HttpContextContract) {}
+    public async update({}: HttpContext) {}
 
-    public async destroy({}: HttpContextContract) {}
+    public async destroy({}: HttpContext) {}
 }

app/Controllers/Http/Admin/LicenseController.ts

@@ -0,0 +1,51 @@
+import type { HttpContext } from '@adonisjs/core/http';
+import License from '#models/license';
+
+export default class LicenseController {
+    public async index({ auth, inertia }: HttpContext) {
+        const direction = 'asc'; // or 'desc'
+        const licenses = await License.query().orderBy('sort_order', direction).exec();
+
+        return inertia.render('Admin/License/Index', {
+            licenses: licenses,
+            can: {
+                edit: await auth.user?.can(['settings']),
+            },
+        });
+    }
+
+    public async down({ request, response }: HttpContext) {
+        const id = request.param('id');
+        const license = await License.findOrFail(id);
+        license.active = false;
+        await license.save();
+
+        // session.flash({ message: 'person has been deactivated!' });
+        return response.flash('License has been deactivated!', 'message').toRoute('settings.license.index')
+    }
+
+    public async up({ request, response }: HttpContext) {
+        const id = request.param('id');
+        const license = await License.findOrFail(id);
+        license.active = true;
+        await license.save();
+
+        // session.flash({ message: 'person has been activated!' });
+        return response.flash('License has been activated!', 'message').toRoute('settings.license.index');
+    }
+
+    // public async edit({ request, inertia }: HttpContext) {
+    //     const id = request.param('id');
+    //     const license = await License.query().where('id', id).firstOrFail();
+
+    //     // const permissions = await Permission.query().pluck('name', 'id');
+    //     // // const userHasRoles = user.roles;
+    //     // const rolerHasPermissions = await role.related('permissions').query().orderBy('name').pluck('id');
+
+    //     return inertia.render('Admin/License/Edit', {
+    //         // permissions: permissions,
+    //         license: license,
+    //         // roleHasPermissions: Object.keys(rolerHasPermissions).map((key) => rolerHasPermissions[key]), //convert object to array with role ids
+    //     });
+    // }
+}

app/Controllers/Http/Admin/MimetypeController.ts

@@ -0,0 +1,141 @@
+import type { HttpContext } from '@adonisjs/core/http';
+import MimeType from '#models/mime_type';
+import vine, { SimpleMessagesProvider } from '@vinejs/vine';
+
+export default class MimetypeController {
+    public async index({ auth, inertia }: HttpContext) {
+        const direction = 'asc'; // or 'desc'
+        const mimetypes = await MimeType.query().orderBy('name', direction).exec();
+
+        return inertia.render('Admin/Mimetype/Index', {
+            mimetypes: mimetypes,
+            can: {
+                create: await auth.user?.can(['settings']),
+                edit: await auth.user?.can(['settings']),
+            },
+        });
+    }
+
+    public async create({ inertia }: HttpContext) {
+        // const permissions = await Permission.query().select('id', 'name').pluck('name', 'id');
+        return inertia.render('Admin/Mimetype/Create', {});
+    }
+
+    public async store({ request, response, session }: HttpContext) {
+        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
+            enabled: vine.boolean(),
+        });
+        // await request.validate({ schema: newDatasetSchema, messages: this.messages });
+        try {
+            //  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);
+            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']);
+        // 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('|');
+        }
+        await MimeType.create(input);
+        // if (request.input('roles')) {
+        //     const roles: Array<number> = request.input('roles');
+        //     await user.related('roles').attach(roles);
+        // }
+
+        session.flash('message', 'MimeType has been created successfully');
+        return response.redirect().toRoute('settings.mimetype.index');
+    }
+
+    public messages = {
+        'minLength': '{{ field }} must be at least {{ min }} characters long',
+        'maxLength': '{{ field }} must be less then {{ max }} characters long',
+        'isUnique': '{{ field }} must be unique, and this value is already taken',
+        'required': '{{ field }} is required',
+        'file_extension.minLength': 'at least {{ min }} mimetypes must be defined',
+        'file_extension.*.string': 'Each file extension must be a valid string', // Adjusted to match the type
+    };
+
+    public async edit({ request, inertia }: HttpContext) {
+        const id = request.param('id');
+        const mimetype = await MimeType.query().where('id', id).firstOrFail();
+
+        // const permissions = await Permission.query().pluck('name', 'id');
+        // // const userHasRoles = user.roles;
+        // const rolerHasPermissions = await role.related('permissions').query().orderBy('name').pluck('id');
+
+        return inertia.render('Admin/Mimetype/Edit', {
+            mimetype: mimetype,
+        });
+    }
+
+    // public async update({ request, response, session }: HttpContext) {
+    //     // node ace make:validator UpdateUser
+    //     const id = request.param('id');
+    //     const role = await Role.query().where('id', id).firstOrFail();
+
+    //     // validate update form
+    //     // await request.validate(UpdateRoleValidator);
+    //     await request.validateUsing(updateRoleValidator, {
+    //         meta: {
+    //             roleId: role.id,
+    //         },
+    //     });
+
+    //     // password is optional
+
+    //     const input = request.only(['name', 'description']);
+    //     await role.merge(input).save();
+    //     // await user.save();
+
+    //     if (request.input('permissions')) {
+    //         const permissions: Array<number> = request.input('permissions');
+    //         await role.related('permissions').sync(permissions);
+    //     }
+
+    //     session.flash('message', 'Role has been updated successfully');
+    //     return response.redirect().toRoute('settings.role.index');
+    // }
+
+    public async down({ request, response }: HttpContext) {
+        const id = request.param('id');
+        const mimetype = await MimeType.findOrFail(id);
+        mimetype.enabled = false;
+        await mimetype.save();
+
+        // session.flash({ message: 'person has been deactivated!' });
+        return response.flash('mimetype  has been deactivated!', 'message').toRoute('settings.mimetype.index');
+    }
+
+    public async up({ request, response }: HttpContext) {
+        const id = request.param('id');
+        const mimetype = await MimeType.findOrFail(id);
+        mimetype.enabled = true;
+        await mimetype.save();
+
+        // session.flash({ message: 'person has been activated!' });
+        return response.flash('mimetype  has been activated!', 'message').toRoute('settings.mimetype.index');
+    }
+
+    // public async edit({ request, inertia }: HttpContext) {
+    //     const id = request.param('id');
+    //     const license = await License.query().where('id', id).firstOrFail();
+
+    //     // const permissions = await Permission.query().pluck('name', 'id');
+    //     // // const userHasRoles = user.roles;
+    //     // const rolerHasPermissions = await role.related('permissions').query().orderBy('name').pluck('id');
+
+    //     return inertia.render('Admin/License/Edit', {
+    //         // permissions: permissions,
+    //         license: license,
+    //         // roleHasPermissions: Object.keys(rolerHasPermissions).map((key) => rolerHasPermissions[key]), //convert object to array with role ids
+    //     });
+    // }
+}

app/Controllers/Http/Admin/RoleController.ts

@@ -1,14 +1,13 @@
-import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
+import type { HttpContext } from '@adonisjs/core/http';
-import Role from 'App/Models/Role';
+import Role from '#models/role';
-import Permission from 'App/Models/Permission';
+import Permission from '#models/permission';
-import type { ModelQueryBuilderContract } from '@ioc:Adonis/Lucid/Orm';
+import { createRoleValidator, updateRoleValidator } from '#validators/role';
-import CreateRoleValidator from 'App/Validators/CreateRoleValidator';
+import type { ModelQueryBuilderContract } from '@adonisjs/lucid/types/model';
-import UpdateRoleValidator from 'App/Validators/UpdateRoleValidator';
+
-import { RenderResponse } from '@ioc:EidelLev/Inertia';
 // import { schema, rules } from '@ioc:Adonis/Core/Validator';
 
 export default class RoleController {
-    public async index({ auth, request, inertia }: HttpContextContract) {
+    public async index({ auth, request, inertia }: HttpContext) {
         let roles: ModelQueryBuilderContract<typeof Role, Role> = Role.query();
 
         if (request.input('search')) {
@@ -48,18 +47,19 @@ export default class RoleController {
         });
     }
 
-    public async create({ inertia }: HttpContextContract) {
+    public async create({ inertia }: HttpContext) {
         const permissions = await Permission.query().select('id', 'name').pluck('name', 'id');
         return inertia.render('Admin/Role/Create', {
             permissions: permissions,
         });
     }
 
-    public async store({ request, response, session }: HttpContextContract) {
+    public async store({ request, response, session }: HttpContext) {
         // node ace make:validator CreateUser
         try {
             //  Step 2 - Validate request body against  the schema
-            await request.validate(CreateRoleValidator);
+            // await request.validate(CreateRoleValidator);
+            await request.validateUsing(createRoleValidator);
             // await request.validate({ schema: roleSchema });
             // console.log({ payload });
         } catch (error) {
@@ -76,10 +76,10 @@ export default class RoleController {
         }
 
         session.flash('message', `Role ${role.name} has been created successfully`);
-        return response.redirect().toRoute('role.index');
+        return response.redirect().toRoute('settings.role.index');
     }
 
-    public async show({ request, inertia }: HttpContextContract): RenderResponse {
+    public async show({ request, inertia }: HttpContext) {
         const id = request.param('id');
         const role = await Role.query().where('id', id).firstOrFail();
 
@@ -94,7 +94,7 @@ export default class RoleController {
         });
     }
 
-    public async edit({ request, inertia }: HttpContextContract) {
+    public async edit({ request, inertia }: HttpContext) {
         const id = request.param('id');
         const role = await Role.query().where('id', id).firstOrFail();
 
@@ -109,13 +109,18 @@ export default class RoleController {
         });
     }
 
-    public async update({ request, response, session }: HttpContextContract) {
+    public async update({ request, response, session }: HttpContext) {
         // node ace make:validator UpdateUser
         const id = request.param('id');
         const role = await Role.query().where('id', id).firstOrFail();
 
         // validate update form
-        await request.validate(UpdateRoleValidator);
+        // await request.validate(UpdateRoleValidator);
+        await request.validateUsing(updateRoleValidator, {
+            meta: {
+                roleId: role.id,
+            },
+        });
 
         // password is optional
 
@@ -129,15 +134,15 @@ export default class RoleController {
         }
 
         session.flash('message', 'Role has been updated successfully');
-        return response.redirect().toRoute('role.index');
+        return response.redirect().toRoute('settings.role.index');
     }
 
-    public async destroy({ request, response, session }: HttpContextContract) {
+    public async destroy({ request, response, session }: HttpContext) {
         const id = request.param('id');
         const role = await Role.findOrFail(id);
         await role.delete();
 
         session.flash('message', `Role ${role.name} has been deleted.`);
-        return response.redirect().toRoute('role.index');
+        return response.redirect().toRoute('settings.role.index');
     }
 }

app/Controllers/Http/Admin/mailsettings_controller.ts

@@ -0,0 +1,103 @@
+import type { HttpContext } from '@adonisjs/core/http';
+import vine from '@vinejs/vine';
+import AppConfig from '#models/appconfig';
+import mail from '@adonisjs/mail/services/main';
+// import config from '@adonisjs/core/services/config';
+// import { configProvider } from '@adonisjs/core';
+// import app from '@adonisjs/core/services/app';
+
+export default class MailSettingsController {
+    /**
+     * Save the email server settings
+     */
+    public async setMailSettings({ request, response }: HttpContext) {
+        const settingsSchema = vine.compile(
+            vine.object({
+                mail_domain: vine.string(),
+                mail_from_address: vine.string(),
+                mail_smtp_mode: vine.string(),
+                mail_smtpsecure: vine.string().optional(),
+                mail_smtphost: vine.string(),
+                mail_smtpport: vine.string(),
+                mail_smtpauth: vine.boolean(),
+                // mail_sendmailmode: vine.string().optional(),
+            }),
+        );
+
+        const validatedData = await request.validateUsing(settingsSchema);
+
+        const configData: any = { ...validatedData };
+
+        if (!validatedData.mail_smtpauth) {
+            configData.mail_smtpname = null;
+            configData.mail_smtppassword = null;
+        }
+
+        // Prepare the settings to be saved
+        const settingsToSave = [
+            { appid: 'settings', configkey: 'default', configvalue: validatedData.mail_smtp_mode, type: 1, lazy: 0 },
+            { appid: 'settings', configkey: 'host', configvalue: validatedData.mail_smtphost, type: 1, lazy: 0 },
+            { appid: 'settings', configkey: 'port', configvalue: validatedData.mail_smtpport, type: 1, lazy: 0 },
+            {
+                appid: 'settings',
+                configkey: 'from.address',
+                configvalue: `${validatedData.mail_from_address}@${validatedData.mail_domain}`,
+                type: 1,
+                lazy: 0,
+            },
+        ];
+
+        // if (validatedData.mail_smtpauth) {
+        //     settingsToSave.push(
+        //         { appid: 'settings', configkey: 'smtp_user', configvalue: validatedData.mail_smtpname, type: 1, lazy: 0 },
+        //         { appid: 'settings', configkey: 'smtp_password', configvalue: validatedData.mail_smtppassword, type: 1, lazy: 0 },
+        //     );
+        // } else {
+        //     settingsToSave.push(
+        //         { appid: 'settings', configkey: 'smtp_user', configvalue: null, type: 1, lazy: 0 },
+        //         { appid: 'settings', configkey: 'smtp_password', configvalue: null, type: 1, lazy: 0 },
+        //     );
+        // }
+
+        // Save or update the settings in the database
+        for (const setting of settingsToSave) {
+            await AppConfig.updateOrCreate(
+                { appid: setting.appid, configkey: setting.configkey },
+                { configvalue: setting.configvalue, type: setting.type, lazy: setting.lazy },
+            );
+        }
+
+        return response.json({ success: true, message: 'Mail settings updated successfully' });
+    }
+
+    /**
+     * Send a test email to ensure settings work
+     */
+    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 test = mail.config.mailers.smtp();
+        if (!userEmail) {
+            return response.badRequest({ message: 'User email is not set. Please update your profile.' });
+        }
+
+        try {
+            await mail.send((message) => {
+                message
+                    // .from(Config.get('mail.from.address'))
+                    .from('tethys@geosphere.at')
+                    .to(userEmail)
+                    .subject('Test Email')
+                    .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();
+        } catch (error) {
+            return response.internalServerError({ message: `Error sending test email: ${error.message}` });
+        }
+    }
+}

app/Controllers/Http/Api/AuthorsController.ts

@@ -1,10 +1,10 @@
-import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
+import type { HttpContext } from '@adonisjs/core/http';
-import Person from 'App/Models/Person';
+import Person from '#models/person';
 // import Dataset from 'App/Models/Dataset';
 
 // node ace make:controller Author
 export default class AuthorsController {
-    public async index({}: HttpContextContract) {
+    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"));
@@ -19,7 +19,7 @@ export default class AuthorsController {
         return authors;
     }
 
-    public async persons({ request }: HttpContextContract) {
+    public async persons({ request }: HttpContext) {
         const authors = Person.query().where('status', true);
 
         if (request.input('filter')) {

app/Controllers/Http/Api/AvatarController.ts

@@ -0,0 +1,65 @@
+import type { HttpContext } from '@adonisjs/core/http';
+import { StatusCodes } from 'http-status-codes';
+// import * as fs from 'fs';
+// import * as path from 'path';
+
+const prefixes = ['von', 'van'];
+
+// node ace make:controller Author
+export default class AvatarController {
+    public async generateAvatar({ request, response }: HttpContext) {
+        try {
+            const { name, background, textColor, size } = request.only(['name', 'background', 'textColor', 'size']);
+
+            // Generate initials
+            // const initials = name
+            //     .split(' ')
+            //     .map((part) => part.charAt(0).toUpperCase())
+            //     .join('');
+            const initials = this.getInitials(name);
+
+            // Define SVG content with dynamic values for initials, background color, text color, and size
+            const svgContent = `
+            <svg width="${size || 50}" height="${size || 50}" xmlns="http://www.w3.org/2000/svg">
+              <rect width="100%" height="100%" fill="#${background || '7F9CF5'}"/>
+              <text x="50%" y="50%" dominant-baseline="middle" text-anchor="middle" font-weight="bold" font-family="Arial, sans-serif" font-size="${
+                  (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');
+
+            return response.send(svgContent);
+        } catch (error) {
+            return response.status(StatusCodes.OK).json({ error: error.message });
+        }
+    }
+
+    private getInitials(name: string) {
+        const parts = name.split(' ');
+        let initials = '';
+
+        if (parts.length >= 2) {
+            const firstName = parts[0];
+            const lastName = parts[parts.length - 1];
+
+            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();
+        }
+
+        return initials;
+    }
+}

app/Controllers/Http/Api/DatasetController.ts

@@ -1,11 +1,11 @@
-import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
+import type { HttpContext } from '@adonisjs/core/http';
 // import Person from 'App/Models/Person';
-import Dataset from 'App/Models/Dataset';
+import Dataset from '#models/dataset';
 import { StatusCodes } from 'http-status-codes';
 
 // node ace make:controller Author
 export default class DatasetController {
-    public async index({}: HttpContextContract) {
+    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"));
@@ -14,7 +14,7 @@ export default class DatasetController {
         return datasets;
     }
 
-    public async findAll({ response }: HttpContextContract) {
+    public async findAll({ response }: HttpContext) {
         try {
             const datasets = await Dataset.query()
                 .where('server_state', 'published')
@@ -29,7 +29,7 @@ export default class DatasetController {
         }
     }
 
-    public async findOne({ params }: HttpContextContract) {
+    public async findOne({ params }: HttpContext) {
         const datasets = await Dataset.query()
             .where('publish_id', params.publish_id)
             .preload('titles')

app/Controllers/Http/Api/FileController.ts

@@ -0,0 +1,54 @@
+import type { HttpContext } from '@adonisjs/core/http';
+import File from '#models/file';
+import { StatusCodes } from 'http-status-codes';
+import * as fs from 'fs';
+import * as path from 'path';
+
+// node ace make:controller Author
+export default class FileController {
+    // @Get("download/:id")
+    public async findOne({ response, params }: HttpContext) {
+        const id = params.id;
+        const file = await File.findOrFail(id);
+        // const file = await File.findOne({
+        //     where: { id: id },
+        // });
+        if (file) {
+            const filePath = '/storage/app/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`,
+                });
+            }
+
+            // res.status(StatusCodes.OK).sendFile(filePath, (err) => {
+            //     // res.setHeader("Content-Type", "application/json");
+            //     // res.removeHeader("Content-Disposition");
+            //     res.status(StatusCodes.NOT_FOUND).send({
+            //         message: `File with id ${id} doesn't exist on file server`,
+            //     });
+            // });
+        } else {
+            response.status(StatusCodes.NOT_FOUND).send({
+                message: `Cannot find File with id=${id}.`,
+            });
+        }
+    }
+}

app/Controllers/Http/Api/HomeController.ts

@@ -1,9 +1,9 @@
-import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
+import type { HttpContext } from '@adonisjs/core/http';
-import Database from '@ioc:Adonis/Lucid/Database';
+import db from '@adonisjs/lucid/services/db';
 import { StatusCodes } from 'http-status-codes';
 
 export default class HomeController {
-    public async findDocumentsPerYear({ response, params }: HttpContextContract) {
+    public async findDocumentsPerYear({ response, params }: HttpContext) {
         const year = params.year;
         const from = parseInt(year);
         const serverState = 'published';
@@ -17,8 +17,8 @@ export default class HomeController {
             //     .preload('authors')
             //     .orderBy('server_date_published');
 
-            const datasets = await Database.from('documents as doc')
+            const datasets = await db.from('documents as doc')
-                .select(['publish_id', 'server_date_published', Database.raw(`date_part('year', server_date_published) as pub_year`)])
+                .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')
                 .andWhereRaw(`date_part('year', server_date_published) = ?`, [from])
@@ -32,17 +32,17 @@ export default class HomeController {
         }
     }
 
-    public async findYears({ response }: HttpContextContract) {
+    public async findYears({ response }: HttpContext) {
         const serverState = 'published';
         // Use raw SQL queries to select all cars which belongs to the user
         try {
-            const datasets = await Database.rawQuery(
+            const datasets = await db.rawQuery(
                 'SELECT distinct EXTRACT(YEAR FROM server_date_published) as published_date FROM gba.documents WHERE server_state = ?',
                 [serverState],
             );
 
             // Pluck the ids of the cars
-            const years = datasets.rows.map((dataset) => dataset.published_date);
+            const years = datasets.rows.map((dataset: any) => dataset.published_date);
             // check if the cars is returned
             // if (years.length > 0) {
             return response.status(StatusCodes.OK).json(years);
@@ -53,4 +53,91 @@ export default class HomeController {
             });
         }
     }
+
+    public async findPublicationsPerMonth({ response }: HttpContext) {
+        const serverState = 'published';
+        // 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)
+            //     .innerJoin('link_documents_persons as ba', 'doc.id', 'ba.document_id')
+            //     .andWhereRaw(`date_part('year', server_date_published) = ?`, [from])
+            //     .groupBy('pub_month');
+            //     // .orderBy('server_date_published');
+
+            const years = [2021, 2022, 2023]; // Add the second year
+
+            const result = await db.from('documents as doc')
+                .select([
+                    db.raw(`date_part('year', server_date_published) as pub_year`),
+                    db.raw(`date_part('month', server_date_published) as pub_month`),
+                    db.raw('COUNT(*) as count'),
+                ])
+                .where('server_state', serverState)
+                // .innerJoin('link_documents_persons as ba', 'doc.id', 'ba.document_id')
+                // .whereIn('pub_year', years) // Filter by both years
+                .whereRaw(`date_part('year', server_date_published) IN (${years.join(',')})`) // Filter by both years
+                .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) => {
+                const { pub_year, pub_month, count } = item;
+
+                if (!acc[pub_year]) {
+                    acc[pub_year] = {
+                        data: Array.from({ length: 12 }).fill(0),
+                        label: pub_year.toString(),
+                        borderColor: this.getRandomHexColor, // pub_year === 2022 ? '#3e95cd' : '#8e5ea2',
+                        fill: false,
+                    };
+                }
+
+                acc[pub_year].data[pub_month - 1] = parseInt(count);
+
+                return acc ;
+            }, {});
+
+            const outputDatasets = Object.entries(inputDatasets).map(([year, data]) => ({
+                data: data.data,
+                label: year,
+                borderColor: data.borderColor,
+                fill: data.fill
+              }));
+
+            const data = {
+                labels: labels,
+                datasets: outputDatasets,
+            };
+
+            return response.json(data);
+        } catch (error) {
+            return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({
+                message: error.message || 'Some error occurred while retrieving datasets.',
+            });
+        }
+    }
+
+    private getRandomHexColor() {
+        const letters = '0123456789ABCDEF';
+        let color = '#';
+    
+        for (let i = 0; i < 6; i++) {
+            color += letters[Math.floor(Math.random() * 16)];
+        }
+    
+        return color;
+    }
+}
+interface ChartDataset {
+    data: Array<number>;
+    label: string;
+    borderColor: string;
+    fill: boolean;
+
 }

app/Controllers/Http/Api/UserController.ts

@@ -0,0 +1,114 @@
+import type { HttpContext } from '@adonisjs/core/http';
+import User from '#models/user';
+import TwoFactorAuthProvider from '#app/services/TwoFactorAuthProvider';
+import { StatusCodes } from 'http-status-codes';
+import { InvalidArgumentException } from 'node-exceptions';
+import { TotpState } from '#contracts/enums';
+import BackupCodeStorage, { SecureRandom } from '#services/backup_code_storage';
+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 enable({ auth, response, request }: HttpContext) {
+        const user = (await User.find(auth.user?.id)) as User;
+        // await user.load('totp_secret');
+        // if (!user.totp_secret) {
+        //     let totpSecret = new TotpSecret();
+        //     user.related('totp_secret').save(totpSecret);
+        //     await user.load('totp_secret');
+        // }
+
+        if (!user) {
+            throw new Error('user not available');
+        }
+        const state: number = request.input('state');
+
+        try {
+            switch (state) {
+                case TotpState.STATE_DISABLED:
+                    // user.twoFactorSecret = null;
+                    // user.twoFactorRecoveryCodes = null;
+                    await BackupCode.deleteCodes(user);
+                    user.twoFactorSecret = '';
+                    // user.twoFactorRecoveryCodes = [''];
+                    await user.save();
+
+                    user.state = TotpState.STATE_DISABLED;
+                    await user.save();
+
+                    let storage = new BackupCodeStorage(new SecureRandom());
+                    let backupState = await storage.getBackupCodesState(user);
+
+                    return response.status(StatusCodes.OK).json({
+                        state: TotpState.STATE_DISABLED,
+                        backupState: backupState,
+                    });
+                case TotpState.STATE_CREATED:
+                    user.twoFactorSecret = TwoFactorAuthProvider.generateSecret(user);
+                    user.state = TotpState.STATE_CREATED;
+                    await user.save();
+
+                    let qrcode = await TwoFactorAuthProvider.generateQrCode(user);
+                    // throw new InvalidArgumentException('code is missing');
+                    return response.status(StatusCodes.OK).json({
+                        state: user.state,
+                        secret: user.twoFactorSecret,
+                        url: qrcode.url,
+                        svg: qrcode.svg,
+                    });
+                case TotpState.STATE_ENABLED:
+                    let code: string = request.input('code');
+                    if (!code) {
+                        throw new InvalidArgumentException('code is missing');
+                    }
+                    const success = await TwoFactorAuthProvider.enable(user, code);
+
+                    return response.status(StatusCodes.OK).json({
+                        state: success ? TotpState.STATE_ENABLED : TotpState.STATE_CREATED,
+                    });
+                default:
+                    throw new InvalidArgumentException('Invalid TOTP state');
+            }
+        } catch (error) {
+            return response.status(StatusCodes.INTERNAL_SERVER_ERROR).json({
+                message: 'Invalid TOTP state',
+            });
+        }
+    }
+
+    // public async fetchRecoveryCodes({ auth, view }) {
+    //     const user = auth?.user;
+
+    //     return view.render('pages/settings', {
+    //         twoFactorEnabled: user.isTwoFactorEnabled,
+    //         recoveryCodes: user.twoFactorRecoveryCodes,
+    //     });
+    // }
+
+    /**
+     * @NoAdminRequired
+     * @PasswordConfirmationRequired
+     *
+     * @return JSONResponse
+     */
+    public async createCodes({ auth, response }: HttpContext) {
+        // $user = $this->userSession->getUser();
+        const user = (await User.find(auth.user?.id)) as User;
+
+        // let codes = TwoFactorAuthProvider.generateRecoveryCodes();
+        let storage = new BackupCodeStorage(new SecureRandom());
+        // $codes = $this->storage->createCodes($user);
+        const codes = await storage.createCodes(user);
+
+        let backupState = await storage.getBackupCodesState(user);
+        // return new JSONResponse([
+        // 	'codes' => $codes,
+        // 	'state' => $this->storage->getBackupCodesState($user),
+        // ]);
+        return response.status(StatusCodes.OK).json({
+            codes: codes,
+            // state: success ? TotpState.STATE_ENABLED : TotpState.STATE_CREATED,
+            backupState: backupState, //storage.getBackupCodesState(user),
+        });
+    }
+}

app/Controllers/Http/Auth/AuthController.ts

@@ -1,25 +1,55 @@
-import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
+import type { HttpContext } from '@adonisjs/core/http';
-// import User from 'App/Models/User';
+import User from '#models/user';
+import BackupCode from '#models/backup_code';
 // import Hash from '@ioc:Adonis/Core/Hash';
 // import InvalidCredentialException from 'App/Exceptions/InvalidCredentialException';
-import AuthValidator from 'App/Validators/AuthValidator';
+import { authValidator } from '#validators/auth';
+import hash from '@adonisjs/core/services/hash';
 
+import TwoFactorAuthProvider from '#app/services/TwoFactorAuthProvider';
+// import { Authenticator } from '@adonisjs/auth';
+// import { LoginState } from 'Contracts/enums';
+// import { StatusCodes } from 'http-status-codes';
+
+// interface MyHttpsContext extends HttpContext {
+//     auth: Authenticator<User>
+//   }
 export default class AuthController {
-    //   login function
+    //   login function{ request, auth, response }:HttpContext
-    public async login({ request, response, auth, session }: HttpContextContract) {
+    public async login({ request, response, auth, session }: HttpContext) {
         // console.log({
         // 	registerBody: request.body(),
         // });
-        await request.validate(AuthValidator);
+        // await request.validate(AuthValidator);
+        await request.validateUsing(authValidator);
 
-        const plainPassword = await request.input('password');
+        // const plainPassword = await request.input('password');
-        const email = await request.input('email');
+        // const email = await request.input('email');
         // grab uid and password values off request body
-        // const { email, password } = request.only(['email', 'password'])
+        const { email, password } = request.only(['email', 'password']);
 
         try {
-            // attempt to login
+            // // attempt to verify credential and login user
-            await auth.use('web').attempt(email, plainPassword);
+            // await auth.use('web').attempt(email, plainPassword);
+
+            // const user = await auth.use('web').verifyCredentials(email, password);
+            const user = await User.verifyCredentials(email, password);
+
+            if (user.isTwoFactorEnabled) {
+                // session.put("login.id", user.id);
+                // return view.render("pages/two-factor-challenge");
+
+                session.flash('user_id', user.id);
+                return response.redirect().back();
+
+                // let state = LoginState.STATE_VALIDATED;
+                // return response.status(StatusCodes.OK).json({
+                //     state: state,
+                //     new_user_id: user.id,
+                // });
+            }
+
+            await auth.use('web').login(user);
         } catch (error) {
             // if login fails, return vague form message and redirect back
             session.flash('message', 'Your username, email, or password is incorrect');
@@ -27,14 +57,68 @@ export default class AuthController {
         }
 
         // otherwise, redirect todashboard
-        response.redirect('/dashboard');
+        response.redirect('/apps/dashboard');
+    }
+
+    public async twoFactorChallenge({ request, session, auth, response }: HttpContext) {
+        const { code, backup_code, login_id } = request.only(['code', 'backup_code', 'login_id']);      
+        const user = await User.query().where('id', login_id).firstOrFail();
+
+        if (code) {
+            const isValid = await TwoFactorAuthProvider.validate(user, code);
+            if (isValid) {
+                // login user and redirect to dashboard
+                await auth.use('web').login(user);
+                response.redirect('/apps/dashboard');
+            } else {
+                session.flash('message', 'Your two-factor code is incorrect');
+            return response.redirect().back();
+            }
+        } else if (backup_code) {
+            const codes: BackupCode[] = await user.getBackupCodes();
+          
+            // const verifiedBackupCodes = await Promise.all(
+            //     codes.map(async (backupCode) => {
+            //         let isVerified = await hash.verify(backupCode.code, backup_code);
+            //         if (isVerified) {
+            //             return backupCode;
+            //         }
+            //     }),
+            // );
+            // const backupCodeToDelete = verifiedBackupCodes.find(Boolean);
+
+            let backupCodeToDelete = null;
+            for (const backupCode of codes) {
+                const isVerified = await hash.verify(backupCode.code, backup_code);
+                if (isVerified) {
+                    backupCodeToDelete = backupCode;
+                    break;
+                }
+            }
+
+            if (backupCodeToDelete) {   
+                    if (backupCodeToDelete.used === false) {
+                        backupCodeToDelete.used = true;
+                        await backupCodeToDelete.save();
+                        console.log(`BackupCode with id ${backupCodeToDelete.id} has been marked as used.`);
+                        await auth.use('web').login(user);
+                        response.redirect('/apps/dashboard');
+                    } else {
+                        session.flash('message', 'BackupCode already used');
+                        return response.redirect().back();
+                    }                              
+            } else {
+                session.flash('message', 'BackupCode not found');
+                return response.redirect().back();
+            }           
+        }
     }
 
     //   logout function
-    public async logout({ auth, response }: HttpContextContract) {
+    public async logout({ auth, response }: HttpContext) {
         // await auth.logout();
         await auth.use('web').logout();
-        response.redirect('/app/login');
+        return response.redirect('/app/login');
         // return response.status(200);
     }
 }

app/Controllers/Http/Auth/UserController.ts

@@ -0,0 +1,138 @@
+import type { HttpContext } from '@adonisjs/core/http';
+import User from '#models/user';
+// import { RenderResponse } from '@ioc:EidelLev/Inertia';
+import TwoFactorAuthProvider from '#app/services/TwoFactorAuthProvider';
+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';
+
+// 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 {
+    /**
+     * Show the user a form to change their personal information & password.
+     *
+     * @return — \Inertia\Response
+     */
+    public async accountInfo({ inertia, auth }: HttpContext) {
+        // const user = auth.user;
+        const user = (await User.find(auth.user?.id)) as User;
+        // const id = request.param('id');
+        // const user = await User.query().where('id', id).firstOrFail();
+
+        let storage = new BackupCodeStorage(new SecureRandom());
+        // const codes=  user.isTwoFactorEnabled? (await user.getBackupCodes()).map((role) => role.code) : [];
+        let backupState = await storage.getBackupCodesState(user);
+
+        return inertia.render('Auth/AccountInfo', {
+            user: user,
+            twoFactorEnabled: user.isTwoFactorEnabled,
+            // code: await TwoFactorAuthProvider.generateQrCode(user),
+            backupState:  backupState,
+        });
+    }
+
+    public async accountInfoStore({ 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) {
+                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.user');
+        } 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;
+
+        user.twoFactorSecret = TwoFactorAuthProvider.generateSecret(user);
+        user.twoFactorRecoveryCodes = await TwoFactorAuthProvider.generateRecoveryCodes();
+        await user.save();
+
+        session.flash('message', 'Two factor authentication enabled.');
+        return response.redirect().back();
+        // return inertia.render('Auth/AccountInfo', {
+        //     // status: {
+        //     //     type: 'success',
+        //     //     message: 'Two factor authentication enabled.',
+        //     // },
+        //     user: user,
+        //     twoFactorEnabled: user.isTwoFactorEnabled,
+        //     code: await TwoFactorAuthProvider.generateQrCode(user),
+        //     recoveryCodes: user.twoFactorRecoveryCodes,
+        // });
+    }
+
+    public async disableTwoFactorAuthentication({ auth, response, session }: HttpContext): Promise<void> {
+        const user: User | undefined = auth.user;
+
+        if (user) {
+            user.twoFactorSecret = null;
+            user.twoFactorRecoveryCodes = null;
+            await user.save();
+            session.flash('message', 'Two-factor authentication disabled.');
+        } else {
+            session.flash('error', 'User not found.');
+        }
+    
+        return response.redirect().back();
+        // return inertia.render('Auth/AccountInfo', {
+        //     // status: {
+        //     //     type: 'success',
+        //     //     message: 'Two factor authentication disabled.',
+        //     // },
+        //     user: user,
+        //     twoFactorEnabled: user.isTwoFactorEnabled,
+        // });
+    }
+
+    // public async fetchRecoveryCodes({ auth, view }) {
+    //     const user = auth?.user;
+
+    //     return view.render('pages/settings', {
+    //         twoFactorEnabled: user.isTwoFactorEnabled,
+    //         recoveryCodes: user.twoFactorRecoveryCodes,
+    //     });
+    // }
+}

app/Controllers/Http/Editor/DatasetController.ts

@@ -0,0 +1,682 @@
+import type { HttpContext } from '@adonisjs/core/http';
+import { Client } from '@opensearch-project/opensearch';
+import User from '#models/user';
+import Dataset from '#models/dataset';
+import DatasetIdentifier from '#models/dataset_identifier';
+import XmlModel from '#app/Library/XmlModel';
+import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
+import { create } from 'xmlbuilder2';
+import { readFileSync } from 'fs';
+import SaxonJS from 'saxon-js';
+import { DateTime } from 'luxon';
+import Index from '#app/Library/Utils/Index';
+import { getDomain } from '#app/utils/utility-functions';
+import { DoiClient } from '#app/Library/Doi/DoiClient';
+import DoiClientException from '#app/exceptions/DoiClientException';
+import logger from '@adonisjs/core/services/logger';
+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';
+// Create a new instance of the client
+const client = new Client({ node: 'http://localhost:9200' }); // replace with your OpenSearch endpoint
+
+export default class DatasetsController {
+    private proc;
+    public messages = {
+        // 'required': '{{ field }} is required',
+        // 'licenses.minLength': 'at least {{ options.minLength }} permission must be defined',
+        'reviewer_id.required': 'reviewer_id must be defined',
+        'publisher_name.required': 'publisher name must be defined',
+    };
+
+    constructor() {
+        this.proc = readFileSync('public/assets2/solr.sef.json');
+        // Load the XSLT file
+        // this.proc = readFileSync('public/assets2/datasetxml2oai.sef.json');
+    }
+
+    // public async index({}: HttpContextContract) {}
+    public async index({ auth, request, inertia }: HttpContext) {
+        const user = (await User.find(auth.user?.id)) as User;
+        const page = request.input('page', 1);
+        let datasets: ModelQueryBuilderContract<typeof Dataset, Dataset> = Dataset.query();
+
+        // if (request.input('search')) {
+        //     // users = users.whereRaw('name like %?%', [request.input('search')])
+        //     const searchTerm = request.input('search');
+        //     datasets.where('name', 'ilike', `%${searchTerm}%`);
+        // }
+
+        if (request.input('sort')) {
+            type SortOrder = 'asc' | 'desc' | undefined;
+            let attribute = request.input('sort');
+            let sortOrder: SortOrder = 'asc';
+
+            if (attribute.substr(0, 1) === '-') {
+                sortOrder = 'desc';
+                // attribute = substr(attribute, 1);
+                attribute = attribute.substr(1);
+            }
+            datasets.orderBy(attribute, sortOrder);
+        } else {
+            // users.orderBy('created_at', 'desc');
+            datasets.orderBy('id', 'asc');
+        }
+
+        // const users = await User.query().orderBy('login').paginate(page, limit);
+        const myDatasets = await datasets
+            .where('server_state', 'released')
+            .orWhere((dQuery) => {
+                dQuery
+                    .whereIn('server_state', ['editor_accepted', 'rejected_reviewer', 'reviewed', 'published'])
+                    .where('editor_id', user.id)
+                    .doesntHave('identifier', 'and');
+            })
+            // .preload('identifier')
+            .preload('titles')
+            .preload('user', (query) => query.select('id', 'login'))
+            .preload('editor', (query) => query.select('id', 'login'))
+            .paginate(page, 10);
+
+        return inertia.render('Editor/Dataset/Index', {
+            datasets: myDatasets.serialize(),
+            filters: request.all(),
+            can: {
+                receive: await auth.user?.can(['dataset-receive']),
+                approve: await auth.user?.can(['dataset-approve']),
+                reject: await auth.user?.can(['dataset-editor-reject']),
+                edit: await auth.user?.can(['dataset-editor-update']),
+                delete: await auth.user?.can(['dataset-editor-delete']),
+                publish: await auth.user?.can(['dataset-publish']),
+            },
+        });
+    }
+
+    public async receive({ request, inertia, response }: HttpContext) {
+        const id = request.param('id');
+        const dataset = await Dataset.query()
+            .where('id', id)
+            .preload('titles')
+            .preload('descriptions')
+            .preload('user', (builder) => {
+                builder.select('id', 'login');
+            })
+
+            .firstOrFail();
+
+        const validStates = ['released'];
+        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 received. Datset has server state ${dataset.server_state}.`,
+                )
+                .redirect()
+                .back();
+        }
+
+        return inertia.render('Editor/Dataset/Receive', {
+            dataset,
+        });
+    }
+
+    public async receiveUpdate({ auth, request, response }: HttpContext) {
+        const id = request.param('id');
+        // const { id } = params;
+        const dataset = await Dataset.findOrFail(id);
+
+        const validStates = ['released'];
+        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(
+                    'warning',
+                    `Invalid server state. Dataset with id ${id} cannot be received by editor. Datset has server state ${dataset.server_state}.`,
+                )
+                .redirect()
+                .toRoute('editor.dataset.list');
+        }
+
+        dataset.server_state = 'editor_accepted';
+        const user = (await User.find(auth.user?.id)) as User;
+        // dataset.editor().associate(user).save();
+        try {
+            await dataset.related('editor').associate(user); // speichert schon ab
+            // await dataset.save();
+            return response.toRoute('editor.dataset.list').flash(`You have accepted dataset ${dataset.id}!`, 'message');
+        } catch (error) {
+            // Handle any errors
+            console.error(error);
+            return response.status(500).json({ error: 'An error occurred while accepting the data.' });
+        }
+    }
+
+    public async approve({ request, inertia, response }: HttpContext) {
+        const id = request.param('id');
+        // $dataset = Dataset::with('user:id,login')->findOrFail($id);
+        const dataset = await Dataset.findOrFail(id);
+
+        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 approved. Datset has server state ${dataset.server_state}.`,
+                )
+                .redirect()
+                .back();
+        }
+
+        const reviewers = await User.query()
+            .whereHas('roles', (builder) => {
+                builder.where('name', 'reviewer');
+            })
+            .pluck('login', 'id');
+
+        return inertia.render('Editor/Dataset/Approve', {
+            dataset,
+            reviewers,
+        });
+    }
+
+    public async approveUpdate({ request, response }: HttpContext) {
+        const approveDatasetSchema = vine.object({
+            reviewer_id: vine.number(),
+        });
+        try {
+            // await request.validate({ schema: approveDatasetSchema, messages: this.messages });
+            const validator = vine.compile(approveDatasetSchema);
+            await request.validateUsing(validator, { messagesProvider: new SimpleMessagesProvider(this.messages) });
+        } catch (error) {
+            // return response.badRequest(error.messages);
+            throw error;
+        }
+        const id = request.param('id');
+        const dataset = await Dataset.findOrFail(id);
+
+        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 approved. Datset has server state ${dataset.server_state}.`,
+                )
+                .redirect()
+                .back();
+        }
+
+        dataset.server_state = 'approved';
+        if (dataset.reject_reviewer_note != null) {
+            dataset.reject_reviewer_note = null;
+        }
+
+        //save main and additional titles
+        const reviewer_id = request.input('reviewer_id', null);
+        dataset.reviewer_id = reviewer_id;
+
+        if (await dataset.save()) {
+            return response.toRoute('editor.dataset.list').flash('message', 'You have approved one dataset!');
+        }
+    }
+
+    public async reject({ request, inertia, response }: HttpContext) {
+        const id = request.param('id');
+        const dataset = await Dataset.query()
+            .where('id', id)
+            // .preload('titles')
+            // .preload('descriptions')
+            .preload('user', (builder) => {
+                builder.select('id', 'login', 'email');
+            })
+            .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 rejected. Datset has server state ${dataset.server_state}.`,
+                )
+                .redirect()
+                .toRoute('editor.dataset.list');
+        }
+
+        return inertia.render('Editor/Dataset/Reject', {
+            dataset,
+        });
+    }
+
+    // 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!;
+
+        const id = request.param('id');
+        const dataset = await Dataset.query()
+            .where('id', id)
+            .preload('user', (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 = ['editor_accepted', 'rejected_reviewer'];
+        if (!validStates.includes(dataset.server_state)) {
+            // throw new Error('Invalid server state!');
+            // return response.flash('warning', 'Invalid server state. Dataset cannot be released to editor').redirect().back();
+            return response
+                .flash(
+                    `Invalid server state. Dataset with id ${id} cannot be rejected. Datset has server state ${dataset.server_state}.`,
+                     'warning'
+                )
+                .redirect()
+                .toRoute('editor.dataset.list');
+        }
+
+        dataset.server_state = 'rejected_editor';
+        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.user.email,
+            validateSMTP: false,
+        });
+        const validRecipientEmail: boolean = validationResult.valid;
+
+        let emailStatusMessage = '';
+
+        if (sendMail == true) {
+            if (dataset.user.email && validRecipientEmail) {
+                try {
+                    await mail.send((message) => {
+                        message.to(dataset.user.email).subject('Dataset Rejection Notification').html(`
+                            <p>Dear ${dataset.user.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 ${dataset.user.email}.`;
+                } catch (error) {
+                    logger.error(error);
+                    return response.flash('Dataset has not been rejected due to an email error: ' + error.message, 'error').toRoute('editor.dataset.list');
+                }
+            } else {
+                emailStatusMessage = ` However, the email could not be sent because the submitter's email address (${dataset.user.email}) is not valid.`;
+            }
+        }
+
+        await dataset.save();
+        return response
+            .flash(
+                `You have successfully rejected dataset ${dataset.id} submitted by ${dataset.user.login}.${emailStatusMessage}`,
+                'message',
+            )
+            .toRoute('editor.dataset.list');
+    }
+
+    public async publish({ request, inertia, response }: HttpContext) {
+        const id = request.param('id');
+
+        const dataset = await Dataset.query()
+            .where('id', id)
+            .preload('titles')
+            .preload('authors')
+            // .preload('persons', (builder) => {
+            //    builder.wherePivot('role', 'author')
+            //  })
+            .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 published. Datset has server state ${dataset.server_state}.`,
+                )
+                .redirect()
+                .back();
+        }
+
+        return inertia.render('Editor/Dataset/Publish', {
+            dataset,
+        });
+    }
+
+    public async publishUpdate({ request, response }: HttpContext) {
+        const publishDatasetSchema = vine.object({
+            publisher_name: vine.string().trim(),
+        });
+        try {
+            // await request.validate({ schema: publishDatasetSchema, messages: this.messages });
+            const validator = vine.compile(publishDatasetSchema);
+            await request.validateUsing(validator, { messagesProvider: new SimpleMessagesProvider(this.messages) });
+        } catch (error) {
+            throw error;
+        }
+        const id = request.param('id');
+        const dataset = await Dataset.findOrFail(id);
+
+        // let test = await Dataset.getMax('publish_id');
+        // const maxPublishId = await Database.from('documents').max('publish_id as max_publish_id').first();
+        // const max = maxPublishId.max_publish_id;
+        const max = await Dataset.getMax('publish_id');
+        let publish_id = 0;
+        if (max != null) {
+            publish_id = max + 1;
+        } else {
+            publish_id = publish_id + 1;
+        }
+        dataset.publish_id = publish_id;
+        dataset.server_state = 'published';
+        dataset.server_date_published = DateTime.now();
+
+        const publisherName = request.input('publisher_name', 'Tethys');
+        dataset.publisher_name = publisherName;
+
+        if (await dataset.save()) {
+            const index_name = 'tethys-records';
+            await Index.indexDocument(dataset, index_name);
+            return response.toRoute('editor.dataset.list').flash('message', 'You have successfully published the dataset!');
+        }
+    }
+
+    public async doiCreate({ request, inertia }: HttpContext) {
+        const id = request.param('id');
+        const dataset = await Dataset.query()
+            .where('id', id)
+            .preload('titles')
+            .preload('descriptions')
+            // .preload('identifier')
+            .preload('authors')
+            .firstOrFail();
+        return inertia.render('Editor/Dataset/Doi', {
+            dataset,
+        });
+    }
+
+    public async doiStore({ request, response }: HttpContext) {
+        const dataId = request.param('publish_id');
+        const dataset = await Dataset.query()
+            // .preload('xmlCache')
+            .where('publish_id', dataId)
+            .firstOrFail();
+        const xmlMeta = (await Index.getDoiRegisterString(dataset)) as string;
+
+        let prefix = '';
+        let base_domain = '';
+        // const datacite_environment = process.env.DATACITE_ENVIRONMENT || 'debug';
+        prefix = process.env.DATACITE_PREFIX || '';
+        base_domain = process.env.BASE_DOMAIN || '';
+
+        // 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 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 ${dataciteResponse?.status}`;
+            // Log the error or handle it as needed
+            throw new DoiClientException(dataciteResponse?.status, message);
+        }
+        // return response.toRoute('editor.dataset.list').flash('message', xmlMeta);
+    }
+
+    public async show({}: HttpContext) {}
+
+    public async edit({}: HttpContext) {}
+
+    // public async update({}: HttpContextContract) {}
+    public async update({ response }: HttpContext) {
+        const id = 273; //request.param('id');
+        const dataset = await Dataset.query().preload('xmlCache').where('id', id).firstOrFail();
+        // add xml elements
+        let xml = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, '<root></root>');
+        const datasetNode = xml.root().ele('Dataset');
+        await this.createXmlRecord(dataset, datasetNode);
+        // const domNode = await this.getDatasetXmlDomNode(dataset);
+        // const xmlString = xml.end({ prettyPrint: true });
+
+        // const data = request.only(['field1', 'field2']); // get it from xslt
+
+        // Create an index with non-default settings.
+        var index_name = 'tethys-features';
+
+        const xmlString = xml.end({ prettyPrint: false });
+        let doc = '';
+        try {
+            const result = await SaxonJS.transform({
+                // stylesheetFileName: `${config.TMP_BASE_DIR}/data-quality/rules/iati.sef.json`,
+                stylesheetText: this.proc,
+                destination: 'serialized',
+                // sourceFileName: sourceFile,
+                sourceText: xmlString,
+                // stylesheetParams: xsltParameter,
+                // logLevel: 10,
+            });
+            doc = result.principalResult;
+        } catch (error) {
+            return response.status(500).json({
+                message: 'An error occurred while creating the user',
+                error: error.message,
+            });
+        }
+
+        // var settings = {
+        //     settings: {
+        //         index: {
+        //             number_of_shards: 4,
+        //             number_of_replicas: 3,
+        //         },
+        //     },
+        // };
+        // var test = await client.indices.create({
+        //     index: index_name,
+        //     body: settings,
+        // });
+
+        // var document = {
+        //     title: 'Sample Document',
+        //     authors: [
+        //         {
+        //             first_name: 'John',
+        //             last_name: 'Doe',
+        //         },
+        //         {
+        //             first_name: 'Jane',
+        //             last_name: 'Smith',
+        //         },
+        //     ],
+        //     year: '2018',
+        //     genre: 'Crime fiction',
+        // };
+
+        // http://localhost:9200/datastets/_doc/1
+
+        // var id = '1';
+
+        try {
+            // console.log(doc);
+            let document = JSON.parse(`${doc}`);
+
+            // https://opensearch.org/docs/2.1/opensearch/supported-field-types/geo-shape/
+            // Define the new document
+            // const document = {
+            //     title: 'Your Document Name',
+            //     id: dataset.publish_id,
+            //     doctype: 'GIS',
+            //     // "location" : {
+            //     //     "type" : "point",
+            //     //     "coordinates" : [74.00, 40.71]
+            //     //   },
+            //     geo_location: {
+            //         type: 'linestring',
+            //         coordinates: [
+            //             [-77.03653, 38.897676],
+            //             [-77.009051, 38.889939],
+            //         ],
+            //     },
+            //     // geo_location: 'BBOX (71.0589, 74.0060, 42.3601, 40.7128)'
+            //     // geo_location: {
+            //     //     type: 'envelope',
+            //     //     coordinates: [
+            //     //         [13.0, 53.0],
+            //     //         [14.0, 52.0],
+            //     //     ], // Define your BBOX coordinates
+            //     // },
+            // };
+
+            // Update the document
+            var test = await client.index({
+                id: dataset.publish_id?.toString(),
+                index: index_name,
+                body: document,
+                refresh: true,
+            });
+
+            // Return the result
+            return response.json(test.body);
+        } catch (error) {
+            // Handle any errors
+            console.error(error);
+            return response.status(500).json({ error: 'An error occurred while updating the data.' });
+        }
+    }
+
+    public async destroy({}: HttpContext) {}
+
+    private async createXmlRecord(dataset: Dataset, datasetNode: XMLBuilder) {
+        const domNode = await this.getDatasetXmlDomNode(dataset);
+        if (domNode) {
+            datasetNode.import(domNode);
+        }
+    }
+
+    private async getDatasetXmlDomNode(dataset: Dataset) {
+        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) {
+            xmlModel.xmlCache = dataset.xmlCache;
+        }
+
+        // return cache.getDomDocument();
+        const domDocument: XMLBuilder | null = await xmlModel.getDomDocument();
+        return domDocument;
+    }
+}

app/Controllers/Http/Editor/deleteDoiMetadata.xml

@@ -0,0 +1,65 @@
+<?xml version="1.0" encoding="utf-8"?>
+<resource xmlns:dc="http://purl.org/dc/elements/1.1/"
+    xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xmlns="http://datacite.org/schema/kernel-4"
+    xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4.3/metadata.xsd">
+    <identifier identifierType="DOI">10.21388/tethys.213</identifier>
+    <creators>
+        <creator>
+            <creatorName nameType="Personal">Moser, Michael</creatorName>
+            <givenName>Michael</givenName>
+            <familyName>Moser</familyName>
+            <affiliation>GBA</affiliation>
+        </creator>
+    </creators>
+    <titles>
+        <title xml:lang="en">rewerewr</title>
+    </titles>
+    <publisher>Tethys RDR</publisher>
+    <publicationYear>2024</publicationYear>
+    <subjects>
+        <subject xml:lang="de">Aletshausen-Langenneufnach Störung</subject>
+        <subject xml:lang="de">Wolfersberg-Moosach Störung</subject>
+        <subject xml:lang="en">wefwef</subject>
+    </subjects>
+    <language>en</language>
+    <contributors>
+        <contributor contributorType="RegistrationAuthority">
+            <contributorName>Jürgen Reitner</contributorName>
+        </contributor>
+    </contributors>   
+    <dates>
+        <date dateType="Created">2023-11-30</date>
+    </dates>
+    <version>1</version>
+    <resourceType resourceTypeGeneral="Dataset">Dataset</resourceType>
+    <alternateIdentifiers>
+        <alternateIdentifier alternateIdentifierType="url">https://www.tethys.at/dataset/213</alternateIdentifier>
+    </alternateIdentifiers>
+    <rightsList>
+        <rights xml:lang="" rightsURI="https://creativecommons.org/licenses/by/4.0/deed.en"
+            schemeURI="https://spdx.org/licenses/" rightsIdentifierScheme="SPDX"
+            rightsIdentifier="CC-BY-4.0">Creative Commons Attribution 4.0 International (CC BY 4.0)</rights>
+        <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
+    </rightsList>
+    <sizes>
+        <size>1 datasets</size>
+    </sizes>
+    <formats>
+        <format>image/png</format>
+    </formats>
+    <descriptions>
+        <description xml:lang="en" descriptionType="Abstract">rewrewr</description>
+    </descriptions>
+    <geoLocations>
+        <geoLocation>
+            <geoLocationBox>
+                <westBoundLongitude>11.71142578125</westBoundLongitude>
+                <eastBoundLongitude>14.414062500000002</eastBoundLongitude>
+                <southBoundLatitude>46.58906908309185</southBoundLatitude>
+                <northBoundLatitude>47.45780853075031</northBoundLatitude>
+            </geoLocationBox>
+        </geoLocation>
+    </geoLocations>
+</resource>

app/Controllers/Http/Oai/OaiController.ts

@@ -1,16 +1,31 @@
-import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
+import type { HttpContext } from '@adonisjs/core/http';
-import { RequestContract } from '@ioc:Adonis/Core/Request';
+// import { RequestContract } from '@ioc:Adonis/Core/Request';
-import { XMLBuilder } from 'xmlbuilder2/lib/interfaces';
+import { Request } from '@adonisjs/core/http';
+import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
 import { create } from 'xmlbuilder2';
 import dayjs, { Dayjs } from 'dayjs';
-import utc from 'dayjs/plugin/utc';
+import utc from 'dayjs/plugin/utc.js';
-import timezone from 'dayjs/plugin/timezone';
+import timezone from 'dayjs/plugin/timezone.js';
 import { readFileSync } from 'fs';
 import { StatusCodes } from 'http-status-codes';
-import { transform } from 'saxon-js';
+import SaxonJS from 'saxon-js';
 // import { Xslt, xmlParse } from 'xslt-processor'
-import { OaiErrorCodes, OaiModelError } from 'App/Exceptions/OaiErrorCodes';
+import { OaiErrorCodes, OaiModelError } from '#app/exceptions/OaiErrorCodes';
-import { OaiModelException } from 'App/Exceptions/OaiModelException';
+import { OaiModelException, BadOaiModelException } from '#app/exceptions/OaiModelException';
+import Dataset from '#models/dataset';
+import Collection from '#models/collection';
+import { getDomain, preg_match } from '#app/utils/utility-functions';
+import XmlModel from '#app/Library/XmlModel';
+import logger from '@adonisjs/core/services/logger';
+import ResumptionToken from '#app/Library/Oai/ResumptionToken';
+// import Config from '@ioc:Adonis/Core/Config';
+import config from '@adonisjs/core/services/config'
+// import { inject } from '@adonisjs/fold';
+import { inject } from '@adonisjs/core'
+// import { TokenWorkerContract } from "MyApp/Models/TokenWorker";
+import TokenWorkerContract from '#library/Oai/TokenWorkerContract';
+import { ModelQueryBuilderContract } from '@adonisjs/lucid/types/model';
+
 
 interface XslTParameter {
     [key: string]: any;
@@ -20,10 +35,20 @@ interface Dictionary {
     [index: string]: string;
 }
 
+interface ListParameter {
+    cursor: number;
+    totalIds: number;
+    start: number;
+    reldocIds: (number | null)[];
+    metadataPrefix: string;
+}
+
+@inject()
 export default class OaiController {
-    // private deliveringDocumentStates = ["published", "deleted"];
+    private deliveringDocumentStates = ['published', 'deleted'];
-    // private sampleRegEx = /^[A-Za-zäüÄÜß0-9\-_.!~]+$/;
+    private sampleRegEx = /^[A-Za-zäüÄÜß0-9\-_.!~]+$/;
     private xsltParameter: XslTParameter;
+
     /**
      * Holds xml representation of document information to be processed.
      *
@@ -32,23 +57,20 @@ export default class OaiController {
     private xml: XMLBuilder;
     private proc;
 
-    constructor() {
+    
+    constructor(public tokenWorker: TokenWorkerContract) {
         // Load the XSLT file
         this.proc = readFileSync('public/assets2/datasetxml2oai.sef.json');
-        // tests
-        // const xslPath = 'assets/datasetxml2oai-pmh.xslt'; // Replace with the actual path to your XSLT file
-        // this.proc = readFileSync(xslPath, 'utf-8');
-        // this.configuration = new Configuration();
         dayjs.extend(utc);
         dayjs.extend(timezone);
     }
 
-    public async index({ response, request }: HttpContextContract): Promise<void> {
+    public async index({ response, request }: HttpContext): Promise<void> {
         this.xml = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, '<root></root>');
 
         // this.proc = new XSLTProcessor();
         // const stylesheet = readFileSync(__dirname + "/datasetxml2oai.sef.json");
-        const xsltParameter = (this.xsltParameter = {});
+        const xsltParameter: XslTParameter = (this.xsltParameter = {});
 
         let oaiRequest: Dictionary = {};
         if (request.method() === 'POST') {
@@ -59,9 +81,16 @@ export default class OaiController {
             xsltParameter['oai_error_code'] = 'unknown';
             xsltParameter['oai_error_message'] = 'Only POST and GET methods are allowed for OAI-PMH.';
         }
+
+        let earliestDateFromDb;
         // const oaiRequest: OaiParameter = request.body;
         try {
-            this.handleRequest(oaiRequest, request);
+            const firstPublishedDataset: Dataset | null = await Dataset.earliestPublicationDate();
+            firstPublishedDataset != null &&
+                (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);
         } catch (error) {
             if (error instanceof OaiModelException) {
                 const code = error.oaiCode;
@@ -80,9 +109,9 @@ export default class OaiController {
 
         const xmlString = this.xml.end({ prettyPrint: true });
 
-        let xmlOutput;
+        let xmlOutput; // = xmlString;
         try {
-            const result = await transform({
+            const result = await SaxonJS.transform({
                 // stylesheetFileName: `${config.TMP_BASE_DIR}/data-quality/rules/iati.sef.json`,
                 stylesheetText: this.proc,
                 destination: 'serialized',
@@ -106,7 +135,7 @@ export default class OaiController {
         response.status(StatusCodes.OK).send(xmlOutput);
     }
 
-    protected handleRequest(oaiRequest: Dictionary, request: RequestContract) {
+    protected async handleRequest(oaiRequest: Dictionary, request: Request) {
         // Setup stylesheet
         // $this->loadStyleSheet('datasetxml2oai-pmh.xslt');
 
@@ -116,7 +145,7 @@ export default class OaiController {
         this.xsltParameter['unixTimestamp'] = now.unix();
 
         // set OAI base url
-        const baseDomain = process.env.BASE_DOMAIN || 'localhost';
+        const baseDomain = process.env.OAI_BASE_DOMAIN || 'localhost';
         this.xsltParameter['baseURL'] = baseDomain + '/oai';
         this.xsltParameter['repURL'] = request.protocol() + '://' + request.hostname();
         this.xsltParameter['downloadLink'] = request.protocol() + '://' + request.hostname() + '/file/download/';
@@ -130,17 +159,15 @@ export default class OaiController {
                 this.handleIdentify();
             } else if (verb === 'ListMetadataFormats') {
                 this.handleListMetadataFormats();
-            }
+            } else if (verb == 'GetRecord') {
-            // else if (verb == "GetRecord") {
+                await this.handleGetRecord(oaiRequest);
-            //     await this.handleGetRecord(oaiRequest);
+            } else if (verb == 'ListRecords') {
-            // } else if (verb == "ListRecords") {
+                await this.handleListRecords(oaiRequest);
-            //     await this.handleListRecords(oaiRequest);
+            } else if (verb == 'ListIdentifiers') {
-            // } else if (verb == "ListIdentifiers") {
+                await this.handleListIdentifiers(oaiRequest);
-            //     await this.handleListIdentifiers(oaiRequest);
+            } else if (verb == 'ListSets') {
-            // } else if (verb == "ListSets") {
+                await this.handleListSets();
-            //     await this.handleListSets();
+            } else {
-            // }
-            else {
                 this.handleIllegalVerb();
             }
         } else {
@@ -182,6 +209,434 @@ export default class OaiController {
         this.xml.root().ele('Datasets');
     }
 
+    protected async handleListSets() {
+        const repIdentifier = 'tethys.at';
+        this.xsltParameter['repIdentifier'] = repIdentifier;
+        const datasetElement = this.xml.root().ele('Datasets');
+
+        const sets: { [key: string]: string } = {
+            'open_access': 'Set for open access licenses',
+            'openaire_data': "OpenAIRE",
+            'doc-type:ResearchData': 'Set for document type ResearchData',
+            ...(await this.getSetsForDatasetTypes()),
+            ...(await this.getSetsForCollections()),
+            // ... await this.getSetsForProjects(),
+        } as Dictionary;
+
+        for (const [key, value] of Object.entries(sets)) {
+            const setElement = datasetElement.ele('Rdr_Sets');
+            setElement.att('Type', key);
+            setElement.att('TypeName', value);
+        }
+    }
+
+    protected async handleGetRecord(oaiRequest: Dictionary) {
+        const repIdentifier = 'tethys.at';
+        this.xsltParameter['repIdentifier'] = repIdentifier;
+
+        const dataId = this.validateAndGetIdentifier(oaiRequest);
+        const dataset = await Dataset.query()
+            .where('publish_id', dataId)
+            .preload('xmlCache')
+            .preload('collections', (builder) => {
+                builder.preload('collectionRole');
+            })
+            .first();
+
+        if (!dataset || !dataset.publish_id) {
+            throw new OaiModelException(
+                StatusCodes.INTERNAL_SERVER_ERROR,
+                'The value of the identifier argument is unknown or illegal in this repository.',
+                OaiErrorCodes.IDDOESNOTEXIST,
+            );
+        }
+
+        const metadataPrefix = this.validateAndGetMetadataPrefix(oaiRequest);
+        this.xsltParameter['oai_metadataPrefix'] = metadataPrefix;
+        // do not deliver datasets which are restricted by document state defined in deliveringStates
+        this.validateDatasetState(dataset);
+
+        // add xml elements
+        const datasetNode = this.xml.root().ele('Datasets');
+        await this.createXmlRecord(dataset, datasetNode);
+    }
+
+    protected async handleListIdentifiers(oaiRequest: Dictionary) {
+        !this.tokenWorker.isConnected && (await this.tokenWorker.connect());
+
+        const maxIdentifier: number = config.get('oai.max.listidentifiers', 100);
+        await this.handleLists(oaiRequest, maxIdentifier);
+    }
+
+    protected async handleListRecords(oaiRequest: Dictionary) {
+        !this.tokenWorker.isConnected && (await this.tokenWorker.connect());
+
+        const maxRecords: number = config.get('oai.max.listrecords', 100);
+        await this.handleLists(oaiRequest, maxRecords);
+    }
+
+    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');
+
+        // list initialisation
+        const numWrapper: ListParameter = {
+            cursor: 0,
+            totalIds: 0,
+            start: maxRecords + 1,
+            reldocIds: [],
+            metadataPrefix: '',
+        };
+
+        // resumptionToken is defined
+        if ('resumptionToken' in oaiRequest) {
+            await this.handleResumptionToken(oaiRequest, maxRecords, numWrapper);
+        } else {
+            // no resumptionToken is given
+            await this.handleNoResumptionToken(oaiRequest, numWrapper);
+        }
+
+        // handling of document ids
+        const restIds = numWrapper.reldocIds as number[];
+        const workIds = restIds.splice(0, maxRecords) as number[]; // array_splice(restIds, 0, maxRecords);
+
+        // 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.',
+                OaiErrorCodes.NORECORDSMATCH,
+            );
+        }
+
+        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);
+        }
+
+        // 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 handleResumptionToken(oaiRequest: Dictionary, maxRecords: number, numWrapper: ListParameter) {
+        const resParam = oaiRequest['resumptionToken']; //e.g. "158886496600000"
+        const token = await this.tokenWorker.get(resParam);
+
+        if (!token) {
+            throw new OaiModelException(StatusCodes.INTERNAL_SERVER_ERROR, 'cache is outdated.', OaiErrorCodes.BADRESUMPTIONTOKEN);
+        }
+
+        numWrapper.cursor = token.startPosition - 1; //startet dann bei Index 10
+        numWrapper.start = token.startPosition + maxRecords;
+        numWrapper.totalIds = token.totalIds;
+        numWrapper.reldocIds = token.documentIds;
+        numWrapper.metadataPrefix = token.metadataPrefix;
+
+        this.xsltParameter['oai_metadataPrefix'] = numWrapper.metadataPrefix;
+    }
+
+    private async handleNoResumptionToken(oaiRequest: Dictionary, numWrapper: ListParameter) {
+        // no resumptionToken is given
+        if ('metadataPrefix' in oaiRequest) {
+            numWrapper.metadataPrefix = oaiRequest['metadataPrefix'];
+        } else {
+            throw new OaiModelException(
+                StatusCodes.INTERNAL_SERVER_ERROR,
+                'The prefix of the metadata argument is unknown.',
+                OaiErrorCodes.BADARGUMENT,
+            );
+        }
+        this.xsltParameter['oai_metadataPrefix'] = numWrapper.metadataPrefix;
+
+        let finder: ModelQueryBuilderContract<typeof Dataset, Dataset> = Dataset.query();
+        // add server state restrictions
+        finder.whereIn('server_state', this.deliveringDocumentStates);
+        if ('set' in oaiRequest) {
+            const set = oaiRequest['set'] as string;
+            const setArray = set.split(':');
+
+            if (setArray[0] == 'data-type') {
+                if (setArray.length == 2 && setArray[1]) {
+                    finder.where('type', setArray[1]);
+                }
+            } else if (setArray[0] == 'open_access') {
+                const openAccessLicences = ['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]);
+                    });
+                }
+            }
+        }
+
+        // const timeZone = "Europe/Vienna"; // Canonical time zone name
+        // &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.length != until.length) {
+                throw new OaiModelException(
+                    StatusCodes.INTERNAL_SERVER_ERROR,
+                    'The request has different granularities for the from and until parameters.',
+                    OaiErrorCodes.BADARGUMENT,
+                );
+            }
+            fromDate.hour() == 0 && (fromDate = fromDate.startOf('day'));
+            untilDate.hour() == 0 && (untilDate = untilDate.endOf('day'));
+
+            finder.whereBetween('server_date_published', [fromDate.format('YYYY-MM-DD HH:mm:ss'), untilDate.format('YYYY-MM-DD HH:mm:ss')]);
+        } else if ('from' in oaiRequest && !('until' in oaiRequest)) {
+            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'));
+
+            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,
+                );
+            } 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'));
+            }
+        }
+
+        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 setParamResumption(res: string, cursor: number, totalIds: number) {
+        const tomorrow = dayjs().add(1, 'day').format('YYYY-MM-DDThh:mm:ss[Z]');
+        this.xsltParameter['dateDelete'] = tomorrow;
+        this.xsltParameter['res'] = res;
+        this.xsltParameter['cursor'] = cursor;
+        this.xsltParameter['totalIds'] = totalIds;
+    }
+
+    private validateAndGetIdentifier(oaiRequest: Dictionary): number {
+        // Identifier references metadata Urn, not plain Id!
+        // Currently implemented as 'oai:foo.bar.de:{docId}' or 'urn:nbn...-123'
+        if (!('identifier' in oaiRequest)) {
+            throw new BadOaiModelException('The prefix of the identifier argument is unknown.');
+        }
+        const dataId = Number(this.getDocumentIdByIdentifier(oaiRequest.identifier));
+        if (isNaN(dataId)) {
+            throw new OaiModelException(
+                StatusCodes.INTERNAL_SERVER_ERROR,
+                'The value of the identifier argument is illegal in this repository.',
+                OaiErrorCodes.BADARGUMENT,
+            );
+        }
+        return dataId;
+    }
+
+    private validateAndGetMetadataPrefix(oaiRequest: Dictionary): string {
+        let metadataPrefix = '';
+        if ('metadataPrefix' in oaiRequest) {
+            metadataPrefix = oaiRequest['metadataPrefix'];
+        } else {
+            throw new OaiModelException(
+                StatusCodes.INTERNAL_SERVER_ERROR,
+                'The prefix of the metadata argument is unknown.',
+                OaiErrorCodes.BADARGUMENT,
+            );
+        }
+        return metadataPrefix;
+    }
+
+    private validateDatasetState(dataset: Dataset): void {
+        if (dataset.server_state == null || !this.deliveringDocumentStates.includes(dataset.server_state)) {
+            throw new OaiModelException(
+                StatusCodes.INTERNAL_SERVER_ERROR,
+                'Document is not available for OAI export!',
+                OaiErrorCodes.NORECORDSMATCH,
+            );
+        }
+    }
+
+    private async createXmlRecord(dataset: Dataset, datasetNode: XMLBuilder) {
+        const domNode = await this.getDatasetXmlDomNode(dataset);
+
+        if (domNode) {
+            // add frontdoor url and data-type
+            dataset.publish_id && this.addLandingPageAttribute(domNode, dataset.publish_id.toString());
+            this.addSpecInformation(domNode, 'data-type:' + dataset.type);
+
+            if (dataset.collections) {
+                for (const coll of dataset.collections) {
+                    const collRole = coll.collectionRole;
+                    this.addSpecInformation(domNode, collRole.oai_name + ':' + coll.number);
+                }
+            }
+
+            datasetNode.import(domNode);
+        }
+    }
+
+    private async getDatasetXmlDomNode(dataset: Dataset) {
+        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) {
+            xmlModel.xmlCache = dataset.xmlCache;
+        }
+
+        // return cache.getDomDocument();
+        const domDocument: XMLBuilder | null = await xmlModel.getDomDocument();
+        return domDocument;
+    }
+
+    private addSpecInformation(domNode: XMLBuilder, information: string) {
+        domNode.ele('SetSpec').att('Value', information);
+    }
+
+    private addLandingPageAttribute(domNode: XMLBuilder, dataid: string) {
+        const baseDomain = process.env.OAI_BASE_DOMAIN || 'localhost';
+        const url = 'https://' + getDomain(baseDomain) + '/dataset/' + dataid;
+        // add attribute du dataset xml element
+        domNode.att('landingpage', url);
+    }
+
+    private getDocumentIdByIdentifier(oaiIdentifier: string): string {
+        const identifierParts: string[] = oaiIdentifier.split(':'); // explode(":", $oaiIdentifier);
+        const dataId: string = identifierParts[2];
+        // switch (identifierParts[0]) {
+        //     case 'oai':
+        //         if (isset($identifierParts[2])) {
+        //             $dataId = $identifierParts[2];
+        //         }
+        //         break;
+        //     default:
+        //         throw new OaiModelException(
+        //             'The prefix of the identifier argument is unknown.',
+        //             OaiModelError::BADARGUMENT
+        //         );
+        //         break;
+        // }
+
+        // if (empty($dataId) or !preg_match('/^\d+$/', $dataId)) {
+        //     throw new OaiModelException(
+        //         'The value of the identifier argument is unknown or illegal in this repository.',
+        //         OaiModelError::IDDOESNOTEXIST
+        //     );
+
+        return dataId;
+    }
+
+    private async getSetsForCollections(): Promise<Dictionary> {
+        const sets: { [key: string]: string } = {} as Dictionary;
+
+        const collections = await Collection.query()
+            .select('name', 'number', 'role_id')
+            .whereHas('collectionRole', (query) => {
+                query.where('visible_oai', true);
+            })
+            .preload('collectionRole');
+
+        collections.forEach((collection) => {
+            // if collection has a collection role (classification like ddc):
+            if (collection.number) {
+                // collection.load('collectionRole');
+                const setSpec = collection.collectionRole?.oai_name + ':' + collection.number;
+                sets[setSpec] = `Set ${collection.number} '${collection.name}'`;
+            }
+        });
+        return sets;
+    }
+
+    private async getSetsForDatasetTypes(): Promise<Dictionary> {
+        const sets: { [key: string]: string } = {} as Dictionary;
+
+        const datasets: Array<Dataset> = await Dataset.query().select('type').where('server_state', 'published');
+
+        datasets.forEach((dataset) => {
+            if (dataset.type && false == preg_match(this.sampleRegEx, dataset.type)) {
+                const msg = `Invalid SetSpec (data-type='${dataset.type}').
+                Allowed characters are [${this.sampleRegEx}].`;
+                // Log::error("OAI-PMH: $msg");
+                logger.error(`OAI-PMH: ${msg}`);
+                return;
+            }
+            const setSpec = 'data-type:' + dataset.type;
+            sets[setSpec] = `Set for document type '${dataset.type}'`;
+        });
+        return sets;
+    }
+
     private handleIllegalVerb() {
         this.xsltParameter['oai_error_code'] = 'badVerb';
         this.xsltParameter['oai_error_message'] = 'The verb provided in the request is illegal.';

app/Controllers/Http/Reviewer/DatasetController.ts

@@ -0,0 +1,310 @@
+import type { HttpContext } from '@adonisjs/core/http';
+import User from '#models/user';
+import Dataset from '#models/dataset';
+import Field from '#app/Library/Field';
+import BaseModel from '#models/base_model';
+import { DateTime } from 'luxon';
+import { ModelQueryBuilderContract } from '@adonisjs/lucid/types/model';
+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';
+
+interface Dictionary {
+    [index: string]: string;
+}
+
+export default class DatasetsController {
+    public async index({ auth, request, inertia }: HttpContext) {
+        const user = (await User.find(auth.user?.id)) as User;
+        const page = request.input('page', 1);
+        let datasets: ModelQueryBuilderContract<typeof Dataset, Dataset> = Dataset.query();
+
+        // if (request.input('search')) {
+        //     // users = users.whereRaw('name like %?%', [request.input('search')])
+        //     const searchTerm = request.input('search');
+        //     datasets.where('name', 'ilike', `%${searchTerm}%`);
+        // }
+
+        if (request.input('sort')) {
+            type SortOrder = 'asc' | 'desc' | undefined;
+            let attribute = request.input('sort');
+            let sortOrder: SortOrder = 'asc';
+
+            if (attribute.substr(0, 1) === '-') {
+                sortOrder = 'desc';
+                // attribute = substr(attribute, 1);
+                attribute = attribute.substr(1);
+            }
+            datasets.orderBy(attribute, sortOrder);
+        } else {
+            // users.orderBy('created_at', 'desc');
+            datasets.orderBy('id', 'asc');
+        }
+
+        // const users = await User.query().orderBy('login').paginate(page, limit);
+        const myDatasets = await datasets
+            .where('server_state', 'approved')
+            .where('reviewer_id', user.id)
+
+            .preload('titles')
+            .preload('user', (query) => query.select('id', 'login'))
+            .preload('editor', (query) => query.select('id', 'login'))
+            .paginate(page, 10);
+
+        return inertia.render('Reviewer/Dataset/Index', {
+            datasets: myDatasets.serialize(),
+            filters: request.all(),
+            can: {
+                review: await auth.user?.can(['dataset-review']),
+                reject: await auth.user?.can(['dataset-review-reject']),
+            },
+        });
+    }
+
+    public async review({ request, inertia, response }: HttpContext) {
+        const id = request.param('id');
+        const dataset = await Dataset.query()
+            .where('id', id)
+            // .preload('titles')
+            // .preload('descriptions')
+            .preload('user', (builder) => {
+                builder.select('id', 'login');
+            })
+            .firstOrFail();
+
+        const validStates = ['approved'];
+        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 ${dataset.server_state}.`,
+                )
+                .redirect()
+                .toRoute('reviewer.dataset.list');
+        }
+
+        const fieldnames: Array<string> = await dataset.describe();
+        const fields: Dictionary = {};
+        for (const fieldName of fieldnames) {
+            const field: Field = dataset.getField(fieldName) as Field;
+            const modelClass = field.getValueModelClass();
+            let fieldValues = field.getValue();
+            let value = '';
+
+            if (fieldValues === null || fieldValues == undefined) {
+                continue;
+            }
+
+            if (modelClass === null) {
+                if (typeof fieldValues === 'number') {
+                    // If the field values are a number, use them as is
+                    value = fieldValues.toString();
+                } else {
+                    // If the field values are not a number, use the replace() function to remove non-printable characters
+                    value = fieldValues.replace(/[\x00-\x08\x0B\x0C\x0E-\x1F\x7F]/g, '\xEF\xBF\xBD ');
+                }
+            } else {
+                if (!Array.isArray(fieldValues)) {
+                    fieldValues = [fieldValues];
+                }
+
+                for (const fieldValue of fieldValues) {
+                    if (fieldValue === null) {
+                        continue;
+                    }
+                    if (modelClass.prototype instanceof BaseModel) {
+                        // this.mapModelAttributes(fieldValue, childNode);
+                        value = '<ul>';
+                        Object.keys(fieldValue).forEach((prop) => {
+                            let modelValue = fieldValue[prop];
+                            // console.log(`${prop}: ${value}`);
+                            if (modelValue != null) {
+                                if (modelValue instanceof DateTime) {
+                                    modelValue = modelValue.toFormat('yyyy-MM-dd HH:mm:ss').trim();
+                                } else {
+                                    modelValue = modelValue.toString().trim();
+                                }
+
+                                // Replace invalid XML-1.0-Characters by UTF-8 replacement character.
+                                modelValue = modelValue.replace(/[\x00-\x08\x0B\x0C\x0E-\x1F\x7F]/g, '\xEF\xBF\xBD ');
+
+                                value = value + '<li>' + prop + ' : ' + modelValue + '</li>';
+                            }
+                        });
+                        value = value + '</ul>';
+                    } else if (modelClass instanceof DateTime) {
+                        // console.log('Value is a luxon date');
+                        // this.mapDateAttributes(fieldValue, childNode);
+                        value = value + ' Year ' + modelClass.year.toString();
+                        value = value + ' Month ' + modelClass.month.toString();
+                        value = value + ' Day ' + modelClass.day.toString();
+                        value = value + ' Hour ' + modelClass.hour.toString();
+                        value = value + ' Minute ' + modelClass.minute.toString();
+                        value = value + ' Second ' + modelClass.second.toString();
+                        value = value + ' UnixTimestamp ' + modelClass.toUnixInteger().toString();
+                        let zoneName = modelClass.zoneName ? modelClass.zoneName : '';
+                        value = value + ' Timezone ' + zoneName;
+                    }
+                }
+            }
+
+            if (value != '') {
+                fields[fieldName] = value;
+            }
+        }
+
+        return inertia.render('Reviewer/Dataset/Review', {
+            dataset,
+            fields: fields,
+        });
+    }
+
+    public async reviewUpdate({ request, response }: HttpContext) {
+        const id = request.param('id');
+        // const { id } = params;
+        const dataset = await Dataset.findOrFail(id);
+
+        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(
+                    'warning',
+                    `Invalid server state. Dataset with id ${id} cannot be reviewed. Datset has server state ${dataset.server_state}.`,
+                )
+                .redirect()
+                .toRoute('reviewer.dataset.list');
+        }
+
+        dataset.server_state = 'reviewed';
+
+        try {
+            // await dataset.related('editor').associate(user); // speichert schon ab
+            await dataset.save();
+            return response.toRoute('reviewer.dataset.list').flash('message', `You have successfully reviewed dataset ${dataset.id}!`);
+        } catch (error) {
+            // Handle any errors
+            console.error(error);
+            return response.status(500).json({ error: 'An error occurred while reviewing the data.' });
+        }
+    }
+
+    public async reject({ request, inertia, response }: HttpContext) {
+        const id = request.param('id');
+        const dataset = await Dataset.query()
+            .where('id', id)
+            // .preload('titles')
+            // .preload('descriptions')
+            .preload('editor', (builder) => {
+                builder.select('id', 'login', 'email');
+            })
+            .firstOrFail();
+
+        const validStates = ['approved'];
+        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. Datset has server state ${dataset.server_state}.`,
+                )
+                .redirect()
+                .toRoute('reviewer.dataset.list');
+        }
+
+        return inertia.render('Reviewer/Dataset/Reject', {
+            dataset,
+        });
+    }
+
+    public async rejectUpdate({ request, response, auth }: HttpContext) {
+        const authUser = auth.user!;
+
+        const id = request.param('id');
+        const dataset = await Dataset.query()
+            .where('id', id)
+            .preload('editor', (builder) => {
+                builder.select('id', 'login', 'email');
+            })
+            .firstOrFail();
+
+        // const newSchema = schema.create({
+        //     server_state: schema.string({ trim: true }),
+        //     reject_reviewer_note: schema.string({ trim: true }, [rules.minLength(10), rules.maxLength(500)]),
+        // });
+        const newSchema = vine.object({
+            server_state: vine.string().trim(),
+            reject_reviewer_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 = ['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(                   
+                    `Invalid server state. Dataset with id ${id} cannot be rejected. Datset has server state ${dataset.server_state}.`,
+                    'warning',
+                )
+                .redirect()
+                .toRoute('reviewer.dataset.list');
+        }
+
+        // dataset.server_state = 'reviewed';
+        dataset.server_state = 'rejected_reviewer';
+        const rejectReviewerNote = request.input('reject_reviewer_note', '');
+        dataset.reject_reviewer_note = rejectReviewerNote;
+
+        // 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.editor.email,
+            validateSMTP: false,
+        });
+        const validRecipientEmail: boolean = validationResult.valid;
+        let emailStatusMessage = '';
+
+        if (sendMail == true) {
+            if (dataset.editor.email && validRecipientEmail) {
+                try {
+                    await mail.send((message) => {
+                        message.to(dataset.editor.email).subject('Dataset Rejection Notification').html(`
+                            <p>Dear editor ${dataset.editor.login},</p>
+                            <p>Your approved dataset with ID ${dataset.id} has been rejected.</p>
+                            <p>Reason for rejection: ${rejectReviewerNote}</p>
+                            <p>Best regards,<br>Your Tethys reviewer: ${authUser.login}</p>
+                        `);
+                    });
+                    emailStatusMessage = ` A rejection email was successfully sent to ${dataset.editor.email}.`;
+                } catch (error) {
+                    logger.error(error);
+                    return response
+                        .flash('Dataset has not been rejected due to an email error: ' + error.message, 'error')
+                        .toRoute('reviewer.dataset.list');
+                }
+            } else {
+                emailStatusMessage = ` However, the email could not be sent because the editor's email address (${dataset.editor.email}) is not valid.`;
+            }
+        }
+
+        await dataset.save();
+
+        return response
+            .toRoute('reviewer.dataset.list')
+            .flash(`You have rejected dataset ${dataset.id}! to editor ${dataset.editor.login}`, 'message');
+    }
+}

app/Controllers/Http/Submitter/PersonController.ts

@@ -1,4 +1,4 @@
-import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
+import type { HttpContext } from '@adonisjs/core/http';
 // import User from 'App/Models/User';
 // import Dataset from 'App/Models/Dataset';
 // import License from 'App/Models/License';
@@ -10,12 +10,11 @@ import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
 // import Collection from 'App/Models/Collection';
 // import { schema, CustomMessages, rules } from '@ioc:Adonis/Core/Validator';
 // import dayjs from 'dayjs';
-import Person from 'App/Models/Person';
+import Person from '#models/person';
-
+import { ModelQueryBuilderContract } from "@adonisjs/lucid/types/model";
-import type { ModelQueryBuilderContract } from '@ioc:Adonis/Lucid/Orm';
 
 export default class PersonController {
-    public async index({ auth, request, inertia }: HttpContextContract) {
+    public async index({ auth, request, inertia }: HttpContext) {
         // const user = (await User.find(auth.user?.id)) as User;
         const page = request.input('page', 1);
         let persons: ModelQueryBuilderContract<typeof Person, Person> = Person.query();

app/Exceptions/Handler.ts

@@ -1,61 +0,0 @@
-/*
-|--------------------------------------------------------------------------
-| Http Exception Handler
-|--------------------------------------------------------------------------
-|
-| AdonisJs will forward all exceptions occurred during an HTTP request to
-| the following class. You can learn more about exception handling by
-| reading docs.
-|
-| The exception handler extends a base `HttpExceptionHandler` which is not
-| mandatory, however it can do lot of heavy lifting to handle the errors
-| properly.
-|
-*/
-
-import { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
-import Logger from '@ioc:Adonis/Core/Logger';
-import HttpExceptionHandler from '@ioc:Adonis/Core/HttpExceptionHandler';
-
-export default class ExceptionHandler extends HttpExceptionHandler {
-    protected statusPages = {
-        '401,403': 'errors/unauthorized',
-        '404': 'errors/not-found',
-        '500..599': 'errors/server-error',
-    };
-
-    constructor() {
-        super(Logger);
-    }
-
-    public async handle(error: any, ctx: HttpContextContract) {
-        const { response, request, inertia } = ctx;
-
-        /**
-         * Handle failed authentication attempt
-         */
-        // if (['E_INVALID_AUTH_PASSWORD', 'E_INVALID_AUTH_UID'].includes(error.code)) {
-        //   session.flash('errors', { login: error.message });
-        //   return response.redirect('/login');
-        // }
-        // if ([401].includes(error.status)) {
-        //   session.flash('errors', { login: error.message });
-        //   return response.redirect('/dashboard');
-        // }
-
-        // https://github.com/inertiajs/inertia-laravel/issues/56
-        if (request.header('X-Inertia') && [500, 503, 404, 403, 401].includes(response.getStatus())) {
-            return inertia.render('Error', {
-                status: response.getStatus(),
-                message: error.message,
-            });
-            // ->toResponse($request)
-            // ->setStatusCode($response->status());
-        }
-
-        /**
-         * Forward rest of the exceptions to the parent class
-         */
-        return super.handle(error, ctx);
-    }
-}

app/FlashResponse.ts

@@ -1,34 +0,0 @@
-import { Response } from '@adonisjs/http-server/build/src/Response';
-import { ServerResponse, IncomingMessage } from 'http';
-import { RouterContract } from '@ioc:Adonis/Core/Route';
-import { EncryptionContract } from '@ioc:Adonis/Core/Encryption';
-import { ResponseConfig, ResponseContract } from '@ioc:Adonis/Core/Response';
-
-class FlashResponse extends Response implements ResponseContract {
-    protected static macros = {};
-    protected static getters = {};
-    constructor(
-        public request: IncomingMessage,
-        public response: ServerResponse,
-        flashEncryption: EncryptionContract,
-        flashConfig: ResponseConfig,
-        flashRouter: RouterContract,
-    ) {
-        super(request, response, flashEncryption, flashConfig, flashRouter);
-    }
-    public nonce: string;
-
-    public flash(key: string, message: any): this {
-        // Store the flash message in the session
-        this.ctx?.session.flash(key, message);
-        return this;
-    }
-
-    public toRoute(route: string): this {
-        // Redirect to the specified route
-        super.redirect().toRoute(route);
-        return this;
-    }
-}
-
-export default FlashResponse;

app/Library/Doi/DoiClient.ts

@@ -0,0 +1,93 @@
+// 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 axios from 'axios';
+
+export class DoiClient implements DoiClientContract {
+    public username: string;
+    public password: string;
+    public serviceUrl: string;
+
+    constructor() {
+        // const datacite_environment = process.env.DATACITE_ENVIRONMENT || 'debug';
+        this.username = process.env.DATACITE_USERNAME || '';
+        this.password = process.env.DATACITE_PASSWORD || '';
+        this.serviceUrl = process.env.DATACITE_SERVICE_URL || '';
+        // this.prefix = process.env.DATACITE_PREFIX || '';
+        // this.base_domain = process.env.BASE_DOMAIN || '';
+
+        if (this.username === '' || this.password === '' || this.serviceUrl === '') {
+            const message = 'issing configuration settings to properly initialize DOI client';
+            logger.error(message);
+            throw new DoiClientException(StatusCodes.BAD_REQUEST, message);
+        }
+    }
+
+    /**
+     * Creates a DOI with the given identifier
+     *
+     * @param doiValue The desired DOI identifier e.g. '10.5072/tethys.999',
+     * @param xmlMeta
+     * @param landingPageUrl e.g. https://www.tethys.at/dataset/1
+     *
+     * @return Promise<AxiosResponse<any>> The http response in the form of a axios response
+     */
+    public async registerDoi(doiValue: string, xmlMeta: string, landingPageUrl: string): Promise<AxiosResponse<any>> {
+        //step 1: register metadata via xml upload
+        // state draft
+        // let response;
+        // let url = `${this.serviceUrl}/metadata/${doiValue}`; //https://mds.test.datacite.org/metadata/10.21388/tethys.213
+        const auth = {
+            username: this.username,
+            password: this.password,
+        };
+        let headers = {
+            'Content-Type': 'application/xml;charset=UTF-8',
+        };
+        try {
+            const metadataResponse = await axios.default.put(`${this.serviceUrl}/metadata/${doiValue}`, xmlMeta, { auth, headers });
+
+            // Response Codes
+            // 201 Created: operation successful
+            // 401 Unauthorised: no login
+            // 403 Forbidden: login problem, quota exceeded
+            // 415 Wrong Content Type : Not including content type in the header.
+            // 422 Unprocessable Entity : invalid XML
+            // let test = metadataResponse.data; // 'OK (10.21388/TETHYS.213)'
+            if (metadataResponse.status !== 201) {
+                const message = `Unexpected DataCite MDS response code ${metadataResponse.status}`;
+                logger.error(message);
+                throw new DoiClientException(metadataResponse.status, message);
+            }
+
+            const doiResponse = await axios.default.put(`${this.serviceUrl}/doi/${doiValue}`, `doi=${doiValue}\nurl=${landingPageUrl}`, {
+                auth,
+                headers,
+            });
+
+            // Response Codes
+            // 201 Created: operation successful
+            // 400 Bad Request: request body must be exactly two lines: DOI and URL; wrong domain, wrong prefix;
+            // 401 Unauthorised: no login
+            // 403 Forbidden: login problem, quota exceeded
+            // 412 Precondition failed: metadata must be uploaded first.
+            if (doiResponse.status !== 201) {
+                const message = `Unexpected DataCite MDS response code ${doiResponse.status}`;
+                logger.error(message);
+                throw new DoiClientException(doiResponse.status, message);
+            }
+
+            return doiResponse;
+        } catch (error) {
+            // const message = `request for registering DOI failed with ${error.message}`;
+            // Handle the error, log it, or rethrow as needed
+            logger.error(error.message);
+            throw new DoiClientException(error.response.status, error.response.data);
+        }
+    }
+}

app/Library/Doi/DoiClientContract.ts

@@ -0,0 +1,13 @@
+// import ResumptionToken from './ResumptionToken';
+import { AxiosResponse } from 'axios';
+
+export default interface DoiClientContract {
+    username: string;
+    password: string;
+    serviceUrl: string;
+    // prefix: string;
+    // base_domain: string;
+    registerDoi(doiValue: string, xmlMeta: string, landingPageUrl: string): Promise<AxiosResponse<any>>;
+    // get(key: string): Promise<ResumptionToken | null>;
+    // set(token: ResumptionToken): Promise<string>;
+}

app/Library/Oai/ResumptionToken.ts

@@ -0,0 +1,51 @@
+export default class ResumptionToken {
+    private _documentIds: number[] = [];
+    private _metadataPrefix = '';
+    private _resumptionId = '';
+    private _startPosition = 0;
+    private _totalIds = 0;
+
+    get key(): string {
+        return this.metadataPrefix + this.startPosition + this.totalIds;
+    }
+
+    get documentIds(): number[] {
+        return this._documentIds;
+    }
+
+    set documentIds(idsToStore: number | number[]) {
+        this._documentIds = Array.isArray(idsToStore) ? idsToStore : [idsToStore];
+    }
+
+    get metadataPrefix(): string {
+        return this._metadataPrefix;
+    }
+
+    set metadataPrefix(value: string) {
+        this._metadataPrefix = value;
+    }
+
+    get resumptionId(): string {
+        return this._resumptionId;
+    }
+
+    set resumptionId(resumptionId: string) {
+        this._resumptionId = resumptionId;
+    }
+
+    get startPosition(): number {
+        return this._startPosition;
+    }
+
+    set startPosition(startPosition: number) {
+        this._startPosition = startPosition;
+    }
+
+    get totalIds(): number {
+        return this._totalIds;
+    }
+
+    set totalIds(totalIds: number) {
+        this._totalIds = totalIds;
+    }
+}

app/Library/Oai/TokenWorkerContract.ts

@@ -0,0 +1,11 @@
+import ResumptionToken from './ResumptionToken.js';
+
+export default abstract class TokenWorkerContract {
+    abstract ttl: number;
+    abstract isConnected: boolean;
+    abstract connect(): void;
+    abstract close(): void;
+    abstract get(key: string): Promise<ResumptionToken | null>;
+    abstract set(token: ResumptionToken): Promise<string>;
+}
+

app/Library/Oai/TokenWorkerSerice.ts

@@ -0,0 +1,95 @@
+import ResumptionToken from './ResumptionToken.js';
+import { createClient, RedisClientType } from 'redis';
+import InternalServerErrorException from '#app/exceptions/InternalServerException';
+import { sprintf } from 'sprintf-js';
+import dayjs from 'dayjs';
+import TokenWorkerContract from './TokenWorkerContract.js';
+
+export default class TokenWorkerService implements TokenWorkerContract {
+    protected filePrefix = 'rs_';
+    protected fileExtension = 'txt';
+
+    private cache: RedisClientType;
+    public ttl: number;
+    private url: string;
+    private connected = false;
+
+    constructor(ttl: number) {
+        this.ttl = ttl; // time to live
+        this.url = process.env.REDIS_URL || 'redis://127.0.0.1:6379';
+    }
+
+    public async connect() {
+        this.cache = createClient({ url: this.url });
+        this.cache.on('error', (err) => {
+            this.connected = false;
+            console.log('[Redis] Redis Client Error: ', err);
+        });
+        this.cache.on('connect', () => {
+            this.connected = true;
+        });
+        await this.cache.connect();
+    }
+
+    public get isConnected(): boolean {
+        return this.connected;
+    }
+
+    public async has(key: string): Promise<boolean> {
+        const result = await this.cache.get(key);
+        return result !== undefined && result !== null;
+    }
+
+    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();
+        let uniqueName: string;
+        let cacheKeyExists: boolean;
+        do {
+            // format values
+            // %s - String
+            // %d - Signed decimal number (negative, zero or positive)
+            // [0-9] (Specifies the minimum width held of to the variable value)
+            uniqueName = sprintf('%s%05d', uniqueId, fc++);
+            cacheKeyExists = await this.has(uniqueName);
+        } while (cacheKeyExists);
+        return uniqueName;
+    }
+
+    public async get(key: string): Promise<ResumptionToken | null> {
+        if (!this.cache) {
+            throw new InternalServerErrorException('Dataset is not available for OAI export!');
+        }
+
+        const result = await this.cache.get(key);
+        return result ? this.parseToken(result) : null;
+    }
+
+    private parseToken(result: string): ResumptionToken {
+        const rToken: ResumptionToken = new ResumptionToken();
+        const parsed = JSON.parse(result);
+        Object.assign(rToken, parsed);
+        return rToken;
+    }
+
+    public del(key: string) {
+        this.cache.del(key);
+    }
+
+    public flush() {
+        this.cache.flushAll();
+    }
+
+    public async close() {
+        await this.cache.disconnect();
+        this.connected = false;
+    }
+}

app/Library/Strategy.ts

@@ -1,8 +1,8 @@
-import { XMLBuilder } from 'xmlbuilder2/lib/interfaces';
+import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
 import { create } from 'xmlbuilder2';
-import Dataset from 'App/Models/Dataset';
+import Dataset from '#models/dataset';
-import Field from './Field';
+import Field from './Field.js';
-import BaseModel from 'App/Models/BaseModel';
+import BaseModel from '#models/base_model';
 import { DateTime } from 'luxon';
 
 export default class Strategy {
@@ -10,7 +10,7 @@ export default class Strategy {
     private config;
     private xml: XMLBuilder;
 
-    constructor(config) {
+    constructor(config: any) {
         this.version = 1.0;
         this.config = config;
     }
@@ -45,11 +45,11 @@ export default class Strategy {
 
         for (const fieldname of fieldsDiff) {
             const field = model.getField(fieldname);
-            this.mapField(field, modelNode);
+            this.mapField(field as Field, modelNode);
         }
     }
 
-    private mapField(field, modelNode: XMLBuilder) {
+    private mapField(field: Field, modelNode: XMLBuilder) {
         const modelClass = field.getValueModelClass();
         let fieldValues = field.getValue();
 
@@ -107,10 +107,10 @@ export default class Strategy {
         childNode.att('Timezone', zoneName);
     }
 
-    private mapModelAttributes(myObject, childNode: XMLBuilder) {
+    private mapModelAttributes(myObject: any, childNode: XMLBuilder) {
         Object.keys(myObject).forEach((prop) => {
             let value = myObject[prop];
-            console.log(`${prop}: ${value}`);
+            // console.log(`${prop}: ${value}`);
             if (value != null) {
                 if (value instanceof DateTime) {
                     value = value.toFormat('yyyy-MM-dd HH:mm:ss').trim();
@@ -161,7 +161,7 @@ export default class Strategy {
         return fieldValues?.toString().trim();
     }
 
-    private createModelNode(model) {
+    private createModelNode(model: Dataset) {
         const className = 'Rdr_' + model.constructor.name.split('\\').pop(); //Rdr_Dataset
         // return dom.createElement(className);
         return this.xml.root().ele(className);

app/Library/Utils/Index.ts

@@ -0,0 +1,197 @@
+import Dataset from '#models/dataset';
+import { Client } from '@opensearch-project/opensearch';
+import { create } from 'xmlbuilder2';
+import SaxonJS from 'saxon-js';
+import XmlModel from '#app/Library/XmlModel';
+import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
+import logger from '@adonisjs/core/services/logger';
+import { readFileSync } from 'fs';
+import { DateTime } from 'luxon';
+// import Config from '@ioc:Adonis/Core/Config';
+import { getDomain } from '#app/utils/utility-functions';
+
+// const opensearchNode = process.env.OPENSEARCH_HOST || 'localhost';
+// const client = new Client({ node: `http://${opensearchNode}` }); // replace with your OpenSearch endpoint
+interface XslTParameter {
+    [key: string]: any;
+}
+export default {
+    // opensearchNode: process.env.OPENSEARCH_HOST || 'localhost',
+    client: new Client({ node: `http://${process.env.OPENSEARCH_HOST || 'localhost'}` }), // replace with your OpenSearch endpoint
+
+    async getDoiRegisterString(dataset: Dataset): Promise<string | undefined> {
+        try {
+            const proc = readFileSync('public/assets2/doi_datacite.sef.json');
+            const xsltParameter: XslTParameter = {};
+            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 });
+
+            // set timestamp
+            const date = DateTime.now();
+            const unixTimestamp = date.toUnixInteger();
+            xsltParameter['unixTimestamp'] = unixTimestamp;
+
+            // set prefix
+            let prefix = '';
+            // let base_domain = '';
+            // const datacite_environment = process.env.DATACITE_ENVIRONMENT || 'debug';
+            // if (datacite_environment === 'debug') {
+            //     prefix = process.env.DATACITE_TEST_PREFIX || '';
+            //     base_domain = process.env.TEST_BASE_DOMAIN || '';
+            // } else if (datacite_environment === 'production') {
+            //     prefix = process.env.DATACITE_PREFIX || '';
+            //     base_domain = process.env.BASE_DOMAIN || '';
+            // }
+            prefix = process.env.DATACITE_PREFIX || '';
+            xsltParameter['prefix'] = prefix;
+
+            const repIdentifier = 'tethys';
+            xsltParameter['repIdentifier'] = repIdentifier;
+
+            let xmlOutput; // = xmlString;
+            try {
+                const result = await SaxonJS.transform({
+                    // stylesheetFileName: `${config.TMP_BASE_DIR}/data-quality/rules/iati.sef.json`,
+                    stylesheetText: proc,
+                    destination: 'serialized',
+                    // sourceFileName: sourceFile,
+                    sourceText: xmlString,
+                    stylesheetParams: xsltParameter,
+                    // logLevel: 10,
+                });
+                xmlOutput = result.principalResult;
+            } catch (error) {
+                logger.error('An error occurred while creating the user', error.message);
+            }
+
+            return xmlOutput;
+        } catch (error) {
+            logger.error(`An error occurred while indexing datsaet with publish_id ${dataset.publish_id}.`);
+        }
+    },
+
+    async indexDocument(dataset: Dataset, index_name: string): Promise<void> {
+        try {
+            const proc = readFileSync('public/assets2/solr.sef.json');
+            const doc: string = await this.getTransformedString(dataset, proc);
+
+            let document = JSON.parse(doc);
+            await this.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}.`);
+        }
+    },
+
+    async getTransformedString(dataset: Dataset, proc: Buffer): Promise<string> {
+        let xml = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, '<root></root>');
+        const datasetNode = xml.root().ele('Dataset');
+        await createXmlRecord(dataset, datasetNode);
+        const xmlString = xml.end({ prettyPrint: false });
+
+        try {
+            const result = await SaxonJS.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 '';
+        }
+    },
+};
+/**
+ * Return the default global focus trap stack
+ *
+ * @return {import('focus-trap').FocusTrap[]}
+ */
+
+// export const indexDocument = async (dataset: Dataset, index_name: string, proc: Buffer): Promise<void> => {
+//     try {
+//         const doc = await getJsonString(dataset, proc);
+
+//         let document = JSON.parse(doc);
+//         await client.index({
+//             id: dataset.publish_id?.toString(),
+//             index: index_name,
+//             body: document,
+//             refresh: true,
+//         });
+//         Logger.info(`dataset with publish_id ${dataset.publish_id} successfully indexed`);
+//     } catch (error) {
+//         Logger.error(`An error occurred while indexing datsaet with publish_id ${dataset.publish_id}.`);
+//     }
+// };
+
+// const getJsonString = async (dataset, proc): Promise<string> => {
+//     let xml = create({ version: '1.0', encoding: 'UTF-8', standalone: true }, '<root></root>');
+//     const datasetNode = xml.root().ele('Dataset');
+//     await createXmlRecord(dataset, datasetNode);
+//     const xmlString = xml.end({ prettyPrint: false });
+
+//     try {
+//         const result = await transform({
+//             stylesheetText: proc,
+//             destination: 'serialized',
+//             sourceText: xmlString,
+//         });
+//         return result.principalResult;
+//     } catch (error) {
+//         Logger.error(`An error occurred while creating the user, error: ${error.message},`);
+//         return '';
+//     }
+// };
+
+const createXmlRecord = async (dataset: Dataset, datasetNode: XMLBuilder): Promise<void> => {
+    const domNode = await getDatasetXmlDomNode(dataset);
+    if (domNode) {
+         // add frontdoor url and data-type
+        dataset.publish_id && addLandingPageAttribute(domNode, dataset.publish_id.toString());
+        addSpecInformation(domNode, 'data-type:' + dataset.type);
+        if (dataset.collections) {
+            for (const coll of dataset.collections) {
+                const collRole = coll.collectionRole;
+                addSpecInformation(domNode, collRole.oai_name + ':' + coll.number);
+            }
+        }
+
+        datasetNode.import(domNode);
+    }
+};
+
+const getDatasetXmlDomNode = async (dataset: Dataset): Promise<XMLBuilder | null> => {
+    const xmlModel = new XmlModel(dataset);
+    // xmlModel.setModel(dataset);
+    xmlModel.excludeEmptyFields();
+    xmlModel.caching = true;
+    // const cache = dataset.xmlCache ? dataset.xmlCache : null;
+    // dataset.load('xmlCache');
+    await dataset.load('xmlCache');
+    if (dataset.xmlCache) {
+        xmlModel.xmlCache = dataset.xmlCache;
+    }
+
+    // return cache.getDomDocument();
+    const domDocument: XMLBuilder | null = await xmlModel.getDomDocument();
+    return domDocument;
+};
+
+const addLandingPageAttribute = (domNode: XMLBuilder, dataid: string) => {
+    const baseDomain = process.env.OAI_BASE_DOMAIN || 'localhost';
+    const url = 'https://' + getDomain(baseDomain) + '/dataset/' + dataid;
+    // add attribute du dataset xml element
+    domNode.att('landingpage', url);
+};
+
+const addSpecInformation= (domNode: XMLBuilder, information: string) => {
+    domNode.ele('SetSpec').att('Value', information);
+};

app/Library/XmlModel.ts

@@ -1,8 +1,9 @@
-import DocumentXmlCache from 'App/Models/DocumentXmlCache';
+import DocumentXmlCache from '#models/DocumentXmlCache';
-import { XMLBuilder } from 'xmlbuilder2/lib/interfaces';
+import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
-import Dataset from 'App/Models/Dataset';
+import Dataset from '#models/dataset';
-import Strategy from './Strategy';
+import Strategy from './Strategy.js';
 import { DateTime } from 'luxon';
+import { builder } from 'xmlbuilder2';
 
 /**
  * This is the description of the interface
@@ -84,10 +85,21 @@ export default class XmlModel {
                 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.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;
     }

app/Middleware/Auth.ts

@@ -1,67 +0,0 @@
-import { AuthenticationException } from '@adonisjs/auth/build/standalone';
-import type { GuardsList } from '@ioc:Adonis/Addons/Auth';
-import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
-
-/**
- * Auth middleware is meant to restrict un-authenticated access to a given route
- * or a group of routes.
- *
- * You must register this middleware inside `start/kernel.ts` file under the list
- * of named middleware.
- */
-export default class AuthMiddleware {
-    /**
-     * The URL to redirect to when request is Unauthorized
-     */
-    protected redirectTo = '/app/login';
-
-    /**
-     * Authenticates the current HTTP request against a custom set of defined
-     * guards.
-     *
-     * The authentication loop stops as soon as the user is authenticated using any
-     * of the mentioned guards and that guard will be used by the rest of the code
-     * during the current request.
-     */
-    protected async authenticate(auth: HttpContextContract['auth'], guards: (keyof GuardsList)[]) {
-        /**
-         * Hold reference to the guard last attempted within the for loop. We pass
-         * the reference of the guard to the "AuthenticationException", so that
-         * it can decide the correct response behavior based upon the guard
-         * driver
-         */
-        let guardLastAttempted: string | undefined;
-
-        for (let guard of guards) {
-            guardLastAttempted = guard;
-
-            if (await auth.use(guard).check()) {
-                /**
-                 * Instruct auth to use the given guard as the default guard for
-                 * the rest of the request, since the user authenticated
-                 * succeeded here
-                 */
-                auth.defaultGuard = guard;
-                return true;
-            }
-        }
-
-        /**
-         * Unable to authenticate using any guard
-         */
-        throw new AuthenticationException('Unauthorized access', 'E_UNAUTHORIZED_ACCESS', guardLastAttempted, this.redirectTo);
-    }
-
-    /**
-     * Handle request
-     */
-    public async handle({ auth }: HttpContextContract, next: () => Promise<void>, customGuards: (keyof GuardsList)[]) {
-        /**
-         * Uses the user defined guards or the default guard mentioned in
-         * the config file
-         */
-        const guards = customGuards.length ? customGuards : [auth.name];
-        await this.authenticate(auth, guards);
-        await next();
-    }
-}

app/Models/File.ts

@@ -1,76 +0,0 @@
-import { DateTime } from 'luxon';
-import {
-    column,
-    hasMany,
-    HasMany,
-    belongsTo,
-    BelongsTo,
-    // manyToMany,
-    // ManyToMany,
-    SnakeCaseNamingStrategy,
-} from '@ioc:Adonis/Lucid/Orm';
-import HashValue from './HashValue';
-import Dataset from './Dataset';
-import BaseModel from './BaseModel';
-
-export default class File extends BaseModel {
-    public static namingStrategy = new SnakeCaseNamingStrategy();
-    public static primaryKey = 'id';
-    public static table = 'document_files';
-    public static selfAssignPrimaryKey = false;
-
-    @column({
-        isPrimary: true,
-    })
-    public id: number;
-
-    @column({})
-    public document_id: number;
-
-    @column({})
-    public pathName: string;
-
-    @column()
-    public label: string;
-
-    @column()
-    public comment: string;
-
-    @column()
-    public mimeType: string;
-
-    @column()
-    public language: string;
-
-    @column()
-    public fileSize: number;
-
-    @column()
-    public visibleInOai: boolean;
-
-    @column()
-    public visibleInFrontdoor: boolean;
-
-    @column()
-    public sortOrder: number;
-
-    @column.dateTime({ autoCreate: true })
-    public createdAt: DateTime;
-
-    @column.dateTime({ autoCreate: true, autoUpdate: true })
-    public updatedAt: DateTime;
-
-    // public function dataset()
-    // {
-    //     return $this->belongsTo(Dataset::class, 'document_id', 'id');
-    // }
-    @belongsTo(() => Dataset, {
-        foreignKey: 'document_id',
-    })
-    public dataset: BelongsTo<typeof Dataset>;
-
-    @hasMany(() => HashValue, {
-        foreignKey: 'file_id',
-    })
-    public hashvalues: HasMany<typeof HashValue>;
-}

app/Models/User.ts

@@ -1,110 +0,0 @@
-import { DateTime } from 'luxon';
-import { column, beforeSave, manyToMany, ManyToMany, hasMany, HasMany } from '@ioc:Adonis/Lucid/Orm';
-import Hash from '@ioc:Adonis/Core/Hash';
-import Role from './Role';
-import Database from '@ioc:Adonis/Lucid/Database';
-import Config from '@ioc:Adonis/Core/Config';
-import Dataset from './Dataset';
-import BaseModel from './BaseModel';
-
-// export default interface IUser {
-// 	id: number;
-// 	login: string;
-// 	email: string;
-// 	// password: string;
-// 	// createdAt: DateTime;
-// 	// updatedAt: DateTime;
-// 	// async (user): Promise<void>;
-// }
-
-const permissionTable = Config.get('rolePermission.permission_table', 'permissions');
-const rolePermissionTable = Config.get('rolePermission.role_permission_table', 'role_has_permissions');
-
-const roleTable = Config.get('rolePermission.role_table', 'roles');
-const userRoleTable = Config.get('rolePermission.user_role_table', 'link_accounts_roles');
-
-export default class User extends BaseModel {
-    public static table = 'accounts';
-
-    @column({ isPrimary: true })
-    public id: number;
-
-    @column()
-    public login: string;
-
-    @column()
-    public email: string;
-
-    @column({ serializeAs: null })
-    public password: string;
-
-    @column.dateTime({ autoCreate: true })
-    public createdAt: DateTime;
-
-    @column.dateTime({ autoCreate: true, autoUpdate: true })
-    public updatedAt: DateTime;
-
-    @beforeSave()
-    public static async hashPassword(user) {
-        if (user.$dirty.password) {
-            user.password = await Hash.make(user.password);
-        }
-    }
-
-    @manyToMany(() => Role, {
-        pivotForeignKey: 'account_id',
-        pivotRelatedForeignKey: 'role_id',
-        pivotTable: 'link_accounts_roles',
-    })
-    public roles: ManyToMany<typeof Role>;
-
-    @hasMany(() => Dataset, {
-        foreignKey: 'account_id',
-    })
-    public datasets: HasMany<typeof Dataset>;
-
-    // https://github.com/adonisjs/core/discussions/1872#discussioncomment-132289
-    public async getRoles(this: User): Promise<string[]> {
-        const test = await this.related('roles').query();
-        return test.map((role) => role.name);
-    }
-
-    public async can(permissionNames: Array<string>): Promise<boolean> {
-        // const permissions = await this.getPermissions()
-        // return Acl.check(expression, operand => _.includes(permissions, operand))
-        const hasPermission = await this.checkHasPermissions(this, permissionNames);
-        return hasPermission;
-    }
-
-    private async checkHasPermissions(user: User, permissionNames: Array<string>): Promise<boolean> {
-        let permissionPlaceHolder = '(';
-        let placeholders = new Array(permissionNames.length).fill('?');
-        permissionPlaceHolder += placeholders.join(',');
-        permissionPlaceHolder += ')';
-
-        let {
-            rows: {
-                0: { permissioncount },
-            },
-        } = await Database.rawQuery(
-            'SELECT count("p"."name") as permissionCount FROM ' +
-                roleTable +
-                ' r INNER JOIN ' +
-                userRoleTable +
-                ' ur ON ur.role_id=r.id AND "ur"."account_id"=? ' +
-                ' INNER JOIN ' +
-                rolePermissionTable +
-                ' rp ON rp.role_id=r.id ' +
-                ' INNER JOIN ' +
-                permissionTable +
-                ' p ON rp.permission_id=p.id AND "p"."name" in ' +
-                permissionPlaceHolder +
-                ' LIMIT 1',
-            [user.id, ...permissionNames],
-        );
-
-        return permissioncount > 0;
-    }
-}
-
-// export default User;

app/Models/utils.ts

@@ -1,19 +0,0 @@
-import Database, {
-    // DatabaseQueryBuilderContract,
-    QueryClientContract,
-    TransactionClientContract,
-} from '@ioc:Adonis/Lucid/Database';
-import Config from '@ioc:Adonis/Core/Config';
-
-export function getUserRoles(userId: number, trx?: TransactionClientContract): Promise<Array<string>> {
-    const { userRole } = Config.get('acl.joinTables');
-    return ((trx || Database) as QueryClientContract | TransactionClientContract)
-        .query()
-        .from('roles')
-        .distinct('roles.slug')
-        .leftJoin(userRole, `${userRole}.role_id`, 'roles.id')
-        .where(`${userRole}.user_id`, userId)
-        .then((res) => {
-            return res.map((r) => r.slug);
-        });
-}

app/Validators/AuthValidator.ts

@@ -1,46 +0,0 @@
-import { schema, CustomMessages, rules } from '@ioc:Adonis/Core/Validator';
-import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
-
-export default class AuthValidator {
-    constructor(protected ctx: HttpContextContract) {}
-
-    /*
-     * Define schema to validate the "shape", "type", "formatting" and "integrity" of data.
-     *
-     * For example:
-     * 1. The username must be of data type string. But then also, it should
-     *    not contain special characters or numbers.
-     *    ```
-     *     schema.string({}, [ rules.alpha() ])
-     *    ```
-     *
-     * 2. The email must be of data type string, formatted as a valid
-     *    email. But also, not used by any other user.
-     *    ```
-     *     schema.string({}, [
-     *       rules.email(),
-     *       rules.unique({ table: 'users', column: 'email' }),
-     *     ])
-     *    ```
-     */
-    public schema = schema.create({
-        email: schema.string({ trim: true }, [
-            rules.email(),
-            // rules.unique({ table: 'accounts', column: 'email' })
-        ]),
-        password: schema.string({}, [rules.minLength(6)]),
-    });
-
-    /**
-     * Custom messages for validation failures. You can make use of dot notation `(.)`
-     * for targeting nested fields and array expressions `(*)` for targeting all
-     * children of an array. For example:
-     *
-     * {
-     *   'profile.username.required': 'Username is required',
-     *   'scores.*.number': 'Define scores as valid numbers'
-     * }
-     *
-     */
-    public messages: CustomMessages = {};
-}

app/Validators/CreateDatasetValidator.ts

@@ -1,178 +0,0 @@
-import { schema, CustomMessages, rules } from '@ioc:Adonis/Core/Validator';
-import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
-import dayjs from 'dayjs';
-import { TitleTypes, DescriptionTypes, RelationTypes, ReferenceIdentifierTypes, ContributorTypes } from 'Contracts/enums';
-
-export default class CreateDatasetValidator {
-    constructor(protected ctx: HttpContextContract) {}
-
-    /*
-     * Define schema to validate the "shape", "type", "formatting" and "integrity" of data.
-     *
-     * For example:
-     * 1. The username must be of data type string. But then also, it should
-     *    not contain special characters or numbers.
-     *    ```
-     *     schema.string({}, [ rules.alpha() ])
-     *    ```
-     *
-     * 2. The email must be of data type string, formatted as a valid
-     *    email. But also, not used by any other user.
-     *    ```
-     *     schema.string({}, [
-     *       rules.email(),
-     *       rules.unique({ table: 'users', column: 'email' }),
-     *     ])
-     *    ```
-     */
-    public schema = schema.create({
-        // first step
-        language: schema.string({ trim: true }, [
-            rules.regex(/^[a-zA-Z0-9-_]+$/), //Must be alphanumeric with hyphens or underscores
-        ]),
-        licenses: schema.array([rules.minLength(1)]).members(schema.number()), // define at least one license for the new dataset
-        rights: schema.string([rules.equalTo('true')]),
-        // second step
-        type: schema.string({ trim: true }, [rules.minLength(3), rules.maxLength(255)]),
-        creating_corporation: schema.string({ trim: true }, [rules.minLength(3), rules.maxLength(255)]),
-        titles: schema.array([rules.minLength(1)]).members(
-            schema.object().members({
-                value: schema.string({ trim: true }, [rules.minLength(3), rules.maxLength(255)]),
-                type: schema.enum(Object.values(TitleTypes)),
-                language: schema.string({ trim: true }, [
-                    rules.minLength(2),
-                    rules.maxLength(255),
-                    rules.translatedLanguage('/language', 'type'),
-                ]),
-            }),
-        ),
-        descriptions: schema.array([rules.minLength(1)]).members(
-            schema.object().members({
-                value: schema.string({ trim: true }, [rules.minLength(3), rules.maxLength(255)]),
-                type: schema.enum(Object.values(DescriptionTypes)),
-                language: schema.string({ trim: true }, [
-                    rules.minLength(2),
-                    rules.maxLength(255),
-                    rules.translatedLanguage('/language', 'type'),
-                ]),
-            }),
-        ),
-        authors: schema.array([rules.minLength(1)]).members(schema.object().members({ email: schema.string({ trim: true }) })),
-        contributors: schema.array.optional().members(
-            schema.object().members({
-                email: schema.string({ trim: true }),
-                pivot_contributor_type: schema.enum(Object.keys(ContributorTypes)),
-            }),
-        ),
-        // third step
-        project_id: schema.number.optional(),
-        embargo_date: schema.date.optional({ format: 'yyyy-MM-dd' }, [rules.after(10, 'days')]),
-        coverage: schema.object().members({
-            x_min: schema.number(),
-            x_max: schema.number(),
-            y_min: schema.number(),
-            y_max: schema.number(),
-            elevation_absolut: schema.number.optional(),
-            elevation_min: schema.number.optional([rules.requiredIfExists('elevation_max')]),
-            elevation_max: schema.number.optional([rules.requiredIfExists('elevation_min')]),
-            depth_absolut: schema.number.optional(),
-            depth_min: schema.number.optional([rules.requiredIfExists('depth_max')]),
-            depth_max: schema.number.optional([rules.requiredIfExists('depth_min')]),
-        }),
-        references: schema.array.optional([rules.uniqueArray('value')]).members(
-            schema.object().members({
-                value: schema.string({ trim: true }, [rules.minLength(3), rules.maxLength(255)]),
-                type: schema.enum(Object.values(ReferenceIdentifierTypes)),
-                relation: schema.enum(Object.values(RelationTypes)),
-                label: schema.string({ trim: true }, [rules.minLength(2), rules.maxLength(255)]),
-            }),
-        ),
-        subjects: schema.array([rules.minLength(3), rules.uniqueArray('value')]).members(
-            schema.object().members({
-                value: schema.string({ trim: true }, [
-                    rules.minLength(3),
-                    rules.maxLength(255),
-                    // rules.unique({ table: 'dataset_subjects', column: 'value' }),
-                ]),
-                // type: schema.enum(Object.values(TitleTypes)),
-                language: schema.string({ trim: true }, [rules.minLength(2), rules.maxLength(255)]),
-            }),
-        ),
-        // file: schema.file({
-        //     size: '100mb',
-        //     extnames: ['jpg', 'gif', 'png'],
-        // }),
-        files: schema.array([rules.minLength(1)]).members(
-            schema.file({
-                size: '100mb',
-                extnames: ['jpg', 'gif', 'png', 'tif', 'pdf'],
-            }),
-        ),
-        // upload: schema.object().members({
-        //     label: schema.string({ trim: true }, [rules.maxLength(255)]),
-
-        //     // label: schema.string({ trim: true }, [
-        //     //     // rules.minLength(3),
-        //     //     // rules.maxLength(255),
-        //     // ]),
-        // }),
-    });
-
-    /**
-     * Custom messages for validation failures. You can make use of dot notation `(.)`
-     * for targeting nested fields and array expressions `(*)` for targeting all
-     * children of an array. For example:
-     *
-     * {
-     *   'profile.username.required': 'Username is required',
-     *   'scores.*.number': 'Define scores as valid numbers'
-     * }
-     *
-     */
-    public messages: CustomMessages = {
-        'minLength': '{{ field }} must be at least {{ options.minLength }} characters long',
-        'maxLength': '{{ field }} must be less then {{ options.maxLength }} characters long',
-        'required': '{{ field }} is required',
-        'unique': '{{ field }} must be unique, and this value is already taken',
-        // 'confirmed': '{{ field }} is not correct',
-        'licenses.minLength': 'at least {{ options.minLength }} permission must be defined',
-        'licenses.*.number': 'Define roles as valid numbers',
-        'rights.equalTo': 'you must agree to continue',
-
-        'titles.0.value.minLength': 'Main Title  must be at least {{ options.minLength }} characters long',
-        'titles.0.value.required': 'Main Title is required',
-        'titles.*.value.required': 'Additional title is required, if defined',
-        'titles.*.type.required': 'Additional title type is required',
-        'titles.*.language.required': 'Additional title language is required',
-        'titles.*.language.translatedLanguage': 'The language of the translated title must be different from the language of the dataset',
-
-        'descriptions.0.value.minLength': 'Main Abstract  must be at least {{ options.minLength }} characters long',
-        'descriptions.0.value.required': 'Main Abstract is required',
-        'descriptions.*.value.required': 'Additional description is required, if defined',
-        'descriptions.*.type.required': 'Additional description type is required',
-        'descriptions.*.language.required': 'Additional description language is required',
-        'descriptions.*.language.translatedLanguage':
-            'The language of the translated description must be different from the language of the dataset',
-
-        'authors.minLength': 'at least {{ options.minLength }} author must be defined',
-        'contributors.*.pivot_contributor_type.required': 'contributor type is required, if defined',
-
-        'after': `{{ field }} must be older than ${dayjs().add(10, 'day')}`,
-
-        'subjects.minLength': 'at least {{ options.minLength }} keywords must be defined',
-        'subjects.uniqueArray': 'The {{ options.array }} array must have unique values based on the {{ options.field }} attribute.',
-        'subjects.*.value.required': 'keyword value is required',
-        'subjects.*.value.minLength': 'keyword value  must be at least {{ options.minLength }} characters long',
-        'subjects.*.type.required': 'keyword type is required',
-        'subjects.*.language.required': 'language of keyword is required',
-
-        'references.*.value.required': 'Additional reference value is required, if defined',
-        'references.*.type.required': 'Additional reference identifier type is required',
-        'references.*.relation.required': 'Additional reference relation type is required',
-        'references.*.label.required': 'Additional reference label is required',
-
-        'files.minLength': 'At least {{ options.minLength }}  file upload is required.',
-        'files.*.size': 'file size is to big',
-        'files.extnames': 'file extension is not supported',
-    };
-}

app/Validators/CreateRoleValidator.ts

@@ -1,69 +0,0 @@
-import { schema, CustomMessages, rules } from '@ioc:Adonis/Core/Validator';
-import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
-
-export default class CreateRoleValidator {
-    constructor(protected ctx: HttpContextContract) {}
-
-    /*
-     * Define schema to validate the "shape", "type", "formatting" and "integrity" of data.
-     *
-     * For example:
-     * 1. The username must be of data type string. But then also, it should
-     *    not contain special characters or numbers.
-     *    ```
-     *     schema.string({}, [ rules.alpha() ])
-     *    ```
-     *
-     * 2. The email must be of data type string, formatted as a valid
-     *    email. But also, not used by any other user.
-     *    ```
-     *     schema.string({}, [
-     *       rules.email(),
-     *       rules.unique({ table: 'users', column: 'email' }),
-     *     ])
-     *    ```
-     */
-    public schema = schema.create({
-        name: schema.string({ trim: true }, [
-            rules.minLength(3),
-            rules.maxLength(255),
-            rules.unique({ table: 'roles', column: 'name' }),
-            rules.regex(/^[a-zA-Z0-9-_]+$/), //Must be alphanumeric with hyphens or underscores
-        ]),
-        display_name: schema.string.optional({ trim: true }, [
-            rules.minLength(3),
-            rules.maxLength(255),
-            rules.unique({ table: 'roles', column: 'name' }),
-            rules.regex(/^[a-zA-Z0-9-_]+$/), //Must be alphanumeric with hyphens or underscores
-        ]),
-        description: schema.string.optional({}, [rules.minLength(3), rules.maxLength(255)]),
-        permissions: schema.array([rules.minLength(1)]).members(schema.number()), // define at least one role for the new role
-    });
-
-    // emails: schema
-    //   .array([rules.minLength(1)])
-    //   .members(
-    //     schema.object().members({ email: schema.string({}, [rules.email()]) })
-    //   ),
-
-    /**
-     * Custom messages for validation failures. You can make use of dot notation `(.)`
-     * for targeting nested fields and array expressions `(*)` for targeting all
-     * children of an array. For example:
-     *
-     * {
-     *   'profile.username.required': 'Username is required',
-     *   'scores.*.number': 'Define scores as valid numbers'
-     * }
-     *
-     */
-    public messages: CustomMessages = {
-        'minLength': '{{ field }} must be at least {{ options.minLength }} characters long',
-        'maxLength': '{{ field }} must be less then {{ options.maxLength }} characters long',
-        'required': '{{ field }} is required',
-        'unique': '{{ field }} must be unique, and this value is already taken',
-        'confirmed': '{{ field }} is not correct',
-        'permissions.minLength': 'at least {{ options.minLength }} permission must be defined',
-        'permissions.*.number': 'Define roles as valid numbers',
-    };
-}

app/Validators/CreateUserValidator.ts

@@ -1,64 +0,0 @@
-import { schema, CustomMessages, rules } from '@ioc:Adonis/Core/Validator';
-import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
-
-export default class CreateUserValidator {
-    constructor(protected ctx: HttpContextContract) {}
-
-    /*
-     * Define schema to validate the "shape", "type", "formatting" and "integrity" of data.
-     *
-     * For example:
-     * 1. The username must be of data type string. But then also, it should
-     *    not contain special characters or numbers.
-     *    ```
-     *     schema.string({}, [ rules.alpha() ])
-     *    ```
-     *
-     * 2. The email must be of data type string, formatted as a valid
-     *    email. But also, not used by any other user.
-     *    ```
-     *     schema.string({}, [
-     *       rules.email(),
-     *       rules.unique({ table: 'users', column: 'email' }),
-     *     ])
-     *    ```
-     */
-    public schema = schema.create({
-        login: schema.string({ trim: true }, [
-            rules.minLength(3),
-            rules.maxLength(50),
-            rules.unique({ table: 'accounts', column: 'login' }),
-            rules.regex(/^[a-zA-Z0-9-_]+$/), //Must be alphanumeric with hyphens or underscores
-        ]),
-        email: schema.string({}, [rules.email(), rules.unique({ table: 'accounts', column: 'email' })]),
-        password: schema.string([rules.confirmed(), rules.minLength(6)]),
-        roles: schema.array([rules.minLength(1)]).members(schema.number()), // define at least one role for the new user
-    });
-
-    // emails: schema
-    //   .array([rules.minLength(1)])
-    //   .members(
-    //     schema.object().members({ email: schema.string({}, [rules.email()]) })
-    //   ),
-
-    /**
-     * Custom messages for validation failures. You can make use of dot notation `(.)`
-     * for targeting nested fields and array expressions `(*)` for targeting all
-     * children of an array. For example:
-     *
-     * {
-     *   'profile.username.required': 'Username is required',
-     *   'scores.*.number': 'Define scores as valid numbers'
-     * }
-     *
-     */
-    public messages: CustomMessages = {
-        'minLength': '{{ field }} must be at least {{ options.minLength }} characters long',
-        'maxLength': '{{ field }} must be less then {{ options.maxLength }} characters long',
-        'required': '{{ field }} is required',
-        'unique': '{{ field }} must be unique, and this value is already taken',
-        'confirmed': '{{ field }} is not correct',
-        'roles.minLength': 'at least {{ options.minLength }} role must be defined',
-        'roles.*.number': 'Define roles as valid numbers',
-    };
-}

app/Validators/UpdateRoleValidator.ts

@@ -1,97 +0,0 @@
-import { schema, CustomMessages, rules } from '@ioc:Adonis/Core/Validator';
-import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
-// import { Request } from '@adonisjs/core/build/standalone';
-
-export default class UpdateRoleValidator {
-    protected ctx: HttpContextContract;
-    public schema;
-
-    constructor(ctx: HttpContextContract) {
-        this.ctx = ctx;
-        this.schema = this.createSchema();
-    }
-
-    // public get schema() {
-    //     return this._schema;
-    // }
-
-    private createSchema() {
-        return schema.create({
-            name: schema.string({ trim: true }, [
-                rules.minLength(3),
-                rules.maxLength(50),
-                rules.unique({
-                    table: 'roles',
-                    column: 'name',
-                    whereNot: { id: this.ctx?.params.id },
-                }),
-                rules.regex(/^[a-zA-Z0-9-_]+$/),
-                //Must be alphanumeric with hyphens or underscores
-            ]),
-            description: schema.string.optional({}, [rules.minLength(3), rules.maxLength(255)]),
-            permissions: schema.array([rules.minLength(1)]).members(schema.number()), // define at least one permission for the new role
-        });
-    }
-
-    /*
-     * Define schema to validate the "shape", "type", "formatting" and "integrity" of data.
-     *
-     * For example:
-     * 1. The username must be of data type string. But then also, it should
-     *    not contain special characters or numbers.
-     *    ```
-     *     schema.string({}, [ rules.alpha() ])
-     *    ```
-     *
-     * 2. The email must be of data type string, formatted as a valid
-     *    email. But also, not used by any other user.
-     *    ```
-     *     schema.string({}, [
-     *       rules.email(),
-     *       rules.unique({ table: 'users', column: 'email' }),
-     *     ])
-     *    ```
-     */
-
-    // public refs = schema.refs({
-    // 	id: this.ctx.params.id
-    // })
-
-    // public schema = schema.create({
-    // 	login: schema.string({ trim: true }, [
-    // 		rules.minLength(3),
-    // 		rules.maxLength(50),
-    // 		rules.unique({
-    //     table: 'accounts',
-    //     column: 'login',
-    // 	// whereNot: { id: this.refs.id }
-    //     whereNot: { id: this.ctx?.params.id },
-    //   }),
-    // 		// rules.regex(/^[a-zA-Z0-9-_]+$/),
-    //   //Must be alphanumeric with hyphens or underscores
-    // 	]),
-    // 	email: schema.string({}, [rules.email(), rules.unique({ table: 'accounts', column: 'email' })]),
-    // 	password: schema.string.optional([rules.confirmed(), rules.minLength(6)]),
-    // 	roles: schema.array([rules.minLength(1)]).members(schema.number()), // define at least one role for the new user
-    // });
-
-    /**
-     * Custom messages for validation failures. You can make use of dot notation `(.)`
-     * for targeting nested fields and array expressions `(*)` for targeting all
-     * children of an array. For example:
-     *
-     * {
-     *   'profile.username.required': 'Username is required',
-     *   'scores.*.number': 'Define scores as valid numbers'
-     * }
-     *
-     */
-    public messages: CustomMessages = {
-        'minLength': '{{ field }} must be at least {{ options.minLength }} characters long',
-        'maxLength': '{{ field }} must be less then {{ options.maxLength }} characters long',
-        'required': '{{ field }} is required',
-        'unique': '{{ field }} must be unique, and this value is already taken',
-        'permissions.minLength': 'at least {{ options.minLength }} permission must be defined',
-        'permissions.*.number': 'Define permissions as valid numbers',
-    };
-}

app/Validators/UpdateUserValidator.ts

@@ -1,103 +0,0 @@
-import { schema, CustomMessages, rules } from '@ioc:Adonis/Core/Validator';
-import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
-// import { Request } from '@adonisjs/core/build/standalone';
-
-export default class UpdateUserValidator {
-    protected ctx: HttpContextContract;
-    public schema;
-
-    constructor(ctx: HttpContextContract) {
-        this.ctx = ctx;
-        this.schema = this.createSchema();
-    }
-
-    // public get schema() {
-    //     return this._schema;
-    // }
-
-    private createSchema() {
-        return schema.create({
-            login: schema.string({ trim: true }, [
-                rules.minLength(3),
-                rules.maxLength(50),
-                rules.unique({
-                    table: 'accounts',
-                    column: 'login',
-                    // whereNot: { id: this.refs.id }
-                    whereNot: { id: this.ctx?.params.id },
-                }),
-                // rules.regex(/^[a-zA-Z0-9-_]+$/),
-                //Must be alphanumeric with hyphens or underscores
-            ]),
-            email: schema.string({}, [
-                rules.email(),
-                rules.unique({ table: 'accounts', column: 'email', whereNot: { id: this.ctx?.params.id } }),
-            ]),
-            password: schema.string.optional([rules.confirmed(), rules.minLength(6)]),
-            roles: schema.array.optional([rules.minLength(1)]).members(schema.number()), // define at least one role for the new user
-        });
-    }
-
-    /*
-     * Define schema to validate the "shape", "type", "formatting" and "integrity" of data.
-     *
-     * For example:
-     * 1. The username must be of data type string. But then also, it should
-     *    not contain special characters or numbers.
-     *    ```
-     *     schema.string({}, [ rules.alpha() ])
-     *    ```
-     *
-     * 2. The email must be of data type string, formatted as a valid
-     *    email. But also, not used by any other user.
-     *    ```
-     *     schema.string({}, [
-     *       rules.email(),
-     *       rules.unique({ table: 'users', column: 'email' }),
-     *     ])
-     *    ```
-     */
-
-    // public refs = schema.refs({
-    // 	id: this.ctx.params.id
-    // })
-
-    // public schema = schema.create({
-    // 	login: schema.string({ trim: true }, [
-    // 		rules.minLength(3),
-    // 		rules.maxLength(50),
-    // 		rules.unique({
-    //     table: 'accounts',
-    //     column: 'login',
-    // 	// whereNot: { id: this.refs.id }
-    //     whereNot: { id: this.ctx?.params.id },
-    //   }),
-    // 		// rules.regex(/^[a-zA-Z0-9-_]+$/),
-    //   //Must be alphanumeric with hyphens or underscores
-    // 	]),
-    // 	email: schema.string({}, [rules.email(), rules.unique({ table: 'accounts', column: 'email' })]),
-    // 	password: schema.string.optional([rules.confirmed(), rules.minLength(6)]),
-    // 	roles: schema.array([rules.minLength(1)]).members(schema.number()), // define at least one role for the new user
-    // });
-
-    /**
-     * Custom messages for validation failures. You can make use of dot notation `(.)`
-     * for targeting nested fields and array expressions `(*)` for targeting all
-     * children of an array. For example:
-     *
-     * {
-     *   'profile.username.required': 'Username is required',
-     *   'scores.*.number': 'Define scores as valid numbers'
-     * }
-     *
-     */
-    public messages: CustomMessages = {
-        'minLength': '{{ field }} must be at least {{ options.minLength }} characters long',
-        'maxLength': '{{ field }} must be less then {{ options.maxLength }} characters long',
-        'required': '{{ field }} is required',
-        'unique': '{{ field }} must be unique, and this value is already taken',
-        'confirmed': '{{ field }} is not correct',
-        'roles.minLength': 'at least {{ options.minLength }} role must be defined',
-        'roles.*.number': 'Define roles as valid numbers',
-    };
-}

app/exceptions/DoiClientException.ts

@@ -0,0 +1,12 @@
+class DoiClientException extends Error {
+    public status: number;
+    public message: string;
+
+    constructor(status: number, message: string) {
+        super(message);
+        this.status = status;
+        this.message = message;
+    }
+}
+
+export default DoiClientException;

app/exceptions/InternalServerException.ts

@@ -1,5 +1,5 @@
 import { StatusCodes } from 'http-status-codes';
-import HTTPException from './HttpException';
+import HTTPException from './HttpException.js';
 
 class InternalServerErrorException extends HTTPException {
     constructor(message?: string) {

app/exceptions/InvalidCredentialException.ts

@@ -1,4 +1,5 @@
-import { Exception } from '@adonisjs/core/build/standalone';
+import { Exception } from "@adonisjs/core/exceptions";
+import { HttpContext } from "@adonisjs/core/http";
 
 /*
 |--------------------------------------------------------------------------
@@ -23,21 +24,21 @@ export default class InvalidCredentialException extends Exception {
      * Unable to find user
      */
     public static invalidUid() {
-        const error = new this('User not found', 400, 'E_INVALID_AUTH_UID');
+        const error = new this('User not found', {status: 400, code: 'E_INVALID_AUTH_UID'});
         return error;
     }
     /**
      * Invalid user password
      */
     public static invalidPassword() {
-        const error = new this('Password mis-match', 400, 'E_INVALID_AUTH_PASSWORD');
+        const error = new this('Password mis-match', {status: 400, code:  'E_INVALID_AUTH_PASSWORD'});
         return error;
     }
 
     /**
      * Flash error message and redirect the user back
      */
-    private respondWithRedirect(error, ctx) {
+    private respondWithRedirect(error: any, ctx: HttpContext) {
         // if (!ctx.session) {
         //     return ctx.response.status(this.status).send(this.responseText);
         // }
@@ -59,7 +60,7 @@ export default class InvalidCredentialException extends Exception {
      * Handle this exception by itself
      */
 
-    public handle(error, ctx) {
+    public handle(error: any, ctx: HttpContext) {
         //  return response.status(403).view.render("errors/unauthorized", {
         //    error: error,
         //  });

app/exceptions/OaiModelException.ts

@@ -1,6 +1,6 @@
 import { StatusCodes } from 'http-status-codes';
 // import HTTPException from './HttpException';
-import { OaiErrorCodes } from './OaiErrorCodes';
+import { OaiErrorCodes } from './OaiErrorCodes.js';
 
 export class ErrorCode {
     public static readonly Unauthenticated = 'Unauthenticated';

app/exceptions/handler.ts

@@ -0,0 +1,125 @@
+/*
+|--------------------------------------------------------------------------
+| Http Exception Handler
+|--------------------------------------------------------------------------
+|
+| AdonisJs will forward all exceptions occurred during an HTTP request to
+| the following class. You can learn more about exception handling by
+| reading docs.
+|
+| The exception handler extends a base `HttpExceptionHandler` which is not
+| mandatory, however it can do lot of heavy lifting to handle the errors
+| properly.
+|
+*/
+import app from '@adonisjs/core/services/app';
+import { HttpContext, ExceptionHandler } from '@adonisjs/core/http';
+// import logger from '@adonisjs/core/services/logger';
+import type { StatusPageRange, StatusPageRenderer } from '@adonisjs/core/types/http';
+
+export default class HttpExceptionHandler extends ExceptionHandler {
+    /**
+     * In debug mode, the exception handler will display verbose errors
+     * with pretty printed stack traces.
+     */
+    protected debug = !app.inProduction;
+
+    /**
+     * Status pages are used to display a custom HTML pages for certain error
+     * codes. You might want to enable them in production only, but feel
+     * free to enable them in development as well.
+     */
+    protected renderStatusPages = true; //app.inProduction;
+
+    /**
+     * Status pages is a collection of error code range and a callback
+     * to return the HTML contents to send as a response.
+     */
+    // protected statusPages: Record<StatusPageRange, StatusPageRenderer> = {
+    //     '401..403': (error, { view }) => {
+    //         return view.render('./errors/unauthorized', { error });
+    //     },
+    //     '404': (error, { view }) => {
+    //         return view.render('./errors/not-found', { error });
+    //     },
+    //     '500..599': (error, { view }) => {
+    //         return view.render('./errors/server-error', { error });
+    //     },
+    // };
+    protected statusPages: Record<StatusPageRange, StatusPageRenderer> = {
+        '404': (error, { inertia }) => {
+            return inertia.render('Errors/ServerError', {
+                error: error.message,
+                code: error.status,
+            });
+        },
+        '401..403': async (error, { inertia }) => {
+            // session.flash('errors', error.message);
+            return inertia.render('Errors/ServerError', {
+                error: error.message,
+                code: error.status,
+            });           
+        },
+        '500..599': (error, { inertia }) => inertia.render('Errors/ServerError', { error: error.message, code: error.status }),
+    };
+
+    // constructor() {
+    //     super(logger);
+    // }
+
+    public async handle(error: any, ctx: HttpContext) {
+        const { response, request, session } = ctx;
+
+        /**
+         * Handle failed authentication attempt
+         */
+        // if (['E_INVALID_AUTH_PASSWORD', 'E_INVALID_AUTH_UID'].includes(error.code)) {
+        //   session.flash('errors', { login: error.message });
+        //   return response.redirect('/login');
+        // }
+        // if ([401].includes(error.status)) {
+        //   session.flash('errors', { login: error.message });
+        //   return response.redirect('/dashboard');
+        // }
+
+        // https://github.com/inertiajs/inertia-laravel/issues/56
+        // let test = response.getStatus(); //200
+        // let header = request.header('X-Inertia'); // true
+        // if (request.header('X-Inertia') && [500, 503, 404, 403, 401, 200].includes(response.getStatus())) {
+        if (request.header('X-Inertia') && [422].includes(error.status)) {
+            // session.flash('errors', error.messages.errors);
+            session.flash('errors', error.messages);
+            return response.redirect().back();
+            // return inertia.render('errors/server_error', {
+            // return inertia.render('errors/server_error', {
+            //     // status: response.getStatus(),
+            //     error: error,
+            // });
+            // ->toResponse($request)
+            // ->setStatusCode($response->status());
+        }
+        // Dynamically change the error templates based on the absence of X-Inertia header
+        // if (!ctx.request.header('X-Inertia')) {
+        //     this.statusPages = {
+        //         '401..403': (error, { view }) => view.render('./errors/unauthorized', { error }),
+        //         '404': (error, { view }) => view.render('./errors/not-found', { error }),
+        //         '500..599': (error, { view }) => view.render('./errors/server-error', { error }),
+        //     };
+        // }
+
+        /**
+         * Forward rest of the exceptions to the parent class
+         */
+        return super.handle(error, ctx);
+    }
+
+    /**
+     * The method is used to report error to the logging service or
+     * the a third party error monitoring service.
+     *
+     * @note You should not attempt to send a response from this method.
+     */
+    async report(error: unknown, ctx: HttpContext) {
+        return super.report(error, ctx);
+    }
+}

app/middleware/Is.ts

@@ -1,11 +1,12 @@
-import { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
+import { HttpContext } from '@adonisjs/core/http';
-import Config from '@ioc:Adonis/Core/Config';
+// import Config from '@ioc:Adonis/Core/Config';
-import Database from '@ioc:Adonis/Lucid/Database';
+import config from '@adonisjs/core/services/config'
-import User from 'App/Models/User';
+import db from '@adonisjs/lucid/services/db';
+import User from '#models/user';
 // import { Exception } from '@adonisjs/core/build/standalone'
 
-const roleTable = Config.get('rolePermission.role_table', 'roles');
+const roleTable = config.get('rolePermission.role_table', 'roles');
-const userRoleTable = Config.get('rolePermission.user_role_table', 'user_roles');
+const userRoleTable = config.get('rolePermission.user_role_table', 'user_roles');
 
 /**
  * Role authentication to check if user has any of the specified roles
@@ -16,7 +17,7 @@ export default class Is {
     /**
      * Handle request
      */
-    public async handle({ auth, response }: HttpContextContract, next: () => Promise<void>, roleNames: string[]) {
+    public async handle({ auth, response }: HttpContext, next: () => Promise<void>, roleNames: string[]) {
         /**
          * Check if user is logged-in or not.
          */
@@ -33,7 +34,8 @@ export default class Is {
             // 401,
             // "E_INVALID_AUTH_UID");
         }
-        await next();
+        // await next();
+        return next()
     }
 
     private async checkHasRoles(user: User, roleNames: Array<string>): Promise<boolean> {
@@ -46,7 +48,7 @@ export default class Is {
             0: {
                 0: { roleCount },
             },
-        } = await Database.rawQuery(
+        } = await db.rawQuery(
             'SELECT count(`ur`.`id`) as roleCount FROM ' +
                 userRoleTable +
                 ' ur INNER JOIN ' +

app/middleware/auth_middleware.ts

@@ -0,0 +1,25 @@
+import type { HttpContext } from '@adonisjs/core/http'
+import type { NextFn } from '@adonisjs/core/types/http'
+import type { Authenticators } from '@adonisjs/auth/types'
+
+/**
+ * Auth middleware is used authenticate HTTP requests and deny
+ * access to unauthenticated users.
+ */
+export default class AuthMiddleware {
+  /**
+   * The URL to redirect to, when authentication fails
+   */
+  redirectTo = '/app/login'
+  
+  async handle(
+    ctx: HttpContext,
+    next: NextFn,
+    options: {
+      guards?: (keyof Authenticators)[]
+    } = {}
+  ) {
+    await ctx.auth.authenticateUsing(options.guards, { loginRoute: this.redirectTo })
+    return next()
+  }
+}

app/middleware/can_middleware.ts

@@ -1,13 +1,14 @@
-import { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
+import { HttpContext } from '@adonisjs/core/http';
-import Config from '@ioc:Adonis/Core/Config';
+// import Config from '@ioc:Adonis/Core/Config';
-import Database from '@ioc:Adonis/Lucid/Database';
+import config from '@adonisjs/core/services/config';
-import User from 'App/Models/User';
+import db from '@adonisjs/lucid/services/db';
-import { Exception } from '@adonisjs/core/build/standalone';
+import User from '#models/user';
+import { Exception } from '@adonisjs/core/exceptions';
 
-const permissionTable = Config.get('rolePermission.permission_table', 'permissions');
+const permissionTable = config.get('rolePermission.permission_table', 'permissions');
-const rolePermissionTable = Config.get('rolePermission.role_permission_table', 'role_has_permissions');
+const rolePermissionTable = config.get('rolePermission.role_permission_table', 'role_has_permissions');
-const roleTable = Config.get('rolePermission.role_table', 'roles');
+const roleTable = config.get('rolePermission.role_table', 'roles');
-const userRoleTable = Config.get('rolePermission.user_role_table', 'link_accounts_roles');
+const userRoleTable = config.get('rolePermission.user_role_table', 'link_accounts_roles');
 
 /**
  * Permission authentication to check if user has any of the specified permissions
@@ -18,7 +19,7 @@ export default class Can {
     /**
      * Handle request
      */
-    public async handle({ auth, response }: HttpContextContract, next: () => Promise<void>, permissionNames: string[]) {
+    public async handle({ auth, response }: HttpContext, next: () => Promise<void>, permissionNames: string[]) {
         /**
          * Check if user is logged-in
          */
@@ -31,9 +32,10 @@ export default class Can {
             // return response.unauthorized({
             // 	error: `Doesn't have required role(s): ${permissionNames.join(',')}`,
             // });
-            throw new Exception(`Doesn't have required permission(s): ${permissionNames.join(',')}`, 401);
+            throw new Exception(`Doesn't have required permission(s): ${permissionNames.join(',')}`, { status: 401 });
         }
-        await next();
+        // await next();
+        return next();
     }
 
     private async checkHasPermissions(user: User, permissionNames: Array<string>): Promise<boolean> {
@@ -66,7 +68,7 @@ export default class Can {
             rows: {
                 0: { permissioncount },
             },
-        } = await Database.rawQuery(
+        } = await db.rawQuery(
             'SELECT count("p"."name") as permissionCount FROM ' +
                 roleTable +
                 ' r INNER JOIN ' +

app/middleware/container_bindings_middleware.ts

@@ -0,0 +1,19 @@
+import { Logger } from '@adonisjs/core/logger';
+import { HttpContext } from '@adonisjs/core/http';
+import { NextFn } from '@adonisjs/core/types/http';
+
+/**
+ * The container bindings middleware binds classes to their request
+ * specific value using the container resolver.
+ *
+ * - We bind "HttpContext" class to the "ctx" object
+ * - And bind "Logger" class to the "ctx.logger" object
+ */
+export default class ContainerBindingsMiddleware {
+    handle(ctx: HttpContext, next: NextFn) {
+        ctx.containerResolver.bindValue(HttpContext, ctx);
+        ctx.containerResolver.bindValue(Logger, ctx.logger);
+
+        return next();
+    }
+}

app/middleware/guest_middleware.ts

@@ -0,0 +1,27 @@
+import type { HttpContext } from '@adonisjs/core/http';
+import type { NextFn } from '@adonisjs/core/types/http';
+import type { Authenticators } from '@adonisjs/auth/types';
+
+/**
+ * Guest middleware is used to deny access to routes that should
+ * be accessed by unauthenticated users.
+ *
+ * For example, the login page should not be accessible if the user
+ * is already logged-in
+ */
+export default class GuestMiddleware {
+    /**
+     * The URL to redirect to when user is logged-in
+     */
+    redirectTo = '/';
+
+    async handle(ctx: HttpContext, next: NextFn, options: { guards?: (keyof Authenticators)[] } = {}) {
+        for (let guard of options.guards || [ctx.auth.defaultGuard]) {
+            if (await ctx.auth.use(guard).check()) {
+                return ctx.response.redirect(this.redirectTo, true);
+            }
+        }
+
+        return next();
+    }
+}

app/middleware/normalize_newlines_middleware.ts

@@ -0,0 +1,43 @@
+/* 
+* This middleware class normalizes newlines in the request input data by replacing 
+* all occurrences of '\r\n' with '\n' recursively for strings, arrays, and objects.
+*/
+import type { HttpContext } from '@adonisjs/core/http';
+import type { NextFn } from '@adonisjs/core/types/http';
+
+export default class NormalizeNewlinesMiddleware {
+    async handle(ctx: HttpContext, next: NextFn) {
+        // Function to recursively normalize newlines
+        const normalizeNewlines = (input: any): any => {
+            if (typeof input === 'string') {
+                return input.replace(/\r\n/g, '\n');
+            } else if (Array.isArray(input)) {
+                return input.map((item) => normalizeNewlines(item));
+            } else if (typeof input === 'object' && input !== null) {
+                for (const key in input) {
+                    input[key] = normalizeNewlines(input[key]);
+                }
+                return input;
+            }
+            return input;
+        };
+        /**
+         * Middleware logic goes here (before the next call)
+         */
+        // console.log(ctx)
+        // Get all request input
+        const input = ctx.request.all();
+
+        // Normalize newlines in text inputs
+        const normalizedInput = normalizeNewlines(input);
+
+        // Replace request input with normalized data
+        ctx.request.updateBody(normalizedInput);
+
+        /**
+         * Call next method in the pipeline and return its output
+         */
+        const output = await next();
+        return output;
+    }
+}

app/middleware/role_middleware.ts

@@ -1,23 +1,25 @@
-import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
+import type { HttpContext } from '@adonisjs/core/http';
-import Database from '@ioc:Adonis/Lucid/Database';
+import db from '@adonisjs/lucid/services/db';
-import Config from '@ioc:Adonis/Core/Config';
+import config from '@adonisjs/core/services/config';
-import User from 'app/Models/User';
+import User from '#models/user';
-import { Exception } from '@adonisjs/core/build/standalone';
+import { Exception } from '@adonisjs/core/exceptions';
 
-const roleTable = Config.get('rolePermission.role_table', 'roles');
+// const roleTable = Config.get('rolePermission.role_table', 'roles');
-const userRoleTable = Config.get('rolePermission.user_role_table', 'link_accounts_roles');
+const roleTable = config.get('rolePermission.role_table', 'roles');
+// const userRoleTable = Config.get('rolePermission.user_role_table', 'link_accounts_roles');
+const userRoleTable = config.get('rolePermission.user_role_table', 'user_roles');
 
 // node ace make:middleware role
 export default class Role {
     // .middleware(['auth', 'role:admin,moderator'])
-    public async handle({ auth, response }: HttpContextContract, next: () => Promise<void>, userRoles: string[]) {
+    public async handle({ auth, response }: HttpContext, next: () => Promise<void>, userRoles: string[]) {
         // Check if user is logged-in or not.
         // let expression = "";
         // if (Array.isArray(args)) {
         // 	expression = args.join(" || ");
         // }
 
-        let user = await auth.user;
+        let user = auth.user as User;
         if (!user) {
             return response.unauthorized({ error: 'Must be logged in' });
         }
@@ -28,7 +30,7 @@ export default class Role {
             // 	error: `Doesn't have required role(s): ${userRoles.join(',')}`,
             // 	// error: `Doesn't have required role(s)`,
             // });
-            throw new Exception(`Doesn't have required role(s): ${userRoles.join(',')}`, 401);
+            throw new Exception(`Doesn't have required role(s): ${userRoles.join(',')}`, { status: 401 });
         }
 
         // code for middleware goes here. ABOVE THE NEXT CALL
@@ -62,7 +64,7 @@ export default class Role {
             rows: {
                 0: { rolecount },
             },
-        } = await Database.rawQuery(
+        } = await db.rawQuery(
             'SELECT count("r"."id") as roleCount FROM ' +
                 roleTable +
                 ' r INNER JOIN ' +

app/middleware/silent_auth.ts

@@ -1,4 +1,4 @@
-import type { HttpContextContract } from '@ioc:Adonis/Core/HttpContext';
+import type { HttpContext } from '@adonisjs/core/http';
 
 /**
  * Silent auth middleware can be used as a global middleware to silent check
@@ -10,7 +10,7 @@ export default class SilentAuthMiddleware {
     /**
      * Handle request
      */
-    public async handle({ auth }: HttpContextContract, next: () => Promise<void>) {
+    public async handle({ auth }: HttpContext, next: () => Promise<void>) {
         /**
          * Check if user is logged-in or not. If yes, then `ctx.auth.user` will be
          * set to the instance of the currently logged in user.

app/middleware/stardust_middleware.ts

@@ -0,0 +1,47 @@
+import type { HttpContext } from '@adonisjs/core/http';
+import type { NextFn } from '@adonisjs/core/types/http';
+
+
+declare global {
+    function myFunction(): boolean;
+    var myVariable: number;
+
+    interface StardustData {
+        pathname?: string;
+        namedRoutes?: Record<string, string>;
+    }
+    var stardust: StardustData;
+}
+
+declare global {}
+export default class StardustMiddleware {
+    async handle(ctx: HttpContext, next: NextFn): Promise<void> {
+        /**
+         * Middleware logic goes here (before the next call)
+         */
+
+        // Check if the request is an API request
+        if (!ctx.request.url().startsWith('/api')) {
+            // Middleware logic for non-API requests
+            const { pathname } = new URL(ctx.request.completeUrl()); // '/', '/app/login'
+            globalThis.myFunction = () => {
+                return true;
+            };
+            globalThis.myVariable = 1;
+
+            globalThis.stardust = {
+                ...globalThis.stardust,
+                pathname,
+            };
+
+            /**
+             * Call next method in the pipeline and return its output
+             */
+            await next();
+        } else {
+            // Skip middleware for API requests
+            await next();
+        }
+    }
+}
+

app/models/DocumentXmlCache.ts

@@ -1,10 +1,10 @@
-import { column, BaseModel, SnakeCaseNamingStrategy, belongsTo, BelongsTo } from '@ioc:Adonis/Lucid/Orm';
+import { column, BaseModel, SnakeCaseNamingStrategy, belongsTo } from '@adonisjs/lucid/orm';
-import Dataset from './Dataset';
+import Dataset from './dataset.js';
 import { builder, create } from 'xmlbuilder2';
-import { XMLBuilder } from 'xmlbuilder2/lib/interfaces';
+import { XMLBuilder } from 'xmlbuilder2/lib/interfaces.js';
-import Database from '@ioc:Adonis/Lucid/Database';
+import db from '@adonisjs/lucid/services/db';
-import dayjs from 'dayjs';
 import { DateTime } from 'luxon';
+import type { BelongsTo } from "@adonisjs/lucid/types/relations";
 
 export default class DocumentXmlCache extends BaseModel {
     public static namingStrategy = new SnakeCaseNamingStrategy();
@@ -87,7 +87,7 @@ export default class DocumentXmlCache extends BaseModel {
     // 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 = Database.from(this.table)
+        const query = db.from(this.table)
             .where('document_id', datasetId)
             .where('server_date_modified', '>=', serverDateModifiedString) // Check if server_date_modified is newer or equal
             .first();

app/models/appconfig.ts

@@ -0,0 +1,33 @@
+import BaseModel from './base_model.js';
+import { column } from '@adonisjs/lucid/orm';
+
+export default class AppConfig extends BaseModel {
+    public static table = 'appconfigs'; // Specify the table name if it differs from the model name
+
+    @column({ isPrimary: true })
+    public id: number;
+
+    @column()
+    public appid: string;
+
+    @column()
+    public configkey: string;
+
+    @column()
+    public configvalue: string | null;
+
+    @column()
+    public type: number;
+
+    @column()
+    public lazy: number;
+
+    // async function setConfig(key: string, value: string) {
+    //     await this.updateOrCreate({ key }, { value })
+    //   }
+
+    // async function getConfig(key: string) {
+    //     const config = await this.findBy('key', key)
+    //     return config ? config.value : null
+    //   }
+}

app/models/backup_code.ts

@@ -0,0 +1,51 @@
+import BaseModel from './base_model.js';
+import { column, SnakeCaseNamingStrategy, belongsTo } from '@adonisjs/lucid/orm';
+import User from './user.js';
+import type { BelongsTo } from '@adonisjs/lucid/types/relations';
+import db from '@adonisjs/lucid/services/db';
+import hash from '@adonisjs/core/services/hash';
+
+export default class BackupCode extends BaseModel {
+    public static table = 'backupcodes';
+    public static namingStrategy = new SnakeCaseNamingStrategy();
+
+    @column({
+        isPrimary: true,
+    })
+    public id: number;
+
+    @column({})
+    public user_id: number;
+
+    @column({
+        // serializeAs: null,
+        // consume: (value: string) => (value ? JSON.parse(encryption.decrypt(value) ?? '{}') : null),
+        // prepare: (value: string) => encryption.encrypt(JSON.stringify(value)),
+    })
+    public code: string;
+
+    @column({})
+    public used: boolean;
+
+    @belongsTo(() => User, {
+        foreignKey: 'user_id',
+    })
+    public user: BelongsTo<typeof User>;
+
+    // public static async getBackupCodes(user: User): Promise<BackupCode[]> {
+    //     return await db.from(this.table).select('id', 'user_id', 'code', 'used').where('user_id', user.id);
+    // }
+
+    public static async deleteCodes(user: User): Promise<void> {
+        await db.from(this.table).where('user_id', user.id).delete();
+    }
+
+    public static async deleteCodesByUserId(uid: string): Promise<void> {
+        await db.from(this.table).where('user_id', uid).delete();
+    }
+
+    // Method to verify password
+    public async verifyCode(plainCode: string) {
+        return await hash.verify(this.code, plainCode);
+    }
+}

app/models/base_model.ts

@@ -1,4 +1,4 @@
-import { BaseModel as LucidBaseModel } from '@ioc:Adonis/Lucid/Orm';
+import { BaseModel as LucidBaseModel } from '@adonisjs/lucid/orm';
 // import { ManyToManyQueryClient } from '@ioc:Adonis/Lucid/Orm';
 
 // export class CustomManyToManyQueryClient extends ManyToManyQueryClient {
@@ -13,7 +13,6 @@ import { BaseModel as LucidBaseModel } from '@ioc:Adonis/Lucid/Orm';
 //   }
 // }
 
-
 /**
  * Helper to find if value is a valid Object or
  * not
@@ -30,6 +29,8 @@ export default class BaseModel extends LucidBaseModel {
      */
     // private fillInvoked: boolean = false;
 
+    [key: string]: any;
+    
     public static fillable: string[] = [];
 
     public fill(attributes: any, allowExtraProperties: boolean = false): this {
@@ -117,9 +118,10 @@ export default class BaseModel extends LucidBaseModel {
 
         return this;
     }
-
 }
 
+
+
 // export class DatasetRelatedBaseModel extends LucidBaseModel {
 //     public dataset: BelongsTo<typeof Dataset>;
 // }

app/models/collection.ts

@@ -1,6 +1,9 @@
-import { column, SnakeCaseNamingStrategy, manyToMany, ManyToMany } from '@ioc:Adonis/Lucid/Orm';
+import { column, SnakeCaseNamingStrategy, manyToMany, belongsTo } from '@adonisjs/lucid/orm';
-import Dataset from './Dataset';
+import Dataset from './dataset.js';
-import BaseModel from './BaseModel';
+import BaseModel from './base_model.js';
+import CollectionRole from './collection_role.js';
+import type { ManyToMany } from "@adonisjs/lucid/types/relations";
+import type { BelongsTo } from "@adonisjs/lucid/types/relations";
 
 export default class Collection extends BaseModel {
     public static namingStrategy = new SnakeCaseNamingStrategy();
@@ -43,4 +46,9 @@ export default class Collection extends BaseModel {
         pivotTable: 'link_documents_collections',
     })
     public datasets: ManyToMany<typeof Dataset>;
+
+    @belongsTo(() => CollectionRole, {
+        foreignKey: 'role_id',
+    })
+    public collectionRole: BelongsTo<typeof CollectionRole>;
 }

app/models/collection_role.ts

@@ -0,0 +1,39 @@
+import { column, SnakeCaseNamingStrategy, hasMany } from '@adonisjs/lucid/orm';
+import BaseModel from './base_model.js';
+import Collection from './collection.js';
+import type { HasMany } from "@adonisjs/lucid/types/relations";
+
+export default class CollectionRole extends BaseModel {
+    public static namingStrategy = new SnakeCaseNamingStrategy();
+    public static primaryKey = 'id';
+    public static table = 'collections_roles';
+    public static fillable: string[] = ['name', 'oai_name', 'visible'];
+
+    @column({
+        isPrimary: true,
+    })
+    public id: number;
+
+    @column({})
+    public name: string;
+
+    @column({})
+    public oai_name?: string;
+
+    @column({})
+    public position: number;
+
+    @column({})
+    public visible: boolean;
+
+    @column({})
+    public visible_frontdoor: boolean;
+
+    @column({})
+    public visible_oai: boolean;
+
+    @hasMany(() => Collection, {
+        foreignKey: 'role_id',
+    })
+    public collections: HasMany<typeof Collection>;
+}

app/models/coverage.ts

@@ -1,7 +1,8 @@
-import { column, SnakeCaseNamingStrategy, belongsTo, BelongsTo } from '@ioc:Adonis/Lucid/Orm';
+import { column, SnakeCaseNamingStrategy, belongsTo } from '@adonisjs/lucid/orm';
 import { DateTime } from 'luxon';
-import Dataset from './Dataset';
+import Dataset from './dataset.js';
-import BaseModel from './BaseModel';
+import BaseModel from './base_model.js';
+import type { BelongsTo } from "@adonisjs/lucid/types/relations";
 
 export default class Coverage extends BaseModel {
     public static namingStrategy = new SnakeCaseNamingStrategy();

app/models/dataset.ts

@@ -2,31 +2,31 @@ import {
     column,
     SnakeCaseNamingStrategy,
     manyToMany,
-    ManyToMany,
     belongsTo,
-    BelongsTo,
     hasMany,
-    HasMany,
     computed,
-    hasOne,
+    hasOne
-    HasOne,
+} from '@adonisjs/lucid/orm';
-} from '@ioc:Adonis/Lucid/Orm';
 import { DateTime } from 'luxon';
 import dayjs from 'dayjs';
-import Person from './Person';
+import Person from './person.js';
-import User from './User';
+import User from './user.js';
-import Title from './Title';
+import Title from './title.js';
-import Description from './Description';
+import Description from './description.js';
-import License from './License';
+import License from './license.js';
-import Subject from './Subject';
+import Subject from './subject.js';
-import File from './File';
+import File from './file.js';
-import Coverage from './Coverage';
+import Coverage from './coverage.js';
-import DatasetReference from './DatasetReference';
+import DatasetReference from './dataset_reference.js';
-import Collection from './Collection';
+import Collection from './collection.js';
-import DatasetIdentifier from './DatasetIdentifier';
+import DatasetIdentifier from './dataset_identifier.js';
-import Project from './Project';
+import Project from './project.js';
-import DocumentXmlCache from './DocumentXmlCache';
+import DocumentXmlCache from './DocumentXmlCache.js';
-import DatasetExtension from 'App/Models/Traits/DatasetExtension'; // Adjust the import path
+import DatasetExtension from '#models/traits/dataset_extension';
+import type { ManyToMany } from "@adonisjs/lucid/types/relations";
+import type { BelongsTo } from "@adonisjs/lucid/types/relations";
+import type { HasMany } from "@adonisjs/lucid/types/relations";
+import type { HasOne } from "@adonisjs/lucid/types/relations";
 
 export default class Dataset extends DatasetExtension {
     public static namingStrategy = new SnakeCaseNamingStrategy();
@@ -46,7 +46,12 @@ export default class Dataset extends DatasetExtension {
     @column({ columnName: 'creating_corporation' })
     public creating_corporation: string;
 
-    @column.dateTime({ columnName: 'embargo_date' })
+    @column.dateTime({ 
+        columnName: 'embargo_date',
+        serialize: (value: Date | null) => {
+            return value ? dayjs(value).format('YYYY-MM-DD') : value;
+        },
+    })
     public embargo_date: DateTime;
 
     @column({})
@@ -55,7 +60,7 @@ export default class Dataset extends DatasetExtension {
     @column({})
     public language: string;
 
-    @column({})
+    @column({columnName: 'publish_id'})
     public publish_id: number | null = null;
 
     @column({})
@@ -95,7 +100,14 @@ export default class Dataset extends DatasetExtension {
     })
     public created_at: DateTime;
 
-    @column.dateTime({ autoCreate: true, autoUpdate: true, columnName: 'server_date_modified' })
+    @column.dateTime({
+        serialize: (value: Date | null) => {
+            return value ? dayjs(value).format('MMMM D YYYY HH:mm a') : value;
+        },
+        autoCreate: true,
+        autoUpdate: true,
+        columnName: 'server_date_modified',
+    })
     public server_date_modified: DateTime;
 
     @manyToMany(() => Person, {
@@ -188,6 +200,15 @@ export default class Dataset extends DatasetExtension {
         return mainTitle ? mainTitle.value : null;
     }
 
+    @computed({
+        serializeAs: 'main_abstract',
+    })
+    public get mainAbstract() {
+        // return `${this.firstName} ${this.lastName}`;
+        const mainTitle = this.descriptions?.find((desc) => desc.type === 'Abstract');
+        return mainTitle ? mainTitle.value : null;
+    }
+
     @manyToMany(() => Person, {
         pivotForeignKey: 'document_id',
         pivotRelatedForeignKey: 'person_id',
@@ -203,7 +224,7 @@ export default class Dataset extends DatasetExtension {
         pivotForeignKey: 'document_id',
         pivotRelatedForeignKey: 'person_id',
         pivotTable: 'link_documents_persons',
-        pivotColumns: ['role', 'sort_order', 'allow_email_contact'],
+        pivotColumns: ['role', 'sort_order', 'allow_email_contact', 'contributor_type'],
         onQuery(query) {
             query.wherePivot('role', 'contributor');
         },
@@ -214,4 +235,44 @@ export default class Dataset extends DatasetExtension {
         foreignKey: 'document_id',
     })
     public xmlCache: HasOne<typeof DocumentXmlCache>;
+
+    /**
+     * Get the account that the dataset belongs to
+     */
+    @belongsTo(() => User, {
+        foreignKey: 'editor_id',
+    })
+    public editor: BelongsTo<typeof User>;
+
+    @belongsTo(() => User, {
+        foreignKey: 'reviewer_id',
+    })
+    public reviewer: BelongsTo<typeof User>;
+
+    static async earliestPublicationDate(): Promise<Dataset | null> {
+        const serverState = 'published';
+
+        const model = await this.query().where('server_state', serverState).orderBy('server_date_published', 'asc').first();
+
+        return model || null;
+    }
+
+    static async getMax (column: string) {
+        let dataset = await this.query().max(column + ' as max_publish_id').firstOrFail();
+        return dataset.$extras.max_publish_id;
+      }
+
+    @computed({
+        serializeAs: 'remaining_time',
+    })
+    public get remainingTime() {
+        const dateFuture = this.server_date_modified.plus({ days: 14 });
+        if (this.server_state === 'approved') {
+            const now = DateTime.now();
+            let duration = dateFuture.diff(now, ['days', 'hours', 'months']).toObject();
+            return duration.days;
+        } else {
+            return 0;
+        }
+    }
 }

app/models/dataset_identifier.ts

@@ -1,7 +1,8 @@
-import { column, SnakeCaseNamingStrategy, belongsTo, BelongsTo } from '@ioc:Adonis/Lucid/Orm';
+import { column, SnakeCaseNamingStrategy, belongsTo } from '@adonisjs/lucid/orm';
 import { DateTime } from 'luxon';
-import Dataset from './Dataset';
+import Dataset from './dataset.js';
-import BaseModel from './BaseModel';
+import BaseModel from './base_model.js';
+import type { BelongsTo } from "@adonisjs/lucid/types/relations";
 
 export default class DatasetIdentifier extends BaseModel {
     public static namingStrategy = new SnakeCaseNamingStrategy();
@@ -20,6 +21,9 @@ export default class DatasetIdentifier extends BaseModel {
     @column({})
     public type: string;
 
+    @column({})
+    public status: string;
+
     @column({})
     public value: string;
 
@@ -38,4 +42,9 @@ export default class DatasetIdentifier extends BaseModel {
         foreignKey: 'dataset_id',
     })
     public dataset: BelongsTo<typeof Dataset>;
+
+    // // Specify the relationships to touch when this model is updated
+    // public static get touches() {
+    //     return ['dataset'];
+    // }
 }

app/models/dataset_reference.ts

@@ -1,7 +1,8 @@
-import { column, SnakeCaseNamingStrategy, belongsTo, BelongsTo } from '@ioc:Adonis/Lucid/Orm';
+import { column, SnakeCaseNamingStrategy, belongsTo } from '@adonisjs/lucid/orm';
 import { DateTime } from 'luxon';
-import Dataset from './Dataset';
+import Dataset from './dataset.js';
-import BaseModel from './BaseModel';
+import BaseModel from './base_model.js';
+import type { BelongsTo } from "@adonisjs/lucid/types/relations";
 
 export default class DatasetReference extends BaseModel {
     public static namingStrategy = new SnakeCaseNamingStrategy();

app/models/description.ts

@@ -1,6 +1,7 @@
-import { column, belongsTo, BelongsTo } from '@ioc:Adonis/Lucid/Orm';
+import { column, belongsTo } from '@adonisjs/lucid/orm';
-import Dataset from './Dataset';
+import Dataset from './dataset.js';
-import BaseModel from './BaseModel';
+import BaseModel from './base_model.js';
+import type { BelongsTo } from "@adonisjs/lucid/types/relations";
 
 export default class Description extends BaseModel {
     public static primaryKey = 'id';
@@ -9,6 +10,11 @@ export default class Description extends BaseModel {
     public static timestamps = false;
     public static fillable: string[] = ['value', 'type', 'language'];
 
+    @column({
+        isPrimary: true,
+    })
+    public id: number;
+    
     @column({})
     public document_id: number;
 

app/models/file.ts

@@ -0,0 +1,184 @@
+import { DateTime } from 'luxon';
+import { column, hasMany, belongsTo, SnakeCaseNamingStrategy, computed } from '@adonisjs/lucid/orm';
+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 type { HasMany } from "@adonisjs/lucid/types/relations";
+import type { BelongsTo } from "@adonisjs/lucid/types/relations";
+// import { TransactionClientContract } from "@adonisjs/lucid/database";
+import { TransactionClientContract } from '@adonisjs/lucid/types/database';
+
+
+
+
+
+export default class File extends BaseModel {
+    // private readonly _data: Uint8Array;
+    // private readonly _type: string;
+    // private readonly _size: number;
+
+    public static namingStrategy = new SnakeCaseNamingStrategy();
+    public static primaryKey = 'id';
+    public static table = 'document_files';
+    public static selfAssignPrimaryKey = false;
+
+    @column({
+        isPrimary: true,
+    })
+    public id: number;
+
+    @column({})
+    public document_id: number;
+
+    @column({})
+    public pathName: string;
+
+    @column()
+    public label: string;
+
+    @column()
+    public comment: string;
+
+    @column()
+    public mimeType: string;
+
+    @column()
+    public language: string;
+
+    @column()
+    public fileSize: number;
+
+    @column()
+    public visibleInOai: boolean;
+
+    @column()
+    public visibleInFrontdoor: boolean;
+
+    @column()
+    public sortOrder: number;
+
+    @column.dateTime({ autoCreate: true })
+    public createdAt: DateTime;
+
+    @column.dateTime({ autoCreate: true, autoUpdate: true })
+    public updatedAt: DateTime;
+
+    // public function dataset()
+    // {
+    //     return $this->belongsTo(Dataset::class, 'document_id', 'id');
+    // }
+    @belongsTo(() => Dataset, {
+        foreignKey: 'document_id',
+    })
+    public dataset: BelongsTo<typeof Dataset>;
+
+    @hasMany(() => HashValue, {
+        foreignKey: 'file_id',
+    })
+    public hashvalues: HasMany<typeof HashValue>;
+
+    @computed({
+        serializeAs: 'filePath',
+    })
+    public get filePath() {
+        return `/storage/app/public/${this.pathName}`;
+        // const mainTitle = this.titles?.find((title) => title.type === 'Main');
+        // return mainTitle ? mainTitle.value : null;
+    }
+
+    @computed({
+        serializeAs: 'size',
+    })
+    public get size() {
+        return this.fileSize;
+    }
+
+    @computed({
+        serializeAs: 'type',
+    })
+    public get type() {
+        return this.mimeType;
+    }
+
+    @computed({
+        serializeAs: 'name',
+    })
+    get name(): string {
+        return this.label;
+    }
+
+    @computed({
+        serializeAs: 'lastModified',
+    })
+    get lastModified(): number {
+        return this.updatedAt.toUnixInteger(); //.toFormat("yyyy-MM-dd'T'HH:mm:ss'Z'");
+    }
+
+    readonly webkitRelativePath: string = '';
+
+    // @computed({
+    //     serializeAs: 'fileData',
+    // })
+    // public get fileData(): string {
+    //     try {
+    //         const fileContent: Buffer = fs.readFileSync(this.filePath);
+    //         // Create a Blob from the file content
+    //         // const blob = new Blob([fileContent], { type: this.type }); // Adjust
+    //         // let fileSrc = URL.createObjectURL(blob);
+    //         // return fileSrc;
+
+    //         // create a JSON string that contains the data in the property "blob"
+    //         const json = JSON.stringify({ blob: fileContent.toString('base64') });
+    //         return json;
+    //     } catch (err) {
+    //         // console.error(`Error reading file: ${err}`);
+    //         return '';
+    //     }
+    // }
+
+    public async createHashValues(trx?: TransactionClientContract) {
+        const hashtypes: string[] = ['md5', 'sha512'];
+
+        for (const type of hashtypes) {
+            const hash = new HashValue();
+            hash.type = type;
+            const hashString = await this._checksumFile(this.filePath, type); // Assuming getRealHash is a method in the same model
+            hash.value = hashString;
+
+            // https://github.com/adonisjs/core/discussions/1872#discussioncomment-132289
+            const file: File = this;
+            if (trx) {
+                await file.useTransaction(trx).related('hashvalues').save(hash); // Save the hash value to the database
+            } else {
+                await file.related('hashvalues').save(hash); // Save the hash value to the database
+            }
+        }
+    }
+
+    public async delete() {
+        if (this.pathName) {
+            // Delete file from additional storage
+            await drive.delete(this.pathName);
+        }
+
+        // Call the original delete method of the BaseModel to remove the record from the database
+        await super.delete();
+    }
+
+    private async _checksumFile(path: string, hashName = 'md5'): Promise<string> {
+        return new Promise((resolve, reject) => {
+            const hash = crypto.createHash(hashName);
+            const stream = fs.createReadStream(path);
+            stream.on('error', (err) => reject(err));
+            stream.on('data', (chunk) => hash.update(chunk));
+            stream.on('end', () => resolve(hash.digest('hex')));
+        });
+    }
+}

app/models/hash_value.ts

@@ -1,9 +1,10 @@
-import { column, BaseModel, belongsTo, BelongsTo, SnakeCaseNamingStrategy } from '@ioc:Adonis/Lucid/Orm';
+import { column, BaseModel, belongsTo, SnakeCaseNamingStrategy } from '@adonisjs/lucid/orm';
-import File from './File';
+import File from './file.js';
+import type { BelongsTo } from "@adonisjs/lucid/types/relations";
 
 export default class HashValue extends BaseModel {
     public static namingStrategy = new SnakeCaseNamingStrategy();
-    public static primaryKey = 'file_id, type';
+    // public static primaryKey = 'file_id,type';
     public static table = 'file_hashvalues';
 
     // static get primaryKey () {
@@ -20,10 +21,10 @@ export default class HashValue extends BaseModel {
     // public id: number;
 
     // Foreign key is still on the same model
-    @column({})
+    @column({ isPrimary: true })
     public file_id: number;
 
-    @column({})
+    @column({ isPrimary: true })
     public type: string;
 
     @column()

app/models/language.ts

@@ -1,5 +1,5 @@
-import { column, SnakeCaseNamingStrategy } from '@ioc:Adonis/Lucid/Orm';
+import { column, SnakeCaseNamingStrategy } from '@adonisjs/lucid/orm';
-import BaseModel from './BaseModel';
+import BaseModel from './base_model.js';
 // import { DateTime } from 'luxon';
 
 export default class Language extends BaseModel {

app/models/license.ts

@@ -1,5 +1,5 @@
-import { column, SnakeCaseNamingStrategy } from '@ioc:Adonis/Lucid/Orm';
+import { column, SnakeCaseNamingStrategy } from '@adonisjs/lucid/orm';
-import BaseModel from './BaseModel';
+import BaseModel from './base_model.js';
 
 export default class License extends BaseModel {
     public static namingStrategy = new SnakeCaseNamingStrategy();

app/models/mime_type.ts

@@ -0,0 +1,40 @@
+import { column, SnakeCaseNamingStrategy } from '@adonisjs/lucid/orm';
+import BaseModel from './base_model.js';
+import { DateTime } from 'luxon';
+
+export default class MimeType extends BaseModel {
+    public static namingStrategy = new SnakeCaseNamingStrategy();
+    public static primaryKey = 'id';
+    public static table = 'mime_types';
+    public static fillable: string[] = ['name', 'file_extension', 'enabled'];
+
+    @column({
+        isPrimary: true,
+    })
+    public id: number;
+
+    @column({})
+    public name: string;
+
+    @column({})
+    public file_extension: string;
+
+    @column({})
+    public enabled: boolean;
+
+    @column.dateTime({
+        autoCreate: true,
+    })
+    public created_at: DateTime;
+
+    @column.dateTime({
+        autoCreate: true,
+        autoUpdate: true,
+    })
+    public updated_at: DateTime;
+
+    // @hasMany(() => Collection, {
+    //     foreignKey: 'role_id',
+    // })
+    // public collections: HasMany<typeof Collection>;
+}

app/models/permission.ts

@@ -1,8 +1,9 @@
-import { column, manyToMany, ManyToMany, SnakeCaseNamingStrategy, beforeUpdate, beforeCreate } from '@ioc:Adonis/Lucid/Orm';
+import { column, manyToMany, SnakeCaseNamingStrategy } from '@adonisjs/lucid/orm';
 import { DateTime } from 'luxon';
 import dayjs from 'dayjs';
-import Role from 'App/Models/Role';
+import Role from '#models/role';
-import BaseModel from './BaseModel';
+import BaseModel from './base_model.js';
+import type { ManyToMany } from "@adonisjs/lucid/types/relations";
 
 export default class Permission extends BaseModel {
     public static namingStrategy = new SnakeCaseNamingStrategy();
@@ -44,12 +45,12 @@ export default class Permission extends BaseModel {
     })
     public updated_at: DateTime;
 
-    @beforeCreate()
+    // @beforeCreate()
-    @beforeUpdate()
+    // @beforeUpdate()
-    public static async resetDate(role) {
+    // public static async resetDate(role) {
-        role.created_at = this.formatDateTime(role.created_at);
+    //     role.created_at = this.formatDateTime(role.created_at);
-        role.updated_at = this.formatDateTime(role.updated_at);
+    //     role.updated_at = this.formatDateTime(role.updated_at);
-    }
+    // }
 
     // public static boot() {
     //   super.boot()
@@ -64,22 +65,22 @@ export default class Permission extends BaseModel {
     //   })
     // }
 
-    private static formatDateTime(datetime) {
+    // private static formatDateTime(datetime) {
-        let value = new Date(datetime);
+    //     let value = new Date(datetime);
-        return datetime
+    //     return datetime
-            ? value.getFullYear() +
+    //         ? value.getFullYear() +
-                  '-' +
+    //               '-' +
-                  (value.getMonth() + 1) +
+    //               (value.getMonth() + 1) +
-                  '-' +
+    //               '-' +
-                  value.getDate() +
+    //               value.getDate() +
-                  ' ' +
+    //               ' ' +
-                  value.getHours() +
+    //               value.getHours() +
-                  ':' +
+    //               ':' +
-                  value.getMinutes() +
+    //               value.getMinutes() +
-                  ':' +
+    //               ':' +
-                  value.getSeconds()
+    //               value.getSeconds()
-            : datetime;
+    //         : datetime;
-    }
+    // }
 
     // @belongsTo(() => Role)
     // public role: BelongsTo<typeof Role>;

app/models/person.ts

@@ -1,8 +1,9 @@
-import { column, SnakeCaseNamingStrategy, computed, manyToMany, ManyToMany } from '@ioc:Adonis/Lucid/Orm';
+import { column, SnakeCaseNamingStrategy, computed, manyToMany } from '@adonisjs/lucid/orm';
 import { DateTime } from 'luxon';
 import dayjs from 'dayjs';
-import Dataset from './Dataset';
+import Dataset from './dataset.js';
-import BaseModel from './BaseModel';
+import BaseModel from './base_model.js';
+import type { ManyToMany } from "@adonisjs/lucid/types/relations";
 
 export default class Person extends BaseModel {
     public static namingStrategy = new SnakeCaseNamingStrategy();
@@ -69,6 +70,12 @@ export default class Person extends BaseModel {
         return stock;
     }
 
+    @computed()
+    public get pivot_contributor_type() {
+        const contributor_type = this.$extras.pivot_contributor_type; //my pivot column name was "stock"
+        return contributor_type;
+    }
+
     @manyToMany(() => Dataset, {
         pivotForeignKey: 'person_id',
         pivotRelatedForeignKey: 'document_id',

app/models/project.ts

@@ -1,6 +1,6 @@
-import { column, SnakeCaseNamingStrategy } from '@ioc:Adonis/Lucid/Orm';
+import { column, SnakeCaseNamingStrategy } from '@adonisjs/lucid/orm';
 import { DateTime } from 'luxon';
-import BaseModel from './BaseModel';
+import BaseModel from './base_model.js';
 
 export default class Project extends BaseModel {
     public static namingStrategy = new SnakeCaseNamingStrategy();

app/models/role.ts

@@ -1,10 +1,11 @@
-import { column, SnakeCaseNamingStrategy, manyToMany, ManyToMany, beforeCreate, beforeUpdate } from '@ioc:Adonis/Lucid/Orm';
+import { column, SnakeCaseNamingStrategy, manyToMany, beforeCreate, beforeUpdate } from '@adonisjs/lucid/orm';
-import BaseModel from './BaseModel';
+import BaseModel from './base_model.js';
 import { DateTime } from 'luxon';
 // import moment from 'moment';
 import dayjs from 'dayjs';
-import User from './User';
+import User from './user.js';
-import Permission from 'App/Models/Permission';
+import Permission from '#models/permission';
+import type { ManyToMany } from "@adonisjs/lucid/types/relations";
 
 export default class Role extends BaseModel {
     public static namingStrategy = new SnakeCaseNamingStrategy();
@@ -46,7 +47,7 @@ export default class Role extends BaseModel {
 
     @beforeCreate()
     @beforeUpdate()
-    public static async resetDate(role) {
+    public static async resetDate(role: Role) {
         role.created_at = this.formatDateTime(role.created_at);
         role.updated_at = this.formatDateTime(role.updated_at);
     }
@@ -64,7 +65,7 @@ export default class Role extends BaseModel {
     // 	});
     // }
 
-    private static formatDateTime(datetime) {
+    private static formatDateTime(datetime: any) {
         let value = new Date(datetime);
         return datetime
             ? value.getFullYear() +

app/models/subject.ts

@@ -1,9 +1,10 @@
-import { column, SnakeCaseNamingStrategy, manyToMany, ManyToMany, beforeCreate, beforeUpdate } from '@ioc:Adonis/Lucid/Orm';
+import { column, SnakeCaseNamingStrategy, manyToMany, computed} from '@adonisjs/lucid/orm';
-import BaseModel from './BaseModel';
+import BaseModel from './base_model.js';
 
 import { DateTime } from 'luxon';
 import dayjs from 'dayjs';
-import Dataset from './Dataset';
+import Dataset from './dataset.js';
+import type { ManyToMany } from "@adonisjs/lucid/types/relations";
 
 export default class Subject extends BaseModel {
     public static namingStrategy = new SnakeCaseNamingStrategy();
@@ -44,28 +45,33 @@ export default class Subject extends BaseModel {
     })
     public updated_at: DateTime;
 
-    @beforeCreate()
+    // @beforeCreate()
-    @beforeUpdate()
+    // @beforeUpdate()
-    public static async resetDate(role) {
+    // public static async resetDate(role) {
-        role.created_at = this.formatDateTime(role.created_at);
+    //     role.created_at = this.formatDateTime(role.created_at);
-        role.updated_at = this.formatDateTime(role.updated_at);
+    //     role.updated_at = this.formatDateTime(role.updated_at);
-    }
+    // }
 
-    private static formatDateTime(datetime) {
+    // private static formatDateTime(datetime) {
-        let value = new Date(datetime);
+    //     let value = new Date(datetime);
-        return datetime
+    //     return datetime
-            ? value.getFullYear() +
+    //         ? value.getFullYear() +
-                  '-' +
+    //               '-' +
-                  (value.getMonth() + 1) +
+    //               (value.getMonth() + 1) +
-                  '-' +
+    //               '-' +
-                  value.getDate() +
+    //               value.getDate() +
-                  ' ' +
+    //               ' ' +
-                  value.getHours() +
+    //               value.getHours() +
-                  ':' +
+    //               ':' +
-                  value.getMinutes() +
+    //               value.getMinutes() +
-                  ':' +
+    //               ':' +
-                  value.getSeconds()
+    //               value.getSeconds()
-            : datetime;
+    //         : datetime;
+    // }
+    @computed()
+    public get dataset_count() : number{
+        const count = this.$extras.datasets_count; //my pivot column name was "stock"
+        return count;
     }
 
     @manyToMany(() => Dataset, {

app/models/title.ts

@@ -1,6 +1,8 @@
-import { column, belongsTo, BelongsTo } from '@ioc:Adonis/Lucid/Orm';
+import { column, belongsTo } from '@adonisjs/lucid/orm';
-import Dataset from './Dataset';
+import Dataset from './dataset.js';
-import BaseModel from './BaseModel';
+import BaseModel from './base_model.js';
+import type { BelongsTo } from "@adonisjs/lucid/types/relations";
+
 // import { DatasetRelatedBaseModel } from './BaseModel';
 
 export default class Title extends BaseModel {
@@ -10,6 +12,11 @@ export default class Title extends BaseModel {
     public static timestamps = false;
     public static fillable: string[] = ['value', 'type', 'language'];
 
+    @column({
+        isPrimary: true,
+    })
+    public id: number;
+
     @column({})
     public document_id: number;
 

app/models/totp_secret.ts

@@ -0,0 +1,65 @@
+import { column, BaseModel, SnakeCaseNamingStrategy, belongsTo } from '@adonisjs/lucid/orm';
+import User from './user.js';
+import { DateTime } from 'luxon';
+import dayjs from 'dayjs';
+// import Encryption from '@ioc:Adonis/Core/Encryption';
+import encryption from '@adonisjs/core/services/encryption';
+import type { BelongsTo } from "@adonisjs/lucid/types/relations";
+
+export default class TotpSecret extends BaseModel {
+    public static namingStrategy = new SnakeCaseNamingStrategy();
+    public static table = 'totp_secrets';
+    // public static fillable: string[] = ['value', 'label', 'type', 'relation'];
+   
+    @column({
+        isPrimary: true,
+    })
+    public id: number;
+
+    @column({})
+    public user_id: number;
+
+    // @column()
+    // public twoFactorSecret: string;
+    @column({
+        serializeAs: null,
+        consume: (value: string) => (value ? JSON.parse(encryption.decrypt(value) ?? '{}') : null),
+        prepare: (value: string) => encryption.encrypt(JSON.stringify(value)),
+    })
+    public twoFactorSecret?: string | null;
+
+    // serializeAs: null removes the model properties from the serialized output.
+    @column({
+        serializeAs: null,
+        consume: (value: string) => (value ? JSON.parse(encryption.decrypt(value) ?? '[]') : []),
+        prepare: (value: string[]) => encryption.encrypt(JSON.stringify(value)),
+    })
+    public twoFactorRecoveryCodes?: string[] | null;
+
+    @column({})
+    public state: number;
+
+    @column.dateTime({
+        serialize: (value: Date | null) => {
+            // return value ? moment(value).format('MMMM Do YYYY, HH:mm:ss') : value;
+            return value ? dayjs(value).format('MMMM D YYYY HH:mm a') : value;
+        },
+        autoCreate: true,
+    })
+    public created_at: DateTime;
+
+    @column.dateTime({
+        serialize: (value: Date | null) => {
+            return value ? dayjs(value).format('MMMM D YYYY HH:mm a') : value;
+        },
+        autoCreate: true,
+        autoUpdate: true,
+    })
+    public updated_at: DateTime;
+
+    @belongsTo(() => User, {
+        foreignKey: 'user_id',
+    })
+    public user: BelongsTo<typeof User>;
+
+}

app/models/traits/dataset_extension.ts

@@ -1,15 +1,15 @@
-import Title from 'App/Models/Title';
+import Title from '#models/title';
-import Description from 'App/Models/Description';
+import Description from '#models/description';
-import License from 'App/Models/License';
+import License from '#models/license';
-import Person from 'App/Models/Person';
+import Person from '#models/person';
-import DatasetReference from 'App/Models/DatasetReference';
+import DatasetReference from '#models/dataset_reference';
-import DatasetIdentifier from 'App/Models/DatasetIdentifier';
+import DatasetIdentifier from '#models/dataset_identifier';
-import Subject from 'App/Models/Subject';
+import Subject from '#models/subject';
-import File from 'App/Models/File';
+import File from '#models/file';
-import Coverage from 'App/Models/Coverage';
+import Coverage from '#models/coverage';
-import Collection from 'App/Models/Collection';
+import Collection from '#models/collection';
-import { BaseModel as LucidBaseModel } from '@ioc:Adonis/Lucid/Orm';
+import { BaseModel as LucidBaseModel } from '@adonisjs/lucid/orm';
-import Field from 'App/Library/Field';
+import Field from '#app/Library/Field';
 import { DateTime } from 'luxon';
 
 // @StaticImplements<LucidModel>()
@@ -30,13 +30,13 @@ export type DatasetRelatedModel =
     | typeof DatasetIdentifier
     | typeof File;
 
-
 export default abstract class DatasetExtension extends LucidBaseModel {
-    public abstract id;
+    public abstract id: number;
     public externalFields: Record<string, any> = this.getExternalFields();
     // which fields shoud#t be published
     protected internalFields: Record<string, any> = {};
     protected fields: Record<string, any> = {};
+    [key: string]: any;
 
     private getExternalFields(): Record<string, any> {
         // External fields definition
@@ -83,7 +83,7 @@ export default abstract class DatasetExtension extends LucidBaseModel {
                     sort_order: 'sort_order',
                     allow_email_contact: 'allow_email_contact',
                 },
-                relation: 'persons',
+                relation: 'contributors',
                 fetch: 'eager',
             },
             Reference: {
@@ -160,7 +160,7 @@ export default abstract class DatasetExtension extends LucidBaseModel {
 
         //      // Initialize available date fields and set up date validator
         //     // if the particular field is present
-        let dateFields = new Array<string>('EmbargoDate', 'CreatedAt', 'ServerDatePublished', 'ServerDateDeleted');
+        let dateFields = new Array<string>('EmbargoDate', 'CreatedAt', 'ServerDateModified', 'ServerDatePublished', 'ServerDateDeleted');
         dateFields.forEach((fieldname) => {
             let dateField = this.getField(fieldname);
             dateField instanceof Field && dateField.setValueModelClass(DateTime.now());
@@ -323,7 +323,7 @@ export default abstract class DatasetExtension extends LucidBaseModel {
     private convertColumnToFieldname(columnName: string): string {
         return columnName
             .split(/[-_]/)
-            .map((word) => (word.charAt(0).toUpperCase() + word.slice(1)))
+            .map((word) => word.charAt(0).toUpperCase() + word.slice(1))
             .join('');
     }
 }

app/models/user.ts

@@ -0,0 +1,180 @@
+import { DateTime } from 'luxon';
+import { withAuthFinder } from '@adonisjs/auth/mixins/lucid';
+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';
+import config from '@adonisjs/core/services/config';
+import Dataset from './dataset.js';
+import BaseModel from './base_model.js';
+// import Encryption from '@ioc:Adonis/Core/Encryption';
+import encryption from '@adonisjs/core/services/encryption';
+import { TotpState } from '#contracts/enums';
+import type { ManyToMany } from '@adonisjs/lucid/types/relations';
+import type { HasMany } from '@adonisjs/lucid/types/relations';
+import { compose } from '@adonisjs/core/helpers';
+import BackupCode from './backup_code.js';
+
+const AuthFinder = withAuthFinder(() => hash.use('laravel'), {
+    uids: ['email'],
+    passwordColumnName: 'password',
+});
+
+// import TotpSecret from './TotpSecret';
+
+// export default interface IUser {
+// 	id: number;
+// 	login: string;
+// 	email: string;
+// 	// password: string;
+// 	// createdAt: DateTime;
+// 	// updatedAt: DateTime;
+// 	// async (user): Promise<void>;
+// }
+
+// const permissionTable = config.get('rolePermission.permission_table', 'permissions');
+// const rolePermissionTable = config.get('rolePermission.role_permission_table', 'role_has_permissions');
+
+// const roleTable = config.get('rolePermission.role_table', 'roles');
+// const userRoleTable = config.get('rolePermission.user_role_table', 'link_accounts_roles');
+
+export default class User extends compose(BaseModel, AuthFinder) {
+    // export default class User extends BaseModel {
+    public static namingStrategy = new SnakeCaseNamingStrategy();
+    public static table = 'accounts';
+
+    @column({ isPrimary: true })
+    public id: number;
+
+    @column()
+    public login: string;
+
+    
+    @column()
+    public firstName: string;
+
+    @column()
+    public lastName: string;
+
+    @column()
+    public email: string;
+
+    @column({ serializeAs: null })
+    public password: string;
+
+    @column.dateTime({ autoCreate: true })
+    public createdAt: DateTime;
+
+    @column.dateTime({ autoCreate: true, autoUpdate: true })
+    public updatedAt: DateTime;
+
+    // serializeAs: null removes the model properties from the serialized output.
+    @column({
+        serializeAs: null,
+        consume: (value: string) => (value ? JSON.parse(encryption.decrypt(value) ?? '{}') : null),
+        prepare: (value: string) => encryption.encrypt(JSON.stringify(value)),
+    })
+    public twoFactorSecret?: string | null;
+
+    // serializeAs: null removes the model properties from the serialized output.
+    @column({
+        serializeAs: null,
+        consume: (value: string) => (value ? JSON.parse(encryption.decrypt(value) ?? '[]') : []),
+        prepare: (value: string[]) => encryption.encrypt(JSON.stringify(value)),
+    })
+    public twoFactorRecoveryCodes?: string[] | null;
+
+    @column({})
+    public state: number;
+
+    // @hasOne(() => TotpSecret, {
+    //     foreignKey: 'user_id',
+    // })
+    // public totp_secret: HasOne<typeof TotpSecret>;
+
+    // @beforeSave()
+    // public static async hashPassword(user: User) {
+    //     if (user.$dirty.password) {
+    //         user.password = await hash.use('laravel').make(user.password);
+    //     }
+    // }
+
+    public get isTwoFactorEnabled(): boolean {
+        return Boolean(this?.twoFactorSecret && this.state == TotpState.STATE_ENABLED);
+        // return Boolean(this.totp_secret?.twoFactorSecret);
+    }
+
+    @manyToMany(() => Role, {
+        pivotForeignKey: 'account_id',
+        pivotRelatedForeignKey: 'role_id',
+        pivotTable: 'link_accounts_roles',
+    })
+    public roles: ManyToMany<typeof Role>;
+
+    @hasMany(() => Dataset, {
+        foreignKey: 'account_id',
+    })
+    public datasets: HasMany<typeof Dataset>;
+
+    @hasMany(() => BackupCode, {
+        foreignKey: 'user_id',
+    })
+    public backupcodes: HasMany<typeof BackupCode>;
+
+    public async getBackupCodes(this: User): Promise<BackupCode[]> {
+        const test = await this.related('backupcodes').query();
+        // return test.map((role) => role.code);
+        return test;
+    }
+
+    // https://github.com/adonisjs/core/discussions/1872#discussioncomment-132289
+    public async getRoles(this: User): Promise<string[]> {
+        const test = await this.related('roles').query();
+        return test.map((role) => role.name);
+    }
+
+    public async can(permissionNames: Array<string>): Promise<boolean> {
+        // const permissions = await this.getPermissions()
+        // return Acl.check(expression, operand => _.includes(permissions, operand))
+        const hasPermission = await this.checkHasPermissions(this, permissionNames);
+        return hasPermission;
+    }
+
+    private async checkHasPermissions(user: User, permissionNames: Array<string>): Promise<boolean> {
+        const permissionTable = config.get('rolePermission.permission_table', 'permissions');
+        const rolePermissionTable = config.get('rolePermission.role_permission_table', 'role_has_permissions');
+
+        const roleTable = config.get('rolePermission.role_table', 'roles');
+        const userRoleTable = config.get('rolePermission.user_role_table', 'link_accounts_roles');
+
+        let permissionPlaceHolder = '(';
+        let placeholders = new Array(permissionNames.length).fill('?');
+        permissionPlaceHolder += placeholders.join(',');
+        permissionPlaceHolder += ')';
+
+        let {
+            rows: {
+                0: { permissioncount },
+            },
+        } = await db.rawQuery(
+            'SELECT count("p"."name") as permissionCount FROM ' +
+                roleTable +
+                ' r INNER JOIN ' +
+                userRoleTable +
+                ' ur ON ur.role_id=r.id AND "ur"."account_id"=? ' +
+                ' INNER JOIN ' +
+                rolePermissionTable +
+                ' rp ON rp.role_id=r.id ' +
+                ' INNER JOIN ' +
+                permissionTable +
+                ' p ON rp.permission_id=p.id AND "p"."name" in ' +
+                permissionPlaceHolder +
+                ' LIMIT 1',
+            [user.id, ...permissionNames],
+        );
+
+        return permissioncount > 0;
+    }
+}
+
+// export default User;

app/models/user_role.ts

@@ -1,8 +1,10 @@
-import { column, BaseModel, belongsTo, BelongsTo, SnakeCaseNamingStrategy } from '@ioc:Adonis/Lucid/Orm';
+import { column, BaseModel, belongsTo, SnakeCaseNamingStrategy } from '@adonisjs/lucid/orm';
 
-import User from 'App/Models/User';
+import User from '#models/user';
-import Role from 'App/Models/Role';
+import Role from '#models/role';
 import { DateTime } from 'luxon';
+import type { BelongsTo } from "@adonisjs/lucid/types/relations";
+
 // import moment from 'moment'
 
 export default class UserRole extends BaseModel {
@@ -49,7 +51,7 @@ export default class UserRole extends BaseModel {
         });
     }
 
-    private static formatDateTime(datetime) {
+    private static formatDateTime(datetime: any) {
         let value = new Date(datetime);
         return datetime
             ? value.getFullYear() +

app/services/TwoFactorAuthProvider.ts

@@ -0,0 +1,128 @@
+// import Config from '@ioc:Adonis/Core/Config';
+// import config from '@adonisjs/core/services/config'
+import env from '#start/env';
+import User from '#models/user';
+import { generateSecret, verifyToken } from 'node-2fa/dist/index.js';
+// import cryptoRandomString from 'crypto-random-string';
+import QRCode from 'qrcode';
+import crypto from 'crypto';
+import { TotpState } from '#contracts/enums';
+
+// npm install node-2fa --save
+// npm install crypto-random-string --save
+// import { cryptoRandomStringAsync } from 'crypto-random-string/index';
+// npm install qrcode --save
+// npm i --save-dev @types/qrcode
+
+class TwoFactorAuthProvider {
+    private issuer: string = env.get('APP_NAME') || 'TethysCloud';
+
+    /**
+     * generateSecret will generate a user-specific 32-character secret.
+     * We’re providing the name of the app and the user’s email as parameters for the function.
+     * This secret key will be used to verify whether the token provided by the user during authentication is valid or not.
+     *
+     * Return the default global focus trap stack     *
+     * @param {User} user user for the secrect
+     * @return {string}
+     */
+    public generateSecret(user: User) {
+        const secret = generateSecret({
+            name: this.issuer,
+            account: user.email,
+        });
+        return secret.secret;
+    }
+
+    /**
+     * We also generated recovery codes which can be used in case we’re unable to retrieve tokens from 2FA applications.
+     * We assign the user a list of recovery codes and each code can be used only once during the authentication process.
+     *   The recovery codes are random strings generated using the cryptoRandomString library.
+     *
+     * Return recovery codes
+     * @return {string[]}
+     */
+    public generateRecoveryCodes(): string[] {
+        const recoveryCodeLimit: number = 8;
+        const codes: string[] = [];
+        for (let i = 0; i < recoveryCodeLimit; i++) {
+            const recoveryCode: string = `${this.secureRandomString()}-${this.secureRandomString()}`;
+            codes.push(recoveryCode);
+        }
+        return codes;
+    }
+
+    private secureRandomString() {
+        // return await cryptoRandomString.async({ length: 10, type: 'hex' });
+        return this.generateRandomString(10, 'hex');
+    }
+
+    private generateRandomString(length: number, type: 'hex' | 'base64' | 'numeric' = 'hex'): string {
+        const byteLength = Math.ceil(length * 0.5); // For hex encoding, each byte generates 2 characters
+        const randomBytes = crypto.randomBytes(byteLength);
+
+        switch (type) {
+            case 'hex':
+                return randomBytes.toString('hex').slice(0, length);
+            case 'base64':
+                return randomBytes.toString('base64').slice(0, length);
+            case 'numeric':
+                return randomBytes
+                    .toString('hex')
+                    .replace(/[a-fA-F]/g, '') // Remove non-numeric characters
+                    .slice(0, length);
+            default:
+                throw new Error('Invalid type specified');
+        }
+    }
+
+    // public async generateQrCode(user: User) : Promise<{svg: string; url: string; secret: string; }> {
+    //     const issuer = encodeURIComponent(this.issuer); // 'TethysCloud'
+    //     // const userName = encodeURIComponent(user.email); // 'rrqx9472%40tethys.at'
+    //     const label = `${this.issuer}:${user.email}`;
+
+    //     const algorithm = encodeURIComponent("SHA256");
+    //     const query = `?secret=${user.twoFactorSecret}&issuer=${issuer}&algorithm=${algorithm}&digits=6`; // '?secret=FEYCLOSO627CB7SMLX6QQ7BP75L7SJ54&issuer=TethysCloud'
+    //     const url = `otpauth://totp/${label}${query}`; // 'otpauth://totp/rrqx9472%40tethys.at?secret=FEYCLOSO627CB7SMLX6QQ7BP75L7SJ54&issuer=TethysCloud'
+    //     const svg = await QRCode.toDataURL(url);
+    //     const secret = user.twoFactorSecret as string;
+    //     return { svg, url, secret };
+    // }
+
+    public async generateQrCode(user: User, twoFactorSecret?: string): Promise<{ svg: string; url: string; secret: string }> {
+        const issuer = encodeURIComponent(this.issuer); // 'TethysCloud'
+        // const userName = encodeURIComponent(user.email); // 'rrqx9472%40tethys.at'
+        const label = `${this.issuer}:${user.email}`;
+
+        // const algorithm = encodeURIComponent('SHA256');
+        const secret = twoFactorSecret ? twoFactorSecret : (user.twoFactorSecret as string);
+        const query = `?secret=${secret}&issuer=${issuer}&digits=6`; // '?secret=FEYCLOSO627CB7SMLX6QQ7BP75L7SJ54&issuer=TethysCloud'
+
+        const url = `otpauth://totp/${label}${query}`; // 'otpauth://totp/rrqx9472%40tethys.at?secret=FEYCLOSO627CB7SMLX6QQ7BP75L7SJ54&issuer=TethysCloud'
+        const svg = await QRCode.toDataURL(url);
+
+        return { svg, url, secret };
+    }
+
+    public async enable(user: User, token: string): Promise<boolean> {
+        const isValid = verifyToken(user.twoFactorSecret as string, token, 1);
+        if (!isValid) {
+            return false;
+        }
+        user.state = TotpState.STATE_ENABLED;
+        if (await user.save()) {
+            return true;
+        }
+        return false;
+    }
+
+    public async validate(user: User, token: string): Promise<boolean> {
+        const isValid = verifyToken(user.twoFactorSecret as string, token, 1);
+        if (isValid) {
+            return true;
+        }
+        return false;
+    }
+}
+
+export default new TwoFactorAuthProvider();

app/services/backup_code_storage.ts

@@ -0,0 +1,136 @@
+import User from '#models/user';
+import BackupCode from '#models/backup_code';
+import hash from '@adonisjs/core/services/hash';
+
+export interface ISecureRandom {
+    CHAR_UPPER: string;
+    CHAR_LOWER: string;
+    CHAR_DIGITS: string;
+    CHAR_SYMBOLS: string;
+    CHAR_ALPHANUMERIC: string;
+    CHAR_HUMAN_READABLE: string;
+
+    /**
+     * Generate a random string of specified length.
+     * @param int $length The length of the generated string
+     * @param string $characters An optional list of characters to use if no character list is
+     * 							specified all valid base64 characters are used.
+     * @return string
+     * @since 8.0.0
+     */
+    generate(length: number, characters?: string): string;
+}
+
+export class SecureRandom implements ISecureRandom {
+    CHAR_UPPER: string = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ';
+    CHAR_LOWER: string = 'abcdefghijklmnopqrstuvwxyz';
+    CHAR_DIGITS: string = '0123456789';
+    CHAR_SYMBOLS: string = '!"#$%&\\\'()*+,-./:;<=>?@[]^_`{|}~';
+    CHAR_ALPHANUMERIC: string = this.CHAR_UPPER + this.CHAR_LOWER + this.CHAR_DIGITS;
+    CHAR_HUMAN_READABLE: string = 'abcdefgijkmnopqrstwxyzABCDEFGHJKLMNPQRSTWXYZ23456789';
+
+    public generate(length: number, characters: string = this.CHAR_ALPHANUMERIC): string {
+        if (length <= 0) {
+            throw new Error('Invalid length specified: ' + length + ' must be bigger than 0');
+        }
+        const maxCharIndex: number = characters.length - 1;
+        let randomString: string = '';
+        while (length > 0) {
+            const randomNumber: number = Math.floor(Math.random() * (maxCharIndex + 1));
+            randomString += characters[randomNumber];
+            length--;
+        }
+        return randomString;
+    }
+}
+
+class BackupCodeStorage {
+    private static CODE_LENGTH: number = 16;
+    // private mapper: BackupCodeMapper;
+    // private hasher: IHasher;
+    private random: ISecureRandom;
+    // private eventDispatcher: IEventDispatcher;
+
+    // constructor(mapper: BackupCodeMapper, random: ISecureRandom, hasher: IHasher, eventDispatcher: IEventDispatcher) {
+    //     this.mapper = mapper;
+    //     this.hasher = hasher;
+    //     this.random = random;
+    //     this.eventDispatcher = eventDispatcher;
+    // }
+    constructor(random: ISecureRandom) {
+        // this.mapper = mapper;
+        // this.hasher = hasher;
+        this.random = random;
+        // this.eventDispatcher = eventDispatcher;
+    }
+
+    public async createCodes(user: User, number: number = 10): Promise<string[]> {
+        let results: string[] = [];
+        // this.mapper.deleteCodes(user);
+        await BackupCode.deleteCodes(user);
+        // user.twoFactorRecoveryCodes = [""];
+
+        // const uid = user.getUID();
+        for (let i = 1; i <= Math.min(number, 20); i++) {
+            const code = this.random.generate(BackupCodeStorage.CODE_LENGTH, this.random.CHAR_HUMAN_READABLE);
+            // const code = crypto
+            //     .randomBytes(Math.ceil(BackupCodeStorage.CODE_LENGTH / 2))
+            //     .toString('hex')
+            //     .slice(0, BackupCodeStorage.CODE_LENGTH);
+            const dbCode = new BackupCode();
+            // dbCode.setUserId(uid);
+          
+            // dbCode.setCode(this.hasher.hash(code));
+            dbCode.code = await hash.make(code);
+            // dbCode.setUsed(0);
+            dbCode.used = false;
+            // this.mapper.insert(dbCode);
+            // await dbCode.save();
+            await dbCode.related('user').associate(user); // speichert schon ab
+            results.push(code);
+        }
+        // this.eventDispatcher.dispatchTyped(new CodesGenerated(user));
+        return results;
+    }
+
+    public async hasBackupCodes(user: User): Promise<boolean> {
+        const codes = await user.getBackupCodes();
+        return codes.length > 0;
+    }
+
+    public async getBackupCodesState(user: User) {
+        // const codes = this.mapper.getBackupCodes(user);
+        // const codes = await user.related('backupcodes').query().exec();
+        const codes: BackupCode[] = await user.getBackupCodes();
+        const total = codes.length;
+        let used: number = 0;
+        codes.forEach((code) => {
+            if (code.used === true) {
+                used++;
+            }
+        });
+        return {
+            enabled: total > 0,
+            total: total,
+            used: used,
+        };
+    }
+
+    // public validateCode(user: User, code: string): boolean {
+    //     const dbCodes = await user.getBackupCodes();
+    //     for (const dbCode of dbCodes) {
+    //         if (parseInt(dbCode.getUsed()) === 0 && this.hasher.verify(code, dbCode.getCode())) {
+    //             dbCode.setUsed(1);
+    //             this.mapper.update(dbCode);
+    //             return true;
+    //         }
+    //     }
+    //     return false;
+    // }
+
+    // public deleteCodes(user: User): void {
+    //     this.mapper.deleteCodes(user);
+    // }
+}
+
+export default BackupCodeStorage;

app/services/drive.ts

@@ -0,0 +1,13 @@
+// import app from './app.js';
+import DriveManager from "#providers/drive/src/drive_manager";
+import app from "@adonisjs/core/services/app";
+
+let drive: DriveManager;
+/**
+ * Returns a singleton instance of the router class from
+ * the container
+ */
+await app.booted(async () => {
+    drive = await app.container.make(DriveManager);
+});
+export { drive as default };

app/utils/utility-functions.ts

@@ -0,0 +1,26 @@
+export function sum(a: number, b: number): number {
+    return a + b;
+}
+
+export function getDomain(host: string): string {
+    // $myhost = strtolower(trim($host));
+    let myHost: string = host.trim().toLocaleLowerCase();
+    // $count = substr_count($myhost, '.');
+    const count: number = myHost.split(',').length - 1;
+
+    if (count == 2) {
+        const words = myHost.split('.');
+        if (words[1].length > 3) {
+            myHost = myHost.split('.', 2)[1];
+        }
+    } else if (count > 2) {
+        myHost = getDomain(myHost.split('.', 2)[1]);
+    }
+    myHost = myHost.replace(new RegExp(/^.*:\/\//i, 'g'), '');
+    return myHost;
+}
+
+export function preg_match(regex: RegExp, str: string) {
+    const result: boolean = regex.test(str);
+    return result;
+}

app/validators/auth.ts

@@ -0,0 +1,20 @@
+import vine from '@vinejs/vine';
+
+// public schema = schema.create({
+//     email: schema.string({ trim: true }, [
+//         rules.email(),
+//         // rules.unique({ table: 'accounts', column: 'email' })
+//     ]),
+//     password: schema.string({}, [rules.minLength(6)]),
+// });
+
+/**
+ * Validates the role's creation action
+ * node ace make:validator role
+ */
+export const authValidator = vine.compile(
+    vine.object({
+        email: vine.string().maxLength(255).email().normalizeEmail(),
+        password: vine.string().trim().minLength(6),
+    }),
+);

app/validators/dataset.ts

@@ -0,0 +1,354 @@
+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();
+// const extensions = enabledExtensions
+//     .map((extension) => {
+//         return extension.file_extension.split('|');
+//     })
+//     .flat();
+
+/**
+ * Validates the dataset's creation action
+ * node ace make:validator dataset
+ */
+export const createDatasetValidator = vine.compile(
+    vine.object({
+        // first step
+        language: vine
+            .string()
+            .trim()
+            .regex(/^[a-zA-Z0-9]+$/),
+        licenses: vine.array(vine.number()).minLength(1), // define at least one license for the new dataset
+        rights: vine.string().in(['true']),
+        // second step
+        type: vine.string().trim().minLength(3).maxLength(255),
+        creating_corporation: vine.string().trim().minLength(3).maxLength(255),
+        titles: vine
+            .array(
+                vine.object({
+                    value: vine.string().trim().minLength(3).maxLength(255),
+                    type: vine.enum(Object.values(TitleTypes)),
+                    language: vine
+                        .string()
+                        .trim()
+                        .minLength(2)
+                        .maxLength(255)
+                        .translatedLanguage({ mainLanguageField: 'language', typeField: 'type' }),
+                }),
+            )
+            .minLength(1),
+        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' }),
+                }),
+            )
+            .minLength(1),
+        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),
+                    last_name: vine.string().trim().minLength(3).maxLength(255),
+                }),
+            )
+            .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),
+                    last_name: vine.string().trim().minLength(3).maxLength(255),
+                    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'),
+        }),
+        references: vine
+            .array(
+                vine.object({
+                    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),
+                }),
+            )
+            .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'),
+        // last step
+        files: vine
+            .array(
+                vine
+                    .myfile({
+                        size: '512mb',
+                        //extnames: extensions,
+                    })
+                    .allowedMimetypeExtensions()
+                    .filenameLength({ clientNameSizeLimit: 100 })
+                    .fileScan({ removeInfected: true }),
+            )
+            .minLength(1),
+    }),
+);
+
+/**
+ * Validates the dataset's update action
+ */
+export const updateDatasetValidator = vine.compile(
+    vine.object({
+        // first step
+        language: vine
+            .string()
+            .trim()
+            .regex(/^[a-zA-Z0-9]+$/),
+        licenses: vine.array(vine.number()).minLength(1), // define at least one license for the new dataset
+        rights: vine.string().in(['true']),
+        // second step
+        type: vine.string().trim().minLength(3).maxLength(255),
+        creating_corporation: vine.string().trim().minLength(3).maxLength(255),
+        titles: vine
+            .array(
+                vine.object({
+                    value: vine.string().trim().minLength(3).maxLength(255),
+                    type: vine.enum(Object.values(TitleTypes)),
+                    language: vine
+                        .string()
+                        .trim()
+                        .minLength(2)
+                        .maxLength(255)
+                        .translatedLanguage({ mainLanguageField: 'language', typeField: 'type' }),
+                }),
+            )
+            .minLength(1),
+        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' }),
+                }),
+            )
+            .minLength(1),
+        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),
+                    last_name: vine.string().trim().minLength(3).maxLength(255),
+                }),
+            )
+            .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),
+                    last_name: vine.string().trim().minLength(3).maxLength(255),
+                    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'),
+        }),
+        references: vine
+            .array(
+                vine.object({
+                    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),
+                }),
+            )
+            .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'),
+        // last step
+        files: vine
+        .array(
+            vine
+                .myfile({
+                    size: '512mb',
+                    //extnames: extensions,
+                })
+                .allowedMimetypeExtensions()
+                .filenameLength({ clientNameSizeLimit: 100 })
+                .fileScan({ removeInfected: true }),
+        ).dependentArrayMinLength({ dependentArray: 'fileInputs', min: 1}),
+        fileInputs: vine
+        .array(
+            vine
+                .object({
+                    label: vine.string().trim().maxLength(100),
+                    //extnames: extensions,
+                })                
+        ),
+    }),
+);
+
+// files: schema.array([rules.minLength(1)]).members(
+//     schema.file({
+//         size: '512mb',
+//         extnames: ['jpg', 'gif', 'png', 'tif', 'pdf', 'zip', 'fgb', 'nc', 'qml', 'ovr', 'gpkg', 'gml', 'gpx', 'kml', 'kmz', 'json'],
+//     }),
+// ),
+
+let messagesProvider = new SimpleMessagesProvider({
+    'minLength': '{{ field }} must be at least {{ min }} characters long',
+    'maxLength': '{{ field }} must be less then {{ max }} characters long',
+    'required': '{{ field }} is required',
+    'unique': '{{ field }} must be unique, and this value is already taken',
+    // 'confirmed': '{{ field }} is not correct',
+    'licenses.minLength': 'at least {{ min }} permission must be defined',
+    'licenses.*.number': 'Define roles as valid numbers',
+    'rights.in': 'you must agree to continue',
+
+    'titles.0.value.minLength': 'Main Title  must be at least {{ min }} characters long',
+    'titles.0.value.maxLength': 'Main Title  must be less than {{ max }} characters long',
+    'titles.0.value.required': 'Main Title is required',
+    'titles.*.value.required': 'Additional title is required, if defined',
+    'titles.*.type.required': 'Additional title type is required',
+    'titles.*.language.required': 'Additional title language is required',
+    'titles.*.language.translatedLanguage': 'The language of the translated title must be different from the language of the dataset',
+
+    'descriptions.0.value.minLength': 'Main Abstract  must be at least {{ min }} characters long',
+    'descriptions.0.value.maxLength': 'Main Abstract  must be less than {{ max }} characters long',
+    'descriptions.0.value.required': 'Main Abstract is required',
+    'descriptions.*.value.required': 'Additional description is required, if defined',
+    'descriptions.*.type.required': 'Additional description type is required',
+    'descriptions.*.language.required': 'Additional description language is required',
+    'descriptions.*.language.translatedLanguage':
+        'The language of the translated description must be different from the language of the dataset',
+
+    'authors.array.minLength': 'at least {{ min }} author must be defined',
+    'authors.distinct': 'The {{ field }} array must have unique values based on the {{ fields }} attribute.',
+    'authors.*.email.isUnique': 'the email of the new creator already exists in the database',
+    'contributors.*.pivot_contributor_type.required': 'contributor type is required, if defined',
+    'contributors.distinct': 'The {{ field }} array must have unique values based on the {{ fields }} attribute.',
+
+    'after': `{{ field }} must be older than ${dayjs().add(10, 'day')}`,
+
+    'subjects.array.minLength': 'at least {{ min }} keywords must be defined',
+    'subjects.*.value.required': 'keyword value is required',
+    'subjects.*.value.minLength': 'keyword value  must be at least {{ min }} characters long',
+    'subjects.*.type.required': 'keyword type is required',
+    'subjects.*.language.required': 'language of keyword is required',
+    'subjects.distinct': 'The {{ field }} array must have unique values based on the {{ fields }} attribute.',
+
+    'references.*.value.required': 'Additional reference value is required, if defined',
+    'references.*.type.required': 'Additional reference identifier type is required',
+    'references.*.relation.required': 'Additional reference relation type is required',
+    'references.*.label.required': 'Additional reference label is required',
+
+    'files.array.minLength': 'At least {{ min }}  file upload is required.',
+    'files.*.size': 'file size is to big',
+    'files.*.extnames': 'file extension is not supported',
+});
+
+createDatasetValidator.messagesProvider = messagesProvider;
+updateDatasetValidator.messagesProvider = messagesProvider;
+// export default createDatasetValidator;

app/validators/role.ts

@@ -0,0 +1,64 @@
+import vine, { SimpleMessagesProvider } from '@vinejs/vine';
+
+/**
+ * Validates the role's creation action
+ * node ace make:validator role
+ */
+export const createRoleValidator = vine.compile(
+    vine.object({
+        name: vine
+            .string()
+            .isUnique({ table: 'roles', column: 'name' })
+            .trim()
+            .minLength(3)
+            .maxLength(255)
+            .regex(/^[a-zA-Z0-9]+$/), //Must be alphanumeric with hyphens or underscores
+        display_name: vine
+            .string()
+            .isUnique({ table: 'roles', column: 'display_name' })
+            .trim()
+            .minLength(3)
+            .maxLength(255)
+            .regex(/^[a-zA-Z0-9]+$/),
+        description: vine.string().trim().escape().minLength(3).maxLength(255).optional(),
+        permissions: vine.array(vine.number()).minLength(1), // define at least one permission for the new role
+    }),
+);
+
+export const updateRoleValidator = vine.withMetaData<{ roleId: number }>().compile(
+    vine.object({
+        name: vine
+            .string()
+            // .unique(async (db, value, field) => {
+            //     const result = await db.from('roles').select('id').whereNot('id', field.meta.roleId).where('name', value).first();
+            //     return result.length ? false : true;
+            // })
+            .isUnique({
+                table: 'roles',
+                column: 'name',
+                whereNot: (field) => field.meta.roleId,
+            })
+            .trim()
+            .minLength(3)
+            .maxLength(255),
+
+        description: vine.string().trim().escape().minLength(3).maxLength(255).optional(),
+        permissions: vine.array(vine.number()).minLength(1), // define at least one permission for the new role
+    }),
+);
+
+let messagesProvider = new SimpleMessagesProvider({
+    // Applicable for all fields
+    'required': 'The {{ field }} field is required',
+    'unique': '{{ field }} must be unique, and this value is already taken',
+    'string': 'The value of {{ field }} field must be a string',
+    'email': 'The value is not a valid email address',
+
+    // 'contacts.0.email.required': 'The primary email of the contact is required',
+    // 'contacts.*.email.required': 'Contact email is required',
+    'permissions.minLength': 'at least {{min }} permission must be defined',
+    'permissions.*.number': 'Define permissions as valid numbers',
+});
+
+createRoleValidator.messagesProvider = messagesProvider;
+updateRoleValidator.messagesProvider = messagesProvider;

app/validators/user.ts

@@ -0,0 +1,64 @@
+import vine, { SimpleMessagesProvider } from '@vinejs/vine';
+
+/**
+ * Validates the role's creation action
+ * node ace make:validator user
+ */
+export const createUserValidator = vine.compile(
+    vine.object({
+        login: vine
+            .string()
+            .trim()
+            .minLength(3)
+            .maxLength(20)
+            .isUnique({ table: 'accounts', column: 'login' })
+            .regex(/^[a-zA-Z0-9]+$/), //Must be alphanumeric with hyphens or underscores
+        first_name: vine.string().trim().minLength(3).maxLength(255),
+        last_name: vine.string().trim().minLength(3).maxLength(255),
+        email: vine.string().maxLength(255).email().normalizeEmail().isUnique({ table: 'accounts', column: 'email' }),
+        password: vine.string().confirmed().trim().minLength(3).maxLength(60),
+        roles: vine.array(vine.number()).minLength(1), // define at least one role for the new user
+    }),
+);
+
+/**
+ * Validates the role's update action
+ * node ace make:validator user
+ */
+export const updateUserValidator = vine.withMetaData<{ objId: number }>().compile(
+    vine.object({
+        login: vine
+            .string()
+            .trim()
+            .minLength(3)
+            .maxLength(20)
+            .isUnique({ table: 'accounts', column: 'login', whereNot: (field) => field.meta.objId }),
+            // .regex(/^[a-zA-Z0-9]+$/), //Must be alphanumeric with hyphens or underscores
+        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', whereNot: (field) => field.meta.objId }),
+        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
+    }),
+);
+
+let messagesProvider = new SimpleMessagesProvider({
+    // Applicable for all fields
+    'required': 'The {{ field }} field is required',
+    'unique': '{{ field }} must be unique, and this value is already taken',
+    'string': 'The value of {{ field }} field must be a string',
+    'email': 'The value is not a valid email address',
+    'minLength': '{{ field }} must be at least {{ min }} characters long',
+    'maxLength': '{{ field }} must be less then {{ max }} characters long',
+    'confirmed': 'Oops! The confirmation of {{ field }} is not correct. Please double-check and ensure they match.',
+    'roles.minLength': 'at least {{ min }} role must be defined',
+    'roles.*.number': 'Define roles as valid numbers',
+});
+
+createUserValidator.messagesProvider = messagesProvider;
+updateUserValidator.messagesProvider = messagesProvider;